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Tao K, Zhou J, Nagarajan P, Tzou PL, Shafer RW. Comprehensive database of HIV mutations selected during antiretroviral in vitro passage experiments. Antiviral Res 2024; 230:105988. [PMID: 39154752 DOI: 10.1016/j.antiviral.2024.105988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 08/20/2024]
Abstract
BACKGROUND In vitro passage experiments are crucial to the development of antiretroviral (ARV) drugs. METHODS We created an online database containing data from 102 published studies in which HIV-1 or HIV-2 was cultured with increasing concentrations of the FDA-approved nucleoside RT inhibitors (NRTIs), nonnucleoside RT inhibitors (NNRTIs), integrase strand transfer inhibitors (INSTIs), protease inhibitors (PIs), capsid inhibitor (CAI) lenacapavir, and nucleoside RT translocation inhibitor (NRTTI) islatravir. We summarized the mutations selected in the subset of passage experiments with NRTIs lamivudine (3TC), emtricitabine (FTC), abacavir (ABC), tenofovir (TFV), and zidovudine (AZT), NNRTIs doravirine (DOR), efavirenz (EFV), and rilpivirine (RPV), INSTIs bictegravir (BIC), cabotegravir (CAB), and dolutegravir (DTG), and PIs atazanavir (ATV), darunavir (DRV), and lopinavir (LPV). Mutations selected in vitro were compared with those selected in persons receiving the same ARV. RESULTS Twenty-seven studies described 89 experiments of wildtype isolates passaged with 3TC, FTC, ABC, TFV, or AZT; sixteen studies described 89 experiments passaged with EFV, RPV, or DOR; eleven studies described 76 experiments passaged with the INSTIs BIC, CAB, or DTG; six studies described 33 experiments passaged with ATV, LPV, or DRV. With several exceptions, mutations selected in two or more experiments were among the most common mutations selected in persons receiving the same ARV. CONCLUSIONS We created a database of published ARV in vitro selection experiments. Mutations emerging from these experiments generally predict those observed in persons receiving the same ARV. However, there are notable differences in mutation frequencies between in vitro and in vivo settings.
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Affiliation(s)
- Kaiming Tao
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Jinru Zhou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Pavithra Nagarajan
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Philip L Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, 94305, USA.
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2
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Ngo W, Peukes JT, Baldwin A, Xue ZW, Hwang S, Stickels RR, Lin Z, Satpathy AT, Wells JA, Schekman R, Nogales E, Doudna JA. Mechanism-guided engineering of a minimal biological particle for genome editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604809. [PMID: 39091760 PMCID: PMC11291128 DOI: 10.1101/2024.07.23.604809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
The widespread application of genome editing to treat or even cure disease requires the delivery of genome editors into the nucleus of target cells. Enveloped Delivery Vehicles (EDVs) are engineered virally-derived particles capable of packaging and delivering CRISPR-Cas9 ribonucleoproteins (RNPs). However, the presence of lentiviral genome encapsulation and replication components in EDVs has obscured the underlying delivery mechanism and precluded particle optimization. Here we show that Cas9 RNP nuclear delivery is independent of the native lentiviral capsid structure. Instead, EDV-mediated genome editing activity corresponds directly to the number of nuclear localization sequences on the Cas9 enzyme. EDV structural analysis using cryo-electron tomography and small molecule inhibitors guided the removal of ~80% of viral residues, creating a minimal EDV (miniEDV) that retains full RNP delivery capability. MiniEDVs are 25% smaller yet package equivalent amounts of Cas9 RNPs relative to the original EDVs, and demonstrated increased editing in cell lines and therapeutically-relevant primary human T cells. These results show that virally-derived particles can be streamlined to create efficacious genome editing delivery vehicles that could simplify production and manufacturing.
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Affiliation(s)
- Wayne Ngo
- Innovative Genomics Institute; University of California, Berkeley; Berkeley CA, USA
- Gladstone Institutes; San Francisco, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley; Berkeley, CA, USA
| | - Julia T. Peukes
- California Institute for Quantitative Biosciences, University of California, Berkeley; Berkeley, CA, USA
| | - Alisha Baldwin
- Innovative Genomics Institute; University of California, Berkeley; Berkeley CA, USA
- Gladstone Institutes; San Francisco, CA, USA
| | - Zhiwei Wayne Xue
- Innovative Genomics Institute; University of California, Berkeley; Berkeley CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, USA
| | - Sidney Hwang
- Department of Pathology, Stanford University; Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology; San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy; San Francisco, CA, USA
| | - Robert R. Stickels
- Department of Pathology, Stanford University; Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology; San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy; San Francisco, CA, USA
| | - Zhi Lin
- Department of Pharmaceutical Chemistry, University of California, San Francisco; San Francisco, CA, USA
| | - Ansuman T. Satpathy
- Department of Pathology, Stanford University; Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology; San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy; San Francisco, CA, USA
| | - James A. Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco; San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco; San Francisco, CA, USA
| | - Randy Schekman
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley; Berkeley CA, USA
| | - Eva Nogales
- California Institute for Quantitative Biosciences, University of California, Berkeley; Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley; Berkeley CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory; Berkeley, CA, USA
| | - Jennifer A. Doudna
- Innovative Genomics Institute; University of California, Berkeley; Berkeley CA, USA
- Gladstone Institutes; San Francisco, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley; Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology; San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley; Berkeley CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory; Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley; Berkeley, CA, USA
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3
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Chaudhari SB, Kumar A, Mankar VH, Banerjee S, Kumar D, Mubarak NM, Dehghani MH. Diverse role, structural trends, and applications of fluorinated sulphonamide compounds in agrochemical and pharmaceutical fields. Heliyon 2024; 10:e32434. [PMID: 38975170 PMCID: PMC11226812 DOI: 10.1016/j.heliyon.2024.e32434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 06/02/2024] [Accepted: 06/04/2024] [Indexed: 07/09/2024] Open
Abstract
Our knowledge of fluorine's unique and complex properties has significantly increased over the past 20 years. Consequently, more sophisticated and innovative techniques have emerged to incorporate this feature into the design of potential drug candidates. In recent years, researchers have become interested in synthesizing fluoro-sulphonamide compounds to discover new chemical entities with distinct and unexpected physical, chemical, and biological characteristics. The fluorinated sulphonamide molecules have shown significant biomedical importance. Their potential is not limited to biomedical applications but also includes crop protection. The discovery of novel fluorine and Sulfur compounds has highlighted their importance in the chemical sector, particularly in the agrochemical and medicinal fields. Recently, several fluorinated sulphonamide derivatives have been developed and frequently used by agriculturalists to produce food for the growing global population. These molecules have also exhibited their potential in health by inhibiting various human diseases. In today's world, it is crucial to have a steady supply of innovative pharmaceutical and agrochemical molecules that are highly effective, less harmful to the environment, and affordable. This review summarizes the available information on the activity of Fluorine and Sulphonamide compounds, which have proven active in pharmaceuticals and agrochemicals with excellent environmental and human health approaches. Moreover, it focuses on the current literature on the chemical structures, the application of fluorinated sulphonamide compounds against various pathological conditions, and their effectiveness in crop protection.
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Affiliation(s)
- Shankar B. Chaudhari
- Department of Chemistry, School of Chemical Engineering and Physical Sciences, Lovely Professional University, Jalandhar, Punjab, India
| | - Anupam Kumar
- Department of Biotechnology, School of Bioengineering and Bio Sciences, Lovely Professional University, Jalandhar, Punjab, India
| | - Viraj H. Mankar
- Department of Chemistry, Queensland University of Technology Brisbane, Australia
| | - Shaibal Banerjee
- Department of Applied Chemistry, Defence Institute of Advanced Technology, (DU), Girinagar, Pune 411025, India
| | - Deepak Kumar
- Department of Chemistry, School of Chemical Engineering and Physical Sciences, Lovely Professional University, Jalandhar, Punjab, India
| | - Nabisab Mujawar Mubarak
- Petroleum and Chemical Engineering, Faculty of Engineering, Universiti Teknologi Brunei, Bandar Seri Begawan, BE1410, Brunei Darussalam
- Department of Biosciences, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - Mohammad Hadi Dehghani
- Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Center for Solid Waste Research, Institute for Environmental Research, Tehran University of Medical Sciences, Tehran, Iran
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4
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Schirra RT, dos Santos NFB, Ganser-Pornillos BK, Pornillos O. Arg18 Substitutions Reveal the Capacity of the HIV-1 Capsid Protein for Non-Fullerene Assembly. Viruses 2024; 16:1038. [PMID: 39066201 PMCID: PMC11281672 DOI: 10.3390/v16071038] [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: 02/14/2024] [Revised: 06/21/2024] [Accepted: 06/22/2024] [Indexed: 07/28/2024] Open
Abstract
In the fullerene cone HIV-1 capsid, the central channels of the hexameric and pentameric capsomers each contain a ring of arginine (Arg18) residues that perform essential roles in capsid assembly and function. In both the hexamer and pentamer, the Arg18 rings coordinate inositol hexakisphosphate, an assembly and stability factor for the capsid. Previously, it was shown that amino-acid substitutions of Arg18 can promote pentamer incorporation into capsid-like particles (CLPs) that spontaneously assemble in vitro under high-salt conditions. Here, we show that these Arg18 mutant CLPs contain a non-canonical pentamer conformation and distinct lattice characteristics that do not follow the fullerene geometry of retroviral capsids. The Arg18 mutant pentamers resemble the hexamer in intra-oligomeric contacts and form a unique tetramer-of-pentamers that allows for incorporation of an octahedral vertex with a cross-shaped opening in the hexagonal capsid lattice. Our findings highlight an unexpected degree of structural plasticity in HIV-1 capsid assembly.
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Affiliation(s)
- Randall T. Schirra
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA (N.F.B.d.S.)
| | - Nayara F. B. dos Santos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA (N.F.B.d.S.)
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Barbie K. Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA (N.F.B.d.S.)
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA (N.F.B.d.S.)
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
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McGraw A, Hillmer G, Choi J, Narayan K, Mehedincu SM, Marquez D, Tibebe H, DeCicco-Skinner KL, Izumi T. Evaluating HIV-1 Infectivity and Virion Maturation across Varied Producer Cells with a Novel FRET-Based Detection and Quantification Assay. Int J Mol Sci 2024; 25:6396. [PMID: 38928103 PMCID: PMC11204348 DOI: 10.3390/ijms25126396] [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: 04/29/2024] [Revised: 05/27/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
The maturation of HIV-1 virions is a crucial process in viral replication. Although T-cells are a primary source of virus production, much of our understanding of virion maturation comes from studies using the HEK293T human embryonic kidney cell line. Notably, there is a lack of comparative analyses between T-cells and HEK293T cells in terms of virion maturation efficiency in existing literature. We previously developed an advanced virion visualization system based on the FRET principle, enabling the effective distinction between immature and mature virions via fluorescence microscopy. In this study, we utilized pseudotyped, single-round infectious viruses tagged with FRET labels (HIV-1 Gag-iFRET∆Env) derived from Jurkat (a human T-lymphocyte cell line) and HEK293T cells to evaluate their virion maturation rates. HEK293T-derived virions demonstrated a maturity rate of 81.79%, consistent with other studies and our previous findings. However, virions originating from Jurkat cells demonstrated a significantly reduced maturation rate of 68.67% (p < 0.0001). Correspondingly, viruses produced from Jurkat cells exhibited significantly reduced infectivity compared to those derived from HEK293T cells, with the relative infectivity measured at 65.3%. This finding is consistent with the observed relative maturation rate of viruses produced by Jurkat cells. These findings suggest that initiation of virion maturation directly correlates with viral infectivity. Our observation highlights the dynamic nature of virus-host interactions and their implications for virion production and infectivity.
