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Joon S, Singla RK, Shen B. In Silico Drug Discovery for Treatment of Virus Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1368:73-93. [DOI: 10.1007/978-981-16-8969-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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2
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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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3
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Antunes DA, Devaurs D, Kavraki LE. Understanding the challenges of protein flexibility in drug design. Expert Opin Drug Discov 2015; 10:1301-13. [DOI: 10.1517/17460441.2015.1094458] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Seçinti H, Seçen H. Synthesis of Two Natural Furan-Cyclized Diarylheptanoidsvia2-Furaldehyde. Helv Chim Acta 2015. [DOI: 10.1002/hlca.201400274] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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McKinney DC, Zhou F, Eyermann CJ, Ferguson AD, Prince DB, Breen J, Giacobbe RA, Lahiri S, Verheijen JC. 4,5-Disubstituted 6-Aryloxy-1,3-dihydrobenzo[c][1,2]oxaboroles Are Broad-Spectrum Serine β-Lactamase Inhibitors. ACS Infect Dis 2015; 1:310-6. [PMID: 27622821 DOI: 10.1021/acsinfecdis.5b00031] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Bacterially expressed β-lactamases are rapidly eroding the clinical utility of the important β-lactam class of antibacterials, significantly impairing our ability to fight serious bacterial infections. This paper describes a study of oxaborole-derived β-lactamase inhibitors in which crystal structures and computational modeling aided in the rational design of analogues with improved spectrum of activity against class A, C, and D enzymes. Crystal structures of two of these inhibitors covalently bound to two different serine β-lactamases, class C Pseudomonas aeruginosa AmpC and class D OXA-10, are described herein. Improved physicochemical properties as well as increased activity against an array of β-lactamases resulted in substantial restoration of susceptibility to ceftazidime in Escherichia coli and Klebsiella pneumoniae.
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Affiliation(s)
- David C. McKinney
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham Massachusetts 02451, United States
| | - Fei Zhou
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham Massachusetts 02451, United States
| | - Charles J. Eyermann
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham Massachusetts 02451, United States
| | | | | | | | - Robert A. Giacobbe
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham Massachusetts 02451, United States
| | - Sushmita Lahiri
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham Massachusetts 02451, United States
| | - Jeroen C. Verheijen
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham Massachusetts 02451, United States
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6
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Virtual Screening and Molecular Dynamics Simulations from a Bank of Molecules of the Amazon Region Against Functional NS3-4A Protease-Helicase Enzyme of Hepatitis C Virus. Appl Biochem Biotechnol 2015; 176:1709-21. [DOI: 10.1007/s12010-015-1672-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 05/17/2015] [Indexed: 10/23/2022]
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7
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Zhao X, Zhang L, Lu X, Li T, Lu K. Synthesis of 2-Aryl and 3-Aryl Benzo[b]furan Thioethers Using Aryl Sulfonyl Hydrazides as Sulfenylation Reagents. J Org Chem 2015; 80:2918-24. [DOI: 10.1021/acs.joc.5b00146] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Xia Zhao
- College
of Chemistry, Tianjin Key Laboratory of Structure and Performance
for Functional Molecules, Tianjin Normal University, Tianjin 300387, China
| | - Lipeng Zhang
- College
of Chemistry, Tianjin Key Laboratory of Structure and Performance
for Functional Molecules, Tianjin Normal University, Tianjin 300387, China
| | - Xiaoyu Lu
- College
of Chemistry, Tianjin Key Laboratory of Structure and Performance
for Functional Molecules, Tianjin Normal University, Tianjin 300387, China
| | - Tianjiao Li
- College
of Chemistry, Tianjin Key Laboratory of Structure and Performance
for Functional Molecules, Tianjin Normal University, Tianjin 300387, China
| | - Kui Lu
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
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Nevagi RJ, Dighe SN, Dighe SN. Biological and medicinal significance of benzofuran. Eur J Med Chem 2014; 97:561-81. [PMID: 26015069 DOI: 10.1016/j.ejmech.2014.10.085] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/15/2014] [Accepted: 10/31/2014] [Indexed: 11/29/2022]
Abstract
This article emphasizes on the importance of benzofuran as a biologically relevant heterocycle. It covers most of the physiologically as well as medicinally important compounds containing benzofuran rings. This article also covers clinically approved drugs containing benzofuran scaffold.
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Affiliation(s)
- Reshma J Nevagi
- Department of Pharmaceutical Chemistry, SMBT College of Pharmacy, Nandi Hills, Dhamangaon, Igatpuri, Nashik 422403, Maharashtra, India
| | - Santosh N Dighe
- Department of Chemistry, Sir Parshurambhau College, Pune 30, Maharashtra, India
| | - Satish N Dighe
- Department of Pharmaceutical Chemistry, Sinhgad College of Pharmacy, Vadgaon (BK), Pune, Maharashtra, India.
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9
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Qiu S, Chen F, Liu Y, Lai L. Discovery of Novel Secretory Phospholipase A2Inhibitors Using Virtual Screen. Chem Biol Drug Des 2014; 84:216-22. [DOI: 10.1111/cbdd.12307] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/11/2014] [Accepted: 02/14/2014] [Indexed: 12/14/2022]
Affiliation(s)
- Shunchen Qiu
- BNLMS; State Key Laboratory of Structural Chemistry for Unstable and Stable Species; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Fangjin Chen
- Center for Quantitative Biology; Peking University; Beijing 100871 China
| | - Ying Liu
- BNLMS; State Key Laboratory of Structural Chemistry for Unstable and Stable Species; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Center for Quantitative Biology; Peking University; Beijing 100871 China
| | - Luhua Lai
- BNLMS; State Key Laboratory of Structural Chemistry for Unstable and Stable Species; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
- Center for Quantitative Biology; Peking University; Beijing 100871 China
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Abstract
Docking methodology aims to predict the experimental binding modes and affinities of small molecules within the binding site of particular receptor targets and is currently used as a standard computational tool in drug design for lead compound optimisation and in virtual screening studies to find novel biologically active molecules. The basic tools of a docking methodology include a search algorithm and an energy scoring function for generating and evaluating ligand poses. In this review, we present the search algorithms and scoring functions most commonly used in current molecular docking methods that focus on protein-ligand applications. We summarise the main topics and recent computational and methodological advances in protein-ligand docking. Protein flexibility, multiple ligand binding modes and the free-energy landscape profile for binding affinity prediction are important and interconnected challenges to be overcome by further methodological developments in the docking field.
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Identification of novel small molecules as inhibitors of hepatitis C virus by structure-based virtual screening. Int J Mol Sci 2013; 14:22845-56. [PMID: 24264035 PMCID: PMC3856094 DOI: 10.3390/ijms141122845] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 11/06/2013] [Accepted: 11/07/2013] [Indexed: 12/30/2022] Open
Abstract
Hepatitis C virus (HCV) NS3/NS4A serine protease is essential for viral replication, which is regarded as a promising drug target for developing direct-acting anti-HCV agents. In this study, sixteen novel compounds with cell-based HCV replicon activity ranging from 3.0 to 28.2 μM (IC50) were successfully identified by means of structure-based virtual screening. Compound 5 and compound 11, with an IC50 of 3.0 μM and 5.1 μM, respectively, are the two most potent molecules with low cytotoxicity.
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12
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Smieško M. DOLINA – Docking Based on a Local Induced-Fit Algorithm: Application toward Small-Molecule Binding to Nuclear Receptors. J Chem Inf Model 2013; 53:1415-23. [DOI: 10.1021/ci400098y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Martin Smieško
- Department of Pharmaceutical
Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
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14
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Yuriev E, Ramsland PA. Latest developments in molecular docking: 2010-2011 in review. J Mol Recognit 2013; 26:215-39. [PMID: 23526775 DOI: 10.1002/jmr.2266] [Citation(s) in RCA: 193] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 01/16/2013] [Accepted: 01/19/2013] [Indexed: 12/28/2022]
Affiliation(s)
- Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences; Monash University; Parkville; VIC; 3052; Australia
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15
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Takaya D, Sato T, Yuki H, Sasaki S, Tanaka A, Yokoyama S, Honma T. Prediction of Ligand-Induced Structural Polymorphism of Receptor Interaction Sites Using Machine Learning. J Chem Inf Model 2013; 53:704-16. [DOI: 10.1021/ci300458g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Daisuke Takaya
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
| | - Tomohiro Sato
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
| | - Hitomi Yuki
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
| | - Shunta Sasaki
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
| | - Akiko Tanaka
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
- Department of Biophysics and
Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Teruki Honma
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama 230-0045, Japan
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Murgueitio MS, Bermudez M, Mortier J, Wolber G. In silico virtual screening approaches for anti-viral drug discovery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2012; 9:e219-25. [PMID: 24990575 PMCID: PMC7105918 DOI: 10.1016/j.ddtec.2012.07.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Despite the considerable advances in medical and pharmaceutical research during the past years, diseases caused by viruses have remained a major burden to public health. Virtual in silico screening has repeatedly proven to be useful to meet the special challenges of antiviral drug discovery. Large virtual compound libraries are filtered by different computational screening methods such as docking, ligand-based similarity searches or pharmacophore-based screening, reducing the number of candidate molecules to a smaller set of promising candidates that are then tested biologically. This rational approach makes the drug discovery process more goal-oriented and saves resources in terms of time and money. In this review we discuss how different virtual screening techniques can be applied to antiviral drug discovery, present recent success stories in this field and finally address the main differences between the methods.:
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Affiliation(s)
- Manuela S Murgueitio
- Freie Universität Berlin, Institute of Pharmacy, Department Pharmaceutical Chemistry, Koenigin-Luise-Str. 2, 14195 Berlin, Germany
| | - Marcel Bermudez
- Freie Universität Berlin, Institute of Pharmacy, Department Pharmaceutical Chemistry, Koenigin-Luise-Str. 2, 14195 Berlin, Germany
| | - Jérémie Mortier
- Freie Universität Berlin, Institute of Pharmacy, Department Pharmaceutical Chemistry, Koenigin-Luise-Str. 2, 14195 Berlin, Germany
| | - Gerhard Wolber
- Freie Universität Berlin, Institute of Pharmacy, Department Pharmaceutical Chemistry, Koenigin-Luise-Str. 2, 14195 Berlin, Germany.
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