1
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Kuzikov M, Reinshagen J, Wycisk K, Corona A, Esposito F, Malune P, Manelfi C, Iaconis D, Beccari A, Tramontano E, Nowotny M, Windshügel B, Gribbon P, Zaliani A. Drug repurposing screen to identify inhibitors of the RNA polymerase (nsp12) and helicase (nsp13) from SARS-CoV-2 replication and transcription complex. Virus Res 2024; 343:199356. [PMID: 38490582 PMCID: PMC10958470 DOI: 10.1016/j.virusres.2024.199356] [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: 08/28/2023] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 03/17/2024]
Abstract
Coronaviruses contain one of the largest genomes among the RNA viruses, coding for 14-16 non-structural proteins (nsp) that are involved in proteolytic processing, genome replication and transcription, and four structural proteins that build the core of the mature virion. Due to conservation across coronaviruses, nsps form a group of promising drug targets as their inhibition directly affects viral replication and, therefore, progression of infection. A minimal but fully functional replication and transcription complex was shown to be formed by one RNA-dependent RNA polymerase (nsp12), one nsp7, two nsp8 accessory subunits, and two helicase (nsp13) enzymes. Our approach involved, targeting nsp12 and nsp13 to allow multiple starting point to interfere with virus infection progression. Here we report a combined in-vitro repurposing screening approach, identifying new and confirming reported SARS-CoV-2 nsp12 and nsp13 inhibitors.
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Affiliation(s)
- Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany; Constructor University, School of Science, Campus Ring 1, 28759 Bremen, Germany.
| | - Jeanette Reinshagen
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Krzysztof Wycisk
- Laboratory of Protein Structure - International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland
| | - Angela Corona
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Francesca Esposito
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Paolo Malune
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Candida Manelfi
- EXSCALATE, Dompé farmaceutici S.p.A., Via Tommaso De Amicis, 95, Napoli, 80131, Italy
| | - Daniela Iaconis
- EXSCALATE, Dompé farmaceutici S.p.A., Via Tommaso De Amicis, 95, Napoli, 80131, Italy
| | - Andrea Beccari
- EXSCALATE, Dompé farmaceutici S.p.A., Via Tommaso De Amicis, 95, Napoli, 80131, Italy
| | - Enzo Tramontano
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Marcin Nowotny
- Laboratory of Protein Structure - International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland
| | - Björn Windshügel
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany; Constructor University, School of Science, Campus Ring 1, 28759 Bremen, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
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2
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Jalencas X, Berg H, Espeland LO, Sreeramulu S, Kinnen F, Richter C, Georgiou C, Yadrykhinsky V, Specker E, Jaudzems K, Miletić T, Harmel R, Gribbon P, Schwalbe H, Brenk R, Jirgensons A, Zaliani A, Mestres J. Design, quality and validation of the EU-OPENSCREEN fragment library poised to a high-throughput screening collection. RSC Med Chem 2024; 15:1176-1188. [PMID: 38665834 PMCID: PMC11042166 DOI: 10.1039/d3md00724c] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/08/2024] [Indexed: 04/28/2024] Open
Abstract
The EU-OPENSCREEN (EU-OS) European Research Infrastructure Consortium (ERIC) is a multinational, not-for-profit initiative that integrates high-capacity screening platforms and chemistry groups across Europe to facilitate research in chemical biology and early drug discovery. Over the years, the EU-OS has assembled a high-throughput screening compound collection, the European Chemical Biology Library (ECBL), that contains approximately 100 000 commercially available small molecules and a growing number of thousands of academic compounds crowdsourced through our network of European and non-European chemists. As an extension of the ECBL, here we describe the computational design, quality control and use case screenings of the European Fragment Screening Library (EFSL) composed of 1056 mini and small chemical fragments selected from a substructure analysis of the ECBL. Access to the EFSL is open to researchers from both academia and industry. Using EFSL, eight fragment screening campaigns using different structural and biophysical methods have successfully identified fragment hits in the last two years. As one of the highlighted projects for antibiotics, we describe the screening by Bio-Layer Interferometry (BLI) of the EFSL, the identification of a 35 μM fragment hit targeting the beta-ketoacyl-ACP synthase 2 (FabF), its binding confirmation to the protein by X-ray crystallography (PDB 8PJ0), its subsequent rapid exploration of its surrounding chemical space through hit-picking of ECBL compounds that contain the fragment hit as a core substructure, and the final binding confirmation of two follow-up hits by X-ray crystallography (PDB 8R0I and 8R1V).
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Affiliation(s)
- Xavier Jalencas
- Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute Parc de Recerca Biomèdica (PRBB), Doctor Aiguader 88 08003 Barcelona Spain
| | - Hannes Berg
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
- Chemical Biology, Goethe University Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
| | - Ludvik Olai Espeland
- Department of Biomedicine, University of Bergen Jonas Lies Vei 91 5020 Bergen Norway
- Department of Chemistry, University of Bergen Allégaten 41 5007 Bergen Norway
| | - Sridhar Sreeramulu
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
- Chemical Biology, Goethe University Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
| | - Franziska Kinnen
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
- Chemical Biology, Goethe University Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
| | - Christian Richter
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
- Chemical Biology, Goethe University Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
| | - Charis Georgiou
- Department of Biomedicine, University of Bergen Jonas Lies Vei 91 5020 Bergen Norway
| | | | - Edgar Specker
- EU-OPENSCREEN ERIC Robert-Rössle Straße 10 13125 Berlin Germany
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis Aizkraules 21 Riga LV-1006 Latvia
| | - Tanja Miletić
- EU-OPENSCREEN ERIC Robert-Rössle Straße 10 13125 Berlin Germany
| | - Robert Harmel
- EU-OPENSCREEN ERIC Robert-Rössle Straße 10 13125 Berlin Germany
| | - Phil Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) Schnackenburgallee 114 22525 Hamburg Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD) Theodor Stern Kai 7 60590 Frankfurt Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
- Chemical Biology, Goethe University Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
- Instruct-ERIC Oxford House, Parkway Court, John Smith Drive Oxford OX4 2JY UK
| | - Ruth Brenk
- Department of Biomedicine, University of Bergen Jonas Lies Vei 91 5020 Bergen Norway
- Computational Biology Unit, University of Bergen Thormøhlensgate 55 5008 Bergen Norway
| | - Aigars Jirgensons
- Latvian Institute of Organic Synthesis Aizkraules 21 Riga LV-1006 Latvia
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) Schnackenburgallee 114 22525 Hamburg Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD) Theodor Stern Kai 7 60590 Frankfurt Germany
| | - Jordi Mestres
- Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute Parc de Recerca Biomèdica (PRBB), Doctor Aiguader 88 08003 Barcelona Spain
- Institut de Quimica Computacional i Catalisi, Facultat de Ciencies, Universitat de Girona Maria Aurelia Capmany 69 17003 Girona Catalonia Spain
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Wang W, Tang J, Zaliani A. Outline and background for the EU-OS solubility prediction challenge. SLAS Discov 2024; 29:100155. [PMID: 38518955 DOI: 10.1016/j.slasd.2024.100155] [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] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/27/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
In June 2022, EU-OS came to the decision to make public a solubility data set of 100+K compounds obtained from several of the EU-OS proprietary screening compound collections. Leveraging on the interest of SLAS for screening scientific development it was decided to launch a joint EUOS-SLAS competition within the chemoinformatics and machine learning (ML) communities. The competition was open to real world computation experts, for the best, most predictive, classification model of compound solubility. The aim of the competition was multiple: from a practical side, the winning model should then serve as a cornerstone for future solubility predictions having used the largest training set so far publicly available. From a higher project perspective, the intent was to focus the energies and experiences, even if professionally not precisely coming from Pharma R&D; to address the issue of how to predict compound solubility. Here we report how the competition was ideated and the practical aspects of conducting it within the Kaggle framework, leveraging of the versatility and the open-source nature of this data science platform. Consideration on results and challenges encountered have been also examined.
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Affiliation(s)
- Wenyu Wang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland; Institute for Molecular Medicine Finland-FIMM, Helsinki Institute of Life Science-HiLIFE, University of Helsinki, Helsinki 00290, Finland; iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki 00290, Finland
| | - Jing Tang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland; iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki 00290, Finland.
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg 22525, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany.
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4
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Albani S, Costanzi E, Hoang GL, Kuzikov M, Frings M, Ansari N, Demitri N, Nguyen TT, Rizzi V, Schulz JB, Bolm C, Zaliani A, Carloni P, Storici P, Rossetti G. Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease. J Chem Inf Model 2024; 64:892-904. [PMID: 38051605 PMCID: PMC10865365 DOI: 10.1021/acs.jcim.3c01497] [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: 09/22/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/07/2023]
Abstract
Many homodimeric enzymes tune their functions by exploiting either negative or positive cooperativity between subunits. In the SARS-CoV-2 Main protease (Mpro) homodimer, the latter has been suggested by symmetry in most of the 500 reported protease/ligand complex structures solved by macromolecular crystallography (MX). Here we apply the latter to both covalent and noncovalent ligands in complex with Mpro. Strikingly, our experiments show that the occupation of both active sites of the dimer originates from an excess of ligands. Indeed, cocrystals obtained using a 1:1 ligand/protomer stoichiometry lead to single occupation only. The empty binding site exhibits a catalytically inactive geometry in solution, as suggested by molecular dynamics simulations. Thus, Mpro operates through negative cooperativity with the asymmetric activity of the catalytic sites. This allows it to function with a wide range of substrate concentrations, making it resistant to saturation and potentially difficult to shut down, all properties advantageous for the virus' adaptability and resistance.
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Affiliation(s)
- Simone Albani
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- Faculty
of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, Aachen 52062, Germany
| | - Elisa Costanzi
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Gia Linh Hoang
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
| | - Maria Kuzikov
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
- Constructor University, School of Science, Campus Ring 1, Bremen 28759, Germany
| | - Marcus Frings
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Narjes Ansari
- Atomistic
Simulations, Italian Institute of Technology, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Nicola Demitri
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Toan T. Nguyen
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Valerio Rizzi
- School
of Pharmaceutical Sciences, University of
Geneva, Rue Michel Servet 1, 1206 Genève, Switzerland
| | - Jörg B. Schulz
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
| | - Carsten Bolm
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Andrea Zaliani
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg 22525, Germany
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
| | - Paolo Carloni
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Paola Storici
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Giulia Rossetti
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
- Jülich
Supercomputing Center (JSC), Forschungszentrum
Jülich, Jülich 52425, Germany
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Li D, Ju F, Wang H, Fan C, Jacob JC, Gul S, Zaliani A, Wartmann T, Polidori MC, Bruns CJ, Zhao Y. Combination of the biomarkers for aging and cancer? - Challenges and current status. Transl Oncol 2023; 38:101783. [PMID: 37716258 PMCID: PMC10514562 DOI: 10.1016/j.tranon.2023.101783] [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: 01/30/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/18/2023] Open
Abstract
The proportion of patients diagnosed with cancer has been shown to rise with the increasing aging global population. Advanced age is a major risk factor for morbidity and mortality in older adults. As individuals experience varying health statuses, particularly with age, it poses a challenge for medical professionals in the cancer field to obtain standardized treatment outcomes. Hence, relying solely on chronological age and disease-related parameters is inadequate for clinical decision-making for elderly patients. With functional, multimorbidity-related, and psychosocial changes that occur with aging, oncologic diseases may develop and be treated differently from younger patients, leading to unique challenges in treatment efficacy and tolerance. To overcome this challenge, personalized therapy using biomarkers has emerged as a promising solution. Various categories of biomarkers, including inflammatory, hematological, metabolic, endocrine, and DNA modification-related indicators, may display features related to both cancer and aging, aiding in the development of innovative therapeutic approaches for patients with cancer in old age. Furthermore, physical functional measurements as non-molecular phenotypic biomarkers are being investigated for their potential complementary role in structured multidomain strategies to combat age-related diseases such as cancer. This review provides insight into the current developments, recent discoveries, and significant challenges in cancer and aging biomarkers, with a specific focus on their application in advanced age.
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Affiliation(s)
- Dai Li
- Department of General, Visceral, Tumor and Transplantation Surgery, University Hospital of Cologne, Kerpener Straße 62, 50937 Cologne, Germany; Department of Anesthesiology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Feng Ju
- Department of General, Visceral, Tumor and Transplantation Surgery, University Hospital of Cologne, Kerpener Straße 62, 50937 Cologne, Germany
| | - Han Wang
- Department of Anesthesiology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Chunfu Fan
- Medical faculty, University of Cologne, Germany
| | | | - Sheraz Gul
- Fraunhofer Institute for Translational Medicine and Pharmacology, Schnackenburgallee 114, d-22525 Hamburg, Germany; Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Hamburg Site, Schnackenburgallee 114, d-22525 Hamburg, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology, Schnackenburgallee 114, d-22525 Hamburg, Germany; Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Hamburg Site, Schnackenburgallee 114, d-22525 Hamburg, Germany
| | - Thomas Wartmann
- Department of General, Visceral und Vascular Surgery, Otto von Guericke University, Magdeburg, Leipziger Str. 44, Magdeburg, 39120, Germany
| | - Maria Cristina Polidori
- Ageing Clinical Research, Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress-Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne Germany
| | - Christiane J Bruns
- Department of General, Visceral, Tumor and Transplantation Surgery, University Hospital of Cologne, Kerpener Straße 62, 50937 Cologne, Germany; Center for Integrated Oncology (CIO) Aachen, Bonn, Cologne and Düsseldorf, Cologne, Germany
| | - Yue Zhao
- Department of General, Visceral, Tumor and Transplantation Surgery, University Hospital of Cologne, Kerpener Straße 62, 50937 Cologne, Germany.
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Reus P, Guthmann H, Uhlig N, Agbaria M, Issmail L, Eberlein V, Nordling-David MM, Jbara-Agbaria D, Ciesek S, Bojkova D, Cinatl J, Burger-Kentischer A, Rupp S, Zaliani A, Grunwald T, Gribbon P, Kannt A, Golomb G. Drug repurposing for the treatment of COVID-19: Targeting nafamostat to the lungs by a liposomal delivery system. J Control Release 2023; 364:654-671. [PMID: 37939853 DOI: 10.1016/j.jconrel.2023.10.050] [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: 07/13/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023]
Abstract
Despite tremendous global efforts since the beginning of the COVID-19 pandemic, still only a limited number of prophylactic and therapeutic options are available. Although vaccination is the most effective measure in preventing morbidity and mortality, there is a need for safe and effective post-infection treatment medication. In this study, we explored a pipeline of 21 potential candidates, examined in the Calu-3 cell line for their antiviral efficacy, for drug repurposing. Ralimetinib and nafamostat, clinically used drugs, have emerged as attractive candidates. Due to the inherent limitations of the selected drugs, we formulated targeted liposomes suitable for both systemic and intranasal administration. Non-targeted and targeted nafamostat liposomes (LipNaf) decorated with an Apolipoprotein B peptide (ApoB-P) as a specific lung-targeting ligand were successfully developed. The developed liposomal formulations of nafamostat were found to possess favorable physicochemical properties including nano size (119-147 nm), long-term stability of the normally rapidly degrading compound in aqueous solution, negligible leakage from the liposomes upon storage, and a neutral surface charge with low polydispersity index (PDI). Both nafamostat and ralimetinib liposomes showed good cellular uptake and lack of cytotoxicity, and non-targeted LipNaf demonstrated enhanced accumulation in the lungs following intranasal (IN) administration in non-infected mice. LipNaf retained its anti-SARS-CoV 2 activity in Calu 3 cells with only a modest decrease, exhibiting complete inhibition at concentrations >100 nM. IN, but not intraperitoneal (IP) treatment with targeted LipNaf resulted in a trend to reduced viral load in the lungs of K18-hACE2 mice compared to targeted empty Lip. Nevertheless, upon removal of outlier data, a statistically significant 1.9-fold reduction in viral load was achieved. This observation further highlights the importance of a targeted delivery into the respiratory tract. In summary, we were able to demonstrate a proof-of-concept of drug repurposing by liposomal formulations with anti-SARS-CoV-2 activity. The biodistribution and bioactivity studies with LipNaf suggest an IN or inhalation route of administration for optimal therapeutic efficacy.