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Affiliation(s)
- Aidan McGraw
- Department of Biology, College of Arts and Sciences, American University, Washington, DC 20016, USA; (A.M.); (G.H.); (J.C.); (K.N.); (S.M.M.); (D.M.); (H.T.); (K.L.D.-S.)
| | - Grace Hillmer
- Department of Biology, College of Arts and Sciences, American University, Washington, DC 20016, USA; (A.M.); (G.H.); (J.C.); (K.N.); (S.M.M.); (D.M.); (H.T.); (K.L.D.-S.)
| | - Jeongpill Choi
- Department of Biology, College of Arts and Sciences, American University, Washington, DC 20016, USA; (A.M.); (G.H.); (J.C.); (K.N.); (S.M.M.); (D.M.); (H.T.); (K.L.D.-S.)
| | - Kedhar Narayan
- Department of Biology, College of Arts and Sciences, American University, Washington, DC 20016, USA; (A.M.); (G.H.); (J.C.); (K.N.); (S.M.M.); (D.M.); (H.T.); (K.L.D.-S.)
| | - Stefania M. Mehedincu
- Department of Biology, College of Arts and Sciences, American University, Washington, DC 20016, USA; (A.M.); (G.H.); (J.C.); (K.N.); (S.M.M.); (D.M.); (H.T.); (K.L.D.-S.)
| | - Dacia Marquez
- Department of Biology, College of Arts and Sciences, American University, Washington, DC 20016, USA; (A.M.); (G.H.); (J.C.); (K.N.); (S.M.M.); (D.M.); (H.T.); (K.L.D.-S.)
| | - Hasset Tibebe
- Department of Biology, College of Arts and Sciences, American University, Washington, DC 20016, USA; (A.M.); (G.H.); (J.C.); (K.N.); (S.M.M.); (D.M.); (H.T.); (K.L.D.-S.)
| | - Kathleen L. DeCicco-Skinner
- Department of Biology, College of Arts and Sciences, American University, Washington, DC 20016, USA; (A.M.); (G.H.); (J.C.); (K.N.); (S.M.M.); (D.M.); (H.T.); (K.L.D.-S.)
| | - Taisuke Izumi
- Department of Biology, College of Arts and Sciences, American University, Washington, DC 20016, USA; (A.M.); (G.H.); (J.C.); (K.N.); (S.M.M.); (D.M.); (H.T.); (K.L.D.-S.)
- District of Columbia Center for AIDS Research, Washington, DC 20052, USA
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6
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Sumner RP, Blest H, Lin M, Maluquer de Motes C, Towers GJ. HIV-1 with gag processing defects activates cGAS sensing. Retrovirology 2024; 21:10. [PMID: 38778414 PMCID: PMC11112816 DOI: 10.1186/s12977-024-00643-0] [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: 04/08/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Detection of viruses by host pattern recognition receptors induces the expression of type I interferon (IFN) and IFN-stimulated genes (ISGs), which suppress viral replication. Numerous studies have described HIV-1 as a poor activator of innate immunity in vitro. The exact role that the viral capsid plays in this immune evasion is not fully understood. RESULTS To better understand the role of the HIV-1 capsid in sensing we tested the effect of making HIV-1 by co-expressing a truncated Gag that encodes the first 107 amino acids of capsid fused with luciferase or GFP, alongside wild type Gag-pol. We found that unlike wild type HIV-1, viral particles produced with a mixture of wild type and truncated Gag fused to luciferase or GFP induced a potent IFN response in THP-1 cells and macrophages. Innate immune activation by Gag-fusion HIV-1 was dependent on reverse transcription and DNA sensor cGAS, suggesting activation of an IFN response by viral DNA. Further investigation revealed incorporation of the Gag-luciferase/GFP fusion proteins into viral particles that correlated with subtle defects in wild type Gag cleavage and a diminished capacity to saturate restriction factor TRIM5α, likely due to aberrant particle formation. We propose that expression of the Gag fusion protein disturbs the correct cleavage and maturation of wild type Gag, yielding viral particles that are unable to effectively shield viral DNA from detection by innate sensors including cGAS. CONCLUSIONS These data highlight the crucial role of capsid in innate evasion and support growing literature that disruption of Gag cleavage and capsid formation induces a viral DNA- and cGAS-dependent innate immune response. Together these data demonstrate a protective role for capsid and suggest that antiviral activity of capsid-targeting antivirals may benefit from enhanced innate and adaptive immunity in vivo.
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Affiliation(s)
- Rebecca P Sumner
- Division of Infection and Immunity, University College London, 90 Gower Street, London, WC1E 6BT, UK.
- Department of Microbial Sciences, University of Surrey, Guildford, GU2 7XH, UK.
| | - Henry Blest
- Division of Infection and Immunity, University College London, 90 Gower Street, London, WC1E 6BT, UK
| | - Meiyin Lin
- Division of Infection and Immunity, University College London, 90 Gower Street, London, WC1E 6BT, UK
| | | | - Greg J Towers
- Division of Infection and Immunity, University College London, 90 Gower Street, London, WC1E 6BT, UK
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7
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Smith RA, Raugi DN, Nixon RS, Seydi M, Margot NA, Callebaut C, Gottlieb GS. Antiviral Activity of Lenacapavir Against Human Immunodeficiency Virus Type 2 (HIV-2) Isolates and Drug-Resistant HIV-2 Mutants. J Infect Dis 2024; 229:1290-1294. [PMID: 38060982 PMCID: PMC11095534 DOI: 10.1093/infdis/jiad562] [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: 07/06/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 03/07/2024] Open
Abstract
The activity of lenacapavir against human immunodeficiency virus type 1 (HIV-1) has been extensively evaluated in vitro, but comparable data for human immunodeficiency virus type 2 (HIV-2) are scarce. We determined the anti-HIV-2 activity of lenacapavir using single-cycle infections of MAGIC-5A cells and multicycle infections of a T-cell line. Lenacapavir exhibited low-nanomolar activity against HIV-2, but was 11- to 14-fold less potent against HIV-2 in comparison to HIV-1. Mutations in HIV-2 that confer resistance to other antiretrovirals did not confer cross-resistance to lenacapavir. Although lenacapavir-containing regimens might be considered for appropriate patients with HIV-2, more frequent viral load and/or CD4 testing may be needed to assess clinical response.
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Affiliation(s)
- Robert A Smith
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Dana N Raugi
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Robert S Nixon
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Moussa Seydi
- Service des Maladies Infectieuses et Tropicales, Centre Hospitalier National Universitaire de Fann, Dakar, Senegal
| | | | | | - Geoffrey S Gottlieb
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
- Department of Global Health, University of Washington, Seattle
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Scott TM, Arnold LM, Powers JA, McCann DA, Christensen DE, Pereira MJ, Zhou W, Torrez RM, Iwasa JH, Kranzusch PJ, Sundquist WI, Johnson JS. Cell-free assays reveal the HIV-1 capsid protects reverse transcripts from cGAS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590513. [PMID: 38712059 PMCID: PMC11071359 DOI: 10.1101/2024.04.22.590513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Retroviruses can be detected by the innate immune sensor cyclic GMP-AMP synthase (cGAS), which recognizes reverse-transcribed DNA and activates an antiviral response. However, the extent to which HIV-1 shields its genome from cGAS recognition remains unclear. To study this process in mechanistic detail, we reconstituted reverse transcription, genome release, and innate immune sensing of HIV-1 in a cell-free system. We found that wild-type HIV-1 capsids protect their genomes from cGAS even after completion of reverse transcription. Viral DNA could be "deprotected" by thermal stress, capsid mutations, or reduced concentrations of inositol hexakisphosphate (IP6) that destabilize the capsid. Strikingly, capsid inhibitors also disrupted viral cores and dramatically potentiated cGAS activity, both in vitro and in cellular infections. Our results provide biochemical evidence that the HIV-1 capsid lattice conceals the genome from cGAS and that chemical or physical disruption of the viral core can expose HIV-1 DNA and activate innate immune signaling.
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Affiliation(s)
- Tiana M. Scott
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Lydia M. Arnold
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Jordan A. Powers
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Delaney A. McCann
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Devin E. Christensen
- Department of Biochemistry, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Miguel J. Pereira
- Department of Biochemistry, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Wen Zhou
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology; Shenzhen, Guangdong 518055, China
| | - Rachel M. Torrez
- Department of Biochemistry, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Janet H. Iwasa
- Department of Biochemistry, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Philip J. Kranzusch
- Department of Microbiology, Harvard Medical School; Boston, MA 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute; Boston, MA 02115, USA
| | - Wesley I. Sundquist
- Department of Biochemistry, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Jarrod S. Johnson
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
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9
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Eschbach JE, Puray-Chavez M, Mohammed S, Wang Q, Xia M, Huang LC, Shan L, Kutluay SB. HIV-1 capsid stability and reverse transcription are finely balanced to minimize sensing of reverse transcription products via the cGAS-STING pathway. mBio 2024; 15:e0034824. [PMID: 38530034 PMCID: PMC11077976 DOI: 10.1128/mbio.00348-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
A critical determinant for early post-entry events, the HIV-1 capsid (CA) protein forms the conical core when it rearranges around the dimeric RNA genome and associated viral proteins. Although mutations in CA have been reported to alter innate immune sensing of HIV-1, a direct link between core stability and sensing of HIV-1 nucleic acids has not been established. Herein, we assessed how manipulating the stability of the CA lattice through chemical and genetic approaches affects innate immune recognition of HIV-1. We found that destabilization of the CA lattice resulted in potent sensing of reverse transcription products when destabilization per se does not completely block reverse transcription. Surprisingly, due to the combined effects of enhanced reverse transcription and defects in nuclear entry, two separate CA mutants that form hyperstable cores induced innate immune sensing more potently than destabilizing CA mutations. At low concentrations that allowed the accumulation of reverse transcription products, CA-targeting compounds GS-CA1 and lenacapavir measurably impacted CA lattice stability in cells and modestly enhanced innate immune sensing of HIV. Interestingly, innate immune activation observed with viruses containing unstable cores was abolished by low doses of lenacapavir. Innate immune activation observed with both hyperstable and unstable CA mutants was dependent on the cGAS-STING DNA-sensing pathway and reverse transcription. Overall, our findings demonstrate that CA lattice stability and reverse transcription are finely balanced to support reverse transcription and minimize cGAS-STING-mediated sensing of the resulting viral DNA. IMPORTANCE In HIV-1 particles, the dimeric RNA genome and associated viral proteins and enzymes are encased in a proteinaceous lattice composed of the viral capsid protein. Herein, we assessed how altering the stability of this capsid lattice through orthogonal genetic and chemical approaches impacts the induction of innate immune responses. Specifically, we found that decreasing capsid lattice stability results in more potent sensing of viral reverse transcription products, but not the genomic RNA, in a cGAS-STING-dependent manner. The recently developed capsid inhibitors lenacapavir and GS-CA1 enhanced the innate immune sensing of HIV-1. Unexpectedly, due to increased levels of reverse transcription and cytosolic accumulation of the resulting viral cDNA, capsid mutants with hyperstable cores also resulted in the potent induction of type I interferon-mediated innate immunity. Our findings suggest that HIV-1 capsid lattice stability and reverse transcription are finely balanced to minimize exposure of reverse transcription products in the cytosol of host cells.
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Affiliation(s)
- Jenna E. Eschbach
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Maritza Puray-Chavez
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Shawn Mohammed
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Qiankun Wang
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Ming Xia
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Lin-Chen Huang
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Liang Shan
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Sebla B. Kutluay
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
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10
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McGraw A, Hillmer G, Choi J, Narayan K, Marquez D, Tibebe H, Izumi T. Evaluating HIV-1 Infectivity and Virion Maturation Across Varied Producer Cells with a Novel FRET-Based Detection and Quantification Assay. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.25.573317. [PMID: 38234844 PMCID: PMC10793453 DOI: 10.1101/2023.12.25.573317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The maturation of HIV-1 virions is a crucial process in viral replication. Although T cells are a primary source of virus production, much of our understanding of virion maturation comes from studies using the HEK293T human embryonic kidney cell line. Notably, there is a lack of comparative analyses between T cells and HEK293T cells in terms of virion maturation efficiency in existing literature. We previously developed an advanced virion visualization system based on the FRET principle, enabling the effective distinction between immature and mature virions via fluorescence microscopy. In this study, we utilized pseudotyped, single-round infectious viruses tagged with FRET labels (HIV-1 Gag-iFRETΔEnv) derived from Jurkat (a human T lymphocyte cell line) and HEK293T cells to evaluate their virion maturation rates. HEK293T-derived virions demonstrated a maturity rate of 81.79%, consistent with other studies and our previous findings. However, virions originating from Jurkat cells demonstrated a significantly reduced maturation rate of 68.67% (p < 0.0001). Correspondingly, viruses produced from Jurkat cells exhibited significantly reduced infectivity compared to those derived from HEK293T cells, with the relative infectivity measured at 65.3%. This finding is consistent with the observed relative maturation rate of viruses produced by Jurkat cells. These findings suggest that initiation of virion maturation directly correlates with viral infectivity. Our observation highlights the dynamic nature of virus-host interactions and their implications for virion production and infectivity.
