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Rashidian A, Dušek J, Drastik M, Smutná L, Fritsche K, Braeuning A, Pijnenburg D, van Beuningen R, Honkakoski P, Poso A, Kronenberger T, Pavek P. Filling the Blank Space: Branched 4-Nonylphenol Isomers Are Responsible for Robust Constitutive Androstane Receptor (CAR) Activation by Nonylphenol. Environ Sci Technol 2024; 58:6913-6923. [PMID: 38593436 DOI: 10.1021/acs.est.3c10096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
4-Nonylphenol (4-NP), a para-substituted phenolic compound with a straight or branched carbon chain, is a ubiquitous environmental pollutant and food contaminant. 4-NP, particularly the branched form, has been identified as an endocrine disruptor (ED) with potent activities on estrogen receptors. Constitutive Androstane Receptor (CAR) is another crucial nuclear receptor that regulates hepatic lipid, glucose, and steroid metabolism and is involved in the ED mechanism of action. An NP mixture has been described as an extremely potent activator of both human and rodent CAR. However, detailed mechanistic aspects of CAR activation by 4-NP are enigmatic, and it is not known if 4-NP can directly interact with the CAR ligand binding domain (LBD). Here, we examined interactions of individual branched (22NP, 33NP, and 353NP) and linear 4-NPs with CAR variants using molecular dynamics (MD) simulations, cellular experiments with various CAR expression constructs, recombinant CAR LBD in a TR-FRET assay, or a differentiated HepaRG hepatocyte cellular model. Our results demonstrate that branched 4-NPs display more stable poses to activate both wild-type CAR1 and CAR3 variant LBDs in MD simulations. Consistently, branched 4-NPs activated CAR3 and CAR1 LBD more efficiently than linear 4-NP. Furthermore, in HepaRG cells, we observed that all 4-NPs upregulated CYP2B6 mRNA, a relevant hallmark for CAR activation. This is the first study to provide detailed insights into the direct interaction between individual 4-NPs and human CAR-LBD, as well as its dominant variant CAR3. The work could contribute to the safer use of individual 4-NPs in many areas of industry.
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Affiliation(s)
- Azam Rashidian
- Department of Internal Medicine VIII, University Hospital of Tübingen, Tübingen, Baden-Württemberg 72076, Germany
| | - Jan Dušek
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, Hradec Kralove 500 05, Czech Republic
- Department of Physiology, Faculty of Medicine in Hradec Kralove, Charles University, Šimkova 870, Hradec Králové 500 03, Czech Republic
| | - Martin Drastik
- Department of Biophysics and Physical Chemistry, Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, Hradec Kralove 500 05, Czech Republic
| | - Lucie Smutná
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, Hradec Kralove 500 05, Czech Republic
| | - Kristin Fritsche
- Department Food Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, Berlin 10589, Germany
| | - Albert Braeuning
- Department Food Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, Berlin 10589, Germany
| | - Dirk Pijnenburg
- PamGene International B.V., Wolvenhoek 10, 's-Hertogenbosch 5211HH, Netherlands
| | - Rinie van Beuningen
- PamGene International B.V., Wolvenhoek 10, 's-Hertogenbosch 5211HH, Netherlands
| | - Paavo Honkakoski
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1 C, Kuopio 72011, Finland
| | - Antti Poso
- Department of Internal Medicine VIII, University Hospital of Tübingen, Tübingen, Baden-Württemberg 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Tübingen 72076, Germany
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen 72076, Germany
| | - Thales Kronenberger
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Tübingen 72076, Germany
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen 72076, Germany
| | - Petr Pavek
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, Hradec Kralove 500 05, Czech Republic
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2
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Karim M, Mishra M, Lo CW, Saul S, Cagirici HB, Tran DHN, Agrawal A, Ghita L, Ojha A, East MP, Gammeltoft KA, Sahoo MK, Johnson GL, Das S, Jochmans D, Cohen CA, Gottwein J, Dye J, Neff N, Pinsky BA, Laitinen T, Pantsar T, Poso A, Zanini F, Jonghe SD, Asquith CRM, Einav S. PIP4K2C inhibition reverses autophagic flux impairment induced by SARS-CoV-2. bioRxiv 2024:2024.04.15.589676. [PMID: 38659941 PMCID: PMC11042293 DOI: 10.1101/2024.04.15.589676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
In search for broad-spectrum antivirals, we discovered a small molecule inhibitor, RMC-113, that potently suppresses the replication of multiple RNA viruses including SARS-CoV-2 in human lung organoids. We demonstrated selective dual inhibition of the lipid kinases PIP4K2C and PIKfyve by RMC-113 and target engagement by its clickable analog. Advanced lipidomics revealed alteration of SARS-CoV-2-induced phosphoinositide signature by RMC-113 and linked its antiviral effect with functional PIP4K2C and PIKfyve inhibition. We discovered PIP4K2C's roles in SARS-CoV-2 entry, RNA replication, and assembly/egress, validating it as a druggable antiviral target. Integrating proteomics, single-cell transcriptomics, and functional assays revealed that PIP4K2C binds SARS-CoV-2 nonstructural protein 6 and regulates virus-induced impairment of autophagic flux. Reversing this autophagic flux impairment is a mechanism of antiviral action of RMC-113. These findings reveal virus-induced autophagy regulation via PIP4K2C, an understudied kinase, and propose dual inhibition of PIP4K2C and PIKfyve as a candidate strategy to combat emerging viruses.
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Affiliation(s)
- Marwah Karim
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Manjari Mishra
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Chieh-Wen Lo
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Sirle Saul
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Halise Busra Cagirici
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Do Hoang Nhu Tran
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Aditi Agrawal
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Luca Ghita
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Amrita Ojha
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
| | - Michael P East
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Karen Anbro Gammeltoft
- Department of Infectious Diseases, University of Copenhagen, Denmark. Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen
- University Hospital-Hvidovre, Hvidovre, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Malaya Kumar Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Gary L Johnson
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Soumita Das
- Biomedical & Nutritional Science, Center for Pathogen Research & Training (CPRT), University of Massachusetts-Lowell, USA
| | - Dirk Jochmans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Courtney A Cohen
- US Army Medical Research Institute of Infectious Diseases, Viral Immunology Branch, Frederick, Maryland, USA
| | - Judith Gottwein
- Department of Infectious Diseases, University of Copenhagen, Denmark. Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen
- University Hospital-Hvidovre, Hvidovre, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - John Dye
- US Army Medical Research Institute of Infectious Diseases, Viral Immunology Branch, Frederick, Maryland, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Benjamin A Pinsky
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Finland
| | - Tatu Pantsar
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Finland
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Finland
| | - Fabio Zanini
- School of Clinical Medicine, UNSW Sydney, Sydney, New South Wales, Australia
- Cellular Genomics Futures Institute, UNSW Sydney, Sydney, New South Wales, Australia
- Evolution and Ecology Research Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | | | - Shirit Einav
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
- Department of Microbiology and Immunology, Stanford University, CA, USA
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3
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Flury P, Breidenbach J, Krüger N, Voget R, Schäkel L, Si Y, Krasniqi V, Calistri S, Olfert M, Sylvester K, Rocha C, Ditzinger R, Rasch A, Pöhlmann S, Kronenberger T, Poso A, Rox K, Laufer SA, Müller CE, Gütschow M, Pillaiyar T. Correction to "Cathepsin-Targeting SARS-CoV-2 Inhibitors: Design, Synthesis, and Biological Activity". ACS Pharmacol Transl Sci 2024; 7:1195-1196. [PMID: 38633592 PMCID: PMC11020060 DOI: 10.1021/acsptsci.4c00095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Indexed: 04/19/2024]
Abstract
[This corrects the article DOI: 10.1021/acsptsci.3c00313.].
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Affiliation(s)
- Philipp Flury
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Julian Breidenbach
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Nadine Krüger
- Infection
Biology Unit, German Primate Center, Leibniz
Institute for Primate Research Göttingen, Kellnerweg 4, Göttingen 37077, Germany
| | - Rabea Voget
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Laura Schäkel
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Yaoyao Si
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Vesa Krasniqi
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Sara Calistri
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Matthias Olfert
- Institute
of Pharmacy, Pharmaceutical (Bio-)Analysis, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Katharina Sylvester
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Cheila Rocha
- Infection
Biology Unit, German Primate Center, Leibniz
Institute for Primate Research Göttingen, Kellnerweg 4, Göttingen 37077, Germany
| | - Raphael Ditzinger
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Alexander Rasch
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Stefan Pöhlmann
- Infection
Biology Unit, German Primate Center, Leibniz
Institute for Primate Research Göttingen, Kellnerweg 4, Göttingen 37077, Germany
- Faculty
of
Biology and Psychology, University Göttingen, Göttingen 37073, Germany
| | - Thales Kronenberger
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Faculty of
Health Sciences, School of Pharmacy, University
of Eastern Finland, Kuopio 70211, Finland
- Excellence
Cluster “Controlling Microbes to Fight Infections” (CMFI), Tübingen 72076, Germany
| | - Antti Poso
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Faculty of
Health Sciences, School of Pharmacy, University
of Eastern Finland, Kuopio 70211, Finland
| | - Katharina Rox
- Department
of Chemical Biology, Helmholtz Centre for
Infection Research (HZI), Braunschweig 38124, Germany
- Partner
Site
Hannover-Braunschweig, German Center for
Infection Research (DZIF), Braunschweig 38124, Germany
| | - Stefan A. Laufer
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Christa E. Müller
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Michael Gütschow
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Thanigaimalai Pillaiyar
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
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4
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Asquith CRM, East MP, Laitinen T, Alamillo-Ferrer C, Hartikainen E, Wells CI, Axtman AD, Drewry DH, Tizzard GJ, Poso A, Willson TM, Johnson GL. Discovery and optimization of narrow spectrum inhibitors of Tousled like kinase 2 (TLK2) using quantitative structure activity relationships. Eur J Med Chem 2024; 271:116357. [PMID: 38636130 DOI: 10.1016/j.ejmech.2024.116357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/24/2024] [Accepted: 03/24/2024] [Indexed: 04/20/2024]
Abstract
The oxindole scaffold has been the center of several kinase drug discovery programs, some of which have led to approved medicines. A series of two oxindole matched pairs from the literature were identified where TLK2 was potently inhibited as an off-target kinase. The oxindole has long been considered a promiscuous kinase inhibitor template, but across these four specific literature oxindoles TLK2 activity was consistent, while the kinome profile was radically different ranging from narrow to broad spectrum kinome coverage. We synthesized a large series of analogues, utilizing quantitative structure-activity relationship (QSAR) analysis, water mapping of the kinase ATP binding sites, kinome profiling, and small-molecule x-ray structural analysis to optimize TLK2 inhibition and kinome selectivity. This resulted in the identification of several narrow spectrum, sub-family selective, chemical tool compounds including 128 (UNC-CA2-103) that could enable elucidation of TLK2 biology.
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Affiliation(s)
- Christopher R M Asquith
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, NC, 27599, USA; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland; Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Michael P East
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, NC, 27599, USA
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Carla Alamillo-Ferrer
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Erkka Hartikainen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Carrow I Wells
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alison D Axtman
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - David H Drewry
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Graham J Tizzard
- UK National Crystallography Service, School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Timothy M Willson
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Gary L Johnson
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, NC, 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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5
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Seizer P, von Ungern-Sternberg SNI, Haug V, Dicenta V, Rosa A, Butt E, Nöthel M, Rohlfing AK, Sigle M, Nawroth PP, Nussbaum C, Sperandio M, Kusch C, Meub M, Sauer M, Münzer P, Bieber K, Stanger A, Mack AF, Huber R, Brand K, Lehners M, Feil R, Poso A, Krutzke K, Schäffer TE, Nieswandt B, Borst O, May AE, Zernecke A, Gawaz M, Heinzmann D. Cyclophilin A is a ligand for RAGE in thrombo-inflammation. Cardiovasc Res 2024; 120:385-402. [PMID: 38175781 DOI: 10.1093/cvr/cvad189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 10/08/2023] [Accepted: 10/20/2023] [Indexed: 01/06/2024] Open
Abstract
AIMS Cyclophilin A (CyPA) induces leucocyte recruitment and platelet activation upon release into the extracellular space. Extracellular CyPA therefore plays a critical role in immuno-inflammatory responses in tissue injury and thrombosis upon platelet activation. To date, CD147 (EMMPRIN) has been described as the primary receptor mediating extracellular effects of CyPA in platelets and leucocytes. The receptor for advanced glycation end products (RAGE) shares inflammatory and prothrombotic properties and has also been found to have similar ligands as CD147. In this study, we investigated the role of RAGE as a previously unknown interaction partner for CyPA. METHODS AND RESULTS Confocal imaging, proximity ligation, co-immunoprecipitation, and atomic force microscopy were performed and demonstrated an interaction of CyPA with RAGE on the cell surface. Static and dynamic cell adhesion and chemotaxis assays towards extracellular CyPA using human leucocytes and leucocytes from RAGE-deficient Ager-/- mice were conducted. Inhibition of RAGE abrogated CyPA-induced effects on leucocyte adhesion and chemotaxis in vitro. Accordingly, Ager-/- mice showed reduced leucocyte recruitment and endothelial adhesion towards CyPA in vivo. In wild-type mice, we observed a downregulation of RAGE on leucocytes when endogenous extracellular CyPA was reduced. We furthermore evaluated the role of RAGE for platelet activation and thrombus formation upon CyPA stimulation. CyPA-induced activation of platelets was found to be dependent on RAGE, as inhibition of RAGE, as well as platelets from Ager-/- mice showed a diminished activation and thrombus formation upon CyPA stimulation. CyPA-induced signalling through RAGE was found to involve central signalling pathways including the adaptor protein MyD88, intracellular Ca2+ signalling, and NF-κB activation. CONCLUSION We propose RAGE as a hitherto unknown receptor for CyPA mediating leucocyte as well as platelet activation. The CyPA-RAGE interaction thus represents a novel mechanism in thrombo-inflammation.
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Affiliation(s)
- Peter Seizer
- Department of Cardiology and Angiology, Universitätsklinikum Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
- Department of Cardiology and Angiology, Ostalbklinikum Aalen, Aalen, Germany
| | - Saskia N I von Ungern-Sternberg
- Department of Cardiology and Angiology, Universitätsklinikum Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
| | - Verena Haug
- Department of Cardiology and Angiology, Universitätsklinikum Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
| | - Valerie Dicenta
- Department of Cardiology and Angiology, Universitätsklinikum Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
| | - Annabelle Rosa
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
| | - Elke Butt
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
| | - Moritz Nöthel
- Department of Internal Medicine II, Cardiology, Pneumology, Angiology, University Hospital Bonn, Bonn, Germany
| | - Anne-Katrin Rohlfing
- Department of Cardiology and Angiology, Universitätsklinikum Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
| | - Manuel Sigle
- Department of Cardiology and Angiology, Universitätsklinikum Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
| | - Peter P Nawroth
- Department of Internal Medicine 1 and Clinical Chemistry, University Hospital of Heidelberg, Heidelberg, Germany
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
- Joint Heidelberg-ICD Translational Diabetes Program, Helmholtz-Zentrum, Munich, Germany
| | - Claudia Nussbaum
- Division of Neonatology, Department of Pediatrics, Dr. von Hauner Children's Hospital, LMU University Hospital, LMU Munich, Munich, Germany
| | - Markus Sperandio
- Institute of Cardiovascular Physiology and Pathophysiology, Ludwig-Maximilians University Munich, Munich, Germany
- German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislauf-Forschung, DZHK), Munich Heart Alliance Partner Site, Munich, Germany
| | - Charly Kusch
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
| | - Mara Meub
- Department of Biotechnology und Biophysics, Julius-Maximilians University, Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology und Biophysics, Julius-Maximilians University, Würzburg, Germany
| | - Patrick Münzer
- Department of Cardiology and Angiology, Universitätsklinikum Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
- DFG Heisenberg Group Cardiovascular Thromboinflammation and Translational Thrombocardiology, University of Tübingen, Tübingen, Germany
| | - Kristin Bieber
- Department of Hematology, Oncology, Immunology und Pulmonology, Universitätsklinikum Tübingen, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Anna Stanger
- Department of Hematology, Oncology, Immunology und Pulmonology, Universitätsklinikum Tübingen, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Andreas F Mack
- Institute of Clinical Anatomy and Cell Analytics, Eberhard Karls University Tübingen, Tübingen, Germany
| | - René Huber
- Institute of Clinical Chemistry, Hannover Medical School, Hannover, Germany
| | - Korbinian Brand
- Institute of Clinical Chemistry, Hannover Medical School, Hannover, Germany
| | - Moritz Lehners
- Interfakultäres Institut für Biochemie, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Robert Feil
- Interfakultäres Institut für Biochemie, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Antti Poso
- Department of Internal Medicine VIII, University Hospital of Tübingen, Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, Tübingen, Germany
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls University, Tübingen, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Tübingen, Germany
- Excellence Cluster 'Controlling Microbes to Fight Infections' (CMFI), Tübingen, Germany
| | - Konstantin Krutzke
- Institute of Applied Physics, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Tilman E Schäffer
- Institute of Applied Physics, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Bernhard Nieswandt
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
- Rudolf Virchow Center, University of Würzburg, Würzburg, Germany
| | - Oliver Borst
- Department of Cardiology and Angiology, Universitätsklinikum Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
- DFG Heisenberg Group Cardiovascular Thromboinflammation and Translational Thrombocardiology, University of Tübingen, Tübingen, Germany
| | - Andreas E May
- Department of Cardiology, Innere Medizin I, Klinikum Memmingen, Memmingen, Germany
| | - Alma Zernecke
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
| | - Meinrad Gawaz
- Department of Cardiology and Angiology, Universitätsklinikum Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
| | - David Heinzmann
- Department of Cardiology and Angiology, Universitätsklinikum Tübingen, Eberhard Karls University Tübingen, Otfried-Müller-Str. 10, 72076 Tübingen, Germany
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6
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Zwirner S, Abu Rmilah AA, Klotz S, Pfaffenroth B, Kloevekorn P, Moschopoulou AA, Schuette S, Haag M, Selig R, Li K, Zhou W, Nelson E, Poso A, Chen H, Amiot B, Jia Y, Minshew A, Michalak G, Cui W, Rist E, Longerich T, Jung B, Felgendreff P, Trompak O, Premsrirut PK, Gries K, Muerdter TE, Heinkele G, Wuestefeld T, Shapiro D, Weissbach M, Koenigsrainer A, Sipos B, Ab E, Zacarias MO, Theisgen S, Gruenheit N, Biskup S, Schwab M, Albrecht W, Laufer S, Nyberg S, Zender L. First-in-class MKK4 inhibitors enhance liver regeneration and prevent liver failure. Cell 2024; 187:1666-1684.e26. [PMID: 38490194 PMCID: PMC11011246 DOI: 10.1016/j.cell.2024.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 03/17/2024]
Abstract
Diminished hepatocyte regeneration is a key feature of acute and chronic liver diseases and after extended liver resections, resulting in the inability to maintain or restore a sufficient functional liver mass. Therapies to restore hepatocyte regeneration are lacking, making liver transplantation the only curative option for end-stage liver disease. Here, we report on the structure-based development and characterization (nuclear magnetic resonance [NMR] spectroscopy) of first-in-class small molecule inhibitors of the dual-specificity kinase MKK4 (MKK4i). MKK4i increased liver regeneration upon hepatectomy in murine and porcine models, allowed for survival of pigs in a lethal 85% hepatectomy model, and showed antisteatotic and antifibrotic effects in liver disease mouse models. A first-in-human phase I trial (European Union Drug Regulating Authorities Clinical Trials [EudraCT] 2021-000193-28) with the clinical candidate HRX215 was conducted and revealed excellent safety and pharmacokinetics. Clinical trials to probe HRX215 for prevention/treatment of liver failure after extensive oncological liver resections or after transplantation of small grafts are warranted.
