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Hasan TN, Naqvi SS, Rehman MU, Ullah R, Ammad M, Arshad N, Ain QU, Perween S, Hussain A. Ginger ring compounds as an inhibitor of spike binding protein of alpha, beta, gamma and delta variants of SARS-CoV-2: An in-silico study. NARRA J 2023; 3:e98. [PMID: 38455706 PMCID: PMC10919719 DOI: 10.52225/narra.v3i1.98] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/01/2023] [Indexed: 03/09/2024]
Abstract
The available drugs against coronavirus disease 2019 (COVOD-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are limited. This study aimed to identify ginger-derived compounds that might neutralize SARS-CoV-2 and prevent its entry into host cells. Ring compounds of ginger were screened against spike (S) protein of alpha, beta, gamma, and delta variants of SARS-CoV-2. The S protein FASTA sequence was retrieved from Global Initiative on Sharing Avian Influenza Data (GISAID) and converted into ".pdb" format using Open Babel tool. A total of 306 compounds were identified from ginger through food and phyto-databases. Out of those, 38 ring compounds were subjected to docking analysis using CB Dock online program which implies AutoDock Vina for docking. The Vina score was recorded, which reflects the affinity between ligands and receptors. Further, the Protein Ligand Interaction Profiler (PLIP) program for detecting the type of interaction between ligand-receptor was used. SwissADME was used to compute druglikeness parameters and pharmacokinetics characteristics. Furthermore, energy minimization was performed by using Swiss PDB Viewer (SPDBV) and energy after minimization was recorded. Molecular dynamic simulation was performed to find the stability of protein-ligand complex and root-mean- square deviation (RMSD) as well as root-mean-square fluctuation (RMSF) were calculated and recorded by using myPresto v5.0. Our study suggested that 17 out of 38 ring compounds of ginger were very likely to bind the S protein of SARS-CoV-2. Seventeen out of 38 ring compounds showed high affinity of binding with S protein of alpha, beta, gamma, and delta variants of SARS-CoV-2. The RMSD showed the stability of the complex was parallel to the S protein monomer. These computer-aided predictions give an insight into the possibility of ginger ring compounds as potential anti-SARS-CoV-2 worthy of in vitro investigations.
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Affiliation(s)
- Tarique N. Hasan
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
- School of Life Sciences, Manipal Academy of Higher Education, Dubai, United Arab Emirates
| | - Syed S. Naqvi
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Mati Ur Rehman
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
- College de Paris, France
| | - Rooh Ullah
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Muhammad Ammad
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Narmeen Arshad
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Qurat Ul Ain
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Shabana Perween
- Pure Health Laboratory, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Arif Hussain
- School of Life Sciences, Manipal Academy of Higher Education, Dubai, United Arab Emirates
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2
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Wang Z, Barnes CO, Gautam R, Cetrulo Lorenzi JC, Mayer CT, Oliveira TY, Ramos V, Cipolla M, Gordon KM, Gristick HB, West AP, Nishimura Y, Raina H, Seaman MS, Gazumyan A, Martin M, Bjorkman PJ, Nussenzweig MC, Escolano A. A broadly neutralizing macaque monoclonal antibody against the HIV-1 V3-Glycan patch. eLife 2020; 9:e61991. [PMID: 33084569 PMCID: PMC7577740 DOI: 10.7554/elife.61991] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/09/2020] [Indexed: 12/22/2022] Open
Abstract
A small fraction of HIV-1- infected humans develop broadly neutralizing antibodies (bNAbs) against HIV-1 that protect macaques from simian immunodeficiency HIV chimeric virus (SHIV). Similarly, a small number of macaques infected with SHIVs develop broadly neutralizing serologic activity, but less is known about the nature of simian antibodies. Here, we report on a monoclonal antibody, Ab1485, isolated from a macaque infected with SHIVAD8 that developed broadly neutralizing serologic activity targeting the V3-glycan region of HIV-1 Env. Ab1485 neutralizes 38.1% of HIV-1 isolates in a 42-pseudovirus panel with a geometric mean IC50 of 0.055 µg/mLl and SHIVAD8 with an IC50 of 0.028 µg/mLl. Ab1485 binds the V3-glycan epitope in a glycan-dependent manner. A 3.5 Å cryo-electron microscopy structure of Ab1485 in complex with a native-like SOSIP Env trimer showed conserved contacts with the N332gp120 glycan and gp120 GDIR peptide motif, but in a distinct Env-binding orientation relative to human V3/N332gp120 glycan-targeting bNAbs. Intravenous infusion of Ab1485 protected macaques from a high dose challenge with SHIVAD8. We conclude that macaques can develop bNAbs against the V3-glycan patch that resemble human V3-glycan bNAbs.