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11
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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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12
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Mulato A, Lansdon E, Aoyama R, Voigt J, Lee M, Liclican A, Lee G, Singer E, Stafford B, Gong R, Murray B, Chan J, Lee J, Xu Y, Ahmadyar S, Gonzalez A, Cho A, Stepan GJ, Schmitz U, Schultz B, Marchand B, Brumshtein B, Wang R, Yu H, Cihlar T, Xu L, Yant SR. Preclinical characterization of a non-peptidomimetic HIV protease inhibitor with improved metabolic stability. Antimicrob Agents Chemother 2024; 68:e0137323. [PMID: 38380945 PMCID: PMC10989020 DOI: 10.1128/aac.01373-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/17/2024] [Indexed: 02/22/2024] Open
Abstract
Protease inhibitors (PIs) remain an important component of antiretroviral therapy for the treatment of HIV-1 infection due to their high genetic barrier to resistance development. Nevertheless, the two most commonly prescribed HIV PIs, atazanavir and darunavir, still require co-administration with a pharmacokinetic boosting agent to maintain sufficient drug plasma levels which can lead to undesirable drug-drug interactions. Herein, we describe GS-9770, a novel investigational non-peptidomimetic HIV PI with unboosted once-daily oral dosing potential due to improvements in its metabolic stability and its pharmacokinetic properties in preclinical animal species. This compound demonstrates potent inhibitory activity and high on-target selectivity for recombinant HIV-1 protease versus other aspartic proteases tested. In cell culture, GS-9770 inhibits Gag polyprotein cleavage and shows nanomolar anti-HIV-1 potency in primary human cells permissive to HIV-1 infection and against a broad range of HIV subtypes. GS-9770 demonstrates an improved resistance profile against a panel of patient-derived HIV-1 isolates with resistance to atazanavir and darunavir. In resistance selection experiments, GS-9770 prevented the emergence of breakthrough HIV-1 variants at all fixed drug concentrations tested and required multiple protease substitutions to enable outgrowth of virus exposed to escalating concentrations of GS-9770. This compound also remained fully active against viruses resistant to drugs from other antiviral classes and showed no in vitro antagonism when combined pairwise with drugs from other antiretroviral classes. Collectively, these preclinical data identify GS-9770 as a potent, non-peptidomimetic once-daily oral HIV PI with potential to overcome the persistent requirement for pharmacological boosting with this class of antiretroviral agents.
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Affiliation(s)
- Andrew Mulato
- Department of Virology, Gilead Sciences, Foster City, California, USA
| | - Eric Lansdon
- Department of Structural Biology and Chemistry, Gilead Sciences, Foster City, California, USA
| | - Ron Aoyama
- Department of Drug Metabolism, Gilead Sciences, Foster City, California, USA
| | - Johannes Voigt
- Department of Structural Biology and Chemistry, Gilead Sciences, Foster City, California, USA
| | - Michael Lee
- Department of Discovery Sciences and Technology, Gilead Sciences, Foster City, California, USA
| | - Albert Liclican
- Department of Discovery Sciences and Technology, Gilead Sciences, Foster City, California, USA
| | - Gary Lee
- Department of Discovery Sciences and Technology, Gilead Sciences, Foster City, California, USA
| | - Eric Singer
- Department of Virology, Gilead Sciences, Foster City, California, USA
| | - Brian Stafford
- Department of Drug Metabolism, Gilead Sciences, Foster City, California, USA
| | - Ruoyu Gong
- Department of Discovery Sciences and Technology, Gilead Sciences, Foster City, California, USA
| | - Bernard Murray
- Department of Drug Metabolism, Gilead Sciences, Foster City, California, USA
| | - Julie Chan
- Department of Discovery Sciences and Technology, Gilead Sciences, Foster City, California, USA
| | - Johnny Lee
- Department of Discovery Sciences and Technology, Gilead Sciences, Foster City, California, USA
| | - Yili Xu
- Department of Discovery Sciences and Technology, Gilead Sciences, Foster City, California, USA
| | - Shekeba Ahmadyar
- Department of Discovery Sciences and Technology, Gilead Sciences, Foster City, California, USA
| | - Ana Gonzalez
- Department of Medicinal Chemistry, Gilead Sciences, Foster City, California, USA
| | - Aesop Cho
- Department of Medicinal Chemistry, Gilead Sciences, Foster City, California, USA
| | - George J. Stepan
- Department of Discovery Sciences and Technology, Gilead Sciences, Foster City, California, USA
| | - Uli Schmitz
- Department of Structural Biology and Chemistry, Gilead Sciences, Foster City, California, USA
| | - Brian Schultz
- Department of Discovery Sciences and Technology, Gilead Sciences, Foster City, California, USA
| | - Bruno Marchand
- Department of Discovery Sciences and Technology, Gilead Sciences, Foster City, California, USA
| | - Boris Brumshtein
- Department of Discovery Sciences and Technology, Gilead Sciences, Foster City, California, USA
| | - Ruth Wang
- Department of Discovery Sciences and Technology, Gilead Sciences, Foster City, California, USA
| | - Helen Yu
- Department of Discovery Sciences and Technology, Gilead Sciences, Foster City, California, USA
| | - Tomas Cihlar
- Department of Virology, Gilead Sciences, Foster City, California, USA
| | - Lianhong Xu
- Department of Medicinal Chemistry, Gilead Sciences, Foster City, California, USA
| | - Stephen R. Yant
- Department of Virology, Gilead Sciences, Foster City, California, USA
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13
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Sever B, Otsuka M, Fujita M, Ciftci H. A Review of FDA-Approved Anti-HIV-1 Drugs, Anti-Gag Compounds, and Potential Strategies for HIV-1 Eradication. Int J Mol Sci 2024; 25:3659. [PMID: 38612471 PMCID: PMC11012182 DOI: 10.3390/ijms25073659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
Acquired immunodeficiency syndrome (AIDS) is an enormous global health threat stemming from human immunodeficiency virus (HIV-1) infection. Up to now, the tremendous advances in combination antiretroviral therapy (cART) have shifted HIV-1 infection from a fatal illness into a manageable chronic disorder. However, the presence of latent reservoirs, the multifaceted nature of HIV-1, drug resistance, severe off-target effects, poor adherence, and high cost restrict the efficacy of current cART targeting the distinct stages of the virus life cycle. Therefore, there is an unmet need for the discovery of new therapeutics that not only bypass the limitations of the current therapy but also protect the body's health at the same time. The main goal for complete HIV-1 eradication is purging latently infected cells from patients' bodies. A potential strategy called "lock-in and apoptosis" targets the budding phase of the life cycle of the virus and leads to susceptibility to apoptosis of HIV-1 infected cells for the elimination of HIV-1 reservoirs and, ultimately, for complete eradication. The current work intends to present the main advantages and disadvantages of United States Food and Drug Administration (FDA)-approved anti-HIV-1 drugs as well as plausible strategies for the design and development of more anti-HIV-1 compounds with better potency, favorable pharmacokinetic profiles, and improved safety issues.
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Affiliation(s)
- Belgin Sever
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskisehir 26470, Türkiye;
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan;
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan;
- Department of Drug Discovery, Science Farm Ltd., Kumamoto 862-0976, Japan
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan;
| | - Halilibrahim Ciftci
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan;
- Department of Drug Discovery, Science Farm Ltd., Kumamoto 862-0976, Japan
- Department of Bioengineering Sciences, Izmir Katip Celebi University, Izmir 35620, Türkiye
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14
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Faysal KMR, Walsh JC, Renner N, Márquez CL, Shah VB, Tuckwell AJ, Christie MP, Parker MW, Turville SG, Towers GJ, James LC, Jacques DA, Böcking T. Pharmacologic hyperstabilisation of the HIV-1 capsid lattice induces capsid failure. eLife 2024; 13:e83605. [PMID: 38347802 PMCID: PMC10863983 DOI: 10.7554/elife.83605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/12/2024] [Indexed: 02/15/2024] Open
Abstract
The HIV-1 capsid has emerged as a tractable target for antiretroviral therapy. Lenacapavir, developed by Gilead Sciences, is the first capsid-targeting drug approved for medical use. Here, we investigate the effect of lenacapavir on HIV capsid stability and uncoating. We employ a single particle approach that simultaneously measures capsid content release and lattice persistence. We demonstrate that lenacapavir's potent antiviral activity is predominantly due to lethal hyperstabilisation of the capsid lattice and resultant loss of compartmentalisation. This study highlights that disrupting capsid metastability is a powerful strategy for the development of novel antivirals.
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Affiliation(s)
- KM Rifat Faysal
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
| | - James C Walsh
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
| | - Nadine Renner
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Chantal L Márquez
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
| | - Vaibhav B Shah
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
| | - Andrew J Tuckwell
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
| | - Michelle P Christie
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourneAustralia
| | - Michael W Parker
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourneAustralia
- Structural Biology Unit, St. Vincent’s Institute of Medical ResearchFitzroyAustralia
| | | | - Greg J Towers
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Leo C James
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - David A Jacques
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
| | - Till Böcking
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, UNSWSydneyAustralia
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15
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Dwivedi R, Prakash P, Kumbhar BV, Balasubramaniam M, Dash C. HIV-1 capsid and viral DNA integration. mBio 2024; 15:e0021222. [PMID: 38085100 PMCID: PMC10790781 DOI: 10.1128/mbio.00212-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE HIV-1 capsid protein (CA)-independently or by recruiting host factors-mediates several key steps of virus replication in the cytoplasm and nucleus of the target cell. Research in the recent years have established that CA is multifunctional and genetically fragile of all the HIV-1 proteins. Accordingly, CA has emerged as a validated and high priority therapeutic target, and the first CA-targeting antiviral drug was recently approved for treating multi-drug resistant HIV-1 infection. However, development of next generation CA inhibitors depends on a better understanding of CA's known roles, as well as probing of CA's novel roles, in HIV-1 replication. In this timely review, we present an updated overview of the current state of our understanding of CA's multifunctional role in HIV-1 replication-with a special emphasis on CA's newfound post-nuclear roles, highlight the pressing knowledge gaps, and discuss directions for future research.
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Affiliation(s)
- Richa Dwivedi
- 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
| | - Prem Prakash
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA
| | - Bajarang Vasant Kumbhar
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS (Deemed to be) University, Mumbai, Maharashtra, India
| | - Muthukumar Balasubramaniam
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, 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, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA
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16
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Hamilton JR, Chen E, Perez BS, Sandoval Espinoza CR, Kang MH, Trinidad M, Ngo W, Doudna JA. In vivo human T cell engineering with enveloped delivery vehicles. Nat Biotechnol 2024:10.1038/s41587-023-02085-z. [PMID: 38212493 PMCID: PMC11236958 DOI: 10.1038/s41587-023-02085-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/01/2023] [Indexed: 01/13/2024]
Abstract
Viruses and virally derived particles have the intrinsic capacity to deliver molecules to cells, but the difficulty of readily altering cell-type selectivity has hindered their use for therapeutic delivery. Here, we show that cell surface marker recognition by antibody fragments displayed on membrane-derived particles encapsulating CRISPR-Cas9 protein and guide RNA can deliver genome editing tools to specific cells. Compared to conventional vectors like adeno-associated virus that rely on evolved capsid tropisms to deliver virally encoded cargo, these Cas9-packaging enveloped delivery vehicles (Cas9-EDVs) leverage predictable antibody-antigen interactions to transiently deliver genome editing machinery selectively to cells of interest. Antibody-targeted Cas9-EDVs preferentially confer genome editing in cognate target cells over bystander cells in mixed populations, both ex vivo and in vivo. By using multiplexed targeting molecules to direct delivery to human T cells, Cas9-EDVs enable the generation of genome-edited chimeric antigen receptor T cells in humanized mice, establishing a programmable delivery modality with the potential for widespread therapeutic utility.
