1
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Irfan A, Faisal S, Ahmad S, Saif MJ, Zahoor AF, Khan SG, Javid J, Al-Hussain SA, Muhammed MT, Zaki MEA. An Exploration of the Inhibitory Mechanism of Rationally Screened Benzofuran-1,3,4-Oxadiazoles and-1,2,4-Triazoles as Inhibitors of NS5B RdRp Hepatitis C Virus through Pharmacoinformatic Approaches. Biomedicines 2023; 11:3085. [PMID: 38002085 PMCID: PMC10669698 DOI: 10.3390/biomedicines11113085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Benzofuran, 1,3,4-oxadiazole, and 1,2,4-triazole are privileged heterocyclic moieties that display the most promising and wide spectrum of biological activities against a wide variety of diseases. In the current study, benzofuran-1,3,4-oxadiazole BF1-BF7 and benzofuran-1,2,4-triazole compounds BF8-BF15 were tested against HCV NS5B RNA-dependent RNA polymerase (RdRp) utilizing structure-based screening via a computer-aided drug design (CADD) approach. A molecular docking approach was applied to evaluate the binding potential of benzofuran-appended 1,3,4-oxadiazole and 1,2,4-triazole BF1-BF15 molecules. Benzofuran-1,3,4-oxadiazole scaffolds BF1-BF7 showed lesser binding affinities (-12.63 to -14.04 Kcal/mol) than benzofuran-1,2,4-triazole scaffolds BF8-BF15 (-14.11 to -16.09 Kcal/mol) against the HCV NS5B enzyme. Molecular docking studies revealed the excellent binding affinity scores exhibited by benzofuran-1,2,4-triazole structural motifs BF-9 (-16.09 Kcal/mol), BF-12 (-15.75 Kcal/mol), and BF-13 (-15.82 Kcal/mol), respectively, which were comparatively better than benzofuran-based HCV NS5B inhibitors' standard reference drug Nesbuvir (-15.42 Kcal/mol). A molecular dynamics simulation assay was also conducted to obtain valuable insights about the enzyme-compounds interaction profile and structural stability, which indicated the strong intermolecular energies of the BF-9+NS5B complex and the BF-12+NS5B complex as per the MM-PBSA method, while the BF-12+NS5B complex was the most stable system as per the MM-GBSA calculation. The drug-likeness and ADMET studies of all the benzofuran-1,2,4-triazole derivatives BF8-BF15 revealed that these compounds possessed good medicinal chemistry profiles in agreement with all the evaluated parameters for being drugs. The molecular docking affinity scores, MM-PBSA/MM-GBSA and MD-simulation stability analysis, drug-likeness profiling, and ADMET study assessment indicated that N-4-fluorophenyl-S-linked benzofuran-1,2,4-triazole BF-12 could be a future promising anti-HCV NS5B RdRp inhibitor therapeutic drug candidate that has a structural agreement with the Nesbuvir standard reference drug.
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Affiliation(s)
- Ali Irfan
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (A.I.); (A.F.Z.)
| | - Shah Faisal
- Department of Chemistry, Islamia College University Peshawar, Peshawar 25120, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University Peshawar, Peshawar 25000, Pakistan
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut P.O. Box 36, Lebanon
- Department of Natural Sciences, Lebanese American University, Beirut P.O. Box 36, Lebanon
| | - Muhammad Jawwad Saif
- Department of Applied Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Ameer Fawad Zahoor
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (A.I.); (A.F.Z.)
| | - Samreen Gul Khan
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (A.I.); (A.F.Z.)
