1
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Sharma Y, Pawar GP, Chaudhari VD. One-Pot Domino Reaction: Direct Access to Polysubstituted 1,4-Benzothiazine 1,1-Dioxide via Water-Gas Shift Reaction Utilizing DMF/H 2O. J Org Chem 2023; 88:701-710. [PMID: 36538787 DOI: 10.1021/acs.joc.2c02171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Benzothiazine 1,1-dioxide (BTDO) is a privileged chemical motif, and its metal-free domino access is in high demand. Current BTDO production methods require costly metal catalysts or harsh reaction conditions. A facile domino approach to BTDO via a water-gas shift reaction (WGSR) employing sodium 2-nitrobenzenesulfinates and α-bromo ketones is presented. This strategy is cost-effective and environmentally beneficial. The optimized reaction conditions demonstrated remarkable chemical tolerance to a wide range of electrically and sterically varied substituents on both coupling partners.
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Affiliation(s)
- Yogesh Sharma
- Division of Medicinal Chemistry, CSIR-Institute of Microbial Technology, Chandigarh 160036, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Ganesh P Pawar
- Division of Medicinal Chemistry, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Vinod D Chaudhari
- Division of Medicinal Chemistry, CSIR-Institute of Microbial Technology, Chandigarh 160036, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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2
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Zhou Z, Zhang J, Zhou E, Ren C, Wang J, Wang Y. Small molecule NS5B RdRp non-nucleoside inhibitors for the treatment of HCV infection: A medicinal chemistry perspective. Eur J Med Chem 2022; 240:114595. [PMID: 35868125 DOI: 10.1016/j.ejmech.2022.114595] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) infection has become a global health problem with enormous risks. Nonstructural protein 5B (NS5B) RNA-dependent RNA polymerase (RdRp) is a component of HCV, which can promote the formation of the viral RNA replication complex and is also an essential part of the replication complex itself. It plays a vital role in the synthesis of the positive and negative strands of HCV RNA. Therefore, the development of small-molecule inhibitors targeting NS5B RdRp is of great value for treating HCV infection-related diseases. Compared with NS5B RdRp nucleoside inhibitors, non-nucleoside inhibitors have more flexible structures, simpler mechanisms of action, and more predictable efficacy and safety of drugs in humans. Technological advances over the past decade have led to remarkable achievements in developing NS5B RdRp inhibitors. This review will summarize the non-nucleoside inhibitors targeting NS5B RdRp developed in the past decade and describe their structure optimization process and structure-activity relationship.
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Affiliation(s)
- Zhilan Zhou
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jifa Zhang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Tianfu Jincheng Laboratory, Chengdu, 610041, Sichuan, China
| | - Enda Zhou
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Changyu Ren
- Department of Pharmacy, Chengdu Fifth People's Hospital, Chengdu, Sichuan, 611130, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, Tennessee, United States
| | - Yuxi Wang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Tianfu Jincheng Laboratory, Chengdu, 610041, Sichuan, China.
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3
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Wei S, Hu X, Du L, Zhao L, Xue H, Liu C, Chou JJ, Zhong J, Tong Y, Wang S, OuYang B. Inhibitor Development against p7 Channel in Hepatitis C Virus. Molecules 2021; 26:1350. [PMID: 33802584 PMCID: PMC7961618 DOI: 10.3390/molecules26051350] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 12/27/2022] Open
Abstract
Hepatitis C Virus (HCV) is the key cause of chronic and severe liver diseases. The recent direct-acting antiviral agents have shown the clinical success on HCV-related diseases, but the rapid HCV mutations of the virus highlight the sustaining necessity to develop new drugs. p7, the viroporin protein from HCV, has been sought after as a potential anti-HCV drug target. Several classes of compounds, such as amantadine and rimantadine have been testified for p7 inhibition. However, the efficacies of these compounds are not high. Here, we screened some novel p7 inhibitors with amantadine scaffold for the inhibitor development. The dissociation constant (Kd) of 42 ARD-series compounds were determined by nuclear magnetic resonance (NMR) titrations. The efficacies of the two best inhibitors, ARD87 and ARD112, were further confirmed using viral production assay. The binding mode analysis and binding stability for the strongest inhibitor were deciphered by molecular dynamics (MD) simulation. These ARD-series compounds together with 49 previously published compounds were further analyzed by molecular docking. Key pharmacophores were identified among the structure-similar compounds. Our studies suggest that different functional groups are highly correlated with the efficacy for inhibiting p7 of HCV, in which hydrophobic interactions are the dominant forces for the inhibition potency. Our findings provide guiding principles for designing higher affinity inhibitors of p7 as potential anti-HCV drug candidates.
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Affiliation(s)
- Shukun Wei
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201203, China; (S.W.); (L.D.); (L.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China; (X.H.); (J.Z.)
| | - Xiaoyou Hu
- University of Chinese Academy of Sciences, Beijing 100049, China; (X.H.); (J.Z.)
- CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lingyu Du
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201203, China; (S.W.); (L.D.); (L.Z.)
| | - Linlin Zhao
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201203, China; (S.W.); (L.D.); (L.Z.)
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA;
| | - Hongjuan Xue
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China;
| | - Chaolun Liu
- ShanghaiTech University, Shanghai 201210, China;
| | - James J. Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA;
| | - Jin Zhong
- University of Chinese Academy of Sciences, Beijing 100049, China; (X.H.); (J.Z.)
- CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- ShanghaiTech University, Shanghai 201210, China;
| | - Yimin Tong
- CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shuqing Wang
- School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Bo OuYang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201203, China; (S.W.); (L.D.); (L.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China; (X.H.); (J.Z.)
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4
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Khalid H, Landry KB, Ijaz B, Ashfaq UA, Ahmed M, Kanwal A, Froeyen M, Mirza MU. Discovery of novel Hepatitis C virus inhibitor targeting multiple allosteric sites of NS5B polymerase. INFECTION GENETICS AND EVOLUTION 2020; 84:104371. [PMID: 32485331 DOI: 10.1016/j.meegid.2020.104371] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 05/13/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
HCV is a viral infection posing a severe global threat when left untreated progress to end-stage liver disease, including cirrhosis and HCC. The NS5B polymerase of HCV is the most potent target that harbors four allosteric binding sites that could interfere with the HCV infection. We present the discovery of a novel synthetic compound that harbors the potential of NS5B polymerase inhibition. All eight compounds belonging to the benzothiazine family of heterocycles displayed no cellular cytotoxicity in HepG2 cells at nontoxic dose concentration (200 μM). Subsequently, among eight compounds of the series, merely compound 5b exhibited significant inhibition of the expression of the HCV NS5B gene as compared to DMSO control in semi-quantitative PCR. Based on our western blot result, 5b at the range of 50, 100 and 200 μM induced 20, 40, and 70% inhibition of NS5B protein respectively. To estimate the binding potential, 5b was docked at respective allosteric sites followed by molecular dynamics (MD) simulations for a period of 20 ns. In addition, binding free energy calculation by MM-GB/PBSA method revealed a conserved interaction profile of residues lining the allosteric sites in agreement with the reported NS5B co-crystallized inhibitors. The presented results provide important information about a novel compound 5b which may facilitate the the discovery of novel inhibitors that tends to target multiple sites on NS5B polymerase.
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Affiliation(s)
- Hina Khalid
- Department of Bioinformatics and Biotechnology, Government College University, 38000 Faisalabad, Pakistan
| | - Koloko Brice Landry
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Bushra Ijaz
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, 38000 Faisalabad, Pakistan.
| | - Matloob Ahmed
- Department of Chemistry, Government College University, 38000 Faisalabad, Pakistan
| | - Afshan Kanwal
- Department of Chemistry, Government College University, 38000 Faisalabad, Pakistan
| | - Matheus Froeyen
- Department of Pharmaceutical Sciences, REGA Institute for Medical Research, Medicinal Chemistry, University of Leuven, 3000 Leuven, Belgium
| | - Muhammad Usman Mirza
- Department of Pharmaceutical Sciences, REGA Institute for Medical Research, Medicinal Chemistry, University of Leuven, 3000 Leuven, Belgium
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5
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Badshah SL, Ahmad N, Ur Rehman A, Khan K, Ullah A, Alsayari A, Muhsinah AB, N Mabkhot Y. Molecular docking and simulation of Zika virus NS3 helicase. BMC Chem 2019; 13:67. [PMID: 31384814 PMCID: PMC6661806 DOI: 10.1186/s13065-019-0582-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 05/02/2019] [Indexed: 02/06/2023] Open
Abstract
The Zika virus (ZIKV) has gained attention for the last few years due to the congenital microcephaly and Guillain–Barre Syndrome that resulted in humans. The non-structural protein-3 (NS3) helicase of ZIKV play an important role in viral RNA replication. In this article, we performed hundred nanosecond molecular dynamics simulation and molecular docking of the NS3 helicase of ZIKV with 1,4-benzothiazine derivatives. The root mean square deviation (RMSD) analyses showed the stability of the NS3 helicase. The simulation showed that the flexible and rigid domains of the protein play a crucial role during the RNA replication process. All such domains with ligand binding pockets can be targeted for drug design. The molecular docking showed that the strong hydrogen bonding and arene-cation interactions are responsible for the binding between NS3 and 1,4-benzothiazine derivatives, which provides a new dimension for potent drug design for ZIKV.
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Affiliation(s)
- Syed Lal Badshah
- 1Department of Chemistry, Islamia College University, Peshawar, Khyber Pakhtunkhwa Pakistan
| | - Nasir Ahmad
- 1Department of Chemistry, Islamia College University, Peshawar, Khyber Pakhtunkhwa Pakistan
| | - Ashfaq Ur Rehman
- 2State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
| | - Khalid Khan
- 1Department of Chemistry, Islamia College University, Peshawar, Khyber Pakhtunkhwa Pakistan
| | - Asad Ullah
- 1Department of Chemistry, Islamia College University, Peshawar, Khyber Pakhtunkhwa Pakistan
| | - Abdulrhman Alsayari
- 3Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, 62529 Saudi Arabia
| | - Abdullatif Bin Muhsinah
- 3Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, 62529 Saudi Arabia
| | - Yahia N Mabkhot
- 4Department of Pharmaceutical Chemistry, College of Pharamacy, King Khalid University, Abha, 61441 Saudi Arabia
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6
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Computational Study of HCV p7 Channel: Insight into a New Strategy for HCV Inhibitor Design. Interdiscip Sci 2018; 11:292-299. [PMID: 30194627 DOI: 10.1007/s12539-018-0306-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/23/2018] [Accepted: 09/03/2018] [Indexed: 10/28/2022]
Abstract
HCV p7 protein is a cation-selective ion channel, playing an essential role during the life cycle of HCV viruses. To understand the cation-selective mechanism, we constructed a hexameric model in lipid bilayers of HCV p7 protein for HCB JFH-1 strain, genotype 2a. In this structural model, His9 and Val6 were key factors for the HCV cation-selective ion channel. The histidine residues at position 9 in the hexameric model formed a first gate for HCV p7 channel, acting as a selectivity filter for cations. The valines mentioned above formed a second gate for HCV p7 channel, serving as a hydrophobic filter for the dehydrated cations. The binding pocket for the channel blockers, e.g., amantadine and rimantadine, was composed of residues 20-26 in H2 helix and 52-60 in H3 helix in i + 2 monomer. However, the molecular volumes for both amantadine and rimantadine were too small for the binding pocket of HCV p7 channel. Thus, designing a compound similar with rimantadine and having much larger volume would be an effective strategy for discovering inhibitors against HCV p7 channel. To achieve this point, we used rimantadine as a structural template to search ChEMBL database for the candidates employing favorable binding affinities to HCV p7 channel. As a result, six candidates were identified to have potential to be novel inhibitors against HCV p7 channel.
