1
|
Alzahrani NS, Almarwani AM. The effect of HIV on patients' lives: a phenomenological qualitative study. Int J Qual Stud Health Well-being 2024; 19:2315634. [PMID: 38340013 PMCID: PMC10860465 DOI: 10.1080/17482631.2024.2315634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 02/04/2024] [Indexed: 02/12/2024] Open
Abstract
INTRODUCTION Human immunodeficiency virus (HIV) infection poses a significant threat to the immune system, compromising the body's ability to combat diseases and infections. The Ministry of Health in Saudi Arabia reported an HIV incidence rate of 3 cases per 10,000 individuals. This study aimed to gain insight into the lived experience of Saudi patients living with HIV. METHODS Employing a qualitative phenomenological approach, this study conducted in-depth interviews with 16 HIV patients (10 men, 6 women) between January 2023 and May 2023. RESULTS Thematic data analysis highlighted three overarching themes and four subthemes. "Fear of the Future" encompassed subthemes including the fear of infecting a family member, fear of marriage, fear of employment recruitment, and fear of scandals. "Hopelessness" reflected the profound emotional state experienced by patients. "Overcoming Adversity" captured the resilience and strength demonstrated by individuals facing the challenges of living with HIV. CONCLUSION Saudi patients diagnosed with HIV encounter numerous obstacles in their daily lives. The fear of the future, including concerns such as infecting family members, marriage prospects, employment opportunities, and potential social repercussions, significantly impacts their overall well-being. By understanding the lived experience of HIV patients in Saudi Arabia, healthcare providers and policymakers can better support and enhance the quality of life for this population.
Collapse
Affiliation(s)
- Naif S. Alzahrani
- Department of Medical Surgical Nursing, College of Nursing, Taibah University, Medina, Saudi Arabia
| | | |
Collapse
|
2
|
K C Y, Pal S, Nitz TJ, Wild C, Gaur R. Construction of a HIV-1 subtype C 3D model using homology modeling and in-silico docking, molecular dynamics simulation, and MM-GBSA calculation of second-generation HIV-1 maturation inhibitor(s). J Biomol Struct Dyn 2024; 42:7150-7159. [PMID: 37489057 DOI: 10.1080/07391102.2023.2238079] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 07/13/2023] [Indexed: 07/26/2023]
Abstract
Maturation inhibitors (MIs) efficiently block HIV-1 maturation by inhibiting the cleavage of the capsid protein and spacer peptide 1 (CA-SP1) leading to the production of immature and non-infectious virus particles. We have previously reported that second-generation MIs were more potent than bevirimat (BVM) against HIV-1 subtype C. In-silico studies on interaction of with BVM and their analogs have been limited to HIV-1 subtype B(5I4T) due to lack of an available 3D structure for HIV-1 subtype C virus. In our current study, we have developed a 3D model of HIV-1C Gag CA-SP1 region using protein homology modeling with HIV-1 subtype B(514T) as a template. The HIV-1 C homology model generated was extensively validated using several online tools and served as a template to perform molecular docking studies with eight well-characterized MIs. The docked complex of HIV-1C and all nine MIs was subjected to molecular dynamics simulation for 100 ns using AMBER and binding free energy calculations were done using MM-GBSA. Based on our data, CV8611 exhibited highest binding energy of -6.5 Kcal/mol among all BVM analogs. CV8611 formed strong interactions with Gly222 and Met235 of HIV-1C Gag CA-SP1 during MD simulation and remained intact. The root mean square deviation and root mean square fluctuation values of the complex were stable during the simulations. Our study is the first to report construction and validation of 3D model for the HIV-1C Gag CA-SP1, which could serve as a crucial tool in the structure-aided design of novel and broadly acting maturation inhibitors.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Yuvraj K C
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, India
| | - Sapna Pal
- Bioinformatics centre, National Institute of Immunology, New Delhi, India
| | - T J Nitz
- DFH Pharma, Gaithersburg, MD, USA
| | | | - Ritu Gaur
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, India
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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.
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Durden H, Preece B, Gallegos R, Saha I, MacArthur B, Petersen A, Peppel W, Saffarian S. Competitive assembly resolves the stoichiometry of essential proteins in infectious HIV-1 virions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.10.584319. [PMID: 38559103 PMCID: PMC10979864 DOI: 10.1101/2024.03.10.584319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
During assembly on the plasma membrane, HIV-1 virions incorporate Gag-Pol as well as gp120/gp41 trimers. The Pol region consists of protease, reverse transcriptase and integrase precursors which are essential enzymes required for maturation, reverse transcription, and integration of the viral genome in the next host. gp120/gp41 trimers catalyze the fusion of the virion with its next host. Only a fraction of released virions are infectious. The stoichiometry of gp120/gp41 and Gag-Pol proteins in HIV virions was previously measured using cryotomography and ratiometric protein analysis, but what is the stoichiometry of these proteins in infectious virions remained to be determined. Here we developed a method based on competition between infectious HIV backbones with noninfectious mutants and measured 100 ± 10 Gag-Pol and 15 ± 3 gp120/gp41 proteins incorporated in infectious virions assembled in HEK293 cells from NL4.3 HIV-1 backbone. Our measurements are in broad agreement with cryotomography and ratiometric protein analysis and therefore stoichiometry of gp120/gp41 and Gag-Pol in infectious virions is the same as all released virions. With the development of appropriate mutants and infectivity assays, our method is applicable to other infectious viruses. Statement of significance There are 30 million people who have succumbed to the AIDS pandemic with 600,000 additional deaths per year. HIV has an accelerated rate of mutational accumulation with the virus mutating out of neutralizing antibodies within the same patient making development of vaccines challenging. Like most enveloped viruses, only a fraction of released virions are infectious and the question of what selects these virions has remained a mystery. The method developed in this article will allow stoichiometric measurements on infectious virions and therefore allows further studies of causes of infectivity.
Collapse
|
8
|
Hikichi Y, Grover JR, Schäfer A, Mothes W, Freed EO. Epistatic pathways can drive HIV-1 escape from integrase strand transfer inhibitors. SCIENCE ADVANCES 2024; 10:eadn0042. [PMID: 38427738 PMCID: PMC10906922 DOI: 10.1126/sciadv.adn0042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
People living with human immunodeficiency virus (HIV) receiving integrase strand transfer inhibitors (INSTIs) have been reported to experience virological failure in the absence of resistance mutations in integrase. To elucidate INSTI resistance mechanisms, we propagated HIV-1 in the presence of escalating concentrations of the INSTI dolutegravir. HIV-1 became resistant to dolutegravir by sequentially acquiring mutations in the envelope glycoprotein (Env) and the nucleocapsid protein. The selected Env mutations enhance the ability of the virus to spread via cell-cell transfer, thereby increasing the multiplicity of infection (MOI). While the selected Env mutations confer broad resistance to multiple classes of antiretrovirals, the fold resistance is ~2 logs higher for INSTIs than for other classes of drugs. We demonstrate that INSTIs are more readily overwhelmed by high MOI than other classes of antiretrovirals. Our findings advance the understanding of how HIV-1 can evolve resistance to antiretrovirals, including the potent INSTIs, in the absence of drug-target gene mutations.
Collapse
Affiliation(s)
- Yuta Hikichi
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jonathan R. Grover
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Alicia Schäfer
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Eric O. Freed
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Banerjee P, Voth GA. Conformational transitions of the HIV-1 Gag polyprotein upon multimerization and gRNA binding. Biophys J 2024; 123:42-56. [PMID: 37978800 PMCID: PMC10808027 DOI: 10.1016/j.bpj.2023.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/25/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023] Open
Abstract
During the HIV-1 assembly process, the Gag polyprotein multimerizes at the producer cell plasma membrane, resulting in the formation of spherical immature virus particles. Gag-genomic RNA (gRNA) interactions play a crucial role in the multimerization process, which is yet to be fully understood. We performed large-scale all-atom molecular dynamics simulations of membrane-bound full-length Gag dimer, hexamer, and 18-mer. The inter-domain dynamic correlation of Gag, quantified by the heterogeneous elastic network model applied to the simulated trajectories, is observed to be altered by implicit gRNA binding, as well as the multimerization state of the Gag. The lateral dynamics of our simulated membrane-bound Gag proteins, with and without gRNA binding, agree with prior experimental data and help to validate our simulation models and methods. The gRNA binding is observed to affect mainly the SP1 domain of the 18-mer and the matrix-capsid linker domain of the hexamer. In the absence of gRNA binding, the independent dynamical motion of the nucleocapsid domain results in a collapsed state of the dimeric Gag. Unlike stable SP1 helices in the six-helix bundle, without IP6 binding, the SP1 domain undergoes a spontaneous helix-to-coil transition in the dimeric Gag. Together, our findings reveal conformational switches of Gag at different stages of the multimerization process and predict that the gRNA binding reinforces an efficient binding surface of Gag for multimerization, and also regulates the dynamic organization of the local membrane region itself.
Collapse
Affiliation(s)
- Puja Banerjee
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois.
| |
Collapse
|
11
|
Loaiza JD, Chvatal-Medina M, Hernandez JC, Rugeles MT. Integrase inhibitors: current protagonists in antiretroviral therapy. Immunotherapy 2023; 15:1477-1495. [PMID: 37822251 DOI: 10.2217/imt-2023-0011] [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] [Indexed: 10/13/2023] Open
Abstract
Since HIV was identified as the etiological agent of AIDS, there have been significant advances in antiretroviral therapy (ART) that has reduced morbidity/mortality. Still, the viral genome's high mutation rate, suboptimal ART regimens, incomplete adherence to therapy and poor control of the viral load generate variants resistant to multiple drugs. Licensing over 30 anti-HIV drugs worldwide, including integrase inhibitors, has marked a milestone since they are potent and well-tolerated drugs. In addition, they favor a faster recovery of CD4+ T cells. They also increase the diversity profile of the gut microbiota and reduce inflammatory markers. All of these highlight the importance of including them in different ART regimens.