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Affiliation(s)
- Philipp Reus
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany; Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Paul-Ehrlich-Straße 40, 60596 Frankfurt am Main, Germany
| | - Hadar Guthmann
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel; The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nadja Uhlig
- Fraunhofer Institute for Cell Therapy und Immunology IZI, Perlickstrasse 1, 04103 Leipzig, Germany
| | - Majd Agbaria
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Leila Issmail
- Fraunhofer Institute for Cell Therapy und Immunology IZI, Perlickstrasse 1, 04103 Leipzig, Germany
| | - Valentina Eberlein
- Fraunhofer Institute for Cell Therapy und Immunology IZI, Perlickstrasse 1, 04103 Leipzig, Germany
| | - Mirjam M Nordling-David
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Doaa Jbara-Agbaria
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Sandra Ciesek
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Paul-Ehrlich-Straße 40, 60596 Frankfurt am Main, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Denisa Bojkova
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Paul-Ehrlich-Straße 40, 60596 Frankfurt am Main, Germany
| | - Jindrich Cinatl
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Paul-Ehrlich-Straße 40, 60596 Frankfurt am Main, Germany
| | - Anke Burger-Kentischer
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Nobelstraße 12, 70569 Stuttgart, Germany
| | - Steffen Rupp
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Nobelstraße 12, 70569 Stuttgart, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Thomas Grunwald
- Fraunhofer Institute for Cell Therapy und Immunology IZI, Perlickstrasse 1, 04103 Leipzig, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Aimo Kannt
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Fraunhofer Innovation Center TheraNova, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Institute for Clinical Pharmacology, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany.
| | - Gershon Golomb
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel; The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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Sharifi MA, Wierer M, Dang TA, Milic J, Moggio A, Sachs N, von Scheidt M, Hinterdobler J, Müller P, Werner J, Stiller B, Aherrahrou Z, Erdmann J, Zaliani A, Graettinger M, Reinshagen J, Gul S, Gribbon P, Maegdefessel L, Bernhagen J, Sager HB, Mann M, Schunkert H, Kessler T. ADAMTS-7 Modulates Atherosclerotic Plaque Formation by Degradation of TIMP-1. Circ Res 2023; 133:674-686. [PMID: 37675562 PMCID: PMC7615141 DOI: 10.1161/circresaha.123.322737] [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: 03/06/2023] [Accepted: 08/23/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND The ADAMTS7 locus was genome-wide significantly associated with coronary artery disease. Lack of the ECM (extracellular matrix) protease ADAMTS-7 (A disintegrin and metalloproteinase-7) was shown to reduce atherosclerotic plaque formation. Here, we sought to identify molecular mechanisms and downstream targets of ADAMTS-7 mediating the risk of atherosclerosis. METHODS Targets of ADAMTS-7 were identified by high-resolution mass spectrometry of atherosclerotic plaques from Apoe-/- and Apoe-/-Adamts7-/- mice. ECM proteins were identified using solubility profiling. Putative targets were validated using immunofluorescence, in vitro degradation assays, coimmunoprecipitation, and Förster resonance energy transfer-based protein-protein interaction assays. ADAMTS7 expression was measured in fibrous caps of human carotid artery plaques. RESULTS In humans, ADAMTS7 expression was higher in caps of unstable as compared to stable carotid plaques. Compared to Apoe-/- mice, atherosclerotic aortas of Apoe-/- mice lacking Adamts-7 (Apoe-/-Adamts7-/-) contained higher protein levels of Timp-1 (tissue inhibitor of metalloprotease-1). In coimmunoprecipitation experiments, the catalytic domain of ADAMTS-7 bound to TIMP-1, which was degraded in the presence of ADAMTS-7 in vitro. ADAMTS-7 reduced the inhibitory capacity of TIMP-1 at its canonical target MMP-9 (matrix metalloprotease-9). As a downstream mechanism, we investigated collagen content in plaques of Apoe-/- and Apoe-/-Adamts7-/- mice after a Western diet. Picrosirius red staining of the aortic root revealed less collagen as a readout of higher MMP-9 activity in Apoe-/- as compared to Apoe-/- Adamts7-/- mice. To facilitate high-throughput screening for ADAMTS-7 inhibitors with the aim of decreasing TIMP-1 degradation, we designed a Förster resonance energy transfer-based assay targeting the ADAMTS-7 catalytic site. CONCLUSIONS ADAMTS-7, which is induced in unstable atherosclerotic plaques, decreases TIMP-1 stability reducing its inhibitory effect on MMP-9, which is known to promote collagen degradation and is likewise associated with coronary artery disease. Disrupting the interaction of ADAMTS-7 and TIMP-1 might be a strategy to increase collagen content and plaque stability for the reduction of atherosclerosis-related events.
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Affiliation(s)
- M. Amin Sharifi
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Tan An Dang
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
| | - Jelena Milic
- Division of Vascular Biology, Institute for Stroke and Dementia Research, Ludwig Maximilian University of Munich, Munich, Germany
| | - Aldo Moggio
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
| | - Nadja Sachs
- Vascular Biology and Experimental Vascular Medicine Unit, Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Moritz von Scheidt
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
| | - Julia Hinterdobler
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
| | - Philipp Müller
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
| | - Julia Werner
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
| | - Barbara Stiller
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
| | - Zouhair Aherrahrou
- Institute for Cardiogenetics and University Heart Centre Lübeck, University of Lübeck, Lübeck, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Hamburg/Kiel/Lübeck, Germany
| | - Jeanette Erdmann
- Institute for Cardiogenetics and University Heart Centre Lübeck, University of Lübeck, Lübeck, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Hamburg/Kiel/Lübeck, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Hamburg, Germany
| | - Mira Graettinger
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Hamburg, Germany
| | - Jeanette Reinshagen
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Hamburg, Germany
| | - Sheraz Gul
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Hamburg, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Hamburg, Germany
| | - Lars Maegdefessel
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
- Vascular Biology and Experimental Vascular Medicine Unit, Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Jürgen Bernhagen
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
- Division of Vascular Biology, Institute for Stroke and Dementia Research, Ludwig Maximilian University of Munich, Munich, Germany
| | - Hendrik B. Sager
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Heribert Schunkert
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
| | - Thorsten Kessler
- Department of Cardiology, German Heart Centre Munich, Technical University of Munich, Munich, Germany
- German Centre for Cardiovascular Research (DZHK e.V.), partner site Munich Heart Alliance, Munich, Germany
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Krix S, DeLong LN, Madan S, Domingo-Fernández D, Ahmad A, Gul S, Zaliani A, Fröhlich H. MultiGML: Multimodal graph machine learning for prediction of adverse drug events. Heliyon 2023; 9:e19441. [PMID: 37681175 PMCID: PMC10481305 DOI: 10.1016/j.heliyon.2023.e19441] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/09/2023] Open
Abstract
Adverse drug events constitute a major challenge for the success of clinical trials. Several computational strategies have been suggested to estimate the risk of adverse drug events in preclinical drug development. While these approaches have demonstrated high utility in practice, they are at the same time limited to specific information sources. Thus, many current computational approaches neglect a wealth of information which results from the integration of different data sources, such as biological protein function, gene expression, chemical compound structure, cell-based imaging and others. In this work we propose an integrative and explainable multi-modal Graph Machine Learning approach (MultiGML), which fuses knowledge graphs with multiple further data modalities to predict drug related adverse events and general drug target-phenotype associations. MultiGML demonstrates excellent prediction performance compared to alternative algorithms, including various traditional knowledge graph embedding techniques. MultiGML distinguishes itself from alternative techniques by providing in-depth explanations of model predictions, which point towards biological mechanisms associated with predictions of an adverse drug event. Hence, MultiGML could be a versatile tool to support decision making in preclinical drug development.
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Affiliation(s)
- Sophia Krix
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53757, Sankt Augustin, Germany
- Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, 53115, Bonn, Germany
- Fraunhofer Center for Machine Learning, Germany
| | - Lauren Nicole DeLong
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53757, Sankt Augustin, Germany
- Artificial Intelligence and its Applications Institute, School of Informatics, University of Edinburgh, 10 Crichton Street, EH8 9AB, UK
| | - Sumit Madan
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53757, Sankt Augustin, Germany
- Department of Computer Science, University of Bonn, 53115, Bonn, Germany
| | - Daniel Domingo-Fernández
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53757, Sankt Augustin, Germany
- Fraunhofer Center for Machine Learning, Germany
- Enveda Biosciences, Boulder, CO, 80301, USA
| | - Ashar Ahmad
- Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, 53115, Bonn, Germany
- Grunenthal GmbH, 52099, Aachen, Germany
| | - Sheraz Gul
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, 22525, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Schnackenburgallee 114, 22525, Hamburg, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, 22525, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Schnackenburgallee 114, 22525, Hamburg, Germany
| | - Holger Fröhlich
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53757, Sankt Augustin, Germany
- Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, 53115, Bonn, Germany
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9
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Karki R, Gadiya Y, Gribbon P, Zaliani A. Pharmacophore-Based Machine Learning Model To Predict Ligand Selectivity for E3 Ligase Binders. ACS Omega 2023; 8:30177-30185. [PMID: 37636935 PMCID: PMC10448689 DOI: 10.1021/acsomega.3c02803] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/06/2023] [Indexed: 08/29/2023]
Abstract
E3 ligases are enzymes that play a critical role in ubiquitin-mediated protein degradation and are involved in various cellular processes. Pharmacophore analysis is a useful approach for predicting E3 ligase binding selectivity, which involves identifying key chemical features necessary for a ligand to interact with a specific protein target cavity. While pharmacophore analysis is not always sufficient to accurately predict ligand binding affinity, it can be a valuable tool for filtering and/or designing focused libraries for screening campaigns. In this study, we present a fast and an inexpensive approach using a pharmacophore fingerprinting scheme known as ErG, which is used in a multi-class machine learning classification model. This model can assign the correct E3 ligase binder to its known E3 ligase and predict the probability of each molecule to bind to different E3 ligases. Practical applications of this approach are demonstrated on commercial libraries such as Asinex for the rational design of E3 ligase binders. The scripts and data associated with this study can be found on GitHub at https://github.com/Fraunhofer-ITMP/E3_binder_Model.
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Affiliation(s)
- Reagon Karki
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Yojana Gadiya
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590 Frankfurt, Germany
- Bonn-Aachen
International Center for Information Technology (B-IT), University of Bonn, 53113 Bonn, Germany
| | - Philip Gribbon
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Andrea Zaliani
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590 Frankfurt, Germany
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10
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Schultz B, DeLong LN, Masny A, Lentzen M, Raschka T, van Dijk D, Zaliani A, Fröhlich H. A machine learning method for the identification and characterization of novel COVID-19 drug targets. Sci Rep 2023; 13:7159. [PMID: 37137934 PMCID: PMC10156718 DOI: 10.1038/s41598-023-34287-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 04/27/2023] [Indexed: 05/05/2023] Open
Abstract
In addition to vaccines, the World Health Organization sees novel medications as an urgent matter to fight the ongoing COVID-19 pandemic. One possible strategy is to identify target proteins, for which a perturbation by an existing compound is likely to benefit COVID-19 patients. In order to contribute to this effort, we present GuiltyTargets-COVID-19 ( https://guiltytargets-covid.eu/ ), a machine learning supported web tool to identify novel candidate drug targets. Using six bulk and three single cell RNA-Seq datasets, together with a lung tissue specific protein-protein interaction network, we demonstrate that GuiltyTargets-COVID-19 is capable of (i) prioritizing meaningful target candidates and assessing their druggability, (ii) unraveling their linkage to known disease mechanisms, (iii) mapping ligands from the ChEMBL database to the identified targets, and (iv) pointing out potential side effects in the case that the mapped ligands correspond to approved drugs. Our example analyses identified 4 potential drug targets from the datasets: AKT3 from both the bulk and single cell RNA-Seq data as well as AKT2, MLKL, and MAPK11 in the single cell experiments. Altogether, we believe that our web tool will facilitate future target identification and drug development for COVID-19, notably in a cell type and tissue specific manner.
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Affiliation(s)
- Bruce Schultz
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53757, Sankt, Augustin, Germany
- Fraunhofer Center for Machine Learning, Sankt, Germany
| | - Lauren Nicole DeLong
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53757, Sankt, Augustin, Germany
- Artificial Intelligence and its Applications Institute, University of Edinburgh School of Informatics, 10 Crichton St, Edinburgh, EH8 9AB, UK
| | - Aliaksandr Masny
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53757, Sankt, Augustin, Germany
- Fraunhofer Center for Machine Learning, Sankt, Germany
| | - Manuel Lentzen
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53757, Sankt, Augustin, Germany
- University of Bonn, Bonn-Aachen Center for IT (b-it), Friedrich Hirzebruch-Allee 6, 53115, Bonn, Germany
| | - Tamara Raschka
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53757, Sankt, Augustin, Germany
- University of Bonn, Bonn-Aachen Center for IT (b-it), Friedrich Hirzebruch-Allee 6, 53115, Bonn, Germany
- Fraunhofer Center for Machine Learning, Sankt, Germany
| | - David van Dijk
- Center for Biomedical Data Science, Yale School of Medicine, Yale University, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacologie (ITMP), Drug Discovery Research ScreeningPort, VolksparkLabs, Schnackenburgallee 114, 22535, Hamburg, Germany
| | - Holger Fröhlich
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53757, Sankt, Augustin, Germany.
- University of Bonn, Bonn-Aachen Center for IT (b-it), Friedrich Hirzebruch-Allee 6, 53115, Bonn, Germany.
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11
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Karki R, Gadiya Y, Zaliani A, Gribbon P. Mpox Knowledge Graph: A comprehensive representation embedding chemical entities and associated biology of Mpox. Bioinformatics Advances 2023; 3:vbad045. [PMID: 37187795 PMCID: PMC10181838 DOI: 10.1093/bioadv/vbad045] [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] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/20/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023]
Abstract
Abstract
The outbreak of Mpox virus (MPXV) infection in May 2022 is declared a global health emergency by WHO. A total of 84330 cases have been confirmed as of 5th January, 2023 and the numbers are on the rise. The MPXV pathophysiology and its underlying mechanisms are unfortunately not yet understood. Likewise, the knowledge of biochemicals and drugs used against MPXV and their downstream effects is sparse. In this work, using Knowledge Graph (KG) representations we have depicted chemical and biological aspects of MPXV. To achieve this, we have collected and rationally assembled several biological study results, assays, drug candidates, and pre-clinical evidence to form a dynamic and comprehensive network. The KG is compliant with FAIR annotations allowing seamless transformation and integration to/with other formats and infrastructures.
Availability and implementation
The programmatic scripts for Mpox KG are publicly available at https://github.com/Fraunhofer-ITMP/mpox-kg. It is hosted publicly at https://doi.org/10.18119/N9SG7D.
