1
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Implications of Fragment-Based Drug Discovery in Tuberculosis and HIV. Pharmaceuticals (Basel) 2022; 15:ph15111415. [PMID: 36422545 PMCID: PMC9692459 DOI: 10.3390/ph15111415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis (TB) remains a global health problem and the emergence of HIV has further worsened it. Long chemotherapy and the emergence of drug-resistance strains of Mycobacterium tuberculosis as well as HIV has aggravated the problem. This demands urgent the need to develop new anti-tuberculosis and antiretrovirals to treat TB and HIV. The lack of diversity in drugs designed using traditional approaches is a major disadvantage and limits the treatment options. Therefore, new technologies and approaches are required to solve the current issues and enhance the production of drugs. Interestingly, fragment-based drug discovery (FBDD) has gained an advantage over high-throughput screenings as FBDD has enabled rapid and efficient progress to develop potent small molecule compounds that specifically bind to the target. Several potent inhibitor compounds of various targets have been developed using FBDD approach and some of them are under progression to clinical trials. In this review, we emphasize some of the important targets of mycobacteria and HIV. We also discussed about the target-based druggable molecules that are identified using the FBDD approach, use of these druggable molecules to identify novel binding sites on the target and assays used to evaluate inhibitory activities of these identified druggable molecules on the biological activity of the targets.
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2
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Design, synthesis and biological evaluation of imidazole and oxazole fragments as HIV-1 integrase-LEDGF/p75 disruptors and inhibitors of microbial pathogens. Bioorg Med Chem 2020; 28:115210. [DOI: 10.1016/j.bmc.2019.115210] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 10/23/2019] [Accepted: 11/05/2019] [Indexed: 12/17/2022]
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3
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Northfield SE, Wielens J, Headey SJ, Williams-Noonan BJ, Mulcair M, Scanlon MJ, Parker MW, Thompson PE, Chalmers DK. Cyclic Hexapeptide Mimics of the LEDGF Integrase Recognition Loop in Complex with HIV-1 Integrase. ChemMedChem 2018; 13:1555-1565. [PMID: 29862651 DOI: 10.1002/cmdc.201800129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/21/2018] [Indexed: 12/18/2022]
Abstract
The p75 splice variant of lens epithelium-derived growth factor (LEDGF) is a 75 kDa protein, which is recruited by the human immunodeficiency virus (HIV) to tether the pre-integration complex to the host chromatin and promote integration of proviral DNA into the host genome. We designed a series of small cyclic peptides that are structural mimics of the LEDGF binding domain, which interact with integrase as potential binding inhibitors. Herein we present the X-ray crystal structures, NMR studies, SPR analysis, and conformational studies of four cyclic peptides bound to the HIV-1 integrase core domain. Although the X-ray studies show that the peptides closely mimic the LEDGF binding loop, the measured affinities of the peptides are in the low millimolar range. Computational analysis using conformational searching and free energy calculations suggest that the low affinity of the peptides is due to mismatch between the low-energy solution and bound conformations.
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Affiliation(s)
- Susan E Northfield
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Jerome Wielens
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia.,ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria, 3065, Australia
| | - Stephen J Headey
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Billy J Williams-Noonan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Mark Mulcair
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Martin J Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Michael W Parker
- ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria, 3065, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria, 3010, Australia
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - David K Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
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4
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A structure-based design approach to advance the allyltyrosine-based series of HIV integrase inhibitors. Tetrahedron 2018. [DOI: 10.1016/j.tet.2017.11.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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5
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Burlein C, Wang C, Xu M, Bhatt T, Stahlhut M, Ou Y, Adam GC, Heath J, Klein DJ, Sanders J, Narayan K, Abeywickrema P, Heo MR, Carroll SS, Grobler JA, Sharma S, Diamond TL, Converso A, Krosky DJ. Discovery of a Distinct Chemical and Mechanistic Class of Allosteric HIV-1 Integrase Inhibitors with Antiretroviral Activity. ACS Chem Biol 2017; 12:2858-2865. [PMID: 29024587 DOI: 10.1021/acschembio.7b00550] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Allosteric integrase inhibitors (ALLINIs) bind to the lens epithelial-derived growth factor (LEDGF) pocket on HIV-1 integrase (IN) and possess potent antiviral effects. Rather than blocking proviral integration, ALLINIs trigger IN conformational changes that have catastrophic effects on viral maturation, rendering the virions assembled in the presence of ALLINIs noninfectious. A high-throughput screen for compounds that disrupt the IN·LEDGF interaction was executed, and extensive triage led to the identification of a t-butylsulfonamide series, as exemplified by 1. The chemical, biochemical, and virological characterization of this series revealed that 1 and its analogs produce an ALLINI-like phenotype through engagement of IN sites distinct from the LEDGF pocket. Key to demonstrating target engagement and differentiating this new series from the existing ALLINIs was the development of a fluorescence polarization probe of IN (FLIPPIN) based on the t-butylsulfonamide series. These findings further solidify the late antiviral mechanism of ALLINIs and point toward opportunities to develop structurally and mechanistically novel antiretroviral agents with unique resistance patterns.