Collapse
Affiliation(s)
- John D Loaiza
- Grupo Inmunovirología, Facultad de medicina, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Mateo Chvatal-Medina
- Grupo Inmunovirología, Facultad de medicina, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Juan C Hernandez
- Infettare, Facultad de medicina, Universidad Cooperativa de Colombia, Medellín, 050012, Colombia
| | - Maria T Rugeles
- Grupo Inmunovirología, Facultad de medicina, Universidad de Antioquia, Medellín, 050010, Colombia
| |
Collapse
|
12
|
Banerjee P, Voth GA. Conformational transitions of the HIV-1 Gag polyprotein upon multimerization and gRNA binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553549. [PMID: 37645781 PMCID: PMC10462060 DOI: 10.1101/2023.08.16.553549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
During the HIV-1 assembly process, the Gag polyprotein multimerizes at the producer cell plasma membrane, resulting in the formation of spherical immature virus particles. Gag-gRNA interactions play a crucial role in the multimerization process, which is yet to be fully understood. We have performed large-scale all-atom molecular dynamics simulations of membrane-bound full-length Gag dimer, hexamer, and 18-mer. The inter-domain dynamic correlation of Gag, quantified by the heterogeneous elastic network model (hENM) applied to the simulated trajectories, is observed to be altered by implicit gRNA binding, as well as the multimerization state of the Gag. The lateral dynamics of our simulated membrane-bound Gag proteins, with and without gRNA binding, agree with prior experimental data and help to validate our simulation models and methods. The gRNA binding is observed to impact mainly the SP1 domain of the 18-mer and the MA-CA linker domain of the hexamer. In the absence of gRNA binding, the independent dynamical motion of the NC domain results in a collapsed state of the dimeric Gag. Unlike stable SP1 helices in the six-helix bundle, without IP6 binding, the SP1 domain undergoes a spontaneous helix-to-coil transition in the dimeric Gag. Together, our findings reveal conformational switches of Gag at different stages of the multimerization process and predict that the gRNA binding reinforces an efficient binding surface of Gag for multimerization, as well as regulates the dynamic organization of the local membrane region itself. Significance Gag(Pr 55 Gag ) polyprotein orchestrates many essential events in HIV-1 assembly, including packaging of the genomic RNA (gRNA) in the immature virion. Although various experimental techniques, such as cryo-ET, X-ray, and NMR, have revealed structural properties of individual domains in the immature Gag clusters, structural and biophysical characterization of a full-length Gag molecule remains a challenge for existing experimental techniques. Using atomistic molecular dynamics simulations of the different model systems of Gag polyprotein, we present here a detailed structural characterization of Gag molecules in different multimerization states and interrogate the synergy between Gag-Gag, Gag-membrane, and Gag-gRNA interactions during the viral assembly process.
Collapse
|
13
|
Guo S, Saha I, Saffarian S, Johnson ME. Structure of the HIV immature lattice allows for essential lattice remodeling within budded virions. eLife 2023; 12:e84881. [PMID: 37435945 PMCID: PMC10361719 DOI: 10.7554/elife.84881] [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: 11/12/2022] [Accepted: 07/12/2023] [Indexed: 07/13/2023] Open
Abstract
For HIV virions to become infectious, the immature lattice of Gag polyproteins attached to the virion membrane must be cleaved. Cleavage cannot initiate without the protease formed by the homo-dimerization of domains linked to Gag. However, only 5% of the Gag polyproteins, termed Gag-Pol, carry this protease domain, and they are embedded within the structured lattice. The mechanism of Gag-Pol dimerization is unknown. Here, we use spatial stochastic computer simulations of the immature Gag lattice as derived from experimental structures, showing that dynamics of the lattice on the membrane is unavoidable due to the missing 1/3 of the spherical protein coat. These dynamics allow for Gag-Pol molecules carrying the protease domains to detach and reattach at new places within the lattice. Surprisingly, dimerization timescales of minutes or less are achievable for realistic binding energies and rates despite retaining most of the large-scale lattice structure. We derive a formula allowing extrapolation of timescales as a function of interaction free energy and binding rate, thus predicting how additional stabilization of the lattice would impact dimerization times. We further show that during assembly, dimerization of Gag-Pol is highly likely and therefore must be actively suppressed to prevent early activation. By direct comparison to recent biochemical measurements within budded virions, we find that only moderately stable hexamer contacts (-12kBT<∆G<-8kBT) retain both the dynamics and lattice structures that are consistent with experiment. These dynamics are likely essential for proper maturation, and our models quantify and predict lattice dynamics and protease dimerization timescales that define a key step in understanding formation of infectious viruses.
Collapse
Affiliation(s)
- Sikao Guo
- TC Jenkins Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| | - Ipsita Saha
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of HealthFrederickUnited States
| | - Saveez Saffarian
- Center for Cell and Genome Science, University of UtahSalt Lake CityUnited States
- Department of Physics and Astronomy, University of UtahSalt Lake CityUnited States
- School of Biological Sciences, University of UtahSalt Lake CityUnited States
| | - Margaret E Johnson
- TC Jenkins Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| |
Collapse
|
14
|
Yoo SW, Waheed AA, Deme P, Tohumeken S, Rais R, Smith MD, DeMarino C, Calabresi PA, Kashanchi F, Freed EO, Slusher BS, Haughey NJ. Inhibition of neutral sphingomyelinase 2 impairs HIV-1 envelope formation and substantially delays or eliminates viral rebound. Proc Natl Acad Sci U S A 2023; 120:e2219543120. [PMID: 37406092 PMCID: PMC10334757 DOI: 10.1073/pnas.2219543120] [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: 11/15/2022] [Accepted: 04/03/2023] [Indexed: 07/07/2023] Open
Abstract
Although HIV-1 Gag is known to drive viral assembly and budding, the precise mechanisms by which the lipid composition of the plasma membrane is remodeled during assembly are incompletely understood. Here, we provide evidence that the sphingomyelin hydrolase neutral sphingomyelinase 2 (nSMase2) interacts with HIV-1 Gag and through the hydrolysis of sphingomyelin creates ceramide that is necessary for proper formation of the viral envelope and viral maturation. Inhibition or depletion of nSMase2 resulted in the production of noninfectious HIV-1 virions with incomplete Gag lattices lacking condensed conical cores. Inhibition of nSMase2 in HIV-1-infected humanized mouse models with a potent and selective inhibitor of nSMase2 termed PDDC [phenyl(R)-(1-(3-(3,4-dimethoxyphenyl)-2, 6-dimethylimidazo[1,2-b]pyridazin-8-yl) pyrrolidin-3-yl)-carbamate] produced a linear reduction in levels of HIV-1 in plasma. If undetectable plasma levels of HIV-1 were achieved with PDDC treatment, viral rebound did not occur for up to 4 wk when PDDC was discontinued. In vivo and tissue culture results suggest that PDDC selectively kills cells with actively replicating HIV-1. Collectively, this work demonstrates that nSMase2 is a critical regulator of HIV-1 replication and suggests that nSMase2 could be an important therapeutic target with the potential to kill HIV-1-infected cells.
Collapse
Affiliation(s)
- Seung-Wan Yoo
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD21210
| | - Abdul A. Waheed
- Virus-Cell Interaction Section, HIV-1 Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD21702
| | - Pragney Deme
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD21210
| | - Sehmus Tohumeken
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD21210
| | - Rana Rais
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Matthew D. Smith
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD21210
| | - Catherine DeMarino
- Laboratory of Molecular Virology, George Mason University, Manassas, VA20110
| | - Peter A. Calabresi
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD21210
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, George Mason University, Manassas, VA20110
| | - Eric O. Freed
- Virus-Cell Interaction Section, HIV-1 Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD21702
| | - Barbara S. Slusher
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD21210
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD21210
- Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD21210
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD21224
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21210
| | - Norman J. Haughey
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD21210
- Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD21210
| |
Collapse
|
15
|
Waheed AA, Zhu Y, Agostino E, Naing L, Hikichi Y, Soheilian F, Yoo SW, Song Y, Zhang P, Slusher BS, Haughey NJ, Freed EO. Neutral sphingomyelinase 2 is required for HIV-1 maturation. Proc Natl Acad Sci U S A 2023; 120:e2219475120. [PMID: 37406093 PMCID: PMC10334776 DOI: 10.1073/pnas.2219475120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/11/2023] [Indexed: 07/07/2023] Open
Abstract
HIV-1 assembly occurs at the inner leaflet of the plasma membrane (PM) in highly ordered membrane microdomains. The size and stability of membrane microdomains is regulated by activity of the sphingomyelin hydrolase neutral sphingomyelinase 2 (nSMase2) that is localized primarily to the inner leaflet of the PM. In this study, we demonstrate that pharmacological inhibition or depletion of nSMase2 in HIV-1-producer cells results in a block in the processing of the major viral structural polyprotein Gag and the production of morphologically aberrant, immature HIV-1 particles with severely impaired infectivity. We find that disruption of nSMase2 also severely inhibits the maturation and infectivity of other primate lentiviruses HIV-2 and simian immunodeficiency virus, has a modest or no effect on nonprimate lentiviruses equine infectious anemia virus and feline immunodeficiency virus, and has no effect on the gammaretrovirus murine leukemia virus. These studies demonstrate a key role for nSMase2 in HIV-1 particle morphogenesis and maturation.
