1
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Martino SD, Petri GL, De Rosa M. Hepatitis C: The Story of a Long Journey through First, Second, and Third Generation NS3/4A Peptidomimetic Inhibitors. What Did We Learn? J Med Chem 2024; 67:885-921. [PMID: 38179950 DOI: 10.1021/acs.jmedchem.3c01971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Hepatitis C viral (HCV) infection is the leading cause of liver failure and still represents a global health burden. Over the past decade, great advancements made HCV curable, and sustained viral remission significantly improved to more than 98%. Historical treatment with pegylated interferon alpha and ribavirin has been displaced by combinations of direct-acting antivirals. These regimens include drugs targeting different stages of the HCV life cycle. However, the emergence of viral resistance remains a big concern. The design of peptidomimetic inhibitors (PIs) able to fit and fill the conserved substrate envelope region within the active site helped avoid contact with the vulnerable sites of the most common resistance-associated substitutions Arg155, Ala156, and Asp168. Herein, we give an overview of HCV NS3 PIs discovered during the past decade, and we deeply discuss the rationale behind the structural optimization efforts essential to achieve pangenotypic activity.
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Affiliation(s)
- Simona Di Martino
- Drug Discovery Unit, Medicinal Chemistry Group, Ri.MED Foundation, Palermo 90133, Italy
| | - Giovanna Li Petri
- Drug Discovery Unit, Medicinal Chemistry Group, Ri.MED Foundation, Palermo 90133, Italy
| | - Maria De Rosa
- Drug Discovery Unit, Medicinal Chemistry Group, Ri.MED Foundation, Palermo 90133, Italy
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2
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Shcherbakov NV, Dar'in DV, Kukushkin VY, Dubovtsev AY. Gold-Catalyzed Nitrene Transfer from Benzofuroxans to N-Allylynamides: Synthesis of 3-Azabicyclo[3.1.0]hexanes. J Org Chem 2021; 86:12964-12972. [PMID: 34472847 DOI: 10.1021/acs.joc.1c01654] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The gold-catalyzed reaction between benzofuroxans, functioning as nitrene transfer reagents, and N-allylynamides leads to 3-azabicyclo[3.1.0]hexan-2-imines. This highly selective annulation proceeds smoothly under mild conditions (5 mol % Ph3PAuNTf2, PhCl, 60 °C) and exhibits high functional group tolerance (21 examples, ≤96% yields). The obtained cyclopropanated products represent a useful synthetic platform with an easily modulated substitution pattern as illustrated by their postmodifications. Intramolecular cyclopropanation of gold α-imino carbene intermediates is suggested as a key step of the catalytic cycle.
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Affiliation(s)
- Nikolay V Shcherbakov
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russian Federation
| | - Dmitry V Dar'in
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russian Federation
| | - Vadim Yu Kukushkin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russian Federation
| | - Alexey Yu Dubovtsev
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya Nab. 7/9, 199034 Saint Petersburg, Russian Federation
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3
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Filatov AS, Wang S, Khoroshilova OV, Lozovskiy SV, Larina AG, Boitsov VM, Stepakov AV. Stereo- and Regioselective 1,3-Dipolar Cycloaddition of the Stable Ninhydrin-Derived Azomethine Ylide to Cyclopropenes: Trapping of Unstable Cyclopropene Dipolarophiles. J Org Chem 2019; 84:7017-7036. [PMID: 31066276 DOI: 10.1021/acs.joc.9b00753] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A stereo- and regioselective 1,3-dipolar cycloaddition of the stable ninhydrin-derived azomethine ylide [2-(3,4-dihydro-2 H-pyrrolium-1-yl)-1-oxo-1 H-inden-3-olate, DHPO] to differently substituted cyclopropenes has been established. As a result, an efficient synthetic protocol was developed for the preparation of biologically relevant spiro[cyclopropa[ a]pyrrolizine-2,2'-indene] derivatives. DHPO has proved to be an effective trap for such highly reactive and unstable substrates as parent cyclopropene, 1-methylcyclopropene, 1-phenylcyclopropene, and 1-halo-2-phenylcyclopropenes. It has also been found that 3-nitro-1,2-diphenylcyclopropene undergoes a nucleophilic substitution reaction in alcohols and thiols to afford 3-alkoxy- and 3-arylthio-substituted 1,2-diphenylcyclopropenes, which can be captured as corresponding 1,3-dipolar cycloadducts in the presence of DHPO. These new approaches provide a straightforward strategy for the synthesis of functionally substituted cyclopropa[ a]pyrrolizine derivatives. The factors governing regio- and stereoselectivity have been revealed by means of quantum mechanical calculations (M11 density functional theory), including previously unreported Nylide- Hcyclopropene second-orbital interactions. The outcome of this work contributes to the study of 1,3-dipolar cycloaddition, as well as enriches chemistry of cyclopropenes and methods for the construction of polycyclic compounds with cyclopropane fragments.
