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Parveen N, Borrenberghs D, Rocha S, Hendrix J. Single Viruses on the Fluorescence Microscope: Imaging Molecular Mobility, Interactions and Structure Sheds New Light on Viral Replication. Viruses 2018; 10:E250. [PMID: 29748498 PMCID: PMC5977243 DOI: 10.3390/v10050250] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/24/2018] [Accepted: 05/04/2018] [Indexed: 12/13/2022] Open
Abstract
Viruses are simple agents exhibiting complex reproductive mechanisms. Decades of research have provided crucial basic insights, antiviral medication and moderately successful gene therapy trials. The most infectious viral particle is, however, not always the most abundant one in a population, questioning the utility of classic ensemble-averaging virology. Indeed, viral replication is often not particularly efficient, prone to errors or containing parallel routes. Here, we review different single-molecule sensitive fluorescence methods that we employ routinely to investigate viruses. We provide a brief overview of the microscopy hardware needed and discuss the different methods and their application. In particular, we review how we applied (i) single-molecule Förster resonance energy transfer (smFRET) to probe the subviral human immunodeficiency virus (HIV-1) integrase (IN) quaternary structure; (ii) single particle tracking to study interactions of the simian virus 40 with membranes; (iii) 3D confocal microscopy and smFRET to quantify the HIV-1 pre-integration complex content and quaternary structure; (iv) image correlation spectroscopy to quantify the cytosolic HIV-1 Gag assembly, and finally; (v) super-resolution microscopy to characterize the interaction of HIV-1 with tetherin during assembly. We hope this review is an incentive for setting up and applying similar single-virus imaging studies in daily virology practice.
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Affiliation(s)
- Nagma Parveen
- Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics Division, Chemistry Department, KU Leuven, B-3001 Leuven, Belgium.
| | - Doortje Borrenberghs
- Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics Division, Chemistry Department, KU Leuven, B-3001 Leuven, Belgium.
| | - Susana Rocha
- Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics Division, Chemistry Department, KU Leuven, B-3001 Leuven, Belgium.
| | - Jelle Hendrix
- Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics Division, Chemistry Department, KU Leuven, B-3001 Leuven, Belgium.
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt University, B-3590 Diepenbeek, Belgium.
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52
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Ciubotaru M, Musat MG, Surleac M, Ionita E, Petrescu AJ, Abele E, Abele R. The Design of New HIV-IN Tethered Bifunctional Inhibitors Using Multiple Microdomain Targeted Docking. Curr Med Chem 2018; 26:2574-2600. [PMID: 29623824 DOI: 10.2174/0929867325666180406114405] [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] [Received: 11/17/2017] [Revised: 03/16/2018] [Accepted: 03/16/2018] [Indexed: 12/17/2022]
Abstract
Currently, used antiretroviral HIV therapy drugs exclusively target critical groups in the enzymes essential for the viral life cycle. Increased mutagenesis of their genes changes these viral enzymes, which once mutated can evade therapeutic targeting, effects which confer drug resistance. To circumvent this, our review addresses a strategy to design and derive HIV-Integrase (HIV-IN) inhibitors which simultaneously target two IN functional domains, rendering it inactive even if the enzyme accumulates many mutations. First we review the enzymatic role of IN to insert the copied viral DNA into a chromosome of the host T lymphocyte, highlighting its main functional and structural features to be subjected to inhibitory action. From a functional and structural perspective we present all classes of HIV-IN inhibitors with their most representative candidates. For each chosen compound we also explain its mechanism of IN inhibition. We use the recently resolved cryo EM IN tetramer intasome DNA complex onto which we dock various reference IN inhibitory chemical scaffolds such as to target adjacent functional IN domains. Pairing compounds with complementary activity, which dock in the vicinity of a IN structural microdomain, we design bifunctional new drugs which may not only be more resilient to IN mutations but also may be more potent inhibitors than their original counterparts. In the end of our review we propose synthesis pathways to link such paired compounds with enhanced synergistic IN inhibitory effects.
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Affiliation(s)
- Mihai Ciubotaru
- Department of Immunology, Colentina Clinical Hospital Research Center, Bucharest, Romania.,Department of Life and Environmental Physics, National Institute for Physics and Nuclear Engineering Horia Hulubei, Bucharest-Magurele, Romania
| | - Mihaela Georgiana Musat
- Department of Immunology, Colentina Clinical Hospital Research Center, Bucharest, Romania.,Department of Biochemistry, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | - Marius Surleac
- Department of Bio-informatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Elena Ionita
- Department of Immunology, Colentina Clinical Hospital Research Center, Bucharest, Romania.,Department of Life and Environmental Physics, National Institute for Physics and Nuclear Engineering Horia Hulubei, Bucharest-Magurele, Romania
| | - Andrei Jose Petrescu
- Department of Bio-informatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Edgars Abele
- Modern Catalysis Method Mihai Ciubotaru group, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Ramona Abele
- Modern Catalysis Method Mihai Ciubotaru group, Latvian Institute of Organic Synthesis, Riga, Latvia
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53
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George A, Gopi Krishna Reddy A, Satyanarayana G, Raghavendra NK. 1,2,3,4-Tetrahydroisoquinolines as inhibitors of HIV-1 integrase and human LEDGF/p75 interaction. Chem Biol Drug Des 2018; 91:1133-1140. [PMID: 29405651 DOI: 10.1111/cbdd.13175] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/14/2018] [Accepted: 01/20/2018] [Indexed: 01/02/2023]
Abstract
Alkaloids are a class of organic compounds with a wide range of biological properties, including anti-HIV activity. The 1,2,3,4-tetrahydroisoquinoline is a ubiquitous structural motif of many alkaloids. Using a short and an efficient route for synthesis, a series of 1,2,3,4-tetrahydroisoquinolines/isoquinolines was developed. These compounds have been analysed for their ability to inhibit an important interaction between HIV-1 integrase enzyme (IN) and human LEDGF/p75 protein (p75) which assists in the viral integration into the active genes. A lead compound 6d is found to inhibit the LEDGF/p75-IN interaction in vitro with an IC50 of ~10 μm. Molecular docking analysis of the isoquinoline 6d reveals its interactions with the LEDGF/p75-binding residues of IN. Based on an order of addition experiment, the binding of 6d or LEDGF/p75 to IN is shown to be mutually exclusive. Also, the activity of 6d in vitro is found to be unaffected by the presence of a non-specific DNA. As reported earlier for the inhibitors of LEDGF/p75-IN interaction, 6d exhibits a potent inhibition of both the early and late stages of HIV-1 replication. Compound 6d differing from the known inhibitors in the chemical moieties and interactions with CCD could potentially be explored further for developing small molecule inhibitors of LEDGF/p75-IN interaction having a higher potency.
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Affiliation(s)
- Anu George
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | | | - Gedu Satyanarayana
- Department of Chemistry, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
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54
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Bonnard D, Le Rouzic E, Eiler S, Amadori C, Orlov I, Bruneau JM, Brias J, Barbion J, Chevreuil F, Spehner D, Chasset S, Ledoussal B, Moreau F, Saïb A, Klaholz BP, Emiliani S, Ruff M, Zamborlini A, Benarous R. Structure-function analyses unravel distinct effects of allosteric inhibitors of HIV-1 integrase on viral maturation and integration. J Biol Chem 2018; 293:6172-6186. [PMID: 29507092 DOI: 10.1074/jbc.m117.816793] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 02/13/2018] [Indexed: 11/06/2022] Open
Abstract
Recently, a new class of HIV-1 integrase (IN) inhibitors with a dual mode of action, called IN-LEDGF/p75 allosteric inhibitors (INLAIs), was described. Designed to interfere with the IN-LEDGF/p75 interaction during viral integration, unexpectedly, their major impact was on virus maturation. This activity has been linked to induction of aberrant IN multimerization, whereas inhibition of the IN-LEDGF/p75 interaction accounts for weaker antiretroviral effect at integration. Because these dual activities result from INLAI binding to IN at a single binding site, we expected that these activities co-evolved together, driven by the affinity for IN. Using an original INLAI, MUT-A, and its activity on an Ala-125 (A125) IN variant, we found that these two activities on A125-IN can be fully dissociated: MUT-A-induced IN multimerization and the formation of eccentric condensates in viral particles, which are responsible for inhibition of virus maturation, were lost, whereas inhibition of the IN-LEDGF/p75 interaction and consequently integration was fully retained. Hence, the mere binding of INLAI to A125 IN is insufficient to promote the conformational changes of IN required for aberrant multimerization. By analyzing the X-ray structures of MUT-A bound to the IN catalytic core domain (CCD) with or without the Ala-125 polymorphism, we discovered that the loss of IN multimerization is due to stabilization of the A125-IN variant CCD dimer, highlighting the importance of the CCD dimerization energy for IN multimerization. Our study reveals that affinity for the LEDGF/p75-binding pocket is not sufficient to induce INLAI-dependent IN multimerization and the associated inhibition of viral maturation.
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Affiliation(s)
- Damien Bonnard
- From Biodim Mutabilis, 93230 Romainville, .,Inserm U944, CNRS UMR 7212, Université Paris Diderot, Conservatoire National des Arts et Métiers, 75010 Paris
| | | | - Sylvia Eiler
- the Centre for Integrative Biology, IGBMC, Inserm, CNRS, Université de Strasbourg, 67404 Illkirch, and
| | - Céline Amadori
- From Biodim Mutabilis, 93230 Romainville.,the Institut Cochin, Inserm U1016, 75014 Paris, France
| | - Igor Orlov
- the Centre for Integrative Biology, IGBMC, Inserm, CNRS, Université de Strasbourg, 67404 Illkirch, and
| | | | | | | | | | - Danièle Spehner
- the Centre for Integrative Biology, IGBMC, Inserm, CNRS, Université de Strasbourg, 67404 Illkirch, and
| | | | | | | | - Ali Saïb
- Inserm U944, CNRS UMR 7212, Université Paris Diderot, Conservatoire National des Arts et Métiers, 75010 Paris
| | - Bruno P Klaholz
- the Centre for Integrative Biology, IGBMC, Inserm, CNRS, Université de Strasbourg, 67404 Illkirch, and
| | | | - Marc Ruff
- the Centre for Integrative Biology, IGBMC, Inserm, CNRS, Université de Strasbourg, 67404 Illkirch, and
| | - Alessia Zamborlini
- Inserm U944, CNRS UMR 7212, Université Paris Diderot, Conservatoire National des Arts et Métiers, 75010 Paris,
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55
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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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56
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Demeulemeester J, Blokken J, De Houwer S, Dirix L, Klaassen H, Marchand A, Chaltin P, Christ F, Debyser Z. Inhibitors of the integrase-transportin-SR2 interaction block HIV nuclear import. Retrovirology 2018; 15:5. [PMID: 29329553 PMCID: PMC5767004 DOI: 10.1186/s12977-018-0389-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 11/20/2017] [Indexed: 12/12/2022] Open
Abstract
Background Combination antiretroviral therapy efficiently suppresses HIV replication in infected patients, transforming HIV/AIDS into a chronic disease. Viral resistance does develop however, especially under suboptimal treatment conditions such as poor adherence. As a consequence, continued exploration of novel targets is paramount to identify novel antivirals that do not suffer from cross-resistance with existing drugs. One new promising class of targets are HIV protein–cofactor interactions. Transportin-SR2 (TRN-SR2) is a β-karyopherin that was recently identified as an HIV-1 cofactor. It has been implicated in nuclear import of the viral pre-integration complex and was confirmed as a direct binding partner of HIV-1 integrase (IN). Nevertheless, consensus on its mechanism of action is yet to be reached. Results Here we describe the development and use of an AlphaScreen-based high-throughput screening cascade for small molecule inhibitors of the HIV-1 IN–TRN-SR2 interaction. False positives and nonspecific protein–protein interaction inhibitors were eliminated through different counterscreens. We identified and confirmed 2 active compound series from an initial screen of 25,608 small molecules. These compounds significantly reduced nuclear import of fluorescently labeled HIV particles. Conclusions Alphascreen-based high-throughput screening can allow the identification of compounds representing a novel class of HIV inhibitors. These results corroborate the role of the IN–TRN-SR2 interaction in nuclear import. These compounds represent the first in class small molecule inhibitors of HIV-1 nuclear import.
