1
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Liashuk OS, Andriashvili VA, Tolmachev AO, Grygorenko OO. Chemoselective Reactions of Functionalized Sulfonyl Halides. CHEM REC 2024; 24:e202300256. [PMID: 37823680 DOI: 10.1002/tcr.202300256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/13/2023] [Indexed: 10/13/2023]
Abstract
Chemoselective transformations of functionalized sulfonyl fluorides and chlorides are surveyed comprehensively. It is shown that sulfonyl fluorides provide an excellent selectivity control in their reactions. Thus, numerous conditions are tolerated by the SO2 F group - from amide and ester formation to directed ortho-lithiation and transition-metal-catalyzed cross-couplings. Meanwhile, sulfur (VI) fluoride exchange (SuFEx) is also compatible with numerous functional groups, thus confirming its title of "another click reaction". On the contrary, with a few exceptions, most transformations of functionalized sulfonyl chlorides typically occur at the SO2 Cl moiety.
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Affiliation(s)
- Oleksandr S Liashuk
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
| | - Vladyslav A Andriashvili
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
| | - Andriy O Tolmachev
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
| | - Oleksandr O Grygorenko
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
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2
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ElHefnawi M, Jo E, Tolba MM, Fares M, Yang J, Shahbaaz M, Windisch MP. Drug repurposing through virtual screening and in vitro validation identifies tigecycline as a novel putative HCV polymerase inhibitor. Virology 2022; 570:9-17. [DOI: 10.1016/j.virol.2022.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/25/2022] [Accepted: 02/26/2022] [Indexed: 10/18/2022]
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3
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Elghoneimy LK, Ismail MI, Boeckler FM, Azzazy HME, Ibrahim TM. Facilitating SARS CoV-2 RNA-Dependent RNA polymerase (RdRp) drug discovery by the aid of HCV NS5B palm subdomain binders: In silico approaches and benchmarking. Comput Biol Med 2021; 134:104468. [PMID: 34015671 PMCID: PMC8111889 DOI: 10.1016/j.compbiomed.2021.104468] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/25/2021] [Accepted: 04/30/2021] [Indexed: 01/18/2023]
Abstract
Corona Virus 2019 Disease (COVID-19) is a rapidly emerging pandemic caused by a newly discovered beta coronavirus, called Sever Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2). SARS CoV-2 is an enveloped, single stranded RNA virus that depends on RNA-dependent RNA polymerase (RdRp) to replicate. Therefore, SARS CoV-2 RdRp is considered as a promising target to cease virus replication. SARS CoV-2 polymerase shows high structural similarity to Hepatitis C Virus-1b genotype (HCV-1b) polymerase. Arising from the high similarity between SARS CoV-2 RdRp and HCV NS5B, we utilized the reported small-molecule binders to the palm subdomain of HCV NS5B (genotype 1b) to generate a high-quality DEKOIS 2.0 benchmark set and conducted a benchmarking analysis against HCV NS5B. The three highly cited and publicly available docking tools AutoDock Vina, FRED and PLANTS were benchmarked. Based on the benchmarking results and analysis via pROC-Chemotype plot, PLANTS showed the best screening performance and can recognize potent binders at the early enrichment. Accordingly, we used PLANTS in a prospective virtual screening to repurpose both the FDA-approved drugs (DrugBank) and the HCV-NS5B palm subdomain binders (BindingDB) for SARS CoV-2 RdRp palm subdomain. Further assessment by molecular dynamics simulations for 50 ns recommended diosmin (from DrugBank) and compound 3 (from BindingDB) to be the best potential binders to SARS CoV-2 RdRp palm subdomain. The best predicted compounds are recommended to be biologically investigated against COVID-19. In conclusion, this work provides in-silico analysis to propose possible SARS CoV-2 RdRp palm subdomain binders recommended as a remedy for COVID-19. Up-to-our knowledge, this study is the first to propose binders at the palm subdomain of SARS CoV2 RdRp. Furthermore, this study delivers an example of how to make use of a high quality custom-made DEKOIS 2.0 benchmark set as a procedure to elevate the virtual screening success rate against a vital target of the rapidly emerging pandemic.