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Affiliation(s)
- Stefan Zwirner
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany; HepaRegeniX GmbH, Tübingen 72072, Germany
| | - Anan A Abu Rmilah
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Sabrina Klotz
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Bent Pfaffenroth
- Department of Pharmaceutical Chemistry, University of Tübingen, Tübingen 72076, Germany
| | - Philip Kloevekorn
- Department of Pharmaceutical Chemistry, University of Tübingen, Tübingen 72076, Germany
| | - Athina A Moschopoulou
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Svenja Schuette
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart 70376, Germany
| | - Roland Selig
- HepaRegeniX GmbH, Tübingen 72072, Germany; Department of Pharmaceutical Chemistry, University of Tübingen, Tübingen 72076, Germany
| | - Kewei Li
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Wei Zhou
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Erek Nelson
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Antti Poso
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany; School of Pharmacy, University of Eastern Finland, Kuopio 70211, Finland; iFIT Cluster of Excellence (EXC 2180) "Image-guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany
| | - Harvey Chen
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Bruce Amiot
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Yao Jia
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Anna Minshew
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Gregory Michalak
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Wei Cui
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Elke Rist
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Thomas Longerich
- Institute of Pathology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | | | - Philipp Felgendreff
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Omelyan Trompak
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | | | - Katharina Gries
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Thomas E Muerdter
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart 70376, Germany
| | - Georg Heinkele
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart 70376, Germany
| | - Torsten Wuestefeld
- Laboratory for In Vivo Genetics & Gene Therapy, Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138672, Singapore; School of Biological Sciences, Nanyang Technological University of Singapore, Singapore 637551, Singapore
| | | | | | - Alfred Koenigsrainer
- iFIT Cluster of Excellence (EXC 2180) "Image-guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany; German Cancer Research Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Department of General-, Visceral, and Transplant Surgery, University Hospital Tübingen, Tübingen 72076, Germany
| | - Bence Sipos
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Eiso Ab
- ZoBio B.V., Leiden 2333 CH, the Netherlands
| | | | | | | | | | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart 70376, Germany; iFIT Cluster of Excellence (EXC 2180) "Image-guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany; Department of Clinical Pharmacology, Pharmacy and Biochemistry, University of Tübingen, Tübingen 72076, Germany
| | | | - Stefan Laufer
- Department of Pharmaceutical Chemistry, University of Tübingen, Tübingen 72076, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), Tübingen 72076, Germany.
| | - Scott Nyberg
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA.
| | - Lars Zender
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany; iFIT Cluster of Excellence (EXC 2180) "Image-guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany; German Cancer Research Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), Tübingen 72076, Germany.
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7
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Rak M, Menge A, Tesch R, Berger LM, Balourdas DI, Shevchenko E, Krämer A, Elson L, Berger BT, Abdi I, Wahl LM, Poso A, Kaiser A, Hanke T, Kronenberger T, Joerger AC, Müller S, Knapp S. Development of Selective Pyrido[2,3- d]pyrimidin-7(8 H)-one-Based Mammalian STE20-Like (MST3/4) Kinase Inhibitors. J Med Chem 2024; 67:3813-3842. [PMID: 38422480 DOI: 10.1021/acs.jmedchem.3c02217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Mammalian STE20-like (MST) kinases 1-4 play key roles in regulating the Hippo and autophagy pathways, and their dysregulation has been implicated in cancer development. In contrast to the well-studied MST1/2, the roles of MST3/4 are less clear, in part due to the lack of potent and selective inhibitors. Here, we re-evaluated literature compounds, and used structure-guided design to optimize the p21-activated kinase (PAK) inhibitor G-5555 (8) to selectively target MST3/4. These efforts resulted in the development of MR24 (24) and MR30 (27) with good kinome-wide selectivity and high cellular potency. The distinct cellular functions of closely related MST kinases can now be elucidated with subfamily-selective chemical tool compounds using a combination of the MST1/2 inhibitor PF-06447475 (2) and the two MST3/4 inhibitors developed. We found that MST3/4-selective inhibition caused a cell-cycle arrest in the G1 phase, whereas MST1/2 inhibition resulted in accumulation of cells in the G2/M phase.
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Affiliation(s)
- Marcel Rak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Amelie Menge
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Roberta Tesch
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Lena M Berger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Dimitrios-Ilias Balourdas
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Ekaterina Shevchenko
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
- German Translational Cancer Network (DKTK) and Frankfurt Cancer Institute (FCI), 60438 Frankfurt am Main, Germany
| | - Lewis Elson
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Benedict-Tilman Berger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Ismahan Abdi
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Laurenz M Wahl
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, 70210 Kuopio, Finland
| | - Astrid Kaiser
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Thomas Hanke
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, 70210 Kuopio, Finland
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
- German Translational Cancer Network (DKTK) and Frankfurt Cancer Institute (FCI), 60438 Frankfurt am Main, Germany
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8
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Bogacheva MS, Kuivanen S, Potdar S, Hassinen A, Huuskonen S, Pöhner I, Luck TJ, Turunen L, Feodoroff M, Szirovicza L, Savijoki K, Saarela J, Tammela P, Paavolainen L, Poso A, Varjosalo M, Kallioniemi O, Pietiäinen V, Vapalahti O. Drug repurposing platform for deciphering the druggable SARS-CoV-2 interactome. Antiviral Res 2024; 223:105813. [PMID: 38272320 DOI: 10.1016/j.antiviral.2024.105813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has heavily challenged the global healthcare system. Despite the vaccination programs, the new virus variants are circulating. Further research is required for understanding of the biology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and for discovery of therapeutic agents against the virus. Here, we took advantage of drug repurposing to identify if existing drugs could inhibit SARS-CoV-2 infection. We established an open high throughput platform for in vitro screening of drugs against SARS-CoV-2 infection. We screened ∼1000 drugs for their ability to inhibit SARS-CoV-2-induced cell death in the African green monkey kidney cell line (Vero-E6), analyzed how the hit compounds affect the viral N (nucleocapsid) protein expression in human cell lines using high-content microscopic imaging and analysis, determined the hit drug targets in silico, and assessed their ability to cause phospholipidosis, which can interfere with the viral replication. Duvelisib was found by in silico interaction assay as a potential drug targeting virus-host protein interactions. The predicted interaction between PARP1 and S protein, affected by Duvelisib, was further validated by immunoprecipitation. Our results represent a rapidly applicable platform for drug repurposing and evaluation of the new emerging viruses' responses to the drugs. Further in silico studies help us to discover the druggable host pathways involved in the infectious cycle of SARS-CoV-2.
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Affiliation(s)
- Mariia S Bogacheva
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland; Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland.
| | - Suvi Kuivanen
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | - Swapnil Potdar
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Antti Hassinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Sini Huuskonen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ina Pöhner
- Faculty of Health Sciences, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Tamara J Luck
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Laura Turunen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Michaela Feodoroff
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland; Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Leonora Szirovicza
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland
| | - Kirsi Savijoki
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Jani Saarela
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Päivi Tammela
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Lassi Paavolainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Antti Poso
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland; Department of Internal Medicine VIII, University Hospital Tubingen, Tubingen, Germany
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland; Science for Life Laboratory (SciLifeLab), Department of Oncology and Pathology, Karolinska Institutet, Solna, Sweden
| | - Vilja Pietiäinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Department of Virology, Medicum, University of Helsinki, Helsinki, Finland; Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland; HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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9
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Wittlinger F, Ogboo BC, Shevchenko E, Damghani T, Pham CD, Schaeffner IK, Oligny BT, Chitnis SP, Beyett TS, Rasch A, Buckley B, Urul DA, Shaurova T, May EW, Schaefer EM, Eck MJ, Hershberger PA, Poso A, Laufer SA, Heppner DE. Linking ATP and allosteric sites to achieve superadditive binding with bivalent EGFR kinase inhibitors. Commun Chem 2024; 7:38. [PMID: 38378740 PMCID: PMC10879502 DOI: 10.1038/s42004-024-01108-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024] Open
Abstract
Bivalent molecules consisting of groups connected through bridging linkers often exhibit strong target binding and unique biological effects. However, developing bivalent inhibitors with the desired activity is challenging due to the dual motif architecture of these molecules and the variability that can be introduced through differing linker structures and geometries. We report a set of alternatively linked bivalent EGFR inhibitors that simultaneously occupy the ATP substrate and allosteric pockets. Crystal structures show that initial and redesigned linkers bridging a trisubstituted imidazole ATP-site inhibitor and dibenzodiazepinone allosteric-site inhibitor proved successful in spanning these sites. The re-engineered linker yielded a compound that exhibited significantly higher potency (~60 pM) against the drug-resistant EGFR L858R/T790M and L858R/T790M/C797S, which was superadditive as compared with the parent molecules. The enhanced potency is attributed to factors stemming from the linker connection to the allosteric-site group and informs strategies to engineer linkers in bivalent agent design.
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Affiliation(s)
- Florian Wittlinger
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Blessing C Ogboo
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Ekaterina Shevchenko
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies" Eberhard Karls Universität Tübingen, 72076, Tübingen, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tübingen, Germany
| | - Tahereh Damghani
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Calvin D Pham
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Ilse K Schaeffner
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Brandon T Oligny
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Surbhi P Chitnis
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Tyler S Beyett
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 5119 Rollins Research Center, 1510 Clifton Rd, Atlanta, GA, 30322, USA
| | - Alexander Rasch
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Brian Buckley
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Daniel A Urul
- AssayQuant Technologies, Inc., Marlboro, MA, 01752, USA
| | - Tatiana Shaurova
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Earl W May
- AssayQuant Technologies, Inc., Marlboro, MA, 01752, USA
| | | | - Michael J Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Pamela A Hershberger
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Antti Poso
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies" Eberhard Karls Universität Tübingen, 72076, Tübingen, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tübingen, Germany
- School of Pharmacy, University of Eastern Finland, 70210, Kuopio, Finland
| | - Stefan A Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies" Eberhard Karls Universität Tübingen, 72076, Tübingen, Germany.
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tübingen, Germany.
| | - David E Heppner
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA.
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.
- Department of Structural Biology, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA.
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10
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Spahn S, Kleinhenz F, Shevchenko E, Stahl A, Rasen Y, Geisler C, Ruhm K, Klaumuenzer M, Kronenberger T, Laufer SA, Sundberg-Malek H, Bui KC, Horger M, Biskup S, Schulze-Osthoff K, Templin M, Malek NP, Poso A, Bitzer M. The molecular interaction pattern of lenvatinib enables inhibition of wild-type or kinase-mutated FGFR2-driven cholangiocarcinoma. Nat Commun 2024; 15:1287. [PMID: 38346946 PMCID: PMC10861557 DOI: 10.1038/s41467-024-45247-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 01/18/2024] [Indexed: 02/15/2024] Open
Abstract
Fibroblast growth factor receptor (FGFR)-2 can be inhibited by FGFR-selective or non-selective tyrosine kinase inhibitors (TKIs). Selective TKIs are approved for cholangiocarcinoma (CCA) with FGFR2 fusions; however, their application is limited by a characteristic pattern of adverse events or evocation of kinase domain mutations. A comprehensive characterization of a patient cohort treated with the non-selective TKI lenvatinib reveals promising efficacy in FGFR2-driven CCA. In a bed-to-bench approach, we investigate FGFR2 fusion proteins bearing critical tumor-relevant point mutations. These mutations confer growth advantage of tumor cells and increased resistance to selective TKIs but remain intriguingly sensitive to lenvatinib. In line with clinical observations, in-silico analyses reveal a more favorable interaction pattern of lenvatinib with FGFR2, including an increased flexibility and ligand efficacy, compared to FGFR-selective TKIs. Finally, the treatment of a patient with progressive disease and a newly developed kinase mutation during therapy with a selective inhibitor results in a striking response to lenvatinib. Our in vitro, in silico, and clinical data suggest that lenvatinib is a promising treatment option for FGFR2-driven CCA, especially when insurmountable adverse reactions of selective TKIs or acquired kinase mutations occur.
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Affiliation(s)
- Stephan Spahn
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany.
| | - Fabian Kleinhenz
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany
| | - Ekaterina Shevchenko
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-University, 72076, Tuebingen, Germany
- Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tuebingen, Germany
| | - Aaron Stahl
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, 72770, Reutlingen, Germany
| | - Yvonne Rasen
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany
| | - Christine Geisler
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany
| | - Kristina Ruhm
- Center for Personalized Medicine, Eberhard-Karls University, 72076, Tuebingen, Germany
| | | | - Thales Kronenberger
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-University, 72076, Tuebingen, Germany
- Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tuebingen, Germany
| | - Stefan A Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-University, 72076, Tuebingen, Germany
- Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tuebingen, Germany
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, 72076, Tuebingen, Germany
| | - Holly Sundberg-Malek
- Center for Personalized Medicine, Eberhard-Karls University, 72076, Tuebingen, Germany
| | - Khac Cuong Bui
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany
| | - Marius Horger
- Department of Diagnostic and Interventional Radiology, Eberhard-Karls University, 72076, Tuebingen, Germany
| | - Saskia Biskup
- CeGaT GmbH and Praxis für Humangenetik, 72076, Tuebingen, Germany
| | - Klaus Schulze-Osthoff
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, 72076, Tuebingen, Germany
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, Eberhard-Karls University, 72076, Tuebingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Markus Templin
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, 72770, Reutlingen, Germany
| | - Nisar P Malek
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany
- Center for Personalized Medicine, Eberhard-Karls University, 72076, Tuebingen, Germany
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, 72076, Tuebingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- M3-Research Center for Malignome, Metabolome and Microbiome, Eberhard-Karls University, 72076, Tuebingen, Germany
| | - Antti Poso
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-University, 72076, Tuebingen, Germany
- Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tuebingen, Germany
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, 72076, Tuebingen, Germany
- School of Pharmacy, University of Eastern Finland, 70210, Kuopio, Finland
| | - Michael Bitzer
- Department of Internal Medicine I, University Hospital Tuebingen, 72076, Tuebingen, Germany.
- Center for Personalized Medicine, Eberhard-Karls University, 72076, Tuebingen, Germany.
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, 72076, Tuebingen, Germany.
- M3-Research Center for Malignome, Metabolome and Microbiome, Eberhard-Karls University, 72076, Tuebingen, Germany.
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11
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Flury P, Breidenbach J, Krüger N, Voget R, Schäkel L, Si Y, Krasniqi V, Calistri S, Olfert M, Sylvester K, Rocha C, Ditzinger R, Rasch A, Pöhlmann S, Kronenberger T, Poso A, Rox K, Laufer SA, Müller CE, Gütschow M, Pillaiyar T. Cathepsin-Targeting SARS-CoV-2 Inhibitors: Design, Synthesis, and Biological Activity. ACS Pharmacol Transl Sci 2024; 7:493-514. [PMID: 38357286 PMCID: PMC10863444 DOI: 10.1021/acsptsci.3c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 02/16/2024]
Abstract
Cathepsins (Cats) are proteases that mediate the successful entry of SARS-CoV-2 into host cells. We designed and synthesized a tailored series of 21 peptidomimetics and evaluated their inhibitory activity against human cathepsins L, B, and S. Structural diversity was realized by combinations of different C-terminal warhead functions and N-terminal capping groups, while a central Leu-Phe fragment was maintained. Several compounds were identified as promising cathepsin L and S inhibitors with Ki values in the low nanomolar to subnanomolar range, for example, the peptide aldehydes 9a and 9b (9a, 2.67 nM, CatL; 0.455 nM, CatS; 9b, 1.76 nM, CatL; 0.512 nM, CatS). The compounds' inhibitory activity against the main protease of SARS-CoV-2 (Mpro) was additionally investigated. Based on the results at CatL, CatS, and Mpro, selected inhibitors were subjected to investigations of their antiviral activity in cell-based assays. In particular, the peptide nitrile 11e exhibited promising antiviral activity with an EC50 value of 38.4 nM in Calu-3 cells without showing cytotoxicity. High metabolic stability and favorable pharmacokinetic properties make 11e suitable for further preclinical development.
