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Kleinpeter A, Mallery DL, Renner N, Albecka A, Klarhof JO, Freed EO, James LC. HIV-1 adapts to lost IP6 coordination through second-site mutations that restore conical capsid assembly. Nat Commun 2024; 15:8017. [PMID: 39271696 PMCID: PMC11399258 DOI: 10.1038/s41467-024-51971-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 08/20/2024] [Indexed: 09/15/2024] Open
Abstract
The HIV-1 capsid is composed of capsid (CA) protein hexamers and pentamers (capsomers) that contain a central pore hypothesised to regulate capsid assembly and facilitate nucleotide import early during post-infection. These pore functions are mediated by two positively charged rings created by CA Arg-18 (R18) and Lys-25 (K25). Here we describe the forced evolution of viruses containing mutations in R18 and K25. Whilst R18 mutants fail to replicate, K25A viruses acquire compensating mutations that restore nearly wild-type replication fitness. These compensating mutations, which rescue reverse transcription and infection without reintroducing lost pore charges, map to three adaptation hot-spots located within and between capsomers. The second-site suppressor mutations act by restoring the formation of pentamers lost upon K25 mutation, enabling closed conical capsid assembly both in vitro and inside virions. These results indicate that there is no intrinsic requirement for K25 in either nucleotide import or capsid assembly. We propose that whilst HIV-1 must maintain a precise hexamer:pentamer equilibrium for proper capsid assembly, compensatory mutations can tune this equilibrium to restore fitness lost by mutation of the central pore.
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Affiliation(s)
- Alex Kleinpeter
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA.
| | - Donna L Mallery
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Nadine Renner
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Anna Albecka
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - J Ole Klarhof
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Eric O Freed
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702-1201, USA.
| | - Leo C James
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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2
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Biswas B, Lai KK, Bracey H, Datta SAK, Harvin D, Sowd GA, Aiken C, Rein A. Essential functions of inositol hexakisphosphate (IP6) in murine leukemia virus replication. mBio 2024; 15:e0115824. [PMID: 38912776 PMCID: PMC11253606 DOI: 10.1128/mbio.01158-24] [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: 04/18/2024] [Accepted: 05/14/2024] [Indexed: 06/25/2024] Open
Abstract
We have investigated the function of inositol hexakisphosphate (IP6) and inositol pentakisphosphate (IP5) in the replication of murine leukemia virus (MLV). While IP6 is known to be critical for the life cycle of HIV-1, its significance in MLV remains unexplored. We find that IP6 is indeed important for MLV replication. It significantly enhances endogenous reverse transcription (ERT) in MLV. Additionally, a pelleting-based assay reveals that IP6 can stabilize MLV cores, thereby facilitating ERT. We find that IP5 and IP6 are packaged in MLV particles. However, unlike HIV-1, MLV depends upon the presence of IP6 and IP5 in target cells for successful infection. This IP6/5 requirement for infection is reflected in impaired reverse transcription observed in IP6/5-deficient cell lines. In summary, our findings demonstrate the importance of capsid stabilization by IP6/5 in the replication of diverse retroviruses; we suggest possible reasons for the differences from HIV-1 that we observed in MLV.IMPORTANCEInositol hexakisphosphate (IP6) is crucial for the assembly and replication of HIV-1. IP6 is packaged in HIV-1 particles and stabilizes the viral core enabling it to synthesize viral DNA early in viral infection. While its importance for HIV-1 is well established, its significance for other retroviruses is unknown. Here we report the role of IP6 in the gammaretrovirus, murine leukemia virus (MLV). We found that like HIV-1, MLV packages IP6, and as in HIV-1, IP6 stabilizes the MLV core thus promoting reverse transcription. Interestingly, we discovered a key difference in the role of IP6 in MLV versus HIV-1: while HIV-1 is not dependent upon IP6 levels in target cells, MLV replication is significantly reduced in IP6-deficient cell lines. We suggest that this difference in IP6 requirements reflects key differences between HIV-1 and MLV replication.
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Affiliation(s)
- Banhi Biswas
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, Frederick, Maryland, USA
| | - Kin Kui Lai
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, Frederick, Maryland, USA
| | - Harrison Bracey
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Siddhartha A. K. Datta
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, Frederick, Maryland, USA
| | - Demetria Harvin
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, Frederick, Maryland, USA
| | - Gregory A. Sowd
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Christopher Aiken
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alan Rein
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, Frederick, Maryland, USA
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3
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Sun F, Chen H, Dai X, Hou Y, Li J, Zhang Y, Huang L, Guo B, Yang D. Liposome-lentivirus for miRNA therapy with molecular mechanism study. J Nanobiotechnology 2024; 22:329. [PMID: 38858736 PMCID: PMC11165871 DOI: 10.1186/s12951-024-02534-0] [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: 02/21/2024] [Accepted: 05/09/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Cancer stem cells (CSCs) play a vital role in the occurrence, maintenance, and recurrence of solid tumors. Although, miR-145-5p can inhibit CSCs survival, poor understanding of the underlying mechanisms hamperes further therapeutic optimization for patients. Lentivirus with remarkable transduction efficiency is the most commonly used RNA carrier in research, but has shown limited tumor-targeting capability. METHODS We have applied liposome to decorate lentivirus surface thereby yielding liposome-lentivirus hybrid-based carriers, termed miR-145-5p-lentivirus nanoliposome (MRL145), and systematically analyzed their potential therapeutic effects on liver CSCs (LCSCs). RESULTS MRL145 exhibited high delivery efficiency and potent anti-tumor efficacy under in vitro and in vivo. Mechanistically, the overexpressed miR-145-5p can significantly suppress the self-renewal, migration, and invasion abilities of LCSCs by targeting Collagen Type IV Alpha 3 Chain (COL4A3). Importantly, COL4A3 can promote phosphorylating GSK-3β at ser 9 (p-GSK-3β S9) to inactivate GSK3β, and facilitate translocation of β-catenin into the nucleus to activate the Wnt/β-catenin pathway, thereby promoting self-renewal, migration, and invasion of LCSCs. Interestingly, COL4A3 could attenuate the cellular autophagy through modulating GSK3β/Gli3/VMP1 axis to promote self-renewal, migration, and invasion of LCSCs. CONCLUSIONS These findings provide new insights in mode of action of miR-145-5p in LCSCs therapy and indicates that liposome-virus hybrid carriers hold great promise in miRNA delivery.
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Affiliation(s)
- Fen Sun
- Institute of Animal Sciences and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250000, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Huaqing Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Xiaoyong Dai
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Precision Medicine and Healthcare Research Center, Tsinghua-Berkeley Shenzhen Institute (TBSI), Tsinghua University, Shenzhen, 518055, Guangdong, China
| | - Yibo Hou
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Jing Li
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Yinghe Zhang
- Shenzhen Key Laboratory of Advanced Functional Carbon Materials Research and Comprehensive Application, School of Science, Harbin Institute of Technology, Shenzhen, 518055, China
| | - Laiqiang Huang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
| | - Bing Guo
- Shenzhen Key Laboratory of Advanced Functional Carbon Materials Research and Comprehensive Application, School of Science, Harbin Institute of Technology, Shenzhen, 518055, China.
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology, Harbin Institute of Technology, Shenzhen, 518055, China.
| | - Dongye Yang
- Division of Gastroenterology and Hepatology, The University of Hongkong-Shenzhen Hospital, Shenzhen, China.
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4
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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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5
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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 PMCID: PMC11257216 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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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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7
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Biswas B, Lai KK, Bracey H, Datta SA, Harvin D, Sowd GA, Aiken C, Rein A. Essential functions of Inositol hexakisphosphate (IP6) in Murine Leukemia Virus replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.581940. [PMID: 38464197 PMCID: PMC10925174 DOI: 10.1101/2024.02.27.581940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
We have investigated the function of inositol hexakisphosphate (IP6) and inositol pentakisphosphate (IP5) in the replication of murine leukemia virus (MLV). While IP6 is known to be critical for the life cycle of HIV-1, its significance in MLV remains unexplored. We find that IP6 is indeed important for MLV replication. It significantly enhances endogenous reverse transcription (ERT) in MLV. Additionally, a pelleting-based assay reveals that IP6 can stabilize MLV cores, thereby facilitating ERT. We find that IP5 and IP6 are packaged in MLV particles. However, unlike HIV-1, MLV depends upon the presence of IP6 and IP5 in target cells for successful infection. This IP6/5 requirement for infection is reflected in impaired reverse transcription observed in IP6/5-deficient cell lines. In summary, our findings demonstrate the importance of capsid stabilization by IP6/5 in the replication of diverse retroviruses; we suggest possible reasons for the differences from HIV-1 that we observed in MLV.
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Affiliation(s)
- Banhi Biswas
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, P.O. Box B, Frederick, MD 21702-1201, USA
| | - Kin Kui Lai
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, P.O. Box B, Frederick, MD 21702-1201, USA
| | - Harrison Bracey
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232-3263, USA
| | - Siddhartha A.K. Datta
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, P.O. Box B, Frederick, MD 21702-1201, USA
| | - Demetria Harvin
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, P.O. Box B, Frederick, MD 21702-1201, USA
| | - Gregory A. Sowd
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232-3263, USA
| | - Christopher Aiken
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232-3263, USA
| | - Alan Rein
- HIV Dynamics and Replication Program, National Cancer Institute-Frederick, P.O. Box B, Frederick, MD 21702-1201, USA
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8
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Lei ZC, Wang X, Yang L, Qu H, Sun Y, Yang Y, Li W, Zhang WB, Cao XY, Fan C, Li G, Wu J, Tian ZQ. What can molecular assembly learn from catalysed assembly in living organisms? Chem Soc Rev 2024; 53:1892-1914. [PMID: 38230701 DOI: 10.1039/d3cs00634d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Molecular assembly is the process of organizing individual molecules into larger structures and complex systems. The self-assembly approach is predominantly utilized in creating artificial molecular assemblies, and was believed to be the primary mode of molecular assembly in living organisms as well. However, it has been shown that the assembly of many biological complexes is "catalysed" by other molecules, rather than relying solely on self-assembly. In this review, we summarize these catalysed-assembly (catassembly) phenomena in living organisms and systematically analyse their mechanisms. We then expand on these phenomena and discuss related concepts, including catalysed-disassembly and catalysed-reassembly. Catassembly proves to be an efficient and highly selective strategy for synergistically controlling and manipulating various noncovalent interactions, especially in hierarchical molecular assemblies. Overreliance on self-assembly may, to some extent, hinder the advancement of artificial molecular assembly with powerful features. Furthermore, inspired by the biological catassembly phenomena, we propose guidelines for designing artificial catassembly systems and developing characterization and theoretical methods, and review pioneering works along this new direction. Overall, this approach may broaden and deepen our understanding of molecular assembly, enabling the construction and control of intelligent assembly systems with advanced functionality.
