1
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Eschbach JE, Puray-Chavez M, Mohammed S, Wang Q, Xia M, Huang LC, Shan L, Kutluay SB. HIV-1 capsid stability and reverse transcription are finely balanced to minimize sensing of reverse transcription products via the cGAS-STING pathway. mBio 2024; 15:e0034824. [PMID: 38530034 PMCID: PMC11077976 DOI: 10.1128/mbio.00348-24] [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: 02/05/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
A critical determinant for early post-entry events, the HIV-1 capsid (CA) protein forms the conical core when it rearranges around the dimeric RNA genome and associated viral proteins. Although mutations in CA have been reported to alter innate immune sensing of HIV-1, a direct link between core stability and sensing of HIV-1 nucleic acids has not been established. Herein, we assessed how manipulating the stability of the CA lattice through chemical and genetic approaches affects innate immune recognition of HIV-1. We found that destabilization of the CA lattice resulted in potent sensing of reverse transcription products when destabilization per se does not completely block reverse transcription. Surprisingly, due to the combined effects of enhanced reverse transcription and defects in nuclear entry, two separate CA mutants that form hyperstable cores induced innate immune sensing more potently than destabilizing CA mutations. At low concentrations that allowed the accumulation of reverse transcription products, CA-targeting compounds GS-CA1 and lenacapavir measurably impacted CA lattice stability in cells and modestly enhanced innate immune sensing of HIV. Interestingly, innate immune activation observed with viruses containing unstable cores was abolished by low doses of lenacapavir. Innate immune activation observed with both hyperstable and unstable CA mutants was dependent on the cGAS-STING DNA-sensing pathway and reverse transcription. Overall, our findings demonstrate that CA lattice stability and reverse transcription are finely balanced to support reverse transcription and minimize cGAS-STING-mediated sensing of the resulting viral DNA. IMPORTANCE In HIV-1 particles, the dimeric RNA genome and associated viral proteins and enzymes are encased in a proteinaceous lattice composed of the viral capsid protein. Herein, we assessed how altering the stability of this capsid lattice through orthogonal genetic and chemical approaches impacts the induction of innate immune responses. Specifically, we found that decreasing capsid lattice stability results in more potent sensing of viral reverse transcription products, but not the genomic RNA, in a cGAS-STING-dependent manner. The recently developed capsid inhibitors lenacapavir and GS-CA1 enhanced the innate immune sensing of HIV-1. Unexpectedly, due to increased levels of reverse transcription and cytosolic accumulation of the resulting viral cDNA, capsid mutants with hyperstable cores also resulted in the potent induction of type I interferon-mediated innate immunity. Our findings suggest that HIV-1 capsid lattice stability and reverse transcription are finely balanced to minimize exposure of reverse transcription products in the cytosol of host cells.
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Affiliation(s)
- Jenna E. Eschbach
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Maritza Puray-Chavez
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Shawn Mohammed
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Qiankun Wang
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Ming Xia
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Lin-Chen Huang
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Liang Shan
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Sebla B. Kutluay
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
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2
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Guedán A, Burley M, Caroe ER, Bishop KN. HIV-1 Capsid Rapidly Induces Long-Lived CPSF6 Puncta in Non-Dividing Cells, but Similar Puncta Already Exist in Uninfected T-Cells. Viruses 2024; 16:670. [PMID: 38793552 PMCID: PMC11125723 DOI: 10.3390/v16050670] [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: 01/30/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
The HIV-1 capsid (CA) protein forms the outer shell of the viral core that is released into the cytoplasm upon infection. CA binds various cellular proteins, including CPSF6, that direct HIV-1 integration into speckle-associated domains in host chromatin. Upon HIV-1 infection, CPSF6 forms puncta in the nucleus. Here, we characterised these CPSF6 puncta further in HeLa cells, T-cells and macrophages and confirmed that integration and reverse transcription are not required for puncta formation. Indeed, we found that puncta formed very rapidly after infection, correlating with the time that CA entered the nucleus. In aphidicolin-treated HeLa cells and macrophages, puncta were detected for the length of the experiment, suggesting that puncta are only lost upon cell division. CA still co-localised with CPSF6 puncta at the latest time points, considerably after the peak of reverse transcription and integration. Intriguingly, the number of puncta induced in macrophages did not correlate with the MOI or the total number of nuclear speckles present in each cell, suggesting that CA/CPSF6 is only directed to a few nuclear speckles. Furthermore, we found that CPSF6 already co-localised with nuclear speckles in uninfected T-cells, suggesting that HIV-1 promotes a natural behaviour of CPSF6.
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Affiliation(s)
| | | | | | - Kate N. Bishop
- Retroviral Replication Laboratory, The Francis Crick Institute, London NW1 1AT, UK; (A.G.); (M.B.); (E.R.C.)
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3
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Taylor IA, Fassati A. The capsid revolution. J Mol Cell Biol 2024; 15:mjad076. [PMID: 38037430 PMCID: PMC11193064 DOI: 10.1093/jmcb/mjad076] [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: 07/25/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/02/2023] Open
Abstract
Lenacapavir, targeting the human immunodeficiency virus type-1 (HIV-1) capsid, is the first-in-class antiretroviral drug recently approved for clinical use. The development of Lenacapavir is attributed to the remarkable progress in our understanding of the capsid protein made during the last few years. Considered little more than a component of the virus shell to be shed early during infection, the capsid has been found to be a key player in the HIV-1 life cycle by interacting with multiple host factors, entering the nucleus, and directing integration. Here, we describe the key advances that led to this 'capsid revolution'.
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Affiliation(s)
- Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ariberto Fassati
- Division of Infection and Immunity, University College London, London WC1E 6JF, UK
- Institute of Immunity and Transplantation, University College London, London NW3 2PP, UK
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4
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Lang S, Fletcher DA, Petit AP, Luise N, Fyfe P, Zuccotto F, Porter D, Hope A, Bellany F, Kerr C, Mackenzie CJ, Wyatt PG, Gray DW. Application of an NMR/Crystallography Fragment Screening Platform for the Assessment and Rapid Discovery of New HIV-CA Binding Fragments. ChemMedChem 2024:e202400025. [PMID: 38581280 DOI: 10.1002/cmdc.202400025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/08/2024]
Abstract
Identification and assessment of novel targets is essential to combat drug resistance in the treatment of HIV/AIDS. HIV Capsid (HIV-CA), the protein playing a major role in both the early and late stages of the viral life cycle, has emerged as an important target. We have applied an NMR fragment screening platform and identified molecules that bind to the N-terminal domain (NTD) of HIV-CA at a site close to the interface with the C-terminal domain (CTD). Using X-ray crystallography, we have been able to obtain crystal structures to identify the binding mode of these compounds. This allowed for rapid progression of the initial, weak binding, fragment starting points to compounds 37 and 38, which have 19F-pKi values of 5.3 and 5.4 respectively.
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Affiliation(s)
- Stuart Lang
- Cresset Discovery, New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG80SSS
| | - Daniel A Fletcher
- BioAscent Discovery Ltd, Bo'Ness Road, Newhouse, Lanarkshire, ML1 5UH
| | | | - Nicola Luise
- Alira Health, Av. De Josep Tarradellas, 123, 7th Floor, 08029, Barcelona, Spain
| | - Paul Fyfe
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
| | - Fabio Zuccotto
- Vertex Pharmaceuticals (Europe) Ltd, 86-88, Jubilee Avenue, Milton Park, Abingdon, Oxfordshire, OX14 4RW
| | - David Porter
- Evotec (UK) Ltd, Dorothy Crowfoot Hodgkin Campus, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ
| | - Anthony Hope
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
| | - Fiona Bellany
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
| | - Catrina Kerr
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
| | | | - Paul G Wyatt
- Sitala Bio Ltd, Unit D6, Grain House Mill Court, Great Shelford, Cambridge, CB22 5LD
| | - David W Gray
- Drug Discovery Unit, University of Dundee, Dow Street, Dundee, DD1 5EH
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5
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Akther T, McFadden WM, Zhang H, Kirby KA, Sarafianos SG, Wang Z. Design and Synthesis of New GS-6207 Subtypes for Targeting HIV-1 Capsid Protein. Int J Mol Sci 2024; 25:3734. [PMID: 38612545 PMCID: PMC11012105 DOI: 10.3390/ijms25073734] [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: 02/06/2024] [Revised: 03/08/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
HIV-1 capsid protein (CA) is the molecular target of the recently FDA-approved long acting injectable (LAI) drug lenacapavir (GS-6207). The quick emergence of CA mutations resistant to GS-6207 necessitates the design and synthesis of novel sub-chemotypes. We have conducted the structure-based design of two new sub-chemotypes combining the scaffold of GS-6207 and the N-terminal cap of PF74 analogs, the other important CA-targeting chemotype. The design was validated via induced-fit molecular docking. More importantly, we have worked out a general synthetic route to allow the modular synthesis of novel GS-6207 subtypes. Significantly, the desired stereochemistry of the skeleton C2 was confirmed via an X-ray crystal structure of the key synthetic intermediate 22a. Although the newly synthesized analogs did not show significant potency, our efforts herein will facilitate the future design and synthesis of novel subtypes with improved potency.
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Affiliation(s)
- Thamina Akther
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA;
| | - William M. McFadden
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (W.M.M.); (H.Z.)
| | - Huanchun Zhang
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (W.M.M.); (H.Z.)
| | - Karen A. Kirby
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (W.M.M.); (H.Z.)
| | - Stefan G. Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (W.M.M.); (H.Z.)
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA;
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6
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McFadden WM, Casey-Moore MC, Bare GAL, Kirby KA, Wen X, Li G, Wang H, Slack RL, Snyder AA, Lorson ZC, Kaufman IL, Cilento ME, Tedbury PR, Gembicky M, Olson AJ, Torbett BE, Sharpless KB, Sarafianos SG. Identification of clickable HIV-1 capsid-targeting probes for viral replication inhibition. Cell Chem Biol 2024; 31:477-486.e7. [PMID: 38518746 DOI: 10.1016/j.chembiol.2024.02.012] [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: 03/06/2023] [Revised: 12/15/2023] [Accepted: 02/27/2024] [Indexed: 03/24/2024]
Abstract
Of the targets for HIV-1 therapeutics, the capsid core is a relatively unexploited but alluring drug target due to its indispensable roles throughout virus replication. Because of this, we aimed to identify "clickable" covalent modifiers of the HIV-1 capsid protein (CA) for future functionalization. We screened a library of fluorosulfate compounds that can undergo sulfur(VI) fluoride exchange (SuFEx) reactions, and five compounds were identified as hits. These molecules were further characterized for antiviral effects. Several compounds impacted in vitro capsid assembly. One compound, BBS-103, covalently bound CA via a SuFEx reaction to Tyr145 and had antiviral activity in cell-based assays by perturbing virus production, but not uncoating. The covalent binding of compounds that target the HIV-1 capsid could aid in the future design of antiretroviral drugs or chemical probes that will help study aspects of HIV-1 replication.
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Affiliation(s)
- William M McFadden
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Mary C Casey-Moore
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Grant A L Bare
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Karen A Kirby
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA; Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Xin Wen
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Gencheng Li
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hua Wang
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ryan L Slack
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Alexa A Snyder
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Zachary C Lorson
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Isabella L Kaufman
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Maria E Cilento
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Philip R Tedbury
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA; Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Milan Gembicky
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92521, United States
| | - Arthur J Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bruce E Torbett
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA
| | - K Barry Sharpless
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Stefan G Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA; Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA.