| | - Jamila Javid
- Department of Chemistry, University of Sialkot, Sialkot 51040, Pakistan
| | - Sami A. Al-Hussain
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13623, Saudi Arabia
| | - Muhammed Tilahun Muhammed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Suleyman Demirel University, Isparta 32260, Turkey
| | - Magdi E. A. Zaki
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13623, Saudi Arabia
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2
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Chen Q, Zhou X, Rehmel J, Steele JP, Svensson KA, Beck JP, Hembre EJ, Hao J. Ensemble Docking Approach to Mitigate Pregnane X Receptor-Mediated CYP3A4 Induction Risk. J Chem Inf Model 2023; 63:173-186. [PMID: 36473234 DOI: 10.1021/acs.jcim.2c01175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Three structurally closely related dopamine D1 receptor positive allosteric modulators (D1 PAMs) based on a tetrahydroisoquinoline (THIQ) scaffold were profiled for their CYP3A4 induction potentials. It was found that the length of the linker at the C5 position greatly affected the potentials of these D1 PAMs as CYP3A4 inducers, and the level of induction correlated well with the activation of the pregnane X receptor (PXR). Based on the published PXR X-ray crystal structures, we built a binding model specifically for these THIQ-scaffold-based D1 PAMs in the PXR ligand-binding pocket via an ensemble docking approach and found the model could explain the observed CYP induction disparity. Combined with our previously reported D1 receptor homology model, which identified the C5 position as pointing toward the solvent-exposed space, our PXR-binding model coincidentally suggested that structural modifications at the C5 position could productively modulate the CYP induction potential while maintaining the D1 PAM potency of these THIQ-based PAMs.
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Affiliation(s)
- Qi Chen
- Discovery Chemistry Research and Technologies, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana46285, United States
| | - Xin Zhou
- Drug Disposition, Lilly Biotechnology Center, Eli Lilly and Company, 10290 Campus Point Drive, San Diego, California92121, United States
| | - Jessica Rehmel
- Drug Disposition, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana46285, United States
| | - James P Steele
- Quantitative Biology, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana46285, United States
| | - Kjell A Svensson
- Neuroscience Discovery, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana46285, United States
| | - James P Beck
- Discovery Chemistry Research and Technologies, Lilly Biotechnology Center, Eli Lilly and Company, 10290 Campus Point Drive, San Diego, California92121, United States
| | - Erik J Hembre
- Discovery Chemistry Research and Technologies, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana46285, United States
| | - Junliang Hao
- Discovery Chemistry Research and Technologies, Lilly Biotechnology Center, Eli Lilly and Company, 10290 Campus Point Drive, San Diego, California92121, United States
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3
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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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4
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Liu T, Beck JP, Hao J. A concise review on hPXR ligand-recognizing residues and structure-based strategies to alleviate hPXR transactivation risk. RSC Med Chem 2022; 13:129-137. [PMID: 35308029 PMCID: PMC8864553 DOI: 10.1039/d1md00348h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/03/2022] [Indexed: 01/21/2023] Open
Abstract
The human pregnane X receptor (hPXR) regulates the expression of major drug metabolizing enzymes. A wide range of drug candidates bind and activate hPXR, and hence are at risk of increasing drug-drug interactions and reducing clinical efficacy. hPXR structural features that function as hot spots for ligand binding are identified and highlighted in this concise review. Based on literature structure-activity relationship data as case studies, structure-based strategies to mitigate hPXR transactivation are summarized for medicinal chemists.
