1
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Singer MR, Dinh T, Levintov L, Annamalai AS, Rey JS, Briganti L, Cook NJ, Pye VE, Taylor IA, Kim K, Engelman AN, Kim B, Perilla JR, Kvaratskhelia M, Cherepanov P. The Drug-Induced Interface That Drives HIV-1 Integrase Hypermultimerization and Loss of Function. mBio 2023; 14:e0356022. [PMID: 36744954 PMCID: PMC9973045 DOI: 10.1128/mbio.03560-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 02/07/2023] Open
Abstract
Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are an emerging class of small molecules that disrupt viral maturation by inducing the aberrant multimerization of IN. Here, we present cocrystal structures of HIV-1 IN with two potent ALLINIs, namely, BI-D and the drug candidate Pirmitegravir. The structures reveal atomistic details of the ALLINI-induced interface between the HIV-1 IN catalytic core and carboxyl-terminal domains (CCD and CTD). Projecting from their principal binding pocket on the IN CCD dimer, the compounds act as molecular glue by engaging a triad of invariant HIV-1 IN CTD residues, namely, Tyr226, Trp235, and Lys266, to nucleate the CTD-CCD interaction. The drug-induced interface involves the CTD SH3-like fold and extends to the beginning of the IN carboxyl-terminal tail region. We show that mutations of HIV-1 IN CTD residues that participate in the interface with the CCD greatly reduce the IN-aggregation properties of Pirmitegravir. Our results explain the mechanism of the ALLINI-induced condensation of HIV-1 IN and provide a reliable template for the rational development of this series of antiretrovirals through the optimization of their key contacts with the viral target. IMPORTANCE Despite the remarkable success of combination antiretroviral therapy, HIV-1 remains among the major causes of human suffering and loss of life in poor and developing nations. To prevail in this drawn-out battle with the pandemic, it is essential to continue developing advanced antiviral agents to fight drug resistant HIV-1 variants. Allosteric integrase inhibitors (ALLINIs) are an emerging class of HIV-1 antagonists that are orthogonal to the current antiretroviral drugs. These small molecules act as highly specific molecular glue, which triggers the aggregation of HIV-1 integrase. In this work, we present high-resolution crystal structures that reveal the crucial interactions made by two potent ALLINIs, namely, BI-D and Pirmitegravir, with HIV-1 integrase. Our results explain the mechanism of drug action and will inform the development of this promising class of small molecules for future use in antiretroviral regimens.
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Affiliation(s)
- Matthew R. Singer
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Tung Dinh
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Lev Levintov
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Arun S. Annamalai
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Juan S. Rey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Lorenzo Briganti
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Nicola J. Cook
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Valerie E. Pye
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Baek Kim
- Center for Drug Discovery, Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Juan R. Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Peter Cherepanov
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Infectious Disease, St-Mary's Campus, Imperial College London, London, United Kingdom
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2
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Maehigashi T, Ahn S, Kim UI, Lindenberger J, Oo A, Koneru PC, Mahboubi B, Engelman AN, Kvaratskhelia M, Kim K, Kim B. A highly potent and safe pyrrolopyridine-based allosteric HIV-1 integrase inhibitor targeting host LEDGF/p75-integrase interaction site. PLoS Pathog 2021; 17:e1009671. [PMID: 34293041 PMCID: PMC8297771 DOI: 10.1371/journal.ppat.1009671] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/27/2021] [Indexed: 12/03/2022] Open
Abstract
Allosteric integrase inhibitors (ALLINIs) are a class of experimental anti-HIV agents that target the noncatalytic sites of the viral integrase (IN) and interfere with the IN-viral RNA interaction during viral maturation. Here, we report a highly potent and safe pyrrolopyridine-based ALLINI, STP0404, displaying picomolar IC50 in human PBMCs with a >24,000 therapeutic index against HIV-1. X-ray structural and biochemical analyses revealed that STP0404 binds to the host LEDGF/p75 protein binding pocket of the IN dimer, which induces aberrant IN oligomerization and blocks the IN-RNA interaction. Consequently, STP0404 inhibits proper localization of HIV-1 RNA genomes in viral particles during viral maturation. Y99H and A128T mutations at the LEDGF/p75 binding pocket render resistance to STP0404. Extensive in vivo pharmacological and toxicity investigations demonstrate that STP0404 harbors outstanding therapeutic and safety properties. Overall, STP0404 is a potent and first-in-class ALLINI that targets LEDGF/p75 binding site and has advanced to a human trial.