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7
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Sun QS, Sun J, Jiang W, Yan CG. Annulation reaction of methyl 2-(benzo[ b ][1,4]thiazin-3-ylidene)acetate with β -nitrostyrenes and 3-nitrochromenes. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.01.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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8
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Bhutia ZT, Das A, Biswas M, Chatterjee A, Banerjee M. 7-Oxa-4-thia-1-aza-bicyclo[3.2.1]octane 4,4-Dioxides: Mechanochemical Synthesis by Tandem Michael Addition-1,3-Dipolar Cycloaddition of Aldoximes and Evaluation of Antibacterial Activities. European J Org Chem 2018. [DOI: 10.1002/ejoc.201701511] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
| | - Avijit Das
- Department of Biological Sciences; BITS; Goa Campus 403726 Pilani India
| | - Malabika Biswas
- Department of Biological Sciences; BITS; Goa Campus 403726 Pilani India
| | | | - Mainak Banerjee
- Department of Chemistry; BITS; Goa Campus 403726 Pilani India
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9
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de Macedo MB, Kimmel R, Urankar D, Gazvoda M, Peixoto A, Cools F, Torfs E, Verschaeve L, Lima ES, Lyčka A, Milićević D, Klásek A, Cos P, Kafka S, Košmrlj J, Cappoen D. Design, synthesis and antitubercular potency of 4-hydroxyquinolin-2(1H)-ones. Eur J Med Chem 2017; 138:491-500. [PMID: 28689097 DOI: 10.1016/j.ejmech.2017.06.061] [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] [Received: 04/30/2017] [Revised: 06/16/2017] [Accepted: 06/28/2017] [Indexed: 10/19/2022]
Abstract
In this study, a 50-membered library of substituted 4-hydroxyquinolin-2(1H)-ones and two closely related analogues was designed, scored in-silico for drug likeness and subsequently synthesized. Thirteen derivatives, all sharing a common 3-phenyl substituent showed minimal inhibitory concentrations against Mycobacterium tuberculosis H37Ra below 10 μM and against Mycobacterium bovis AN5A below 15 μM but were inactive against faster growing mycobacterial species. None of these selected derivatives showed significant acute toxicity against MRC-5 cells or early signs of genotoxicity in the Vitotox™ assay at the active concentration range. The structure activity study relation provided some insight in the further favourable substitution pattern at the 4-hydroxyquinolin-2(1H)-one scaffold and finally 6-fluoro-4-hydroxy-3-phenylquinolin-2(1H)-one (38) was selected as the most promising member of the library with a MIC of 3.2 μM and a CC50 against MRC-5 of 67.4 μM.
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Affiliation(s)
- Maíra Bidart de Macedo
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), S7, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Roman Kimmel
- Faculty of Technology, Tomas Bata University, Vavrečkova 275, CZ-760 01 Zlín, Czech Republic
| | - Damijana Urankar
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Martin Gazvoda
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Antonio Peixoto
- Centre National de la Recherche Scientifique, IPBS, UMR 5089, F-31077 Toulouse, France; Univ. Toulouse, UPS, F-31000 Toulouse, France
| | - Freya Cools
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), S7, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Eveline Torfs
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), S7, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Luc Verschaeve
- Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Emerson Silva Lima
- Faculty of Pharmaceutical Sciences, Federal Univeristy of Amazonas, Avenida General Rodrigo Otávio Campos de Jordão, 6200, Coroado, Manaus 69077-000, Amazonas, Brazil
| | - Antonín Lyčka
- Faculty of Science, University of Hradec Králové, Rokitanského 62, CZ-500 03 Hradec Králové III, Czech Republic
| | - David Milićević
- Faculty of Technology, Tomas Bata University, Vavrečkova 275, CZ-760 01 Zlín, Czech Republic
| | - Antonín Klásek
- Faculty of Technology, Tomas Bata University, Vavrečkova 275, CZ-760 01 Zlín, Czech Republic
| | - Paul Cos
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), S7, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Stanislav Kafka
- Faculty of Technology, Tomas Bata University, Vavrečkova 275, CZ-760 01 Zlín, Czech Republic.
| | - Janez Košmrlj
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.
| | - Davie Cappoen
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), S7, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium.
