1
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Pillaiyar T, Wozniak M, Abboud D, Rasch A, Liebing AD, Poso A, Kronenberger T, Stäubert C, Laufer SA, Hanson J. Development of Ligands for the Super Conserved Orphan G Protein-Coupled Receptor GPR27 with Improved Efficacy and Potency. J Med Chem 2023; 66:17118-17137. [PMID: 38060818 DOI: 10.1021/acs.jmedchem.3c02030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
The orphan G protein-coupled receptor GPR27 appears to play a role in insulin production, secretion, lipid metabolism, neuronal plasticity, and l-lactate homeostasis. However, investigations on the function of GPR27 are impaired by the lack of potent and efficacious agonists. We describe herein the development of di- and trisubstituted benzamide derivatives 4a-e, 7a-z, and 7aa-ai, which display GPR27-specific activity in a β-arrestin 2 recruitment-based assay. Highlighted compounds are PT-91 (7p: pEC50 6.15; Emax 100%) and 7ab (pEC50 6.56; Emax 99%). A putative binding mode was revealed by the docking studies of 7p and 7ab with a GPR27 homology model. The novel active compounds exhibited no GPR27-mediated activation of G proteins, indicating that the receptor may possess an atypical profile. Compound 7p displays high metabolic stability and brain exposure in mice. Thus, 7p represents a novel tool to investigate the elusive pharmacology of GPR27 and assess its potential as a drug target.
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Affiliation(s)
- Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Monika Wozniak
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, B-4000 Liège, Belgium
| | - Dayana Abboud
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, B-4000 Liège, Belgium
| | - Alexander Rasch
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Aenne-Dorothea Liebing
- Rudolf Schönheimer Institute of Biochemistry, Faculty of Medicine, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Claudia Stäubert
- Rudolf Schönheimer Institute of Biochemistry, Faculty of Medicine, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany
| | - Stefan A Laufer
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Julien Hanson
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, B-4000 Liège, Belgium
- Laboratory of Medicinal Chemistry, Centre for Interdisciplinary Research on Medicines (CIRM), University of Liège, B-4000 Liège, Belgium
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2
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Figuerola-Asencio L, Morales P, Zhao P, Hurst DP, Sayed SS, Colón KL, Gómez-Cañas M, Fernández-Ruiz J, Croatt MP, Reggio PH, Abood ME, Jagerovic N. Thienopyrimidine Derivatives as GPR55 Receptor Antagonists: Insight into Structure-Activity Relationship. ACS Med Chem Lett 2022; 14:18-25. [PMID: 36655130 PMCID: PMC9841585 DOI: 10.1021/acsmedchemlett.2c00325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022] Open
Abstract
GPR55 is an orphan G-protein coupled receptor involved in various pathophysiological conditions. However, there are only a few noncannabinoid GPR55 ligands reported so far. The lack of potent and selective GPR55 ligands precludes a deep exploration of this receptor. The studies presented here focused on a thienopyrimidine scaffold based on the GPR55 antagonist ML192, previously discovered by high-throughput screening. The GPR55 activities of the new synthesized compounds were assessed using β-arrestin recruitment assays in Chinese hamster ovary cells overexpressing human GPR55. Some derivatives were identified as GPR55 antagonists with functional efficacy and selectivity versus CB1 and CB2 cannabinoid receptors.
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Affiliation(s)
- Laura Figuerola-Asencio
- Instituto
de Química Médica, Consejo
Superior de Investigaciones Científicas, 28006Madrid, Spain
| | - Paula Morales
- Instituto
de Química Médica, Consejo
Superior de Investigaciones Científicas, 28006Madrid, Spain
| | - Pingwei Zhao
- Center
for Substance Abuse Research, Temple University, Philadelphia, Pennsylvania19122, United States
| | - Dow P. Hurst
- Center
for Drug Discovery, Department of Chemistry and Biochemistry, University North Carolina, Greensboro, North Carolina27599, United States
| | - Sommayah S. Sayed
- Center
for Drug Discovery, Department of Chemistry and Biochemistry, University North Carolina, Greensboro, North Carolina27599, United States
| | - Katsuya L. Colón
- Center
for Drug Discovery, Department of Chemistry and Biochemistry, University North Carolina, Greensboro, North Carolina27599, United States
| | - María Gómez-Cañas
- Department
of Biochemistry and Molecular Biology, Faculty of Medicine, Complutense University, CIBERNED and IRYCIS, 28040Madrid, Spain
| | - Javier Fernández-Ruiz
- Department
of Biochemistry and Molecular Biology, Faculty of Medicine, Complutense University, CIBERNED and IRYCIS, 28040Madrid, Spain
| | - Mitchell P. Croatt
- Center
for Drug Discovery, Department of Chemistry and Biochemistry, University North Carolina, Greensboro, North Carolina27599, United States
| | - Patricia H. Reggio
- Center
for Drug Discovery, Department of Chemistry and Biochemistry, University North Carolina, Greensboro, North Carolina27599, United States,E-mail:
| | - Mary E. Abood
- Center
for Substance Abuse Research, Temple University, Philadelphia, Pennsylvania19122, United States,E-mail:
| | - Nadine Jagerovic
- Instituto
de Química Médica, Consejo
Superior de Investigaciones Científicas, 28006Madrid, Spain,E-mail:
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3
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Obubeid FO, Eltigani MM, Mukhtar RM, Ibrahim RA, Alzain MA, Elbadawi FA, Ghaboosh H, Alzain AA. Dual targeting inhibitors for HIV-1 capsid and cyclophilin A: molecular docking, molecular dynamics, and quantum mechanics. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2097673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Fauad O. Obubeid
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Maha M. Eltigani
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Rua M. Mukhtar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Reham A. Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Muna A. Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Fatima A. Elbadawi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Hiba Ghaboosh
- Department of Pharmaceutics, University of Gezira, Wad Madani, Sudan
| | - Abdulrahim A. Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
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4
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Han J, Kyu Lee M, Jang Y, Cho WJ, Kim M. Repurposing of cyclophilin A inhibitors as broad-spectrum antiviral agents. Drug Discov Today 2022; 27:1895-1912. [PMID: 35609743 PMCID: PMC9123807 DOI: 10.1016/j.drudis.2022.05.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 03/30/2022] [Accepted: 05/18/2022] [Indexed: 12/28/2022]
Abstract
Cyclophilin A (CypA) is linked to diverse human diseases including viral infections. With the worldwide emergence of severe acute respiratory coronavirus 2 (SARS-CoV-2), drug repurposing has been highlighted as a strategy with the potential to speed up antiviral development. Because CypA acts as a proviral component in hepatitis C virus, coronavirus and HIV, its inhibitors have been suggested as potential treatments for these infections. Here, we review the structure of cyclosporin A and sanglifehrin A analogs as well as synthetic micromolecules inhibiting CypA; and we discuss their broad-spectrum antiviral efficacy in the context of the virus lifecycle.