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Affiliation(s)
- Tatsuya Maehigashi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | | | - Uk-Il Kim
- ST Pharm Co., Ltd., Seoul, South Korea
| | - Jared Lindenberger
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Adrian Oo
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Pratibha C. Koneru
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Bijan Mahboubi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | | | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, United States of America
- Center for Drug Discovery, Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
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3
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Kumar D, Sharma P, Shabu, Kaur R, Lobe MMM, Gupta GK, Ntie-Kang F. In search of therapeutic candidates for HIV/AIDS: rational approaches, design strategies, structure-activity relationship and mechanistic insights. RSC Adv 2021; 11:17936-17964. [PMID: 35480193 PMCID: PMC9033207 DOI: 10.1039/d0ra10655k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 04/19/2021] [Indexed: 12/23/2022] Open
Abstract
The HIV/AIDS pandemic is a serious threat to the health and development of mankind, which has affected about 37.9 million people worldwide. The increasing negative health, economic and social impacts of this disease have led to the search for new therapeutic candidates for the mitigation of AIDS/HIV. However, to date, there is still no treatment that can cure this disease. Furthermore, the clinically available drugs have numerous severe side effects. Hence, the synthesis of novel agents from natural leads is one of the rational approaches to obtain new drugs in modern medicinal chemistry. This review article is an effort to summarize recent developments with regards to the discovery of novel analogs with promising biological potential against HIV/AIDS. Herein, we also aim to discuss prospective directions on the progress of more credible and specific analogues. Besides presenting design strategies, the present communication also highlights the structure-activity relationship together with the structural features of the most promising molecules, their IC50 values, mechanistic insights and some interesting key findings revealed during their biological evaluation. The interactions with the amino acid residues of the enzymes responsible for HIV-1 inhibition are also discussed. This collection will be of great interest for researchers working in this area.
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Affiliation(s)
- Dinesh Kumar
- Sri Sai College of Pharmacy Manawala Amritsar-143001 Punjab India +91-9988902489
| | - Pooja Sharma
- Sri Sai College of Pharmacy Manawala Amritsar-143001 Punjab India +91-9988902489
- Department of Pharmaceutical Sciences and Drug Research, Punjabi University Patiala India
| | - Shabu
- Indian Institute of Integrative Medicine (CSIR-IIIM) Canal Road Jammu 180001 India
| | - Ramandeep Kaur
- Sri Sai College of Pharmacy Manawala Amritsar-143001 Punjab India +91-9988902489
| | - Maloba M M Lobe
- Department of Chemistry, Faculty of Science, University of Buea P. O. Box 63 Buea Cameroon +237 685625811
| | - Girish K Gupta
- Department of Pharmaceutical Chemistry, Sri Sai College of Pharmacy Badhani Pathankot-145001 Punjab India
| | - Fidele Ntie-Kang
- Department of Chemistry, Faculty of Science, University of Buea P. O. Box 63 Buea Cameroon +237 685625811
- Institute for Pharmacy, Martin-Luther-Universität Halle-Wittenberg Kurt-Mothes-Str. 3 06120 Halle (Saale) Germany +49 3455525043
- Institute of Botany, Technical University of Dresden Zellescher Weg 20b 01062 Dresden Germany
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4
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Elliott JL, Eschbach JE, Koneru PC, Li W, Puray-Chavez M, Townsend D, Lawson DQ, Engelman AN, Kvaratskhelia M, Kutluay SB. Integrase-RNA interactions underscore the critical role of integrase in HIV-1 virion morphogenesis. eLife 2020; 9:54311. [PMID: 32960169 PMCID: PMC7671690 DOI: 10.7554/elife.54311] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 09/22/2020] [Indexed: 01/29/2023] Open
Abstract
A large number of human immunodeficiency virus 1 (HIV-1) integrase (IN) alterations, referred to as class II substitutions, exhibit pleiotropic effects during virus replication. However, the underlying mechanism for the class II phenotype is not known. Here we demonstrate that all tested class II IN substitutions compromised IN-RNA binding in virions by one of the three distinct mechanisms: (i) markedly reducing IN levels thus precluding the formation of IN complexes with viral RNA; (ii) adversely affecting functional IN multimerization and consequently impairing IN binding to viral RNA; and (iii) directly compromising IN-RNA interactions without substantially affecting IN levels or functional IN multimerization. Inhibition of IN-RNA interactions resulted in the mislocalization of viral ribonucleoprotein complexes outside the capsid lattice, which led to premature degradation of the viral genome and IN in target cells. Collectively, our studies uncover causal mechanisms for the class II phenotype and highlight an essential role of IN-RNA interactions for accurate virion maturation.