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Affiliation(s)
- Tao Liu
- Discovery Chemistry Research & Technologies, Eli Lilly and Company, Lilly Biotechnology Center 10290 Campus Point Drive San Diego CA 92121 USA
| | - James P Beck
- Discovery Chemistry Research & Technologies, Eli Lilly and Company, Lilly Biotechnology Center 10290 Campus Point Drive San Diego CA 92121 USA
| | - Junliang Hao
- Discovery Chemistry Research & Technologies, Eli Lilly and Company, Lilly Biotechnology Center 10290 Campus Point Drive San Diego CA 92121 USA
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5
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Tian Y, Shang Y, Su W. DBU‐Catalyzed Regioselective
α
‐Alkylation of Enones Using the Vinylogous Strategy. ASIAN J ORG CHEM 2021. [DOI: 10.1002/ajoc.202100293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yawei Tian
- College of Chemistry Fuzhou University 2 Xueyuan Road Fuzhou Fujian 350108 P. R. China
- State Key Laboratory of Structural Chemistry Center for Excellence in Molecular Synthesis Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Yangqiao West Road 155 Fuzhou Fujian 350002 P. R. China
| | - Yaping Shang
- State Key Laboratory of Structural Chemistry Center for Excellence in Molecular Synthesis Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Yangqiao West Road 155 Fuzhou Fujian 350002 P. R. China
| | - Weiping Su
- College of Chemistry Fuzhou University 2 Xueyuan Road Fuzhou Fujian 350108 P. R. China
- State Key Laboratory of Structural Chemistry Center for Excellence in Molecular Synthesis Fujian Institute of Research on the Structure of Matter Chinese Academy of Sciences Yangqiao West Road 155 Fuzhou Fujian 350002 P. R. China
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6
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Hall A, Chanteux H, Ménochet K, Ledecq M, Schulze MSED. Designing Out PXR Activity on Drug Discovery Projects: A Review of Structure-Based Methods, Empirical and Computational Approaches. J Med Chem 2021; 64:6413-6522. [PMID: 34003642 DOI: 10.1021/acs.jmedchem.0c02245] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This perspective discusses the role of pregnane xenobiotic receptor (PXR) in drug discovery and the impact of its activation on CYP3A4 induction. The use of structural biology to reduce PXR activity on drug discovery projects has become more common in recent years. Analysis of this work highlights several important molecular interactions, and the resultant structural modifications to reduce PXR activity are summarized. The computational approaches undertaken to support the design of new drugs devoid of PXR activation potential are also discussed. Finally, the SAR of empirical design strategies to reduce PXR activity is reviewed, and the key SAR transformations are discussed and summarized. In conclusion, this perspective demonstrates that PXR activity can be greatly diminished or negated on active drug discovery projects with the knowledge now available. This perspective should be useful to anyone who seeks to reduce PXR activity on a drug discovery project.
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Affiliation(s)
- Adrian Hall
- UCB, Avenue de l'Industrie, Braine-L'Alleud 1420, Belgium
| | | | | | - Marie Ledecq
- UCB, Avenue de l'Industrie, Braine-L'Alleud 1420, Belgium
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7
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Masaret GS. Convenient synthesis and anticancer evaluation of novel pyrazolyl‐thiophene, thieno[3,2‐
b
]pyridine, pyrazolo[3,4‐
d
]thieno[3,2‐
b
]pyridine and pyrano[2,3‐
d
]thieno[3,2‐
b
]pyridine derivatives. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Ghada S. Masaret
- Chemistry Department College of Applied Sciences, Umm Al‐Qura University Makkah Saudi Arabia
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8
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Cartier A, Levernier E, Corcé V, Fukuyama T, Dhimane A, Ollivier C, Ryu I, Fensterbank L. Carbonylation of Alkyl Radicals Derived from Organosilicates through Visible‐Light Photoredox Catalysis. Angew Chem Int Ed Engl 2019; 58:1789-1793. [DOI: 10.1002/anie.201811858] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Alex Cartier
- Department of ChemistryGraduate School of ScienceOsaka Prefecture University Sakai Osaka 599-8531 Japan
| | - Etienne Levernier
- Sorbonne UniversitéCNRSInstitut Parisien de Chimie Moléculaire 4 Place Jussieu, CC 229 75252 Paris Cedex 05 France
| | - Vincent Corcé
- Sorbonne UniversitéCNRSInstitut Parisien de Chimie Moléculaire 4 Place Jussieu, CC 229 75252 Paris Cedex 05 France
| | - Takahide Fukuyama
- Department of ChemistryGraduate School of ScienceOsaka Prefecture University Sakai Osaka 599-8531 Japan