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Affiliation(s)
- Laila K Elghoneimy
- Department of Chemistry, School of Sciences and Engineering, American University in Cairo, AUC Avenue, SSE # 1184, P.O. Box 74, New Cairo, 11835, Egypt
| | - Muhammad I Ismail
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt, Al-Sherouk City, Cairo-Suez Desert Road, 11837, Cairo, Egypt
| | - Frank M Boeckler
- Department of Pharmacy, Eberhard-Karls University, Auf der Morgenstelle 8, 72076, Tuebingen, Germany
| | - Hassan M E Azzazy
- Department of Chemistry, School of Sciences and Engineering, American University in Cairo, AUC Avenue, SSE # 1184, P.O. Box 74, New Cairo, 11835, Egypt
| | - Tamer M Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt.
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4
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Chang L, Zhu GY, Yang T, Zhao XL, Shi M, Zhao MX. Organocatalytic asymmetric formal [3 + 2] cycloaddition reaction of isocyanoacetates with saccharin-derived 1-azadienes. Org Biomol Chem 2021; 19:3687-3697. [PMID: 33908569 DOI: 10.1039/d1ob00115a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
An efficient organocatalytic diastereo- and enantioselective formal [3 + 2] cycloaddition reaction of α-isocyanoacetates with saccharin-derived 1-azadienes catalyzed by a dihydroquinine derived squaramide catalyst has been investigated, and it furnished the corresponding directly linked benzo[d]isothiazole 1,1-dioxide-dihydropyrroles with two adjacent tertiary-quaternary stereocenters in high yields (up to 98%), with moderate to excellent stereoselectivities (up to >20 : 1 dr and 97% ee) under mild conditions.
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Affiliation(s)
- Li Chang
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.
| | - Guang-Yu Zhu
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.
| | - Ting Yang
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.
| | - Xiao-Li Zhao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Min Shi
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China. and State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Road, Shanghai 200032, China
| | - Mei-Xin Zhao
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China.
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5
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Tosstorff A, Cole JC, Taylor R, Harris SF, Kuhn B. Identification of Noncompetitive Protein–Ligand Interactions for Structural Optimization. J Chem Inf Model 2020; 60:6595-6611. [DOI: 10.1021/acs.jcim.0c00858] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Andreas Tosstorff
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
| | - Jason C. Cole
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
| | - Robin Taylor
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
| | - Seth F. Harris
- Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Bernd Kuhn
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
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6
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Facile synthesis of tricyclic isoxazole-fused benzo[b]thiophene 1,1-dioxide derivatives via 1,3-dipolar cycloaddition. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151943] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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7
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Chen XL, Tang BC, He C, Ma JT, Zhuang SY, Wu YD, Wu AX. Rongalite as a sulfone source: a novel copper-catalyzed sulfur dioxide anion incorporation process. Chem Commun (Camb) 2020; 56:13653-13656. [DOI: 10.1039/d0cc05800a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A novel copper-catalyzed sulfur dioxide anion incorporation cascade for the synthesis of 1-thiaflavanone sulfones has been disclosed using rongalite as an economic and safe sulfone source.
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Affiliation(s)
- Xiang-Long Chen
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
| | - Bo-Cheng Tang
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
| | - Cai He
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
| | - Jin-Tian Ma
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
| | - Shi-Yi Zhuang
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
| | - Yan-Dong Wu
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
| | - An-Xin Wu
- Key Laboratory of Pesticide & Chemical Biology
- Ministry of Education
- College of Chemistry
- Central China Normal University
- Wuhan 430079
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8
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Murray AB, Quadri M, Li H, McKenna R, Horenstein NA. Synthesis of saccharin-glycoconjugates targeting carbonic anhydrase using a one-pot cyclization/deprotection strategy. Carbohydr Res 2019; 476:65-70. [PMID: 30921738 DOI: 10.1016/j.carres.2019.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/23/2019] [Accepted: 03/02/2019] [Indexed: 11/26/2022]
Abstract
Carbonic anhydrase IX (CA IX) has been identified as a biomarker and drug target for several malignant tumors due to its role in cancer cell growth and proliferation. Simple cyclic sulfonamides, like saccharin (SAC), have shown up to a 60-fold selectivity towards CA IX over other ubiquitous CA isoforms, with greater selectivity obtained applying the "tail-approach" to derivatize SAC with a methylene triazole linker that connected to a "tail" beta glucoside. These modifications of SAC led to an increased selectivity of more than 1000-fold towards CA IX, whereas clinically available CA inhibitors show little to no isoform selectivity. As part of our interest in the development of new CA inhibitors, we found the existing synthetic protocol, which relies on a N-tert-butyl saccharin intermediate, to be problematic in the final deprotection steps. We therefore describe an alternative approach to the synthesis of these compounds featuring a gentle "one pot" deprotection/cyclization as the final synthetic step, and report new galactosyl and glucosyl conjugates with low to mid nM inhibition of CA IX.