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Affiliation(s)
- Jinhe Han
- College of Pharmacy, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Myoung Kyu Lee
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Yejin Jang
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Won-Jea Cho
- College of Pharmacy, Chonnam National University, Gwangju, 61186, Republic of Korea.
| | - Meeheyin Kim
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea; Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Republic of Korea.
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5
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Hermann T, Hochegger P, Dolensky J, Seebacher W, Saf R, Kaiser M, Mäser P, Weis R. New Acyl Derivatives of 3-Aminofurazanes and Their Antiplasmodial Activities. Pharmaceuticals (Basel) 2021; 14:ph14050412. [PMID: 33925485 PMCID: PMC8145535 DOI: 10.3390/ph14050412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/21/2021] [Accepted: 04/24/2021] [Indexed: 11/16/2022] Open
Abstract
An N-acylated furazan-3-amine of a Medicines for Malaria Venture (MMV) project has shown activity against different strains of Plasmodium falciparum. Seventeen new derivatives were prepared and tested in vitro for their activities against blood stages of two strains of Plasmodium falciparum. Several structure-activity relationships were revealed. The activity strongly depended on the nature of the acyl moiety. Only benzamides showed promising activity. The substitution pattern of their phenyl ring affected the activity and the cytotoxicity of compounds. In addition, physicochemical parameters were calculated (log P, log D, ligand efficiency) or determined experimentally (permeability) via a PAMPA. The N-(4-(3,4-diethoxyphenyl)-1,2,5-oxadiazol-3-yl)-3-(trifluoromethyl)benzamide possessed good physicochemical properties and showed high antiplasmodial activity against a chloroquine-sensitive strain (IC50(NF54) = 0.019 µM) and even higher antiplasmodial activity against a multiresistant strain (IC50(K1) = 0.007 µM). Compared to the MMV compound, the permeability and the activity against the multiresistant strain were improved.
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Affiliation(s)
- Theresa Hermann
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Schubertstraße 1, A-8010 Graz, Austria; (T.H.); (J.D.); (W.S.); (R.W.)
| | - Patrick Hochegger
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Schubertstraße 1, A-8010 Graz, Austria; (T.H.); (J.D.); (W.S.); (R.W.)
- Correspondence: ; Tel.: +43-316-380-5379; Fax: +43-316-380-9846
| | - Johanna Dolensky
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Schubertstraße 1, A-8010 Graz, Austria; (T.H.); (J.D.); (W.S.); (R.W.)
| | - Werner Seebacher
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Schubertstraße 1, A-8010 Graz, Austria; (T.H.); (J.D.); (W.S.); (R.W.)
| | - Robert Saf
- Institute for Chemistry and Technology of Materials (ICTM), Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria;
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Socinstraße 57, CH-4002 Basel, Switzerland; (M.K.); (P.M.)
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute, Socinstraße 57, CH-4002 Basel, Switzerland; (M.K.); (P.M.)
| | - Robert Weis
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Schubertstraße 1, A-8010 Graz, Austria; (T.H.); (J.D.); (W.S.); (R.W.)