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7
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Garza CM, Holcomb M, Santos-Martins D, Torbett BE, Forli S. IP6 and PF74 affect HIV-1 Capsid Stability through Modulation of Hexamer-Hexamer Tilt Angle Preference. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.11.584513. [PMID: 38559213 PMCID: PMC10979974 DOI: 10.1101/2024.03.11.584513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The HIV-1 capsid is an irregularly shaped complex of about 1200 protein chains containing the viral genome and several viral proteins. Together, these components are the key to unlocking passage into the nucleus, allowing for permanent integration of the viral genome into the host cell genome. Recent interest into the role of the capsid in viral replication has been driven by the approval of the first-in-class drug lenacapavir, which marks the first drug approved to target a non-enzymatic HIV-1 viral protein. In addition to lenacapavir, other small molecules such as the drug-like compound PF74, and the anionic sugar inositolhexakisphosphate (IP6), are known to impact capsid stability, and although this is widely accepted as a therapeutic effect, the mechanisms through which they do so remain unknown. In this study, we employed a systematic atomistic simulation approach to study the impact of molecules bound to hexamers at the central pore (IP6) and the FG-binding site (PF74) on capsid oligomer dynamics, compared to apo hexamers and pentamers. We found that neither small molecule had a sizeable impact on the free energy of binding of the interface between neighboring hexamers but that both had impacts on the free energy profiles of performing angular deformations to the pair of oligomers akin to the variations in curvature along the irregular surface of the capsid. The IP6 cofactor, on one hand, stabilizes a pair of neighboring hexamers in their flattest configurations, whereas without IP6, the hexamers prefer a high tilt angle between them. On the other hand, having PF74 bound introduces a strong preference for intermediate tilt angles. These results suggest that structural instability is a natural feature of the HIV-1 capsid which is modulated by molecules bound in either the central pore or the FG-binding site. Such modulators, despite sharing many of the same effects on non-bonded interactions at the various protein-protein interfaces, have decidedly different effects on the flexibility of the complex. This study provides a detailed model of the HIV-1 capsid and its interactions with small molecules, informing structure-based drug design, as well as experimental design and interpretation.
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8
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Layish B, Goli R, Flick H, Huang SW, Zhang RZ, Kvaratskhelia M, Kane M. Virus specificity and nucleoporin requirements for MX2 activity are affected by GTPase function and capsid-CypA interactions. PLoS Pathog 2024; 20:e1011830. [PMID: 38512975 PMCID: PMC10986937 DOI: 10.1371/journal.ppat.1011830] [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: 11/15/2023] [Revised: 04/02/2024] [Accepted: 02/29/2024] [Indexed: 03/23/2024] Open
Abstract
Human myxovirus resistance 2 (MX2/MXB) is an interferon-induced GTPase that inhibits human immunodeficiency virus-1 (HIV-1) infection by preventing nuclear import of the viral preintegration complex. The HIV-1 capsid (CA) is the major viral determinant for sensitivity to MX2, and complex interactions between MX2, CA, nucleoporins (Nups), cyclophilin A (CypA), and other cellular proteins influence the outcome of viral infection. To explore the interactions between MX2, the viral CA, and CypA, we utilized a CRISPR-Cas9/AAV approach to generate CypA knock-out cell lines as well as cells that express CypA from its endogenous locus, but with specific point mutations that would abrogate CA binding but should not affect enzymatic activity or cellular function. We found that infection of CypA knock-out and point mutant cell lines with wild-type HIV-1 and CA mutants recapitulated the phenotypes observed upon cyclosporine A (CsA) addition, indicating that effects of CsA treatment are the direct result of blocking CA-CypA interactions and are therefore independent from potential interactions between CypA and MX2 or other cellular proteins. Notably, abrogation of GTP hydrolysis by MX2 conferred enhanced antiviral activity when CA-CypA interactions were abolished, and this effect was not mediated by the CA-binding residues in the GTPase domain, or by phosphorylation of MX2 at position T151. We additionally found that elimination of GTPase activity also altered the Nup requirements for MX2 activity. Our data demonstrate that the antiviral activity of MX2 is affected by CypA-CA interactions in a virus-specific and GTPase activity-dependent manner. These findings further highlight the importance of the GTPase domain of MX2 in regulation of substrate specificity and interaction with nucleocytoplasmic trafficking pathways.
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Affiliation(s)
- Bailey Layish
- Department of Pediatrics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Ram Goli
- Department of Pediatrics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Haley Flick
- Department of Pediatrics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Szu-Wei Huang
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Robert Z. Zhang
- Department of Pediatrics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Melissa Kane
- Department of Pediatrics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
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9
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Tsurutani N, Momose F, Ogawa K, Sano K, Morikawa Y. Intracellular trafficking of HIV-1 Gag via Syntaxin 6-positive compartments/vesicles: Involvement in tumor necrosis factor secretion. J Biol Chem 2024; 300:105687. [PMID: 38280430 PMCID: PMC10891346 DOI: 10.1016/j.jbc.2024.105687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/29/2024] Open
Abstract
HIV-1 Gag protein is synthesized in the cytosol and is transported to the plasma membrane, where viral particle assembly and budding occur. Endosomes are alternative sites of Gag accumulation. However, the intracellular transport pathways and carriers for Gag have not been clarified. We show here that Syntaxin6 (Syx6), a soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) involved in membrane fusion in post-Golgi networks, is a molecule responsible for Gag trafficking and also for tumor necrosis factor-α (TNFα) secretion and that Gag and TNFα are cotransported via Syx6-positive compartments/vesicles. Confocal and live-cell imaging revealed that Gag colocalized and cotrafficked with Syx6, a fraction of which localizes in early and recycling endosomes. Syx6 knockdown reduced HIV-1 particle production, with Gag distributed diffusely throughout the cytoplasm. Coimmunoprecipitation and pulldown show that Gag binds to Syx6, but not its SNARE partners or their assembly complexes, suggesting that Gag preferentially binds free Syx6. The Gag matrix domain and the Syx6 SNARE domain are responsible for the interaction and cotrafficking. In immune cells, Syx6 knockdown/knockout similarly impaired HIV-1 production. Interestingly, HIV-1 infection facilitated TNFα secretion, and this enhancement did not occur in Syx6-depleted cells. Confocal and live-cell imaging revealed that TNFα and Gag partially colocalized and were cotransported via Syx6-positive compartments/vesicles. Biochemical analyses indicate that TNFα directly binds the C-terminal domain of Syx6. Altogether, our data provide evidence that both Gag and TNFα make use of Syx6-mediated trafficking machinery and suggest that Gag expression does not inhibit but rather facilitates TNFα secretion in HIV-1 infection.
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Affiliation(s)
- Naomi Tsurutani
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Fumitaka Momose
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Keiji Ogawa
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Kouichi Sano
- Osaka Medical and Pharmaceutical University, Takatsuki, Osaka, Japan
| | - Yuko Morikawa
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan.
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10
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Piacentini J, Allen DS, Ganser-Pornillos BK, Chanda SK, Yoh SM, Pornillos O. Molecular Determinants of PQBP1 Binding to the HIV-1 Capsid Lattice. J Mol Biol 2024; 436:168409. [PMID: 38128824 PMCID: PMC10885737 DOI: 10.1016/j.jmb.2023.168409] [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: 08/25/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) stimulates innate immune responses upon infection, including cyclic GMP-AMP synthase (cGAS) signaling that results in type I interferon production. HIV-1-induced activation of cGAS requires the host cell factor polyglutamine binding protein 1 (PQBP1), an intrinsically disordered protein that bridges capsid recognition and cGAS recruitment. However, the molecular details of PQBP1 interactions with the HIV-1 capsid and their functional implications remain poorly understood. Here, we show that PQBP1 binds to HIV-1 capsids through charge complementing contacts between acidic residues in the N-terminal region of PQBP1 and an arginine ring in the central channel of the HIV-1 CA hexamer that makes up the viral capsid. These studies reveal the molecular details of PQBP1's primary interaction with the HIV-1 capsid and suggest that additional elements are likely to contribute to stable capsid binding.
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Affiliation(s)
- Juliana Piacentini
- University of Virginia, Department of Molecular Physiology & Biological Physics, Charlottesville, VA, USA
| | - Dale S Allen
- The Scripps Research Institute, Department of Immunology and Microbiology, La Jolla, CA, USA
| | - Barbie K Ganser-Pornillos
- University of Virginia, Department of Molecular Physiology & Biological Physics, Charlottesville, VA, USA; University of Utah, Department of Biochemistry, Salt Lake City, UT, USA
| | - Sumit K Chanda
- The Scripps Research Institute, Department of Immunology and Microbiology, La Jolla, CA, USA
| | - Sunnie M Yoh
- The Scripps Research Institute, Department of Immunology and Microbiology, La Jolla, CA, USA.
| | - Owen Pornillos
- University of Virginia, Department of Molecular Physiology & Biological Physics, Charlottesville, VA, USA; University of Utah, Department of Biochemistry, Salt Lake City, UT, USA.
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11
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Sha H, Zhu F. Hexagonal Lattices of HIV Capsid Proteins Explored by Simulations Based on a Thermodynamically Consistent Model. J Phys Chem B 2024; 128:960-972. [PMID: 38251836 DOI: 10.1021/acs.jpcb.3c06881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
HIV capsid proteins (CAs) may self-assemble into a variety of shapes under in vivo and in vitro conditions. Here, we employed simulations based on a residue-level coarse-grained (CG) model with full conformational flexibility to investigate hexagonal lattices, which are the underlying structural pattern for CA aggregations. Facilitated by enhanced sampling simulations to rigorously calculate CA dimerization and polymerization affinities, we calibrated our model to reproduce the experimentally measured affinities. Using the calibrated model, we performed unbiased simulations on several large systems consisting of 1512 CA subunits, allowing reversible binding and unbinding of the CAs in a thermodynamically consistent manner. In one simulation, a preassembled hexagonal CA sheet developed spontaneous curvatures reminiscent of those observed in experiments, and the edges of the sheet exhibited local curvatures larger than those of the interior. In other simulations starting with randomly distributed CAs at different concentrations, existing CA assemblies grew by binding free capsomeres to the edges and by merging with other assemblies. At high CA concentrations, rapid establishment of predominant aggregates was followed by much slower adjustments toward more regular hexagonal lattices, with increasing numbers of intact CA hexamers and pentamers being formed. Our approach of adapting a general CG model to specific systems by using experimental binding data represents a practical and effective strategy for simulating and elucidating intricate protein aggregations.
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Affiliation(s)
- Hao Sha
- Department of Physics, Indiana University─Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Fangqiang Zhu
- Department of Physics, Indiana University─Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
- Biochemical and Biophysical Systems Group, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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12
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Jang S, Engelman AN. Capsid-host interactions for HIV-1 ingress. Microbiol Mol Biol Rev 2023; 87:e0004822. [PMID: 37750702 PMCID: PMC10732038 DOI: 10.1128/mmbr.00048-22] [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: 09/27/2023] Open
Abstract
The HIV-1 capsid, composed of approximately 1,200 copies of the capsid protein, encases genomic RNA alongside viral nucleocapsid, reverse transcriptase, and integrase proteins. After cell entry, the capsid interacts with a myriad of host factors to traverse the cell cytoplasm, pass through the nuclear pore complex (NPC), and then traffic to chromosomal sites for viral DNA integration. Integration may very well require the dissolution of the capsid, but where and when this uncoating event occurs remains hotly debated. Based on size constraints, a long-prevailing view was that uncoating preceded nuclear transport, but recent research has indicated that the capsid may remain largely intact during nuclear import, with perhaps some structural remodeling required for NPC traversal. Completion of reverse transcription in the nucleus may further aid capsid uncoating. One canonical type of host factor, typified by CPSF6, leverages a Phe-Gly (FG) motif to bind capsid. Recent research has shown these peptides reside amid prion-like domains (PrLDs), which are stretches of protein sequence devoid of charged residues. Intermolecular PrLD interactions along the exterior of the capsid shell impart avid host factor binding for productive HIV-1 infection. Herein we overview capsid-host interactions implicated in HIV-1 ingress and discuss important research questions moving forward. Highlighting clinical relevance, the long-acting ultrapotent inhibitor lenacapavir, which engages the same capsid binding pocket as FG host factors, was recently approved to treat people living with HIV.
