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Abuelizz HA, Marzouk M, Bakheit AH, Al-Salahi R. Investigation of some benzoquinazoline and quinazoline derivatives as novel inhibitors of HCV-NS3/4A protease: biological, molecular docking and QSAR studies. RSC Adv 2020; 10:35820-35830. [PMID: 35517076 PMCID: PMC9056986 DOI: 10.1039/d0ra05604a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/14/2020] [Indexed: 12/12/2022] Open
Abstract
Morbidity and mortality due to hepatitis C virus (HCV) is a globe health concern. Hence, there is a persistent demand to design and optimize current HCV therapy and develop novel agents. HCV NS3/A4 protease plays an essential role in HCV life cycle and replication. Thus, HCV NS3/A4 protease inhibitors are one of the best therapeutic targets for the identification of novel candidate drugs. Recent studies have shown some benzoquinazolines as potent antiviral agents and promising HAV-3C protease inhibitors. In the present study, a series of benzo[g]quinazolines (1–13) and their quinazoline analogues (14–17) were evaluated for their HCV-NS3/4A inhibitory activities using in vitro assay. Our results revealed that the target compounds inhibited the activity of the NS3/4A enzyme, (IC50 = 6.41 ± 0.12 to 78.80 ± 1.70 μM) in comparison to telaprevir (IC50 = 1.72 ± 0.03 μM) as a reference drug. Compounds 1, 2, 3, 9, 10 and 13 showed the highest activity (IC50 = 11.02 ± 0.25, 6.41 ± 0.12, 9.35 ± 0.19, 9.08 ± 0.20, 16.03 ± 0.34 and 7.21 ± 0.15 μM, respectively). Molecular docking was performed to study the binding modes of the docked-chosen benzo[g]quinazolines, hydrogen bonding, and amino acid residues at the catalytic triad of the NS3/4A enzyme of HCV. The QSAR was determined to explore the relationships between the molecular structures of the targets and their biological activities by developing prediction models among the known HCV NS3/A4 inhibitors and then to predict the inhibitory activity of the target molecules synthesized. HCV NS3/A4 protease inhibitors are one of the best therapeutic targets for the identification of novel candidate drugs. A series of benzo[g]quinazolines and their quinazoline analogues were evaluated for their HCV-NS3/4A inhibitory activities.![]()
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Affiliation(s)
- Hatem A Abuelizz
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University PO Box 2457 Riyadh 11451 Saudi Arabia
| | - Mohamed Marzouk
- Chemistry of Natural Products Group, Center of Excellence for Advanced Sciences, National Research Centre 33 El-Bohouth St. (Former El-Tahrir St.), Dokki Cairo 12622 Egypt
| | - Ahmed H Bakheit
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University PO Box 2457 Riyadh 11451 Saudi Arabia .,Department of Chemistry, Faculty of Science and Technology, El-Neelain University P.O. Box 12702 Khartoum 11121 Sudan
| | - Rashad Al-Salahi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University PO Box 2457 Riyadh 11451 Saudi Arabia
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Venkatesan A, Prabhu Dass J F. Review on chemogenomic approaches towards hepatitis C viral targets. J Cell Biochem 2019; 120:12167-12181. [PMID: 30887580 DOI: 10.1002/jcb.28581] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 01/09/2019] [Accepted: 01/14/2019] [Indexed: 12/18/2022]
Abstract
Hepatitis C virus (HCV) is the most prevalent viral pathogen that infects more than 185 million people worldwide. HCV infection leads to chronic liver diseases such as liver cirrhosis and hepatocellular carcinoma. Direct-acting antivirals (DAAs) are the recent combination therapy for HCV infection with reduced side effects than prior therapies. Sustained virological response (SVR) acts as a gold standard marker to monitor the success of antiviral treatment. Older treatment therapies attain 50-55% of SVR compared with DAAs which attain around 90-95%. The current review emphasizes the recent chemogenomic updates that have been unfolded through structure-based drug design of HCV drug target proteins (NS3/4A, NS5A, and NS5B) and ligand-based drug design of DAAs in achieving a stable HCV viral treatment strategies.