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6
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Pan WJ, Wang ZX. Palladium-Catalyzed C−H Benzylation of (Benzo)oxazoles with Benzylic Quaternary Ammonium Triflates. ASIAN J ORG CHEM 2018. [DOI: 10.1002/ajoc.201800264] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Wen-Jing Pan
- CAS Key Laboratory of Soft Matter Chemistry, and Department of Chemistry; University of Science and Technology of China; Hefei Anhui 230026 P.R. China
| | - Zhong-Xia Wang
- CAS Key Laboratory of Soft Matter Chemistry, and Department of Chemistry; University of Science and Technology of China; Hefei Anhui 230026 P.R. China
- Collaborative Innovation Center of Chemical Science, and Engineering (Tianjin); Tianjin 300072 P.R. China
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7
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Zhu L, Luo K, Li K, Jin Y, Lin J. Design, synthesis and biological evaluation of 2-phenylquinoline-4-carboxamide derivatives as a new class of tubulin polymerization inhibitors. Bioorg Med Chem 2017; 25:5939-5951. [DOI: 10.1016/j.bmc.2017.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 12/15/2022]
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8
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Majee D, Guin S, Biswas S, Samanta S. A Metal-Free Based New Approach to 2,4-Disubstituted Pyridines via One-Pot Sequential Reaction of Cyclic Sulfamidate Imines with β-Substituted Acroleins. ChemistrySelect 2017. [DOI: 10.1002/slct.201700733] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Debashis Majee
- Discipline of Chemistry; Indian Institute of Technology Indore; Simrol 453552, Madhya Pradesh India
| | - Soumitra Guin
- Discipline of Chemistry; Indian Institute of Technology Indore; Simrol 453552, Madhya Pradesh India
| | - Soumen Biswas
- Discipline of Chemistry; Indian Institute of Technology Indore; Simrol 453552, Madhya Pradesh India
| | - Sampak Samanta
- Discipline of Chemistry; Indian Institute of Technology Indore; Simrol 453552, Madhya Pradesh India
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9
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Wear MA, Nowicki MW, Blackburn EA, McNae IW, Walkinshaw MD. Thermo-kinetic analysis space expansion for cyclophilin-ligand interactions - identification of a new nonpeptide inhibitor using Biacore™ T200. FEBS Open Bio 2017; 7:533-549. [PMID: 28396838 PMCID: PMC5377415 DOI: 10.1002/2211-5463.12201] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/18/2017] [Accepted: 01/23/2017] [Indexed: 12/31/2022] Open
Abstract
We have established a refined methodology for generating surface plasmon resonance sensor surfaces of recombinant his‐tagged human cyclophilin‐A. Our orientation‐specific stabilisation approach captures his‐tagged protein under ‘physiological conditions’ (150 mm NaCl, pH 7.5) and covalently stabilises it on Ni2+‐nitrilotriacetic acid surfaces, very briefly activated for primary amine‐coupling reactions, producing very stable and active surfaces (≥ 95% specific activity) of cyclophilin‐A. Variation in protein concentration with the same contact time allows straightforward generation of variable density surfaces, with essentially no loss of activity, making the protocol easily adaptable for studying numerous interactions; from very small fragments, ~ 100 Da, to large protein ligands. This new method results in an increased stability and activity of the immobilised protein and allowed us to expand the thermo‐kinetic analysis space, and to determine accurate and robust thermodynamic parameters for the cyclophilin‐A–cyclosporin‐A interaction. Furthermore, the increased sensitivity of the surface allowed identification of a new nonpeptide inhibitor of cyclophilin‐A, from a screen of a fragment library. This fragment, 2,3‐diaminopyridine, bound specifically with a mean affinity of 248 ± 60 μm. The X‐ray structure of this 109‐Da fragment bound in the active site of cyclophilin‐A was solved to a resolution of 1.25 Å (PDB: 5LUD), providing new insight into the molecular details for a potential new series of nonpeptide cyclophilin‐A inhibitors.
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Affiliation(s)
- Martin A Wear
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
| | - Matthew W Nowicki
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
| | - Elizabeth A Blackburn
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
| | - Iain W McNae
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
| | - Malcolm D Walkinshaw
- The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK
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10
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Chen L, Chen S, Gui C, Shen J, Shen X, Jiang H. Discovering Severe Acute Respiratory Syndrome Coronavirus 3CL Protease Inhibitors: Virtual Screening, Surface Plasmon Resonance, and Fluorescence Resonance Energy Transfer Assays. ACTA ACUST UNITED AC 2016; 11:915-21. [PMID: 17092912 PMCID: PMC9050464 DOI: 10.1177/1087057106293295] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
An integrated system has been developed for discovering potent inhibitors of severe acute respiratory syndrome coronavirus 3C-like protease (SARS-CoV 3CLpro) by virtual screening correlating with surface plasmon resonance (SPR) and fluorescence resonance energy transfer (FRET) technologies-based assays. The authors screened 81,287 small molecular compounds against SPECS database by virtual screening; 256 compounds were subsequently selected for biological evaluation. Through SPR technology-based assay, 52 from these 256 compounds were discovered to show binding to SARS-CoV 3CLpro. The enzymatic inhibition activities of these 52 SARS-CoV 3CLpro binders were further applied to FRET-based assay, and IC50 values were determined. Based on this integrated assay platform, 8 new SARS-CoV 3CLpro inhibitors were discovered. The fact that the obtained IC50 values for the inhibitors are in good accordance with the discovered dissociation equilibrium constants (KDs) assayed by SPR implied the reliability of this platform. Our current work is hoped to supply a powerful approach in the discovery of potent SARS-CoV 3CLpro inhibitors, and the determined inhibitors could be used as possible lead compounds for further research.
