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Han D, Zhao F, Chen Y, Xue Y, Bao K, Chang Y, Lu J, Wang M, Liu T, Gao Q, Cui W, Xu Y. Distinct Characteristic Binding Modes of Benzofuran Core Inhibitors to Diverse Genotypes of Hepatitis C Virus NS5B Polymerase: A Molecular Simulation Study. Int J Mol Sci 2024; 25:8028. [PMID: 39125602 PMCID: PMC11311972 DOI: 10.3390/ijms25158028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024] Open
Abstract
The benzofuran core inhibitors HCV-796, BMS-929075, MK-8876, compound 2, and compound 9B exhibit good pan-genotypic activity against various genotypes of NS5B polymerase. To elucidate their mechanism of action, multiple molecular simulation methods were used to investigate the complex systems of these inhibitors binding to GT1a, 1b, 2a, and 2b NS5B polymerases. The calculation results indicated that these five inhibitors can not only interact with the residues in the palm II subdomain of NS5B polymerase, but also with the residues in the palm I subdomain or the palm I/III overlap region. Interestingly, the binding of inhibitors with longer substituents at the C5 position (BMS-929075, MK-8876, compound 2, and compound 9B) to the GT1a and 2b NS5B polymerases exhibits different binding patterns compared to the binding to the GT1b and 2a NS5B polymerases. The interactions between the para-fluorophenyl groups at the C2 positions of the inhibitors and the residues at the binding pockets, together with the interactions between the substituents at the C5 positions and the residues at the reverse β-fold (residues 441-456), play a key role in recognition and the induction of the binding. The relevant studies could provide valuable information for further research and development of novel anti-HCV benzofuran core pan-genotypic inhibitors.
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Affiliation(s)
- Di Han
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Fang Zhao
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Yifan Chen
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Yiwei Xue
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Ke Bao
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Yuxiao Chang
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Jiarui Lu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Meiting Wang
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Taigang Liu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
| | - Qinghe Gao
- School of Pharmacy, Xinxiang Medical University, Xinxiang 453003, China;
| | - Wei Cui
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China;
| | - Yongtao Xu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China; (F.Z.); (Y.C.); (Y.X.); (K.B.); (Y.C.); (J.L.); (M.W.); (T.L.)
- Henan International Joint Laboratory of Neural Information Analysis and Drug Intelligent Design, Xinxiang 453003, China
- Xinxiang Key Laboratory of Biomedical Information Research, Xinxiang 453003, China
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2
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Ahmad G, Sohail M, Bilal M, Rasool N, Qamar MU, Ciurea C, Marceanu LG, Misarca C. N-Heterocycles as Promising Antiviral Agents: A Comprehensive Overview. Molecules 2024; 29:2232. [PMID: 38792094 PMCID: PMC11123935 DOI: 10.3390/molecules29102232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/22/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
Viruses are a real threat to every organism at any stage of life leading to extensive infections and casualties. N-heterocycles can affect the viral life cycle at many points, including viral entrance into host cells, viral genome replication, and the production of novel viral species. Certain N-heterocycles can also stimulate the host's immune system, producing antiviral cytokines and chemokines that can stop the reproduction of viruses. This review focused on recent five- or six-membered synthetic N-heterocyclic molecules showing antiviral activity through SAR analyses. The review will assist in identifying robust scaffolds that might be utilized to create effective antiviral drugs with either no or few side effects.
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Affiliation(s)
- Gulraiz Ahmad
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan; (G.A.); (M.S.)
| | - Maria Sohail
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan; (G.A.); (M.S.)
| | - Muhammad Bilal
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China;
| | - Nasir Rasool
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan; (G.A.); (M.S.)
| | - Muhammad Usman Qamar
- Institute of Microbiology, Faculty of Life Sciences, Government College University, Faisalabad 38000, Pakistan;
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
- Department of Microbiology and Molecular Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Codrut Ciurea
- Faculty of Medicine, Transilvania University of Brasov, 500036 Brasov, Romania; (L.G.M.)
| | - Luigi Geo Marceanu
- Faculty of Medicine, Transilvania University of Brasov, 500036 Brasov, Romania; (L.G.M.)
| | - Catalin Misarca
- Faculty of Medicine, Transilvania University of Brasov, 500036 Brasov, Romania; (L.G.M.)
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3
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Recent Advances in the Synthesis of C2‐Functionalized Pyridines and Quinolines Using
N
‐Oxide Chemistry. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000910] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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4
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Wang D, Huang M, Li G, Zheng S, Yu P. Scalable synthesis of a tetrasubstituted 7-azabenzofuran as a key intermediate for a class of potent HCV NS5B inhibitors. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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5
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O’Byrne SN, Eduful BJ, Willson TM, Drewry DH. Concise, gram-scale synthesis of furo[2,3- b]pyridines with functional handles for chemoselective cross-coupling. Tetrahedron Lett 2020; 61:152353. [PMID: 33012852 PMCID: PMC7526865 DOI: 10.1016/j.tetlet.2020.152353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A concise 4-step synthesis of furo[2,3-b]pyridines, with handles in the 3- and 5-positions for palladium mediated cross-coupling reactions, is described. The synthetic route has been optimized, with only one step requiring purification by column chromatography. The route is amenable to scale-up, and was successfully executed on a multi-gram scale. Furopyridines are of growing interest in medicinal chemistry, and this route should enable easy access to the core for structure-activity relationship (SAR) studies.
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Affiliation(s)
- Sean N. O’Byrne
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Benjamin J. Eduful
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Timothy M. Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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6
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Fu C, Li G, Shen M, Zhang L, Yu P, Wang D. Facile and Efficient Synthesis of Tri‐ and Tetrasubstituted 7‐Azabenzofuran Derivatives. ASIAN J ORG CHEM 2020. [DOI: 10.1002/ajoc.202000131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Chunsheng Fu
- Shanxi Biological Institute Co. Ltd No. 50, Shifan Street, Xiaodian District Taiyuan Shanxi 030006 China
| | - Gaoyu Li
- College of BiotechnologyTianjin University of Science and Technology No. 29, 13th Avenue, TEDA Tianjin 300457 China
| | - Meng Shen
- College of BiotechnologyTianjin University of Science and Technology No. 29, 13th Avenue, TEDA Tianjin 300457 China
| | - Longxia Zhang
- Shanxi Biological Institute Co. Ltd No. 50, Shifan Street, Xiaodian District Taiyuan Shanxi 030006 China
| | - Peng Yu
- College of BiotechnologyTianjin University of Science and Technology No. 29, 13th Avenue, TEDA Tianjin 300457 China
| | - Dong Wang
- College of BiotechnologyTianjin University of Science and Technology No. 29, 13th Avenue, TEDA Tianjin 300457 China
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7
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Yeung KS, Beno BR, Mosure K, Zhu J, Grant-Young KA, Parcella K, Anjanappa P, Bora RO, Selvakumar K, Wang YK, Fang H, Krause R, Rigat K, Liu M, Lemm J, Sheriff S, Witmer M, Tredup J, Jardel A, Kish K, Parker D, Haskell R, Santone K, Meanwell NA, Soars MG, Roberts SB, Kadow JF. Structure-Property Basis for Solving Transporter-Mediated Efflux and Pan-Genotypic Inhibition in HCV NS5B Inhibitors. ACS Med Chem Lett 2018; 9:1217-1222. [PMID: 30613329 DOI: 10.1021/acsmedchemlett.8b00379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/05/2018] [Indexed: 01/07/2023] Open
Abstract
In solving the P-gp and BCRP transporter-mediated efflux issue in a series of benzofuran-derived pan-genotypic palm site inhibitors of the hepatitis C virus NS5B replicase, it was found that close attention to physicochemical properties was essential. In these compounds, where both molecular weight (MW >579) and TPSA (>110 Å2) were high, attenuation of polar surface area together with weakening of hydrogen bond acceptor strength of the molecule provided a higher intrinsic membrane permeability and more desirable Caco-2 parameters, as demonstrated by trifluoroacetamide 11 and the benchmark N-ethylamino analog 12. In addition, the tendency of these inhibitors to form intramolecular hydrogen bonds potentially contributes favorably to the improved membrane permeability and absorption. The functional group minimization that resolved the efflux problem simultaneously maintained potent inhibitory activity toward a gt-2 HCV replicon due to a switching of the role of substituents in interacting with the Gln414 binding pocket, as observed in gt-2a NS5B/inhibitor complex cocrystal structures, thus increasing the efficiency of the optimization. Noteworthy, a novel intermolecular S=O···C=O n → π* type interaction between the ligand sulfonamide oxygen atom and the carbonyl moiety of the side chain of Gln414 was observed. The insights from these structure-property studies and crystallography information provided a direction for optimization in a campaign to identify second generation pan-genotypic NS5B inhibitors.
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Affiliation(s)
- Kap-Sun Yeung
- Bristol-Myers Squibb Research and Development, P.O.
Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Brett R. Beno
- Bristol-Myers Squibb Research and Development, P.O.
Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Kathy Mosure
- Bristol-Myers Squibb Research and Development, P.O.
Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Juliang Zhu
- Bristol-Myers Squibb Research and Development, P.O.
Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Katherine A. Grant-Young
- Bristol-Myers Squibb Research and Development, P.O.
Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Kyle Parcella
- Bristol-Myers Squibb Research and Development, P.O.
Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Prakash Anjanappa
- Department of Discovery Chemistry, Biocon Bristol-Myers Squibb Research and Development Center, Biocon Park, Jigani Link Road, Bommasandra IV, Bangalore 560099, India
| | - Rajesh Onkardas Bora
- Department of Discovery Chemistry, Biocon Bristol-Myers Squibb Research and Development Center, Biocon Park, Jigani Link Road, Bommasandra IV, Bangalore 560099, India
| | - Kumaravel Selvakumar
- Department of Discovery Chemistry, Biocon Bristol-Myers Squibb Research and Development Center, Biocon Park, Jigani Link Road, Bommasandra IV, Bangalore 560099, India
| | - Ying-Kai Wang
- Bristol-Myers Squibb Research and Development, P.O.
Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Hua Fang
- Bristol-Myers Squibb Research and Development, P.O.
Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Rudolph Krause
- Bristol-Myers Squibb Research and Development, P.O.
Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Karen Rigat
- Bristol-Myers Squibb Research and Development, P.O.
Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Mengping Liu
- Bristol-Myers Squibb Research and Development, P.O.
Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Julie Lemm
- Bristol-Myers Squibb Research and Development, P.O.
Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Steven Sheriff
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Mark Witmer
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Jeffrey Tredup
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Adam Jardel
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Kevin Kish
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Dawn Parker
- Bristol-Myers Squibb Research and Development, P.O.
Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Roy Haskell
- Bristol-Myers Squibb Research and Development, P.O.
Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Kenneth Santone
- Bristol-Myers Squibb Research and Development, P.O.
Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Nicholas A. Meanwell
- Bristol-Myers Squibb Research and Development, P.O.
Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Matthew G. Soars
- Bristol-Myers Squibb Research and Development, P.O.
Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Susan B. Roberts
- Bristol-Myers Squibb Research and Development, P.O.
Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - John F. Kadow
- Bristol-Myers Squibb Research and Development, P.O.
Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
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8
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Ashraf MU, Iman K, Khalid MF, Salman HM, Shafi T, Rafi M, Javaid N, Hussain R, Ahmad F, Shahzad-Ul-Hussan S, Mirza S, Shafiq M, Afzal S, Hamera S, Anwar S, Qazi R, Idrees M, Qureshi SA, Chaudhary SU. Evolution of efficacious pangenotypic hepatitis C virus therapies. Med Res Rev 2018; 39:1091-1136. [PMID: 30506705 DOI: 10.1002/med.21554] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 10/11/2018] [Accepted: 10/11/2018] [Indexed: 12/12/2022]
Abstract
Hepatitis C compromises the quality of life of more than 350 million individuals worldwide. Over the last decade, therapeutic regimens for treating hepatitis C virus (HCV) infections have undergone rapid advancements. Initially, structure-based drug design was used to develop molecules that inhibit viral enzymes. Subsequently, establishment of cell-based replicon systems enabled investigations into various stages of HCV life cycle including its entry, replication, translation, and assembly, as well as role of host proteins. Collectively, these approaches have facilitated identification of important molecules that are deemed essential for HCV life cycle. The expanded set of putative virus and host-encoded targets has brought us one step closer to developing robust strategies for efficacious, pangenotypic, and well-tolerated medicines against HCV. Herein, we provide an overview of the development of various classes of virus and host-directed therapies that are currently in use along with others that are undergoing clinical evaluation.
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Affiliation(s)
- Muhammad Usman Ashraf
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.,Virology Laboratory, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Kanzal Iman
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Farhan Khalid
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.,Department of Biomedical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Hafiz Muhammad Salman
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.,Plant Biotechnology Laboratory, Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Talha Shafi
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Momal Rafi
- Department of Statistics, University of Gujrat, Gujrat, Pakistan
| | - Nida Javaid
- Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Rashid Hussain
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Fayyaz Ahmad
- Department of Statistics, University of Gujrat, Gujrat, Pakistan
| | | | - Shaper Mirza
- Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Shafiq
- Plant Biotechnology Laboratory, Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Samia Afzal
- Virology Laboratory, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Sadia Hamera
- Department of Plant Genetics, Institute of Life Sciences, University of Rostock, Germany
| | - Saima Anwar
- Department of Biomedical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Romena Qazi
- Department of Pathology, Shaukat Khanum Memorial Cancer Hospital & Research Centre, Lahore, Pakistan
| | - Muhammad Idrees
- Virology Laboratory, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.,Hazara University, Mansehra, Pakistan
| | - Sohail A Qureshi
- Institute of Integrative Biosciences, CECOS-University of Information Technology and Emerging Sciences, Peshawar, Pakistan
| | - Safee Ullah Chaudhary
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
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9
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Recent advance in oxazole-based medicinal chemistry. Eur J Med Chem 2018; 144:444-492. [DOI: 10.1016/j.ejmech.2017.12.044] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/04/2017] [Accepted: 12/13/2017] [Indexed: 01/09/2023]
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10
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Zhuo X, Wang YZ, Yeung KS, Zhu J, Huang XS, Parcella KE, Eastman KJ, Kadow JF, Meanwell NA, Shu YZ, Johnson BM. Bioactivation of cyclopropyl rings by P450: an observation encountered during the optimisation of a series of hepatitis C virus NS5B inhibitors. Xenobiotica 2017; 48:1215-1226. [PMID: 29182424 DOI: 10.1080/00498254.2017.1409915] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
1. Due to its unique C-C and C-H bonding properties, conformational preferences and relative hydrophilicity, the cyclopropyl ring has been used as a synthetic building block in drug discovery to modulate potency and drug-like properties. During an effort to discover inhibitors of the hepatitis C virus non-structural protein 5B with improved potency and genotype-coverage profiles, the use of a pyrimidinylcyclopropylbenzamide moiety linked to a C6-substituted benzofuran or azabenzofuran core scaffold was explored in an effort to balance antiviral potency and metabolic stability. 2. In vitro metabolism studies of two compounds from this C6-substituted series revealed an NADPH-dependent bioactivation pathway leading to the formation of multiple glutathione (GSH) conjugates. Analysis of these conjugates by LC-MS and NMR demonstrated that the cyclopropyl group was the site of bioactivation. Based on the putative structures and molecular weights of the cyclopropyl-GSH conjugates, a multi-step mechanism was proposed to explain the formation of these metabolites by P450. This mechanism involves hydrogen atom abstraction to form a cyclopropyl radical, followed by a ring opening rearrangement and reaction with GSH. 3. These findings provided important information to the medicinal chemistry team which responded by replacing the cyclopropyl ring with a gem-dimethyl group. Subsequent compounds bearing this feature were shown to avert the bioactivation pathways in question.
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Affiliation(s)
- Xiaoliang Zhuo
- a Departments of Pharmaceutical Candidate Optimisation , Bristol-Myers Squibb Research and Development , Wallingford , CT , USA and
| | - Ying-Zi Wang
- a Departments of Pharmaceutical Candidate Optimisation , Bristol-Myers Squibb Research and Development , Wallingford , CT , USA and
| | - Kap-Sun Yeung
- b Discovery Chemistry and Molecular Technologies , Bristol-Myers Squibb Research and Development , Wallingford , CT , USA
| | - Juliang Zhu
- b Discovery Chemistry and Molecular Technologies , Bristol-Myers Squibb Research and Development , Wallingford , CT , USA
| | - Xiaohua Stella Huang
- a Departments of Pharmaceutical Candidate Optimisation , Bristol-Myers Squibb Research and Development , Wallingford , CT , USA and
| | - Kyle E Parcella
- b Discovery Chemistry and Molecular Technologies , Bristol-Myers Squibb Research and Development , Wallingford , CT , USA
| | - Kyle J Eastman
- b Discovery Chemistry and Molecular Technologies , Bristol-Myers Squibb Research and Development , Wallingford , CT , USA
| | - John F Kadow
- b Discovery Chemistry and Molecular Technologies , Bristol-Myers Squibb Research and Development , Wallingford , CT , USA
| | - Nicholas A Meanwell
- b Discovery Chemistry and Molecular Technologies , Bristol-Myers Squibb Research and Development , Wallingford , CT , USA
| | - Yue-Zhong Shu
- a Departments of Pharmaceutical Candidate Optimisation , Bristol-Myers Squibb Research and Development , Wallingford , CT , USA and
| | - Benjamin M Johnson
- a Departments of Pharmaceutical Candidate Optimisation , Bristol-Myers Squibb Research and Development , Wallingford , CT , USA and
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11
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Bessa LM, Launay H, Dujardin M, Cantrelle FX, Lippens G, Landrieu I, Schneider R, Hanoulle X. NMR reveals the intrinsically disordered domain 2 of NS5A protein as an allosteric regulator of the hepatitis C virus RNA polymerase NS5B. J Biol Chem 2017; 292:18024-18043. [PMID: 28912275 DOI: 10.1074/jbc.m117.813766] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/06/2017] [Indexed: 12/13/2022] Open
Abstract
Non-structural protein 5B (NS5B) is the RNA-dependent RNA polymerase that catalyzes replication of the hepatitis C virus (HCV) RNA genome and therefore is central for its life cycle. NS5B interacts with the intrinsically disordered domain 2 of NS5A (NS5A-D2), another essential multifunctional HCV protein that is required for RNA replication. As a result, these two proteins represent important targets for anti-HCV chemotherapies. Despite this importance and the existence of NS5B crystal structures, our understanding of the conformational and dynamic behavior of NS5B in solution and its relationship with NS5A-D2 remains incomplete. To address these points, we report the first detailed NMR spectroscopic study of HCV NS5B lacking its membrane anchor (NS5BΔ21). Analysis of constructs with selective isotope labeling of the δ1 methyl groups of isoleucine side chains demonstrates that, in solution, NS5BΔ21 is highly dynamic but predominantly adopts a closed conformation. The addition of NS5A-D2 leads to spectral changes indicative of binding to both allosteric thumb sites I and II of NS5BΔ21 and induces long-range perturbations that affect the RNA-binding properties of the polymerase. We compared these modifications with the short- and long-range effects triggered in NS5BΔ21 upon binding of filibuvir, an allosteric inhibitor. We demonstrate that filibuvir-bound NS5BΔ21 is strongly impaired in the binding of both NS5A-D2 and RNA. NS5A-D2 induces conformational and functional perturbations in NS5B similar to those triggered by filibuvir. Thus, our work highlights NS5A-D2 as an allosteric regulator of the HCV polymerase and provides new insight into the dynamics of NS5B in solution.
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Affiliation(s)
- Luiza M Bessa
- From the University of Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France
| | - Hélène Launay
- From the University of Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France
| | - Marie Dujardin
- From the University of Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France
| | - François-Xavier Cantrelle
- From the University of Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France
| | - Guy Lippens
- From the University of Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France
| | - Isabelle Landrieu
- From the University of Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France
| | - Robert Schneider
- From the University of Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France
| | - Xavier Hanoulle
- From the University of Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, 59000 Lille, France
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12
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Parcella K, Eastman K, Yeung KS, Grant-Young KA, Zhu J, Wang T, Zhang Z, Yin Z, Parker D, Mosure K, Fang H, Wang YK, Lemm J, Zhuo X, Hanumegowda U, Liu M, Rigat K, Donoso M, Tuttle M, Zvyaga T, Haarhoff Z, Meanwell NA, Soars MG, Roberts SB, Kadow JF. Improving Metabolic Stability with Deuterium: The Discovery of BMT-052, a Pan-genotypic HCV NS5B Polymerase Inhibitor. ACS Med Chem Lett 2017; 8:771-774. [PMID: 28740615 DOI: 10.1021/acsmedchemlett.7b00211] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/29/2017] [Indexed: 12/31/2022] Open
Abstract
Iterative structure-activity analyses in a class of highly functionalized furo[2,3-b]pyridines led to the identification of the second generation pan-genotypic hepatitis C virus NS5B polymerase primer grip inhibitor BMT-052 (14), a potential clinical candidate. The key challenge of poor metabolic stability was overcome by strategic incorporation of deuterium at potential metabolic soft spots. The preclinical profile and status of BMT-052 (14) is described.
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Affiliation(s)
- Kyle Parcella
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Kyle Eastman
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Kap-Sun Yeung
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Katharine A. Grant-Young
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Juliang Zhu
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Tao Wang
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Zhongxing Zhang
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Zhiwei Yin
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Dawn Parker
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Kathy Mosure
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Hua Fang
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Ying-Kai Wang
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Julie Lemm
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Xiaoliang Zhuo
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Umesh Hanumegowda
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Mengping Liu
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Karen Rigat
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Maria Donoso
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Maria Tuttle
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Tatyana Zvyaga
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Zuzana Haarhoff
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Nicholas A. Meanwell
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Matthew G. Soars
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - Susan B. Roberts
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
| | - John F. Kadow
- Bristol-Myers Squibb Research and Development, 5 Research
Parkway, Wallingford, Connecticut 06492, United States
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13
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Yeung KS, Beno BR, Parcella K, Bender JA, Grant-Young KA, Nickel A, Gunaga P, Anjanappa P, Bora RO, Selvakumar K, Rigat K, Wang YK, Liu M, Lemm J, Mosure K, Sheriff S, Wan C, Witmer M, Kish K, Hanumegowda U, Zhuo X, Shu YZ, Parker D, Haskell R, Ng A, Gao Q, Colston E, Raybon J, Grasela DM, Santone K, Gao M, Meanwell NA, Sinz M, Soars MG, Knipe JO, Roberts SB, Kadow JF. Discovery of a Hepatitis C Virus NS5B Replicase Palm Site Allosteric Inhibitor (BMS-929075) Advanced to Phase 1 Clinical Studies. J Med Chem 2017; 60:4369-4385. [PMID: 28430437 DOI: 10.1021/acs.jmedchem.7b00328] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The hepatitis C virus (HCV) NS5B replicase is a prime target for the development of direct-acting antiviral drugs for the treatment of chronic HCV infection. Inspired by the overlay of bound structures of three structurally distinct NS5B palm site allosteric inhibitors, the high-throughput screening hit anthranilic acid 4, the known benzofuran analogue 5, and the benzothiadiazine derivative 6, an optimization process utilizing the simple benzofuran template 7 as a starting point for a fragment growing approach was pursued. A delicate balance of molecular properties achieved via disciplined lipophilicity changes was essential to achieve both high affinity binding and a stringent targeted absorption, distribution, metabolism, and excretion profile. These efforts led to the discovery of BMS-929075 (37), which maintained ligand efficiency relative to early leads, demonstrated efficacy in a triple combination regimen in HCV replicon cells, and exhibited consistently high oral bioavailability and pharmacokinetic parameters across preclinical animal species. The human PK properties from the Phase I clinical studies of 37 were better than anticipated and suggest promising potential for QD administration.
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Affiliation(s)
- Kap-Sun Yeung
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Brett R Beno
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Kyle Parcella
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - John A Bender
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Katherine A Grant-Young
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Andrew Nickel
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Prashantha Gunaga
- Department of Discovery Chemistry, Biocon Bristol-Myers Squibb Research and Development Center , Biocon Park, Jigani Link Road, Bommasandra IV, Bangalore 560099, India
| | - Prakash Anjanappa
- Department of Discovery Chemistry, Biocon Bristol-Myers Squibb Research and Development Center , Biocon Park, Jigani Link Road, Bommasandra IV, Bangalore 560099, India
| | - Rajesh Onkardas Bora
- Department of Discovery Chemistry, Biocon Bristol-Myers Squibb Research and Development Center , Biocon Park, Jigani Link Road, Bommasandra IV, Bangalore 560099, India
| | - Kumaravel Selvakumar
- Department of Discovery Chemistry, Biocon Bristol-Myers Squibb Research and Development Center , Biocon Park, Jigani Link Road, Bommasandra IV, Bangalore 560099, India
| | - Karen Rigat
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Ying-Kai Wang
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Mengping Liu
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Julie Lemm
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Kathy Mosure
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Steven Sheriff
- Bristol-Myers Squibb Research and Development , P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Changhong Wan
- Bristol-Myers Squibb Research and Development , P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Mark Witmer
- Bristol-Myers Squibb Research and Development , P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Kevin Kish
- Bristol-Myers Squibb Research and Development , P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Umesh Hanumegowda
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Xiaoliang Zhuo
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Yue-Zhong Shu
- Bristol-Myers Squibb Research and Development , P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Dawn Parker
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Roy Haskell
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Alicia Ng
- Bristol-Myers Squibb Research and Development , P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Qi Gao
- Bristol-Myers Squibb Research and Development , 1 Squibb Drive, New Brunswick, New Jersey 08901, United States
| | - Elizabeth Colston
- Bristol-Myers Squibb Research and Development , P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Joseph Raybon
- Bristol-Myers Squibb Research and Development , P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Dennis M Grasela
- Bristol-Myers Squibb Research and Development , P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Kenneth Santone
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Min Gao
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Nicholas A Meanwell
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Michael Sinz
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Matthew G Soars
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jay O Knipe
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Susan B Roberts
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - John F Kadow
- Bristol-Myers Squibb Research and Development , P.O. Box 5100, 5 Research Parkway, Wallingford, Connecticut 06492, United States
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