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Affiliation(s)
- Jennifer R Hamilton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Azalea Therapeutics, Berkeley, CA, USA
| | - Evelyn Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Azalea Therapeutics, Berkeley, CA, USA
| | - Barbara S Perez
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Cindy R Sandoval Espinoza
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Min Hyung Kang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Marena Trinidad
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Wayne Ngo
- Gladstone Institutes, San Francisco, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Gladstone Institutes, San Francisco, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
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17
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Twarock R, Towers GJ, Stockley PG. Molecular frustration: a hypothesis for regulation of viral infections. Trends Microbiol 2024; 32:17-26. [PMID: 37507296 DOI: 10.1016/j.tim.2023.07.003] [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: 11/30/2022] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
The recent revolution in imaging techniques and results from RNA footprinting in situ reveal how the bacteriophage MS2 genome regulates both particle assembly and genome release. We have proposed a model in which multiple packaging signal (PS) RNA-coat protein (CP) contacts orchestrate different stages of a viral life cycle. Programmed formation and release of specific PS contacts with CP regulates viral particle assembly and genome uncoating during cell entry. We hypothesize that molecular frustration, a concept introduced to understand protein folding, can be used to better rationalize how PSs function in both particle assembly and genome release. More broadly this concept may explain the directionality of viral life cycles, for example, the roles of host cofactors in HIV infection. We propose that this is a universal principle in virology that explains mechanisms of host-virus interaction and suggests diverse therapeutic interventions.
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Affiliation(s)
- Reidun Twarock
- Departments of Mathematics and Biology & York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Greg J Towers
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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18
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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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19
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Sun L, Zhang T, Xu S, Zhang X, Zhan P, Liu X. Bibliometric analysis and visualization of research trends on HIV-1 capsid inhibitors (2000-2022). Front Pharmacol 2023; 14:1282090. [PMID: 37936907 PMCID: PMC10626487 DOI: 10.3389/fphar.2023.1282090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/16/2023] [Indexed: 11/09/2023] Open
Abstract
Background: Acquired immunodeficiency syndrome (AIDS) has seriously endangered human life and health, the main pathogenic agent is human immunodeficiency virus type 1 (HIV-1). The combination antiretroviral therapy (cART) has shown serious drug resistance and side effects, and the discovery of HIV-1 capsid inhibitors is an effective way to solve the problem. Recent studies have shown significant progress in the research of HIV-1 capsid inhibitors. However, there is still a lack of comprehensive overview of bibliometric analysis in this field. This study aimed to provide the research trends and hotspots of HIV-1 capsid inhibitors. Method: Publications related to HIV-1 capsid inhibitors from 2000 to 2022 were searched on the Web of Science Core Collection (WoSCC) database and screened according to inclusion criteria. VOSviewer was conducted to evaluate the results. Results: 96 publications from 25 countries were finally included, and the number of annual publications related to HIV-1 capsid inhibitors showed an increasing trend. The United States was the most productive country with the most publication number, H-index, and total citation number, as well as the widest international cooperation. The most popular journal in this field was Journal of Virology. Drexel University was the most productive institution, and Simon Cocklin participated in the most publications. Keywords co-occurrence analysis exhibited that studying the molecular mechanism of capsid protein, discovering drug candidates, and improving antiretroviral therapy are the main and hot topics in this field. Conclusion: This is the first bibliometric study in the field of HIV-1 capsid inhibitors, which comprehensively analyzed the research trends and hotspots in this direction. This work is expected to provide the scientific community with new insights to promote the research of HIV-1 capsid inhibitors.
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Affiliation(s)
- Lin Sun
- Department of Pharmacy, Qilu Hospital of Shandong University, Jinan, Shandong, China
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, China
| | - Tongchao Zhang
- Clinical Research Center of Shandong University, Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Shujing Xu
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, China
| | - Xujie Zhang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, China
| | - Peng Zhan
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, China
| | - Xinyong Liu
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, China
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20
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Deshpande A, Bryer AJ, Andino J, Shi J, Hong J, Torres C, Harel S, Francis AC, Perilla JR, Aiken C, Rousso I. Elasticity of the HIV-1 Core Facilitates Nuclear Entry and Infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560083. [PMID: 37808653 PMCID: PMC10557754 DOI: 10.1101/2023.09.29.560083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
HIV-1 infection requires passage of the viral core through the nuclear pore of the cell, a process that depends on functions of the viral capsid 1,2 . Recent studies have shown that HIV- 1 cores enter the nucleus prior to capsid disassembly 3-5 . Interactions with the nuclear pore complex are necessary but not sufficient for nuclear entry, and the mechanism by which the viral core traverses the comparably sized nuclear pore is unknown. Here we show that the HIV-1 core is highly elastic and that this property is linked to nuclear entry and infectivity. Using atomic force microscopy-based approaches, we found that purified wild type cores rapidly returned to their normal conical morphology following a severe compression. Results from independently performed molecular dynamic simulations of the mature HIV-1 capsid also revealed its elastic property. Analysis of four HIV-1 capsid mutants that exhibit impaired nuclear entry revealed that the mutant viral cores are brittle. Suppressors of the mutants restored elasticity and rescued infectivity and nuclear entry. Elasticity was also reduced by treatment of cores with the capsid-targeting compound PF74 and the antiviral drug lenacapavir. Our results indicate that capsid elasticity is a fundamental property of the HIV-1 core that enables its passage through the nuclear pore complex, thereby facilitating infection. These results provide new insights into the mechanisms of HIV-1 nuclear entry and the antiviral mechanisms of HIV-1 capsid inhibitors.
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21
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Swanstrom AE, Gorelick RJ, Welker JL, Schmidt F, Lu B, Wang K, Rowe W, Breed MW, Killoran KE, Kramer JA, Donohue D, Roser JD, Bieniasz PD, Hatziioannou T, Pyle C, Thomas JA, Trubey CM, Zheng J, Blair W, Yant SR, Lifson JD, Del Prete GQ. Long-acting lenacapavir protects macaques against intravenous challenge with simian-tropic HIV. EBioMedicine 2023; 95:104764. [PMID: 37625266 PMCID: PMC10470178 DOI: 10.1016/j.ebiom.2023.104764] [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: 03/27/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Long-acting subcutaneous lenacapavir (LEN), a first-in-class HIV capsid inhibitor approved by the US FDA for the treatment of multidrug-resistant HIV-1 with twice yearly dosing, is under investigation for HIV-1 pre-exposure prophylaxis (PrEP). We previously derived a simian-tropic HIV-1 clone (stHIV-A19) that encodes an HIV-1 capsid and replicates to high titres in pigtail macaques (PTM), resulting in a nonhuman primate model well-suited for evaluating LEN PrEP in vivo. METHODS Lenacapavir potency against stHIV-A19 in PTM peripheral blood mononuclear cells in vitro was determined and subcutaneous LEN pharmacokinetics were evaluated in naïve PTMs in vivo. To evaluate the protective efficacy of LEN PrEP, naïve PTMs received either a single subcutaneous injection of LEN (25 mg/kg, N = 3) or vehicle (N = 4) 30 days before a high-dose intravenous challenge with stHIV-A19, or 7 daily subcutaneous injections of a 3-drug control PrEP regimen starting 3 days before stHIV-A19 challenge (N = 3). FINDINGS In vitro, LEN showed potent antiviral activity against stHIV-A19, comparable to its potency against HIV-1. In vivo, subcutaneous LEN displayed sustained plasma drug exposures in PTMs. Following stHIV-A19 challenge, while all vehicle control animals became productively infected, all LEN and 3-drug control PrEP animals were protected from infection. INTERPRETATION These findings highlight the utility of the stHIV-A19/PTM model and support the clinical development of long-acting LEN for PrEP in humans. FUNDING Gilead Sciences as part of a Cooperative Research and Development Agreement between Gilead Sciences and Frederick National Lab; federal funds from the National Cancer Institute, National Institutes of Health, under Contract No. 75N91019D00024/HHSN261201500003I; NIH grant R01AI078788.
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Affiliation(s)
- Adrienne E Swanstrom
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jorden L Welker
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, Rockefeller University, New York, NY, USA
| | - Bing Lu
- Gilead Sciences, Foster City, CA, USA
| | | | | | - Matthew W Breed
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kristin E Killoran
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joshua A Kramer
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Duncan Donohue
- DMS Applies Information Management Sciences, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - James D Roser
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, Rockefeller University, New York, NY, USA
| | | | - Cathi Pyle
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - James A Thomas
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Charles M Trubey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jim Zheng
- Gilead Sciences, Foster City, CA, USA
| | | | | | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Gregory Q Del Prete
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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22
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Han S, Lu Y. Fluorine in anti-HIV drugs approved by FDA from 1981 to 2023. Eur J Med Chem 2023; 258:115586. [PMID: 37393791 DOI: 10.1016/j.ejmech.2023.115586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 07/04/2023]
Abstract
Human immunodeficiency virus (HIV) is the etiological agent of acquired immunodeficiency syndrome (AIDS). Nowadays, FDA has approved over thirty antiretroviral drugs grouped in six categories. Interestingly, one-third of these drugs contain different number of fluorine atoms. The introduction of fluorine to obtain drug-like compounds is a well-accepted strategy in medicinal chemistry. In this review, we summarized 11 fluorine-containing anti-HIV drugs, focusing on their efficacy, resistance, safety, and specific roles of fluorine in the development of each drug. These examples may be of help for the discovery of new drug candidates bearing fluorine in their structures.
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Affiliation(s)
- Sheng Han
- School of Medicine, Shanghai University, Shanghai, China.
| | - Yiming Lu
- School of Medicine, Shanghai University, Shanghai, China; Department of Critical Care Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.
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23
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Xue G, Yu HJ, Buffone C, Huang SW, Lee K, Goh SL, Gres AT, Guney MH, Sarafianos SG, Luban J, Diaz-Griffero F, KewalRamani VN. The HIV-1 capsid core is an opportunistic nuclear import receptor. Nat Commun 2023; 14:3782. [PMID: 37355754 PMCID: PMC10290713 DOI: 10.1038/s41467-023-39146-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/01/2023] [Indexed: 06/26/2023] Open
Abstract
The movement of viruses and other large macromolecular cargo through nuclear pore complexes (NPCs) is poorly understood. The human immunodeficiency virus type 1 (HIV-1) provides an attractive model to interrogate this process. HIV-1 capsid (CA), the chief structural component of the viral core, is a critical determinant in nuclear transport of the virus. HIV-1 interactions with NPCs are dependent on CA, which makes direct contact with nucleoporins (Nups). Here we identify Nup35, Nup153, and POM121 to coordinately support HIV-1 nuclear entry. For Nup35 and POM121, this dependence was dependent cyclophilin A (CypA) interaction with CA. Mutation of CA or removal of soluble host factors changed the interaction with the NPC. Nup35 and POM121 make direct interactions with HIV-1 CA via regions containing phenylalanine glycine motifs (FG-motifs). Collectively, these findings provide additional evidence that the HIV-1 CA core functions as a macromolecular nuclear transport receptor (NTR) that exploits soluble host factors to modulate NPC requirements during nuclear invasion.
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Affiliation(s)
- Guangai Xue
- Model Development Section, Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Hyun Jae Yu
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD, 21702, USA
| | - Cindy Buffone
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Szu-Wei Huang
- Model Development Section, Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - KyeongEun Lee
- Model Development Section, Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Shih Lin Goh
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Anna T Gres
- Bond Life Sciences Center, Chemistry, University of Missouri, Columbia, MO, 65201, USA
| | - Mehmet Hakan Guney
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Stefan G Sarafianos
- Bond Life Sciences Center, Chemistry, University of Missouri, Columbia, MO, 65201, USA
- Bond Life Sciences Center, MMI, Biochemistry, University of Missouri, Columbia, MO, 65201, USA
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Vineet N KewalRamani
- Model Development Section, Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA.