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Affiliation(s)
- Sooin Jang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - 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
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13
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Azemin WA, Ishak NF, Saedin MAA, Shamsir MS, Razali SA. Molecular docking and simulation studies of Chloroquine, Rimantadine and CAP-1 as potential repurposed antivirals for decapod iridescent virus 1 (DIV1). FISH AND SHELLFISH IMMUNOLOGY REPORTS 2023; 5:100120. [PMID: 37854946 PMCID: PMC10579962 DOI: 10.1016/j.fsirep.2023.100120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023] Open
Abstract
Drug repurposing is a methodology of identifying new therapeutic use for existing drugs. It is a highly efficient, time and cost-saving strategy that offers an alternative approach to the traditional drug discovery process. Past in-silico studies involving molecular docking have been successful in identifying potential repurposed drugs for the various treatment of diseases including aquaculture diseases. The emerging shrimp hemocyte iridescent virus (SHIV) or Decapod iridescent virus 1 (DIV1) is a viral pathogen that causes severe disease and high mortality (80 %) in farmed shrimps caused serious economic losses and presents a new threat to the shrimp farming industry. Therefore, effective antiviral drugs are critically needed to control DIV1 infections. The aim of this study is to investigate the interaction of potential existing antiviral drugs, Chloroquine, Rimantadine, and CAP-1 with DIV1 major capsid protein (MCP) with the intention of exploring the potential of drug repurposing. The interaction of the DIV1 MCP and three antivirals were characterised and analysed using molecular docking and molecular dynamics simulation. The results showed that CAP-1 is a more promising candidate against DIV1 with the lowest binding energy of -8.46 kcal/mol and is more stable compared to others. We speculate that CAP-1 binding may induce the conformational changes in the DIV1 MCP structure by phosphorylating multiple residues (His123, Tyr162, and Thr395) and ultimately block the viral assembly and maturation of DIV1 MCP. To the best of our knowledge, this is the first report regarding the structural characterisation of DIV1 MCP docked with repurposing drugs.
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Affiliation(s)
- Wan-Atirah Azemin
- School of Biological Sciences, Universiti Sains Malaysia, Pulau, Minden, Pinang 11800, Malaysia
| | - Nur Farahin Ishak
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Nerus, Kuala, Terengganu 21030, Malaysia
| | - Mohamad Amirul Asyraf Saedin
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Nerus, Kuala, Terengganu 21030, Malaysia
| | - Mohd Shahir Shamsir
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, UTM, Johor Bahru 81310, Malaysia
| | - Siti Aisyah Razali
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Nerus, Kuala, Terengganu 21030, Malaysia
- Biological Security and Sustainability Research Interest Group (BIOSES), Universiti Malaysia Terengganu, Nerus, Kuala, Terengganu 21030, Malaysia
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14
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Gruenke PR, Mayer MD, Aneja R, Song Z, Burke DH, Heng X, Lange MJ. Differentiation SELEX approach identifies RNA aptamers with different specificities for HIV-1 capsid assembly forms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571135. [PMID: 38168417 PMCID: PMC10760009 DOI: 10.1101/2023.12.11.571135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The HIV-1 capsid protein (CA) assumes distinct assembly forms during replication, each presenting unique, solvent-accessible surfaces that facilitate multifaceted functions and host factor interactions. However, contributions of individual CA assemblies remain unclear, as the evaluation of CA in cells presents several technical challenges. To address this need, we sought to identify CA assembly form-specific aptamers. Aptamer subsets with different specificities emerged from within a highly converged, pre-enriched aptamer library previously selected to bind the CA hexamer lattice. Subsets were either highly specific for CA lattice or bound both CA lattice and CA hexamer. We further evaluated four representatives to reveal aptamer structural features required for binding, highlighting interesting features and challenges in aptamer structure determination. Importantly, our aptamers bind biologically relevant forms of CA and we demonstrate aptamer-mediated affinity purification of CA from cell lysates without virus or host modification. Thus, we have identified CA assembly form-specific aptamers that represent exciting new tools for the study of CA.
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15
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Badieyan S, Lichon D, Andreas MP, Gillies JP, Peng W, Shi J, DeSantis ME, Aiken CR, Böcking T, Giessen TW, Campbell EM, Cianfrocco MA. HIV-1 binds dynein directly to hijack microtubule transport machinery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555335. [PMID: 37693451 PMCID: PMC10491134 DOI: 10.1101/2023.08.29.555335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Viruses exploit host cytoskeletal elements and motor proteins for trafficking through the dense cytoplasm. Yet the molecular mechanism that describes how viruses connect to the motor machinery is unknown. Here, we demonstrate the first example of viral microtubule trafficking from purified components: HIV-1 hijacking microtubule transport machinery. We discover that HIV-1 directly binds to the retrograde microtubule-associated motor, dynein, and not via a cargo adaptor, as previously suggested. Moreover, we show that HIV-1 motility is supported by multiple, diverse dynein cargo adaptors as HIV-1 binds to dynein light and intermediate chains on dynein's tail. Further, we demonstrate that multiple dynein motors tethered to rigid cargoes, like HIV-1 capsids, display reduced motility, distinct from the behavior of multiple motors on membranous cargoes. Our results introduce a new model of viral trafficking wherein a pathogen opportunistically 'hijacks' the microtubule transport machinery for motility, enabling multiple transport pathways through the host cytoplasm.
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Affiliation(s)
| | - Drew Lichon
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, IL, USA
| | - Michael P Andreas
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - John P Gillies
- Department of Molecular, Cellular, and Developmental Biology, College of Literature, Sciences, and the Arts, University of Michigan, Ann Arbor, MI USA
| | - Wang Peng
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Jiong Shi
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Morgan E DeSantis
- Department of Molecular, Cellular, and Developmental Biology, College of Literature, Sciences, and the Arts, University of Michigan, Ann Arbor, MI USA
| | - Christopher R Aiken
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Till Böcking
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Tobias W Giessen
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Edward M Campbell
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, IL, USA
| | - Michael A Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
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16
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Gao X, McFadden WM, Wen X, Emanuelli A, Lorson ZC, Zheng H, Kirby KA, Sarafianos SG. Use of TSAR, Thermal Shift Analysis in R, to identify Folic Acid as a Molecule that Interacts with HIV-1 Capsid. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569293. [PMID: 38076946 PMCID: PMC10705415 DOI: 10.1101/2023.11.29.569293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Thermal shift assay (TSA) is a versatile biophysical technique for studying protein interactions. Here, we report a free, open-source software tool TSAR (Thermal Shift Analysis in R) to expedite and automate the analysis of thermal shift data derived either from individual experiments or large screens of chemical libraries. The TSAR package incorporates multiple, dynamic workflows to facilitate the analysis of TSA data and returns publication-ready graphics or processed results. Further, the package includes a graphic user interface (GUI) that enables easy use by non-programmers, aiming to simplify TSA analysis while diversifying visualization. To exemplify the utility of TSAR we screened a chemical library of vitamins to identify molecules that interact with the capsid protein (CA) of human immunodeficiency virus type 1 (HIV-1). Our data show that hexameric CA interacts with folic acid in vitro.
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Affiliation(s)
- X. Gao
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Children’s Healthcare of Atlanta, Atlanta, GA
| | - W. M. McFadden
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Children’s Healthcare of Atlanta, Atlanta, GA
| | - X. Wen
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Children’s Healthcare of Atlanta, Atlanta, GA
| | - A. Emanuelli
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Children’s Healthcare of Atlanta, Atlanta, GA
| | - Z. C. Lorson
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Children’s Healthcare of Atlanta, Atlanta, GA
| | - H. Zheng
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Children’s Healthcare of Atlanta, Atlanta, GA
| | - K. A. Kirby
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Children’s Healthcare of Atlanta, Atlanta, GA
| | - S. G. Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Children’s Healthcare of Atlanta, Atlanta, GA
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17
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Layish B, Goli R, Flick H, Huang SW, Zhang RZ, Kvaratskhelia M, Kane M. Virus specificity and nucleoporin requirements for MX2 activity are affected by GTPase function and capsid-CypA interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567336. [PMID: 38014352 PMCID: PMC10680775 DOI: 10.1101/2023.11.16.567336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Human myxovirus resistance 2 (MX2/MXB) is an interferon-induced GTPase that inhibits human immunodeficiency virus-1 (HIV-1) infection by preventing nuclear import of the viral preintegration complex. The HIV-1 capsid (CA) is the major viral determinant for sensitivity to MX2, and complex interactions between MX2, CA, nucleoporins (Nups), cyclophilin A (CypA), and other cellular proteins influence the outcome of viral infection. To explore the interactions between MX2, the viral CA, and CypA, we utilized a CRISPR-Cas9/AAV approach to generate CypA knock-out cell lines as well as cells that express CypA from its endogenous locus, but with specific point mutations that would abrogate CA binding but should not affect enzymatic activity or cellular function. We found that infection of CypA knock-out and point mutant cell lines with wild-type HIV-1 and CA mutants recapitulated the phenotypes observed upon cyclosporine A (CsA) addition, indicating that effects of CsA treatment are the direct result of blocking CA-CypA interactions and are therefore independent from potential interactions between CypA and MX2 or other cellular proteins. Notably, abrogation of GTP hydrolysis by MX2 conferred enhanced antiviral activity when CA-CypA interactions were abolished, and this effect was not mediated by the CA-binding residues in the GTPase domain, or by phosphorylation of MX2 at position T151. We additionally found that elimination of GTPase activity also altered the Nup requirements for MX2 activity. Our data demonstrate that the antiviral activity of MX2 is affected by CypA-CA interactions in a virus-specific and GTPase activity-dependent manner. These findings further highlight the importance of the GTPase domain of MX2 in regulation of substrate specificity and interaction with nucleocytoplasmic trafficking pathways.
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Affiliation(s)
- Bailey Layish
- Department of Pediatrics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Ram Goli
- Department of Pediatrics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Haley Flick
- Department of Pediatrics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Szu-Wei Huang
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Robert Z Zhang
- Department of Pediatrics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Melissa Kane
- Department of Pediatrics, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
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18
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Zhang DW, Xu XS, Zhou R, Fu Z. Modulation of HIV-1 capsid multimerization by sennoside A and sennoside B via interaction with the NTD/CTD interface in capsid hexamer. Front Microbiol 2023; 14:1270258. [PMID: 37817748 PMCID: PMC10561090 DOI: 10.3389/fmicb.2023.1270258] [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: 07/31/2023] [Accepted: 09/11/2023] [Indexed: 10/12/2023] Open
Abstract
Small molecules that bind to the pocket targeted by a peptide, termed capsid assembly inhibitor (CAI), have shown antiviral effects with unique mechanisms of action. We report the discovery of two natural compounds, sennoside A (SA) and sennoside B (SB), derived from medicinal plants that bind to this pocket in the C-terminal domain of capsid (CA CTD). Both SA and SB were identified via a drug-screening campaign that utilized a time-resolved fluorescence resonance energy transfer assay. They inhibited the HIV-1 CA CTD/CAI interaction at sub-micromolar concentrations of 0.18 μM and 0.08 μM, respectively. Mutation of key residues (including Tyr 169, Leu 211, Asn 183, and Glu 187) in the CA CTD decreased their binding affinity to the CA monomer, from 1.35-fold to 4.17-fold. Furthermore, both compounds induced CA assembly in vitro and bound directly to the CA hexamer, suggesting that they interact with CA beyond the CA CTD. Molecular docking showed that both compounds were bound to the N-terminal domain (NTD)/CTD interface between adjacent protomers within the CA hexamer. SA established a hydrogen-bonding network with residues N57, V59, Q63, K70, and N74 of CA1-NTD and Q179 of CA2-CTD. SB formed hydrogen bonds with the N53, N70, and N74 residues of CA1-NTD, and the A177and Q179 residues of CA2-CTD. Both compounds, acting as glue, can bring αH4 in the NTD and αH9 in the CTD of the NTD/CTD interface close to each other. Collectively, our research indicates that SA and SB, which enhance CA assembly, could serve as novel chemical tools to identify agents that modulate HIV-1 CA assembly. These natural compounds may potentially lead to the development of new antiviral therapies with unique mechanisms of action.