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Affiliation(s)
- Akilah B Murray
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Marta Quadri
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, 32611, USA
| | - Haoxi Li
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, 32611, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Nicole A Horenstein
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, 32611, USA.
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9
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Ma Y, Wang K, Zhang D, Sun P. Solvent Controlled Transformation between Sulfonyl Hydrazides and Alkynes: Divergent Synthesis of Benzo[
b
]thiophene‐1,1‐dioxides and (E)‐β‐iodo Vinylsulfones. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201801258] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yue Ma
- Artemisinin Research Center and Institute of Chinese Materia MedicaChina Academy of Chinese Medical Sciences Beijing 100700 People's Republic of China
| | - Kun Wang
- Artemisinin Research Center and Institute of Chinese Materia MedicaChina Academy of Chinese Medical Sciences Beijing 100700 People's Republic of China
| | - Dong Zhang
- Artemisinin Research Center and Institute of Chinese Materia MedicaChina Academy of Chinese Medical Sciences Beijing 100700 People's Republic of China
| | - Peng Sun
- Artemisinin Research Center and Institute of Chinese Materia MedicaChina Academy of Chinese Medical Sciences Beijing 100700 People's Republic of China
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10
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Wang AF, Hao WJ, Zhu YL, Li G, Zhou P, Tu SJ, Jiang B. Double SO 2 Insertion into 1,7-Diynes Leading to Functionalized Naphtho[1,2- c]thiophene 2,2-dioxides. ACS OMEGA 2018; 3:1482-1491. [PMID: 31458474 PMCID: PMC6641491 DOI: 10.1021/acsomega.7b01789] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/23/2018] [Indexed: 05/04/2023]
Abstract
A novel metal-free double SO2 insertion/multicomponent bicyclization cascade of benzene-linked 1,7-diynes has been established by treatment with aryldiazonium tetrafluoroborates and DABCO-bis(sulfur dioxide) under redox-neutral conditions, providing a range of dual sulfone-containing naphtho[1,2-c]thiophene 2,2-dioxides with generally high stereoselectivity. The reaction pathway is proposed to proceed through the sequence of arylsulfonyl-radical-induced 6-exo-dig/5-endo-trig bicyclization, H-abstraction, and diazotization.
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Affiliation(s)
- Ai-Fang Wang
- School
of Chemistry & Materials Science, Jiangsu
Normal University, Xuzhou 221116, P. R. China
| | - Wen-Juan Hao
- School
of Chemistry & Materials Science, Jiangsu
Normal University, Xuzhou 221116, P. R. China
- E-mail: (W.-J.H.)
| | - Yi-Long Zhu
- School
of Chemistry & Materials Science, Jiangsu
Normal University, Xuzhou 221116, P. R. China
| | - Guigen Li
- Institute
of Chemistry & BioMedical Sciences, Nanjing University, Nanjing 210093, P. R. China
- Department
of Chemistry and Biochemistry, Texas Tech
University, Lubbock, Texas 79409-1061, United States
| | - Peng Zhou
- Institute
of Chemistry & BioMedical Sciences, Nanjing University, Nanjing 210093, P. R. China
| | - Shu-Jiang Tu
- School
of Chemistry & Materials Science, Jiangsu
Normal University, Xuzhou 221116, P. R. China
- E-mail: (S.-J.T.)
| | - Bo Jiang
- School
of Chemistry & Materials Science, Jiangsu
Normal University, Xuzhou 221116, P. R. China
- E-mail: (B.J.)