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24
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Chatzidaki I, Curteis T, Luedke H, Mezzio DJ, Rhee MS, McArthur E, Eddowes LA. Indirect Treatment Comparisons of Lenacapavir Plus Optimized Background Regimen Versus Other Treatments for Multidrug-Resistant Human Immunodeficiency Virus. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2023; 26:810-822. [PMID: 36566886 DOI: 10.1016/j.jval.2022.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 12/05/2022] [Accepted: 12/15/2022] [Indexed: 06/04/2023]
Abstract
BACKGROUND/AIMS Heavily treatment-experienced (HTE) people with human immunodeficiency virus (HIV) (PWH) may not achieve virologic suppression (VS) with combination antiretroviral therapy due to multidrug resistance (MDR), intolerance, and safety concerns. These PWH often receive highly individualized treatment regimens, but these regimens may not enable PWH to achieve VS, thereby halting disease progression. Novel medications are required for treating individuals with MDR HIV. Lenacapavir (LEN), a first-in-class HIV capsid inhibitor, is under investigation for the treatment of HTE individuals with MDR HIV in the phase 2/3 CAPELLA study. This study aimed to compare LEN plus optimized background regimen (OBR) with fostemsavir (FTR) + OBR, ibalizumab (IBA) + OBR, and OBR alone in terms of VS, CD4 cell count change from baseline, immunologic recovery, and discontinuation due to adverse events, using indirect treatment comparisons. METHODS A systematic review identified clinical evidence on HIV-1 treatments in HTE PWH. A feasibility assessment evaluated the identified studies for indirect treatment comparison analyses based on population characteristics, interventions, comparators, and outcomes of interest. Unanchored simulated treatment comparisons of LEN + OBR versus comparators were conducted. RESULTS LEN + OBR had 6.57 times higher odds of VS at weeks 24 to 28 than FTR + OBR (95% confidence interval [CI] 1.34-32.28), 8.93 times higher odds of VS than IBA + OBR (95% CI 2.07-38.46), and 12.74 times higher odds of VS than OBR alone (95% CI 1.70-95.37). Change from baseline in CD4 cell count was similar across LEN + OBR, FTR + OBR, and IBA + OBR. CONCLUSION LEN + OBR has statistically significantly greater odds of VS at weeks 24 to 28 than its comparators and represents a novel treatment for people with MDR HIV.
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25
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Lynch DL, Pavlova A, Fan Z, Gumbart JC. Understanding Virus Structure and Dynamics through Molecular Simulations. J Chem Theory Comput 2023. [PMID: 37192279 DOI: 10.1021/acs.jctc.3c00116] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Viral outbreaks remain a serious threat to human and animal populations and motivate the continued development of antiviral drugs and vaccines, which in turn benefits from a detailed understanding of both viral structure and dynamics. While great strides have been made in characterizing these systems experimentally, molecular simulations have proven to be an essential, complementary approach. In this work, we review the contributions of molecular simulations to the understanding of viral structure, functional dynamics, and processes related to the viral life cycle. Approaches ranging from coarse-grained to all-atom representations are discussed, including current efforts at modeling complete viral systems. Overall, this review demonstrates that computational virology plays an essential role in understanding these systems.
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Affiliation(s)
- Diane L Lynch
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zixing Fan
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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26
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Schirra RT, Dos Santos NFB, Zadrozny KK, Kucharska I, Ganser-Pornillos BK, Pornillos O. A molecular switch modulates assembly and host factor binding of the HIV-1 capsid. Nat Struct Mol Biol 2023; 30:383-390. [PMID: 36759579 PMCID: PMC10023569 DOI: 10.1038/s41594-022-00913-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 12/20/2022] [Indexed: 02/11/2023]
Abstract
The HIV-1 capsid is a fullerene cone made of quasi-equivalent hexamers and pentamers of the viral CA protein. Typically, quasi-equivalent assembly of viral capsid subunits is controlled by a molecular switch. Here, we identify a Thr-Val-Gly-Gly motif that modulates CA hexamer/pentamer switching by folding into a 310 helix in the pentamer and random coil in the hexamer. Manipulating the coil/helix configuration of the motif allowed us to control pentamer and hexamer formation in a predictable manner, thus proving its function as a molecular switch. Importantly, the switch also remodels the common binding site for host factors that are critical for viral replication and the new ultra-potent HIV-1 inhibitor lenacapavir. This study reveals that a critical assembly element also modulates the post-assembly and viral replication functions of the HIV-1 capsid and provides new insights on capsid function and inhibition.
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Affiliation(s)
- Randall T Schirra
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Nayara F B Dos Santos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Kaneil K Zadrozny
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Iga Kucharska
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
- The Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Barbie K Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
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27
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Hwang KS, Seo EU, Choi N, Kim J, Kim HN. 3D engineered tissue models for studying human-specific infectious viral diseases. Bioact Mater 2023; 21:576-594. [PMID: 36204281 PMCID: PMC9519398 DOI: 10.1016/j.bioactmat.2022.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/13/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022] Open
Abstract
Viral infections cause damage to various organ systems by inducing organ-specific symptoms or systemic multi-organ damage. Depending on the infection route and virus type, infectious diseases are classified as respiratory, nervous, immune, digestive, or skin infections. Since these infectious diseases can widely spread in the community and their catastrophic effects are severe, identification of their causative agent and mechanisms underlying their pathogenesis is an urgent necessity. Although infection-associated mechanisms have been studied in two-dimensional (2D) cell culture models and animal models, they have shown limitations in organ-specific or human-associated pathogenesis, and the development of a human-organ-mimetic system is required. Recently, three-dimensional (3D) engineered tissue models, which can present human organ-like physiology in terms of the 3D structure, utilization of human-originated cells, recapitulation of physiological stimuli, and tight cell–cell interactions, were developed. Furthermore, recent studies have shown that these models can recapitulate infection-associated pathologies. In this review, we summarized the recent advances in 3D engineered tissue models that mimic organ-specific viral infections. First, we briefly described the limitations of the current 2D and animal models in recapitulating human-specific viral infection pathology. Next, we provided an overview of recently reported viral infection models, focusing particularly on organ-specific infection pathologies. Finally, a future perspective that must be pursued to reconstitute more human-specific infectious diseases is presented. 3D in vitro models are different from the traditional model in the infection process. Human-specific infection research requires a 3D microenvironment and human cells. 3D in vitro infectious models can be useful for basic research on infectious disease. 3D in vitro infectious models recapitulate the complex cell-virus-immune interaction.
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Affiliation(s)
- Kyeong Seob Hwang
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
- School of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Eun U Seo
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, Republic of Korea
| | - Nakwon Choi
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Republic of Korea
| | - Jongbaeg Kim
- School of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea
- Corresponding author.
| | - Hong Nam Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
- School of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea
- Yonsei-KIST Convergence Research Institute, Yonsei University, Seoul, 03722, Republic of Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, Republic of Korea
- Corresponding author. Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea.
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28
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Zhang DW, Xie L, Xu XS, Li Y, Xu X. A Broad-Spectrum Antiviral Molecule, Protoporphyrin IX, Acts as a Moderator of HIV-1 Capsid Assembly by Targeting the Capsid Hexamer. Microbiol Spectr 2023; 11:e0266322. [PMID: 36475726 PMCID: PMC9927277 DOI: 10.1128/spectrum.02663-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The capsid protein (CA), an essential component of human immunodeficiency virus type 1 (HIV-1), represents an appealing target for antivirals. Small molecules targeting the CAI-binding cavity in the C-terminal domain of HIV-1 CA (CA CTD) confer potent antiviral activities. In this study, we report that a small molecule, protoporphyrin IX (PPIX), targets the HIV-1 CA by binding to this pocket. PPIX was identified via in vitro drug screening, using a homogeneous and time-resolved fluorescence-based assay. CA multimerization and a biolayer interferometry (BLI) assay showed that PPIX promoted CA multimerization and bound directly to CA. The binding model of PPIX to CA CTD revealed that PPIX forms hydrogen bonds with the L211and E212 residues in the CA CTD. Moreover, the BLI assay demonstrated that this compound preferentially binds to the CA hexamer versus the monomer. The superposition of the CAI CTD-PPIX complex and the hexameric CA structure suggests that PPIX binds to the interface formed by the NTD and the CTD between adjacent protomers in the CA hexamer via the T72 and E212 residues, serving as a glue to enhance the multimerization of CA. Taken together, our studies demonstrate that PPIX, a hexamer-targeted CA assembly enhancer, should be a new chemical probe for the discovery of modulators of the HIV-1 capsid assembly. IMPORTANCE CA and its assembled viral core play essential roles in distinct steps during HIV-1 replication, including reverse transcription, integration, nuclear entry, virus assembly, and maturation through CA-CA or CA-host factor interactions. These functions of CA are fundamental for HIV-1 pathogenesis, making it an appealing target for antiviral therapy. In the present study, we identified protoporphyrin IX (PPIX) as a candidate CA modulator that can promote CA assembly and prefers binding the CA hexamer versus the monomer. PPIX, like a glue, bound at the interfaces between CA subunits to accelerate CA multimerization. Therefore, PPIX could be used as a new lead for a CA modulator, and it holds potential research applications.
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Affiliation(s)
- Da-Wei Zhang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Liangxu Xie
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Xiao-Shuang Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Yimin Li
- College of Pharmacy and Key Laboratory for Research and Development of “Qin Medicine” of Shaanxi Administration of Chinese Medicine, Shaanxi University of Chinese Medicine, Xixian New District, China
| | - Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
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29
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Gillis EP, Parcella K, Bowsher M, Cook JH, Iwuagwu C, Naidu BN, Patel M, Peese K, Huang H, Valera L, Wang C, Kieltyka K, Parker DD, Simmermacher J, Arnoult E, Nolte RT, Wang L, Bender JA, Frennesson DB, Saulnier M, Wang AX, Meanwell NA, Belema M, Hanumegowda U, Jenkins S, Krystal M, Kadow JF, Cockett M, Fridell R. Potent Long-Acting Inhibitors Targeting the HIV-1 Capsid Based on a Versatile Quinazolin-4-one Scaffold. J Med Chem 2023; 66:1941-1954. [PMID: 36719971 DOI: 10.1021/acs.jmedchem.2c01732] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Long-acting (LA) human immunodeficiency virus-1 (HIV-1) antiretroviral therapy characterized by a ≥1 month dosing interval offers significant advantages over daily oral therapy. However, the criteria for compounds that enter clinical development are high. Exceptional potency and low plasma clearance are required to meet dose size requirements; excellent chemical stability and/or crystalline form stability is required to meet formulation requirements, and new antivirals in HIV-1 therapy need to be largely free of side effects and drug-drug interactions. In view of these challenges, the discovery that capsid inhibitors comprising a quinazolinone core tolerate a wide range of structural modifications while maintaining picomolar potency against HIV-1 infection in vitro, are assembled efficiently in a multi-component reaction, and can be isolated in a stereochemically pure form is reported herein. The detailed characterization of a prototypical compound, GSK878, is presented, including an X-ray co-crystal structure and subcutaneous and intramuscular pharmacokinetic data in rats and dogs.