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Affiliation(s)
- Da-Wei Zhang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Xiao-Shuang Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Rui Zhou
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiguo Fu
- Department of Orthopedics, Changzhou Hospital of Traditional Chinese Medicine, Changzhou, China
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19
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Gres AT, Kirby KA, McFadden WM, Du H, Liu D, Xu C, Bryer AJ, Perilla JR, Shi J, Aiken C, Fu X, Zhang P, Francis AC, Melikyan GB, Sarafianos SG. Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization. Nat Commun 2023; 14:5614. [PMID: 37699872 PMCID: PMC10497533 DOI: 10.1038/s41467-023-41197-7] [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: 11/25/2020] [Accepted: 08/25/2023] [Indexed: 09/14/2023] Open
Abstract
HIV-1 capsid (CA) stability is important for viral replication. E45A and P38A mutations enhance and reduce core stability, thus impairing infectivity. Second-site mutations R132T and T216I rescue infectivity. Capsid lattice stability was studied by solving seven crystal structures (in native background), including P38A, P38A/T216I, E45A, E45A/R132T CA, using molecular dynamics simulations of lattices, cryo-electron microscopy of assemblies, time-resolved imaging of uncoating, biophysical and biochemical characterization of assembly and stability. We report pronounced and subtle, short- and long-range rearrangements: (1) A38 destabilized hexamers by loosening interactions between flanking CA protomers in P38A but not P38A/T216I structures. (2) Two E45A structures showed unexpected stabilizing CANTD-CANTD inter-hexamer interactions, variable R18-ring pore sizes, and flipped N-terminal β-hairpin. (3) Altered conformations of E45Aa α9-helices compared to WT, E45A/R132T, WTPF74, WTNup153, and WTCPSF6 decreased PF74, CPSF6, and Nup153 binding, and was reversed in E45A/R132T. (4) An environmentally sensitive electrostatic repulsion between E45 and D51 affected lattice stability, flexibility, ion and water permeabilities, electrostatics, and recognition of host factors.
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Affiliation(s)
- Anna T Gres
- C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Karen A Kirby
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - William M McFadden
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Haijuan Du
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Dandan Liu
- C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO, USA
| | - Chaoyi Xu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Alexander J Bryer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
- Department of Physics & Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jiong Shi
- Department of Pathology, Immunology & Microbiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christopher Aiken
- Department of Pathology, Immunology & Microbiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiaofeng Fu
- Department of Structural Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Peijun Zhang
- Department of Structural Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, UK
- Electron Bio-Imaging Centre, Diamond Light Sources, Harwell Science and Innovation Campus, Didcot, UK
| | - Ashwanth C Francis
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | - Gregory B Melikyan
- Children's Healthcare of Atlanta, Atlanta, GA, USA
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | - Stefan G Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
- Children's Healthcare of Atlanta, Atlanta, GA, USA.
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO, USA.
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20
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Huang Y, Zhang Y, Ni T. Towards in situ high-resolution imaging of viruses and macromolecular complexes using cryo-electron tomography. J Struct Biol 2023; 215:108000. [PMID: 37467823 DOI: 10.1016/j.jsb.2023.108000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/15/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
Cryo-electron tomography and subtomogram averaging are rising and fast-evolving imaging techniques to study biological events, providing structural information at an unprecedented resolution while preserving spatial correlation in their native contexts. The latest technology and methodology development ranging from sample preparation to data collection and data processing, has enabled significant advancement in its applications to various biological systems. This review provides an overview of the current technology development enabling high-resolution structural study in situ, highlighting the use of a priori information of biological samples to assess the quality of subtomogram averaging pipeline. We exemplify the applications of this technique to understanding viruses and principles of macromolecule assembly using different biological systems, ranging from in vitro to in situ samples, which provide structural information at different resolutions and contexts.
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Affiliation(s)
- Yixin Huang
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Yu Zhang
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Tao Ni
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region.
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21
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Highland CM, Tan A, Ricaña CL, Briggs JAG, Dick RA. Structural insights into HIV-1 polyanion-dependent capsid lattice formation revealed by single particle cryo-EM. Proc Natl Acad Sci U S A 2023; 120:e2220545120. [PMID: 37094124 PMCID: PMC10160977 DOI: 10.1073/pnas.2220545120] [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: 12/02/2022] [Accepted: 03/12/2023] [Indexed: 04/26/2023] Open
Abstract
The HIV-1 capsid houses the viral genome and interacts extensively with host cell proteins throughout the viral life cycle. It is composed of capsid protein (CA), which assembles into a conical fullerene lattice composed of roughly 200 CA hexamers and 12 CA pentamers. Previous structural analyses of individual CA hexamers and pentamers have provided valuable insight into capsid structure and function, but detailed structural information about these assemblies in the broader context of the capsid lattice is lacking. In this study, we combined cryoelectron tomography and single particle analysis (SPA) cryoelectron microscopy to determine structures of continuous regions of the capsid lattice containing both hexamers and pentamers. We also developed a method of liposome scaffold-based in vitro lattice assembly ("lattice templating") that enabled us to directly study the lattice under a wider range of conditions than has previously been possible. Using this approach, we identified a critical role for inositol hexakisphosphate in pentamer formation and determined the structure of the CA lattice bound to the capsid-targeting antiretroviral drug GS-6207 (lenacapavir). Our work reveals key structural details of the mature HIV-1 CA lattice and establishes the combination of lattice templating and SPA as a robust strategy for studying retroviral capsid structure and capsid interactions with host proteins and antiviral compounds.
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Affiliation(s)
- Carolyn M. Highland
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY14853
| | - Aaron Tan
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, CambridgeCB2 0QH, UK
| | - Clifton L. Ricaña
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
| | - John A. G. Briggs
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, CambridgeCB2 0QH, UK
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Munich82512, Germany
| | - Robert A. Dick
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
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22
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Tao K, Rhee SY, Tzou PL, Osman ZA, Pond SLK, Holmes SP, Shafer RW. HIV-1 Group M Capsid Amino Acid Variability: Implications for Sequence Quality Control of Genotypic Resistance Testing. Viruses 2023; 15:992. [PMID: 37112972 PMCID: PMC10143361 DOI: 10.3390/v15040992] [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: 03/22/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND With the approval of the HIV-1 capsid inhibitor, lenacapavir, capsid sequencing will be required for managing lenacapavir-experienced individuals with detectable viremia. Successful sequence interpretation will require examining new capsid sequences in the context of previously published sequence data. METHODS We analyzed published HIV-1 group M capsid sequences from 21,012 capsid-inhibitor naïve individuals to characterize amino acid variability at each position and influence of subtype and cytotoxic T lymphocyte (CTL) selection pressure. We determined the distributions of usual mutations, defined as amino acid differences from the group M consensus, with a prevalence ≥ 0.1%. Co-evolving mutations were identified using a phylogenetically-informed Bayesian graphical model method. RESULTS 162 (70.1%) positions had no usual mutations (45.9%) or only conservative usual mutations with a positive BLOSUM62 score (24.2%). Variability correlated independently with subtype-specific amino acid occurrence (Spearman rho = 0.83; p < 1 × 10-9) and the number of times positions were reported to contain an HLA-associated polymorphism, an indicator of CTL pressure (rho = 0.43; p = 0.0002). CONCLUSIONS Knowing the distribution of usual capsid mutations is essential for sequence quality control. Comparing capsid sequences from lenacapavir-treated and lenacapavir-naïve individuals will enable the identification of additional mutations potentially associated with lenacapavir therapy.
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Affiliation(s)
- Kaiming Tao
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Philip L. Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Zachary A. Osman
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | | | - Susan P. Holmes
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
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23
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Zhao S, Zhang X, da Silva-Júnior EF, Zhan P, Liu X. Computer-aided drug design in seeking viral capsid modulators. Drug Discov Today 2023; 28:103581. [PMID: 37030533 DOI: 10.1016/j.drudis.2023.103581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/16/2023] [Accepted: 03/30/2023] [Indexed: 04/09/2023]
Abstract
Approved or licensed antiviral drugs have limited applications because of their drug resistance and severe adverse effects. By contrast, by stabilizing or destroying the viral capsid, compounds known as capsid modulators prevent viral replication by acting on new targets and, therefore, overcoming the problem of clinical drug resistance. For example. computer-aided drug design (CADD) methods, using strategies based on structures of biological targets (structure-based drug design; SBDD), such as docking, molecular dynamics (MD) simulations, and virtual screening (VS), have provided opportunities for fast and effective development of viral capsid modulators. In this review, we summarize the application of CADD in the discovery, optimization, and mechanism prediction of capsid-targeting small molecules, providing new insights into antiviral drug discovery modalities. Teaser: Computer-aided drug design will accelerate the development of viral capsid regulators, which brings new hope for the treatment of refractory viral diseases.
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Affiliation(s)
- Shujie Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xujie Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Edeildo Ferreira da Silva-Júnior
- Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, 57072-970 Maceió, Alagoas, Brazil.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
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24
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Schirra RT, Dos Santos NFB, Zadrozny KK, Kucharska I, Ganser-Pornillos BK, Pornillos O. A molecular switch modulates assembly and host factor binding of the HIV-1 capsid. Nat Struct Mol Biol 2023; 30:383-390. [PMID: 36759579 PMCID: PMC10023569 DOI: 10.1038/s41594-022-00913-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 12/20/2022] [Indexed: 02/11/2023]
Abstract
The HIV-1 capsid is a fullerene cone made of quasi-equivalent hexamers and pentamers of the viral CA protein. Typically, quasi-equivalent assembly of viral capsid subunits is controlled by a molecular switch. Here, we identify a Thr-Val-Gly-Gly motif that modulates CA hexamer/pentamer switching by folding into a 310 helix in the pentamer and random coil in the hexamer. Manipulating the coil/helix configuration of the motif allowed us to control pentamer and hexamer formation in a predictable manner, thus proving its function as a molecular switch. Importantly, the switch also remodels the common binding site for host factors that are critical for viral replication and the new ultra-potent HIV-1 inhibitor lenacapavir. This study reveals that a critical assembly element also modulates the post-assembly and viral replication functions of the HIV-1 capsid and provides new insights on capsid function and inhibition.
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Affiliation(s)
- Randall T Schirra
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Nayara F B Dos Santos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Kaneil K Zadrozny
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Iga Kucharska
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
- The Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Barbie K Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
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25
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Gillis EP, Parcella K, Bowsher M, Cook JH, Iwuagwu C, Naidu BN, Patel M, Peese K, Huang H, Valera L, Wang C, Kieltyka K, Parker DD, Simmermacher J, Arnoult E, Nolte RT, Wang L, Bender JA, Frennesson DB, Saulnier M, Wang AX, Meanwell NA, Belema M, Hanumegowda U, Jenkins S, Krystal M, Kadow JF, Cockett M, Fridell R. Potent Long-Acting Inhibitors Targeting the HIV-1 Capsid Based on a Versatile Quinazolin-4-one Scaffold. J Med Chem 2023; 66:1941-1954. [PMID: 36719971 DOI: 10.1021/acs.jmedchem.2c01732] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Long-acting (LA) human immunodeficiency virus-1 (HIV-1) antiretroviral therapy characterized by a ≥1 month dosing interval offers significant advantages over daily oral therapy. However, the criteria for compounds that enter clinical development are high. Exceptional potency and low plasma clearance are required to meet dose size requirements; excellent chemical stability and/or crystalline form stability is required to meet formulation requirements, and new antivirals in HIV-1 therapy need to be largely free of side effects and drug-drug interactions. In view of these challenges, the discovery that capsid inhibitors comprising a quinazolinone core tolerate a wide range of structural modifications while maintaining picomolar potency against HIV-1 infection in vitro, are assembled efficiently in a multi-component reaction, and can be isolated in a stereochemically pure form is reported herein. The detailed characterization of a prototypical compound, GSK878, is presented, including an X-ray co-crystal structure and subcutaneous and intramuscular pharmacokinetic data in rats and dogs.