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Affiliation(s)
- Philipp Flury
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Julian Breidenbach
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Nadine Krüger
- Infection
Biology Unit, German Primate Center, Leibniz
Institute for Primate Research Göttingen, Kellnerweg 4, Göttingen 37077, Germany
| | - Rabea Voget
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Laura Schäkel
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Yaoyao Si
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Vesa Krasniqi
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Sara Calistri
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Matthias Olfert
- Faculty
of Biology and Psychology, University Göttingen, Göttingen 37073, Germany
| | - Katharina Sylvester
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Cheila Rocha
- Infection
Biology Unit, German Primate Center, Leibniz
Institute for Primate Research Göttingen, Kellnerweg 4, Göttingen 37077, Germany
| | - Raphael Ditzinger
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Alexander Rasch
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Stefan Pöhlmann
- Infection
Biology Unit, German Primate Center, Leibniz
Institute for Primate Research Göttingen, Kellnerweg 4, Göttingen 37077, Germany
- Faculty
of Biology and Psychology, University Göttingen, Göttingen 37073, Germany
| | - Thales Kronenberger
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Faculty
of Health Sciences, School of Pharmacy, University of Eastern Finland, Kuopio 70211, Finland
- Excellence
Cluster “Controlling Microbes to Fight Infections” (CMFI), Tübingen 72076, Germany
| | - Antti Poso
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Faculty
of Health Sciences, School of Pharmacy, University of Eastern Finland, Kuopio 70211, Finland
| | - Katharina Rox
- Department
of Chemical Biology, Helmholtz Centre for
Infection Research (HZI), Braunschweig 38124, Germany
- Partner
Site Hannover-Braunschweig, German Center
for Infection Research (DZIF), Braunschweig 38124, Germany
| | - Stefan A. Laufer
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Christa E. Müller
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Michael Gütschow
- PharmaCenter
Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53121, Germany
| | - Thanigaimalai Pillaiyar
- Institute
of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen
Center for Academic Drug Discovery, Eberhard
Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
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12
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Deen AJ, Adinolfi S, Härkönen J, Patinen T, Liu X, Laitinen T, Takabe P, Kainulainen K, Pasonen-Seppänen S, Gawriyski LM, Arasu UT, Selvarajan I, Mäkinen P, Laitinen H, Kansanen E, Kaikkonen MU, Poso A, Varjosalo M, Levonen AL. Oncogenic KEAP1 mutations activate TRAF2-NFκB signaling to prevent apoptosis in lung cancer cells. Redox Biol 2024; 69:103031. [PMID: 38184997 PMCID: PMC10808971 DOI: 10.1016/j.redox.2024.103031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024] Open
Abstract
The Kelch-like ECH-associated protein 1 (KEAP1) - Nuclear factor erythroid 2 -related factor 2 (NRF2) pathway is the major transcriptional stress response system in cells against oxidative and electrophilic stress. NRF2 is frequently constitutively active in many cancers, rendering the cells resistant to chemo- and radiotherapy. Loss-of-function (LOF) mutations in the repressor protein KEAP1 are common in non-small cell lung cancer, particularly adenocarcinoma. While the mutations can occur throughout the gene, they are enriched in certain areas, indicating that these may have unique functional importance. In this study, we show that in the GSEA analysis of TCGA lung adenocarcinoma RNA-seq data, the KEAP1 mutations in R320 and R470 were associated with enhanced Tumor Necrosis Factor alpha (TNFα) - Nuclear Factor kappa subunit B (NFκB) signaling as well as MYC and MTORC1 pathways. To address the functional role of these hotspot mutations, affinity purification and mass spectrometry (AP-MS) analysis of wild type (wt) KEAP1 and its mutation forms, R320Q and R470C were employed to interrogate differences in the protein interactome. We identified TNF receptor associated factor 2 (TRAF2) as a putative protein interaction partner. Both mutant KEAP1 forms showed increased interaction with TRAF2 and other anti-apoptotic proteins, suggesting that apoptosis signalling could be affected by the protein interactions. A549 lung adenocarcinoma cells overexpressing mutant KEAP1 showed high TRAF2-mediated NFκB activity and increased protection against apoptosis, XIAP being one of the key proteins involved in anti-apoptotic signalling. To conclude, KEAP1 R320Q and R470C and its interaction with TRAF2 leads to activation of NFκB pathway, thereby protecting against apoptosis.
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Affiliation(s)
- Ashik Jawahar Deen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Simone Adinolfi
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Jouni Härkönen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland; Department of Pathology, Hospital Nova of Central Finland, Jyväskylä, 40620, Finland
| | - Tommi Patinen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Xiaonan Liu
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Tuomo Laitinen
- School of Pharmacy, University of Eastern Finland, Kuopio, 70211, Finland
| | - Piia Takabe
- Institute of Biomedicine, University of Eastern Finland, Kuopio, 70211, Finland
| | - Kirsi Kainulainen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, 70211, Finland
| | | | - Lisa M Gawriyski
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Uma Thanigai Arasu
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Ilakya Selvarajan
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Petri Mäkinen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Hanna Laitinen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Emilia Kansanen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland; Science Service Centre, Kuopio University Hospital, Kuopio, 70211, Finland
| | - Minna U Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, Kuopio, 70211, Finland; Department of Internal Medicine VIII, University Hospital Tübingen, Tübingen, 72076, Germany
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Anna-Liisa Levonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland.
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13
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Serafim MSM, Kronenberger T, Rocha REO, Rosa ADRA, Mello TLG, Poso A, Ferreira RS, Abrahão JS, Kroon EG, Mota BEF, Maltarollo VG. Aminopyrimidine Derivatives as Multiflavivirus Antiviral Compounds Identified from a Consensus Virtual Screening Approach. J Chem Inf Model 2024; 64:393-411. [PMID: 38194508 DOI: 10.1021/acs.jcim.3c01505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Around three billion people are at risk of infection by the dengue virus (DENV) and potentially other flaviviruses. Worldwide outbreaks of DENV, Zika virus (ZIKV), and yellow fever virus (YFV), the lack of antiviral drugs, and limitations on vaccine usage emphasize the need for novel antiviral research. Here, we propose a consensus virtual screening approach to discover potential protease inhibitors (NS3pro) against different flavivirus. We employed an in silico combination of a hologram quantitative structure-activity relationship (HQSAR) model and molecular docking on characterized binding sites followed by molecular dynamics (MD) simulations, which filtered a data set of 7.6 million compounds to 2,775 hits. Lastly, docking and MD simulations selected six final potential NS3pro inhibitors with stable interactions along the simulations. Five compounds had their antiviral activity confirmed against ZIKV, YFV, DENV-2, and DENV-3 (ranging from 4.21 ± 0.14 to 37.51 ± 0.8 μM), displaying aggregator characteristics for enzymatic inhibition against ZIKV NS3pro (ranging from 28 ± 7 to 70 ± 7 μM). Taken together, the compounds identified in this approach may contribute to the design of promising candidates to treat different flavivirus infections.
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Affiliation(s)
- Mateus Sá Magalhães Serafim
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Rafael Eduardo Oliveira Rocha
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Amanda Del Rio Abreu Rosa
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Thaysa Lara Gonçalves Mello
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
- Department of Medical Oncology and Pneumology, University Hospital of Tübingen, Tübingen 70211, Germany
| | - Rafaela Salgado Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Jonatas Santos Abrahão
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Erna Geessien Kroon
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Bruno Eduardo Fernandes Mota
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Vinícius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
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14
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Pylkkö T, Tomašič T, Poso A, Tammela P. Virtual Screening Assisted Search for Inhibitors of the Translocated Intimin Receptor of Enteropathogenic Escherichia Coli. Chembiochem 2024; 25:e202300638. [PMID: 37971396 DOI: 10.1002/cbic.202300638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/03/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023]
Abstract
This study aimed to identify inhibitors of the translocated intimin receptor (Tir) of enteropathogenic Escherichia coli (EPEC). EPEC is an intestinal pathogen that causes diarrhea and is a major health concern worldwide. Because Tir is a key virulence factor involved in EPEC pathogenesis, inhibiting its function is a potential strategy for controlling EPEC infections. Virtual screening was applied to chemical libraries to search for compounds that inhibit Tir-mediated bacterial adherence to host cells. Three sites were targeted using the cocrystal structure published earlier. A selection of compounds was then assessed in a cell-based infection model and fluorescence microscopy assay. The results of this study provide a basis for further optimization and testing of Tir inhibitors as potential therapeutic agents for EPEC infections.
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Affiliation(s)
- Tuomas Pylkkö
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
| | - Tihomir Tomašič
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
| | - Päivi Tammela
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
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15
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Waitman KB, de Almeida LC, Primi MC, Carlos JAEG, Ruiz C, Kronenberger T, Laufer S, Goettert MI, Poso A, Vassiliades SV, de Souza VAM, Toledo MFZJ, Hassimotto NMA, Cameron MD, Bannister TD, Costa-Lotufo LV, Machado-Neto JA, Tavares MT, Parise-Filho R. HDAC specificity and kinase off-targeting by purine-benzohydroxamate anti-hematological tumor agents. Eur J Med Chem 2024; 263:115935. [PMID: 37989057 DOI: 10.1016/j.ejmech.2023.115935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 11/23/2023]
Abstract
A series of hybrid inhibitors, combining pharmacophores of known kinase inhibitors bearing anilino-purines (ruxolitinib, ibrutinib) and benzohydroxamate HDAC inhibitors (nexturastat A), were generated in the present study. The compounds have been synthesized and tested against solid and hematological tumor cell lines. Compounds 4d-f were the most promising in cytotoxicity assays (IC50 ≤ 50 nM) vs. hematological cells and displayed moderate activity in solid tumor models (EC50 = 9.3-21.7 μM). Compound 4d potently inhibited multiple kinase targets of interest for anticancer effects, including JAK2, JAK3, HDAC1, and HDAC6. Molecular dynamics simulations showed that 4d has stable interactions with HDAC and members of the JAK family, with differences in the hinge binding energy conferring selectivity for JAK3 and JAK2 over JAK1. The kinase inhibition profile of compounds 4d-f allows selective cytotoxicity, with minimal effects on non-tumorigenic cells. Moreover, these compounds have favorable pharmacokinetic profiles, with high stability in human liver microsomes (e.g., see t1/2: >120 min for 4f), low intrinsic clearance, and lack of significant inhibition of four major CYP450 isoforms.
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Affiliation(s)
- Karoline B Waitman
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Larissa C de Almeida
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marina C Primi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, United States
| | - Jorge A E G Carlos
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Claudia Ruiz
- Department of Molecular Medicine, Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, 33458, United States
| | - Thales Kronenberger
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), 72076, Tübingen, Germany; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland; Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), 72076, Tübingen, Germany
| | - Stefan Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), 72076, Tübingen, Germany
| | - Marcia Ines Goettert
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), 72076, Tübingen, Germany
| | - Antti Poso
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), 72076, Tübingen, Germany; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland; Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), 72076, Tübingen, Germany
| | - Sandra V Vassiliades
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Vinícius A M de Souza
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Mônica F Z J Toledo
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Neuza M A Hassimotto
- Food Research Center-(FoRC-CEPID) and Department of Food Science and Nutrition, Faculty of Pharmaceutical Science, University of São Paulo, São Paulo, SP, Brazil
| | - Michael D Cameron
- Department of Molecular Medicine, Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, 33458, United States
| | - Thomas D Bannister
- Department of Molecular Medicine, Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, 33458, United States
| | - Letícia V Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - João A Machado-Neto
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maurício T Tavares
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, United States.
| | - Roberto Parise-Filho
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.
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16
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Pillaiyar T, Wozniak M, Abboud D, Rasch A, Liebing AD, Poso A, Kronenberger T, Stäubert C, Laufer SA, Hanson J. Development of Ligands for the Super Conserved Orphan G Protein-Coupled Receptor GPR27 with Improved Efficacy and Potency. J Med Chem 2023; 66:17118-17137. [PMID: 38060818 DOI: 10.1021/acs.jmedchem.3c02030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
The orphan G protein-coupled receptor GPR27 appears to play a role in insulin production, secretion, lipid metabolism, neuronal plasticity, and l-lactate homeostasis. However, investigations on the function of GPR27 are impaired by the lack of potent and efficacious agonists. We describe herein the development of di- and trisubstituted benzamide derivatives 4a-e, 7a-z, and 7aa-ai, which display GPR27-specific activity in a β-arrestin 2 recruitment-based assay. Highlighted compounds are PT-91 (7p: pEC50 6.15; Emax 100%) and 7ab (pEC50 6.56; Emax 99%). A putative binding mode was revealed by the docking studies of 7p and 7ab with a GPR27 homology model. The novel active compounds exhibited no GPR27-mediated activation of G proteins, indicating that the receptor may possess an atypical profile. Compound 7p displays high metabolic stability and brain exposure in mice. Thus, 7p represents a novel tool to investigate the elusive pharmacology of GPR27 and assess its potential as a drug target.
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Affiliation(s)
- Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Monika Wozniak
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, B-4000 Liège, Belgium
| | - Dayana Abboud
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, B-4000 Liège, Belgium
| | - Alexander Rasch
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Aenne-Dorothea Liebing
- Rudolf Schönheimer Institute of Biochemistry, Faculty of Medicine, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Claudia Stäubert
- Rudolf Schönheimer Institute of Biochemistry, Faculty of Medicine, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany
| | - Stefan A Laufer
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Julien Hanson
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, B-4000 Liège, Belgium
- Laboratory of Medicinal Chemistry, Centre for Interdisciplinary Research on Medicines (CIRM), University of Liège, B-4000 Liège, Belgium
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17
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Asquith CRM, East MP, Laitinen T, Alamillo-Ferrer C, Hartikainen E, Wells CI, Axtman AD, Drewry DH, Tizzard GJ, Poso A, Willson TM, Johnson GL. Discovery and Optimization of Narrow Spectrum Inhibitors of Tousled Like Kinase 2 (TLK2) Using Quantitative Structure Activity Relationships. bioRxiv 2023:2023.12.28.573261. [PMID: 38234837 PMCID: PMC10793458 DOI: 10.1101/2023.12.28.573261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The oxindole scaffold has been the center of several kinase drug discovery programs, some of which have led to approved medicines. A series of two oxindole matched pairs from the literature were identified where TLK2 was a potent off-target kinase. The oxindole has long been considered a promiscuous inhibitor template, but across these 4 specific literature oxindoles TLK2 activity was consistent, while the kinome profile was radically different from narrow to broad spectrum coverage. We synthesized a large series of analogues and through quantitative structure-activity relationship (QSAR) analysis, water mapping of the kinase ATP binding sites, small-molecule x-ray structural analysis and kinome profiling, narrow spectrum, sub-family selective, chemical tool compounds were identified to enable elucidation of TLK2 biology.
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Affiliation(s)
- Christopher R M Asquith
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, NC 27599, USA
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael P East
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Carla Alamillo-Ferrer
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Erkka Hartikainen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Carrow I Wells
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alison D Axtman
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David H Drewry
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Graham J Tizzard
- UK National Crystallography Service, School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Timothy M Willson
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Gary L Johnson
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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18
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Joiner JD, Steinchen W, Mozer N, Kronenberger T, Bange G, Poso A, Wagner S, Hartmann MD. HilE represses the activity of the Salmonella virulence regulator HilD via a mechanism distinct from that of intestinal long-chain fatty acids. J Biol Chem 2023; 299:105387. [PMID: 37890783 PMCID: PMC10696396 DOI: 10.1016/j.jbc.2023.105387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The expression of virulence factors essential for the invasion of host cells by Salmonella enterica is tightly controlled by a network of transcription regulators. The AraC/XylS transcription factor HilD is the main integration point of environmental signals into this regulatory network, with many factors affecting HilD activity. Long-chain fatty acids, which are highly abundant throughout the host intestine, directly bind to and repress HilD, acting as environmental cues to coordinate virulence gene expression. The regulatory protein HilE also negatively regulates HilD activity, through a protein-protein interaction. Both of these regulators inhibit HilD dimerization, preventing HilD from binding to target DNA. We investigated the structural basis of these mechanisms of HilD repression. Long-chain fatty acids bind to a conserved pocket in HilD, in a comparable manner to that reported for other AraC/XylS regulators, whereas HilE forms a stable heterodimer with HilD by binding to the HilD dimerization interface. Our results highlight two distinct, mutually exclusive mechanisms by which HilD activity is repressed, which could be exploited for the development of new antivirulence leads.