| | - Anne‐Lise Dhimane
- Sorbonne UniversitéCNRSInstitut Parisien de Chimie Moléculaire 4 Place Jussieu, CC 229 75252 Paris Cedex 05 France
| | - Cyril Ollivier
- Sorbonne UniversitéCNRSInstitut Parisien de Chimie Moléculaire 4 Place Jussieu, CC 229 75252 Paris Cedex 05 France
| | - Ilhyong Ryu
- Department of ChemistryGraduate School of ScienceOsaka Prefecture University Sakai Osaka 599-8531 Japan
- Department of Applied ChemistryNational Chiao Tung University Hsinchu Taiwan
| | - Louis Fensterbank
- Sorbonne UniversitéCNRSInstitut Parisien de Chimie Moléculaire 4 Place Jussieu, CC 229 75252 Paris Cedex 05 France
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9
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Cartier A, Levernier E, Corcé V, Fukuyama T, Dhimane A, Ollivier C, Ryu I, Fensterbank L. Carbonylation of Alkyl Radicals Derived from Organosilicates through Visible‐Light Photoredox Catalysis. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201811858] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Alex Cartier
- Department of ChemistryGraduate School of ScienceOsaka Prefecture University Sakai Osaka 599-8531 Japan
| | - Etienne Levernier
- Sorbonne UniversitéCNRSInstitut Parisien de Chimie Moléculaire 4 Place Jussieu, CC 229 75252 Paris Cedex 05 France
| | - Vincent Corcé
- Sorbonne UniversitéCNRSInstitut Parisien de Chimie Moléculaire 4 Place Jussieu, CC 229 75252 Paris Cedex 05 France
| | - Takahide Fukuyama
- Department of ChemistryGraduate School of ScienceOsaka Prefecture University Sakai Osaka 599-8531 Japan
| | - Anne‐Lise Dhimane
- Sorbonne UniversitéCNRSInstitut Parisien de Chimie Moléculaire 4 Place Jussieu, CC 229 75252 Paris Cedex 05 France
| | - Cyril Ollivier
- Sorbonne UniversitéCNRSInstitut Parisien de Chimie Moléculaire 4 Place Jussieu, CC 229 75252 Paris Cedex 05 France
| | - Ilhyong Ryu
- Department of ChemistryGraduate School of ScienceOsaka Prefecture University Sakai Osaka 599-8531 Japan
- Department of Applied ChemistryNational Chiao Tung University Hsinchu Taiwan
| | - Louis Fensterbank
- Sorbonne UniversitéCNRSInstitut Parisien de Chimie Moléculaire 4 Place Jussieu, CC 229 75252 Paris Cedex 05 France
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10
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Nedolya NA, Tarasova OA, Albanov AI, Trofimov BA. A New Facet of Azatriene Reactivity: A Short Cut to 5-Amino-3-methyl-4-(1H-pyrrol-1-yl)thiophene-2-carboxylates and 5-Amino-3-methyl-4-(1H-pyrrol-1-yl)thiophene-2-carbonitriles. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800268] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nina A. Nedolya
- A. E. Favorsky Irkutsk Institute of Chemistry; Siberian Branch; Russian Academy of Sciences; 1 Favorsky Str. 664033 Irkutsk Russian Federation
| | - Olga A. Tarasova
- A. E. Favorsky Irkutsk Institute of Chemistry; Siberian Branch; Russian Academy of Sciences; 1 Favorsky Str. 664033 Irkutsk Russian Federation
| | - Alexander I. Albanov
- A. E. Favorsky Irkutsk Institute of Chemistry; Siberian Branch; Russian Academy of Sciences; 1 Favorsky Str. 664033 Irkutsk Russian Federation
| | - Boris A. Trofimov
- A. E. Favorsky Irkutsk Institute of Chemistry; Siberian Branch; Russian Academy of Sciences; 1 Favorsky Str. 664033 Irkutsk Russian Federation
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11
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Li P, Dorsch W, Lauffer DJ, Bilimoria D, Chauret N, Court JJ, Das SK, Denis F, Mani N, Nanthakumar S, Nicolas O, Rao BG, Ronkin S, Selliah S, Shawgo RS, Stearns R, Tang Q, Waal ND, Green J. Discovery of Novel Allosteric HCV NS5B Inhibitors. 2. Lactam-Containing Thiophene Carboxylates. ACS Med Chem Lett 2017; 8:251-255. [PMID: 28197321 DOI: 10.1021/acsmedchemlett.6b00479] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/26/2017] [Indexed: 12/14/2022] Open
Abstract
Lomibuvir (1) is a non-nucleoside, allosteric inhibitor of the hepatitis C virus NS5B polymerase with demonstrated clinical efficacy. Further development efforts within this class of inhibitor focused on improving the antiviral activity and physicochemical and pharmacokinetic properties. Recently, we reported the development of this series, leading to compound 2, a molecule with comparable potency and an improved physicochemical profile relative to 1. Further exploration of the amino amide-derived side chain led to a series of lactam derivatives, inspired by the X-ray crystal structure of related thiophene carboxylate inhibitors. This series, exemplified by 12f, provided 3-5-fold improvement in potency against HCV replication, as measured by replicon assays. The synthesis, structure-activity relationships, in vitro ADME characterization, and in vivo evaluation of this novel series are discussed.