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Affiliation(s)
- Zhi-Chao Lei
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xinchang Wang
- School of Electronic Science and Engineering, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, P. R. China
| | - Liulin Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - Hang Qu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - Yibin Sun
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Yang Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - Wei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Xiao-Yu Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science, Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jiarui Wu
- Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, P. R. China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, P. R. China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, 310024, P. R. China
| | - Zhong-Qun Tian
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
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9
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Gifford LB, Melikyan GB. HIV-1 Capsid Uncoating Is a Multistep Process That Proceeds through Defect Formation Followed by Disassembly of the Capsid Lattice. ACS NANO 2024; 18:2928-2947. [PMID: 38241476 PMCID: PMC10832047 DOI: 10.1021/acsnano.3c07678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/21/2024]
Abstract
The HIV-1 core consists of a cone-shaped capsid shell made of capsid protein (CA) hexamers and pentamers encapsulating the viral genome. HIV-1 capsid disassembly, referred to as uncoating, is important for productive infection; however, the location, timing, and regulation of uncoating remain controversial. Here, we employ amber codon suppression to directly label CA. In addition, a fluid phase fluorescent probe is incorporated into the viral core to detect small defects in the capsid lattice. This double-labeling strategy enables the visualization of uncoating of single cores in vitro and in living cells, which we found to always proceed through at least two distinct steps─the formation of a defect in the capsid lattice that initiates gradual loss of CA below a detectable level. Importantly, intact cores containing the fluid phase and CA fluorescent markers enter and uncoat in the nucleus, as evidenced by a sequential loss of both markers, prior to establishing productive infection. This two-step uncoating process is observed in different cells, including a macrophage line. Notably, the lag between the release of fluid phase marker and terminal loss of CA appears to be independent of the cell type or reverse transcription and is much longer (>5-fold) for nuclear capsids compared to cell-free cores or cores in the cytosol, suggesting that the capsid lattice is stabilized by capsid-binding nuclear factors. Our results imply that intact HIV-1 cores enter the cell nucleus and that uncoating is initiated through a localized defect in the capsid lattice prior to a global loss of CA.
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Affiliation(s)
- Levi B. Gifford
- Department
of Pediatrics, Emory University School of
Medicine, Atlanta, Georgia 30322, United States
| | - Gregory B. Melikyan
- Department
of Pediatrics, Emory University School of
Medicine, Atlanta, Georgia 30322, United States
- Children’s
Healthcare of Atlanta, Atlanta, Georgia 30322, United States
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10
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Padron A, Prakash P, Pandhare J, Luban J, Aiken C, Balasubramaniam M, Dash C. Emerging role of cyclophilin A in HIV-1 infection: from producer cell to the target cell nucleus. J Virol 2023; 97:e0073223. [PMID: 37843371 PMCID: PMC10688351 DOI: 10.1128/jvi.00732-23] [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: 10/17/2023] Open
Abstract
The HIV-1 genome encodes a small number of proteins with structural, enzymatic, regulatory, and accessory functions. These viral proteins interact with a number of host factors to promote the early and late stages of HIV-1 infection. During the early stages of infection, interactions between the viral proteins and host factors enable HIV-1 to enter the target cell, traverse the cytosol, dock at the nuclear pore, gain access to the nucleus, and integrate into the host genome. Similarly, the viral proteins recruit another set of host factors during the late stages of infection to orchestrate HIV-1 transcription, translation, assembly, and release of progeny virions. Among the host factors implicated in HIV-1 infection, Cyclophilin A (CypA) was identified as the first host factor to be packaged within HIV-1 particles. It is now well established that CypA promotes HIV-1 infection by directly binding to the viral capsid. Mechanistic models to pinpoint CypA's role have spanned from an effect in the producer cell to the early steps of infection in the target cell. In this review, we will describe our understanding of the role(s) of CypA in HIV-1 infection, highlight the current knowledge gaps, and discuss the potential role of this host factor in the post-nuclear entry steps of HIV-1 infection.
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Affiliation(s)
- Adrian Padron
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
- School of Graduate Studies, Meharry Medical College, Nashville, Tennessee, USA
| | - Prem Prakash
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Jui Pandhare
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
- School of Graduate Studies, Meharry Medical College, Nashville, Tennessee, USA
| | - Jeremy Luban
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Chris Aiken
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Muthukumar Balasubramaniam
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Chandravanu Dash
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
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11
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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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12
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Meanwell NA. Sub-stoichiometric Modulation of Viral Targets-Potent Antiviral Agents That Exploit Target Vulnerability. ACS Med Chem Lett 2023; 14:1021-1030. [PMID: 37583823 PMCID: PMC10424314 DOI: 10.1021/acsmedchemlett.3c00279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 06/30/2023] [Indexed: 08/17/2023] Open
Abstract
The modulation of oligomeric viral targets at sub-stoichiometric ratios of drug to target has been advocated for its efficacy and potency, but there are only a limited number of documented examples. In this Viewpoint, we summarize the invention of the HIV-1 maturation inhibitor fipravirimat and discuss the emerging details around the mode of action of this class of drug that reflects inhibition of a protein composed of 1,300-1,600 monomers that interact in a cooperative fashion. Similarly, the HCV NS5A inhibitor daclatasvir has been shown to act in a highly sub-stoichiometric fashion, inhibiting viral replication at concentrations that are ∼23,500 lower than that of the protein target.
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13
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Waheed AA, Zhu Y, Agostino E, Naing L, Hikichi Y, Soheilian F, Yoo SW, Song Y, Zhang P, Slusher BS, Haughey NJ, Freed EO. Neutral sphingomyelinase 2 is required for HIV-1 maturation. Proc Natl Acad Sci U S A 2023; 120:e2219475120. [PMID: 37406093 PMCID: PMC10334776 DOI: 10.1073/pnas.2219475120] [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: 11/18/2022] [Accepted: 04/11/2023] [Indexed: 07/07/2023] Open
Abstract
HIV-1 assembly occurs at the inner leaflet of the plasma membrane (PM) in highly ordered membrane microdomains. The size and stability of membrane microdomains is regulated by activity of the sphingomyelin hydrolase neutral sphingomyelinase 2 (nSMase2) that is localized primarily to the inner leaflet of the PM. In this study, we demonstrate that pharmacological inhibition or depletion of nSMase2 in HIV-1-producer cells results in a block in the processing of the major viral structural polyprotein Gag and the production of morphologically aberrant, immature HIV-1 particles with severely impaired infectivity. We find that disruption of nSMase2 also severely inhibits the maturation and infectivity of other primate lentiviruses HIV-2 and simian immunodeficiency virus, has a modest or no effect on nonprimate lentiviruses equine infectious anemia virus and feline immunodeficiency virus, and has no effect on the gammaretrovirus murine leukemia virus. These studies demonstrate a key role for nSMase2 in HIV-1 particle morphogenesis and maturation.
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Affiliation(s)
- Abdul A. Waheed
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Yanan Zhu
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, OxfordOX3 7BN, United Kingdom
| | - Eva Agostino
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Lwar Naing
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Yuta Hikichi
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Ferri Soheilian
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD21702
| | - Seung-Wan Yoo
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Yun Song
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, DidcotOX11 0DE, United Kingdom
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, OxfordOX3 7BN, United Kingdom
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, DidcotOX11 0DE, United Kingdom
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, OxfordOX3 7BN, United Kingdom
| | - Barbara S. Slusher
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Norman J. Haughey
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Eric O. Freed
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
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14
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Papa G, Albecka A, Mallery D, Vaysburd M, Renner N, James LC. IP6-stabilised HIV capsids evade cGAS/STING-mediated host immune sensing. EMBO Rep 2023; 24:e56275. [PMID: 36970882 PMCID: PMC10157305 DOI: 10.15252/embr.202256275] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/06/2023] [Accepted: 03/10/2023] [Indexed: 03/29/2023] Open
Abstract
HIV-1 uses inositol hexakisphosphate (IP6) to build a metastable capsid capable of delivering its genome into the host nucleus. Here, we show that viruses that are unable to package IP6 lack capsid protection and are detected by innate immunity, resulting in the activation of an antiviral state that inhibits infection. Disrupting IP6 enrichment results in defective capsids that trigger cytokine and chemokine responses during infection of both primary macrophages and T-cell lines. Restoring IP6 enrichment with a single mutation rescues the ability of HIV-1 to infect cells without being detected. Using a combination of capsid mutants and CRISPR-derived knockout cell lines for RNA and DNA sensors, we show that immune sensing is dependent upon the cGAS-STING axis and independent of capsid detection. Sensing requires the synthesis of viral DNA and is prevented by reverse transcriptase inhibitors or reverse transcriptase active-site mutation. These results demonstrate that IP6 is required to build capsids that can successfully transit the cell and avoid host innate immune sensing.
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Affiliation(s)
- Guido Papa
- MRC Laboratory of Molecular Biology, Protein & Nucleic Acid DivisionCambridgeUK
| | - Anna Albecka
- MRC Laboratory of Molecular Biology, Protein & Nucleic Acid DivisionCambridgeUK
| | - Donna Mallery
- MRC Laboratory of Molecular Biology, Protein & Nucleic Acid DivisionCambridgeUK
| | - Marina Vaysburd
- MRC Laboratory of Molecular Biology, Protein & Nucleic Acid DivisionCambridgeUK
| | - Nadine Renner
- MRC Laboratory of Molecular Biology, Protein & Nucleic Acid DivisionCambridgeUK
| | - Leo C James
- MRC Laboratory of Molecular Biology, Protein & Nucleic Acid DivisionCambridgeUK
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15
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Stacey JCV, Tan A, Lu JM, James LC, Dick RA, Briggs JAG. Two structural switches in HIV-1 capsid regulate capsid curvature and host factor binding. Proc Natl Acad Sci U S A 2023; 120:e2220557120. [PMID: 37040417 PMCID: PMC10120081 DOI: 10.1073/pnas.2220557120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 04/12/2023] Open
Abstract
The mature HIV-1 capsid protects the viral genome and interacts with host proteins to travel from the cell periphery into the nucleus. To achieve this, the capsid protein, CA, constructs conical capsids from a lattice of hexamers and pentamers, and engages in and then relinquishes multiple interactions with cellular proteins in an orchestrated fashion. Cellular host factors including Nup153, CPSF6, and Sec24C engage the same pocket within CA hexamers. How CA assembles pentamers and hexamers of different curvatures, how CA oligomerization states or curvature might modulate host-protein interactions, and how binding of multiple cofactors to a single site is coordinated, all remain to be elucidated. Here, using single-particle cryoEM, we have determined the structure of the mature HIV-1 CA pentamer and hexamer from conical CA-IP6 polyhedra to ~3 Å resolution. We also determined structures of hexamers in the context of multiple lattice curvatures and number of pentamer contacts. Comparison of these structures, bound or not to host protein peptides, revealed two structural switches within HIV-1 CA that modulate peptide binding according to CA lattice curvature and whether CA is hexameric or pentameric. These observations suggest that the conical HIV-1 capsid has different host-protein binding properties at different positions on its surface, which may facilitate cell entry and represent an evolutionary advantage of conical morphology.