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Affiliation(s)
- Eric P Gillis
- Discovery Chemistry, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Kyle Parcella
- Discovery Chemistry, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Michael Bowsher
- Discovery Chemistry, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - James H Cook
- Discovery Chemistry, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Christiana Iwuagwu
- Discovery Chemistry, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - B Narasimhulu Naidu
- Discovery Chemistry, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Manoj Patel
- Discovery Chemistry, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Kevin Peese
- Discovery Chemistry, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Haichang Huang
- Discovery Biology, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Lourdes Valera
- Discovery Biology, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Chunfu Wang
- Discovery Biology, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Kasia Kieltyka
- Discovery Pharmaceutics, DMPK and Toxicology, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Dawn D Parker
- Discovery Pharmaceutics, DMPK and Toxicology, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Jean Simmermacher
- Discovery Pharmaceutics, DMPK and Toxicology, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Eric Arnoult
- Molecular Design, GSK, Collegeville, Pennsylvania 19426, United States
| | - Robert T Nolte
- Protein Cellular and Structural Sciences, GSK, Collegeville, Pennsylvania 19426, United States
| | - Liping Wang
- Protein Cellular and Structural Sciences, GSK, Collegeville, Pennsylvania 19426, United States
| | - John A Bender
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey 08543, United States
| | - David B Frennesson
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Cambridge, Massachusetts 02142, United States
| | - Mark Saulnier
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey 08543, United States
| | - Alan Xiangdong Wang
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey 08543, United States
| | - Nicholas A Meanwell
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey 08543, United States
| | - Makonen Belema
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey 08543, United States
| | - Umesh Hanumegowda
- Discovery Pharmaceutics, DMPK and Toxicology, ViiV Healthcare, Branford, Connecticut 06405, United States.,ViiV Discovery, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Susan Jenkins
- Discovery Pharmaceutics, DMPK and Toxicology, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Mark Krystal
- Discovery Biology, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - John F Kadow
- Discovery Chemistry, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Mark Cockett
- ViiV Discovery, ViiV Healthcare, Branford, Connecticut 06405, United States
| | - Robert Fridell
- Discovery Biology, ViiV Healthcare, Branford, Connecticut 06405, United States
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Ndashimye E, Reyes PS, Arts EJ. New antiretroviral inhibitors and HIV-1 drug resistance: more focus on 90% HIV-1 isolates? FEMS Microbiol Rev 2023; 47:fuac040. [PMID: 36130204 PMCID: PMC9841967 DOI: 10.1093/femsre/fuac040] [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: 07/25/2022] [Revised: 09/13/2022] [Accepted: 09/18/2022] [Indexed: 01/21/2023] Open
Abstract
Combined HIV antiretroviral therapy (cART) has been effective except if drug resistance emerges. As cART has been rolled out in low-income countries, drug resistance has emerged at higher rates than observed in high income countries due to factors including initial use of these less tolerated cART regimens, intermittent disruptions in drug supply, and insufficient treatment monitoring. These socioeconomic factors impacting drug resistance are compounded by viral mechanistic differences by divergent HIV-1 non-B subtypes compared to HIV-1 subtype B that largely infects the high-income countries (just 10% of 37 million infected). This review compares the inhibition and resistance of diverse HIV-1 subtypes and strains to the various approved drugs as well as novel inhibitors in clinical trials. Initial sequence variations and differences in replicative fitness between HIV-1 subtypes pushes strains through different fitness landscapes to escape from drug selective pressure. The discussions here provide insight to patient care givers and policy makers on how best to use currently approved ART options and reduce the emergence of drug resistance in ∼33 million individuals infected with HIV-1 subtype A, C, D, G, and recombinants forms. Unfortunately, over 98% of the literature on cART resistance relates to HIV-1 subtype B.
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Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
- Joint Clinical Research Centre, -Center for AIDS Research Laboratories, 256, Kampala, Uganda
| | - Paul S Reyes
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University Schulich School of Medicine & Dentistry, Western University, N6A 3K7, London, Ontario, Canada
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Kobayakawa T, Yokoyama M, Tsuji K, Fujino M, Kurakami M, Onishi T, Boku S, Ishii T, Miura Y, Shinohara K, Kishihara Y, Ohashi N, Kotani O, Murakami T, Sato H, Tamamura H. Low-molecular-weight anti-HIV-1 agents targeting HIV-1 capsid proteins. RSC Adv 2023; 13:2156-2167. [PMID: 36712613 PMCID: PMC9834766 DOI: 10.1039/d2ra06837k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 01/02/2023] [Indexed: 01/15/2023] Open
Abstract
The HIV-1 capsid is a shell that encapsulates viral RNA, and forms a conical structure by assembling oligomers of capsid (CA) proteins. Since the CA proteins are highly conserved among many strains of HIV-1, the inhibition of the CA function could be an appropriate goal for suppression of HIV-1 replication, but to date, no drug targeting CA has been developed. Hydrophobic interactions between two CA molecules through Trp184 and Met185 in the protein are known to be indispensable for conformational stabilization of the CA multimer. In our previous study, a small molecule designed by in silico screening as a dipeptide mimic of Trp184 and Met185 in the interaction site was synthesized and found to have significant anti-HIV-1 activity. In the present study, molecules with different scaffolds based on a dipeptide mimic of Trp184 and Met185 have been designed and synthesized. Their significant anti-HIV activity and their advantages compared to the previous compounds were examined. The present results should be useful in the design of novel CA-targeting anti-HIV agents.
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Affiliation(s)
- Takuya Kobayakawa
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) 2-3-10 Kandasurugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Masaru Yokoyama
- Pathogen Genomics Center, National Institute of Infectious Diseases Musashimurayama 208-0011 Tokyo Japan
| | - Kohei Tsuji
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) 2-3-10 Kandasurugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Masayuki Fujino
- AIDS Research Center, National Institute of Infectious Diseases Shinjuku-ku Tokyo 162-8640 Japan
| | - Masaki Kurakami
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) 2-3-10 Kandasurugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Takato Onishi
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) 2-3-10 Kandasurugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Sayaka Boku
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) 2-3-10 Kandasurugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Takahiro Ishii
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) 2-3-10 Kandasurugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Yutaro Miura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) 2-3-10 Kandasurugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Kouki Shinohara
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) 2-3-10 Kandasurugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Yuki Kishihara
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) 2-3-10 Kandasurugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Nami Ohashi
- Showa Pharmaceutical University Machida 194-8543 Tokyo Japan
| | - Osamu Kotani
- Pathogen Genomics Center, National Institute of Infectious Diseases Musashimurayama 208-0011 Tokyo Japan
| | - Tsutomu Murakami
- AIDS Research Center, National Institute of Infectious Diseases Shinjuku-ku Tokyo 162-8640 Japan
| | - Hironori Sato
- Pathogen Genomics Center, National Institute of Infectious Diseases Musashimurayama 208-0011 Tokyo Japan
| | - Hirokazu Tamamura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU) 2-3-10 Kandasurugadai, Chiyoda-ku Tokyo 101-0062 Japan
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Ding D, Xu S, Zhang X, Jiang X, Cocklin S, Dick A, Zhan P, Liu X. The discovery and design of novel HIV-1 capsid modulators and future perspectives. Expert Opin Drug Discov 2023; 18:5-12. [PMID: 36480372 DOI: 10.1080/17460441.2023.2157401] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Although combination antiretroviral therapy (cART) has achieved significant success in treating HIV, the emergence of multidrug-resistant viruses and cumulative medication toxicity make it necessary to find new classes of antiretroviral agents with novel mechanisms of action. With high sequence conservation, the HIV-1 capsid (CA) protein has attracted attention as a prospective therapeutic target due to its crucial structural and regulatory functions in the HIV-1 replication cycle. AREA COVERED Herein, the authors provide a cutting-edge overview of current advances in the design and discovery of CA modulators, PF74, GS-6207 and their derivativeswhich targets a therapeutically attractive NTD-CTD interprotomer pocket within the hexameric configuration of HIV-1 CA. The discovery and development of these compounds, and derivatives thereof, have provided valuable information for the design of second-generation CA-targeting antivirals. EXPERT OPINION Despite some successes in designing and discovering HIV-1 CA modulators, more studies are required to decipher which chemical groups confer specific desirable properties. The future of CA-modulating compounds may lie in covalent inhibition and the creation of proteolysis-targeting chimeras (PROTACs). Moreover, biological interrogation of the process of CA uncoating, virus-host interactions, and studies on the lattice-binding restriction factors may improve our knowledge of HIV-1 CA and support the design of new antiviral agents.
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Affiliation(s)
- Dang Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Xujie Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Simon Cocklin
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Alexej Dick
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan, PR China
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Madhu P, Davey NE, Ivarsson Y. How viral proteins bind short linear motifs and intrinsically disordered domains. Essays Biochem 2022; 66:EBC20220047. [PMID: 36504386 DOI: 10.1042/ebc20220047] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 02/11/2024]
Abstract
Viruses are the obligate intracellular parasites that exploit the host cellular machinery to replicate their genome. During the viral life cycle viruses manipulate the host cell through interactions with host proteins. Many of these protein-protein interactions are mediated through the recognition of host globular domains by short linear motifs (SLiMs), or longer intrinsically disordered domains (IDD), in the disordered regions of viral proteins. However, viruses also employ their own globular domains for binding to SLiMs and IDDs present in host proteins or virus proteins. In this review, we focus on the different strategies adopted by viruses to utilize proteins or protein domains for binding to the disordered regions of human or/and viral ligands. With a set of examples, we describe viral domains that bind human SLiMs. We also provide examples of viral proteins that bind to SLiMs, or IDDs, of viral proteins as a part of complex assembly and regulation of protein functions. The protein-protein interactions are often crucial for viral replication, and may thus offer possibilities for innovative inhibitor design.
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Affiliation(s)
- Priyanka Madhu
- Department of Chemistry, BMC, Uppsala University, Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, London, U.K
| | - Ylva Ivarsson
- Department of Chemistry, BMC, Uppsala University, Uppsala, Sweden
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Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection. Nat Commun 2022; 13:5879. [PMID: 36202818 PMCID: PMC9537594 DOI: 10.1038/s41467-022-33662-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/27/2022] [Indexed: 12/24/2022] Open
Abstract
Cellular proteins CPSF6, NUP153 and SEC24C play crucial roles in HIV-1 infection. While weak interactions of short phenylalanine-glycine (FG) containing peptides with isolated capsid hexamers have been characterized, how these cellular factors functionally engage with biologically relevant mature HIV-1 capsid lattices is unknown. Here we show that prion-like low complexity regions (LCRs) enable avid CPSF6, NUP153 and SEC24C binding to capsid lattices. Structural studies revealed that multivalent CPSF6 assembly is mediated by LCR-LCR interactions, which are templated by binding of CPSF6 FG peptides to a subset of hydrophobic capsid pockets positioned along adjoining hexamers. In infected cells, avid CPSF6 LCR-mediated binding to HIV-1 cores is essential for functional virus-host interactions. The investigational drug lenacapavir accesses unoccupied hydrophobic pockets in the complex to potently impair HIV-1 inside the nucleus without displacing the tightly bound cellular cofactor from virus cores. These results establish previously undescribed mechanisms of virus-host interactions and antiviral action.
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Abstract
Lenacapavir (LEN) is a long-acting, highly potent HIV-1 capsid (CA) inhibitor. The evolution of viral variants under the genetic pressure of LEN identified Q67H, N74D, and Q67H/N74D CA substitutions as the main resistance associated mutations (RAMs). Here, we determined high-resolution structures of CA hexamers containing these RAMs in the absence and presence of LEN. Our findings reveal that the Q67H change induces a conformational switch, which adversely affects the inhibitor binding. In the unliganded protein, the His67 side chain adopts the closed conformation by projecting into the inhibitor binding pocket and thereby creating steric hindrance with respect to LEN. Upon the inhibitor binding, the His67 side chain repositions to the open conformation that closely resembles the Gln67 side chain in the WT protein. We propose that the switch from the closed conformation to the open conformation, which is needed to accommodate LEN, accounts for the reduced inhibitor potency with respect to the Q67H CA variant. The N74D CA change results in the loss of a direct hydrogen bond and in induced electrostatic repulsions between CA and LEN. The double Q67H/N74D substitutions exhibited cumulative effects of respective single amino acid changes. An examination of LEN binding kinetics to CA hexamers revealed that Q67H and N74D CA changes adversely influenced the inhibitor binding affinity (KD) by primarily affecting the dissociation rate constant (koff). We used these structural and mechanistic findings to rationally modify LEN. The resulting analog exhibited increased potency against the Q67H/N74D viral variant. Thus, our studies provide a means for the development of second-generation inhibitors with enhanced barriers to resistance.