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Affiliation(s)
- Jonas Demeulemeester
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Kapucijnenvoer 33, VCTB +5, Bus 7001, 3000, Leuven, Flanders, Belgium.,The Francis Crick Institute, London, UK
| | - Jolien Blokken
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Kapucijnenvoer 33, VCTB +5, Bus 7001, 3000, Leuven, Flanders, Belgium
| | - Stéphanie De Houwer
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Kapucijnenvoer 33, VCTB +5, Bus 7001, 3000, Leuven, Flanders, Belgium
| | - Lieve Dirix
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Kapucijnenvoer 33, VCTB +5, Bus 7001, 3000, Leuven, Flanders, Belgium
| | - Hugo Klaassen
- Center for Innovation and Stimulation of Drug Discovery (CISTIM), Leuven, Belgium
| | - Arnaud Marchand
- Center for Innovation and Stimulation of Drug Discovery (CISTIM), Leuven, Belgium
| | - Patrick Chaltin
- Center for Innovation and Stimulation of Drug Discovery (CISTIM), Leuven, Belgium.,Center for Drug Design and Development (CD3), KU Leuven R&D, Leuven, Belgium
| | - Frauke Christ
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Kapucijnenvoer 33, VCTB +5, Bus 7001, 3000, Leuven, Flanders, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Kapucijnenvoer 33, VCTB +5, Bus 7001, 3000, Leuven, Flanders, Belgium.
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57
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Hoyte AC, Jamin AV, Koneru PC, Kobe MJ, Larue RC, Fuchs JR, Engelman AN, Kvaratskhelia M. Resistance to pyridine-based inhibitor KF116 reveals an unexpected role of integrase in HIV-1 Gag-Pol polyprotein proteolytic processing. J Biol Chem 2017; 292:19814-19825. [PMID: 28972144 PMCID: PMC5712621 DOI: 10.1074/jbc.m117.816645] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 09/27/2017] [Indexed: 11/06/2022] Open
Abstract
The pyridine-based multimerization selective HIV-1 integrase (IN) inhibitors (MINIs) are a distinct subclass of allosteric IN inhibitors. MINIs potently inhibit HIV-1 replication during virion maturation by inducing hyper- or aberrant IN multimerization but are largely ineffective during the early steps of viral replication. Here, we investigated the mechanism for the evolution of a triple IN substitution (T124N/V165I/T174I) that emerges in cell culture with a representative MINI, KF116. We show that HIV-1 NL4-3(IN T124N/V165I/T174I) confers marked (>2000-fold) resistance to KF116. Two IN substitutions (T124N/T174I) directly weaken inhibitor binding at the dimer interface of the catalytic core domain but at the same time markedly impair HIV-1 replication capacity. Unexpectedly, T124N/T174I IN substitutions inhibited proteolytic processing of HIV-1 polyproteins Gag and Gag-Pol, resulting in immature virions. Strikingly, the addition of the third IN substitution (V165I) restored polyprotein processing, virus particle maturation, and significant levels of replication capacity. These results reveal an unanticipated role of IN for polyprotein proteolytic processing during virion morphogenesis. The complex evolutionary pathway for the emergence of resistant viruses, which includes the need for the compensatory V165I IN substitution, highlights a relatively high genetic barrier exerted by MINI KF116. Additionally, we have solved the X-ray structure of the drug-resistant catalytic core domain protein, which provides means for rational development of second-generation MINIs.
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Affiliation(s)
- Ashley C Hoyte
- From the Center for Retrovirus Research and
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado 80045, and
| | - Augusta V Jamin
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215
| | - Pratibha C Koneru
- From the Center for Retrovirus Research and
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado 80045, and
| | | | | | - James R Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215
| | - Mamuka Kvaratskhelia
- From the Center for Retrovirus Research and
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado 80045, and
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58
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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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59
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Amadori C, van der Velden YU, Bonnard D, Orlov I, van Bel N, Le Rouzic E, Miralles L, Brias J, Chevreuil F, Spehner D, Chasset S, Ledoussal B, Mayr L, Moreau F, García F, Gatell J, Zamborlini A, Emiliani S, Ruff M, Klaholz BP, Moog C, Berkhout B, Plana M, Benarous R. The HIV-1 integrase-LEDGF allosteric inhibitor MUT-A: resistance profile, impairment of virus maturation and infectivity but without influence on RNA packaging or virus immunoreactivity. Retrovirology 2017; 14:50. [PMID: 29121950 PMCID: PMC5680779 DOI: 10.1186/s12977-017-0373-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/27/2017] [Indexed: 01/22/2023] Open
Abstract
Background
HIV-1 Integrase (IN) interacts with the cellular co-factor LEDGF/p75 and tethers the HIV preintegration complex to the host genome enabling integration. Recently a new class of IN inhibitors was described, the IN-LEDGF allosteric inhibitors (INLAIs). Designed to interfere with the IN-LEDGF interaction during integration, the major impact of these inhibitors was surprisingly found on virus maturation, causing a reverse transcription defect in target cells. Results
Here we describe the MUT-A compound as a genuine INLAI with an original chemical structure based on a new type of scaffold, a thiophene ring. MUT-A has all characteristics of INLAI compounds such as inhibition of IN-LEDGF/p75 interaction, IN multimerization, dual antiretroviral (ARV) activities, normal packaging of genomic viral RNA and complete Gag protein maturation. MUT-A has more potent ARV activity compared to other INLAIs previously reported, but similar profile of resistance mutations and absence of ARV activity on SIV. HIV-1 virions produced in the presence of MUT-A were non-infectious with the formation of eccentric condensates outside of the core. In studying the immunoreactivity of these non-infectious virions, we found that inactivated HIV-1 particles were captured by anti-HIV-specific neutralizing and non-neutralizing antibodies (b12, 2G12, PGT121, 4D4, 10-1074, 10E8, VRC01) with efficiencies comparable to non-treated virus. Autologous CD4+ T lymphocyte proliferation and cytokine induction by monocyte-derived dendritic cells (MDDC) pulsed either with MUT-A-inactivated HIV or non-treated HIV were also comparable. Conclusions
Although strongly defective in infectivity, HIV-1 virions produced in the presence of the MUT-A INLAI have a normal protein and genomic RNA content as well as B and T cell immunoreactivities comparable to non-treated HIV-1. These inactivated viruses might form an attractive new approach in vaccine research in an attempt to study if this new type of immunogen could elicit an immune response against HIV-1 in animal models. Electronic supplementary material The online version of this article (10.1186/s12977-017-0373-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Céline Amadori
- Biodim Mutabilis, 93230, Romainville, France.,INSERM, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France.,University Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Yme Ubeles van der Velden
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Igor Orlov
- Centre for Integrative Biology, IGBMC, CNRS, INSERM, University of Strasbourg, Strasbourg, France
| | - Nikki van Bel
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Laia Miralles
- AIDS Research Group, IDIBAPS, Hospital Clinic, Barcelona, Spain
| | - Julie Brias
- Biodim Mutabilis, 93230, Romainville, France
| | | | - Daniele Spehner
- Centre for Integrative Biology, IGBMC, CNRS, INSERM, University of Strasbourg, Strasbourg, France
| | | | | | | | | | - Felipe García
- AIDS Research Group, IDIBAPS, Hospital Clinic, Barcelona, Spain
| | - José Gatell
- AIDS Research Group, IDIBAPS, Hospital Clinic, Barcelona, Spain
| | - Alessia Zamborlini
- CNRS, UMR7212, INSERM U944, Université Paris Diderot, Conservatoire National des Arts et Métiers, Paris, France
| | - Stéphane Emiliani
- INSERM, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France.,University Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Marc Ruff
- Centre for Integrative Biology, IGBMC, CNRS, INSERM, University of Strasbourg, Strasbourg, France
| | - Bruno P Klaholz
- Centre for Integrative Biology, IGBMC, CNRS, INSERM, University of Strasbourg, Strasbourg, France
| | | | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Montserrat Plana
- AIDS Research Group, IDIBAPS, Hospital Clinic, Barcelona, Spain.
| | - Richard Benarous
- Biodim Mutabilis, 93230, Romainville, France. .,, 19 rue de Croulebarbe, 75013, Paris, France.
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60
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Panwar U, Singh SK. Structure-based virtual screening toward the discovery of novel inhibitors for impeding the protein-protein interaction between HIV-1 integrase and human lens epithelium-derived growth factor (LEDGF/p75). J Biomol Struct Dyn 2017; 36:3199-3217. [PMID: 28948865 DOI: 10.1080/07391102.2017.1384400] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
HIV-1 integrase is a unique promising component of the viral replication cycle, catalyzing the integration of reverse transcribed viral cDNA into the host cell genome. Generally, IN activity requires both viral as well as a cellular co-factor in the processing replication cycle. Among them, the human lens epithelium-derived growth factor (LEDGF/p75) represented as promising cellular co-factor which supports the viral replication by tethering IN to the chromatin. Due to its major importance in the early steps of HIV replication, the interaction between IN and LEDGF/p75 has become a pleasing target for anti-HIV drug discovery. The present study involves the finding of novel inhibitor based on the information of dimeric CCD of IN in complex with known inhibitor, which were carried out by applying a structure-based virtual screening concept with molecular docking. Additionally, Free binding energy, ADME properties, PAINS analysis, Density Functional Theory, and Enrichment Calculations were performed on selected compounds for getting a best lead molecule. On the basis of these analyses, the current study proposes top 3 compounds: Enamine-Z742267384, Maybridge-HTS02400, and Specs-AE-848/37125099 with acceptable pharmacological properties and enhanced binding affinity to inhibit the interaction between IN and LEDGF/p75. Furthermore, Simulation studies were carried out on these molecules to expose their dynamics behavior and stability. We expect that the findings obtained here could be future therapeutic agents and may provide an outline for the experimental studies to stimulate the innovative strategy for research community.
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Affiliation(s)
- Umesh Panwar
- a Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics , Alagappa University , Karaikudi 630004 , Tamil Nadu , India
| | - Sanjeev Kumar Singh
- a Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics , Alagappa University , Karaikudi 630004 , Tamil Nadu , India
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61
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Bueno MTD, Reyes D, Llano M. LEDGF/p75 Deficiency Increases Deletions at the HIV-1 cDNA Ends. Viruses 2017; 9:v9090259. [PMID: 28914817 PMCID: PMC5618025 DOI: 10.3390/v9090259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 09/08/2017] [Accepted: 09/12/2017] [Indexed: 11/17/2022] Open
Abstract
Processing of unintegrated linear HIV-1 cDNA by the host DNA repair system results in its degradation and/or circularization. As a consequence, deficient viral cDNA integration generally leads to an increase in the levels of HIV-1 cDNA circles containing one or two long terminal repeats (LTRs). Intriguingly, impaired HIV-1 integration in LEDGF/p75-deficient cells does not result in a correspondent increase in viral cDNA circles. We postulate that increased degradation of unintegrated linear viral cDNA in cells lacking the lens epithelium-derived growth factor (LEDGF/p75) account for this inconsistency. To evaluate this hypothesis, we characterized the nucleotide sequence spanning 2-LTR junctions isolated from LEDGF/p75-deficient and control cells. LEDGF/p75 deficiency resulted in a significant increase in the frequency of 2-LTRs harboring large deletions. Of note, these deletions were dependent on the 3′ processing activity of integrase and were not originated by aberrant reverse transcription. Our findings suggest a novel role of LEDGF/p75 in protecting the unintegrated 3′ processed linear HIV-1 cDNA from exonucleolytic degradation.
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Affiliation(s)
- Murilo T D Bueno
- Department of Biological Sciences, University of Texas at El Paso. El Paso, TX 79968, USA.
| | - Daniel Reyes
- Department of Biological Sciences, University of Texas at El Paso. El Paso, TX 79968, USA.
| | - Manuel Llano
- Department of Biological Sciences, University of Texas at El Paso. El Paso, TX 79968, USA.