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Affiliation(s)
- Christine Burlein
- Pharmacology, ‡Discovery Chemistry, §Screening and Protein Science, ∥Structural Chemistry, and ⊥Infectious Disease Biology, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Cheng Wang
- Pharmacology, ‡Discovery Chemistry, §Screening and Protein Science, ∥Structural Chemistry, and ⊥Infectious Disease Biology, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Min Xu
- Pharmacology, ‡Discovery Chemistry, §Screening and Protein Science, ∥Structural Chemistry, and ⊥Infectious Disease Biology, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Triveni Bhatt
- Pharmacology, ‡Discovery Chemistry, §Screening and Protein Science, ∥Structural Chemistry, and ⊥Infectious Disease Biology, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Mark Stahlhut
- Pharmacology, ‡Discovery Chemistry, §Screening and Protein Science, ∥Structural Chemistry, and ⊥Infectious Disease Biology, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Yangsi Ou
- Pharmacology, ‡Discovery Chemistry, §Screening and Protein Science, ∥Structural Chemistry, and ⊥Infectious Disease Biology, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Gregory C. Adam
- Pharmacology, ‡Discovery Chemistry, §Screening and Protein Science, ∥Structural Chemistry, and ⊥Infectious Disease Biology, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Jeffrey Heath
- Pharmacology, ‡Discovery Chemistry, §Screening and Protein Science, ∥Structural Chemistry, and ⊥Infectious Disease Biology, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Daniel J. Klein
- Pharmacology, ‡Discovery Chemistry, §Screening and Protein Science, ∥Structural Chemistry, and ⊥Infectious Disease Biology, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - John Sanders
- Pharmacology, ‡Discovery Chemistry, §Screening and Protein Science, ∥Structural Chemistry, and ⊥Infectious Disease Biology, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Kartik Narayan
- Pharmacology, ‡Discovery Chemistry, §Screening and Protein Science, ∥Structural Chemistry, and ⊥Infectious Disease Biology, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Pravien Abeywickrema
- Pharmacology, ‡Discovery Chemistry, §Screening and Protein Science, ∥Structural Chemistry, and ⊥Infectious Disease Biology, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Mee Ra Heo
- Pharmacology, ‡Discovery Chemistry, §Screening and Protein Science, ∥Structural Chemistry, and ⊥Infectious Disease Biology, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Steven S. Carroll
- Pharmacology, ‡Discovery Chemistry, §Screening and Protein Science, ∥Structural Chemistry, and ⊥Infectious Disease Biology, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Jay A. Grobler
- Pharmacology, ‡Discovery Chemistry, §Screening and Protein Science, ∥Structural Chemistry, and ⊥Infectious Disease Biology, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Sujata Sharma
- Pharmacology, ‡Discovery Chemistry, §Screening and Protein Science, ∥Structural Chemistry, and ⊥Infectious Disease Biology, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Tracy L. Diamond
- Pharmacology, ‡Discovery Chemistry, §Screening and Protein Science, ∥Structural Chemistry, and ⊥Infectious Disease Biology, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Antonella Converso
- Pharmacology, ‡Discovery Chemistry, §Screening and Protein Science, ∥Structural Chemistry, and ⊥Infectious Disease Biology, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Daniel J. Krosky
- Pharmacology, ‡Discovery Chemistry, §Screening and Protein Science, ∥Structural Chemistry, and ⊥Infectious Disease Biology, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
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6
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Abd El Razik HA, Badr MH, Atta AH, Mouneir SM, Abu-Serie MM. Benzodioxole-Pyrazole Hybrids as Anti-Inflammatory and Analgesic Agents with COX-1,2/5-LOX Inhibition and Antioxidant Potential. Arch Pharm (Weinheim) 2017; 350. [DOI: 10.1002/ardp.201700026] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/09/2017] [Accepted: 03/17/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Heba A. Abd El Razik