Collapse
Affiliation(s)
- Abdul A. Waheed
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Yanan Zhu
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, OxfordOX3 7BN, United Kingdom
| | - Eva Agostino
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Lwar Naing
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Yuta Hikichi
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| | - Ferri Soheilian
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD21702
| | - Seung-Wan Yoo
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Yun Song
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, DidcotOX11 0DE, United Kingdom
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, OxfordOX3 7BN, United Kingdom
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, DidcotOX11 0DE, United Kingdom
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, OxfordOX3 7BN, United Kingdom
| | - Barbara S. Slusher
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Johns Hopkins Drug Discovery, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Norman J. Haughey
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Eric O. Freed
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD21702
| |
Collapse
|
16
|
Kleinpeter AB, Zhu Y, Mallery DL, Ablan SD, Chen L, Hardenbrook N, Saiardi A, James LC, Zhang P, Freed EO. The Effect of Inositol Hexakisphosphate on HIV-1 Particle Production and Infectivity can be Modulated by Mutations that Affect the Stability of the Immature Gag Lattice. J Mol Biol 2023; 435:168037. [PMID: 37330292 PMCID: PMC10544863 DOI: 10.1016/j.jmb.2023.168037] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 06/19/2023]
Abstract
The assembly of an HIV-1 particle begins with the construction of a spherical lattice composed of hexamer subunits of the Gag polyprotein. The cellular metabolite inositol hexakisphosphate (IP6) binds and stabilizes the immature Gag lattice via an interaction with the six-helix bundle (6HB), a crucial structural feature of Gag hexamers that modulates both virus assembly and infectivity. The 6HB must be stable enough to promote immature Gag lattice formation, but also flexible enough to be accessible to the viral protease, which cleaves the 6HB during particle maturation. 6HB cleavage liberates the capsid (CA) domain of Gag from the adjacent spacer peptide 1 (SP1) and IP6 from its binding site. This pool of IP6 molecules then promotes the assembly of CA into the mature conical capsid that is required for infection. Depletion of IP6 in virus-producer cells results in severe defects in assembly and infectivity of wild-type (WT) virions. Here we show that in an SP1 double mutant (M4L/T8I) with a hyperstable 6HB, IP6 can block virion infectivity by preventing CA-SP1 processing. Thus, depletion of IP6 in virus-producer cells markedly increases M4L/T8I CA-SP1 processing and infectivity. We also show that the introduction of the M4L/T8I mutations partially rescues the assembly and infectivity defects induced by IP6 depletion on WT virions, likely by increasing the affinity of the immature lattice for limiting IP6. These findings reinforce the importance of the 6HB in virus assembly, maturation, and infection and highlight the ability of IP6 to modulate 6HB stability.
Collapse
Affiliation(s)
- Alex B Kleinpeter
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA. https://twitter.com/AlexKleinpeter
| | - Yanan Zhu
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Donna L Mallery
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Sherimay D Ablan
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Long Chen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Nathan Hardenbrook
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Adolfo Saiardi
- Laboratory for Molecular Cell Biology, University College London, London, UK. https://twitter.com/SaiardiLab
| | - Leo C James
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. https://twitter.com/JamesLab9
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; 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
| | - Eric O Freed
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA.
| |
Collapse
|
17
|
Tao K, Rhee SY, Tzou PL, Osman ZA, Pond SLK, Holmes SP, Shafer RW. HIV-1 Group M Capsid Amino Acid Variability: Implications for Sequence Quality Control of Genotypic Resistance Testing. Viruses 2023; 15:992. [PMID: 37112972 PMCID: PMC10143361 DOI: 10.3390/v15040992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND With the approval of the HIV-1 capsid inhibitor, lenacapavir, capsid sequencing will be required for managing lenacapavir-experienced individuals with detectable viremia. Successful sequence interpretation will require examining new capsid sequences in the context of previously published sequence data. METHODS We analyzed published HIV-1 group M capsid sequences from 21,012 capsid-inhibitor naïve individuals to characterize amino acid variability at each position and influence of subtype and cytotoxic T lymphocyte (CTL) selection pressure. We determined the distributions of usual mutations, defined as amino acid differences from the group M consensus, with a prevalence ≥ 0.1%. Co-evolving mutations were identified using a phylogenetically-informed Bayesian graphical model method. RESULTS 162 (70.1%) positions had no usual mutations (45.9%) or only conservative usual mutations with a positive BLOSUM62 score (24.2%). Variability correlated independently with subtype-specific amino acid occurrence (Spearman rho = 0.83; p < 1 × 10-9) and the number of times positions were reported to contain an HLA-associated polymorphism, an indicator of CTL pressure (rho = 0.43; p = 0.0002). CONCLUSIONS Knowing the distribution of usual capsid mutations is essential for sequence quality control. Comparing capsid sequences from lenacapavir-treated and lenacapavir-naïve individuals will enable the identification of additional mutations potentially associated with lenacapavir therapy.
Collapse
Affiliation(s)
- Kaiming Tao
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Philip L. Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Zachary A. Osman
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | | | - Susan P. Holmes
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
18
|
Mohamed S, Boulmé R, Sayada C. From Capillary Electrophoresis to Deep Sequencing: An Improved HIV-1 Drug Resistance Assessment Solution Using In Vitro Diagnostic (IVD) Assays and Software. Viruses 2023; 15:v15020571. [PMID: 36851783 PMCID: PMC9965321 DOI: 10.3390/v15020571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Drug-resistance mutations were mostly detected using capillary electrophoresis sequencing, which does not detect minor variants with a frequency below 20%. Next-Generation Sequencing (NGS) can now detect additional mutations which can be useful for HIV-1 drug resistance interpretation. The objective of this study was to evaluate the performances of CE-IVD assays for HIV-1 drug-resistance assessment both for target-specific and whole-genome sequencing, using standardized end-to-end solution platforms. METHODS A total of 301 clinical samples were prepared, extracted, and amplified for the three HIV-1 genomic targets, Protease (PR), Reverse Transcriptase (RT), and Integrase (INT), using the CE-IVD DeepChek® Assays; and then 19 clinical samples, using the CE-IVD DeepChek® HIV Whole Genome Assay, were sequenced on the NGS iSeq100 and MiSeq (Illumina, San Diego, CA, USA). Sequences were compared to those obtained by capillary electrophoresis. Quality control for Molecular Diagnostics (QCMD) samples was added to validate the clinical accuracy of these in vitro diagnostics (IVDs). Nineteen clinical samples were then tested with the same sample collection, handling, and measurement procedure for evaluating the use of NGS for whole-genome HIV-1. Sequencing analyzer outputs were submitted to a downstream CE-IVD standalone software tailored for HIV-1 analysis and interpretation. RESULTS The limits of range detection were 1000 to 106 cp/mL for the HIV-1 target-specific sequencing. The median coverage per sample for the three amplicons (PR/RT and INT) was 13,237 reads. High analytical reproducibility and repeatability were evidenced by a positive percent agreement of 100%. Duplicated samples in two distinct NGS runs were 100% homologous. NGS detected all the mutations found by capillary electrophoresis and identified additional resistance variants. A perfect accuracy score with the QCMD panel detection of drug-resistance mutations was obtained. CONCLUSIONS This study is the first evaluation of the DeepChek® Assays for targets specific (PR/RT and INT) and whole genome. A cutoff of 3% allowed for a better characterization of the viral population by identifying additional resistance mutations and improving the HIV-1 drug-resistance interpretation. The use of whole-genome sequencing is an additional and complementary tool to detect mutations in newly infected untreated patients and heavily experienced patients, both with higher HIV-1 viral-load profiles, to offer new insight and treatment strategies, especially using the new HIV-1 capsid/maturation inhibitors and to assess the potential clinical impact of mutations in the HIV-1 genome outside of the usual HIV-1 targets (RT/PR and INT).
Collapse
Affiliation(s)
| | | | - Chalom Sayada
- Advanced Biological Laboratories (ABL), 2550 Luxembourg, Luxembourg
| |
Collapse
|
19
|
Perkins MV, Joseph S, Dittmer DP, Mackman N. Cardiovascular Disease and Thrombosis in HIV Infection. Arterioscler Thromb Vasc Biol 2023; 43:175-191. [PMID: 36453273 PMCID: PMC10165851 DOI: 10.1161/atvbaha.122.318232] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022]
Abstract
HIV infection has transitioned from an acute, fatal disease to a chronic one managed by antiretroviral therapy. Thus, the aging population of people living with HIV (PLWH) continues to expand. HIV infection results in a dysregulated immune system, wherein CD4+ T cells are depleted, particularly in the gastrointestinal tract, disrupting the gut epithelial barrier. Long-term HIV infection is associated with chronic inflammation through potentially direct mechanisms caused by viral replication or exposure to viral proteins and indirect mechanisms resulting from increased translocation of microbial products from the intestine or exposure to antiretroviral therapy. Chronic inflammation (as marked by IL [interleukin]-6 and CRP [C-reactive protein]) in PLWH promotes endothelial cell dysfunction and atherosclerosis. PLWH show significantly increased rates of cardiovascular disease, such as myocardial infarction (risk ratio, 1.79 [95% CI, 1.54-2.08]) and stroke (risk ratio, 2.56 [95% CI, 1.43-4.61]). In addition, PLWH have increased levels of the coagulation biomarker D-dimer and have a two to ten-fold increased risk of venous thromboembolism compared with the general population. Several small clinical trials analyzed the effect of different antithrombotic agents on platelet activation, coagulation, inflammation, and immune cell activation. Although some markers for coagulation were reduced, most agents failed to reduce inflammatory markers in PLWH. More studies are needed to understand the underlying mechanisms driving inflammation in PLWH to create better therapies for lowering chronic inflammation in PLWH. Such therapies can potentially reduce atherosclerosis, cardiovascular disease, and thrombosis rates in PLWH and thus overall mortality in this population.