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62
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George A, Raghavendra NK. L368F/V408F double mutant of IBD of LEDGF/p75 retains interaction with M178I mutant of HIV-1 integrase. Biochem Biophys Res Commun 2017; 490:271-275. [DOI: 10.1016/j.bbrc.2017.06.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 06/09/2017] [Indexed: 01/15/2023]
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63
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Structural basis for the potent inhibition of the HIV integrase-LEDGF/p75 protein-protein interaction. J Mol Graph Model 2017; 75:189-198. [PMID: 28582696 DOI: 10.1016/j.jmgm.2017.05.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/23/2017] [Accepted: 05/24/2017] [Indexed: 11/20/2022]
Abstract
Integrase (IN) constitutes one of the key enzymes involved in the lifecycle of the Human Immunodeficiency Virus (HIV), the etiological agent of AIDS. The biological role of IN strongly depends on the recognition and binding of cellular cofactors belonging to the infected host cell. Thus, the inhibition of the protein-protein interaction (PPI) between IN and cellular cofactors has been envisioned as a promising therapeutic target. In the present work we explore a structure-activity relationship for a set of 14 compounds reported as inhibitors of the PPI between IN and the lens epithelium-derived growth factor (LEDGF/p75). Our results demonstrate that the possibility to adopt the bioactive conformation capable of interacting with the hotspots IN-LEDGF/p75 hotspots residues constitutes a critical feature to obtain a potent inhibition. A ligand efficiency (|Lig-Eff|) quantitative descriptor combining both interaction energetics and conformational requirements was developed and correlated with the reported biological activity. Our results contribute to the rational development of IN-LEDGF/p75 interaction inhibitors providing a solid quantitative structure-activity relationship aimed for the screening of new IN-LEDGF/p75 interaction inhibitors.
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64
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Structural Basis for Inhibitor-Induced Aggregation of HIV Integrase. PLoS Biol 2016; 14:e1002584. [PMID: 27935939 PMCID: PMC5147827 DOI: 10.1371/journal.pbio.1002584] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 11/14/2016] [Indexed: 11/19/2022] Open
Abstract
The allosteric inhibitors of integrase (termed ALLINIs) interfere with HIV replication by binding to the viral-encoded integrase (IN) protein. Surprisingly, ALLINIs interfere not with DNA integration but with viral particle assembly late during HIV replication. To investigate the ALLINI inhibitory mechanism, we crystallized full-length HIV-1 IN bound to the ALLINI GSK1264 and determined the structure of the complex at 4.4 Å resolution. The structure shows GSK1264 buried between the IN C-terminal domain (CTD) and the catalytic core domain. In the crystal lattice, the interacting domains are contributed by two different dimers so that IN forms an open polymer mediated by inhibitor-bridged contacts; the N-terminal domains do not participate and are structurally disordered. Engineered amino acid substitutions at the inhibitor interface blocked ALLINI-induced multimerization. HIV escape mutants with reduced sensitivity to ALLINIs commonly altered amino acids at or near the inhibitor-bound interface, and these substitutions also diminished IN multimerization. We propose that ALLINIs inhibit particle assembly by stimulating inappropriate polymerization of IN via interactions between the catalytic core domain and the CTD and that understanding the interface involved offers new routes to inhibitor optimization. A new crystal structure of the HIV integrase enzyme in complex with the allosteric inhibitor GSK1264 explains how the drug induces aggregation of the viral protein. A promising new class of antivirals called “ALLINIs” (allosteric inhibitors of integrase) potently inhibits HIV replication. Like other drugs, ALLINIs seem to target also the HIV-1 integrase (IN), which is crucial for the replication of this virus, but instead of acting at early phases of HIV replication, they interfere with viral particle assembly and maturation that occur at late stages and induce aggregation of IN. Despite these findings, the structural bases for the effects are still unknown. In this study, we crystallized full-length HIV-1 IN in complex with an ALLINI called GSK1264 and determined its structure to 4.4 Å. The structure reveals for the first time the complete ALLINI-binding interface, comprised of both IN C-terminal and catalytic core domains. These domains are contributed from neighboring IN dimers, revealing an open polymeric conformation mediated by inhibitor-bridged contacts. Substitutions at this interface block ALLINI-induced multimerization, and we find that escape mutants against this class of drug lie at or near this interface. We propose that ALLINIs catalyze formation of an open IN polymer, which in turn interferes with viral particle assembly.
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65
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Antiviral Activity of Bictegravir (GS-9883), a Novel Potent HIV-1 Integrase Strand Transfer Inhibitor with an Improved Resistance Profile. Antimicrob Agents Chemother 2016; 60:7086-7097. [PMID: 27645238 PMCID: PMC5118987 DOI: 10.1128/aac.01474-16] [Citation(s) in RCA: 189] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/02/2016] [Indexed: 11/28/2022] Open
Abstract
Bictegravir (BIC; GS-9883), a novel, potent, once-daily, unboosted inhibitor of HIV-1 integrase (IN), specifically targets IN strand transfer activity (50% inhibitory concentration [IC50] of 7.5 ± 0.3 nM) and HIV-1 integration in cells. BIC exhibits potent and selective in vitro antiretroviral activity in both T-cell lines and primary human T lymphocytes, with 50% effective concentrations ranging from 1.5 to 2.4 nM and selectivity indices up to 8,700 relative to cytotoxicity. BIC exhibits synergistic in vitro antiviral effects in pairwise combinations with tenofovir alafenamide, emtricitabine, or darunavir and maintains potent antiviral activity against HIV-1 variants resistant to other classes of antiretrovirals. BIC displayed an in vitro resistance profile that was markedly improved compared to the integrase strand transfer inhibitors (INSTIs) raltegravir (RAL) and elvitegravir (EVG), and comparable to that of dolutegravir (DTG), against nine INSTI-resistant site-directed HIV-1 mutants. BIC displayed statistically improved antiviral activity relative to EVG, RAL, and DTG against a panel of 47 patient-derived HIV-1 isolates with high-level INSTI resistance; 13 of 47 tested isolates exhibited >2-fold lower resistance to BIC than DTG. In dose-escalation experiments conducted in vitro, BIC and DTG exhibited higher barriers to resistance than EVG, selecting for HIV-1 variants with reduced phenotypic susceptibility at days 71, 87, and 20, respectively. A recombinant virus with the BIC-selected M50I/R263K dual mutations in IN exhibited only 2.8-fold reduced susceptibility to BIC compared to wild-type virus. All BIC-selected variants exhibited low to intermediate levels of cross-resistance to RAL, DTG, and EVG (<8-fold) but remained susceptible to other classes of antiretrovirals. A high barrier to in vitro resistance emergence for both BIC and DTG was also observed in viral breakthrough studies in the presence of constant clinically relevant drug concentrations. The overall virologic profile of BIC supports its ongoing clinical investigation in combination with other antiretroviral agents for both treatment-naive and -experienced HIV-infected patients.
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66
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Borrenberghs D, Dirix L, De Wit F, Rocha S, Blokken J, De Houwer S, Gijsbers R, Christ F, Hofkens J, Hendrix J, Debyser Z. Dynamic Oligomerization of Integrase Orchestrates HIV Nuclear Entry. Sci Rep 2016; 6:36485. [PMID: 27830755 PMCID: PMC5103197 DOI: 10.1038/srep36485] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/04/2016] [Indexed: 11/16/2022] Open
Abstract
Nuclear entry is a selective, dynamic process granting the HIV-1 pre-integration complex (PIC) access to the chromatin. Classical analysis of nuclear entry of heterogeneous viral particles only yields averaged information. We now have employed single-virus fluorescence methods to follow the fate of single viral pre-integration complexes (PICs) during infection by visualizing HIV-1 integrase (IN). Nuclear entry is associated with a reduction in the number of IN molecules in the complexes while the interaction with LEDGF/p75 enhances IN oligomerization in the nucleus. Addition of LEDGINs, small molecule inhibitors of the IN-LEDGF/p75 interaction, during virus production, prematurely stabilizes a higher-order IN multimeric state, resulting in stable IN multimers resistant to a reduction in IN content and defective for nuclear entry. This suggests that a stringent size restriction determines nuclear pore entry. Taken together, this work demonstrates the power of single-virus imaging providing crucial insights in HIV replication and enabling mechanism-of-action studies.
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Affiliation(s)
- Doortje Borrenberghs
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium.,Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, 3001, Belgium
| | - Lieve Dirix
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium.,Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, 3001, Belgium
| | - Flore De Wit
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Susana Rocha
- Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, 3001, Belgium
| | - Jolien Blokken
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Stéphanie De Houwer
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Rik Gijsbers
- Laboratory for Viral Vector Technology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Frauke Christ
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Johan Hofkens
- Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, 3001, Belgium
| | - Jelle Hendrix
- Laboratory for Photochemistry and Spectroscopy, Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, 3001, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
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67
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Spearman P. HIV-1 Gag as an Antiviral Target: Development of Assembly and Maturation Inhibitors. Curr Top Med Chem 2016; 16:1154-66. [PMID: 26329615 DOI: 10.2174/1568026615666150902102143] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/18/2015] [Accepted: 06/21/2015] [Indexed: 01/10/2023]
Abstract
HIV-1 Gag is the master orchestrator of particle assembly. The central role of Gag at multiple stages of the HIV lifecycle has led to efforts to develop drugs that directly target Gag and prevent the formation and release of infectious particles. Until recently, however, only the catalytic site protease inhibitors have been available to inhibit late stages of HIV replication. This review summarizes the current state of development of antivirals that target Gag or disrupt late events in the retrovirus lifecycle such as maturation of the viral capsid. Maturation inhibitors represent an exciting new series of antiviral compounds, including those that specifically target CA-SP1 cleavage and the allosteric integrase inhibitors that inhibit maturation by a completely different mechanism. Numerous small molecules and peptides targeting CA have been studied in attempts to disrupt steps in assembly. Efforts to target CA have recently gained considerable momentum from the development of small molecules that bind CA and alter capsid stability at the post-entry stage of the lifecycle. Efforts to develop antivirals that inhibit incorporation of genomic RNA or to inhibit late budding events remain in preliminary stages of development. Overall, the development of novel antivirals targeting Gag and the late stages in HIV replication appears much closer to success than ever, with the new maturation inhibitors leading the way.
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Affiliation(s)
- Paul Spearman
- Department of Pediatrics; Pediatric Infectious Diseases, Emory University, 2015 Uppergate Drive, Atlanta, GA 30322.
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68
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Zhang FH, Debnath B, Xu ZL, Yang LM, Song LR, Zheng YT, Neamati N, Long YQ. Discovery of novel 3-hydroxypicolinamides as selective inhibitors of HIV-1 integrase-LEDGF/p75 interaction. Eur J Med Chem 2016; 125:1051-1063. [PMID: 27810592 DOI: 10.1016/j.ejmech.2016.10.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 09/27/2016] [Accepted: 10/19/2016] [Indexed: 12/27/2022]
Abstract
Currently, three HIV-1 integrase (IN) active site-directed inhibitors are in clinical use for the treatment of HIV infection. However, emergence of drug resistance mutations have limited the promise of a long-term cure. As an alternative, allosteric inhibition of IN activity has drawn great attention and several of such inhibitors are under early stage clinical development. Specifically, inhibitors of IN and the cellular cofactor LEDGF/p75 remarkably diminish proviral integration in cells and deliver a potent reduction in viral replicative capacity. Distinct from the extensively studied 2-(quinolin-3-yl) acetic acid or 1H-indol-3-yl-2-hydroxy-4-oxobut-2-enoic acid chemotypes, this study discloses a new class of selective IN-LEDGF/p75 inhibitors without the carboxylic acid functionality. More significantly, 3-hydroxypicolinamides also show low micromolar inhibition against IN dimerization, providing novel dual IN inhibitors with in vitro therapeutically selective antiviral effect for further development. Finally, our shape-based ROCS pharmacophore model of the 3-hydroxypicolinamide class of compounds provides a new insight into the binding mode of these novel IN-LEDGF/p75 inhibitors.
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Affiliation(s)
- Feng-Hua Zhang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Bikash Debnath
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109-2800, USA
| | - Zhong-Liang Xu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Liu-Meng Yang
- Laboratory of Molecular Immunopharmacology, Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Li-Rui Song
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yong-Tang Zheng
- Laboratory of Molecular Immunopharmacology, Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109-2800, USA.
| | - Ya-Qiu Long
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
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69
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The Multifaceted Contributions of Chromatin to HIV-1 Integration, Transcription, and Latency. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 328:197-252. [PMID: 28069134 DOI: 10.1016/bs.ircmb.2016.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The capacity of the human immunodeficiency virus (HIV-1) to establish latent infections constitutes a major barrier to the development of a cure for HIV-1. In latent infection, replication competent HIV-1 provirus is integrated within the host genome but remains silent, masking the infected cells from the activity of the host immune response. Despite the progress in elucidating the molecular players that regulate HIV-1 gene expression, the mechanisms driving the establishment and maintenance of latency are still not fully understood. Transcription from the HIV-1 genome occurs in the context of chromatin and is subjected to the same regulatory mechanisms that drive cellular gene expression. Much like in eukaryotic genes, the nucleosomal landscape of the HIV-1 promoter and its position within genomic chromatin are determinants of its transcriptional activity. Understanding the multilayered chromatin-mediated mechanisms that underpin HIV-1 integration and expression is of utmost importance for the development of therapeutic strategies aimed at reducing the pool of latently infected cells. In this review, we discuss the impact of chromatin structure on viral integration, transcriptional regulation and latency, and the host factors that influence HIV-1 replication by regulating chromatin organization. Finally, we describe therapeutic strategies under development to target the chromatin-HIV-1 interplay.