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Boswell MT, Nazziwa J, Kuroki K, Palm A, Karlson S, Månsson F, Biague A, da Silva ZJ, Onyango CO, de Silva TI, Jaye A, Norrgren H, Medstrand P, Jansson M, Maenaka K, Rowland-Jones SL, Esbjörnsson J. Intrahost evolution of the HIV-2 capsid correlates with progression to AIDS. Virus Evol 2022; 8:veac075. [PMID: 36533148 PMCID: PMC9753047 DOI: 10.1093/ve/veac075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/24/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2023] Open
Abstract
HIV-2 infection will progress to AIDS in most patients without treatment, albeit at approximately half the rate of HIV-1 infection. HIV-2 capsid (p26) amino acid polymorphisms are associated with lower viral loads and enhanced processing of T cell epitopes, which may lead to protective Gag-specific T cell responses common in slower progressors. Lower virus evolutionary rates, and positive selection on conserved residues in HIV-2 env have been associated with slower progression to AIDS. In this study we analysed 369 heterochronous HIV-2 p26 sequences from 12 participants with a median age of 30 years at enrolment. CD4% change over time was used to stratify participants into relative faster and slower progressor groups. We analysed p26 sequence diversity evolution, measured site-specific selection pressures and evolutionary rates, and determined if these evolutionary parameters were associated with progression status. Faster progressors had lower CD4% and faster CD4% decline rates. Median pairwise sequence diversity was higher in faster progressors (5.7x10-3 versus 1.4x10-3 base substitutions per site, P<0.001). p26 evolved under negative selection in both groups (dN/dS=0.12). Median virus evolutionary rates were higher in faster than slower progressors - synonymous rates: 4.6x10-3 vs. 2.3x10-3; and nonsynonymous rates: 6.9x10-4 vs. 2.7x10-4 substitutions/site/year, respectively. Virus evolutionary rates correlated negatively with CD4% change rates (ρ = -0.8, P=0.02), but not CD4% level. The signature amino acid at p26 positions 6, 12 and 119 differed between faster (6A, 12I, 119A) and slower (6G, 12V, 119P) progressors. These amino acid positions clustered near to the TRIM5α/p26 hexamer interface surface. p26 evolutionary rates were associated with progression to AIDS and were mostly driven by synonymous substitutions. Nonsynonymous evolutionary rates were an order of magnitude lower than synonymous rates, with limited amino acid sequence evolution over time within hosts. These results indicate HIV-2 p26 may be an attractive therapeutic target.
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Affiliation(s)
- M T Boswell
- Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, OX3 7FZ, Oxford, UK
| | - J Nazziwa
- Department of Translational Medicine, Lund University, Sölvegatan 17, 223 62, Lund, Sweden
| | - K Kuroki
- Faculty of Pharmaceutical Sciences and Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - A Palm
- Department of Translational Medicine, Lund University, Sölvegatan 17, 223 62, Lund, Sweden
| | - S Karlson
- Department of Translational Medicine, Lund University, Sölvegatan 17, 223 62, Lund, Sweden
| | - F Månsson
- Department of Translational Medicine, Lund University, Sölvegatan 17, 223 62, Lund, Sweden
| | - A Biague
- National Public Health Laboratory, V94M+HM4, Bissau, Guinea-Bissau
| | - Z J da Silva
- National Public Health Laboratory, V94M+HM4, Bissau, Guinea-Bissau
| | - C O Onyango
- US Centres for Disease Control, KEMRI Complex, Mbagathi Road off Mbagathi Way PO Box 606-00621, Kenya
| | - T I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, The Medical School, University of Sheffield, Beech Hill Rd, S10 2RX, Sheffield, UK
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara P. O. Box 273, Banjul, The Gambia
| | - A Jaye
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara P. O. Box 273, Banjul, The Gambia
| | - H Norrgren
- Department of Clinical Sciences Lund, Lund University, Sölvegatan 19, 221 84 Lund, Sweden
| | - P Medstrand
- Department of Translational Medicine, Lund University, Sölvegatan 17, 223 62, Lund, Sweden
| | - M Jansson
- Department of Laboratory Medicine, Lund University, Sölvegatan 19, Sweden
| | - K Maenaka
- Faculty of Pharmaceutical Sciences and Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - S L Rowland-Jones
- Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, OX3 7FZ, Oxford, UK
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara P. O. Box 273, Banjul, The Gambia
| | - J Esbjörnsson
- Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, OX3 7FZ, Oxford, UK
- Department of Translational Medicine, Lund University, Sölvegatan 17, 223 62, Lund, Sweden
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Müller TG, Zila V, Müller B, Kräusslich HG. Nuclear Capsid Uncoating and Reverse Transcription of HIV-1. Annu Rev Virol 2022; 9:261-284. [PMID: 35704745 DOI: 10.1146/annurev-virology-020922-110929] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
After cell entry, human immunodeficiency virus type 1 (HIV-1) replication involves reverse transcription of the RNA genome, nuclear import of the subviral complex without nuclear envelope breakdown, and integration of the viral complementary DNA into the host genome. Here, we discuss recent evidence indicating that completion of reverse transcription and viral genome uncoating occur in the nucleus rather than in the cytoplasm, as previously thought, and suggest a testable model for nuclear import and uncoating. Multiple recent studies indicated that the cone-shaped capsid, which encases the genome and replication proteins, not only serves as a reaction container for reverse transcription and as a shield from innate immune sensors but also may constitute the elusive HIV-1 nuclear import factor. Rupture of the capsid may be triggered in the nucleus by completion of reverse transcription, by yet-unknown nuclear factors, or by physical damage, and it appears to occur in close temporal and spatial association with the integration process. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Thorsten G Müller
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany;
| | - Vojtech Zila
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany;
| | - Barbara Müller
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany;
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, Heidelberg University, Heidelberg, Germany; .,German Center for Infection Research, Heidelberg, Germany
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Troyano-Hernáez P, Reinosa R, Holguín Á. HIV Capsid Protein Genetic Diversity Across HIV-1 Variants and Impact on New Capsid-Inhibitor Lenacapavir. Front Microbiol 2022; 13:854974. [PMID: 35495642 PMCID: PMC9039614 DOI: 10.3389/fmicb.2022.854974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/09/2022] [Indexed: 12/17/2022] Open
Abstract
The HIV p24 capsid protein has an essential, structural, and functional role in the viral replication cycle, being an interesting target for vaccine design, diagnostic tests, and new antiretroviral drugs (ARVs). The HIV-1 variability poses a challenge for the accuracy and efficiency of diagnostic and treatment tools. This study analyzes p24 diversity among HIV-1 variants and within its secondary structure in HIV-1 M, O, P, and N groups. All available HIV-1 p24 nucleotide sequences were downloaded from the Los Alamos HIV Sequence Database, selecting 23,671 sequences belonging to groups O, N, P, and M (9 subtypes, 7 sub-sub types, and 109 circulating recombinant forms or CRFs). Using a bioinformatics tool developed in our laboratory (EpiMolBio program), we analyzed the amino acid conservation compared to the HXB2 subtype B reference sequence and the V-markers, or amino acid changes that were specific for each variant with at least 10 available sequences. We inferred the p24 consensus sequence for HIV-1 and for each group to analyze the overall conservation in p24 main structural regions, reporting the percentage of substitutions per variant affecting the capsid assembly and molecule-binding, including those associated with resistance to the new capsid-inhibitor lenacapavir, and the key residues involved in lenacapavir-p24 interaction, according to the bibliography. Although the overall structure of p24 was highly conserved, the conservation in the secondary structure varied between HIV-1 variants and the type of secondary structure. All HIV-1 variants presented >80% amino acid conservation vs. HXB2 reference sequence, except for group M sub-subtype F1 (69.27%). Mutants affecting the capsid assembly or lenacapavir capsid-binding were found in <1% of the p24 consensus sequence. Our study reports the HIV-1 variants carrying 14 unique single V-markers in 9/38 group M variants and the level of p24 conservation in each secondary structure region among the 4 HIV-1 groups and group M variants, revealing no natural resistance to lenacapavir in any HIV-1 variant. We present a thorough analysis of p24 variability among all HIV-1 variants circulating to date. Since p24 genetic variability can impact the viral replication cycle and the efficacy of new p24-based diagnostic, therapeutic, and vaccine strategies, conservation studies must consider all HIV-1 variants circulating worldwide.
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Affiliation(s)
- Paloma Troyano-Hernáez
- HIV-1 Molecular Epidemiology Laboratory, Department of Microbiology, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, CIBER en Epidemiología y Salud Pública (CIBERESP), Red en Investigación Translacional en Infecciones Pediátricas (RITIP), Madrid, Spain
| | - Roberto Reinosa
- HIV-1 Molecular Epidemiology Laboratory, Department of Microbiology, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, CIBER en Epidemiología y Salud Pública (CIBERESP), Red en Investigación Translacional en Infecciones Pediátricas (RITIP), Madrid, Spain
| | - África Holguín
- HIV-1 Molecular Epidemiology Laboratory, Department of Microbiology, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, CIBER en Epidemiología y Salud Pública (CIBERESP), Red en Investigación Translacional en Infecciones Pediátricas (RITIP), Madrid, Spain
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Moonmuang S, Maniratanachote R, Chetprayoon P, Sornsuwan K, Thongkum W, Chupradit K, Tayapiwatana C. Specific Interaction of DARPin with HIV-1 CA NTD Disturbs the Distribution of Gag, RNA Packaging, and Tetraspanin Remodelling in the Membrane. Viruses 2022; 14:v14040824. [PMID: 35458554 PMCID: PMC9025900 DOI: 10.3390/v14040824] [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: 03/06/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 11/22/2022] Open
Abstract
A designed repeat scaffold protein (AnkGAG1D4) recognizing the human immunodeficiency virus-1 (HIV-1) capsid (CA) was formerly established with antiviral assembly. Here, we investigated the molecular mechanism of AnkGAG1D4 function during the late stages of the HIV-1 replication cycle. By applying stimulated emission-depletion (STED) microscopy, Gag polymerisation was interrupted at the plasma membrane. Disturbance of Gag polymerisation triggered Gag accumulation inside producer cells and trapping of the CD81 tetraspanin on the plasma membrane. Moreover, reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) experiments were performed to validate the packaging efficiency of RNAs. Our results advocated that AnkGAG1D4 interfered with the Gag precursor protein from selecting HIV-1 and cellular RNAs for encapsidation into viral particles. These findings convey additional information on the antiviral activity of AnkGAG1D4 at late stages of the HIV-1 life cycle, which is potential for an alternative anti-HIV molecule.
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Affiliation(s)
- Sutpirat Moonmuang
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (S.M.); (K.S.); (W.T.); (K.C.)
- Department of Medical Technology, Division of Clinical Immunology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Rawiwan Maniratanachote
- Toxicology and Bio Evaluation Service Center (TBES), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (R.M.); (P.C.)
| | - Paninee Chetprayoon
- Toxicology and Bio Evaluation Service Center (TBES), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand; (R.M.); (P.C.)
| | - Kanokporn Sornsuwan
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (S.M.); (K.S.); (W.T.); (K.C.)
| | - Weeraya Thongkum
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (S.M.); (K.S.); (W.T.); (K.C.)
- Center of Innovative Immunodiagnostic Development, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Koollawat Chupradit
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (S.M.); (K.S.); (W.T.); (K.C.)
- Siriraj Center for Regenerative Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Chatchai Tayapiwatana
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand; (S.M.); (K.S.); (W.T.); (K.C.)
- Department of Medical Technology, Division of Clinical Immunology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Innovative Immunodiagnostic Development, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence:
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A functional map of HIV-host interactions in primary human T cells. Nat Commun 2022; 13:1752. [PMID: 35365639 PMCID: PMC8976027 DOI: 10.1038/s41467-022-29346-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/08/2022] [Indexed: 02/07/2023] Open
Abstract
Human Immunodeficiency Virus (HIV) relies on host molecular machinery for replication. Systematic attempts to genetically or biochemically define these host factors have yielded hundreds of candidates, but few have been functionally validated in primary cells. Here, we target 426 genes previously implicated in the HIV lifecycle through protein interaction studies for CRISPR-Cas9-mediated knock-out in primary human CD4+ T cells in order to systematically assess their functional roles in HIV replication. We achieve efficient knockout (>50% of alleles) in 364 of the targeted genes and identify 86 candidate host factors that alter HIV infection. 47 of these factors validate by multiplex gene editing in independent donors, including 23 factors with restrictive activity. Both gene editing efficiencies and HIV-1 phenotypes are highly concordant among independent donors. Importantly, over half of these factors have not been previously described to play a functional role in HIV replication, providing numerous novel avenues for understanding HIV biology. These data further suggest that host-pathogen protein-protein interaction datasets offer an enriched source of candidates for functional host factor discovery and provide an improved understanding of the mechanics of HIV replication in primary T cells.