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10
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Paparin JL, Amador A, Badaroux E, Bot S, Caillet C, Convard T, Da Costa D, Dukhan D, Griffe L, Griffon JF, LaColla M, Leroy F, Liuzzi M, Giulia Loi A, McCarville J, Mascia V, Milhau J, Onidi L, Pierra C, Rahali R, Rosinosky E, Sais E, Seifer M, Surleraux D, Standring D, Dousson CB. Discovery of benzophosphadiazine drug candidate IDX375: A novel hepatitis C allosteric NS5B RdRp inhibitor. Bioorg Med Chem Lett 2017; 27:2634-2640. [PMID: 28416131 DOI: 10.1016/j.bmcl.2017.01.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/06/2017] [Accepted: 01/08/2017] [Indexed: 11/15/2022]
Abstract
Hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRp) plays a central role in virus replication. NS5B has no functional equivalent in mammalian cells, and as a consequence is an attractive target for selective inhibition. This paper describes the discovery of a novel family of HCV NS5B non-nucleoside inhibitors inspired by the bioisosterism between sulfonamide and phosphonamide. Systematic structural optimization in this new series led to the identification of IDX375, a potent non-nucleoside inhibitor that is selective for genotypes 1a and 1b. The structure and binding domain of IDX375 were confirmed by X-ray co-crystalisation study.
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Affiliation(s)
- Jean-Laurent Paparin
- Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP50001, 34189 Montpellier Cedex 4, France.
| | | | | | - Stéphanie Bot
- Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP50001, 34189 Montpellier Cedex 4, France
| | | | - Thierry Convard
- Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP50001, 34189 Montpellier Cedex 4, France
| | - Daniel Da Costa
- Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP50001, 34189 Montpellier Cedex 4, France
| | - David Dukhan
- Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP50001, 34189 Montpellier Cedex 4, France
| | | | - Jean-François Griffon
- Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP50001, 34189 Montpellier Cedex 4, France
| | | | | | | | | | | | | | - Julien Milhau
- Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP50001, 34189 Montpellier Cedex 4, France
| | | | - Claire Pierra
- Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP50001, 34189 Montpellier Cedex 4, France
| | - Rachid Rahali
- Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP50001, 34189 Montpellier Cedex 4, France
| | | | | | | | | | | | - Cyril B Dousson
- Idenix SARL, an MSD Company, Medicinal Chemistry Laboratory, Cap Gamma, 1682 rue de la Valsière, BP50001, 34189 Montpellier Cedex 4, France
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11
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Ismail NSM, Elzahabi HSA, Sabry P, Baselious FN, AbdelMalak AS, Hanna F. A study of the allosteric inhibition of HCV RNA-dependent RNA polymerase and implementing virtual screening for the selection of promising dual-site inhibitors with low resistance potential. J Recept Signal Transduct Res 2016; 37:341-354. [PMID: 27829320 DOI: 10.1080/10799893.2016.1248293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Structure-based pharmacophores were generated and validated using the bioactive conformations of different co-crystallized enzyme-inhibitor complexes for allosteric palm-1 and thumb-2 inhibitors of NS5B. Two pharmacophore models were obtained, one for palm-1 inhibitors with sensitivity = 0.929 and specificity = 0.983, and the other for thumb-2 inhibitors with sensitivity = 1 and specificity = 0.979. In addition, a quantitative structure activity relationship (QSAR) models were developed based on using the values of different scoring functions as descriptors predicting the activity on both allosteric binding sites (palm-1 and thumb-2). QSAR studies revealed good predictive and statistically significant two descriptor models (r2 = .837, r2adjusted = .792 and r2prediction = .688 for palm-1 model and r2 = .927, r2adjusted = .908 and r2prediction = .779 for thumb-2 model). External validation for the QSAR models assured their prediction power with r2ext = .72 and .89 for palm-1 and thumb-2, respectively. Different docking protocols were examined for their validity to predict the correct binding poses of inhibitors inside their respective binding sites. Virtual screening was carried out on ZINC database using the generated pharmacophores, the selected valid docking algorithms and QSAR models to find compounds that could theoretically bind to both sites simultaneously.