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Affiliation(s)
- Pan Li
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Warren Dorsch
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - David J. Lauffer
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Darius Bilimoria
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Nathalie Chauret
- Vertex Pharmaceuticals (Canada) Incorporated, 275 Boulevard Armand Frappier, Laval, Quebec H7 V 4A7, Canada
| | - John J. Court
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Sanjoy Kumar Das
- Vertex Pharmaceuticals (Canada) Incorporated, 275 Boulevard Armand Frappier, Laval, Quebec H7 V 4A7, Canada
| | - Francois Denis
- Vertex Pharmaceuticals (Canada) Incorporated, 275 Boulevard Armand Frappier, Laval, Quebec H7 V 4A7, Canada
| | - Nagraj Mani
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Suganthini Nanthakumar
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Olivier Nicolas
- Vertex Pharmaceuticals (Canada) Incorporated, 275 Boulevard Armand Frappier, Laval, Quebec H7 V 4A7, Canada
| | - B. Govinda Rao
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Steven Ronkin
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Subajini Selliah
- Vertex Pharmaceuticals (Canada) Incorporated, 275 Boulevard Armand Frappier, Laval, Quebec H7 V 4A7, Canada
| | - Rebecca S. Shawgo
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Ralph Stearns
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Qing Tang
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Nathan D. Waal
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Jeremy Green
- Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States
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12
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Antiviral Nucleotide Incorporation by Recombinant Human Mitochondrial RNA Polymerase Is Predictive of Increased In Vivo Mitochondrial Toxicity Risk. Antimicrob Agents Chemother 2016; 60:7077-7085. [PMID: 27645237 DOI: 10.1128/aac.01253-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/20/2016] [Indexed: 02/07/2023] Open
Abstract
Nucleoside or nucleotide inhibitors are a highly successful class of antivirals due to selectivity, potency, broad coverage, and high barrier to resistance. Nucleosides are the backbone of combination treatments for HIV, hepatitis B virus, and, since the FDA approval of sofosbuvir in 2013, also for hepatitis C virus (HCV). However, many promising nucleotide inhibitors have advanced to clinical trials only to be terminated due to unexpected toxicity. Here we describe the in vitro pharmacology of compound 1, a monophosphate prodrug of a 2'-ethynyluridine developed for the treatment of HCV. Compound 1 inhibits multiple HCV genotypes in vitro (50% effective concentration [EC50], 0.05 to 0.1 μM) with a selectivity index of >300 (50% cytotoxic concentration [CC50], 30 μM in MT-4 cells). The active triphosphate metabolite of compound 1, compound 2, does not inhibit human α, β, or γ DNA polymerases but was a substrate for incorporation by the human mitochondrial RNA polymerase (POLRMT). In dog, the oral administration of compound 1 resulted in elevated serum liver enzymes and microscopic changes in the liver. Transmission electron microscopy showed significant mitochondrial swelling and lipid accumulation in hepatocytes. Gene expression analysis revealed dose-proportional gene signature changes linked to loss of hepatic function and increased mitochondrial dysfunction. The potential of in vivo toxicity through mitochondrial polymerase incorporation by nucleoside analogs has been previously shown. This study shows that even moderate levels of nucleotide analog incorporation by POLRMT increase the risk of in vivo mitochondrial dysfunction. Based on these results, further development of compound 1 as an anti-HCV compound was terminated.