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Affiliation(s)
- James C. V. Stacey
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried82512, Germany
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QU, United Kingdom
| | - Aaron Tan
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QU, United Kingdom
| | - John M. Lu
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QU, United Kingdom
| | - Leo C. James
- PNAC Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QU, United Kingdom
| | - Robert A. Dick
- Department of Molecular Biology and Genetics, Cornell University, IthacaNY14853
| | - John A. G. Briggs
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried82512, Germany
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QU, United Kingdom
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16
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Shen Q, Kumari S, Xu C, Jang S, Shi J, Burdick RC, Levintov L, Xiong Q, Wu C, Devarkar SC, Tian T, Tripler TN, Hu Y, Yuan S, Temple J, Feng Q, Lusk CP, Aiken C, Engelman AN, Perilla JR, Pathak VK, Lin C, Xiong Y. The capsid lattice engages a bipartite NUP153 motif to mediate nuclear entry of HIV-1 cores. Proc Natl Acad Sci U S A 2023; 120:e2202815120. [PMID: 36943880 PMCID: PMC10068764 DOI: 10.1073/pnas.2202815120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 01/30/2023] [Indexed: 03/23/2023] Open
Abstract
Increasing evidence has suggested that the HIV-1 capsid enters the nucleus in a largely assembled, intact form. However, not much is known about how the cone-shaped capsid interacts with the nucleoporins (NUPs) in the nuclear pore for crossing the nuclear pore complex. Here, we elucidate how NUP153 binds HIV-1 capsid by engaging the assembled capsid protein (CA) lattice. A bipartite motif containing both canonical and noncanonical interaction modules was identified at the C-terminal tail region of NUP153. The canonical cargo-targeting phenylalanine-glycine (FG) motif engaged the CA hexamer. By contrast, a previously unidentified triple-arginine (RRR) motif in NUP153 targeted HIV-1 capsid at the CA tri-hexamer interface in the capsid. HIV-1 infection studies indicated that both FG- and RRR-motifs were important for the nuclear import of HIV-1 cores. Moreover, the presence of NUP153 stabilized tubular CA assemblies in vitro. Our results provide molecular-level mechanistic evidence that NUP153 contributes to the entry of the intact capsid into the nucleus.
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Affiliation(s)
- Qi Shen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
- Nanobiology Institute, Yale University, West Haven, CT06516
| | - Sushila Kumari
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD21702
| | - Chaoyi Xu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE19716
| | - Sooin Jang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
| | - Jiong Shi
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN37232
| | - Ryan C. Burdick
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD21702
| | - Lev Levintov
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE19716
| | - Qiancheng Xiong
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
- Nanobiology Institute, Yale University, West Haven, CT06516
| | - Chunxiang Wu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Swapnil C. Devarkar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Taoran Tian
- Nanobiology Institute, Yale University, West Haven, CT06516
| | - Therese N. Tripler
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Yingxia Hu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Shuai Yuan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Joshua Temple
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Qingzhou Feng
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
- Nanobiology Institute, Yale University, West Haven, CT06516
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
| | - Christopher Aiken
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN37232
| | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
| | - Juan R. Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE19716
| | - Vinay K. Pathak
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD21702
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, New Haven, CT06520
- Nanobiology Institute, Yale University, West Haven, CT06516
- Department of Biomedical Engineering, Yale University, New Haven, CT06511
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
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17
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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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18
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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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19
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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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20
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Zhang X, Sun L, Xu S, Shao X, Li Z, Ding D, Jiang X, Zhao S, Cocklin S, Clercq ED, Pannecouque C, Dick A, Liu X, Zhan P. Design, Synthesis, and Mechanistic Study of 2-Pyridone-Bearing Phenylalanine Derivatives as Novel HIV Capsid Modulators. Molecules 2022; 27:molecules27217640. [PMID: 36364467 PMCID: PMC9658817 DOI: 10.3390/molecules27217640] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
The AIDS pandemic is still of importance. HIV-1 and HIV-2 are the causative agents of this pandemic, and in the absence of a viable vaccine, drugs are continually required to provide quality of life for infected patients. The HIV capsid (CA) protein performs critical functions in the life cycle of HIV-1 and HIV-2, is broadly conserved across major strains and subtypes, and is underexploited. Therefore, it has become a therapeutic target of interest. Here, we report a novel series of 2-pyridone-bearing phenylalanine derivatives as HIV capsid modulators. Compound FTC-2 is the most potent anti-HIV-1 compound in the new series of compounds, with acceptable cytotoxicity in MT-4 cells (selectivity index HIV-1 > 49.57; HIV-2 > 17.08). However, compound TD-1a has the lowest EC50 in the anti-HIV-2 assays (EC50 = 4.86 ± 1.71 μM; CC50= 86.54 ± 29.24 μM). A water solubility test found that TD-1a showed a moderately increased water solubility compared with PF74, while the water solubility of FTC-2 was improved hundreds of times. Furthermore, we use molecular simulation studies to provide insight into the molecular contacts between the new compounds and HIV CA. We also computationally predict drug-like properties and metabolic stability for FTC-2 and TD-1a. Based on this analysis, TD-1a is predicted to have improved drug-like properties and metabolic stability over PF74. This study increases the repertoire of CA modulators and has important implications for developing anti-HIV agents with novel mechanisms, especially those that inhibit the often overlooked HIV-2.
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Affiliation(s)
- Xujie Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
- Department of Pharmacy, Qilu Hospital of Shandong University, 107 West Culture Road, Jinan 250012, China
| | - Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Xiaoyu Shao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Ziyi Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Dang Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Shujie Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Simon Cocklin
- Specifica, Inc., 1607 Alcaldesa Street, Santa Fe, NM 87501, USA
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 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 19102, 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, Shandong University, 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, Shandong University, 44 West Culture Road, Jinan 250012, China
- Correspondence: (C.P.); (A.D.); (X.L.); (P.Z.)
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21
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Regueiro-Ren A, Sit SY, Chen Y, Chen J, Swidorski JJ, Liu Z, Venables BL, Sin N, Hartz RA, Protack T, Lin Z, Zhang S, Li Z, Wu DR, Li P, Kempson J, Hou X, Gupta A, Rampulla R, Mathur A, Park H, Sarjeant A, Benitex Y, Rahematpura S, Parker D, Phillips T, Haskell R, Jenkins S, Santone KS, Cockett M, Hanumegowda U, Dicker I, Meanwell NA, Krystal M. The Discovery of GSK3640254, a Next-Generation Inhibitor of HIV-1 Maturation. J Med Chem 2022; 65:11927-11948. [PMID: 36044257 DOI: 10.1021/acs.jmedchem.2c00879] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
GSK3640254 is an HIV-1 maturation inhibitor (MI) that exhibits significantly improved antiviral activity toward a range of clinically relevant polymorphic variants with reduced sensitivity toward the second-generation MI GSK3532795 (BMS-955176). The key structural difference between GSK3640254 and its predecessor is the replacement of the para-substituted benzoic acid moiety attached at the C-3 position of the triterpenoid core with a cyclohex-3-ene-1-carboxylic acid substituted with a CH2F moiety at the carbon atom α- to the pharmacophoric carboxylic acid. This structural element provided a new vector with which to explore structure-activity relationships (SARs) and led to compounds with improved polymorphic coverage while preserving pharmacokinetic (PK) properties. The approach to the design of GSK3640254, the development of a synthetic route and its preclinical profile are discussed. GSK3640254 is currently in phase IIb clinical trials after demonstrating a dose-related reduction in HIV-1 viral load over 7-10 days of dosing to HIV-1-infected subjects.
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Affiliation(s)
- Alicia Regueiro-Ren
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey08543, United States
| | - Sing-Yuen Sit
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Yan Chen
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Jie Chen
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Jacob J Swidorski
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Zheng Liu
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Brian L Venables
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Ny Sin
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Richard A Hartz
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Tricia Protack
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Zeyu Lin
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Sharon Zhang
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Zhufang Li
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Dauh-Rurng Wu
- Department of Discovery Synthesis, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey08543, United States
| | - Peng Li
- Department of Discovery Synthesis, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey08543, United States
| | - James Kempson
- Department of Discovery Synthesis, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey08543, United States
| | - Xiaoping Hou
- Department of Discovery Synthesis, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey08543, United States
| | - Anuradha Gupta
- Department of Discovery Synthesis; Bristol Myers Squibb Research and Early Development, Bangalore 560099, India
| | - Richard Rampulla
- Department of Discovery Synthesis, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey08543, United States
| | - Arvind Mathur
- Department of Discovery Synthesis, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey08543, United States
| | - Hyunsoo Park
- Bristol Myers Squibb Chemical and Synthetic Development, New Brunswick, New Jersey08901, United States
| | - Amy Sarjeant
- Bristol Myers Squibb Chemical and Synthetic Development, New Brunswick, New Jersey08901, United States
| | - Yulia Benitex
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Sandhya Rahematpura
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Dawn Parker
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Thomas Phillips
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Roy Haskell
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Susan Jenkins
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Kenneth S Santone
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Mark Cockett
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Umesh Hanumegowda
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Ira Dicker
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Nicholas A Meanwell
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey08543, United States
| | - Mark Krystal
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
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22
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Yuan L, Gao F, Lv Z, Nayak D, Nayak A, Santos Bury PD, Cano KE, Jia L, Oleinik N, Atilgan FC, Ogretmen B, Williams KM, Davies C, El Oualid F, Wasmuth EV, Olsen SK. Crystal structures reveal catalytic and regulatory mechanisms of the dual-specificity ubiquitin/FAT10 E1 enzyme Uba6. Nat Commun 2022; 13:4880. [PMID: 35986001 PMCID: PMC9391358 DOI: 10.1038/s41467-022-32613-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 08/08/2022] [Indexed: 11/11/2022] Open
Abstract
The E1 enzyme Uba6 initiates signal transduction by activating ubiquitin and the ubiquitin-like protein FAT10 in a two-step process involving sequential catalysis of adenylation and thioester bond formation. To gain mechanistic insights into these processes, we determined the crystal structure of a human Uba6/ubiquitin complex. Two distinct architectures of the complex are observed: one in which Uba6 adopts an open conformation with the active site configured for catalysis of adenylation, and a second drastically different closed conformation in which the adenylation active site is disassembled and reconfigured for catalysis of thioester bond formation. Surprisingly, an inositol hexakisphosphate (InsP6) molecule binds to a previously unidentified allosteric site on Uba6. Our structural, biochemical, and biophysical data indicate that InsP6 allosterically inhibits Uba6 activity by altering interconversion of the open and closed conformations of Uba6 while also enhancing its stability. In addition to revealing the molecular mechanisms of catalysis by Uba6 and allosteric regulation of its activities, our structures provide a framework for developing Uba6-specific inhibitors and raise the possibility of allosteric regulation of other E1s by naturally occurring cellular metabolites.
