1
|
Kephart SM, Hom N, Lee KK. Visualizing intermediate stages of viral membrane fusion by cryo-electron tomography. Trends Biochem Sci 2024:S0968-0004(24)00160-9. [PMID: 39054240 DOI: 10.1016/j.tibs.2024.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/07/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024]
Abstract
Protein-mediated membrane fusion is the dynamic process where specialized protein machinery undergoes dramatic conformational changes that drive two membrane bilayers together, leading to lipid mixing and opening of a fusion pore between previously separate membrane-bound compartments. Membrane fusion is an essential stage of enveloped virus entry that results in viral genome delivery into host cells. Recent studies applying cryo-electron microscopy techniques in a time-resolved fashion provide unprecedented glimpses into the interaction of viral fusion proteins and membranes, revealing fusion intermediate states from the initiation of fusion to release of the viral genome. In combination with complementary structural, biophysical, and computation modeling approaches, these advances are shedding new light on the mechanics and dynamics of protein-mediated membrane fusion.
Collapse
Affiliation(s)
- Sally M Kephart
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Nancy Hom
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA; Biological Structure Physics and Design Graduate Program, University of Washington, Seattle, WA, USA.
| |
Collapse
|
2
|
Webb NE, Sevareid CM, Sanchez C, Tobin NH, Aldrovandi GM. Natural Variation in HIV-1 Entry Kinetics Map to Specific Residues and Reveal an Interdependence Between Attachment and Fusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600587. [PMID: 38979136 PMCID: PMC11230229 DOI: 10.1101/2024.06.25.600587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
HIV-1 entry kinetics reflect the fluid motion of the HIV envelope glycoprotein through at least three major structural configurations that drive virus-cell membrane fusion. The lifetime of each state is an important component of potency for inhibitors that target them. We used the time-of-addition inhibitor assay and a novel analytical strategy to define the kinetics of pre-hairpin exposure (using T20) and co-receptor engagement (via. maraviroc), through a characteristic delay metric, across a variety of naturally occurring HIV Env isolates. Among 257 distinct HIV-1 envelope isolates we found a remarkable breadth of T20 and maraviroc delays ranging from as early as 30 seconds to as late as 60 minutes. The most extreme delays were observed among transmission-linked clade C isolates. We identified four single-residue determinants of late T20 and maraviroc delays that are associated with either receptor engagement or gp41 function. Comparison of these delays with T20 sensitivity suggest co-receptor engagement and fusogenic activity in gp41 act cooperatively but sequentially to drive entry. Our findings support current models of entry where co-receptor engagement drives gp41 eclipse and have strong implications for the design of entry inhibitors and antibodies that target transient entry states. Author Summary The first step of HIV-1 infection is entry, where virus-cell membrane fusion is driven by the HIV-1 envelope glycoprotein through a series of conformational changes. Some of the most broadly active entry inhibitors work by binding conformations that exist only transiently during entry. The lifetimes of these states and the kinetics of entry are important elements of inhibitor activity for which little is known. We demonstrate a remarkable range of kinetics among 257 diverse HIV-1 isolates and find that this phenotype is highly flexible, with multiple single-residue determinants. Examination of the kinetics of two conformational landmarks shed light on novel kinetic features that offer new details about the role of co-receptor engagement and provide a framework to explain entry inhibitor synergy.
Collapse
|
3
|
Tam EH, Peng Y, Cheah MXY, Yan C, Xiao T. Neutralizing antibodies to block viral entry and for identification of entry inhibitors. Antiviral Res 2024; 224:105834. [PMID: 38369246 DOI: 10.1016/j.antiviral.2024.105834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 02/20/2024]
Abstract
Neutralizing antibodies (NAbs) are naturally produced by our immune system to combat viral infections. Clinically, neutralizing antibodies with potent efficacy and high specificity have been extensively used to prevent and treat a wide variety of viral infections, including Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), Human Immunodeficiency Virus (HIV), Dengue Virus (DENV) and Hepatitis B Virus (HBV). An overwhelmingly large subset of clinically effective NAbs operates by targeting viral envelope proteins to inhibit viral entry into the host cell. Binding of viral envelope protein to the host receptor is a critical rate limiting step triggering a cascade of downstream events, including endocytosis, membrane fusion and pore formation to allow viral entry. In recent years, improved structural knowledge on these processes have allowed researchers to also leverage NAbs as an indispensable tool in guiding discovery of novel antiviral entry inhibitors, providing drug candidates with high efficacy and pan-genus specificity. This review will summarize the latest progresses on the applications of NAbs as effective entry inhibitors and as important tools to develop antiviral therapeutics by high-throughput drug screenings, rational design of peptidic entry inhibitor mimicking NAbs and in silico computational modeling approaches.