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Affiliation(s)
- Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Rajeev Gautam
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | | | - Christian T Mayer
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Kristie M Gordon
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Yoshiaki Nishimura
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Henna Raina
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical CenterBostonUnited States
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
| | - Malcolm Martin
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical Institute. The Rockefeller UniversityNew YorkUnited States
| | - Amelia Escolano
- Laboratory of Molecular Immunology, The Rockefeller UniversityNew YorkUnited States
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3
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Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 2020. [PMID: 32697968 DOI: 10.1016/j.cell.2020.06.043s] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to introduction of the G614 variant. The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage. We found that the G614 variant grows to a higher titer as pseudotyped virions. In infected individuals, G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, but not with increased disease severity. These findings illuminate changes important for a mechanistic understanding of the virus and support continuing surveillance of Spike mutations to aid with development of immunological interventions.
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Affiliation(s)
- Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA.
| | - Will M Fischer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Hyejin Yoon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - James Theiler
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Werner Abfalterer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nick Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Elena E Giorgi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Tanmoy Bhattacharya
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Brian Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Matthew D Parker
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - David G Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Cariad M Evans
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Timothy M Freeman
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Charlene McDanal
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Lautaro G Perez
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Haili Tang
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Alex Moon-Walker
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Program in Virology, Harvard University, Boston, MA 02115, USA; Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Sean P Whelan
- Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Celia C LaBranche
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
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4
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Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 2020; 182:812-827.e19. [PMID: 32697968 PMCID: PMC7332439 DOI: 10.1016/j.cell.2020.06.043] [Citation(s) in RCA: 2785] [Impact Index Per Article: 696.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/10/2020] [Accepted: 06/26/2020] [Indexed: 02/08/2023]
Abstract
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to introduction of the G614 variant. The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage. We found that the G614 variant grows to a higher titer as pseudotyped virions. In infected individuals, G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, but not with increased disease severity. These findings illuminate changes important for a mechanistic understanding of the virus and support continuing surveillance of Spike mutations to aid with development of immunological interventions.
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Affiliation(s)
- Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA.
| | - Will M Fischer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Hyejin Yoon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - James Theiler
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Werner Abfalterer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nick Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Elena E Giorgi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Tanmoy Bhattacharya
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Brian Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Matthew D Parker
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - David G Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Cariad M Evans
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Timothy M Freeman
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Charlene McDanal
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Lautaro G Perez
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Haili Tang
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Alex Moon-Walker
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Program in Virology, Harvard University, Boston, MA 02115, USA; Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Sean P Whelan
- Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Celia C LaBranche
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
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5
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Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 2020. [PMID: 32697968 DOI: 10.1016/j.cell.2020.06.043%0asummary] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to introduction of the G614 variant. The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage. We found that the G614 variant grows to a higher titer as pseudotyped virions. In infected individuals, G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, but not with increased disease severity. These findings illuminate changes important for a mechanistic understanding of the virus and support continuing surveillance of Spike mutations to aid with development of immunological interventions.