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Affiliation(s)
- Eric P Gillis
- Discovery Chemistry, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Kyle Parcella
- Discovery Chemistry, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Michael Bowsher
- Discovery Chemistry, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - James H Cook
- Discovery Chemistry, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Christiana Iwuagwu
- Discovery Chemistry, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - B Narasimhulu Naidu
- Discovery Chemistry, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Manoj Patel
- Discovery Chemistry, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Kevin Peese
- Discovery Chemistry, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Haichang Huang
- Discovery Biology, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Lourdes Valera
- Discovery Biology, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Chunfu Wang
- Discovery Biology, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Kasia Kieltyka
- Discovery Pharmaceutics, DMPK and Toxicology, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Dawn D Parker
- Discovery Pharmaceutics, DMPK and Toxicology, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Jean Simmermacher
- Discovery Pharmaceutics, DMPK and Toxicology, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Eric Arnoult
- Molecular Design, GSK, Collegeville, Pennsylvania 19426, United States
| | - Robert T Nolte
- Protein Cellular and Structural Sciences, GSK, Collegeville, Pennsylvania 19426, United States
| | - Liping Wang
- Protein Cellular and Structural Sciences, GSK, Collegeville, Pennsylvania 19426, United States
| | - John A Bender
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey 08543, United States
| | - David B Frennesson
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Cambridge, Massachusetts 02142, United States
| | - Mark Saulnier
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey 08543, United States
| | - Alan Xiangdong Wang
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey 08543, United States
| | - Nicholas A Meanwell
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey 08543, United States
| | - Makonen Belema
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey 08543, United States
| | - Umesh Hanumegowda
- Discovery Pharmaceutics, DMPK and Toxicology, ViiV Healthcare, Branford, Connecticut 06405, United States.,ViiV Discovery, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Susan Jenkins
- Discovery Pharmaceutics, DMPK and Toxicology, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Mark Krystal
- Discovery Biology, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - John F Kadow
- Discovery Chemistry, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Mark Cockett
- ViiV Discovery, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Robert Fridell
- Discovery Biology, ViiV Healthcare, Branford, Connecticut 06405, United States
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26
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Lei X, Gonçalves-Carneiro D, Zang TM, Bieniasz PD. Initiation of HIV-1 Gag lattice assembly is required for recognition of the viral genome packaging signal. eLife 2023; 12:e83548. [PMID: 36688533 PMCID: PMC9908077 DOI: 10.7554/elife.83548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
The encapsidation of HIV-1 gRNA into virions is enabled by the binding of the nucleocapsid (NC) domain of the HIV-1 Gag polyprotein to the structured viral RNA packaging signal (Ψ) at the 5' end of the viral genome. However, the subcellular location and oligomeric status of Gag during the initial Gag-Ψ encounter remain uncertain. Domains other than NC, such as capsid (CA), may therefore indirectly affect RNA recognition. To investigate the contribution of Gag domains to Ψ recognition in a cellular environment, we performed protein-protein crosslinking and protein-RNA crosslinking immunoprecipitation coupled with sequencing (CLIP-seq) experiments. We demonstrate that NC alone does not bind specifically to Ψ in living cells, whereas full-length Gag and a CANC subdomain bind to Ψ with high specificity. Perturbation of the Ψ RNA structure or NC zinc fingers affected CANC:Ψ binding specificity. Notably, CANC variants with substitutions that disrupt CA:CA dimer, trimer, or hexamer interfaces in the immature Gag lattice also affected RNA binding, and mutants that were unable to assemble a nascent Gag lattice were unable to specifically bind to Ψ. Artificially multimerized NC domains did not specifically bind Ψ. CA variants with substitutions in inositol phosphate coordinating residues that prevent CA hexamerization were also deficient in Ψ binding and second-site revertant mutants that restored CA assembly also restored specific binding to Ψ. Overall, these data indicate that the correct assembly of a nascent immature CA lattice is required for the specific interaction between Gag and Ψ in cells.
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Affiliation(s)
- Xiao Lei
- Laboratory of Retrovirology, Rockefeller UniversityNew YorkUnited States
| | | | - Trinity M Zang
- Laboratory of Retrovirology, Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical Institute, The Rockefeller UniversityNew York, New YorkUnited States
| | - Paul D Bieniasz
- Laboratory of Retrovirology, Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical Institute, The Rockefeller UniversityNew York, New YorkUnited States
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27
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Kobayakawa T, Yokoyama M, Tsuji K, Fujino M, Kurakami M, Onishi T, Boku S, Ishii T, Miura Y, Shinohara K, Kishihara Y, Ohashi N, Kotani O, Murakami T, Sato H, Tamamura H. Low-molecular-weight anti-HIV-1 agents targeting HIV-1 capsid proteins. RSC Adv 2023; 13:2156-2167. [PMID: 36712613 PMCID: PMC9834766 DOI: 10.1039/d2ra06837k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 01/02/2023] [Indexed: 01/15/2023] Open
Abstract
The HIV-1 capsid is a shell that encapsulates viral RNA, and forms a conical structure by assembling oligomers of capsid (CA) proteins. Since the CA proteins are highly conserved among many strains of HIV-1, the inhibition of the CA function could be an appropriate goal for suppression of HIV-1 replication, but to date, no drug targeting CA has been developed. Hydrophobic interactions between two CA molecules through Trp184 and Met185 in the protein are known to be indispensable for conformational stabilization of the CA multimer. In our previous study, a small molecule designed by in silico screening as a dipeptide mimic of Trp184 and Met185 in the interaction site was synthesized and found to have significant anti-HIV-1 activity. In the present study, molecules with different scaffolds based on a dipeptide mimic of Trp184 and Met185 have been designed and synthesized. Their significant anti-HIV activity and their advantages compared to the previous compounds were examined. The present results should be useful in the design of novel CA-targeting anti-HIV agents.
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Affiliation(s)
- Takuya Kobayakawa
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU)2-3-10 Kandasurugadai, Chiyoda-kuTokyo 101-0062Japan
| | - Masaru Yokoyama
- Pathogen Genomics Center, National Institute of Infectious DiseasesMusashimurayama 208-0011TokyoJapan
| | - Kohei Tsuji
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU)2-3-10 Kandasurugadai, Chiyoda-kuTokyo 101-0062Japan
| | - Masayuki Fujino
- AIDS Research Center, National Institute of Infectious DiseasesShinjuku-kuTokyo 162-8640Japan
| | - Masaki Kurakami
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU)2-3-10 Kandasurugadai, Chiyoda-kuTokyo 101-0062Japan
| | - Takato Onishi
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU)2-3-10 Kandasurugadai, Chiyoda-kuTokyo 101-0062Japan
| | - Sayaka Boku
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU)2-3-10 Kandasurugadai, Chiyoda-kuTokyo 101-0062Japan
| | - Takahiro Ishii
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU)2-3-10 Kandasurugadai, Chiyoda-kuTokyo 101-0062Japan
| | - Yutaro Miura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU)2-3-10 Kandasurugadai, Chiyoda-kuTokyo 101-0062Japan
| | - Kouki Shinohara
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU)2-3-10 Kandasurugadai, Chiyoda-kuTokyo 101-0062Japan
| | - Yuki Kishihara
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU)2-3-10 Kandasurugadai, Chiyoda-kuTokyo 101-0062Japan
| | - Nami Ohashi
- Showa Pharmaceutical UniversityMachida 194-8543TokyoJapan
| | - Osamu Kotani
- Pathogen Genomics Center, National Institute of Infectious DiseasesMusashimurayama 208-0011TokyoJapan
| | - Tsutomu Murakami
- AIDS Research Center, National Institute of Infectious DiseasesShinjuku-kuTokyo 162-8640Japan
| | - Hironori Sato
- Pathogen Genomics Center, National Institute of Infectious DiseasesMusashimurayama 208-0011TokyoJapan
| | - Hirokazu Tamamura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU)2-3-10 Kandasurugadai, Chiyoda-kuTokyo 101-0062Japan
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28
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Gupta M, Pak AJ, Voth GA. Critical mechanistic features of HIV-1 viral capsid assembly. SCIENCE ADVANCES 2023; 9:eadd7434. [PMID: 36608139 PMCID: PMC9821859 DOI: 10.1126/sciadv.add7434 10.1126/sciadv.add7434] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/08/2022] [Indexed: 11/04/2023]
Abstract
The maturation of HIV-1 capsid protein (CA) into a cone-shaped lattice capsid is critical for viral infectivity. CA can self-assemble into a range of capsid morphologies made of ~175 to 250 hexamers and 12 pentamers. The cellular polyanion inositol hexakisphosphate (IP6) has recently been demonstrated to facilitate conical capsid formation by coordinating a ring of arginine residues within the central cavity of capsid hexamers and pentamers. However, the kinetic interplay of events during IP6 and CA coassembly is unclear. In this work, we use coarse-grained molecular dynamics simulations to elucidate the molecular mechanism of capsid formation, including the role played by IP6. We show that IP6, in small quantities at first, promotes curvature generation by trapping pentameric defects in the growing lattice and shifts assembly behavior toward kinetically favored outcomes. Our analysis also suggests that IP6 can stabilize metastable capsid intermediates and can induce structural pleomorphism in mature capsids.
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Affiliation(s)
- Manish Gupta
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
| | | | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
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29
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Gupta M, Pak AJ, Voth GA. Critical mechanistic features of HIV-1 viral capsid assembly. SCIENCE ADVANCES 2023; 9:eadd7434. [PMID: 36608139 PMCID: PMC9821859 DOI: 10.1126/sciadv.add7434+10.1126/sciadv.add7434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/08/2022] [Indexed: 01/21/2024]
Abstract
The maturation of HIV-1 capsid protein (CA) into a cone-shaped lattice capsid is critical for viral infectivity. CA can self-assemble into a range of capsid morphologies made of ~175 to 250 hexamers and 12 pentamers. The cellular polyanion inositol hexakisphosphate (IP6) has recently been demonstrated to facilitate conical capsid formation by coordinating a ring of arginine residues within the central cavity of capsid hexamers and pentamers. However, the kinetic interplay of events during IP6 and CA coassembly is unclear. In this work, we use coarse-grained molecular dynamics simulations to elucidate the molecular mechanism of capsid formation, including the role played by IP6. We show that IP6, in small quantities at first, promotes curvature generation by trapping pentameric defects in the growing lattice and shifts assembly behavior toward kinetically favored outcomes. Our analysis also suggests that IP6 can stabilize metastable capsid intermediates and can induce structural pleomorphism in mature capsids.
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Affiliation(s)
- Manish Gupta
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
| | | | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
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30
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Gupta M, Pak AJ, Voth GA. Critical mechanistic features of HIV-1 viral capsid assembly. SCIENCE ADVANCES 2023; 9:eadd7434. [PMID: 36608139 PMCID: PMC9821859 DOI: 10.1126/sciadv.add7434] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/08/2022] [Indexed: 05/29/2023]
Abstract
The maturation of HIV-1 capsid protein (CA) into a cone-shaped lattice capsid is critical for viral infectivity. CA can self-assemble into a range of capsid morphologies made of ~175 to 250 hexamers and 12 pentamers. The cellular polyanion inositol hexakisphosphate (IP6) has recently been demonstrated to facilitate conical capsid formation by coordinating a ring of arginine residues within the central cavity of capsid hexamers and pentamers. However, the kinetic interplay of events during IP6 and CA coassembly is unclear. In this work, we use coarse-grained molecular dynamics simulations to elucidate the molecular mechanism of capsid formation, including the role played by IP6. We show that IP6, in small quantities at first, promotes curvature generation by trapping pentameric defects in the growing lattice and shifts assembly behavior toward kinetically favored outcomes. Our analysis also suggests that IP6 can stabilize metastable capsid intermediates and can induce structural pleomorphism in mature capsids.
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31
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Rochal SB, Konevtsova OV, Roshal DS, Božič A, Golushko IY, Podgornik R. Packing and trimer-to-dimer protein reconstruction in icosahedral viral shells with a single type of symmetrical structural unit. NANOSCALE ADVANCES 2022; 4:4677-4688. [PMID: 36341291 PMCID: PMC9595183 DOI: 10.1039/d2na00461e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Understanding the principles of protein packing and the mechanisms driving morphological transformations in virus shells (capsids) during their maturation can be pivotal for the development of new antiviral strategies. Here, we study how these principles and mechanisms manifest themselves in icosahedral viral capsids assembled from identical symmetric structural units (capsomeres). To rationalize such shells, we model capsomers as symmetrical groups of identical particles interacting with a short-range potential typical of the classic Tammes problem. The capsomere particles are assumed to retain their relative positions on the vertices of planar polygons placed on the spherical shell and to interact only with the particles from other capsomeres. Minimization of the interaction energy enforces equal distances between the nearest particles belonging to neighboring capsomeres and minimizes the number of different local environments. Thus, our model implements the Caspar and Klug quasi-equivalence principle and leads to packings strikingly similar to real capsids. We then study a reconstruction of protein trimers into dimers in a Flavivirus shell during its maturation, connecting the relevant structural changes with the modifications of the electrostatic charges of proteins, wrought by the oxidative switch in the bathing solution that is essential for the process. We highlight the key role of pr peptides in the shell reconstruction and show that the highly ordered arrangement of these subunits in the dimeric state is energetically favored at a low pH level. We also discuss the electrostatic mechanisms controlling the release of pr peptides in the last irreversible step of the maturation process.
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Affiliation(s)
- Sergei B Rochal
- Physics Faculty, Southern Federal University Rostov-on-Don Russia
| | | | - Daria S Roshal
- Physics Faculty, Southern Federal University Rostov-on-Don Russia
| | - Anže Božič
- Department of Theoretical Physics, Jožef Stefan Institute SI-1000 Ljubljana Slovenia
| | - Ivan Yu Golushko
- Physics Faculty, Southern Federal University Rostov-on-Don Russia
| | - Rudolf Podgornik
- Department of Theoretical Physics, Jožef Stefan Institute SI-1000 Ljubljana Slovenia
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana SI-1000 Ljubljana Slovenia
- School of Physical Sciences and Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences Beijing 100049 China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences Beijing 100190 China
- Wenzhou Institute of the University of Chinese Academy of Sciences Wenzhou Zhejiang 325000 China
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32
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Yang H, Talledge N, Arndt WG, Zhang W, Mansky LM. Human Immunodeficiency Virus Type 2 Capsid Protein Mutagenesis Reveals Amino Acid Residues Important for Virus Particle Assembly. J Mol Biol 2022; 434:167753. [PMID: 35868362 PMCID: PMC11057910 DOI: 10.1016/j.jmb.2022.167753] [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: 05/11/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 11/16/2022]
Abstract
Human immunodeficiency virus (HIV) Gag drives virus particle assembly. The capsid (CA) domain is critical for Gag multimerization mediated by protein-protein interactions. The Gag protein interaction network defines critical aspects of the retroviral lifecycle at steps such as particle assembly and maturation. Previous studies have demonstrated that the immature particle morphology of HIV-2 is intriguingly distinct relative to that of HIV-1. Based upon this observation, we sought to determine the amino acid residues important for virus assembly that might help explain the differences between HIV-1 and HIV-2. To do this, we conducted site-directed mutagenesis of targeted locations in the HIV-2 CA domain of Gag and analyzed various aspects of virus particle assembly. A panel of 31 site-directed mutants of residues that reside at the HIV-2 CA inter-hexamer interface, intra-hexamer interface and CA inter-domain linker were created and analyzed for their effects on the efficiency of particle production, particle morphology, particle infectivity, Gag subcellular distribution and in vitro protein assembly. Seven conserved residues between HIV-1 and HIV-2 (L19, A41, I152, K153, K157, N194, D196) and two non-conserved residues (G38, N127) were found to significantly impact Gag multimerization and particle assembly. Taken together, these observations complement structural analyses of immature HIV-2 particle morphology and Gag lattice organization as well as provide important comparative insights into the key amino acid residues that can help explain the observed differences between HIV immature particle morphology and its association with virus replication and particle infectivity.
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Affiliation(s)
- Huixin Yang
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Comparative Molecular Biosciences Graduate Program, University of Minnesota - Twin Cities, St. Paul, MN 55108, USA
| | - Nathaniel Talledge
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Division of Basic Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - William G Arndt
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Division of Basic Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Biochemistry, Molecular Biology & Biophysics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Wei Zhang
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Division of Basic Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Characterization Facility, College of Sciences and Engineering, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA.
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Division of Basic Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Comparative Molecular Biosciences Graduate Program, University of Minnesota - Twin Cities, St. Paul, MN 55108, USA; Biochemistry, Molecular Biology & Biophysics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA.
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Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection. Nat Commun 2022; 13:5879. [PMID: 36202818 PMCID: PMC9537594 DOI: 10.1038/s41467-022-33662-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/27/2022] [Indexed: 12/24/2022] Open
Abstract
Cellular proteins CPSF6, NUP153 and SEC24C play crucial roles in HIV-1 infection. While weak interactions of short phenylalanine-glycine (FG) containing peptides with isolated capsid hexamers have been characterized, how these cellular factors functionally engage with biologically relevant mature HIV-1 capsid lattices is unknown. Here we show that prion-like low complexity regions (LCRs) enable avid CPSF6, NUP153 and SEC24C binding to capsid lattices. Structural studies revealed that multivalent CPSF6 assembly is mediated by LCR-LCR interactions, which are templated by binding of CPSF6 FG peptides to a subset of hydrophobic capsid pockets positioned along adjoining hexamers. In infected cells, avid CPSF6 LCR-mediated binding to HIV-1 cores is essential for functional virus-host interactions. The investigational drug lenacapavir accesses unoccupied hydrophobic pockets in the complex to potently impair HIV-1 inside the nucleus without displacing the tightly bound cellular cofactor from virus cores. These results establish previously undescribed mechanisms of virus-host interactions and antiviral action.
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Abstract
Lenacapavir (LEN) is a long-acting, highly potent HIV-1 capsid (CA) inhibitor. The evolution of viral variants under the genetic pressure of LEN identified Q67H, N74D, and Q67H/N74D CA substitutions as the main resistance associated mutations (RAMs). Here, we determined high-resolution structures of CA hexamers containing these RAMs in the absence and presence of LEN. Our findings reveal that the Q67H change induces a conformational switch, which adversely affects the inhibitor binding. In the unliganded protein, the His67 side chain adopts the closed conformation by projecting into the inhibitor binding pocket and thereby creating steric hindrance with respect to LEN. Upon the inhibitor binding, the His67 side chain repositions to the open conformation that closely resembles the Gln67 side chain in the WT protein. We propose that the switch from the closed conformation to the open conformation, which is needed to accommodate LEN, accounts for the reduced inhibitor potency with respect to the Q67H CA variant. The N74D CA change results in the loss of a direct hydrogen bond and in induced electrostatic repulsions between CA and LEN. The double Q67H/N74D substitutions exhibited cumulative effects of respective single amino acid changes. An examination of LEN binding kinetics to CA hexamers revealed that Q67H and N74D CA changes adversely influenced the inhibitor binding affinity (KD) by primarily affecting the dissociation rate constant (koff). We used these structural and mechanistic findings to rationally modify LEN. The resulting analog exhibited increased potency against the Q67H/N74D viral variant. Thus, our studies provide a means for the development of second-generation inhibitors with enhanced barriers to resistance.
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Ji X, Li J, Sharma PP, Jiang X, Rathi B, Gao Z, Hu L, Kang D, De Clercq E, Cocklin S, Liu C, Pannecouque C, Dick A, Liu X, Zhan P. Design, Synthesis and Structure-Activity Relationships of Phenylalanine-Containing Peptidomimetics as Novel HIV-1 Capsid Binders Based on Ugi Four-Component Reaction. Molecules 2022; 27:molecules27185995. [PMID: 36144727 PMCID: PMC9502897 DOI: 10.3390/molecules27185995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/09/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022] Open
Abstract
As a key structural protein, HIV capsid (CA) protein plays multiple roles in the HIV life cycle, and is considered a promising target for anti-HIV treatment. Based on the structural information of CA modulator PF-74 bound to HIV-1 CA hexamer, 18 novel phenylalanine derivatives were synthesized via the Ugi four-component reaction. In vitro anti-HIV activity assays showed that most compounds exhibited low-micromolar-inhibitory potency against HIV. Among them, compound I-19 exhibited the best anti-HIV-1 activity (EC50 = 2.53 ± 0.84 μM, CC50 = 107.61 ± 27.43 μM). In addition, I-14 displayed excellent HIV-2 inhibitory activity (EC50 = 2.30 ± 0.11 μM, CC50 > 189.32 μM) with relatively low cytotoxicity, being more potent than that of the approved drug nevirapine (EC50 > 15.02 μM, CC50 > 15.2 μM). Additionally, surface plasmon resonance (SPR) binding assays demonstrated direct binding to the HIV CA protein. Moreover, molecular docking and molecular dynamics simulations provided additional information on the binding mode of I-19 to HIV-1 CA. In summary, we further explored the structure—activity relationships (SARs) and selectivity of anti-HIV-1/HIV-2 of PF-74 derivatives, which is conducive to discovering efficient anti-HIV drugs.
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Affiliation(s)
- Xiangkai Ji
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Jing Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Prem Prakash Sharma
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi 110007, India
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, Delhi 110007, India
| | - Zhen Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Lide Hu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan 250012, China
| | - Erik De Clercq
- Laboratory of Virology and Chemotherapym, Rega Institute for Medical Research, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Simon Cocklin
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19104, USA
| | - Chuanfeng Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Christophe Pannecouque
- Laboratory of Virology and Chemotherapym, Rega Institute for Medical Research, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
- Correspondence: (C.P.); (A.D.); (X.L.); (P.Z.)
| | - Alexej Dick
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19104, USA
- Correspondence: (C.P.); (A.D.); (X.L.); (P.Z.)
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan 250012, China
- Correspondence: (C.P.); (A.D.); (X.L.); (P.Z.)
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, Jinan 250012, China
- Correspondence: (C.P.); (A.D.); (X.L.); (P.Z.)
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Defining the HIV Capsid Binding Site of Nucleoporin 153. mSphere 2022; 7:e0031022. [PMID: 36040047 PMCID: PMC9599535 DOI: 10.1128/msphere.00310-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The interaction between the HIV-1 capsid and human nucleoporin 153 (NUP153) is vital for delivering the HIV-1 preintegration complex into the nucleus via the nuclear pore complex. The interaction with the capsid requires a phenylalanine/glycine-containing motif in the C-terminus of NUP153 (NUP153C). This study used molecular modeling and biochemical assays to comprehensively determine the amino acids in NUP153 that are important for capsid interaction. Molecular dynamics, FoldX, and PyRosetta simulations delineated the minimal capsid binding motif of NUP153 based on the known structure of NUP153 bound to the HIV-1 capsid hexamer. Computational predictions were experimentally validated by testing the interaction of NUP153 with capsid using an in vitro binding assay and a cell-based TRIM-NUP153C restriction assay. This work identified eight amino acids from P1411 to G1418 that stably engage with capsid, with significant correlations between the interactions predicted by molecular models and empirical experiments. This validated the usefulness of this multidisciplinary approach to rapidly characterize the interaction between human proteins and the HIV-1 capsid. IMPORTANCE The human immunodeficiency virus (HIV) can infect nondividing cells by interacting with the host nuclear pore complex. The host nuclear pore protein NUP153 directly interacts with the HIV capsid to promote viral nuclear entry. This study used a multidisciplinary approach combining computational and experimental techniques to comprehensively map the effect of mutating the amino acids of NUP153 on HIV capsid interaction. This work showed a significant correlation between computational and empirical data sets, revealing that the HIV capsid interacted specifically with only six amino acids of NUP153. The simplicity of the interaction motif suggested other FG-containing motifs could also interact with the HIV-1 capsid. Furthermore, it was predicted that naturally occurring polymorphisms in human and nonhuman primates would disrupt NUP153 interaction with capsid, potentially protecting certain populations from HIV-1 infection.
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37
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Wang W, Li Y, Zhang Z, Wei W. Human immunodeficiency virus-1 core: The Trojan horse in virus–host interaction. Front Microbiol 2022; 13:1002476. [PMID: 36106078 PMCID: PMC9465167 DOI: 10.3389/fmicb.2022.1002476] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) is the major cause of acquired immunodeficiency syndrome (AIDs) worldwide. In HIV-1 infection, innate immunity is the first defensive line for immune recognition and viral clearance to ensure the normal biological function of the host cell and body health. Under the strong selected pressure generated by the human body over thousands of years, HIV has evolved strategies to counteract and deceive the innate immune system into completing its lifecycle. Recently, several studies have demonstrated that HIV capsid core which is thought to be a protector of the cone structure of genomic RNA, also plays an essential role in escaping innate immunity surveillance. This mini-review summarizes the function of capsid in viral immune evasion, and the comprehensive elucidation of capsid-host cell innate immunity interaction could promote our understanding of HIV-1’s pathogenic mechanism and provide insights for HIV-1 treatment in clinical therapy.
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Affiliation(s)
- Wei Wang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Yan Li
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhe Zhang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Wei Wei
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Translational Medicine, First Hospital, Jilin University, Changchun, Jilin, China
- *Correspondence: Wei Wei,
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38
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Direct Capsid Labeling of Infectious HIV-1 by Genetic Code Expansion Allows Detection of Largely Complete Nuclear Capsids and Suggests Nuclear Entry of HIV-1 Complexes via Common Routes. mBio 2022; 13:e0195922. [PMID: 35972146 PMCID: PMC9600849 DOI: 10.1128/mbio.01959-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The cone-shaped mature HIV-1 capsid is the main orchestrator of early viral replication. After cytosolic entry, it transports the viral replication complex along microtubules toward the nucleus. While it was initially believed that the reverse transcribed genome is released from the capsid in the cytosol, recent observations indicate that a high amount of capsid protein (CA) remains associated with subviral complexes during import through the nuclear pore complex (NPC). Observation of postentry events via microscopic detection of HIV-1 CA is challenging, since epitope shielding limits immunodetection and the genetic fragility of CA hampers direct labeling approaches. Here, we present a minimally invasive strategy based on genetic code expansion and click chemistry that allows for site-directed fluorescent labeling of HIV-1 CA, while retaining virus morphology and infectivity. Thereby, we could directly visualize virions and subviral complexes using advanced microscopy, including nanoscopy and correlative imaging. Quantification of signal intensities of subviral complexes revealed an amount of CA associated with nuclear complexes in HeLa-derived cells and primary T cells consistent with a complete capsid and showed that treatment with the small molecule inhibitor PF74 did not result in capsid dissociation from nuclear complexes. Cone-shaped objects detected in the nucleus by electron tomography were clearly identified as capsid-derived structures by correlative microscopy. High-resolution imaging revealed dose-dependent clustering of nuclear capsids, suggesting that incoming particles may follow common entry routes.
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39
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Yoh SM, Mamede JI, Lau D, Ahn N, Sánchez-Aparicio MT, Temple J, Tuckwell A, Fuchs NV, Cianci GC, Riva L, Curry H, Yin X, Gambut S, Simons LM, Hultquist JF, König R, Xiong Y, García-Sastre A, Böcking T, Hope TJ, Chanda SK. Recognition of HIV-1 capsid by PQBP1 licenses an innate immune sensing of nascent HIV-1 DNA. Mol Cell 2022; 82:2871-2884.e6. [PMID: 35809572 PMCID: PMC9552964 DOI: 10.1016/j.molcel.2022.06.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/22/2022] [Accepted: 06/07/2022] [Indexed: 12/21/2022]
Abstract
We have previously described polyglutamine-binding protein 1 (PQBP1) as an adapter required for the cyclic GMP-AMP synthase (cGAS)-mediated innate response to the human immunodeficiency virus 1 (HIV-1) and other lentiviruses. Cytoplasmic HIV-1 DNA is a transient and low-abundance pathogen-associated molecular pattern (PAMP), and the mechanism for its detection and verification is not fully understood. Here, we show a two-factor authentication strategy by the innate surveillance machinery to selectively respond to the low concentration of HIV-1 DNA, while distinguishing these species from extranuclear DNA molecules. We find that, upon HIV-1 infection, PQBP1 decorates the intact viral capsid, and this serves as a primary verification step for the viral nucleic acid cargo. As reverse transcription and capsid disassembly initiate, cGAS is recruited to the capsid in a PQBP1-dependent manner. This positions cGAS at the site of PAMP generation and sanctions its response to a low-abundance DNA PAMP.
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Affiliation(s)
- Sunnie M Yoh
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA.
| | - João I Mamede
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612, USA
| | - Derrick Lau
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Narae Ahn
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Maria T Sánchez-Aparicio
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joshua Temple
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Andrew Tuckwell
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Nina V Fuchs
- Host-Pathogen Interaction, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Gianguido C Cianci
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Laura Riva
- Calibr, a Division of The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Heather Curry
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Xin Yin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, P.R. China
| | - Stéphanie Gambut
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612, USA
| | - Lacy M Simons
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Renate König
- Host-Pathogen Interaction, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Till Böcking
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Thomas J Hope
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sumit K Chanda
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA.
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The HIV-1 Gag Protein Displays Extensive Functional and Structural Roles in Virus Replication and Infectivity. Int J Mol Sci 2022; 23:ijms23147569. [PMID: 35886917 PMCID: PMC9323242 DOI: 10.3390/ijms23147569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/15/2022] [Accepted: 06/19/2022] [Indexed: 01/10/2023] Open
Abstract
Once merely thought of as the protein responsible for the overall physical nature of the human immunodeficiency virus type 1 (HIV-1), the Gag polyprotein has since been elucidated to have several roles in viral replication and functionality. Over the years, extensive research into the polyproteins’ structure has revealed that Gag can mediate its own trafficking to the plasma membrane, it can interact with several host factors and can even aid in viral genome packaging. Not surprisingly, Gag has also been associated with HIV-1 drug resistance and even treatment failure. Therefore, this review provides an extensive overview of the structural and functional roles of the HIV-1 Gag domains in virion integrity, functionality and infectivity.
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41
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Obubeid FO, Eltigani MM, Mukhtar RM, Ibrahim RA, Alzain MA, Elbadawi FA, Ghaboosh H, Alzain AA. Dual targeting inhibitors for HIV-1 capsid and cyclophilin A: molecular docking, molecular dynamics, and quantum mechanics. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2097673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Fauad O. Obubeid
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Maha M. Eltigani
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Rua M. Mukhtar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Reham A. Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Muna A. Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Fatima A. Elbadawi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Hiba Ghaboosh
- Department of Pharmaceutics, University of Gezira, Wad Madani, Sudan
| | - Abdulrahim A. Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
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42
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Identification of 2-(4-N,N-Dimethylaminophenyl)-5-methyl-1-phenethyl-1H-benzimidazole targeting HIV-1 CA capsid protein and inhibiting HIV-1 replication in cellulo. BMC Pharmacol Toxicol 2022; 23:43. [PMID: 35765101 PMCID: PMC9241302 DOI: 10.1186/s40360-022-00581-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 05/30/2022] [Indexed: 11/29/2022] Open
Abstract
The capsid (CA) subunit of the HIV-1 Gag polyprotein is involved in several steps of the viral cycle, from the assembly of new viral particles to the protection of the viral genome until it enters into the nucleus of newly infected cells. As such, it represents an interesting therapeutic target to tackle HIV infection. In this study, we screened hundreds of compounds with a low cost of synthesis for their ability to interfere with Gag assembly in vitro. Representatives of the most promising families of compounds were then tested for their ability to inhibit HIV-1 replication in cellulo. From these molecules, a hit compound from the benzimidazole family with high metabolic stability and low toxicity, 2-(4-N,N-dimethylaminophenyl)-5-methyl-1-phenethyl-1H-benzimidazole (696), appeared to block HIV-1 replication with an IC50 of 3 µM. Quantitative PCR experiments demonstrated that 696 does not block HIV-1 infection before the end of reverse transcription, and molecular docking confirmed that 696 is likely to bind at the interface between two monomers of CA and interfere with capsid oligomerization. Altogether, 696 represents a promising lead molecule for the development of a new series of HIV-1 inhibitors.
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43
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Tasneem N, Szyszka TN, Jenner EN, Lau YH. How Pore Architecture Regulates the Function of Nanoscale Protein Compartments. ACS NANO 2022; 16:8540-8556. [PMID: 35583458 DOI: 10.1021/acsnano.2c02178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Self-assembling proteins can form porous compartments that adopt well-defined architectures at the nanoscale. In nature, protein compartments act as semipermeable barriers to enable spatial separation and organization of complex biochemical processes. The compartment pores play a key role in their overall function by selectively controlling the influx and efflux of important biomolecular species. By engineering the pores, the functionality of compartments can be tuned to facilitate non-native applications, such as artificial nanoreactors for catalysis. In this review, we analyze how protein structure determines the porosity and impacts the function of both native and engineered compartments, highlighting the wealth of structural data recently obtained by cryo-EM and X-ray crystallography. Through this analysis, we offer perspectives on how current structural insights can inform future studies into the design of artificial protein compartments as nanoreactors with tunable porosity and function.
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Affiliation(s)
- Nuren Tasneem
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
| | - Taylor N Szyszka
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
- University of Sydney Nano Institute, Camperdown, New South Wales 2006, Australia
| | - Eric N Jenner
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Eastern Avenue, Camperdown, New South Wales 2006, Australia
- University of Sydney Nano Institute, Camperdown, New South Wales 2006, Australia
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44
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Nicastro G, Lucci M, Oregioni A, Kelly G, Frenkiel TA, Taylor IA. CP-MAS and solution NMR studies of allosteric communication in CA-assemblies of HIV-1. J Mol Biol 2022; 434:167691. [PMID: 35738429 DOI: 10.1016/j.jmb.2022.167691] [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: 05/13/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 10/18/2022]
Abstract
Solution and solid-state NMR spectroscopy are highly complementary techniques for studying structure and dynamics in very high molecular weight systems. Here we have analysed the dynamics of HIV-1 capsid (CA) assemblies in presence of the cofactors IP6 and ATPγS and the host-factor CPSF6 using a combination of solution state and cross polarisation magic angle spinning (CP-MAS) solid-state NMR. In particular, dynamical effects on ns to µs and µs to ms timescales are observed revealing diverse motions in assembled CA. Using CP-MAS NMR, we exploited the sensitivity of the amide/Cα-Cβ backbone chemical shifts in DARR and NCA spectra to observe the plasticity of the HIV-1 CA tubular assemblies and also map the binding of cofactors and the dynamics of cofactor-CA complexes. In solution, we measured how the addition of host- and co-factors to CA -hexamers perturbed the chemical shifts and relaxation properties of CA-Ile and -Met methyl groups using transverse-relaxation-optimized NMR spectroscopy to exploit the sensitivity of methyl groups as probes in high-molecular weight proteins. These data show how dynamics of the CA protein assembly over a range of spatial and temporal scales play a critical role in CA function. Moreover, we show that binding of IP6, ATPγS and CPSF6 results in local chemical shift as well as dynamic changes for a significant, contiguous portion of CA, highlighting how allosteric pathways communicate ligand interactions between adjacent CA protomers.
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Affiliation(s)
- Giuseppe Nicastro
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Massimo Lucci
- CIRMMP, University of Florence, Via L. Sacconi, 6 50019 Sesto Fiorentino (FI), Italy
| | - Alain Oregioni
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Tom A Frenkiel
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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45
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Pak A, Gupta M, Yeager M, Voth GA. Inositol Hexakisphosphate (IP6) Accelerates Immature HIV-1 Gag Protein Assembly toward Kinetically Trapped Morphologies. J Am Chem Soc 2022; 144:10417-10428. [PMID: 35666943 PMCID: PMC9204763 DOI: 10.1021/jacs.2c02568] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
During the late stages of the HIV-1 lifecycle, immature virions are produced by the concerted activity of Gag polyproteins, primarily mediated by the capsid (CA) and spacer peptide 1 (SP1) domains, which assemble into a spherical lattice, package viral genomic RNA, and deform the plasma membrane. Recently, inositol hexakisphosphate (IP6) has been identified as an essential assembly cofactor that efficiently produces both immature virions in vivo and immature virus-like particles in vitro. To date, however, several distinct mechanistic roles for IP6 have been proposed on the basis of independent functional, structural, and kinetic studies. In this work, we investigate the molecular influence of IP6 on the structural outcomes and dynamics of CA/SP1 assembly using coarse-grained (CG) molecular dynamics (MD) simulations and free energy calculations. Here, we derive a bottom-up, low-resolution, and implicit-solvent CG model of CA/SP1 and IP6, and simulate their assembly under conditions that emulate both in vitro and in vivo systems. Our analysis identifies IP6 as an assembly accelerant that promotes curvature generation and fissure-like defects throughout the lattice. Our findings suggest that IP6 induces kinetically trapped immature morphologies, which may be physiologically important for later stages of viral morphogenesis and potentially useful for virus-like particle technologies.
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Affiliation(s)
- Alexander
J. Pak
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, Institute
for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Manish Gupta
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, Institute
for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Mark Yeager
- Department
of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States,Center
for Membrane Biology, University of Virginia
School of Medicine, Charlottesville, Virginia 22908, United States, United States,Cardiovascular
Research Center, University of Virginia
School of Medicine, Charlottesville, Virginia 22908, United States,Department
of Medicine, Division of Cardiovascular Medicine, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
| | - Gregory A. Voth
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, Institute
for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States,E-mail:
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46
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Markússon S, Hallin EI, Bustad HJ, Raasakka A, Xu J, Muruganandam G, Loris R, Martinez A, Bramham CR, Kursula P. High-affinity anti-Arc nanobodies provide tools for structural and functional studies. PLoS One 2022; 17:e0269281. [PMID: 35671319 PMCID: PMC9173642 DOI: 10.1371/journal.pone.0269281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/17/2022] [Indexed: 11/19/2022] Open
Abstract
Activity-regulated cytoskeleton-associated protein (Arc) is a multidomain protein of retroviral origin with a vital role in the regulation of synaptic plasticity and memory formation in mammals. However, the mechanistic and structural basis of Arc function is poorly understood. Arc has an N-terminal domain (NTD) involved in membrane binding and a C-terminal domain (CTD) that binds postsynaptic protein ligands. In addition, the NTD and CTD both function in Arc oligomerisation, including assembly of retrovirus-like capsids involved in intercellular signalling. To obtain new tools for studies on Arc structure and function, we produced and characterised six high-affinity anti-Arc nanobodies (Nb). The CTD of rat and human Arc were both crystallised in ternary complexes with two Nbs. One Nb bound deep into the stargazin-binding pocket of Arc CTD and suggested competitive binding with Arc ligand peptides. The crystallisation of the human Arc CTD in two different conformations, accompanied by SAXS data and molecular dynamics simulations, paints a dynamic picture of the mammalian Arc CTD. The collapsed conformation closely resembles Drosophila Arc in capsids, suggesting that we have trapped a capsid-like conformation of the human Arc CTD. Our data obtained with the help of anti-Arc Nbs suggest that structural dynamics of the CTD and dimerisation of the NTD may promote the formation of capsids. Taken together, the recombinant high-affinity anti-Arc Nbs are versatile tools that can be further developed for studying mammalian Arc structure and function, as well as mechanisms of Arc capsid formation, both in vitro and in vivo. For example, the Nbs could serve as a genetically encoded tools for inhibition of endogenous Arc interactions in the study of neuronal function and plasticity.
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Affiliation(s)
| | - Erik I. Hallin
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Ju Xu
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Gopinath Muruganandam
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Department of Bioengineering Sciences, Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - Remy Loris
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Department of Bioengineering Sciences, Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | | | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
- * E-mail:
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47
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Ramesh D, Mohanty AK, De A, Vijayakumar BG, Sethumadhavan A, Muthuvel SK, Mani M, Kannan T. Uracil derivatives as HIV-1 capsid protein inhibitors: design, in silico, in vitro and cytotoxicity studies. RSC Adv 2022; 12:17466-17480. [PMID: 35765450 PMCID: PMC9190787 DOI: 10.1039/d2ra02450k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/29/2022] [Indexed: 11/24/2022] Open
Abstract
A series of novel uracil derivatives such as bispyrimidine dione and tetrapyrimidine dione derivatives were designed based on the existing four-point pharmacophore model as effective HIV capsid protein inhibitors. The compounds were initially docked with an HIV capsid protein monomer to rationalize the ideas of design and to find the potential binding modes. The successful design and computational studies led to the synthesis of bispyrimidine dione and tetrapyrimidine dione derivatives from uracil and aromatic aldehydes in the presence of HCl using novel methodology. The in vitro evaluation in HIV p24 assay revealed five potential uracil derivatives with IC50 values ranging from 191.5 μg ml−1 to 62.5 μg ml−1. The meta-chloro substituted uracil compound 9a showed promising activity with an IC50 value of 62.5 μg ml−1 which is well correlated with the computational studies. As expected, all the active compounds were noncytotoxic in BA/F3 and Mo7e cell lines highlighting the thoughtful design. The structure activity relationship indicates the position priority and lower log P values as the possible cause of inhibitory potential of the uracil compounds. The paper describes the design, synthesis, computational and biological validation of a series of novel uracil derivatives as effective HIV capsid protein inhibitors.![]()
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Affiliation(s)
- Deepthi Ramesh
- Department of Chemistry, Pondicherry University Kalapet Puducherry-605014 India
| | - Amaresh Kumar Mohanty
- Department of Bioinformatics, Pondicherry University Kalapet Puducherry-605014 India
| | - Anirban De
- Department of Chemistry, Pondicherry University Kalapet Puducherry-605014 India
| | | | | | - Suresh Kumar Muthuvel
- Department of Bioinformatics, Pondicherry University Kalapet Puducherry-605014 India
| | - Maheswaran Mani
- Department of Microbiology, Pondicherry University Kalapet Puducherry-605014 India
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48
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Dick A, Meuser ME, Cocklin S. Clade-Specific Alterations within the HIV-1 Capsid Protein with Implications for Nuclear Translocation. Biomolecules 2022; 12:biom12050695. [PMID: 35625621 PMCID: PMC9138599 DOI: 10.3390/biom12050695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 11/16/2022] Open
Abstract
The HIV-1 capsid (CA) protein has emerged as an attractive therapeutic target. However, all inhibitor designs and structural analyses for this essential HIV-1 protein have focused on the clade B HIV-1 (NL4-3) variant. This study creates, overproduces, purifies, and characterizes the CA proteins from clade A1, A2, B, C, and D isolates. These new CA constructs represent novel reagents that can be used in future CA-targeted inhibitor design and to investigate CA proteins’ structural and biochemical properties from genetically diverse HIV-1 subtypes. Moreover, we used surface plasmon resonance (SPR) spectrometry and computational modeling to examine inter-clade differences in CA assembly and binding of PF-74, CPSF-6, and NUP-153. Interestingly, we found that HIV-1 CA from clade A1 does not bind to NUP-153, suggesting that the import of CA core structures through the nuclear pore complex may be altered for viruses from this clade. Overall, we have demonstrated that in silico generated models of the HIV-1 CA protein from clades other than the prototypically used clade B have utility in understanding and predicting biology and antiviral drug design and mechanism of action.
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Affiliation(s)
- Alexej Dick
- Correspondence: (A.D.); (S.C.); Tel.: +1-215-762-7234 (A.D. & S.C.); Fax: +1-215-762-4452 (A.D. & S.C.)
| | | | - Simon Cocklin
- Correspondence: (A.D.); (S.C.); Tel.: +1-215-762-7234 (A.D. & S.C.); Fax: +1-215-762-4452 (A.D. & S.C.)
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49
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Sun Q, Biswas A, Vijayan RSK, Craveur P, Forli S, Olson AJ, Castaner AE, Kirby KA, Sarafianos SG, Deng N, Levy R. Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid. J Comput Aided Mol Des 2022; 36:193-203. [PMID: 35262811 PMCID: PMC8904208 DOI: 10.1007/s10822-022-00446-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/24/2022] [Indexed: 02/07/2023]
Abstract
We have identified novel HIV-1 capsid inhibitors targeting the PF74 binding site. Acting as the building block of the HIV-1 capsid core, the HIV-1 capsid protein plays an important role in the viral life cycle and is an attractive target for antiviral development. A structure-based virtual screening workflow for hit identification was employed, which includes docking 1.6 million commercially-available drug-like compounds from the ZINC database to the capsid dimer, followed by applying two absolute binding free energy (ABFE) filters on the 500 top-ranked molecules from docking. The first employs the Binding Energy Distribution Analysis Method (BEDAM) in implicit solvent. The top-ranked compounds are then refined using the Double Decoupling method in explicit solvent. Both docking and BEDAM refinement were carried out on the IBM World Community Grid as part of the FightAIDS@Home project. Using this virtual screening workflow, we identified 24 molecules with calculated binding free energies between − 6 and − 12 kcal/mol. We performed thermal shift assays on these molecules to examine their potential effects on the stability of HIV-1 capsid hexamer and found that two compounds, ZINC520357473 and ZINC4119064 increased the melting point of the latter by 14.8 °C and 33 °C, respectively. These results support the conclusion that the two ZINC compounds are primary hits targeting the capsid dimer interface. Our simulations also suggest that the two hit molecules may bind at the capsid dimer interface by occupying a new sub-pocket that has not been exploited by existing CA inhibitors. The possible causes for why other top-scored compounds suggested by ABFE filters failed to show measurable activity are discussed.
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Affiliation(s)
- Qinfang Sun
- Center for Biophysics and Computational Biology and Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
| | - Avik Biswas
- Center for Biophysics and Computational Biology and Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
| | - R S K Vijayan
- Institute for Applied Cancer Science, MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Pierrick Craveur
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Arthur J Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Andres Emanuelli Castaner
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Karen A Kirby
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Nanjie Deng
- Department of Chemistry and Physical Sciences, Pace University, New York, NY, 10038, USA.
| | - Ronald Levy
- Center for Biophysics and Computational Biology and Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
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50
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Lerner G, Weaver N, Anokhin B, Spearman P. Advances in HIV-1 Assembly. Viruses 2022; 14:v14030478. [PMID: 35336885 PMCID: PMC8952333 DOI: 10.3390/v14030478] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/10/2022] Open
Abstract
The assembly of HIV-1 particles is a concerted and dynamic process that takes place on the plasma membrane of infected cells. An abundance of recent discoveries has advanced our understanding of the complex sequence of events leading to HIV-1 particle assembly, budding, and release. Structural studies have illuminated key features of assembly and maturation, including the dramatic structural transition that occurs between the immature Gag lattice and the formation of the mature viral capsid core. The critical role of inositol hexakisphosphate (IP6) in the assembly of both the immature and mature Gag lattice has been elucidated. The structural basis for selective packaging of genomic RNA into virions has been revealed. This review will provide an overview of the HIV-1 assembly process, with a focus on recent advances in the field, and will point out areas where questions remain that can benefit from future investigation.
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