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Affiliation(s)
- Alexander S Filatov
- Institute of Chemistry , Saint Petersburg State University , Universitetsky pr. 26 , 198504 St. Petersburg , Russian Federation
| | - Siqi Wang
- Institute of Chemistry , Saint Petersburg State University , Universitetsky pr. 26 , 198504 St. Petersburg , Russian Federation
| | - Olesya V Khoroshilova
- Institute of Chemistry , Saint Petersburg State University , Universitetsky pr. 26 , 198504 St. Petersburg , Russian Federation
| | - Stanislav V Lozovskiy
- Institute of Chemistry , Saint Petersburg State University , Universitetsky pr. 26 , 198504 St. Petersburg , Russian Federation
| | - Anna G Larina
- Institute of Chemistry , Saint Petersburg State University , Universitetsky pr. 26 , 198504 St. Petersburg , Russian Federation
| | - Vitali M Boitsov
- Saint Petersburg Academic University , ul. Khlopina 8/3 , 194021 St. Petersburg , Russian Federation.,Pavlov First Saint Petersburg State Medical University , ul. L'va Tolstogo 6/8 , 197022 St. Petersburg , Russian Federation
| | - Alexander V Stepakov
- Institute of Chemistry , Saint Petersburg State University , Universitetsky pr. 26 , 198504 St. Petersburg , Russian Federation.,Saint Petersburg State Institute of Technology , Moskovskii pr. 26 , 190013 St. Petersburg , Russian Federation
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4
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Konstantinidou M, Kurpiewska K, Kalinowska-Tłuscik J, Dömling A. Glutarimide Alkaloids Through Multicomponent Reaction Chemistry. European J Org Chem 2018. [DOI: 10.1002/ejoc.201801276] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | - Katarzyna Kurpiewska
- Faculty of Chemistry; Jagiellonian University; 3 Ingardena Street 30-060 Krakow Poland
| | | | - Alexander Dömling
- Drug Design; University of Groningen; A. Deusinglaan 1 9713 AV Groningen The Netherlands
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5
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Belfrage AK, Abdurakhmanov E, Åkerblom E, Brandt P, Alogheli H, Neyts J, Danielson UH, Sandström A. Pan-NS3 protease inhibitors of hepatitis C virus based on an R3-elongated pyrazinone scaffold. Eur J Med Chem 2018; 148:453-464. [DOI: 10.1016/j.ejmech.2018.02.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 01/20/2018] [Accepted: 02/10/2018] [Indexed: 02/07/2023]
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6
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Maslivetc V, Barrett C, Aksenov NA, Rubina M, Rubin M. Intramolecular nucleophilic addition of carbanions generated from N-benzylamides to cyclopropenes. Org Biomol Chem 2018; 16:285-294. [PMID: 29242861 PMCID: PMC5755969 DOI: 10.1039/c7ob02068f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An unusual reaction is described, involving a formal intramolecular nucleophilic substitution of bromocyclopropanes with nitrogen ylides generated in situ from N-benzyl carboxamides. It is shown that this reaction involves cyclopropene intermediates and allows for the facile and expeditious preparation of 3-azabicyclo[3.1.0]hexan-2-one scaffolds.