Collapse
Affiliation(s)
- Megan V. Perkins
- UNC Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah Joseph
- UNC Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dirk P. Dittmer
- UNC Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nigel Mackman
- UNC Blood Research Center, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Division of Hematology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| |
Collapse
|
20
|
Anti-HIV Potential of Beesioside I Derivatives as Maturation Inhibitors: Synthesis, 3D-QSAR, Molecular Docking and Molecular Dynamics Simulations. Int J Mol Sci 2023; 24:ijms24021430. [PMID: 36674943 PMCID: PMC9867151 DOI: 10.3390/ijms24021430] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
HIV-1 maturation is the final step in the retroviral lifecycle that is regulated by the proteolytic cleavage of the Gag precursor protein. As a first-in-class HIV-1 maturation inhibitor (MI), bevirimat blocks virion maturation by disrupting capsid-spacer peptide 1 (CA-SP1) cleavage, which acts as the target of MIs. Previous alterations of beesioside I (1) produced (20S,24S)-15ꞵ,16ꞵ-diacetoxy-18,24; 20,24-diepoxy-9,19-cyclolanostane-3ꞵ,25-diol 3-O-3′,3′-dimethylsuccinate (3, DSC), showing similar anti-HIV potency compared to bevirimat. To ascertain the binding modes of this derivative, further modification of compound 1 was conducted. Three-dimensional quantitative structure−activity relationship (3D-QSAR) analysis combined with docking simulations and molecular dynamics (MD) were conducted. Five new derivatives were synthesized, among which compound 3b showed significant activity against HIV-1NL4-3 with an EC50 value of 0.28 µM. The developed 3D-QSAR model resulted in great predictive ability with training set (r2 = 0.99, q2 = 0.55). Molecular docking studies were complementary to the 3D-QSAR analysis, showing that DSC was differently bound to CA-SP1 with higher affinity than that of bevirimat. MD studies revealed that the complex of the ligand and the protein was stable, with root mean square deviation (RMSD) values <2.5 Å. The above results provided valuable insights into the potential of DSC as a prototype to develop new antiviral agents.
Collapse
|
21
|
Role of TLRs in HIV-1 Infection and Potential of TLR Agonists in HIV-1 Vaccine Development and Treatment Strategies. Pathogens 2023; 12:pathogens12010092. [PMID: 36678440 PMCID: PMC9866513 DOI: 10.3390/pathogens12010092] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Toll-like receptors (TLRs), as a family of pattern recognition receptors, play an important role in the recognition of HIV-1 molecular structures by various cells of the innate immune system, but also provide a functional association with subsequent mechanisms of adaptive immunity. TLR7 and TLR8 play a particularly important role in the innate immune response to RNA viruses due to their ability to recognise GU-rich single-stranded RNA molecules and subsequently activate intracellular signalling pathways resulting in expression of genes coding for various biological response modifiers (interferons, proinflammatory cytokines, chemokines). The aim of this review is to summarise the most recent knowledge on the role of TLRs in the innate immune response to HIV-1 and the role of TLR gene polymorphisms in the biology and in the clinical aspects of HIV infections. In addition, the role of TLR agonists as latency reversing agents in research to treat HIV infections and as immunomodulators in HIV vaccine research will be discussed.
Collapse
|
22
|
Smith RA, Raugi DN, Nixon RS, Song J, Seydi M, Gottlieb GS. Intrinsic resistance of HIV-2 and SIV to the maturation inhibitor GSK2838232. PLoS One 2023; 18:e0280568. [PMID: 36652466 PMCID: PMC9847912 DOI: 10.1371/journal.pone.0280568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/02/2023] [Indexed: 01/19/2023] Open
Abstract
GSK2838232 (GSK232) is a novel maturation inhibitor that blocks the proteolytic cleavage of HIV-1 Gag at the junction of capsid and spacer peptide 1 (CA/SP1), rendering newly-formed virions non-infectious. To our knowledge, GSK232 has not been tested against HIV-2, and there are limited data regarding the susceptibility of HIV-2 to other HIV-1 maturation inhibitors. To assess the potential utility of GSK232 as an option for HIV-2 treatment, we determined the activity of the compound against a panel of HIV-1, HIV-2, and SIV isolates in culture. GSK232 was highly active against HIV-1 isolates from group M subtypes A, B, C, D, F, and group O, with IC50 values ranging from 0.25-0.92 nM in spreading (multi-cycle) assays and 1.5-2.8 nM in a single cycle of infection. In contrast, HIV-2 isolates from groups A, B, and CRF01_AB, and SIV isolates SIVmac239, SIVmac251, and SIVagm.sab-2, were highly resistant to GSK232. To determine the role of CA/SP1 in the observed phenotypes, we constructed a mutant of HIV-2ROD9 in which the sequence of CA/SP1 was modified to match the corresponding sequence found in HIV-1. The resulting variant was fully susceptible to GSK232 in the single-cycle assay (IC50 = 1.8 nM). Collectively, our data indicate that the HIV-2 and SIV isolates tested in our study are intrinsically resistant to GSK232, and that the determinants of resistance map to CA/SP1. The molecular mechanism(s) responsible for the differential susceptibility of HIV-1 and HIV-2/SIV to GSK232 require further investigation.
Collapse
Affiliation(s)
- Robert A. Smith
- Center for Emerging and Reemerging Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Dana N. Raugi
- Center for Emerging and Reemerging Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Robert S. Nixon
- Center for Emerging and Reemerging Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Jennifer Song
- Center for Emerging and Reemerging Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Moussa Seydi
- Service des Maladies Infectieuses et Tropicales, CHNU de Fann, Dakar, Senegal
| | - Geoffrey S. Gottlieb
- Center for Emerging and Reemerging Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | | |
Collapse
|
23
|
Qiu L, Bhutoria S, Kalpana GV, Zou X. Computational Modeling of IN-CTD/TAR Complex to Elucidate Additional Strategies to Inhibit HIV-1 Replication. Methods Mol Biol 2023; 2610:75-84. [PMID: 36534283 PMCID: PMC10067014 DOI: 10.1007/978-1-0716-2895-9_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
HIV-1 integrase (IN) is a key enzyme that is essential for mediating the insertion of retroviral DNA into the host chromosome. IN also exhibits additional functions which are not fully elucidated, including its ability to bind to viral genomic RNA. Lack of binding of IN to RNA within the virions has been shown to be associated with production of morphologically defective virus particles. However, the exact structure of HIV-1 IN bound to RNA is not known. Based on the studies that C-terminal domain (CTD) of IN binds to TAR RNA region and based on the observation that TAR and the host factor INI1 binding to IN-CTD are identical, we computationally modelled the IN-CTD/TAR complex structure. Computational modeling of nucleic acid binding to proteins is a valuable method to understand the macromolecular interaction when experimental methods of solving the complex structures are not feasible. The current model of the IN-CTD/TAR complex may facilitate further understanding of this interaction and may lead to therapeutic targeting of IN-CTD/RNA interactions to inhibit HIV-1 replication.
Collapse
Affiliation(s)
- Liming Qiu
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Savita Bhutoria
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Ganjam V Kalpana
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Xiaoqin Zou
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Johnson MM, Jones CE, Clark DN. The Effect of Treatment-Associated Mutations on HIV Replication and Transmission Cycles. Viruses 2022; 15:107. [PMID: 36680147 PMCID: PMC9861436 DOI: 10.3390/v15010107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/21/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
HIV/AIDS mortality has been decreasing over the last decade. While promising, this decrease correlated directly with increased use of antiretroviral drugs. As a natural consequence of its high mutation rate, treatments provide selection pressure that promotes the natural selection of escape mutants. Individuals may acquire drug-naive strains, or those that have already mutated due to treatment. Even within a host, mutation affects HIV tropism, where initial infection begins with R5-tropic virus, but the clinical transition to AIDS correlates with mutations that lead to an X4-tropic switch. Furthermore, the high mutation rate of HIV has spelled failure for all attempts at an effective vaccine. Pre-exposure drugs are currently the most effective drug-based preventatives, but their effectiveness is also threatened by viral mutation. From attachment and entry to assembly and release, the steps in the replication cycle are also discussed to describe the drug mechanisms and mutations that arise due to those drugs. Revealing the patterns of HIV-1 mutations, their effects, and the coordinated attempt to understand and control them will lead to effective use of current preventative measures and treatment options, as well as the development of new ones.
Collapse
Affiliation(s)
- Madison M. Johnson
- Department of Microbiology, Weber State University, Ogden, UT 84408, USA
| | | | | |
Collapse
|
26
|
Hartz RA, Xu L, Sit SY, Chen J, Venables BL, Lin Z, Zhang S, Li Z, Parker D, Simmons TS, Jenkins S, Hanumegowda UM, Dicker I, Krystal M, Meanwell NA, Regueiro-Ren A. Synthesis, Structure-Activity Relationships, and In Vivo Evaluation of Novel C-17 Amine Derivatives Based on GSK3640254 as HIV-1 Maturation Inhibitors with Broad Spectrum Activity. J Med Chem 2022; 65:15935-15966. [PMID: 36441509 DOI: 10.1021/acs.jmedchem.2c01618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An investigation of the structure-activity relationships of a series of HIV-1 maturation inhibitors (MIs) based on GSK3640254 (4) was conducted by incorporating novel C-17 amine substituents to reduce the overall basicity of the resultant analogues. We found that replacement of the distal amine on the C-17 sidechain present in 4 with a tertiary alcohol in combination with either a heterocyclic ring system or a cyclohexyl ring substituted with polar groups provided potent wild-type HIV-1 MIs that also retained excellent potency against a T332S/V362I/prR41G variant, a laboratory strain that served as a surrogate to assess HIV-1 polymorphic virus coverage. Compound 26 exhibited broad-spectrum HIV-1 activity against an expanded panel of clinically relevant Gag polymorphic viruses and had the most desirable overall profile in this series of compounds. In pharmacokinetic studies, 26 had low clearance and exhibited 24 and 31% oral bioavailability in rats and dogs, respectively.