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11
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Chen Y, Aurell CJ, Pettersen A, Lewis RJ, Hayes MA, Lepistö M, Jonson AC, Leek H, Thunberg L. Saccharin Aza Bioisosteres-Synthesis and Preclinical Property Comparisons. ACS Med Chem Lett 2017. [PMID: 28626531 DOI: 10.1021/acsmedchemlett.7b00137] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Saccharin is a well-known scaffold in drug discovery. Herein, we report the synthesis and preclinical property comparisons of three bioisosteres of saccharin: aza-pseudosaccharins (cluster B), and two new types of aza-saccharins (clusters C and D). We demonstrate a convenient protocol to selectively synthesize products in cluster C or D when primary amines are used. Preclinical characterization of selected matched-pair products is reported. Through comparison of two diastereomers, we highlight how stereochemistry affects the preclinical properties. Given that saccharin-based derivatives are widely used in many chemistry fields, we foresee that structures exemplified by clusters C and D offer new opportunities for novel drug design, creating a chiral center on the sulfur atom and the option of substitution at two different nitrogens.
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Affiliation(s)
- Yantao Chen
- Medicinal Chemistry, Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development, AstraZeneca R&D Gothenburg, 431 83 Mölndal, Sweden
| | - Carl-Johan Aurell
- Large Scale Chemistry, Early Chemical Development, Pharmaceutical Sciences, AstraZeneca R&D Gothenburg, 431 83 Mölndal, Sweden
| | - Anna Pettersen
- Pharmaceutical Technology
and Development, Product Development, AstraZeneca Operations Gothenburg, 431 83 Mölndal, Sweden
| | - Richard J. Lewis
- Medicinal Chemistry, Respiratory, Inflammation and Autoimmunity, Innovative Medicines and Early Development, AstraZeneca R&D Gothenburg, 431 83 Mölndal, Sweden
| | - Martin A. Hayes
- DMPK, Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development, AstraZeneca R&D Gothenburg, 431 83 Mölndal, Sweden
| | - Matti Lepistö
- Medicinal Chemistry, Respiratory, Inflammation and Autoimmunity, Innovative Medicines and Early Development, AstraZeneca R&D Gothenburg, 431 83 Mölndal, Sweden
| | - Anna C. Jonson
- Medicinal Chemistry, Respiratory, Inflammation and Autoimmunity, Innovative Medicines and Early Development, AstraZeneca R&D Gothenburg, 431 83 Mölndal, Sweden
| | - Hanna Leek
- Medicinal Chemistry, Respiratory, Inflammation and Autoimmunity, Innovative Medicines and Early Development, AstraZeneca R&D Gothenburg, 431 83 Mölndal, Sweden
| | - Linda Thunberg
- Medicinal Chemistry, Respiratory, Inflammation and Autoimmunity, Innovative Medicines and Early Development, AstraZeneca R&D Gothenburg, 431 83 Mölndal, Sweden
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12
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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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13
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Wei Y, Li J, Qing J, Huang M, Wu M, Gao F, Li D, Hong Z, Kong L, Huang W, Lin J. Discovery of Novel Hepatitis C Virus NS5B Polymerase Inhibitors by Combining Random Forest, Multiple e-Pharmacophore Modeling and Docking. PLoS One 2016; 11:e0148181. [PMID: 26845440 PMCID: PMC4742222 DOI: 10.1371/journal.pone.0148181] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 01/14/2016] [Indexed: 02/07/2023] Open
Abstract
The NS5B polymerase is one of the most attractive targets for developing new drugs to block Hepatitis C virus (HCV) infection. We describe the discovery of novel potent HCV NS5B polymerase inhibitors by employing a virtual screening (VS) approach, which is based on random forest (RB-VS), e-pharmacophore (PB-VS), and docking (DB-VS) methods. In the RB-VS stage, after feature selection, a model with 16 descriptors was used. In the PB-VS stage, six energy-based pharmacophore (e-pharmacophore) models from different crystal structures of the NS5B polymerase with ligands binding at the palm I, thumb I and thumb II regions were used. In the DB-VS stage, the Glide SP and XP docking protocols with default parameters were employed. In the virtual screening approach, the RB-VS, PB-VS and DB-VS methods were applied in increasing order of complexity to screen the InterBioScreen database. From the final hits, we selected 5 compounds for further anti-HCV activity and cellular cytotoxicity assay. All 5 compounds were found to inhibit NS5B polymerase with IC50 values of 2.01-23.84 μM and displayed anti-HCV activities with EC50 values ranging from 1.61 to 21.88 μM, and all compounds displayed no cellular cytotoxicity (CC50 > 100 μM) except compound N2, which displayed weak cytotoxicity with a CC50 value of 51.3 μM. The hit compound N2 had the best antiviral activity against HCV, with a selective index of 32.1. The 5 hit compounds with new scaffolds could potentially serve as NS5B polymerase inhibitors through further optimization and development.