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Affiliation(s)
- Lingmin Yuan
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Fei Gao
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Department of Research & Development, Beijing IPE Center for Clinical Laboratory CO, Beijing, 100176, China
| | - Zongyang Lv
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Digant Nayak
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Anindita Nayak
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Priscila Dos Santos Bury
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Kristin E Cano
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Lijia Jia
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Natalia Oleinik
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Firdevs Cansu Atilgan
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Besim Ogretmen
- Department of Biochemistry & Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Katelyn M Williams
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Christopher Davies
- Department of Biochemistry & Molecular Biology, University of South Alabama, Mobile, AL, 36688, USA
| | - Farid El Oualid
- UbiQ Bio B.V., Science Park 408, 1098 XH, Amsterdam, The Netherlands
| | - Elizabeth V Wasmuth
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Shaun K Olsen
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
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23
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Rousso I, Deshpande A. Applications of Atomic Force Microscopy in HIV-1 Research. Viruses 2022; 14:v14030648. [PMID: 35337055 PMCID: PMC8955997 DOI: 10.3390/v14030648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 12/10/2022] Open
Abstract
Obtaining an understanding of the mechanism underlying the interrelations between the structure and function of HIV-1 is of pivotal importance. In previous decades, this mechanism was addressed extensively in a variety of studies using conventional approaches. More recently, atomic force microscopy, which is a relatively new technique with unique capabilities, has been utilized to study HIV-1 biology. Atomic force microscopy can generate high-resolution images at the nanometer-scale and analyze the mechanical properties of individual HIV-1 virions, virus components (e.g., capsids), and infected live cells under near-physiological environments. This review describes the working principles and various imaging and analysis modes of atomic force microscopy, and elaborates on its distinctive contributions to HIV-1 research in areas such as mechanobiology and the physics of infection.
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24
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McFadden WM, Snyder AA, Kirby KA, Tedbury PR, Raj M, Wang Z, Sarafianos SG. Rotten to the core: antivirals targeting the HIV-1 capsid core. Retrovirology 2021; 18:41. [PMID: 34937567 PMCID: PMC8693499 DOI: 10.1186/s12977-021-00583-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/09/2021] [Indexed: 12/20/2022] Open
Abstract
The capsid core of HIV-1 is a large macromolecular assembly that surrounds the viral genome and is an essential component of the infectious virus. In addition to its multiple roles throughout the viral life cycle, the capsid interacts with multiple host factors. Owing to its indispensable nature, the HIV-1 capsid has been the target of numerous antiretrovirals, though most capsid-targeting molecules have not had clinical success until recently. Lenacapavir, a long-acting drug that targets the HIV-1 capsid, is currently undergoing phase 2/3 clinical trials, making it the most successful capsid inhibitor to-date. In this review, we detail the role of the HIV-1 capsid protein in the virus life cycle, categorize antiviral compounds based on their targeting of five sites within the HIV-1 capsid, and discuss their molecular interactions and mechanisms of action. The diverse range of inhibition mechanisms provides insight into possible new strategies for designing novel HIV-1 drugs and furthers our understanding of HIV-1 biology. ![]()
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Affiliation(s)
- William M McFadden
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Alexa A Snyder
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 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
| | - Philip R Tedbury
- 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
| | - Monika Raj
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, 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.
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25
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Zhang X, Sun L, Meuser ME, Zalloum WA, Xu S, Huang T, Cherukupalli S, Jiang X, Ding X, Tao Y, Kang D, De Clercq E, Pannecouque C, Dick A, Cocklin S, Liu X, Zhan P. Design, synthesis, and mechanism study of dimerized phenylalanine derivatives as novel HIV-1 capsid inhibitors. Eur J Med Chem 2021; 226:113848. [PMID: 34592608 DOI: 10.1016/j.ejmech.2021.113848] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 12/16/2022]
Abstract
HIV-1 capsid (CA) plays indispensable and multiple roles in the life cycle of HIV-1, become an attractive target in antiviral therapy. Herein, we report the design, synthesis, and mechanism study of a novel series of dimerized phenylalanine derivatives as HIV-1 capsid inhibitors using 2-piperazineone or 2,5-piperazinedione as a linker. The structure-activity relationship (SAR) indicated that dimerized phenylalanines were more potent than monomers of the same chemotype. Further, the inclusion of fluorine substituted phenylalanine and methoxyl substituted aniline was found to be beneficial for antiviral activity. From the synthesized series, Q-c4 was found to be the most potent compound with an EC50 value of 0.57 μM, comparable to PF74. Interestingly, Q-c4 demonstrated a slightly higher affinity to the CA monomer than the CA hexamer, commensurate with its more significant effect in the late-stage of the HIV-1 lifecycle. Competitive SPR experiments with peptides from CPSF6 and NUP153 revealed that Q-c4 binds to the interprotomer pocket of hexameric CA as designed. Single-round infection assays showed that Q-c4 interferes with the HIV-1 life cycle in a dual-stage manner, affecting both pre-and post-integration. Stability assays in human plasma and human liver microsomes indicated that although Q-c4 has improved stability over PF74, this kind of inhibitor still requires further optimization. And the results of the online molinspiration software predicted that Q-c4 has desirable physicochemical properties but some properties still have some violation from the Lipinski rule of five. Overall, the dimerized phenylalanines are promising novel platforms for developing future HIV-1 CA inhibitors with considerable potential for optimization.
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Affiliation(s)
- 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
| | - Lin Sun
- 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
| | - Megan E Meuser
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Waleed A Zalloum
- Department of Pharmacy, Faculty of Health Science, American University of Madaba, P.O Box 2882, Amman, 11821, Jordan
| | - Shujing Xu
- 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
| | - Tianguang Huang
- 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
| | - Srinivasulu Cherukupalli
- 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
| | - Xiangyi Jiang
- 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
| | - Xiao Ding
- 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
| | - Yucen Tao
- 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
| | - Dongwei Kang
- 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
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000, Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000, Leuven, Belgium.
| | - Alexej Dick
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA.
| | - Simon Cocklin
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA.
| | - 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.
| | - 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.
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26
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Stephan Oroszlan and the Proteolytic Processing of Retroviral Proteins: Following A Pro. Viruses 2021; 13:v13112218. [PMID: 34835024 PMCID: PMC8621278 DOI: 10.3390/v13112218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/22/2021] [Accepted: 10/24/2021] [Indexed: 12/26/2022] Open
Abstract
Steve Oroszlan determined the sequences at the ends of virion proteins for a number of different retroviruses. This work led to the insight that the amino-terminal amino acid of the mature viral CA protein is always proline. In this remembrance, we review Steve’s work that led to this insight and show how that insight was a necessary precursor to the work we have done in the subsequent years exploring the cleavage rate determinants of viral protease processing sites and the multiple roles the amino-terminal proline of CA plays after protease cleavage liberates it from its position in a protease processing site.
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27
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Saito A, Yamashita M. HIV-1 capsid variability: viral exploitation and evasion of capsid-binding molecules. Retrovirology 2021; 18:32. [PMID: 34702294 PMCID: PMC8549334 DOI: 10.1186/s12977-021-00577-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/13/2021] [Indexed: 11/17/2022] Open
Abstract
The HIV-1 capsid, a conical shell encasing viral nucleoprotein complexes, is involved in multiple post-entry processes during viral replication. Many host factors can directly bind to the HIV-1 capsid protein (CA) and either promote or prevent HIV-1 infection. The viral capsid is currently being explored as a novel target for therapeutic interventions. In the past few decades, significant progress has been made in our understanding of the capsid–host interactions and mechanisms of action of capsid-targeting antivirals. At the same time, a large number of different viral capsids, which derive from many HIV-1 mutants, naturally occurring variants, or diverse lentiviruses, have been characterized for their interactions with capsid-binding molecules in great detail utilizing various experimental techniques. This review provides an overview of how sequence variation in CA influences phenotypic properties of HIV-1. We will focus on sequence differences that alter capsid–host interactions and give a brief account of drug resistant mutations in CA and their mutational effects on viral phenotypes. Increased knowledge of the sequence-function relationship of CA helps us deepen our understanding of the adaptive potential of the viral capsid.
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Affiliation(s)
- Akatsuki Saito
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, Japan.,Center for Animal Disease Control, University of Miyazaki, Miyazaki, Miyazaki, Japan
| | - Masahiro Yamashita
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly. Viruses 2021; 13:v13091853. [PMID: 34578434 PMCID: PMC8473085 DOI: 10.3390/v13091853] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 11/17/2022] Open
Abstract
The small cellular molecule inositol hexakisphosphate (IP6) has been known for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like particles. However, the molecular details underlying this effect have been determined only recently, with the identification of the IP6 binding site in the immature Gag lattice. IP6 also promotes formation of the mature capsid protein (CA) lattice via a second IP6 binding site, and enhances core stability, creating a favorable environment for reverse transcription. IP6 also enhances assembly of other retroviruses, from both the Lentivirus and the Alpharetrovirus genera. These findings suggest that IP6 may have a conserved function throughout the family Retroviridae. Here, we discuss the different steps in the viral life cycle that are influenced by IP6, and describe in detail how IP6 interacts with the immature and mature lattices of different retroviruses.