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Affiliation(s)
- Jennifer L Elliott
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, United States
| | - Jenna E Eschbach
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, United States
| | - Pratibha C Koneru
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, United States
| | - Wen Li
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, United States.,Department of Medicine, Harvard Medical School, Boston, United States
| | - Maritza Puray-Chavez
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, United States
| | - Dana Townsend
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, United States
| | - Dana Q Lawson
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, United States
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, United States.,Department of Medicine, Harvard Medical School, Boston, United States
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, United States
| | - Sebla B Kutluay
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, United States
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5
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Elliott JL, Kutluay SB. Going beyond Integration: The Emerging Role of HIV-1 Integrase in Virion Morphogenesis. Viruses 2020; 12:E1005. [PMID: 32916894 PMCID: PMC7551943 DOI: 10.3390/v12091005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 12/22/2022] Open
Abstract
The HIV-1 integrase enzyme (IN) plays a critical role in the viral life cycle by integrating the reverse-transcribed viral DNA into the host chromosome. This function of IN has been well studied, and the knowledge gained has informed the design of small molecule inhibitors that now form key components of antiretroviral therapy regimens. Recent discoveries unveiled that IN has an under-studied yet equally vital second function in human immunodeficiency virus type 1 (HIV-1) replication. This involves IN binding to the viral RNA genome in virions, which is necessary for proper virion maturation and morphogenesis. Inhibition of IN binding to the viral RNA genome results in mislocalization of the viral genome inside the virus particle, and its premature exposure and degradation in target cells. The roles of IN in integration and virion morphogenesis share a number of common elements, including interaction with viral nucleic acids and assembly of higher-order IN multimers. Herein we describe these two functions of IN within the context of the HIV-1 life cycle, how IN binding to the viral genome is coordinated by the major structural protein, Gag, and discuss the value of targeting the second role of IN in virion morphogenesis.
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Affiliation(s)
| | - Sebla B. Kutluay
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA;
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6
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Koneru PC, Francis AC, Deng N, Rebensburg SV, Hoyte AC, Lindenberger J, Adu-Ampratwum D, Larue RC, Wempe MF, Engelman AN, Lyumkis D, Fuchs JR, Levy RM, Melikyan GB, Kvaratskhelia M. HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors. eLife 2019; 8:46344. [PMID: 31120420 PMCID: PMC6581505 DOI: 10.7554/elife.46344] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 05/22/2019] [Indexed: 12/13/2022] Open
Abstract
Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are a promising new class of antiretroviral agents that disrupt proper viral maturation by inducing hyper-multimerization of IN. Here we show that lead pyridine-based ALLINI KF116 exhibits striking selectivity for IN tetramers versus lower order protein oligomers. IN structural features that are essential for its functional tetramerization and HIV-1 replication are also critically important for KF116 mediated higher-order IN multimerization. Live cell imaging of single viral particles revealed that KF116 treatment during virion production compromises the tight association of IN with capsid cores during subsequent infection of target cells. We have synthesized the highly active (-)-KF116 enantiomer, which displayed EC50 of ~7 nM against wild type HIV-1 and ~10 fold higher, sub-nM activity against a clinically relevant dolutegravir resistant mutant virus suggesting potential clinical benefits for complementing dolutegravir therapy with pyridine-based ALLINIs. HIV-1 inserts its genetic code into human genomes, turning healthy cells into virus factories. To do this, the virus uses an enzyme called integrase. Front-line treatments against HIV-1 called “integrase strand-transfer inhibitors” stop this enzyme from working. These inhibitors have helped to revolutionize the treatment of HIV/AIDS by protecting the cells from new infections. But, the emergence of drug resistance remains a serious problem. As the virus evolves, it changes the shape of its integrase protein, substantially reducing the effectiveness of the current therapies. One way to overcome this problem is to develop other therapies that can kill the drug resistant viruses by targeting different parts of the integrase protein. It should be much harder for the virus to evolve the right combination of changes to escape two or more treatments at once. A promising class of new compounds are “allosteric integrase inhibitors”. These chemical compounds target a part of the integrase enzyme that the other treatments do not yet reach. Rather than stopping the integrase enzyme from inserting the viral code into the human genome, the new inhibitors make integrase proteins clump together and prevent the formation of infectious viruses. At the moment, these compounds are still experimental. Before they are ready for use in people, researchers need to better understand how they work, and there are several open questions to answer. Integrase proteins work in groups of four and it is not clear how the new compounds make the integrases form large clumps, or what this does to the virus. Understanding this should allow scientists to develop improved versions of the drugs. To answer these questions, Koneru et al. first examined two of the new compounds. A combination of molecular analysis and computer modelling revealed how they work. The compounds link many separate groups of four integrases with each other to form larger and larger clumps, essentially a snowball effect. Live images of infected cells showed that the clumps of integrase get stuck outside of the virus’s protective casing. This leaves them exposed, allowing the cell to destroy the integrase enzymes. Koneru et al. also made a new compound, called (-)-KF116. Not only was this compound able to tackle normal HIV-1, it could block viruses resistant to the other type of integrase treatment. In fact, in laboratory tests, it was 10 times more powerful against these resistant viruses. Together, these findings help to explain how allosteric integrase inhibitors work, taking scientists a step closer to bringing them into the clinic. In the future, new versions of the compounds, like (-)-KF116, could help to tackle drug resistance in HIV-1.