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Affiliation(s)
- Vladimir Maslivetc
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr., Lawrence, KS 66045-7582, USA.
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7
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Yuan Y, Zheng ZJ, Ye F, Ma JH, Xu Z, Bai XF, Li L, Xu LW. Highly efficient desymmetrization of cyclopropenes to azabicyclo[3.1.0]hexanes with five continuous stereogenic centers by copper-catalyzed [3 + 2] cycloadditions. Org Chem Front 2018. [DOI: 10.1039/c8qo00761f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An unprecedented copper-catalyzed desymmetrization/cycloaddition reaction of 1,1-disubstituted cyclopropenes provides an efficient access to azabicyclo[3.1.0]hexanes bearing five continuous carbon-stereogenic centers.
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Affiliation(s)
- Yang Yuan
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education
- Hangzhou Normal University
- P. R. China
| | - Zhan-Jiang Zheng
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education
- Hangzhou Normal University
- P. R. China
| | - Fei Ye
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education
- Hangzhou Normal University
- P. R. China
| | - Jun-Han Ma
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education
- Hangzhou Normal University
- P. R. China
| | - Zheng Xu
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education
- Hangzhou Normal University
- P. R. China
| | - Xing-Feng Bai
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education
- Hangzhou Normal University
- P. R. China
| | - Li Li
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education
- Hangzhou Normal University
- P. R. China
| | - Li-Wen Xu
- Key Laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education
- Hangzhou Normal University
- P. R. China
- State Key Laboratory for Oxo Synthesis and Selective Oxidation
- Suzhou Research Institute and Lanzhou Institute of Chemical Physics
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8
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Konnert L, Lamaty F, Martinez J, Colacino E. Recent Advances in the Synthesis of Hydantoins: The State of the Art of a Valuable Scaffold. Chem Rev 2017. [PMID: 28644621 DOI: 10.1021/acs.chemrev.7b00067] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The review highlights the hydantoin syntheses presented from the point of view of the preparation methods. Novel synthetic routes to various hydantoin structures, the advances brought to the classical methods in the aim of producing more sustainable and environmentally friendly procedures for the preparation of these biomolecules, and a critical comparison of the different synthetic approaches developed in the last twelve years are also described. The review is composed of 95 schemes, 8 figures and 528 references for the last 12 years and includes the description of the hydantoin-based marketed drugs and clinical candidates.
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Affiliation(s)
- Laure Konnert
- Université de Montpellier, Institut des Biomolécules Max Mousseron UMR 5247 CNRS - Universités Montpellier - ENSCM , Place E. Bataillon, Campus Triolet, cc 1703, 34095 Montpellier, France
| | - Frédéric Lamaty
- Université de Montpellier, Institut des Biomolécules Max Mousseron UMR 5247 CNRS - Universités Montpellier - ENSCM , Place E. Bataillon, Campus Triolet, cc 1703, 34095 Montpellier, France
| | - Jean Martinez
- Université de Montpellier, Institut des Biomolécules Max Mousseron UMR 5247 CNRS - Universités Montpellier - ENSCM , Place E. Bataillon, Campus Triolet, cc 1703, 34095 Montpellier, France
| | - Evelina Colacino
- Université de Montpellier, Institut des Biomolécules Max Mousseron UMR 5247 CNRS - Universités Montpellier - ENSCM , Place E. Bataillon, Campus Triolet, cc 1703, 34095 Montpellier, France
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9
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Abstract
Chirality is a key factor in the safety and efficacy of many drug products and thus the production of single enantiomers of drug intermediates and drugs has become important and state of the art in the pharmaceutical industry. There has been an increasing awareness of the enormous potential of microorganisms and enzymes (biocatalysts) for the transformation of synthetic chemicals with high chemo-, regio- and enatioselectivities providing products in high yields and purity. In this article, biocatalytic processes are described for the synthesis of key chiral intermediates for development pharmaceuticals.
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Affiliation(s)
- Ramesh N Patel
- SLRP Associates, LLC, Consultation in Biocatalysis and Biotechnology, 572 Cabot Hill Road, Bridgewater, NJ 08807, USA.