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Abstract
Here, we used a fluorescent protein that is free in solution and is trapped in nuclear HIV-1 capsids to demonstrate that the capsids retain integrity and prevent mixing of macromolecules within the viral core and the cellular environment until just before integration. We also found that capsid integrity is maintained until just minutes before disassembly in the nucleus, revealing that uncoating proceeds rapidly after integrity loss. These valuable insights into the early stage of HIV-1 replication indicate that intact HIV-1 capsids are imported through nuclear pores, that reverse transcription is mostly completed within intact capsids, and that preintegration complex-host interactions facilitating integration and target site selection must occur within a short time frame between capsid disassembly and integration. We recently reported that HIV-1 cores that retained >94% of their capsid (CA) protein entered the nucleus and disassembled (uncoated) near their integration site <1.5 h before integration. However, whether the nuclear capsids lost their integrity by rupturing or a small loss of CA before capsid disassembly was unclear. Here, we utilized a previously reported vector in which green fluorescent protein is inserted in HIV-1 Gag (iGFP); proteolytic processing efficiently releases GFP, some of which remains trapped inside capsids and serves as a fluid phase content marker that is released when the capsids lose their integrity. We found that nuclear capsids retained their integrity until shortly before integration and lost their GFP content marker ∼1 to 3 min before loss of capsid-associated mRuby-tagged cleavage and polyadenylation specificity factor 6 (mRuby-CPSF6). In contrast, loss of GFP fused to CA and mRuby-CPSF6 occurred simultaneously, indicating that viral cores retain their integrity until just minutes before uncoating. Our results indicate that HIV-1 evolved to retain its capsid integrity and maintain a separation between macromolecules in the viral core and the nuclear environment until uncoating occurs just before integration. These observations imply that intact HIV-1 capsids are imported through nuclear pores; that reverse transcription occurs in an intact capsid; and that interactions between the preintegration complex and LEDGF/p75, and possibly other host factors that facilitate integration, must occur during the short time period between loss of capsid integrity and integration.
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AlBurtamani N, Paul A, Fassati A. The Role of Capsid in the Early Steps of HIV-1 Infection: New Insights into the Core of the Matter. Viruses 2021; 13:v13061161. [PMID: 34204384 PMCID: PMC8234406 DOI: 10.3390/v13061161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 01/27/2023] Open
Abstract
In recent years, major advances in research and experimental approaches have significantly increased our knowledge on the role of the HIV-1 capsid in the virus life cycle, from reverse transcription to integration and gene expression. This makes the capsid protein a good pharmacological target to inhibit HIV-1 replication. This review covers our current understanding of the role of the viral capsid in the HIV-1 life cycle and its interaction with different host factors that enable reverse transcription, trafficking towards the nucleus, nuclear import and integration into host chromosomes. It also describes different promising small molecules, some of them in clinical trials, as potential targets for HIV-1 therapy.
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HIV-1 uncoating occurs via a series of rapid biomechanical changes in the core related to individual stages of reverse transcription. J Virol 2021; 95:JVI.00166-21. [PMID: 33692202 PMCID: PMC8139671 DOI: 10.1128/jvi.00166-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The HIV core consists of the viral genome and associated proteins encased by a cone-shaped protein shell termed the capsid. Successful infection requires reverse transcription of the viral genome and disassembly of the capsid shell within a cell in a process known as uncoating. The integrity of the viral capsid is critical for reverse transcription, yet the viral capsid must be breached to release the nascent viral DNA prior to integration. We employed atomic force microscopy to study the stiffness changes in HIV-1 cores during reverse transcription in vitro in reactions containing the capsid-stabilizing host metabolite IP6 Cores exhibited a series of stiffness spikes, with up to three spikes typically occurring between 10-30, 40-80, and 120-160 minutes after initiation of reverse transcription. Addition of the reverse transcriptase (RT) inhibitor efavirenz eliminated the appearance of these spikes and the subsequent disassembly of the capsid, thus establishing that both result from reverse transcription. Using timed addition of efavirenz, and analysis of an RNAseH-defective RT mutant, we established that the first stiffness spike requires minus-strand strong stop DNA synthesis, with subsequent spikes requiring later stages of reverse transcription. Additional rapid AFM imaging experiments revealed repeated morphological changes in cores that were temporally correlated with the observed stiffness spikes. Our study reveals discrete mechanical changes in the viral core that are likely related to specific stages of reverse transcription. These reverse-transcription-induced changes in the capsid progressively remodel the viral core to prime it for temporally accurate uncoating in target cells.ImportanceFor successful infection, the HIV-1 genome, which is enclosed inside a capsid shell, must be reverse transcribed into double-stranded DNA and released from the capsid (in a process known as uncoating) before it can be integrated into the target cell genome. The mechanism of HIV-1 uncoating is a pivotal question of long standing. Using atomic force microscopy to analyze individual HIV-1 cores during reverse transcription, we observe a reproducible pattern of stiffness spikes. These spikes were shown to be associated with distinct stages of the reverse transcription reaction. Our findings suggest that these reverse-transcription-induced alterations gradually prepared the core for uncoating at the right time and location in target cells.
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Lev S, Bowring B, Desmarini D, Djordjevic JT. Inositol polyphosphate-protein interactions: Implications for microbial pathogenicity. Cell Microbiol 2021; 23:e13325. [PMID: 33721399 PMCID: PMC9286782 DOI: 10.1111/cmi.13325] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/03/2021] [Accepted: 03/07/2021] [Indexed: 11/29/2022]
Abstract
Inositol polyphosphates (IPs) and inositol pyrophosphates (PP-IPs) regulate diverse cellular processes in eukaryotic cells. IPs and PP-IPs are highly negatively charged and exert their biological effects by interacting with specific protein targets. Studies performed predominantly in mammalian cells and model yeasts have shown that IPs and PP-IPs modulate target function through allosteric regulation, by promoting intra- and intermolecular stabilization and, in the case of PP-IPs, by donating a phosphate from their pyrophosphate (PP) group to the target protein. Technological advances in genetics have extended studies of IP function to microbial pathogens and demonstrated that disrupting PP-IP biosynthesis and PP-IP-protein interaction has a profound impact on pathogenicity. This review summarises the complexity of IP-mediated regulation in eukaryotes, including microbial pathogens. It also highlights examples of poor conservation of IP-protein interaction outcome despite the presence of conserved IP-binding domains in eukaryotic proteomes.
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Affiliation(s)
- Sophie Lev
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia.,Sydney Medical School-Westmead, University of Sydney, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia
| | - Bethany Bowring
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia.,Sydney Medical School-Westmead, University of Sydney, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia
| | - Desmarini Desmarini
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia.,Sydney Medical School-Westmead, University of Sydney, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia
| | - Julianne Teresa Djordjevic
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia.,Sydney Medical School-Westmead, University of Sydney, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia
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Addressing Antiretroviral Drug Resistance with Host-Targeting Drugs-First Steps towards Developing a Host-Targeting HIV-1 Assembly Inhibitor. Viruses 2021; 13:v13030451. [PMID: 33802145 PMCID: PMC8001593 DOI: 10.3390/v13030451] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022] Open
Abstract
The concerning increase in HIV-1 resistance argues for prioritizing the development of host-targeting antiviral drugs because such drugs can offer high genetic barriers to the selection of drug-resistant viral variants. Targeting host proteins could also yield drugs that act on viral life cycle events that have proven elusive to inhibition, such as intracellular events of HIV-1 immature capsid assembly. Here, we review small molecule inhibitors identified primarily through HIV-1 self-assembly screens and describe how all act either narrowly post-entry or broadly on early and late events of the HIV-1 life cycle. We propose that a different screening approach could identify compounds that specifically inhibit HIV-1 Gag assembly, as was observed when a potent rabies virus inhibitor was identified using a host-catalyzed rabies assembly screen. As an example of this possibility, we discuss an antiretroviral small molecule recently identified using a screen that recapitulates the host-catalyzed HIV-1 capsid assembly pathway. This chemotype potently blocks HIV-1 replication in T cells by specifically inhibiting immature HIV-1 capsid assembly but fails to select for resistant viral variants over 37 passages, suggesting a host protein target. Development of such small molecules could yield novel host-targeting antiretroviral drugs and provide insight into chronic diseases resulting from dysregulation of host machinery targeted by these drugs.
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Zhuang S, Torbett BE. Interactions of HIV-1 Capsid with Host Factors and Their Implications for Developing Novel Therapeutics. Viruses 2021; 13:417. [PMID: 33807824 PMCID: PMC8001122 DOI: 10.3390/v13030417] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/21/2021] [Accepted: 02/25/2021] [Indexed: 12/11/2022] Open
Abstract
The Human Immunodeficiency Virus type 1 (HIV-1) virion contains a conical shell, termed capsid, encasing the viral RNA genome. After cellular entry of the virion, the capsid is released and ensures the protection and delivery of the HIV-1 genome to the host nucleus for integration. The capsid relies on many virus-host factor interactions which are regulated spatiotemporally throughout the course of infection. In this paper, we will review the current understanding of the highly dynamic HIV-1 capsid-host interplay during the early stages of viral replication, namely intracellular capsid trafficking after viral fusion, nuclear import, uncoating, and integration of the viral genome into host chromatin. Conventional anti-retroviral therapies primarily target HIV-1 enzymes. Insights of capsid structure have resulted in a first-in-class, long-acting capsid-targeting inhibitor, GS-6207 (Lenacapavir). This inhibitor binds at the interface between capsid protein subunits, a site known to bind host factors, interferes with capsid nuclear import, HIV particle assembly, and ordered assembly. Our review will highlight capsid structure, the host factors that interact with capsid, and high-throughput screening techniques, specifically genomic and proteomic approaches, that have been and can be used to identify host factors that interact with capsid. Better structural and mechanistic insights into the capsid-host factor interactions will significantly inform the understanding of HIV-1 pathogenesis and the development of capsid-centric antiretroviral therapeutics.