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Affiliation(s)
- Yu Wei
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China
| | - Jinlong Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China
- High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biomedicine and Technology, Tianjin, 300457, China
| | - Jie Qing
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Mingjie Huang
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ming Wu
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Fenghua Gao
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Dongmei Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China
| | - Zhangyong Hong
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Lingbao Kong
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
- * E-mail: (JPL); (WH); (LK)
| | - Weiqiang Huang
- PracticaChem-China, Tianjin, 300192, PR China
- * E-mail: (JPL); (WH); (LK)
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, 300071, China
- High-Throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biomedicine and Technology, Tianjin, 300457, China
- * E-mail: (JPL); (WH); (LK)
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14
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Mao R, Zheng D, Xia H, Wu J. Copper(i)-catalyzed sulfonylation of (2-alkynylaryl)boronic acids with DABSO. Org Chem Front 2016. [DOI: 10.1039/c6qo00070c] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The scaffold of benzo[b]thiophene 1,1-dioxides can be easily constructed through a copper(i)-catalyzed insertion of sulfur dioxide into (2-alkynylaryl)boronic acids. The reaction proceeds via insertion of sulfur dioxide and subsequent intramolecular 5-endo cyclization.
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Affiliation(s)
- Runyu Mao
- Department of Chemistry
- Fudan University
- Shanghai 200433
- China
| | - Danqing Zheng
- Department of Chemistry
- Fudan University
- Shanghai 200433
- China
| | - Hongguang Xia
- Department of Biochemistry and Molecular Biology
- Zhejiang University School of Medicine
- Hangzhou 310058
- China
| | - Jie Wu
- Department of Chemistry
- Fudan University
- Shanghai 200433
- China
- State Key Laboratory of Organometallic Chemistry
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15
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Luo Y, Pan X, Chen C, Yao L, Wu J. An unexpected reaction of 2-alkynylaryldiazonium tetrafluoroborate with sulfur dioxide. Chem Commun (Camb) 2015; 51:180-2. [PMID: 25387522 DOI: 10.1039/c4cc07938h] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
An unexpected result from the reaction of 2-alkynylaryldiazonium tetrafluoroborate with sulfur dioxide is described. In the presence of morpholin-4-amine, this transformation catalyzed by copper(i) bromide proceeds through insertion of sulfur dioxide and intramolecular 5-endo cyclization, leading to benzo[b]thiophene 1,1-dioxides in moderate to good yields.
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Affiliation(s)
- Yong Luo
- Department of Chemistry
- Fudan University
- Shanghai 200433
- China
| | - Xiaolin Pan
- Department of Chemistry
- Fudan University
- Shanghai 200433
- China
| | - Chen Chen
- Obstetrics and Gynecology Hospital
- Fudan University
- Shanghai 200011
- China
| | - Liangqing Yao
- Obstetrics and Gynecology Hospital
- Fudan University
- Shanghai 200011
- China
| | - Jie Wu
- Department of Chemistry
- Fudan University
- Shanghai 200433
- China
- State Key Laboratory of Organometallic Chemistry
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16
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Dürüst Y, Sağırlı A, Kariuki BM, Knight DW. [1,3]-Dipolar cycloaddition of N-aryl sydnones to benzothiophene 1,1-dioxide, 1-cyclopropylprop-2-yn-1-ol and 1-(prop-2-ynyl)-1H-indole. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.04.083] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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Yu H, Fang Y, Lu X, Liu Y, Zhang H. Combined 3D-QSAR, molecular docking, molecular dynamics simulation, and binding free energy calculation studies on the 5-hydroxy-2H-pyridazin-3-one derivatives as HCV NS5B polymerase inhibitors. Chem Biol Drug Des 2013; 83:89-105. [PMID: 23941500 DOI: 10.1111/cbdd.12203] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Revised: 06/08/2013] [Accepted: 06/19/2013] [Indexed: 12/14/2022]
Abstract
The NS5B RNA-dependent RNA polymerase (RdRP) is a promising therapeutic target for developing novel anti-hepatitis C virus (HCV) drugs. In this work, a combined molecular modeling study was performed on a series of 193 5-hydroxy-2H-pyridazin-3-one derivatives as inhibitors of HCV NS5B Polymerase. The best 3D-QSAR models, including CoMFA and CoMSIA, are based on receptor (or docking). Furthermore, a 40-ns molecular dynamics (MD) simulation and binding free energy calculations using docked structures of NS5B with ten compounds, which have diverse structures and pIC50 values, were employed to determine the detailed binding process and to compare the binding modes of the inhibitors with different activities. On one side, the stability and rationality of molecular docking and 3D-QSAR results were validated by MD simulation. The binding free energies calculated by the MM-PBSA method gave a good correlation with the experimental biological activity. On the other side, by analyzing some differences between the molecular docking and the MD simulation results, we can find that the MD simulation could also remedy the defects of molecular docking. The analyses of the combined molecular modeling results have identified that Tyr448, Ser556, and Asp318 are the key amino acid residues in the NS5B binding pocket. The results from this study can provide some insights into the development of novel potent NS5B inhibitors.