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Affiliation(s)
- Nasser S M Ismail
- a Pharmaceutical Chemistry Department, Faculty of Pharmaceutical Sciences and Pharmaceutical Industries , Future University , Cairo , Egypt
| | - Heba S A Elzahabi
- b Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Al-Azhar University , Cairo , Egypt
| | - Peter Sabry
- c National Organization for Drug Control and Research , Dokki , Cairo , Egypt
| | - Fady N Baselious
- d Department of Research and Development , Global Napi Pharmaceuticals , 6th October City , Giza , Egypt
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12
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Fülöpová V, Krchňáková A, Schütznerová E, Zajíček J, Krchňák V. Ring Contraction of 2,5-Dihydrobenzo[f][1,2,5]thiadiazepine 1,1-Dioxides: Access to 4H-Benzo[b][1,4]thiazine 1,1-Dioxides. J Org Chem 2015; 80:1795-801. [DOI: 10.1021/jo502713k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Veronika Fülöpová
- Department of Organic
Chemistry, Institute of Molecular and Translational Medicine, Faculty
of Science, Palacky University, 17. Listopadu 12, 771 46 Olomouc, Czech Republic
| | - Anna Krchňáková
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Center, Notre Dame, Indiana 46556, United States
| | - Eva Schütznerová
- Department of Organic
Chemistry, Institute of Molecular and Translational Medicine, Faculty
of Science, Palacky University, 17. Listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jaroslav Zajíček
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Center, Notre Dame, Indiana 46556, United States
| | - Viktor Krchňák
- Department of Organic
Chemistry, Institute of Molecular and Translational Medicine, Faculty
of Science, Palacky University, 17. Listopadu 12, 771 46 Olomouc, Czech Republic
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Center, Notre Dame, Indiana 46556, United States
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13
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Talamas FX, Abbot SC, Anand S, Brameld KA, Carter DS, Chen J, Davis D, de Vicente J, Fung AD, Gong L, Harris SF, Inbar P, Labadie SS, Lee EK, Lemoine R, Le Pogam S, Leveque V, Li J, McIntosh J, Nájera I, Park J, Railkar A, Rajyaguru S, Sangi M, Schoenfeld RC, Staben LR, Tan Y, Taygerly JP, Villaseñor AG, Weller PE. Discovery of N-[4-[6-tert-butyl-5-methoxy-8-(6-methoxy-2-oxo-1H-pyridin-3-yl)-3-quinolyl]phenyl]methanesulfonamide (RG7109), a potent inhibitor of the hepatitis C virus NS5B polymerase. J Med Chem 2014; 57:1914-31. [PMID: 24195700 PMCID: PMC3954946 DOI: 10.1021/jm401329s] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In the past few years, there have been many advances in the efforts to cure patients with hepatitis C virus (HCV). The ultimate goal of these efforts is to develop a combination therapy consisting of only direct-antiviral agents (DAAs). In this paper, we discuss our efforts that led to the identification of a bicyclic template with potent activity against the NS5B polymerase, a critical enzyme on the life cycle of HCV. In continuation of our exploration to improve the stilbene series, the 3,5,6,8-tetrasubstituted quinoline core was identified as replacement of the stilbene moiety. 6-Methoxy-2(1H)-pyridone was identified among several heterocyclic headgroups to have the best potency. Solubility of the template was improved by replacing a planar aryl linker with a saturated pyrrolidine. Profiling of the most promising compounds led to the identification of quinoline 41 (RG7109), which was selected for advancement to clinical development.
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Affiliation(s)
- Francisco X. Talamas
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Sarah C. Abbot
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Shalini Anand
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Ken A. Brameld
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - David S. Carter
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Jun Chen
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Dana Davis
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Javier de Vicente
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Amy D. Fung
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Leyi Gong
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Seth F. Harris
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Petra Inbar
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Sharada S. Labadie
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Eun K. Lee
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Remy Lemoine
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Sophie Le Pogam
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Vincent Leveque
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Jim Li
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Joel McIntosh
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Isabel Nájera
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Jaehyeon Park
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Aruna Railkar
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Sonal Rajyaguru
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Michael Sangi
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Ryan C. Schoenfeld
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Leanna R. Staben
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Yunchou Tan
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Joshua P. Taygerly
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Armando G. Villaseñor
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Paul E. Weller
- Hoffmann-La Roche Inc., Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States
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14
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Wang M, Zhong M, Yan A, Li L, Yu C. Quantitative structure and bioactivity relationship study on HCV NS5B polymerase inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2013; 25:1-15. [PMID: 24283437 DOI: 10.1080/1062936x.2013.820790] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Several QSAR (quantitative structure-activity relationship) models for predicting the inhibitory activity of 333 hepatitis C virus (HCV) NS5B polymerase inhibitors were developed. All the inhibitors are HCV polymerase non-nucleoside analogue inhibitors (NNIs) fitting into the pocket of the NNI III binding site. For each molecule, global descriptors and 2D property autocorrelation descriptors were calculated from the program ADRIANA.Code. Pearson correlation analysis was used to select the significant descriptors for building models. The whole dataset was split into a training set and a test set randomly or using a Kohonen's self-organizing map (SOM). Then, the inhibitory activity of 333 HCV NS5B polymerase inhibitors was predicted using multilinear regression (MLR) analysis and support vector machine (SVM) method, respectively. For the test set of the best model (Model 2B), correlation coefficient of 0.91 was achieved. Some molecular descriptors, such as molecular complexity (Complexity), the number of hydrogen bonding donors (HDon) and the solubility of the molecule in water (log S) were found to be very important factors which determined the bioactivity of the HCV NS5B inhibitors. Some other molecular properties such as electrostatic and charge properties also played important roles in the interaction between the ligand and the protein. The selected molecular descriptors were further confirmed by analysing the interaction between two representative inhibitors and the polymerase in their crystal structures.