Collapse
Affiliation(s)
- Ee Hong Tam
- School of Biological Sciences, Nanyang Technological University 637551, Singapore; Institute of Structural Biology, Nanyang Technological University 636921, Singapore
| | - Yu Peng
- School of Biological Sciences, Nanyang Technological University 637551, Singapore; Institute of Structural Biology, Nanyang Technological University 636921, Singapore
| | - Megan Xin Yan Cheah
- Institute of Molecular and Cell Biology, A*STAR (Agency of Science, Technology and Research) 138673, Singapore
| | - Chuan Yan
- Institute of Molecular and Cell Biology, A*STAR (Agency of Science, Technology and Research) 138673, Singapore
| | - Tianshu Xiao
- School of Biological Sciences, Nanyang Technological University 637551, Singapore; Institute of Structural Biology, Nanyang Technological University 636921, Singapore.
| |
Collapse
|
4
|
Dam KMA, Fan C, Yang Z, Bjorkman PJ. Intermediate conformations of CD4-bound HIV-1 Env heterotrimers. Nature 2023; 623:1017-1025. [PMID: 37993719 PMCID: PMC10686819 DOI: 10.1038/s41586-023-06639-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/13/2023] [Indexed: 11/24/2023]
Abstract
HIV-1 envelope (Env) exhibits distinct conformational changes in response to host receptor (CD4) engagement. Env, a trimer of gp120 and gp41 heterodimers, has been structurally characterized in a closed, prefusion conformation with closely associated gp120s and coreceptor binding sites on gp120 V3 hidden by V1V2 loops1-4 and in fully saturated CD4-bound open Env conformations with changes including outwardly rotated gp120s and displaced V1V2 loops3-9. To investigate changes resulting from substoichiometric CD4 binding, we solved single-particle cryo-electron microscopy (cryo-EM) structures of soluble, native-like heterotrimeric Envs bound to one or two CD4 molecules. Most of the Env trimers bound to one CD4 adopted the closed, prefusion Env state, with a minority exhibiting a heterogeneous partially open Env conformation. When bound to two CD4s, the CD4-bound gp120s exhibited an open Env conformation including a four-stranded gp120 bridging sheet and displaced gp120 V1V2 loops that expose the coreceptor sites on V3. The third gp120 adopted an intermediate, occluded-open state10 that showed gp120 outward rotation but maintained the prefusion three-stranded gp120 bridging sheet with only partial V1V2 displacement and V3 exposure. We conclude that most of the engagements with one CD4 molecule were insufficient to stimulate CD4-induced conformational changes, whereas binding two CD4 molecules led to Env opening in CD4-bound protomers only. The substoichiometric CD4-bound soluble Env heterotrimer structures resembled counterparts derived from a cryo-electron tomography study of complexes between virion-bound Envs and membrane-anchored CD4 (ref. 11), validating their physiological relevance. Together, these results illuminate intermediate conformations of HIV-1 Env and illustrate its structural plasticity.
Collapse
Affiliation(s)
- Kim-Marie A Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| |
Collapse
|
5
|
Abstract
There are at least 21 families of enveloped viruses that infect mammals, and many contain members of high concern for global human health. All enveloped viruses have a dedicated fusion protein or fusion complex that enacts the critical genome-releasing membrane fusion event that is essential before viral replication within the host cell interior can begin. Because all enveloped viruses enter cells by fusion, it behooves us to know how viral fusion proteins function. Viral fusion proteins are also major targets of neutralizing antibodies, and hence they serve as key vaccine immunogens. Here we review current concepts about viral membrane fusion proteins focusing on how they are triggered, structural intermediates between pre- and postfusion forms, and their interplay with the lipid bilayers they engage. We also discuss cellular and therapeutic interventions that thwart virus-cell membrane fusion.
