301
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Gray JL, von Delft F, Brennan PE. Targeting the Small GTPase Superfamily through Their Regulatory Proteins. Angew Chem Int Ed Engl 2020; 59:6342-6366. [PMID: 30869179 PMCID: PMC7204875 DOI: 10.1002/anie.201900585] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/11/2019] [Indexed: 12/11/2022]
Abstract
The Ras superfamily of small GTPases are guanine-nucleotide-dependent switches essential for numerous cellular processes. Mutations or dysregulation of these proteins are associated with many diseases, but unsuccessful attempts to target the small GTPases directly have resulted in them being classed as "undruggable". The GTP-dependent signaling of these proteins is controlled by their regulators; guanine nucleotide exchange factors (GEFs), GTPase activating proteins (GAPs), and in the Rho and Rab subfamilies, guanine nucleotide dissociation inhibitors (GDIs). This review covers the recent small molecule and biologics strategies to target the small GTPases through their regulators. It seeks to critically re-evaluate recent chemical biology practice, such as the presence of PAINs motifs and the cell-based readout using compounds that are weakly potent or of unknown specificity. It highlights the vast scope of potential approaches for targeting the small GTPases in the future through their regulatory proteins.
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Affiliation(s)
- Janine L. Gray
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordOld Road CampusOxfordOX3 7FZUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0QXUK
| | - Frank von Delft
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0QXUK
- Department of BiochemistryUniversity of JohannesburgAuckland Park2006South Africa
| | - Paul E. Brennan
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordOld Road CampusOxfordOX3 7FZUK
- Alzheimer's Research (UK) Oxford Drug Discovery InstituteNuffield Department of MedicineUniversity of OxfordOxfordOX3 7FZUK
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302
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Jenkinson S, Schmidt F, Rosenbrier Ribeiro L, Delaunois A, Valentin JP. A practical guide to secondary pharmacology in drug discovery. J Pharmacol Toxicol Methods 2020; 105:106869. [PMID: 32302774 DOI: 10.1016/j.vascn.2020.106869] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/21/2020] [Accepted: 04/03/2020] [Indexed: 01/29/2023]
Abstract
Secondary pharmacological profiling is increasingly applied in pharmaceutical drug discovery to address unwanted pharmacological side effects of drug candidates before entering the clinic. Regulators, drug makers and patients share a demand for deep characterization of secondary pharmacology effects of novel drugs and their metabolites. The scope of such profiling has therefore expanded substantially in the past two decades, leading to the implementation of broad in silico profiling methods and focused in vitro off-target screening panels, to identify liabilities, but also opportunities, as early as possible. The pharmaceutical industry applies such panels at all stages of drug discovery routinely up to early development. Nevertheless, target composition, screening technologies, assay formats, interpretation and scheduling of panels can vary significantly between companies in the absence of dedicated guidelines. To contribute towards best practices in secondary pharmacology profiling, this review aims to summarize the state-of-the art in this field. Considerations are discussed with respect to panel design, screening strategy, implementation and interpretation of the data, including regulatory perspectives. The cascaded, or integrated, use of in silico and off-target profiling allows to exploit synergies for comprehensive safety assessment of drug candidates.
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Affiliation(s)
- Stephen Jenkinson
- Drug Safety Research and Development, Pfizer Inc., La Jolla, CA 92121, United States of America.
| | - Friedemann Schmidt
- Sanofi, R&D Preclinical Safety, Industriepark Höchst, 65926 Frankfurt/Main, Germany
| | - Lyn Rosenbrier Ribeiro
- Medicines Discovery Catapult, Block 35, Mereside, Alderley Park, Alderley Edge, SK10 4TG, United Kingdom
| | - Annie Delaunois
- UCB BioPharma SRL, Early Solutions, Development Science, Non-Clinical Safety, 1420 Braine L'Alleud, Walloon Region, Belgium
| | - Jean-Pierre Valentin
- UCB BioPharma SRL, Early Solutions, Development Science, Non-Clinical Safety, 1420 Braine L'Alleud, Walloon Region, Belgium
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303
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Alteen MG, Gros C, Meek RW, Cardoso DA, Busmann JA, Sangouard G, Deen MC, Tan H, Shen DL, Russell CC, Davies GJ, Robinson PJ, McCluskey A, Vocadlo DJ. A Direct Fluorescent Activity Assay for Glycosyltransferases Enables Convenient High‐Throughput Screening: Application to
O
‐GlcNAc Transferase. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000621] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Matthew G. Alteen
- Department of Chemistry Simon Fraser University Burnaby BC V5A 1S6 Canada
| | - Christina Gros
- Department of Chemistry Simon Fraser University Burnaby BC V5A 1S6 Canada
| | - Richard W. Meek
- York Structural Biology Laboratory Department of Chemistry University of York York YO10 5DD UK
| | - David A. Cardoso
- Children's Medical Research Institute The University of Sydney Sydney NSW 2145 Australia
| | - Jil A. Busmann
- Department of Molecular Biology and Biochemistry Simon Fraser University Burnaby BC V5A 1S6 Canada
| | - Gontran Sangouard
- Department of Chemistry Simon Fraser University Burnaby BC V5A 1S6 Canada
| | - Matthew C. Deen
- Department of Chemistry Simon Fraser University Burnaby BC V5A 1S6 Canada
| | - Hong‐Yee Tan
- Department of Chemistry Simon Fraser University Burnaby BC V5A 1S6 Canada
| | - David L. Shen
- Department of Molecular Biology and Biochemistry Simon Fraser University Burnaby BC V5A 1S6 Canada
| | - Cecilia C. Russell
- Chemistry, School of Environmental and Life Sciences The University of Newcastle University Drive Callaghan NSW 2308 Australia
| | - Gideon J. Davies
- York Structural Biology Laboratory Department of Chemistry University of York York YO10 5DD UK
| | - Phillip J. Robinson
- Children's Medical Research Institute The University of Sydney Sydney NSW 2145 Australia
| | - Adam McCluskey
- Chemistry, School of Environmental and Life Sciences The University of Newcastle University Drive Callaghan NSW 2308 Australia
| | - David J. Vocadlo
- Department of Chemistry Simon Fraser University Burnaby BC V5A 1S6 Canada
- Department of Molecular Biology and Biochemistry Simon Fraser University Burnaby BC V5A 1S6 Canada
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304
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Cascioferro S, Parrino B, Carbone D, Schillaci D, Giovannetti E, Cirrincione G, Diana P. Thiazoles, Their Benzofused Systems, and Thiazolidinone Derivatives: Versatile and Promising Tools to Combat Antibiotic Resistance. J Med Chem 2020; 63:7923-7956. [PMID: 32208685 PMCID: PMC7997583 DOI: 10.1021/acs.jmedchem.9b01245] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Thiazoles,
their benzofused systems, and thiazolidinone derivatives
are widely recognized as nuclei of great value for obtaining molecules
with various biological activities, including analgesic, anti-inflammatory,
anti-HIV, antidiabetic, antitumor, and antimicrobial. In particular,
in the past decade, many compounds bearing these heterocycles have
been studied for their promising antibacterial properties due to their
action on different microbial targets. Here we assess the recent development
of this class of compounds to address mechanisms underlying antibiotic
resistance at both bacterial-cell and community levels (biofilms).
We also explore the SAR and the prospective clinical application of
thiazole and its benzofused derivatives, which act as inhibitors of
mechanisms underlying antibiotic resistance in the treatment of severe
drug-resistant infections. In addition, we examined all bacterial
targets involved in their antimicrobial activity reporting, when described,
their spontaneous frequencies of resistance.
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Affiliation(s)
- Stella Cascioferro
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Barbara Parrino
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Daniela Carbone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Domenico Schillaci
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Elisa Giovannetti
- Department of Medical Oncology, VU University Medical Center, Cancer Center Amsterdam, DeBoelelaan 1117, 1081HV, Amsterdam, The Netherlands.,Cancer Pharmacology Lab, Fondazione Pisana per la Scienza, via Giovannini 13, 56017 San Giuliano Terme, Pisa, Italy
| | - Girolamo Cirrincione
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Patrizia Diana
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
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305
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Alteen MG, Gros C, Meek RW, Cardoso DA, Busmann JA, Sangouard G, Deen MC, Tan H, Shen DL, Russell CC, Davies GJ, Robinson PJ, McCluskey A, Vocadlo DJ. A Direct Fluorescent Activity Assay for Glycosyltransferases Enables Convenient High‐Throughput Screening: Application toO‐GlcNAc Transferase. Angew Chem Int Ed Engl 2020; 59:9601-9609. [DOI: 10.1002/anie.202000621] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/13/2020] [Indexed: 12/27/2022]
Affiliation(s)
- Matthew G. Alteen
- Department of ChemistrySimon Fraser University Burnaby BC V5A 1S6 Canada
| | - Christina Gros
- Department of ChemistrySimon Fraser University Burnaby BC V5A 1S6 Canada
| | - Richard W. Meek
- York Structural Biology LaboratoryDepartment of ChemistryUniversity of York York YO10 5DD UK
| | - David A. Cardoso
- Children's Medical Research InstituteThe University of Sydney Sydney NSW 2145 Australia
| | - Jil A. Busmann
- Department of Molecular Biology and BiochemistrySimon Fraser University Burnaby BC V5A 1S6 Canada
| | - Gontran Sangouard
- Department of ChemistrySimon Fraser University Burnaby BC V5A 1S6 Canada
| | - Matthew C. Deen
- Department of ChemistrySimon Fraser University Burnaby BC V5A 1S6 Canada
| | - Hong‐Yee Tan
- Department of ChemistrySimon Fraser University Burnaby BC V5A 1S6 Canada
| | - David L. Shen
- Department of Molecular Biology and BiochemistrySimon Fraser University Burnaby BC V5A 1S6 Canada
| | - Cecilia C. Russell
- Chemistry, School of Environmental and Life SciencesThe University of Newcastle University Drive Callaghan NSW 2308 Australia
| | - Gideon J. Davies
- York Structural Biology LaboratoryDepartment of ChemistryUniversity of York York YO10 5DD UK
| | - Phillip J. Robinson
- Children's Medical Research InstituteThe University of Sydney Sydney NSW 2145 Australia
| | - Adam McCluskey
- Chemistry, School of Environmental and Life SciencesThe University of Newcastle University Drive Callaghan NSW 2308 Australia
| | - David J. Vocadlo
- Department of ChemistrySimon Fraser University Burnaby BC V5A 1S6 Canada
- Department of Molecular Biology and BiochemistrySimon Fraser University Burnaby BC V5A 1S6 Canada
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306
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Divan A, Sibi MP, Tulin A. Structurally unique PARP-1 inhibitors for the treatment of prostate cancer. Pharmacol Res Perspect 2020; 8:e00586. [PMID: 32342655 PMCID: PMC7186898 DOI: 10.1002/prp2.586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 03/03/2020] [Accepted: 03/13/2020] [Indexed: 11/23/2022] Open
Abstract
The prognosis for metastatic castration-resistant prostate cancer is unfavorable, and although Poly(ADP)-ribose polymerase-1 (PARP-1) inhibitors have shown efficacy in the treatment of androgen-receptor dependent malignancies, the limited number of options present obstacles for patients that are not responsive to these treatments. Here we utilize an integrated screening strategy that combines cellular screening assays, informatics, in silico computational approaches, and dose-response testing for reducing a compound library of confirmed PARP-1 inhibitors. Six hundred and sixty-four validated PARP-1 inhibitors were reduced to 9 small molecules with favorable physicochemical/ADME properties, unique chemical fingerprints, high dissimilarity to existing drugs, few off-target effects, and dose-responsivity in the 1 µmol/L - 20 µmol/L range. The top 9 unique molecules identified by our integrated screening strategy will be selected for further preclinical development including cytotoxicity testing, effects on mitosis, structure-activity relationship, physicochemical/ADME studies, and in vivo testing.