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10
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Discovery of a series of novel compounds with moderate anti-hepatitis C virus NS3 protease activity in vitro. Bioorg Med Chem 2015; 23:5539-45. [PMID: 26238980 DOI: 10.1016/j.bmc.2015.07.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/16/2015] [Accepted: 07/17/2015] [Indexed: 01/02/2023]
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11
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Belfrage AK, Gising J, Svensson F, Åkerblom E, Sköld C, Sandström A. Efficient and Selective Palladium-Catalysed C-3 Urea Couplings to 3,5-Dichloro-2(1H)-pyrazinones. European J Org Chem 2015. [DOI: 10.1002/ejoc.201403405] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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12
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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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13
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Lv HS, Zhang JH, Xie YS, Zhao BX. Synthesis and X-ray Crystal Structure of Novel (3E,4E)-1-aryl-3,4-bis[(benzo[d][1,3]dioxol-5-yl)methylidene]pyrrolidene-2,5-dione. JOURNAL OF CHEMICAL RESEARCH 2013. [DOI: 10.3184/174751913x13686149475125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A series of novel (3E,4E)-1-aryl-3,4-bis[(benzo[d][1,3]dioxol-5-yl)methylidene]pyrrolidene-2,5-dione derivatives was synthesised and characterised by IR, 1H NMR and HRMS. Moreover, the molecular structure of (3E,4E)-3,4-bis [(benzo[d][1,3]dioxol-5-yl)methylene]-1-(4-ethoxyphenyl)pyrrolidine-2,5-dione was confirmed by the X-ray crystal structure determination.
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Affiliation(s)
- Hong-Shui Lv
- Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China
| | - Jin-Hua Zhang
- Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China
| | - Yong-Sheng Xie
- Department of Chemical and Environment Engineering, Chongqing Three Gorges University, Chongqing 404000, P. R. China
| | - Bao-Xiang Zhao
- Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, P. R. China
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14
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Trembling PM, Tanwar S, Dusheiko GM. Boceprevir: an oral protease inhibitor for the treatment of chronic HCV infection. Expert Rev Anti Infect Ther 2012; 10:269-79. [PMID: 22397560 DOI: 10.1586/eri.12.8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Chronic hepatitis C (CHC) virus infection affects more than 170 million people globally. The aim of treatment of CHC is to affect sustained elimination of the virus (a sustained virological response [SVR]). The success and duration of therapy with interferon is dependent on HCV genotype. The current standard of care comprises combined treatment with pegylated interferon and ribavirin. Rates of SVR in patients with genotype 1 infection, the least responsive group, are less than 50%. Boceprevir is a ketoamide protease inhibitor that binds reversibly to the HCV nonstructural NS3 protease active site inhibiting intracellular viral replication. Phase III clinical studies have demonstrated that, in combination with the current standard of care, boceprevir significantly increases the SVR rate in both treatment-naive and previously treated patients with genotype 1 CHC. Both the US FDA and EMA have approved boceprevir for the treatment of genotype 1 CHC: the first directly-acting antiviral drug to be licensed for this indication. This article will review the pharmacology and pharmacodynamics of boceprevir, the efficacy and safety of the drug, and explore possible future developments in the management of CHC.
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Affiliation(s)
- Paul M Trembling
- Centre for Hepatology, UCL Medical School, Royal Free Hospital, Rowland Hill Street, London, NW3 2PF, UK
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15
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C-6 aryl substituted 4-quinolone-3-carboxylic acids as inhibitors of hepatitis C virus. Bioorg Med Chem 2012; 20:4790-800. [PMID: 22748708 DOI: 10.1016/j.bmc.2012.05.066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 05/21/2012] [Accepted: 05/29/2012] [Indexed: 12/20/2022]
Abstract
Quinolone-3-carboxylic acid represents a highly privileged chemotype in medicinal chemistry and has been extensively explored as antibiotics and antivirals targeting human immunodeficiency virus (HIV) integrase (IN). Herein we describe the synthesis and anti-hepatitis C virus (HCV) profile of a series of C-6 aryl substituted 4-quinlone-3-carboxylic acid analogues. Significant inhibition was observed with a few analogues at low micromolar range against HCV replicon in cell culture and a reduction in replicon RNA was confirmed through an RT-qPCR assay. Interestingly, evaluation of analogues as inhibitors of NS5B in a biochemical assay yielded only modest inhibitory activities, suggesting that a different mechanism of action could operate in cell culture.