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Affiliation(s)
- Shentian Zhuang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA;
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Bruce E. Torbett
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA;
- 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 98105, USA
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Scoca V, Di Nunzio F. The HIV-1 Capsid: From Structural Component to Key Factor for Host Nuclear Invasion. Viruses 2021; 13:273. [PMID: 33578999 PMCID: PMC7916756 DOI: 10.3390/v13020273] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 02/07/2023] Open
Abstract
Since the discovery of HIV-1, the viral capsid has been recognized to have an important role as a structural protein that holds the viral genome, together with viral proteins essential for viral life cycle, such as the reverse transcriptase (RT) and the integrase (IN). The reverse transcription process takes place between the cytoplasm and the nucleus of the host cell, thus the Reverse Transcription Complexes (RTCs)/Pre-integration Complexes (PICs) are hosted in intact or partial cores. Early biochemical assays failed to identify the viral CA associated to the RTC/PIC, possibly due to the stringent detergent conditions used to fractionate the cells or to isolate the viral complexes. More recently, it has been observed that some host partners of capsid, such as Nup153 and CPSF6, can only bind multimeric CA proteins organized in hexamers. Those host factors are mainly located in the nuclear compartment, suggesting the entrance of the viral CA as multimeric structure inside the nucleus. Recent data show CA complexes within the nucleus having a different morphology from the cytoplasmic ones, clearly highlighting the remodeling of the viral cores during nuclear translocation. Thus, the multimeric CA complexes lead the viral genome into the host nuclear compartment, piloting the intranuclear journey of HIV-1 in order to successfully replicate. The aim of this review is to discuss and analyze the main discoveries to date that uncover the viral capsid as a key player in the reverse transcription and PIC maturation until the viral DNA integration into the host genome.
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Affiliation(s)
- Viviana Scoca
- Advanced Molecular Virology and Retroviral Dynamics Group, Department of Virology Pasteur Institute, 75015 Paris, France;
- BioSPC Doctoral School, Universitè de Paris, 75015 Paris, France
| | - Francesca Di Nunzio
- Advanced Molecular Virology and Retroviral Dynamics Group, Department of Virology Pasteur Institute, 75015 Paris, France;
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Wilbourne M, Zhang P. Visualizing HIV-1 Capsid and Its Interactions with Antivirals and Host Factors. Viruses 2021; 13:246. [PMID: 33557422 PMCID: PMC7914784 DOI: 10.3390/v13020246] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 02/03/2023] Open
Abstract
Understanding of the construction and function of the HIV capsid has advanced considerably in the last decade. This is due in large part to the development of more sophisticated structural techniques, particularly cryo-electron microscopy (cryoEM) and cryo-electron tomography (cryoET). The capsid is known to be a pleomorphic fullerene cone comprised of capsid protein monomers arranged into 200-250 hexamers and 12 pentamers. The latter of these induce high curvature necessary to close the cone at both ends. CryoEM/cryoET, NMR, and X-ray crystallography have collectively described these interactions to atomic or near-atomic resolutions. Further, these techniques have helped to clarify the role the HIV capsid plays in several parts of the viral life cycle, from reverse transcription to nuclear entry and integration into the host chromosome. This includes visualizing the capsid bound to host factors. Multiple proteins have been shown to interact with the capsid. Cyclophilin A, nucleoporins, and CPSF6 promote viral infectivity, while MxB and Trim5α diminish the viral infectivity. Finally, structural insights into the intra- and intermolecular interactions that govern capsid function have enabled development of small molecules, peptides, and truncated proteins to disrupt or stabilize the capsid to inhibit HIV replication. The most promising of these, GS6207, is now in clinical trial.
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Affiliation(s)
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
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Application of Advanced Light Microscopy to the Study of HIV and Its Interactions with the Host. Viruses 2021; 13:v13020223. [PMID: 33535486 PMCID: PMC7912744 DOI: 10.3390/v13020223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 11/24/2022] Open
Abstract
This review highlights the significant observations of human immunodeficiency virus (HIV) assembly, release and maturation made possible with advanced light microscopy techniques. The advances in technology which now enables these light microscopy measurements are discussed with special emphasis on live imaging approaches including Total Internal Reflection Fluorescence (TIRF), high-resolution light microscopy techniques including PALM and STORM and single molecule measurements, including Fluorescence Resonance Energy Transfer (FRET). The review concludes with a discussion on what new insights and understanding can be expected from these measurements.
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Structure, Function, and Interactions of the HIV-1 Capsid Protein. Life (Basel) 2021; 11:life11020100. [PMID: 33572761 PMCID: PMC7910843 DOI: 10.3390/life11020100] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 11/30/2022] Open
Abstract
The capsid (CA) protein of the human immunodeficiency virus type 1 (HIV-1) is an essential structural component of a virion and facilitates many crucial life cycle steps through interactions with host cell factors. Capsid shields the reverse transcription complex from restriction factors while it enables trafficking to the nucleus by hijacking various adaptor proteins, such as FEZ1 and BICD2. In addition, the capsid facilitates the import and localization of the viral complex in the nucleus through interaction with NUP153, NUP358, TNPO3, and CPSF-6. In the later stages of the HIV-1 life cycle, CA plays an essential role in the maturation step as a constituent of the Gag polyprotein. In the final phase of maturation, Gag is cleaved, and CA is released, allowing for the assembly of CA into a fullerene cone, known as the capsid core. The fullerene cone consists of ~250 CA hexamers and 12 CA pentamers and encloses the viral genome and other essential viral proteins for the next round of infection. As research continues to elucidate the role of CA in the HIV-1 life cycle and the importance of the capsid protein becomes more apparent, CA displays potential as a therapeutic target for the development of HIV-1 inhibitors.
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Identification of an Antiretroviral Small Molecule That Appears To Be a Host-Targeting Inhibitor of HIV-1 Assembly. J Virol 2021; 95:JVI.00883-20. [PMID: 33148797 PMCID: PMC7925099 DOI: 10.1128/jvi.00883-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 10/25/2020] [Indexed: 12/16/2022] Open
Abstract
Given the projected increase in multidrug-resistant HIV-1, there is an urgent need for development of antiretrovirals that act on virus life cycle stages not targeted by drugs currently in use. Host-targeting compounds are of particular interest because they can offer a high barrier to resistance. Here, we report identification of two related small molecules that inhibit HIV-1 late events, a part of the HIV-1 life cycle for which potent and specific inhibitors are lacking. This chemotype was discovered using cell-free protein synthesis and assembly systems that recapitulate intracellular host-catalyzed viral capsid assembly pathways. These compounds inhibit replication of HIV-1 in human T cell lines and peripheral blood mononuclear cells, and are effective against a primary isolate. They reduce virus production, likely by inhibiting a posttranslational step in HIV-1 Gag assembly. Notably, the compound colocalizes with HIV-1 Gag in situ; however, unexpectedly, selection experiments failed to identify compound-specific resistance mutations in gag or pol, even though known resistance mutations developed upon parallel nelfinavir selection. Thus, we hypothesized that instead of binding to Gag directly, these compounds localize to assembly intermediates, the intracellular multiprotein complexes containing Gag and host factors that form during immature HIV-1 capsid assembly. Indeed, imaging of infected cells shows compound colocalized with two host enzymes found in assembly intermediates, ABCE1 and DDX6, but not two host proteins found in other complexes. While the exact target and mechanism of action of this chemotype remain to be determined, our findings suggest that these compounds represent first-in-class, host-targeting inhibitors of intracellular events in HIV-1 assembly.IMPORTANCE The success of antiretroviral treatment for HIV-1 is at risk of being undermined by the growing problem of drug resistance. Thus, there is a need to identify antiretrovirals that act on viral life cycle stages not targeted by drugs in use, such as the events of HIV-1 Gag assembly. To address this gap, we developed a compound screen that recapitulates the intracellular events of HIV-1 assembly, including virus-host interactions that promote assembly. This effort led to the identification of a new chemotype that inhibits HIV-1 replication at nanomolar concentrations, likely by acting on assembly. This compound colocalized with Gag and two host enzymes that facilitate capsid assembly. However, resistance selection did not result in compound-specific mutations in gag, suggesting that the chemotype does not directly target Gag. We hypothesize that this chemotype represents a first-in-class inhibitor of virus production that acts by targeting a virus-host complex important for HIV-1 Gag assembly.
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Chen W, Jiang J, Gong L, Shu Z, Xiang D, Zhang X, Bi K, Diao H. Hepatitis B virus P protein initiates glycolytic bypass in HBV-related hepatocellular carcinoma via a FOXO3/miRNA-30b-5p/MINPP1 axis. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:1. [PMID: 33390177 PMCID: PMC7779247 DOI: 10.1186/s13046-020-01803-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/07/2020] [Indexed: 12/11/2022]
Abstract
Background Hepatitis B virus (HBV) infection is a crucial risk factor for hepatocellular carcinoma (HCC). However, its underlying mechanism remains understudied. Methods Microarray analysis was conducted to compare the genes and miRNAs in liver tissue from HBV-positive and HBV-negative HCC patients. Biological functions of these biomarkers in HBV-related HCC were validated via in vitro and in vivo experiments. Furthermore, we investigated the effect of HBV on the proliferation and migration of tumor cells in HBV-positive HCC tissue. Bioinformatics analysis was then performed to validate the clinical value of the biomarkers in a large HCC cohort. Results We found that a gene, MINPP1 from the glycolytic bypass metabolic pathway, has an important biological function in the development of HBV-positive HCC. MINPP1 is down-regulated in HBV-positive HCC and could inhibit the proliferation and migration of the tumor cells. Meanwhile, miRNA-30b-5p was found to be a stimulator for the proliferation of tumor cell through glycolytic bypass in HBV-positive HCC. More importantly, miRNA-30b-5p could significantly downregulate MINPP1 expression. Metabolic experiments showed that the miRNA-30b-5p/MINPP1 axis is able to accelerate the conversion of glucose to lactate and 2,3-bisphosphoglycerate (2,3-BPG). In the HBV-negative HCC cells, miRNA-30b-5p/MINPP1 could not regulate the glycolytic bypass to promote the tumorigenesis. However, once HBV was introduced into these cells, miRNA-30b-5p/MINPP1 significantly enhanced the proliferation, migration of tumor cells, and promoted the glycolytic bypass. We further revealed that HBV infection promoted the expression of miRNA-30b-5p through the interaction of HBV protein P (HBp) with FOXO3. Bioinformatics analysis on a large cohort dataset showed that high expression of MINPP1 was associated with favorable survival of HBV-positive HCC patients, which could lead to a slower progress of this disease. Conclusion Our study found that the HBp/FOXO3/miRNA-30b-5p/MINPP1 axis contributes to the development of HBV-positive HCC cells through the glycolytic bypass. We also presented miRNA-30b-5p/MINPP1 as a novel biomarker for HBV-positive HCC early diagnosis and a potential pharmaceutical target for antitumor therapy. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-020-01803-8.