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Affiliation(s)
- Ali Divan
- School of Medicine & Health SciencesUniversity of North DakotaGrand ForksNDUSA
| | | | - Alexei Tulin
- School of Medicine & Health SciencesUniversity of North DakotaGrand ForksNDUSA
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307
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Xu G, Yang Y, Yang Y, Song G, Li S, Zhang J, Yang W, Wang LL, Weng Z, Zuo Z. The discovery, design and synthesis of potent agonists of adenylyl cyclase type 2 by virtual screening combining biological evaluation. Eur J Med Chem 2020; 191:112115. [DOI: 10.1016/j.ejmech.2020.112115] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/30/2020] [Accepted: 02/02/2020] [Indexed: 01/02/2023]
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308
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Osella MI, Salazar MO, Gamarra MD, Moreno DM, Lambertucci F, Frances DE, Furlan RLE. Arylsulfonyl histamine derivatives as powerful and selective α-glucosidase inhibitors. RSC Med Chem 2020; 11:518-527. [PMID: 33479653 PMCID: PMC7489258 DOI: 10.1039/c9md00559e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/17/2020] [Indexed: 12/24/2022] Open
Abstract
A series of simple N-arylbenzenesulfonyl histamine derivatives were prepared and screened against α-glucosidase. Inhibition was in the micromolar range for several N α,N τ-di-arylsulfonyl compounds, with N α,N τ-di-4-trifluorobenzenesulfonyl histamine (IId) being the best inhibitor. Compound IId is a reversible and competitive α-glucosidase inhibitor, and presented good selectivity with respect to other target enzymes, including β-glucosidase and α-amylase, and interesting predicted physicochemical properties. Docking studies have been run to postulate ligand-enzyme interactions to account for the experimental results. In vivo, compound IId produced a similar hypoglycemic effect to acarbose with half of its dose.
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Affiliation(s)
- M I Osella
- Farmacognosia , Departamento de Química Orgánica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Suipacha 531 , Rosario S2002LRK , Argentina .
| | - M O Salazar
- Farmacognosia , Departamento de Química Orgánica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Suipacha 531 , Rosario S2002LRK , Argentina .
| | - M D Gamarra
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN, CONICET-UBA) , Departamento de Biológica , Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Ciudad Universitaria , Intendente Guiraldes 2160 , Ciudad Autónoma de Buenos Aires C1428EGA , Argentina
| | - D M Moreno
- Instituto de Química Rosario (IQUIR, CONICET-UNR) , Área Química General e Inorgánica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Suipacha 531 , Rosario S2002LRK , Argentina
| | - F Lambertucci
- Instituto de Fisiología Experimental (IFISE, CONICET-UNR) , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Suipacha 531 , Rosario S2002LRK , Argentina
| | - D E Frances
- Instituto de Fisiología Experimental (IFISE, CONICET-UNR) , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Suipacha 531 , Rosario S2002LRK , Argentina
| | - R L E Furlan
- Farmacognosia , Departamento de Química Orgánica , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Suipacha 531 , Rosario S2002LRK , Argentina .
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309
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Gorgulla C, Boeszoermenyi A, Wang ZF, Fischer PD, Coote PW, Padmanabha Das KM, Malets YS, Radchenko DS, Moroz YS, Scott DA, Fackeldey K, Hoffmann M, Iavniuk I, Wagner G, Arthanari H. An open-source drug discovery platform enables ultra-large virtual screens. Nature 2020; 580:663-668. [PMID: 32152607 PMCID: PMC8352709 DOI: 10.1038/s41586-020-2117-z] [Citation(s) in RCA: 295] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 02/27/2020] [Indexed: 12/21/2022]
Abstract
On average, an approved drug currently costs US$2-3 billion and takes more than 10 years to develop1. In part, this is due to expensive and time-consuming wet-laboratory experiments, poor initial hit compounds and the high attrition rates in the (pre-)clinical phases. Structure-based virtual screening has the potential to mitigate these problems. With structure-based virtual screening, the quality of the hits improves with the number of compounds screened2. However, despite the fact that large databases of compounds exist, the ability to carry out large-scale structure-based virtual screening on computer clusters in an accessible, efficient and flexible manner has remained difficult. Here we describe VirtualFlow, a highly automated and versatile open-source platform with perfect scaling behaviour that is able to prepare and efficiently screen ultra-large libraries of compounds. VirtualFlow is able to use a variety of the most powerful docking programs. Using VirtualFlow, we prepared one of the largest and freely available ready-to-dock ligand libraries, with more than 1.4 billion commercially available molecules. To demonstrate the power of VirtualFlow, we screened more than 1 billion compounds and identified a set of structurally diverse molecules that bind to KEAP1 with submicromolar affinity. One of the lead inhibitors (iKeap1) engages KEAP1 with nanomolar affinity (dissociation constant (Kd) = 114 nM) and disrupts the interaction between KEAP1 and the transcription factor NRF2. This illustrates the potential of VirtualFlow to access vast regions of the chemical space and identify molecules that bind with high affinity to target proteins.
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Affiliation(s)
- Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA.
- Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Andras Boeszoermenyi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zi-Fu Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Patrick D Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Paul W Coote
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Krishna M Padmanabha Das
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yehor S Malets
- Enamine, Kyiv, Ukraine
- National Taras Shevchenko University of Kyiv, Kyiv, Ukraine
| | - Dmytro S Radchenko
- Enamine, Kyiv, Ukraine
- National Taras Shevchenko University of Kyiv, Kyiv, Ukraine
| | - Yurii S Moroz
- National Taras Shevchenko University of Kyiv, Kyiv, Ukraine
- Chemspace, Kyiv, Ukraine
| | - David A Scott
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Konstantin Fackeldey
- Zuse Institute Berlin, Berlin, Germany
- Institute of Mathematics, Technical University Berlin, Berlin, Germany
| | - Moritz Hoffmann
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | | | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
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310
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Nunes FO, de Almeida JM, Ferreira AMT, da Cruz LA, Jacob CMB, Garcez WS, Garcez FR. Antitrypanosomal butanolides from Aiouea trinervis. EXCLI JOURNAL 2020; 19:323-333. [PMID: 32327956 PMCID: PMC7174576 DOI: 10.17179/excli2020-1088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 02/26/2020] [Indexed: 11/21/2022]
Abstract
In a search for new antitrypanosomal agents in the Brazilian flora, the ethanol extract of the xylopodium from Aiouea trinervis (Lauraceae) exhibited in vitro activity against the epimastigote forms of Trypanosoma cruzi, the etiological agent of Chagas disease. Bioassay-guided chromatographic fractionation of the ethanol extract afforded three butanolides, isoobtusilactone A (1), epilitsenolide C2 (2), and epilitsenolide C1 (3). Butanolides 1 and 3 were more active against T. cruzi epimastigotes than the reference drug benznidazole (by 8.9-fold and 3.2-fold, respectively), while 2 proved inactive. Compounds 1 and 3 showed low cytotoxicity in mammalian Vero cells (CC50> 156 μmol L-1) and high selectivity index (SI) values for epimastigotes (SI = 56.8 and 28.6, respectively), and 1 was more selective than benznidazole (SI = 46.5). Butanolide 1 at 24 μmol L-1 also led to cell cycle alterations in epimastigote forms, and inhibited the growth of amastigote cells in more than 70 %. In silico ADMET properties of 1 were also analyzed and predicted favorable drug-like characteristics. This butanolide also complied with Lipinski's rule of five and was not predicted as interference compound (PAINS). This is the first report on the isolation of these bioactive butanolides under the guidance of in vitro trypanocidal activity against T. cruzi.
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Affiliation(s)
- Felipe Oliveira Nunes
- Instituto de Química, Universidade Federal de Mato Grosso do Sul, Av. Senador Filinto Muller 1555, 79074-460 Campo Grande-MS, Brazil
| | - Júlio Menta de Almeida
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Av. Costa e Silva s/n, 79070-900 Campo Grande-MS, Brazil
| | - Alda Maria Teixeira Ferreira
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Av. Costa e Silva s/n, 79070-900 Campo Grande-MS, Brazil
| | - Letícia Alves da Cruz
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Av. Costa e Silva s/n, 79070-900 Campo Grande-MS, Brazil
| | - Camila Mareti Bonin Jacob
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Av. Costa e Silva s/n, 79070-900 Campo Grande-MS, Brazil
| | - Walmir Silva Garcez
- Instituto de Química, Universidade Federal de Mato Grosso do Sul, Av. Senador Filinto Muller 1555, 79074-460 Campo Grande-MS, Brazil
| | - Fernanda Rodrigues Garcez
- Instituto de Química, Universidade Federal de Mato Grosso do Sul, Av. Senador Filinto Muller 1555, 79074-460 Campo Grande-MS, Brazil
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311
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Méndez D, Urra FA, Millas-Vargas JP, Alarcón M, Rodríguez-Lavado J, Palomo I, Trostchansky A, Araya-Maturana R, Fuentes E. Synthesis of antiplatelet ortho-carbonyl hydroquinones with differential action on platelet aggregation stimulated by collagen or TRAP-6. Eur J Med Chem 2020; 192:112187. [PMID: 32155530 DOI: 10.1016/j.ejmech.2020.112187] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 02/07/2023]
Abstract
Cardiovascular diseases are the leading cause of death in the world. Platelets have a major role in cardiovascular events as they bind to the damaged endothelium activating and forming thrombi. Although some hydroquinone scaffold-containing compounds have known antiplatelet activities, currently there is a lack of evidence on the antiplatelet activity of hydroquinones carrying electron attractor groups. In this work, we evaluate the antiplatelet effect of a series of ortho-carbonyl hydroquinone derivatives on cytotoxicity and function of human platelets, using collagen and thrombin receptor activator peptide 6 (TRAP-6) as agonists. Our structure-activity relationship study shows that gem-diethyl/methyl substitutions and the addition/modifications of the third ring of ortho-carbonyl hydroquinone scaffold influence on the selective index (IC50 TRAP-6/IC50 Collagen) and the inhibitory capacity of platelet aggregation. Compounds 3 and 8 inhibit agonist-induced platelet aggregation in a non-competitive manner with IC50 values of 1.77 ± 2.09 μM (collagen) and 11.88 ± 4.59 μM (TRAP-6), respectively and show no cytotoxicity. Both compounds do not affect intracellular calcium levels and mitochondrial bioenergetics. Consistently, they reduce the expression of P-selectin, activation of glycoprotein IIb/IIIa, and release of adenosine triphosphate and CD63 from platelet. Our findings may be used for further development of new drugs in platelet-related thrombosis diseases.
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Affiliation(s)
- Diego Méndez
- Thrombosis Research Center, Medical Technology School, Department of Clinical Biochemistry and Immunohaematology, Faculty of Health Sciences, Universidad de Talca, Talca, Chile
| | - Félix A Urra
- Molecular and Clinical Pharmacology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile; Network for Snake Venom Research and Drug Discovery, Santiago, Chile.
| | - Juan Pablo Millas-Vargas
- Instituto de Química de Recursos Naturales, Programa de Investigación Asociativa en Cáncer Gástrico (PIA-CG), Universidad de Talca, Talca, Chile
| | - Marcelo Alarcón
- Thrombosis Research Center, Medical Technology School, Department of Clinical Biochemistry and Immunohaematology, Faculty of Health Sciences, Universidad de Talca, Talca, Chile
| | - Julio Rodríguez-Lavado
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Iván Palomo
- Thrombosis Research Center, Medical Technology School, Department of Clinical Biochemistry and Immunohaematology, Faculty of Health Sciences, Universidad de Talca, Talca, Chile
| | - Andrés Trostchansky
- Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Ramiro Araya-Maturana
- Thrombosis Research Center, Medical Technology School, Department of Clinical Biochemistry and Immunohaematology, Faculty of Health Sciences, Universidad de Talca, Talca, Chile; Instituto de Química de Recursos Naturales, Programa de Investigación Asociativa en Cáncer Gástrico (PIA-CG), Universidad de Talca, Talca, Chile; Network for Snake Venom Research and Drug Discovery, Santiago, Chile.
| | - Eduardo Fuentes
- Thrombosis Research Center, Medical Technology School, Department of Clinical Biochemistry and Immunohaematology, Faculty of Health Sciences, Universidad de Talca, Talca, Chile.