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Affiliation(s)
- Haijing Yu
- Key Laboratory of Radiopharmaceuticals of Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
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18
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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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19
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Multiple virtual screening approaches for finding new hepatitis C virus RNA-dependent RNA polymerase inhibitors: structure-based screens and molecular dynamics for the pursue of new poly pharmacological inhibitors. BMC Bioinformatics 2012; 13 Suppl 17:S5. [PMID: 23282180 PMCID: PMC3521232 DOI: 10.1186/1471-2105-13-s17-s5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The RNA polymerase NS5B of Hepatitis C virus (HCV) is a well-characterised drug target with an active site and four allosteric binding sites. This work presents a workflow for virtual screening and its application to Drug Bank screening targeting the Hepatitis C Virus (HCV) RNA polymerase non-nucleoside binding sites. Potential polypharmacological drugs are sought with predicted active inhibition on viral replication, and with proven positive pharmaco-clinical profiles. The approach adopted was receptor-based. Docking screens, guided with contact pharmacophores and neural-network activity prediction models on all allosteric binding sites and MD simulations, constituted our analysis workflow for identification of potential hits. Steps included: 1) using a two-phase docking screen with Surflex and Glide Xp. 2) Ranking based on scores, and important H interactions. 3) a machine-learning target-trained artificial neural network PIC prediction model used for ranking. This provided a better correlation of IC50 values of the training sets for each site with different docking scores and sub-scores. 4) interaction pharmacophores-through retrospective analysis of protein-inhibitor complex X-ray structures for the interaction pharmacophore (common interaction modes) of inhibitors for the five non-nucleoside binding sites were constructed. These were used for filtering the hits according to the critical binding feature of formerly reported inhibitors. This filtration process resulted in identification of potential new inhibitors as well as formerly reported ones for the thumb II and Palm I sites (HCV-81) NS5B binding sites. Eventually molecular dynamics simulations were carried out, confirming the binding hypothesis and resulting in 4 hits.
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20
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Van Tonder J, Gohain M, Loganathan N, Bezuidenhoudt BCB. 2,5-Dihexyl-thio-phene 1,1-dioxide. Acta Crystallogr Sect E Struct Rep Online 2012; 68:o3437. [PMID: 23476254 PMCID: PMC3589018 DOI: 10.1107/s1600536812046867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 11/14/2012] [Indexed: 11/10/2022]
Abstract
In the title mol-ecule, C16H28O2S, the two n-hexyl groups are in all-trans conformations. Their C atoms are situated close to the plane of the thio-phene ring with a maximum deviation of 0.718 (6) Å for one of the terminal methyl groups. In the crystal, a short C-H⋯O contact is observed between thio-phene 1,1-dioxide groups.