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70
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Nakamura T, Campbell JR, Moore AR, Otsu S, Aikawa H, Tamamura H, Mitsuya H. Development and validation of a cell-based assay system to assess human immunodeficiency virus type 1 integrase multimerization. J Virol Methods 2016; 236:196-206. [PMID: 27474494 PMCID: PMC8188399 DOI: 10.1016/j.jviromet.2016.07.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 07/22/2016] [Accepted: 07/22/2016] [Indexed: 12/26/2022]
Abstract
Multimerization of HIV-1 integrase (IN) subunits is required for the concerted integration of HIV-1 proviral DNA into the host genome. Thus, the disruption of IN multimerization represents a new avenue for intervening HIV-1 infection. Here, we generated a cell-based assay system to assess IN multimerization using a newly constructed bimolecular fluorescence complementation (BiFC-IN) system. BiFC-IN proteins were efficient in emitting fluorescence, and amino acid (AA) substitutions associated with IN multimerization attenuated fluorescence, suggesting that the BiFC-IN system may be useful for evaluating the profile of IN multimerization. A recently reported non-catalytic site IN inhibitor (NCINI), which allosterically induces IN over-multimerization/aggregation, significantly increased fluorescence in the BiFC-IN system. An IN's substitution, A128T, associated with viral resistance to NCINIs, decreased the NCINI-induced increase of fluorescence, suggesting that A128T reduces the potential for IN over-multimerization. Moreover, E11K and F181T substitutions known to inhibit IN tetramerization also reduced the NCINI-induced fluorescence increase, suggesting that NCINI-induced IN over-multimerization was more likely to occur from tetramer subunits than from dimer subunits. The present study demonstrates that our cell-based BiFC-IN system may be useful in elucidating the profile of IN multimerization, and also help evaluate and identify novel compounds that disrupt IN multimerization in living cells.
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Affiliation(s)
- Tomofumi Nakamura
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Medical Sciences, Kumamoto 860-8556, Japan
| | - Joseph R Campbell
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Medical Sciences, Kumamoto 860-8556, Japan
| | - Amber R Moore
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Medical Sciences, Kumamoto 860-8556, Japan
| | - Sachiko Otsu
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Medical Sciences, Kumamoto 860-8556, Japan
| | - Haruo Aikawa
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Hirokazu Tamamura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Hiroaki Mitsuya
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Medical Sciences, Kumamoto 860-8556, Japan; Experimental Retrovirology Section, National Center for Global Health and Medicine Research Institute, Shinjuku, Tokyo 162-8655, Japan; HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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71
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Patel D, Antwi J, Koneru PC, Serrao E, Forli S, Kessl JJ, Feng L, Deng N, Levy RM, Fuchs JR, Olson AJ, Engelman AN, Bauman JD, Kvaratskhelia M, Arnold E. A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain. J Biol Chem 2016; 291:23569-23577. [PMID: 27645997 DOI: 10.1074/jbc.m116.753384] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Indexed: 12/29/2022] Open
Abstract
HIV-1 integrase (IN) is essential for virus replication and represents an important multifunctional therapeutic target. Recently discovered quinoline-based allosteric IN inhibitors (ALLINIs) potently impair HIV-1 replication and are currently in clinical trials. ALLINIs exhibit a multimodal mechanism of action by inducing aberrant IN multimerization during virion morphogenesis and by competing with IN for binding to its cognate cellular cofactor LEDGF/p75 during early steps of HIV-1 infection. However, quinoline-based ALLINIs impose a low genetic barrier for the evolution of resistant phenotypes, which highlights a need for discovery of second-generation inhibitors. Using crystallographic screening of a library of 971 fragments against the HIV-1 IN catalytic core domain (CCD) followed by a fragment expansion approach, we have identified thiophenecarboxylic acid derivatives that bind at the CCD-CCD dimer interface at the principal lens epithelium-derived growth factor (LEDGF)/p75 binding pocket. The most active derivative (5) inhibited LEDGF/p75-dependent HIV-1 IN activity in vitro with an IC50 of 72 μm and impaired HIV-1 infection of T cells at an EC50 of 36 μm The identified lead compound, with a relatively small molecular weight (221 Da), provides an optimal building block for developing a new class of inhibitors. Furthermore, although structurally distinct thiophenecarboxylic acid derivatives target a similar pocket at the IN dimer interface as the quinoline-based ALLINIs, the lead compound, 5, inhibited IN mutants that confer resistance to quinoline-based compounds. Collectively, our findings provide a plausible path for structure-based development of second-generation ALLINIs.
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Affiliation(s)
- Disha Patel
- From the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854
| | - Janet Antwi
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy and
| | - Pratibha C Koneru
- Center for Retrovirus Research and College of Pharmacy, Ohio State University, Columbus, Ohio 43210
| | - Erik Serrao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215
| | - Stefano Forli
- Molecular Graphics Laboratory, Department of Integrative Structural and Computational Biology, MB-112, The Scripps Research Institute, La Jolla, California 92037
| | - Jacques J Kessl
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, and
| | - Lei Feng
- Center for Retrovirus Research and College of Pharmacy, Ohio State University, Columbus, Ohio 43210
| | - Nanjie Deng
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
| | - Ronald M Levy
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, Pennsylvania 19122
| | - James R Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy and
| | - Arthur J Olson
- Molecular Graphics Laboratory, Department of Integrative Structural and Computational Biology, MB-112, The Scripps Research Institute, La Jolla, California 92037
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215
| | - Joseph D Bauman
- From the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and College of Pharmacy, Ohio State University, Columbus, Ohio 43210,
| | - Eddy Arnold
- From the Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey 08854,
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Thermodynamic instability of viral proteins is a pathogen-associated molecular pattern targeted by human defensins. Sci Rep 2016; 6:32499. [PMID: 27581352 PMCID: PMC5007486 DOI: 10.1038/srep32499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 08/08/2016] [Indexed: 11/21/2022] Open
Abstract
Human defensins are innate immune defense peptides with a remarkably broad repertoire of anti-pathogen activities. In addition to modulating immune response, inflammation, and angiogenesis, disintegrating bacterial membranes, and inactivating bacterial toxins, defensins are known to intercept various viruses at different stages of their life cycles, while remaining relatively benign towards human cells and proteins. Recently we have found that human defensins inactivate proteinaceous bacterial toxins by taking advantage of their low thermodynamic stability and acting as natural “anti-chaperones”, i.e. destabilizing the native conformation of the toxins. In the present study we tested various proteins produced by several viruses (HIV-1, PFV, and TEV) and found them to be susceptible to destabilizing effects of human α-defensins HNP-1 and HD-5 and the synthetic θ-defensin RC-101, but not β-defensins hBD-1 and hBD-2 or structurally related plant-derived peptides. Defensin-induced unfolding promoted exposure of hydrophobic groups otherwise confined to the core of the viral proteins. This resulted in precipitation, an enhanced susceptibility to proteolytic cleavage, and a loss of viral protein activities. We propose, that defensins recognize and target a common and essential physico-chemical property shared by many bacterial toxins and viral proteins – the intrinsically low thermodynamic protein stability.
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Patel PA, Kvaratskhelia N, Mansour Y, Antwi J, Feng L, Koneru P, Kobe MJ, Jena N, Shi G, Mohamed MS, Li C, Kessl JJ, Fuchs JR. Indole-based allosteric inhibitors of HIV-1 integrase. Bioorg Med Chem Lett 2016; 26:4748-4752. [PMID: 27568085 DOI: 10.1016/j.bmcl.2016.08.037] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/11/2016] [Accepted: 08/12/2016] [Indexed: 11/15/2022]
Abstract
Employing a scaffold hopping approach, a series of allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) have been synthesized based on an indole scaffold. These compounds incorporate the key elements utilized in quinoline-based ALLINIs for binding to the IN dimer interface at the principal LEDGF/p75 binding pocket. The most potent of these compounds displayed good activity in the LEDGF/p75 dependent integration assay (IC50=4.5μM) and, as predicted based on the geometry of the five- versus six-membered ring, retained activity against the A128T IN mutant that confers resistance to many quinoline-based ALLINIs.
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Affiliation(s)
- Pratiq A Patel
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Department of Chemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Nina Kvaratskhelia
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Yara Mansour
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Janet Antwi
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Lei Feng
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Pratibha Koneru
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Mathew J Kobe
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Nivedita Jena
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Guqin Shi
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Mosaad S Mohamed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Chenglong Li
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Jacques J Kessl
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States.
| | - James R Fuchs
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States.
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Agharbaoui FE, Hoyte AC, Ferro S, Gitto R, Buemi MR, Fuchs JR, Kvaratskhelia M, De Luca L. Computational and synthetic approaches for developing Lavendustin B derivatives as allosteric inhibitors of HIV-1 integrase. Eur J Med Chem 2016; 123:673-683. [PMID: 27517812 DOI: 10.1016/j.ejmech.2016.07.077] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/25/2016] [Accepted: 07/31/2016] [Indexed: 01/26/2023]
Abstract
Through structure-based virtual screening and subsequent activity assays of selected natural products, Lavendustin B was previously identified as an inhibitor of HIV-1 integrase (IN) interaction with its cognate cellular cofactor, lens epithelium-derived growth factor (LEDGF/p75). In order to improve the inhibitory potency we have employed in silico-based approaches. Particularly, a series of new analogues was designed and docked into the LEDGF/p75 binding pocket of HIV-1 IN. To identify promising leads we used the Molecular Mechanics energies combined with the Generalized Born and Surface Area continuum solvation (MM-GBSA) method, molecular dynamics simulations and analysis of hydrogen bond occupancies. On the basis of these studies, six analogues of Lavendustine B, containing the benzylamino-hydroxybenzoic scaffold, were selected for synthesis and structure activity-relationship (SAR) studies. Our results demonstrated a good correlation between computational and experimental data, and all six analogues displayed an improved potency for inhibiting IN binding to LEDGF/p75 in vitro to respect to the parent compound Lavendustin B. Additionally, these analogs show to inhibit weakly LEDGF/p75-independent IN catalytic activity suggesting a multimodal allosteric mechanism of action. Nevertheless, for the synthesized compounds similar profiles for HIV-1 inhibition and cytoxicity were highlighted. Taken together, our studies elucidated the mode of action of Lavendustin B analogs and provided a path for their further development as a new promising class of HIV-1 integrase inhibitors.
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Affiliation(s)
- Fatima E Agharbaoui
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche e Ambientali (CHIBIOFARAM), Polo Universitario SS. Annunziata, Università di Messina, Viale Annunziata, I-98168, Messina, Italy; Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA; Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA.
| | - Ashley C Hoyte
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
| | - Stefania Ferro
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche e Ambientali (CHIBIOFARAM), Polo Universitario SS. Annunziata, Università di Messina, Viale Annunziata, I-98168, Messina, Italy
| | - Rosaria Gitto
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche e Ambientali (CHIBIOFARAM), Polo Universitario SS. Annunziata, Università di Messina, Viale Annunziata, I-98168, Messina, Italy
| | - Maria Rosa Buemi
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche e Ambientali (CHIBIOFARAM), Polo Universitario SS. Annunziata, Università di Messina, Viale Annunziata, I-98168, Messina, Italy
| | - James R Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
| | - Laura De Luca
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche e Ambientali (CHIBIOFARAM), Polo Universitario SS. Annunziata, Università di Messina, Viale Annunziata, I-98168, Messina, Italy.