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312
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Schein CH. Repurposing approved drugs on the pathway to novel therapies. Med Res Rev 2020; 40:586-605. [PMID: 31432544 PMCID: PMC7018532 DOI: 10.1002/med.21627] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/17/2019] [Accepted: 07/26/2019] [Indexed: 12/22/2022]
Abstract
The time and cost of developing new drugs have led many groups to limit their search for therapeutics to compounds that have previously been approved for human use. Many "repurposed" drugs, such as derivatives of thalidomide, antibiotics, and antivirals have had clinical success in treatment areas well beyond their original approved use. These include applications in treating antibiotic-resistant organisms, viruses, cancers and to prevent burn scarring. The major theoretical justification for reusing approved drugs is that they have known modes of action and controllable side effects. Coadministering antibiotics with inhibitors of bacterial toxins or enzymes that mediate multidrug resistance can greatly enhance their activity. Drugs that control host cell pathways, including inflammation, tumor necrosis factor, interferons, and autophagy, can reduce the "cytokine storm" response to injury, control infection, and aid in cancer therapy. An active compound, even if previously approved for human use, will be a poor clinical candidate if it lacks specificity for the new target, has poor solubility or can cause serious side effects. Synergistic combinations can reduce the dosages of the individual components to lower reactivity. Preclinical analysis should take into account that severely ill patients with comorbidities will be more sensitive to side effects than healthy trial subjects. Once an active, approved drug has been identified, collaboration with medicinal chemists can aid in finding derivatives with better physicochemical properties, specificity, and efficacy, to provide novel therapies for cancers, emerging and rare diseases.
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Affiliation(s)
- Catherine H Schein
- Department of Biochemistry and Molecular Biology, Institute for Human Infection and Immunity (IHII), University of Texas Medical Branch at Galveston, Galveston, Texas
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313
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Xenobiotics, Trace Metals and Genetics in the Pathogenesis of Tauopathies. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17041269. [PMID: 32079163 PMCID: PMC7068520 DOI: 10.3390/ijerph17041269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 11/17/2022]
Abstract
Tauopathies are a disease group characterized by either pathological accumulation or release of fragments of hyperphosphorylated tau proteins originating from the central nervous system. The tau hypotheses of Parkinson’s and Alzheimer’s diseases contain a clinically diverse spectrum of tauopathies. Studies of case records of various tauopathies may reveal clinical phenotype characteristics of the disease. In addition, improved understanding of different tauopathies would disclose environmental factors, such as xenobiotics and trace metals, that can precipitate or modify the progression of the disorder. Important for diagnostics and monitoring of these disorders is a further development of adequate biomarkers, including refined neuroimaging, or proteomics. Our goal is to provide an in-depth review of the current literature regarding the pathophysiological roles of tau proteins and the pathogenic factors leading to various tauopathies, with the perspective of future advances in potential therapeutic strategies.
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314
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Abstract
Here, we describe our action plan for hit identification (APHID) that guides the process of hit triage, with elimination of less tractable hits and retention of more tractable hits. We exemplify the process with reference to our high-throughput screening (HTS) campaign against the enzyme, KAT6A, that resulted in successful identification of a tractable hit. We hope that APHID could serve as a useful, concise and digestible guide for those involved in HTS and hit triage, especially those that are relatively new to this exciting and continually evolving technology.
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315
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Peterková L, Kmoníčková E, Ruml T, Rimpelová S. Sarco/Endoplasmic Reticulum Calcium ATPase Inhibitors: Beyond Anticancer Perspective. J Med Chem 2020; 63:1937-1963. [PMID: 32030976 DOI: 10.1021/acs.jmedchem.9b01509] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The sarco/endoplasmic reticulum calcium ATPase (SERCA), which plays a key role in the maintenance of Ca2+ ion homeostasis, is an extensively studied enzyme, the inhibition of which has a considerable impact on cell life and death decision. To date, several SERCA inhibitors have been thoroughly studied and the most notable one, a derivative of the sesquiterpene lactone thapsigargin, is gradually approaching a clinical application. Meanwhile, new compounds with SERCA-inhibiting properties of natural, synthetic, or semisynthetic origin are being discovered and/or developed; some of these might also be suitable for the development of new drugs with improved performance. This review brings an up-to-date comprehensive overview of recently discovered compounds with the potential of SERCA inhibition, discusses their mechanism of action, and highlights their potential clinical applications, such as cancer treatment.
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Affiliation(s)
- Lucie Peterková
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, 166 28, Prague 6, Czech Republic
| | - Eva Kmoníčková
- Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00 Pilsen, Czech Republic
| | - Tomáš Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, 166 28, Prague 6, Czech Republic
| | - Silvie Rimpelová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, 166 28, Prague 6, Czech Republic.,Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00 Pilsen, Czech Republic
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316
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Abstract
The cyclic-AMP response element binding protein (CREB) is an important nuclear transcription factor and has been shown to be overexpressed and/or over-activated in many different cancer types, suggesting that targeting CREB is a novel approach for developing cancer therapies. Our lab discovered the first cell-permeable small molecule inhibitor of CREB, from which we further developed a potent CREB inhibitor with in vivo anti-cancer activity. In this article, we detailed our biochemical and cell-based bioassays to assess different small molecule CREB inhibitors.
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Affiliation(s)
- Bingbing X Li
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, United States.
| | - Xiangshu Xiao
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, United States.
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317
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Bruder M, Polo G, Trivella DBB. Natural allosteric modulators and their biological targets: molecular signatures and mechanisms. Nat Prod Rep 2020; 37:488-514. [PMID: 32048675 DOI: 10.1039/c9np00064j] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: 2008 to 2018Over the last decade more than two hundred single natural products were confirmed as natural allosteric modulators (alloNPs) of proteins. The compounds are presented and discussed with the support of a chemical space, constructed using a principal component analysis (PCA) of molecular descriptors from chemical compounds of distinct databases. This analysis showed that alloNPs are dispersed throughout the majority of the chemical space defined by natural products in general. Moreover, a cluster of alloNPs was shown to occupy a region almost devoid of allosteric modulators retrieved from a dataset composed mainly of synthetic compounds, further highlighting the importance to explore the entire natural chemical space for probing allosteric mechanisms. The protein targets which alloNPs bind to comprised 81 different proteins, which were classified into 5 major groups, with enzymes, in particular hydrolases, being the main representative group. The review also brings a critical interpretation on the mechanisms by which alloNPs display their molecular action on proteins. In the latter analysis, alloNPs were classified according to their final effect on the target protein, resulting in 3 major categories: (i) local alteration of the orthosteric site; (ii) global alteration in protein dynamics that change function; and (iii) oligomer stabilisation or protein complex destabilisation via protein-protein interaction in sites distant from the orthosteric site. G-protein coupled receptors (GPCRs), which use a combination of the three types of allosteric regulation found, were also probed by natural products. In summary, the natural allosteric modulators reviewed herein emphasise their importance for exploring alternative chemotherapeutic strategies, potentially pushing the boundaries of the druggable space of pharmacologically relevant drug targets.
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Affiliation(s)
- Marjorie Bruder
- Brazilian Biosciences National Laboratory (LNBio), National Centre for Research in Energy and Materials (CNPEM), 13083-970 Campinas, SP, Brazil.
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318
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Gao K, Oerlemans R, Groves MR. Theory and applications of differential scanning fluorimetry in early-stage drug discovery. Biophys Rev 2020; 12:85-104. [PMID: 32006251 PMCID: PMC7040159 DOI: 10.1007/s12551-020-00619-2] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
Differential scanning fluorimetry (DSF) is an accessible, rapid, and economical biophysical technique that has seen many applications over the years, ranging from protein folding state detection to the identification of ligands that bind to the target protein. In this review, we discuss the theory, applications, and limitations of DSF, including the latest applications of DSF by ourselves and other researchers. We show that DSF is a powerful high-throughput tool in early drug discovery efforts. We place DSF in the context of other biophysical methods frequently used in drug discovery and highlight their benefits and downsides. We illustrate the uses of DSF in protein buffer optimization for stability, refolding, and crystallization purposes and provide several examples of each. We also show the use of DSF in a more downstream application, where it is used as an in vivo validation tool of ligand-target interaction in cell assays. Although DSF is a potent tool in buffer optimization and large chemical library screens when it comes to ligand-binding validation and optimization, orthogonal techniques are recommended as DSF is prone to false positives and negatives.
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Affiliation(s)
- Kai Gao
- Structure Biology in Drug Design, Drug Design Group XB20, Departments of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Rick Oerlemans
- Structure Biology in Drug Design, Drug Design Group XB20, Departments of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Matthew R Groves
- Structure Biology in Drug Design, Drug Design Group XB20, Departments of Pharmacy, University of Groningen, Groningen, The Netherlands.
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319
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Silvestri I, Lyu H, Fata F, Banta PR, Mattei B, Ippoliti R, Bellelli A, Pitari G, Ardini M, Petukhova V, Thatcher GRJ, Petukhov PA, Williams DL, Angelucci F. Ectopic suicide inhibition of thioredoxin glutathione reductase. Free Radic Biol Med 2020; 147:200-211. [PMID: 31870799 PMCID: PMC7583042 DOI: 10.1016/j.freeradbiomed.2019.12.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/13/2019] [Accepted: 12/17/2019] [Indexed: 02/07/2023]
Abstract
Selective suicide inhibitors represent a seductively attractive approach for inactivation of therapeutically relevant enzymes since they are generally devoid of off-target toxicity in vivo. While most suicide inhibitors are converted to reactive species at enzyme active sites, theoretically bioactivation can also occur in ectopic (secondary) sites that have no known function. Here, we report an example of such an "ectopic suicide inhibition", an unprecedented bioactivation mechanism of a suicide inhibitor carried out by a non-catalytic site of thioredoxin glutathione reductase (TGR). TGR is a promising drug target to treat schistosomiasis, a devastating human parasitic disease. Utilizing hits selected from a high throughput screening campaign, time-resolved X-ray crystallography, molecular dynamics, mass spectrometry, molecular modeling, protein mutagenesis and functional studies, we find that 2-naphtholmethylamino derivatives bound to this novel ectopic site of Schistosoma mansoni (Sm)TGR are transformed to covalent modifiers and react with its mobile selenocysteine-containing C-terminal arm. In particular, one 2-naphtholmethylamino compound is able to specifically induce the pro-oxidant activity in the inhibited enzyme. Since some 2-naphtholmethylamino analogues show worm killing activity and the ectopic site is not conserved in human orthologues, a general approach to development of novel and selective anti-parasitic therapeutics against schistosoma is proposed.