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry; Alexandria University; Alexandria Egypt
| | - Mona H. Badr
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry; Alexandria University; Alexandria Egypt
| | - Attia H. Atta
- Faculty of Veterinary Medicine, Department of Pharmacology; Cairo University; Cairo Egypt
| | - Samar M. Mouneir
- Faculty of Veterinary Medicine, Department of Pharmacology; Cairo University; Cairo Egypt
| | - Marwa M. Abu-Serie
- Genetic Engineering and Biotechnology Research Institute (GEBRI); City for Scientific Research and Technology Application, Borg El-Arab; Alexandria Egypt
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7
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Doak BC, Norton RS, Scanlon MJ. The ways and means of fragment-based drug design. Pharmacol Ther 2016; 167:28-37. [DOI: 10.1016/j.pharmthera.2016.07.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 07/08/2016] [Indexed: 12/21/2022]
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8
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Zhan P, Pannecouque C, De Clercq E, Liu X. Anti-HIV Drug Discovery and Development: Current Innovations and Future Trends. J Med Chem 2015; 59:2849-78. [PMID: 26509831 DOI: 10.1021/acs.jmedchem.5b00497] [Citation(s) in RCA: 229] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The early effectiveness of combinatorial antiretroviral therapy (cART) in the treatment of HIV infection has been compromised to some extent by rapid development of multidrug-resistant HIV strains, poor bioavailability, and cumulative toxicities, and so there is a need for alternative strategies of antiretroviral drug discovery and additional therapeutic agents with novel action modes or targets. From this perspective, we first review current strategies of antiretroviral drug discovery and optimization, with the aid of selected examples from the recent literature. We highlight the development of phosphate ester-based prodrugs as a means to improve the aqueous solubility of HIV inhibitors, and the introduction of the substrate envelope hypothesis as a new approach for overcoming HIV drug resistance. Finally, we discuss future directions for research, including opportunities for exploitation of novel antiretroviral targets, and the strategy of activation of latent HIV reservoirs as a means to eradicate the virus.
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Affiliation(s)
- Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Katholieke Universiteit Leuven , Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Katholieke Universiteit Leuven , Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
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9
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Esposito F, Tintori C, Martini R, Christ F, Debyser Z, Ferrarese R, Cabiddu G, Corona A, Ceresola ER, Calcaterra A, Iovine V, Botta B, Clementi M, Canducci F, Botta M, Tramontano E. Kuwanon-L as a New Allosteric HIV-1 Integrase Inhibitor: Molecular Modeling and Biological Evaluation. Chembiochem 2015; 16:2507-12. [PMID: 26360521 DOI: 10.1002/cbic.201500385] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Indexed: 12/22/2022]
Abstract
HIV-1 integrase (IN) active site inhibitors are the latest class of drugs approved for HIV treatment. The selection of IN strand-transfer drug-resistant HIV strains in patients supports the development of new agents that are active as allosteric IN inhibitors. Here, a docking-based virtual screening has been applied to a small library of natural ligands to identify new allosteric IN inhibitors that target the sucrose binding pocket. From theoretical studies, kuwanon-L emerged as the most promising binder and was thus selected for biological studies. Biochemical studies showed that kuwanon-L is able to inhibit the HIV-1 IN catalytic activity in the absence and in the presence of LEDGF/p75 protein, the IN dimerization, and the IN/LEDGF binding. Kuwanon-L also inhibited HIV-1 replication in cell cultures. Overall, docking and biochemical results suggest that kuwanon-L binds to an allosteric binding pocket and can be considered an attractive lead for the development of new allosteric IN antiviral agents.