Supplementary information
Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Reagon Karki
- Discovery Research ScreeningPort, Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) , Schnackenburgallee 114, 22525 Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD) , Theodor Stern Kai 7, Frankfurt, 60590, Germany
| | - Yojana Gadiya
- Discovery Research ScreeningPort, Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) , Schnackenburgallee 114, 22525 Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD) , Theodor Stern Kai 7, Frankfurt, 60590, Germany
| | - Andrea Zaliani
- Discovery Research ScreeningPort, Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) , Schnackenburgallee 114, 22525 Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD) , Theodor Stern Kai 7, Frankfurt, 60590, Germany
| | - Philip Gribbon
- Discovery Research ScreeningPort, Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) , Schnackenburgallee 114, 22525 Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD) , Theodor Stern Kai 7, Frankfurt, 60590, Germany
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12
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Gadiya Y, Zaliani A, Gribbon P, Hofmann-Apitius M. PEMT: a patent enrichment tool for drug discovery. Bioinformatics 2023; 39:btac716. [PMID: 36322820 PMCID: PMC9805556 DOI: 10.1093/bioinformatics/btac716] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/10/2022] [Accepted: 11/01/2022] [Indexed: 11/11/2022] Open
Abstract
MOTIVATION Drug discovery practitioners in industry and academia use semantic tools to extract information from online scientific literature to generate new insights into targets, therapeutics and diseases. However, due to complexities in access and analysis, patent-based literature is often overlooked as a source of information. As drug discovery is a highly competitive field, naturally, tools that tap into patent literature can provide any actor in the field an advantage in terms of better informed decision-making. Hence, we aim to facilitate access to patent literature through the creation of an automatic tool for extracting information from patents described in existing public resources. RESULTS Here, we present PEMT, a novel patent enrichment tool, that takes advantage of public databases like ChEMBL and SureChEMBL to extract relevant patent information linked to chemical structures and/or gene names described through FAIR principles and metadata annotations. PEMT aims at supporting drug discovery and research by establishing a patent landscape around genes of interest. The pharmaceutical focus of the tool is mainly due to the subselection of International Patent Classification codes, but in principle, it can be used for other patent fields, provided that a link between a concept and chemical structure is investigated. Finally, we demonstrate a use-case in rare diseases by generating a gene-patent list based on the epidemiological prevalence of these diseases and exploring their underlying patent landscapes. AVAILABILITY AND IMPLEMENTATION PEMT is an open-source Python tool and its source code and PyPi package are available at https://github.com/Fraunhofer-ITMP/PEMT and https://pypi.org/project/PEMT/, respectively. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yojana Gadiya
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Hamburg 22525, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Frankfurt 60590, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Hamburg 22525, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Frankfurt 60590, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Hamburg 22525, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Frankfurt 60590, Germany
| | - Martin Hofmann-Apitius
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin 53754, Germany
- Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, Bonn 53113, Germany
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13
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Pelliccia S, Cerchia C, Esposito F, Cannalire R, Corona A, Costanzi E, Kuzikov M, Gribbon P, Zaliani A, Brindisi M, Storici P, Tramontano E, Summa V. Easy access to α-ketoamides as SARS-CoV-2 and MERS M pro inhibitors via the PADAM oxidation route. Eur J Med Chem 2022; 244:114853. [PMID: 36332546 PMCID: PMC9575579 DOI: 10.1016/j.ejmech.2022.114853] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/28/2022]
Abstract
SARS-CoV-2 caused worldwide the current outbreak called COVID-19. Despite multiple countermeasures implemented, there is an urgent global need for new potent and efficient antiviral drugs against this pathogen. In this context, the main protease (Mpro) of SARS-CoV-2 is an essential viral enzyme and plays a pivotal role in viral replication and transcription. Its specific cleavage of polypeptides after a glutamine residue has been considered as a key element to design novel antiviral drugs. Herein, we reported the design, synthesis and structure-activity relationships of novel α-ketoamides as covalent reversible inhibitors of Mpro, exploiting the PADAM oxidation route. The reported compounds showed μM to nM activities in enzymatic and in the antiviral cell-based assays against SARS-CoV-2 Mpro. In order to assess inhibitors’ binding mode, two co-crystal structures of SARS-CoV-2 Mpro in complex with our inhibitors were solved, which confirmed the covalent binding of the keto amide moiety to the catalytic Cys145 residue of Mpro. Finally, in order to interrogate potential broad-spectrum properties, we assessed a selection of compounds against MERS Mpro where they showed nM inhibitory potency, thus highlighting their potential as broad-spectrum coronavirus inhibitors.
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Affiliation(s)
- Sveva Pelliccia
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy,Corresponding author
| | - Carmen Cerchia
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy
| | - Francesca Esposito
- Dipartimento di Scienze della Vita e dell'Ambiente, Cittadella Universitaria di Monserrato, Cagliari, Monserrato, SS-554, Italy
| | - Rolando Cannalire
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy
| | - Angela Corona
- Dipartimento di Scienze della Vita e dell'Ambiente, Cittadella Universitaria di Monserrato, Cagliari, Monserrato, SS-554, Italy
| | - Elisa Costanzi
- Protein Facility, Elettra - Sincrotrone Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, Trieste, Basovizza, 34149, Italy
| | - Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg, 22525, Germany,Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759, Bremen, Germany,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg, 22525, Germany,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg, 22525, Germany,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Margherita Brindisi
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy
| | - Paola Storici
- Protein Facility, Elettra - Sincrotrone Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, Trieste, Basovizza, 34149, Italy
| | - Enzo Tramontano
- Dipartimento di Scienze della Vita e dell'Ambiente, Cittadella Universitaria di Monserrato, Cagliari, Monserrato, SS-554, Italy
| | - Vincenzo Summa
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy,Corresponding author
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14
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Linden T, Hanses F, Domingo-Fernández D, DeLong LN, Kodamullil AT, Schneider J, Vehreschild MJGT, Lanznaster J, Ruethrich MM, Borgmann S, Hower M, Wille K, Feldt T, Rieg S, Hertenstein B, Wyen C, Roemmele C, Vehreschild JJ, Jakob CEM, Stecher M, Kuzikov M, Zaliani A, Fröhlich H. Corrigendum to "Machine Learning Based Prediction of COVID-19 Mortality Suggests Repositioning of Anticancer Drug for Treating Severe Cases"[Artificial Intelligence in Life Sciences] 1(2021), 100020. Artif Intell Life Sci 2022; 2:100032. [PMID: 35156080 PMCID: PMC8824443 DOI: 10.1016/j.ailsci.2022.100032] [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] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
[This corrects the article DOI: 10.1016/j.ailsci.2021.100020.].
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Affiliation(s)
- Thomas Linden
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53757, Sankt Augustin, Germany
- University of Bonn, Bonn-Aachen International Center for IT, Friedrich Hirzebruch-Allee 6, 53115, Bonn, Germany
| | - Frank Hanses
- Emergency Department, University Hospital Regensburg, 93053 Regensburg, Germany
- Department for Infectious Diseases and Infection Control, University Hospital Regensburg, Germany
| | - Daniel Domingo-Fernández
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53757, Sankt Augustin, Germany
| | - Lauren Nicole DeLong
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53757, Sankt Augustin, Germany
- University of Bonn, Bonn-Aachen International Center for IT, Friedrich Hirzebruch-Allee 6, 53115, Bonn, Germany
| | - Alpha Tom Kodamullil
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53757, Sankt Augustin, Germany
| | - Jochen Schneider
- Department of Internal Medicine II, School of Medicine, Technical University of Munich, University Hospital rechts der Isar, 81675 Munich, Germany
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Julia Lanznaster
- Department of Internal Medicine II, Hospital Passau, Innstraße 76, 94032 Passau, Germany
| | - Maria Madeleine Ruethrich
- Department of Internal Medicine II, Hematology and Medical Oncology, University Hospital Jena, 07747 Jena, Germany
| | - Stefan Borgmann
- Department of Infectious Diseases and Infection Control, Hospital Ingolstadt, 85049 Ingolstadt, Germany
| | - Martin Hower
- Department of Pneumology, Infectious Diseases and Intensive Care, Klinikum Dortmund gGmbH, Hospital of University Witten / Herdecke, 44137 Dortmund, Germany
| | - Kai Wille
- University Clinic for Haematology, Oncology, Haemostaseology and Palliative Care, Johannes Wesling Medical Centre Minden, 32429 Minden, Germany
| | - Torsten Feldt
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Siegbert Rieg
- Division of Infectious Diseases, Department of Medicine II, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, 79106 Freiburg, Germany
| | - Bernd Hertenstein
- Department of Hematology and Oncology, Klinikum Bremen-Mitte, 28205 Bremen, Germany
| | | | - Christoph Roemmele
- Internal Medicine III - Gastroenterology and Infectious Diseases, University Hospital Augsburg, 86156 Augsburg, Germany
| | - Jörg Janne Vehreschild
- Department II of Internal Medicine, Hematology/Oncology, Goethe University, Frankfurt, 60590 Frankfurt am Main, Germany
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
- German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Carolin E M Jakob
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
- German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Melanie Stecher
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
- German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacologie (ITMP), VolksparkLabs, Schnackenburgallee 114, 22535 Hamburg, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacologie (ITMP), VolksparkLabs, Schnackenburgallee 114, 22535 Hamburg, Germany
| | - Holger Fröhlich
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53757, Sankt Augustin, Germany
- University of Bonn, Bonn-Aachen International Center for IT, Friedrich Hirzebruch-Allee 6, 53115, Bonn, Germany
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15
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Berg H, Wirtz Martin MA, Altincekic N, Alshamleh I, Kaur Bains J, Blechar J, Ceylan B, de Jesus V, Dhamotharan K, Fuks C, Gande SL, Hargittay B, Hohmann KF, Hutchinson MT, Korn SM, Krishnathas R, Kutz F, Linhard V, Matzel T, Meiser N, Niesteruk A, Pyper DJ, Schulte L, Trucks S, Azzaoui K, Blommers MJJ, Gadiya Y, Karki R, Zaliani A, Gribbon P, Almeida MDS, Anobom CD, Bula AL, Buetikofer M, Caruso ÍP, Felli IC, Da Poian AT, de Amorim GC, Fourkiotis NK, Gallo A, Ghosh D, Gomes-Neto F, Gorbatyuk O, Hao B, Kurauskas V, Lecoq L, Li Y, Mebus-Antunes NC, Mompean M, Neves-Martins TC, Ninot-Pedrosa M, Pinheiro AS, Pontoriero L, Pustovalova Y, Riek R, Robertson A, Abi Saad MJ, Treviño MA, Tsika AC, Almeida FC, Bax A, Henzler-Wildman K, Hoch JC, Jaudzems K, Laurents DV, Orts J, Pieratelli R, Spyroulias GA, Duchardt-Ferner E, Ferner J, Fuertig B, Hengesbach M, Löhr F, Qureshi N, Richter C, Saxena K, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Woehnert J, Schwalbe H. Comprehensive Fragment Screening of the SARS‐CoV‐2 Proteome Explores Novel Chemical Space for Drug Development. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205858] [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: 11/09/2022]
Affiliation(s)
- Hannes Berg
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Nadide Altincekic
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Islam Alshamleh
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Jasleen Kaur Bains
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julius Blechar
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Betül Ceylan
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Vanessa de Jesus
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Christin Fuks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Santosh L. Gande
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Bruno Hargittay
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Marie T. Hutchinson
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Robin Krishnathas
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Felicitas Kutz
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Verena Linhard
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Tobias Matzel
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nathalie Meiser
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Niesteruk
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Dennis J. Pyper
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Linda Schulte
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Sven Trucks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Kamal Azzaoui
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Marcel J J Blommers
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Yojana Gadiya
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Drug Discovery Research ScreeningPort Screening Unit GERMANY
| | - Reagon Karki
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Marcius da Silva Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institue for Medical Biochemistry BRAZIL
| | - Cristiane Dinis Anobom
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Anna Lina Bula
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Institute of Organic Synthesis LATVIA
| | - Matthias Buetikofer
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute für Physikalische Chemie GERMANY
| | - Ícaro Putinhon Caruso
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics BRAZIL
| | - Isabella Caterina Felli
- University of Florence: Universita degli Studi di Firenze Magnetic Resonance Center (CERM) ITALY
| | - Andrea T Da Poian
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics GERMANY
| | - Gisele Cardoso de Amorim
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Multidisciplinary Center for Research in Biology BRAZIL
| | - Nikolaos K Fourkiotis
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Angelo Gallo
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Dhiman Ghosh
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | | | - Oksana Gorbatyuk
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Bing Hao
- UConn Health Department of Molecular Biology and Biopyhsics UNITED STATES
| | - Vilius Kurauskas
- UW Madison: University of Wisconsin Madison Department of Biochemistry UNITED STATES
| | - Lauriane Lecoq
- Universite de Lyon Molecular Microbiology and Structural Biochemistry FRANCE
| | - Yunfeng Li
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Nathane Cunha Mebus-Antunes
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Miguel Mompean
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Thais Cristtina Neves-Martins
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Marti Ninot-Pedrosa
- Universite Lyon 1 IUT Lyon 1 Molecular Microbiology and Structural Biochemistry FRANCE
| | - Anderson S Pinheiro
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Letizia Pontoriero
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Yulia Pustovalova
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Roland Riek
- ETH Zürich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | - Angus Robertson
- NIAMDD: National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | - Marie Jose Abi Saad
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Miguel A Treviño
- CSIC: Consejo Superior de Investigaciones Cientificas "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Aikaterini C Tsika
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Fabio C.L. Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Ad Bax
- National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | | | - Jeffrey C Hoch
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Kristaps Jaudzems
- Institute of Organic Synthesis of the Latvian Academy of Sciences: Latvijas Organiskas sintezes instituts Institute for Organic Chemistry LATVIA
| | - Douglas V Laurents
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Julien Orts
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Roberta Pieratelli
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Georgios A Spyroulias
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | | | - Jan Ferner
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Boris Fuertig
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Martin Hengesbach
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Frank Löhr
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nusrat Qureshi
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Christian Richter
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Krishna Saxena
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Andreas Schlundt
- Goethe-Universitat Frankfurt am Main Department for Biosciences GERMANY
| | - Sridhar Sreeramulu
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Wacker
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julia E Weigand
- TU Darmstadt: Technische Universitat Darmstadt Department of Biology GERMANY
| | | | - Jens Woehnert
- Goethe-Universitat Frankfurt am Main Department of Biological Sciences GERMANY
| | - Harald Schwalbe
- Goethe-Universitat Frankfurt am Main Institut für Organische Chemie und Chemische Biologie Max-von-Laue-Str. 7 60438 Frankfurt GERMANY
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16
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Berg H, Wirtz Martin MA, Altincekic N, Alshamleh I, Kaur Bains J, Blechar J, Ceylan B, de Jesus V, Dhamotharan K, Fuks C, Gande SL, Hargittay B, Hohmann KF, Hutchinson MT, Korn SM, Krishnathas R, Kutz F, Linhard V, Matzel T, Meiser N, Niesteruk A, Pyper DJ, Schulte L, Trucks S, Azzaoui K, Blommers MJJ, Gadiya Y, Karki R, Zaliani A, Gribbon P, Almeida MDS, Anobom CD, Bula AL, Buetikofer M, Caruso ÍP, Felli IC, Da Poian AT, de Amorim GC, Fourkiotis NK, Gallo A, Ghosh D, Gomes-Neto F, Gorbatyuk O, Hao B, Kurauskas V, Lecoq L, Li Y, Mebus-Antunes NC, Mompean M, Neves-Martins TC, Ninot-Pedrosa M, Pinheiro AS, Pontoriero L, Pustovalova Y, Riek R, Robertson A, Abi Saad MJ, Treviño MA, Tsika AC, Almeida FC, Bax A, Henzler-Wildman K, Hoch JC, Jaudzems K, Laurents DV, Orts J, Pieratelli R, Spyroulias GA, Duchardt-Ferner E, Ferner J, Fuertig B, Hengesbach M, Löhr F, Qureshi N, Richter C, Saxena K, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Woehnert J, Schwalbe H. Comprehensive Fragment Screening of the SARS‐CoV‐2 Proteome Explores Novel Chemical Space for Drug Development. Angew Chem Int Ed Engl 2022; 61:e202205858. [PMID: 36115062 PMCID: PMC9539013 DOI: 10.1002/anie.202205858] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Indexed: 11/17/2022]
Abstract
SARS‐CoV‐2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti‐virals. Within the international Covid19‐NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80% of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR‐detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure‐based drug design against the SCoV2 proteome.
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Affiliation(s)
- Hannes Berg
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Nadide Altincekic
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Islam Alshamleh
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Jasleen Kaur Bains
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julius Blechar
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Betül Ceylan
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Vanessa de Jesus
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Christin Fuks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Santosh L. Gande
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Bruno Hargittay
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Marie T. Hutchinson
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | | | - Robin Krishnathas
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Felicitas Kutz
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Verena Linhard
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Tobias Matzel
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nathalie Meiser
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Niesteruk
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Dennis J. Pyper
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Linda Schulte
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Sven Trucks
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Kamal Azzaoui
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Marcel J J Blommers
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Yojana Gadiya
- Fraunhofer Institute for Molecular Biology and Applied Ecology ScreeningPort: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Drug Discovery Research ScreeningPort Screening Unit GERMANY
| | - Reagon Karki
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP: Fraunhofer-Institut fur Translationale Medizin und Pharmakologie ITMP Screening Unit GERMANY
| | - Marcius da Silva Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institue for Medical Biochemistry BRAZIL
| | - Cristiane Dinis Anobom
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Anna Lina Bula
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Institute of Organic Synthesis LATVIA
| | - Matthias Buetikofer
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute für Physikalische Chemie GERMANY
| | - Ícaro Putinhon Caruso
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics BRAZIL
| | - Isabella Caterina Felli
- University of Florence: Universita degli Studi di Firenze Magnetic Resonance Center (CERM) ITALY
| | - Andrea T Da Poian
- Sao Paulo State University Julio de Mesquita Filho: Universidade Estadual Paulista Julio de Mesquita Filho Department of Physics GERMANY
| | - Gisele Cardoso de Amorim
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Multidisciplinary Center for Research in Biology BRAZIL
| | - Nikolaos K Fourkiotis
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Angelo Gallo
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Dhiman Ghosh
- ETH Zurich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | | | - Oksana Gorbatyuk
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Bing Hao
- UConn Health Department of Molecular Biology and Biopyhsics UNITED STATES
| | - Vilius Kurauskas
- UW Madison: University of Wisconsin Madison Department of Biochemistry UNITED STATES
| | - Lauriane Lecoq
- Universite de Lyon Molecular Microbiology and Structural Biochemistry FRANCE
| | - Yunfeng Li
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Nathane Cunha Mebus-Antunes
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Miguel Mompean
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Thais Cristtina Neves-Martins
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Marti Ninot-Pedrosa
- Universite Lyon 1 IUT Lyon 1 Molecular Microbiology and Structural Biochemistry FRANCE
| | - Anderson S Pinheiro
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Department of Biochemistry BRAZIL
| | - Letizia Pontoriero
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Yulia Pustovalova
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Roland Riek
- ETH Zürich: Eidgenossische Technische Hochschule Zurich Institute for Physical Chemistry SWITZERLAND
| | - Angus Robertson
- NIAMDD: National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | - Marie Jose Abi Saad
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Miguel A Treviño
- CSIC: Consejo Superior de Investigaciones Cientificas "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Aikaterini C Tsika
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | - Fabio C.L. Almeida
- Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro Institute of Medical Biochemistry BRAZIL
| | - Ad Bax
- National Institute of Diabetes and Digestive and Kidney Diseases Laboratory of Chemical Physics UNITED STATES
| | | | - Jeffrey C Hoch
- UConn Health Department of Molecular Biology and Biophysics UNITED STATES
| | - Kristaps Jaudzems
- Institute of Organic Synthesis of the Latvian Academy of Sciences: Latvijas Organiskas sintezes instituts Institute for Organic Chemistry LATVIA
| | - Douglas V Laurents
- Estacion Biologica de Donana CSIC "Rocasolano" Institute for Physical Chemistry SPAIN
| | - Julien Orts
- University of Vienna: Universitat Wien Department of Pharmaceutical Sciences AUSTRIA
| | - Roberta Pieratelli
- University of Florence: Universita degli Studi di Firenze Center for Magnetic Resonance ITALY
| | - Georgios A Spyroulias
- University of Patras - Patras Campus: Panepistemio Patron Department of Pharmacy GREECE
| | | | - Jan Ferner
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Boris Fuertig
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Martin Hengesbach
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Frank Löhr
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Nusrat Qureshi
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Christian Richter
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Krishna Saxena
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Andreas Schlundt
- Goethe-Universitat Frankfurt am Main Department for Biosciences GERMANY
| | - Sridhar Sreeramulu
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Anna Wacker
- Goethe-Universitat Frankfurt am Main Biochemistry, Chemistry, Pharmacy GERMANY
| | - Julia E Weigand
- TU Darmstadt: Technische Universitat Darmstadt Department of Biology GERMANY
| | | | - Jens Woehnert
- Goethe-Universitat Frankfurt am Main Department of Biological Sciences GERMANY
| | - Harald Schwalbe
- Goethe-Universitat Frankfurt am Main Institut für Organische Chemie und Chemische Biologie Max-von-Laue-Str. 7 60438 Frankfurt GERMANY
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17
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Zaliani A, Vangeel L, Reinshagen J, Iaconis D, Kuzikov M, Keminer O, Wolf M, Ellinger B, Esposito F, Corona A, Tramontano E, Manelfi C, Herzog K, Jochmans D, De Jonghe S, Chiu W, Francken T, Schepers J, Collard C, Abbasi K, Claussen C, Summa V, Beccari AR, Neyts J, Gribbon P, Leyssen P. Cytopathic SARS-CoV-2 screening on VERO-E6 cells in a large-scale repurposing effort. Sci Data 2022; 9:405. [PMID: 35831315 PMCID: PMC9279437 DOI: 10.1038/s41597-022-01532-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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] [Received: 01/22/2021] [Accepted: 06/29/2022] [Indexed: 01/13/2023] Open
Abstract
Worldwide, there are intensive efforts to identify repurposed drugs as potential therapies against SARS-CoV-2 infection and the associated COVID-19 disease. To date, the anti-inflammatory drug dexamethasone and (to a lesser extent) the RNA-polymerase inhibitor remdesivir have been shown to be effective in reducing mortality and patient time to recovery, respectively, in patients. Here, we report the results of a phenotypic screening campaign within an EU-funded project (H2020-EXSCALATE4COV) aimed at extending the repertoire of anti-COVID therapeutics through repurposing of available compounds and highlighting compounds with new mechanisms of action against viral infection. We screened 8702 molecules from different repurposing libraries, to reveal 110 compounds with an anti-cytopathic IC50 < 20 µM. From this group, 18 with a safety index greater than 2 are also marketed drugs, making them suitable for further study as potential therapies against COVID-19. Our result supports the idea that a systematic approach to repurposing is a valid strategy to accelerate the necessary drug discovery process. Measurement(s) | Cytopathic Effect | Technology Type(s) | confocal fluorescence microscopy | Factor Type(s) | Cellular toxicity | Sample Characteristic - Organism | Chlorocebus sabaeus | Sample Characteristic - Environment | continuant | Sample Characteristic - Location | Belgium |
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Affiliation(s)
- Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany. .,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany.
| | - Laura Vangeel
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
| | - Jeanette Reinshagen
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany.,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Daniela Iaconis
- Dompé Farmaceutici SpA, via Campo di Pile, 67100, L'Aquila, Italy
| | - Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany.,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Oliver Keminer
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany.,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Markus Wolf
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany.,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Bernhard Ellinger
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany.,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Francesca Esposito
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS554, 09042, Monserrato, Cagliari, Italy
| | - Angela Corona
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS554, 09042, Monserrato, Cagliari, Italy
| | - Enzo Tramontano
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS554, 09042, Monserrato, Cagliari, Italy
| | - Candida Manelfi
- Dompé Farmaceutici SpA, via Campo di Pile, 67100, L'Aquila, Italy
| | - Katja Herzog
- EU-OPENSCREEN ERIC, Campus Berlin Buch, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Dirk Jochmans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
| | - Winston Chiu
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
| | - Thibault Francken
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
| | - Joost Schepers
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
| | - Caroline Collard
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
| | - Kayvan Abbasi
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
| | - Carsten Claussen
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany.,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Vincenzo Summa
- Department of Excellence of Pharmacy, University of Naples Federico II, Via D. Montesano, 49, 80131, Naples, Italy
| | - Andrea R Beccari
- Dompé Farmaceutici SpA, via Campo di Pile, 67100, L'Aquila, Italy
| | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Discovery Research ScreeningPort, Schnackenburgallee 114, 22525, Hamburg, Germany.,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596, Frankfurt am Main, Germany
| | - Pieter Leyssen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium
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18
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Kuzikov M, Woens J, Zaliani A, Hambach J, Eden T, Fehse B, Ellinger B, Riecken K. High-throughput drug screening allowed identification of entry inhibitors specifically targeting different routes of SARS-CoV-2 Delta and Omicron/BA.1. Biomed Pharmacother 2022; 151:113104. [PMID: 35643072 PMCID: PMC9108036 DOI: 10.1016/j.biopha.2022.113104] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/04/2022] [Accepted: 05/10/2022] [Indexed: 01/25/2023] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2) has continuously evolved, resulting in the emergence of several variants of concern (VOCs). To study mechanisms of viral entry and potentially identify specific inhibitors, we pseudotyped lentiviral vectors with different SARS-CoV-2 VOC spike variants (D614G, Alpha, Beta, Delta, Omicron/BA.1), responsible for receptor binding and membrane fusion. These SARS-CoV-2 lentiviral pseudoviruses were applied to screen 774 FDA-approved drugs. For the assay we decided to use CaCo2 cells, since they equally allow cell entry through both the direct membrane fusion pathway mediated by TMPRSS2 and the endocytosis pathway mediated by cathepsin-L. The active molecules which showed stronger differences in their potency to inhibit certain SARS-CoV-2 VOCs included antagonists of G-protein coupled receptors, like phenothiazine-derived antipsychotic compounds such as Chlorpromazine, with highest activity against the Omicron pseudovirus. In general, our data showed that the various VOCs differ in their preferences for cell entry, and we were able to identify synergistic combinations of inhibitors. Notably, Omicron singled out by relying primarily on the endocytosis pathway while Delta preferred cell entry via membrane fusion. In conclusion, our data provide new insights into different entry preferences of SARS-CoV-2 VOCs, which might help to identify new drug targets.
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Affiliation(s)
- Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, 22525 Hamburg, Germany,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany,Department of Life Sciences and Chemistry, Jacobs University Bremen, 28759 Bremen, Germany
| | - Jannis Woens
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, 22525 Hamburg, Germany,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Julia Hambach
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Thomas Eden
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Boris Fehse
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 20246 Hamburg, Germany
| | - Bernhard Ellinger
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, 22525 Hamburg, Germany,Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany,Corresponding author at: Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Kristoffer Riecken
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany,Correspondence to: Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
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19
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Alharbi E, Gadiya Y, Henderson D, Zaliani A, Delfin-Rossaro A, Cambon-Thomsen A, Kohler M, Witt G, Welter D, Juty N, Jay C, Engkvist O, Goble C, Reilly DS, Satagopam V, Ioannidis V, Gu W, Gribbon P. Selection of data sets for FAIRification in drug discovery and development: Which, why, and how? Drug Discov Today 2022; 27:2080-2085. [PMID: 35595012 PMCID: PMC9236643 DOI: 10.1016/j.drudis.2022.05.010] [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] [Received: 01/14/2022] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 11/30/2022]
Abstract
Research organisations are focussed on quantifying the costs and benefits of implementing FAIR. Criteria used for the selection of data for FAIRification can be opaque and inconsistent. FAIRification effort depends on individual skills, competencies, resources, and time available. FAIRification should satisfy reuse scenarios, and lead to scientific and economic impacts. Organisational challenges include providing training to individuals and developing a FAIR organisation culture.
Despite the intuitive value of adopting the Findable, Accessible, Interoperable, and Reusable (FAIR) principles in both academic and industrial sectors, challenges exist in resourcing, balancing long- versus short-term priorities, and achieving technical implementation. This situation is exacerbated by the unclear mechanisms by which costs and benefits can be assessed when decisions on FAIR are made. Scientific and research and development (R&D) leadership need reliable evidence of the potential benefits and information on effective implementation mechanisms and remediating strategies. In this article, we describe procedures for cost–benefit evaluation, and identify best-practice approaches to support the decision-making process involved in FAIR implementation.
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Affiliation(s)
- Ebtisam Alharbi
- Department of Computer Science, The University of Manchester, Oxford Road, Manchester, UK
| | - Yojana Gadiya
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Cluster of Excellence for Immune Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - David Henderson
- Bayer AG, Research & Development, Pharmaceuticals, Müllerstrasse 178, 13353 Berlin, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Cluster of Excellence for Immune Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | | | | | - Manfred Kohler
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Cluster of Excellence for Immune Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Gesa Witt
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Cluster of Excellence for Immune Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Danielle Welter
- Luxembourg Centre for Systems Biomedicine, ELIXIR Luxembourg, University of Luxembourg, L-4367 Belval, Luxembourg
| | - Nick Juty
- Department of Computer Science, The University of Manchester, Oxford Road, Manchester, UK
| | - Caroline Jay
- Department of Computer Science, The University of Manchester, Oxford Road, Manchester, UK
| | - Ola Engkvist
- Discovery Sciences, R&D, AstraZeneca, SE-43183 Mölndal, Sweden
| | - Carole Goble
- Department of Computer Science, The University of Manchester, Oxford Road, Manchester, UK
| | - Dorothy S Reilly
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Venkata Satagopam
- Luxembourg Centre for Systems Biomedicine, ELIXIR Luxembourg, University of Luxembourg, L-4367 Belval, Luxembourg
| | - Vassilios Ioannidis
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, 1015 Lausanne, Switzerland.
| | - Wei Gu
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland.
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany; Fraunhofer Cluster of Excellence for Immune Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590 Frankfurt, Germany.
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20
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Corona A, Wycisk K, Talarico C, Manelfi C, Milia J, Cannalire R, Esposito F, Gribbon P, Zaliani A, Iaconis D, Beccari AR, Summa V, Nowotny M, Tramontano E. Natural Compounds Inhibit SARS-CoV-2 nsp13 Unwinding and ATPase Enzyme Activities. ACS Pharmacol Transl Sci 2022; 5:226-239. [PMID: 35434533 PMCID: PMC9003574 DOI: 10.1021/acsptsci.1c00253] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [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: 11/29/2021] [Indexed: 12/27/2022]
Abstract
![]()
SARS-CoV-2 infection
is still spreading worldwide, and new antiviral
therapies are an urgent need to complement the approved vaccine preparations.
SARS-CoV-2 nps13 helicase is a validated drug target participating
in the viral replication complex and possessing two associated activities:
RNA unwinding and 5′-triphosphatase. In the search of SARS-CoV-2
direct antiviral agents, we established biochemical assays for both
SARS-CoV-2 nps13-associated enzyme activities and screened both in silico and in vitro a small in-house
library of natural compounds. Myricetin, quercetin, kaempferol, and
flavanone were found to inhibit the SARS-CoV-2 nps13 unwinding activity
at nanomolar concentrations, while licoflavone C was shown to block
both SARS-CoV-2 nps13 activities at micromolar concentrations. Mode
of action studies showed that all compounds are nsp13 noncompetitive
inhibitors versus ATP, while computational studies suggested that
they can bind both nucleotide and 5′-RNA nsp13 binding sites,
with licoflavone C showing a unique pattern of interaction with nsp13
amino acid residues. Overall, we report for the first time natural
flavonoids as selective inhibitors of SARS-CoV-2 nps13 helicase with
low micromolar activity.
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Affiliation(s)
- Angela Corona
- Dipartimento di Scienze della vita e dell'ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, SS-554, 09042 Monserrato, Cagliari, Italy
| | - Krzysztof Wycisk
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Ks. Trojdena 4, Warsaw 02-109, Poland
| | - Carmine Talarico
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Candida Manelfi
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Jessica Milia
- Dipartimento di Scienze della vita e dell'ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, SS-554, 09042 Monserrato, Cagliari, Italy
| | - Rolando Cannalire
- Department of Pharmacy, University of Napoli "Federico II", via D. Montesano 49, Napoli 80131, Italy
| | - Francesca Esposito
- Dipartimento di Scienze della vita e dell'ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, SS-554, 09042 Monserrato, Cagliari, Italy
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany.,Fraunhofer Cluster of Excellence for Immune Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany.,Fraunhofer Cluster of Excellence for Immune Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Daniela Iaconis
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Andrea R Beccari
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Vincenzo Summa
- Department of Pharmacy, University of Napoli "Federico II", via D. Montesano 49, Napoli 80131, Italy
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Ks. Trojdena 4, Warsaw 02-109, Poland
| | - Enzo Tramontano
- Dipartimento di Scienze della vita e dell'ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, SS-554, 09042 Monserrato, Cagliari, Italy
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21
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Khorchani T, Gadiya Y, Witt G, Lanzillotta D, Claussen C, Zaliani A. SASC: A simple approach to synthetic cohorts for generating longitudinal observational patient cohorts from COVID-19 clinical data. Patterns 2022; 3:100453. [PMID: 35156066 PMCID: PMC8825316 DOI: 10.1016/j.patter.2022.100453] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/26/2021] [Accepted: 01/28/2022] [Indexed: 11/20/2022]
Abstract
One of the impacts of the coronavirus disease 2019 (COVID-19) pandemic has been a push for researchers to better exploit synthetic data and accelerate the design, analysis, and modeling of clinical trials. The unprecedented clinical efforts caused by COVID-19’s emergence will certainly boost future robust and innovative approaches of statistical sciences applied to clinical fields. Here, we report the development of SASC, a simple but efficient approach to generate COVID-19-related synthetic clinical data through a web application. SASC takes basic summary statistics for each group of patients and attempts to generate single variables according to internal correlations. To assess the “reliability” of the results, statistical comparisons with Synthea, a known synthetic patient generator tool, and, more importantly, with clinical data of real COVID-19 patients are provided. The source code and web application are available on GitHub, Zenodo, and Mendeley Data. From summaries of grouped variables, it is possible to generate synthetic data Similarity between real and virtual cohorts visualized with Kaplan-Meyer plots Shiny app for tuning and downloading the synthetic cohort provided to users SASC performances and result accuracies are similar to or better than Synthea results
Virtual cohorts built on synthetic data have received attention lately as they can change the way we work with clinical data. Generating synthetic data very close to "real-world" data without having ethical restrictions can considerably help data analysts in several aspects such as didactic efforts, statistical modeling, and assessments of interventions. We developed SASC, a tool that uses summary statistics of real clinical data to produce synthetic data having the same or a very close summary to the reference variables. SASC displays a performance comparable with, or superior to, that of other virtual cohort tools like Synthea and allows users to optimize the synthetic dataset produced through a Shiny visualizer application interactively.
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Affiliation(s)
- Takoua Khorchani
- Department of Human Biology, Claude Bernard Lyon1 University, 8 Rockefeller Avenue, 69008 Lyon, France
- Corresponding author
| | - Yojana Gadiya
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune Mediated Diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Gesa Witt
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune Mediated Diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Delia Lanzillotta
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune Mediated Diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Carsten Claussen
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune Mediated Diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune Mediated Diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
- Corresponding author
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22
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Krasemann S, Haferkamp U, Pfefferle S, Woo MS, Heinrich F, Schweizer M, Appelt-Menzel A, Cubukova A, Barenberg J, Leu J, Hartmann K, Thies E, Littau JL, Sepulveda-Falla D, Zhang L, Ton K, Liang Y, Matschke J, Ricklefs F, Sauvigny T, Sperhake J, Fitzek A, Gerhartl A, Brachner A, Geiger N, König EM, Bodem J, Franzenburg S, Franke A, Moese S, Müller FJ, Geisslinger G, Claussen C, Kannt A, Zaliani A, Gribbon P, Ondruschka B, Neuhaus W, Friese MA, Glatzel M, Pless O. The blood-brain barrier is dysregulated in COVID-19 and serves as a CNS entry route for SARS-CoV-2. Stem Cell Reports 2022; 17:307-320. [PMID: 35063125 PMCID: PMC8772030 DOI: 10.1016/j.stemcr.2021.12.011] [Citation(s) in RCA: 113] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/11/2022] Open
Abstract
Neurological complications are common in COVID-19. Although SARS-CoV-2 has been detected in patients’ brain tissues, its entry routes and resulting consequences are not well understood. Here, we show a pronounced upregulation of interferon signaling pathways of the neurovascular unit in fatal COVID-19. By investigating the susceptibility of human induced pluripotent stem cell (hiPSC)-derived brain capillary endothelial-like cells (BCECs) to SARS-CoV-2 infection, we found that BCECs were infected and recapitulated transcriptional changes detected in vivo. While BCECs were not compromised in their paracellular tightness, we found SARS-CoV-2 in the basolateral compartment in transwell assays after apical infection, suggesting active replication and transcellular transport of virus across the blood-brain barrier (BBB) in vitro. Moreover, entry of SARS-CoV-2 into BCECs could be reduced by anti-spike-, anti-angiotensin-converting enzyme 2 (ACE2)-, and anti-neuropilin-1 (NRP1)-specific antibodies or the transmembrane protease serine subtype 2 (TMPRSS2) inhibitor nafamostat. Together, our data provide strong support for SARS-CoV-2 brain entry across the BBB resulting in increased interferon signaling. IFNγ signaling is upregulated in COVID-19 human neurovascular unit SARS-CoV-2-infected hiPS-BCECs display similar upregulation of IFNγ signaling SARS-CoV-2 replicates in hiPS-BCECs and is released while barrier remains intact SARS-CoV-2 infection of hiPS-BCECs is decreased by antibodies and protease inhibitors
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23
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Linden T, Hanses F, Domingo-Fernández D, DeLong LN, Kodamullil AT, Schneider J, Vehreschild MJGT, Lanznaster J, Ruethrich MM, Borgmann S, Hower M, Wille K, Feldt T, Rieg S, Hertenstein B, Wyen C, Roemmele C, Vehreschild JJ, Jakob CEM, Stecher M, Kuzikov M, Zaliani A, Fröhlich H. Machine Learning Based Prediction of COVID-19 Mortality Suggests Repositioning of Anticancer Drug for Treating Severe Cases. Artif Intell Life Sci 2021; 1:100020. [PMID: 34988543 PMCID: PMC8677630 DOI: 10.1016/j.ailsci.2021.100020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 02/08/2023]
Abstract
Despite available vaccinations COVID-19 case numbers around the world are still growing, and effective medications against severe cases are lacking. In this work, we developed a machine learning model which predicts mortality for COVID-19 patients using data from the multi-center 'Lean European Open Survey on SARS-CoV-2-infected patients' (LEOSS) observational study (>100 active sites in Europe, primarily in Germany), resulting into an AUC of almost 80%. We showed that molecular mechanisms related to dementia, one of the relevant predictors in our model, intersect with those associated to COVID-19. Most notably, among these molecules was tyrosine kinase 2 (TYK2), a protein that has been patented as drug target in Alzheimer's Disease but also genetically associated with severe COVID-19 outcomes. We experimentally verified that anti-cancer drugs Sorafenib and Regorafenib showed a clear anti-cytopathic effect in Caco2 and VERO-E6 cells and can thus be regarded as potential treatments against COVID-19. Altogether, our work demonstrates that interpretation of machine learning based risk models can point towards drug targets and new treatment options, which are strongly needed for COVID-19.
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Affiliation(s)
- Thomas Linden
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53757 Sankt Augustin, Germany
- University of Bonn, Bonn-Aachen International Center for IT, Friedrich Hirzebruch-Allee 6, 53115 Bonn, Germany
| | - Frank Hanses
- Emergency Department, University Hospital Regensburg, 93053 Regensburg, Germany
- Department for Infectious Diseases and Infection Control, University Hospital Regensburg, Germany
| | - Daniel Domingo-Fernández
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53757 Sankt Augustin, Germany
| | - Lauren Nicole DeLong
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53757 Sankt Augustin, Germany
- University of Bonn, Bonn-Aachen International Center for IT, Friedrich Hirzebruch-Allee 6, 53115 Bonn, Germany
| | - Alpha Tom Kodamullil
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53757 Sankt Augustin, Germany
| | - Jochen Schneider
- Technical University of Munich, School of Medicine, University Hospital rechts der Isar, Department of Internal Medicine II, 81675 Munich, Germany
| | - Maria J G T Vehreschild
- Department II of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, 60590 Frankfurt, Germany
| | - Julia Lanznaster
- Department of Internal Medicine II, Hospital Passau, Innstraße 76, 94032 Passau, Germany
| | - Maria Madeleine Ruethrich
- Institute for Infection Medicine and Hospital Hygiene, University Hospital Jena, 07743 Jena, Germany
| | - Stefan Borgmann
- Department of Infectious Diseases and Infection Control, Hospital Ingolstadt, 85049 Ingolstadt, Germany
| | - Martin Hower
- Department of Pneumology, Infectious Diseases and Intensive Care, Klinikum Dortmund gGmbH, Hospital of University Witten / Herdecke, 44137 Dortmund, Germany
| | - Kai Wille
- University Clinic for Haematology, Oncology, Haemostaseology and Palliative Care, Johannes Wesling Medical Centre Minden, 32429 Minden, Germany
| | - Torsten Feldt
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Siegbert Rieg
- Department of Medicine II, University Hospital Freiburg, 79110 Freiburg, Germany
| | - Bernd Hertenstein
- Department of Medicine II, University Hospital Freiburg, 79110 Freiburg, Germany
| | - Christoph Wyen
- Christoph Wyen, Praxis am Ebertplatz Cologne, 50668 Cologne, Germany
| | - Christoph Roemmele
- Internal Medicine III - Gastroenterology and Infectious Diseases, University Hospital Augsburg, 86156 Augsburg, Germany
| | - Jörg Janne Vehreschild
- Department II of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University, 60590 Frankfurt, Germany
| | - Carolin E M Jakob
- Department I for Internal Medicine, University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
| | - Melanie Stecher
- Fraunhofer Institute for Translational Medicine and Pharmacologie (ITMP), VolksparkLabs, Schnackenburgallee 114, 22535 Hamburg, Germany
| | - Maria Kuzikov
- Department for Infectious Diseases and Infection Control, University Hospital Regensburg, Germany
| | - Andrea Zaliani
- Department for Infectious Diseases and Infection Control, University Hospital Regensburg, Germany
| | - Holger Fröhlich
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, 53757 Sankt Augustin, Germany
- University of Bonn, Bonn-Aachen International Center for IT, Friedrich Hirzebruch-Allee 6, 53115 Bonn, Germany
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24
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Costanzi E, Kuzikov M, Esposito F, Albani S, Demitri N, Giabbai B, Camasta M, Tramontano E, Rossetti G, Zaliani A, Storici P. Structural and Biochemical Analysis of the Dual Inhibition of MG-132 against SARS-CoV-2 Main Protease (Mpro/3CLpro) and Human Cathepsin-L. Int J Mol Sci 2021; 22:11779. [PMID: 34769210 PMCID: PMC8583849 DOI: 10.3390/ijms222111779] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [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: 09/29/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 12/26/2022] Open
Abstract
After almost two years from its first evidence, the COVID-19 pandemic continues to afflict people worldwide, highlighting the need for multiple antiviral strategies. SARS-CoV-2 main protease (Mpro/3CLpro) is a recognized promising target for the development of effective drugs. Because single target inhibition might not be sufficient to block SARS-CoV-2 infection and replication, multi enzymatic-based therapies may provide a better strategy. Here we present a structural and biochemical characterization of the binding mode of MG-132 to both the main protease of SARS-CoV-2, and to the human Cathepsin-L, suggesting thus an interesting scaffold for the development of double-inhibitors. X-ray diffraction data show that MG-132 well fits into the Mpro active site, forming a covalent bond with Cys145 independently from reducing agents and crystallization conditions. Docking of MG-132 into Cathepsin-L well-matches with a covalent binding to the catalytic cysteine. Accordingly, MG-132 inhibits Cathepsin-L with nanomolar potency and reversibly inhibits Mpro with micromolar potency, but with a prolonged residency time. We compared the apo and MG-132-inhibited structures of Mpro solved in different space groups and we identified a new apo structure that features several similarities with the inhibited ones, offering interesting perspectives for future drug design and in silico efforts.
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Affiliation(s)
- Elisa Costanzi
- Elettra—Sincrotrone Trieste, 34149 Trieste, Italy; (E.C.); (N.D.); (B.G.)
| | - Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), 22525 Hamburg, Germany; (M.K.); (A.Z.)
- Department of Life Sciences and Chemistry, Jacobs University Bremen GmbH, 28759 Bremen, Germany
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy; (F.E.); (M.C.); (E.T.)
| | - Simone Albani
- Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5) “Computational Biomedicine”, Forschungszentrum Jülich, 52425 Jülich, Germany; (S.A.); (G.R.)
- Department of Biology, Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062 Aachen, Germany
| | - Nicola Demitri
- Elettra—Sincrotrone Trieste, 34149 Trieste, Italy; (E.C.); (N.D.); (B.G.)
| | - Barbara Giabbai
- Elettra—Sincrotrone Trieste, 34149 Trieste, Italy; (E.C.); (N.D.); (B.G.)
| | - Marianna Camasta
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy; (F.E.); (M.C.); (E.T.)
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, 09124 Cagliari, Italy; (F.E.); (M.C.); (E.T.)
| | - Giulia Rossetti
- Institute for Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations (IAS-5) “Computational Biomedicine”, Forschungszentrum Jülich, 52425 Jülich, Germany; (S.A.); (G.R.)
- Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich, 52425 Jülich, Germany
- Department of Neurology, Faculty of Medicine, RWTH Aachen University, 52074 Aachen, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), 22525 Hamburg, Germany; (M.K.); (A.Z.)
| | - Paola Storici
- Elettra—Sincrotrone Trieste, 34149 Trieste, Italy; (E.C.); (N.D.); (B.G.)
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25
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Tanoli Z, Aldahdooh J, Alam F, Wang Y, Seemab U, Fratelli M, Pavlis P, Hajduch M, Bietrix F, Gribbon P, Zaliani A, Hall MD, Shen M, Brimacombe K, Kulesskiy E, Saarela J, Wennerberg K, Vähä-Koskela M, Tang J. Minimal information for chemosensitivity assays (MICHA): a next-generation pipeline to enable the FAIRification of drug screening experiments. Brief Bioinform 2021; 23:6361039. [PMID: 34472587 PMCID: PMC8769689 DOI: 10.1093/bib/bbab350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/03/2021] [Accepted: 08/02/2021] [Indexed: 12/29/2022] Open
Abstract
Chemosensitivity assays are commonly used for preclinical drug discovery and clinical trial optimization. However, data from independent assays are often discordant, largely attributed to uncharacterized variation in the experimental materials and protocols. We report here the launching of Minimal Information for Chemosensitivity Assays (MICHA), accessed via https://micha-protocol.org. Distinguished from existing efforts that are often lacking support from data integration tools, MICHA can automatically extract publicly available information to facilitate the assay annotation including: 1) compounds, 2) samples, 3) reagents and 4) data processing methods. For example, MICHA provides an integrative web server and database to obtain compound annotation including chemical structures, targets and disease indications. In addition, the annotation of cell line samples, assay protocols and literature references can be greatly eased by retrieving manually curated catalogues. Once the annotation is complete, MICHA can export a report that conforms to the FAIR principle (Findable, Accessible, Interoperable and Reusable) of drug screening studies. To consolidate the utility of MICHA, we provide FAIRified protocols from five major cancer drug screening studies as well as six recently conducted COVID-19 studies. With the MICHA web server and database, we envisage a wider adoption of a community-driven effort to improve the open access of drug sensitivity assays.
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Affiliation(s)
- Ziaurrehman Tanoli
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | - Jehad Aldahdooh
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | - Farhan Alam
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | - Yinyin Wang
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | - Umair Seemab
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | | | - Petr Pavlis
- Institute of Molecular and Translational Medicine, Czech
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Czech
| | | | - Philip Gribbon
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Germany
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, USA
| | - Min Shen
- National Center for Advancing Translational Sciences, USA
| | | | - Evgeny Kulesskiy
- Institute for Molecular Medicine Finland, University of Helsinki, Finland
| | - Jani Saarela
- Institute for Molecular Medicine Finland, University of Helsinki, Finland
| | - Krister Wennerberg
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Denmark
| | | | - Jing Tang
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
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26
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Tanoli Z, Aldahdooh J, Alam F, Wang Y, Seemab U, Fratelli M, Pavlis P, Hajduch M, Bietrix F, Gribbon P, Zaliani A, Hall MD, Shen M, Brimacombe K, Kulesskiy E, Saarela J, Wennerberg K, Vähä-Koskela M, Tang J. Minimal information for Chemosensitivity assays (MICHA): A next-generation pipeline to enable the FAIRification of drug screening experiments. bioRxiv 2021. [PMID: 33300000 PMCID: PMC7724669 DOI: 10.1101/2020.12.03.409409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Chemosensitivity assays are commonly used for preclinical drug discovery and clinical trial optimization. However, data from independent assays are often discordant, largely attributed to uncharacterized variation in the experimental materials and protocols. We report here the launching of MICHA (Minimal Information for Chemosensitivity Assays), accessed via https://micha-protocol.org. Distinguished from existing efforts that are often lacking support from data integration tools, MICHA can automatically extract publicly available information to facilitate the assay annotation including: 1) compounds, 2) samples, 3) reagents, and 4) data processing methods. For example, MICHA provides an integrative web server and database to obtain compound annotation including chemical structures, targets, and disease indications. In addition, the annotation of cell line samples, assay protocols and literature references can be greatly eased by retrieving manually curated catalogues. Once the annotation is complete, MICHA can export a report that conforms to the FAIR principle (Findable, Accessible, Interoperable and Reusable) of drug screening studies. To consolidate the utility of MICHA, we provide FAIRified protocols from five major cancer drug screening studies, as well as six recently conducted COVID-19 studies. With the MICHA webserver and database, we envisage a wider adoption of a community-driven effort to improve the open access of drug sensitivity assays.