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Affiliation(s)
- Ilaria Silvestri
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, Italy
| | - Haining Lyu
- Dept. of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Francesca Fata
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, Italy
| | - Paul R Banta
- Dept. of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Benedetta Mattei
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, Italy
| | - Rodolfo Ippoliti
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, Italy
| | - Andrea Bellelli
- Dept. of Biochemical Sciences, Sapienza University of Rome, Italy
| | - Giuseppina Pitari
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, Italy
| | - Matteo Ardini
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, Italy
| | - Valentina Petukhova
- Dept. of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Gregory R J Thatcher
- Dept. of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Pavel A Petukhov
- Dept. of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA.
| | - David L Williams
- Dept. of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA.
| | - Francesco Angelucci
- Dept. of Life, Health and Environmental Sciences, University of L'Aquila, Italy.
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320
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Gray JL, Delft F, Brennan PE. Targeting der kleinen GTPasen über ihre regulatorischen Proteine. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201900585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Janine L. Gray
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Old Road Campus Oxford OX3 7FZ Großbritannien
- Diamond Light Source Harwell Science and Innovation Campus Didcot OX11 0QX Großbritannien
| | - Frank Delft
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Diamond Light Source Harwell Science and Innovation Campus Didcot OX11 0QX Großbritannien
- Department of BiochemistryUniversity of Johannesburg Auckland Park 2006 Südafrika
| | - Paul E. Brennan
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Old Road Campus Oxford OX3 7FZ Großbritannien
- Alzheimer's Research (UK) Oxford Drug Discovery InstituteNuffield Department of MedicineUniversity of Oxford Oxford OX3 7FZ Großbritannien
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321
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Yang ZY, He JH, Lu AP, Hou TJ, Cao DS. Application of Negative Design To Design a More Desirable Virtual Screening Library. J Med Chem 2020; 63:4411-4429. [DOI: 10.1021/acs.jmedchem.9b01476] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Zi-Yi Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Jun-Hong He
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Ai-Ping Lu
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, SAR, P. R. China
| | - Ting-Jun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Dong-Sheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, SAR, P. R. China
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322
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Abdeldayem A, Raouf YS, Constantinescu SN, Moriggl R, Gunning PT. Advances in covalent kinase inhibitors. Chem Soc Rev 2020; 49:2617-2687. [DOI: 10.1039/c9cs00720b] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This comprehensive review details recent advances, challenges and innovations in covalent kinase inhibition within a 10 year period (2007–2018).
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Affiliation(s)
- Ayah Abdeldayem
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
| | - Yasir S. Raouf
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
| | | | - Richard Moriggl
- Institute of Animal Breeding and Genetics
- University of Veterinary Medicine
- 1210 Vienna
- Austria
| | - Patrick T. Gunning
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
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323
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Zhu H, Lee OW, Shah P, Jadhav A, Xu X, Patnaik S, Shen M, Hall MD. Identification of Activators of Human Fumarate Hydratase by Quantitative High-Throughput Screening. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:43-56. [PMID: 31522598 PMCID: PMC7340117 DOI: 10.1177/2472555219873559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Fumarate hydratase (FH) is a metabolic enzyme that is part of the Krebs cycle and reversibly catalyzes the hydration of fumarate to malate. Mutations of the FH gene have been associated with fumarate hydratase deficiency (FHD), hereditary leiomyomatosis and renal cell cancer (HLRCC), and other diseases. Currently, there are no high-quality small-molecule probes for studying human FH. To address this, we developed a quantitative high-throughput screening (qHTS) FH assay and screened a total of 57,037 compounds from in-house libraries in dose-response. While no inhibitors of FH were confirmed, a series of phenyl-pyrrolo-pyrimidine-diones were identified as activators of human FH. These compounds were not substrates of FH, were inactive in a malate dehydrogenase counterscreen, and showed no detectable reduction-oxidation activity. The binding of two compounds from the series to human FH was confirmed by microscale thermophoresis. The low hit rate in this screening campaign confirmed that FH is a "tough target" to modulate, and the small-molecule activators of human FH reported here may serve as a starting point for further optimization and development into cellular probes of human FH and potential drug candidates.
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Affiliation(s)
- Hu Zhu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Olivia W Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Pranav Shah
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Xin Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Samarjit Patnaik
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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324
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Perkins KR, Atilho RM, Moon MH, Breaker RR. Employing a ZTP Riboswitch to Detect Bacterial Folate Biosynthesis Inhibitors in a Small Molecule High-Throughput Screen. ACS Chem Biol 2019; 14:2841-2850. [PMID: 31609568 DOI: 10.1021/acschembio.9b00713] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Various riboswitch classes are being discovered that precisely monitor the status of important biological processes, including metabolic pathway function, signaling for physiological adaptations, and responses to toxic agents. Biochemical components for some of these processes might make excellent targets for the development of novel antibacterial molecules, which can be broadly sought by using phenotypic drug discovery (PDD) methods. However, PDD data do not normally provide clues regarding the target for each hit compound. We have developed and validated a robust fluorescent reporter system based on a ZTP riboswitch that identifies numerous folate biosynthesis inhibitors with high sensitivity and precision. The utility of the riboswitch-based PDD strategy was evaluated using Escherichia coli bacteria by conducting a 128 310-compound high-throughput screen, which identified 78 sulfanilamide derivatives among the many initial hits. Similarly, representatives of other riboswitch classes could be employed to rapidly match antibacterial hits with the biological processes they target.
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Affiliation(s)
- Kevin R. Perkins
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, United States
| | - Ruben M. Atilho
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, United States
| | - Michelle H. Moon
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8103, United States
| | - Ronald R. Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, United States
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, United States
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, United States
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325
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Pobbati AV, Mejuch T, Chakraborty S, Karatas H, Bharath SR, Guéret SM, Goy PA, Hahne G, Pahl A, Sievers S, Guccione E, Song H, Waldmann H, Hong W. Identification of Quinolinols as Activators of TEAD-Dependent Transcription. ACS Chem Biol 2019; 14:2909-2921. [PMID: 31742995 DOI: 10.1021/acschembio.9b00786] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The transcriptional co-regulators YAP (Yes-associated protein) and TAZ (transcriptional coactivator with PDZ-binding motif) are the vertebrate downstream effectors of the Hippo signaling pathway that controls various physiological and pathological processes. YAP and TAZ pair with the TEAD (TEA domain) family of transcription factors to initiate transcription. We previously identified a tractable pocket in TEADs, which has been physiologically shown to bind palmitate. Herein, a TEAD-palmitate interaction screen was developed to select small molecules occupying the palmitate-binding pocket (PBP) of TEADs. We show that quinolinols were TEAD-binding compounds that augment YAP/TAZ-TEAD activity, which was verified using TEAD reporter assay, RT-qPCR, and RNA-Seq analyses. Structure-activity relationship investigations uncovered the quinolinol substituents that are necessary for TEAD activation. We reveal a novel mechanism where quinolinols stabilize YAP/TAZ protein levels by occupying the PBP. The enhancement of YAP activity by quinolinols accelerates the in vivo wound closure in a mouse wound-healing model. Although small molecules that occupy the PBP have been shown to inhibit YAP/TAZ-TEAD activity, leveraging PBP to activate TEADs is a novel approach.
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Affiliation(s)
- Ajaybabu V. Pobbati
- Department of Multi-Modal Molecular (M3) Biology, Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673 Singapore
| | - Tom Mejuch
- Department of Chemical Biology, Max Planck Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Sayan Chakraborty
- Department of Multi-Modal Molecular (M3) Biology, Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673 Singapore
| | - Hacer Karatas
- Department of Chemical Biology, Max Planck Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Sakshibeedu R. Bharath
- Department of Multi-Modal Molecular (M3) Biology, Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673 Singapore
| | - Stéphanie M. Guéret
- AstraZeneca−Max Planck Institute Satellite Unit, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Pierre-Alexis Goy
- Department of Multi-Modal Molecular (M3) Biology, Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673 Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 119077 Singapore
| | - Gernot Hahne
- Department of Chemical Biology, Max Planck Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Axel Pahl
- Department of Chemical Biology, Max Planck Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Sonja Sievers
- Department of Chemical Biology, Max Planck Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Ernesto Guccione
- Department of Multi-Modal Molecular (M3) Biology, Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673 Singapore
| | - Haiwei Song
- Department of Multi-Modal Molecular (M3) Biology, Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673 Singapore
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
- Technische Universität Dortmund, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Wanjin Hong
- Department of Multi-Modal Molecular (M3) Biology, Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673 Singapore
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326
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Shen L, Pelletier J. Selective targeting of the DEAD-box RNA helicase eukaryotic initiation factor (eIF) 4A by natural products. Nat Prod Rep 2019; 37:609-616. [PMID: 31782447 DOI: 10.1039/c9np00052f] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: up to 2019Pharmacological targeting of eukaryotic mRNA translation initiation is a promising approach for cancer therapy, since several signaling pathways that are commonly deregulated during tumor progression converge on this process. The DEAD-box helicase, eukaryotic initiation factor (eIF) 4A, is essential for translation initiation and facilitates the loading of the 43S pre-initiation complex onto mRNAs. Hippuristanol, rocaglates, and pateamine A are natural products that each target eIF4A by interfering with the helicase's RNA-binding activity in distinct manners. They exert a selective change in gene expression that results in potent anti-tumorigenic activity in pre-clinical studies. This review will provide an update on the molecular mechanisms of action of these natural products.
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Affiliation(s)
- Leo Shen
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada.
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327
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Kodadek T, Paciaroni NG, Balzarini M, Dickson P. Beyond protein binding: recent advances in screening DNA-encoded libraries. Chem Commun (Camb) 2019; 55:13330-13341. [PMID: 31633708 PMCID: PMC6939232 DOI: 10.1039/c9cc06256d] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNA-encoded library (DEL) screening has emerged as an important method for early stage drug and probe molecule discovery. The vast majority of screens using DELs have been relatively simple binding assays. The library is incubated with a target molecule, which is almost always a protein, and the DNAs that remain associated with the target after thorough washing are amplified and deep sequenced to reveal the chemical structures of the ligands they encode. Recently however, a number of different screening formats have been introduced that demand more than simple binding. These include a format that demands hits exhibit high selectivity for target vs. off-targets, a protocol to screen for enzyme inhibitors and another to identify organocatalysts in a DEL. These and other novel assay formats are reviewed in this article. We also consider some of the most significant remaining challenges in DEL assay development.
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Affiliation(s)
- Thomas Kodadek
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Nicholas G Paciaroni
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Madeline Balzarini
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Paige Dickson
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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328
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Abrusán G, Marsh JA. Ligands and Receptors with Broad Binding Capabilities Have Common Structural Characteristics: An Antibiotic Design Perspective. J Med Chem 2019; 62:9357-9374. [PMID: 31188598 PMCID: PMC6858282 DOI: 10.1021/acs.jmedchem.9b00220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Indexed: 01/08/2023]
Abstract
The spread of antibiotic resistance is one of the most serious global public-health problems. Here we show that a particular class of homomers with binding sites spanning multiple protein chains is particularly suitable for targeting by broad-spectrum antibacterial agents because due to the slow evolutionary change of such binding pockets, ligands of such homomers are much more likely to bind their homologs than ligands of monomers, or homomers with a single-chain binding site. Additionally, using de novo ligand design and deep learning, we show that the chemical compounds that can bind several different receptors have common structural characteristics and that halogens and fragments similar to the building blocks existing antimicrobials are overrepresented in them. Finally, we show that binding multiple receptors selects for flexible compounds, which are less likely to accumulate in Gram-negative bacteria; thus there is trade-off between reducing the emergence of resistance by multitargeting and broad-spectrum antibacterial activity.
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Affiliation(s)
- György Abrusán
- MRC Human Genetics Unit, Institute
of Genetics and Molecular Medicine, University
of Edinburgh, Crewe Road, Edinburgh EH4 2XU, U.K.
| | - Joseph A. Marsh
- MRC Human Genetics Unit, Institute
of Genetics and Molecular Medicine, University
of Edinburgh, Crewe Road, Edinburgh EH4 2XU, U.K.
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329
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Engelhardt H, Böse D, Petronczki M, Scharn D, Bader G, Baum A, Bergner A, Chong E, Döbel S, Egger G, Engelhardt C, Ettmayer P, Fuchs JE, Gerstberger T, Gonnella N, Grimm A, Grondal E, Haddad N, Hopfgartner B, Kousek R, Krawiec M, Kriz M, Lamarre L, Leung J, Mayer M, Patel ND, Simov BP, Reeves JT, Schnitzer R, Schrenk A, Sharps B, Solca F, Stadtmüller H, Tan Z, Wunberg T, Zoephel A, McConnell DB. Start Selective and Rigidify: The Discovery Path toward a Next Generation of EGFR Tyrosine Kinase Inhibitors. J Med Chem 2019; 62:10272-10293. [PMID: 31689114 DOI: 10.1021/acs.jmedchem.9b01169] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The epidermal growth factor receptor (EGFR), when carrying an activating mutation like del19 or L858R, acts as an oncogenic driver in a subset of lung tumors. While tumor responses to tyrosine kinase inhibitors (TKIs) are accompanied by marked tumor shrinkage, the response is usually not durable. Most patients relapse within two years of therapy often due to acquisition of an additional mutation in EGFR kinase domain that confers resistance to TKIs. Crucially, oncogenic EGFR harboring both resistance mutations, T790M and C797S, can no longer be inhibited by currently approved EGFR TKIs. Here, we describe the discovery of BI-4020, which is a noncovalent, wild-type EGFR sparing, macrocyclic TKI. BI-4020 potently inhibits the above-described EGFR variants and induces tumor regressions in a cross-resistant EGFRdel19 T790M C797S xenograft model. Key was the identification of a highly selective but moderately potent benzimidazole followed by complete rigidification of the molecule through macrocyclization.
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Affiliation(s)
- Harald Engelhardt
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Dietrich Böse
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Mark Petronczki
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Dirk Scharn
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Anke Baum
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Andreas Bergner
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Eugene Chong
- Boehringer Ingelheim Pharmaceuticals, Inc. , 900 Ridgebury Road , Ridgefield , Connecticut 06877 , United States
| | - Sandra Döbel
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Georg Egger
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Christian Engelhardt
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Peter Ettmayer
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Julian E Fuchs
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Thomas Gerstberger
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Nina Gonnella
- Boehringer Ingelheim Pharmaceuticals, Inc. , 900 Ridgebury Road , Ridgefield , Connecticut 06877 , United States
| | - Andreas Grimm
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Elisabeth Grondal
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Nizar Haddad
- Boehringer Ingelheim Pharmaceuticals, Inc. , 900 Ridgebury Road , Ridgefield , Connecticut 06877 , United States
| | - Barbara Hopfgartner
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Roland Kousek
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Mariusz Krawiec
- Boehringer Ingelheim Pharmaceuticals, Inc. , 900 Ridgebury Road , Ridgefield , Connecticut 06877 , United States
| | - Monika Kriz
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Lyne Lamarre
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Joyce Leung
- Boehringer Ingelheim Pharmaceuticals, Inc. , 900 Ridgebury Road , Ridgefield , Connecticut 06877 , United States
| | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Nitinchandra D Patel
- Boehringer Ingelheim Pharmaceuticals, Inc. , 900 Ridgebury Road , Ridgefield , Connecticut 06877 , United States
| | - Biljana Peric Simov
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Jonathan T Reeves
- Boehringer Ingelheim Pharmaceuticals, Inc. , 900 Ridgebury Road , Ridgefield , Connecticut 06877 , United States
| | - Renate Schnitzer
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Andreas Schrenk
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Bernadette Sharps
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Flavio Solca
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Heinz Stadtmüller
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Zhulin Tan
- Boehringer Ingelheim Pharmaceuticals, Inc. , 900 Ridgebury Road , Ridgefield , Connecticut 06877 , United States
| | - Tobias Wunberg
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Andreas Zoephel
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
| | - Darryl B McConnell
- Boehringer Ingelheim RCV GmbH & Co KG , Dr-Boehringer-Gasse 5-11 , Vienna 1120 , Austria
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330
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Immune Checkpoint PD-1/PD-L1 CTLA-4/CD80 are Blocked by Rhus verniciflua Stokes and its Active Compounds. Molecules 2019; 24:molecules24224062. [PMID: 31717574 PMCID: PMC6891444 DOI: 10.3390/molecules24224062] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 01/24/2023] Open
Abstract
The bark of Rhus verniciflua Stokes (RVS) has been used to treat cancer in Korean herbal medicine. When we screened for PD-1 and CTLA-4 immune checkpoint inhibitors (PD-1/PD-L1 CTLA-4/CD80) from around 800 herbal extracts using competitive Enzyme-Linked Immunosorbent Assay (ELISA), we found that RVS blocked both the PD-1/PD-L1 and the CTLA-4/CD80 interactions. To identify the active compounds from RVS, we performed bioactivity-guided fractionation, and the ethyl acetate (EtOAc) fraction of RVS proved to be the most effective at blocking the PD-1/PD-L1 and CTLA-4/CD80 interactions. In addition, we isolated and identified 20 major compounds in the EtOAc fraction of RVS and then examined the blocking effects of these 20 compounds on PD-1/PD-L1 and CTLA-4/CD80. Among them, four compounds [eriodictyol (7) > fisetin (9) > quercetin (18) > liquiritigenin (13)] blocked the interaction of PD-1/PD-L1 on competitive ELISA. In addition, four different compounds [protocatechuic acid (2) > caffeic acid (19) > taxifolin (5) > butin (6)] blocked the interaction of CTLA-4/CD80. Our findings suggest that RVS and its components could be used as a potential immune checkpoint inhibitor blockade and could be developed for immuno-oncological therapeutics.
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331
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Musyoka T, Bishop ÖT. South African Abietane Diterpenoids and Their Analogs as Potential Antimalarials: Novel Insights from Hybrid Computational Approaches. Molecules 2019; 24:E4036. [PMID: 31703388 PMCID: PMC6891524 DOI: 10.3390/molecules24224036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/28/2019] [Accepted: 10/31/2019] [Indexed: 12/31/2022] Open
Abstract
The hemoglobin degradation process in Plasmodium parasites is vital for nutrient acquisition required for their growth and proliferation. In P. falciparum, falcipains (FP-2 and FP-3) are the major hemoglobinases, and remain attractive antimalarial drug targets. Other Plasmodium species also possess highly homologous proteins to FP-2 and FP-3. Although several inhibitors have been designed against these proteins, none has been commercialized due to associated toxicity on human cathepsins (Cat-K, Cat-L and Cat-S). Despite the two enzyme groups sharing a common structural fold and catalytic mechanism, distinct active site variations have been identified, and can be exploited for drug development. Here, we utilize in silico approaches to screen 628 compounds from the South African natural sources to identify potential hits that can selectively inhibit the plasmodial proteases. Using docking studies, seven abietane diterpenoids, binding strongly to the plasmodial proteases, and three additional analogs from PubChem were identified. Important residues involved in ligand stabilization were identified for all potential hits through binding pose analysis and their energetic contribution determined by binding free energy calculations. The identified compounds present important scaffolds that could be further developed as plasmodial protease inhibitors. Previous laboratory assays showed the effect of the seven diterpenoids as antimalarials. Here, for the first time, we demonstrate that their possible mechanism of action could be by interacting with falcipains and their plasmodial homologs. Dynamic residue network (DRN) analysis on the plasmodial proteases identified functionally important residues, including a region with high betweenness centrality, which had previously been proposed as a potential allosteric site in FP-2.
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Affiliation(s)
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa;
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332
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David L, Arús-Pous J, Karlsson J, Engkvist O, Bjerrum EJ, Kogej T, Kriegl JM, Beck B, Chen H. Applications of Deep-Learning in Exploiting Large-Scale and Heterogeneous Compound Data in Industrial Pharmaceutical Research. Front Pharmacol 2019; 10:1303. [PMID: 31749705 PMCID: PMC6848277 DOI: 10.3389/fphar.2019.01303] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/14/2019] [Indexed: 12/21/2022] Open
Abstract
In recent years, the development of high-throughput screening (HTS) technologies and their establishment in an industrialized environment have given scientists the possibility to test millions of molecules and profile them against a multitude of biological targets in a short period of time, generating data in a much faster pace and with a higher quality than before. Besides the structure activity data from traditional bioassays, more complex assays such as transcriptomics profiling or imaging have also been established as routine profiling experiments thanks to the advancement of Next Generation Sequencing or automated microscopy technologies. In industrial pharmaceutical research, these technologies are typically established in conjunction with automated platforms in order to enable efficient handling of screening collections of thousands to millions of compounds. To exploit the ever-growing amount of data that are generated by these approaches, computational techniques are constantly evolving. In this regard, artificial intelligence technologies such as deep learning and machine learning methods play a key role in cheminformatics and bio-image analytics fields to address activity prediction, scaffold hopping, de novo molecule design, reaction/retrosynthesis predictions, or high content screening analysis. Herein we summarize the current state of analyzing large-scale compound data in industrial pharmaceutical research and describe the impact it has had on the drug discovery process over the last two decades, with a specific focus on deep-learning technologies.
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Affiliation(s)
- Laurianne David
- Hit Discovery, Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
- Department of Life Science Informatics, B-IT, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Josep Arús-Pous
- Hit Discovery, Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Johan Karlsson
- Quantitative Biology, Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Ola Engkvist
- Hit Discovery, Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Esben Jannik Bjerrum
- Hit Discovery, Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Thierry Kogej
- Hit Discovery, Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
| | - Jan M. Kriegl
- Department of Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Bernd Beck
- Department of Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Hongming Chen
- Hit Discovery, Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, Gothenburg, Sweden
- Chemistry and Chemical Biology Centre, Guangzhou Regenerative Medicine and Health – Guangdong Laboratory, Guangzhou, China
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333
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Cheminformatics Explorations of Natural Products. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2019; 110:1-35. [PMID: 31621009 DOI: 10.1007/978-3-030-14632-0_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The chemistry of natural products is fascinating and has continuously attracted the attention of the scientific community for many reasons including, but not limited to, biosynthesis pathways, chemical diversity, the source of bioactive compounds and their marked impact on drug discovery. There is a broad range of experimental and computational techniques (molecular modeling and cheminformatics) that have evolved over the years and have assisted the investigation of natural products. Herein, we discuss cheminformatics strategies to explore the chemistry and applications of natural products. Since the potential synergisms between cheminformatics and natural products are vast, we will focus on three major aspects: (1) exploration of the chemical space of natural products to identify bioactive compounds, with emphasis on drug discovery; (2) assessment of the toxicity profile of natural products; and (3) diversity analysis of natural product collections and the design of chemical collections inspired by natural sources.
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334
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Potowski M, Losch F, Wünnemann E, Dahmen JK, Chines S, Brunschweiger A. Screening of metal ions and organocatalysts on solid support-coupled DNA oligonucleotides guides design of DNA-encoded reactions. Chem Sci 2019; 10:10481-10492. [PMID: 32055372 PMCID: PMC7003951 DOI: 10.1039/c9sc04708e] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/17/2019] [Indexed: 12/27/2022] Open
Abstract
DNA-encoded compound libraries are widely used in drug discovery. Screening of catalysts for compatibility with solid phase-coupled DNA sequences guided the selection of encoded reactions, exemplified by a Zn(II)-mediated aza-Diels–Alder reaction.
DNA-encoded compound libraries are a widely used technology for target-based small molecule screening. Generally, these libraries are synthesized by solution phase combinatorial chemistry requiring aqueous solvent mixtures and reactions that are orthogonal to DNA reactivity. Initiating library synthesis with readily available controlled pore glass-coupled DNA barcodes benefits from enhanced DNA stability due to nucleobase protection and choice of dry organic solvents for encoded compound synthesis. We screened the compatibility of solid-phase coupled DNA sequences with 53 metal salts and organic reagents. This screening experiment suggests design of encoded library synthesis. Here, we show the reaction optimization and scope of three sp3-bond containing heterocyclic scaffolds synthesized on controlled pore glass-connected DNA sequences. A ZnCl2-promoted aza-Diels–Alder reaction with Danishefsky's diene furnished diverse substituted DNA-tagged pyridones, and a phosphoric acid organocatalyst allowed for synthesis of tetrahydroquinolines by the Povarov reaction and pyrimidinones by the Biginelli reaction, respectively. These three reactions caused low levels of DNA depurination and cover broad and only partially overlapping chemical space though using one set of DNA-coupled starting materials.
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Affiliation(s)
- Marco Potowski
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Florian Losch
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Elena Wünnemann
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Janina K Dahmen
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Silvia Chines
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
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335
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Wei Z, Xie Z, Kuvelkar R, Shah V, Bateman K, McLaren DG, Cooks RG. High‐Throughput Bioassays using “Dip‐and‐Go” Multiplexed Electrospray Mass Spectrometry. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Zhenwei Wei
- Aston LabsDepartment of ChemistryPurdue University 560 Oval Drive West Lafayette IN 47906-1393 USA
| | - Zhuoer Xie
- Aston LabsDepartment of ChemistryPurdue University 560 Oval Drive West Lafayette IN 47906-1393 USA
| | - Reshma Kuvelkar
- Merck & Co., Inc. 2000 Galloping Hill Road Kenilworth NJ 07033 USA
| | - Vinit Shah
- Merck & Co., Inc. 2000 Galloping Hill Road Kenilworth NJ 07033 USA
| | - Kevin Bateman
- Merck & Co., Inc. 2000 Galloping Hill Road Kenilworth NJ 07033 USA
| | - David G. McLaren
- Merck & Co., Inc. 2000 Galloping Hill Road Kenilworth NJ 07033 USA
| | - R. Graham Cooks
- Aston LabsDepartment of ChemistryPurdue University 560 Oval Drive West Lafayette IN 47906-1393 USA
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336
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Wei Z, Xie Z, Kuvelkar R, Shah V, Bateman K, McLaren DG, Cooks RG. High-Throughput Bioassays using "Dip-and-Go" Multiplexed Electrospray Mass Spectrometry. Angew Chem Int Ed Engl 2019; 58:17594-17598. [PMID: 31589796 DOI: 10.1002/anie.201909047] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Indexed: 12/16/2022]
Abstract
A multiplexed system based on inductive nanoelectrospray mass spectrometry (nESI-MS) has been developed for high-throughput screening (HTS) bioassays. This system combines inductive nESI and field amplification micro-electrophoresis to achieve a "dip-and-go" sample loading and purification strategy that enables nESI-MS based HTS assays in 96-well microtiter plates. The combination of inductive nESI and micro-electrophoresis makes it possible to perform efficient in situ separations and clean-up of biological samples. The sensitivity of the system is such that quantitative analysis of peptides from 1-10 000 nm can be performed in a biological matrix. A prototype of the automation system has been developed to handle 12 samples (one row of a microtiter plate) at a time. The sample loading and electrophoretic clean-up of biosamples can be done in parallel within 20 s followed by MS analysis at a rate of 1.3 to 3.5 s per sample. The system was used successfully for the quantitative analysis of BACE1-catalyzed peptide hydrolysis, a prototypical HTS assay of relevance to drug discovery. IC50 values for this system were in agreement with LC-MS but recorded in times more than an order of magnitude shorter.
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Affiliation(s)
- Zhenwei Wei
- Aston Labs, Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47906-1393, USA
| | - Zhuoer Xie
- Aston Labs, Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47906-1393, USA
| | - Reshma Kuvelkar
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Vinit Shah
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Kevin Bateman
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - David G McLaren
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - R Graham Cooks
- Aston Labs, Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47906-1393, USA
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337
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David L, Walsh J, Sturm N, Feierberg I, Nissink JWM, Chen H, Bajorath J, Engkvist O. Identification of Compounds That Interfere with High-Throughput Screening Assay Technologies. ChemMedChem 2019; 14:1795-1802. [PMID: 31479198 PMCID: PMC6856845 DOI: 10.1002/cmdc.201900395] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/21/2019] [Indexed: 01/23/2023]
Abstract
A significant challenge in high-throughput screening (HTS) campaigns is the identification of assay technology interference compounds. A Compound Interfering with an Assay Technology (CIAT) gives false readouts in many assays. CIATs are often considered viable hits and investigated in follow-up studies, thus impeding research and wasting resources. In this study, we developed a machine-learning (ML) model to predict CIATs for three assay technologies. The model was trained on known CIATs and non-CIATs (NCIATs) identified in artefact assays and described by their 2D structural descriptors. Usual methods identifying CIATs are based on statistical analysis of historical primary screening data and do not consider experimental assays identifying CIATs. Our results show successful prediction of CIATs for existing and novel compounds and provide a complementary and wider set of predicted CIATs compared to BSF, a published structure-independent model, and to the PAINS substructural filters. Our analysis is an example of how well-curated datasets can provide powerful predictive models despite their relatively small size.
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Affiliation(s)
- Laurianne David
- Hit Discovery, Discovery Sciences, R&D BioPharmaceuticalsAstraZeneca GoteborgPepparedsleden 1431 83MölndalSweden
- Department of Life Science Informatics, B-ITLIMES Program Unit Chemical Biology and Medicinal ChemistryRheinische Friedrich-Wilhelms-Universität BonnEndenicher Allee 19c53115BonnGermany
| | - Jarrod Walsh
- Hit Discovery, Discovery Sciences, R&D BioPharmaceuticalsAstraZeneca CambridgeAlderley ParkMacclesfieldSK10 4TGUK
| | - Noé Sturm
- Data Science and AI, Drug Safety & Metabolism, R&D BioPharmaceuticalsAstraZeneca GothenburgPepparedsleden 1431 83MölndalSweden
| | - Isabella Feierberg
- Hit Discovery, Discovery Sciences, R&D BioPharmaceuticalsAstraZeneca Boston35 Gatehouse DriveWalthamMA02451USA
| | - J. Willem M. Nissink
- Computational Chemistry, Oncology R&DAstraZenecaCambridge Science Park, Milton RoadCambridgeCB4 0WGUK
| | - Hongming Chen
- Hit Discovery, Discovery Sciences, R&D BioPharmaceuticalsAstraZeneca GoteborgPepparedsleden 1431 83MölndalSweden
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-ITLIMES Program Unit Chemical Biology and Medicinal ChemistryRheinische Friedrich-Wilhelms-Universität BonnEndenicher Allee 19c53115BonnGermany
| | - Ola Engkvist
- Hit Discovery, Discovery Sciences, R&D BioPharmaceuticalsAstraZeneca GoteborgPepparedsleden 1431 83MölndalSweden
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338
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Recent Advances in Selective and Irreversible Covalent Ligand Development and Validation. Cell Chem Biol 2019; 26:1486-1500. [PMID: 31631011 DOI: 10.1016/j.chembiol.2019.09.012] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/06/2019] [Accepted: 09/26/2019] [Indexed: 12/20/2022]
Abstract
Some of the most widely used drugs, such as aspirin and penicillin, are covalent drugs. Covalent binding can improve potency, selectivity, and duration of the effects, but the intrinsic reactivity represents a potential liability and may result in idiosyncratic toxicity. For decades, the cons were believed to outweigh the pros, and covalent targeting was deprioritized in drug discovery. Recently, several covalent inhibitors have been approved for cancer treatment, thus rebooting the field. In this review, we briefly reflect on the history of selective covalent targeting, and provide a comprehensive overview of emerging developments from a chemical biology stand-point. Our discussion will reflect on efforts to validate irreversible covalent ligands, expand the scope of targets, and discover new ligands and warheads. We conclude with a brief commentary of remaining limitations and emerging opportunities in selective covalent targeting.
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339
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Balogun EO, Inaoka DK, Shiba T, Tsuge C, May B, Sato T, Kido Y, Nara T, Aoki T, Honma T, Tanaka A, Inoue M, Matsuoka S, Michels PAM, Watanabe YI, Moore AL, Harada S, Kita K. Discovery of trypanocidal coumarins with dual inhibition of both the glycerol kinase and alternative oxidase of Trypanosoma brucei brucei. FASEB J 2019; 33:13002-13013. [PMID: 31525300 DOI: 10.1096/fj.201901342r] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
African trypanosomiasis, sleeping sickness in humans or nagana in animals, is a potentially fatal neglected tropical disease and a threat to 65 million human lives and 100 million small and large livestock animals in sub-Saharan Africa. Available treatments for this devastating disease are few and have limited efficacy, prompting the search for new drug candidates. Simultaneous inhibition of the trypanosomal glycerol kinase (TGK) and trypanosomal alternative oxidase (TAO) is considered a validated strategy toward the development of new drugs. Our goal is to develop a TGK-specific inhibitor for coadministration with ascofuranone (AF), the most potent TAO inhibitor. Here, we report on the identification of novel compounds with inhibitory potency against TGK. Importantly, one of these compounds (compound 17) and its derivatives (17a and 17b) killed trypanosomes even in the absence of AF. Inhibition kinetics revealed that derivative 17b is a mixed-type and competitive inhibitor for TGK and TAO, respectively. Structural data revealed the molecular basis of this dual inhibitory action, which, in our opinion, will aid in the successful development of a promising drug to treat trypanosomiasis. Although the EC50 of compound 17b against trypanosome cells was 1.77 µM, it had no effect on cultured human cells, even at 50 µM.-Balogun, E. O., Inaoka, D. K., Shiba, T., Tsuge, C., May, B., Sato, T., Kido, Y., Nara, T., Aoki, T., Honma, T., Tanaka, A., Inoue, M., Matsuoka, S., Michels, P. A. M., Watanabe, Y.-I., Moore, A. L., Harada, S., Kita, K. Discovery of trypanocidal coumarins with dual inhibition of both the glycerol kinase and alternative oxidase of Trypanosoma brucei brucei.
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Affiliation(s)
- Emmanuel Oluwadare Balogun
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria.,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daniel Ken Inaoka
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,School of Tropical Medicine and Global Health Nagasaki University, Nagasaki, Japan.,Department of Molecular Infection Dynamics, Shionogi Global Infectious Disease Division, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Chiaki Tsuge
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Benjamin May
- Biochemistry and Medicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Tomohiro Sato
- Systems and Structural Biology Center, Riken, Yokohama, Japan
| | - Yasutoshi Kido
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria.,Department of Parasitology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Takeshi Nara
- Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, Tokyo, Japan
| | - Takashi Aoki
- Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, Tokyo, Japan
| | - Teruki Honma
- Systems and Structural Biology Center, Riken, Yokohama, Japan
| | - Akiko Tanaka
- Systems and Structural Biology Center, Riken, Yokohama, Japan
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Shigeru Matsuoka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Paul A M Michels
- Centre for Immunity, Infection, and Evolution School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Yoh-Ichi Watanabe
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Anthony L Moore
- Biochemistry and Medicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,School of Tropical Medicine and Global Health Nagasaki University, Nagasaki, Japan.,Department of Molecular Infection Dynamics, Shionogi Global Infectious Disease Division, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
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340
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Kanlaya R, Thongboonkerd V. Molecular Mechanisms of Epigallocatechin-3-Gallate for Prevention of Chronic Kidney Disease and Renal Fibrosis: Preclinical Evidence. Curr Dev Nutr 2019; 3:nzz101. [PMID: 31555758 PMCID: PMC6752729 DOI: 10.1093/cdn/nzz101] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/28/2019] [Indexed: 02/07/2023] Open
Abstract
Chronic kidney disease (CKD) is a common public health problem worldwide characterized by gradual decline of renal function over months/years accompanied by renal fibrosis and failure in tissue wound healing after sustained injury. Patients with CKD frequently present with profound signs/symptoms that require medical treatment, mostly culminating in hemodialysis and renal transplantation. To prevent CKD more efficiently, there is an urgent need for better understanding of the pathogenic mechanisms and molecular pathways of the disease pathogenesis and progression, and for developing novel therapeutic targets. Recently, several lines of evidence have shown that epigallocatechin-3-gallate (EGCG), an abundant phytochemical polyphenol derived from Camellia sinensis, might be a promising bioactive compound for prevention of CKD development/progression. This review summarizes current knowledge of molecular mechanisms underlying renoprotective roles of EGCG in CKD based on available preclinical evidence (from both in vitro and in vivo animal studies), particularly its antioxidant property through preservation of mitochondrial function and activation of Nrf2 (nuclear factor erythroid 2-related factor 2)/HO-1 (heme oxygenase-1) signaling, anti-inflammatory activity, and protective effect against epithelial mesenchymal transition. Finally, future perspectives, challenges, and concerns regarding its clinical use in CKD and renal fibrosis are discussed.
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Affiliation(s)
- Rattiyaporn Kanlaya
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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341
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Tran KT, Pallesen JS, Solbak SMØ, Narayanan D, Baig A, Zang J, Aguayo-Orozco A, Carmona RMC, Garcia AD, Bach A. A Comparative Assessment Study of Known Small-Molecule Keap1-Nrf2 Protein-Protein Interaction Inhibitors: Chemical Synthesis, Binding Properties, and Cellular Activity. J Med Chem 2019; 62:8028-8052. [PMID: 31411465 DOI: 10.1021/acs.jmedchem.9b00723] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Inhibiting the protein-protein interaction (PPI) between the transcription factor Nrf2 and its repressor protein Keap1 has emerged as a promising strategy to target oxidative stress in diseases, including central nervous system (CNS) disorders. Numerous non-covalent small-molecule Keap1-Nrf2 PPI inhibitors have been reported to date, but many feature suboptimal physicochemical properties for permeating the blood-brain barrier, while others contain problematic structural moieties. Here, we present the first side-by-side assessment of all reported Keap1-Nrf2 PPI inhibitor classes using fluorescence polarization, thermal shift assay, and surface plasmon resonance-and further evaluate the compounds in an NQO1 induction cell assay and in counter tests for nonspecific activities. Surprisingly, half of the compounds were inactive or deviated substantially from reported activities, while we confirm the cross-assay activities for others. Through this study, we have identified the most promising Keap1-Nrf2 inhibitors that can serve as pharmacological probes or starting points for developing CNS-active Keap1 inhibitors.
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Affiliation(s)
- Kim T Tran
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - Jakob S Pallesen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - Sara M Ø Solbak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - Dilip Narayanan
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - Amina Baig
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - Jie Zang
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - Alejandro Aguayo-Orozco
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - Rosa M C Carmona
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - Anthony D Garcia
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark.,École Nationale Supérieure de Chimie de Rennes , 11 Allée de Beaulieu , CS 50837, Rennes Cedex 7 35708 , France
| | - Anders Bach
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
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342
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Dantas RF, Evangelista TCS, Neves BJ, Senger MR, Andrade CH, Ferreira SB, Silva-Junior FP. Dealing with frequent hitters in drug discovery: a multidisciplinary view on the issue of filtering compounds on biological screenings. Expert Opin Drug Discov 2019; 14:1269-1282. [DOI: 10.1080/17460441.2019.1654453] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Rafael Ferreira Dantas
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Tereza Cristina Santos Evangelista
- LaSOPB – Laboratório de Síntese Orgânica e Prospecção Biológica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruno Junior Neves
- LabChem – Laboratory of Cheminformatics, Centro Universitário de Anápolis, UniEVANGÉLICA, Anápolis, Brazil
| | - Mario Roberto Senger
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Carolina Horta Andrade
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
| | - Sabrina Baptista Ferreira
- LaSOPB – Laboratório de Síntese Orgânica e Prospecção Biológica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Floriano Paes Silva-Junior
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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343
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Amato G, Wiethe R, Manke A, Vasukuttan V, Snyder R, Runyon S, Maitra R. Functionalized 6-(piperidin-1-yl)-8,9-diphenyl purines as inverse agonists of the CB1 receptor - SAR efforts towards selectivity and peripheralization. Bioorg Med Chem 2019; 27:3632-3649. [PMID: 31301950 DOI: 10.1016/j.bmc.2019.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/18/2019] [Accepted: 07/02/2019] [Indexed: 10/26/2022]
Abstract
Antagonists of type 1 cannabinoid receptors (CB1) may be useful in treating diabetes, hepatic disorders, and fibrosis. Otenabant (1) is a potent and selective CB1 inverse agonist that was under investigation as an anti-obesity agent, but its development was halted once adverse effects associated with another marketed inverse agonist rimonabant (2) became known. Non-tissue selective antagonists of CB1 that have high levels of brain penetration produce adverse effects in a small subset of patients including anxiety, depression and suicidal ideation. Currently, efforts are underway to produce compounds that have limited brain penetration. In this report, novel analogs of 1 are explored to develop and test strategies for peripheralization. The piperidine of 1 is studied as a linker, which is functionalized with alkyl, heteroalkyl, aryl and heteroaryl groups using a connector in the form of an amine, amide, sulfonamide, sulfamide, carbamate, oxime, amidine, or guanidine. We also report more polar replacements for the 4-chlorophenyl group in the 9-position of the purine core, which improve calculated physical properties of the molecules. These studies resulted in compounds such as 75 that are potent inverse agonists of hCB1 with exceptional selectivity for hCB1 over hCB2. SAR studies revealed ways to adjust physical properties to limit brain exposure.
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Affiliation(s)
- George Amato
- Discovery Science and Technology, RTI International, 3040 Cornwallis Rd., Research Triangle Park, NC 27709-2194, USA
| | - Robert Wiethe
- Discovery Science and Technology, RTI International, 3040 Cornwallis Rd., Research Triangle Park, NC 27709-2194, USA
| | - Amruta Manke
- Discovery Science and Technology, RTI International, 3040 Cornwallis Rd., Research Triangle Park, NC 27709-2194, USA
| | - Vineetha Vasukuttan
- Discovery Science and Technology, RTI International, 3040 Cornwallis Rd., Research Triangle Park, NC 27709-2194, USA
| | - Rodney Snyder
- Discovery Science and Technology, RTI International, 3040 Cornwallis Rd., Research Triangle Park, NC 27709-2194, USA
| | - Scott Runyon
- Discovery Science and Technology, RTI International, 3040 Cornwallis Rd., Research Triangle Park, NC 27709-2194, USA
| | - Rangan Maitra
- Discovery Science and Technology, RTI International, 3040 Cornwallis Rd., Research Triangle Park, NC 27709-2194, USA.
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344
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Bamborough P, Chung CW, Demont EH, Bridges AM, Craggs PD, Dixon DP, Francis P, Furze RC, Grandi P, Jones EJ, Karamshi B, Locke K, Lucas SCC, Michon AM, Mitchell DJ, Pogány P, Prinjha RK, Rau C, Roa AM, Roberts AD, Sheppard RJ, Watson RJ. A Qualified Success: Discovery of a New Series of ATAD2 Bromodomain Inhibitors with a Novel Binding Mode Using High-Throughput Screening and Hit Qualification. J Med Chem 2019; 62:7506-7525. [PMID: 31398032 DOI: 10.1021/acs.jmedchem.9b00673] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The bromodomain of ATAD2 has proved to be one of the least-tractable proteins within this target class. Here, we describe the discovery of a new class of inhibitors by high-throughput screening and show how the difficulties encountered in establishing a screening triage capable of finding progressible hits were overcome by data-driven optimization. Despite the prevalence of nonspecific hits and an exceptionally low progressible hit rate (0.001%), our optimized hit qualification strategy employing orthogonal biophysical methods enabled us to identify a single active series. The compounds have a novel ATAD2 binding mode with noncanonical features including the displacement of all conserved water molecules within the active site and a halogen-bonding interaction. In addition to reporting this new series and preliminary structure-activity relationship, we demonstrate the value of diversity screening to complement the knowledge-based approach used in our previous ATAD2 work. We also exemplify tactics that can increase the chance of success when seeking new chemical starting points for novel and less-tractable targets.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Paola Grandi
- Cellzome , Meyerhofstrasse 1 , Heidelberg 69117 , Germany
| | | | | | | | | | | | | | | | | | - Christina Rau
- Cellzome , Meyerhofstrasse 1 , Heidelberg 69117 , Germany
| | - Ana Maria Roa
- GlaxoSmithKline Tres Cantos , 28760 Tres Cantos , Madrid , Spain
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345
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King JB, Carter AC, Dai W, Lee JW, Kil YS, Du L, Helff SK, Cai S, Huddle BC, Cichewicz RH. Design and Application of a High-Throughput, High-Content Screening System for Natural Product Inhibitors of the Human Parasite Trichomonas vaginalis. ACS Infect Dis 2019; 5:1456-1470. [PMID: 31265248 PMCID: PMC10782576 DOI: 10.1021/acsinfecdis.9b00156] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It is estimated that Trichomonas vaginalis affects an astonishing 3.9% of the world's population, and while many of those infected are asymptomatic, progression of the disease can lead to serious health problems. Currently, the nitroimidazoles constitute the only drug class approved to treat trichomoniasis in the United States, which makes the spread of drug resistance a realistic concern. We developed a new image-based, high-throughput, and high-content assay for testing natural products (purified compounds and extracts) for antitrichomonal activity. Applying this assay system to a library of fungal natural product extracts led to the identification of three general classes of natural product inhibitors that exhibited moderate to strong activities against T. vaginalis: anthraquinones, xanthone-anthraquinone heterodimers, and decalin-linked tetramic-acid-containing metabolites. The tetramate natural products emerged as the most promising candidate molecules with pyrrolocin A (51) exhibiting potent activity against the parasite (EC50 = 60 nM), yet this metabolite showed limited toxicity to mammalian cell lines (selectivity index values of 100 and 167 versus 3T3 fibroblast and Ect1 normal cervical cells, respectively). The imaging-based assay system is a powerful tool for the bioassay-guided purification of single-component antitrichomonal biomolecules from complex natural product mixtures.
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Affiliation(s)
- Jarrod B. King
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, 101 Stephenson Parkway, Room 1000, University of Oklahoma, Norman, Oklahoma, 73019, United States
| | - Adam C. Carter
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, 101 Stephenson Parkway, Room 1000, University of Oklahoma, Norman, Oklahoma, 73019, United States
| | - Wentao Dai
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, 101 Stephenson Parkway, Room 1000, University of Oklahoma, Norman, Oklahoma, 73019, United States
| | - Jin Woo Lee
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, 101 Stephenson Parkway, Room 1000, University of Oklahoma, Norman, Oklahoma, 73019, United States
| | - Yun-Seo Kil
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, 101 Stephenson Parkway, Room 1000, University of Oklahoma, Norman, Oklahoma, 73019, United States
| | - Lin Du
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, 101 Stephenson Parkway, Room 1000, University of Oklahoma, Norman, Oklahoma, 73019, United States
| | - Sara K. Helff
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, 101 Stephenson Parkway, Room 1000, University of Oklahoma, Norman, Oklahoma, 73019, United States
| | - Shengxin Cai
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, 101 Stephenson Parkway, Room 1000, University of Oklahoma, Norman, Oklahoma, 73019, United States
| | - Brandt C. Huddle
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, 101 Stephenson Parkway, Room 1000, University of Oklahoma, Norman, Oklahoma, 73019, United States
| | - Robert H. Cichewicz
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, 101 Stephenson Parkway, Room 1000, University of Oklahoma, Norman, Oklahoma, 73019, United States
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346
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Li X, Payne DT, Ampolu B, Bland N, Brown JT, Dutton MJ, Fitton CA, Gulliver A, Hale L, Hamza D, Jones G, Lane R, Leach AG, Male L, Merisor EG, Morton MJ, Quy AS, Roberts R, Scarll R, Schulz-Utermoehl T, Stankovic T, Stevenson B, Fossey JS, Agathanggelou A. Derivatisation of parthenolide to address chemoresistant chronic lymphocytic leukaemia. MEDCHEMCOMM 2019; 10:1379-1390. [PMID: 32952998 PMCID: PMC7478165 DOI: 10.1039/c9md00297a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/03/2019] [Indexed: 12/13/2022]
Abstract
Parthenolide is a natural product that exhibits anti-leukaemic activity, however, its clinical use is limited by its poor bioavailability. It may be extracted from feverfew and protocols for growing, extracting and derivatising it are reported. A novel parthenolide derivative with good bioavailability and pharmacological properties was identified through a screening cascade based on in vitro anti-leukaemic activity and calculated "drug-likeness" properties, in vitro and in vivo pharmacokinetics studies and hERG liability testing. In vitro studies showed the most promising derivative to have comparable anti-leukaemic activity to DMAPT, a previously described parthenolide derivative. The newly identified compound was shown to have pro-oxidant activity and in silico molecular docking studies indicate a prodrug mode of action. A synthesis scheme is presented for the production of amine 7 used in the generation of 5f.
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Affiliation(s)
- Xingjian Li
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Daniel T Payne
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Badarinath Ampolu
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Nicholas Bland
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Jane T Brown
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Mark J Dutton
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Catherine A Fitton
- Institute for Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Abigail Gulliver
- Winterbourne Botanic Garden, University of Birmingham, 58 Edgbaston Park Road, Edgbaston, Birmingham, West Midlands B15 2RT, UK
| | - Lee Hale
- Winterbourne Botanic Garden, University of Birmingham, 58 Edgbaston Park Road, Edgbaston, Birmingham, West Midlands B15 2RT, UK
| | - Daniel Hamza
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Geraint Jones
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Rebecca Lane
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Andrew G Leach
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Louise Male
- X-Ray Crystallography Facility, School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK
| | - Elena G Merisor
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - Michael J Morton
- ApconiX Ltd, Alderly Park, Nether Alderly, Cheshire, SK10 4TG, UK
| | - Alex S Quy
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Ruth Roberts
- ApconiX Ltd, Alderly Park, Nether Alderly, Cheshire, SK10 4TG, UK
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK
| | - Rosanna Scarll
- Institute for Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | | | - Tatjana Stankovic
- Institute for Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Brett Stevenson
- Sygnature Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham, NG1 1GR, UK
| | - John S Fossey
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
| | - Angelo Agathanggelou
- Institute for Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, UK.
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347
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Anticancer properties of 5Z-(4-fluorobenzylidene)-2-(4-hydroxyphenylamino)-thiazol-4-one. Sci Rep 2019; 9:10609. [PMID: 31337851 PMCID: PMC6650463 DOI: 10.1038/s41598-019-47177-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/09/2019] [Indexed: 11/09/2022] Open
Abstract
4-thiazolidinones, which are privileged structures in medicinal chemistry, comprise the well-known class of heterocycles and are a source of new drug-like compounds. Undoubtedly, the 5-bulky-substituted-2,4-thiazolidinediones - a class of antihyperglycemic glitazones, which are peroxisome proliferator-activated receptor gamma (PPARγ) agonists, are the most described group among them. As there are various chemically distinct 4-thiazolidinones, different subtypes have been selected for studies; however, their main pharmacological profiles are similar. The aim of this study was to evaluate the anticancer activity of 5Z-(4-fluorobenzylidene)-2-(4-hydroxyphenylamino)-thiazol-4-one (Les-236) in four human cancer cell lines, A549, SCC-15, SH-SY5Y, and CACO-2, and investigate its impact on the production of reactive oxygen species (ROS) and the apoptotic process as well as cytotoxicity and metabolism in these cell lines. The cell lines were exposed to increasing concentrations (1 nM to 100 µM) of the studied compound for 6, 24, and 48 h, and later, ROS production, cell viability, caspase-3 activity, and cell metabolism were examined. The obtained results showed that the studied compound decreased the production of ROS, increased the release of lactate dehydrogenase, and decreased cell metabolism/proliferation in all the five cell lines at micromolar concentrations. Interestingly, over a wide range of concentrations (from 1 nM to 100 µM), Les-236 was able to increase the activity of caspase-3 in BJ (after 6 h of exposure), A549, CACO-2, and SCC-15 (after 48 h of exposure) cell lines which could be an effect of the activation of PPARγ-dependent pathways.
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348
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Miller TW, Amason JD, Garcin ED, Lamy L, Dranchak PK, Macarthur R, Braisted J, Rubin JS, Burgess TL, Farrell CL, Roberts DD, Inglese J. Quantitative high-throughput screening assays for the discovery and development of SIRPα-CD47 interaction inhibitors. PLoS One 2019; 14:e0218897. [PMID: 31276567 PMCID: PMC6611588 DOI: 10.1371/journal.pone.0218897] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 06/11/2019] [Indexed: 02/06/2023] Open
Abstract
CD47 is an immune checkpoint molecule that downregulates key aspects of both the innate and adaptive anti-tumor immune response via its counter receptor SIRPα, and it is expressed at high levels in a wide variety of tumor types. This has led to the development of biologics that inhibit SIRPα engagement including humanized CD47 antibodies and a soluble SIRPα decoy receptor that are currently undergoing clinical trials. Unfortunately, toxicological issues, including anemia related to on-target mechanisms, are barriers to their clinical advancement. Another potential issue with large biologics that bind CD47 is perturbation of CD47 signaling through its high-affinity interaction with the matricellular protein thrombospondin-1 (TSP1). One approach to avoid these shortcomings is to identify and develop small molecule molecular probes and pretherapeutic agents that would (1) selectively target SIRPα or TSP1 interactions with CD47, (2) provide a route to optimize pharmacokinetics, reduce on-target toxicity and maximize tissue penetration, and (3) allow more flexible routes of administration. As the first step toward this goal, we report the development of an automated quantitative high-throughput screening (qHTS) assay platform capable of screening large diverse drug-like chemical libraries to discover novel small molecules that inhibit CD47-SIRPα interaction. Using time-resolved Förster resonance energy transfer (TR-FRET) and bead-based luminescent oxygen channeling assay formats (AlphaScreen), we developed biochemical assays, optimized their performance, and individually tested them in small-molecule library screening. Based on performance and low false positive rate, the LANCE TR-FRET assay was employed in a ~90,000 compound library qHTS, while the AlphaScreen oxygen channeling assay served as a cross-validation orthogonal assay for follow-up characterization. With this multi-assay strategy, we successfully eliminated compounds that interfered with the assays and identified five compounds that inhibit the CD47-SIRPα interaction; these compounds will be further characterized and later disclosed. Importantly, our results validate the large library qHTS for antagonists of CD47-SIRPα interaction and suggest broad applicability of this approach to screen chemical libraries for other protein-protein interaction modulators.
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Affiliation(s)
- Thomas W. Miller
- Paradigm Shift Therapeutics LLC, Rockville, Maryland, United States of America
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Joshua D. Amason
- Paradigm Shift Therapeutics LLC, Rockville, Maryland, United States of America
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Elsa D. Garcin
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Catonsville, Maryland, United States of America
| | - Laurence Lamy
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Patricia K. Dranchak
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Ryan Macarthur
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - John Braisted
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Jeffrey S. Rubin
- Paradigm Shift Therapeutics LLC, Rockville, Maryland, United States of America
| | - Teresa L. Burgess
- Paradigm Shift Therapeutics LLC, Rockville, Maryland, United States of America
| | | | - David D. Roberts
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - James Inglese
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
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349
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Chinsembu KC. Chemical diversity and activity profiles of HIV-1 reverse transcriptase inhibitors from plants. REVISTA BRASILEIRA DE FARMACOGNOSIA-BRAZILIAN JOURNAL OF PHARMACOGNOSY 2019. [DOI: 10.1016/j.bjp.2018.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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350
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Amato G, Manke A, Wiethe R, Vasukuttan V, Snyder R, Yueh YL, Decker A, Runyon S, Maitra R. Functionalized 6-(Piperidin-1-yl)-8,9-Diphenyl Purines as Peripherally Restricted Inverse Agonists of the CB1 Receptor. J Med Chem 2019; 62:6330-6345. [PMID: 31185168 DOI: 10.1021/acs.jmedchem.9b00727] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Peripherally restricted CB1 receptor antagonists may be useful in treating metabolic syndrome, diabetes, liver diseases, and gastrointestinal disorders. Clinical development of the centrally acting CB1 inverse agonist otenabant (1) was halted due to its potential of producing adverse effects. SAR studies of 1 are reported herein with the objective of producing peripherally restricted analogues. Crystal structures of hCB1 and docking studies with 1 indicate that the piperidine group could be functionalized at the 4-position to access a binding pocket that can accommodate both polar and nonpolar groups. The piperidine is studied as a linker, functionalized with alkyl, heteroalkyl, aryl, and heteroaryl groups using a urea connector. Orally bioavailable and peripherally selective compounds have been produced that are potent inverse agonists of hCB1 with exceptional selectivity for hCB1 over hCB2. Compound 38 blocked alcohol-induced liver steatosis in mice and has good ADME properties for further development.
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Affiliation(s)
- George Amato
- Discovery Science and Technology , RTI International , 3040 Cornwallis Road , Research Triangle Park , North Carolina 27709-2194 , United States
| | - Amruta Manke
- Discovery Science and Technology , RTI International , 3040 Cornwallis Road , Research Triangle Park , North Carolina 27709-2194 , United States
| | - Robert Wiethe
- Discovery Science and Technology , RTI International , 3040 Cornwallis Road , Research Triangle Park , North Carolina 27709-2194 , United States
| | - Vineetha Vasukuttan
- Discovery Science and Technology , RTI International , 3040 Cornwallis Road , Research Triangle Park , North Carolina 27709-2194 , United States
| | - Rodney Snyder
- Discovery Science and Technology , RTI International , 3040 Cornwallis Road , Research Triangle Park , North Carolina 27709-2194 , United States
| | - Yun Lan Yueh
- Discovery Science and Technology , RTI International , 3040 Cornwallis Road , Research Triangle Park , North Carolina 27709-2194 , United States
| | - Ann Decker
- Discovery Science and Technology , RTI International , 3040 Cornwallis Road , Research Triangle Park , North Carolina 27709-2194 , United States
| | - Scott Runyon
- Discovery Science and Technology , RTI International , 3040 Cornwallis Road , Research Triangle Park , North Carolina 27709-2194 , United States
| | - Rangan Maitra
- Discovery Science and Technology , RTI International , 3040 Cornwallis Road , Research Triangle Park , North Carolina 27709-2194 , United States
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