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Affiliation(s)
- Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS 554, 09042, Monserrato, Cagliari, Italy
| | - Cristina Tintori
- Department of Biotechnologies, Chemical and Pharmacy, University of Siena, via Alcide de Gasperi 2, 53100, Siena, Italy
| | - Riccardo Martini
- Department of Biotechnologies, Chemical and Pharmacy, University of Siena, via Alcide de Gasperi 2, 53100, Siena, Italy
| | - Frauke Christ
- Laboratory for Molecular Virology and Gene Therapy, KU Leuven, 3000, Leuven, Flanders, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, KU Leuven, 3000, Leuven, Flanders, Belgium
| | - Roberto Ferrarese
- Laboratory of Virology, San Raffaele Hospital, IRCCS, via Olgettina 60, 20132, Milano, Italy
| | - Gianluigi Cabiddu
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS 554, 09042, Monserrato, Cagliari, Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS 554, 09042, Monserrato, Cagliari, Italy
| | - Elisa Rita Ceresola
- Laboratory of Virology, San Raffaele Hospital, IRCCS, via Olgettina 60, 20132, Milano, Italy
| | - Andrea Calcaterra
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Valentina Iovine
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Bruno Botta
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Massimo Clementi
- Laboratory of Virology, San Raffaele Hospital, IRCCS, via Olgettina 60, 20132, Milano, Italy
| | - Filippo Canducci
- Laboratory of Virology, San Raffaele Hospital, IRCCS, via Olgettina 60, 20132, Milano, Italy.,Department of Department of Biotechnology and Life Sciences, University of Insubria, via Ravasi 2, 21100, Varese, Italy
| | - Maurizio Botta
- Department of Biotechnologies, Chemical and Pharmacy, University of Siena, via Alcide de Gasperi 2, 53100, Siena, Italy.
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS 554, 09042, Monserrato, Cagliari, Italy.
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10
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Northfield SE, Mountford SJ, Wielens J, Liu M, Zhang L, Herzog H, Holliday ND, Scanlon MJ, Parker MW, Chalmers DK, Thompson PE. Propargyloxyproline Regio- and Stereoisomers for Click-Conjugation of Peptides: Synthesis and Application in Linear and Cyclic Peptides. Aust J Chem 2015. [DOI: 10.1071/ch15146] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The use of the click reaction for the introduction of conjugate groups, such as affinity or fluorescent labels, to a peptide for the study of peptide biochemistry and pharmacology is widespread. However, the nature and location of substituted 1,2,3-triazoles in peptide sequences may markedly affect conformation or binding as compared with native sequences. We have examined the preparation and application of propargyloxyproline (Pop) residues as a precursor to such peptide conjugates. Pop residues are available in a range of regio- and stereoisomers from hydroxyproline precursors and are readily prepared in Fmoc-protected form. They can be incorporated routinely in peptide synthesis and broadly retain the conformational properties of the parent proline containing peptides. This is exemplified by the preparation of biotin- and fluorophore-labelled peptides derived from linear and cyclic peptides.
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11
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Li Y, Xuan S, Feng Y, Yan A. Targeting HIV-1 integrase with strand transfer inhibitors. Drug Discov Today 2014; 20:435-49. [PMID: 25486307 DOI: 10.1016/j.drudis.2014.12.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 11/14/2014] [Accepted: 12/01/2014] [Indexed: 01/03/2023]
Abstract
HIV-1 integrase (IN) is a retroviral enzyme essential for integration of genetic material into the DNA of the host cell and hence for viral replication. The absence of an equivalent enzyme in humans makes IN an interesting target for anti-HIV drug design. This review briefly overviews the structural and functional properties of HIV-1 IN. We analyze the binding modes of the established drugs, clinical candidates and a comprehensive library of leads based on innovative chemical scaffolds of HIV-1 IN strand transfer inhibitors (INSTIs). Computational clustering techniques are applied for identifying structural features relating to bioactivity. From bio- and chemo-informatics analyses, we provide novel insights into structure-activity relationships of INSTIs and elaborate new strategies for design of innovative inhibitors.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, 15 BeiSanHuan East Road, P.O. Box 53, Beijing 100029, PR China
| | - Shouyi Xuan
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, 15 BeiSanHuan East Road, P.O. Box 53, Beijing 100029, PR China
| | - Yue Feng
- Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, 15 BeiSanHuan East Road, P.O. Box 53, Beijing 100029, PR China
| | - Aixia Yan
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, 15 BeiSanHuan East Road, P.O. Box 53, Beijing 100029, PR China.