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75
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Sun L, Gao P, Zhan P, Liu X. Pyrazolo[1,5-a]pyrimidine-based macrocycles as novel HIV-1 inhibitors: a patent evaluation of WO2015123182. Expert Opin Ther Pat 2016; 26:979-86. [PMID: 27398994 DOI: 10.1080/13543776.2016.1210127] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The emergence of drug resistance in Combination Antiretroviral Therapy (cART) confirms a continuing need to investigate novel HIV-1 inhibitors with unexplored mechanisms of action. Recently, a series of pyrazolopyrimidine-based macrocyclic compounds were reported as inhibitors of HIV-1 replication disclosed in the patent WO2015123182. Most of the disclosed compounds possessed in vitro antiviral potency in single-digit nanomolar range, which were determined by MT-2 cell assay. Then, the structural diversity, pharmacophore similarity of HIV-1 IN-LEDGF/p75 inhibitors, and implications for drug design were analyzed. In the end of this article, a glimpse of some macrocycles as potent antiviral agents (drug candidates) was provided. Some strategies and technologies enabling macrocycle design were also described. We expect that further development of these macrocyclic compounds will offer new anti-HIV-1 drug candidates.
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Affiliation(s)
- Lin Sun
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
| | - Ping Gao
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
| | - Peng Zhan
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
| | - Xinyong Liu
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
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76
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Feng L, Dharmarajan V, Serrao E, Hoyte A, Larue RC, Slaughter A, Sharma A, Plumb MR, Kessl JJ, Fuchs JR, Bushman FD, Engelman AN, Griffin PR, Kvaratskhelia M. The Competitive Interplay between Allosteric HIV-1 Integrase Inhibitor BI/D and LEDGF/p75 during the Early Stage of HIV-1 Replication Adversely Affects Inhibitor Potency. ACS Chem Biol 2016; 11:1313-21. [PMID: 26910179 DOI: 10.1021/acschembio.6b00167] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Allosteric HIV-1 integrase inhibitors (ALLINIs) have recently emerged as a promising class of antiretroviral agents and are currently in clinical trials. In infected cells, ALLINIs potently inhibit viral replication by impairing virus particle maturation but surprisingly exhibit a reduced EC50 for inhibiting HIV-1 integration in target cells. To better understand the reduced antiviral activity of ALLINIs during the early stage of HIV-1 replication, we investigated the competitive interplay between a potent representative ALLINI, BI/D, and LEDGF/p75 with HIV-1 integrase. While the principal binding sites of BI/D and LEDGF/p75 overlap at the integrase catalytic core domain dimer interface, we show that the inhibitor and the cellular cofactor induce markedly different multimerization patterns of full-length integrase. LEDGF/p75 stabilizes an integrase tetramer through the additional interactions with the integrase N-terminal domain, whereas BI/D induces protein-protein interactions in C-terminal segments that lead to aberrant, higher-order integrase multimerization. We demonstrate that LEDGF/p75 binds HIV-1 integrase with significantly higher affinity than BI/D and that the cellular protein is able to reverse the inhibitor induced aberrant, higher-order integrase multimerization in a dose-dependent manner in vitro. Consistent with these observations, alterations of the cellular levels of LEDGF/p75 markedly affected BI/D EC50 values during the early steps of HIV-1 replication. Furthermore, genome-wide sequencing of HIV-1 integration sites in infected cells demonstrate that LEDGF/p75-dependent integration site selection is adversely affected by BI/D treatment. Taken together, our studies elucidate structural and mechanistic details of the interplay between LEDGF/p75 and BI/D during the early stage of HIV-1 replication.
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Affiliation(s)
- Lei Feng
- Center for Retrovirus Research and College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Venkatasubramanian Dharmarajan
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
| | - Erik Serrao
- Department
of Cancer Immunology and Virology, Dana-Farber Cancer Institute and
Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Ashley Hoyte
- Center for Retrovirus Research and College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ross C. Larue
- Center for Retrovirus Research and College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Alison Slaughter
- Center for Retrovirus Research and College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Amit Sharma
- Center for Retrovirus Research and College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Matthew R. Plumb
- Center for Retrovirus Research and College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jacques J. Kessl
- Center for Retrovirus Research and College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - James R. Fuchs
- Division of Medicinal Chemistry and Pharmacognosy,
College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Frederic D. Bushman
- Perelman School of Medicine, Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Alan N. Engelman
- Department
of Cancer Immunology and Virology, Dana-Farber Cancer Institute and
Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Patrick R. Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and College
of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
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77
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Abstract
The integration of a DNA copy of the viral RNA genome into host chromatin is the defining step of retroviral replication. This enzymatic process is catalyzed by the virus-encoded integrase protein, which is conserved among retroviruses and LTR-retrotransposons. Retroviral integration proceeds via two integrase activities: 3'-processing of the viral DNA ends, followed by the strand transfer of the processed ends into host cell chromosomal DNA. Herein we review the molecular mechanism of retroviral DNA integration, with an emphasis on reaction chemistries and architectures of the nucleoprotein complexes involved. We additionally discuss the latest advances on anti-integrase drug development for the treatment of AIDS and the utility of integrating retroviral vectors in gene therapy applications.
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Affiliation(s)
- Paul Lesbats
- Clare Hall Laboratories, The Francis Crick Institute , Blanche Lane, South Mimms, EN6 3LD, U.K
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School , 450 Brookline Avenue, Boston, Massachusetts 02215 United States
| | - Peter Cherepanov
- Clare Hall Laboratories, The Francis Crick Institute , Blanche Lane, South Mimms, EN6 3LD, U.K.,Imperial College London , St-Mary's Campus, Norfolk Place, London, W2 1PG, U.K
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78
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Vranckx LS, Demeulemeester J, Saleh S, Boll A, Vansant G, Schrijvers R, Weydert C, Battivelli E, Verdin E, Cereseto A, Christ F, Gijsbers R, Debyser Z. LEDGIN-mediated Inhibition of Integrase-LEDGF/p75 Interaction Reduces Reactivation of Residual Latent HIV. EBioMedicine 2016; 8:248-264. [PMID: 27428435 PMCID: PMC4919729 DOI: 10.1016/j.ebiom.2016.04.039] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 04/19/2016] [Accepted: 04/28/2016] [Indexed: 12/20/2022] Open
Abstract
Persistence of latent, replication-competent Human Immunodeficiency Virus type 1 (HIV-1) provirus is the main impediment towards a cure for HIV/AIDS (Acquired Immune Deficiency Syndrome). Therefore, different therapeutic strategies to eliminate the viral reservoirs are currently being explored. We here propose a novel strategy to reduce the replicating HIV reservoir during primary HIV infection by means of drug-induced retargeting of HIV integration. A novel class of integration inhibitors, referred to as LEDGINs, inhibit the interaction between HIV integrase and the LEDGF/p75 host cofactor, the main determinant of lentiviral integration site selection. We show for the first time that LEDGF/p75 depletion hampers HIV-1 reactivation in cell culture. Next we demonstrate that LEDGINs relocate and retarget HIV integration resulting in a HIV reservoir that is refractory to reactivation by different latency-reversing agents. Taken together, these results support the potential of integrase inhibitors that modulate integration site targeting to reduce the likeliness of viral rebound. LEDGF/p75 depletion hampers HIV reactivation in cell culture. LEDGINs relocate and retarget authentic HIV integration. LEDGIN treatment results in quiescent residual HIV provirus which is less susceptible to reactivation. LEDGIN treatment during primary HIV infection may lead to an HIV remission.
Different strategies to cure HIV infection are being explored. Although complete eradication of the HIV provirus is the ultimate goal, disease remission allowing treatment interruption without viral rebound would constitute a significant leap forward. HIV integration site selection is orchestrated by LEDGF/p75. The advent of LEDGINs, that block the interaction between integrase and LEDGF/p75, allowed us to examine the hypothesis that interference with HIV integration site selection would yield integration sites that are less optimal for productive infection. Here we provide evidence in cell culture that LEDGIN treatment during acute HIV infection yields an HIV reservoir refractory to reactivation.
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Affiliation(s)
- Lenard S Vranckx
- Laboratory of Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, Kapucijnenvoer 33 VTCB +5, 3000 Leuven, Flanders, Belgium.
| | - Jonas Demeulemeester
- Laboratory of Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, Kapucijnenvoer 33 VTCB +5, 3000 Leuven, Flanders, Belgium.
| | - Suha Saleh
- Laboratory of Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, Kapucijnenvoer 33 VTCB +5, 3000 Leuven, Flanders, Belgium.
| | - Annegret Boll
- Laboratory of Molecular Virology, Centre for Integrative Biology (CIBIO), University of Trento, Via delle Regole 101, 38123 Trento, Italy.
| | - Gerlinde Vansant
- Laboratory of Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, Kapucijnenvoer 33 VTCB +5, 3000 Leuven, Flanders, Belgium.
| | - Rik Schrijvers
- Laboratory of Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, Kapucijnenvoer 33 VTCB +5, 3000 Leuven, Flanders, Belgium; Laboratory of Clinical Immunology, Department of Microbiology and Immunology, KU Leuven, Herestraat 49, 3000 Leuven, Flanders, Belgium.
| | - Caroline Weydert
- Laboratory of Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, Kapucijnenvoer 33 VTCB +5, 3000 Leuven, Flanders, Belgium.
| | - Emilie Battivelli
- Gladstone Institute of Virology and Immunology, University of California, 1650 Owens St., 94158 San Francisco, CA, USA.
| | - Eric Verdin
- Gladstone Institute of Virology and Immunology, University of California, 1650 Owens St., 94158 San Francisco, CA, USA.
| | - Anna Cereseto
- Laboratory of Molecular Virology, Centre for Integrative Biology (CIBIO), University of Trento, Via delle Regole 101, 38123 Trento, Italy.
| | - Frauke Christ
- Laboratory of Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, Kapucijnenvoer 33 VTCB +5, 3000 Leuven, Flanders, Belgium.
| | - Rik Gijsbers
- Laboratory of Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, Kapucijnenvoer 33 VTCB +5, 3000 Leuven, Flanders, Belgium.
| | - Zeger Debyser
- Laboratory of Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, Kapucijnenvoer 33 VTCB +5, 3000 Leuven, Flanders, Belgium.
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79
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Abstract
The retroviral integrases are virally encoded, specialized recombinases that catalyze the insertion of viral DNA into the host cell's DNA, a process that is essential for virus propagation. We have learned a great deal since the existence of an integrated form of retroviral DNA (the provirus) was first proposed by Howard Temin in 1964. Initial studies focused on the genetics and biochemistry of avian and murine virus DNA integration, but the pace of discovery increased substantially with advances in technology, and an influx of investigators focused on the human immunodeficiency virus. We begin with a brief account of the scientific landscape in which some of the earliest discoveries were made, and summarize research that led to our current understanding of the biochemistry of integration. A more detailed account of recent analyses of integrase structure follows, as they have provided valuable insights into enzyme function and raised important new questions.
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Affiliation(s)
- Mark D Andrake
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111; ,
| | - Anna Marie Skalka
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111; ,
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Fontana J, Jurado KA, Cheng N, Ly NL, Fuchs JR, Gorelick RJ, Engelman AN, Steven AC. Distribution and Redistribution of HIV-1 Nucleocapsid Protein in Immature, Mature, and Integrase-Inhibited Virions: a Role for Integrase in Maturation. J Virol 2015; 89:9765-80. [PMID: 26178982 PMCID: PMC4577894 DOI: 10.1128/jvi.01522-15] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 07/09/2015] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED During virion maturation, HIV-1 capsid protein assembles into a conical core containing the viral ribonucleoprotein (vRNP) complex, thought to be composed mainly of the viral RNA and nucleocapsid protein (NC). After infection, the viral RNA is reverse transcribed into double-stranded DNA, which is then incorporated into host chromosomes by integrase (IN) catalysis. Certain IN mutations (class II) and antiviral drugs (allosteric IN inhibitors [ALLINIs]) adversely affect maturation, resulting in virions that contain "eccentric condensates," electron-dense aggregates located outside seemingly empty capsids. Here we demonstrate that in addition to this mislocalization of electron density, a class II IN mutation and ALLINIs each increase the fraction of virions with malformed capsids (from ∼ 12% to ∼ 53%). Eccentric condensates have a high NC content, as demonstrated by "tomo-bubblegram" imaging, a novel labeling technique that exploits the susceptibility of NC to radiation damage. Tomo-bubblegrams also localized NC inside wild-type cores and lining the spherical Gag shell in immature virions. We conclude that eccentric condensates represent nonpackaged vRNPs and that either genetic or pharmacological inhibition of IN can impair vRNP incorporation into mature cores. Supplying IN in trans as part of a Vpr-IN fusion protein partially restored the formation of conical cores with internal electron density and the infectivity of a class II IN deletion mutant virus. Moreover, the ability of ALLINIs to induce eccentric condensate formation required both IN and viral RNA. Based on these observations, we propose a role for IN in initiating core morphogenesis and vRNP incorporation into the mature core during HIV-1 maturation. IMPORTANCE Maturation, a process essential for HIV-1 infectivity, involves core assembly, whereby the viral ribonucleoprotein (vRNP, composed of vRNA and nucleocapsid protein [NC]) is packaged into a conical capsid. Allosteric integrase inhibitors (ALLINIs) affect multiple viral processes. We have characterized ALLINIs and integrase mutants that have the same phenotype. First, by comparing the effects of ALLINIs on several steps of the viral cycle, we show that inhibition of maturation accounts for compound potency. Second, by using cryoelectron tomography, we find that ALLINIs impair conical capsid assembly. Third, by developing tomo-bubblegram imaging, which specifically labels NC protein, we find that ALLINIs block vRNP packaging; instead, vRNPs form "eccentric condensates" outside the core. Fourth, malformed cores, typical of integrase-deleted virus, are partially replaced by conical cores when integrase is supplied in trans. Fifth, vRNA is necessary for ALLINI-induced eccentric condensate formation. These observations suggest that integrase is involved in capsid morphogenesis and vRNP packaging.
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Affiliation(s)
- Juan Fontana
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kellie A Jurado
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Naiqian Cheng
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Ngoc L Ly
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - James R Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Alan N Engelman
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Alasdair C Steven
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
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81
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Impact of Chromatin on HIV Replication. Genes (Basel) 2015; 6:957-76. [PMID: 26437430 PMCID: PMC4690024 DOI: 10.3390/genes6040957] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/14/2015] [Accepted: 09/22/2015] [Indexed: 12/22/2022] Open
Abstract
Chromatin influences Human Immunodeficiency Virus (HIV) integration and replication. This review highlights critical host factors that influence chromatin structure and organization and that also impact HIV integration, transcriptional regulation and latency. Furthermore, recent attempts to target chromatin associated factors to reduce the HIV proviral load are discussed.
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82
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Tesina P, Čermáková K, Hořejší M, Procházková K, Fábry M, Sharma S, Christ F, Demeulemeester J, Debyser Z, Rijck JD, Veverka V, Řezáčová P. Multiple cellular proteins interact with LEDGF/p75 through a conserved unstructured consensus motif. Nat Commun 2015; 6:7968. [PMID: 26245978 DOI: 10.1038/ncomms8968] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 07/01/2015] [Indexed: 01/09/2023] Open
Abstract
Lens epithelium-derived growth factor (LEDGF/p75) is an epigenetic reader and attractive therapeutic target involved in HIV integration and the development of mixed lineage leukaemia (MLL1) fusion-driven leukaemia. Besides HIV integrase and the MLL1-menin complex, LEDGF/p75 interacts with various cellular proteins via its integrase binding domain (IBD). Here we present structural characterization of IBD interactions with transcriptional repressor JPO2 and domesticated transposase PogZ, and show that the PogZ interaction is nearly identical to the interaction of LEDGF/p75 with MLL1. The interaction with the IBD is maintained by an intrinsically disordered IBD-binding motif (IBM) common to all known cellular partners of LEDGF/p75. In addition, based on IBM conservation, we identify and validate IWS1 as a novel LEDGF/p75 interaction partner. Our results also reveal how HIV integrase efficiently displaces cellular binding partners from LEDGF/p75. Finally, the similar binding modes of LEDGF/p75 interaction partners represent a new challenge for the development of selective interaction inhibitors.
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Affiliation(s)
- Petr Tesina
- Institute of Organic Chemistry and Biochemistry of the ASCR, v.v.i., Flemingovo nam. 2, 166 10 Prague, Czech Republic.,Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, 128 44 Prague, Czech Republic.,Institute of Molecular Genetics of the ASCR, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic
| | - Kateřina Čermáková
- KU Leuven, Molecular Virology and Gene Therapy, Kapucijnenvoer 33, B-3000 Leuven, Belgium
| | - Magdalena Hořejší
- Institute of Molecular Genetics of the ASCR, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic
| | - Kateřina Procházková
- Institute of Organic Chemistry and Biochemistry of the ASCR, v.v.i., Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics of the ASCR, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic
| | - Subhalakshmi Sharma
- KU Leuven, Molecular Virology and Gene Therapy, Kapucijnenvoer 33, B-3000 Leuven, Belgium
| | - Frauke Christ
- KU Leuven, Molecular Virology and Gene Therapy, Kapucijnenvoer 33, B-3000 Leuven, Belgium
| | - Jonas Demeulemeester
- KU Leuven, Molecular Virology and Gene Therapy, Kapucijnenvoer 33, B-3000 Leuven, Belgium
| | - Zeger Debyser
- KU Leuven, Molecular Virology and Gene Therapy, Kapucijnenvoer 33, B-3000 Leuven, Belgium
| | - Jan De Rijck
- KU Leuven, Molecular Virology and Gene Therapy, Kapucijnenvoer 33, B-3000 Leuven, Belgium
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry of the ASCR, v.v.i., Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry of the ASCR, v.v.i., Flemingovo nam. 2, 166 10 Prague, Czech Republic.,Institute of Molecular Genetics of the ASCR, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic
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Fischer G, Rossmann M, Hyvönen M. Alternative modulation of protein-protein interactions by small molecules. Curr Opin Biotechnol 2015; 35:78-85. [PMID: 25935873 PMCID: PMC4728186 DOI: 10.1016/j.copbio.2015.04.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/08/2015] [Accepted: 04/09/2015] [Indexed: 01/05/2023]
Abstract
Protein–protein interactions can be modulated by more than orthosteric disruption. Modulator categories: ‘orthosteric versus allosteric’ and ‘disrupting versus stabilising’. Interfacial binders exert secondary effects. Non-competitive modulation is a way around low affinity molecules. Non-competitive modulators require tailored screening strategies.
Protein–protein interactions (PPI) have become increasingly popular drug targets, with a number of promising compounds currently in clinical trials. Recent research shows, that PPIs can be modulated in more ways than direct inhibition, where novel non-competitive modes of action promise a solution for the difficult nature of PPI drug discovery. Here, we review recently discovered PPI modulators in light of their mode of action and categorise them as disrupting versus stabilising, orthosteric versus allosteric and by their ability to affect the proteins’ dynamics. We also give recent examples of compounds successful in the clinic, analyse their physicochemical properties and discuss how to overcome the hurdles in discovering alternative modes of modulation.
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Affiliation(s)
- Gerhard Fischer
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Maxim Rossmann
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
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84
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Novel near-infrared BiFC systems from a bacterial phytochrome for imaging protein interactions and drug evaluation under physiological conditions. Biomaterials 2015; 48:97-107. [DOI: 10.1016/j.biomaterials.2015.01.038] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/20/2014] [Accepted: 01/20/2015] [Indexed: 11/23/2022]
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85
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Desimmie BA, Weydert C, Schrijvers R, Vets S, Demeulemeester J, Proost P, Paron I, De Rijck J, Mast J, Bannert N, Gijsbers R, Christ F, Debyser Z. HIV-1 IN/Pol recruits LEDGF/p75 into viral particles. Retrovirology 2015; 12:16. [PMID: 25809198 PMCID: PMC4357141 DOI: 10.1186/s12977-014-0134-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/22/2014] [Indexed: 01/12/2023] Open
Abstract
Background The dynamic interaction between HIV and its host governs the replication of the virus and the study of the virus-host interplay is key to understand the viral lifecycle. The host factor lens epithelium-derived growth factor (LEDGF/p75) tethers the HIV preintegration complex to the chromatin through a direct interaction with integrase (IN). Small molecules that bind the LEDGF/p75 binding pocket of the HIV IN dimer (LEDGINs) block HIV replication through a multimodal mechanism impacting early and late stage replication including HIV maturation. Furthermore, LEDGF/p75 has been identified as a Pol interaction partner. This raised the question whether LEDGF/p75 besides acting as a molecular tether in the target cell, also affects late steps of HIV replication. Results LEDGF/p75 is recruited into HIV-1 particles through direct interaction with the viral IN (or Pol polyprotein) and is a substrate for HIV-1 protease. Incubation in the presence of HIV-1 protease inhibitors resulted in detection of full-length LEDGF/p75 in purified viral particles. We also demonstrate that inhibition of LEDGF/p75-IN interaction by specific mutants or LEDGINs precludes incorporation of LEDGF/p75 in virions, underscoring the specificity of the uptake. LEDGF/p75 depletion did however not result in altered LEDGIN potency. Conclusion Together, these results provide evidence for an IN/Pol mediated uptake of LEDGF/p75 in viral particles and a specific cleavage by HIV protease. Understanding of the possible role of LEDGF/p75 or its cleavage fragments in the viral particle awaits further experimentation. Electronic supplementary material The online version of this article (doi:10.1186/s12977-014-0134-4) contains supplementary material, which is available to authorized users.
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86
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Feng L, Larue RC, Slaughter A, Kessl JJ, Kvaratskhelia M. HIV-1 integrase multimerization as a therapeutic target. Curr Top Microbiol Immunol 2015; 389:93-119. [PMID: 25778682 PMCID: PMC4791179 DOI: 10.1007/82_2015_439] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Multimeric HIV-1 integrase (IN) plays an essential, multifunctional role in virus replication and serves as an important therapeutic target. Structural and biochemical studies have revealed the importance of the ordered interplay between IN molecules for its function. In the presence of viral DNA ends, individual IN subunits assemble into a tetramer and form a stable synaptic complex (SSC), which mediates integration of the reverse transcribed HIV-1 genome into chromatin. Cellular chromatin-associated protein LEDGF/p75 engages the IN tetramer in the SSC and directs HIV-1 integration into active genes. A mechanism to deregulate the productive interplay between IN subunits with small molecule inhibitors has recently received considerable attention. Most notably, allosteric IN inhibitors (ALLINIs) have been shown to bind to the IN dimer interface at the LEDGF/p75 binding pocket, stabilize interacting IN subunits, and promote aberrant, higher order IN multimerization. Consequently, these compounds impair formation of the SSC and associated LEDGF/p75-independent IN catalytic activities as well as inhibit LEDGF/p75 binding to the SSC in vitro. However, in infected cells, ALLINIs more potently impaired correct maturation of virus particles than the integration step. ALLINI treatments induced aberrant, higher order IN multimerization in virions and resulted in eccentric, non-infectious virus particles. These studies have suggested that the correctly ordered IN structure is important for virus particle morphogenesis and highlighted IN multimerization as a plausible therapeutic target for developing new inhibitors to enhance treatment options for HIV-1-infected patients.
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Affiliation(s)
- Lei Feng
- The Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Ross C. Larue
- The Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Alison Slaughter
- The Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Jacques J. Kessl
- The Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Mamuka Kvaratskhelia
- The Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
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87
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Host factors for retroviral integration site selection. Trends Biochem Sci 2014; 40:108-16. [PMID: 25555456 DOI: 10.1016/j.tibs.2014.12.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/15/2014] [Accepted: 12/02/2014] [Indexed: 11/22/2022]
Abstract
To achieve productive infection, retroviruses such as HIV stably integrate their reverse transcribed RNA genome into a host chromosome. Each retroviral family preferentially integrates near a unique subset of genomic features. HIV integrase (IN) is targeted to the body of active transcription units through interaction with lens epithelium-derived growth factor (LEDGF/p75). We describe the successful effort to develop inhibitors of the interaction between IN and LEDGF/p75, referred to as LEDGINs. Gammaretroviruses display a distinct integration pattern. Recently, BET (bromo- and extraterminal domain) proteins were identified as the LEDGF/p75 counterparts that target the integration of gammaretroviruses. The identification of the chromatin-readers LEDGF/p75 and BET as cellular cofactors that orchestrate lentiviral or gammaretroviral integration opens new avenues to developing safer viral vectors for gene therapy.
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88
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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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Slaughter A, Jurado KA, Deng N, Feng L, Kessl JJ, Shkriabai N, Larue RC, Fadel HJ, Patel PA, Jena N, Fuchs JR, Poeschla E, Levy RM, Engelman A, Kvaratskhelia M. The mechanism of H171T resistance reveals the importance of Nδ-protonated His171 for the binding of allosteric inhibitor BI-D to HIV-1 integrase. Retrovirology 2014; 11:100. [PMID: 25421939 PMCID: PMC4251946 DOI: 10.1186/s12977-014-0100-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/24/2014] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are an important new class of anti-HIV-1 agents. ALLINIs bind at the IN catalytic core domain (CCD) dimer interface occupying the principal binding pocket of its cellular cofactor LEDGF/p75. Consequently, ALLINIs inhibit HIV-1 IN interaction with LEDGF/p75 as well as promote aberrant IN multimerization. Selection of viral strains emerging under the inhibitor pressure has revealed mutations at the IN dimer interface near the inhibitor binding site. RESULTS We have investigated the effects of one of the most prevalent substitutions, H171T IN, selected under increasing pressure of ALLINI BI-D. Virus containing the H171T IN substitution exhibited an ~68-fold resistance to BI-D treatment in infected cells. These results correlated with ~84-fold reduced affinity for BI-D binding to recombinant H171T IN CCD protein compared to its wild type (WT) counterpart. However, the H171T IN substitution only modestly affected IN-LEDGF/p75 binding and allowed HIV-1 containing this substitution to replicate at near WT levels. The x-ray crystal structures of BI-D binding to WT and H171T IN CCD dimers coupled with binding free energy calculations revealed the importance of the Nδ- protonated imidazole group of His171 for hydrogen bonding to the BI-D tert-butoxy ether oxygen and establishing electrostatic interactions with the inhibitor carboxylic acid, whereas these interactions were compromised upon substitution to Thr171. CONCLUSIONS Our findings reveal a distinct mechanism of resistance for the H171T IN mutation to ALLINI BI-D and indicate a previously undescribed role of the His171 side chain for binding the inhibitor.
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Affiliation(s)
- Alison Slaughter
- Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, 496 W. 12th Ave, 508 Riffe Building, Columbus, OH 43210 USA
| | - Kellie A Jurado
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA 02215 USA
| | - Nanjie Deng
- Department of Chemistry and Center for Biophysics and Computational Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122 USA
| | - Lei Feng
- Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, 496 W. 12th Ave, 508 Riffe Building, Columbus, OH 43210 USA
| | - Jacques J Kessl
- Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, 496 W. 12th Ave, 508 Riffe Building, Columbus, OH 43210 USA
| | - Nikoloz Shkriabai
- Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, 496 W. 12th Ave, 508 Riffe Building, Columbus, OH 43210 USA
| | - Ross C Larue
- Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, 496 W. 12th Ave, 508 Riffe Building, Columbus, OH 43210 USA
| | - Hind J Fadel
- Department of Molecular Medicine & Division of Infectious Diseases, Mayo Clinic College of Medicine, Rochester, MN 55905 USA
| | - Pratiq A Patel
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210 USA
| | - Nivedita Jena
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210 USA
| | - James R Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210 USA
| | - Eric Poeschla
- Department of Molecular Medicine & Division of Infectious Diseases, Mayo Clinic College of Medicine, Rochester, MN 55905 USA
| | - Ronald M Levy
- Department of Chemistry and Center for Biophysics and Computational Biology, College of Science and Technology, Temple University, Philadelphia, PA 19122 USA
| | - Alan Engelman
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA 02215 USA
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy, The Ohio State University, 496 W. 12th Ave, 508 Riffe Building, Columbus, OH 43210 USA
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Dobard C, Sharma S, Parikh UM, West R, Taylor A, Martin A, Pau CP, Hanson DL, Lipscomb J, Smith J, Novembre F, Hazuda D, Garcia-Lerma JG, Heneine W. Postexposure protection of macaques from vaginal SHIV infection by topical integrase inhibitors. Sci Transl Med 2014; 6:227ra35. [PMID: 24622515 DOI: 10.1126/scitranslmed.3007701] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Coitally delivered microbicide gels containing antiretroviral drugs are important for HIV prevention. However, to date, microbicides have contained entry or reverse transcriptase inhibitors that block early steps in virus infection and thus need to be given as a preexposure dose that interferes with sexual practices and may limit compliance. Integrase inhibitors block late steps after virus infection and therefore are more suitable for post-coital dosing. We first determined the kinetics of strand transfer in vitro and confirmed that integration begins about 6 hours after infection. We then used a repeat-challenge macaque model to assess efficacy of vaginal gels containing integrase strand transfer inhibitors when applied before or after simian/human immunodeficiency virus (SHIV) challenge. We showed that gel containing the strand transfer inhibitor L-870812 protected two of three macaques when applied 30 min before SHIV challenge. We next evaluated the efficacy of 1% raltegravir gel and demonstrated its ability to protect macaques when applied 3 hours after SHIV exposure (five of six protected; P < 0.05, Fisher's exact test). Breakthrough infections showed no evidence of drug resistance in plasma or vaginal secretions despite continued gel dosing after infection. We documented rapid vaginal absorption reflecting a short pharmacological lag time and noted that vaginal, but not plasma, virus load was substantially reduced in the breakthrough infection after raltegravir gel treatment. We provide a proof of concept that topically applied integrase inhibitors protect against vaginal SHIV infection when administered shortly before or 3 hours after virus exposure.
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Affiliation(s)
- Charles Dobard
- Laboratory Branch, Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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Kvaratskhelia M, Sharma A, Larue RC, Serrao E, Engelman A. Molecular mechanisms of retroviral integration site selection. Nucleic Acids Res 2014; 42:10209-25. [PMID: 25147212 PMCID: PMC4176367 DOI: 10.1093/nar/gku769] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Retroviral replication proceeds through an obligate integrated DNA provirus, making retroviral vectors attractive vehicles for human gene-therapy. Though most of the host cell genome is available for integration, the process of integration site selection is not random. Retroviruses differ in their choice of chromatin-associated features and also prefer particular nucleotide sequences at the point of insertion. Lentiviruses including HIV-1 preferentially integrate within the bodies of active genes, whereas the prototypical gammaretrovirus Moloney murine leukemia virus (MoMLV) favors strong enhancers and active gene promoter regions. Integration is catalyzed by the viral integrase protein, and recent research has demonstrated that HIV-1 and MoMLV targeting preferences are in large part guided by integrase-interacting host factors (LEDGF/p75 for HIV-1 and BET proteins for MoMLV) that tether viral intasomes to chromatin. In each case, the selectivity of epigenetic marks on histones recognized by the protein tether helps to determine the integration distribution. In contrast, nucleotide preferences at integration sites seem to be governed by the ability for the integrase protein to locally bend the DNA duplex for pairwise insertion of the viral DNA ends. We discuss approaches to alter integration site selection that could potentially improve the safety of retroviral vectors in the clinic.
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Affiliation(s)
- Mamuka Kvaratskhelia
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Amit Sharma
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Ross C Larue
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Erik Serrao
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Alan Engelman
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
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92
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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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93
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Shkriabai N, Dharmarajan V, Slaughter A, Kessl JJ, Larue RC, Feng L, Fuchs JR, Griffin PR, Kvaratskhelia M. A critical role of the C-terminal segment for allosteric inhibitor-induced aberrant multimerization of HIV-1 integrase. J Biol Chem 2014; 289:26430-26440. [PMID: 25118283 DOI: 10.1074/jbc.m114.589572] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are a promising class of antiretroviral agents for clinical development. Although ALLINIs promote aberrant IN multimerization and inhibit IN interaction with its cellular cofactor LEDGF/p75 with comparable potencies in vitro, their primary mechanism of action in infected cells is through inducing aberrant multimerization of IN. Crystal structures have shown that ALLINIs bind at the IN catalytic core domain dimer interface and bridge two interacting subunits. However, how these interactions promote higher-order protein multimerization is not clear. Here, we used mass spectrometry-based protein footprinting to monitor surface topology changes in full-length WT and the drug-resistant A128T mutant INs in the presence of ALLINI-2. These experiments have identified protein-protein interactions that extend beyond the direct inhibitor binding site and which lead to aberrant multimerization of WT but not A128T IN. Specifically, we demonstrate that C-terminal residues Lys-264 and Lys-266 play an important role in the inhibitor induced aberrant multimerization of the WT protein. Our findings provide structural clues for exploiting IN multimerization as a new, attractive therapeutic target and are expected to facilitate development of improved inhibitors.
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Affiliation(s)
- Nikoloz Shkriabai
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio 43210
| | | | - Alison Slaughter
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio 43210
| | - Jacques J Kessl
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio 43210
| | - Ross C Larue
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio 43210
| | - Lei Feng
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio 43210
| | - James R Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210
| | - Patrick R Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458, and
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio 43210,.
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van Bel N, van der Velden Y, Bonnard D, Le Rouzic E, Das AT, Benarous R, Berkhout B. The allosteric HIV-1 integrase inhibitor BI-D affects virion maturation but does not influence packaging of a functional RNA genome. PLoS One 2014; 9:e103552. [PMID: 25072705 PMCID: PMC4114784 DOI: 10.1371/journal.pone.0103552] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 05/20/2014] [Indexed: 12/30/2022] Open
Abstract
The viral integrase (IN) is an essential protein for HIV-1 replication. IN inserts the viral dsDNA into the host chromosome, thereby aided by the cellular co-factor LEDGF/p75. Recently a new class of integrase inhibitors was described: allosteric IN inhibitors (ALLINIs). Although designed to interfere with the IN-LEDGF/p75 interaction to block HIV DNA integration during the early phase of HIV-1 replication, the major impact was surprisingly found on the process of virus maturation during the late phase, causing a reverse transcription defect upon infection of target cells. Virus particles produced in the presence of an ALLINI are misformed with the ribonucleoprotein located outside the virus core. Virus assembly and maturation are highly orchestrated and regulated processes in which several viral proteins and RNA molecules closely interact. It is therefore of interest to study whether ALLINIs have unpredicted pleiotropic effects on these RNA-related processes. We confirm that the ALLINI BI-D inhibits virus replication and that the produced virus is non-infectious. Furthermore, we show that the wild-type level of HIV-1 genomic RNA is packaged in virions and these genomes are in a dimeric state. The tRNAlys3 primer for reverse transcription was properly placed on this genomic RNA and could be extended ex vivo. In addition, the packaged reverse transcriptase enzyme was fully active when extracted from virions. As the RNA and enzyme components for reverse transcription are properly present in virions produced in the presence of BI-D, the inhibition of reverse transcription is likely to reflect the mislocalization of the components in the aberrant virus particle.
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Affiliation(s)
- Nikki van Bel
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Yme van der Velden
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | | | | | - Atze T. Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- * E-mail:
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Gupta K, Brady T, Dyer BM, Malani N, Hwang Y, Male F, Nolte RT, Wang L, Velthuisen E, Jeffrey J, Van Duyne GD, Bushman FD. Allosteric inhibition of human immunodeficiency virus integrase: late block during viral replication and abnormal multimerization involving specific protein domains. J Biol Chem 2014; 289:20477-88. [PMID: 24904063 PMCID: PMC4110260 DOI: 10.1074/jbc.m114.551119] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 06/03/2014] [Indexed: 11/06/2022] Open
Abstract
HIV-1 replication in the presence of antiviral agents results in evolution of drug-resistant variants, motivating the search for additional drug classes. Here we report studies of GSK1264, which was identified as a compound that disrupts the interaction between HIV-1 integrase (IN) and the cellular factor lens epithelium-derived growth factor (LEDGF)/p75. GSK1264 displayed potent antiviral activity and was found to bind at the site occupied by LEDGF/p75 on IN by x-ray crystallography. Assays of HIV replication in the presence of GSK1264 showed only modest inhibition of the early infection steps and little effect on integration targeting, which is guided by the LEDGF/p75-IN interaction. In contrast, inhibition of late replication steps was more potent. Particle production was normal, but particles showed reduced infectivity. GSK1264 promoted aggregation of IN and preformed LEDGF/p75-IN complexes, suggesting a mechanism of inhibition. LEDGF/p75 was not displaced from IN during aggregation, indicating trapping of LEDGF/p75 in aggregates. Aggregation assays with truncated IN variants revealed that a construct with catalytic and C-terminal domains of IN only formed an open polymer associated with efficient drug-induced aggregation. These data suggest that the allosteric inhibitors of IN are promising antiviral agents and provide new information on their mechanism of action.
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Affiliation(s)
- Kushol Gupta
- the Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, and
| | - Troy Brady
- From the Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6076
| | - Benjamin M. Dyer
- From the Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6076
| | - Nirav Malani
- From the Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6076
| | - Young Hwang
- From the Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6076
| | - Frances Male
- From the Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6076
| | | | | | - Emile Velthuisen
- the HIV Discovery Performance Unit, Infectious Disease Therapy Area Unit, GlaxoSmithKline, Research Triangle Park, North Carolina 27709
| | - Jerry Jeffrey
- the HIV Discovery Performance Unit, Infectious Disease Therapy Area Unit, GlaxoSmithKline, Research Triangle Park, North Carolina 27709
| | - Gregory D. Van Duyne
- the Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, and
| | - Frederic D. Bushman
- From the Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6076
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96
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Harrison AT, Kriel FH, Papathanasopoulos MA, Mosebi S, Abrahams S, Hewer R. The Evaluation of Statins as Potential Inhibitors of the LEDGF/p75-HIV-1 Integrase interaction. Chem Biol Drug Des 2014; 85:290-5. [DOI: 10.1111/cbdd.12384] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 05/03/2014] [Accepted: 06/18/2014] [Indexed: 12/13/2022]
Affiliation(s)
- Angela T. Harrison
- CMDD; Advanced Materials Division; Mintek; Private bag X3015 Randburg Johannesburg 2125 South Africa
- HIV Pathogenesis Research Laboratory; Department of Molecular Medicine and Haematology; University of Witwatersrand Medical School; 7 York Road Parktown Johannesburg 2193 South Africa
| | - Frederik H. Kriel
- CMDD; Advanced Materials Division; Mintek; Private bag X3015 Randburg Johannesburg 2125 South Africa
| | - Maria A. Papathanasopoulos
- HIV Pathogenesis Research Laboratory; Department of Molecular Medicine and Haematology; University of Witwatersrand Medical School; 7 York Road Parktown Johannesburg 2193 South Africa
| | - Salerwe Mosebi
- CMDD; Advanced Materials Division; Mintek; Private bag X3015 Randburg Johannesburg 2125 South Africa
| | - Shaakira Abrahams
- CMDD; Advanced Materials Division; Mintek; Private bag X3015 Randburg Johannesburg 2125 South Africa
- HIV Pathogenesis Research Laboratory; Department of Molecular Medicine and Haematology; University of Witwatersrand Medical School; 7 York Road Parktown Johannesburg 2193 South Africa
| | - Raymond Hewer
- CMDD; Advanced Materials Division; Mintek; Private bag X3015 Randburg Johannesburg 2125 South Africa
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97
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TALEN knockout of the PSIP1 gene in human cells: analyses of HIV-1 replication and allosteric integrase inhibitor mechanism. J Virol 2014; 88:9704-17. [PMID: 24942577 DOI: 10.1128/jvi.01397-14] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED HIV-1 utilizes the cellular protein LEDGF/p75 as a chromosome docking and integration cofactor. The LEDGF/p75 gene, PSIP1, is a potential therapeutic target because, like CCR5, depletion of LEDGF/p75 is tolerated well by human CD4+ T cells, and knockout mice have normal immune systems. RNA interference (RNAi) has been useful for studying LEDGF/p75, but the potent cofactor activity of small protein residua can be confounding. Here, in human cells with utility for HIV research (293T and Jurkat), we used transcription activator-like effector nucleases (TALENs) to completely eradicate all LEDGF/p75 expression. We performed two kinds of PSIP1 knockouts: whole-gene deletion and deletion of the integrase binding domain (IBD)-encoding exons. HIV-1 integration was inhibited, and spreading viral replication was severely impaired in PSIP1-/- Jurkat cells infected at high multiplicity. Furthermore, frameshifting the gene in the first coding exon with a single TALEN pair yielded trace LEDGF/p75 levels that were virologically active, affirming the cofactor's potency and the value of definitive gene or IBD exon segment deletion. Some recent studies have suggested that LEDGF/p75 may participate in HIV-1 assembly. However, we determined that assembly of infectious viral particles is normal in PSIP1-/- cells. The potency of an allosteric integrase inhibitor, ALLINI-2, for rendering produced virions noninfectious was also unaffected by total eradication of cellular LEDGF/p75. We conclude that HIV-1 particle assembly and the main ALLINI mechanism are LEDGF/p75 independent. The block to HIV-1 propagation in PSIP1-/- human CD4+ T cells raises the possibility of gene targeting PSIP1 combinatorially with CCR5 for HIV-1 cure. IMPORTANCE LEDGF/p75 dependence is universally conserved in the retroviral genus Lentivirus. Once inside the nucleus, lentiviral preintegration complexes are thought to attach to the chromosome when integrase binds to LEDGF/p75. This tethering process is largely responsible for the 2-fold preference for integration into active genes, but the cofactor's full role in the lentiviral life cycle is not yet clear. Effective knockdowns are difficult because even trace residua of this tightly chromatin-bound protein can support integration cofactor function. Here, in experimentally useful human cell lines, we used TALENs to definitively eradicate LEDGF/p75 by deleting either all of PSIP1 or the exons that code for the integrase binding domain. HIV-1 replication was severely impaired in these PSIP1 knockout cells. Experiments in these cells also excluded a role for LEDGF/p75 in HIV-1 assembly and showed that the main ALLINI mechanism is LEDGF/p75 independent. Site-specific gene targeting of PSIP1 may have therapeutic potential for HIV-1 disease.
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98
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Fader LD, Carson R, Morin S, Bilodeau F, Chabot C, Halmos T, Bailey MD, Kawai SH, Coulombe R, Laplante S, Mekhssian K, Jakalian A, Garneau M, Duan J, Mason SW, Simoneau B, Fenwick C, Tsantrizos Y, Yoakim C. Minimizing the Contribution of Enterohepatic Recirculation to Clearance in Rat for the NCINI Class of Inhibitors of HIV. ACS Med Chem Lett 2014; 5:711-6. [PMID: 24944749 DOI: 10.1021/ml500110j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 04/16/2014] [Indexed: 12/12/2022] Open
Abstract
A scaffold replacement approach was used to identifying the pyridine series of noncatalytic site integrase inhibitors. These molecules bind with higher affinity to a tetrameric form compared to a dimeric form of integrase. Optimization of the C6 and C4 positions revealed that viruses harboring T124 or A124 amino acid substitutions are highly susceptible to these inhibitors, but viruses having the N124 amino acid substitution are about 100-fold less susceptible. Compound 20 had EC50 values <10 nM against viruses having T124 or A124 substitutions in IN and >800 nM in viruses having N124 substitions. Compound 20 had an excellent in vitro ADME profile and demonstrated reduced contribution of biliary excretion to in vivo clearance compared to BI 224436, the lead compound from the quinoline series of NCINIs.
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Affiliation(s)
- Lee D. Fader
- Research and Development, Boehringer Ingelheim (Canada), Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Rebekah Carson
- Research and Development, Boehringer Ingelheim (Canada), Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Sébastien Morin
- Research and Development, Boehringer Ingelheim (Canada), Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - François Bilodeau
- Research and Development, Boehringer Ingelheim (Canada), Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Catherine Chabot
- Research and Development, Boehringer Ingelheim (Canada), Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Ted Halmos
- Research and Development, Boehringer Ingelheim (Canada), Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Murray D. Bailey
- Research and Development, Boehringer Ingelheim (Canada), Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Stephen H. Kawai
- Research and Development, Boehringer Ingelheim (Canada), Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - René Coulombe
- Research and Development, Boehringer Ingelheim (Canada), Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Steven Laplante
- Research and Development, Boehringer Ingelheim (Canada), Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Kevork Mekhssian
- Research and Development, Boehringer Ingelheim (Canada), Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Araz Jakalian
- Research and Development, Boehringer Ingelheim (Canada), Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Michel Garneau
- Research and Development, Boehringer Ingelheim (Canada), Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Jianmin Duan
- Research and Development, Boehringer Ingelheim (Canada), Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Stephen W. Mason
- Research and Development, Boehringer Ingelheim (Canada), Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Bruno Simoneau
- Research and Development, Boehringer Ingelheim (Canada), Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Craig Fenwick
- Research and Development, Boehringer Ingelheim (Canada), Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Youla Tsantrizos
- Research and Development, Boehringer Ingelheim (Canada), Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
| | - Christiane Yoakim
- Research and Development, Boehringer Ingelheim (Canada), Ltd., 2100 Cunard Street, Laval, Québec H7S 2G5, Canada
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99
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Sharma A, Slaughter A, Jena N, Feng L, Kessl JJ, Fadel HJ, Malani N, Male F, Wu L, Poeschla E, Bushman FD, Fuchs JR, Kvaratskhelia M. A new class of multimerization selective inhibitors of HIV-1 integrase. PLoS Pathog 2014; 10:e1004171. [PMID: 24874515 PMCID: PMC4038613 DOI: 10.1371/journal.ppat.1004171] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 04/22/2014] [Indexed: 12/20/2022] Open
Abstract
The quinoline-based allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are promising candidates for clinically useful antiviral agents. Studies using these compounds have highlighted the role of IN in both early and late stages of virus replication. However, dissecting the exact mechanism of action of the quinoline-based ALLINIs has been complicated by the multifunctional nature of these inhibitors because they both inhibit IN binding with its cofactor LEDGF/p75 and promote aberrant IN multimerization with similar potencies in vitro. Here we report design of small molecules that allowed us to probe the role of HIV-1 IN multimerization independently from IN-LEDGF/p75 interactions in infected cells. We altered the rigid quinoline moiety in ALLINIs and designed pyridine-based molecules with a rotatable single bond to allow these compounds to bridge between interacting IN subunits optimally and promote oligomerization. The most potent pyridine-based inhibitor, KF116, potently (EC50 of 0.024 µM) blocked HIV-1 replication by inducing aberrant IN multimerization in virus particles, whereas it was not effective when added to target cells. Furthermore, KF116 inhibited the HIV-1 IN variant with the A128T substitution, which confers resistance to the majority of quinoline-based ALLINIs. A genome-wide HIV-1 integration site analysis demonstrated that addition of KF116 to target or producer cells did not affect LEDGF/p75-dependent HIV-1 integration in host chromosomes, indicating that this compound is not detectably inhibiting IN-LEDGF/p75 binding. These findings delineate the significance of correctly ordered IN structure for HIV-1 particle morphogenesis and demonstrate feasibility of exploiting IN multimerization as a therapeutic target. Furthermore, pyridine-based compounds present a novel class of multimerization selective IN inhibitors as investigational probes for HIV-1 molecular biology. The administration of highly active-antiretroviral therapy (HAART) has changed what was once a terminal disease into a manageable chronic infection. The success of HAART is manifested by reduced mortality and morbidity of HIV-1 infected patients. However, evolution of HIV-1 strains resistant to current therapies is a major clinical problem in the fight against AIDS. Therefore, new inhibitors with novel mechanisms of action are needed. One such mechanism is to target multimerization of HIV-1 integrase. In the present study, we report the design of pyridine-based small molecules that contain a rotatable single bond to allow optimal bridging between interacting integrase subunits. As a result, pyridine-based compounds stabilized interacting IN subunits and promoted aberrant, higher order integrase multimerization. The most potent compound, KF116, potently inhibited HIV-1 replication by interfering with proper maturation of HIV-1 particles, whereas KF116 at therapeutically relevant (submicromolar) concentrations had no detectable effects on LEDGF/p75 mediated HIV-1 integration. Our findings highlight HIV-1 integrase multimerization as a plausible therapeutic target and offer a path for designing improved inhibitors for potential clinical use.
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Affiliation(s)
- Amit Sharma
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America
| | - Alison Slaughter
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America
| | - Nivedita Jena
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America
| | - Lei Feng
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America
| | - Jacques J. Kessl
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America
| | - Hind J. Fadel
- Department of Molecular Medicine & Division of Infectious Diseases, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Nirav Malani
- Perelman School of Medicine, Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Frances Male
- Perelman School of Medicine, Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Li Wu
- Center for Retrovirus Research and Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Eric Poeschla
- Department of Molecular Medicine & Division of Infectious Diseases, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Frederic D. Bushman
- Perelman School of Medicine, Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - James R. Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research and College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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100
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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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