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Affiliation(s)
- Wenbiao Chen
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Disease, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Jingjing Jiang
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Disease, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Lan Gong
- Microbiome Research Centre, St George and Sutherland Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Zheyue Shu
- Department of Surgery, First Affiliated Hospital, Division of Hepatobiliary & Pancreatic Surgery, Zhejiang University School of Medicine, Hangzhou, 310000, China.,Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, 310000, China
| | - Dairong Xiang
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Disease, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Xujun Zhang
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Disease, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Kefan Bi
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Disease, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Hongyan Diao
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Disease, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China.
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Xu C, Fischer DK, Rankovic S, Li W, Dick RA, Runge B, Zadorozhnyi R, Ahn J, Aiken C, Polenova T, Engelman AN, Ambrose Z, Rousso I, Perilla JR. Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis. PLoS Biol 2020; 18:e3001015. [PMID: 33332391 PMCID: PMC7775124 DOI: 10.1371/journal.pbio.3001015] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 12/31/2020] [Accepted: 11/26/2020] [Indexed: 02/07/2023] Open
Abstract
Reverse transcription, an essential event in the HIV-1 life cycle, requires deoxynucleotide triphosphates (dNTPs) to fuel DNA synthesis, thus requiring penetration of dNTPs into the viral capsid. The central cavity of the capsid protein (CA) hexamer reveals itself as a plausible channel that allows the passage of dNTPs into assembled capsids. Nevertheless, the molecular mechanism of nucleotide import into the capsid remains unknown. Employing all-atom molecular dynamics (MD) simulations, we established that cooperative binding between nucleotides inside a CA hexamer cavity results in energetically favorable conditions for passive translocation of dNTPs into the HIV-1 capsid. Furthermore, binding of the host cell metabolite inositol hexakisphosphate (IP6) enhances dNTP import, while binding of synthesized molecules like benzenehexacarboxylic acid (BHC) inhibits it. The enhancing effect on reverse transcription by IP6 and the consequences of interactions between CA and nucleotides were corroborated using atomic force microscopy, transmission electron microscopy, and virological assays. Collectively, our results provide an atomistic description of the permeability of the HIV-1 capsid to small molecules and reveal a novel mechanism for the involvement of metabolites in HIV-1 capsid stabilization, nucleotide import, and reverse transcription. This study shows that the HIV-1 capsid protein, in addition to its structural role, regulates reverse transcription, an essential metabolic process of the virus, by mediating the import of nucleotides. In addition, host cell metabolites such as inositol phosphates are recruited by the capsid to regulate viral DNA synthesis.
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Affiliation(s)
- Chaoyi Xu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, United States of America
- Pittsburgh Center for HIV Protein Interactions (PCHPI), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Douglas K. Fischer
- Pittsburgh Center for HIV Protein Interactions (PCHPI), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Sanela Rankovic
- Department of Physiology and Cell Biology, Ben-Gurion University of Negev, Beer Sheva, Israel
| | - Wen Li
- Pittsburgh Center for HIV Protein Interactions (PCHPI), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert A. Dick
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Brent Runge
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, United States of America
- Pittsburgh Center for HIV Protein Interactions (PCHPI), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Roman Zadorozhnyi
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, United States of America
- Pittsburgh Center for HIV Protein Interactions (PCHPI), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Jinwoo Ahn
- Pittsburgh Center for HIV Protein Interactions (PCHPI), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Christopher Aiken
- Pittsburgh Center for HIV Protein Interactions (PCHPI), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, United States of America
- Pittsburgh Center for HIV Protein Interactions (PCHPI), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Alan N. Engelman
- Pittsburgh Center for HIV Protein Interactions (PCHPI), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Zandrea Ambrose
- Pittsburgh Center for HIV Protein Interactions (PCHPI), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (ZA); (IR); (JRP)
| | - Itay Rousso
- Department of Physiology and Cell Biology, Ben-Gurion University of Negev, Beer Sheva, Israel
- * E-mail: (ZA); (IR); (JRP)
| | - Juan R. Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, United States of America
- Pittsburgh Center for HIV Protein Interactions (PCHPI), University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (ZA); (IR); (JRP)
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42
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Maffucci T, Falasca M. Signalling Properties of Inositol Polyphosphates. Molecules 2020; 25:molecules25225281. [PMID: 33198256 PMCID: PMC7696153 DOI: 10.3390/molecules25225281] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 12/16/2022] Open
Abstract
Several studies have identified specific signalling functions for inositol polyphosphates (IPs) in different cell types and have led to the accumulation of new information regarding their cellular roles as well as new insights into their cellular production. These studies have revealed that interaction of IPs with several proteins is critical for stabilization of protein complexes and for modulation of enzymatic activity. This has not only revealed their importance in regulation of several cellular processes but it has also highlighted the possibility of new pharmacological interventions in multiple diseases, including cancer. In this review, we describe some of the intracellular roles of IPs and we discuss the pharmacological opportunities that modulation of IPs levels can provide.
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Affiliation(s)
- Tania Maffucci
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
- Correspondence: (T.M.); (M.F.); Tel.: +61-08-92669712 (M.F.)
| | - Marco Falasca
- School of Pharmacy and Biomedical Sciences, CHIRI, Curtin University, Perth 6102, Australia
- Correspondence: (T.M.); (M.F.); Tel.: +61-08-92669712 (M.F.)
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43
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Christensen DE, Ganser-Pornillos BK, Johnson JS, Pornillos O, Sundquist WI. Reconstitution and visualization of HIV-1 capsid-dependent replication and integration in vitro. Science 2020; 370:eabc8420. [PMID: 33033190 PMCID: PMC8022914 DOI: 10.1126/science.abc8420] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/31/2020] [Indexed: 12/18/2022]
Abstract
During the first half of the viral life cycle, HIV-1 reverse transcribes its RNA genome and integrates the double-stranded DNA copy into a host cell chromosome. Despite progress in characterizing and inhibiting these processes, in situ mechanistic and structural studies remain challenging. This is because these operations are executed by individual viral preintegration complexes deep within cells. We therefore reconstituted and imaged the early stages of HIV-1 replication in a cell-free system. HIV-1 cores released from permeabilized virions supported efficient, capsid-dependent endogenous reverse transcription to produce double-stranded DNA genomes, which sometimes looped out from ruptured capsid walls. Concerted integration of both viral DNA ends into a target plasmid then proceeded in a cell extract-dependent reaction. This reconstituted system uncovers the role of the capsid in templating replication.
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Affiliation(s)
- Devin E Christensen
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Barbie K Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Jarrod S Johnson
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA.
| | - Wesley I Sundquist
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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44
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Yu A, Lee EMY, Jin J, Voth GA. Atomic-scale characterization of mature HIV-1 capsid stabilization by inositol hexakisphosphate (IP 6). SCIENCE ADVANCES 2020; 6:eabc6465. [PMID: 32938668 PMCID: PMC7494349 DOI: 10.1126/sciadv.abc6465] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/20/2020] [Indexed: 05/16/2023]
Abstract
Inositol hexakisphosphates (IP6) are cellular cofactors that promote the assembly of mature capsids of HIV. These negatively charged molecules coordinate an electropositive ring of arginines at the center of pores distributed throughout the capsid surface. Kinetic studies indicate that the binding of IP6 increases the stable lifetimes of the capsid by several orders of magnitude from minutes to hours. Using all-atom molecular dynamics simulations, we uncover the mechanisms that underlie the unusually high stability of mature capsids in complex with IP6 We find that capsid hexamers and pentamers have differential binding modes for IP6 Ligand density calculations show three sites of interaction with IP6 including at a known capsid inhibitor binding pocket. Free energy calculations demonstrate that IP6 preferentially stabilizes pentamers over hexamers to enhance fullerene modes of assembly. These results elucidate the molecular role of IP6 in stabilizing and assembling the retroviral capsid.
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Affiliation(s)
- Alvin Yu
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Elizabeth M Y Lee
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
| | - Jaehyeok Jin
- 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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45
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Ricana CL, Lyddon TD, Dick RA, Johnson MC. Primate lentiviruses require Inositol hexakisphosphate (IP6) or inositol pentakisphosphate (IP5) for the production of viral particles. PLoS Pathog 2020; 16:e1008646. [PMID: 32776974 PMCID: PMC7446826 DOI: 10.1371/journal.ppat.1008646] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/20/2020] [Accepted: 06/26/2020] [Indexed: 11/18/2022] Open
Abstract
Inositol hexakisphosphate (IP6) potently stimulates HIV-1 particle assembly in vitro and infectious particle production in vivo. However, knockout cells lacking inositol-pentakisphosphate 2-kinase (IPPK-KO), the enzyme that produces IP6 by phosphorylation of inositol pentakisphosphate (IP5), were still able to produce infectious HIV-1 particles at a greatly reduced rate. HIV-1 in vitro assembly can also be stimulated to a lesser extent with IP5, but until recently, it was not known if IP5 could also function in promoting assembly in vivo. Here we addressed whether there is an absolute requirement for IP6 or IP5 in the production of infectious HIV-1 particles. IPPK-KO cells expressed no detectable IP6 but elevated IP5 levels and displayed a 20-100-fold reduction in infectious particle production, correlating with lost virus release. Transient transfection of an IPPK expression vector stimulated infectious particle production and release in IPPK-KO but not wildtype cells. Several attempts to make IP6/IP5 deficient stable cells were not successful, but transient expression of the enzyme multiple inositol polyphosphate phosphatase-1 (MINPP1) into IPPK-KOs resulted in near ablation of IP6 and IP5. Under these conditions, we found that HIV-1 infectious particle production and virus release were essentially abolished (1000-fold reduction) demonstrating an IP6/IP5 requirement. However, other retroviruses including a Gammaretrovirus, a Betaretrovirus, and two non-primate Lentiviruses displayed only a modest (3-fold) reduction in infectious particle production from IPPK-KOs and were not significantly altered by expression of IPPK or MINPP1. The only other retrovirus found to show a clear IP6/IP5 dependence was the primate (macaque) Lentivirus Simian Immunodeficiency Virus, which displayed similar sensitivity as HIV-1. We were not able to determine if producer cell IP6/IP5 is required at additional steps beyond assembly because viral particles devoid of both molecules could not be generated. Finally, we found that loss of IP6/IP5 in viral target cells had no effect on permissivity to HIV-1 infection.