Collapse
Affiliation(s)
- Richard A Hartz
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Li Xu
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Sing-Yuen Sit
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Jie Chen
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Brian L Venables
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Zeyu Lin
- Department of Virology, Bristol Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Sharon Zhang
- Department of Virology, Bristol Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Zhufang Li
- Department of Virology, Bristol Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Dawn Parker
- Department of Metabolism and Pharmacokinetics, Bristol Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Tara S Simmons
- Department of Metabolism and Pharmacokinetics, Bristol Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Susan Jenkins
- Department of Metabolism and Pharmacokinetics, Bristol Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Umesh M Hanumegowda
- Department of Metabolism and Pharmacokinetics, Bristol Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Ira Dicker
- Department of Virology, Bristol Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Mark Krystal
- Department of Virology, Bristol Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Nicholas A Meanwell
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Alicia Regueiro-Ren
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| |
Collapse
|
27
|
The C-Terminal Domain of RNase H and the C-Terminus Amino Acid Residue Regulate Virus Release and Autoprocessing of a Defective HIV-1 Possessing M50I and V151I Changes in Integrase. Viruses 2022; 14:v14122687. [PMID: 36560691 PMCID: PMC9788298 DOI: 10.3390/v14122687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
Previously, we reported that an HIV-1 variant containing Met-to-Ile change at codon 50 and Val-to-Ile mutation at codon 151 of integrase (IN), HIV(IN:M50I/V151I), was an impaired virus. Despite the mutations being in IN, the virus release was significantly suppressed (p < 0.0001) and the initiation of autoprocessing was inhibited; the mechanism of the defect remains unknown. In the current study, we attempted to identify the critical domains or amino acid (aa) residue(s) that promote defects in HIV(IN:M50I/V151I), using a series of variants, including truncated or aa-substituted RNase H (RH) or IN. The results demonstrated that virus release and the initiation of autoprocessing were regulated by the C-terminal domains (CTDs) of RH and IN. Further studies illustrated that Asp at codon 109 of RH CTD and Asp at the C terminus of IN induces the defect. This result indicated that the CTDs of RH and IN in GagPol and particular aa positions in RH and IN regulated the virus release and the initiation of autoprocessing, and these sites could be potential targets for the development of new therapies.
Collapse
|
28
|
Regueiro-Ren A, Sit SY, Chen Y, Chen J, Swidorski JJ, Liu Z, Venables BL, Sin N, Hartz RA, Protack T, Lin Z, Zhang S, Li Z, Wu DR, Li P, Kempson J, Hou X, Gupta A, Rampulla R, Mathur A, Park H, Sarjeant A, Benitex Y, Rahematpura S, Parker D, Phillips T, Haskell R, Jenkins S, Santone KS, Cockett M, Hanumegowda U, Dicker I, Meanwell NA, Krystal M. The Discovery of GSK3640254, a Next-Generation Inhibitor of HIV-1 Maturation. J Med Chem 2022; 65:11927-11948. [PMID: 36044257 DOI: 10.1021/acs.jmedchem.2c00879] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
GSK3640254 is an HIV-1 maturation inhibitor (MI) that exhibits significantly improved antiviral activity toward a range of clinically relevant polymorphic variants with reduced sensitivity toward the second-generation MI GSK3532795 (BMS-955176). The key structural difference between GSK3640254 and its predecessor is the replacement of the para-substituted benzoic acid moiety attached at the C-3 position of the triterpenoid core with a cyclohex-3-ene-1-carboxylic acid substituted with a CH2F moiety at the carbon atom α- to the pharmacophoric carboxylic acid. This structural element provided a new vector with which to explore structure-activity relationships (SARs) and led to compounds with improved polymorphic coverage while preserving pharmacokinetic (PK) properties. The approach to the design of GSK3640254, the development of a synthetic route and its preclinical profile are discussed. GSK3640254 is currently in phase IIb clinical trials after demonstrating a dose-related reduction in HIV-1 viral load over 7-10 days of dosing to HIV-1-infected subjects.
Collapse
Affiliation(s)
- Alicia Regueiro-Ren
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey08543, United States
| | - Sing-Yuen Sit
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Yan Chen
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Jie Chen
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Jacob J Swidorski
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Zheng Liu
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Brian L Venables
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Ny Sin
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Richard A Hartz
- Department of Discovery Chemistry, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Tricia Protack
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Zeyu Lin
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Sharon Zhang
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Zhufang Li
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Dauh-Rurng Wu
- Department of Discovery Synthesis, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey08543, United States
| | - Peng Li
- Department of Discovery Synthesis, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey08543, United States
| | - James Kempson
- Department of Discovery Synthesis, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey08543, United States
| | - Xiaoping Hou
- Department of Discovery Synthesis, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey08543, United States
| | - Anuradha Gupta
- Department of Discovery Synthesis; Bristol Myers Squibb Research and Early Development, Bangalore 560099, India
| | - Richard Rampulla
- Department of Discovery Synthesis, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey08543, United States
| | - Arvind Mathur
- Department of Discovery Synthesis, Bristol Myers Squibb Research and Early Development, PO Box 4000, Princeton, New Jersey08543, United States
| | - Hyunsoo Park
- Bristol Myers Squibb Chemical and Synthetic Development, New Brunswick, New Jersey08901, United States
| | - Amy Sarjeant
- Bristol Myers Squibb Chemical and Synthetic Development, New Brunswick, New Jersey08901, United States
| | - Yulia Benitex
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Sandhya Rahematpura
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Dawn Parker
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Thomas Phillips
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Roy Haskell
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Susan Jenkins
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Kenneth S Santone
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Mark Cockett
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Umesh Hanumegowda
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Ira Dicker
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| | - Nicholas A Meanwell
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey08543, United States
| | - Mark Krystal
- Department of Virology, Bristol Myers Squibb Research and Early Development, 5 Research Parkway, Wallingford, Connecticut06492, United States
| |
Collapse
|
29
|
Metabolite Identification of HIV-1 Capsid Modulators PF74 and 11L in Human Liver Microsomes. Metabolites 2022; 12:metabo12080752. [PMID: 36005624 PMCID: PMC9412436 DOI: 10.3390/metabo12080752] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
PF74 and 11L, as potent modulators of the HIV-1 capsid protein, have been demonstrated to act at both early and late stages in the HIV-1 life cycle. However, their clearance is high in human liver microsomes (HLMs). The main goal of this study was to clarify the metabolism of PF74 and 11L in HLMs, and provide guidance for future structural optimization. To accomplish this, the phase-I metabolites of PF74 and 11L, resulting from in vitro incubation with HLMs, were investigated via ultra-performance liquid chromatography–ultraviolet–high-resolution mass spectrometry (UPLC–UV–HRMS). The results show that 17 phase-I metabolites were putatively annotated for PF74, whereas 16 phase-I metabolites were found for 11L. The main metabolic pathways of PF74 in HLMs were oxidation and demethylation, and the secondary metabolic pathway was hydrolysis; thus, the di-oxidation and demethylation products (M7, M9, M11, and M14) were found to be major metabolites of PF74 in HLMs. In comparison, the main metabolic pathways of 11L in HLMs were oxidation, demethylation, dehydrogenation, and oxidative deamination, with M6′, M11′, M15′, and M16′ as the main metabolites. We suggest that the indole ring and N-methyl group of PF74, and the aniline group, benzene ring R1′, N-methyl, and methoxy group of 11L, were the main metabolic soft spots. Therefore, our research illuminates structural optimization options in seeking improved HIV-1 CA modulators.
Collapse
|
30
|
Antiviral Activity and Mechanisms of Seaweeds Bioactive Compounds on Enveloped Viruses-A Review. Mar Drugs 2022; 20:md20060385. [PMID: 35736188 PMCID: PMC9228758 DOI: 10.3390/md20060385] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 12/13/2022] Open
Abstract
In the last decades, the interest in seaweed has significantly increased. Bioactive compounds from seaweed’s currently receive major attention from pharmaceutical companies as they express several interesting biological activities which are beneficial for humans. The structural diversity of seaweed metabolites provides diverse biological activities which are expressed through diverse mechanisms of actions. This review mainly focuses on the antiviral activity of seaweed’s extracts, highlighting the mechanisms of actions of some seaweed molecules against infection caused by different types of enveloped viruses: influenza, Lentivirus (HIV-1), Herpes viruses, and coronaviruses. Seaweed metabolites with antiviral properties can act trough different pathways by increasing the host’s defense system or through targeting and blocking virus replication before it enters host cells. Several studies have already established the large antiviral spectrum of seaweed’s bioactive compounds. Throughout this review, antiviral mechanisms and medical applications of seaweed’s bioactive compounds are analyzed, suggesting seaweed’s potential source of antiviral compounds for the formulation of novel and natural antiviral drugs.