Collapse
Affiliation(s)
- Judith M White
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia, USA;
| | - Amanda E Ward
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Laura Odongo
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Lukas K Tamm
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| |
Collapse
|
6
|
Su R, Zeng J, Marcink TC, Porotto M, Moscona A, O’Shaughnessy B. Host Cell Membrane Capture by the SARS-CoV-2 Spike Protein Fusion Intermediate. ACS CENTRAL SCIENCE 2023; 9:1213-1228. [PMID: 37396856 PMCID: PMC10255576 DOI: 10.1021/acscentsci.3c00158] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Indexed: 07/04/2023]
Abstract
Cell entry by SARS-CoV-2 is accomplished by the S2 subunit of the spike S protein on the virion surface by capture of the host cell membrane and fusion with the viral envelope. Capture and fusion require the prefusion S2 to transit to its potent fusogenic form, the fusion intermediate (FI). However, the FI structure is unknown, detailed computational models of the FI are unavailable, and the mechanisms and timing of membrane capture and fusion are not established. Here, we constructed a full-length model of the SARS-CoV-2 FI by extrapolating from known SARS-CoV-2 pre- and postfusion structures. In atomistic and coarse-grained molecular dynamics simulations the FI was remarkably flexible and executed giant bending and extensional fluctuations due to three hinges in the C-terminal base. The simulated configurations and their giant fluctuations are quantitatively consistent with SARS-CoV-2 FI configurations measured recently using cryo-electron tomography. Simulations suggested a host cell membrane capture time of ∼2 ms. Isolated fusion peptide simulations identified an N-terminal helix that directed and maintained binding to the membrane but grossly underestimated the binding time, showing that the fusion peptide environment is radically altered when attached to its host fusion protein. The large configurational fluctuations of the FI generated a substantial exploration volume that aided capture of the target membrane, and may set the waiting time for fluctuation-triggered refolding of the FI that draws the viral envelope and host cell membrane together for fusion. These results describe the FI as machinery that uses massive configurational fluctuations for efficient membrane capture and suggest novel potential drug targets.
Collapse
Affiliation(s)
- Rui Su
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Jin Zeng
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Tara C. Marcink
- Department
of Pediatrics, Columbia University Vagelos
College of Physicians & Surgeons, New York, New York 10032, United States
- Center
for Host−Pathogen Interaction, Columbia
University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States
| | - Matteo Porotto
- Department
of Pediatrics, Columbia University Vagelos
College of Physicians & Surgeons, New York, New York 10032, United States
- Center
for Host−Pathogen Interaction, Columbia
University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States
- Department
of Experimental Medicine, University of
Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | - Anne Moscona
- Department
of Pediatrics, Columbia University Vagelos
College of Physicians & Surgeons, New York, New York 10032, United States
- Center
for Host−Pathogen Interaction, Columbia
University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States
- Department
of Microbiology & Immunology, Columbia
University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States
- Department
of Physiology, Columbia University Vagelos
College of Physicians & Surgeons, New York, New York 10032, United States
| | - Ben O’Shaughnessy
- Department
of Chemical Engineering, Columbia University, New York, New York 10027, United States
| |
Collapse
|
7
|
Bruun TUJ, Tang S, Erwin G, Deis L, Fernandez D, Kim PS. Structure-guided stabilization improves the ability of the HIV-1 gp41 hydrophobic pocket to elicit neutralizing antibodies. J Biol Chem 2023; 299:103062. [PMID: 36841484 PMCID: PMC10064241 DOI: 10.1016/j.jbc.2023.103062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023] Open
Abstract
The hydrophobic pocket found in the N-heptad repeat (NHR) region of HIV-1 gp41 is a highly conserved epitope that is the target of various HIV-1-neutralizing monoclonal antibodies. Although the high conservation of the pocket makes it an attractive vaccine candidate, it has been challenging to elicit potent anti-NHR antibodies via immunization. Here, we solved a high-resolution structure of the NHR mimetic IQN17, and, consistent with previous ligand-bound gp41 pocket structures, we observed remarkable conformational plasticity of the pocket. The high malleability of this pocket led us to test whether we could improve the immunogenicity of the gp41 pocket by stabilizing its conformation. We show that the addition of five amino acids at the C terminus of IQN17, to generate IQN22, introduces a stabilizing salt bridge at the base of the peptide that rigidifies the pocket. Mice immunized with IQN22 elicited higher avidity antibodies against the gp41 pocket and a more potent, albeit still weak, neutralizing response against HIV-1 compared with IQN17. Stabilized epitope-focused immunogens could serve as the basis for future HIV-1 fusion-inhibiting vaccines.