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Affiliation(s)
- Joe D Joiner
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology, Philipps University of Marburg, Marburg, Germany; Department of Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Nick Mozer
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Thales Kronenberger
- Department of Internal Medicine VIII, University Hospital Tübingen, Tübingen, Germany; Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Eberhard Karls University Tübingen, Tübingen, Germany; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland; Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen, Germany
| | - Gert Bange
- Center for Synthetic Microbiology, Philipps University of Marburg, Marburg, Germany; Department of Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Antti Poso
- Department of Internal Medicine VIII, University Hospital Tübingen, Tübingen, Germany; Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Eberhard Karls University Tübingen, Tübingen, Germany; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Samuel Wagner
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany; Partner-site Tübingen, German Center for Infection Research (DZIF), Tübingen, Germany
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany; Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
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19
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Tavares MT, Krüger A, Yan SLR, Waitman KB, Gomes VM, de Oliveira DS, Paz F, Hilscher S, Schutkowski M, Sippl W, Ruiz C, Toledo MFZJ, Hassimotto NMA, Machado-Neto JA, Poso A, Cameron MD, Bannister TD, Palmisano G, Wrenger C, Kronenberger T, Parise-Filho R. 1,3-Diphenylureido hydroxamate as a promising scaffold for generation of potent antimalarial histone deacetylase inhibitors. Sci Rep 2023; 13:21006. [PMID: 38030668 PMCID: PMC10687260 DOI: 10.1038/s41598-023-47959-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023] Open
Abstract
We report a series of 1,3-diphenylureido hydroxamate HDAC inhibitors evaluated against sensitive and drug-resistant P. falciparum strains. Compounds 8a-d show potent antiplasmodial activity, indicating that a phenyl spacer allows improved potency relative to cinnamyl and di-hydrocinnamyl linkers. In vitro, mechanistic studies demonstrated target activity for PfHDAC1 on a recombinant level, which agreed with cell quantification of the acetylated histone levels. Compounds 6c, 7c, and 8c, identified as the most active in phenotypic assays and PfHDAC1 enzymatic inhibition. Compound 8c stands out as a remarkable inhibitor, displaying an impressive 85% inhibition of PfHDAC1, with an IC50 value of 0.74 µM in the phenotypic screening on Pf3D7 and 0.8 µM against multidrug-resistant PfDd2 parasites. Despite its potent inhibition of PfHDAC1, 8c remains the least active on human HDAC1, displaying remarkable selectivity. In silico studies suggest that the phenyl linker has an ideal length in the series for permitting effective interactions of the hydroxamate with PfHDAC1 and that this compound series could bind as well as in HsHDAC1. Taken together, these results highlight the potential of diphenylurea hydroxamates as a privileged scaffold for the generation of potent antimalarial HDAC inhibitors with improved selectivity over human HDACs.
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Affiliation(s)
- Maurício T Tavares
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Arne Krüger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, 05508-900, Brazil
| | - Sun L Rei Yan
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, 05508-900, Brazil
| | - Karoline B Waitman
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 580, São Paulo, 05508-000, Brazil
| | - Vinícius M Gomes
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, Brazil
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia
| | - Daffiny Sumam de Oliveira
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, 05508-900, Brazil
| | - Franciarli Paz
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, 05508-900, Brazil
| | - Sebastian Hilscher
- Faculty of Biosciences, Martin-Luther-University of Halle-Wittenberg, 06120, Halle/Saale, Germany
| | - Mike Schutkowski
- Faculty of Biosciences, Martin-Luther-University of Halle-Wittenberg, 06120, Halle/Saale, Germany
| | - Wolfgang Sippl
- Faculty of Biosciences, Martin-Luther-University of Halle-Wittenberg, 06120, Halle/Saale, Germany
| | - Claudia Ruiz
- Department of Molecular Medicine, The Herbert Wertheim Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Mônica F Z J Toledo
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 580, São Paulo, 05508-000, Brazil
| | - Neuza M A Hassimotto
- Food Research Center-(FoRC-CEPID) and Department of Food Science and Nutrition, Faculty of Pharmaceutical Science, University of São Paulo, São Paulo, SP, Brazil
| | - João A Machado-Neto
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Antti Poso
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland
| | - Michael D Cameron
- Department of Molecular Medicine, The Herbert Wertheim Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Thomas D Bannister
- Department of Molecular Medicine, The Herbert Wertheim Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Giuseppe Palmisano
- GlycoProteomics Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, Brazil
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, 05508-900, Brazil.
| | - Thales Kronenberger
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.
- Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tübingen, Germany.
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211, Kuopio, Finland.
| | - Roberto Parise-Filho
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 580, São Paulo, 05508-000, Brazil.
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20
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Tonduru AK, Maljaei SH, Adla SK, Anamea L, Tampio J, Králová A, Jalkanen AJ, Espada C, Santos IF, Montaser AB, Rautio J, Kronenberger T, Poso A, Huttunen KM. Targeting Glial Cells by Organic Anion-Transporting Polypeptide 1C1 (OATP1C1)-Utilizing l-Thyroxine-Derived Prodrugs. J Med Chem 2023; 66:15094-15114. [PMID: 37930268 PMCID: PMC10683023 DOI: 10.1021/acs.jmedchem.3c01026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
OATP1C1 (organic anion-transporting polypeptide 1C1) transports thyroid hormones, particularly thyroxine (T4), into human astrocytes. In this study, we investigated the potential of utilizing OATP1C1 to improve the delivery of anti-inflammatory drugs into glial cells. We designed and synthesized eight novel prodrugs by incorporating T4 and 3,5-diiodo-l-tyrosine (DIT) as promoieties to selected anti-inflammatory drugs. The prodrug uptake in OATP1C1-expressing human U-87MG glioma cells demonstrated higher accumulation with T4 promoiety compared to those with DIT promoiety or the parent drugs themselves. In silico models of OATP1C1 suggested dynamic binding for the prodrugs, wherein the pose changed from vertical to horizontal. The predicted binding energies correlated with the transport profiles, with T4 derivatives exhibiting higher binding energies when compared to prodrugs with a DIT promoiety. Interestingly, the prodrugs also showed utilization of oatp1a4/1a5/1a6 in mouse primary astrocytes, which was further supported by docking studies and a great potential for improved brain drug delivery.
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Affiliation(s)
- Arun Kumar Tonduru
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Seyed Hamed Maljaei
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Santosh Kumar Adla
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Landry Anamea
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Janne Tampio
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Adéla Králová
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Aaro J. Jalkanen
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Catarina Espada
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Inês Falcato Santos
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Ahmed B. Montaser
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Jarkko Rautio
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Thales Kronenberger
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
- Department
of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical
Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle
8, 72076 Tuebingen, Germany
- Tuebingen
Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tuebingen, Germany
| | - Antti Poso
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
- Department
of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical
Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle
8, 72076 Tuebingen, Germany
- Tuebingen
Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tuebingen, Germany
- Department
of Internal Medicine VIII, University Hospital
Tübingen, DE 72076 Tübingen, Germany
- Cluster
of Excellence iFIT (EXC 2180) “Image-Guided and Functionally
Instructed Tumor Therapies”, University
of Tübingen, 72076 Tübingen, Germany
| | - Kristiina M. Huttunen
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
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21
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Dutra JDP, Scheiffer G, Kronenberger T, Gomes LJC, Zanzarini I, dos Santos KK, Tonduru AK, Poso A, Rego FGDM, Picheth G, Valdameri G, Moure VR. Structural and molecular characterization of lopinavir and ivermectin as breast cancer resistance protein (BCRP/ABCG2) inhibitors. EXCLI J 2023; 22:1155-1172. [PMID: 38204967 PMCID: PMC10776880 DOI: 10.17179/excli2023-6427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/02/2023] [Indexed: 01/12/2024]
Abstract
A current clinical challenge in cancer is multidrug resistance (MDR) mediated by ABC transporters. Breast cancer resistance protein (BCRP) or ABCG2 transporter is one of the most important ABC transporters implicated in MDR and the use of inhibitors is a promising approach to overcome the resistance in cancer. This study aimed to characterize the molecular mechanism of ABCG2 inhibitors identified by a repurposing drug strategy using antiviral, anti-inflammatory and antiparasitic agents. Lopinavir and ivermectin can be considered as pan-inhibitors of ABC transporters, since both compounds inhibited ABCG2, P-glycoprotein and MRP1. They inhibited ABCG2 activity showing IC50 values of 25.5 and 23.4 µM, respectively. These drugs were highly cytotoxic and not transported by ABCG2. Additionally, these drugs increased the 5D3 antibody binding and did not affect the mRNA and protein expression levels. Cell-based analysis of the type of inhibition suggested a non-competitive inhibition, which was further corroborated by in silico approaches of molecular docking and molecular dynamics simulations. These results showed an overlap of the lopinavir and ivermectin binding sites on ABCG2, mainly interacting with E446 residue. However, the substrate mitoxantrone occupies a different site, binding to the F436 region, closer to the L554/L555 plug. In conclusion, these results revealed the mechanistic basis of lopinavir and ivermectin interaction with ABCG2. See also the Graphical abstract(Fig. 1).
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Affiliation(s)
- Julia de Paula Dutra
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
| | - Gustavo Scheiffer
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
| | - Thales Kronenberger
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
- (a) Department of Internal Medicine VIII, University Hospital Tuebingen, Otfried-Müller-Strasse 14, Tuebingen DE 72076, Germany, (b) Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany, (c) Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, 72076 Tuebingen, Germany, (d) Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tuebingen, Germany
| | - Lucas Julian Cruz Gomes
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
| | - Isadora Zanzarini
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
| | - Kelly Karoline dos Santos
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
| | - Arun K. Tonduru
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
- (a) Department of Internal Medicine VIII, University Hospital Tuebingen, Otfried-Müller-Strasse 14, Tuebingen DE 72076, Germany, (b) Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany, (c) Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, 72076 Tuebingen, Germany, (d) Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tuebingen, Germany
| | | | - Geraldo Picheth
- Graduate Program in Pharmaceutical Sciences, Federal University of Parana, Curitiba, PR, Brazil
| | - Glaucio Valdameri
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
| | - Vivian Rotuno Moure
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
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22
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Sivula T, Yetukuri L, Kalliokoski T, Käsnänen H, Poso A, Pöhner I. Machine Learning-Boosted Docking Enables the Efficient Structure-Based Virtual Screening of Giga-Scale Enumerated Chemical Libraries. J Chem Inf Model 2023; 63:5773-5783. [PMID: 37655823 PMCID: PMC10523430 DOI: 10.1021/acs.jcim.3c01239] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Indexed: 09/02/2023]
Abstract
The emergence of ultra-large screening libraries, filled to the brim with billions of readily available compounds, poses a growing challenge for docking-based virtual screening. Machine learning (ML)-boosted strategies like the tool HASTEN combine rapid ML prediction with the brute-force docking of small fractions of such libraries to increase screening throughput and take on giga-scale libraries. In our case study of an anti-bacterial chaperone and an anti-viral kinase, we first generated a brute-force docking baseline for 1.56 billion compounds in the Enamine REAL lead-like library with the fast Glide high-throughput virtual screening protocol. With HASTEN, we observed robust recall of 90% of the true 1000 top-scoring virtual hits in both targets when docking only 1% of the entire library. This reduction of the required docking experiments by 99% significantly shortens the screening time. In the kinase target, the employment of a hydrogen bonding constraint resulted in a major proportion of unsuccessful docking attempts and hampered ML predictions. We demonstrate the optimization potential in the treatment of failed compounds when performing ML-boosted screening and benchmark and showcase HASTEN as a fast and robust tool in a growing arsenal of approaches to unlock the chemical space covered by giga-scale screening libraries for everyday drug discovery campaigns.
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Affiliation(s)
- Toni Sivula
- School
of Pharmacy, University of Eastern Finland, Kuopio FI-70211, Finland
| | | | - Tuomo Kalliokoski
- Computational
Medicine Design, Orion Pharma, Orionintie 1A, Espoo FI-02101, Finland
| | - Heikki Käsnänen
- Computational
Medicine Design, Orion Pharma, Orionintie 1A, Espoo FI-02101, Finland
| | - Antti Poso
- School
of Pharmacy, University of Eastern Finland, Kuopio FI-70211, Finland
- Department
of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical
Sciences, Eberhard Karls University, Tübingen DE-72076, Germany
- Cluster
of Excellence iFIT (EXC 2180) “Image-Guided and Functionally
Instructed Tumor Therapies”, University
of Tübingen, Tübingen DE-72076, Germany
- Tübingen
Center for Academic Drug Discovery & Development (TüCAD2), Tübingen DE-72076, Germany
| | - Ina Pöhner
- School
of Pharmacy, University of Eastern Finland, Kuopio FI-70211, Finland
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23
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Heppner D, Wittlinger F, Ogboo B, Shevchenko E, Damghani T, Pham C, Schaeffner I, Oligny B, Chitnis S, Beyett T, Rasch A, Buckley B, Urul D, Shaurova T, May E, Schaefer E, Eck M, Hershberger P, Poso A, Laufer S. Linking ATP and allosteric sites to achieve superadditive binding with bivalent EGFR kinase inhibitors. Res Sq 2023:rs.3.rs-3286949. [PMID: 37790373 PMCID: PMC10543509 DOI: 10.21203/rs.3.rs-3286949/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Bivalent molecules consisting of groups connected through bridging linkers often exhibit strong target binding and unique biological effects. However, developing bivalent inhibitors with the desired activity is challenging due to the dual motif architecture of these molecules and the variability that can be introduced through differing linker structures and geometries. We report a set of alternatively linked bivalent EGFR inhibitors that simultaneously occupy the ATP substrate and allosteric pockets. Crystal structures show that initial and redesigned linkers bridging a trisubstituted imidazole ATP-site inhibitor and dibenzodiazepinone allosteric-site inhibitor proved successful in spanning these sites. The reengineered linker yielded a compound that exhibited significantly higher potency (~60 pM) against the drug-resistant EGFR L858R/T790M and L858R/T790M/C797S, which was superadditive as compared with the parent molecules. The enhanced potency is attributed to factors stemming from the linker connection to the allosteric-site group and informs strategies to engineer linkers in bivalent agent design.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Michael Eck
- Dana-Farber Cancer Institute & Department of Biological Chemistry and Molecular Pharmacology at Harvard Medical School
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24
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Rak M, Tesch R, Berger LM, Shevchenko E, Raab M, Tjaden A, Zhubi R, Balourdas DI, Joerger AC, Poso A, Krämer A, Elson L, Lučić A, Kronenberger T, Hanke T, Strebhardt K, Sanhaji M, Knapp S. Shifting the selectivity of pyrido[2,3-d]pyrimidin-7(8H)-one inhibitors towards the salt-inducible kinase (SIK) subfamily. Eur J Med Chem 2023; 254:115347. [PMID: 37094449 DOI: 10.1016/j.ejmech.2023.115347] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/27/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023]
Abstract
Salt-inducible kinases 1-3 (SIK1-3) are key regulators of the LKB1-AMPK pathway and play an important role in cellular homeostasis. Dysregulation of any of the three isoforms has been associated with tumorigenesis in liver, breast, and ovarian cancers. We have recently developed the dual pan-SIK/group I p21-activated kinase (PAK) chemical probe MRIA9. However, inhibition of p21-activated kinases has been associated with cardiotoxicity in vivo, which complicates the use of MRIA9 as a tool compound. Here, we present a structure-based approach involving the back-pocket and gatekeeper residues, for narrowing the selectivity of pyrido[2,3-d]pyrimidin-7(8H)-one-based inhibitors towards SIK kinases, eliminating PAK activity. Optimization was guided by high-resolution crystal structure analysis and computational methods, resulting in a pan-SIK inhibitor, MR22, which no longer exhibited activity on STE group kinases and displayed excellent selectivity in a representative kinase panel. MR22-dependent SIK inhibition led to centrosome dissociation and subsequent cell-cycle arrest in ovarian cancer cells, as observed with MRIA9, conclusively linking these phenotypic effects to SIK inhibition. Taken together, MR22 represents a valuable tool compound for studying SIK kinase function in cells.
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Affiliation(s)
- Marcel Rak
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Roberta Tesch
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Lena M Berger
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Ekaterina Shevchenko
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen, 72076, Germany; School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, Kuopio, 70210, Finland
| | - Monika Raab
- Department of Obstetrics and Gynaecology, School of Medicine, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany
| | - Amelie Tjaden
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Rezart Zhubi
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Dimitrios-Ilias Balourdas
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen, 72076, Germany; School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, Kuopio, 70210, Finland
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany; German Translational Cancer Network (DKTK) and Frankfurt Cancer Institute (FCI), Frankfurt am Main, 60438, Germany
| | - Lewis Elson
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Aleksandar Lučić
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen, 72076, Germany; School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, Kuopio, 70210, Finland
| | - Thomas Hanke
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany
| | - Klaus Strebhardt
- Department of Obstetrics and Gynaecology, School of Medicine, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany
| | - Mourad Sanhaji
- Department of Obstetrics and Gynaecology, School of Medicine, Johann Wolfgang Goethe University, Theodor-Stern-Kai 7, Frankfurt am Main, 60590, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, Frankfurt am Main, 60438, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 15, Frankfurt am Main, 60438, Germany; German Translational Cancer Network (DKTK) and Frankfurt Cancer Institute (FCI), Frankfurt am Main, 60438, Germany.
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25
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Ouyang X, D'Agostino PM, Wahlsten M, Delbaje E, Jokela J, Permi P, Gaiani G, Poso A, Bartos P, Gulder TAM, Koistinen H, Fewer DP. Direct pathway cloning and expression of the radiosumin biosynthetic gene cluster. Org Biomol Chem 2023. [PMID: 37259568 DOI: 10.1039/d3ob00385j] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Radiosumins are a structurally diverse family of low molecular weight natural products that are produced by cyanobacteria and exhibit potent serine protease inhibition. Members of this family are dipeptides characterized by the presence of two similar non-proteinogenic amino acids. Here we used a comparative bioinformatic analysis to identify radiosumin biosynthetic gene clusters from the genomes of 13 filamentous cyanobacteria. We used direct pathway cloning to capture and express the entire 16.8 kb radiosumin biosynthetic gene cluster from Dolichospermum planctonicum UHCC 0167 in Escherichia coli. Bioinformatic analysis demonstrates that radiosumins represent a new group of chorismate-derived non-aromatic secondary metabolites. High-resolution liquid chromatography-mass spectrometry, nuclear magnetic resonance spectroscopy and chemical degradation analysis revealed that cyanobacteria produce a cocktail of novel radiosumins. We report the chemical structure of radiosumin D, an N-methyl dipeptide, containing a special Aayp (2-amino-3-(4-amino-2-cyclohexen-1-ylidene) propionic acid) with R configuration that differs from radiosumin A-C, an N-Me derivative of Aayp (Amyp) and two acetyl groups. Radiosumin C inhibits all three human trypsin isoforms at micromolar concentrations with preference for trypsin-1 and -3 (IC50 values from 1.7 μM to >7.2 μM). These results provide a biosynthetic logic to explore the genetic and chemical diversity of the radiosumin family and suggest that these natural products may be a source of drug leads for selective human serine proteases inhibitors.