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16
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Li T, Liang J, Ambrogelly A, Brennan T, Gloor G, Huisman G, Lalonde J, Lekhal A, Mijts B, Muley S, Newman L, Tobin M, Wong G, Zaks A, Zhang X. Efficient, chemoenzymatic process for manufacture of the Boceprevir bicyclic [3.1.0]proline intermediate based on amine oxidase-catalyzed desymmetrization. J Am Chem Soc 2012; 134:6467-72. [PMID: 22409428 DOI: 10.1021/ja3010495] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The key structural feature in Boceprevir, Merck's new drug treatment for hepatitis C, is the bicyclic [3.1.0]proline moiety "P2". During the discovery and development stages, the P2 fragment was produced by a classical resolution approach. As the drug candidate advanced through clinical trials and approached regulatory approval and commercialization, Codexis and Schering-Plough (now Merck) jointly developed a chemoenzymatic asymmetric synthesis of P2 where the net reaction was an oxidative Strecker reaction. The key part of this reaction sequence is an enzymatic oxidative desymmetrization of the prochiral amine substrate.
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Affiliation(s)
- Tao Li
- Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, USA.
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Synthesis of 5-benzyl-2-phenylpyrazolo[1,5-a]pyrazin-4,6(5H,7H)-dione derivatives and discovery of an apoptosis inducer for H322 lung cancer cells. Bioorg Med Chem Lett 2012; 22:844-9. [DOI: 10.1016/j.bmcl.2011.12.049] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 12/07/2011] [Accepted: 12/09/2011] [Indexed: 11/18/2022]
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18
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Chen YL, Tang J, Kesler MJ, Sham YY, Vince R, Geraghty RJ, Wang Z. The design, synthesis and biological evaluations of C-6 or C-7 substituted 2-hydroxyisoquinoline-1,3-diones as inhibitors of hepatitis C virus. Bioorg Med Chem 2011; 20:467-79. [PMID: 22100256 DOI: 10.1016/j.bmc.2011.10.058] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 10/13/2011] [Accepted: 10/18/2011] [Indexed: 12/14/2022]
Abstract
C7-Substituted 2-hydroxyisoquinoline-1,3-diones inhibit the strand transfer of HIV integrase (IN) and the reverse-transcriptase-associated ribonuclease H (RNH). Hepatitis C virus (HCV) NS5B polymerase shares a similar active site fold to RNH and IN, suggesting that N-hydroxyimides could be useful inhibitor scaffolds of HCV via targeting the NS5B. Herein we describe the design, chemical synthesis, replicon and biochemical assays, and molecular docking of C-6 or C-7 aryl substituted 2-hydroxyisoquinoline-1,3-diones as novel HCV inhibitors. The synthesis involved an improved and clean cyclization method, which allowed the convenient preparation of various analogs. Biological studies revealed that the C-6 analogs, a previously unknown chemotype, consistently inhibit both HCV replicon and recombinant NS5B at low micromolar range. Molecular modeling studies suggest that these inhibitors may bind to the NS5B active site.