Collapse
Affiliation(s)
- Theodora U J Bruun
- Sarafan ChEM-H, Stanford University, Stanford, California, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Shaogeng Tang
- Sarafan ChEM-H, Stanford University, Stanford, California, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Graham Erwin
- Sarafan ChEM-H, Stanford University, Stanford, California, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Lindsay Deis
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Daniel Fernandez
- Sarafan ChEM-H, Stanford University, Stanford, California, USA; Chem-H Macromolecular Structure Knowledge Center (MSKC), Stanford University, Stanford, California, USA
| | - Peter S Kim
- Sarafan ChEM-H, Stanford University, Stanford, California, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA; Chan Zuckerberg Biohub, San Francisco, California, USA.
| |
Collapse
|
8
|
Bell BN, Bruun TUJ, Friedland N, Kim PS. HIV-1 prehairpin intermediate inhibitors show efficacy independent of neutralization tier. Proc Natl Acad Sci U S A 2023; 120:e2215792120. [PMID: 36795752 PMCID: PMC9974412 DOI: 10.1073/pnas.2215792120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023] Open
Abstract
HIV-1 strains are categorized into one of three neutralization tiers based on the relative ease by which they are neutralized by plasma from HIV-1-infected donors not on antiretroviral therapy; tier-1 strains are particularly sensitive to neutralization while tier-2 and tier-3 strains are increasingly difficult to neutralize. Most broadly neutralizing antibodies (bnAbs) previously described target the native prefusion conformation of HIV-1 Envelope (Env), but the relevance of the tiered categories for inhibitors targeting another Env conformation, the prehairpin intermediate, is not well understood. Here, we show that two inhibitors targeting distinct highly conserved regions of the prehairpin intermediate have strikingly consistent neutralization potencies (within ~100-fold for a given inhibitor) against strains in all three neutralization tiers of HIV-1; in contrast, best-in-class bnAbs targeting diverse Env epitopes vary by more than 10,000-fold in potency against these strains. Our results indicate that antisera-based HIV-1 neutralization tiers are not relevant for inhibitors targeting the prehairpin intermediate and highlight the potential for therapies and vaccine efforts targeting this conformation.
Collapse
Affiliation(s)
- Benjamin N. Bell
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Theodora U. J. Bruun
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
| | - Natalia Friedland
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
| | - Peter S. Kim
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
- Chan Zuckerberg Biohub, San Francisco, CA94158
| |
Collapse
|
9
|
Enhancing HIV-1 Neutralization by Increasing the Local Concentration of Membrane-Proximal External Region-Directed Broadly Neutralizing Antibodies. J Virol 2023; 97:e0164722. [PMID: 36541800 PMCID: PMC9888200 DOI: 10.1128/jvi.01647-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Broadly neutralizing antibodies (bNAbs) against the membrane-proximal external region (MPER) of the gp41 component of the human immunodeficiency virus type 1 (HIV-1) envelope (Env) are characterized by long, hydrophobic, heavy chain complementarity-determining region 3s (HCDR3s) that interact with the MPER and some viral membrane lipids to achieve increased local concentrations. Here, we show that increasing the local concentration of MPER-directed bNAbs at the cell surface via binding to the high-affinity Fc receptor FcγRI potentiates their ability to prevent viral entry in a manner analogous to the previously reported observation wherein the lipid-binding activity of MPER bNAbs increases their concentration at the viral surface membrane. However, binding of MPER-directed bNAb 10E8 to FcγRI abolishes the neutralization synergy that is seen with the N-heptad repeat (NHR)-targeting antibody D5_AR and NHR-targeting small molecule enfuvirtide (T20), possibly due to decreased accessibility of the NHR in the FcγRI-10E8-MPER complex. Taken together, our results suggest that lipid-binding activity and FcγRI-mediated potentiation function in concert to improve the potency of MPER-directed bNAbs by increasing their local concentration near the site of viral fusion. Therefore, lipid binding may not be a strict requirement for potent neutralization by MPER-targeting bNAbs, as alternative methods can achieve similar increases in local concentrations while avoiding potential liabilities associated with immunologic host tolerance. IMPORTANCE The trimeric glycoprotein Env, the only viral protein expressed on the surface of HIV-1, is the target of broadly neutralizing antibodies and the focus of most vaccine development efforts. Broadly neutralizing antibodies targeting the membrane proximal external region (MPER) of Env show lipid-binding characteristics, and modulating this interaction affects neutralization. In this study, we tested the neutralization potencies of variants of the MPER-targeting antibody 10E8 with different viral-membrane-binding and host FcγRI-binding capabilities. Our results suggest that binding to both lipid and FcγRI improves the neutralization potency of MPER-directed antibodies by concentrating the antibodies at sites of viral fusion. As such, lipid binding may not be uniquely required for MPER-targeting broadly neutralizing antibodies, as alternative methods to increase local concentration can achieve similar improvements in potency.