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Affiliation(s)
- Xiaodan Ouyang
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
| | - Paul M D'Agostino
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069 Dresden, Germany
| | - Matti Wahlsten
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
| | - Endrews Delbaje
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil
| | - Jouni Jokela
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
| | - Perttu Permi
- Department of Chemistry, University of Jyväskylä, Finland
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Finland
| | - Greta Gaiani
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
| | - Antti Poso
- Kuopio Campus, School of Pharmacy, University of Eastern Finland, Finland
| | - Piia Bartos
- Kuopio Campus, School of Pharmacy, University of Eastern Finland, Finland
| | - Tobias A M Gulder
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069 Dresden, Germany
| | - Hannu Koistinen
- Department of Clinical Chemistry and Haematology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Helsinki FIN-00014, Finland
| | - David P Fewer
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
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26
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Maltarollo VG, da Silva EB, Kronenberger T, Sena Andrade MM, de Lima Marques GV, Cândido Oliveira NJ, Santos LH, Oliveira Rezende Júnior CD, Cassiano Martinho AC, Skinner D, Fajtová P, M Fernandes TH, Silveira Dos Santos ED, Rodrigues Gazolla PA, Martins de Souza AP, da Silva ML, Dos Santos FS, Lavorato SN, Oliveira Bretas AC, Carvalho DT, Franco LL, Luedtke S, Giardini MA, Poso A, Dias LC, Podust LM, Alves RJ, McKerrow J, Andrade SF, Teixeira RR, Siqueira-Neto JL, O'Donoghue A, de Oliveira RB, Ferreira RS. Structure-based discovery of thiosemicarbazones as SARS-CoV-2 main protease inhibitors. Future Med Chem 2023; 15:959-985. [PMID: 37435731 DOI: 10.4155/fmc-2023-0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023] Open
Abstract
Aim: Discovery of novel SARS-CoV-2 main protease (Mpro) inhibitors using a structure-based drug discovery strategy. Materials & methods: Virtual screening employing covalent and noncovalent docking was performed to discover Mpro inhibitors, which were subsequently evaluated in biochemical and cellular assays. Results: 91 virtual hits were selected for biochemical assays, and four were confirmed as reversible inhibitors of SARS CoV-2 Mpro with IC50 values of 0.4-3 μM. They were also shown to inhibit SARS-CoV-1 Mpro and human cathepsin L. Molecular dynamics simulations indicated the stability of the Mpro inhibitor complexes and the interaction of ligands at the subsites. Conclusion: This approach led to the discovery of novel thiosemicarbazones as potent SARS-CoV-2 Mpro inhibitors.
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Affiliation(s)
- Vinícius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Elany Barbosa da Silva
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Thales Kronenberger
- Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany
- Cluster of Excellence iFIT (EXC 2180) 'Image-Guided & Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, 72076, Germany
- Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, Tübingen, 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Marina Mol Sena Andrade
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Gabriel V de Lima Marques
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Nereu J Cândido Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Lucianna H Santos
- Department of Biochemistry & Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Celso de Oliveira Rezende Júnior
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, 38400-902, Brazil
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo, 13083-970, Brazil
| | - Ana C Cassiano Martinho
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, 38400-902, Brazil
| | - Danielle Skinner
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
- Institute of Organic Chemistry & Biochemistry, Academy of Sciences of the Czech Republic, Prague, 16610, Czech Republic
| | - Thaís H M Fernandes
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
- Pharmaceutical Synthesis Group (PHARSG), Departamento de Produção de Matéria-Prima, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
| | - Eduardo da Silveira Dos Santos
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
- Pharmaceutical Synthesis Group (PHARSG), Departamento de Produção de Matéria-Prima, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
| | - Poliana A Rodrigues Gazolla
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Ana P Martins de Souza
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Milene Lopes da Silva
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Fabíola S Dos Santos
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Stefânia N Lavorato
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
- Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Barreiras, Bahia, 47810-047, Brazil
| | - Ana C Oliveira Bretas
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Diogo Teixeira Carvalho
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Lucas Lopardi Franco
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Stephanie Luedtke
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Miriam A Giardini
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Antti Poso
- Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany
- Cluster of Excellence iFIT (EXC 2180) 'Image-Guided & Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, 72076, Germany
- Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, Tübingen, 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Luiz C Dias
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo, 13083-970, Brazil
| | - Larissa M Podust
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Ricardo J Alves
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - James McKerrow
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Saulo F Andrade
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
- Pharmaceutical Synthesis Group (PHARSG), Departamento de Produção de Matéria-Prima, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
| | - Róbson R Teixeira
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Jair L Siqueira-Neto
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Anthony O'Donoghue
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Renata B de Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Rafaela S Ferreira
- Department of Biochemistry & Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
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27
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Dimitrov T, Moschopoulou AA, Seidel L, Kronenberger T, Kudolo M, Poso A, Geibel C, Wölffing P, Dauch D, Zender L, Schollmeyer D, Bajorath J, Forster M, Laufer S. Design and Optimization of Novel Benzimidazole- and Imidazo[4,5- b]pyridine-Based ATM Kinase Inhibitors with Subnanomolar Activities. J Med Chem 2023. [PMID: 37226670 DOI: 10.1021/acs.jmedchem.2c02104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The ATM kinase is a promising target in cancer treatment as an important regulator of the cellular response to DNA double-strand breaks. In this work, we present a new class of specific benzimidazole-based ATM inhibitors with picomolar potency against the isolated enzyme and favorable selectivity within relative PIKK and PI3K kinases. We could identify two promising inhibitor subgroups with significantly different physicochemical properties, which we developed simultaneously. These efforts lead to numerous highly active inhibitors with picomolar enzymatic activities. Furthermore, initial low cellular activities on A549 cells could be increased significantly in numerous examples resulting in cellular IC50 values in the subnanomolar range. Further characterization of the highly potent inhibitors 90 und 93 revealed promising pharmacokinetic properties and strong activities in organoids in combination with etoposide. Additionally, 93 showed no off-target activities within a kinome-representative mini kinase panel, with favorable selectivities within the PIKK- and PI3K-families.
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Affiliation(s)
- Teodor Dimitrov
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität, Tübingen 72076, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany
| | - Athina Anastasia Moschopoulou
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital of Tübingen, Tübingen 72076, Germany
- German Cancer Research Consortium (DKTK), Partner Site Tübingen, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Lennart Seidel
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität, Tübingen 72076, Germany
| | - Thales Kronenberger
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität, Tübingen 72076, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Tübingen 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Mark Kudolo
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität, Tübingen 72076, Germany
| | - Antti Poso
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität, Tübingen 72076, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Tübingen 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Christian Geibel
- Department of Pharmaceutical (Bio-)Analysis, Institute of Pharmaceutical Sciences, Eberhard Karls Universität, Tübingen 72076, Germany
| | - Pascal Wölffing
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Tübingen 72076, Germany
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital of Tübingen, Tübingen 72076, Germany
| | - Daniel Dauch
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Tübingen 72076, Germany
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital of Tübingen, Tübingen 72076, Germany
| | - Lars Zender
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital of Tübingen, Tübingen 72076, Germany
- German Cancer Research Consortium (DKTK), Partner Site Tübingen, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Dieter Schollmeyer
- Department Chemie, Johannes Gutenberg-Universitaet Mainz, Zentrale Analytik, Duesbergweg 10-14, Mainz 55099, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Friedrich-Hirzebruch-Allee 5/6, Bonn D-53115, Germany
| | - Michael Forster
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität, Tübingen 72076, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany
| | - Stefan Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität, Tübingen 72076, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Tübingen 72076, Germany
- German Cancer Research Consortium (DKTK), Partner Site Tübingen, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
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28
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Valdameri G, Kita DH, Dutra JDP, Gomes DL, Tonduru AK, Kronenberger T, Gavinho B, Rossi IV, Carvalho MMD, Pérès B, Zattoni IF, Rego FGDM, Picheth G, Freitas RAD, Poso A, Ambudkar SV, Ramirez MI, Boumendjel A, Moure VR. Characterization of Potent ABCG2 Inhibitor Derived from Chromone: From the Mechanism of Inhibition to Human Extracellular Vesicles for Drug Delivery. Pharmaceutics 2023; 15:pharmaceutics15041259. [PMID: 37111745 PMCID: PMC10144134 DOI: 10.3390/pharmaceutics15041259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
Inhibition of ABC transporters is a promising approach to overcome multidrug resistance in cancer. Herein, we report the characterization of a potent ABCG2 inhibitor, namely, chromone 4a (C4a). Molecular docking and in vitro assays using ABCG2 and P-glycoprotein (P-gp) expressing membrane vesicles of insect cells revealed that C4a interacts with both transporters, while showing selectivity toward ABCG2 using cell-based transport assays. C4a inhibited the ABCG2-mediated efflux of different substrates and molecular dynamic simulations demonstrated that C4a binds in the Ko143-binding pocket. Liposomes and extracellular vesicles (EVs) of Giardia intestinalis and human blood were used to successfully bypass the poor water solubility and delivery of C4a as assessed by inhibition of the ABCG2 function. Human blood EVs also promoted delivery of the well-known P-gp inhibitor, elacridar. Here, for the first time, we demonstrated the potential use of plasma circulating EVs for drug delivery of hydrophobic drugs targeting membrane proteins.
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Affiliation(s)
- Glaucio Valdameri
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba 80210-170, PR, Brazil
| | - Diogo Henrique Kita
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba 80210-170, PR, Brazil
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4256, USA
| | - Julia de Paula Dutra
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba 80210-170, PR, Brazil
| | - Diego Lima Gomes
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba 80210-170, PR, Brazil
| | - Arun Kumar Tonduru
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Thales Kronenberger
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Bruno Gavinho
- Microbiology, Parasitology and Pathology Program, Federal University of Parana, Curitiba 81530-000, PR, Brazil
| | - Izadora Volpato Rossi
- Cell and Molecular Biology Program, Federal University of Parana, Curitiba 81530-000, PR, Brazil
| | - Mariana Mazetto de Carvalho
- Biopol, Graduate Program in Pharmaceutical Sciences, Federal University of Parana, Curitiba 80210-170, PR, Brazil
| | - Basile Pérès
- Département de Pharmacochimie Moléculaire UMR 5063, Université Grenoble Alpes, 38041 Grenoble, France
| | - Ingrid Fatima Zattoni
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba 80210-170, PR, Brazil
| | | | - Geraldo Picheth
- Graduate Program in Pharmaceutical Sciences, Federal University of Parana, Curitiba 80210-170, PR, Brazil
| | - Rilton Alves de Freitas
- Biopol, Graduate Program in Pharmaceutical Sciences, Federal University of Parana, Curitiba 80210-170, PR, Brazil
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Suresh V Ambudkar
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4256, USA
| | - Marcel I Ramirez
- Laboratory of Cell Biology, Carlos Chagas Institute, Fiocruz, Curitiba 81310-020, PR, Brazil
| | | | - Vivian Rotuno Moure
- Graduate Program in Pharmaceutical Sciences, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba 80210-170, PR, Brazil
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29
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Ferreira GM, Kronenberger T, Maltarollo VG, Poso A, de Moura Gatti F, Almeida VM, Marana SR, Lopes CD, Tezuka DY, de Albuquerque S, da Silva Emery F, Trossini GHG. Trypanosoma cruzi Sirtuin 2 as a Relevant Druggable Target: New Inhibitors Developed by Computer-Aided Drug Design. Pharmaceuticals (Basel) 2023; 16:ph16030428. [PMID: 36986527 PMCID: PMC10057528 DOI: 10.3390/ph16030428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/17/2023] [Accepted: 03/03/2023] [Indexed: 03/14/2023] Open
Abstract
Trypanosoma cruzi, the etiological agent of Chagas disease, relies on finely coordinated epigenetic regulation during the transition between hosts. Herein we targeted the silent information regulator 2 (Sir2) enzyme, a NAD+-dependent class III histone deacetylase, to interfere with the parasites’ cell cycle. A combination of molecular modelling with on-target experimental validation was used to discover new inhibitors from commercially available compound libraries. We selected six inhibitors from the virtual screening, which were validated on the recombinant Sir2 enzyme. The most potent inhibitor (CDMS-01, IC50 = 40 μM) was chosen as a potential lead compound.
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Affiliation(s)
- Glaucio Monteiro Ferreira
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo, Av Prof Lineu Prestes 580, Building. 13, São Paulo 05508-000, SP, Brazil; (G.M.F.)
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, Av Prof Lineu Prestes 580, Building. 17, São Paulo 05508-000, SP, Brazil
| | - Thales Kronenberger
- Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, 72076 Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Vinicius Gonçalves Maltarollo
- Department of Pharmaceutical Products, Faculty of Pharmacy, Federal University of Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte 31270-901, MG, Brazil
| | - Antti Poso
- Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, 72076 Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Fernando de Moura Gatti
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo, Av Prof Lineu Prestes 580, Building. 13, São Paulo 05508-000, SP, Brazil; (G.M.F.)
| | - Vitor Medeiros Almeida
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av Prof Lineu Prestes 748, Building 12, São Paulo 05508-000, SP, Brazil; (V.M.A.)
| | - Sandro Roberto Marana
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av Prof Lineu Prestes 748, Building 12, São Paulo 05508-000, SP, Brazil; (V.M.A.)
| | - Carla Duque Lopes
- Department of Clinical Toxicological and Bromatological Analysis, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, Ribeirão Preto 14040-903, SP, Brazil
| | - Daiane Yukie Tezuka
- Department of Clinical Toxicological and Bromatological Analysis, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, Ribeirão Preto 14040-903, SP, Brazil
| | - Sérgio de Albuquerque
- Department of Clinical Toxicological and Bromatological Analysis, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, Ribeirão Preto 14040-903, SP, Brazil
| | - Flavio da Silva Emery
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, Ribeirão Preto 14040-903, SP, Brazil
- Correspondence: (F.d.S.E.); (G.H.G.T.); Tel.: +55-11-3091-3793 (G.H.G.T.)
| | - Gustavo Henrique Goulart Trossini
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo, Av Prof Lineu Prestes 580, Building. 13, São Paulo 05508-000, SP, Brazil; (G.M.F.)
- Correspondence: (F.d.S.E.); (G.H.G.T.); Tel.: +55-11-3091-3793 (G.H.G.T.)
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30
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Díaz‐Holguín A, Rashidian A, Pijnenburg D, Monteiro Ferreira G, Stefela A, Kaspar M, Kudova E, Poso A, van Beuningen R, Pavek P, Kronenberger T. Front Cover: When Two Become One: Conformational Changes in FXR/RXR Heterodimers Bound to Steroidal Antagonists (ChemMedChem 4/2023). ChemMedChem 2023. [DOI: 10.1002/cmdc.202300056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Affiliation(s)
- Alejandro Díaz‐Holguín
- School of Pharmacy Faculty of Health Sciences University of Eastern Finland Kuopio 70211 Finland
- Current address: Science for Life Laboratory Department of Cell and Molecular Biology Uppsala University 75124 Uppsala Sweden
| | - Azam Rashidian
- Institute of Pharmacy Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2) Eberhard Karls University Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Internal Medicine VIII University Hospital of Tübingen Otfried-Müller-Strasse 14 72076 Tübingen Germany
| | - Dirk Pijnenburg
- PamGene International B.V. Wolvenhoek 10 5211HH ‘s-Hertogenbosch Netherlands
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses School of Pharmaceutical Sciences University of São Paulo Av. Prof. Lineu Prestes 580 05508-000 São Paulo Brazil
| | - Alzbeta Stefela
- Department of Pharmacology and Toxicology Charles University Heyrovskeho 1203 50005 Hradec Kralove Czechia
| | - Miroslav Kaspar
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 542/2 16000 Prague Czechia
- Faculty of Sciences Charles University in Prague Albertov 6 Prague 2 12843 Czechia
| | - Eva Kudova
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 542/2 16000 Prague Czechia
| | - Antti Poso
- Institute of Pharmacy Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2) Eberhard Karls University Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Internal Medicine VIII University Hospital of Tübingen Otfried-Müller-Strasse 14 72076 Tübingen Germany
- School of Pharmacy Faculty of Health Sciences University of Eastern Finland Kuopio 70211 Finland
| | - Rinie van Beuningen
- PamGene International B.V. Wolvenhoek 10 5211HH ‘s-Hertogenbosch Netherlands
| | - Petr Pavek
- Department of Pharmacology and Toxicology Charles University Heyrovskeho 1203 50005 Hradec Kralove Czechia
| | - Thales Kronenberger
- Institute of Pharmacy Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2) Eberhard Karls University Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Internal Medicine VIII University Hospital of Tübingen Otfried-Müller-Strasse 14 72076 Tübingen Germany
- School of Pharmacy Faculty of Health Sciences University of Eastern Finland Kuopio 70211 Finland
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31
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Díaz-Holguín A, Rashidian A, Pijnenburg D, Monteiro Ferreira G, Stefela A, Kaspar M, Kudova E, Poso A, van Beuningen R, Pavek P, Kronenberger T. When Two Become One: Conformational Changes in FXR/RXR Heterodimers Bound to Steroidal Antagonists. ChemMedChem 2023; 18:e202200556. [PMID: 36398403 DOI: 10.1002/cmdc.202200556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/15/2022] [Indexed: 11/19/2022]
Abstract
Farnesoid X receptor (FXR) is a nuclear receptor with an essential role in regulating bile acid synthesis and cholesterol homeostasis. FXR activation by agonists is explained by an αAF-2-trapping mechanism; however, antagonism mechanisms are diverse. We discuss microsecond molecular dynamics (MD) simulations investigating our recently reported FXR antagonists 2a and 2 h. We study the antagonist-induced conformational changes in the FXR ligand-binding domain, when compared to the synthetic (GW4064) or steroidal (chenodeoxycholic acid, CDCA) FXR agonists in the FXR monomer or FXR/RXR heterodimer r, and in the presence and absence of the coactivator. Our MD data suggest ligand-specific influence on conformations of different FXR-LBD regions, including the α5/α6 region, αAF-2, and α9-11. Changes in the heterodimerization interface induced by antagonists seem to be associated with αAF-2 destabilization, which prevents both co-activator and co-repressor recruitment. Our results provide new insights into the conformational behaviour of FXR, suggesting that FXR antagonism/agonism shift requires a deeper assessment than originally proposed by crystal structures.
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Affiliation(s)
- Alejandro Díaz-Holguín
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, 70211, Finland.,Current address: Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, 75124, Uppsala, Sweden
| | - Azam Rashidian
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,Department of Internal Medicine VIII, University Hospital of Tübingen, Otfried-Müller-Strasse 14, 72076, Tübingen, Germany
| | - Dirk Pijnenburg
- PamGene International B.V., Wolvenhoek 10, 5211HH, 's-Hertogenbosch, Netherlands
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 580, 05508-000, São Paulo, Brazil
| | - Alzbeta Stefela
- Department of Pharmacology and Toxicology, Charles University, Heyrovskeho 1203, 50005, Hradec Kralove, Czechia
| | - Miroslav Kaspar
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 16000, Prague, Czechia.,Faculty of Sciences, Charles University in Prague, Albertov 6, Prague 2, 12843, Czechia
| | - Eva Kudova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 16000, Prague, Czechia
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,Department of Internal Medicine VIII, University Hospital of Tübingen, Otfried-Müller-Strasse 14, 72076, Tübingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Rinie van Beuningen
- PamGene International B.V., Wolvenhoek 10, 5211HH, 's-Hertogenbosch, Netherlands
| | - Petr Pavek
- Department of Pharmacology and Toxicology, Charles University, Heyrovskeho 1203, 50005, Hradec Kralove, Czechia
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,Department of Internal Medicine VIII, University Hospital of Tübingen, Otfried-Müller-Strasse 14, 72076, Tübingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, 70211, Finland
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32
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Huttunen J, Kronenberger T, Montaser AB, Králová A, Terasaki T, Poso A, Huttunen KM. Sodium-Dependent Neutral Amino Acid Transporter 2 Can Serve as a Tertiary Carrier for l-Type Amino Acid Transporter 1-Utilizing Prodrugs. Mol Pharm 2023; 20:1331-1346. [PMID: 36688491 PMCID: PMC9906736 DOI: 10.1021/acs.molpharmaceut.2c00948] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Membrane transporters are the key determinants of the homeostasis of endogenous compounds in the cells and their exposure to drugs. However, the substrate specificities of distinct transporters can overlap. In the present study, the interactions of l-type amino acid transporter 1 (LAT1)-utilizing prodrugs with sodium-coupled neutral amino acid transporter 2 (SNAT2) were explored. The results showed that the cellular uptake of LAT1-utilizing prodrugs into a human breast cancer cell line, MCF-7 cells, was mediated via SNATs as the uptake was increased at higher pH (8.5), decreased in the absence of sodium, and inhibited in the presence of unselective SNAT-inhibitor, (α-(methylamino)isobutyric acid, MeAIB). Moreover, docking the compounds to a SNAT2 homology model (inward-open conformation) and further molecular dynamics simulations and the subsequent trajectory and principal component analyses confirmed the chemical features supporting the interactions of the studied compounds with SNAT2, which was found to be the main SNAT expressed in MCF-7 cells.
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Affiliation(s)
- Johanna Huttunen
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.
Box 1627, FI-70211 Kuopio, Finland
| | - Thales Kronenberger
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.
Box 1627, FI-70211 Kuopio, Finland,Department
of Internal Medicine VIII, University Hospital
Tübingen, Otfried-Müller-Strasse
14, DE 72076 Tübingen, Germany,Department
of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical
Sciences, Eberhard-Karls-Universität,
Tübingen, Auf
der Morgenstelle 8, 72076 Tübingen, Germany,Cluster
of Excellence iFIT (EXC 2180) “Image-Guided and Functionally
Instructed Tumor Therapies”, University
of Tübingen, 72076 Tübingen, Germany,Tübingen
Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tübingen, Germany
| | - Ahmed B. Montaser
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.
Box 1627, FI-70211 Kuopio, Finland
| | - Adéla Králová
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.
Box 1627, FI-70211 Kuopio, Finland
| | - Tetsuya Terasaki
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.
Box 1627, FI-70211 Kuopio, Finland
| | - Antti Poso
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.
Box 1627, FI-70211 Kuopio, Finland,Department
of Internal Medicine VIII, University Hospital
Tübingen, Otfried-Müller-Strasse
14, DE 72076 Tübingen, Germany,Department
of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical
Sciences, Eberhard-Karls-Universität,
Tübingen, Auf
der Morgenstelle 8, 72076 Tübingen, Germany,Cluster
of Excellence iFIT (EXC 2180) “Image-Guided and Functionally
Instructed Tumor Therapies”, University
of Tübingen, 72076 Tübingen, Germany,Tübingen
Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tübingen, Germany
| | - Kristiina M. Huttunen
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.
Box 1627, FI-70211 Kuopio, Finland,
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33
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Bahrami K, Järvinen J, Laitinen T, Reinisalo M, Honkakoski P, Poso A, Huttunen KM, Rautio J. Structural Features Affecting the Interactions and Transportability of LAT1-Targeted Phenylalanine Drug Conjugates. Mol Pharm 2023; 20:206-218. [PMID: 36394563 PMCID: PMC9811466 DOI: 10.1021/acs.molpharmaceut.2c00594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
L-type amino acid transporter 1 (LAT1) transfers essential amino acids across cell membranes. Owing to its predominant expression in the blood-brain barrier and tumor cells, LAT1 has been exploited for drug delivery and targeting to the central nervous system (CNS) and various cancers. Although the interactions of amino acids and their mimicking compounds with LAT1 have been extensively investigated, the specific structural features for an optimal drug scaffold have not yet been determined. Here, we evaluated a series of LAT1-targeted drug-phenylalanine conjugates (ligands) by determining their uptake rates by in vitro studies and investigating their interaction with LAT1 via induced-fit docking. Combining the experimental and computational data, we concluded that although LAT1 can accommodate various types of structures, smaller compounds are preferred. As the ligand size increased, its flexibility became more crucial in determining the compound's transportability and interactions. Compounds with linear or planar structures exhibited reduced uptake; those with rigid lipophilic structures lacked interactions and likely utilized other transport mechanisms for cellular entry. Introducing polar groups between aromatic structures enhanced interactions. Interestingly, compounds with a carbamate bond in the aromatic ring's para-position displayed very good transport efficiencies for the larger compounds. Compared to the ester bond, the corresponding amide bond had superior hydrogen bond acceptor properties and increased interactions. A reverse amide bond was less favorable than a direct amide bond for interactions with LAT1. The present information can be applied broadly to design appropriate CNS or antineoplastic drug candidates with a prodrug strategy and to discover novel LAT1 inhibitors used either as direct or adjuvant cancer therapy.
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Los B, Ferreira GM, Borges JB, Kronenberger T, Oliveira VFD, Dagli-Hernandez C, Bortolin RH, Gonçalves RM, Faludi AA, Mori AA, Barbosa TKA, Freitas RCCD, Jannes CE, Pereira ADC, Bastos GM, Poso A, Hirata RDC, Hirata MH. Effects of PCSK9 missense variants on molecular conformation and biological activity in transfected HEK293FT cells. Gene 2023; 851:146979. [DOI: 10.1016/j.gene.2022.146979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/30/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
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35
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Santos LH, Kronenberger T, Almeida RG, Silva EB, Rocha REO, Oliveira JC, Barreto LV, Skinner D, Fajtová P, Giardini MA, Woodworth B, Bardine C, Lourenço AL, Craik CS, Poso A, Podust LM, McKerrow JH, Siqueira-Neto JL, O’Donoghue AJ, da Silva
Júnior EN, Ferreira RS. Structure-Based Identification of Naphthoquinones and Derivatives as Novel Inhibitors of Main Protease M pro and Papain-like Protease PL pro of SARS-CoV-2. J Chem Inf Model 2022; 62:6553-6573. [PMID: 35960688 PMCID: PMC9397563 DOI: 10.1021/acs.jcim.2c00693] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Indexed: 01/07/2023]
Abstract
The worldwide COVID-19 pandemic caused by the coronavirus SARS-CoV-2 urgently demands novel direct antiviral treatments. The main protease (Mpro) and papain-like protease (PLpro) are attractive drug targets among coronaviruses due to their essential role in processing the polyproteins translated from the viral RNA. In this study, we virtually screened 688 naphthoquinoidal compounds and derivatives against Mpro of SARS-CoV-2. Twenty-four derivatives were selected and evaluated in biochemical assays against Mpro using a novel fluorogenic substrate. In parallel, these compounds were also assayed with SARS-CoV-2 PLpro. Four compounds inhibited Mpro with half-maximal inhibitory concentration (IC50) values between 0.41 μM and 9.0 μM. In addition, three compounds inhibited PLpro with IC50 ranging from 1.9 μM to 3.3 μM. To verify the specificity of Mpro and PLpro inhibitors, our experiments included an assessment of common causes of false positives such as aggregation, high compound fluorescence, and inhibition by enzyme oxidation. Altogether, we confirmed novel classes of specific Mpro and PLpro inhibitors. Molecular dynamics simulations suggest stable binding modes for Mpro inhibitors with frequent interactions with residues in the S1 and S2 pockets of the active site. For two PLpro inhibitors, interactions occur in the S3 and S4 pockets. In summary, our structure-based computational and biochemical approach identified novel naphthoquinonal scaffolds that can be further explored as SARS-CoV-2 antivirals.
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Affiliation(s)
- Lucianna H. Santos
- Department of Biochemistry and Immunology,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
| | - Thales Kronenberger
- Department of Oncology and Pneumonology, Internal
Medicine VIII, University Hospital Tübingen,
Otfried-Müller-Straße 10, DE72076 Tübingen,
Germany
- School of Pharmacy, Faculty of Health Sciences,
University of Eastern Finland, 70211 Kuopio,
Finland
- Institute of Pharmacy, Pharmaceutical/Medicinal
Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2),
Eberhard Karls University Tübingen, Auf der
Morgenstelle 8, 72076 Tübingen, Germany
| | - Renata G. Almeida
- Institute of Exact Sciences, Department of Chemistry,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
| | - Elany B. Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - Rafael E. O. Rocha
- Department of Biochemistry and Immunology,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
| | - Joyce C. Oliveira
- Institute of Exact Sciences, Department of Chemistry,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
| | - Luiza V. Barreto
- Department of Biochemistry and Immunology,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
| | - Danielle Skinner
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
- Institute of Organic Chemistry and Biochemistry,
Academy of Sciences of the Czech Republic, 16610 Prague,
Czech Republic
| | - Miriam A. Giardini
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - Brendon Woodworth
- Department of Medicine, Division of Infectious
Diseases, University of California San Diego, La Jolla,
California 92093, United States
| | - Conner Bardine
- Department of Pharmaceutical Chemistry,
University of California San Francisco, San Francisco,
California 94143, United States
| | - André L. Lourenço
- Department of Pharmaceutical Chemistry,
University of California San Francisco, San Francisco,
California 94143, United States
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry,
University of California San Francisco, San Francisco,
California 94143, United States
| | - Antti Poso
- Department of Oncology and Pneumonology, Internal
Medicine VIII, University Hospital Tübingen,
Otfried-Müller-Straße 10, DE72076 Tübingen,
Germany
- School of Pharmacy, Faculty of Health Sciences,
University of Eastern Finland, 70211 Kuopio,
Finland
| | - Larissa M. Podust
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - James H. McKerrow
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - Jair L. Siqueira-Neto
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, 9500 Gilman Drive, La
Jolla, California 92093-0657, United States
| | - Eufrânio N. da Silva
Júnior
- Institute of Exact Sciences, Department of Chemistry,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
| | - Rafaela S. Ferreira
- Department of Biochemistry and Immunology,
Federal University of Minas Gerais, Belo Horizonte, Minas
Gerais 31270-901, Brazil
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36
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Abstract
It is crucial for molecular dynamics simulations of biomembranes that the force field parameters give a realistic model of the membrane behavior. In this study, we examined the OPLS3e force field for the carbon-hydrogen order parameters SCH of POPC (1-palmitoyl-2-oleoylphosphatidylcholine) lipid bilayers at varying hydration conditions and ion concentrations. The results show that OPLS3e behaves similarly to the CHARMM36 force field and relatively accurately follows the experimentally measured SCH for the lipid headgroup, the glycerol backbone, and the acyl tails. Thus, OPLS3e is a good choice for POPC bilayer simulations under many biologically relevant conditions. The exception are systems with an abundancy of ions, as similarly to most other force fields OPLS3e strongly overestimates the membrane-binding of cations, especially Ca2+. This leads to undesirable positive charge of the membrane surface and drastically lowers the concentration of Ca2+ in the surrounding solvent, which might cause issues in systems sensitive to correct charge distribution profiles across the membrane.
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Affiliation(s)
- Milla Kurki
- School
of Pharmacy, University of Eastern Finland, Kuopio Campus, Yliopistonranta 1
C, P.O. Box 1627, 70211 Kuopio, Finland
| | - Antti Poso
- School
of Pharmacy, University of Eastern Finland, Kuopio Campus, Yliopistonranta 1
C, P.O. Box 1627, 70211 Kuopio, Finland
| | - Piia Bartos
- School
of Pharmacy, University of Eastern Finland, Kuopio Campus, Yliopistonranta 1
C, P.O. Box 1627, 70211 Kuopio, Finland,
| | - Markus S. Miettinen
- Department
of Chemistry, University of Bergen, 5007 Bergen, Norway,Computational
Biology Unit, Department of Informatics, University of Bergen, 5007 Bergen, Norway
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37
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Imberg L, Platte S, Erbacher C, Daniliuc CG, Kalinina SA, Dörner W, Poso A, Karst U, Kalinin DV. Amide-functionalized 1,2,4-Triazol-5-amines as Covalent Inhibitors of Blood Coagulation Factor XIIa and Thrombin. ACS Pharmacol Transl Sci 2022; 5:1318-1347. [PMID: 36524012 PMCID: PMC9745896 DOI: 10.1021/acsptsci.2c00204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Indexed: 12/05/2022]
Abstract
To counteract thrombosis, new safe and efficient antithrombotics are required. We herein report the design, synthesis, and biological activity of a series of amide-functionalized acylated 1,2,4-triazol-5-amines as selective inhibitors of blood coagulation factor XIIa and thrombin. The introduction of an amide moiety into the main scaffold of 3-aryl aminotriazoles added certain three-dimensional properties to synthesized compounds and allowed them to reach binding sites in FXIIa and thrombin previously unaddressed by non-functionalized 1,2,4-triazol-5-amines. Among synthesized compounds, one quinoxaline-derived aminotriazole bearing N-butylamide moiety inhibited FXIIa with the IC50 value of 28 nM, whereas the N-phenylamide-derived aminotriazole inhibited thrombin with the IC50 value of 41 nM. Performed mass-shift experiments and molecular modeling studies proved the covalent mechanism of FXIIa and thrombin inhibition by synthesized compounds. In plasma coagulation tests, developed aminotriazoles showed anticoagulant properties mainly affecting the intrinsic blood coagulation pathway, activation of which is associated with thrombosis but is negligible for hemostasis.
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Affiliation(s)
- Lukas Imberg
- Institute
of Pharmaceutical and Medicinal Chemistry, University of Münster, Münster 48149, Germany
| | - Simon Platte
- Institute
of Pharmaceutical and Medicinal Chemistry, University of Münster, Münster 48149, Germany
| | - Catharina Erbacher
- Institute
of Inorganic and Analytical Chemistry, University
of Münster, Münster 48149, Germany
| | | | | | - Wolfgang Dörner
- Institute
of Biochemistry, University of Münster, Münster 48149, Germany
| | - Antti Poso
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
- Department
of Internal Medicine VIII, University Hospital
Tübingen, Tübingen 72076, Germany
| | - Uwe Karst
- Institute
of Inorganic and Analytical Chemistry, University
of Münster, Münster 48149, Germany
| | - Dmitrii V. Kalinin
- Institute
of Pharmaceutical and Medicinal Chemistry, University of Münster, Münster 48149, Germany
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38
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Maltarollo VG, Shevchenko E, Lima IDDM, Cino EA, Ferreira GM, Poso A, Kronenberger T. Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels. J Chem Inf Model 2022; 62:5746-5761. [PMID: 36343333 DOI: 10.1021/acs.jcim.2c01178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The enzyme enoyl-ACP reductase (FabI) is the limiting step of the membrane's fatty acid biosynthesis in bacteria and a druggable target for novel antibacterial agents. The FabI active form is a homotetramer, which displays the highest affinity to inhibitors. Herein, molecular dynamics studies were carried out using the structure of FabI in complex with known inhibitors to investigate their effects on tetramerization. Our results suggest that multimerization is essential for the integrity of the catalytic site and that inhibitor binding enables the multimerization by stabilizing the substrate binding loop (SBL, L:195-200) coupled with changes in the H4/5 (QR interface). We also observed that AFN-1252 (naphtpyridinone derivative) promotes unique conformational changes affecting monomer-monomer interfaces. These changes are induced by AFN-1252 interaction with key residues in the binding sites (Ala95, Tyr146, and Tyr156). In addition, the analysis of water trajectories indicated that AFN-1252 complexes allow more water molecules to enter the binding site than triclosan and MUT056399 complexes. FabI-AFN-1252 simulations show accumulation of water molecules near the Tyr146/147 pocket, which can become a hotspot to the design of novel FabI inhibitors.
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Affiliation(s)
- Vinicius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Ekaterina Shevchenko
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, DE72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tübingen, Germany
| | - Igor Daniel de Miranda Lima
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil
| | - Elio A Cino
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Brazil
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av Prof Lineu Prestes 580, 05508-000 São Paulo, Brazil
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, DE72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tübingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, DE72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tübingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
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39
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Bayrak A, Mohr F, Kolb K, Szpakowska M, Shevchenko E, Dicenta V, Rohlfing AK, Kudolo M, Pantsar T, Günther M, Kaczor AA, Poso A, Chevigné A, Pillaiyar T, Gawaz M, Laufer SA. Discovery and Development of First-in-Class ACKR3/CXCR7 Superagonists for Platelet Degranulation Modulation. J Med Chem 2022; 65:13365-13384. [PMID: 36150079 DOI: 10.1021/acs.jmedchem.2c01198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The atypical chemokine receptor 3 (ACKR3), formerly known as CXC-chemokine receptor 7 (CXCR7), has been postulated to regulate platelet function and thrombus formation. Herein, we report the discovery and development of first-in-class ACKR3 agonists, which demonstrated superagonistic properties with Emax values of up to 160% compared to the endogenous reference ligand CXCL12 in a β-arrestin recruitment assay. Initial in silico screening using an ACKR3 homology model identified two hits, C10 (EC50 19.1 μM) and C11 (EC50 = 11.4 μM). Based on these hits, extensive structure-activity relationship studies were conducted by synthesis and testing of derivatives. It resulted in the identification of the novel thiadiazolopyrimidinone-based compounds 26 (LN5972, EC50 = 3.4 μM) and 27 (LN6023, EC50 = 3.5 μM). These compounds are selective for ACKR3 versus CXCR4 and show metabolic stability. In a platelet degranulation assay, these agonists effectively reduced P-selectin expression by up to 97%, suggesting potential candidates for the treatment of platelet-mediated thrombosis.
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Affiliation(s)
- Alp Bayrak
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Florian Mohr
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Kyra Kolb
- Department of Internal Medicine III, Cardiology and Angiology, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076 Tübingen, Germany
| | - Martyna Szpakowska
- Department of Infection and Immunity, Immuno-Pharmacology and Interactomics, Luxembourg Institute of Health (LIH), L-4354 Esch-sur-Alzette, Luxembourg
| | - Ekaterina Shevchenko
- Department of Internal Medicine VIII, Oncology and Pneumology, University Hospital Tübingen, Otfried-Müller-Strasse 14, 72076 Tübingen, Germany
| | - Valerie Dicenta
- Department of Internal Medicine III, Cardiology and Angiology, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076 Tübingen, Germany
| | - Anne-Katrin Rohlfing
- Department of Internal Medicine III, Cardiology and Angiology, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076 Tübingen, Germany
| | - Mark Kudolo
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Tatu Pantsar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,School of Pharmacy, University of Eastern Finland, P.O. BOX 1627, 70211 Kuopio, Finland
| | - Marcel Günther
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Agnieszka A Kaczor
- School of Pharmacy, University of Eastern Finland, P.O. BOX 1627, 70211 Kuopio, Finland.,Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodzki St., PL-20093 Lublin, Poland
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, P.O. BOX 1627, 70211 Kuopio, Finland.,Department of Internal Medicine VIII, Oncology and Pneumology, University Hospital Tübingen, Otfried-Müller-Strasse 14, 72076 Tübingen, Germany
| | - Andy Chevigné
- Department of Infection and Immunity, Immuno-Pharmacology and Interactomics, Luxembourg Institute of Health (LIH), L-4354 Esch-sur-Alzette, Luxembourg
| | - Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Meinrad Gawaz
- Department of Internal Medicine III, Cardiology and Angiology, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076 Tübingen, Germany
| | - Stefan A Laufer
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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40
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Laitinen T, Meili T, Koyioni M, Koutentis PA, Poso A, Hofmann-Lehmann R, Asquith CRM. Synthesis and evaluation of 1,2,3-dithiazole inhibitors of the nucleocapsid protein of feline immunodeficiency virus (FIV) as a model for HIV infection. Bioorg Med Chem 2022; 68:116834. [PMID: 35653871 DOI: 10.1016/j.bmc.2022.116834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/13/2022] [Accepted: 05/13/2022] [Indexed: 11/17/2022]
Abstract
We disclose a series of potent anti-viral 1,2,3-dithiazoles, accessed through a succinct synthetic approach from 4,5-dichloro-1,2,3-dithiazolium chloride (Appel's salt). A series of small libraries of compounds were screened against feline immunodeficiency virus (FIV) infected cells as a model for HIV. This approach highlighted new structure activity relationship understanding and led to the development of sub-micro molar anti-viral compounds with reduced toxicity. In addition, insight into the mechanistic progress of this system is provided via advanced QM-MM modelling. The 1,2,3-dithiazole represents a versatile scaffold with potential for further development to treat both FIV and HIV.
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Affiliation(s)
- Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Theres Meili
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich 8057, Switzerland
| | - Maria Koyioni
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | | | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland; Department of Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Strasse 14, 72076 Tübingen, Germany
| | - Regina Hofmann-Lehmann
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Christopher R M Asquith
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland; Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, NC 27599, USA.
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41
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Pillaiyar T, Flury P, Krüger N, Su H, Schäkel L, Barbosa Da Silva E, Eppler O, Kronenberger T, Nie T, Luedtke S, Rocha C, Sylvester K, Petry MR, McKerrow JH, Poso A, Pöhlmann S, Gütschow M, O’Donoghue AJ, Xu Y, Müller CE, Laufer SA. Small-Molecule Thioesters as SARS-CoV-2 Main Protease Inhibitors: Enzyme Inhibition, Structure-Activity Relationships, Antiviral Activity, and X-ray Structure Determination. J Med Chem 2022; 65:9376-9395. [PMID: 35709506 PMCID: PMC9216242 DOI: 10.1021/acs.jmedchem.2c00636] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Indexed: 02/08/2023]
Abstract
The main protease (Mpro, 3CLpro) of SARS-CoV-2 is an attractive target in coronaviruses because of its crucial involvement in viral replication and transcription. Here, we report on the design, synthesis, and structure-activity relationships of novel small-molecule thioesters as SARS-CoV-2 Mpro inhibitors. Compounds 3w and 3x exhibited excellent SARS-CoV-2 Mpro inhibition with kinac/Ki of 58,700 M-1 s-1 (Ki = 0.0141 μM) and 27,200 M-1 s-1 (Ki = 0.0332 μM), respectively. In Calu-3 and Vero76 cells, compounds 3h, 3i, 3l, 3r, 3v, 3w, and 3x displayed antiviral activity in the nanomolar range without host cell toxicity. Co-crystallization of 3w and 3af with SARS-CoV-2 Mpro was accomplished, and the X-ray structures showed covalent binding with the catalytic Cys145 residue of the protease. The potent SARS-CoV-2 Mpro inhibitors also inhibited the Mpro of other beta-coronaviruses, including SARS-CoV-1 and MERS-CoV, indicating that they might be useful to treat a broader range of coronaviral infections.
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Affiliation(s)
- Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal
Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls
University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
Cluster of Excellence iFIT (EXC 2180) “Image-Guided & Functionally Instructed
Tumor Therapies”, University of Tübingen,
Tübingen 72076, Germany
| | - Philipp Flury
- Institute of Pharmacy, Pharmaceutical/Medicinal
Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls
University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
Cluster of Excellence iFIT (EXC 2180) “Image-Guided & Functionally Instructed
Tumor Therapies”, University of Tübingen,
Tübingen 72076, Germany
| | - Nadine Krüger
- Infection Biology Unit, German Primate
Center, Leibniz Institute for Primate Research Göttingen,
Kellnerweg 4, Göttingen 37077, Germany
| | - Haixia Su
- CAS Key Laboratory of Receptor Research, and Stake Key
Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese
Academy of Sciences, Shanghai 201203, China
| | - Laura Schäkel
- PharmaCenter Bonn, Pharmaceutical Institute,
Pharmaceutical & Medicinal Chemistry, University of Bonn,
An der Immenburg 4, Bonn D-53121, Germany
| | - Elany Barbosa Da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
| | - Olga Eppler
- Institute of Pharmacy, Pharmaceutical/Medicinal
Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls
University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
Cluster of Excellence iFIT (EXC 2180) “Image-Guided & Functionally Instructed
Tumor Therapies”, University of Tübingen,
Tübingen 72076, Germany
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal
Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls
University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
Cluster of Excellence iFIT (EXC 2180) “Image-Guided & Functionally Instructed
Tumor Therapies”, University of Tübingen,
Tübingen 72076, Germany
| | - Tianqing Nie
- CAS Key Laboratory of Receptor Research, and Stake Key
Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese
Academy of Sciences, Shanghai 201203, China
| | - Stephanie Luedtke
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
| | - Cheila Rocha
- Infection Biology Unit, German Primate
Center, Leibniz Institute for Primate Research Göttingen,
Kellnerweg 4, Göttingen 37077, Germany
| | - Katharina Sylvester
- PharmaCenter Bonn, Pharmaceutical Institute,
Pharmaceutical & Medicinal Chemistry, University of Bonn,
An der Immenburg 4, Bonn D-53121, Germany
| | - Marvin R.I. Petry
- PharmaCenter Bonn, Pharmaceutical Institute,
Pharmaceutical & Medicinal Chemistry, University of Bonn,
An der Immenburg 4, Bonn D-53121, Germany
| | - James H. McKerrow
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal
Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls
University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
Cluster of Excellence iFIT (EXC 2180) “Image-Guided & Functionally Instructed
Tumor Therapies”, University of Tübingen,
Tübingen 72076, Germany
- School of Pharmacy, Faculty of Health Sciences,
University of Eastern Finland, Kuopio 70211,
Finland
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate
Center, Leibniz Institute for Primate Research Göttingen,
Kellnerweg 4, Göttingen 37077, Germany
- Faculty of Biology and Psychology,
University Göttingen,Göttingen 37073,
Germany
| | - Michael Gütschow
- PharmaCenter Bonn, Pharmaceutical Institute,
Pharmaceutical & Medicinal Chemistry, University of Bonn,
An der Immenburg 4, Bonn D-53121, Germany
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences,
University of California San Diego, La Jolla, California
92093, United States
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, and Stake Key
Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese
Academy of Sciences, Shanghai 201203, China
| | - Christa E. Müller
- PharmaCenter Bonn, Pharmaceutical Institute,
Pharmaceutical & Medicinal Chemistry, University of Bonn,
An der Immenburg 4, Bonn D-53121, Germany
| | - Stefan A. Laufer
- Institute of Pharmacy, Pharmaceutical/Medicinal
Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls
University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
Cluster of Excellence iFIT (EXC 2180) “Image-Guided & Functionally Instructed
Tumor Therapies”, University of Tübingen,
Tübingen 72076, Germany
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42
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Ferreira GM, Pillaiyar T, Hirata MH, Poso A, Kronenberger T. Inhibitor induced conformational changes in SARS-COV-2 papain-like protease. Sci Rep 2022; 12:11585. [PMID: 35803957 PMCID: PMC9270405 DOI: 10.1038/s41598-022-15181-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/20/2022] [Indexed: 01/24/2023] Open
Abstract
SARS-CoV-2's papain-like protease (PLpro) interaction with ligands has recently been explored with a myriad of crystal structures. We used molecular dynamics (MD) simulations to study different PLpro-ligand complexes, their ligand-induced conformational changes, and interactions. We focused on inhibitors reported with known IC50 against PLpro, namely GRL-0617, XR8-89, PLP_Snyder530, and Sander's recently published compound 7 (CPD7), and compared these trajectories against the apostructure (Apo), with a total of around 60 µs worth simulation data. We aimed to study the conformational changes using molecular dynamics simulations for the inhibitors in the PLpro. PCA analyses and the MSM models revealed distinct conformations of PLpro in the absence/presence of ligands and proposed that BL2-loop contributes to the accessibility of these inhibitors. Further, bulkier substituents closer to Tyr268 and Gln269 could improve inhibition of SARS-CoV-2 PLpro by occupying the region between BL2-groove and BL2-loop, but we also expand on the relevance of exploring multiple PLpro sub-pockets to improve inhibition.
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Affiliation(s)
- Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av Prof Lineu Prestes 580, São Paulo, 05508-000, Brazil
| | - Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Mario Hiroyuki Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av Prof Lineu Prestes 580, São Paulo, 05508-000, Brazil
| | - Antti Poso
- Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, 72076, Tübingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany. .,Department of Oncology and Pneumonology, Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Straße 10, 72076, Tübingen, Germany. .,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland. .,Tübingen Center for Academic Drug Discovery and Development (TüCAD2), 72076, Tübingen, Germany.
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43
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Laitinen T, Meili T, Koyioni M, Koutentis PA, Poso A, Hofmann-Lehmann R, Asquith CR. Corrigendum to “Synthesis and evaluation of 1,2,3-dithiazole inhibitors of the nucleocapsid protein of feline immunodeficiency virus (FIV) as a model for HIV infection” [Bioorg. Med. Chem. 68 (2022) 116834]. Bioorg Med Chem 2022; 71:116948. [DOI: 10.1016/j.bmc.2022.116948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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44
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Targowska-Duda KM, Maj M, Drączkowski P, Budzyńska B, Boguszewska-Czubara A, Wróbel TM, Laitinen T, Kaczmar P, Poso A, Kaczor AA. WaterMap guided structure-based virtual screening for acetylcholinesterase inhibitors. ChemMedChem 2022; 17:e202100721. [PMID: 35157366 DOI: 10.1002/cmdc.202100721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/11/2022] [Indexed: 11/11/2022]
Abstract
Structure-based virtual screening of the Enamine database of 1.7 million compounds followed by WaterMap calculations (a molecular dynamics simulation-based method) was applied to identify novel AChE inhibitors. The inhibitory potency of 29 selected compounds against electric eel (ee) AChE was determined using the Ellman's method. Three compounds were found active (success rate 10%). For the most potent compound (~40% of inhibition at 10 μM), 20 derivatives were discovered based on the Enamine similarity search. Finally, five compounds were found promising (IC 50 ranged from 6.3 µM to 17.5 µM) inhibitors of AChE. The performed similarity and fragment analysis confirmed significant structural novelty of novel AChE inhibitors. Toxicity/safety of selected compounds was determined in zebrafish model.
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Affiliation(s)
| | - Maciej Maj
- Medical University of Lublin: Uniwersytet Medyczny w Lublinie, Department of Biopharmacy, POLAND
| | - Piotr Drączkowski
- Medical University of Lublin: Uniwersytet Medyczny w Lublinie, Department of Synthesis and Chemical Technology of Pharmaceutical Substances, POLAND
| | - Barbara Budzyńska
- Medical University of Lublin: Uniwersytet Medyczny w Lublinie, Independent Laboratory of Behavioral Studies, POLAND
| | - Anna Boguszewska-Czubara
- Medical University of Lublin: Uniwersytet Medyczny w Lublinie, Department of Medical Chemistry, POLAND
| | - Tomasz M Wróbel
- Medical University of Lublin: Uniwersytet Medyczny w Lublinie, Department of Synthesis and Chemical Technology of Pharmaceutical Substances, POLAND
| | - Tuomo Laitinen
- University of Eastern Finland - Kuopio Campus: Ita-Suomen yliopisto - Kuopion kampus, School of Pharmacy, FINLAND
| | - Patrycja Kaczmar
- Medical University of Lublin: Uniwersytet Medyczny w Lublinie, Department of Biopharmacy, POLAND
| | - Antti Poso
- University of Eastern Finland - Kuopio Campus: Ita-Suomen yliopisto - Kuopion kampus, School of Pharmacy, FINLAND
| | - Agnieszka Anna Kaczor
- Medical University of Lublin, Department of Synthesis and Chemical Technology of Pharmaceutical Substances, 4A Chodzki St, 20093, Lublin, POLAND
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45
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Santos LH, Kronenberger T, Almeida RG, Silva EB, Rocha REO, Oliveira JC, Barreto LV, Skinner D, Fajtová P, Giardini MA, Woodworth B, Bardine C, Lourenço AL, Craik CS, Poso A, Podust LM, McKerrow JH, Siqueira-Neto JL, O'Donoghue AJ, da Silva Júnior EN, Ferreira RS. Structure-based identification of naphthoquinones and derivatives as novel inhibitors of main protease Mpro and papain-like protease PLpro of SARS-CoV-2. bioRxiv 2022:2022.01.05.475095. [PMID: 35018373 PMCID: PMC8750648 DOI: 10.1101/2022.01.05.475095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The worldwide COVID-19 pandemic caused by the coronavirus SARS-CoV-2 urgently demands novel direct antiviral treatments. The main protease (Mpro) and papain-like protease (PLpro) are attractive drug targets among coronaviruses due to their essential role in processing the polyproteins translated from the viral RNA. In the present work, we virtually screened 688 naphthoquinoidal compounds and derivatives against Mpro of SARS-CoV-2. Twenty-four derivatives were selected and evaluated in biochemical assays against Mpro using a novel fluorogenic substrate. In parallel, these compounds were also assayed with SARS-CoV-2 PLpro. Four compounds inhibited Mpro with half-maximal inhibitory concentration (IC 50 ) values between 0.41 µM and 66 µM. In addition, eight compounds inhibited PLpro with IC 50 ranging from 1.7 µM to 46 µM. Molecular dynamics simulations suggest stable binding modes for Mpro inhibitors with frequent interactions with residues in the S1 and S2 pockets of the active site. For two PLpro inhibitors, interactions occur in the S3 and S4 pockets. In summary, our structure-based computational and biochemical approach identified novel naphthoquinonal scaffolds that can be further explored as SARS-CoV-2 antivirals.
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46
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Laine LJ, Mäki-Jouppila JHE, Kutvonen E, Tiikkainen P, Nyholm TKM, Tien JF, Umbreit NT, Härmä V, Kallio L, Davis TN, Asbury CL, Poso A, Gorbsky GJ, Kallio MJ. VTT-006, an anti-mitotic compound, binds to the Ndc80 complex and suppresses cancer cell growth in vitro. Oncoscience 2021; 8:134-153. [PMID: 34926718 PMCID: PMC8667816 DOI: 10.18632/oncoscience.549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/01/2021] [Indexed: 11/25/2022] Open
Abstract
Hec1 (Highly expressed in cancer 1) resides in the outer kinetochore where it works to facilitate proper kinetochore-microtubule interactions during mitosis. Hec1 is overexpressed in various cancers and its expression shows correlation with high tumour grade and poor patient prognosis. Chemical perturbation of Hec1 is anticipated to impair kinetochore-microtubule binding, activate the spindle assembly checkpoint (spindle checkpoint) and thereby suppress cell proliferation. In this study, we performed high-throughput screen to identify novel small molecules that target the Hec1 calponin homology domain (CHD), which is needed for normal microtubule attachments. 4 million compounds were first virtually fitted against the CHD, and the best hit molecules were evaluated in vitro. These approaches led to the identification of VTT-006, a 1,2-disubstituted-tetrahydro-beta-carboline derivative, which showed binding to recombinant Ndc80 complex and modulated Hec1 association with microtubules in vitro. VTT-006 treatment resulted in chromosome congression defects, reduced chromosome oscillations and induced loss of inter-kinetochore tension. Cells remained arrested in mitosis with an active spindle checkpoint for several hours before undergoing cell death. VTT-006 suppressed the growth of several cancer cell lines and enhanced the sensitivity of HeLa cells to Taxol. Our findings propose that VTT-006 is a potential anti-mitotic compound that disrupts M phase, impairs kinetochore-microtubule interactions, and activates the spindle checkpoint.
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Affiliation(s)
- Leena J Laine
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland.,Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland.,These authors contributed equally to this work
| | - Jenni H E Mäki-Jouppila
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland.,Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland.,Drug Research Doctoral Programme, University of Turku, Finland.,Department of Pharmacology, Drug Development and Therapeutics, University of Turku, Turku, Finland.,These authors contributed equally to this work
| | - Emma Kutvonen
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland.,Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Pekka Tiikkainen
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland
| | | | - Jerry F Tien
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Neil T Umbreit
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Ville Härmä
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland
| | - Lila Kallio
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Gary J Gorbsky
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Marko J Kallio
- VTT Health, VTT Technical Research Centre of Finland Ltd., Otaniemi, Finland.,Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
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47
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Hellinen L, Koskela A, Vattulainen E, Liukkonen M, Wegler C, Treyer A, Handin N, Svensson R, Myöhänen T, Poso A, Kaarniranta K, Artursson P, Urtti A. Inhibition of prolyl oligopeptidase: A promising pathway to prevent the progression of age-related macular degeneration. Biomed Pharmacother 2021; 146:112501. [PMID: 34891119 DOI: 10.1016/j.biopha.2021.112501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 01/18/2023] Open
Abstract
Dry age-related macular degeneration (AMD) is a currently untreatable vision threatening disease. Impaired proteasomal clearance and autophagy in the retinal pigment epithelium (RPE) and subsequent photoreceptor damage are connected with dry AMD, but detailed pathophysiology is still unclear. In this paper, we discover inhibition of cytosolic protease, prolyl oligopeptidase (PREP), as a potential pathway to treat dry AMD. We showed that PREP inhibitor exposure induced autophagy in the RPE cells, shown by increased LC3-II levels and decreased p62 levels. PREP inhibitor treatment increased total levels of autophagic vacuoles in the RPE cells. Global proteomics was used to examine the phenotype of a commonly used cell model displaying AMD characteristics, oxidative stress and altered protein metabolism, in vitro. These RPE cells displayed induced protein aggregation and clear alterations in macromolecule metabolism, confirming the relevance of the cell model. Differences in intracellular target engagement of PREP inhibitors were observed with cellular thermal shift assay (CETSA). These differences were explained by intracellular drug exposure (the unbound cellular partition coefficient, Kpuu). Importantly, our data is in line with previous observations regarding the discrepancy between PREP's cleaving activity and outcomes in autophagy. This highlights the need to further explore PREP's role in autophagy so that more effective compounds can be designed to battle diseases in which autophagy induction is needed. The present work is the first report investigating the PREP pathway in the RPE and we predict that the PREP inhibitors can be further optimized for treatment of dry AMD.
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Affiliation(s)
- Laura Hellinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70210 Kuopio, Finland; Department of Pharmacy, Uppsala University, 751 23 Uppsala, Sweden
| | - Ali Koskela
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 , Finland
| | - Elina Vattulainen
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 , Finland
| | - Mikko Liukkonen
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 , Finland
| | - Christine Wegler
- Department of Pharmacy, Uppsala University, 751 23 Uppsala, Sweden; Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Uppsala University, 751 23 Uppsala, Sweden
| | - Andrea Treyer
- Department of Pharmacy, Uppsala University, 751 23 Uppsala, Sweden
| | - Niklas Handin
- Department of Pharmacy, Uppsala University, 751 23 Uppsala, Sweden
| | - Richard Svensson
- Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Uppsala University, 751 23 Uppsala, Sweden
| | - Timo Myöhänen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70210 Kuopio, Finland; Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, Finland
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70210 Kuopio, Finland
| | - Kai Kaarniranta
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 , Finland; Department of Ophthalmology, Kuopio University Hospital, P.O. Box 1777, FIN-70211 Kuopio, Finland
| | - Per Artursson
- Department of Pharmacy, Uppsala University, 751 23 Uppsala, Sweden; Uppsala University Drug Optimization and Pharmaceutical Profiling Platform, Uppsala University, 751 23 Uppsala, Sweden; Science for Life Laboratory Drug Discovery and Development Platform, Uppsala University, 751 23 Uppsala, Sweden
| | - Arto Urtti
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70210 Kuopio, Finland; Drug Research Programme, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland; Laboratory of Biohybrid Technologies, Institute of Chemistry, St. Petersburg State University, Peterhoff, St. Petersburg 198504, Russia.
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48
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Ahmed MN, Wahlsten M, Jokela J, Nees M, Stenman UH, Alvarenga DO, Strandin T, Sivonen K, Poso A, Permi P, Metsä-Ketelä M, Koistinen H, Fewer DP. Potent Inhibitor of Human Trypsins from the Aeruginosin Family of Natural Products. ACS Chem Biol 2021; 16:2537-2546. [PMID: 34661384 PMCID: PMC8609519 DOI: 10.1021/acschembio.1c00611] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Serine proteases
regulate many physiological processes and play
a key role in a variety of cancers. Aeruginosins are a family of natural
products produced by cyanobacteria that exhibit pronounced structural
diversity and potent serine protease inhibition. Here, we sequenced
the complete genome of Nodularia sphaerocarpa UHCC 0038 and identified the 43.7 kb suomilide biosynthetic gene
cluster. Bioinformatic analysis demonstrated that suomilide belongs
to the aeruginosin family of natural products. We identified 103 complete
aeruginosin biosynthetic gene clusters from 12 cyanobacterial genera
and showed that they encode an unexpected chemical diversity. Surprisingly,
purified suomilide inhibited human trypsin-2 and -3, with IC50 values of 4.7 and 11.5 nM, respectively, while trypsin-1 was inhibited
with an IC50 of 104 nM. Molecular dynamics simulations
suggested that suomilide has a long residence time when bound to trypsins.
This was confirmed experimentally for trypsin-1 and -3 (residence
times of 1.5 and 57 min, respectively). Suomilide also inhibited the
invasion of aggressive and metastatic PC-3M prostate cancer cells
without affecting cell proliferation. The potent inhibition of trypsin-3,
together with a long residence time and the ability to inhibit prostate
cancer cell invasion, makes suomilide an attractive drug lead for
targeting cancers that overexpress trypsin-3. These results substantially
broaden the genetic and chemical diversity of the aeruginosin family
and suggest that aeruginosins may be a source of selective inhibitors
of human serine proteases.
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Affiliation(s)
- Muhammad N. Ahmed
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Biocenter 1, P.O. Box 56, Helsinki FIN-00014, Finland
- Department of Clinical Chemistry and Haematology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 8, P.O. Box 63, Helsinki FIN-00014, Finland
| | - Matti Wahlsten
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Biocenter 1, P.O. Box 56, Helsinki FIN-00014, Finland
| | - Jouni Jokela
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Biocenter 1, P.O. Box 56, Helsinki FIN-00014, Finland
| | - Matthias Nees
- Department of Biochemistry and Molecular Biology, Medical University in Lublin, ul. Chodzki 1, Lublin 20-093, Poland
- Institute of Biomedicine and Western Cancer Centre FICAN West, University of Turku, Turku 20101, Finland
| | - Ulf-Håkan Stenman
- Department of Clinical Chemistry and Haematology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 8, P.O. Box 63, Helsinki FIN-00014, Finland
| | - Danillo O. Alvarenga
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Biocenter 1, P.O. Box 56, Helsinki FIN-00014, Finland
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Tomas Strandin
- Department of Virology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, Helsinki FIN-00014, Finland
| | - Kaarina Sivonen
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Biocenter 1, P.O. Box 56, Helsinki FIN-00014, Finland
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, P.O. Box 1627, Kuopio FIN-70211, Finland
- Dept. of Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Strasse 14, Tübingen DE-72076, Germany
| | - Perttu Permi
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Jyväskylä FI-40014, Finland
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, P.O. Box
35, Jyväskylä FI-40014, Finland
| | - Mikko Metsä-Ketelä
- Department of Biochemistry, University of Turku, Turku FIN-20014, Finland
| | - Hannu Koistinen
- Department of Clinical Chemistry and Haematology, Faculty of Medicine, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 8, P.O. Box 63, Helsinki FIN-00014, Finland
| | - David P. Fewer
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 9, Biocenter 1, P.O. Box 56, Helsinki FIN-00014, Finland
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49
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Liu X, Huuskonen S, Laitinen T, Redchuk T, Bogacheva M, Salokas K, Pöhner I, Öhman T, Tonduru AK, Hassinen A, Gawriyski L, Keskitalo S, Vartiainen MK, Pietiäinen V, Poso A, Varjosalo M. SARS-CoV-2-host proteome interactions for antiviral drug discovery. Mol Syst Biol 2021; 17:e10396. [PMID: 34709727 PMCID: PMC8552907 DOI: 10.15252/msb.202110396] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 12/20/2022] Open
Abstract
Treatment options for COVID-19, caused by SARS-CoV-2, remain limited. Understanding viral pathogenesis at the molecular level is critical to develop effective therapy. Some recent studies have explored SARS-CoV-2-host interactomes and provided great resources for understanding viral replication. However, host proteins that functionally associate with SARS-CoV-2 are localized in the corresponding subnetwork within the comprehensive human interactome. Therefore, constructing a downstream network including all potential viral receptors, host cell proteases, and cofactors is necessary and should be used as an additional criterion for the validation of critical host machineries used for viral processing. This study applied both affinity purification mass spectrometry (AP-MS) and the complementary proximity-based labeling MS method (BioID-MS) on 29 viral ORFs and 18 host proteins with potential roles in viral replication to map the interactions relevant to viral processing. The analysis yields a list of 693 hub proteins sharing interactions with both viral baits and host baits and revealed their biological significance for SARS-CoV-2. Those hub proteins then served as a rational resource for drug repurposing via a virtual screening approach. The overall process resulted in the suggested repurposing of 59 compounds for 15 protein targets. Furthermore, antiviral effects of some candidate drugs were observed in vitro validation using image-based drug screen with infectious SARS-CoV-2. In addition, our results suggest that the antiviral activity of methotrexate could be associated with its inhibitory effect on specific protein-protein interactions.
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Affiliation(s)
- Xiaonan Liu
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
| | - Sini Huuskonen
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
| | - Tuomo Laitinen
- School of PharmacyUniversity of Eastern FinlandKuopioFinland
| | - Taras Redchuk
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
| | - Mariia Bogacheva
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
- Institute for Molecular Medicine FinlandUniversity of HelsinkiHelsinkiFinland
- Department of VirologyUniversity of HelsinkiHelsinkiFinland
| | - Kari Salokas
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
| | - Ina Pöhner
- School of PharmacyUniversity of Eastern FinlandKuopioFinland
| | - Tiina Öhman
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
| | | | - Antti Hassinen
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
- Institute for Molecular Medicine FinlandUniversity of HelsinkiHelsinkiFinland
| | - Lisa Gawriyski
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
| | - Salla Keskitalo
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
| | - Maria K Vartiainen
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
| | - Vilja Pietiäinen
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
- Institute for Molecular Medicine FinlandUniversity of HelsinkiHelsinkiFinland
| | - Antti Poso
- School of PharmacyUniversity of Eastern FinlandKuopioFinland
- Department of Internal Medicine VIIIUniversity Hospital TübingenTübingenGermany
| | - Markku Varjosalo
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
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50
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Zattoni IF, Kronenberger T, Kita DH, Guanaes LD, Guimarães MM, de Oliveira Prado L, Ziasch M, Vesga LC, Gomes de Moraes Rego F, Picheth G, Gonçalves MB, Noseda MD, Ducatti DRB, Poso A, Robey RW, Ambudkar SV, Moure VR, Gonçalves AG, Valdameri G. A new porphyrin as selective substrate-based inhibitor of breast cancer resistance protein (BCRP/ABCG2). Chem Biol Interact 2021; 351:109718. [PMID: 34717915 DOI: 10.1016/j.cbi.2021.109718] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/25/2022]
Abstract
The ABCG2 transporter plays a pivotal role in multidrug resistance, however, no clinical trial using specific ABCG2 inhibitors have been successful. Although ABC transporters actively extrude a wide variety of substrates, photodynamic therapeutic agents with porphyrinic scaffolds are exclusively transported by ABCG2. In this work, we describe for the first time a porphyrin derivative (4B) inhibitor of ABCG2 and capable to overcome multidrug resistance in vitro. The inhibition was time-dependent and 4B was not itself transported by ABCG2. Independently of the substrate, the porphyrin 4B showed an IC50 value of 1.6 μM and a mixed type of inhibition. This compound inhibited the ATPase activity and increased the binding of the conformational-sensitive antibody 5D3. A thermostability assay confirmed allosteric protein changes triggered by the porphyrin. Long-timescale molecular dynamics simulations revealed a different behavior between the ABCG2 porphyrinic substrate pheophorbide a and the porphyrin 4B. Pheophorbide a was able to bind in three different protein sites but 4B showed one binding conformation with a strong ionic interaction with GLU446. The inhibition was selective toward ABCG2, since no inhibition was observed for P-glycoprotein and MRP1. Finally, this compound successfully chemosensitized cells that overexpress ABCG2. These findings reinforce that substrates may be a privileged source of chemical scaffolds for identification of new inhibitors of multidrug resistance-linked ABC transporters.
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Affiliation(s)
- Ingrid Fatima Zattoni
- Pharmaceutical Sciences Graduate Program, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil
| | - Thales Kronenberger
- School of Pharmacy, University of Eastern Finland, Faculty of Health Sciences, Kuopio, 70211, Finland; Department of Medical Oncology and Pneumology, Internal Medicine VIII, University Hospital of Tübingen, Otfried-Müller-Strasse 14, 72076, Tübingen, Germany
| | - Diogo Henrique Kita
- Pharmaceutical Sciences Graduate Program, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil; Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | - Melanie Ziasch
- Department of Clinical Analysis, Federal University of Parana, Curitiba, PR, Brazil
| | - Luis C Vesga
- School of Pharmacy, University of Eastern Finland, Faculty of Health Sciences, Kuopio, 70211, Finland; Research Group in Biochemistry and Microbiology (GIBIM), School of Chemistry, Industrial University of Santander, A.A. 678, Bucaramanga, Colombia; Research Group on Organic Compounds of Medicinal Interest (CODEIM), Technological Park of Guatiguara, Industrial University of Santander, A. A. 678, Piedecuesta, Colombia
| | | | - Geraldo Picheth
- Department of Clinical Analysis, Federal University of Parana, Curitiba, PR, Brazil
| | - Marcos Brown Gonçalves
- Department of Physics, Federal Technological University of Paraná, 80230-901 Curitiba, Parana, Brazil
| | - Miguel D Noseda
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Diogo R B Ducatti
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, Faculty of Health Sciences, Kuopio, 70211, Finland; Department of Medical Oncology and Pneumology, Internal Medicine VIII, University Hospital of Tübingen, Otfried-Müller-Strasse 14, 72076, Tübingen, Germany
| | - Robert W Robey
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Suresh V Ambudkar
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vivian Rotuno Moure
- Pharmaceutical Sciences Graduate Program, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil; Department of Clinical Analysis, Federal University of Parana, Curitiba, PR, Brazil
| | | | - Glaucio Valdameri
- Pharmaceutical Sciences Graduate Program, Laboratory of Cancer Drug Resistance, Federal University of Parana, Curitiba, PR, Brazil; Department of Clinical Analysis, Federal University of Parana, Curitiba, PR, Brazil.
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