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12
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Tiefenbrunn T, Stout CD. Towards novel therapeutics for HIV through fragment-based screening and drug design. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 116:124-40. [DOI: 10.1016/j.pbiomolbio.2014.09.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 09/15/2014] [Accepted: 09/29/2014] [Indexed: 12/17/2022]
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13
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García-Sosa AT, Maran U. Improving the use of ranking in virtual screening against HIV-1 integrase with triangular numbers and including ligand profiling with antitargets. J Chem Inf Model 2014; 54:3172-85. [PMID: 25303089 DOI: 10.1021/ci500300u] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A delicate balance exists between a drug molecule's toxicity and its activity. Indeed, efficacy, toxicity, and side effect problems are a common cause for the termination of drug candidate compounds and development projects. To address this, an antitarget interaction profile is built and combined with virtual screening and cross docking for new inhibitors of HIV-1 integrase, in order to consider possible off-target interactions as early as possible in a drug or hit discovery program. New ranking techniques using triangular numbers improve ranking information on the compounds and recovery of known inhibitors into the top compounds using different docking programs. This improved ranking arises from using consensus of ranks between docking programs and ligand efficiencies to derive a new rank, instead of using absolute score values, or average of ranks. The triangular number rerank also allowed the objective combination of results from several protein targets or screen conditions and several programs. Triangular number reranking conserves more information than other reranking methods such as average of scores or averages of ranks. In addition, the use of triangular numbers for reranking makes possible the use of thresholds with a justified leeway based on the number of available known inhibitors, so that the majority of the compounds above the threshold in ranks compare to the compounds that have known experimentally determined biological activity. The battery of anti- or off-targets can be tailored to specific molecular or drug design challenges. In silico filters can thus be deployed in successive stages, for prefiltering, activity profiling, and for further analysis and triaging of libraries of compounds.
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14
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Kong Y, Xuan S, Yan A. Computational models on quantitative prediction of bioactivity of HIV-1 integrase 3' processing inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2014; 25:729-746. [PMID: 25121566 DOI: 10.1080/1062936x.2014.942695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this study, four computational quantitative structure-activity relationship (QSAR) models were built to predict the bioactivity of 3' processing (3'P) inhibitors of HIV-1 integrase. Some 453 inhibitors whose bioactivity values were detected by the radiolabelling method were collected. The molecular structures were represented with MOE descriptors. In total, 21 descriptors were selected for modelling. All inhibitors were divided into a training set and a test set with two methods: (1) by a Kohonen's self-organizing map (SOM); (2) by a random selection. For every training set and test set, a multilinear regression (MLR) analysis and a support vector machine (SVM) were used to establish models, respectively. For the training/test set divided by SOM, the correlation coefficients (r) were over 0.84, and for the training/test set split randomly, the r values were over 0.86. Some molecular properties such as hydrogen bond donor capacity, atomic partial charge properties, molecular refractivity, the number of aromatic bonds and molecular surface area, volume and shape properties played important roles for inhibiting 3' processing step of HIV-1 integrase.
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Affiliation(s)
- Y Kong
- a State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering , Beijing University of Chemical Technology , Beijing , China
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15
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Kang D, Song Y, Chen W, Zhan P, Liu X. “Old Dogs with New Tricks”: exploiting alternative mechanisms of action and new drug design strategies for clinically validated HIV targets. MOLECULAR BIOSYSTEMS 2014; 10:1998-2022. [DOI: 10.1039/c4mb00147h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Costi R, Métifiot M, Chung S, Cuzzucoli Crucitti G, Maddali K, Pescatori L, Messore A, Madia VN, Pupo G, Scipione L, Tortorella S, Di Leva FS, Cosconati S, Marinelli L, Novellino E, Le Grice SFJ, Corona A, Pommier Y, Marchand C, Di Santo R. Basic quinolinonyl diketo acid derivatives as inhibitors of HIV integrase and their activity against RNase H function of reverse transcriptase. J Med Chem 2014; 57:3223-34. [PMID: 24684270 PMCID: PMC4203401 DOI: 10.1021/jm5001503] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
A series
of antiviral basic quinolinonyl diketo acid derivatives
were developed as inhibitors of HIV-1 IN. Compounds 12d,f,i inhibited HIV-1 IN with IC50 values below 100 nM for strand transfer and showed a 2 order of
magnitude selectivity over 3′-processing. These strand transfer
selective inhibitors also inhibited HIV-1 RNase H with low micromolar
potencies. Molecular modeling studies based on both the HIV-1 IN and
RNase H catalytic core domains provided new structural insights for
the future development of these compounds as dual HIV-1 IN and RNase
H inhibitors.
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Affiliation(s)
- Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma , P.le Aldo Moro 5, I-00185 Roma, Italy
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Perryman AL, Santiago DN, Forli S, Martins DS, Olson AJ. Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge. J Comput Aided Mol Des 2014; 28:429-441. [PMID: 24493410 DOI: 10.1007/s10822-014-9709-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 01/11/2014] [Indexed: 01/01/2023]
Abstract
To rigorously assess the tools and protocols that can be used to understand and predict macromolecular recognition, and to gain more structural insight into three newly discovered allosteric binding sites on a critical drug target involved in the treatment of HIV infections, the Olson and Levy labs collaborated on the SAMPL4 challenge. This computational blind challenge involved predicting protein-ligand binding against the three allosteric sites of HIV integrase (IN), a viral enzyme for which two drugs (that target the active site) have been approved by the FDA. Positive control cross-docking experiments were utilized to select 13 receptor models out of an initial ensemble of 41 different crystal structures of HIV IN. These 13 models of the targets were selected using our new "Rank Difference Ratio" metric. The first stage of SAMPL4 involved using virtual screens to identify 62 active, allosteric IN inhibitors out of a set of 321 compounds. The second stage involved predicting the binding site(s) and crystallographic binding mode(s) for 57 of these inhibitors. Our team submitted four entries for the first stage that utilized: (1) AutoDock Vina (AD Vina) plus visual inspection; (2) a new common pharmacophore engine; (3) BEDAM replica exchange free energy simulations, and a Consensus approach that combined the predictions of all three strategies. Even with the SAMPL4's very challenging compound library that displayed a significantly lower amount of structural diversity than most libraries that are conventionally employed in prospective virtual screens, these approaches produced hit rates of 24, 25, 34, and 27 %, respectively, on a set with 19 % declared binders. Our only entry for the second stage challenge was based on the results of AD Vina plus visual inspection, and it ranked third place overall according to several different metrics provided by the SAMPL4 organizers. The successful results displayed by these approaches highlight the utility of the computational structure-based drug discovery tools and strategies that are being developed to advance the goals of the newly created, multi-institution, NIH-funded center called the "HIV Interaction and Viral Evolution Center".
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Affiliation(s)
- Alexander L Perryman
- Department of Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel N Santiago
- Department of Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Stefano Forli
- Department of Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Diogo Santos Martins
- Department of Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Arthur J Olson
- Department of Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
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Xuan S, Wang M, Kang H, Kirchmair J, Tan L, Yan A. Support Vector Machine (SVM) Models for Predicting Inhibitors of the 3′ Processing Step of HIV-1 Integrase. Mol Inform 2013; 32:811-26. [DOI: 10.1002/minf.201300107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 07/26/2013] [Indexed: 01/24/2023]
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Serrao E, Debnath B, Otake H, Kuang Y, Christ F, Debyser Z, Neamati N. Fragment-based discovery of 8-hydroxyquinoline inhibitors of the HIV-1 integrase-lens epithelium-derived growth factor/p75 (IN-LEDGF/p75) interaction. J Med Chem 2013; 56:2311-22. [PMID: 23445471 DOI: 10.1021/jm301632e] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
On the basis of an initial molecular modeling study suggesting the favorable binding of the "privileged" fragment 8-hydroxyquinoline with HIV-1 integrase (IN) at the IN-lens epithelium-derived growth factor/p75 (LEDGF/p75) interface , we developed a set of modified 8-hydroxyquinoline fragments demonstrating micromolar IC50 values for inhibition of the IN-LEDGF/p75 interaction, but significant cytotoxicity was associated with these initial compounds. Diverse modifications at the C5 and C7 carbons of the 8-hydroxyquinoline core improved potency, but reduction of diversity to only modifications at the C5 position ultimately yielded potent inhibitors with low cytotoxicity. Two of these particular compounds, 5-((p-tolylamino)methyl)quinolin-8-ol and 5-(((3,4-dimethylphenyl)amino)methyl)quinolin-8-ol, inhibited viral replication in MT-4 cells with low micromolar EC50. This is the first study providing evidence for 8-hydroxyquinolines as novel inhibitors of the IN-LEDGF/p75 interaction. Our lead compounds are druglike, have low molecular weights, and are amenable to various substitutions suitable for enhancing their potency and selectivity.