Collapse
|
31
|
Xu S, Sun L, Zalloum WA, Zhang X, Huang T, Ding D, Tao Y, Zhao F, Gao S, Kang D, De Clercq E, Pannecouque C, Dick A, Cocklin S, Liu X, Zhan P. From design to biological mechanism evaluation of phenylalanine-bearing HIV-1 capsid inhibitors targeting a vital assembly interface. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.06.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
32
|
Balasubramaniam M, Davids BO, Bryer A, Xu C, Thapa S, Shi J, Aiken C, Pandhare J, Perilla JR, Dash C. HIV-1 mutants that escape the cytotoxic T-lymphocytes are defective in viral DNA integration. PNAS NEXUS 2022; 1:pgac064. [PMID: 35719891 PMCID: PMC9198661 DOI: 10.1093/pnasnexus/pgac064] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/17/2022] [Indexed: 12/02/2022]
Abstract
HIV-1 replication is durably controlled without antiretroviral therapy (ART) in certain infected individuals called elite controllers (ECs). These individuals express specific human leukocyte antigens (HLA) that tag HIV-infected cells for elimination by presenting viral epitopes to CD8+ cytotoxic T-lymphocytes (CTL). In HIV-infected individuals expressing HLA-B27, CTLs primarily target the viral capsid protein (CA)-derived KK10 epitope. While selection of CA mutation R264K helps HIV-1 escape this potent CTL response, the accompanying fitness cost severely diminishes virus infectivity. Interestingly, selection of a compensatory CA mutation S173A restores HIV-1 replication. However, the molecular mechanism(s) underlying HIV-1 escape from this ART-free virus control by CTLs is not fully understood. Here, we report that the R264K mutation-associated infectivity defect arises primarily from impaired HIV-1 DNA integration, which is restored by the S173A mutation. Unexpectedly, the integration defect of the R264K variant was also restored upon depletion of the host cyclophilin A. These findings reveal a nuclear crosstalk between CA and HIV-1 integration as well as identify a previously unknown role of cyclophilin A in viral DNA integration. Finally, our study identifies a novel immune escape mechanism of an HIV-1 variant escaping a CA-directed CTL response.
Collapse
Affiliation(s)
| | - Benem-Orom Davids
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, TN - 37208, USA
| | - Alex Bryer
- Department of Chemistry, University of Delaware, Newark, DE - 19716, USA
| | - Chaoyi Xu
- Department of Chemistry, University of Delaware, Newark, DE - 19716, USA
| | - Santosh Thapa
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, TN - 37208, USA
| | - Jiong Shi
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN - 37232, USA
| | - Christopher Aiken
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN - 37232, USA
| | - Jui Pandhare
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, TN - 37208, USA
| | - Juan R Perilla
- Department of Chemistry, University of Delaware, Newark, DE - 19716, USA
| | - Chandravanu Dash
- The Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, TN - 37208, USA
| |
Collapse
|
33
|
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.
Collapse
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:
| |
Collapse
|
34
|
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] [MESH Headings] [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.
Collapse
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.
| |
Collapse
|
35
|
Lerner G, Weaver N, Anokhin B, Spearman P. Advances in HIV-1 Assembly. Viruses 2022; 14:v14030478. [PMID: 35336885 PMCID: PMC8952333 DOI: 10.3390/v14030478] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/10/2022] Open
Abstract
The assembly of HIV-1 particles is a concerted and dynamic process that takes place on the plasma membrane of infected cells. An abundance of recent discoveries has advanced our understanding of the complex sequence of events leading to HIV-1 particle assembly, budding, and release. Structural studies have illuminated key features of assembly and maturation, including the dramatic structural transition that occurs between the immature Gag lattice and the formation of the mature viral capsid core. The critical role of inositol hexakisphosphate (IP6) in the assembly of both the immature and mature Gag lattice has been elucidated. The structural basis for selective packaging of genomic RNA into virions has been revealed. This review will provide an overview of the HIV-1 assembly process, with a focus on recent advances in the field, and will point out areas where questions remain that can benefit from future investigation.
Collapse
|
36
|
van Heuvel Y, Schatz S, Rosengarten JF, Stitz J. Infectious RNA: Human Immunodeficiency Virus (HIV) Biology, Therapeutic Intervention, and the Quest for a Vaccine. Toxins (Basel) 2022; 14:toxins14020138. [PMID: 35202165 PMCID: PMC8876946 DOI: 10.3390/toxins14020138] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/02/2022] [Accepted: 02/09/2022] [Indexed: 11/16/2022] Open
Abstract
Different mechanisms mediate the toxicity of RNA. Genomic retroviral mRNA hijacks infected host cell factors to enable virus replication. The viral genomic RNA of the human immunodeficiency virus (HIV) encompasses nine genes encoding in less than 10 kb all proteins needed for replication in susceptible host cells. To do so, the genomic RNA undergoes complex alternative splicing to facilitate the synthesis of the structural, accessory, and regulatory proteins. However, HIV strongly relies on the host cell machinery recruiting cellular factors to complete its replication cycle. Antiretroviral therapy (ART) targets different steps in the cycle, preventing disease progression to the acquired immunodeficiency syndrome (AIDS). The comprehension of the host immune system interaction with the virus has fostered the development of a variety of vaccine platforms. Despite encouraging provisional results in vaccine trials, no effective vaccine has been developed, yet. However, novel promising vaccine platforms are currently under investigation.
Collapse
Affiliation(s)
- Yasemin van Heuvel
- Research Group Pharmaceutical Biotechnology, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Chempark Leverkusen, Kaiser-Wilhelm-Allee, 51368 Leverkusen, Germany; (Y.v.H.); (S.S.); (J.F.R.)
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 3-9, 30167 Hannover, Germany
| | - Stefanie Schatz
- Research Group Pharmaceutical Biotechnology, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Chempark Leverkusen, Kaiser-Wilhelm-Allee, 51368 Leverkusen, Germany; (Y.v.H.); (S.S.); (J.F.R.)
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 3-9, 30167 Hannover, Germany
| | - Jamila Franca Rosengarten
- Research Group Pharmaceutical Biotechnology, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Chempark Leverkusen, Kaiser-Wilhelm-Allee, 51368 Leverkusen, Germany; (Y.v.H.); (S.S.); (J.F.R.)
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 3-9, 30167 Hannover, Germany
| | - Jörn Stitz
- Research Group Pharmaceutical Biotechnology, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Chempark Leverkusen, Kaiser-Wilhelm-Allee, 51368 Leverkusen, Germany; (Y.v.H.); (S.S.); (J.F.R.)
- Correspondence:
| |
Collapse
|
37
|
Gilmer O, Mailler E, Paillart JC, Mouhand A, Tisné C, Mak J, Smyth RP, Marquet R, Vivet-Boudou V. Structural maturation of the HIV-1 RNA 5' untranslated region by Pr55 Gag and its maturation products. RNA Biol 2022; 19:191-205. [PMID: 35067194 PMCID: PMC8786341 DOI: 10.1080/15476286.2021.2021677] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Maturation of the HIV-1 viral particles shortly after budding is required for infectivity. During this process, the Pr55Gag precursor undergoes a cascade of proteolytic cleavages, and whilst the structural rearrangements of the viral proteins are well understood, the concomitant maturation of the genomic RNA (gRNA) structure is unexplored, despite evidence that it is required for infectivity. To get insight into this process, we systematically analysed the interactions between Pr55Gag or its maturation products (NCp15, NCp9 and NCp7) and the 5ʹ gRNA region and their structural consequences, in vitro. We show that Pr55Gag and its maturation products mostly bind at different RNA sites and with different contributions of their two zinc knuckle domains. Importantly, these proteins have different transient and permanent effects on the RNA structure, the late NCp9 and NCp7 inducing dramatic structural rearrangements. Altogether, our results reveal the distinct contributions of the different Pr55Gag maturation products on the gRNA structural maturation.
Collapse
Affiliation(s)
- Orian Gilmer
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, IBMC, Strasbourg, France
| | - Elodie Mailler
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, IBMC, Strasbourg, France
| | - Jean-Christophe Paillart
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, IBMC, Strasbourg, France
| | - Assia Mouhand
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-chimique, Paris, France
| | - Carine Tisné
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-chimique, Paris, France
| | - Johnson Mak
- Institute for Glycomics, Griffith University, Gold Coast, Australia
| | - Redmond P Smyth
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, IBMC, Strasbourg, France
| | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, IBMC, Strasbourg, France
| | - Valérie Vivet-Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, IBMC, Strasbourg, France
| |
Collapse
|
38
|
HIV-1 and HTLV-1 Transmission Modes: Mechanisms and Importance for Virus Spread. Viruses 2022; 14:v14010152. [PMID: 35062355 PMCID: PMC8779814 DOI: 10.3390/v14010152] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 12/13/2022] Open
Abstract
So far, only two retroviruses, human immunodeficiency virus (HIV) (type 1 and 2) and human T-cell lymphotropic virus type 1 (HTLV-1), have been recognized as pathogenic for humans. Both viruses mainly infect CD4+ T lymphocytes. HIV replication induces the apoptosis of CD4 lymphocytes, leading to the development of acquired immunodeficiency syndrome (AIDS). After a long clinical latency period, HTLV-1 can transform lymphocytes, with subsequent uncontrolled proliferation and the manifestation of a disease called adult T-cell leukemia (ATLL). Certain infected patients develop neurological autoimmune disorder called HTLV-1-associated myelopathy, also known as tropical spastic paraparesis (HAM/TSP). Both viruses are transmitted between individuals via blood transfusion, tissue/organ transplantation, breastfeeding, and sexual intercourse. Within the host, these viruses can spread utilizing either cell-free or cell-to-cell modes of transmission. In this review, we discuss the mechanisms and importance of each mode of transmission for the biology of HIV-1 and HTLV-1.
Collapse
|
39
|
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. ![]()
Collapse
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.
| |
Collapse
|
40
|
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.
Collapse
|
41
|
Yang J, Hao M, Khan MA, Rehman MT, Highbarger HC, Chen Q, Goswami S, Sherman BT, Rehm CA, Dewar RL, Chang W, Imamichi T. A Combination of M50I and V151I Polymorphic Mutations in HIV-1 Subtype B Integrase Results in Defects in Autoprocessing. Viruses 2021; 13:2331. [PMID: 34835137 PMCID: PMC8625782 DOI: 10.3390/v13112331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/15/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
We have recently reported that a recombinant HIV-1NL4.3 containing Met-to-Ile change at codon 50 of integrase (IN) (IN:M50I) exhibits suppression of the virus release below 0.5% of WT HIV, and the released viral particles are replication-incompetent due to defects in Gag/GagPol processing by inhibition of the initiation of autoprocessing of GagPol polyproteins in the virions and leads to replication-incompetent viruses. The coexisting Ser-to-Asn change at codon 17 of IN or Asn-to-Ser mutation at codon 79 of RNaseH (RH) compensated the defective IN:M50I phenotype, suggesting that both IN and RH regulate an HIV infectability. In the current study, to elucidate a distribution of the three mutations during anti-retroviral therapy among patients, we performed a population analysis using 529 plasma virus RNA sequences obtained through the MiSeq. The result demonstrated that 14 plasma HIVs contained IN:M50I without the compensatory mutations. Comparing the sequences of the 14 viruses with that of the defective virus illustrated that only Val-to-Ile change at codon 151 of IN (IN:V151I) existed in the recombinant virus. This IN:V151I is known as a polymorphic mutation and was derived from HIVNL4.3 backbone. A back-mutation at 151 from Ile-to-Val in the defective virus recovered HIV replication capability, and Western Blotting assay displayed that the back-mutation restored Gag/GagPol processing in viral particles. These results demonstrate that a combination of IN:M50I and IN:V151I mutations, but not IN:M50I alone, produces a defective virus.
Collapse
Affiliation(s)
- Jun Yang
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory, Frederick, MD 21702, USA; (J.Y.); (M.H.); (Q.C.); (S.G.); (B.T.S.); (W.C.)
| | - Ming Hao
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory, Frederick, MD 21702, USA; (J.Y.); (M.H.); (Q.C.); (S.G.); (B.T.S.); (W.C.)
| | - Muhammad A. Khan
- Virus Isolation and Serology Laboratory, Frederick National Laboratory, Frederick, MD 21702, USA; (M.A.K.); (M.T.R.); (H.C.H.); (R.L.D.)
| | - Muhammad T. Rehman
- Virus Isolation and Serology Laboratory, Frederick National Laboratory, Frederick, MD 21702, USA; (M.A.K.); (M.T.R.); (H.C.H.); (R.L.D.)
| | - Helene C. Highbarger
- Virus Isolation and Serology Laboratory, Frederick National Laboratory, Frederick, MD 21702, USA; (M.A.K.); (M.T.R.); (H.C.H.); (R.L.D.)
| | - Qian Chen
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory, Frederick, MD 21702, USA; (J.Y.); (M.H.); (Q.C.); (S.G.); (B.T.S.); (W.C.)
| | - Suranjana Goswami
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory, Frederick, MD 21702, USA; (J.Y.); (M.H.); (Q.C.); (S.G.); (B.T.S.); (W.C.)
| | - Brad T. Sherman
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory, Frederick, MD 21702, USA; (J.Y.); (M.H.); (Q.C.); (S.G.); (B.T.S.); (W.C.)
| | - Catherine A. Rehm
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA;
| | - Robin L. Dewar
- Virus Isolation and Serology Laboratory, Frederick National Laboratory, Frederick, MD 21702, USA; (M.A.K.); (M.T.R.); (H.C.H.); (R.L.D.)
| | - Weizhong Chang
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory, Frederick, MD 21702, USA; (J.Y.); (M.H.); (Q.C.); (S.G.); (B.T.S.); (W.C.)
| | - Tomozumi Imamichi
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory, Frederick, MD 21702, USA; (J.Y.); (M.H.); (Q.C.); (S.G.); (B.T.S.); (W.C.)
| |
Collapse
|
42
|
Rey JS, Li W, Bryer AJ, Beatson H, Lantz C, Engelman AN, Perilla JR. Deep-learning in situ classification of HIV-1 virion morphology. Comput Struct Biotechnol J 2021; 19:5688-5700. [PMID: 34765089 PMCID: PMC8554174 DOI: 10.1016/j.csbj.2021.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 01/04/2023] Open
Abstract
Efficient classifier capable of overcoming inherent problems of small-data training sets. Automated detection and classification of HIV-1 particle morphology from transmission electron micrographs. Three orders of magnitude speed increase in data processing with negligible loss in accuracy.
Transmission electron microscopy (TEM) has a multitude of uses in biomedical imaging due to its ability to discern ultrastructure morphology at the nanometer scale. Through its ability to directly visualize virus particles, TEM has for several decades been an invaluable tool in the virologist’s toolbox. As applied to HIV-1 research, TEM is critical to evaluate activities of inhibitors that block the maturation and morphogenesis steps of the virus lifecycle. However, both the preparation and analysis of TEM micrographs requires time consuming manual labor. Through the dedicated use of computer vision frameworks and machine learning techniques, we have developed a convolutional neural network backbone of a two-stage Region Based Convolutional Neural Network (RCNN) capable of identifying, segmenting and classifying HIV-1 virions at different stages of maturation and morphogenesis. Our results outperformed common RCNN backbones, achieving 80.0% mean Average Precision on a diverse set of micrographs comprising different experimental samples and magnifications. We expect that this tool will be of interest to a broad range of researchers.
Collapse
Affiliation(s)
- Juan S Rey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Wen Li
- Department of Medicine, Harvard Medical School, Boston, MA, United States.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Alexander J Bryer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Hagan Beatson
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Christian Lantz
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Alan N Engelman
- Department of Medicine, Harvard Medical School, Boston, MA, United States.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States.,Data Science Institute, University of Delaware, Newark, DE, United States
| |
Collapse
|
43
|
Menéndez-Arias L, Delgado R. Update and latest advances in antiretroviral therapy. Trends Pharmacol Sci 2021; 43:16-29. [PMID: 34742581 DOI: 10.1016/j.tips.2021.10.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 12/27/2022]
Abstract
Since the first cases of AIDS appeared in 1981, human immunodeficiency virus type 1 (HIV-1) infection has reached pandemic proportions. Forty years later, research has led to the approval of more than 30 antiretroviral drugs, while combination therapies have turned HIV-1 infection into a chronic, but manageable disease. Still, drug toxicity and acquired and transmitted drug resistance remain as major threats to therapy success. In this review, we provide an overview on currently available anti-HIV drugs and the latest developments in antiretroviral therapy, focused on new antiretroviral agents acting on known and unexploited antiviral targets, prevention therapies aimed to improve available drug combinations, and research on new long-acting therapies, particularly those involving novel drug candidates such as lenacapavir or islatravir.
Collapse
Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas y Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | - Rafael Delgado
- Laboratory of Molecular Microbiology. Instituto de Investigación Hospital 12 de Octubre (Imas12) and The University Complutense School of Medicine, Madrid, Spain.
| |
Collapse
|
44
|
Niklasch M, Zimmermann P, Nassal M. The Hepatitis B Virus Nucleocapsid-Dynamic Compartment for Infectious Virus Production and New Antiviral Target. Biomedicines 2021; 9:1577. [PMID: 34829806 PMCID: PMC8615760 DOI: 10.3390/biomedicines9111577] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV) is a small enveloped DNA virus which replicates its tiny 3.2 kb genome by reverse transcription inside an icosahedral nucleocapsid, formed by a single ~180 amino acid capsid, or core, protein (Cp). HBV causes chronic hepatitis B (CHB), a severe liver disease responsible for nearly a million deaths each year. Most of HBV's only seven primary gene products are multifunctional. Though less obvious than for the multi-domain polymerase, P protein, this is equally crucial for Cp with its multiple roles in the viral life-cycle. Cp provides a stable genome container during extracellular phases, allows for directed intracellular genome transport and timely release from the capsid, and subsequent assembly of new nucleocapsids around P protein and the pregenomic (pg) RNA, forming a distinct compartment for reverse transcription. These opposing features are enabled by dynamic post-transcriptional modifications of Cp which result in dynamic structural alterations. Their perturbation by capsid assembly modulators (CAMs) is a promising new antiviral concept. CAMs inappropriately accelerate assembly and/or distort the capsid shell. We summarize the functional, biochemical, and structural dynamics of Cp, and discuss the therapeutic potential of CAMs based on clinical data. Presently, CAMs appear as a valuable addition but not a substitute for existing therapies. However, as part of rational combination therapies CAMs may bring the ambitious goal of a cure for CHB closer to reality.
Collapse
Affiliation(s)
| | | | - Michael Nassal
- Internal Medicine II/Molecular Biology, University Hospital Freiburg, Hugstetter Str. 55, D-79106 Freiburg, Germany; (M.N.); (P.Z.)
| |
Collapse
|
45
|
Saito A, Yamashita M. HIV-1 capsid variability: viral exploitation and evasion of capsid-binding molecules. Retrovirology 2021; 18:32. [PMID: 34702294 PMCID: PMC8549334 DOI: 10.1186/s12977-021-00577-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/13/2021] [Indexed: 11/17/2022] Open
Abstract
The HIV-1 capsid, a conical shell encasing viral nucleoprotein complexes, is involved in multiple post-entry processes during viral replication. Many host factors can directly bind to the HIV-1 capsid protein (CA) and either promote or prevent HIV-1 infection. The viral capsid is currently being explored as a novel target for therapeutic interventions. In the past few decades, significant progress has been made in our understanding of the capsid–host interactions and mechanisms of action of capsid-targeting antivirals. At the same time, a large number of different viral capsids, which derive from many HIV-1 mutants, naturally occurring variants, or diverse lentiviruses, have been characterized for their interactions with capsid-binding molecules in great detail utilizing various experimental techniques. This review provides an overview of how sequence variation in CA influences phenotypic properties of HIV-1. We will focus on sequence differences that alter capsid–host interactions and give a brief account of drug resistant mutations in CA and their mutational effects on viral phenotypes. Increased knowledge of the sequence-function relationship of CA helps us deepen our understanding of the adaptive potential of the viral capsid.
Collapse
Affiliation(s)
- Akatsuki Saito
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, Japan.,Center for Animal Disease Control, University of Miyazaki, Miyazaki, Miyazaki, Japan
| | - Masahiro Yamashita
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
| |
Collapse
|
46
|
mRNA Trafficking in the Nervous System: A Key Mechanism of the Involvement of Activity-Regulated Cytoskeleton-Associated Protein (Arc) in Synaptic Plasticity. Neural Plast 2021; 2021:3468795. [PMID: 34603440 PMCID: PMC8486535 DOI: 10.1155/2021/3468795] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/15/2021] [Accepted: 09/07/2021] [Indexed: 12/18/2022] Open
Abstract
Synaptic activity mediates information storage and memory consolidation in the brain and requires a fast de novo synthesis of mRNAs in the nucleus and proteins in synapses. Intracellular localization of a protein can be achieved by mRNA trafficking and localized translation. Activity-regulated cytoskeleton-associated protein (Arc) is a master regulator of synaptic plasticity and plays an important role in controlling large signaling networks implicated in learning, memory consolidation, and behavior. Transcription of the Arc gene may be induced by a short behavioral event, resulting in synaptic activation. Arc mRNA is exported into the cytoplasm and can be trafficked into the dendrite of an activated synapse where it is docked and translated. The structure of Arc is similar to the viral GAG (group-specific antigen) protein, and phylogenic analysis suggests that Arc may originate from the family of Ty3/Gypsy retrotransposons. Therefore, Arc might evolve through “domestication” of retroviruses. Arc can form a capsid-like structure that encapsulates a retrovirus-like sentence in the 3′-UTR (untranslated region) of Arc mRNA. Such complex can be loaded into extracellular vesicles and transported to other neurons or muscle cells carrying not only genetic information but also regulatory signals within neuronal networks. Therefore, Arc mRNA inter- and intramolecular trafficking is essential for the modulation of synaptic activity required for memory consolidation and cognitive functions. Recent studies with single-molecule imaging in live neurons confirmed and extended the role of Arc mRNA trafficking in synaptic plasticity.
Collapse
|
47
|
Saha I, Preece B, Peterson A, Durden H, MacArthur B, Lowe J, Belnap D, Vershinin M, Saffarian S. Gag-Gag Interactions Are Insufficient to Fully Stabilize and Order the Immature HIV Gag Lattice. Viruses 2021; 13:1946. [PMID: 34696376 PMCID: PMC8540168 DOI: 10.3390/v13101946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
Immature HIV virions harbor a lattice of Gag molecules with significant ordering in CA-NTD, CA-CTD and SP1 regions. This ordering plays a major role during HIV maturation. To test the condition in which the Gag lattice forms in vivo, we assembled virus like particles (VLPs) by expressing only HIV Gag in mammalian cells. Here we show that these VLPs incorporate a similar number of Gag molecules compared to immature HIV virions. However, within these VLPs, Gag molecules diffuse with a pseudo-diffusion rate of 10 nm2/s, this pseudo-diffusion is abrogated in the presence of melittin and is sensitive to mutations within the SP1 region. Using cryotomography, we show that unlike immature HIV virions, in the Gag lattice of VLPs the CA-CTD and SP1 regions are significantly less ordered. Our observations suggest that within immature HIV virions, other viral factors in addition to Gag, contribute to ordering in the CA-CTD and SP1 regions.
Collapse
Affiliation(s)
- Ipsita Saha
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA;
| | - Benjamin Preece
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA; (B.P.); (A.P.); (H.D.); (B.M.); (M.V.)
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Abby Peterson
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA; (B.P.); (A.P.); (H.D.); (B.M.); (M.V.)
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Haley Durden
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA; (B.P.); (A.P.); (H.D.); (B.M.); (M.V.)
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Brian MacArthur
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA; (B.P.); (A.P.); (H.D.); (B.M.); (M.V.)
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Jake Lowe
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; (J.L.); (D.B.)
| | - David Belnap
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; (J.L.); (D.B.)
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael Vershinin
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA; (B.P.); (A.P.); (H.D.); (B.M.); (M.V.)
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; (J.L.); (D.B.)
| | - Saveez Saffarian
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA; (B.P.); (A.P.); (H.D.); (B.M.); (M.V.)
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA; (J.L.); (D.B.)
| |
Collapse
|
48
|
Duerr R, Crosse KM, Valero-Jimenez AM, Dittmann M. SARS-CoV-2 Portrayed against HIV: Contrary Viral Strategies in Similar Disguise. Microorganisms 2021; 9:1389. [PMID: 34198973 PMCID: PMC8307803 DOI: 10.3390/microorganisms9071389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 and HIV are zoonotic viruses that rapidly reached pandemic scale, causing global losses and fear. The COVID-19 and AIDS pandemics ignited massive efforts worldwide to develop antiviral strategies and characterize viral architectures, biological and immunological properties, and clinical outcomes. Although both viruses have a comparable appearance as enveloped viruses with positive-stranded RNA and envelope spikes mediating cellular entry, the entry process, downstream biological and immunological pathways, clinical outcomes, and disease courses are strikingly different. This review provides a systemic comparison of both viruses' structural and functional characteristics, delineating their distinct strategies for efficient spread.
Collapse
Affiliation(s)
- Ralf Duerr
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA; (K.M.C.); (A.M.V.-J.); (M.D.)
| | | | | | | |
Collapse
|
49
|
Perilla JR, Hadden-Perilla JA, Gronenborn AM, Polenova T. Integrative structural biology of HIV-1 capsid protein assemblies: combining experiment and computation. Curr Opin Virol 2021; 48:57-64. [PMID: 33901736 DOI: 10.1016/j.coviro.2021.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/11/2021] [Accepted: 03/20/2021] [Indexed: 12/31/2022]
Abstract
HIV-1 is the causative agent of acquired immunodeficiency syndrome (AIDS), a global pandemic that has claimed 32.7 million lives since 1981. Despite decades of research, there is no cure for the disease, with 38 million people currently infected with HIV. Attractive therapeutic targets for drug development are mature HIV-1 capsids, immature Gag polyprotein assemblies, and Gag maturation intermediates, although their complex architectures, pleomorphism, and dynamics render these assemblies challenging for structural biology. The recent development of integrative approaches, combining experimental and computational methods has enabled atomic-level characterization of structures and dynamics of capsid and Gag assemblies, and revealed their interactions with small-molecule inhibitors and host factors. These structures provide important insights that will guide the development of capsid and maturation inhibitors.
Collapse
Affiliation(s)
- Juan R Perilla
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Jodi A Hadden-Perilla
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE, United States
| | - Angela M Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States; Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States.
| | - Tatyana Polenova
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
| |
Collapse
|
50
|
Ghimire D, Kc Y, Timilsina U, Goel K, Nitz TJ, Wild CT, Gaur R. A single G10T polymorphism in HIV-1 subtype C Gag-SP1 regulates sensitivity to maturation inhibitors. Retrovirology 2021; 18:9. [PMID: 33836787 PMCID: PMC8033686 DOI: 10.1186/s12977-021-00553-5] [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: 12/18/2020] [Accepted: 03/23/2021] [Indexed: 08/30/2023] Open
Abstract
BACKGROUND Maturation inhibitors (MIs) potently block HIV-1 maturation by inhibiting the cleavage of the capsid protein and spacer peptide 1 (CA-SP1). Bevirimat (BVM), a highly efficacious first-in-class MI against HIV-1 subtype B isolates, elicited sub-optimal efficacy in clinical trials due to polymorphisms in the CA-SP1 region of the Gag protein (SP1:V7A). HIV-1 subtype C inherently contains this polymorphism thus conferring BVM resistance, however it displayed sensitivity to second generation BVM analogs. RESULTS In this study, we have assessed the efficacy of three novel second-generation MIs (BVM analogs: CV-8611, CV-8612, CV-8613) against HIV-1 subtype B and C isolates. The BVM analogs were potent inhibitors of both HIV-1 subtype B (NL4-3) and subtype C (K3016) viruses. Serial passaging of the subtype C, K3016 virus strain in the presence of BVM analogs led to identification of two mutant viruses-Gag SP1:A1V and CA:I201V. While the SP1:A1V mutant was resistant to the MIs, the CA:I120V mutant displayed partial resistance and a MI-dependent phenotype. Further analysis of the activity of the BVM analogs against two additional HIV-1 subtype C strains, IndieC1 and ZM247 revealed that they had reduced sensitivity as compared to K3016. Sequence analysis of the three viruses identified two polymorphisms at SP1 residues 9 and 10 (K3016: N9, G10; IndieC1/ZM247: S9, T10). The N9S and S9N mutants had no change in MI-sensitivity. On the other hand, replacing glycine at residue 10 with threonine in K3016 reduced its MI sensitivity whereas introducing glycine at SP1 10 in place of threonine in IndieC1 and ZM247 significantly enhanced their MI sensitivity. Thus, the specific glycine residue 10 of SP1 in the HIV-1 subtype C viruses determined sensitivity towards BVM analogs. CONCLUSIONS We have identified an association of a specific glycine at position 10 of Gag-SP1 with an MI susceptible phenotype of HIV-1 subtype C viruses. Our findings have highlighted that HIV-1 subtype C viruses, which were inherently resistant to BVM, may also be similarly predisposed to exhibit a significant degree of resistance to second-generation BVM analogs. Our work has strongly suggested that genetic differences between HIV-1 subtypes may produce variable MI sensitivity that needs to be considered in the development of novel, potent, broadly-active MIs.
Collapse
Affiliation(s)
- Dibya Ghimire
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India
| | - Yuvraj Kc
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India
| | - Uddhav Timilsina
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India.,Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, 14203, USA
| | - Kriti Goel
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India
| | - T J Nitz
- DFH Pharma, Gaithersburg, MD, 20886, USA
| | | | - Ritu Gaur
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, 110021, India.
| |
Collapse
|