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Affiliation(s)
- Clifton L Ricana
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America
| | - Terri D Lyddon
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America
| | - Robert A Dick
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Marc C Johnson
- Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America
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46
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Wen Y, Feigenson GW, Vogt VM, Dick RA. Mechanisms of PI(4,5)P2 Enrichment in HIV-1 Viral Membranes. J Mol Biol 2020; 432:5343-5364. [PMID: 32739462 PMCID: PMC8262684 DOI: 10.1016/j.jmb.2020.07.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/12/2020] [Accepted: 07/26/2020] [Indexed: 01/10/2023]
Abstract
Phosphatidylinositol 4,5-bisphosphate (PIP2) is critical for HIV-1 virus assembly. The viral membrane is enriched in PIP2, suggesting that the virus assembles at PIP2-rich microdomains. We showed previously that in model membranes PIP2 can form nanoscopic clusters bridged by multivalent cations. Here, using purified proteins we quantitated the binding of HIV-1 Gag-related proteins to giant unilamellar vesicles containing either clustered or free PIP2. Myristoylated MA strongly preferred binding to clustered PIP2. By contrast, unmyristoylated HIV-1 MA, RSV MA, and a PH domain all preferred to interact with free PIP2. We also found that HIV-1 Gag multimerization promotes PIP2 clustering. Truncated Gag proteins comprising the MA, CA, and SP domains (MACASP) or the MA and CA domains (MACA) induced self-quenching of acyl chain-labeled fluorescent PIP2 in liposomes, implying clustering. However, HIV-1 MA itself did not induce PIP2 clustering. A CA inter-hexamer dimer interface mutation led to a loss of induced PIP2 clustering in MACA, indicating the importance of protein multimerization. Cryo-electron tomography of liposomes with bound MACA showed an amorphous protein layer on the membrane surface. Thus, it appears that while protein–protein interactions are required for PIP2 clustering, formation of a regular lattice is not. Protein-induced PIP2 clustering and multivalent cation-induced PIP2 clustering are additive. Taken together, these results provide the first evidence that HIV-1 Gag can selectively target pre-existing PIP2-enriched domains of the plasma membrane for viral assembly, and that Gag multimerization can further enrich PIP2 at assembly sites. These effects could explain the observed PIP2 enrichment in HIV-1.
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Affiliation(s)
- Yi Wen
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Gerald W Feigenson
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Volker M Vogt
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Robert A Dick
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA.
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47
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PF74 and Its Novel Derivatives Stabilize Hexameric Lattice of HIV-1 Mature-Like Particles. Molecules 2020; 25:molecules25081895. [PMID: 32325987 PMCID: PMC7221806 DOI: 10.3390/molecules25081895] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/09/2020] [Accepted: 04/15/2020] [Indexed: 01/23/2023] Open
Abstract
A major structural retroviral protein, capsid protein (CA), is able to oligomerize into two different hexameric lattices, which makes this protein a key component for both the early and late stages of HIV-1 replication. During the late stage, the CA protein, as part of the Gag polyprotein precursor, facilitates protein–protein interactions that lead to the assembly of immature particles. Following protease activation and Gag polyprotein processing, CA also drives the assembly of the mature viral core. In the early stage of infection, the role of the CA protein is distinct. It controls the disassembly of the mature CA hexameric lattice i.e., uncoating, which is critical for the reverse transcription of the single-stranded RNA genome into double stranded DNA. These properties make CA a very attractive target for small molecule functioning as inhibitors of HIV-1 particle assembly and/or disassembly. Of these, inhibitors containing the PF74 scaffold have been extensively studied. In this study, we reported a series of modifications of the PF74 molecule and its characterization through a combination of biochemical and structural approaches. Our data supported the hypothesis that PF74 stabilizes the mature HIV-1 CA hexameric lattice. We identified derivatives with a higher in vitro stabilization activity in comparison to the original PF74 molecule.
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48
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Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FKM. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLoS Pathog 2020; 16:e1008277. [PMID: 31986188 PMCID: PMC7004409 DOI: 10.1371/journal.ppat.1008277] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 02/06/2020] [Accepted: 12/11/2019] [Indexed: 01/11/2023] Open
Abstract
Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly.
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MESH Headings
- Amino Acid Sequence
- Animals
- Electron Microscope Tomography
- Equine Infectious Anemia/metabolism
- Equine Infectious Anemia/virology
- Gene Products, gag/chemistry
- Gene Products, gag/genetics
- Gene Products, gag/metabolism
- HIV Infections/metabolism
- HIV Infections/virology
- HIV-1/genetics
- HIV-1/physiology
- HIV-1/ultrastructure
- Horses
- Host-Pathogen Interactions
- Infectious Anemia Virus, Equine/chemistry
- Infectious Anemia Virus, Equine/genetics
- Infectious Anemia Virus, Equine/physiology
- Infectious Anemia Virus, Equine/ultrastructure
- Phytic Acid/metabolism
- Sequence Alignment
- Virion/genetics
- Virion/physiology
- Virion/ultrastructure
- Virus Assembly
- gag Gene Products, Human Immunodeficiency Virus/chemistry
- gag Gene Products, Human Immunodeficiency Virus/genetics
- gag Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Robert A. Dick
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail: (RAD); (FKMS)
| | - Chaoyi Xu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, United States of America
| | - Dustin R. Morado
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Clifton L. Ricana
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, United States of America
| | - Terri D. Lyddon
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, United States of America
| | - Arianna M. Broad
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - J. Ryan Feathers
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Marc C. Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, United States of America
| | - Volker M. Vogt
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Juan R. Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, United States of America
| | - John A. G. Briggs
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Florian K. M. Schur
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- * E-mail: (RAD); (FKMS)
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49
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Dostálková A, Hadravová R, Kaufman F, Křížová I, Škach K, Flegel M, Hrabal R, Ruml T, Rumlová M. A simple, high-throughput stabilization assay to test HIV-1 uncoating inhibitors. Sci Rep 2019; 9:17076. [PMID: 31745222 PMCID: PMC6863892 DOI: 10.1038/s41598-019-53483-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/30/2019] [Indexed: 02/04/2023] Open
Abstract
Shortly after entering the cell, HIV-1 copies its genomic RNA into double-stranded DNA in a process known as reverse transcription. This process starts inside a core consisting of an enclosed lattice of capsid proteins that protect the viral RNA from cytosolic sensors and degradation pathways. To accomplish reverse transcription and integrate cDNA into the host cell genome, the capsid shell needs to be disassembled, or uncoated. Premature or delayed uncoating attenuates reverse transcription and blocks HIV-1 infectivity. Small molecules that bind to the capsid lattice of the HIV-1 core and either destabilize or stabilize its structure could thus function as effective HIV-1 inhibitors. To screen for such compounds, we modified our recently developed FAITH assay to allow direct assessment of the stability of in vitro preassembled HIV-1 capsid-nucleocapsid (CANC) tubular particles. This new assay is a high-throughput fluorescence method based on measuring the amount of nucleic acid released from CANC complexes under disassembly conditions. The amount of disassembled CANC particles and released nucleic acid is proportional to the fluorescence signal, from which the relative percentage of CANC stability can be calculated. We consider our assay a potentially powerful tool for in vitro screening for compounds that alter HIV disassembly.
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Affiliation(s)
- Alžběta Dostálková
- Department of Biotechnology, University of Chemistry and Technology, Prague, 166 28, Czech Republic
| | - Romana Hadravová
- Department of Biotechnology, University of Chemistry and Technology, Prague, 166 28, Czech Republic
- Institute of Organic Chemistry and Biochemistry IOCB Research Centre & Gilead Sciences, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10, Prague, Czech Republic
| | - Filip Kaufman
- Department of Biotechnology, University of Chemistry and Technology, Prague, 166 28, Czech Republic
| | - Ivana Křížová
- Department of Biotechnology, University of Chemistry and Technology, Prague, 166 28, Czech Republic
| | - Kryštof Škach
- Department of Chemistry of Natural Compounds University of Chemistry and Technology, Prague, 166 28, Prague, Czech Republic
| | - Martin Flegel
- Department of Chemistry of Natural Compounds University of Chemistry and Technology, Prague, 166 28, Prague, Czech Republic
| | - Richard Hrabal
- NMR Laboratory, University of Chemistry and Technology, Prague, 166 28, Prague, Czech Republic
| | - Tomáš Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, 166 28, Prague, Czech Republic
| | - Michaela Rumlová
- Department of Biotechnology, University of Chemistry and Technology, Prague, 166 28, Czech Republic.
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50
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Huang PT, Summers BJ, Xu C, Perilla JR, Malikov V, Naghavi MH, Xiong Y. FEZ1 Is Recruited to a Conserved Cofactor Site on Capsid to Promote HIV-1 Trafficking. Cell Rep 2019; 28:2373-2385.e7. [PMID: 31422020 PMCID: PMC6736649 DOI: 10.1016/j.celrep.2019.07.079] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 05/08/2019] [Accepted: 07/22/2019] [Indexed: 12/31/2022] Open
Abstract
HIV-1 uses the microtubule network to traffic the viral capsid core toward the nucleus. Viral nuclear trafficking and infectivity require the kinesin-1 adaptor protein FEZ1. Here, we demonstrate that FEZ1 directly interacts with the HIV-1 capsid and specifically binds capsid protein (CA) hexamers. FEZ1 contains multiple acidic, poly-glutamate stretches that interact with the positively charged central pore of CA hexamers. The FEZ1-capsid interaction directly competes with nucleotides and inositol hexaphosphate (IP6) that bind at the same location. In addition, all-atom molecular dynamic (MD) simulations establish the molecular details of FEZ1-capsid interactions. Functionally, mutation of the FEZ1 capsid-interacting residues significantly reduces trafficking of HIV-1 particles toward the nucleus and early infection. These findings support a model in which the central capsid hexamer pore is a general HIV-1 cofactor-binding hub and FEZ1 serves as a unique CA hexamer pattern sensor to recognize this site and promote capsid trafficking in the cell.
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Affiliation(s)
- Pei-Tzu Huang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Brady James Summers
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Chaoyi Xu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Viacheslav Malikov
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Mojgan H Naghavi
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
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