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Affiliation(s)
- Arthi Venkatesan
- Department of Integrative Biology, School of BioSciences and Technology (SBST), VIT, Vellore, Tamil Nadu, India
| | - Febin Prabhu Dass J
- Department of Integrative Biology, School of BioSciences and Technology (SBST), VIT, Vellore, Tamil Nadu, India
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Shunmugam L, Soliman MES. Targeting HCV polymerase: a structural and dynamic perspective into the mechanism of selective covalent inhibition. RSC Adv 2018; 8:42210-42222. [PMID: 35558797 PMCID: PMC9092151 DOI: 10.1039/c8ra07346e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/30/2018] [Indexed: 12/16/2022] Open
Abstract
Background: Concerns have been raised over the emerging pandemic status of hepatitis C virus (HCV). Current available drugs lack specificity, stability and potency. The HCV NS5B RNA-dependent RNA polymerase (RdRp) is a vital component in viral replication and is often targeted in antiviral therapies. Recent experimental procedures have led to the discovery of a novel covalent RdRp inhibitor, compound 47, which selectively targets cysteine 366 of the HCV RdRp and exhibits promising pharmacokinetic outcomes. Selective covalent inhibition of HCV is, however, a highly neglected subject in the literature, that is reinforced by the lack of efficient structure-based drug design protocols. In this paper, an atomistic insight into a novel selective approach to inhibit HCV RdRp is provided. Methodology/Results: Covalent molecular dynamic analyses revealed the inhibitory mechanism of compound 47 on the RdRp. Inhibitor binding induced distinctive internal movements resulting in the disruption of normal physiological interdomain interactions. Conclusion: Compound 47 stimulates reorganization of key protein elements required for RNA transcription, thus hampering viral replication as well as disrupting the overall conformation of HCV. This study will open new lines of approach for the design of novel selective inhibitors against HCV as well as other viral families.
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Affiliation(s)
- Letitia Shunmugam
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal Westville Campus Durban 4001 South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal Westville Campus Durban 4001 South Africa
- School of Health Sciences, University of KwaZulu-Natal Westville Campus Durban 4001 South Africa +27 (0) 31 260 7872 +27 (0) 31 260 8048
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Balachandran A, Wong R, Stoilov P, Pan S, Blencowe B, Cheung P, Harrigan PR, Cochrane A. Identification of small molecule modulators of HIV-1 Tat and Rev protein accumulation. Retrovirology 2017; 14:7. [PMID: 28122580 PMCID: PMC5267425 DOI: 10.1186/s12977-017-0330-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 01/04/2017] [Indexed: 11/10/2022] Open
Abstract
Background HIV-1 replication is critically dependent upon controlled processing of its RNA and the activities provided by its encoded regulatory factors Tat and Rev. A screen of small molecule modulators of RNA processing identified several which inhibited virus gene expression, affecting both relative abundance of specific HIV-1 RNAs and the levels of Tat and Rev proteins. Results The screen for small molecules modulators of HIV-1 gene expression at the post-transcriptional level identified three (a pyrimidin-7-amine, biphenylcarboxamide, and benzohydrazide, designated 791, 833, and 892, respectively) that not only reduce expression of HIV-1 Gag and Env and alter the accumulation of viral RNAs, but also dramatically decrease Tat and Rev levels. Analyses of viral RNA levels by qRTPCR and RTPCR indicated that the loss of either protein could not be attributed to changes in abundance of the mRNAs encoding these factors. However, addition of the proteasome inhibitor MG132 did result in significant restoration of Tat expression, indicating that the compounds are affecting Tat synthesis and/or degradation. Tests in the context of replicating HIV-1 in PBMCs confirmed that 791 significantly reduced virus replication. Parallel analyses of the effect of the compounds on host gene expression revealed only minor changes in either mRNA abundance or alternative splicing. Subsequent tests suggest that 791 may function by reducing levels of the Tat/Rev chaperone Nap1. Conclusions The three compounds examined (791, 833, 892), despite their lack of structural similarity, all suppressed HIV-1 gene expression by preventing accumulation of two key HIV-1 regulatory factors, Tat and Rev. These findings demonstrate that selective disruption of HIV-1 gene expression can be achieved. Electronic supplementary material The online version of this article (doi:10.1186/s12977-017-0330-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ahalya Balachandran
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON, M5S1A8, Canada
| | - Raymond Wong
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Peter Stoilov
- Department of Biochemistry, University of West Virginia, Morgantown, WV, USA
| | - Sandy Pan
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Benjamin Blencowe
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON, M5S1A8, Canada.,Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Peter Cheung
- British Columbia Centre for Excellence in HIV/AIDS, 608-1081 Burrard St., Vancouver, BC, Canada
| | - P Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, 608-1081 Burrard St., Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON, M5S1A8, Canada.