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Affiliation(s)
- Johannes Van Tonder
- Department of Chemistry, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa
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21
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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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22
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Lardy MA, LeBrun L, Bullard D, Kissinger C, Gobbi A. Building a Three-Dimensional Model of CYP2C9 Inhibition Using the Autocorrelator: An Autonomous Model Generator. J Chem Inf Model 2012; 52:1328-36. [DOI: 10.1021/ci200558e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Laurie LeBrun
- Anadys Pharmaceuticals, Inc., San Diego, CA, United States
| | - Drew Bullard
- Anadys Pharmaceuticals, Inc., San Diego, CA, United States
| | | | - Alberto Gobbi
- Anadys Pharmaceuticals, Inc., San Diego, CA, United States
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23
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Mahmoud AH, Mohamed Abouzid KA, El Ella DAERA, Hamid Ismail MA. Optimization of Benzoisothiazole dioxide inhibitory activity of the NS5B polymerase of HCV genotype 4 using ligand-steered homological modeling, reaction-driven scaffold-hopping and Enovo workflow. Bioinformation 2011; 7:328-33. [PMID: 22355232 PMCID: PMC3280486 DOI: 10.6026/97320630007328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 11/18/2011] [Indexed: 11/27/2022] Open
Abstract
Infection caused by hepatitis C virus (HCV) is a significant world health problem for which novel therapies are in urgent demand. The virus is highly prevalent in the Middle East and Africa particularly Egypt with more than 90% of infections due to genotype 4. Nonstructural (NS5B) viral proteins have emerged as an attractive target for HCV antivirals discovery. A potent class of inhibitors having benzisothiazole dioxide scaffold has been identified on this target, however they were mainly active on genotype 1 while exhibiting much lowered activity on other genotypes due to the high degree of mutation of its binding site. Based on this fact, we employed a novel strategy to optimize this class on genotype 4. This strategy depends on using a refined ligand-steered homological model of this genotype to study the mutation binding energies of the binding site amino acid residues, the essential features for interaction and provide a structure-based pharmacophore model that can aid optimization. This model was applied on a focused library which was generated using a reaction-driven scaffold-hopping strategy. The hits retrieved were subjected to Enovo pipeline pilot optimization workflow that employs R-group enumeration, core-constrained protein docking using modified CDOCKER and finally ranking of poses using an accurate molecular mechanics generalized Born with surface area method.
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Affiliation(s)
- Amr Hamed Mahmoud
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
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24
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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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25
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Antonow D, Marrafa T, Dawood I, Ahmed T, Haque MR, Thurston DE, Zinzalla G. Facile oxidation of electron-poor benzo[b]thiophenes to the corresponding sulfones with an aqueous solution of H2O2 and P2O5. Chem Commun (Camb) 2010; 46:2289-91. [DOI: 10.1039/b924333j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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de Vicente J, Hendricks RT, Smith DB, Fell JB, Fischer J, Spencer SR, Stengel PJ, Mohr P, Robinson JE, Blake JF, Hilgenkamp RK, Yee C, Adjabeng G, Elworthy TR, Li J, Wang B, Bamberg JT, Harris SF, Wong A, Leveque VJP, Najera I, Le Pogam S, Rajyaguru S, Ao-Ieong G, Alexandrova L, Larrabee S, Brandl M, Briggs A, Sukhtankar S, Farrell R. Non-nucleoside inhibitors of HCV polymerase NS5B. Part 4: structure-based design, synthesis, and biological evaluation of benzo[d]isothiazole-1,1-dioxides. Bioorg Med Chem Lett 2009; 19:5652-6. [PMID: 19709881 DOI: 10.1016/j.bmcl.2009.08.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2009] [Revised: 08/04/2009] [Accepted: 08/05/2009] [Indexed: 12/09/2022]
Abstract
A series of benzo[d]isothiazole-1,1-dioxides were designed and evaluated as inhibitors of HCV polymerase NS5B. Structure-based design led to the incorporation of a high affinity methyl sulfonamide group. Structure-activity relationship (SAR) studies of this series revealed analogues with submicromolar potencies in the HCV replicon assay and moderate pharmacokinetic properties. SAR studies combined with structure based drug design focused on the sulfonamide region led to a novel and potent cyclic analogue.
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Affiliation(s)
- Javier de Vicente
- Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, CA 94304, USA.
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27
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3-Hydroxyisoquinolines as inhibitors of HCV NS5b RNA-dependent RNA polymerase. Bioorg Med Chem Lett 2009; 19:410-4. [PMID: 19070486 DOI: 10.1016/j.bmcl.2008.11.060] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Revised: 11/13/2008] [Accepted: 11/17/2008] [Indexed: 12/17/2022]
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