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Affiliation(s)
- Erik Serrao
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California , 1985 Zonal Avenue, Los Angeles, California 90089, USA
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Wielens J, Headey SJ, Rhodes DI, Mulder RJ, Dolezal O, Deadman JJ, Newman J, Chalmers DK, Parker MW, Peat TS, Scanlon MJ. Parallel screening of low molecular weight fragment libraries: do differences in methodology affect hit identification? ACTA ACUST UNITED AC 2012; 18:147-59. [PMID: 23139382 DOI: 10.1177/1087057112465979] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fragment screening is becoming widely accepted as a technique to identify hit compounds for the development of novel lead compounds. In neighboring laboratories, we have recently, and independently, performed a fragment screening campaign on the HIV-1 integrase core domain (IN) using similar commercially purchased fragment libraries. The two campaigns used different screening methods for the preliminary identification of fragment hits; one used saturation transfer difference nuclear magnetic resonance spectroscopy (STD-NMR), and the other used surface plasmon resonance (SPR) spectroscopy. Both initial screens were followed by X-ray crystallography. Using the STD-NMR/X-ray approach, 15 IN/fragment complexes were identified, whereas the SPR/X-ray approach found 6 complexes. In this article, we compare the approaches that were taken by each group and the results obtained, and we look at what factors could potentially influence the final results. We find that despite using different approaches with little overlap of initial hits, both approaches identified binding sites on IN that provided a basis for fragment-based lead discovery and further lead development. Comparison of hits identified in the two studies highlights a key role for both the conditions under which fragment binding is measured and the criteria selected to classify hits.
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Tintori C, Demeulemeester J, Franchi L, Massa S, Debyser Z, Christ F, Botta M. Discovery of small molecule HIV-1 integrase dimerization inhibitors. Bioorg Med Chem Lett 2012; 22:3109-14. [PMID: 22483582 DOI: 10.1016/j.bmcl.2012.03.064] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Revised: 03/15/2012] [Accepted: 03/15/2012] [Indexed: 10/28/2022]
Abstract
Human immunodeficiency virus-1 integrase (HIV-1 IN) inserts the viral DNA into host cell chromatin in a multistep process. This enzyme exists in equilibrium between monomeric, dimeric, tetrameric and high order oligomeric states. However, monomers of IN are not capable of supporting its catalytic functions and the active form has been shown to be at least a dimer. As a consequence, the development of inhibitors targeting IN dimerization constitutes a promising novel antiviral strategy. In this work, we successfully combined different computational techniques in order to identify small molecule inhibitors of IN dimerization. Additionally, a novel AlphaScreen-based IN dimerization assay was used to evaluate the inhibitory activities of the selected compounds. To the best of our knowledge, this study represents the first successful virtual screening and evaluation of small molecule HIV-1 IN dimerization inhibitors, which may serve as attractive hit compounds for the development of novel anti-HIV.
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Affiliation(s)
- Cristina Tintori
- Dipartimento Farmaco Chimico Tecnologico, University of Siena, Via Alcide de Gasperi 2, I-53100 Siena, Italy
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Demeulemeester J, Christ F, De Maeyer M, Debyser Z. Fueling HIV-1 integrase drug design with structural insights. DRUG DISCOVERY TODAY. TECHNOLOGIES 2012; 9:e175-e226. [PMID: 24064310 DOI: 10.1016/j.ddtec.2012.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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