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41
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42
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Domínguez-Zotes S, Valbuena A, Mateu MG. Antiviral compounds modulate elasticity, strength and material fatigue of a virus capsid framework. Biophys J 2022; 121:919-931. [PMID: 35151634 PMCID: PMC8943814 DOI: 10.1016/j.bpj.2022.02.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/18/2022] [Accepted: 02/09/2022] [Indexed: 11/30/2022] Open
Abstract
This study investigates whether the biochemical and antiviral effects of organic compounds that bind different sites in the mature human immunodeficiency virus capsid may be related to the modulation of different mechanical properties of the protein lattice from which the capsid is built. Mechanical force was used as a probe to quantify, in atomic force microscopy experiments at physiological pH and ionic strength, ligand-mediated changes in capsid lattice elasticity, breathing, strength against local dislocation by mechanical stress, and resistance to material fatigue. The results indicate that the effects of the tested compounds on assembly or biochemical stability can be linked, from a physics-based perspective, to their interference with the mechanical behavior of the viral capsid framework. The antivirals CAP-1 and CAI-55 increased the intrinsic elasticity and breathing of the capsid protein lattice and may entropically decrease the probability of the capsid protein to assemble into a functionally competent conformation. Antiviral PF74 increased the resistance of the capsid protein lattice to disruption by mechanical stress and material fatigue and may enthalpically strengthen the basal capsid lattice against breakage and disintegration. This study provides proof of concept that the interrogation of the mechanical properties of the nanostructured protein material that makes a virus capsid may provide fundamental insights into the biophysical action of capsid-binding antiviral agents. The implications for drug design by specifically targeting the biomechanics of viruses are discussed.
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Affiliation(s)
- Santos Domínguez-Zotes
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
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Yu A, Lee EMY, Briggs JAG, Ganser-Pornillos BK, Pornillos O, Voth GA. Strain and rupture of HIV-1 capsids during uncoating. Proc Natl Acad Sci U S A 2022; 119:e2117781119. [PMID: 35238630 PMCID: PMC8915963 DOI: 10.1073/pnas.2117781119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/25/2022] [Indexed: 12/18/2022] Open
Abstract
SignificanceThe mature capsids of HIV-1 are transiently stable complexes that self-assemble around the viral genome during maturation, and uncoat to release preintegration complexes that archive a double-stranded DNA copy of the virus in the host cell genome. However, a detailed view of how HIV cores rupture remains lacking. Here, we elucidate the physical properties involved in capsid rupture using a combination of large-scale all-atom molecular dynamics simulations and cryo-electron tomography. We find that intrinsic strain on the capsid forms highly correlated patterns along the capsid surface, along which cracks propagate. Capsid rigidity also increases with high strain. Our findings provide fundamental insight into viral capsid uncoating.
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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
| | - Elizabeth M. Y. Lee
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637
| | - John A. G. Briggs
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Barbie K. Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903
| | - 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
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44
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In PrEP: Long-acting antivirals for HIV prevention. Cell Host Microbe 2022; 30:148-150. [PMID: 35143766 DOI: 10.1016/j.chom.2022.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two recent publications (Vidal et al., 2021; Xue et al., 2022) report highly potent inhibitors as candidates for HIV pre-exposure prophylaxis (PrEP). They provide strong evidence that administration of long-acting capsid or fusion inhibitors as PrEP offers robust protection against simian-human immunodeficiency virus in the rhesus macaque model of HIV infection.
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Selyutina A, Hu P, Miller S, Simons LM, Yu HJ, Hultquist JF, Lee K, KewalRamani VN, Diaz-Griffero F. GS-CA1 and lenacapavir stabilize the HIV-1 core and modulate the core interaction with cellular factors. iScience 2022; 25:103593. [PMID: 35005542 PMCID: PMC8718827 DOI: 10.1016/j.isci.2021.103593] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/11/2021] [Accepted: 12/07/2021] [Indexed: 12/02/2022] Open
Abstract
The HIV-1 capsid is the target for the antiviral drugs GS-CA1 and Lenacapavir (GS-6207). We investigated the mechanism by which GS-CA1 and GS-6207 inhibit HIV-1 infection. HIV-1 inhibition by GS-CA1 did not require CPSF6 in CD4+ T cells. Contrary to PF74 that accelerates uncoating of HIV-1, GS-CA1 and GS-6207 stabilized the core. GS-CA1, unlike PF74, allowed the core to enter the nucleus, which agrees with the fact that GS-CA1 inhibits infection after reverse transcription. Unlike PF74, GS-CA1 did not disaggregate preformed CPSF6 complexes in nuclear speckles, suggesting that PF74 and GS-CA1 have different mechanisms of action. GS-CA1 stabilized the HIV-1 core, possibly by inducing a conformational shift in the core; in agreement, HIV-1 cores bearing N74D regained their ability to bind CPSF6 in the presence of GS-CA1. We showed that GS-CA1 binds to the HIV-1 core, changes its conformation, stabilizes the core, and thereby prevents viral uncoating and infection. GS-CA1 and Lenacapavir (GS-6207) stabilizes the HIV-1 core during infection GS-CA1/GS-6207 inhibit the interaction of the HIV-1 core with host factors GS-CA1/GS-6207 do not disaggregate preformed CPSF6 complexes in nuclear speckles GS-CA1/GS-6207 affects the dynamic surface of the HIV-1 core
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Affiliation(s)
- Anastasia Selyutina
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1301 Morris Park - Price Center 501, Bronx, NY 10461, USA
| | - Pan Hu
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1301 Morris Park - Price Center 501, Bronx, NY 10461, USA
| | - Sorin Miller
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Lacy M Simons
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Hyun Jae Yu
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD 21702, USA
| | - Judd F Hultquist
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - KyeongEun Lee
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Vineet N KewalRamani
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1301 Morris Park - Price Center 501, Bronx, NY 10461, USA
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46
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Targeting the Virus Capsid as a Tool to Fight RNA Viruses. Viruses 2022; 14:v14020174. [PMID: 35215767 PMCID: PMC8879806 DOI: 10.3390/v14020174] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 12/10/2022] Open
Abstract
Several strategies have been developed to fight viral infections, not only in humans but also in animals and plants. Some of them are based on the development of efficient vaccines, to target the virus by developed antibodies, others focus on finding antiviral compounds with activities that inhibit selected virus replication steps. Currently, there is an increasing number of antiviral drugs on the market; however, some have unpleasant side effects, are toxic to cells, or the viruses quickly develop resistance to them. As the current situation shows, the combination of multiple antiviral strategies or the combination of the use of various compounds within one strategy is very important. The most desirable are combinations of drugs that inhibit different steps in the virus life cycle. This is an important issue especially for RNA viruses, which replicate their genomes using error-prone RNA polymerases and rapidly develop mutants resistant to applied antiviral compounds. Here, we focus on compounds targeting viral structural capsid proteins, thereby inhibiting virus assembly or disassembly, virus binding to cellular receptors, or acting by inhibiting other virus replication mechanisms. This review is an update of existing papers on a similar topic, by focusing on the most recent advances in the rapidly evolving research of compounds targeting capsid proteins of RNA viruses.
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Vidal SJ, Bekerman E, Hansen D, Lu B, Wang K, Mwangi J, Rowe W, Campigotto F, Zheng J, Kato D, Chandrashekar A, Barrett J, Patel S, Wan H, Anioke T, Mercado NB, Nkolola JP, Ferguson MJ, Rinaldi WJ, Callebaut C, Blair W, Cihlar T, Geleziunas R, Yant SR, Barouch DH. Long-acting capsid inhibitor protects macaques from repeat SHIV challenges. Nature 2022; 601:612-616. [PMID: 34875675 PMCID: PMC8753592 DOI: 10.1038/s41586-021-04279-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/24/2021] [Indexed: 11/11/2022]
Abstract
Because no currently available vaccine can prevent HIV infection, pre-exposure prophylaxis (PrEP) with antiretrovirals (ARVs) is an important tool for combating the HIV pandemic1,2. Long-acting ARVs promise to build on the success of current PrEP strategies, which must be taken daily, by reducing the frequency of administration3. GS-CA1 is a small-molecule HIV capsid inhibitor with picomolar antiviral potency against a broad array of HIV strains, including variants resistant to existing ARVs, and has shown long-acting therapeutic potential in a mouse model of HIV infection4. Here we show that a single subcutaneous administration of GS-CA1 provides long-term protection against repeated rectal simian-human immunodeficiency virus (SHIV) challenges in rhesus macaques. Whereas all control animals became infected after 15 weekly challenges, a single 300 mg kg-1 dose of GS-CA1 provided per-exposure infection risk reduction of 97% for 24 weeks. Pharmacokinetic analysis showed a correlation between GS-CA1 plasma concentration and protection from SHIV challenges. GS-CA1 levels greater than twice the rhesus plasma protein-adjusted 95% effective concentration conferred 100% protection in this model. These proof-of-concept data support the development of capsid inhibitors as a novel long-acting PrEP strategy in humans.
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Affiliation(s)
- Samuel J Vidal
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Brigham and Women's Hospital and Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Bing Lu
- Gilead Sciences, Foster City, CA, USA
| | | | | | | | | | - Jim Zheng
- Gilead Sciences, Foster City, CA, USA
| | | | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Julia Barrett
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Shivani Patel
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Huahua Wan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Tochi Anioke
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Noe B Mercado
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Joseph P Nkolola
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | | | | | | | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
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48
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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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49
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Ricaña CL, Dick RA. Inositol Phosphates and Retroviral Assembly: A Cellular Perspective. Viruses 2021; 13:v13122516. [PMID: 34960784 PMCID: PMC8703376 DOI: 10.3390/v13122516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 12/13/2022] Open
Abstract
Understanding the molecular mechanisms of retroviral assembly has been a decades-long endeavor. With the recent discovery of inositol hexakisphosphate (IP6) acting as an assembly co-factor for human immunodeficiency virus (HIV), great strides have been made in retroviral research. In this review, the enzymatic pathways to synthesize and metabolize inositol phosphates (IPs) relevant to retroviral assembly are discussed. The functions of these enzymes and IPs are outlined in the context of the cellular biology important for retroviruses. Lastly, the recent advances in understanding the role of IPs in retroviral biology are surveyed.
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50
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Ni T, Zhu Y, Yang Z, Xu C, Chaban Y, Nesterova T, Ning J, Böcking T, Parker MW, Monnie C, Ahn J, Perilla JR, Zhang P. Structure of native HIV-1 cores and their interactions with IP6 and CypA. SCIENCE ADVANCES 2021; 7:eabj5715. [PMID: 34797722 PMCID: PMC8604400 DOI: 10.1126/sciadv.abj5715] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/01/2021] [Indexed: 05/24/2023]
Abstract
The viral capsid plays essential roles in HIV replication and is a major platform engaging host factors. To overcome challenges in study native capsid structure, we used the perfringolysin O to perforate the membrane of HIV-1 particles, thus allowing host proteins and small molecules to access the native capsid while improving cryo–electron microscopy image quality. Using cryo–electron tomography and subtomogram averaging, we determined the structures of native capsomers in the presence and absence of inositol hexakisphosphate (IP6) and cyclophilin A and constructed an all-atom model of a complete HIV-1 capsid. Our structures reveal two IP6 binding sites and modes of cyclophilin A interactions. Free energy calculations substantiate the two binding sites at R18 and K25 and further show a prohibitive energy barrier for IP6 to pass through the pentamer. Our results demonstrate that perfringolysin O perforation is a valuable tool for structural analyses of enveloped virus capsids and interactions with host cell factors.
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Affiliation(s)
- Tao Ni
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Yanan Zhu
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Zhengyi Yang
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Chaoyi Xu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Yuriy Chaban
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Tanya Nesterova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Jiying Ning
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Till Böcking
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, UNSW, Sydney, Australia
| | - Michael W. Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
- St. Vincent’s Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Christina Monnie
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jinwoo Ahn
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Juan R. Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - 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
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7BN, UK
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