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Montermoso S, Eilers G, Allen A, Sharp R, Hwang Y, Bushman FD, Gupta K, Duyne GV. Structural Impact of Ex Vivo Resistance Mutations on HIV-1 Integrase Polymers Induced by Allosteric Inhibitors. J Mol Biol 2025; 437:169224. [PMID: 40409709 DOI: 10.1016/j.jmb.2025.169224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2025] [Revised: 05/15/2025] [Accepted: 05/16/2025] [Indexed: 05/25/2025]
Abstract
HIV-1 integrase (IN) is targeted by two classes of antivirals: integrase strand transfer inhibitors (INSTIs), which bind to the active site within the catalytic core domain (CCD), and allosteric integrase inhibitors (ALLINIs), which bind at the CCD dimer interface. ALLINIs were initially designed to disrupt interactions with the cellular cofactor LEDGF/p75, but it has become clear that ALLINIs primarily act by promoting formation of aberrant integrase polymers. The ALLINIs achieve this by stabilizing ectopic intermolecular interactions between the CCD dimer and the integrase carboxy-terminal domain (CTD), which disrupts viral maturation. Previously, we determined the structure of full-length HIV-1 IN bound to the ALLINI GSK1264 at 4.4 Å resolution, revealing its polymerization mechanism. More recently, we reported the X-ray crystal structure of a minimal ternary complex between CCD, CTD, and the ALLINI BI-224436 at a higher resolution. In this study, we improve the original 4.4 Å structure using this higher-resolution information and report two new structures of full-length HIV-1 IN harboring escape mutations in the CCD (Trp131Cys) or CTD (Asn222Lys) bound with the prototype ALLINI BI-D at 4.5 Å. These structures reveal perturbations to the tertiary organization associated with escape substitutions, which correlate with their reduced ability to form ectopic ALLINI-induced polymers in vitro. These findings suggest a general structural mechanism of ALLINI resistance and provide insights for the design of improved ALLINIs.
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Affiliation(s)
- Saira Montermoso
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Graduate Group in Biochemistry, Biophysics, and Chemical Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Grant Eilers
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Audrey Allen
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Robert Sharp
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Young Hwang
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
| | - Gregory Van Duyne
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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2
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Kalpana GV, Ernst E, Haldar S. TAR RNA Mimicry of INI1 and Its Influence on Non-Integration Function of HIV-1 Integrase. Viruses 2025; 17:693. [PMID: 40431704 PMCID: PMC12115661 DOI: 10.3390/v17050693] [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: 03/07/2025] [Revised: 05/06/2025] [Accepted: 05/07/2025] [Indexed: 05/29/2025] Open
Abstract
HIV-1 integrase (IN), an essential viral protein that catalyzes integration, also influences non-integration functions such as particle production and morphogenesis. The mechanism by which non-integration functions are mediated is not completely understood. Several factors influence these non-integration functions, including the ability of IN to bind to viral RNA. INI1 is an integrase-binding host factor that influences HIV-1 replication at multiple stages, including particle production and particle morphogenesis. IN mutants defective for binding to INI1 are also defective for particle morphogenesis, similar to RNA-binding-defective IN mutants. Studies have indicated that the highly conserved Repeat (Rpt) 1, the IN-binding domain of INI1, structurally mimics TAR RNA, and that Rpt1 and TAR RNA compete for binding to IN. Based on the RNA mimicry, we propose that INI1 may function as a "place-holder" for viral RNA to facilitate proper ribonucleoprotein complex formation required during the assembly and particle morphogenesis of the HIV-1 virus. These studies suggest that drugs that target IN/INI1 interaction may lead to dual inhibition of both IN/INI1 and IN/RNA interactions to curb HIV-1 replication.
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Affiliation(s)
- Ganjam V. Kalpana
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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3
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Ay S, Burlaud-Gaillard J, Gazi A, Tatirovsky Y, Cuche C, Diana JS, Scoca V, Di Santo JP, Roingeard P, Mammano F, Di Nunzio F. In vivo HIV-1 nuclear condensates safeguard against cGAS and license reverse transcription. EMBO J 2025; 44:166-199. [PMID: 39623137 PMCID: PMC11697293 DOI: 10.1038/s44318-024-00316-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 11/05/2024] [Accepted: 11/07/2024] [Indexed: 01/04/2025] Open
Abstract
Entry of viral capsids into the nucleus induces the formation of biomolecular condensates called HIV-1 membraneless organelles (HIV-1-MLOs). Several questions remain about their persistence, in vivo formation, composition, and function. Our study reveals that HIV-1-MLOs persisted for several weeks in infected cells, and their abundance correlated with viral infectivity. Using an appropriate animal model, we show that HIV-1-MLOs were formed in vivo during acute infection. To explore the viral structures present within these biomolecular condensates, we used a combination of double immunogold labeling, electron microscopy and tomography, and unveiled a diverse array of viral core structures. Our functional analyses showed that HIV-1-MLOs remained stable during treatment with a reverse transcriptase inhibitor, maintaining the virus in a dormant state. Drug withdrawal restored reverse transcription, promoting efficient virus replication akin to that observed in latently infected patients on antiretroviral therapy. However, when HIV-1 MLOs were deliberately disassembled by pharmacological treatment, we observed a complete loss of viral infectivity. Our findings show that HIV-1 MLOs shield the final reverse transcription product from host immune detection.
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Affiliation(s)
- Selen Ay
- Institut Pasteur, Advanced Molecular Virology Unit, Department of Virology, Université Paris Cité, 75015, Paris, France
| | - Julien Burlaud-Gaillard
- Inserm U1259 MAVIVHe, Université de Tours and CHRU de Tours, Tours, France
- Plate-Forme IBiSA de Microscopie Electronique, Université de Tours and CHRU de Tours, Tours, France
| | - Anastasia Gazi
- Institut Pasteur, Université Paris Cité, Ultrastructural BioImaging Facility, 75015, Paris, France
| | - Yevgeniy Tatirovsky
- Innate Immunity Unit, Institut Pasteur, Université Paris Cité, Inserm U1223, Paris, France
- Vaccine Research Institute, Université Paris Est, Inserm U955, Créteil, France
| | - Celine Cuche
- Institut Pasteur, Advanced Molecular Virology Unit, Department of Virology, Université Paris Cité, 75015, Paris, France
| | - Jean-Sebastien Diana
- Institut Pasteur, Advanced Molecular Virology Unit, Department of Virology, Université Paris Cité, 75015, Paris, France
| | - Viviana Scoca
- Institut Pasteur, Advanced Molecular Virology Unit, Department of Virology, Université Paris Cité, 75015, Paris, France
| | - James P Di Santo
- Innate Immunity Unit, Institut Pasteur, Université Paris Cité, Inserm U1223, Paris, France
| | - Philippe Roingeard
- Inserm U1259 MAVIVHe, Université de Tours and CHRU de Tours, Tours, France
- Plate-Forme IBiSA de Microscopie Electronique, Université de Tours and CHRU de Tours, Tours, France
| | - Fabrizio Mammano
- Inserm U1259 MAVIVHe, Université de Tours and CHRU de Tours, Tours, France
| | - Francesca Di Nunzio
- Institut Pasteur, Advanced Molecular Virology Unit, Department of Virology, Université Paris Cité, 75015, Paris, France.
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4
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Park K, Lee D, Jeong J, Lee S, Kim S, Ahn K. Human immunodeficiency virus-1 induces host genomic R-loops and preferentially integrates its genome near the R-loop regions. eLife 2024; 13:RP97348. [PMID: 39630854 PMCID: PMC11616997 DOI: 10.7554/elife.97348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2024] Open
Abstract
Although HIV-1 integration sites favor active transcription units in the human genome, high-resolution analysis of individual HIV-1 integration sites has shown that the virus can integrate into a variety of host genomic locations, including non-genic regions. The invisible infection by HIV-1 integrating into non-genic regions, challenging the traditional understanding of HIV-1 integration site selection, is more problematic because they are selected for preservation in the host genome during prolonged antiretroviral therapies. Here, we showed that HIV-1 integrates its viral genome into the vicinity of R-loops, a genomic structure composed of DNA-RNA hybrids. VSV-G-pseudotyped HIV-1 infection initiates the formation of R-loops in both genic and non-genic regions of the host genome and preferentially integrates into R-loop-rich regions. Using a HeLa cell model that can independently control transcriptional activity and R-loop formation, we demonstrated that the exogenous formation of R-loops directs HIV-1 integration-targeting sites. We also found that HIV-1 integrase proteins physically bind to the host genomic R-loops. These findings provide novel insights into the mechanisms underlying retroviral integration and the new strategies for antiretroviral therapy against HIV-1 latent infection.
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Affiliation(s)
- Kiwon Park
- Center for RNA Research, Institute for Basic ScienceSeoulRepublic of Korea
- School of Biological Sciences, Seoul National UniversitySeoulRepublic of Korea
| | - Dohoon Lee
- Bioinformatics Institute, Seoul National UniversitySeoulRepublic of Korea
- BK21 FOUR Intelligence Computing, Seoul National UniversitySeoulRepublic of Korea
| | - Jiseok Jeong
- Center for RNA Research, Institute for Basic ScienceSeoulRepublic of Korea
- School of Biological Sciences, Seoul National UniversitySeoulRepublic of Korea
| | - Sungwon Lee
- Center for RNA Research, Institute for Basic ScienceSeoulRepublic of Korea
- School of Biological Sciences, Seoul National UniversitySeoulRepublic of Korea
| | - Sun Kim
- Department of Computer Science and Engineering, Seoul National UniversitySeoulRepublic of Korea
| | - Kwangseog Ahn
- Center for RNA Research, Institute for Basic ScienceSeoulRepublic of Korea
- School of Biological Sciences, Seoul National UniversitySeoulRepublic of Korea
- SNU Institute for Virus Research, Seoul National UniversitySeoulRepublic of Korea
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5
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Wei X, Lipscomb JT, Tino AS, Cong ME, Ruone S, Bentz ML, Sheth M, Garcia-Lerma G, Johnson JA. HIV Replication Under High-Level Cabotegravir Is Associated with the Appearance of 3'-PPT Mutations, Circular DNA Transcription and Recombination. Viruses 2024; 16:1874. [PMID: 39772184 PMCID: PMC11680205 DOI: 10.3390/v16121874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2024] [Revised: 11/21/2024] [Accepted: 11/27/2024] [Indexed: 01/30/2025] Open
Abstract
The HIV integrase inhibitor, dolutegravir (DTG), in the absence of eliciting integrase (int) resistance, has been reported to select mutations in the virus 3'-polypurine tract (3'-PPT) adjacent to the 3'-LTR U3. An analog of DTG, cabotegravir (CAB), has a high genetic barrier to drug resistance and is used in formulations for treatment and long-acting pre-exposure prophylaxis. We examined whether mutations observed for DTG would emerge in vitro with CAB. HIV-1IIIB was cultured in paired experiments of continuous high (300 nM) CAB initiated 2 h or 24 h after infection. After eight months of CAB treatment, no int resistance was detected. Conversely, HIV RNA 3'-PPT mutants were detected within one month and were the majority virus by day 98. The appearance of 3'-PPT variants coincided with a rapid accumulation of HIV 1-LTR and 2-LTR circles. RNA amplification from the 3'-LTR TAR identified transcripts crossing 2-LTR circle junctions, which incorporated the adjacent U5 sequence identical to the 3'-PPT mutants. 3'-PPT variants were only identified in LTR circles and transcripts. Additionally, we found evidence of linear HIV and LTR circle recombination with human DNA at motifs homologous to 3'-PPT sequences. HIV persistence under CAB was associated with transcription and recombination of LTR circle sequences.
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Affiliation(s)
- Xierong Wei
- Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (X.W.); (J.T.L.); (A.S.T.); (M.-e.C.); (S.R.); (G.G.-L.)
| | - Jonathan T. Lipscomb
- Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (X.W.); (J.T.L.); (A.S.T.); (M.-e.C.); (S.R.); (G.G.-L.)
| | - Ariana Santos Tino
- Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (X.W.); (J.T.L.); (A.S.T.); (M.-e.C.); (S.R.); (G.G.-L.)