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Affiliation(s)
- Ziaurrehman Tanoli
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | - Jehad Aldahdooh
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | - Farhan Alam
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | - Yinyin Wang
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | - Umair Seemab
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
| | | | - Petr Pavlis
- Institute of Molecular and Translational Medicine, Czech
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Czech
| | | | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology, Hamburg, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology, Hamburg, Germany
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, U.S.A
| | - Min Shen
- National Center for Advancing Translational Sciences, U.S.A
| | | | - Evgeny Kulesskiy
- Institute for Molecular Medicine Finland, University of Helsinki, Finland
| | - Jani Saarela
- Institute for Molecular Medicine Finland, University of Helsinki, Finland
| | - Krister Wennerberg
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Denmark
| | | | - Jing Tang
- Research Program in Systems Oncology, Faculty of medicine, University of Helsinki, Finland
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27
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Kuzikov M, Costanzi E, Reinshagen J, Esposito F, Vangeel L, Wolf M, Ellinger B, Claussen C, Geisslinger G, Corona A, Iaconis D, Talarico C, Manelfi C, Cannalire R, Rossetti G, Gossen J, Albani S, Musiani F, Herzog K, Ye Y, Giabbai B, Demitri N, Jochmans D, Jonghe SD, Rymenants J, Summa V, Tramontano E, Beccari AR, Leyssen P, Storici P, Neyts J, Gribbon P, Zaliani A. Identification of Inhibitors of SARS-CoV-2 3CL-Pro Enzymatic Activity Using a Small Molecule in Vitro Repurposing Screen. ACS Pharmacol Transl Sci 2021; 4:1096-1110. [PMID: 35287429 PMCID: PMC7986981 DOI: 10.1021/acsptsci.0c00216] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Indexed: 02/08/2023]
Abstract
Compound repurposing is an important strategy for the identification of effective treatment options against SARS-CoV-2 infection and COVID-19 disease. In this regard, SARS-CoV-2 main protease (3CL-Pro), also termed M-Pro, is an attractive drug target as it plays a central role in viral replication by processing the viral polyproteins pp1a and pp1ab at multiple distinct cleavage sites. We here report the results of a repurposing program involving 8.7 K compounds containing marketed drugs, clinical and preclinical candidates, and small molecules regarded as safe in humans. We confirmed previously reported inhibitors of 3CL-Pro and have identified 62 additional compounds with IC50 values below 1 μM and profiled their selectivity toward chymotrypsin and 3CL-Pro from the Middle East respiratory syndrome virus. A subset of eight inhibitors showed anticytopathic effect in a Vero-E6 cell line, and the compounds thioguanosine and MG-132 were analyzed for their predicted binding characteristics to SARS-CoV-2 3CL-Pro. The X-ray crystal structure of the complex of myricetin and SARS-Cov-2 3CL-Pro was solved at a resolution of 1.77 Å, showing that myricetin is covalently bound to the catalytic Cys145 and therefore inhibiting its enzymatic activity.
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Affiliation(s)
- Maria Kuzikov
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Elisa Costanzi
- Elettra-Sincrotrone
Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Jeanette Reinshagen
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Francesca Esposito
- Dipartimento
di Scienze della vita e dell’ambiente, Cittadella Universitaria di Monserrato, SS-554 Monserrato, Cagliari, Italy
| | - Laura Vangeel
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Markus Wolf
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Bernhard Ellinger
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Carsten Claussen
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Gerd Geisslinger
- Fraunhofer Institute for Translational Medicine and
Pharmacology
ITMP, Theodor Stern Kai
7, 60596 Frankfurt
am Main, Germany
- Institute
of Clinical Pharmacology, Goethe-University, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Angela Corona
- Dipartimento
di Scienze della vita e dell’ambiente, Cittadella Universitaria di Monserrato, SS-554 Monserrato, Cagliari, Italy
| | - Daniela Iaconis
- Dompé
Farmaceutici SpA, via Campo di Pile, 67100 L’Aquila, Italy
| | - Carmine Talarico
- Dompé
Farmaceutici SpA, via Campo di Pile, 67100 L’Aquila, Italy
| | - Candida Manelfi
- Dompé
Farmaceutici SpA, via Campo di Pile, 67100 L’Aquila, Italy
| | - Rolando Cannalire
- Department
of Pharmacy, University of Naples Federico
II, Via D. Montesano,
49, 80131 Naples, Italy
| | - Giulia Rossetti
- Institute
of Neuroscience and Medicine (INM-9)/Institute for Advanced Simulation
(IAS-5) and Jülich Supercomputing Centre (JSC) Forschungszentrum
Jülich, D-52425 Jülich, Germany
- Faculty
of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Jonas Gossen
- Institute
of Neuroscience and Medicine (INM-9)/Institute for Advanced Simulation
(IAS-5) and Jülich Supercomputing Centre (JSC) Forschungszentrum
Jülich, D-52425 Jülich, Germany
| | - Simone Albani
- Institute
of Neuroscience and Medicine (INM-9)/Institute for Advanced Simulation
(IAS-5) and Jülich Supercomputing Centre (JSC) Forschungszentrum
Jülich, D-52425 Jülich, Germany
| | - Francesco Musiani
- Laboratory
of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40216 Bologna, Italy
| | - Katja Herzog
- EU-OPENSCREEN
ERIC, Robert-Rössle-Straße
10, 13125 Berlin, Germany
| | - Yang Ye
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Barbara Giabbai
- Elettra-Sincrotrone
Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Nicola Demitri
- Elettra-Sincrotrone
Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Dirk Jochmans
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Steven De Jonghe
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Jasper Rymenants
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Vincenzo Summa
- Department
of Pharmacy, University of Naples Federico
II, Via D. Montesano,
49, 80131 Naples, Italy
| | - Enzo Tramontano
- Dipartimento
di Scienze della vita e dell’ambiente, Cittadella Universitaria di Monserrato, SS-554 Monserrato, Cagliari, Italy
| | | | - Pieter Leyssen
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Paola Storici
- Elettra-Sincrotrone
Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Johan Neyts
- Department
of Microbiology, Immunology and Transplantation, Rega Institute for
Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Philip Gribbon
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Andrea Zaliani
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
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28
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Gossen J, Albani S, Hanke A, Joseph BP, Bergh C, Kuzikov M, Costanzi E, Manelfi C, Storici P, Gribbon P, Beccari AR, Talarico C, Spyrakis F, Lindahl E, Zaliani A, Carloni P, Wade RC, Musiani F, Kokh DB, Rossetti G. A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics. ACS Pharmacol Transl Sci 2021; 4:1079-1095. [PMID: 34136757 PMCID: PMC8009102 DOI: 10.1021/acsptsci.0c00215] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Indexed: 12/27/2022]
Abstract
The SARS-CoV-2 coronavirus outbreak continues to spread at a rapid rate worldwide. The main protease (Mpro) is an attractive target for anti-COVID-19 agents. Unexpected difficulties have been encountered in the design of specific inhibitors. Here, by analyzing an ensemble of ∼30 000 SARS-CoV-2 Mpro conformations from crystallographic studies and molecular simulations, we show that small structural variations in the binding site dramatically impact ligand binding properties. Hence, traditional druggability indices fail to adequately discriminate between highly and poorly druggable conformations of the binding site. By performing ∼200 virtual screenings of compound libraries on selected protein structures, we redefine the protein's druggability as the consensus chemical space arising from the multiple conformations of the binding site formed upon ligand binding. This procedure revealed a unique SARS-CoV-2 Mpro blueprint that led to a definition of a specific structure-based pharmacophore. The latter explains the poor transferability of potent SARS-CoV Mpro inhibitors to SARS-CoV-2 Mpro, despite the identical sequences of the active sites. Importantly, application of the pharmacophore predicted novel high affinity inhibitors of SARS-CoV-2 Mpro, that were validated by in vitro assays performed here and by a newly solved X-ray crystal structure. These results provide a strong basis for effective rational drug design campaigns against SARS-CoV-2 Mpro and a new computational approach to screen protein targets with malleable binding sites.
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Affiliation(s)
- Jonas Gossen
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich, 52425, Germany
- Institute
for Advanced Simulations (IAS-5) “Computational biomedicine”, Forschungszentrum Jülich, Jülich, 52425, Germany
- Faculty of
Mathematics, Computer Science and Natural Sciences, RWTH Aachen, Aachen, 52062, Germany
| | - Simone Albani
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich, 52425, Germany
- Institute
for Advanced Simulations (IAS-5) “Computational biomedicine”, Forschungszentrum Jülich, Jülich, 52425, Germany
- Faculty of
Mathematics, Computer Science and Natural Sciences, RWTH Aachen, Aachen, 52062, Germany
| | - Anton Hanke
- Molecular
and Cellular Modeling Group, Heidelberg
Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, Heidelberg, 69118, Germany
- Institute
of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany
| | - Benjamin P. Joseph
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich, 52425, Germany
- Institute
for Advanced Simulations (IAS-5) “Computational biomedicine”, Forschungszentrum Jülich, Jülich, 52425, Germany
- Faculty of
Mathematics, Computer Science and Natural Sciences, RWTH Aachen, Aachen, 52062, Germany
| | - Cathrine Bergh
- Science for
Life Laboratory & Swedish e-Science Research Center, Department
of Applied Physics, KTH Royal Institute
of Technology, Stockholm, 11428, Sweden
| | - Maria Kuzikov
- Department
of Screening Port, Fraunhofer Institute
for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, Hamburg, 22525, Germany
| | - Elisa Costanzi
- Elettra-Sincrotrone
Trieste S.C.p.A., SS 14-km 163,5 in AREA Science Park, Basovizza,
Trieste, 34149, Italy
| | - Candida Manelfi
- Dompé
Farmaceutici SpA, Via Campo di Pile, L’Aquila, 67100, Italy
| | - Paola Storici
- Elettra-Sincrotrone
Trieste S.C.p.A., SS 14-km 163,5 in AREA Science Park, Basovizza,
Trieste, 34149, Italy
| | - Philip Gribbon
- Department
of Screening Port, Fraunhofer Institute
for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, Hamburg, 22525, Germany
| | | | - Carmine Talarico
- Dompé
Farmaceutici SpA, Via Campo di Pile, L’Aquila, 67100, Italy
| | - Francesca Spyrakis
- Department
of Drug Science and Technology, University
of Turin, via Giuria
9, Turin, 10125, Italy
| | - Erik Lindahl
- Science for
Life Laboratory & Swedish e-Science Research Center, Department
of Applied Physics, KTH Royal Institute
of Technology, Stockholm, 11428, Sweden
- Science
for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, SE-106 91, Sweden
| | - Andrea Zaliani
- Department
of Screening Port, Fraunhofer Institute
for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, Hamburg, 22525, Germany
| | - Paolo Carloni
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich, 52425, Germany
- Institute
for Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich, Jülich, 52425, Germany
- Institute
for Advanced Simulations (IAS-5) “Computational biomedicine”, Forschungszentrum Jülich, Jülich, 52425, Germany
- Faculty of
Mathematics, Computer Science and Natural Sciences, RWTH Aachen, Aachen, 52062, Germany
| | - Rebecca C. Wade
- Molecular
and Cellular Modeling Group, Heidelberg
Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, Heidelberg, 69118, Germany
- Zentrum
für Molekulare Biologie der University Heidelberg, DKFZ-ZMBH
Alliance, INF 282, Heidelberg, 69120, Germany
- Interdisciplinary
Center for Scientific Computing (IWR), Heidelberg
University, INF 368, Heidelberg, 69120, Germany
| | - Francesco Musiani
- Laboratory
of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Daria B. Kokh
- Molecular
and Cellular Modeling Group, Heidelberg
Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, Heidelberg, 69118, Germany
| | - Giulia Rossetti
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich, 52425, Germany
- Institute
for Advanced Simulations (IAS-5) “Computational biomedicine”, Forschungszentrum Jülich, Jülich, 52425, Germany
- Jülich
Supercomputing Center (JSC), Forschungszentrum
Jülich, Jülich, 52425, Germany
- Department
of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, RWTH Aachen University, Aachen, 44517, Germany
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29
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Kuzikov M, Costanzi E, Reinshagen J, Esposito F, Vangeel L, Wolf M, Ellinger B, Claussen C, Geisslinger G, Corona A, Iaconis D, Talarico C, Manelfi C, Cannalire R, Rossetti G, Gossen J, Albani S, Musiani F, Herzog K, Ye Y, Giabbai B, Demitri N, Jochmans D, Jonghe SD, Rymenants J, Summa V, Tramontano E, Beccari AR, Leyssen P, Storici P, Neyts J, Gribbon P, Zaliani A. Identification of Inhibitors of SARS-CoV-2 3CL-Pro Enzymatic Activity Using a Small Molecule in Vitro Repurposing Screen. ACS Pharmacol Transl Sci 2021; 4:1096-1110. [PMID: 35287429 DOI: 10.1101/2020.12.16.422677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Indexed: 05/18/2023]
Abstract
Compound repurposing is an important strategy for the identification of effective treatment options against SARS-CoV-2 infection and COVID-19 disease. In this regard, SARS-CoV-2 main protease (3CL-Pro), also termed M-Pro, is an attractive drug target as it plays a central role in viral replication by processing the viral polyproteins pp1a and pp1ab at multiple distinct cleavage sites. We here report the results of a repurposing program involving 8.7 K compounds containing marketed drugs, clinical and preclinical candidates, and small molecules regarded as safe in humans. We confirmed previously reported inhibitors of 3CL-Pro and have identified 62 additional compounds with IC50 values below 1 μM and profiled their selectivity toward chymotrypsin and 3CL-Pro from the Middle East respiratory syndrome virus. A subset of eight inhibitors showed anticytopathic effect in a Vero-E6 cell line, and the compounds thioguanosine and MG-132 were analyzed for their predicted binding characteristics to SARS-CoV-2 3CL-Pro. The X-ray crystal structure of the complex of myricetin and SARS-Cov-2 3CL-Pro was solved at a resolution of 1.77 Å, showing that myricetin is covalently bound to the catalytic Cys145 and therefore inhibiting its enzymatic activity.
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Affiliation(s)
- Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Elisa Costanzi
- Elettra-Sincrotrone Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Jeanette Reinshagen
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Francesca Esposito
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554 Monserrato, Cagliari, Italy
| | - Laura Vangeel
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Markus Wolf
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Bernhard Ellinger
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Carsten Claussen
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Gerd Geisslinger
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor Stern Kai 7, 60596 Frankfurt am Main, Germany
- Institute of Clinical Pharmacology, Goethe-University, Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Angela Corona
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554 Monserrato, Cagliari, Italy
| | - Daniela Iaconis
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Carmine Talarico
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Candida Manelfi
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Rolando Cannalire
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano, 49, 80131 Naples, Italy
| | - Giulia Rossetti
- Institute of Neuroscience and Medicine (INM-9)/Institute for Advanced Simulation (IAS-5) and Jülich Supercomputing Centre (JSC) Forschungszentrum Jülich, D-52425 Jülich, Germany
- Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Jonas Gossen
- Institute of Neuroscience and Medicine (INM-9)/Institute for Advanced Simulation (IAS-5) and Jülich Supercomputing Centre (JSC) Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Simone Albani
- Institute of Neuroscience and Medicine (INM-9)/Institute for Advanced Simulation (IAS-5) and Jülich Supercomputing Centre (JSC) Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40216 Bologna, Italy
| | - Katja Herzog
- EU-OPENSCREEN ERIC, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Yang Ye
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Barbara Giabbai
- Elettra-Sincrotrone Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Nicola Demitri
- Elettra-Sincrotrone Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Dirk Jochmans
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Steven De Jonghe
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Jasper Rymenants
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Vincenzo Summa
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano, 49, 80131 Naples, Italy
| | - Enzo Tramontano
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554 Monserrato, Cagliari, Italy
| | - Andrea R Beccari
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Pieter Leyssen
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Paola Storici
- Elettra-Sincrotrone Trieste S.C.p.A., SS 14 - km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Johan Neyts
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
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30
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Schultz B, Zaliani A, Ebeling C, Reinshagen J, Bojkova D, Lage-Rupprecht V, Karki R, Lukassen S, Gadiya Y, Ravindra NG, Das S, Baksi S, Domingo-Fernández D, Lentzen M, Strivens M, Raschka T, Cinatl J, DeLong LN, Gribbon P, Geisslinger G, Ciesek S, van Dijk D, Gardner S, Kodamullil AT, Fröhlich H, Peitsch M, Jacobs M, Hoeng J, Eils R, Claussen C, Hofmann-Apitius M. A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization. Sci Rep 2021; 11:11049. [PMID: 34040048 PMCID: PMC8155020 DOI: 10.1038/s41598-021-90296-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 10/01/2020] [Accepted: 05/04/2021] [Indexed: 02/08/2023] Open
Abstract
The SARS-CoV-2 pandemic has challenged researchers at a global scale. The scientific community's massive response has resulted in a flood of experiments, analyses, hypotheses, and publications, especially in the field of drug repurposing. However, many of the proposed therapeutic compounds obtained from SARS-CoV-2 specific assays are not in agreement and thus demonstrate the need for a singular source of COVID-19 related information from which a rational selection of drug repurposing candidates can be made. In this paper, we present the COVID-19 PHARMACOME, a comprehensive drug-target-mechanism graph generated from a compilation of 10 separate disease maps and sources of experimental data focused on SARS-CoV-2/COVID-19 pathophysiology. By applying our systematic approach, we were able to predict the synergistic effect of specific drug pairs, such as Remdesivir and Thioguanosine or Nelfinavir and Raloxifene, on SARS-CoV-2 infection. Experimental validation of our results demonstrate that our graph can be used to not only explore the involved mechanistic pathways, but also to identify novel combinations of drug repurposing candidates.
