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Bai H, Lewitus E, Li Y, Thomas PV, Zemil M, Merbah M, Peterson CE, Thuraisamy T, Rees PA, Hajduczki A, Dussupt V, Slike B, Mendez-Rivera L, Schmid A, Kavusak E, Rao M, Smith G, Frey J, Sims A, Wieczorek L, Polonis V, Krebs SJ, Ake JA, Vasan S, Bolton DL, Joyce MG, Townsley S, Rolland M. Contemporary HIV-1 consensus Env with AI-assisted redesigned hypervariable loops promote antibody binding. Nat Commun 2024; 15:3924. [PMID: 38724518 PMCID: PMC11082178 DOI: 10.1038/s41467-024-48139-x] [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: 06/26/2023] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
An effective HIV-1 vaccine must elicit broadly neutralizing antibodies (bnAbs) against highly diverse Envelope glycoproteins (Env). Since Env with the longest hypervariable (HV) loops is more resistant to the cognate bnAbs than Env with shorter HV loops, we redesigned hypervariable loops for updated Env consensus sequences of subtypes B and C and CRF01_AE. Using modeling with AlphaFold2, we reduced the length of V1, V2, and V5 HV loops while maintaining the integrity of the Env structure and glycan shield, and modified the V4 HV loop. Spacers are designed to limit strain-specific targeting. All updated Env are infectious as pseudoviruses. Preliminary structural characterization suggests that the modified HV loops have a limited impact on Env's conformation. Binding assays show improved binding to modified subtype B and CRF01_AE Env but not to subtype C Env. Neutralization assays show increases in sensitivity to bnAbs, although not always consistently across clades. Strikingly, the HV loop modification renders the resistant CRF01_AE Env sensitive to 10-1074 despite the absence of a glycan at N332.
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Affiliation(s)
- Hongjun Bai
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Eric Lewitus
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Yifan Li
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Paul V Thomas
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Michelle Zemil
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Mélanie Merbah
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Caroline E Peterson
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Thujitha Thuraisamy
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Phyllis A Rees
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Agnes Hajduczki
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Vincent Dussupt
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Bonnie Slike
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Letzibeth Mendez-Rivera
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Annika Schmid
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Erin Kavusak
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Mekhala Rao
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Gabriel Smith
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Jessica Frey
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Alicea Sims
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Lindsay Wieczorek
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Victoria Polonis
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Shelly J Krebs
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Julie A Ake
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Sandhya Vasan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Diane L Bolton
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - M Gordon Joyce
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Samantha Townsley
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA
| | - Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, 20817, USA.
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Lewitus E, Li Y, Bai H, Pham P, Rolland M. HIV-1 Gag, Pol, and Env diversified with limited adaptation since the 1980s. mBio 2024; 15:e0174923. [PMID: 38329340 PMCID: PMC10936417 DOI: 10.1128/mbio.01749-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/02/2024] [Indexed: 02/09/2024] Open
Abstract
Knowledge of HIV-1 global sequence diversity is critical for developing an effective prophylactic against HIV-1 infection. We developed the Hervé platform to analyze and visualize trends in HIV-1 diversification. Using Hervé, we analyzed 4,830 Env, 4,407 Gag, and 3,002 Pol publicly available independent sequences corresponding to subtypes A1, A6, B, C, D, F1, and G and circulating recombinant forms (CRFs) 01_AE, 02_AG, and 07_BC; sequences were sampled between 1980 and 2020 from 82 countries. HIV-1 diversified with a median of 1.82 amino acid substitutions per year in Env, 0.297 in Gag, and 0.779 in Pol. Yet, Env subtype B diversification plateaued post-2000. Pairwise diversity within subtypes and CRFs increased by 41.82% (range = 24.85%-54.41%) in Env, 56.93% (15.38%-89.16%) in Gag, and 46.12% (11.70%-70.57%) in Pol. Consensus sequences based on sequences sampled in each decade remained relatively stable over time. Similarly, at antibody epitope sites, only 0-8 residues that were minority variants became consensus over time in any subtype/CRF and only one known drug resistance mutation site differed from the reference (subtype G). The apparent contradiction between the fast diversification of HIV-1 and its limited adaptation illustrates that HIV-1 evolution is not directional and its consensus is at the intersection of millions of within-host selective processes occurring in a star-like manner. While a consensus sequence is a better representation of HIV-1 diversity than any individual sequence, consensus sequences have progressively become more distant from the circulating sequences they represent. IMPORTANCE Global surveillance of HIV-1 sequences is critical for designing relevant prophylactic and therapeutic interventions to infection. We designed an open-source platform, Hervé, for analyzing and visualizing the diversification dynamics of HIV-1 protein sequences. We characterized the evolution of over 12,000 HIV-1 Env, Gag, and Pol protein sequences from 1980-2020 and found that, despite a steady increase in intra-subtype and circulating recombinant form diversity, the most frequent residue at each site, i.e., the consensus, has varied only moderately.