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Affiliation(s)
- Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA.
| | - Will M Fischer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Hyejin Yoon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - James Theiler
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Werner Abfalterer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nick Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Elena E Giorgi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Tanmoy Bhattacharya
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Brian Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Matthew D Parker
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - David G Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Cariad M Evans
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Timothy M Freeman
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Charlene McDanal
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Lautaro G Perez
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Haili Tang
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Alex Moon-Walker
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Program in Virology, Harvard University, Boston, MA 02115, USA; Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Sean P Whelan
- Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Celia C LaBranche
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
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Abstract
Neutralizing antibodies against human immunodeficiency virus subtype 1 (HIV-1) bind to its envelope glycoprotein (Env). Half of the molecular mass of Env is carbohydrate making it one of the most heavily glycosylated proteins known in nature. HIV-1 Env glycans are derived from the host and present a formidable challenge for host anti-glycan antibody induction. Anti-glycan antibody induction is challenging because anti-HIV-1 glycan antibodies should recognize Env antigen while not acquiring autoreactivity. Thus, the glycan network on HIV-1 Env is referred to as the glycan shield. Despite the challenges presented by immune recognition of host-derived glycans, neutralizing antibodies capable of binding the glycans on HIV-1 Env can be generated by the host immune system in the setting of HIV-1 infection. In particular, a cluster of high mannose glycans, including an N-linked glycan at position 332, form the high mannose patch and are targeted by a variety of broadly neutralizing antibodies. These high mannose patch-directed HIV-1 antibodies can be categorized into distinct categories based on their antibody paratope structure, neutralization activity, and glycan and peptide reactivity. Below we will compare and contrast each of these classes of HIV-1 glycan-dependent antibodies and describe vaccine design efforts to elicit each of these antibody types.
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7
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Falkenhagen A, Joshi S. HIV Entry and Its Inhibition by Bifunctional Antiviral Proteins. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 13:347-364. [PMID: 30340139 PMCID: PMC6197789 DOI: 10.1016/j.omtn.2018.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 09/05/2018] [Accepted: 09/05/2018] [Indexed: 12/14/2022]
Abstract
HIV entry is a highly specific and time-sensitive process that can be divided into receptor binding, coreceptor binding, and membrane fusion. Bifunctional antiviral proteins (bAVPs) exploit the multi-step nature of the HIV entry process by binding to two different extracellular targets. They are generated by expressing a fusion protein containing two entry inhibitors with a flexible linker. The resulting fusion proteins exhibit exceptional neutralization potency and broad cross-clade inhibition. In this review, we summarize the HIV entry process and provide an overview of the design, antiviral potency, and methods of delivery of bAVPs. Additionally, we discuss the advantages and limitations of bAVPs for HIV prevention and treatment.
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Affiliation(s)
- Alexander Falkenhagen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E2, Canada
| | - Sadhna Joshi
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E2, Canada.
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8
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Abstract
INTRODUCTION Despite many recent advances in the HIV prevention landscape, an effective vaccine remains the most promising tool to end the HIV-1 pandemic. Areas covered: This review summarizes past HIV vaccine efficacy trials and current vaccine strategies as well as new approaches about to move into first-in-human trials. Expert opinion: Despite many setbacks in early HIV vaccine efficacy trials, the success of RV144 has provided the glimmer of hope necessary to invigorate the vaccine field, and has led to the development of a large number of vaccine strategies aiming at inducing an array of different immune responses. The follow-up pox-protein trials, developed to replicate and enhance the polyfunctional antibody responses induced by the RV144 regimen, are already reaching efficacy trials, while a large body of work providing a more complete understanding of the development of broadly neutralizing antibodies is now being translated into immunogen design using several different strategies. T-cell based vaccines, fallen out of favor after Ad5-based trials showed increased infection rates in Ad5 seropositive vaccine recipients, are experiencing a comeback based in part on the promising results from non-human primate challenge studies using rhCMV-based immunogens. This diverse array of vaccine candidates may finally allow us to identify a broadly effective HIV vaccine able to contain the epidemic.
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Affiliation(s)
- Kristen W Cohen
- a Vaccine and Infectious Disease Division , Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Nicole Frahm
- a Vaccine and Infectious Disease Division , Fred Hutchinson Cancer Research Center , Seattle , WA , USA.,b Department of Global Health , University of Washington , Seattle , WA , USA
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9
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van den Kerkhof TLGM, de Taeye SW, Boeser-Nunnink BD, Burton DR, Kootstra NA, Schuitemaker H, Sanders RW, van Gils MJ. HIV-1 escapes from N332-directed antibody neutralization in an elite neutralizer by envelope glycoprotein elongation and introduction of unusual disulfide bonds. Retrovirology 2016; 13:48. [PMID: 27388013 PMCID: PMC4936165 DOI: 10.1186/s12977-016-0279-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 06/21/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Current HIV-1 immunogens are unable to induce antibodies that can neutralize a broad range of HIV-1 (broadly neutralizing antibodies; bNAbs). However, such antibodies are elicited in 10-30 % of HIV-1 infected individuals, and the co-evolution of the virus and the humoral immune responses in these individuals has attracted attention, because they can provide clues for vaccine design. RESULTS Here we characterized the NAb responses and envelope glycoprotein evolution in an HIV-1 infected "elite neutralizer" of the Amsterdam Cohort Studies on HIV-1 infection and AIDS who developed an unusually potent bNAb response rapidly after infection. The NAb response was dependent on the N332-glycan and viral resistance against the N332-glycan dependent bNAb PGT135 developed over time but viral escape did not occur at or near this glycan. In contrast, the virus likely escaped by increasing V1 length, with up to 21 amino acids, accompanied by the introduction of 1-3 additional glycans, as well as 2-4 additional cysteine residues within V1. CONCLUSIONS In the individual studied here, HIV-1 escaped from N332-glycan directed NAb responses without changing the epitope itself, but by elongating a variable loop that shields this epitope.
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Affiliation(s)
- Tom L G M van den Kerkhof
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands.,Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Steven W de Taeye
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Brigitte D Boeser-Nunnink
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Dennis R Burton
- Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Neeltje A Kootstra
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands.,Janssen Pharmaceuticals, 2333 CN, Leiden, The Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands. .,Department of Microbiology and Immunology, Weill Medical College, Cornell University, New York, NY, 10065, USA.
| | - Marit J van Gils
- Department of Microbiology and Immunology, Weill Medical College, Cornell University, New York, NY, 10065, USA.
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10
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Krumm SA, Mohammed H, Le KM, Crispin M, Wrin T, Poignard P, Burton DR, Doores KJ. Mechanisms of escape from the PGT128 family of anti-HIV broadly neutralizing antibodies. Retrovirology 2016; 13:8. [PMID: 26837192 PMCID: PMC4736637 DOI: 10.1186/s12977-016-0241-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/18/2016] [Indexed: 11/26/2022] Open
Abstract
Background Broadly neutralizing antibodies (bnAbs) directed against the mannose-patch on the HIV envelope glycoprotein gp120 have several features that make them desirable targets for vaccine design. The PGT125-131 bnAb family is of particular interest due to its superior breadth and potency. The overlapping epitopes recognized by this family are intricate and neutralization requires interaction with at least two N-linked glycans (N332/N334, N295 or N301) in addition to backbone-mediated contact with the 323IGDIR327 motif of the V3 loop. We have recently shown that this bnAb family consists of two distinct antibody classes that can bind alternate arrangements of glycans in the mannose-patch in the absence of N332 thereby limiting viral escape. This led us to further investigate viral resistance and escape mechanisms to the PGT125-131 bnAb family. Results Using an escape virus isolated from the PGT125-131 donor as a guide, we show that mutating both the V3 core protein epitope and repositioning critical N-linked glycosylation sites are required to restore neutralization sensitivity. Interestingly, neutralization sensitivity could be restored via different routes for the two distinct bnAb classes within the PGT125-131 family, which may have been important in generating the divergence in recognition. We demonstrate that the observed V3 mutations confer neutralization resistance in other virus strains through both gain-of-function and escape studies. Furthermore, we show that the V3 loop is important in facilitating promiscuous binding to glycans within the mannose-patch. Conclusions These data highlight the importance of the V3 loop in the design of immunogens aimed at inducing broad and potent bnAbs that can bind promiscuously to the mannose-patch. Electronic supplementary material The online version of this article (doi:10.1186/s12977-016-0241-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefanie A Krumm
- Department of Infectious Diseases, King's College London School of Medicine, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK.
| | - Hajer Mohammed
- Department of Infectious Diseases, King's College London School of Medicine, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK.
| | - Khoa M Le
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, USA. .,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA. .,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, USA.
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | - Terri Wrin
- Monogram Biosciences, Laboratory Corporation of America(R) Holdings, South San Francisco, CA, USA.
| | - Pascal Poignard
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, USA. .,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
| | - Dennis R Burton
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, USA. .,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA. .,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, USA. .,Ragon Institute of MGH, MIT and Harvard, Cambridge, USA.
| | - Katie J Doores
- Department of Infectious Diseases, King's College London School of Medicine, Guy's Hospital, Great Maze Pond, London, SE1 9RT, UK.
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11
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Inhibitory Effect of Individual or Combinations of Broadly Neutralizing Antibodies and Antiviral Reagents against Cell-Free and Cell-to-Cell HIV-1 Transmission. J Virol 2015; 89:7813-28. [PMID: 25995259 DOI: 10.1128/jvi.00783-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 05/11/2015] [Indexed: 12/18/2022] Open
Abstract
UNLABELLED To date, most therapeutic and vaccine candidates for human immunodeficiency virus type 1 (HIV-1) are evaluated preclinically for efficacy against cell-free viral challenges. However, cell-associated HIV-1 is suggested to be a major contributor to sexual transmission by mucosal routes. To determine if neutralizing antibodies or inhibitors block cell-free and cell-associated virus transmission of diverse HIV-1 strains with different efficiencies, we tested 12 different antibodies and five inhibitors against four green fluorescent protein (GFP)-labeled HIV-1 envelope (Env) variants from transmitted/founder (T/F) or chronic infection isolates. We evaluated antibody/inhibitor-mediated virus neutralization using either TZM-bl target cells, in which infectivity was determined by virus-driven luciferase expression, or A3R5 lymphoblastoid target cells, in which infectivity was evaluated by GFP expression. In both the TZM-bl and A3R5 assays, cell-free virus or infected CD4+ lymphocytes were used as targets for neutralization. We further hypothesized that the combined use of specific neutralizing antibodies targeting HIV-1 Env would more effectively prevent cell-associated virus transmission than the use of individual antibodies. The tested antibody combinations included two gp120-directed antibodies, VRC01 and PG9, or VRC01 with the gp41-directed antibody 10E8. Our results demonstrated that cell-associated virus was less sensitive to neutralizing antibodies and inhibitors, particularly using the A3R5 neutralization assay, and the potencies of these neutralizing agents differed among Env variants. A combination of different neutralizing antibodies that target specific sites on gp120 led to a significant reduction in cell-associated virus transmission. These assays will help identify ideal combinations of broadly neutralizing antibodies to use for passive preventive antibody administration and further characterize targets for the most effective neutralizing antibodies/inhibitors. IMPORTANCE Prevention of the transmission of human immunodeficiency virus type 1 (HIV-1) remains a prominent goal of HIV research. The relative contribution of HIV-1 within an infected cell versus cell-free HIV-1 to virus transmission remains debated. It has been suggested that cell-associated virus is more efficient at transmitting HIV-1 and more difficult to neutralize than cell-free virus. Several broadly neutralizing antibodies and retroviral inhibitors are currently being studied as potential therapies against HIV-1 transmission. The present study demonstrates a decrease in neutralizing antibody and inhibitor efficiencies against cell-associated compared to cell-free HIV-1 transmission among different strains of HIV-1. We also observed a significant reduction in virus transmission using a combination of two different neutralizing antibodies that target specific sites on the outermost region of HIV-1, the virus envelope. Therefore, our findings support the use of antibody combinations against both cell-free and cell-associated virus in future candidate therapy regimens.
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Acharya P, Lusvarghi S, Bewley CA, Kwong PD. HIV-1 gp120 as a therapeutic target: navigating a moving labyrinth. Expert Opin Ther Targets 2015; 19:765-83. [PMID: 25724219 DOI: 10.1517/14728222.2015.1010513] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION The HIV-1 gp120 envelope (Env) glycoprotein mediates attachment of virus to human target cells that display requisite receptors, CD4 and co-receptor, generally CCR5. Despite high-affinity interactions with host receptors and proof-of-principle by the drug maraviroc that interference with CCR5 provides therapeutic benefit, no licensed drug currently targets gp120. AREAS COVERED An overview of the role of gp120 in HIV-1 entry and of sites of potential gp120 vulnerability to therapeutic inhibition is presented. Viral defenses that protect these sites and turn gp120 into a moving labyrinth are discussed together with strategies for circumventing these defenses to allow therapeutic targeting of gp120 sites of vulnerability. EXPERT OPINION The gp120 envelope glycoprotein interacts with host proteins through multiple interfaces and has conserved structural features at these interaction sites. In spite of this, targeting gp120 for therapeutic purposes is challenging. Env mechanisms that have evolved to evade the humoral immune response also shield it from potential therapeutics. Nevertheless, substantial progress has been made in understanding HIV-1 gp120 structure and its interactions with host receptors, and in developing therapeutic leads that potently neutralize diverse HIV-1 strains. Synergies between advances in understanding, needs for therapeutics against novel viral targets and characteristics of breadth and potency for a number of gp120-targetting lead molecules bodes well for gp120 as a HIV-1 therapeutic target.
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Affiliation(s)
- Priyamvada Acharya
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Vaccine Research Center, Structural Biology Section , Room 4609B, 40 Convent Drive, Bethesda, MD 20892 , USA
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13
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Early preservation of CXCR5+ PD-1+ helper T cells and B cell activation predict the breadth of neutralizing antibody responses in chronic HIV-1 infection. J Virol 2014; 88:13310-21. [PMID: 25210168 DOI: 10.1128/jvi.02186-14] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Much is known about the characteristics of broadly neutralizing antibodies (bNAbs) generated during HIV-1 infection, but little is known about immunological mechanisms responsible for their development in only a minority of those infected by HIV-1. By monitoring longitudinally a cohort of HIV-1-infected subjects, we observed that the preservation of CXCR5(+) CD4(+) T helper cell frequencies and activation status of B cells during the first year of infection correlates with the maximum breadth of plasma neutralizing antibody responses during chronic infection independently of viral load. Although, during the first year of infection, no differences were observed in the abilities of peripheral CXCR5(+) CD4(+) T helper cells to induce antibody secretion by autologous naive B cells, higher frequencies of class-switched antibodies were detected in cocultures of CXCR5(+) CD4(+) T and B cells from the subjects who later developed broadly neutralizing antibody responses than those who did not. Furthermore, B cells from the former subjects had higher expression of AICDA than B cells from the latter subjects, and transcript levels correlated with the frequency of CXCR5(+) CD4(+) T cells. Thus, the early preservation of CXCR5(+) CD4(+) T cells and B cell function are central to the development of bNAbs. Our study provides a possible explanation for their infrequent generation during HIV-1 infection. IMPORTANCE Broadly neutralizing antibodies are developed by HIV-1-infected subjects, but so far (and despite intensive efforts over the past 3 decades) they have not been elicited by immunization. Understanding how bNAbs are generated during natural HIV-1 infection and why only some HIV-1-infected subjects generate such antibodies will assist our efforts to elicit bNAbs by immunization. CXCR5(+) PD-1(+) CD4(+) T cells are critical for the development of high-affinity antigen-specific antibody responses. In our study, we found that the HIV-1-infected subjects who develop bNAbs have a higher frequency of peripheral CXCR5(+) PD-1(+) CD4(+) T cells in early infection and also that this frequency mirrored what was observed in uninfected subjects and correlated with the level of B cell activation across subjects. Our study highlights the critical role helper T cell function has in the elicitation of broadly neutralizing antibody responses in the context of HIV infection.
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Shingai M, Nishimura Y, Klein F, Mouquet H, Donau OK, Plishka R, Buckler-White A, Piatak M, Lifson JD, Dimitrov D, Nussenzweig MC, Martin MA. Antibody-mediated immunotherapy of macaques chronically infected with SHIV suppresses viraemia. Nature 2013; 503:277-80. [PMID: 24172896 PMCID: PMC4133787 DOI: 10.1038/nature12746] [Citation(s) in RCA: 378] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 10/11/2013] [Indexed: 02/07/2023]
Abstract
Neutralizing antibodies can confer immunity to primate lentiviruses by blocking infection in macaque models of AIDS. However, earlier studies of anti-human immunodeficiency virus type 1 (HIV-1) neutralizing antibodies administered to infected individuals or humanized mice reported poor control of virus replication and the rapid emergence of resistant variants. A new generation of anti-HIV-1 monoclonal antibodies, possessing extraordinary potency and breadth of neutralizing activity, has recently been isolated from infected individuals. These neutralizing antibodies target different regions of the HIV-1 envelope glycoprotein including the CD4-binding site, glycans located in the V1/V2, V3 and V4 regions, and the membrane proximal external region of gp41 (refs 9-14). Here we have examined two of the new antibodies, directed to the CD4-binding site and the V3 region (3BNC117 and 10-1074, respectively), for their ability to block infection and suppress viraemia in macaques infected with the R5 tropic simian-human immunodeficiency virus (SHIV)-AD8, which emulates many of the pathogenic and immunogenic properties of HIV-1 during infections of rhesus macaques. Either antibody alone can potently block virus acquisition. When administered individually to recently infected macaques, the 10-1074 antibody caused a rapid decline in virus load to undetectable levels for 4-7 days, followed by virus rebound during which neutralization-resistant variants became detectable. When administered together, a single treatment rapidly suppressed plasma viraemia for 3-5 weeks in some long-term chronically SHIV-infected animals with low CD4(+) T-cell levels. A second cycle of anti-HIV-1 monoclonal antibody therapy, administered to two previously treated animals, successfully controlled virus rebound. These results indicate that immunotherapy or a combination of immunotherapy plus conventional antiretroviral drugs might be useful as a treatment for chronically HIV-1-infected individuals experiencing immune dysfunction.
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Affiliation(s)
- Masashi Shingai
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Yoshiaki Nishimura
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Florian Klein
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065 USA
| | - Hugo Mouquet
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, France
| | - Olivia K. Donau
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Ronald Plishka
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Alicia Buckler-White
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Michael Piatak
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Dimiter Dimitrov
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065 USA
- Howard Hughes Medical Institute
| | - Malcolm A. Martin
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
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Julien JP, Cupo A, Sok D, Stanfield RL, Lyumkis D, Deller MC, Klasse PJ, Burton DR, Sanders RW, Moore JP, Ward AB, Wilson IA. Crystal structure of a soluble cleaved HIV-1 envelope trimer. Science 2013; 342:1477-83. [PMID: 24179159 DOI: 10.1126/science.1245625] [Citation(s) in RCA: 698] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
HIV-1 entry into CD4(+) target cells is mediated by cleaved envelope glycoprotein (Env) trimers that have been challenging to characterize structurally. Here, we describe the crystal structure at 4.7 angstroms of a soluble, cleaved Env trimer that is stabilized and antigenically near-native (termed the BG505 SOSIP.664 gp140 trimer) in complex with a potent broadly neutralizing antibody, PGT122. The structure shows a prefusion state of gp41, the interaction between the component gp120 and gp41 subunits, and how a close association between the gp120 V1/V2/V3 loops stabilizes the trimer apex around the threefold axis. The complete epitope of PGT122 on the trimer involves gp120 V1, V3, and several surrounding glycans. This trimer structure advances our understanding of how Env functions and is presented to the immune system, and provides a blueprint for structure-based vaccine design.
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Affiliation(s)
- Jean-Philippe Julien
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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