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Affiliation(s)
- Yue-Lei Chen
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware St. SE, MMC 204, Minneapolis, MN 55455, USA
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19
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Abstract
The use of Quantitative Structure-Activity Relationship models to address problems in drug discovery has a mixed history, generally resulting from the misapplication of QSAR models that were either poorly constructed or used outside of their domains of applicability. This situation has motivated the development of a variety of model performance metrics (r(2), PRESS r(2), F-tests, etc.) designed to increase user confidence in the validity of QSAR predictions. In a typical workflow scenario, QSAR models are created and validated on training sets of molecules using metrics such as Leave-One-Out or many-fold cross-validation methods that attempt to assess their internal consistency. However, few current validation methods are designed to directly address the stability of QSAR predictions in response to changes in the information content of the training set. Since the main purpose of QSAR is to quickly and accurately estimate a property of interest for an untested set of molecules, it makes sense to have a means at hand to correctly set user expectations of model performance. In fact, the numerical value of a molecular prediction is often less important to the end user than knowing the rank order of that set of molecules according to their predicted end point values. Consequently, a means for characterizing the stability of predicted rank order is an important component of predictive QSAR. Unfortunately, none of the many validation metrics currently available directly measure the stability of rank order prediction, making the development of an additional metric that can quantify model stability a high priority. To address this need, this work examines the stabilities of QSAR rank order models created from representative data sets, descriptor sets, and modeling methods that were then assessed using Kendall Tau as a rank order metric, upon which the Shannon entropy was evaluated as a means of quantifying rank-order stability. Random removal of data from the training set, also known as Data Truncation Analysis (DTA), was used as a means for systematically reducing the information content of each training set while examining both rank order performance and rank order stability in the face of training set data loss. The premise for DTA ROE model evaluation is that the response of a model to incremental loss of training information will be indicative of the quality and sufficiency of its training set, learning method, and descriptor types to cover a particular domain of applicability. This process is termed a "rank order entropy" evaluation or ROE. By analogy with information theory, an unstable rank order model displays a high level of implicit entropy, while a QSAR rank order model which remains nearly unchanged during training set reductions would show low entropy. In this work, the ROE metric was applied to 71 data sets of different sizes and was found to reveal more information about the behavior of the models than traditional metrics alone. Stable, or consistently performing models, did not necessarily predict rank order well. Models that performed well in rank order did not necessarily perform well in traditional metrics. In the end, it was shown that ROE metrics suggested that some QSAR models that are typically used should be discarded. ROE evaluation helps to discern which combinations of data set, descriptor set, and modeling methods lead to usable models in prioritization schemes and provides confidence in the use of a particular model within a specific domain of applicability.
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Liu Q, Zhou H, Liu L, Chen X, Zhu R, Cao Z. Multi-target QSAR modelling in the analysis and design of HIV-HCV co-inhibitors: an in-silico study. BMC Bioinformatics 2011; 12:294. [PMID: 21774796 PMCID: PMC3167801 DOI: 10.1186/1471-2105-12-294] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 07/20/2011] [Indexed: 12/13/2022] Open
Abstract
Background HIV and HCV infections have become the leading global public-health threats. Even more remarkable, HIV-HCV co-infection is rapidly emerging as a major cause of morbidity and mortality throughout the world, due to the common rapid mutation characteristics of the two viruses as well as their similar complex influence to immunology system. Although considerable progresses have been made on the study of the infection of HIV and HCV respectively, few researches have been conducted on the investigation of the molecular mechanism of their co-infection and designing of the multi-target co-inhibitors for the two viruses simultaneously. Results In our study, a multi-target Quantitative Structure-Activity Relationship (QSAR) study of the inhibitors for HIV-HCV co-infection were addressed with an in-silico machine learning technique, i.e. multi-task learning, to help to guide the co-inhibitor design. Firstly, an integrated dataset with 3 HIV inhibitor subsets targeted on protease, integrase and reverse transcriptase respectively, together with another 6 subsets of 2 HCV inhibitors targeted on NS3 serine protease and NS5B polymerase respectively were compiled. Secondly, an efficient multi-target QSAR modelling of HIV-HCV co-inhibitors was performed by applying an accelerated gradient method based multi-task learning on the whole 9 datasets. Furthermore, by solving the L-1-infinity regularized optimization, the Drug-like index features for compound description were ranked according to their joint importance in multi-target QSAR modelling of HIV and HCV. Finally, a drug structure-activity simulation for investigating the relationships between compound structures and binding affinities was presented based on our multiple target analysis, which is then providing several novel clues for the design of multi-target HIV-HCV co-inhibitors with increasing likelihood of successful therapies on HIV, HCV and HIV-HCV co-infection. Conclusions The framework presented in our study provided an efficient way to identify and design inhibitors that simultaneously and selectively bind to multiple targets from multiple viruses with high affinity, and will definitely shed new lights on the future work of inhibitor synthesis for multi-target HIV, HCV, and HIV-HCV co-infection treatments.