Collapse
|
10
|
Dam KMA, Fan C, Yang Z, Bjorkman PJ. Structural characterization of HIV-1 Env heterotrimers bound to one or two CD4 receptors reveals intermediate Env conformations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525985. [PMID: 36747804 PMCID: PMC9900888 DOI: 10.1101/2023.01.27.525985] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
HIV-1 envelope (Env) exhibits distinct conformational changes in response to host receptor (CD4) engagement. Env, a trimer of gp120/gp41 heterodimers, has been structurally characterized in a closed, prefusion conformation with closely associated gp120s and coreceptor binding sites on gp120 V3 hidden by V1V2 loops, and in fully-saturated CD4-bound open Env conformations with changes including outwardly rotated gp120s and displaced V1V2 loops. To investigate changes resulting from sub-stoichiometric CD4 binding, we solved 3.4Å and 3.9Å single-particle cryo-EM structures of soluble, native-like Envs bound to one or two CD4 molecules. Env trimer bound to one CD4 adopted the closed, prefusion Env state. When bound to two CD4s, the CD4-bound gp120s exhibited an open Env conformation including a four-stranded gp120 bridging sheet and displaced gp120 V1V2 loops that expose the coreceptor sites on V3. The third gp120 adopted an intermediate, occluded-open state that included gp120 outward rotation but maintained the prefusion, three-stranded gp120 bridging sheet and showed only partial V1V2 displacement and V3 exposure. We conclude that engagement of one CD4 molecule was insufficient to stimulate CD4-induced conformational changes, while binding two CD4 molecules led to Env opening in CD4-bound protomers only. Together, these results illuminate HIV-1 Env intermediate conformations and illustrate the structural plasticity of HIV-1 Env.
Collapse
Affiliation(s)
- Kim-Marie A Dam
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Present address: Department of Molecular and Cell Biology, University of California, 13 Berkeley, CA 94720, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| |
Collapse
|
11
|
Abstract
Human immunodeficiency virus type 1 (HIV-1) envelope (Env), a heterotrimer of gp120-gp41 subunits, mediates fusion of the viral and host cell membranes after interactions with the host receptor CD4 and a coreceptor. CD4 binding induces rearrangements in Env trimer, resulting in a CD4-induced (CD4i) open Env conformation. Structural studies of antibodies isolated from infected donors have defined antibody-Env interactions, with one class of antibodies specifically recognizing the CD4i open Env conformation. In this study, we characterized a group of monoclonal antibodies isolated from HIV-1 infected donors (V2i MAbs) that displayed characteristics of CD4i antibodies. Binding experiments demonstrated that the V2i MAbs preferentially recognize CD4-bound open Env trimers. Structural characterizations of V2i MAb-Env-CD4 trimer complexes using single-particle cryo-electron microscopy showed recognition by V2i MAbs using different angles of approach to the gp120 V1V2 domain and the β2/β3 strands on a CD4i open conformation Env with no direct interactions of the MAbs with CD4. We also characterized CG10, a CD4i antibody that was raised in mice immunized with a gp120-CD4 complex, bound to an Env trimer plus CD4. CG10 exhibited characteristics similar to those of the V2i antibodies, i.e., recognition of the open Env conformation, but showed direct contacts to both CD4 and gp120. Structural comparisons of these and previously characterized CD4i antibody interactions with Env provide a suggested mechanism for how these antibodies are elicited during HIV-1 infection. IMPORTANCE The RV144 HIV-1 clinical vaccination trial showed modest protection against viral infection. Antibody responses to the V1V2 region of HIV-1 Env gp120 were correlated inversely with the risk of infection, and data from three other clinical vaccine trials suggested a similar signal. In addition, antibodies targeting V1V2 have been correlated with protections from simian immunodeficiency virus (SIV) and simian-human immunodeficiency virus (SHIV) infections in nonhuman primates. We structurally characterized V2i antibodies directed against V1V2 isolated from HIV-1 infected humans in complex with open Env trimers bound to the host receptor CD4. We also characterized a CD4i antibody that interacts with CD4 as well as the gp120 subunit of an open Env trimer. Our study suggests how V2i and CD4i antibodies were elicited during HIV-1 infection.