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Affiliation(s)
- Pratibha C Koneru
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, United States
| | - Ashwanth C Francis
- Division of Infectious Diseases, Department of Pediatrics, Emory University, Atlanta, United States
| | - Nanjie Deng
- Department of Chemistry and Physical Sciences, Pace University, New York, United States
| | - Stephanie V Rebensburg
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, United States
| | - Ashley C Hoyte
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, United States
| | - Jared Lindenberger
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, United States
| | | | - Ross C Larue
- College of Pharmacy, The Ohio State University, Columbus, United States
| | - Michael F Wempe
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Aurora, United States
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, United States.,Department of Medicine, Harvard Medical School, Boston, United States
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, United States
| | - James R Fuchs
- College of Pharmacy, The Ohio State University, Columbus, United States
| | - Ronald M Levy
- Department of Chemistry, Temple University, Philadelphia, United States
| | - Gregory B Melikyan
- Division of Infectious Diseases, Department of Pediatrics, Emory University, Atlanta, United States
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, United States
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7
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Bieniasz PD, Kutluay SB. CLIP-related methodologies and their application to retrovirology. Retrovirology 2018; 15:35. [PMID: 29716635 PMCID: PMC5930818 DOI: 10.1186/s12977-018-0417-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 04/17/2018] [Indexed: 01/28/2023] Open
Abstract
Virtually every step of HIV-1 replication and numerous cellular antiviral defense mechanisms are regulated by the binding of a viral or cellular RNA-binding protein (RBP) to distinct sequence or structural elements on HIV-1 RNAs. Until recently, these protein-RNA interactions were studied largely by in vitro binding assays complemented with genetics approaches. However, these methods are highly limited in the identification of the relevant targets of RBPs in physiologically relevant settings. Development of crosslinking-immunoprecipitation sequencing (CLIP) methodology has revolutionized the analysis of protein-nucleic acid complexes. CLIP combines immunoprecipitation of covalently crosslinked protein-RNA complexes with high-throughput sequencing, providing a global account of RNA sequences bound by a RBP of interest in cells (or virions) at near-nucleotide resolution. Numerous variants of the CLIP protocol have recently been developed, some with major improvements over the original. Herein, we briefly review these methodologies and give examples of how CLIP has been successfully applied to retrovirology research.
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Affiliation(s)
- Paul D. Bieniasz
- Howard Hughes Medical Institute and Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065 USA
| | - Sebla B. Kutluay
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110 USA
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8
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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: 25] [Impact Index Per Article: 4.2] [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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9
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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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10
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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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11
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Allosteric HIV-1 Integrase Inhibitors Lead to Premature Degradation of the Viral RNA Genome and Integrase in Target Cells. J Virol 2017; 91:JVI.00821-17. [PMID: 28615207 DOI: 10.1128/jvi.00821-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 05/23/2017] [Indexed: 12/23/2022] Open
Abstract
Recent evidence indicates that inhibition of HIV-1 integrase (IN) binding to the viral RNA genome by allosteric integrase inhibitors (ALLINIs) or through mutations within IN yields aberrant particles in which the viral ribonucleoprotein complexes (vRNPs) are eccentrically localized outside the capsid lattice. These particles are noninfectious and are blocked at an early reverse transcription stage in target cells. However, the basis of this reverse transcription defect is unknown. Here, we show that the viral RNA genome and IN from ALLINI-treated virions are prematurely degraded in target cells, whereas reverse transcriptase remains active and stably associated with the capsid lattice. The aberrantly shaped cores in ALLINI-treated particles can efficiently saturate and be degraded by a restricting TRIM5 protein, indicating that they are still composed of capsid proteins arranged in a hexagonal lattice. Notably, the fates of viral core components follow a similar pattern in cells infected with eccentric particles generated by mutations within IN that inhibit its binding to the viral RNA genome. We propose that IN-RNA interactions allow packaging of both the viral RNA genome and IN within the protective capsid lattice to ensure subsequent reverse transcription and productive infection in target cells. Conversely, disruption of these interactions by ALLINIs or mutations in IN leads to premature degradation of both the viral RNA genome and IN, as well as the spatial separation of reverse transcriptase from the viral genome during early steps of infection.IMPORTANCE Recent evidence indicates that HIV-1 integrase (IN) plays a key role during particle maturation by binding to the viral RNA genome. Inhibition of IN-RNA interactions yields aberrant particles with the viral ribonucleoprotein complexes (vRNPs) eccentrically localized outside the conical capsid lattice. Although these particles contain all of the components necessary for reverse transcription, they are blocked at an early reverse transcription stage in target cells. To explain the basis of this defect, we tracked the fates of multiple viral components in infected cells. Here, we show that the viral RNA genome and IN in eccentric particles are prematurely degraded, whereas reverse transcriptase remains active and stably associated within the capsid lattice. We propose that IN-RNA interactions ensure the packaging of both vRNPs and IN within the protective capsid cores to facilitate subsequent reverse transcription and productive infection in target cells.
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12
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Kessl JJ, Kutluay SB, Townsend D, Rebensburg S, Slaughter A, Larue RC, Shkriabai N, Bakouche N, Fuchs JR, Bieniasz PD, Kvaratskhelia M. HIV-1 Integrase Binds the Viral RNA Genome and Is Essential during Virion Morphogenesis. Cell 2016; 166:1257-1268.e12. [PMID: 27565348 DOI: 10.1016/j.cell.2016.07.044] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/16/2016] [Accepted: 07/26/2016] [Indexed: 10/21/2022]
Abstract
While an essential role of HIV-1 integrase (IN) for integration of viral cDNA into human chromosome is established, studies with IN mutants and allosteric IN inhibitors (ALLINIs) have suggested that IN can also influence viral particle maturation. However, it has remained enigmatic as to how IN contributes to virion morphogenesis. Here, we demonstrate that IN directly binds the viral RNA genome in virions. These interactions have specificity, as IN exhibits distinct preference for select viral RNA structural elements. We show that IN substitutions that selectively impair its binding to viral RNA result in eccentric, non-infectious virions without affecting nucleocapsid-RNA interactions. Likewise, ALLINIs impair IN binding to viral RNA in virions of wild-type, but not escape mutant, virus. These results reveal an unexpected biological role of IN binding to the viral RNA genome during virion morphogenesis and elucidate the mode of action of ALLINIs.
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Affiliation(s)
- Jacques J Kessl
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Sebla B Kutluay
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, Rockefeller University, New York, NY 10016, USA
| | - Dana Townsend
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stephanie Rebensburg
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Alison Slaughter
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Ross C Larue
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Nikoloz Shkriabai
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Nordine Bakouche
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - James R Fuchs
- College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, Rockefeller University, New York, NY 10016, USA; Howard Hughes Medical Institute, Aaron Diamond AIDS Research Center, Rockefeller University, New York, NY 10016, USA
| | - Mamuka Kvaratskhelia
- Center for Retrovirus Research, Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Ohio State University, Columbus, OH 43210, USA.
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13
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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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14
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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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15
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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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16
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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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17
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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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18
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Design, synthesis and activity evaluation of novel peptide fusion inhibitors targeting HIV-1 gp41. Bioorg Med Chem 2016; 24:201-6. [DOI: 10.1016/j.bmc.2015.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 11/05/2015] [Accepted: 12/02/2015] [Indexed: 11/19/2022]
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19
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van Bel N, Ghabri A, Das AT, Berkhout B. The HIV-1 leader RNA is exquisitely sensitive to structural changes. Virology 2015; 483:236-52. [DOI: 10.1016/j.virol.2015.03.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 03/05/2015] [Accepted: 03/27/2015] [Indexed: 01/14/2023]
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