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Affiliation(s)
- M Wang
- a State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering , Beijing University of Chemical Technology , Beijing , China
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15
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Schoenfeld RC, Bourdet DL, Brameld KA, Chin E, de Vicente J, Fung A, Harris SF, Lee EK, Le Pogam S, Leveque V, Li J, Lui AST, Najera I, Rajyaguru S, Sangi M, Steiner S, Talamas FX, Taygerly JP, Zhao J. Discovery of a novel series of potent non-nucleoside inhibitors of hepatitis C virus NS5B. J Med Chem 2013; 56:8163-82. [PMID: 24069953 DOI: 10.1021/jm401266k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Hepatitis C virus (HCV) is a major global public health problem. While the current standard of care, a direct-acting antiviral (DAA) protease inhibitor taken in combination with pegylated interferon and ribavirin, represents a major advancement in recent years, an unmet medical need still exists for treatment modalities that improve upon both efficacy and tolerability. Toward those ends, much effort has continued to focus on the discovery of new DAAs, with the ultimate goal to provide interferon-free combinations. The RNA-dependent RNA polymerase enzyme NS5B represents one such DAA therapeutic target for inhibition that has attracted much interest over the past decade. Herein, we report the discovery and optimization of a novel series of inhibitors of HCV NS5B, through the use of structure-based design applied to a fragment-derived starting point. Issues of potency, pharmacokinetics, and early safety were addressed in order to provide a clinical candidate in fluoropyridone 19.
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Affiliation(s)
- Ryan C Schoenfeld
- Pharma Research & Early Development, Hoffmann-La Roche Inc. , 340 Kingsland Street, Nutley, New Jersey 07110, United States
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16
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Accounting for Target Flexibility and Water Molecules by Docking to Ensembles of Target Structures: The HCV NS5B Palm Site I Inhibitors Case Study. J Chem Inf Model 2013; 54:481-97. [DOI: 10.1021/ci400367m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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17
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Weidlich IE, Filippov IV, Brown J, Kaushik-Basu N, Krishnan R, Nicklaus MC, Thorpe IF. Inhibitors for the hepatitis C virus RNA polymerase explored by SAR with advanced machine learning methods. Bioorg Med Chem 2013; 21:3127-37. [PMID: 23608107 PMCID: PMC3653294 DOI: 10.1016/j.bmc.2013.03.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/10/2013] [Accepted: 03/18/2013] [Indexed: 12/30/2022]
Abstract
Hepatitis C virus (HCV) is a global health challenge, affecting approximately 200 million people worldwide. In this study we developed SAR models with advanced machine learning classifiers Random Forest and k Nearest Neighbor Simulated Annealing for 679 small molecules with measured inhibition activity for NS5B genotype 1b. The activity was expressed as a binary value (active/inactive), where actives were considered molecules with IC50 ≤0.95 μM. We applied our SAR models to various drug-like databases and identified novel chemical scaffolds for NS5B inhibitors. Subsequent in vitro antiviral assays suggested a new activity for an existing prodrug, Candesartan cilexetil, which is currently used to treat hypertension and heart failure but has not been previously tested for anti-HCV activity. We also identified NS5B inhibitors with two novel non-nucleoside chemical motifs.
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Affiliation(s)
- Iwona E. Weidlich
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Frederick National Laboratory for Cancer Research, 376 Boyles Street, Frederick, MD 21702
- Computational Drug Design Systems (CODDES) LLC, Rockville, MD
| | - Igor V. Filippov
- Chemical Biology Laboratory, Center for Cancer Research, SAIC-Frederick, Inc., 376 Boyles Street, Frederick, MD 21702
| | - Jodian Brown
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250
| | - Neerja Kaushik-Basu
- Department of Biochemistry and Molecular Biology, UMDNJ New Jersey Medical School, 185 South Orange Ave, Newark, NJ 07103
| | - Ramalingam Krishnan
- Department of Biochemistry and Molecular Biology, UMDNJ New Jersey Medical School, 185 South Orange Ave, Newark, NJ 07103
| | - Marc C. Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Frederick National Laboratory for Cancer Research, 376 Boyles Street, Frederick, MD 21702
| | - Ian F. Thorpe
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250
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18
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Talamas FX, Ao-Ieong G, Brameld KA, Chin E, de Vicente J, Dunn JP, Ghate M, Giannetti AM, Harris SF, Labadie SS, Leveque V, Li J, Lui AST, McCaleb KL, Nájera I, Schoenfeld RC, Wang B, Wong A. De novo fragment design: a medicinal chemistry approach to fragment-based lead generation. J Med Chem 2013; 56:3115-9. [PMID: 23509929 DOI: 10.1021/jm4002605] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The use of fragments with low binding affinity for their targets as starting points has received much attention recently. Screening of fragment libraries has been the most common method to find attractive starting points. Herein, we describe a unique, alternative approach to generating fragment leads. A binding model was developed and a set of guidelines were then selected to use this model to design fragments, enabling our discovery of a novel fragment with high LE.
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Affiliation(s)
- Francisco X Talamas
- Hoffmann-La Roche Inc, Pharma Research & Early Development, 340 Kingsland Street, Nutley, New Jersey 07110, United States.
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19
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Barreca ML, Manfroni G, Leyssen P, Winquist J, Kaushik-Basu N, Paeshuyse J, Krishnan R, Iraci N, Sabatini S, Tabarrini O, Basu A, Danielson UH, Neyts J, Cecchetti V. Structure-based discovery of pyrazolobenzothiazine derivatives as inhibitors of hepatitis C virus replication. J Med Chem 2013; 56:2270-82. [PMID: 23409936 DOI: 10.1021/jm301643a] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The NS5B RNA-dependent RNA polymerase is an attractive target for the development of novel and selective inhibitors of hepatitis C virus replication. To identify novel structural hits as anti-HCV agents, we performed structure-based virtual screening of our in-house library followed by rational drug design, organic synthesis, and biological testing. These studies led to the identification of pyrazolobenzothiazine scaffold as a suitable template for obtaining novel anti-HCV agents targeting the NS5B polymerase. The best compound of this series was the meta-fluoro-N-1-phenyl pyrazolobenzothiazine derivative 4a, which exhibited an EC50 = 3.6 μM, EC90 = 25.6 μM, and CC50 > 180 μM in the Huh 9-13 replicon system, thus providing a good starting point for further hit evolution.