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Affiliation(s)
- Eric Lewitus
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Yifan Li
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Hongjun Bai
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Phuc Pham
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
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Qiao J, Peng Q, Qian F, You Q, Feng L, Hu S, Liu W, Huang L, Shu X, Sun B. HIV-1 Vpr protein upregulates microRNA-210-5p expression to induce G2 arrest by targeting TGIF2. PLoS One 2021; 16:e0261971. [PMID: 34965271 PMCID: PMC8716043 DOI: 10.1371/journal.pone.0261971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/14/2021] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs) are important molecules that mediate virus-host interactions, mainly by regulating gene expression via gene silencing. Here, we demonstrated that HIV-1 infection upregulated miR-210-5p in HIV-1-inoculated cell lines and in the serum of HIV-1-infected individuals. Luciferase reporter assays and western blotting confirmed that a target protein of miR-210-5p, TGIF2, is regulated by HIV-1 infection. Furthermore, HIV-1 Vpr protein induced miR-210-5p expression. The use of a miR-210-5p inhibitor and TGIF2 overexpression showed that Vpr upregulated miR-210-5p and thereby downregulated TGIF2, which might be one of the mechanisms used by Vpr to induce G2 arrest. Moreover, we identified a transcription factor, NF-κB p50, which upregulated miR-210-5p in response to Vpr protein. In conclusion, we identified a mechanism whereby miR-210-5p, which is induced upon HIV-1 infection, targets TGIF2. This pathway was initiated by Vpr protein activating NF-κB p50, which promoted G2 arrest. These alterations orchestrated by miRNA provide new evidence on how HIV-1 interacts with its host during infection and increase our understanding of the mechanism by which Vpr regulates the cell cycle.
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Affiliation(s)
- Jialu Qiao
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Qian Peng
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Feng Qian
- Division of HIV/AIDS, The Second Affiliated Hospital of Soochow University, Soochow, China
| | - Qiang You
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Lingyan Feng
- Department of Immunology, School of Medicine, Jianghan University, Wuhan, China
| | - Song Hu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Wei Liu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Lixia Huang
- Department of Immunology, School of Medicine, Jianghan University, Wuhan, China
| | - Xiji Shu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
- * E-mail: (BS); (XS)
| | - Binlian Sun
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
- * E-mail: (BS); (XS)
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Xie Y, Xie L, Chen A, Wu S, Mo Y, Guo X, Zeng C, Huang X, He J. Anti-HIV/SIV activity of icariin and its metabolite anhydroicaritin mainly involve reverse transcriptase. Eur J Pharmacol 2020; 884:173327. [PMID: 32726656 DOI: 10.1016/j.ejphar.2020.173327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 11/26/2022]
Abstract
AIDS, a serious fatal disease caused by the human immunodeficiency virus (HIV), is an epidemic disease for which no effective vaccine has been established. The current therapeutic interventions for AIDS have limited efficacy because they are unable to clear HIV infections and the continuous occurrence of resistant HIV strains. Therefore, the exploitation of new drugs to prevent the spread of AIDS remains a high priority. In this study, the effects of icariin and its metabolite anhydroicaritin on SIV/HIV replication were investigated. In CEM × 174 cells and PBMC cells, both icariin and anhydroicaritin can significantly inhibit HIV-1 or SIVmac251 replication. Furthermore, molecular docking studies revealed that icariin and anhydroicaritin can act on both HIV reverse transcriptase and protease but could not bind to integrase. Reverse transcriptase and protease inhibition biological assays showed that both icariin and anhydroicaritin could significantly inhibit only HIV reverse transcriptase. In summary, the two compounds can significantly inhibit HIV/SIV in vitro and their targets may be mainly involved with HIV reverse transcriptase.
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Affiliation(s)
- Yanzheng Xie
- Science and Technology Innovation Centre, Guangzhou University of Chinese Medicine, Guangzhou, China; Lingnan Medical Research Centre, Guangzhou University of Chinese Medicine, Guangzhou, China; The Second Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lei Xie
- Science and Technology Innovation Centre, Guangzhou University of Chinese Medicine, Guangzhou, China; Lingnan Medical Research Centre, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ailan Chen
- Guangzhou Women and Children' Medical Centre, Guangzhou, China
| | - Shengnan Wu
- Science and Technology Innovation Centre, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuxiao Mo
- Science and Technology Innovation Centre, Guangzhou University of Chinese Medicine, Guangzhou, China; Lingnan Medical Research Centre, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaoqiang Guo
- Science and Technology Innovation Centre, Guangzhou University of Chinese Medicine, Guangzhou, China; Lingnan Medical Research Centre, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Changchun Zeng
- School of Biomedical Technology, Guilin Medical University, Guilin, China
| | - Xinan Huang
- Science and Technology Innovation Centre, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jinyang He
- Science and Technology Innovation Centre, Guangzhou University of Chinese Medicine, Guangzhou, China; Lingnan Medical Research Centre, Guangzhou University of Chinese Medicine, Guangzhou, China.
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