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13
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Court JJ, Poisson C, Ardzinski A, Bilimoria D, Chan L, Chandupatla K, Chauret N, Collier PN, Das SK, Denis F, Dorsch W, Iyer G, Lauffer D, L'Heureux L, Li P, Luisi BS, Mani N, Nanthakumar S, Nicolas O, Rao BG, Ronkin S, Selliah S, Shawgo RS, Tang Q, Waal ND, Yannopoulos CG, Green J. Discovery of Novel Thiophene-Based, Thumb Pocket 2 Allosteric Inhibitors of the Hepatitis C NS5B Polymerase with Improved Potency and Physicochemical Profiles. J Med Chem 2016; 59:6293-302. [PMID: 27366941 DOI: 10.1021/acs.jmedchem.6b00541] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The hepatitis C viral proteins NS3/4A protease, NS5B polymerase, and NS5A are clinically validated targets for direct-acting antiviral therapies. The NS5B polymerase may be inhibited directly through the action of nucleosides or nucleotide analogues or allosterically at a number of well-defined sites. Herein we describe the further development of a series of thiophene carboxylate allosteric inhibitors of NS5B polymerase that act at the thumb pocket 2 site. Lomibuvir (1) is an allosteric HCV NS5B inhibitor that has demonstrated excellent antiviral activity and potential clinical utility in combination with other direct acting antiviral agents. Efforts to further explore and develop this series led to compound 23, a compound with comparable potency and improved physicochemical properties.
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Affiliation(s)
- John J Court
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Carl Poisson
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Andrzej Ardzinski
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Darius Bilimoria
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Laval Chan
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Kishan Chandupatla
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Nathalie Chauret
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Philip N Collier
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Sanjoy Kumar Das
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Francois Denis
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Warren Dorsch
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Ganesh Iyer
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - David Lauffer
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Lucille L'Heureux
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Pan Li
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Brian S Luisi
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Nagraj Mani
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Suganthi Nanthakumar
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Olivier Nicolas
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - B Govinda Rao
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Steven Ronkin
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Subajini Selliah
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Rebecca S Shawgo
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Qing Tang
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Nathan D Waal
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Constantin G Yannopoulos
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Jeremy Green
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
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Zhao C, Wang Y, Ma S. Recent advances on the synthesis of hepatitis C virus NS5B RNA-dependent RNA-polymerase inhibitors. Eur J Med Chem 2015; 102:188-214. [PMID: 26276434 DOI: 10.1016/j.ejmech.2015.07.046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 07/23/2015] [Accepted: 07/28/2015] [Indexed: 02/07/2023]
Abstract
Hepatitis C is a viral liver infection considered as the major cause of cirrhosis and hepatocellular carcinoma (HCC). The HCV NS5B polymerase, an RNA-dependent RNA polymerase, is essential for HCV replication, which is able to catalyze the synthesis of positive (genomic) and negative (template) strand HCV RNA, but has no functional equivalent in mammalian cells. Therefore, the NS5B polymerase has emerged as an attractive target for the development of specifically targeted antiviral therapy for HCV (DAA, for direct-acting antivirals). Recently, a growing number of compounds have been reported as the NS5B polymerase inhibitors, some of which especially have been licensed in clinical trials. This review describes recent advances on the synthesis of the NS5B polymerase inhibitors, focusing on the merits and demerits of their synthetic methods. In particular, inspiration from the synthesis and the future direction of the NS5B polymerase inhibitors are highlighted.
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Affiliation(s)
- Can Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, PR China
| | - Yinhu Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, PR China
| | - Shutao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, PR China.
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