Collapse
|
12
|
Pang W, Lu Y, Zhao YB, Shen F, Fan CF, Wang Q, He WQ, He XY, Li ZK, Chen TT, Yang CX, Li YZ, Xiao SX, Zhao ZJ, Huang XS, Luo RH, Yang LM, Zhang M, Dong XQ, Li MH, Feng XL, Zhou QC, Qu W, Jiang S, Ouyang S, Zheng YT. A variant-proof SARS-CoV-2 vaccine targeting HR1 domain in S2 subunit of spike protein. Cell Res 2022; 32:1068-1085. [PMID: 36357786 PMCID: PMC9648449 DOI: 10.1038/s41422-022-00746-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022] Open
Abstract
The emerging SARS-CoV-2 variants, commonly with many mutations in S1 subunit of spike (S) protein are weakening the efficacy of the current vaccines and antibody therapeutics. This calls for the variant-proof SARS-CoV-2 vaccines targeting the more conserved regions in S protein. Here, we designed a recombinant subunit vaccine, HR121, targeting the conserved HR1 domain in S2 subunit of S protein. HR121 consisting of HR1-linker1-HR2-linker2-HR1, is conformationally and functionally analogous to the HR1 domain present in the fusion intermediate conformation of S2 subunit. Immunization with HR121 in rabbits and rhesus macaques elicited highly potent cross-neutralizing antibodies against SARS-CoV-2 and its variants, particularly Omicron sublineages. Vaccination with HR121 achieved near-full protections against prototype SARS-CoV-2 infection in hACE2 transgenic mice, Syrian golden hamsters and rhesus macaques, and effective protection against Omicron BA.2 infection in Syrian golden hamsters. This study demonstrates that HR121 is a promising candidate of variant-proof SARS-CoV-2 vaccine with a novel conserved target in the S2 subunit for application against current and future SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Wei Pang
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, China
| | - Ying Lu
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, China
| | - Yan-Bo Zhao
- grid.411503.20000 0000 9271 2478The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian China
| | - Fan Shen
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, China
| | - Chang-Fa Fan
- grid.410749.f0000 0004 0577 6238Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control, Beijing, China
| | - Qian Wang
- grid.8547.e0000 0001 0125 2443Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wen-Qiang He
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, China
| | - Xiao-Yan He
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, China
| | - Ze-Kai Li
- grid.411503.20000 0000 9271 2478The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian China
| | - Tao-Tao Chen
- grid.411503.20000 0000 9271 2478The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian China
| | - Cui-Xian Yang
- grid.508267.eYunnan Provincial Infectious Disease Hospital, Kunming, Yunnan China
| | - You-Zhi Li
- grid.411503.20000 0000 9271 2478The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian China
| | - Si-Xuan Xiao
- grid.411503.20000 0000 9271 2478The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian China
| | - Zu-Jiang Zhao
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, China
| | - Xu-Sheng Huang
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, China
| | - Rong-Hua Luo
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China
| | - Liu-Meng Yang
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China
| | - Mi Zhang
- grid.508267.eYunnan Provincial Infectious Disease Hospital, Kunming, Yunnan China
| | - Xing-Qi Dong
- grid.508267.eYunnan Provincial Infectious Disease Hospital, Kunming, Yunnan China
| | - Ming-Hua Li
- grid.9227.e0000000119573309Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China
| | - Xiao-Li Feng
- grid.9227.e0000000119573309Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China
| | - Qing-Cui Zhou
- grid.9227.e0000000119573309Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China
| | - Wang Qu
- grid.9227.e0000000119573309Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China.
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. .,University of the Chinese Academy of Sciences, Beijing, China. .,Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
| |
Collapse
|
13
|
Yang K, Wang C, Kreutzberger AJB, Ojha R, Kuivanen S, Couoh-Cardel S, Muratcioglu S, Eisen TJ, White KI, