1
|
Wang Q, Zhang S, Nguyen HT, Sodroski J. Inhibition of human immunodeficiency virus (HIV-1) infectivity by expression of poorly or broadly neutralizing antibodies against Env in virus-producing cells. J Virol 2024; 98:e0159423. [PMID: 38289101 PMCID: PMC10878270 DOI: 10.1128/jvi.01594-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/19/2023] [Indexed: 02/21/2024] Open
Abstract
The human immunodeficiency virus (HIV-1) envelope (Env) glycoprotein precursor (gp160) trimerizes, is modified by high-mannose glycans in the endoplasmic reticulum, and is transported via Golgi and non-Golgi secretory pathways to the infected cell surface. In the Golgi, gp160 is partially modified by complex carbohydrates and proteolytically cleaved to produce the mature functional Env trimer, which is preferentially incorporated into virions. Broadly neutralizing antibodies (bNAbs) generally recognize the cleaved Env trimer, whereas poorly neutralizing antibodies (pNAbs) bind the conformationally flexible gp160. We found that expression of bNAbs, pNAbs, or soluble/membrane forms of the receptor, CD4, in cells producing HIV-1 all decreased viral infectivity. Four patterns of co-expressed ligand:Env were observed: (i) ligands (CD4, soluble CD4-Ig, and some pNAbs) that specifically recognize the CD4-bound Env conformation resulted in uncleaved Envs lacking complex glycans that were not incorporated into virions; (ii) other pNAbs produced Envs with some complex carbohydrates and severe defects in cleavage, which were relieved by brefeldin A treatment; (iii) bNAbs that recognize gp160 as well as mature Envs resulted in Envs with some complex carbohydrates and moderate decreases in virion Env cleavage; and (iv) bNAbs that preferentially recognize mature Envs produced cleaved Envs with complex glycans in cells and on virions. The low infectivity observed upon co-expression of pNAbs or CD4 could be explained by disruption of Env trafficking, reducing the level of Env and/or increasing the fraction of uncleaved Env on virions. In addition to bNAb effects on virion Env cleavage, the secreted bNAbs neutralized the co-expressed viruses.IMPORTANCEThe Env trimers on the HIV-1 mediate virus entry into host cells. Env is synthesized in infected cells, modified by complex sugars, and cleaved to form a mature, functional Env, which is incorporated into virus particles. Env elicits antibodies in infected individuals, some of which can neutralize the virus. We found that antibodies co-expressed in the virus-producing cell can disrupt Env transit to the proper compartment for cleavage and sugar modification and, in some cases, block incorporation into viruses. These studies provide insights into the processes by which Env becomes functional in the virus-producing cell and may assist attempts to interfere with these events to inhibit HIV-1 infection.
Collapse
Affiliation(s)
- Qian Wang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Hanh T. Nguyen
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
2
|
Parthasarathy D, Pothula KR, Dam KMA, Ratnapriya S, Benet HC, Parsons R, Huang X, Sammour S, Janowska K, Harris M, Sacco S, Sodroski J, Bridges MD, Hubbell WL, Acharya P, Herschhorn A. Conformational flexibility of HIV-1 envelope glycoproteins modulates transmitted / founder sensitivity to broadly neutralizing antibodies. bioRxiv 2023:2023.09.13.557082. [PMID: 37745449 PMCID: PMC10515946 DOI: 10.1101/2023.09.13.557082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
HIV-1 envelope glycoproteins (Envs) mediate viral entry and are the sole target of neutralizing antibodies. Envs of most primary HIV-1 strains exist in a closed conformation and occasionally sample more open states. Thus, current knowledge guides immunogen design to mimic the closed Env conformation as the preferred target for eliciting broadly neutralizing antibodies (bnAbs) to block HIV-1 entry. Here we show that Env-preferred conformations of 6 out of 13 (46%) transmitted/founder (T/F) strains tested are incompletely closed. As a result, entry of these T/Fs into target cells is sensitive to antibodies that recognize internal epitopes exposed on open Env conformations. A cryo-electron microscopy structure of unliganded, incompletely closed T/F Envs (1059-SOSIP) at 3.6 Å resolution exhibits an asymmetric configuration of Env protomers with increased sampling of states with incompletely closed trimer apex. Double electron-electron resonance spectroscopy provided further evidence for enriched occupancy of more open Env conformations. Consistent with conformational flexibility, 1059 Envs were associated with resistance to most bnAbs that exhibit reduced potency against functional Env intermediates. To follow the fate of incompletely closed Env in patients, we reconstructed de novo the post-transmission evolutionary pathway of a second T/F Env (CH040), which is sensitive to the V3-targeting antibody 19b and highly resistant to most bnAbs. Evolved viruses exhibited increased resistance to cold, soluble CD4 and 19b, all of which correlate with closing of the adapted Env trimer. Lastly, we show a correlation between efficient neutralization of multiple Env conformations and increased antiviral breadth of CD4-binding site (CD4bs) bnAbs. In particular, N6 bnAb, which uniquely recognizes different Env conformations, efficiently neutralizes 50% of the HIV-1 strains that were resistant to VRC01 and transmitted during the first-in-humans antibody-mediated prevention trial (HVTN 704). VRC01-resistant Envs are incompletely closed based on their sensitivity to cold and on partial sensitivity to antibodies targeting internal, typically occluded, epitopes. Most VRC01-resistant Envs retain the VRC01 epitope according to VRC01 binding to their gp120 subunit at concentrations that have no significant effect on virus entry, and they exhibit cross resistance to other CD4bs bnAbs that poorly recognize functional Env intermediates. Our findings refine current knowledge of Env conformational states and provide guidance for developing new strategies for bnAb immunotherapy and Env-based immunogen design.
Collapse
Affiliation(s)
- Durgadevi Parthasarathy
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
- These authors contributed equally: Durgadevi Parthasarathy and Karunakar Reddy Pothula
| | - Karunakar Reddy Pothula
- Duke Human Vaccine Institute, Durham, NC, USA
- These authors contributed equally: Durgadevi Parthasarathy and Karunakar Reddy Pothula
| | - Kim-Marie A. Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sneha Ratnapriya
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Héctor Cervera Benet
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | | | - Xiao Huang
- Duke Human Vaccine Institute, Durham, NC, USA
| | | | | | - Miranda Harris
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Samuel Sacco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Present address: Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Michael D. Bridges
- Jules Stein Eye Institute, University of California, Los Angeles, CA, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Wayne L. Hubbell
- Jules Stein Eye Institute, University of California, Los Angeles, CA, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC, USA
- Department of Surgery, and Department of Biochemistry, Duke University, Durham, NC, USA
| | - Alon Herschhorn
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
- Microbiology, Immunology, and Cancer Biology Graduate Program; The College of Veterinary Medicine Graduate Program; and the Molecular Pharmacology and Therapeutics Graduate Program, University of Minnesota, Minneapolis, MN, USA
| |
Collapse
|
3
|
Anang S, Zhang S, Fritschi C, Chiu TJ, Yang D, Smith III AB, Madani N, Sodroski J. V3 tip determinants of susceptibility to inhibition by CD4-mimetic compounds in natural clade A human immunodeficiency virus (HIV-1) envelope glycoproteins. J Virol 2023; 97:e0117123. [PMID: 37888980 PMCID: PMC10688366 DOI: 10.1128/jvi.01171-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE CD4-mimetic compounds (CD4mcs) are small-molecule inhibitors of human immunodeficiency virus (HIV-1) entry into host cells. CD4mcs target a pocket on the viral envelope glycoprotein (Env) spike that is used for binding to the receptor, CD4, and is highly conserved among HIV-1 strains. Nonetheless, naturally occurring HIV-1 strains exhibit a wide range of sensitivities to CD4mcs. Our study identifies changes distant from the binding pocket that can influence the susceptibility of natural HIV-1 strains to the antiviral effects of multiple CD4mcs. We relate the antiviral potency of the CD4mc against this panel of HIV-1 variants to the ability of the CD4mc to activate entry-related changes in Env conformation prematurely. These findings will guide efforts to improve the potency and breadth of CD4mcs against natural HIV-1 variants.
Collapse
Affiliation(s)
- Saumya Anang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Christopher Fritschi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ta-Jung Chiu
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Derek Yang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Amos B. Smith III
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Navid Madani
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
4
|
Wang K, Zhang S, Go EP, Ding H, Wang WL, Nguyen HT, Kappes JC, Desaire H, Sodroski J, Mao Y. Asymmetric conformations of cleaved HIV-1 envelope glycoprotein trimers in styrene-maleic acid lipid nanoparticles. Commun Biol 2023; 6:535. [PMID: 37202420 PMCID: PMC10195785 DOI: 10.1038/s42003-023-04916-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/04/2023] [Indexed: 05/20/2023] Open
Abstract
During virus entry, the pretriggered human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer initially transits into a default intermediate state (DIS) that remains structurally uncharacterized. Here, we present cryo-EM structures at near-atomic resolution of two cleaved full-length HIV-1 Env trimers purified from cell membranes in styrene-maleic acid lipid nanoparticles without antibodies or receptors. The cleaved Env trimers exhibited tighter subunit packing than uncleaved trimers. Cleaved and uncleaved Env trimers assumed remarkably consistent yet distinct asymmetric conformations, with one smaller and two larger opening angles. Breaking conformational symmetry is allosterically coupled with dynamic helical transformations of the gp41 N-terminal heptad repeat (HR1N) regions in two protomers and with trimer tilting in the membrane. The broken symmetry of the DIS potentially assists Env binding to two CD4 receptors-while resisting antibody binding-and promotes extension of the gp41 HR1 helical coiled-coil, which relocates the fusion peptide closer to the target cell membrane.
Collapse
Affiliation(s)
- Kunyu Wang
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, Beijing, China
- Peking-Tsinghua Joint Center for Life Science, Peking University, Beijing, China
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Eden P Go
- Department of Chemistry, University of Kansas, Lawrence, KS, USA
| | - Haitao Ding
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Wei Li Wang
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, Beijing, China
| | - Hanh T Nguyen
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - John C Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, AL, USA
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, KS, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Youdong Mao
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, Beijing, China.
- Peking-Tsinghua Joint Center for Life Science, Peking University, Beijing, China.
- Center for Quantitative Biology, Academy of Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- National Biomedical Imaging Center, Peking University, Beijing, China.
| |
Collapse
|
5
|
Viox E, Richard J, Clark N, Grandea A, Hammad I, Janaka S, Crosno K, Capuano S, Pagliuzza A, Gaudette F, Bourassa C, Fritschi C, III AS, Chomont N, Sodroski J, Finzi A, Evans D, Paiardini M. PP 8.13 – 00191 Investigating the Impact of CD4 mimetic BNM-III-170 on SHIV-infected Rhesus Macaques. J Virus Erad 2022. [DOI: 10.1016/j.jve.2022.100293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
|
6
|
Li W, Chen Y, Prévost J, Ullah I, Lu M, Gong SY, Tauzin A, Gasser R, Vézina D, Anand SP, Goyette G, Chaterjee D, Ding S, Tolbert WD, Grunst MW, Bo Y, Zhang S, Richard J, Zhou F, Huang RK, Esser L, Zeher A, Côté M, Kumar P, Sodroski J, Xia D, Uchil PD, Pazgier M, Finzi A, Mothes W. Structural basis and mode of action for two broadly neutralizing antibodies against SARS-CoV-2 emerging variants of concern. Cell Rep 2022; 38:110210. [PMID: 34971573 PMCID: PMC8673750 DOI: 10.1016/j.celrep.2021.110210] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/26/2021] [Accepted: 12/13/2021] [Indexed: 01/15/2023] Open
Abstract
Emerging variants of concern for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can transmit more efficiently and partially evade protective immune responses, thus necessitating continued refinement of antibody therapies and immunogen design. Here, we elucidate the structural basis and mode of action for two potent SARS-CoV-2 spike (S)-neutralizing monoclonal antibodies, CV3-1 and CV3-25, which remain effective against emerging variants of concern in vitro and in vivo. CV3-1 binds to the (485-GFN-487) loop within the receptor-binding domain (RBD) in the "RBD-up" position and triggers potent shedding of the S1 subunit. In contrast, CV3-25 inhibits membrane fusion by binding to an epitope in the stem helix region of the S2 subunit that is highly conserved among β-coronaviruses. Thus, vaccine immunogen designs that incorporate the conserved regions in the RBD and stem helix region are candidates to elicit pan-coronavirus protective immune responses.
Collapse
Affiliation(s)
- Wenwei Li
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yaozong Chen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Jérémie Prévost
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Irfan Ullah
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Maolin Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Shang Yu Gong
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Alexandra Tauzin
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Romain Gasser
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Dani Vézina
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Sai Priya Anand
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | | | | | - Shilei Ding
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - William D Tolbert
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Michael W Grunst
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yuxia Bo
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan Richard
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Fei Zhou
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rick K Huang
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lothar Esser
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Allison Zeher
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Di Xia
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pradeep D Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA.
| | - Andrés Finzi
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada.
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06520, USA.
| |
Collapse
|
7
|
Zhang S, Wang K, Wang WL, Nguyen HT, Chen S, Lu M, Go EP, Ding H, Steinbock RT, Desaire H, Kappes JC, Sodroski J, Mao Y. Asymmetric Structures and Conformational Plasticity of the Uncleaved Full-Length Human Immunodeficiency Virus Envelope Glycoprotein Trimer. J Virol 2021; 95:e0052921. [PMID: 34549974 PMCID: PMC8610584 DOI: 10.1128/jvi.00529-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/06/2021] [Indexed: 11/20/2022] Open
Abstract
The functional human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer [(gp120/gp41)3] is produced by cleavage of a conformationally flexible gp160 precursor. gp160 cleavage or the binding of BMS-806, an entry inhibitor, stabilizes the pretriggered, "closed" (state 1) conformation recognized by rarely elicited broadly neutralizing antibodies. Poorly neutralizing antibodies (pNAbs) elicited at high titers during natural infection recognize more "open" Env conformations (states 2 and 3) induced by binding the receptor, CD4. We found that BMS-806 treatment and cross-linking decreased the exposure of pNAb epitopes on cell surface gp160; however, after detergent solubilization, cross-linked and BMS-806-treated gp160 sampled non-state-1 conformations that could be recognized by pNAbs. Cryo-electron microscopy of the purified BMS-806-bound gp160 revealed two hitherto unknown asymmetric trimer conformations, providing insights into the allosteric coupling between trimer opening and structural variation in the gp41 HR1N region. The individual protomer structures in the asymmetric gp160 trimers resemble those of other genetically modified or antibody-bound cleaved HIV-1 Env trimers, which have been suggested to assume state-2-like conformations. Asymmetry of the uncleaved Env potentially exposes surfaces of the trimer to pNAbs. To evaluate the effect of stabilizing a state-1-like conformation of the membrane Env precursor, we treated cells expressing wild-type HIV-1 Env with BMS-806. BMS-806 treatment decreased both gp160 cleavage and the addition of complex glycans, implying that gp160 conformational flexibility contributes to the efficiency of these processes. Selective pressure to maintain flexibility in the precursor of functional Env allows the uncleaved Env to sample asymmetric conformations that potentially skew host antibody responses toward pNAbs. IMPORTANCE The envelope glycoprotein (Env) trimers on the surface of human immunodeficiency virus (HIV-1) mediate the entry of the virus into host cells and serve as targets for neutralizing antibodies. The functional Env trimer is produced by cleavage of the gp160 precursor in the infected cell. We found that the HIV-1 Env precursor is highly plastic, allowing it to assume different asymmetric shapes. This conformational plasticity is potentially important for Env cleavage and proper modification by sugars. Having a flexible, asymmetric Env precursor that can misdirect host antibody responses without compromising virus infectivity would be an advantage for a persistent virus like HIV-1.
Collapse
Affiliation(s)
- Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Kunyu Wang
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
| | - Wei Li Wang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
- Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Hanh T. Nguyen
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Shuobing Chen
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
| | - Maolin Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Eden P. Go
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Haitao Ding
- Department of Medicine, University of Alabama at Birmingham, Alabama, USA
| | - Robert T. Steinbock
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - John C. Kappes
- Department of Medicine, University of Alabama at Birmingham, Alabama, USA
- Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, Alabama, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing, China
- Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| |
Collapse
|
8
|
Ratnapriya S, Harris M, Chov A, Herbert ZT, Vrbanac V, Deruaz M, Achuthan V, Engelman AN, Sodroski J, Herschhorn A. Intra- and extra-cellular environments contribute to the fate of HIV-1 infection. Cell Rep 2021; 36:109622. [PMID: 34469717 PMCID: PMC8463096 DOI: 10.1016/j.celrep.2021.109622] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 06/07/2021] [Accepted: 08/06/2021] [Indexed: 11/18/2022] Open
Abstract
HIV-1 entry into host cells leads to one of the following three alternative fates: (1) HIV-1 elimination by restriction factors, (2) establishment of HIV-1 latency, or (3) active viral replication in target cells. Here, we report the development of an improved system for monitoring HIV-1 fate at single-cell and population levels and show the diverse applications of this system to study specific aspects of HIV-1 fate in different cell types and under different environments. An analysis of the transcriptome of infected, primary CD4+ T cells that support alternative fates of HIV-1 identifies differential gene expression signatures in these cells. Small molecules are able to selectively target cells that support viral replication with no significant effect on viral latency. In addition, HIV-1 fate varies in different tissues following infection of humanized mice in vivo. Altogether, these studies indicate that intra- and extra-cellular environments contribute to the fate of HIV-1 infection.
Collapse
Affiliation(s)
- Sneha Ratnapriya
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Miranda Harris
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Angela Chov
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Zachary T Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Vladimir Vrbanac
- Humanized Immune System Mouse Program, Ragon Institute of MGH, MIT and Harvard, and Center for Immunology and Inflammatory Disease, Cambridge, MA 02139, USA
| | - Maud Deruaz
- Humanized Immune System Mouse Program, Ragon Institute of MGH, MIT and Harvard, and Center for Immunology and Inflammatory Disease, Cambridge, MA 02139, USA
| | - Vasudevan Achuthan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Alon Herschhorn
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA.
| |
Collapse
|
9
|
Go EP, Zhang S, Ding H, Kappes JC, Sodroski J, Desaire H. The opportunity cost of automated glycopeptide analysis: case study profiling the SARS-CoV-2 S glycoprotein. Anal Bioanal Chem 2021; 413:7215-7227. [PMID: 34448030 PMCID: PMC8390178 DOI: 10.1007/s00216-021-03621-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/29/2021] [Accepted: 08/16/2021] [Indexed: 11/29/2022]
Abstract
Glycosylation analysis of viral glycoproteins contributes significantly to vaccine design and development. Among other benefits, glycosylation analysis allows vaccine developers to assess the impact of construct design or producer cell line choices for vaccine production, and it is a key measure by which glycoproteins that are produced for use in vaccination can be compared to their native viral forms. Because many viral glycoproteins are multiply glycosylated, glycopeptide analysis is a preferrable approach for mapping the glycans, yet the analysis of glycopeptide data can be cumbersome and requires the expertise of an experienced analyst. In recent years, a commercial software product, Byonic, has been implemented in several instances to facilitate glycopeptide analysis on viral glycoproteins and other glycoproteomics data sets, and the purpose of the study herein is to determine the strengths and limitations of using this software, particularly in cases relevant to vaccine development. The glycopeptides from a recombinantly expressed trimeric S glycoprotein of the SARS-CoV-2 virus were first analyzed using an expert-based analysis strategy; subsequently, analysis of the same data set was completed using Byonic. Careful assessment of instances where the two methods produced different results revealed that the glycopeptide assignments from Byonic contained more false positives than true positives, even when the data were assessed using a 1% false discovery rate. The work herein provides a roadmap for removing the spurious assignments that Byonic generates, and it provides an assessment of the opportunity cost for relying on automated assignments for glycopeptide data sets from viral glycoproteins.
Collapse
Affiliation(s)
- Eden P Go
- Department of Chemistry, University of Kansas, Lawrence, KS, 66049, USA
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, 02215, USA
| | - Haitao Ding
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - John C Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.,Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, AL, 35233, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, 02215, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, KS, 66049, USA.
| |
Collapse
|
10
|
Li W, Chen Y, Prévost J, Ullah I, Lu M, Gong SY, Tauzin A, Gasser R, Vézina D, Anand SP, Goyette G, Chaterjee D, Ding S, Tolbert WD, Grunst MW, Bo Y, Zhang S, Richard J, Zhou F, Huang RK, Esser L, Zeher A, Côté M, Kumar P, Sodroski J, Xia D, Uchil PD, Pazgier M, Finzi A, Mothes W. Structural Basis and Mode of Action for Two Broadly Neutralizing Antibodies Against SARS-CoV-2 Emerging Variants of Concern. bioRxiv 2021:2021.08.02.454546. [PMID: 34373853 PMCID: PMC8351775 DOI: 10.1101/2021.08.02.454546] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Emerging variants of concern for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can transmit more efficiently and partially evade protective immune responses, thus necessitating continued refinement of antibody therapies and immunogen design. Here we elucidate the structural basis and mode of action for two potent SARS-CoV-2 Spike (S) neutralizing monoclonal antibodies CV3-1 and CV3-25 that remained effective against emerging variants of concern in vitro and in vivo. CV3-1 bound to the (485-GFN-487) loop within the receptor-binding domain (RBD) in the "RBD-up" position and triggered potent shedding of the S1 subunit. In contrast, CV3-25 inhibited membrane fusion by binding to an epitope in the stem helix region of the S2 subunit that is highly conserved among β-coronaviruses. Thus, vaccine immunogen designs that incorporate the conserved regions in RBD and stem helix region are candidates to elicit pan-coronavirus protective immune responses.
Collapse
Affiliation(s)
- Wenwei Li
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Yaozong Chen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Jérémie Prévost
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Irfan Ullah
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520
| | - Maolin Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Shang Yu Gong
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Alexandra Tauzin
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Romain Gasser
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Dani Vézina
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Sai Priya Anand
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | | | | | - Shilei Ding
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - William D. Tolbert
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Michael W. Grunst
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Yuxia Bo
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Jonathan Richard
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Fei Zhou
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rick K. Huang
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lothar Esser
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Allison Zeher
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, and Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Di Xia
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pradeep D. Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| |
Collapse
|
11
|
Rajashekar JK, Richard J, Beloor J, Prévost J, Anand SP, Beaudoin-Bussières G, Shan L, Herndler-Brandstetter D, Gendron-Lepage G, Medjahed H, Bourassa C, Gaudette F, Ullah I, Symmes K, Peric A, Lindemuth E, Bibollet-Ruche F, Park J, Chen HC, Kaufmann DE, Hahn BH, Sodroski J, Pazgier M, Flavell RA, Smith AB, Finzi A, Kumar P. Modulating HIV-1 envelope glycoprotein conformation to decrease the HIV-1 reservoir. Cell Host Microbe 2021; 29:904-916.e6. [PMID: 34019804 PMCID: PMC8214472 DOI: 10.1016/j.chom.2021.04.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 02/01/2021] [Accepted: 04/20/2021] [Indexed: 11/21/2022]
Abstract
Small CD4-mimetic compounds (CD4mc) sensitize HIV-1-infected cells to antibody-dependent cellular cytotoxicity (ADCC) by facilitating antibody recognition of epitopes that are otherwise occluded on the unliganded viral envelope (Env). Combining CD4mc with two families of CD4-induced (CD4i) antibodies, which are frequently found in plasma of HIV-1-infected individuals, stabilizes Env in a conformation that is vulnerable to ADCC. We employed new-generation SRG-15 humanized mice, supporting natural killer (NK) cell and Fc-effector functions to demonstrate that brief treatment with CD4mc and CD4i-Abs significantly decreases HIV-1 replication, the virus reservoir and viral rebound after ART interruption. These effects required Fc-effector functions and NK cells, highlighting the importance of ADCC. Viral rebound was also suppressed in HIV-1+-donor cell-derived humanized mice supplemented with autologous HIV-1+-donor-derived plasma and CD4mc. These results indicate that CD4mc could have therapeutic utility in infected individuals for decreasing the size of the HIV-1 reservoir and/or achieving a functional cure.
Collapse
Affiliation(s)
- Jyothi K Rajashekar
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Canada
| | - Jagadish Beloor
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Canada
| | - Sai Priya Anand
- Centre de Recherche du CHUM, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University Montreal, Montreal, QC, Canada
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Canada
| | - Liang Shan
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | | | | | | | | | | | - Irfan Ullah
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Kelly Symmes
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew Peric
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Emily Lindemuth
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Frederic Bibollet-Ruche
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jun Park
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Hung-Ching Chen
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM, Montreal, QC, Canada; Department of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, and Department of Microbiology and Immunobiology, Division of AIDS, Harvard Medical School, Boston, MA, USA; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Marzena Pazgier
- Infectious Diseases Division, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
| | - Amos B Smith
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA.
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Canada; Department of Microbiology and Immunology, McGill University Montreal, Montreal, QC, Canada.
| | - Priti Kumar
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA.
| |
Collapse
|
12
|
Zhang S, Go EP, Ding H, Anang S, Kappes JC, Desaire H, Sodroski J. Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. bioRxiv 2021. [PMID: 33821278 PMCID: PMC8020978 DOI: 10.1101/2021.04.01.438120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The SARS-CoV-2 coronavirus, the etiologic agent of COVID-19, uses its spike (S) glycoprotein anchored in the viral membrane to enter host cells. The S glycoprotein is the major target for neutralizing antibodies elicited by natural infection and by vaccines. Approximately 35% of the SARS-CoV-2 S glycoprotein consists of carbohydrate, which can influence virus infectivity and susceptibility to antibody inhibition. We found that virus-like particles produced by coexpression of SARS-CoV-2 S, M, E and N proteins contained spike glycoproteins that were extensively modified by complex carbohydrates. We used a fucose-selective lectin to enrich the Golgi-resident fraction of a wild-type SARS-CoV-2 S glycoprotein trimer, and determined its glycosylation and disulfide bond profile. Compared with soluble or solubilized S glycoproteins modified to prevent proteolytic cleavage and to retain a prefusion conformation, more of the wild-type S glycoprotein N-linked glycans are processed to complex forms. Even Asn 234, a significant percentage of which is decorated by high-mannose glycans on soluble and virion S trimers, is predominantly modified in the Golgi by processed glycans. Three incompletely occupied sites of O-linked glycosylation were detected. Viruses pseudotyped with natural variants of the serine/threonine residues implicated in O-linked glycosylation were generally infectious and exhibited sensitivity to neutralization by soluble ACE2 and convalescent antisera comparable to that of the wild-type virus. Unlike other natural cysteine variants, a Cys15Phe (C15F) mutant retained partial, but unstable, infectivity. These findings enhance our understanding of the Golgi processing of the native SARS-CoV-2 S glycoprotein carbohydrates and could assist the design of interventions.
Collapse
|
13
|
Nguyen HT, Zhang S, Wang Q, Anang S, Wang J, Ding H, Kappes JC, Sodroski J. Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. J Virol 2021; 95:JVI.02304-20. [PMID: 33310888 PMCID: PMC8092844 DOI: 10.1128/jvi.02304-20] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 01/06/2023] Open
Abstract
SARS-CoV-2, a betacoronavirus, is the cause of the COVID-19 pandemic. The SARS-CoV-2 spike (S) glycoprotein trimer mediates virus entry into host cells and cytopathic effects (syncytium formation). We studied the contribution of several S glycoprotein features to these functions, focusing on those that differ among related coronaviruses. Acquisition of the furin cleavage site by the SARS-CoV-2 S glycoprotein decreased virus stability and infectivity, but greatly enhanced syncytium-forming ability. Notably, the D614G change found in globally predominant SARS-CoV-2 strains increased infectivity, modestly enhanced responsiveness to the ACE2 receptor and susceptibility to neutralizing sera, and tightened association of the S1 subunit with the trimer. Apparently, these two features of the SARS-CoV-2 S glycoprotein, the furin cleavage site and D614G, have evolved to balance virus infectivity, stability, cytopathicity and antibody vulnerability. Although the endodomain (cytoplasmic tail) of the S2 subunit was not absolutely required for virus entry or syncytium formation, alteration of palmitoylated cysteine residues in the cytoplasmic tail decreased the efficiency of these processes. As proteolytic cleavage contributes to the activation of the SARS-CoV-2 S glycoprotein, we evaluated the ability of protease inhibitors to suppress S glycoprotein function. Matrix metalloprotease inhibitors suppressed S-mediated cell-cell fusion, but not virus entry. Synergy between inhibitors of matrix metalloproteases and TMPRSS2 suggests that both host proteases can activate the S glycoprotein during the process of syncytium formation. These results provide insights into SARS-CoV-2 S glycoprotein-host cell interactions that likely contribute to the transmission and pathogenicity of this pandemic agent.IMPORTANCE The development of an effective and durable SARS-CoV-2 vaccine is essential for combating the growing COVID-19 pandemic. The SARS-CoV-2 spike (S) glycoprotein is the main target of neutralizing antibodies elicited during virus infection or following vaccination. Knowledge of the spike glycoprotein evolution, function and interactions with host factors will help researchers to develop effective vaccine immunogens and treatments. Here we identify key features of the spike glycoprotein, including the furin cleavage site and the D614G natural mutation, that modulate viral cytopathic effects, infectivity and sensitivity to inhibition. We also identify two inhibitors of host metalloproteases that block S-mediated cell-cell fusion, a process that contributes to the destruction of the virus-infected cell.
Collapse
Affiliation(s)
- Hanh T Nguyen
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02215, USA
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02215, USA
| | - Qian Wang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02215, USA
| | - Saumya Anang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02215, USA
| | - Jia Wang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02215, USA
| | - Haitao Ding
- Department of Medicine, University of Alabama at Birmingham, AL 35294, USA
- Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, AL 35233, USA
| | - John C Kappes
- Department of Medicine, University of Alabama at Birmingham, AL 35294, USA
- Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, AL 35233, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02215, USA
| |
Collapse
|
14
|
Wang P, Liu L, Nair MS, Yin MT, Luo Y, Wang Q, Yuan T, Mori K, Solis AG, Yamashita M, Garg A, Purpura LJ, Laracy JC, Yu J, Joshua-Tor L, Sodroski J, Huang Y, Ho DD. SARS-CoV-2 neutralizing antibody responses are more robust in patients with severe disease. Emerg Microbes Infect 2020; 9:2091-2093. [PMID: 32930052 PMCID: PMC7534308 DOI: 10.1080/22221751.2020.1823890] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We studied plasma antibody responses of 35 patients about 1 month after SARS-CoV-2 infection. Titers of antibodies binding to the viral nucleocapsid and spike proteins were significantly higher in patients with severe disease. Likewise, mean antibody neutralization titers against SARS-CoV-2 pseudovirus and live virus were higher in the sicker patients, by ∼5-fold and ∼7-fold, respectively. These findings have important implications for those pursuing plasma therapy, isolation of neutralizing monoclonal antibodies, and determinants of immunity.
Collapse
Affiliation(s)
- Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Michael T Yin
- Division of Infectious Diseases, Department of Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yang Luo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Qian Wang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Ting Yuan
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Kanako Mori
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Axel Guzman Solis
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Masahiro Yamashita
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Ankur Garg
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Lawrence J Purpura
- Division of Infectious Diseases, Department of Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Justin C Laracy
- Division of Infectious Diseases, Department of Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jian Yu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Leemor Joshua-Tor
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| |
Collapse
|
15
|
Prévost J, Tolbert WD, Medjahed H, Sherburn RT, Madani N, Zoubchenok D, Gendron-Lepage G, Gaffney AE, Grenier MC, Kirk S, Vergara N, Han C, Mann BT, Chénine AL, Ahmed A, Chaiken I, Kirchhoff F, Hahn BH, Haim H, Abrams CF, Smith AB, Sodroski J, Pazgier M, Finzi A. The HIV-1 Env gp120 Inner Domain Shapes the Phe43 Cavity and the CD4 Binding Site. mBio 2020; 11:e00280-20. [PMID: 32457241 PMCID: PMC7251204 DOI: 10.1128/mbio.00280-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/24/2020] [Indexed: 12/22/2022] Open
Abstract
The HIV-1 envelope glycoproteins (Env) undergo conformational changes upon interaction of the gp120 exterior glycoprotein with the CD4 receptor. The gp120 inner domain topological layers facilitate the transition of Env to the CD4-bound conformation. CD4 engages gp120 by introducing its phenylalanine 43 (Phe43) in a cavity ("the Phe43 cavity") located at the interface between the inner and outer gp120 domains. Small CD4-mimetic compounds (CD4mc) can bind within the Phe43 cavity and trigger conformational changes similar to those induced by CD4. Crystal structures of CD4mc in complex with a modified CRF01_AE gp120 core revealed the importance of these gp120 inner domain layers in stabilizing the Phe43 cavity and shaping the CD4 binding site. Our studies reveal a complex interplay between the gp120 inner domain and the Phe43 cavity and generate useful information for the development of more-potent CD4mc.IMPORTANCE The Phe43 cavity of HIV-1 envelope glycoproteins (Env) is an attractive druggable target. New promising compounds, including small CD4 mimetics (CD4mc), were shown to insert deeply into this cavity. Here, we identify a new network of residues that helps to shape this highly conserved CD4 binding pocket and characterize the structural determinants responsible for Env sensitivity to small CD4 mimetics.
Collapse
Affiliation(s)
- Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - William D Tolbert
- Infectious Diseases Division, Department of Medicine of Uniformed Services, University of the Health Sciences, Bethesda, Maryland, USA
| | | | - Rebekah T Sherburn
- Infectious Diseases Division, Department of Medicine of Uniformed Services, University of the Health Sciences, Bethesda, Maryland, USA
| | - Navid Madani
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Daria Zoubchenok
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | | | - Althea E Gaffney
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Melissa C Grenier
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sharon Kirk
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Natasha Vergara
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Changze Han
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Brendan T Mann
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of the Military Medicine, Bethesda, Maryland, USA
| | - Agnès L Chénine
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of the Military Medicine, Bethesda, Maryland, USA
| | - Adel Ahmed
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Irwin Chaiken
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hillel Haim
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Cameron F Abrams
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Amos B Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Marzena Pazgier
- Infectious Diseases Division, Department of Medicine of Uniformed Services, University of the Health Sciences, Bethesda, Maryland, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| |
Collapse
|
16
|
Ding S, Grenier MC, Tolbert WD, Vézina D, Sherburn R, Richard J, Prévost J, Chapleau JP, Gendron-Lepage G, Medjahed H, Abrams C, Sodroski J, Pazgier M, Smith AB, Finzi A. A New Family of Small-Molecule CD4-Mimetic Compounds Contacts Highly Conserved Aspartic Acid 368 of HIV-1 gp120 and Mediates Antibody-Dependent Cellular Cytotoxicity. J Virol 2019; 93:e01325-19. [PMID: 31554684 PMCID: PMC6880173 DOI: 10.1128/jvi.01325-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 09/18/2019] [Indexed: 12/20/2022] Open
Abstract
The HIV-1 envelope glycoprotein (Env) trimer mediates virus entry into cells. The "closed" conformation of Env is resistant to nonneutralizing antibodies (nnAbs). These antibodies mostly recognize occluded epitopes that can be exposed upon binding of CD4 or small-molecule CD4 mimetics (CD4mc). Here, we describe a new family of small molecules that expose Env to nnAbs and sensitize infected cells to antibody-dependent cellular cytotoxicity (ADCC). These compounds have a limited capacity to inhibit virus infection directly but are able to sensitize viral particles to neutralization by otherwise nonneutralizing antibodies. Structural analysis shows that some analogs of this family of CD4mc engage the gp120 Phe43 cavity by contacting the highly conserved D368 residue, making them attractive scaffolds for drug development.IMPORTANCE HIV-1 has evolved multiple strategies to avoid humoral responses. One efficient mechanism is to keep its envelope glycoprotein (Env) in its "closed" conformation. Here, we report on a new family of small molecules that are able to "open up" Env, thus exposing vulnerable epitopes. This new family of molecules binds in the Phe43 cavity and contacts the highly conserved D368 residue. The structural and biological attributes of molecules of this family make them good candidates for drug development.
Collapse
Affiliation(s)
- Shilei Ding
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Melissa C Grenier
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - William D Tolbert
- Infectious Diseases Division, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Dani Vézina
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Rebekah Sherburn
- Infectious Diseases Division, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Jean-Philippe Chapleau
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | | | | | - Cameron Abrams
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Marzena Pazgier
- Infectious Diseases Division, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Amos B Smith
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| |
Collapse
|
17
|
Alsahafi N, Bakouche N, Kazemi M, Richard J, Ding S, Bhattacharyya S, Das D, Anand SP, Prévost J, Tolbert WD, Lu H, Medjahed H, Gendron-Lepage G, Ortega Delgado GG, Kirk S, Melillo B, Mothes W, Sodroski J, Smith AB, Kaufmann DE, Wu X, Pazgier M, Rouiller I, Finzi A, Munro JB. An Asymmetric Opening of HIV-1 Envelope Mediates Antibody-Dependent Cellular Cytotoxicity. Cell Host Microbe 2019; 25:578-587.e5. [PMID: 30974085 DOI: 10.1016/j.chom.2019.03.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 12/03/2018] [Accepted: 02/28/2019] [Indexed: 10/27/2022]
Abstract
The HIV-1 envelope glycoprotein (Env) (gp120-gp41)3 is the target for neutralizing antibodies and antibody-dependent cellular cytotoxicity (ADCC). HIV-1 Env is flexible, sampling different conformational states. Before engaging CD4, Env adopts a closed conformation (State 1) that is largely antibody resistant. CD4 binding induces an intermediate state (State 2), followed by an open conformation (State 3) that is susceptible to engagement by antibodies that recognize otherwise occluded epitopes. We investigate conformational changes in Env that induce ADCC in the presence of a small-molecule CD4-mimetic compound (CD4mc). We uncover an asymmetric Env conformation (State 2A) recognized by antibodies targeting the conserved gp120 inner domain and mediating ADCC. Sera from HIV+ individuals contain these antibodies, which can stabilize Env State 2A in combination with CD4mc. Additionally, triggering State 2A on HIV-infected primary CD4+ T cells exposes epitopes that induce ADCC. Strategies that induce this Env conformation may represent approaches to fight HIV-1 infection.
Collapse
Affiliation(s)
- Nirmin Alsahafi
- Centre de Recherche du CHUM, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Nordine Bakouche
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Mohsen Kazemi
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Shilei Ding
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Sudipta Bhattacharyya
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Durba Das
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Sai Priya Anand
- Centre de Recherche du CHUM, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - William D Tolbert
- Infectious Diseases Division, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Hong Lu
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, USA
| | | | | | | | - Sharon Kirk
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Bruno Melillo
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Amos B Smith
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada; Department of Medicine, Université de Montréal, Montreal, QC, Canada; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueling Wu
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, USA
| | - Marzena Pazgier
- Infectious Diseases Division, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Isabelle Rouiller
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada.
| | - James B Munro
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.
| |
Collapse
|
18
|
Ding S, Gasser R, Gendron-Lepage G, Medjahed H, Tolbert WD, Sodroski J, Pazgier M, Finzi A. CD4 Incorporation into HIV-1 Viral Particles Exposes Envelope Epitopes Recognized by CD4-Induced Antibodies. J Virol 2019; 93:e01403-19. [PMID: 31484748 PMCID: PMC6819941 DOI: 10.1128/jvi.01403-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 08/29/2019] [Indexed: 12/23/2022] Open
Abstract
CD4 downregulation on infected cells is a highly conserved function of primate lentiviruses. It has been shown to positively impact viral replication by a variety of mechanisms, including enhanced viral release and infectivity, decrease of cell reinfection, and protection from antibody-dependent cellular cytotoxicity (ADCC), which is often mediated by antibodies that require CD4 to change envelope (Env) conformation. Here, we report that incorporation of CD4 into HIV-1 viral particles affects Env conformation resulting in the exposure of occluded epitopes recognized by CD4-induced antibodies. This translates into enhanced neutralization susceptibility by these otherwise nonneutralizing antibodies but is prevented by the HIV-1 Nef accessory protein. Altogether, these findings suggest that another functional consequence of Nef-mediated CD4 downregulation is the protection of viral particles from neutralization by commonly elicited CD4-induced antibodies.IMPORTANCE It has been well established that Env-CD4 complexes expose epitopes recognized by commonly elicited CD4-induced antibodies at the surface of HIV-1-infected cells, rendering them vulnerable to ADCC responses. Here, we show that CD4 incorporation has a profound impact on Env conformation at the surface of viral particles. Incorporated CD4 exposes CD4-induced epitopes on Env, rendering HIV-1 susceptible to neutralization by otherwise nonneutralizing antibodies.
Collapse
Affiliation(s)
- Shilei Ding
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Romain Gasser
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | | | | | - William D Tolbert
- Infectious Diseases Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Marzena Pazgier
- Infectious Diseases Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| |
Collapse
|
19
|
Zhao C, Princiotto AM, Nguyen HT, Zou S, Zhao ML, Zhang S, Herschhorn A, Farrell M, Pahil K, Melillo B, Sambasivarao SV, Abrams C, Smith AB, Madani N, Sodroski J. Strain-Dependent Activation and Inhibition of Human Immunodeficiency Virus Entry by a Specific PF-68742 Stereoisomer. J Virol 2019; 93:e01197-19. [PMID: 31391272 PMCID: PMC6803283 DOI: 10.1128/jvi.01197-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 08/03/2019] [Indexed: 12/27/2022] Open
Abstract
Human immunodeficiency virus (HIV-1) entry into cells is mediated by the viral envelope glycoprotein (Env) trimer, which consists of three gp120 exterior glycoproteins and three gp41 transmembrane glycoproteins. When gp120 binds sequentially to the receptors CD4 and CCR5 on the target cell, the metastable Env trimer is triggered to undergo entry-related conformational changes. PF-68742 is a small molecule that inhibits the infection of a subset of HIV-1 strains by interfering with an Env function other than receptor binding. Determinants of HIV-1 resistance to PF-68742 map to the disulfide loop and fusion peptide of gp41. Of the four possible PF-68742 stereoisomers, only one, MF275, inhibited the infection of CD4-positive CCR5-positive cells by some HIV-1 strains. MF275 inhibition of these HIV-1 strains occurred after CD4 binding but before the formation of the gp41 six-helix bundle. Unexpectedly, MF275 activated the infection of CD4-negative CCR5-positive cells by several HIV-1 strains resistant to the inhibitory effects of the compound in CD4-positive target cells. In contrast to CD4 complementation by CD4-mimetic compounds, activation of CD4-independent infection by MF275 did not depend upon the availability of the gp120 Phe 43 cavity. Sensitivity to inhibitors indicates that MF275-activated virus entry requires formation/exposure of the gp41 heptad repeat (HR1) as well as CCR5 binding. MF275 apparently activates a virus entry pathway parallel to that triggered by CD4 and CD4-mimetic compounds. Strain-dependent divergence in Env conformational transitions allows different outcomes, inhibition or activation, in response to MF275. Understanding the mechanisms of MF275 activity should assist efforts to optimize its utility.IMPORTANCE Envelope glycoprotein (Env) spikes on the surface of human immunodeficiency virus (HIV-1) bind target cell receptors, triggering changes in the shape of Env. We studied a small molecule, MF275, that also induced shape changes in Env. The consequences of MF275 interaction with Env depended on the HIV-1 strain, with infection by some viruses inhibited and infection by other viruses enhanced. These studies reveal the strain-dependent diversity of HIV-1 Envs as they undergo shape changes in proceeding down the entry pathway. Appreciation of this diversity will assist attempts to develop broadly active inhibitors of HIV-1 entry.
Collapse
Affiliation(s)
- Connie Zhao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Amy M Princiotto
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Hanh T Nguyen
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Shitao Zou
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Meiqing Lily Zhao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Alon Herschhorn
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Mark Farrell
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Karanbir Pahil
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Bruno Melillo
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Somisetti V Sambasivarao
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania, USA
| | - Cameron Abrams
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania, USA
| | - Amos B Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Navid Madani
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| |
Collapse
|
20
|
Wang WL, Yu Z, Castillo-Menendez LR, Sodroski J, Mao Y. Robustness of signal detection in cryo-electron microscopy via a bi-objective-function approach. BMC Bioinformatics 2019; 20:169. [PMID: 30943890 PMCID: PMC6446299 DOI: 10.1186/s12859-019-2714-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/04/2019] [Indexed: 12/22/2022] Open
Abstract
Background The detection of weak signals and selection of single particles from low-contrast micrographs of frozen hydrated biomolecules by cryo-electron microscopy (cryo-EM) represents a major practical bottleneck in cryo-EM data analysis. Template-based particle picking by an objective function using fast local correlation (FLC) allows computational extraction of a large number of candidate particles from micrographs. Another independent objective function based on maximum likelihood estimates (MLE) can be used to align the images and verify the presence of a signal in the selected particles. Despite the widespread applications of the two objective functions, an optimal combination of their utilities has not been exploited. Here we propose a bi-objective function (BOF) approach that combines both FLC and MLE and explore the potential advantages and limitations of BOF in signal detection from cryo-EM data. Results The robustness of the BOF strategy in particle selection and verification was systematically examined with both simulated and experimental cryo-EM data. We investigated how the performance of the BOF approach is quantitatively affected by the signal-to-noise ratio (SNR) of cryo-EM data and by the choice of initialization for FLC and MLE. We quantitatively pinpointed the critical SNR (~ 0.005), at which the BOF approach starts losing its ability to select and verify particles reliably. We found that the use of a Gaussian model to initialize the MLE suppresses the adverse effects of reference dependency in the FLC function used for template-matching. Conclusion The BOF approach, which combines two distinct objective functions, provides a sensitive way to verify particles for downstream cryo-EM structure analysis. Importantly, reference dependency of the FLC does not necessarily transfer to the MLE, enabling the robust detection of weak signals. Our insights into the numerical behavior of the BOF approach can be used to improve automation efficiency in the cryo-EM data processing pipeline for high-resolution structural determination. Electronic supplementary material The online version of this article (10.1186/s12859-019-2714-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Wei Li Wang
- Intel® Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.,State Key Laboratory of Artificial Microstructures and Mesoscopic Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Zhou Yu
- Graduate School of Arts and Sciences, Department of Cellular and Molecular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Luis R Castillo-Menendez
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Youdong Mao
- Intel® Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. .,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA. .,State Key Laboratory of Artificial Microstructures and Mesoscopic Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
| |
Collapse
|
21
|
Zhao C, Princiotto A, Farrell M, Smith III AB, Madani N, Sodroski J. 540. Investigating the Mechanism of a Unique Human Immunodeficiency Virus-1 (HIV-1) Entry Inhibitor, MF275. Open Forum Infect Dis 2018. [PMCID: PMC6255539 DOI: 10.1093/ofid/ofy210.549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Methods Results Conclusion Disclosures
Collapse
Affiliation(s)
- Connie Zhao
- Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Amy Princiotto
- Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mark Farrell
- Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amos B Smith III
- Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Navid Madani
- Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Joseph Sodroski
- Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| |
Collapse
|
22
|
Princiotto AM, Vrbanac VD, Melillo B, Park J, Tager AM, Smith AB, Sodroski J, Madani N. A Small-Molecule CD4-Mimetic Compound Protects Bone Marrow-Liver-Thymus Humanized Mice From HIV-1 Infection. J Infect Dis 2018; 218:471-475. [PMID: 29617845 PMCID: PMC6049021 DOI: 10.1093/infdis/jiy174] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/28/2018] [Indexed: 11/13/2022] Open
Abstract
Background Small-molecule CD4-mimetic compounds (CD4mc) inhibit human immunodeficiency virus (HIV-1) entry by blocking binding to the CD4 receptor and by premature triggering of the viral envelope glycoprotein (Env) spike. Methods The efficacy of a CD4mc in protecting bone marrow-liver-thymus (BLT) humanized mice from vaginal HIV-1 challenge was evaluated. Results Intravaginal application of the CD4mc JP-III-48, either before or simultaneously with virus challenge, protected BLT humanized mice from HIV-1JR-CSF infection in a dose- dependent manner. Conclusion The direct antiviral effects of a CD4mc prevent HIV-1 infection in a murine model of sexual transmission.
Collapse
Affiliation(s)
- Amy M Princiotto
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Vladimir D Vrbanac
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Boston, Massachusetts
| | - Bruno Melillo
- Department of Chemistry, University of Pennsylvania, Philadelphia
| | - Jongwoo Park
- Department of Chemistry, University of Pennsylvania, Philadelphia
| | - Andrew M Tager
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Boston, Massachusetts
| | - Amos B Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Navid Madani
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
23
|
Bowder D, Hollingsead H, Durst K, Hu D, Wei W, Wiggins J, Medjahed H, Finzi A, Sodroski J, Xiang SH. Contribution of the gp120 V3 loop to envelope glycoprotein trimer stability in primate immunodeficiency viruses. Virology 2018; 521:158-168. [PMID: 29936340 PMCID: PMC6053598 DOI: 10.1016/j.virol.2018.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/09/2018] [Accepted: 06/11/2018] [Indexed: 02/06/2023]
Abstract
The V3 loop of the human immunodeficiency virus type 1 (HIV-1) gp120 exterior envelope glycoprotein (Env) becomes exposed after CD4 binding and contacts the coreceptor to mediate viral entry. Prior to CD4 engagement, a hydrophobic patch located at the tip of the V3 loop stabilizes the non-covalent association of gp120 with the Env trimer of HIV-1 subtype B strains. Here, we show that this conserved hydrophobic patch (amino acid residues 307, 309 and 317) contributes to gp120-trimer association in HIV-1 subtype C, HIV-2 and SIV. Changes that reduced the hydrophobicity of these V3 residues resulted in increased gp120 shedding and decreased Env-mediated cell-cell fusion and virus entry in the different primate immunodeficiency viruses tested. Thus, the hydrophobic patch is an evolutionarily conserved element in the tip of the gp120 V3 loop that plays an essential role in maintaining the stability of the pre-triggered Env trimer in diverse primate immunodeficiency viruses. The V3-loop of HIV-1 gp120 contributes to Env trimer stability and viral entry. The hydrophobic patch in the tip of the V3 loop is critical for pre-triggered Env trimer stability. The hydrophobic patch is a conserved motif in primate immunodeficiency viruses.
Collapse
Affiliation(s)
- Dane Bowder
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, United States; School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Haley Hollingsead
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, United States; School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Kate Durst
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, United States; School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Duoyi Hu
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, United States; School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Wenzhong Wei
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, United States; School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Joshua Wiggins
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, United States; School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Halima Medjahed
- Centre de Recherche du CHUM, Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Andrés Finzi
- Centre de Recherche du CHUM, Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, United States; Department of Microbiology and Immunobiology, Division of AIDS, Harvard Medical School, Boston, MA 02215, United States; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, United States
| | - Shi-Hua Xiang
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, United States; School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, United States.
| |
Collapse
|
24
|
Madani N, Princiotto AM, Mach L, Ding S, Prevost J, Richard J, Hora B, Sutherland L, Zhao CA, Conn BP, Bradley T, Moody MA, Melillo B, Finzi A, Haynes BF, Smith Iii AB, Santra S, Sodroski J. A CD4-mimetic compound enhances vaccine efficacy against stringent immunodeficiency virus challenge. Nat Commun 2018; 9:2363. [PMID: 29915222 PMCID: PMC6006336 DOI: 10.1038/s41467-018-04758-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 05/23/2018] [Indexed: 11/09/2022] Open
Abstract
The envelope glycoprotein (Env) trimer ((gp120/gp41)3) mediates human immunodeficiency virus (HIV-1) entry into cells. The “closed,” antibody-resistant Env trimer is driven to more open conformations by binding the host receptor, CD4. Broadly neutralizing antibodies that recognize conserved elements of the closed Env are potentially protective, but are elicited inefficiently. HIV-1 has evolved multiple mechanisms to evade readily elicited antibodies against more open Env conformations. Small-molecule CD4-mimetic compounds (CD4mc) bind the HIV-1 gp120 Env and promote conformational changes similar to those induced by CD4, exposing conserved Env elements to antibodies. Here, we show that a CD4mc synergizes with antibodies elicited by monomeric HIV-1 gp120 to protect monkeys from multiple high-dose intrarectal challenges with a heterologous simian-human immunodeficiency virus (SHIV). The protective immune response persists for at least six months after vaccination. CD4mc should increase the protective efficacy of any HIV-1 Env vaccine that elicits antibodies against CD4-induced conformations of Env. The HIV Env trimer exhibits a closed confirmation and restricts access to known antibody binding sites. Here the authors show that a small-molecule CD4-mimetic compound binds the HIV Env trimer and enhances antibody-mediated protection in a non-human primate model of infection.
Collapse
Affiliation(s)
- Navid Madani
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. .,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA. .,Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, 02115, USA.
| | - Amy M Princiotto
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Linh Mach
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Shilei Ding
- Centre de Recherche du CHUM, Montreal, QC, H2X 0A9, Canada.,Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, H2X 0A9, Canada
| | - Jérémie Prevost
- Centre de Recherche du CHUM, Montreal, QC, H2X 0A9, Canada.,Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, H2X 0A9, Canada
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, QC, H2X 0A9, Canada.,Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, H2X 0A9, Canada
| | - Bhavna Hora
- Department of Medicine, Department of Immunology, Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA
| | - Laura Sutherland
- Department of Medicine, Department of Immunology, Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA
| | - Connie A Zhao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Brandon P Conn
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Todd Bradley
- Department of Medicine, Department of Immunology, Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA
| | - M Anthony Moody
- Department of Medicine, Department of Immunology, Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA
| | - Bruno Melillo
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC, H2X 0A9, Canada.,Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, H2X 0A9, Canada
| | - Barton F Haynes
- Department of Medicine, Department of Immunology, Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710, USA
| | - Amos B Smith Iii
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Sampa Santra
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. .,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA. .,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| |
Collapse
|
25
|
Dong Y, Chen S, Zhang S, Sodroski J, Yang Z, Liu D, Mao Y. Frontispiz: Folding DNA into a Lipid-Conjugated Nanobarrel for Controlled Reconstitution of Membrane Proteins. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201880861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yuanchen Dong
- Department of Cancer Immunology and Virology; Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology; Harvard Medical School; Boston MA 02115 USA
- Intel Parallel Computing Center for Structural Biology; Dana-Farber Cancer Institute; Boston MA 02215 USA
| | - Shuobing Chen
- Intel Parallel Computing Center for Structural Biology; Dana-Farber Cancer Institute; Boston MA 02215 USA
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics; Institute of Condensed Matter and Material Physics; School of Physics, and Center for Quantitative Biology; Peking University; Beijing 100871 China
| | - Shijian Zhang
- Department of Cancer Immunology and Virology; Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology; Harvard Medical School; Boston MA 02115 USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology; Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology; Harvard Medical School; Boston MA 02115 USA
| | - Zhongqiang Yang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education; Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education; Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Youdong Mao
- Department of Cancer Immunology and Virology; Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology; Harvard Medical School; Boston MA 02115 USA
- Intel Parallel Computing Center for Structural Biology; Dana-Farber Cancer Institute; Boston MA 02215 USA
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics; Institute of Condensed Matter and Material Physics; School of Physics, and Center for Quantitative Biology; Peking University; Beijing 100871 China
| |
Collapse
|
26
|
Dong Y, Chen S, Zhang S, Sodroski J, Yang Z, Liu D, Mao Y. Frontispiece: Folding DNA into a Lipid-Conjugated Nanobarrel for Controlled Reconstitution of Membrane Proteins. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/anie.201880861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yuanchen Dong
- Department of Cancer Immunology and Virology; Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology; Harvard Medical School; Boston MA 02115 USA
- Intel Parallel Computing Center for Structural Biology; Dana-Farber Cancer Institute; Boston MA 02215 USA
| | - Shuobing Chen
- Intel Parallel Computing Center for Structural Biology; Dana-Farber Cancer Institute; Boston MA 02215 USA
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics; Institute of Condensed Matter and Material Physics; School of Physics, and Center for Quantitative Biology; Peking University; Beijing 100871 China
| | - Shijian Zhang
- Department of Cancer Immunology and Virology; Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology; Harvard Medical School; Boston MA 02115 USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology; Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology; Harvard Medical School; Boston MA 02115 USA
| | - Zhongqiang Yang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education; Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education; Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Youdong Mao
- Department of Cancer Immunology and Virology; Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology; Harvard Medical School; Boston MA 02115 USA
- Intel Parallel Computing Center for Structural Biology; Dana-Farber Cancer Institute; Boston MA 02215 USA
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics; Institute of Condensed Matter and Material Physics; School of Physics, and Center for Quantitative Biology; Peking University; Beijing 100871 China
| |
Collapse
|
27
|
Lu M, Ma X, Luis R. CM, Ermel U, Daniel S. T, Gorman J, Reichard N, Wang K, Grover J, Finzi A, Munro JB, Kwong PD, Blanchard SC, Sodroski J, Mothes W. Single-Molecule FRET Reveals an Additional Conformational State of HIV-1 Envelope Glycoprotein Critical for Vaccine Design. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
28
|
Dong Y, Chen S, Zhang S, Sodroski J, Yang Z, Liu D, Mao Y. Folding DNA into a Lipid-Conjugated Nanobarrel for Controlled Reconstitution of Membrane Proteins. Angew Chem Int Ed Engl 2018; 57:2072-2076. [PMID: 29266648 DOI: 10.1002/anie.201710147] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 12/06/2017] [Indexed: 12/21/2022]
Abstract
Building upon DNA origami technology, we introduce a method to reconstitute a single membrane protein into a self-assembled DNA nanobarrel that scaffolds a nanodisc-like lipid environment. Compared with the membrane-scaffolding-protein nanodisc technique, our approach gives rise to defined stoichiometry, controlled sizes, as well as enhanced stability and homogeneity in membrane protein reconstitution. We further demonstrate potential applications of the DNA nanobarrels in the structural analysis of membrane proteins.
Collapse
Affiliation(s)
- Yuanchen Dong
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.,Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Shuobing Chen
- Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter and Material Physics, School of Physics, and Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Zhongqiang Yang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.,Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter and Material Physics, School of Physics, and Center for Quantitative Biology, Peking University, Beijing, 100871, China
| |
Collapse
|
29
|
Dong Y, Chen S, Zhang S, Sodroski J, Yang Z, Liu D, Mao Y. Folding DNA into a Lipid-Conjugated Nanobarrel for Controlled Reconstitution of Membrane Proteins. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201710147] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yuanchen Dong
- Department of Cancer Immunology and Virology; Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology; Harvard Medical School; Boston MA 02115 USA
- Intel Parallel Computing Center for Structural Biology; Dana-Farber Cancer Institute; Boston MA 02215 USA
| | - Shuobing Chen
- Intel Parallel Computing Center for Structural Biology; Dana-Farber Cancer Institute; Boston MA 02215 USA
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics; Institute of Condensed Matter and Material Physics; School of Physics, and Center for Quantitative Biology; Peking University; Beijing 100871 China
| | - Shijian Zhang
- Department of Cancer Immunology and Virology; Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology; Harvard Medical School; Boston MA 02115 USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology; Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology; Harvard Medical School; Boston MA 02115 USA
| | - Zhongqiang Yang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education; Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education; Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Youdong Mao
- Department of Cancer Immunology and Virology; Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology; Harvard Medical School; Boston MA 02115 USA
- Intel Parallel Computing Center for Structural Biology; Dana-Farber Cancer Institute; Boston MA 02215 USA
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics; Institute of Condensed Matter and Material Physics; School of Physics, and Center for Quantitative Biology; Peking University; Beijing 100871 China
| |
Collapse
|
30
|
Alam SM, Aussedat B, Vohra Y, Meyerhoff RR, Cale EM, Walkowicz WE, Radakovich NA, Anasti K, Armand L, Parks R, Sutherland L, Scearce R, Joyce MG, Pancera M, Druz A, Georgiev IS, Von Holle T, Eaton A, Fox C, Reed SG, Louder M, Bailer RT, Morris L, Abdool-Karim SS, Cohen M, Liao HX, Montefiori DC, Park PK, Fernández-Tejada A, Wiehe K, Santra S, Kepler TB, Saunders KO, Sodroski J, Kwong PD, Mascola JR, Bonsignori M, Moody MA, Danishefsky S, Haynes BF. Mimicry of an HIV broadly neutralizing antibody epitope with a synthetic glycopeptide. Sci Transl Med 2017; 9:9/381/eaai7521. [PMID: 28298421 DOI: 10.1126/scitranslmed.aai7521] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 08/18/2016] [Accepted: 01/31/2017] [Indexed: 12/20/2022]
Abstract
A goal for an HIV-1 vaccine is to overcome virus variability by inducing broadly neutralizing antibodies (bnAbs). One key target of bnAbs is the glycan-polypeptide at the base of the envelope (Env) third variable loop (V3). We have designed and synthesized a homogeneous minimal immunogen with high-mannose glycans reflective of a native Env V3-glycan bnAb epitope (Man9-V3). V3-glycan bnAbs bound to Man9-V3 glycopeptide and native-like gp140 trimers with similar affinities. Fluorophore-labeled Man9-V3 glycopeptides bound to bnAb memory B cells and were able to be used to isolate a V3-glycan bnAb from an HIV-1-infected individual. In rhesus macaques, immunization with Man9-V3 induced V3-glycan-targeted antibodies. Thus, the Man9-V3 glycopeptide closely mimics an HIV-1 V3-glycan bnAb epitope and can be used to isolate V3-glycan bnAbs.
Collapse
Affiliation(s)
- S Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Baptiste Aussedat
- Department of Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yusuf Vohra
- Department of Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - R Ryan Meyerhoff
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Evan M Cale
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - William E Walkowicz
- Department of Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nathan A Radakovich
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kara Anasti
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Lawrence Armand
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Laura Sutherland
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Richard Scearce
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - M Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marie Pancera
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aliaksandr Druz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivelin S Georgiev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tarra Von Holle
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amanda Eaton
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Christopher Fox
- Infectious Disease Research Institute, Seattle, WA 98102, USA
| | - Steven G Reed
- Infectious Disease Research Institute, Seattle, WA 98102, USA
| | - Mark Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lynn Morris
- National Institute for Communicable Diseases, Johannesburg 2131, South Africa.,Center for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban 4013, South Africa
| | - Salim S Abdool-Karim
- National Institute for Communicable Diseases, Johannesburg 2131, South Africa.,Center for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban 4013, South Africa
| | - Myron Cohen
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Peter K Park
- Department of Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sampa Santra
- Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joseph Sodroski
- Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Samuel Danishefsky
- Department of Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.,Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| |
Collapse
|
31
|
Pancera M, Lai YT, Bylund T, Druz A, Narpala S, O’Dell S, Schön A, Bailer RT, Chuang GY, Geng H, Louder MK, Rawi R, Soumana DI, Finzi A, Herschhorn A, Madani N, Sodroski J, Freire E, Langley DR, Mascola JR, McDermott AB, Kwong PD. Crystal structures of trimeric HIV envelope with entry inhibitors BMS-378806 and BMS-626529. Nat Chem Biol 2017; 13:1115-1122. [PMID: 28825711 PMCID: PMC5676566 DOI: 10.1038/nchembio.2460] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 07/19/2017] [Indexed: 01/27/2023]
Abstract
The HIV-1 envelope (Env) spike is a conformational machine that transitions between prefusion (closed, CD4- and CCR5-bound) and postfusion states to facilitate HIV-1 entry into cells. Although the prefusion closed conformation is a potential target for inhibition, development of small-molecule leads has been stymied by difficulties in obtaining structural information. Here, we report crystal structures at 3.8-Å resolution of an HIV-1-Env trimer with BMS-378806 and a derivative BMS-626529 for which a prodrug version is currently in Phase III clinical trials. Both lead candidates recognized an induced binding pocket that was mostly excluded from solvent and comprised of Env elements from a conserved helix and the β20-21 hairpin. In both structures, the β20-21 region assumed a conformation distinct from prefusion-closed and CD4-bound states. Together with biophysical and antigenicity characterizations, the structures illuminate the allosteric and competitive mechanisms by which these small-molecule leads inhibit CD4-induced structural changes in Env.
Collapse
Affiliation(s)
- Marie Pancera
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Yen-Ting Lai
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Aliaksandr Druz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Sandeep Narpala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Sijy O’Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Arne Schön
- Department of Biology, Johns Hopkins University, Baltimore, Maryland
| | - Robert T. Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Hui Geng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Mark K. Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Djade I. Soumana
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Andrés Finzi
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Alon Herschhorn
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Navid Madani
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ernesto Freire
- Department of Biology, Johns Hopkins University, Baltimore, Maryland
| | - David R. Langley
- Computer Assisted Drug Design, Bristol-Myers Squibb, Research and Development, Wallingford, Connecticut
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Adrian B. McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| |
Collapse
|
32
|
Abstract
The human immunodeficiency virus type 1 (HIV-1) envelope glycoproteins (Env) mediate viral entry and are the sole target of neutralizing antibodies. Recent studies show that the metastable HIV-1 Env trimer can transit among three conformational states: State 1, State 3, and State 2, corresponding to the “closed”, “open” and intermediate conformations, respectively. During virus entry, binding to the CD4 receptor drives Env from state 1 to state 3. In the unliganded Env, transitions from the closed (State 1) conformation are restrained by intramolecular interactions among different Env residues, which regulate HIV-1 Env conformation. Releasing the specific restraints on State 1 Env leads to increased occupancy of State 2, which is a functional conformation on the entry pathway and an obligate intermediate between State 1 and State 3. Frequent sampling of intermediate State 2 allows HIV-1 to infect cells expressing low levels of CD4, and leads to resistance to several broadly neutralizing antibodies as well as small-molecule inhibitors. Recent findings provide new mechanistic insights into the function and inhibition of HIV-1 Env and will contribute to the development of new therapeutic and prophylactic interventions to combat HIV-1.
Collapse
Affiliation(s)
- Alon Herschhorn
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, 02215, MA, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, 02215, MA, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, 02215, MA, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, 02215, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, 02215, MA, USA
| |
Collapse
|
33
|
Espy N, Pacheco B, Sodroski J. Adaptation of HIV-1 to cells with low expression of the CCR5 coreceptor. Virology 2017; 508:90-107. [PMID: 28521215 DOI: 10.1016/j.virol.2017.04.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 04/27/2017] [Accepted: 04/28/2017] [Indexed: 11/19/2022]
Abstract
The binding of the human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer ((gp120/gp41)3) to the receptors CD4 and CCR5 triggers virus entry into host cells. To identify Env regions that respond to CCR5 binding, HIV-1 was serially passaged on a CD4-positive canine cell line expressing progressively lower levels of CCR5. HIV-1 replication was observed in cells expressing ~1300 CCR5 molecules/cell. Env changes that conferred this low-CCR5 replication phenotype were located outside of the known CCR5-binding region of the gp120 Env subunit and did not apparently increase CCR5 binding affinity. The adaptation-associated changes, located in the gp120 α1 helix and in the gp41 HR1 heptad repeat and membrane-proximal external region (MPER), enhanced HIV-1 replication in cells at all levels of CCR5 expression. The adapted Envs exhibited a greater propensity to undergo conformational changes, as evidenced by increased exposure of conserved regions near the CD4- and CCR5-binding sites.
Collapse
Affiliation(s)
- Nicole Espy
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Beatriz Pacheco
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Joseph Sodroski
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
34
|
Ding S, Verly MM, Princiotto A, Melillo B, Moody AM, Bradley T, Easterhoff D, Roger M, Hahn BH, Madani N, Smith AB, Haynes BF, Sodroski J, Finzi A. Short Communication: Small-Molecule CD4 Mimetics Sensitize HIV-1-Infected Cells to Antibody-Dependent Cellular Cytotoxicity by Antibodies Elicited by Multiple Envelope Glycoprotein Immunogens in Nonhuman Primates. AIDS Res Hum Retroviruses 2017; 33:428-431. [PMID: 27846736 DOI: 10.1089/aid.2016.0246] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Recent studies have linked antibody Fc-mediated effector functions with control of human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus infections. Interestingly, the presence of antibodies with potent antibody-dependent cellular cytotoxicity (ADCC) activity in RV144 vaccine trial participants correlated inversely with HIV-1 acquisition risk. These antibodies were recently found to recognize epitopes on the HIV-1 envelope (Env) glycoprotein exposed upon Env-CD4 binding. Accordingly, small-molecule CD4 mimetics (CD4mc) that induce Env to sample the CD4-bound conformation were shown to sensitize HIV-1-infected cells to ADCC mediated by sera from HIV-1-infected individuals. However, it remains unknown whether antibodies elicited through immunization can also mediate CD4mc-induced ADCC. In this study, we tested the capacity of CD4mc to sensitize HIV-1-infected cells to ADCC by sera from Env-vaccinated nonhuman primates using a FACS-based ADCC assay. In parallel, we evaluated the ability of CD4mc to sensitize HIV-1 viral particles to neutralization by sera from these immunized animals. We found that the vaccine-induced antibodies were able to mediate ADCC and viral neutralization in the presence, but not the absence, of CD4mc. Thus, CD4mc are capable of sensitizing HIV-1-infected cells to ADCC and infectious viral particles to neutralization by easy-to-elicit antibodies that are otherwise unable to mediate these activities.
Collapse
Affiliation(s)
- Shilei Ding
- Centre de Recherche du CHUM, Montreal, Canada
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Canada
| | - Myriam M. Verly
- Centre de Recherche du CHUM, Montreal, Canada
- McGill University, Montreal, Canada
| | - Amy Princiotto
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
| | - Bruno Melillo
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anthony M. Moody
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina
| | - Todd Bradley
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina
| | - David Easterhoff
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina
| | - Michel Roger
- Centre de Recherche du CHUM, Montreal, Canada
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Canada
| | - Beatrice H. Hahn
- Department of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Navid Madani
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
| | - Amos B. Smith
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, Canada
- Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Canada
- McGill University, Montreal, Canada
| |
Collapse
|
35
|
Witt KC, Castillo-Menendez L, Ding H, Espy N, Zhang S, Kappes JC, Sodroski J. Antigenic characterization of the human immunodeficiency virus (HIV-1) envelope glycoprotein precursor incorporated into nanodiscs. PLoS One 2017; 12:e0170672. [PMID: 28151945 PMCID: PMC5289478 DOI: 10.1371/journal.pone.0170672] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/09/2017] [Indexed: 01/13/2023] Open
Abstract
The entry of human immunodeficiency virus (HIV-1) into host cells is mediated by the viral envelope glycoproteins (Envs), which are derived by the proteolytic cleavage of a trimeric gp160 Env precursor. The mature Env trimer is a major target for entry inhibitors and vaccine-induced neutralizing antibodies. Env interstrain variability, conformational flexibility and heavy glycosylation contribute to evasion of the host immune response, and create challenges for structural characterization and vaccine development. Here we investigate variables associated with reconstitution of the HIV-1 Env precursor into nanodiscs, nanoscale lipid bilayer discs enclosed by membrane scaffolding proteins. We identified detergents, as well as lipids similar in composition to the viral lipidome, that allowed efficient formation of Env-nanodiscs (Env-NDs). Env-NDs were created with the full-length Env precursor and with an Env precursor with the majority of the cytoplasmic tail intact. The self-association of Env-NDs was decreased by glutaraldehyde crosslinking. The Env-NDs exhibited an antigenic profile expected for the HIV-1 Env precursor. Env-NDs were recognized by broadly neutralizing antibodies. Of note, neutralizing antibody epitopes in the gp41 membrane-proximal external region and in the gp120:gp41 interface were well exposed on Env-NDs compared with Env expressed on cell surfaces. Most Env epitopes recognized by non-neutralizing antibodies were masked on the Env-NDs. This antigenic profile was stable for several days, exhibiting a considerably longer half-life than that of Env solubilized in detergents. Negative selection with weak neutralizing antibodies could be used to improve the antigenic profile of the Env-NDs. Finally, we show that lipid adjuvants can be incorporated into Env-NDs. These results indicate that Env-NDs represent a potentially useful platform for investigating the structural, functional and antigenic properties of the HIV-1 Env trimer in a membrane context.
Collapse
Affiliation(s)
- Kristen C. Witt
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Department of Microbiology & Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | - Luis Castillo-Menendez
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Department of Microbiology & Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | - Haitao Ding
- Departments of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Nicole Espy
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Department of Microbiology & Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | - Shijian Zhang
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Department of Microbiology & Immunobiology, Harvard Medical School, Boston, MA, United States of America
| | - John C. Kappes
- Departments of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States of America
- Birmingham Veterans Affairs Medical Center, Research Service, Birmingham, AL, United States of America
| | - Joseph Sodroski
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Department of Microbiology & Immunobiology, Harvard Medical School, Boston, MA, United States of America
- Department of Immunology & Infectious Diseases, Harvard School of Public Health, Boston, MA, United States of America
- * E-mail:
| |
Collapse
|
36
|
Richard J, Pacheco B, Gohain N, Veillette M, Ding S, Alsahafi N, Tolbert WD, Prévost J, Chapleau JP, Coutu M, Jia M, Brassard N, Park J, Courter JR, Melillo B, Martin L, Tremblay C, Hahn BH, Kaufmann DE, Wu X, Smith AB, Sodroski J, Pazgier M, Finzi A. Co-receptor Binding Site Antibodies Enable CD4-Mimetics to Expose Conserved Anti-cluster A ADCC Epitopes on HIV-1 Envelope Glycoproteins. EBioMedicine 2016; 12:208-218. [PMID: 27633463 PMCID: PMC5078604 DOI: 10.1016/j.ebiom.2016.09.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 09/07/2016] [Accepted: 09/07/2016] [Indexed: 11/06/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) has evolved a sophisticated strategy to conceal conserved epitopes of its envelope glycoproteins (Env) recognized by antibody-dependent cellular cytotoxicity (ADCC)-mediating antibodies. These antibodies, which are present in the sera of most HIV-1-infected individuals, preferentially recognize Env in its CD4-bound conformation. Accordingly, recent studies showed that small CD4-mimetics (CD4mc) able to “push” Env into this conformation sensitize HIV-1-infected cells to ADCC mediated by HIV + sera. Here we test whether CD4mc also expose epitopes recognized by anti-cluster A monoclonal antibodies such as A32, thought to be responsible for the majority of ADCC activity present in HIV + sera and linked to decreased HIV-1 transmission in the RV144 trial. We made the surprising observation that CD4mc are unable to enhance recognition of HIV-1-infected cells by this family of antibodies in the absence of antibodies such as 17b, which binds a highly conserved CD4-induced epitope overlapping the co-receptor binding site (CoRBS). Our results indicate that CD4mc initially open the trimeric Env enough to allow the binding of CoRBS antibodies but not anti-cluster A antibodies. CoRBS antibody binding further opens the trimeric Env, allowing anti-cluster A antibody interaction and sensitization of infected cells to ADCC. Therefore, ADCC responses mediated by cluster A antibodies in HIV-positive sera involve a sequential opening of the Env trimer on the surface of HIV-1-infected cells. The understanding of the conformational changes required to expose these vulnerable Env epitopes might be important in the design of new strategies aimed at fighting HIV-1. CD4-mimetics fail to enhance recognition of infected cells by anti-cluster A antibodies (Abs). Co-receptor binding site Abs in conjunction with CD4-mimetics allow binding of Env by anti-cluster A Abs. Co-receptor binding site Abs help CD4-mimetics sensitize HIV-1-infected cells to ADCC.
HIV-1 developed sophisticated strategies to conceal vulnerable epitopes of its envelope glycoproteins (Env) recognized by antibody-dependent cellular cytotoxicity (ADCC)-mediating antibodies. CD4-mimetics (CD4mc) were shown to sensitize HIV-1-infected cells to ADCC induced by HIV + sera. Here we show that this response requires a sequential opening of Env at the surface of HIV-1-infected cells. Co-receptor binding site antibodies, also present in HIV + sera, are required to expose ADCC-mediating epitopes recognized by anti-cluster A antibodies upon CD4mc addition. The understanding of the conformational changes required to expose anti-cluster A epitopes might be important in the design of new strategies aimed at fighting HIV-1.
Collapse
Affiliation(s)
- Jonathan Richard
- Centre de Recherche du CHUM, QC H2X 0A9, Canada; Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC H2X 0A9, Canada.
| | | | - Neelakshi Gohain
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Maxime Veillette
- Centre de Recherche du CHUM, QC H2X 0A9, Canada; Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Shilei Ding
- Centre de Recherche du CHUM, QC H2X 0A9, Canada; Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Nirmin Alsahafi
- Centre de Recherche du CHUM, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - William D Tolbert
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jérémie Prévost
- Centre de Recherche du CHUM, QC H2X 0A9, Canada; Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Jean-Philippe Chapleau
- Centre de Recherche du CHUM, QC H2X 0A9, Canada; Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | | | - Manxue Jia
- Aaron Diamond AIDS Research Center, Affiliate of the Rockefeller University, New York, NY, USA
| | | | - Jongwoo Park
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Joel R Courter
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Bruno Melillo
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Loïc Martin
- CEA, iBiTecS, Service d'Ingénierie Moléculaire des Protéines, Gif sur Yvette, France
| | - Cécile Tremblay
- Centre de Recherche du CHUM, QC H2X 0A9, Canada; Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6076, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6076, USA
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM, QC H2X 0A9, Canada; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA 02139-3583, USA; Department of Medicine, Université de Montréal, Montreal, QC H3C 3T5, Canada; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueling Wu
- Aaron Diamond AIDS Research Center, Affiliate of the Rockefeller University, New York, NY, USA
| | - Amos B Smith
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Division of AIDS, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Marzena Pazgier
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, QC H2X 0A9, Canada; Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada.
| |
Collapse
|
37
|
Bradley T, Trama A, Tumba N, Gray E, Lu X, Madani N, Jahanbakhsh F, Eaton A, Xia SM, Parks R, Lloyd KE, Sutherland LL, Scearce RM, Bowman CM, Barnett S, Abdool-Karim SS, Boyd SD, Melillo B, Smith AB, Sodroski J, Kepler TB, Alam SM, Gao F, Bonsignori M, Liao HX, Moody MA, Montefiori D, Santra S, Morris L, Haynes BF. Amino Acid Changes in the HIV-1 gp41 Membrane Proximal Region Control Virus Neutralization Sensitivity. EBioMedicine 2016; 12:196-207. [PMID: 27612593 PMCID: PMC5078591 DOI: 10.1016/j.ebiom.2016.08.045] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 08/26/2016] [Accepted: 08/30/2016] [Indexed: 01/21/2023] Open
Abstract
Most HIV-1 vaccines elicit neutralizing antibodies that are active against highly sensitive (tier-1) viruses or rare cases of vaccine-matched neutralization-resistant (tier-2) viruses, but no vaccine has induced antibodies that can broadly neutralize heterologous tier-2 viruses. In this study, we isolated antibodies from an HIV-1-infected individual that targeted the gp41 membrane-proximal external region (MPER) that may have selected single-residue changes in viral variants in the MPER that resulted in neutralization sensitivity to antibodies targeting distal epitopes on the HIV-1 Env. Similarly, a single change in the MPER in a second virus from another infected-individual also conferred enhanced neutralization sensitivity. These gp41 single-residue changes thus transformed tier-2 viruses into tier-1 viruses that were sensitive to vaccine-elicited tier-1 neutralizing antibodies. These data demonstrate that Env amino acid changes within the MPER bnAb epitope of naturally-selected escape viruses can increase neutralization sensitivity to multiple types of neutralizing antibodies, and underscore the critical importance of the MPER for maintaining the integrity of the tier-2 HIV-1 trimer. Amino acid changes in the HIV gp41 MPER can regulate neutralization sensitivity of distal epitopes. MPER antibodies isolated early are resistant to MPER changes that enhance neutralization sensitivity. HIV gp41 MPER is critical for determining overall HIV envelope conformations.
The HIV-1 envelope protein (Env) is the primary target for neutralizing antibodies. Most HIV-1 vaccines elicit neutralizing antibodies that are active against highly neutralization-sensitive (tier-1) or rare vaccine-matched more neutralization-resistant (tier-2) viruses, but no vaccine has induced antibodies that can broadly neutralize heterologous tier-2 viruses. In this study, we identified changes that occurred in two HIV-1-infected individuals in the membrane proximal region of the HIV-1 Env that resulted in neutralization sensitivity to antibodies targeting distal epitopes on the HIV Env. These single-residue changes thus transformed tier-2 viruses into tier-1 viruses, highlighting the importance of MPER residues in maintaining neutralization-resistant virus.
Collapse
Affiliation(s)
- Todd Bradley
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA.
| | - Ashley Trama
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Nancy Tumba
- National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - Elin Gray
- National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Navid Madani
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | - Amanda Eaton
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Shi-Mao Xia
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Krissey E Lloyd
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Laura L Sutherland
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Richard M Scearce
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Cindy M Bowman
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Susan Barnett
- Novartis Vaccines and Diagnostics, Inc., Cambridge, MA, USA
| | - Salim S Abdool-Karim
- Center for AIDS Program of Research in South Africa, University of KwaZulu-Natal, Durban 4013, South Africa; Columbia University, New York, NY 10032, USA
| | | | - Bruno Melillo
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amos B Smith
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joseph Sodroski
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | - S Munir Alam
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Feng Gao
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - David Montefiori
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Sampa Santra
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Lynn Morris
- National Institute for Communicable Diseases, Johannesburg 2131, South Africa; Center for AIDS Program of Research in South Africa, University of KwaZulu-Natal, Durban 4013, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2131, South Africa
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA.
| |
Collapse
|
38
|
Melillo B, Liang S, Park J, Schön A, Courter JR, LaLonde JM, Wendler DJ, Princiotto AM, Seaman MS, Freire E, Sodroski J, Madani N, Hendrickson WA, Smith AB. Small-Molecule CD4-Mimics: Structure-Based Optimization of HIV-1 Entry Inhibition. ACS Med Chem Lett 2016; 7:330-4. [PMID: 26985324 DOI: 10.1021/acsmedchemlett.5b00471] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/13/2016] [Indexed: 11/29/2022] Open
Abstract
The optimization, based on computational, thermodynamic, and crystallographic data, of a series of small-molecule ligands of the Phe43 cavity of the envelope glycoprotein gp120 of human immunodeficiency virus (HIV) has been achieved. Importantly, biological evaluation revealed that the small-molecule CD4 mimics (4-7) inhibit HIV-1 entry into target cells with both significantly higher potency and neutralization breadth than previous congeners, while maintaining high selectivity for the target virus. Their binding mode was characterized via thermodynamic and crystallographic studies.
Collapse
Affiliation(s)
- Bruno Melillo
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | | | - Jongwoo Park
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Arne Schön
- Department
of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joel R. Courter
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Judith M. LaLonde
- Department
of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United States
| | - Daniel J. Wendler
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | | | | | - Ernesto Freire
- Department
of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joseph Sodroski
- Department
of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, United States
| | | | | | - Amos B. Smith
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
39
|
Haynes BF, Shaw GM, Korber B, Kelsoe G, Sodroski J, Hahn BH, Borrow P, McMichael AJ. HIV-Host Interactions: Implications for Vaccine Design. Cell Host Microbe 2016; 19:292-303. [PMID: 26922989 DOI: 10.1016/j.chom.2016.02.002] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Development of an effective AIDS vaccine is a global priority. However, the extreme diversity of HIV type 1 (HIV-1), which is a consequence of its propensity to mutate to escape immune responses, along with host factors that prevent the elicitation of protective immune responses, continue to hinder vaccine development. Breakthroughs in understanding of the biology of the transmitted virus, the structure and nature of its envelope trimer, vaccine-induced CD8 T cell control in primates, and host control of broadly neutralizing antibody elicitation have given rise to new vaccine strategies. Despite this promise, emerging data from preclinical trials reinforce the need for additional insight into virus-host biology in order to facilitate the development of a successful vaccine.
Collapse
Affiliation(s)
- Barton F Haynes
- Department of Medicine, Duke University, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Duke University Human Vaccine Institute, Duke University, Durham, NC 27710, USA.
| | - George M Shaw
- Departments of Medicine and Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Garnett Kelsoe
- Department of Immunology, Duke University, Durham, NC 27710, USA; Duke University Human Vaccine Institute, Duke University, Durham, NC 27710, USA
| | - Joseph Sodroski
- Dana Farber-Cancer Institute, Harvard Medical School, Harvard University, Boston, MA 02215, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| |
Collapse
|
40
|
Richard J, Veillette M, Ding S, Zoubchenok D, Alsahafi N, Coutu M, Brassard N, Park J, Courter JR, Melillo B, Smith AB, Shaw GM, Hahn BH, Sodroski J, Kaufmann DE, Finzi A. Small CD4 Mimetics Prevent HIV-1 Uninfected Bystander CD4 + T Cell Killing Mediated by Antibody-dependent Cell-mediated Cytotoxicity. EBioMedicine 2015; 3:122-134. [PMID: 26870823 PMCID: PMC4739418 DOI: 10.1016/j.ebiom.2015.12.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/07/2015] [Accepted: 12/08/2015] [Indexed: 02/06/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection causes a progressive depletion of CD4 + T cells. Despite its importance for HIV-1 pathogenesis, the precise mechanisms underlying CD4 + T-cell depletion remain incompletely understood. Here we make the surprising observation that antibody-dependent cell-mediated cytotoxicity (ADCC) mediates the death of uninfected bystander CD4 + T cells in cultures of HIV-1-infected cells. While HIV-1-infected cells are protected from ADCC by the action of the viral Vpu and Nef proteins, uninfected bystander CD4 + T cells bind gp120 shed from productively infected cells and are efficiently recognized by ADCC-mediating antibodies. Thus, gp120 shedding represents a viral mechanism to divert ADCC responses towards uninfected bystander CD4 + T cells. Importantly, CD4-mimetic molecules redirect ADCC responses from uninfected bystander cells to HIV-1-infected cells; therefore, CD4-mimetic compounds might have therapeutic utility in new strategies aimed at specifically eliminating HIV-1-infected cells. Gp120 shed from productively-infected cells binds to bystander CD4 + T cells. Gp120-coated bystander cells are highly sensitivity to ADCC responses mediated by CD4-induced antibodies. Small-molecule CD4-mimetics redirect CD4-induced antibodies to HIV-1-infected cells.
The hallmark of human immunodeficiency virus type 1 (HIV-1) infection is the progressive depletion of CD4 + T cells. Using cultures of HIV-1-infected cells, we observed that a part of the machinery that the virus uses to infect cells (gp120) binds to uninfected cells. Antibodies elicited during the course of the infection against the gp120 can recognize uninfected cells and redirect an immune response to them that results in their elimination. Importantly, this phenomenon can be blocked with a small CD4-mimetic compound that abrogates the binding of gp120 to uninfected cells and redirects the immune system to infected cells.
Collapse
Affiliation(s)
- Jonathan Richard
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Maxime Veillette
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Shilei Ding
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Daria Zoubchenok
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Nirmin Alsahafi
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Mathieu Coutu
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | | | - Jongwoo Park
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Joel R Courter
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Bruno Melillo
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Amos B Smith
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - George M Shaw
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6076, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6076, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology and Immunobiology, Division of AIDS, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA 02139-3583, USA; Department of Medicine, Université de Montréal, Montreal, QC H3C 3T5, Canada; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada.
| |
Collapse
|
41
|
Sodroski J, Wyatt R, Olshevsky U, Olshevsky V, Moore J. Conformation of the HIV-1 gp120 Envelope Glycoprotein. Antibiotics and Chemotherapy 2015. [DOI: 10.1159/000425175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
42
|
Pancera M, Druz A, Zhou T, O'Dell S, Louder M, Madani N, Herschhorn A, Sodroski J, Mascola JR, Kwong PD. Structure of BMS-806, a Small-molecule HIV-1 Entry Inhibitor, Bound to BG505 SOSIP.664 HIV-1 Env Trimer. AIDS Res Hum Retroviruses 2014. [DOI: 10.1089/aid.2014.5307c.abstract] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Marie Pancera
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Aliaksandr Druz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Mark Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Navid Madani
- Dana Farber Cancer Institute, Boston, MA, United States
| | | | | | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
43
|
Haim H, Salas I, McGee K, Eichelberger N, Winter E, Pacheco B, Sodroski J. Modeling virus- and antibody-specific factors to predict human immunodeficiency virus neutralization efficiency. Cell Host Microbe 2014; 14:547-58. [PMID: 24237700 DOI: 10.1016/j.chom.2013.10.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 08/14/2013] [Accepted: 10/16/2013] [Indexed: 10/26/2022]
Abstract
Efforts to prevent human immunodeficiency virus type 1 (HIV-1) infection would benefit from understanding the factors that govern virus neutralization by antibodies. We present a mechanistic model for HIV-1 neutralization that includes both virus and antibody parameters. Variations in epitope integrity on the viral envelope glycoprotein (Env) trimer and Env reactivity to bound antibody influence neutralization susceptibility. In addition, we define an antibody-specific parameter, the perturbation factor (PF), that describes the degree of conformational change in the Env trimer required for a given antibody to bind. Minimally perturbing (low-PF) antibodies can efficiently neutralize viruses with a broad range of Env reactivities due to fast on-rates and high affinity for Env. Highly perturbing (high-PF) antibodies inhibit only viruses with reactive (perturbation-sensitive) Envs, often through irreversible mechanisms. Accounting for these quantifiable viral and antibody-associated parameters helps to predict the observed profiles of HIV-1 neutralization by antibodies with a wide range of potencies.
Collapse
Affiliation(s)
- Hillel Haim
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02215, USA; Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | | | | | | | | | | | | |
Collapse
|
44
|
Courter JR, Madani N, Sodroski J, Schön A, Freire E, Kwong PD, Hendrickson WA, Chaiken IM, LaLonde JM, Smith AB. Structure-based design, synthesis and validation of CD4-mimetic small molecule inhibitors of HIV-1 entry: conversion of a viral entry agonist to an antagonist. Acc Chem Res 2014; 47:1228-37. [PMID: 24502450 PMCID: PMC3993944 DOI: 10.1021/ar4002735] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
This
Account provides an overview of a multidisciplinary consortium focused
on structure-based strategies to devise small molecule antagonists
of HIV-1 entry into human T-cells, which if successful would hold
considerable promise for the development of prophylactic modalities
to prevent HIV transmission and thereby alter the course of the AIDS
pandemic. Entry of the human immunodeficiency virus (HIV) into
target T-cells entails an interaction between CD4 on the host T-cell
and gp120, a component of the trimeric envelope glycoprotein spike
on the virion surface. The resultant interaction initiates a series
of conformational changes within the envelope spike that permits binding
to a chemokine receptor, formation of the gp41 fusion complex, and
cell entry. A hydrophobic cavity at the CD4–gp120 interface,
defined by X-ray crystallography, provided an initial site for small
molecule antagonist design. This site however has evolved to facilitate
viral entry. As such, the binding of prospective small molecule inhibitors
within this gp120 cavity can inadvertently trigger an allosteric entry
signal. Structural characterization of the CD4–gp120
interface, which provided the foundation for small molecule structure-based
inhibitor design, will be presented first. An integrated approach
combining biochemical, virological, structural, computational, and
synthetic studies, along with a detailed analysis of ligand binding
energetics, revealed that modestly active small molecule inhibitors
of HIV entry can also promote viral entry into cells lacking the CD4
receptor protein; these competitive inhibitors were termed small molecule
CD4 mimetics. Related congeners were subsequently identified with
both improved binding affinity and more potent viral entry inhibition.
Further assessment of the affinity-enhanced small molecule CD4 mimetics
demonstrated
that premature initiation of conformational change within the viral envelope spike, prior to cell encounter, can lead to irreversible
deactivation of viral entry machinery. Related congeners, which bind the same gp120 site, possess different propensities to elicit the
allosteric response that underlies the undesired enhancement of CD4-independent viral entry. Subsequently, key hotspots in the CD4–gp120 interface were categorized using mutagenesis and isothermal titration calorimetry according to the capacity to increase binding affinity without triggering the allosteric signal. This analysis, combined with cocrystal structures of small molecule viral entry agonists with gp120, led to the development of fully functional antagonists of HIV-1 entry. Additional structure-based design exploiting two hotspots followed by synthesis has now yielded low micromolar inhibitors of viral entry.
Collapse
Affiliation(s)
- Joel R. Courter
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Navid Madani
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, Massachusetts 02115, United States
| | - Joseph Sodroski
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Immunology, Harvard Medical School, Department of Immunology and Infectious Diseases, Harvard School of Public Health, Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts 02115, United States
| | - Arne Schön
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ernesto Freire
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics and Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, United States
| | - Irwin M. Chaiken
- Department of Biochemistry and Molecular
Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Judith M. LaLonde
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United States
| | - Amos B. Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
45
|
LaLonde JM, Le-Khac M, Jones DM, Courter JR, Park J, Schön A, Princiotto AM, Wu X, Mascola JR, Freire E, Sodroski J, Madani N, Hendrickson WA, Smith AB. Structure-Based Design and Synthesis of an HIV-1 Entry Inhibitor Exploiting X-Ray and Thermodynamic Characterization. ACS Med Chem Lett 2013; 4:338-343. [PMID: 23667716 DOI: 10.1021/ml300407y] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The design, synthesis, thermodynamic and crystallographic characterization of a potent, broad spectrum, second-generation HIV-1 entry inhibitor that engages conserved carbonyl hydrogen bonds within gp120 has been achieved. The optimized antagonist exhibits a sub-micromolar binding affinity (110 nM) and inhibits viral entry of clade B and C viruses (IC50 geometric mean titer of 1.7 and 14.0 μM, respectively), without promoting CD4-independent viral entry. thermodynamic signatures indicate a binding preference for the (R,R)-over the (S,S)-enantiomer. The crystal structure of the small molecule-gp120 complex reveals the displacement of crystallographic water and the formation of a hydrogen bond with a backbone carbonyl of the bridging sheet. Thus, structure-based design and synthesis targeting the highly conserved and structurally characterized CD4:gp120 interface is an effective tactic to enhance the neutralization potency of small molecule HIV-1 entry inhibitors.
Collapse
Affiliation(s)
- Judith M. LaLonde
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United
States
| | | | - David M. Jones
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| | - Joel R. Courter
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| | - Jongwoo Park
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| | - Arne Schön
- Department
of Biology, The Johns Hopkins University, Baltimore, Maryland 21218,
United States
| | - Amy M. Princiotto
- Department of Cancer
Immunology and
AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Xueling Wu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda,
Maryland 20892, United States
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda,
Maryland 20892, United States
| | - Ernesto Freire
- Department
of Biology, The Johns Hopkins University, Baltimore, Maryland 21218,
United States
| | - Joseph Sodroski
- Department of Cancer
Immunology and
AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Microbiology and
Immunobiology, Harvard Medical School; Department of Immunology and
Infectious Diseases, Harvard School of Public Health; Ragon Institute
of MGH, MIT, and Harvard, Boston, Massachusetts 02115, United States
| | - Navid Madani
- Department of Cancer
Immunology and
AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Wayne A. Hendrickson
- Department of Physiology and
Cellular Biophysics, Columbia University, New York, New York 10032, United States
| | - Amos B. Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
19104, United States
| |
Collapse
|
46
|
Xiang SH, Pacheco B, Bowder D, Yuan W, Sodroski J. Characterization of a dual-tropic human immunodeficiency virus (HIV-1) strain derived from the prototypical X4 isolate HXBc2. Virology 2013; 438:5-13. [PMID: 23369572 DOI: 10.1016/j.virol.2013.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 12/21/2012] [Accepted: 01/02/2013] [Indexed: 11/25/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) coreceptor usage and tropism can be modulated by the V3 loop sequence of the gp120 exterior envelope glycoprotein. For coreceptors, R5 viruses use CCR5, X4 viruses use CXCR4, and dual-tropic (R5X4) viruses use either CCR5 or CXCR4. To understand the requirements for dual tropism, we derived and analyzed a dual-tropic variant of an X4 virus. Changes in the V3 base, which allow gp120 to interact with the tyrosine-sulfated CCR5 N-terminus, and deletion of residues 310/311 in the V3 tip were necessary for efficient CCR5 binding and utilization. Thus, both sets of V3 changes allowed CCR5 utilization with retention of the ability to use CXCR4. We also found that the stable association of gp120 with the trimeric envelope glycoprotein complex in R5X4 viruses, as in X4 viruses, is less sensitive to V3 loop changes than gp120-trimer association in R5 viruses.
Collapse
Affiliation(s)
- Shi-hua Xiang
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute and Department of Microbiology and Immunobiology, Division of AIDS, Harvard Medical School, Boston, MA 02215, USA.
| | | | | | | | | |
Collapse
|
47
|
Zhuang K, Finzi A, Toma J, Frantzell A, Huang W, Sodroski J, Cheng-Mayer C. Identification of interdependent variables that influence coreceptor switch in R5 SHIV(SF162P3N)-infected macaques. Retrovirology 2012; 9:106. [PMID: 23237529 PMCID: PMC3528637 DOI: 10.1186/1742-4690-9-106] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 12/05/2012] [Indexed: 11/18/2022] Open
Abstract
Background We previously reported that adoption of an “open” envelope glycoprotein (Env) to expose the CD4 binding site for efficient receptor binding and infection of cell targets such as macrophages that express low levels of the receptor represents an early event in the process of coreceptor switch in two rapidly progressing (RP) R5 SHIVSF162P3N-infected rhesus macaques, releasing or reducing Env structural constraints that have been suggested to limit the pathways available for a change in coreceptor preference. Here we extended these studies to two additional RP monkeys with coreceptor switch and three without to confirm and identify additional factors that facilitated the process of phenotypic conversion. Results We found that regardless of coreceptor switching, R5 viruses in SHIVSF162P3N-infected RP macaques evolved over time to infect macrophages more efficiently; this was accompanied by increased sCD4 sensitivity, with structural changes in the CD4 binding site, the V3 loop and/or the fusion domain of their Envs that are suggestive of better CD4 contact, CCR5 usage and/or virus fusion. However, sCD4-sensitive variants with improved CD4 binding were observed only in RPs with coreceptor switch. Furthermore, cumulative viral load was higher in RPs with than in those without phenotypic switch, with the latter maintaining a longer period of seroconversion. Conclusions Our data suggest that the increased virus replication in the RPs with R5-to-X4 conversion increased the rate of virus evolution and reduction in the availability of target cells with optimal CD4 expression heightened the competition for binding to the receptor. In the absence of immunological restrictions, variants that adopt an “open” Env to expose the CD4 binding site for better CD4 use are selected, allowing structural changes that confer CXCR4-use to be manifested. Viral load, change in target cell population during the course of infection and host immune response therefore are interdependent variables that influence R5 virus evolution and coreceptor switch in SHIVSF162P3N-infected rhesus macaques. Because an "open" Env conformation also renders the virus more susceptible to antibody neutralization, our findings help to explain the infrequent and late appearance of X4 virus in HIV-1 infection when the immune system deteriorates.
Collapse
Affiliation(s)
- Ke Zhuang
- Aaron Diamond AIDS Research Center, New York, NY, USA
| | | | | | | | | | | | | |
Collapse
|
48
|
Tuzer F, Madani N, Kamanna K, Zentner I, LaLonde J, Holmes A, Upton E, Rajagopal S, McFadden K, Contarino M, Sodroski J, Chaiken I. HIV-1 Env gp120 structural determinants for peptide triazole dual receptor site antagonism. Proteins 2012; 81:271-90. [PMID: 23011758 DOI: 10.1002/prot.24184] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 08/18/2012] [Accepted: 09/03/2012] [Indexed: 11/09/2022]
Abstract
Despite advances in HIV therapy, viral resistance and side-effects with current drug regimens require targeting new components of the virus. Dual antagonist peptide triazoles (PT) are a novel class of HIV-1 inhibitors that specifically target the gp120 component of the viral spike and inhibit its interaction with both of its cell surface protein ligands, namely the initial receptor CD4 and the co-receptor (CCR5/CXCR4), thus preventing viral entry. Following an initial survey of 19 gp120 alanine mutants by ELISA, we screened 11 mutants for their importance in binding to, and inhibition by the PT KR21 using surface plasmon resonance. Key mutants were purified and tested for their effects on the peptide's affinity and its ability to inhibit binding of CD4 and the co-receptor surrogate mAb 17b. Effects of the mutations on KR21 viral neutralization were measured by single-round cell infection assays. Two mutations, D474A and T257A, caused large-scale loss of KR21 binding, as well as losses in both CD4/17b and viral inhibition by KR21. A set of other Ala mutants revealed more moderate losses in direct binding affinity and inhibition sensitivity to KR21. The cluster of sensitive residues defines a PT functional epitope. This site is in a conserved region of gp120 that overlaps the CD4 binding site and is distant from the co-receptor/17b binding site, suggesting an allosteric mode of inhibition for the latter. The arrangement and sequence conservation of the residues in the functional epitope explain the breadth of antiviral activity, and improve the potential for rational inhibitor development.
Collapse
Affiliation(s)
- Ferit Tuzer
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Moody M, Drinker MS, Gurley TC, Amos JD, Eudailey JA, Armand LC, Parks R, Gray ES, Morris L, Finzi A, Yang X, Sodroski J, Liao H, Tomaras GD, Montefiori DC, Haynes BF. Isolation of a clonal lineage of IgA broadly neutralizing antibodies from a chronically infected Tanzanian subject. Retrovirology 2012. [PMCID: PMC3441298 DOI: 10.1186/1742-4690-9-s2-o35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
50
|
LaLonde JM, Kwon YD, Jones DM, Sun AW, Courter JR, Soeta T, Kobayashi T, Princiotto AM, Wu X, Schön A, Freire E, Kwong PD, Mascola JR, Sodroski J, Madani N, Smith AB. Structure-based design, synthesis, and characterization of dual hotspot small-molecule HIV-1 entry inhibitors. J Med Chem 2012; 55:4382-96. [PMID: 22497421 PMCID: PMC3376652 DOI: 10.1021/jm300265j] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cellular infection by HIV-1 is initiated with a binding event between the viral envelope glycoprotein gp120 and the cellular receptor protein CD4. The CD4-gp120 interface is dominated by two hotspots: a hydrophobic gp120 cavity capped by Phe43(CD4) and an electrostatic interaction between residues Arg59(CD4) and Asp368(gp120). The CD4 mimetic small-molecule NBD-556 (1) binds within the gp120 cavity; however, 1 and related congeners demonstrate limited viral neutralization breadth. Herein, we report the design, synthesis, characterization, and X-ray structures of gp120 in complex with small molecules that simultaneously engage both binding hotspots. The compounds specifically inhibit viral infection of 42 tier 2 clades B and C viruses and are shown to be antagonists of entry into CD4-negative cells. Dual hotspot design thus provides both a means to enhance neutralization potency of HIV-1 entry inhibitors and a novel structural paradigm for inhibiting the CD4-gp120 protein-protein interaction.
Collapse
Affiliation(s)
- Judith M. LaLonde
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010
| | - Young Do Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda MD 20892
| | - David M. Jones
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Alexander W. Sun
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Joel R. Courter
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Takahiro Soeta
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Toyoharu Kobayashi
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Amy M. Princiotto
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02115
| | - Xueling Wu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda MD 20892
| | - Arne Schön
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218
| | - Ernesto Freire
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda MD 20892
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda MD 20892
| | - Joseph Sodroski
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02115
- Department of Microbiology and Immunology, Harvard Medical School; Department of Immunology and Infectious Diseases, Harvard School of Public Health; Ragon Institute of MGH, MIT and Harvard, Boston, MA 02115
| | - Navid Madani
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Ave., Boston, MA 02115
| | - Amos B. Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| |
Collapse
|