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Affiliation(s)
- Lili Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Shuai Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Chunshan Gui
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jianhua Shen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xu Shen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
- Address reprint requests to: Xu Shen Drug Discovery and Design Center State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203 E-mail: or
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
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11
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Identification of Spongionella compounds as cyclosporine A mimics. Pharmacol Res 2016; 107:407-414. [DOI: 10.1016/j.phrs.2016.03.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 03/03/2016] [Accepted: 03/03/2016] [Indexed: 01/29/2023]
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12
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Yan W, Qing J, Mei H, Mao F, Huang J, Zhu J, Jiang H, Liu L, Zhang L, Li J. Discovery of Novel Small Molecule Anti-HCV Agents via the CypA Inhibitory Mechanism Using O-Acylation-Directed Lead Optimization. Molecules 2015; 20:10342-59. [PMID: 26053489 PMCID: PMC6272715 DOI: 10.3390/molecules200610342] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 12/15/2022] Open
Abstract
In this work, the relationship between cyclophilin A (CypA) and HCV prompted us to screen a series of small molecule CypA inhibitors which were previously reported by our group. Among them, compound 1, discovered as a non-immunosuppressive anti-HCV agent with an EC50 value of 0.67 μM in a virus assay, was selected for further study. Subsequent chemical modification by O-acylation led to a novel class of molecules, among which compound 25 demonstrated the most potent anti-HCV activity in the virus assay (EC50 = 0.19 μM), but low cytotoxicity and hERG cardiac toxicity. The following studies (a solution stability assay and a simple pharmacokinetic test together with a CypA enzyme inhibition assay) preliminarily indicated that 25 was a prodrug of 1. To the best of our knowledge, 25 is probably the most potent currently reported small molecule anti-HCV agent acting via the CypA inhibitory mechanism. Consequently, our study has provided a new potential small molecule for curing HCV infection.
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Affiliation(s)
- Wenzhong Yan
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.
| | - Jie Qing
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China.
- School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Hanbing Mei
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.
| | - Fei Mao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.
| | - Jin Huang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.
| | - Jin Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.
| | - Hualiang Jiang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China.
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China.
| | - Linqi Zhang
- School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Jian Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.
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Mutahir S, Yar M, Khan MA, Ullah N, Shahzad SA, Khan IU, Mehmood RA, Ashraf M, Nasar R, Pontiki E. Synthesis, characterization, lipoxygenase inhibitory activity and in silico molecular docking of biaryl bis(benzenesulfonamide) and indol-3-yl-hydrazide derivatives. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2014. [DOI: 10.1007/s13738-014-0573-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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14
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Tang Y, Zhu W, Chen K, Jiang H. New technologies in computer-aided drug design: Toward target identification and new chemical entity discovery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2014; 3:307-13. [PMID: 24980533 PMCID: PMC7185835 DOI: 10.1016/j.ddtec.2006.09.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In the postgenomic era, computer-aided drug design (CADD) has considerably extended its range of applications, spanning almost all stages in the drug discovery pipeline, from target identification to lead discovery, from lead optimization to preclinical or clinical trials. Two new technologies of CADD associated with target identification and new chemical entity discovery will be the focus of this review. Li-he Zhang – School of Pharmaceutical Science, Peking University, Beijing, China Kaixian Chen – Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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Affiliation(s)
- Yun Tang
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Weiliang Zhu
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Kaixian Chen
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
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15
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Okawara T, Islam R, Imran Hossain M, Okamoto Y, Nagamatsu T, Anraku K. Facile Synthesis of 2-Phenylquinoline-4-carboxamide Derivatives with Variant Structural Features. HETEROCYCLES 2014. [DOI: 10.3987/com-14-12939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Peel M, Scribner A. Optimization of Cyclophilin Inhibitors for Use in Antiviral Therapy. SUCCESSFUL STRATEGIES FOR THE DISCOVERY OF ANTIVIRAL DRUGS 2013. [DOI: 10.1039/9781849737814-00384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Cyclophilins are members of the Propyl Peptidase Isomerase (PPIase) family of proteins and have recently been found to be required for efficient replication and/or infectivity of several viruses. Cyclosporine A (CsA), the prototypical inhibitor of cyclophilins has shown good activity against several key viruses, including HIV‐1 and HCV, however the immunosuppressive activity of CsA precludes its use as an effective anti‐viral agent. Structural information derived from the ternary complex formed by CsA, cyclophilin A and calcineurin has allowed the design of non‐immunosuppressive derivatives of CsA that retain, and in some cases improve, antiviral activity toward hepatitis C. Chemical modification of CsA has led to compounds with improved pharmacokinetic properties and with reduced drug‐drug interaction potential. Non‐CsA derived inhibitors of cyclophilin A have recently been identified and hold promise as synthetically more tractable leads for cyclophilin‐based discovery projects.
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Affiliation(s)
- Michael Peel
- SCYNEXIS Inc., Research Triangle Park, NC 27709 USA
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17
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Ou-Yang SS, Lu JY, Kong XQ, Liang ZJ, Luo C, Jiang H. Computational drug discovery. Acta Pharmacol Sin 2012; 33:1131-40. [PMID: 22922346 PMCID: PMC4003107 DOI: 10.1038/aps.2012.109] [Citation(s) in RCA: 164] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 07/08/2012] [Indexed: 01/09/2023] Open
Abstract
Computational drug discovery is an effective strategy for accelerating and economizing drug discovery and development process. Because of the dramatic increase in the availability of biological macromolecule and small molecule information, the applicability of computational drug discovery has been extended and broadly applied to nearly every stage in the drug discovery and development workflow, including target identification and validation, lead discovery and optimization and preclinical tests. Over the past decades, computational drug discovery methods such as molecular docking, pharmacophore modeling and mapping, de novo design, molecular similarity calculation and sequence-based virtual screening have been greatly improved. In this review, we present an overview of these important computational methods, platforms and successful applications in this field.
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Affiliation(s)
- Si-sheng Ou-Yang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jun-yan Lu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiang-qian Kong
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhong-jie Liang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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18
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Acevedo O, Ambrose Z, Flaherty PT, Aamer H, Jain P, Sambasivarao SV. Identification of HIV inhibitors guided by free energy perturbation calculations. Curr Pharm Des 2012; 18:1199-216. [PMID: 22316150 DOI: 10.2174/138161212799436421] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 12/06/2011] [Indexed: 01/14/2023]
Abstract
Free energy perturbation (FEP) theory coupled to molecular dynamics (MD) or Monte Carlo (MC) statistical mechanics offers a theoretically precise method for determining the free energy differences of related biological inhibitors. Traditionally requiring extensive computational resources and expertise, it is only recently that its impact is being felt in drug discovery. A review of computer-aided anti-HIV efforts employing FEP calculations is provided here that describes early and recent successes in the design of human immunodeficiency virus type 1 (HIV-1) protease and non-nucleoside reverse transcriptase inhibitors. In addition, our ongoing work developing and optimizing leads for small molecule inhibitors of cyclophilin A (CypA) is highlighted as an update on the current capabilities of the field. CypA has been shown to aid HIV-1 replication by catalyzing the cis/trans isomerization of a conserved Gly-Pro motif in the Nterminal domain of HIV-1 capsid (CA) protein. In the absence of a functional CypA, e.g., by the addition of an inhibitor such as cyclosporine A (CsA), HIV-1 has reduced infectivity. Our simulations of acylurea-based and 1-indanylketone-based CypA inhibitors have determined that their nanomolar and micromolar binding affinities, respectively, are tied to their ability to stabilize Arg55 and Asn102. A structurally novel 1-(2,6-dichlorobenzamido) indole core was proposed to maximize these interactions. FEP-guided optimization, experimental synthesis, and biological testing of lead compounds for toxicity and inhibition of wild-type HIV-1 and CA mutants have demonstrated a dose-dependent inhibition of HIV-1 infection in two cell lines. While the inhibition is modest compared to CsA, the results are encouraging.
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Affiliation(s)
- Orlando Acevedo
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA.
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19
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Merdanovic M, Clausen T, Kaiser M, Huber R, Ehrmann M. Protein quality control in the bacterial periplasm. Annu Rev Microbiol 2012; 65:149-68. [PMID: 21639788 DOI: 10.1146/annurev-micro-090110-102925] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein quality control involves sensing and treatment of defective or incomplete protein structures. Misfolded or mislocalized proteins trigger dedicated signal transduction cascades that upregulate the production of protein quality-control factors. Corresponding proteases and chaperones either degrade or repair damaged proteins, thereby reducing the level of aggregation-prone molecules. Because the periplasm of gram-negative bacteria is particularly exposed to environmental changes and respective protein-folding stresses connected with the presence of detergents, low or high osmolarity of the medium, elevated temperatures, and the host's immune response, fine-tuned protein quality control systems are essential for survival under these unfavorable conditions. This review discusses recent advances in the identification and characterization of the key cellular factors and the emerging general principles of the underlying molecular mechanisms.
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Affiliation(s)
- Melisa Merdanovic
- Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, 45117 Essen, Germany.
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20
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Xu B, Ding J, Chen KX, Miao ZH, Huang H, Liu H, Luo XM. Advances in Cancer Chemotherapeutic Drug Research in China. RECENT ADVANCES IN CANCER RESEARCH AND THERAPY 2012. [PMCID: PMC7158183 DOI: 10.1016/b978-0-12-397833-2.00012-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Bin Xu
- Corresponding author: Bin Xu, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zi Road, Shanghai 201203, People’s Republic of China. Tel: O21-54920515 (o), 13501793936 (mobile), Fax: 021-54920568, e-mail:
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21
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Zhang YL, Zhang J, Jiang N, Lu YH, Wang L, Xu SH, Wang W, Zhang GF, Xu Q, Ge HM, Ma J, Song YC, Tan RX. Immunosuppressive polyketides from mantis-associated Daldinia eschscholzii. J Am Chem Soc 2011; 133:5931-40. [PMID: 21434637 DOI: 10.1021/ja110932p] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Polyketides with unknown architectures are highly desired for the discovery of new drugs and agrochemicals. Here, the mantis-associated Daldinia eschscholzii, a fungus known to produce immunosuppressants dalesconols A and B, was found to simultaneously generate four novel skeletons capable of shaping the unusual chemistry of the fungal polyketides, of which seven were structurally unique and substantially immunosuppressive. In particular, the scaled-up fermentation of the microbe enabled the structural characterization of minor or "transitional" intermediate polyketides that allowed the reasonable recognition of the four biosynthetic pathways initiated by condensations of four, five, six and eight acetate units, respectively. Furthermore, the decarbonylation reaction of triketone, as in the case of daeschol A, was described for the first time, in addition to the structural correction of sporothrin C and nodulone. The work provided a set of novel immunosuppressive molecules that are of significance to drug discovery.
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Affiliation(s)
- Ying L Zhang
- Institute of Functional Biomolecules, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, PR China
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22
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Chen K, Tan Z, He M, Li J, Tang S, Hewlett I, Yu F, Jin Y, Yang M. Structure-Activity Relationships (SAR) Research of Thiourea Derivatives as Dual Inhibitors Targeting both HIV-1 Capsid and Human Cyclophilin A. Chem Biol Drug Des 2010; 76:25-33. [DOI: 10.1111/j.1747-0285.2010.00981.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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23
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Screening and evaluation of thiourea derivatives for their HIV capsid and human cyclophilin A inhibitory activity. Med Chem Res 2010. [DOI: 10.1007/s00044-010-9315-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Wang S, Yan J, Wang X, Yang Z, Lin F, Zhang T. Synthesis and evaluation of the alpha-glucosidase inhibitory activity of 3-[4-(phenylsulfonamido)benzoyl]-2H-1-benzopyran-2-one derivatives. Eur J Med Chem 2009; 45:1250-5. [PMID: 20045223 DOI: 10.1016/j.ejmech.2009.12.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2009] [Revised: 12/08/2009] [Accepted: 12/12/2009] [Indexed: 10/20/2022]
Abstract
In the course of studies directed toward the discovery of novel non-sugar alpha-glucosidase inhibitors for the treatment of diabetes, a series of 3-[4-(phenylsulfonamido)benzoyl]-2H-1-benzopyran-2-one derivatives was synthesized and evaluated as alpha-glucosidase inhibitors. Most compounds showed good inhibitory activity with IC(50) values ranging from 0.0645 microM to 26.746 microM. 7-Hydroxy-6-methoxy-3-[4-(4-methylphenylsulfonamido)benzoyl]-2H-1-benzopyran-2-one 7u manifested the most potent inhibitory activity with an IC(50) value of 0.0645 microM.
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Affiliation(s)
- Shaojie Wang
- Key Laboratory of New Drugs Design and Discovery of Liaoning Province, Shenyang Pharmaceutical University, 103 Culture Road, Shenhe District, Shenyang 110016, China.
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Ni S, Yuan Y, Huang J, Mao X, Lv M, Zhu J, Shen X, Pei J, Lai L, Jiang H, Li J. Discovering potent small molecule inhibitors of cyclophilin A using de novo drug design approach. J Med Chem 2009; 52:5295-8. [PMID: 19691347 DOI: 10.1021/jm9008295] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
This work describes an integrated approach of de novo drug design, chemical synthesis, and bioassay for quick identification of a series of novel small molecule cyclophilin A (CypA) inhibitors (1-3). The activities of the two most potent CypA inhibitors (3h and 3i) are 2.59 and 1.52 nM, respectively, which are about 16 and 27 times more potent than that of cyclosporin A. This study clearly demonstrates the power of our de novo drug design strategy and the related program LigBuilder 2.0 in drug discovery.
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Affiliation(s)
- Shuaishuai Ni
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
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26
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Li J, Tan Z, Tang S, Hewlett I, Pang R, He M, He S, Tian B, Chen K, Yang M. Discovery of dual inhibitors targeting both HIV-1 capsid and human cyclophilin A to inhibit the assembly and uncoating of the viral capsid. Bioorg Med Chem 2009; 17:3177-88. [PMID: 19328002 DOI: 10.1016/j.bmc.2009.02.051] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 02/19/2009] [Accepted: 02/21/2009] [Indexed: 12/21/2022]
Abstract
HIV-1 assembly and disassembly (uncoating) processes are critical for the HIV-1 replication. HIV-1 capsid (CA) and human cyclophilin A (CypA) play essential roles in these processes. We designed and synthesized a series of thiourea compounds as HIV-1 assembly and disassembly dual inhibitors targeting both HIV-1 CA protein and human CypA. The SIV-induced syncytium antiviral evaluation indicated that all of the inhibitors displayed antiviral activities in SIV-infected CEM cells at the concentration of 0.6-15.8 microM for 50% of maximum effective rate. Their abilities to bind CA and CypA were determined by ultraviolet spectroscopic analysis, fluorescence binding affinity and PPIase inhibition assay. Assembly studies in vitro demonstrated that the compounds could potently disrupt CA assembly with a dose-dependent manner. All of these molecules could bind CypA with binding affinities (Kd values) of 51.0-512.8 microM. Fifteen of the CypA binding compounds showed potent PPIase inhibitory activities (IC(50) values<1 microM) while they could not bind either to HIV-1 Protease or to HIV-1 Integrase in the enzyme assays. These results suggested that 15 compounds could block HIV-1 replication by inhibiting the PPIase activity of CypA to interfere with capsid disassembly and disrupting CA assembly.
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Affiliation(s)
- Jiebo Li
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, PO Box 261, Beijing 100191, China
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Fan F, Zhu J, Ni S, Cheng J, Tang Y, Kang C, Li J, Jiang H. Refinement and 3D-QSAR Studies of Inhibitors of Cyclophilin A Containing Amide Linker. QSAR & COMBINATORIAL SCIENCE 2009; 28:183-193. [PMID: 32327951 PMCID: PMC7168557 DOI: 10.1002/qsar.200860076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Revised: 09/27/2008] [Accepted: 10/02/2008] [Indexed: 11/07/2022]
Abstract
Cyclophilin A (CypA) is a ubiquitous cellular enzyme playing essential role in many biological processes, and the discovery of CypA inhibitor is now of special interest in the treatment of immunological disorders. In this work, molecular modeling studies were performed to develop a predictive Common Pharmacophore Hypothesis (CPH) and use it for alignment in 3D-QSAR studies using CoMFA and CoMSIA. A total of 30 compounds containing an amide fragment as the key linker, consisting of 17 of our previously discovered CypA inhibitors and 13 other inhibitors reported in the literature, were selected for pharmacophore refinement and 3D-QSAR studies. The best pharmacophore hypothesis AADR, which had two hydrogen bond acceptors, a hydrogen bond donor, and an aromatic ring, was obtained and used for the alignment of molecules in CoMFA and CoMSIA model development. The models showed a good r 2 value of 0.992 and 0.949 for CoMFA and CoMSIA, respectively. The contour maps of the models were analyzed to give structural insight for activity improvement of future novel CypA inhibitors. The CPH can also provide a powerful template for virtual screening and design of new CypA inhibitors.
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Affiliation(s)
- Feng Fan
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China, Tel.: +86‐21‐64252945
- Shanghai Key Laboratory of Chemical Biology, East China University of Science and Technology, PO Box 544, 130 Meilong Road, Shanghai 200237, China
| | - Jin Zhu
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China, Tel.: +86‐21‐64252945
| | - Shuaishuai Ni
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China, Tel.: +86‐21‐64252945
| | - Jiagao Cheng
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China, Tel.: +86‐21‐64252945
- Shanghai Key Laboratory of Chemical Biology, East China University of Science and Technology, PO Box 544, 130 Meilong Road, Shanghai 200237, China
| | - Yun Tang
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China, Tel.: +86‐21‐64252945
| | - Congmin Kang
- College of Chemical Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 260042, China
| | - Jian Li
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China, Tel.: +86‐21‐64252945
| | - Hualiang Jiang
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China, Tel.: +86‐21‐64252945
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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Lead Discovery Using Virtual Screening. TOPICS IN MEDICINAL CHEMISTRY 2009. [PMCID: PMC7176223 DOI: 10.1007/7355_2009_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The practice of virtual screening (VS) to identify chemical leads to known or novel targets is becoming a core function of the computational chemist within industry. By employing a range of techniques, when attempting to identify compounds with activity against a biological target, a small focused subset of a larger collection of compounds can be identified and tested, often with results much better than selecting a similar number of compounds at random. We will review the key methods available, their relative success, and provide practical insights into best practices and key gaps. We will also argue that the capability of VS methods has grown to a point where fuller integration with experimental methods, including HTS, could increase the effectiveness of both.
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Discovery of a novel CCR5 antagonist lead compound through fragment assembly. Molecules 2008; 13:2426-41. [PMID: 18830165 PMCID: PMC6245477 DOI: 10.3390/molecules13102426] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Revised: 09/18/2008] [Accepted: 09/18/2008] [Indexed: 11/21/2022] Open
Abstract
CCR5, as the major co-receptor for HIV-1 entry, is an attractive novel target for the pharmaceutical industry in the HIV-1 therapeutic area. In this study, based on the structures of maraviroc and 1,4-bis(4-(7-chloroquinolin-4-yl)piperazin-1-yl)butane-1,4- dione (1), which was identified using structure-based virtual screening in conjunction with a calcium mobilization assay, a series of novel small molecule CCR5 antagonists have been designed and synthesized through fragment assembly. Preliminary SARs were obtained, which are in good agreement with the molecular binding model and should prove helpful for future antagonist design. The novel scaffold presented here might also be useful in the development of maraviroc-derived second generation CCR5 antagonists.
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Deng G, Li W, Shen J, Jiang H, Chen K, Liu H. Pyrazolidine-3,5-dione derivatives as potent non-steroidal agonists of farnesoid X receptor: virtual screening, synthesis, and biological evaluation. Bioorg Med Chem Lett 2008; 18:5497-502. [PMID: 18815030 DOI: 10.1016/j.bmcl.2008.09.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Revised: 07/02/2008] [Accepted: 09/05/2008] [Indexed: 01/17/2023]
Abstract
The identification of a novel pyrazolidine-3,5-dione based scaffold hit compound as Farnesoid X receptor (FXR) partial or full agonist has been accomplished by means of virtual screening techniques. A series of pyrazolidine-3,5-dione derivatives (1a-u and 7) was designed, synthesized, and evaluated by a cell-based luciferase transactivation assay for their agonistic activities against FXR. Most of them showed agonistic potencies and 10 of them (1a, 1b, 1d-f, 1j, 1n, 1t, 5b, and 7) exhibited lower EC(50) values than the reference drug CDCA. Molecular modeling studies for the representative compounds 1a, 1d, 1f, 1j, 1n, 1u, 5b, and 7 were also presented. The novel structural scaffold has provided a new direction for finding potent and selective FXR partial and full agonists (referred to as 'selective bile acid receptor modulators', SBARMs).
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Affiliation(s)
- Guanghui Deng
- Drug Discovery and Design Centre, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Graduate School of the Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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Fraser HL, Hopper DW, Kutterer KM, Crombie AL. Chapter 6.1 Six-membered ring systems: pyridine and benzo derivatives. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s0959-6380(08)80014-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Chen S, Zhao X, Tan J, Lu H, Qi Z, Huang Q, Zeng X, Zhang M, Jiang S, Jiang H, Yu L. Structure-based identification of small molecule compounds targeting cell cyclophilin A with anti-HIV-1 activity. Eur J Pharmacol 2007; 565:54-9. [PMID: 17449029 PMCID: PMC3033441 DOI: 10.1016/j.ejphar.2007.03.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Revised: 03/02/2007] [Accepted: 03/06/2007] [Indexed: 10/23/2022]
Abstract
Cyclophilin A acts as protein folding chaperones and intracellular transports in many cellular processes. Previous studies have shown that cyclophilin A can interact with HIV-1 (human immunodeficiency virus type 1) gag protein and enhance viral infectivity. Many cyclophilin A inhibitors such as cyclosporin A can inhibit HIV-1 replication in vitro. Here, we report a structure-based identification of novel non-peptidic cyclophilin A inhibitors as anti-HIV lead compounds. Following a computer-aided virtual screening and subsequent surface plasmon resonance (SPR) analysis, 12 low molecular weight cyclophilin A ligands were selected for further evaluation of their in vitro inhibition of peptidyl-prolyl cis-trans isomerase (PPIase) activity of cyclophilin A and HIV-1 replication. Five of these compounds (FD5, FD8, FD9, FD10 and FD12) exhibited inhibition against both PPIase activity and HIV-1 infection. These active compounds will be used as leads for structure and activity relationship (SAR) and optimization studies in order to design more effective anti-HIV-1 therapeutics, and as probes for investigating the effect of cyclophilins on HIV-1 replication.
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Affiliation(s)
- Shuai Chen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, People’s Republic of China
| | - Xuemei Zhao
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, People’s Republic of China
| | - Jinzhi Tan
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Chinese Academy of Sciences, People's Republic of China
| | - Hong Lu
- Laboratory of Viral Immunology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10021, USA
| | - Zhi Qi
- Laboratory of Viral Immunology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10021, USA
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, People’s Republic of China
| | - Xianzhuo Zeng
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, People’s Republic of China
| | - Mingjun Zhang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, People’s Republic of China
| | - Shibo Jiang
- Laboratory of Viral Immunology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10021, USA
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Chinese Academy of Sciences, People's Republic of China
- Corresponding Authors: Long Yu; Phone: 86-21-65643954; Fax: 86-21-65643250; , Hualiang Jiang; Phone: 86-21-50806600, ext 1210; Fax: 86-21-50807088;
| | - Long Yu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, People’s Republic of China
- Corresponding Authors: Long Yu; Phone: 86-21-65643954; Fax: 86-21-65643250; , Hualiang Jiang; Phone: 86-21-50806600, ext 1210; Fax: 86-21-50807088;
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33
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Rich RL, Myszka DG. Survey of the year 2006 commercial optical biosensor literature. J Mol Recognit 2007; 20:300-66. [DOI: 10.1002/jmr.862] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Fara DC, Oprea TI, Prossnitz ER, Bologa CG, Edwards BS, Sklar LA. Integration of virtual and physical screening. DRUG DISCOVERY TODAY. TECHNOLOGIES 2006; 3:377-385. [PMID: 38620118 PMCID: PMC7105924 DOI: 10.1016/j.ddtec.2006.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
High-throughput screening (HTS) represents the dominant technique for the identification of new lead compounds in current drug discovery. It consists of physical screening (PS) of large libraries of chemicals against one or more specific biological targets. Virtual screening (VS) is a strategy for in silico evaluation of chemical libraries for a given target, and can be integrated to focus the PS process. The present work addresses the integration of both PS and VS, respectively.
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Affiliation(s)
- Dan C. Fara
- Department of Biochemistry and Molecular Biology, Division of Biocomputing, University of New Mexico, Health Sciences Center, Albuquerque, NM 87131, USA
| | - Tudor I. Oprea
- Department of Biochemistry and Molecular Biology, Division of Biocomputing, University of New Mexico, Health Sciences Center, Albuquerque, NM 87131, USA
| | - Eric R. Prossnitz
- Department of Cell Biology and Physiology, University of New Mexico, Health Sciences Center, Albuquerque, NM 87131, USA
| | - Cristian G. Bologa
- Department of Biochemistry and Molecular Biology, Division of Biocomputing, University of New Mexico, Health Sciences Center, Albuquerque, NM 87131, USA
| | - Bruce S. Edwards
- Cancer Research and Treatment Center and Department of Pathology, University of New Mexico, Health Sciences Center, Albuquerque, NM 87131, USA
| | - Larry A. Sklar
- Cancer Research and Treatment Center and Department of Pathology, University of New Mexico, Health Sciences Center, Albuquerque, NM 87131, USA
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Li J, Tan JZ, Chen LL, Zhang J, Shen X, Mei CL, Fu LL, Lin LP, Ding J, Xiong B, Xiong XS, Liu H, Luo XM, Jiang HL. Design, synthesis and antitumor evaluation of a new series of N-substituted-thiourea derivatives. Acta Pharmacol Sin 2006; 27:1259-71. [PMID: 16923349 DOI: 10.1111/j.1745-7254.2006.00437.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
AIM To design and synthesize a novel class of protein tyrosine kinase inhibitors, featuring the N-(2-oxo-1,2-dihydroquinolin-3-yl-methyl)-thiourea framework. METHODS First, compounds 1 and 2 were identified using the virtual screening approach in conjunction with binding assay based on surface plasmon resonance. Subsequently, 3 regions of compounds 1 and 2 were selected for chemical modification. All compounds were characterized potent inhibitory activities toward the human lung adenocarcinoma cell line SPAC1. RESULTS Forty new compounds (1-2, 3a-g, 4a-w, and 5a-l) were designed, synthesized and bioassayed. Six compounds (1, 3e, 4l, 4w, 5a, and 5b) were found to show promising inhibitory activity against the SPAC1 tumor cell line. The inhibitory activity of compound 5a increases approximately 10 times more than that of the original compound 1. CONCLUSION This study provides a promising new template with potential antitumor activity.
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Affiliation(s)
- Jian Li
- Drug Discovery and Design Centre, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China
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