- Anyar Inc., 2113 Lewis Turner Blvd, Fort Walton Beach, FL 32547, USA
| | - Mian-er Cong
- Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (X.W.); (J.T.L.); (A.S.T.); (M.-e.C.); (S.R.); (G.G.-L.)
| | - Susan Ruone
- Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (X.W.); (J.T.L.); (A.S.T.); (M.-e.C.); (S.R.); (G.G.-L.)
| | - Meghan L. Bentz
- Advanced Diagnostics and Biotechnologies Branch, Division of Core Laboratory Services and Response, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (M.L.B.); (M.S.)
| | - Mili Sheth
- Advanced Diagnostics and Biotechnologies Branch, Division of Core Laboratory Services and Response, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (M.L.B.); (M.S.)
| | - Gerardo Garcia-Lerma
- Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (X.W.); (J.T.L.); (A.S.T.); (M.-e.C.); (S.R.); (G.G.-L.)
| | - Jeffrey A. Johnson
- Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; (X.W.); (J.T.L.); (A.S.T.); (M.-e.C.); (S.R.); (G.G.-L.)
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6
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Wu H, Fujioka Y, Sakaguchi S, Suzuki Y, Nakano T. Electron Tomography as a Tool to Study SARS-CoV-2 Morphology. Int J Mol Sci 2024; 25:11762. [PMID: 39519314 PMCID: PMC11547116 DOI: 10.3390/ijms252111762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Revised: 10/29/2024] [Accepted: 10/30/2024] [Indexed: 11/16/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel betacoronavirus, is the causative agent of COVID-19, which has caused economic and social disruption worldwide. To date, many drugs and vaccines have been developed for the treatment and prevention of COVID-19 and have effectively controlled the global epidemic of SARS-CoV-2. However, SARS-CoV-2 is highly mutable, leading to the emergence of new variants that may counteract current therapeutic measures. Electron microscopy (EM) is a valuable technique for obtaining ultrastructural information about the intracellular process of virus replication. In particular, EM allows us to visualize the morphological and subcellular changes during virion formation, which would provide a promising avenue for the development of antiviral agents effective against new SARS-CoV-2 variants. In this review, we present our recent findings using transmission electron microscopy (TEM) combined with electron tomography (ET) to reveal the morphologically distinct types of SARS-CoV-2 particles, demonstrating that TEM and ET are valuable tools for visually understanding the maturation status of SARS-CoV-2 in infected cells. This review also discusses the application of EM analysis to the evaluation of genetically engineered RNA viruses.
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Affiliation(s)
- Hong Wu
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka 565-0871, Japan; (Y.F.); (S.S.); (T.N.)
| | | | | | - Youichi Suzuki
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka 565-0871, Japan; (Y.F.); (S.S.); (T.N.)
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7
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Schemelev AN, Davydenko VS, Ostankova YV, Reingardt DE, Serikova EN, Zueva EB, Totolian AA. Involvement of Human Cellular Proteins and Structures in Realization of the HIV Life Cycle: A Comprehensive Review, 2024. Viruses 2024; 16:1682. [PMID: 39599797 PMCID: PMC11599013 DOI: 10.3390/v16111682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 10/25/2024] [Accepted: 10/26/2024] [Indexed: 11/29/2024] Open
Abstract
Human immunodeficiency virus (HIV) continues to be a global health challenge, with over 38 million people infected by the end of 2022. HIV-1, the predominant strain, primarily targets and depletes CD4+ T cells, leading to immunodeficiency and subsequent vulnerability to opportunistic infections. Despite the progress made in antiretroviral therapy (ART), drug resistance and treatment-related toxicity necessitate novel therapeutic strategies. This review delves into the intricate interplay between HIV-1 and host cellular proteins throughout the viral life cycle, highlighting key host factors that facilitate viral entry, replication, integration, and immune evasion. A focus is placed on actual findings regarding the preintegration complex, nuclear import, and the role of cellular cofactors such as FEZ1, BICD2, and NPC components in viral transport and genome integration. Additionally, the mechanisms of immune evasion via HIV-1 proteins Nef and Vpu, and their interaction with host MHC molecules and interferon signaling pathways, are explored. By examining these host-virus interactions, this review underscores the importance of host-targeted therapies in complementing ART, with a particular emphasis on the potential of genetic research and host protein stability in developing innovative treatments for HIV/AIDS.
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Affiliation(s)
- Alexandr N. Schemelev
- St. Petersburg Pasteur Institute, St. Petersburg 197101, Russia; (V.S.D.); (Y.V.O.); (D.E.R.); (E.N.S.); (E.B.Z.); (A.A.T.)
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8
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Patacchini E, Madia VN, Albano A, Ruggieri G, Messore A, Ialongo D, Saccoliti F, Scipione L, Cosconati S, Koneru PC, Haney R, Kvaratskhelia M, Di Santo R, Costi R. Quinolinonyl Derivatives as Dual Inhibitors of the HIV-1 Integrase Catalytic Site and Integrase-RNA interactions. ACS Med Chem Lett 2024; 15:1533-1540. [PMID: 39291012 PMCID: PMC11403752 DOI: 10.1021/acsmedchemlett.4c00268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 08/01/2024] [Accepted: 08/01/2024] [Indexed: 09/19/2024] Open
Abstract
The HIV-1 integrase (IN) plays a critical role in the viral lifecycle by integrating the viral DNA into the host chromosome. The catalytic function of IN has been exploited as a target, with five drugs acting as active site binders (IN strand transfer inhibitors, INSTIs). However, IN mutations conferring low-level resistance to INSTIs have been reported. Therefore, new IN inhibitors with different mechanisms of action are needed. The allosteric inhibition of IN, exerted by allosteric IN inhibitors (ALLINIs), is gaining interest. ALLINIs inhibit IN by inducing aberrant IN multimerization with different mechanisms. Furthermore, recent discoveries unveiled that IN has an under-studied yet equally vital second function. This involves IN binding to the RNA genome in virions, necessary for proper virion maturation. In this work, we describe a series of quinolinonyl derivatives as inhibitors of both the IN catalytic functions and IN-RNA interactions, which impair both early and late steps of viral replication.
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Affiliation(s)
- Elisa Patacchini
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Valentina Noemi Madia
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Aurora Albano
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Giuseppe Ruggieri
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Antonella Messore
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Davide Ialongo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Francesco Saccoliti
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Luigi Scipione
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Pratibha C Koneru
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Reed Haney
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado 80045, United States
| | - Roberto Di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
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9
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Li M, Li Z, Chen X, Cui Y, Engelman AN, Craigie R. HIV-1 Intasomes Assembled with Excess Integrase C-Terminal Domain Protein Facilitate Structural Studies by Cryo-EM and Reveal the Role of the Integrase C-Terminal Tail in HIV-1 Integration. Viruses 2024; 16:1166. [PMID: 39066328 PMCID: PMC11281638 DOI: 10.3390/v16071166] [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: 06/26/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Retroviral integration is mediated by intasome nucleoprotein complexes wherein a pair of viral DNA ends are bridged together by a multimer of integrase (IN). Atomic-resolution structures of HIV-1 intasomes provide detailed insights into the mechanism of integration and inhibition by clinical IN inhibitors. However, previously described HIV-1 intasomes are highly heterogeneous and have the tendency to form stacks, which is a limiting factor in determining high-resolution cryo-EM maps. We have assembled HIV-1 intasomes in the presence of excess IN C-terminal domain protein, which was readily incorporated into the intasomes. The purified intasomes were largely homogeneous and exhibited minimal stacking tendencies. The cryo-EM map resolution was further improved to 2.01 Å, which will greatly facilitate structural studies of IN inhibitor action and drug resistance mechanisms. The C-terminal 18 residues of HIV-1 IN, which are critical for virus replication and integration in vitro, have not been well resolved in previous intasome structures, and its function remains unclear. We show that the C-terminal tail participates in intasome assembly, resides within the intasome core, and forms a small alpha helix (residues 271-276). Mutations that disrupt alpha helix integrity impede IN activity in vitro and disrupt HIV-1 infection at the step of viral DNA integration.
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Affiliation(s)
- Min Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhen Li
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; (Z.L.); (A.N.E.)
| | - Xuemin Chen
- School of Life Sciences, Anhui University, Hefei 230601, China;
| | - Yanxiang Cui
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; (Z.L.); (A.N.E.)
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Robert Craigie
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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10
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Batisse C, Lapaillerie D, Humbert N, Real E, Zhu R, Mély Y, Parissi V, Ruff M, Batisse J. Integrase-LEDGF/p75 complex triggers the formation of biomolecular condensates that modulate HIV-1 integration efficiency in vitro. J Biol Chem 2024; 300:107374. [PMID: 38762180 PMCID: PMC11208922 DOI: 10.1016/j.jbc.2024.107374] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 04/27/2024] [Accepted: 05/04/2024] [Indexed: 05/20/2024] Open
Abstract
The pre-integration steps of the HIV-1 viral cycle are some of the most valuable targets of recent therapeutic innovations. HIV-1 integrase (IN) displays multiple functions, thanks to its considerable conformational flexibility. Recently, such flexible proteins have been characterized by their ability to form biomolecular condensates as a result of Liquid-Liquid-Phase-Separation (LLPS), allowing them to evolve in a restricted microenvironment within cells called membrane-less organelles (MLO). The LLPS context constitutes a more physiological approach to study the integration of molecular mechanisms performed by intasomes (complexes containing viral DNA, IN, and its cellular cofactor LEDGF/p75). We investigated here if such complexes can form LLPS in vitro and if IN enzymatic activities were affected by this LLPS environment. We observed that the LLPS formed by IN-LEDGF/p75 functional complexes modulate the in vitro IN activities. While the 3'-processing of viral DNA ends was drastically reduced inside LLPS, viral DNA strand transfer was strongly enhanced. These two catalytic IN activities appear thus tightly regulated by the environment encountered by intasomes.
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Affiliation(s)
- Claire Batisse
- Department of Integrated Structural Biology, Chromatin Stability and DNA Mobility, IGBMC, U-596 INSERM, UMR-7104 CNRS, University of Strasbourg, Illkirch Cedex, France; GDR CNRS 2194 "DYNAVIR" (Viral DNA Integration and Chromatin Dynamics Network), France
| | - Delphine Lapaillerie
- Fundamental Microbiology and Pathogenicity Laboratory (MFP), UMR-5234 CNRS-University of Bordeaux, Bordeaux, France; GDR CNRS 2194 "DYNAVIR" (Viral DNA Integration and Chromatin Dynamics Network), France
| | - Nicolas Humbert
- Laboratory of Bioimaging and Pathologies, CNRS UMR 7021, Faculty of Pharmacy, University of Strasbourg, Illkirch Cedex, France
| | - Eleonore Real
- Laboratory of Bioimaging and Pathologies, CNRS UMR 7021, Faculty of Pharmacy, University of Strasbourg, Illkirch Cedex, France
| | - Rui Zhu
- Department of Integrated Structural Biology, Chromatin Stability and DNA Mobility, IGBMC, U-596 INSERM, UMR-7104 CNRS, University of Strasbourg, Illkirch Cedex, France; GDR CNRS 2194 "DYNAVIR" (Viral DNA Integration and Chromatin Dynamics Network), France
| | - Yves Mély
- Laboratory of Bioimaging and Pathologies, CNRS UMR 7021, Faculty of Pharmacy, University of Strasbourg, Illkirch Cedex, France
| | - Vincent Parissi
- Fundamental Microbiology and Pathogenicity Laboratory (MFP), UMR-5234 CNRS-University of Bordeaux, Bordeaux, France; GDR CNRS 2194 "DYNAVIR" (Viral DNA Integration and Chromatin Dynamics Network), France.
| | - Marc Ruff
- Department of Integrated Structural Biology, Chromatin Stability and DNA Mobility, IGBMC, U-596 INSERM, UMR-7104 CNRS, University of Strasbourg, Illkirch Cedex, France; GDR CNRS 2194 "DYNAVIR" (Viral DNA Integration and Chromatin Dynamics Network), France.
| | - Julien Batisse
- Department of Integrated Structural Biology, Chromatin Stability and DNA Mobility, IGBMC, U-596 INSERM, UMR-7104 CNRS, University of Strasbourg, Illkirch Cedex, France; GDR CNRS 2194 "DYNAVIR" (Viral DNA Integration and Chromatin Dynamics Network), France.
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11
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Li M, Yang R, Chen X, Wang H, Ghirlando R, Dimitriadis EK, Craigie R. HIV-1 Integrase Assembles Multiple Species of Stable Synaptic Complex Intasomes That Are Active for Concerted DNA Integration In vitro. J Mol Biol 2024; 436:168557. [PMID: 38582148 PMCID: PMC11134455 DOI: 10.1016/j.jmb.2024.168557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/08/2024]
Abstract
Retroviral DNA integration is mediated by nucleoprotein complexes (intasomes) in which a pair of viral DNA ends are bridged by a multimer of integrase (IN). Most of the high-resolution structures of HIV-1 intasomes are based on an HIV-1 IN with an Sso7d protein domain fused to the N-terminus. Sso7d-IN aggregates much less than wild-type IN and has been critical for structural studies of HIV-1 intasomes. Unexpectedly, these structures revealed that the common core architecture that mediates catalysis could be assembled in various ways, giving rise to both tetrameric and dodecameric intasomes, together with other less well-characterized species. This differs from related retroviruses that assemble unique multimeric intasomes, although the number of protomers in the intasome varies between viruses. The question of whether the additional Sso7d domain contributes to the heterogeneity of HIV-1 intasomes is therefore raised. We have addressed this by biochemical and structural studies of intasomes assembled with wild-type HIV-1 IN. Negative stain and cryo-EM reveal a similar range of multimeric intasome species as with Sso7d-IN with the same common core architecture. Stacks of intasomes resulting from domain swapping are also seen with both wild-type and Sso7d-IN intasomes. The propensity to assemble multimeric intasome species is, therefore, an intrinsic property of HIV-1 IN and is not conferred by the presence of the Sso7d domain. The recently solved intasome structures of different retroviral species, which have been reported to be tetrameric, octameric, dodecameric, and hexadecameric, highlight how a common intasome core architecture can be assembled in different ways for catalysis.
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Affiliation(s)
- Min Li
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Renbin Yang
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xuemin Chen
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaibin Wang
- Laboratory of Cell and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emilios K Dimitriadis
- Laboratory of Bioengineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert Craigie
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
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12
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Grandgenett DP, Engelman AN. Brief Histories of Retroviral Integration Research and Associated International Conferences. Viruses 2024; 16:604. [PMID: 38675945 PMCID: PMC11054761 DOI: 10.3390/v16040604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
The field of retroviral integration research has a long history that started with the provirus hypothesis and subsequent discoveries of the retroviral reverse transcriptase and integrase enzymes. Because both enzymes are essential for retroviral replication, they became valued targets in the effort to discover effective compounds to inhibit HIV-1 replication. In 2007, the first integrase strand transfer inhibitor was licensed for clinical use, and subsequently approved second-generation integrase inhibitors are now commonly co-formulated with reverse transcriptase inhibitors to treat people living with HIV. International meetings specifically focused on integrase and retroviral integration research first convened in 1995, and this paper is part of the Viruses Special Issue on the 7th International Conference on Retroviral Integration, which was held in Boulder Colorado in the summer of 2023. Herein, we overview key historical developments in the field, especially as they pertain to the development of the strand transfer inhibitor drug class. Starting from the mid-1990s, research advancements are presented through the lens of the international conferences. Our overview highlights the impact that regularly scheduled, subject-specific international meetings can have on community-building and, as a result, on field-specific collaborations and scientific advancements.
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Affiliation(s)
- Duane P. Grandgenett
- Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St. Louis, MO 63104, USA
| | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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13
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Kikhai TF, Agapkina YY, Prikazchikova TA, Vdovina MV, Shekhtman SP, Fomicheva SV, Korolev SP, Gottikh MB. Role of I182, R187, and K188 Amino Acid Residues in the Catalytic Domain of HIV-1 Integrase in the Processes of Reverse Transcription and Integration. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:462-473. [PMID: 38648766 DOI: 10.1134/s0006297924030076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 04/25/2024]
Abstract
Structural organization of HIV-1 integrase is based on a tetramer formed by two protein dimers. Within this tetramer, the catalytic domain of one subunit of the first dimer interacts with the N-terminal domain of the second dimer subunit. It is the tetrameric structure that allows both ends of the viral DNA to be correctly positioned relative to the cellular DNA and to realize catalytic functions of integrase, namely 3'-processing and strand transfer. However, during the HIV-1 replicative cycle, integrase is responsible not only for the integration stage, it is also involved in reverse transcription and is necessary at the stage of capsid formation of the newly formed virions. It has been suggested that HIV-1 integrase is a structurally dynamic protein and its biological functions depend on its structure. Accordingly, studying interactions between the domains of integrase that provide its tetrameric structure is important for understanding its multiple functions. In this work, we investigated the role of three amino acids of the catalytic domain, I182, R187, and K188, located in the contact region of two integrase dimers in the tetramer structure, in reverse transcription and integration. It has been shown that the R187 residue is extremely important for formation of the correct integrase structure, which is necessary at all stages of its functional activity. The I182 residue is necessary for successful integration and is not important for reverse transcription, while the K188 residue, on the contrary, is involved in formation of the integrase structure, which is important for the effective reverse transcription.
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Affiliation(s)
- Tatiana F Kikhai
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Yulia Yu Agapkina
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | | | - Maria V Vdovina
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Sofia P Shekhtman
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Sofia V Fomicheva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Sergey P Korolev
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Marina B Gottikh
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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14
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Sun J, Kessl JJ. Optimizing the Multimerization Properties of Quinoline-Based Allosteric HIV-1 Integrase Inhibitors. Viruses 2024; 16:200. [PMID: 38399977 PMCID: PMC10892445 DOI: 10.3390/v16020200] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Allosteric HIV-1 Integrase (IN) Inhibitors or ALLINIs bind at the dimer interface of the IN, away from the enzymatic catalytic site, and disable viral replication by inducing over-multimerization of IN. Interestingly, these inhibitors are capable of impacting both the early and late stages of viral replication. To better understand the important binding features of multi-substituted quinoline-based ALLINIs, we have surveyed published studies on IN multimerization and antiviral properties of various substituted quinolines at the 4, 6, 7, and 8 positions. Here we show how the efficacy of these inhibitors can be modulated by the nature of the substitutions at those positions. These features not only improve the overall antiviral potencies of these compounds but also significantly shift the selectivity toward the viral maturation stage. Thus, to fully maximize the potency of ALLINIs, the interactions between the inhibitor and multiple IN subunits need to be simultaneously optimized.
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Affiliation(s)
- Jian Sun
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Jacques J. Kessl
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, USA
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15
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Jing T, Shan Z, Dinh T, Biswas A, Jang S, Greenwood J, Li M, Zhang Z, Gray G, Shin HJ, Zhou B, Passos D, Aiyer S, Li Z, Craigie R, Engelman AN, Kvaratskhelia M, Lyumkis D. Oligomeric HIV-1 Integrase Structures Reveal Functional Plasticity for Intasome Assembly and RNA Binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577436. [PMID: 38328132 PMCID: PMC10849644 DOI: 10.1101/2024.01.26.577436] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Integrase (IN) performs dual essential roles during HIV-1 replication. During ingress, IN functions within an oligomeric "intasome" assembly to catalyze viral DNA integration into host chromatin. During late stages of infection, tetrameric IN binds viral RNA and orchestrates the condensation of ribonucleoprotein complexes into the capsid core. The molecular architectures of HIV-1 IN assemblies that mediate these distinct events remain unknown. Furthermore, the tetramer is an important antiviral target for allosteric IN inhibitors. Here, we determined cryo-EM structures of wildtype HIV-1 IN tetramers and intasome hexadecamers. Our structures unveil a remarkable plasticity that leverages IN C-terminal domains and abutting linkers to assemble functionally distinct oligomeric forms. Alteration of a newly recognized conserved interface revealed that both IN functions track with tetramerization in vitro and during HIV-1 infection. Collectively, our findings reveal how IN plasticity orchestrates its diverse molecular functions, suggest a working model for IN-viral RNA binding, and provide atomic blueprints for allosteric IN inhibitor development.
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Affiliation(s)
- Tao Jing
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Zelin Shan
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Tung Dinh
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Avik Biswas
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Sooin Jang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Juliet Greenwood
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Min Li
- National Institutes of Health, National Institute of Diabetes and Digestive Diseases, Bethesda, MD, 20892, USA
| | - Zeyuan Zhang
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Gennavieve Gray
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Hye Jeong Shin
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Bo Zhou
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Dario Passos
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Sriram Aiyer
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Zhen Li
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Robert Craigie
- National Institutes of Health, National Institute of Diabetes and Digestive Diseases, Bethesda, MD, 20892, USA
| | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
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16
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Miklík D, Grim J, Elleder D, Hejnar J. Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models. Genome Res 2023; 33:1395-1408. [PMID: 37463751 PMCID: PMC10547254 DOI: 10.1101/gr.277694.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/12/2023] [Indexed: 07/20/2023]
Abstract
A weak palindromic nucleotide motif is the hallmark of retroviral integration site alignments. Given that the majority of target sequences are not palindromic, the current model explains the symmetry by an overlap of the nonpalindromic motif present on one of the half-sites of the sequences. Here, we show that the implementation of multicomponent mixture models allows for different interpretations consistent with the existence of both palindromic and nonpalindromic submotifs in the sets of integration site sequences. We further show that the weak palindromic motifs result from freely combined site-specific submotifs restricted to only a few positions proximal to the site of integration. The submotifs are formed by either palindrome-forming nucleotide preference or nucleotide exclusion. Using the mixture models, we also identify HIV-1-favored palindromic sequences in Alu repeats serving as local hotspots for integration. The application of the novel statistical approach provides deeper insight into the selection of retroviral integration sites and may prove to be a valuable tool in the analysis of any type of DNA motifs.
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Affiliation(s)
- Dalibor Miklík
- Laboratory of Viral and Cellular Genetics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic
| | - Jiří Grim
- Pattern Recognition Department, Institute of Information Theory and Automation of the Czech Academy of Sciences, Prague 8, 182 08, Czech Republic
| | - Daniel Elleder
- Laboratory of Viral and Cellular Genetics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic
| | - Jiří Hejnar
- Laboratory of Viral and Cellular Genetics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic;
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17
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Lannes L, Furman CM, Hickman AB, Dyda F. Zinc-finger BED domains drive the formation of the active Hermes transpososome by asymmetric DNA binding. Nat Commun 2023; 14:4470. [PMID: 37491363 PMCID: PMC10368747 DOI: 10.1038/s41467-023-40210-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 07/18/2023] [Indexed: 07/27/2023] Open
Abstract
The Hermes DNA transposon is a member of the eukaryotic hAT superfamily, and its transposase forms a ring-shaped tetramer of dimers. Our investigation, combining biochemical, crystallography and cryo-electron microscopy, and in-cell assays, shows that the full-length Hermes octamer extensively interacts with its transposon left-end through multiple BED domains of three Hermes protomers contributed by three dimers explaining the role of the unusual higher-order assembly. By contrast, the right-end is bound to no BED domains at all. Thus, this work supports a model in which Hermes multimerizes to gather enough BED domains to find its left-end among the abundant genomic DNA, facilitating the subsequent interaction with the right-end.
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Affiliation(s)
- Laurie Lannes
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Christopher M Furman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alison B Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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18
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Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke TR, Levy RM, Hughes SH, Craigie R, Lyumkis D. Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants. SCIENCE ADVANCES 2023; 9:eadg5953. [PMID: 37478179 PMCID: PMC11803526 DOI: 10.1126/sciadv.adg5953] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/16/2023] [Indexed: 07/23/2023]
Abstract
HIV-1 infection depends on the integration of viral DNA into host chromatin. Integration is mediated by the viral enzyme integrase and is blocked by integrase strand transfer inhibitors (INSTIs), first-line antiretroviral therapeutics widely used in the clinic. Resistance to even the best INSTIs is a problem, and the mechanisms of resistance are poorly understood. Here, we analyze combinations of the mutations E138K, G140A/S, and Q148H/K/R, which confer resistance to INSTIs. The investigational drug 4d more effectively inhibited the mutants compared with the approved drug Dolutegravir (DTG). We present 11 new cryo-EM structures of drug-resistant HIV-1 intasomes bound to DTG or 4d, with better than 3-Å resolution. These structures, complemented with free energy simulations, virology, and enzymology, explain the mechanisms of DTG resistance involving E138K + G140A/S + Q148H/K/R and show why 4d maintains potency better than DTG. These data establish a foundation for further development of INSTIs that potently inhibit resistant forms in integrase.
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Affiliation(s)
- Min Li
- National Institute of Diabetes and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Zelin Shan
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Steven J. Smith
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Qinfang Sun
- Center for Biophysics and Computational Biology, and Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Avik Biswas
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Center for Biophysics and Computational Biology and Department of Physics, Temple University, Philadelphia, PA 19122, USA
| | - Indrani Choudhuri
- Center for Biophysics and Computational Biology, and Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | | | - Allan Haldane
- Center for Biophysics and Computational Biology and Department of Physics, Temple University, Philadelphia, PA 19122, USA
| | - Nanjie Deng
- Department of Chemistry and Physical Sciences, Pace University, New York, NY, 10038, USA
| | - Zhaoyang Li
- National Institute of Diabetes and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xue Zhi Zhao
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Lorenzo Briganti
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Terrence R. Burke
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Ronald M. Levy
- Center for Biophysics and Computational Biology and Department of Physics, Temple University, Philadelphia, PA 19122, USA
| | - Stephen H. Hughes
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Robert Craigie
- National Institute of Diabetes and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
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19
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Corona A, Meleddu R, Delelis O, Subra F, Cottiglia F, Esposito F, Distinto S, Maccioni E, Tramontano E. 5-Nitro-3-(2-(4-phenylthiazol-2-yl)hydrazineylidene)indolin-2-one derivatives inhibit HIV-1 replication by a multitarget mechanism of action. Front Cell Infect Microbiol 2023; 13:1193280. [PMID: 37424782 PMCID: PMC10328743 DOI: 10.3389/fcimb.2023.1193280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/25/2023] [Indexed: 07/11/2023] Open
Abstract
In the effort to identify and develop new HIV-1 inhibitors endowed with innovative mechanisms, we focused our attention on the possibility to target more than one viral encoded enzymatic function with a single molecule. In this respect, we have previously identified by virtual screening a new indolinone-based scaffold for dual allosteric inhibitors targeting both reverse transcriptase-associated functions: polymerase and RNase H. Pursuing with the structural optimization of these dual inhibitors, we synthesized a series of 35 new 3-[2-(4-aryl-1,3-thiazol-2-ylidene)hydrazin-1-ylidene]1-indol-2-one and 3-[3-methyl-4-arylthiazol-2-ylidene)hydrazine-1-ylidene)indolin-2-one derivatives, which maintain their dual inhibitory activity in the low micromolar range. Interestingly, compounds 1a, 3a, 10a, and 9b are able to block HIV-1 replication with EC50 < 20 µM. Mechanism of action studies showed that such compounds could block HIV-1 integrase. In particular, compound 10a is the most promising for further multitarget compound development.
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Affiliation(s)
- Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Rita Meleddu
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Olivier Delelis
- Laboratory of Biology and Applied Pharmacology (LBPA), Ecole Normale Supérieure (ENS) Cachan, Centre National de la Recherche Scientifique (CNRS), Cachan, France
| | - Frederic Subra
- Laboratory of Biology and Applied Pharmacology (LBPA), Ecole Normale Supérieure (ENS) Cachan, Centre National de la Recherche Scientifique (CNRS), Cachan, France
| | - Filippo Cottiglia
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Simona Distinto
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Elias Maccioni
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
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20
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Bera S, Shi K, Aihara H, Grandgenett DP, Pandey KK. Molecular determinants for Rous sarcoma virus intasome assemblies involved in retroviral integration. J Biol Chem 2023; 299:104730. [PMID: 37084813 PMCID: PMC10209032 DOI: 10.1016/j.jbc.2023.104730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/13/2023] [Accepted: 04/16/2023] [Indexed: 04/23/2023] Open
Abstract
Integration of retroviral DNA into the host genome involves the formation of integrase (IN)-DNA complexes termed intasomes. Further characterization of these complexes is needed to understand their assembly process. Here, we report the single-particle cryo-EM structure of the Rous sarcoma virus (RSV) strand transfer complex (STC) intasome produced with IN and a preassembled viral/target DNA substrate at 3.36 Å resolution. The conserved intasome core region consisting of IN subunits contributing active sites interacting with viral/target DNA has a resolution of 3 Å. Our structure demonstrated the flexibility of the distal IN subunits relative to the IN subunits in the conserved intasome core, similar to results previously shown with the RSV octameric cleaved synaptic complex intasome produced with IN and viral DNA only. An extensive analysis of higher resolution STC structure helped in the identification of nucleoprotein interactions important for intasome assembly. Using structure-function studies, we determined the mechanisms of several IN-DNA interactions critical for assembly of both RSV intasomes. We determined the role of IN residues R244, Y246, and S124 in cleaved synaptic complex and STC intasome assemblies and their catalytic activities, demonstrating differential effects. Taken together, these studies advance our understanding of different RSV intasome structures and molecular determinants involved in their assembly.
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Affiliation(s)
- Sibes Bera
- Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St Louis, Missouri, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Duane P Grandgenett
- Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St Louis, Missouri, USA
| | - Krishan K Pandey
- Department of Molecular Microbiology and Immunology, School of Medicine, Saint Louis University, St Louis, Missouri, USA.
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21
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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: 1.0] [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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22
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Overmars RJ, Krullaars Z, Mesplède T. Investigational drugs for HIV: trends, opportunities and key players. Expert Opin Investig Drugs 2023; 32:127-139. [PMID: 36751107 DOI: 10.1080/13543784.2023.2178415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
INTRODUCTION Since the first antiretroviral drug was described, the field of HIV treatment and prevention has undergone two drug-based revolutions: the first one, enabled by the virtually concomitant discovery of non-nucleoside reverse transcriptase and protease inhibitors, was the inception of combined antiretroviral therapy. The second followed the creation of integrase strand-transfer inhibitors with improved safety, potency, and resistance profiles. Long-acting antiretroviral drugs, including broadly neutralizing antibodies, now offer the opportunity for a third transformational change in HIV management. AREAS COVERED Our review focused on HIV treatment and prevention with investigational drugs that offer the potential for infrequent dosing, including drugs not yet approved for clinical use. We also discussed approved drugs for which administration modalities or formulations are being optimized. We performed a literature search in published manuscripts, conference communications, and registered clinical trials. EXPERT OPINION While the field focuses on extending dosing intervals, we identify drug tissue penetration as an understudied opportunity to improve HIV care. We repeat that self-administration remains an essential milestone to reach the full potential of long-acting drugs. Treatments and prevention strategies based on broadly neutralizing antibodies require a deeper understanding of their antiretroviral properties.
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Affiliation(s)
- Ronald J Overmars
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Zoë Krullaars
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Thibault Mesplède
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
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23
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Mbhele N, Gordon M. Structural effects of HIV-1 subtype C integrase mutations on the activity of integrase strand transfer inhibitors in South African patients. J Biomol Struct Dyn 2022; 40:12546-12556. [PMID: 34488561 DOI: 10.1080/07391102.2021.1972840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
HIV-1 integrase enzyme is responsible for the integration of viral DNA into the host genomic DNA. Integrase strand transfer inhibitors (INSTIs) are highly potent antiretroviral agents that inhibit this process, and are internationally approved for the treatment of both naïve and treated HIV-1 patients. However, their long-term efficacy is threatened by development of drug resistance strains resulting in resistance mutations. This work aimed to examine the effect of INSTI resistance-associated mutations (RAMs) and polymorphisms on the structure of HIV-1 subtype C (HIV-1C) integrase. Genetic analysis was performed on seven HIV-1C infected individuals with virologic failure after at least 6 months of INSTI-based antiretroviral therapy, presenting at the King Edward VIII hospital in Durban, South Africa. These were compared with sequences from 41 INSTI-naïve isolates. Integrase structures of selected isolates were modeled on the SWISS model online server. Molecular docking and dynamics simulations were also conducted using AutoDock-Vina and AMBER 18 force fields, respectively. Only one INSTI-treated isolate (14.28%) harboured major mutations (G140A + Q148R) as well as the E157Q minor mutation. Interestingly, S119T and V151I were only found in patients failing raltegravir (an INSTI drug). Molecular modeling and docking showed that RAMs and polymorphisms associated with INSTI-based therapy affect protein stability and this is supported by their weakened hydrogen-bond interactions compared to the wild-type. To the best of our knowledge, this is the first study to identify a double mutant in the 140's loop region from South African HIV-1C isolates and study its effects on Raltegravir, Elvitegravir, and Dolutegravir binding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nokuzola Mbhele
- Department of Virology, College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa
| | - Michelle Gordon
- Department of Virology, College of Health Sciences, University of KwaZulu-Natal, Doris Duke Medical Research Institute, Durban, South Africa
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24
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Barkova A, Adhya I, Conesa C, Asif-Laidin A, Bonnet A, Rabut E, Chagneau C, Lesage P, Acker J. A proteomic screen of Ty1 integrase partners identifies the protein kinase CK2 as a regulator of Ty1 retrotransposition. Mob DNA 2022; 13:26. [PMCID: PMC9673352 DOI: 10.1186/s13100-022-00284-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/13/2022] [Indexed: 11/19/2022] Open
Abstract
Abstract
Background
Transposable elements are ubiquitous and play a fundamental role in shaping genomes during evolution. Since excessive transposition can be mutagenic, mechanisms exist in the cells to keep these mobile elements under control. Although many cellular factors regulating the mobility of the retrovirus-like transposon Ty1 in Saccharomyces cerevisiae have been identified in genetic screens, only very few of them interact physically with Ty1 integrase (IN).
Results
Here, we perform a proteomic screen to establish Ty1 IN interactome. Among the 265 potential interacting partners, we focus our study on the conserved CK2 kinase. We confirm the interaction between IN and CK2, demonstrate that IN is a substrate of CK2 in vitro and identify the modified residues. We find that Ty1 IN is phosphorylated in vivo and that these modifications are dependent in part on CK2. No significant change in Ty1 retromobility could be observed when we introduce phospho-ablative mutations that prevent IN phosphorylation by CK2 in vitro. However, the absence of CK2 holoenzyme results in a strong stimulation of Ty1 retrotransposition, characterized by an increase in Ty1 mRNA and protein levels and a high accumulation of cDNA.
Conclusion
Our study shows that Ty1 IN is phosphorylated, as observed for retroviral INs and highlights an important role of CK2 in the regulation of Ty1 retrotransposition. In addition, the proteomic approach enabled the identification of many new Ty1 IN interacting partners, whose potential role in the control of Ty1 mobility will be interesting to study.
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25
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Shema Mugisha C, Dinh T, Kumar A, Tenneti K, Eschbach JE, Davis K, Gifford R, Kvaratskhelia M, Kutluay SB. Emergence of Compensatory Mutations Reveals the Importance of Electrostatic Interactions between HIV-1 Integrase and Genomic RNA. mBio 2022; 13:e0043122. [PMID: 35975921 PMCID: PMC9601147 DOI: 10.1128/mbio.00431-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/27/2022] [Indexed: 01/11/2023] Open
Abstract
HIV-1 integrase (IN) has a noncatalytic function in virion maturation through its binding to the viral RNA genome (gRNA). Class II IN substitutions inhibit IN-gRNA binding and result in the formation of virions with aberrant morphologies marked by mislocalization of the gRNA between the capsid lattice and the lipid envelope. These viruses are noninfectious due to a block at an early reverse transcription stage in target cells. HIV-1 IN utilizes basic residues within its C-terminal domain (CTD) to bind to the gRNA; however, the molecular nature of how these residues mediate gRNA binding and whether other regions of IN are involved remain unknown. To address this, we have isolated compensatory substitutions in the background of a class II IN mutant virus bearing R269A/K273A substitutions within the IN-CTD. We found that the nearby D256N and D270N compensatory substitutions restored the ability of IN to bind gRNA and led to the formation of mature infectious virions. Reinstating the local positive charge of the IN-CTD through individual D256R, D256K, D278R, and D279R substitutions was sufficient to specifically restore IN-gRNA binding and reverse transcription for the IN R269A/K273A as well as the IN R262A/R263A class II mutants. Structural modeling suggested that compensatory substitutions in the D256 residue created an additional interaction interface for gRNA binding, whereas other substitutions acted locally within the unstructured C-terminal tail of IN. Taken together, our findings highlight the essential role of CTD in gRNA binding and reveal the importance of pliable electrostatic interactions between the IN-CTD and the gRNA. IMPORTANCE In addition to its catalytic function, HIV-1 integrase (IN) binds to the viral RNA genome (gRNA) through positively charged residues (i.e., R262, R263, R269, K273) within its C-terminal domain (CTD) and regulates proper virion maturation. Mutation of these residues results in the formation of morphologically aberrant viruses blocked at an early reverse transcription stage in cells. Here we show that compensatory substitutions in nearby negatively charged aspartic acid residues (i.e., D256N, D270N) restore the ability of IN to bind gRNA for these mutant viruses and result in the formation of accurately matured infectious virions. Similarly, individual charge reversal substitutions at D256 as well as other nearby positions (i.e., D278, D279) are all sufficient to enable the respective IN mutants to bind gRNA, and subsequently restore reverse transcription and virion infectivity. Taken together, our findings reveal the importance of highly pliable electrostatic interactions in IN-gRNA binding.
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Affiliation(s)
- Christian Shema Mugisha
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Tung Dinh
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Abhishek Kumar
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Kasyap Tenneti
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Jenna E. Eschbach
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Keanu Davis
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Robert Gifford
- MRC-University of Glasgow Centre for Virus Research, Bearsden, Glasgow, United Kingdom
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Sebla B. Kutluay
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
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26
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Complex Relationships between HIV-1 Integrase and Its Cellular Partners. Int J Mol Sci 2022; 23:ijms232012341. [PMID: 36293197 PMCID: PMC9603942 DOI: 10.3390/ijms232012341] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
RNA viruses, in pursuit of genome miniaturization, tend to employ cellular proteins to facilitate their replication. HIV-1, one of the most well-studied retroviruses, is not an exception. There is numerous evidence that the exploitation of cellular machinery relies on nucleic acid-protein and protein-protein interactions. Apart from Vpr, Vif, and Nef proteins that are known to regulate cellular functioning via interaction with cell components, another viral protein, integrase, appears to be crucial for proper virus-cell dialog at different stages of the viral life cycle. The goal of this review is to summarize and systematize existing data on known cellular partners of HIV-1 integrase and their role in the HIV-1 life cycle.
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Jóźwik IK, Li W, Zhang DW, Wong D, Grawenhoff J, Ballandras-Colas A, Aiyer S, Cherepanov P, Engelman A, Lyumkis D. B-to-A transition in target DNA during retroviral integration. Nucleic Acids Res 2022; 50:8898-8918. [PMID: 35947647 PMCID: PMC9410886 DOI: 10.1093/nar/gkac644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 01/21/2023] Open
Abstract
Integration into host target DNA (tDNA), a hallmark of retroviral replication, is mediated by the intasome, a multimer of integrase (IN) assembled on viral DNA (vDNA) ends. To ascertain aspects of tDNA recognition during integration, we have solved the 3.5 Å resolution cryo-EM structure of the mouse mammary tumor virus (MMTV) strand transfer complex (STC) intasome. The tDNA adopts an A-like conformation in the region encompassing the sites of vDNA joining, which exposes the sugar-phosphate backbone for IN-mediated strand transfer. Examination of existing retroviral STC structures revealed conservation of A-form tDNA in the analogous regions of these complexes. Furthermore, analyses of sequence preferences in genomic integration sites selectively targeted by six different retroviruses highlighted consistent propensity for A-philic sequences at the sites of vDNA joining. Our structure additionally revealed several novel MMTV IN-DNA interactions, as well as contacts seen in prior STC structures, including conserved Pro125 and Tyr149 residues interacting with tDNA. In infected cells, Pro125 substitutions impacted the global pattern of MMTV integration without significantly altering local base sequence preferences at vDNA insertion sites. Collectively, these data advance our understanding of retroviral intasome structure and function, as well as factors that influence patterns of vDNA integration in genomic DNA.
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Affiliation(s)
- Ilona K Jóźwik
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Wen Li
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA 02215, USA,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Da-Wei Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA 02215, USA,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA,Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Doris Wong
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA 02215, USA
| | - Julia Grawenhoff
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA 02215, USA
| | | | - Sriram Aiyer
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK,Department of Infectious Disease, St-Mary's Campus, Imperial College London, London W2 1PG, UK
| | - Alan N Engelman
- Correspondence may also be addressed to Alan N. Engelman. Tel: +1 617 632 4361; Fax: +1 617 632 4338;
| | - Dmitry Lyumkis
- To whom correspondence should be addressed. Tel: +1 858 453 4100 (Ext 1155);
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28
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Sawant AA, Jadav SS, Nayani K, Mainkar PS. Development of Synthetic Approaches Towards HIV Integrase Strand Transfer Inhibitors (INSTIs). ChemistrySelect 2022. [DOI: 10.1002/slct.202201915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ashwini Amol Sawant
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Surender Singh Jadav
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
- Department of Applied Biology CSIR-Indian Institute of Chemical Technology Tarnaka Uppal Road Hyderabad 500037 India
| | - Kiranmai Nayani
- Department of Organic Synthesis and Process Chemistry CSIR-Indian Institute of Chemical Technology Tarnaka Uppal Road Hyderabad 500037 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Prathama S. Mainkar
- Department of Organic Synthesis and Process Chemistry CSIR-Indian Institute of Chemical Technology Tarnaka Uppal Road Hyderabad 500037 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
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29
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Localization and functions of native and eGFP-tagged capsid proteins in HIV-1 particles. PLoS Pathog 2022; 18:e1010754. [PMID: 35951676 PMCID: PMC9426931 DOI: 10.1371/journal.ppat.1010754] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/30/2022] [Accepted: 07/21/2022] [Indexed: 12/24/2022] Open
Abstract
In infectious HIV-1 particles, the capsid protein (CA) forms a cone-shaped shell called the capsid, which encases the viral ribonucleoprotein complex (vRNP). Following cellular entry, the capsid is disassembled through a poorly understood process referred to as uncoating, which is required to release the reverse transcribed HIV-1 genome for integration into host chromatin. Whereas single virus imaging using indirect CA labeling techniques suggested uncoating to occur in the cytoplasm or at the nuclear pore, a recent study using eGFP-tagged CA reported uncoating in the nucleus. To delineate the HIV-1 uncoating site, we investigated the mechanism of eGFP-tagged CA incorporation into capsids and the utility of this fluorescent marker for visualizing HIV-1 uncoating. We find that virion incorporated eGFP-tagged CA is effectively excluded from the capsid shell, and that a subset of the tagged CA is vRNP associated. These results thus imply that eGFP-tagged CA is not a direct marker for capsid uncoating. We further show that native CA co-immunoprecipitates with vRNP components, providing a basis for retention of eGFP-tagged and untagged CA by sub-viral complexes in the nucleus. Moreover, we find that functional viral replication complexes become accessible to integrase-interacting host factors at the nuclear pore, leading to inhibition of infection and demonstrating capsid permeabilization prior to nuclear import. Finally, we find that HIV-1 cores containing a mixture of wild-type and mutant CA interact differently with cytoplasmic versus nuclear pools of the CA-binding host cofactor CPSF6. Our results suggest that capsid remodeling (including a loss of capsid integrity) is the predominant pathway for HIV-1 nuclear entry and provide new insights into the mechanism of CA retention in the nucleus via interaction with vRNP components. The timing, location and mechanisms of HIV-1 capsid disassembly which is referred to as uncoating remains unclear. Direct labeling of HIV-1 capsids, by incorporating a few green fluorescent proteins (GFP) tagged capsid protein (CA) into virions allows to image the spatio-temporal loss of HIV-1 CA during virus infection. However, the localization and functions of a few virion incorporated eGFP-tagged CA proteins remain unclear, since <50% of virus packaged CA proteins participate to form the conical capsid shell that protects the HIV-1 genome. Here we developed several approaches to test the localization and function of eGFP-tagged CA proteins in virions. We found that eGFP-tagged CA proteins are excluded from the conical capsid shell and that a subset of these proteins is associated with the viral ribonucleoprotein complex (vRNPs), through direct interactions between CA and vRNP components. eGFP-tagged CA is retained in the nucleus by virtue of vRNP association and is unlikely to report on HIV-1 capsid disassembly. We also found that HIV-1 capsids become permeabilized and are remodeled during their transport into the nucleus. Our study provides new insights into the ability of CA to interact with vRNPs for its retention in the nucleus and highlights capsid remodeling as a preferred pathway for HIV-1 entry into the nucleus.
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30
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Rocchi C, Gouet P, Parissi V, Fiorini F. The C-Terminal Domain of HIV-1 Integrase: A Swiss Army Knife for the Virus? Viruses 2022; 14:v14071397. [PMID: 35891378 PMCID: PMC9316232 DOI: 10.3390/v14071397] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 12/31/2022] Open
Abstract
Retroviral integrase is a multimeric enzyme that catalyzes the integration of reverse-transcribed viral DNA into the cellular genome. Beyond integration, the Human immunodeficiency virus type 1 (HIV-1) integrase is also involved in many other steps of the viral life cycle, such as reverse transcription, nuclear import, virion morphogenesis and proviral transcription. All these additional functions seem to depend on the action of the integrase C-terminal domain (CTD) that works as a molecular hub, interacting with many different viral and cellular partners. In this review, we discuss structural issues concerning the CTD, with particular attention paid to its interaction with nucleic acids. We also provide a detailed map of post-translational modifications and interaction with molecular partners.
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Affiliation(s)
- Cecilia Rocchi
- Molecular Microbiology and Structural Biochemistry (MMSB), CNRS, University of Lyon 1, UMR 5086, 69367 Lyon, France; (C.R.); (P.G.)
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), 33076 Bordeaux, France;
| | - Patrice Gouet
- Molecular Microbiology and Structural Biochemistry (MMSB), CNRS, University of Lyon 1, UMR 5086, 69367 Lyon, France; (C.R.); (P.G.)
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), 33076 Bordeaux, France;
| | - Vincent Parissi
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), 33076 Bordeaux, France;
- Fundamental Microbiology and Pathogenicity (MFP), CNRS, University of Bordeaux, UMR5234, 33405 Bordeaux, France
| | - Francesca Fiorini
- Molecular Microbiology and Structural Biochemistry (MMSB), CNRS, University of Lyon 1, UMR 5086, 69367 Lyon, France; (C.R.); (P.G.)
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), 33076 Bordeaux, France;
- Correspondence: ; Tel.: +33-4-72722624; Fax: +33-4-72722616
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Ballandras-Colas A, Chivukula V, Gruszka DT, Shan Z, Singh PK, Pye VE, McLean RK, Bedwell GJ, Li W, Nans A, Cook NJ, Fadel HJ, Poeschla EM, Griffiths DJ, Vargas J, Taylor IA, Lyumkis D, Yardimci H, Engelman AN, Cherepanov P. Multivalent interactions essential for lentiviral integrase function. Nat Commun 2022; 13:2416. [PMID: 35504909 PMCID: PMC9065133 DOI: 10.1038/s41467-022-29928-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/07/2022] [Indexed: 12/24/2022] Open
Abstract
A multimer of retroviral integrase (IN) synapses viral DNA ends within a stable intasome nucleoprotein complex for integration into a host cell genome. Reconstitution of the intasome from the maedi-visna virus (MVV), an ovine lentivirus, revealed a large assembly containing sixteen IN subunits1. Herein, we report cryo-EM structures of the lentiviral intasome prior to engagement of target DNA and following strand transfer, refined at 3.4 and 3.5 Å resolution, respectively. The structures elucidate details of the protein-protein and protein-DNA interfaces involved in lentiviral intasome formation. We show that the homomeric interfaces involved in IN hexadecamer formation and the α-helical configuration of the linker connecting the C-terminal and catalytic core domains are critical for MVV IN strand transfer activity in vitro and for virus infectivity. Single-molecule microscopy in conjunction with photobleaching reveals that the MVV intasome can bind a variable number, up to sixteen molecules, of the lentivirus-specific host factor LEDGF/p75. Concordantly, ablation of endogenous LEDGF/p75 results in gross redistribution of MVV integration sites in human and ovine cells. Our data confirm the importance of the expanded architecture observed in cryo-EM studies of lentiviral intasomes and suggest that this organization underlies multivalent interactions with chromatin for integration targeting to active genes.
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Affiliation(s)
- Allison Ballandras-Colas
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Institut de Biologie Structurale (IBS) CNRS, CEA, University Grenoble, Grenoble, France
| | - Vidya Chivukula
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Dominika T Gruszka
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, London, UK
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics and Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Zelin Shan
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Parmit K Singh
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Valerie E Pye
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Rebecca K McLean
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, UK
- The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, UK
| | - Gregory J Bedwell
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Wen Li
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Nicola J Cook
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Hind J Fadel
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN, USA
| | - Eric M Poeschla
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - David J Griffiths
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, UK
| | - Javier Vargas
- Departmento de Óptica, Universidad Complutense de Madrid, Madrid, Spain
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, UK
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Hasan Yardimci
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, London, UK.
| | - Alan N Engelman
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK.
- Department of Infectious Disease, St-Mary's Campus, Imperial College London, London, UK.
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32
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Engelman AN, Kvaratskhelia M. Multimodal Functionalities of HIV-1 Integrase. Viruses 2022; 14:926. [PMID: 35632668 PMCID: PMC9144474 DOI: 10.3390/v14050926] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 01/11/2023] Open
Abstract
Integrase is the retroviral protein responsible for integrating reverse transcripts into cellular genomes. Co-packaged with viral RNA and reverse transcriptase into capsid-encased viral cores, human immunodeficiency virus 1 (HIV-1) integrase has long been implicated in reverse transcription and virion maturation. However, the underlying mechanisms of integrase in these non-catalytic-related viral replication steps have remained elusive. Recent results have shown that integrase binds genomic RNA in virions, and that mutational or pharmacological disruption of integrase-RNA binding yields eccentric virion particles with ribonucleoprotein complexes situated outside of the capsid shell. Such viruses are defective for reverse transcription due to preferential loss of integrase and viral RNA from infected target cells. Parallel research has revealed defective integrase-RNA binding and eccentric particle formation as common features of class II integrase mutant viruses, a phenotypic grouping of viruses that display defects at steps beyond integration. In light of these new findings, we propose three new subclasses of class II mutant viruses (a, b, and c), all of which are defective for integrase-RNA binding and particle morphogenesis, but differ based on distinct underlying mechanisms exhibited by the associated integrase mutant proteins. We also assess how these findings inform the role of integrase in HIV-1 particle maturation.
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Affiliation(s)
- Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
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Ilgova E, Galkin S, Khrenova M, Serebryakova M, Gottikh M, Anisenko A. Complex of HIV-1 Integrase with Cellular Ku Protein: Interaction Interface and Search for Inhibitors. Int J Mol Sci 2022; 23:ijms23062908. [PMID: 35328329 PMCID: PMC8951179 DOI: 10.3390/ijms23062908] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 12/27/2022] Open
Abstract
The interaction of HIV-1 integrase and the cellular Ku70 protein is necessary for HIV replication due to its positive effect on post-integration DNA repair. We have previously described in detail the Ku70 binding site within integrase. However, the integrase binding site in Ku70 remained poorly characterized. Here, using a peptide fishing assay and site-directed mutagenesis, we have identified residues I72, S73, and I76 of Ku70 as key for integrase binding. The molecular dynamics studies have revealed a possible way for IN to bind to Ku70, which is consistent with experimental data. According to this model, residues I72 and I76 of Ku70 form a "leucine zipper" with integrase residues, and, therefore, their concealment by low-molecular-weight compounds should impede the Ku70 interaction with integrase. We have identified such compounds by molecular docking and have confirmed their capacity to inhibit the formation of the integrase complex with Ku70. Our data demonstrate that the site of IN binding within Ku70 identified in the present work may be used for further search for inhibitors of the integrase binding to Ku70.
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Affiliation(s)
- Ekaterina Ilgova
- Chemistry Department, Lomonosov Moscow State University, 119992 Moscow, Russia; (E.I.); (S.G.); (M.K.); (M.G.)
| | - Simon Galkin
- Chemistry Department, Lomonosov Moscow State University, 119992 Moscow, Russia; (E.I.); (S.G.); (M.K.); (M.G.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Maria Khrenova
- Chemistry Department, Lomonosov Moscow State University, 119992 Moscow, Russia; (E.I.); (S.G.); (M.K.); (M.G.)
- Research Centre of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Marina Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia;
| | - Marina Gottikh
- Chemistry Department, Lomonosov Moscow State University, 119992 Moscow, Russia; (E.I.); (S.G.); (M.K.); (M.G.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia;
| | - Andrey Anisenko
- Chemistry Department, Lomonosov Moscow State University, 119992 Moscow, Russia; (E.I.); (S.G.); (M.K.); (M.G.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia;
- Correspondence:
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Ha CHX, Lee NK, Rahman T, Hwang SS, Yam WK, Chee XW. Repurposing FDA-approved drugs as HIV-1 integrase inhibitors: an in silico investigation. J Biomol Struct Dyn 2022; 41:2146-2159. [PMID: 35067186 DOI: 10.1080/07391102.2022.2028677] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Human Immunodeficiency Virus (HIV) infection is a global pandemic that has claimed 33 million lives to-date. One of the most efficacious treatments for naïve or pretreated HIV patients is the HIV integrase strand transfer inhibitors (INSTIs). However, given that HIV treatment is life-long, the emergence of HIV strains resistant to INSTIs is an imminent challenge. In this work, we showed two best regression QSAR models that were constructed using a boosted Random Forest algorithm (r2 = 0.998, q210CV = 0.721, q2external_test = 0.754) and a boosted K* algorithm (r2 = 0.987, q210CV = 0.721, q2external_test = 0.758) to predict the pIC50 values of INSTIs. Subsequently, the regression QSAR models were deployed against the Drugbank database for drug repositioning. The top-ranked compounds were further evaluated for their target engagement activity using molecular docking studies and accelerated Molecular Dynamics simulation. Lastly, their potential as INSTIs were also evaluated from our literature search. Our study offers the first example of a large-scale regression QSAR modelling effort for discovering highly active INSTIs to combat HIV infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Christopher Heng Xuan Ha
- Faculty of Engineering, Computing and Science, Swinburne University of Technology, Sarawak, Malaysia
| | - Nung Kion Lee
- Faculty of Cognitive Sciences and Human Development, Universiti Malaysia Sarawak, Sarawak, Malaysia
| | - Taufiq Rahman
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Siaw San Hwang
- Faculty of Engineering, Computing and Science, Swinburne University of Technology, Sarawak, Malaysia
| | - Wai Keat Yam
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Kuala Lumpur, Malaysia
| | - Xavier Wezen Chee
- Faculty of Engineering, Computing and Science, Swinburne University of Technology, Sarawak, Malaysia
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Integrase Inhibitor Resistance Mechanisms and Structural Characteristics in Antiretroviral Therapy-Experienced, Integrase Inhibitor-Naive Adults with HIV-1 Infection Treated with Dolutegravir plus Two Nucleoside Reverse Transcriptase Inhibitors in the DAWNING Study. Antimicrob Agents Chemother 2022; 66:e0164321. [PMID: 34694877 PMCID: PMC8765460 DOI: 10.1128/aac.01643-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
At week 48 in the phase IIIb DAWNING study, the integrase strand transfer inhibitor (INSTI) dolutegravir plus 2 nucleoside reverse transcriptase inhibitors demonstrated superiority to ritonavir-boosted lopinavir in achieving virologic suppression in adults with HIV-1 who failed first-line therapy. Here, we report emergent HIV-1 drug resistance and mechanistic underpinnings among dolutegravir-treated adults in DAWNING. Population viral genotyping, phenotyping, and clonal analyses were performed on participants meeting confirmed virologic withdrawal (CVW) criteria on dolutegravir-containing regimens. Dolutegravir binding to and structural changes in HIV-1 integrase-DNA complexes with INSTI resistance-associated substitutions were evaluated. Of participants who received dolutegravir through week 48 plus an additional 110 weeks for this assessment, 6 met CVW criteria with treatment-emergent INSTI resistance-associated substitutions and 1 had R263R/K at baseline but not at CVW. All 7 achieved HIV-1 RNA levels of <400 copies/mL (5 achieved <50 copies/mL) before CVW. Treatment-emergent G118R was detected in 5 participants, occurring with ≥2 other integrase substitutions, including R263R/K, in 3 participants and without other integrase substitutions in 2 participants. G118R or R263K increased the rate of dolutegravir dissociation from integrase-DNA complexes versus wild-type but retained prolonged binding. Overall, among treatment-experienced adults who received dolutegravir in DAWNING, 6 of 314 participants developed treatment-emergent INSTI resistance-associated substitutions, with a change in in vitro dolutegravir resistance of >10-fold and reduced viral replication capacity versus baseline levels. This study demonstrates that the pathway to dolutegravir resistance is a challenging balance between HIV-1 phenotypic change and associated loss of viral fitness. (This study has been registered at ClinicalTrials.gov under identifier NCT02227238.).
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Abstract
A hallmark of retroviral replication is establishment of the proviral state, wherein a DNA copy of the viral RNA genome is stably incorporated into a host cell chromosome. Integrase is the viral enzyme responsible for the catalytic steps involved in this process, and integrase strand transfer inhibitors are widely used to treat people living with HIV. Over the past decade, a series of X-ray crystallography and cryogenic electron microscopy studies have revealed the structural basis of retroviral DNA integration. A variable number of integrase molecules congregate on viral DNA ends to assemble a conserved intasome core machine that facilitates integration. The structures additionally informed on the modes of integrase inhibitor action and the means by which HIV acquires drug resistance. Recent years have witnessed the development of allosteric integrase inhibitors, a highly promising class of small molecules that antagonize viral morphogenesis. In this Review, we explore recent insights into the organization and mechanism of the retroviral integration machinery and highlight open questions as well as new directions in the field.
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Miskey C, Kesselring L, Querques I, Abrusán G, Barabas O, Ivics Z. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2807-2825. [PMID: 35188569 PMCID: PMC8934666 DOI: 10.1093/nar/gkac092] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/24/2022] [Accepted: 02/08/2022] [Indexed: 11/14/2022] Open
Abstract
The Sleeping Beauty (SB) transposon system is a popular tool for genome engineering, but random integration into the genome carries a certain genotoxic risk in therapeutic applications. Here we investigate the role of amino acids H187, P247 and K248 in target site selection of the SB transposase. Structural modeling implicates these three amino acids located in positions analogous to amino acids with established functions in target site selection in retroviral integrases and transposases. Saturation mutagenesis of these residues in the SB transposase yielded variants with altered target site selection properties. Transposon integration profiling of several mutants reveals increased specificity of integrations into palindromic AT repeat target sequences in genomic regions characterized by high DNA bendability. The H187V and K248R mutants redirect integrations away from exons, transcriptional regulatory elements and nucleosomal DNA in the human genome, suggesting enhanced safety and thus utility of these SB variants in gene therapy applications.
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Affiliation(s)
| | | | - Irma Querques
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - György Abrusán
- Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged 6726, Hungary
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
| | - Zoltán Ivics
- To whom correspondence should be addressed. Tel: +49 6103 77 6000; Fax: +49 6103 77 1280;
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Prototype Foamy Virus Integrase Displays Unique Biochemical Activities among Retroviral Integrases. Biomolecules 2021; 11:biom11121910. [PMID: 34944553 PMCID: PMC8699820 DOI: 10.3390/biom11121910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/13/2021] [Accepted: 12/17/2021] [Indexed: 12/01/2022] Open
Abstract
Integrases of different retroviruses assemble as functional complexes with varying multimers of the protein. Retroviral integrases require a divalent metal cation to perform one-step transesterification catalysis. Tetrameric prototype foamy virus (PFV) intasomes assembled from purified integrase and viral DNA oligonucleotides were characterized for their activity in the presence of different cations. While most retroviral integrases are inactive in calcium, PFV intasomes appear to be uniquely capable of catalysis in calcium. The PFV intasomes also contrast with other retroviral integrases by displaying an inverse correlation of activity with increasing manganese beginning at relatively low concentrations. The intasomes were found to be significantly more active in the presence of chloride co-ions compared to acetate. While HIV-1 integrase appears to commit to a target DNA within 20 s, PFV intasomes do not commit to target DNA during their reaction lifetime. Together, these data highlight the unique biochemical activities of PFV integrase compared to other retroviral integrases.
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Passos DO, Li M, Craigie R, Lyumkis D. Retroviral integrase: Structure, mechanism, and inhibition. Enzymes 2021; 50:249-300. [PMID: 34861940 DOI: 10.1016/bs.enz.2021.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The retroviral protein Integrase (IN) catalyzes concerted integration of viral DNA into host chromatin to establish a permanent infection in the target cell. We learned a great deal about the mechanism of catalytic integration through structure/function studies over the previous four decades of IN research. As one of three essential retroviral enzymes, IN has also been targeted by antiretroviral drugs to treat HIV-infected individuals. Inhibitors blocking the catalytic integration reaction are now state-of-the-art drugs within the antiretroviral therapy toolkit. HIV-1 IN also performs intriguing non-catalytic functions that are relevant to the late stages of the viral replication cycle, yet this aspect remains poorly understood. There are also novel allosteric inhibitors targeting non-enzymatic functions of IN that induce a block in the late stages of the viral replication cycle. In this chapter, we will discuss the function, structure, and inhibition of retroviral IN proteins, highlighting remaining challenges and outstanding questions.
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Affiliation(s)
| | - Min Li
- National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Robert Craigie
- National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, La Jolla, CA, United States; The Scripps Research Institute, La Jolla, CA, United States.
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Find and cut-and-transfer (FiCAT) mammalian genome engineering. Nat Commun 2021; 12:7071. [PMID: 34862378 PMCID: PMC8642419 DOI: 10.1038/s41467-021-27183-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 11/09/2021] [Indexed: 12/26/2022] Open
Abstract
While multiple technologies for small allele genome editing exist, robust technologies for targeted integration of large DNA fragments in mammalian genomes are still missing. Here we develop a gene delivery tool (FiCAT) combining the precision of a CRISPR-Cas9 (find module), and the payload transfer efficiency of an engineered piggyBac transposase (cut-and-transfer module). FiCAT combines the functionality of Cas9 DNA scanning and targeting DNA, with piggyBac donor DNA processing and transfer capacity. PiggyBac functional domains are engineered providing increased on-target integration while reducing off-target events. We demonstrate efficient delivery and programmable insertion of small and large payloads in cellulo (human (Hek293T, K-562) and mouse (C2C12)) and in vivo in mouse liver. Finally, we evolve more efficient versions of FiCAT by generating a targeted diversity of 394,000 variants and undergoing 4 rounds of evolution. In this work, we develop a precise and efficient targeted insertion of multi kilobase DNA fragments in mammalian genomes. Mammalian genome engineering has advanced tremendously over the last decade, however there is still a need for robust gene writing with size scaling capacity. Here the authors present Find Cut-and-Transfer (FiCAT) technology to delivery large targeted payload insertion in cell lines and in vivo in mouse models.
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Abascal-Palacios G, Jochem L, Pla-Prats C, Beuron F, Vannini A. Structural basis of Ty3 retrotransposon integration at RNA Polymerase III-transcribed genes. Nat Commun 2021; 12:6992. [PMID: 34848735 PMCID: PMC8632968 DOI: 10.1038/s41467-021-27338-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/15/2021] [Indexed: 12/29/2022] Open
Abstract
Retrotransposons are endogenous elements that have the ability to mobilise their DNA between different locations in the host genome. The Ty3 retrotransposon integrates with an exquisite specificity in a narrow window upstream of RNA Polymerase (Pol) III-transcribed genes, representing a paradigm for harmless targeted integration. Here we present the cryo-EM reconstruction at 4.0 Å of an active Ty3 strand transfer complex bound to TFIIIB transcription factor and a tRNA gene. The structure unravels the molecular mechanisms underlying Ty3 targeting specificity at Pol III-transcribed genes and sheds light into the architecture of retrotransposon machinery during integration. Ty3 intasome contacts a region of TBP, a subunit of TFIIIB, which is blocked by NC2 transcription regulator in RNA Pol II-transcribed genes. A newly-identified chromodomain on Ty3 integrase interacts with TFIIIB and the tRNA gene, defining with extreme precision the integration site position.
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Affiliation(s)
| | - Laura Jochem
- Division of Structural Biology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Carlos Pla-Prats
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer Research, London, SW7 3RP, UK.
- Human Technopole, 20157, Milan, Italy.
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Liu S, Koneru PC, Li W, Pathirage C, Engelman AN, Kvaratskhelia M, Musier-Forsyth K. HIV-1 integrase binding to genomic RNA 5'-UTR induces local structural changes in vitro and in virio. Retrovirology 2021; 18:37. [PMID: 34809662 PMCID: PMC8609798 DOI: 10.1186/s12977-021-00582-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 11/03/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND During HIV-1 maturation, Gag and Gag-Pol polyproteins are proteolytically cleaved and the capsid protein polymerizes to form the honeycomb capsid lattice. HIV-1 integrase (IN) binds the viral genomic RNA (gRNA) and impairment of IN-gRNA binding leads to mis-localization of the nucleocapsid protein (NC)-condensed viral ribonucleoprotein complex outside the capsid core. IN and NC were previously demonstrated to bind to the gRNA in an orthogonal manner in virio; however, the effect of IN binding alone or simultaneous binding of both proteins on gRNA structure is not yet well understood. RESULTS Using crosslinking-coupled selective 2'-hydroxyl acylation analyzed by primer extension (XL-SHAPE), we characterized the interaction of IN and NC with the HIV-1 gRNA 5'-untranslated region (5'-UTR). NC preferentially bound to the packaging signal (Psi) and a UG-rich region in U5, irrespective of the presence of IN. IN alone also bound to Psi but pre-incubation with NC largely abolished this interaction. In contrast, IN specifically bound to and affected the nucleotide (nt) dynamics of the apical loop of the transactivation response element (TAR) and the polyA hairpin even in the presence of NC. SHAPE probing of the 5'-UTR RNA in virions produced from allosteric IN inhibitor (ALLINI)-treated cells revealed that while the global secondary structure of the 5'-UTR remained unaltered, the inhibitor treatment induced local reactivity differences, including changes in the apical loop of TAR that are consistent with the in vitro results. CONCLUSIONS Overall, the binding interactions of NC and IN with the 5'-UTR are largely orthogonal in vitro. This study, together with previous probing experiments, suggests that IN and NC binding in vitro and in virio lead to only local structural changes in the regions of the 5'-UTR probed here. Accordingly, disruption of IN-gRNA binding by ALLINI treatment results in local rather than global secondary structure changes of the 5'-UTR in eccentric virus particles.
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Affiliation(s)
- Shuohui Liu
- grid.261331.40000 0001 2285 7943Department of Chemistry and Biochemistry, Centers for RNA Biology and Retroviral Research, The Ohio State University, Columbus, OH USA
| | - Pratibha C. Koneru
- grid.430503.10000 0001 0703 675XDivision of Infectious Diseases, School of Medicine, University of Colorado, Aurora, CO USA
| | - Wen Li
- grid.65499.370000 0001 2106 9910Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Harvard Medical School, Boston, MA USA
| | - Chathuri Pathirage
- grid.261331.40000 0001 2285 7943Department of Chemistry and Biochemistry, Centers for RNA Biology and Retroviral Research, The Ohio State University, Columbus, OH USA
| | - Alan N. Engelman
- grid.65499.370000 0001 2106 9910Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Medicine, Harvard Medical School, Boston, MA USA
| | - Mamuka Kvaratskhelia
- grid.430503.10000 0001 0703 675XDivision of Infectious Diseases, School of Medicine, University of Colorado, Aurora, CO USA
| | - Karin Musier-Forsyth
- grid.261331.40000 0001 2285 7943Department of Chemistry and Biochemistry, Centers for RNA Biology and Retroviral Research, The Ohio State University, Columbus, OH USA
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43
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Emergence of Resistance in HIV-1 Integrase With Dolutegravir Treatment in a Pediatric Population From the IMPAACT P1093 Study. Antimicrob Agents Chemother 2021; 66:e0164521. [PMID: 34694878 PMCID: PMC8765298 DOI: 10.1128/aac.01645-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
P1093 is a multicenter, open-label, phase I/II study of pharmacokinetics, safety, and tolerability of dolutegravir plus an optimized background regimen in pediatric participants aged 4 weeks to <18 years with HIV-1. Most participants were highly treatment experienced. We report the mechanisms of emergent integrase strand transfer inhibitor (INSTI) resistance among adolescents and children receiving dolutegravir. Plasma was collected at screening and near protocol-defined virologic failure (PDVF) for population- and, for some samples, clonal-level integrase genotyping, phenotyping, and replication capacity. HIV-1 RNA was assessed in all available plasma samples. Phylogenetic analysis of clonal integrase sequences and homology modeling of HIV-1 intasome complexes containing resistance-associated substitutions were performed. Treatment-emergent INSTI resistance was detected in 8 participants who met PDVF criteria. Rare INSTI resistance-associated substitutions G118R or R263K developed in 6 participants. On-study secondary integrase substitutions E157Q or L74I were observed in 2 participants. G118R reduced dolutegravir susceptibility and integrase replication capacity greater than R263K and demonstrated greater reduction in susceptibility and integrase replication capacity when present with specific secondary integrase substitutions, including L74M, T66I, and E138E/K. Continuing evolution after R263K acquisition led to reduced dolutegravir susceptibility and integrase replication capacity. Structural examination revealed potential mechanisms for G118R- and R263K-mediated INSTI resistance. G118R or R263K INSTI resistance substitutions, which are distinct to second-generation INSTIs, were detected in adolescents and children with prior virologic failure who received dolutegravir. This study provides additional molecular and structural characterization of integrase to aid in the understanding of INSTI resistance mechanisms in antiretroviral-experienced populations (ClinicalTrials.gov identifier: NCT01302847).
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Sui H, Hao M, Chang W, Imamichi T. The Role of Ku70 as a Cytosolic DNA Sensor in Innate Immunity and Beyond. Front Cell Infect Microbiol 2021; 11:761983. [PMID: 34746031 PMCID: PMC8566972 DOI: 10.3389/fcimb.2021.761983] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/06/2021] [Indexed: 12/24/2022] Open
Abstract
Human Ku70 is a well-known endogenous nuclear protein involved in the non-homologous end joining pathway to repair double-stranded breaks in DNA. However, Ku70 has been studied in multiple contexts and grown into a multifunctional protein. In addition to the extensive functional study of Ku70 in DNA repair process, many studies have emphasized the role of Ku70 in various other cellular processes, including apoptosis, aging, and HIV replication. In this review, we focus on discussing the role of Ku70 in inducing interferons and proinflammatory cytokines as a cytosolic DNA sensor. We explored the unique structure of Ku70 binding with DNA; illustrated, with evidence, how Ku70, as a nuclear protein, responds to extracellular DNA stimulation; and summarized the mechanisms of the Ku70-involved innate immune response pathway. Finally, we discussed several new strategies to modulate Ku70-mediated innate immune response and highlighted some potential physiological insights based on the role of Ku70 in innate immunity.
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Affiliation(s)
- Hongyan Sui
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | | | | | - Tomozumi Imamichi
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
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Nguyen PQ, Conesa C, Rabut E, Bragagnolo G, Gouzerh C, Fernández-Tornero C, Lesage P, Reguera J, Acker J. Ty1 integrase is composed of an active N-terminal domain and a large disordered C-terminal module dispensable for its activity in vitro. J Biol Chem 2021; 297:101093. [PMID: 34416236 PMCID: PMC8487063 DOI: 10.1016/j.jbc.2021.101093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/05/2021] [Accepted: 08/16/2021] [Indexed: 11/16/2022] Open
Abstract
Long-terminal repeat (LTR) retrotransposons are genetic elements that, like retroviruses, replicate by reverse transcription of an RNA intermediate into a complementary DNA (cDNA) that is next integrated into the host genome by their own integrase. The Ty1 LTR retrotransposon has proven to be a reliable working model to investigate retroelement integration site preference. However, the low yield of recombinant Ty1 integrase production reported so far has been a major obstacle for structural studies. Here we analyze the biophysical and biochemical properties of a stable and functional recombinant Ty1 integrase highly expressed in E.coli. The recombinant protein is monomeric and has an elongated shape harboring the three-domain structure common to all retroviral integrases at the N-terminal half, an extra folded region, and a large intrinsically disordered region at the C-terminal half. Recombinant Ty1 integrase efficiently catalyzes concerted integration in vitro, and the N-terminal domain displays similar activity. These studies that will facilitate structural analyses may allow elucidating the molecular mechanisms governing Ty1 specific integration into safe places in the genome.
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Affiliation(s)
| | - Christine Conesa
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Elise Rabut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Célia Gouzerh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Pascale Lesage
- INSERM U944, CNRS UMR 7212, Genomes and Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Juan Reguera
- Aix-Marseille Université, CNRS, AFMB UMR 7257, Marseille, France; INSERM, AFMB UMR7257, Marseille, France.
| | - Joël Acker
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France.
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Smith SJ, Zhao XZ, Passos DO, Pye VE, Cherepanov P, Lyumkis D, Burke TR, Hughes SH. HIV-1 Integrase Inhibitors with Modifications That Affect Their Potencies against Drug Resistant Integrase Mutants. ACS Infect Dis 2021; 7:1469-1482. [PMID: 33686850 PMCID: PMC8205226 DOI: 10.1021/acsinfecdis.0c00819] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
![]()
Integrase strand transfer inhibitors
(INSTIs) block the integration
step of the retroviral lifecycle and are first-line drugs used for
the treatment of HIV-1/AIDS. INSTIs have a polycyclic core with heteroatom
triads, chelate the metal ions at the active site, and have a halobenzyl
group that interacts with viral DNA attached to the core by a flexible
linker. The most broadly effective INSTIs inhibit both wild-type (WT)
integrase (IN) and a variety of well-known mutants. However, because
there are mutations that reduce the potency of all of the available
INSTIs, new and better compounds are needed. Models based on recent
structures of HIV-1 and red-capped mangabey SIV INs suggest modifications
in the INSTI structures that could enhance interactions with the 3′-terminal
adenosine of the viral DNA, which could improve performance against
INSTI resistant mutants. We designed and tested a series of INSTIs
having modifications to their naphthyridine scaffold. One of the new
compounds retained good potency against an expanded panel of HIV-1
IN mutants that we tested. Our results suggest the possibility of
designing inhibitors that combine the best features of the existing
compounds, which could provide additional efficacy against known HIV-1
IN mutants.
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Affiliation(s)
- Steven J. Smith
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Dario Oliveira Passos
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Valerie E. Pye
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
- St Mary’s Hospital, Department of Infectious Disease, Imperial College London, Section of Virology, Norfolk Place, London W2 1PG, U.K
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Terrence R. Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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Smith SJ, Zhao XZ, Passos DO, Pye VE, Cherepanov P, Lyumkis D, Burke TR, Hughes SH. HIV-1 Integrase Inhibitors with Modifications That Affect Their Potencies against Drug Resistant Integrase Mutants. ACS Infect Dis 2021. [PMID: 33686850 DOI: 10.1021/acsinfecdis.0c00819/suppl_file/id0c00819_liveslides.mp4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2023]
Abstract
Integrase strand transfer inhibitors (INSTIs) block the integration step of the retroviral lifecycle and are first-line drugs used for the treatment of HIV-1/AIDS. INSTIs have a polycyclic core with heteroatom triads, chelate the metal ions at the active site, and have a halobenzyl group that interacts with viral DNA attached to the core by a flexible linker. The most broadly effective INSTIs inhibit both wild-type (WT) integrase (IN) and a variety of well-known mutants. However, because there are mutations that reduce the potency of all of the available INSTIs, new and better compounds are needed. Models based on recent structures of HIV-1 and red-capped mangabey SIV INs suggest modifications in the INSTI structures that could enhance interactions with the 3'-terminal adenosine of the viral DNA, which could improve performance against INSTI resistant mutants. We designed and tested a series of INSTIs having modifications to their naphthyridine scaffold. One of the new compounds retained good potency against an expanded panel of HIV-1 IN mutants that we tested. Our results suggest the possibility of designing inhibitors that combine the best features of the existing compounds, which could provide additional efficacy against known HIV-1 IN mutants.
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Affiliation(s)
- Steven J Smith
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Dario Oliveira Passos
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Valerie E Pye
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, U.K
- St Mary's Hospital, Department of Infectious Disease, Imperial College London, Section of Virology, Norfolk Place, London W2 1PG, U.K
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Terrence R Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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48
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Engelman KD, Engelman AN. Long-Acting Cabotegravir for HIV/AIDS Prophylaxis. Biochemistry 2021; 60:1731-1740. [PMID: 34029457 DOI: 10.1021/acs.biochem.1c00157] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The retrovirus HIV-1 is the etiological agent of the decades-long AIDS pandemic. Although vaccination is the most common preexposure route to prevent acquisition of viral disease, scalable efficacious vaccination strategies have yet to be developed for HIV-1. By contrast, small molecule inhibitors of the HIV-1 enzymes reverse transcriptase, integrase, and protease have been developed that effectively block virus replication. Three different drug compounds are commonly prescribed for people living with HIV as once-daily oral tablets. Once-daily pills composed of two different reverse transcriptase inhibitors are moreover approved as preexposure prophylaxis (PrEP) treatment for virus naïve individuals who may partake in behaviors associated with increased risk of HIV-1 acquisition such as unprotected sex or injection drug use. Long-acting (LA) injectable HIV-1 enzyme inhibitors are at the same time being developed to sidestep adherence noncompliance issues that can arise from self-administered once-daily oral dosing regimens. Cabotegravir (CAB)-LA, which inhibits integrase strand transfer activity, has in recent clinical trials been shown to prevent HIV-1 acquisition more effectively than once-daily oral dosed reverse transcriptase inhibitors. In this Perspective, we examine bench to bedside aspects of CAB-LA treatment and development, starting from the biochemical basis of HIV-1 integration and pharmacological inhibition of integrase catalysis. We also review the results of recent clinical trials that evaluated CAB-LA, as well as the promises and challenges that surround its use for HIV/AIDS PrEP.
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Affiliation(s)
- Kathleen D Engelman
- MassBiologics, University of Massachusetts Medical School, 460 Walk Hill Street, Boston, Massachusetts 02126, United States
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States.,Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, United States
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Yoder KE, Rabe AJ, Fishel R, Larue RC. Strategies for Targeting Retroviral Integration for Safer Gene Therapy: Advances and Challenges. Front Mol Biosci 2021; 8:662331. [PMID: 34055882 PMCID: PMC8149907 DOI: 10.3389/fmolb.2021.662331] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022] Open
Abstract
Retroviruses are obligate intracellular parasites that must integrate a copy of the viral genome into the host DNA. The integration reaction is performed by the viral enzyme integrase in complex with the two ends of the viral cDNA genome and yields an integrated provirus. Retroviral vector particles are attractive gene therapy delivery tools due to their stable integration. However, some retroviral integration events may dysregulate host oncogenes leading to cancer in gene therapy patients. Multiple strategies to target retroviral integration, particularly to genetic safe harbors, have been tested with limited success. Attempts to target integration may be limited by the multimerization of integrase or the presence of host co-factors for integration. Several retroviral integration complexes have evolved a mechanism of tethering to chromatin via a host protein. Integration host co-factors bind chromatin, anchoring the complex and allowing integration. The tethering factor allows for both close proximity to the target DNA and specificity of targeting. Each retrovirus appears to have distinct preferences for DNA sequence and chromatin features at the integration site. Tethering factors determine the preference for chromatin features, but do not affect the subtle sequence preference at the integration site. The sequence preference is likely intrinsic to the integrase protein. New developments may uncouple the requirement for a tethering factor and increase the ability to redirect retroviral integration.
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Affiliation(s)
- Kristine E Yoder
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Anthony J Rabe
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Richard Fishel
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Ross C Larue
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
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50
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Dixit U, Bhutoria S, Wu X, Qiu L, Spira M, Mathew S, Harris R, Adams LJ, Cahill S, Pathak R, Rajesh Kumar P, Nguyen M, Acharya SA, Brenowitz M, Almo SC, Zou X, Steven AC, Cowburn D, Girvin M, Kalpana GV. INI1/SMARCB1 Rpt1 domain mimics TAR RNA in binding to integrase to facilitate HIV-1 replication. Nat Commun 2021; 12:2743. [PMID: 33980829 PMCID: PMC8115288 DOI: 10.1038/s41467-021-22733-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/24/2021] [Indexed: 11/09/2022] Open
Abstract
INI1/SMARCB1 binds to HIV-1 integrase (IN) through its Rpt1 domain and exhibits multifaceted role in HIV-1 replication. Determining the NMR structure of INI1-Rpt1 and modeling its interaction with the IN-C-terminal domain (IN-CTD) reveal that INI1-Rpt1/IN-CTD interface residues overlap with those required for IN/RNA interaction. Mutational analyses validate our model and indicate that the same IN residues are involved in both INI1 and RNA binding. INI1-Rpt1 and TAR RNA compete with each other for IN binding with similar IC50 values. INI1-interaction-defective IN mutant viruses are impaired for incorporation of INI1 into virions and for particle morphogenesis. Computational modeling of IN-CTD/TAR complex indicates that the TAR interface phosphates overlap with negatively charged surface residues of INI1-Rpt1 in three-dimensional space, suggesting that INI1-Rpt1 domain structurally mimics TAR. This possible mimicry between INI1-Rpt1 and TAR explains the mechanism by which INI1/SMARCB1 influences HIV-1 late events and suggests additional strategies to inhibit HIV-1 replication.
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Affiliation(s)
- Updesh Dixit
- Department of Genetics, Albert Einstein College of Medicine, New York City, NY, USA
| | - Savita Bhutoria
- Department of Genetics, Albert Einstein College of Medicine, New York City, NY, USA
| | - Xuhong Wu
- Department of Genetics, Albert Einstein College of Medicine, New York City, NY, USA
| | - Liming Qiu
- Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Menachem Spira
- Department of Genetics, Albert Einstein College of Medicine, New York City, NY, USA
| | - Sheeba Mathew
- Department of Genetics, Albert Einstein College of Medicine, New York City, NY, USA
| | - Richard Harris
- Department of Biochemistry, Albert Einstein College of Medicine, New York City, NY, USA
| | - Lucas J Adams
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sean Cahill
- Department of Biochemistry, Albert Einstein College of Medicine, New York City, NY, USA
| | - Rajiv Pathak
- Department of Genetics, Albert Einstein College of Medicine, New York City, NY, USA
| | - P Rajesh Kumar
- Department of Biochemistry, Albert Einstein College of Medicine, New York City, NY, USA
| | - Minh Nguyen
- Department of Genetics, Albert Einstein College of Medicine, New York City, NY, USA
| | - Seetharama A Acharya
- Department of Anatomy & Structural Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Michael Brenowitz
- Department of Biochemistry, Albert Einstein College of Medicine, New York City, NY, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, New York City, NY, USA
| | - Xiaoqin Zou
- Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Alasdair C Steven
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, New York City, NY, USA
| | - Mark Girvin
- Department of Biochemistry, Albert Einstein College of Medicine, New York City, NY, USA
| | - Ganjam V Kalpana
- Department of Genetics, Albert Einstein College of Medicine, New York City, NY, USA.
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