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Affiliation(s)
- Bruce Schultz
- Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany
| | - Andrea Zaliani
- ScreeningPort, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 22525, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune Mediated Diseases, CIMD, External Partner Site, 22525, Hamburg, Germany
| | - Christian Ebeling
- Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany
| | - Jeanette Reinshagen
- ScreeningPort, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 22525, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune Mediated Diseases, CIMD, External Partner Site, 22525, Hamburg, Germany
| | - Denisa Bojkova
- Institute for Medical Virology, University Hospital Frankfurt, 60590, Frankfurt am Main, Germany
| | - Vanessa Lage-Rupprecht
- Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany
| | - Reagon Karki
- Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany
| | - Sören Lukassen
- Center for Digital Health, Berlin Institute of Health (BIH), Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Yojana Gadiya
- Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany
| | - Neal G Ravindra
- Center for Biomedical Data Science, Yale School of Medicine, Yale University, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Sayoni Das
- Unit 8B Bankside, PrecisionLife Ltd., Hanborough Business Park, Long Hanborough, Oxfordshire, OX29 8LJ, UK
| | - Shounak Baksi
- Causality BioModels Pvt Ltd., Kinfra Hi-Tech Park, Kerala Technology Innovation Zone- KTIZ, Kalamassery, Cochin, 683503, India
| | - Daniel Domingo-Fernández
- Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany
| | - Manuel Lentzen
- Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany
| | - Mark Strivens
- Unit 8B Bankside, PrecisionLife Ltd., Hanborough Business Park, Long Hanborough, Oxfordshire, OX29 8LJ, UK
| | - Tamara Raschka
- Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany
| | - Jindrich Cinatl
- Institute for Medical Virology, University Hospital Frankfurt, 60590, Frankfurt am Main, Germany
| | - Lauren Nicole DeLong
- Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany
| | - Phil Gribbon
- ScreeningPort, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 22525, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune Mediated Diseases, CIMD, External Partner Site, 22525, Hamburg, Germany
| | - Gerd Geisslinger
- Fraunhofer Cluster of Excellence for Immune Mediated Diseases, CIMD, External Partner Site, 22525, Hamburg, Germany
- Pharmazentrum Frankfurt/ZAFES, Institut Für Klinische Pharmakologie, Klinikum Der Goethe-Universität Frankfurt, 60590, Frankfurt am Main, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 60596, Frankfurt am Main, Germany
| | - Sandra Ciesek
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 60596, Frankfurt am Main, Germany
- Institute for Medical Virology, University Hospital Frankfurt, 60590, Frankfurt am Main, Germany
- DZIF, German Centre for Infection Research, External Partner Site, 60596, Frankfurt am Main, Germany
| | - David van Dijk
- Center for Biomedical Data Science, Yale School of Medicine, Yale University, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Steve Gardner
- Unit 8B Bankside, PrecisionLife Ltd., Hanborough Business Park, Long Hanborough, Oxfordshire, OX29 8LJ, UK
| | - Alpha Tom Kodamullil
- Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany
| | - Holger Fröhlich
- Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany
| | - Manuel Peitsch
- Philipp Morris International R&D, Biological Systems Research, R&D Innovation Cube T1517.07, Quai Jeanrenaud 5, 2000, Neuchâte, Switzerland
| | - Marc Jacobs
- Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany
| | - Julia Hoeng
- Philipp Morris International R&D, Biological Systems Research, R&D Innovation Cube T1517.07, Quai Jeanrenaud 5, 2000, Neuchâte, Switzerland
| | - Roland Eils
- Center for Digital Health, Berlin Institute of Health (BIH), Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Carsten Claussen
- ScreeningPort, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 22525, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune Mediated Diseases, CIMD, External Partner Site, 22525, Hamburg, Germany
| | - Martin Hofmann-Apitius
- Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Department of Bioinformatics, Institutszentrum Birlinghoven, 53754, Sankt Augustin, Germany.
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31
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Günther S, Reinke PYA, Fernández-García Y, Lieske J, Lane TJ, Ginn HM, Koua FHM, Ehrt C, Ewert W, Oberthuer D, Yefanov O, Meier S, Lorenzen K, Krichel B, Kopicki JD, Gelisio L, Brehm W, Dunkel I, Seychell B, Gieseler H, Norton-Baker B, Escudero-Pérez B, Domaracky M, Saouane S, Tolstikova A, White TA, Hänle A, Groessler M, Fleckenstein H, Trost F, Galchenkova M, Gevorkov Y, Li C, Awel S, Peck A, Barthelmess M, Schlünzen F, Lourdu Xavier P, Werner N, Andaleeb H, Ullah N, Falke S, Srinivasan V, França BA, Schwinzer M, Brognaro H, Rogers C, Melo D, Zaitseva-Doyle JJ, Knoska J, Peña-Murillo GE, Mashhour AR, Hennicke V, Fischer P, Hakanpää J, Meyer J, Gribbon P, Ellinger B, Kuzikov M, Wolf M, Beccari AR, Bourenkov G, von Stetten D, Pompidor G, Bento I, Panneerselvam S, Karpics I, Schneider TR, Garcia-Alai MM, Niebling S, Günther C, Schmidt C, Schubert R, Han H, Boger J, Monteiro DCF, Zhang L, Sun X, Pletzer-Zelgert J, Wollenhaupt J, Feiler CG, Weiss MS, Schulz EC, Mehrabi P, Karničar K, Usenik A, Loboda J, Tidow H, Chari A, Hilgenfeld R, Uetrecht C, Cox R, Zaliani A, Beck T, Rarey M, Günther S, Turk D, Hinrichs W, Chapman HN, Pearson AR, Betzel C, Meents A. X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science 2021; 372:642-646. [PMID: 33811162 PMCID: PMC8224385 DOI: 10.1126/science.abf7945] [Citation(s) in RCA: 203] [Impact Index Per Article: 67.7] [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: 11/20/2020] [Accepted: 03/29/2021] [Indexed: 12/17/2022]
Abstract
The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput x-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for viral replication. In contrast to commonly applied x-ray fragment screening experiments with molecules of low complexity, our screen tested already-approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to Mpro In subsequent cell-based viral reduction assays, one peptidomimetic and six nonpeptidic compounds showed antiviral activity at nontoxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.
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Affiliation(s)
- Sebastian Günther
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
| | - Patrick Y A Reinke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Yaiza Fernández-García
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany
| | - Julia Lieske
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Thomas J Lane
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Helen M Ginn
- Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Faisal H M Koua
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Christiane Ehrt
- Universität Hamburg, Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany
| | - Wiebke Ewert
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Susanne Meier
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | | | - Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, 20251 Hamburg, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, 20251 Hamburg, Germany
| | - Luca Gelisio
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Ilona Dunkel
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Brandon Seychell
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
| | - Henry Gieseler
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Brenna Norton-Baker
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Chemistry, UC Irvine, Irvine, CA 92697-2025, USA
| | - Beatriz Escudero-Pérez
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany
| | - Martin Domaracky
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Sofiane Saouane
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Alexandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Anna Hänle
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Michael Groessler
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Fabian Trost
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Vision Systems, Hamburg University of Technology, 21071 Hamburg, Germany
| | - Chufeng Li
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Salah Awel
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Ariana Peck
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Miriam Barthelmess
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Frank Schlünzen
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - P Lourdu Xavier
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Nadine Werner
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Hina Andaleeb
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Najeeb Ullah
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Sven Falke
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Vasundara Srinivasan
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Bruno Alves França
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Martin Schwinzer
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Hévila Brognaro
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Cromarte Rogers
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Diogo Melo
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Joanna J Zaitseva-Doyle
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Gisel E Peña-Murillo
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Aida Rahmani Mashhour
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Vincent Hennicke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Pontus Fischer
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Johanna Hakanpää
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Jan Meyer
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Bernhard Ellinger
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Markus Wolf
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | | | - Gleb Bourenkov
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - David von Stetten
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Isabel Bento
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Ivars Karpics
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | | | - Stephan Niebling
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Christian Günther
- EMBL Outstation Hamburg, c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | | | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Huijong Han
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Juliane Boger
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
| | - Diana C F Monteiro
- Hauptmann Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Linlin Zhang
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany
| | - Xinyuanyuan Sun
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany
| | | | - Jan Wollenhaupt
- Helmholtz Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Christian G Feiler
- Helmholtz Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Manfred S Weiss
- Helmholtz Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Eike-Christian Schulz
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Pedram Mehrabi
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Katarina Karničar
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Aleksandra Usenik
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Jure Loboda
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Henning Tidow
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Ashwin Chari
- Research Group for Structural Biochemistry and Mechanisms, Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine, University of Lübeck, 23562 Lübeck, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562 Lübeck, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, 20251 Hamburg, Germany
| | - Russell Cox
- Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Tobias Beck
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany
| | - Dusan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Winfried Hinrichs
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
- Universität Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Physics, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Arwen R Pearson
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Institut für Nanostruktur- und Festkörperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Christian Betzel
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, 22607 Hamburg, Germany
| | - Alke Meents
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
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Ellinger B, Bojkova D, Zaliani A, Cinatl J, Claussen C, Westhaus S, Keminer O, Reinshagen J, Kuzikov M, Wolf M, Geisslinger G, Gribbon P, Ciesek S. A SARS-CoV-2 cytopathicity dataset generated by high-content screening of a large drug repurposing collection. Sci Data 2021; 8:70. [PMID: 33637768 PMCID: PMC7910569 DOI: 10.1038/s41597-021-00848-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [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: 10/08/2020] [Accepted: 01/15/2021] [Indexed: 02/08/2023] Open
Abstract
SARS-CoV-2 is a novel coronavirus responsible for the COVID-19 pandemic, in which acute respiratory infections are associated with high socio-economic burden. We applied high-content screening to a well-defined collection of 5632 compounds including 3488 that have undergone previous clinical investigations across 600 indications. The compounds were screened by microscopy for their ability to inhibit SARS-CoV-2 cytopathicity in the human epithelial colorectal adenocarcinoma cell line, Caco-2. The primary screen identified 258 hits that inhibited cytopathicity by more than 75%, most of which were not previously known to be active against SARS-CoV-2 in vitro. These compounds were tested in an eight-point dose response screen using the same image-based cytopathicity readout. For the 67 most active molecules, cytotoxicity data were generated to confirm activity against SARS-CoV-2. We verified the ability of known inhibitors camostat, nafamostat, lopinavir, mefloquine, papaverine and cetylpyridinium to reduce the cytopathic effects of SARS-CoV-2, providing confidence in the validity of the assay. The high-content screening data are suitable for reanalysis across numerous drug classes and indications and may yield additional insights into SARS-CoV-2 mechanisms and potential therapeutic strategies.
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Affiliation(s)
- Bernhard Ellinger
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Hamburg, 22525, Germany.
| | - Denisa Bojkova
- University Hospital Frankfurt, 60590, Frankfurt am Main, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Hamburg, 22525, Germany
| | - Jindrich Cinatl
- University Hospital Frankfurt, 60590, Frankfurt am Main, Germany
| | - Carsten Claussen
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Hamburg, 22525, Germany
- Fraunhofer Cluster of Excellence for Immune Mediated Diseases CIMD, Frankfurt am Main, 60596, Germany
| | - Sandra Westhaus
- University Hospital Frankfurt, 60590, Frankfurt am Main, Germany
| | - Oliver Keminer
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Hamburg, 22525, Germany
| | - Jeanette Reinshagen
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Hamburg, 22525, Germany
| | - Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Hamburg, 22525, Germany
| | - Markus Wolf
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Hamburg, 22525, Germany
| | - Gerd Geisslinger
- Pharmazentrum Frankfurt/ZAFES, Institut für Klinische Pharmakologie, Klinikum der Goethe-Universität Frankfurt, 60590, Frankfurt am Main, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 60596, Frankfurt am Main, Germany
- Fraunhofer Cluster of Excellence for Immune Mediated Diseases CIMD, Frankfurt am Main, 60596, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Hamburg, 22525, Germany
- Fraunhofer Cluster of Excellence for Immune Mediated Diseases CIMD, Frankfurt am Main, 60596, Germany
| | - Sandra Ciesek
- University Hospital Frankfurt, 60590, Frankfurt am Main, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 60596, Frankfurt am Main, Germany
- DZIF, German Centre for Infection Research, External partner site, 60596, Frankfurt am Main, Germany
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Maculins T, Garcia-Pardo J, Skenderovic A, Gebel J, Putyrski M, Vorobyov A, Busse P, Varga G, Kuzikov M, Zaliani A, Rahighi S, Schaeffer V, Parnham MJ, Sidhu SS, Ernst A, Dötsch V, Akutsu M, Dikic I. Discovery of Protein-Protein Interaction Inhibitors by Integrating Protein Engineering and Chemical Screening Platforms. Cell Chem Biol 2020; 27:1441-1451.e7. [PMID: 32726587 DOI: 10.1016/j.chembiol.2020.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 05/21/2020] [Revised: 06/24/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023]
Abstract
Protein-protein interactions (PPIs) govern intracellular life, and identification of PPI inhibitors is challenging. Roadblocks in assay development stemming from weak binding affinities of natural PPIs impede progress in this field. We postulated that enhancing binding affinity of natural PPIs via protein engineering will aid assay development and hit discovery. This proof-of-principle study targets PPI between linear ubiquitin chains and NEMO UBAN domain, which activates NF-κB signaling. Using phage display, we generated ubiquitin variants that bind to the functional UBAN epitope with high affinity, act as competitive inhibitors, and structurally maintain the existing PPI interface. When utilized in assay development, variants enable generation of robust cell-based assays for chemical screening. Top compounds identified using this approach directly bind to UBAN and dampen NF-κB signaling. This study illustrates advantages of integrating protein engineering and chemical screening in hit identification, a development that we anticipate will have wide application in drug discovery.
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Affiliation(s)
- Timurs Maculins
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany.
| | - Javier Garcia-Pardo
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | | | - Jakob Gebel
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Mateusz Putyrski
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Andrew Vorobyov
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Philipp Busse
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Gabor Varga
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Maria Kuzikov
- Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, Hamburg, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, Hamburg, Germany
| | - Simin Rahighi
- Chapman University School of Pharmacy (CUSP), Harry and Diane Rinker Health Science Campus, Chapman University, Irvine, CA 92618, USA
| | | | - Michael J Parnham
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Andreas Ernst
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Masato Akutsu
- Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany.
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Carlisi E, Bossi D, Zaliani A, Dalla Toffola E. Persistent hiccup after surgical resection of a brainstem arteriovenous malformation: a case successfully treated with gabapentin during rehabilitation. Case report. Eur J Phys Rehabil Med 2012; 48:289-291. [PMID: 22083264] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Persistent hiccup rarely occurs during rehabilitation, but its management can prove to be very difficult, particularly in presence of associated dysphagia, requiring longer hospitalization and higher risk of severe clinical complications. We present a case of persistent hiccup after surgical resection of a brainstem arteriovenous malformation successfully treated with gabapentin during rehabilitation.
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Affiliation(s)
- E Carlisi
- Physical Medicine and Rehabilitation Unit, I.R.C.C.S. Policlinico San Matteo Foundation, Pavia, Italy.
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35
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Grädler U, Fuchss T, Ulrich WR, Boer R, Strub A, Hesslinger C, Anézo C, Diederichs K, Zaliani A. Novel nanomolar imidazo[4,5-b]pyridines as selective nitric oxide synthase (iNOS) inhibitors: SAR and structural insights. Bioorg Med Chem Lett 2011; 21:4228-32. [PMID: 21684157 DOI: 10.1016/j.bmcl.2011.05.073] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 05/18/2011] [Accepted: 05/20/2011] [Indexed: 10/18/2022]
Abstract
Inducible arginine oxidation and subsequent NO production by correspondent synthase (iNOS) are important cellular answers to proinflammatory signals. Prolonged NO production has been proved in higher organisms to cause stroke or septic shock. Several classes of potent NOS inhibitors have been reported, most of them targeting the arginine binding site of the oxygenase domain. Here we disclose the SAR and the rational design of potent and selective iNOS inhibitors which may be useful as anti-inflammatory drugs.
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Affiliation(s)
- Ulrich Grädler
- Nycomed GmbH, Byk-Gulden-Str. 2, D-78467 Konstanz, Germany.
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Schotten T, Berthold H, Thiem J, Zaliani A. Spiro-Annelated Zn-Phthalocyanine: A Novel Building Block for Molecular Architecture? SYNTHESIS-STUTTGART 2010. [DOI: 10.1055/s-0030-1258209] [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: 10/19/2022]
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Velankar AD, Quintini G, Prabhu A, Weber A, Hunaeus G, Voland B, Wuest M, Orjeda C, Harel D, Varghese S, Gore V, Patil M, Gayke D, Herdemann M, Heit I, Zaliani A. Synthesis and biological evaluation of novel (4 or 5-aryl)pyrazolyl-indoles as inhibitors of interleukin-2 inducible T-cell kinase (ITK). Bioorg Med Chem 2010; 18:4547-59. [PMID: 20472447 DOI: 10.1016/j.bmc.2010.04.056] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 04/19/2010] [Accepted: 04/20/2010] [Indexed: 11/17/2022]
Abstract
Interleukin-2 inducible T-cell kinase (ITK) is one of five kinases that belong to the Tec kinase family that plays an important role in T-cell and mast cell signaling. Various reports point to a role of ITK in the treatment of allergic asthma. For example, it was shown that mice lacking ITK have reduced airway hyperresponsiveness, inflammation and tracheal responses in an allergic asthma model. In this article, we disclose novel ITK inhibitors based on (4 or 5-aryl)pyrazolyl-indole scaffold that were also found to be selective for ITK over other kinases like IRK, CDK2, GSK3ss and PKA.
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Affiliation(s)
- Avdhoot D Velankar
- Global Discovery, Nycomed Pharma Pvt. Ltd, Andheri (East), Mumbai, Maharashtra, India.
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39
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Zaliani A, Boda K, Seidel T, Herwig A, Schwab CH, Gasteiger J, Claußen H, Lemmen C, Degen J, Pärn J, Rarey M. Second-generation de novo design: a view from a medicinal chemist perspective. J Comput Aided Mol Des 2009; 23:593-602. [DOI: 10.1007/s10822-009-9291-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Accepted: 06/03/2009] [Indexed: 12/11/2022]
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40
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Zaliani A, Mueller C, Rarey M. Prediction of kinase inhibitors cross-reaction on the basis of kinase ATP cavity similarities: a study using PKSIM protein similarity score. Chem Cent J 2008. [PMCID: PMC4236213 DOI: 10.1186/1752-153x-2-s1-p19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Abstract
On the basis of the recently introduced reduced graph concept of ErG (extending reduced graphs), a straightforward weighting approach to include additional (e.g., structural or SAR) knowledge into similarity searching procedures for virtual screening (wErG) is proposed. This simple procedure is exemplified with three data sets, for which interaction patterns available from X-ray structures of native or peptidomimetic ligands with their target protein are used to significantly improve retrieval rates of known actives from the MDL Drug Report database. The results are compared to those of other virtual screening techniques such as Daylight fingerprints, FTrees, UNITY, and various FlexX docking protocols. Here, it is shown that wErG exhibits a very good and stable performance independent of the target structure. On the basis of this (and the fact that ErG retrieves structurally more dissimilar compounds due to its potential to perform scaffold-hopping), the combination of wErG and FlexX is successfully explored. Overall, wErG is not only an easily applicable weighting procedure that efficiently identifies actives in large data sets but it is also straightforward to understand for both medicinal and computational chemists and can, therefore, be driven by several aspects of project-related knowledge (e.g., X-ray, NMR, SAR, and site-directed mutagenesis) in a very early stage of the hit identification process.
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Affiliation(s)
- Nikolaus Stiefl
- Eli Lilly Research Laboratories, Essener Bogen 7, D-22419 Hamburg, Germany.
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43
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Abstract
An extended reduced graph approach (ErG) is presented that uses pharmacophore-type node descriptions to encode the relevant molecular properties. The basic idea of the method can be described as a hybrid approach of reduced graphs (Gillet et al. J. Chem. Inf. Comput. Sci. 2003, 43, 338-345) and binding property pairs (Kearsley et al. J. Chem. Inf. Comput. Sci. 1996, 36, 118-127). However, specific extension modifications to correctly describe the pharmacophoric properties, size, and shape of the molecules under study result in a very stable and good performance as compared to DAYLIGHT fingerprints (DFP). This is exemplified for 11 activity classes of the MDL Drug Data Report database, for which ErG performs as well or better than DFP in 10 cases. On the basis of the example data sets, the ability of ErG to switch from one chemotype to another (often referred to as "scaffold hopping") is highlighted. Additionally, possible pitfalls of reduced graph approaches as well as suitable solutions are discussed with the help of example structures. Overall, it is shown that ErG is a widely applicable method capable of identifying structurally diverse actives for a given active search query. This diversity is achieved by a high degree of molecular abstraction, which in turn results in a low dimensional descriptor vector that allows very low computation times for similarity searches.
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Efanov AM, Barrett DG, Brenner MB, Briggs SL, Delaunois A, Durbin JD, Giese U, Guo H, Radloff M, Gil GS, Sewing S, Wang Y, Weichert A, Zaliani A, Gromada J. A novel glucokinase activator modulates pancreatic islet and hepatocyte function. Endocrinology 2005; 146:3696-701. [PMID: 15919746 DOI: 10.1210/en.2005-0377] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The glucose-sensing enzyme glucokinase (GK) plays a key role in glucose metabolism. We report here the effects of a novel glucokinase activator, LY2121260. The activator enhanced GK activity via binding to the allosteric site located in the hinge region of the enzyme. LY2121260 stimulated insulin secretion in a glucose-dependent manner in pancreatic beta-cells and increased glucose use in rat hepatocytes. In addition, incubation of beta-cells with the GK activator resulted in increased GK protein levels, suggesting that enhanced insulin secretion on chronic treatment with a GK activator may be due to not only changed enzyme kinetics but also elevated enzyme levels. Animals treated with LY2121260 showed an improved glucose tolerance after oral glucose challenge. These results support the concept that GK activators represent a new class of compounds that increase both insulin secretion and hepatic glucose use and in doing so may prove to be effective agents for the control of blood glucose levels in patients with type 2 diabetes.
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Affiliation(s)
- Alexander M Efanov
- Lilly Research Laboratories, Eli Lilly & Company, Essener Bogen 7, 22419 Hamburg, Germany.
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45
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Abstract
We describe a method for docking of a scaffold-based series and present its advantages over docking of individual ligands, for determining the binding mode of a molecular scaffold in a binding site. The method has been applied to eight different scaffolds of protein kinase inhibitors (PKI). A single analog of each of these eight scaffolds was previously crystallized with different protein kinases. We have used FlexX to dock a set of molecules that share the same scaffold, rather than docking a single molecule. The main mode of binding is determined by the mode of binding of the largest cluster among the docked molecules that share a scaffold. Clustering is based on our 'nearest single neighbor' method [J. Chem. Inf. Comput. Sci., 43 (2003) 208-217]. Additional criteria are applied in those cases in which more than one significant binding mode is found. Using the proposed method, most of the crystallographic binding modes of these scaffolds were reconstructed. Alternative modes, that have not been detected yet by experiments, could also be identified. The method was applied to predict the binding mode of an additional molecular scaffold that was not yet reported and the predicted binding mode has been found to be very similar to experimental results for a closely related scaffold. We suggest that this approach be used as a virtual screening tool for scaffold-based design processes.
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Affiliation(s)
- Doron Chema
- Department of Medicinal Chemistry, David R. Bloom Center for Pharmacy, School of Pharmacy, Hebrew University of Jerusalem 91120, Israel
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46
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Leoni F, Zaliani A, Bertolini G, Porro G, Pagani P, Pozzi P, Donà G, Fossati G, Sozzani S, Azam T, Bufler P, Fantuzzi G, Goncharov I, Kim SH, Pomerantz BJ, Reznikov LL, Siegmund B, Dinarello CA, Mascagni P. The antitumor histone deacetylase inhibitor suberoylanilide hydroxamic acid exhibits antiinflammatory properties via suppression of cytokines. Proc Natl Acad Sci U S A 2002; 99:2995-3000. [PMID: 11867742 PMCID: PMC122461 DOI: 10.1073/pnas.052702999] [Citation(s) in RCA: 401] [Impact Index Per Article: 18.2] [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] [Indexed: 01/12/2023] Open
Abstract
Suberoylanilide hydroxamic acid (SAHA) is a hydroxamic acid-containing hybrid polar molecule; SAHA specifically binds to and inhibits the activity of histone deacetylase. Although SAHA, like other inhibitors of histone deacetylase, exhibits antitumor effects by increasing expression of genes regulating tumor survival, we found that SAHA reduces the production of proinflammatory cytokines in vivo and in vitro. A single oral administration of SAHA to mice dose-dependently reduced circulating TNF-alpha, IL-1-beta, IL-6, and IFN-gamma induced by lipopolysaccharide (LPS). Administration of SAHA also reduced hepatic cellular injury in mice following i.v. injection of Con A. SAHA inhibited nitric oxide release in mouse macrophages stimulated by the combination of TNF-alpha plus IFN-gamma. Human peripheral blood mononuclear cells stimulated with LPS in the presence of SAHA released less TNF-alpha, IL-1-beta, IL-12, and IFN-gamma (50% reduction at 100-200 nM). The production of IFN-gamma stimulated by IL-18 plus IL-12 was also inhibited by SAHA (85% at 200 nM). However, SAHA did not affect LPS-induced synthesis of the IL-1-beta precursor, the IL-1 receptor antagonist, or the chemokine IL-8. In addition, IFN-gamma induced by anti-CD3 was not suppressed by SAHA. Steady-state mRNA levels for LPS-induced TNF-alpha and IFN-gamma in peripheral blood mononuclear cells were markedly decreased, whereas IL-8 and IL-1-beta mRNA levels were unaffected. Because SAHA exhibits antiinflammatory properties in vivo and in vitro, inhibitors of histone deacetylase may stimulate the expression of genes that control the synthesis of cytokines and nitric oxide or hyperacetylate other targets.
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MESH Headings
- Animals
- Anti-Inflammatory Agents, Non-Steroidal/administration & dosage
- Anti-Inflammatory Agents, Non-Steroidal/pharmacology
- Antineoplastic Agents/administration & dosage
- Antineoplastic Agents/pharmacology
- CD3 Complex/metabolism
- Cell Division/drug effects
- Cells, Cultured
- Concanavalin A/pharmacology
- Cytokines/genetics
- Cytokines/metabolism
- Enzyme Inhibitors/administration & dosage
- Enzyme Inhibitors/pharmacology
- Hepatocytes/drug effects
- Histone Deacetylase Inhibitors
- Humans
- Hydroxamic Acids/administration & dosage
- Hydroxamic Acids/pharmacology
- Interferon-gamma/metabolism
- Interferon-gamma/pharmacology
- Interleukin-1/metabolism
- Interleukin-12/biosynthesis
- Leukocytes, Mononuclear/cytology
- Leukocytes, Mononuclear/drug effects
- Leukocytes, Mononuclear/metabolism
- Lipopolysaccharides/pharmacology
- Liver/drug effects
- Liver/injuries
- Macrophages, Peritoneal/drug effects
- Macrophages, Peritoneal/metabolism
- Mice
- Mice, Inbred BALB C
- Mitogens/pharmacology
- Nitric Oxide/biosynthesis
- RNA, Messenger/metabolism
- Tumor Cells, Cultured
- Tumor Necrosis Factor-alpha/metabolism
- Tumor Necrosis Factor-alpha/pharmacology
- Vorinostat
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Affiliation(s)
- Flavio Leoni
- Italfarmaco, SpA., 20092 Cinisello Balsamo, Italy.
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47
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Minghetti P, Casiraghi A, Cilurzo F, Montanari L, Monzani MV, Bertolini G, Zaliani A. Solvation enthalpies as descriptors of structure--in vitro percutaneous permeation relationship of benzoxazinones regioisomers. Farmaco 2000; 55:563-8. [PMID: 11132734 DOI: 10.1016/s0014-827x(00)00048-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The aim of this work was to correlate the in vitro human skin permeability, expressed as the permeability coefficient (Kp), and some physicochemical parameters of a new series of benzoxazinones. The in vitro human skin permeability of 14 substances, including regioisomers with CH3, OH, OCH3, and Cl groups in different positions on the aromatic ring, was determined. The modified Franz diffusion cell method was used. The Kp values were in the range 0.14-8.24 cm/h, showing a strong dependence on the position and type of substituent. Physicochemical descriptors usually referred in literature, such as log P, molecular weight and volume (MV), hydrogen bond donor (Hd) and acceptor activity (Ha), and molecular refractivity were considered, with the addition of solvation enthalpy (delta deltaHsolv). Delta deltaHsolv is defined as the difference between formation enthalpies in water and octanol. The algorithm with the best correlation between Kp and physicochemical descriptors was calculated, taking into account the differences observed among the regioisomers. The algorithm obtained with delta deltaHsolv had a good correlation (r2 = 0.749, F = 16.43, P = 0.0005), comparable with the equation, proposed by Potts and Guy, based on MV, Hd and Ha (r2 = 0.830, F = 16.3, P = 0.0004).
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Affiliation(s)
- P Minghetti
- Istituto di Chimica Farmaceutica e Tossicologica, Università degli Studi di Milano, Milan, Italy.
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48
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Abstract
The recently proposed MS-WHIM indices, a set of theoretical descriptors containing information about size, shape and electrostatic distribution of a molecule, have been further investigated. The main objectives of this work were: (i) to confirm the descriptive power of MS-WHIM in modelling specific biological interactions, (ii) to analyse the dependence of MS-WHIM on the type of atomic charges used for computing electrostatic potential and (iii) to compare the performances of MS-WHIM with those provided by other global 3D molecular descriptors. The spatial autocorrelation of atomic and molecular surface properties were selected for comparison purposes. WHIM-based and autocorrelation-based vectors were calculated for two molecular sets from the literature, namely a series of 18 HIV-1 reverse transcriptase inhibitors and a set of 36 sulphonamide endothelin inhibitors. PLS was adopted to derive statistical predictive models that were validated by means of cross-validation. The reported results confirmed that MS-WHIM indices are able to provide meaningful statistical correlations with biological activity. MS-WHIM descriptors are sensitive to the type of partial atomic charges applied and improved models were obtained using more accurate charges. Moreover for both the datasets, MS-WHIM results, in terms of fitting and predictive power of PLS models, were superior to those from autocorrelation. Finally, the strengths/weaknesses of global 3D-QSAR descriptors over local CoMFA-like methods, as well as the main differences between WHIM-based and autocorrelation-based vectors, are discussed.
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Affiliation(s)
- E Gancia
- Italfarmaco Research Centre, Milan, Italy.
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49
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Affiliation(s)
- A. Zaliani
- Computer Chemistry, Italfarmaco Research Center, via dei lavoratori 54, I-20092 Cinisello Balsamo, Milan, Italy
| | - E. Gancia
- Computer Chemistry, Italfarmaco Research Center, via dei lavoratori 54, I-20092 Cinisello Balsamo, Milan, Italy
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50
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Zaliani A, Pinori M, Ball HL, DiGregorio G, Cremonesi P, Mascagni P. The interaction of myristylated peptides with the catalytic domain of protein kinase C revealed by their sequence palindromy and the identification of a myristyl binding site. Protein Eng 1998; 11:803-10. [PMID: 9796830 DOI: 10.1093/protein/11.9.803] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Using a model of the enzyme structure and the results from a series of free and myristylated peptides, we provide evidence that peptides corresponding to the pseudosubstrate sequence of protein kinase C bind to the enzyme substrate binding site in an essentially extended conformation. This and the nearly symmetrical location of positive charges around the substrate phosphoritable site allow the peptide to bind to the enzyme in either an N-to-C orientation or its C-to-N opposite orientation. The latter is favoured by a change in residue chirality or when the peptide bears a myristoyl chain at its N-terminus. A myristyl binding site was also identified in the enzyme structure and its location in a region proximal to the C-terminal residue of pseudosubstrate bound in the N-to-C direction suggested that C-myristylation of peptide substrates should be more effective than N-myristoylation in antagonizing the enzyme. A peptide (H-RFARKGALRQKN-CONH-Myr) which contains the myristyl chain covalently linked to the C-terminal residue of the pseudosubstrate was thus made and shown to be a potent inhibitor of the histone kinase reaction of protein kinase C and the phosphorylation of p47 in intact cells.
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Affiliation(s)
- A Zaliani
- Italfarmaco Research Centre, Milan, Italy
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