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Affiliation(s)
- Qi Liu
- College of Life Science and Biotechnology, Tongji University, 200092, China
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Venkatraman S, Velazquez F, Wu W, Blackman M, Madison V, Njoroge FG. Potent ketoamide inhibitors of HCV NS3 protease derived from quaternized P1 groups. Bioorg Med Chem Lett 2010; 20:2151-5. [DOI: 10.1016/j.bmcl.2010.02.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 02/10/2010] [Accepted: 02/10/2010] [Indexed: 10/19/2022]
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22
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Nair LG, Bogen S, Ruan S, Pan W, Pike R, Tong X, Cheng KC, Guo Z, Doll RJ, Njoroge FG. Towards the second generation of Boceprevir: Dithianes as an alternative P2 substituent for 2,2-dimethyl cycloproyl proline in HCV NS3 protease inhibitors. Bioorg Med Chem Lett 2010; 20:1689-92. [DOI: 10.1016/j.bmcl.2010.01.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 01/08/2010] [Accepted: 01/11/2010] [Indexed: 01/03/2023]
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23
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Nair LG, Bogen S, Doll RJ, Shih NY, Njoroge FG. Synthesis of sterically hindered 3,5,5-trimethyl 2,6-dioxo tetrahydro pyrimidine as HCV protease inhibitors. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2009.12.129] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Bogen SL, Arasappan A, Velazquez F, Blackman M, Huelgas R, Pan W, Siegel E, Nair LG, Venkatraman S, Guo Z, Doll R, Shih NY, Njoroge FG. Discovery of potent sulfonamide P4-capped ketoamide second generation inhibitors of hepatitis C virus NS3 serine protease with favorable pharmacokinetic profiles in preclinical species. Bioorg Med Chem 2010; 18:1854-65. [PMID: 20149666 DOI: 10.1016/j.bmc.2010.01.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 01/16/2010] [Indexed: 12/28/2022]
Abstract
Hepatitis is a disease characterized by inflammation of the liver, usually producing swelling and, in many cases, permanent damage to liver tissues. Viral hepatitis C (HCV), a small (+)-RNA virus, infects chronically 3% of the world's population. Boceprevir, SCH 503034, (1) our first generation HCV inhibitor, has already established proof-of- concept and is currently in late stage (phase III) clinical trials. In view of the positive data from our first generation compound, further work aimed at optimizing its overall profile was undertaken. Herein, we report that extension of our earlier inhibitor to the P(4) pocket by introducing a new sulfonamide moiety and optimization of the P1/P(1)' capping led to the discovery of a novel series of inhibitors of the HCV NS3 serine protease. Optimization of the P(1) residue significantly improved potency and selectivity. The combination of optimal moieties led to the discovery of compound 47 which, in addition to being a potent inhibitor of HCV subgenomic RNA replication, was also found to have good PK profile in rat, dog and monkey.
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Affiliation(s)
- Stéphane L Bogen
- Department of Medicinal Chemistry, Merck Research Labs, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.
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P4 capped amides and lactams as HCV NS3 protease inhibitors with improved potency and DMPK profile. Bioorg Med Chem Lett 2010; 20:567-70. [DOI: 10.1016/j.bmcl.2009.11.094] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 11/17/2009] [Accepted: 11/18/2009] [Indexed: 11/22/2022]
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Potent aza-peptide derived inhibitors of HCV NS3 protease. Bioorg Med Chem Lett 2009; 19:4760-3. [DOI: 10.1016/j.bmcl.2009.06.060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 06/08/2009] [Accepted: 06/15/2009] [Indexed: 12/24/2022]
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Meanwell NA, Kadow JF, Scola PM. Chapter 20 Progress towards the Discovery and Development of Specifically Targeted Inhibitors of Hepatitis C Virus. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2009. [DOI: 10.1016/s0065-7743(09)04420-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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