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Thai KM, Dong QH, Nguyen TTL, Le DP, Le MT, Tran TD. Computational Approaches for the Discovery of Novel Hepatitis C Virus NS3/4A and NS5B Inhibitors. Oncology 2017. [DOI: 10.4018/978-1-5225-0549-5.ch017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nonstructural 5B (NS5B) polymerase and Nonstructural 3/4A (NS3/4A) protease have proven to be promising targets for the development of anti-HCV (Hepatitis C Virus) agents. The NS5B polymerase is of paramount importance in HCV viral replication; therefore, employing NS5B inhibitors was considered an effective way for the treatment of HCV. Identifying inhibitors against NS3/4A serine protease represents another attractive approach applied in anti-HCV drug discovery, which is evidenced by its crucial role of in the biogenesis of the viral replication activity. In this chapter, many different computational approaches including Quantitative Structure-Activity Relationship (QSAR) and virtual screening in anti-HCV drug discovery were considered and discussed in detail. Virtual Screening (VS) techniques, including ligand-based and structure-based, and QSAR have been utilized for the discovery of NS5B inhibitors. Moreover, using various in silico protocols and workflows, a number of studies have been conducted with an aim of identifying potential NS3/4A blockage agents.
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Affiliation(s)
| | | | | | - Duy-Phong Le
- University of Medicine and Pharmacy at HCMC, Vietnam
| | - Minh-Tri Le
- University of Medicine and Pharmacy at HCMC, Vietnam
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Li M, Wen F, Zhao S, Wang P, Li S, Zhang Y, Zheng N, Wang J. Exploring the Molecular Basis for Binding of Inhibitors by Threonyl-tRNA Synthetase from Brucella abortus: A Virtual Screening Study. Int J Mol Sci 2016; 17:E1078. [PMID: 27447614 PMCID: PMC4964454 DOI: 10.3390/ijms17071078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/19/2016] [Accepted: 06/29/2016] [Indexed: 01/18/2023] Open
Abstract
Targeting threonyl-tRNA synthetase (ThrRS) of Brucella abortus is a promising approach to developing small-molecule drugs against bovine brucellosis. Using the BLASTp algorithm, we identified ThrRS from Escherichia coli (EThrRS, PDB ID 1QF6), which is 51% identical to ThrRS from Brucella abortus (BaThrRS) at the amino acid sequence level. EThrRS was used as the template to construct a BaThrRS homology model which was optimized using molecular dynamics simulations. To determine the residues important for substrate ATP binding, we identified the ATP-binding regions of BaThrRS, docked ATP to the protein, and identified the residues whose side chains surrounded bound ATP. We then used the binding site of ATP to virtually screen for BaThrRS inhibitors and got seven leads. We further characterized the BaThrRS-binding site of the compound with the highest predicted inhibitory activity. Our results should facilitate future experimental effects to find novel drugs for use against bovine brucellosis.
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Affiliation(s)
- Ming Li
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Fang Wen
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Shengguo Zhao
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Pengpeng Wang
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Songli Li
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Yangdong Zhang
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Nan Zheng
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Jiaqi Wang
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Abstract
It is now plausible to dock libraries of 10 million molecules against targets over several days or weeks. When the molecules screened are commercially available, they may be rapidly tested to find new leads. Although docking retains important liabilities (it cannot calculate affinities accurately nor even reliably rank order high-scoring molecules), it can often can distinguish likely from unlikely ligands, often with hit rates above 10%. Here we summarize the improvements in libraries, target quality, and methods that have supported these advances, and the open access resources that make docking accessible. Recent docking screens for new ligands are sketched, as are the binding, crystallographic, and in vivo assays that support them. Like any technique, controls are crucial, and key experimental ones are reviewed. With such controls, docking campaigns can find ligands with new chemotypes, often revealing the new biology that may be docking's greatest impact over the next few years.
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Affiliation(s)
- John J Irwin
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
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Jazayeri A, Dias JM, Marshall FH. From G Protein-coupled Receptor Structure Resolution to Rational Drug Design. J Biol Chem 2015; 290:19489-95. [PMID: 26100628 DOI: 10.1074/jbc.r115.668251] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A number of recent technical solutions have led to significant advances in G protein-coupled receptor (GPCR) structural biology. Apart from a detailed mechanistic view of receptor activation, the new structures have revealed novel ligand binding sites. Together, these insights provide avenues for rational drug design to modulate the activities of these important drug targets. The application of structural data to GPCR drug discovery ushers in an exciting era with the potential to improve existing drugs and discover new ones. In this review, we focus on technical solutions that have accelerated GPCR crystallography as well as some of the salient findings from structures that are relevant to drug discovery. Finally, we outline some of the approaches used in GPCR structure based drug design.
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Affiliation(s)
- Ali Jazayeri
- From Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden City AL7 3AX, United Kingdom
| | - Joao M Dias
- From Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden City AL7 3AX, United Kingdom
| | - Fiona H Marshall
- From Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden City AL7 3AX, United Kingdom
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