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Affiliation(s)
- Maria Letizia Barreca
- Dipartimento di Chimica e Tecnologia del Farmaco, Sezione di Chimica Farmaceutica II, Università degli Studi di Perugia, Via del Liceo 1, 06123 Perugia, Italy.
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20
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Keyvani H, Fazlalipour M, Monavari SHR, Mollaie HR. Hepatitis C Virus - Proteins, Diagnosis, Treatment and New Approaches for Vaccine Development. Asian Pac J Cancer Prev 2012. [DOI: 10.7314/apjcp.2012.13.12.5917] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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21
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Davis BC, Thorpe IF. Thumb inhibitor binding eliminates functionally important dynamics in the hepatitis C virus RNA polymerase. Proteins 2012; 81:40-52. [PMID: 22855387 DOI: 10.1002/prot.24154] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/12/2012] [Accepted: 07/23/2012] [Indexed: 11/09/2022]
Abstract
Hepatitis C virus (HCV) has infected almost 200 million people worldwide, typically causing chronic liver damage and severe complications such as liver failure. Currently, there are few approved treatments for viral infection. Thus, the HCV RNA-dependent RNA polymerase (gene product NS5B) has emerged as an important target for small molecule therapeutics. Potential therapeutic agents include allosteric inhibitors that bind distal to the enzyme active site. While their mechanism of action is not conclusively known, it has been suggested that certain inhibitors prevent a conformational change in NS5B that is crucial for RNA replication. To gain insight into the molecular origin of long-range allosteric inhibition of NS5B, we employed molecular dynamics simulations of the enzyme with and without an inhibitor bound to the thumb domain. These studies indicate that the presence of an inhibitor in the thumb domain alters both the structure and internal motions of NS5B. Principal components analysis identified motions that are severely attenuated by inhibitor binding. These motions may have functional relevance by facilitating interactions between NS5B and RNA template or nascent RNA duplex, with presence of the ligand leading to enzyme conformations with narrower and thus less accessible RNA binding channels. This study provides the first evidence for a mechanistic basis of allosteric inhibition in NS5B. Moreover, we present evidence that allosteric inhibition of NS5B results from intrinsic features of the enzyme free energy landscape, suggesting a common mechanism for the action of diverse allosteric ligands.
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Affiliation(s)
- Brittny C Davis
- Department of Chemistry and Biochemistry, University of Maryland-Baltimore County, Baltimore, Maryland 21250, USA
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22
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Inhibition of NaV1.6 sodium channel currents by a novel series of 1,4-disubstituted-triazole derivatives obtained via copper-catalyzed click chemistry. Bioorg Med Chem Lett 2012; 22:6401-4. [PMID: 22981330 DOI: 10.1016/j.bmcl.2012.08.067] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 08/15/2012] [Accepted: 08/16/2012] [Indexed: 12/30/2022]
Abstract
We have synthesized and evaluated a series of 1,4-disubstituted-triazole derivatives for inhibition of the rat Na(V)1.6 sodium channel isoform, an isoform thought to play an important role in controlling neuronal firing. Starting from a series of 2,4(1H)-diarylimidazoles previously published, we decided to extend the SAR study by replacing the imidazole with a different heterocyclic scaffold and by varying the aryl substituents on the central aromatic ring. The 1,4-disubstituted 1,2,3-triazoles were prepared employing the copper-catalyzed azide-alkyne cycloaddition (CuAAC). Many of the new molecules were able to block the rNa(v)1.6 currents at 10 μM by over 20%, displaying IC(50) values ranging in the low micromolar, thus indicating that triazole can efficiently replace the central heterocyclic core. Moreover, the introduction of a long chain at C4 of the central triazole seems beneficial for increased rNa(v)1.6 current block, whereas the length of N1 substituent seems less crucial for inhibition, as long as a phenyl ring is not direcly connected to the triazole. These results provide additional information on the structural features necessary for block of the voltage-gated sodium channels. These new data will be exploited in the preparation of new compounds and could result in potentially useful AEDs.
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23
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Haudecoeur R, Peuchmaur M, Ahmed-Belkacem A, Pawlotsky JM, Boumendjel A. Structure-Activity Relationships in the Development of Allosteric Hepatitis C Virus RNA-Dependent RNA Polymerase Inhibitors: Ten Years of Research. Med Res Rev 2012; 33:934-84. [DOI: 10.1002/med.21271] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Romain Haudecoeur
- Département de Pharmacochimie Moléculaire; Université de Grenoble/CNRS; UMR 5063, BP 53; 38041; Grenoble Cedex 9; France
| | - Marine Peuchmaur
- Département de Pharmacochimie Moléculaire; Université de Grenoble/CNRS; UMR 5063, BP 53; 38041; Grenoble Cedex 9; France
| | | | | | - Ahcène Boumendjel
- Département de Pharmacochimie Moléculaire; Université de Grenoble/CNRS; UMR 5063, BP 53; 38041; Grenoble Cedex 9; France
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24
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Classification of HCV NS5B polymerase inhibitors using support vector machine. Int J Mol Sci 2012; 13:4033-4047. [PMID: 22605964 PMCID: PMC3344200 DOI: 10.3390/ijms13044033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 02/03/2012] [Accepted: 03/19/2012] [Indexed: 12/29/2022] Open
Abstract
Using a support vector machine (SVM), three classification models were built to predict whether a compound is an active or weakly active inhibitor based on a dataset of 386 hepatitis C virus (HCV) NS5B polymerase NNIs (non-nucleoside analogue inhibitors) fitting into the pocket of the NNI III binding site. For each molecule, global descriptors, 2D and 3D property autocorrelation descriptors were calculated from the program ADRIANA.Code. Three models were developed with the combination of different types of descriptors. Model 2 based on 16 global and 2D autocorrelation descriptors gave the highest prediction accuracy of 88.24% and MCC (Matthews correlation coefficient) of 0.789 on test set. Model 1 based on 13 global descriptors showed the highest prediction accuracy of 86.25% and MCC of 0.732 on external test set (including 80 compounds). Some molecular properties such as molecular shape descriptors (InertiaZ, InertiaX and Span), number of rotatable bonds (NRotBond), water solubility (LogS), and hydrogen bonding related descriptors performed important roles in the interactions between the ligand and NS5B polymerase.
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25
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Recent advances in drug discovery of benzothiadiazine and related analogs as HCV NS5B polymerase inhibitors. Bioorg Med Chem 2011; 19:4690-703. [PMID: 21798747 DOI: 10.1016/j.bmc.2011.06.079] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/22/2011] [Accepted: 06/27/2011] [Indexed: 01/27/2023]
Abstract
Hepatitis C virus (HCV) is a major health burden, with an estimated 170 million chronically infected individuals worldwide, and a leading cause of liver transplantation. Patients are at increased risk of developing liver cirrhosis, hepatocellular carcinoma and even liver failure. In the past two decades, several approaches have been adopted to inhibit non-structural viral proteins. The RNA-dependent RNA polymerase (NS5B) of HCV is one of the attractive validated targets for development of new drugs to block HCV infection. In this review, we report the recent progress made towards identifying and developing benzothiadiazines as HCV NS5B polymerase inhibitors. The substituted benzothiadiazine class was identified by HTS in 2002 as an NS5B inhibitor. Further optimization and modification of the core has improved the potency and pharmacokinetic properties of substituted benzothiadiazines. Research on palm site-binding benzothiadiazine analogs and related derivatives and analogs is discussed in this article.
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26
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Hepatitis C NS5B polymerase inhibitors: Functional equivalents for the benzothiadiazine moiety. Bioorg Med Chem Lett 2011; 21:1876-9. [DOI: 10.1016/j.bmcl.2010.12.067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 12/09/2010] [Accepted: 12/15/2010] [Indexed: 11/19/2022]
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27
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Non-nucleoside inhibitors of hepatitis C virus polymerase: current progress and future challenges. Future Med Chem 2010; 2:121-41. [DOI: 10.4155/fmc.09.148] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The current standard of care for hepatitis C virus (HCV) infection is a combination of PEGylated interferon and ribavirin, which offer limited efficacy and significant side effects. Novel HCV-specific inhibitors, including those directed at the viral polymerase, have become the focus of HCV drug-discovery efforts in the past decade. In addition to the active site targeted by traditional nucleoside inhibitors, at least four different allosteric-binding sites have been reported for the HCV polymerase, which offer ample opportunities for small-molecule inhibitors. In this review, we summarize the recent progress in the discovery of non-nucleoside HCV polymerase inhibitors with a focus on novel chemical matters, their clinical efficacy, safety and potential for combination therapy.
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28
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Ruebsam F, Murphy DE, Tran CV, Li LS, Zhao J, Dragovich PS, McGuire HM, Xiang AX, Sun Z, Ayida BK, Blazel JK, Kim SH, Zhou Y, Han Q, Kissinger CR, Webber SE, Showalter RE, Shah AM, Tsan M, Patel RA, Thompson PA, Lebrun LA, Hou HJ, Kamran R, Sergeeva MV, Bartkowski DM, Nolan TG, Norris DA, Khandurina J, Brooks J, Okamoto E, Kirkovsky L. Discovery of tricyclic 5,6-dihydro-1H-pyridin-2-ones as novel, potent, and orally bioavailable inhibitors of HCV NS5B polymerase. Bioorg Med Chem Lett 2009; 19:6404-12. [PMID: 19818610 DOI: 10.1016/j.bmcl.2009.09.045] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Revised: 09/13/2009] [Accepted: 09/14/2009] [Indexed: 11/27/2022]
Abstract
A novel series of non-nucleoside small molecules containing a tricyclic dihydropyridinone structural motif was identified as potent HCV NS5B polymerase inhibitors. Driven by structure-based design and building on our previous efforts in related series of molecules, we undertook extensive SAR studies, in which we identified a number of metabolically stable and very potent compounds in genotype 1a and 1b replicon assays. This work culminated in the discovery of several inhibitors, which combined potent in vitro antiviral activity against both 1a and 1b genotypes, metabolic stability, good oral bioavailability, and high C(12) (PO)/EC(50) ratios.
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Affiliation(s)
- Frank Ruebsam
- Department of Medicinal Chemistry, Anadys Pharmaceuticals, Inc., 5871 Oberlin Drive, Suite 200, San Diego, CA 92121, USA.
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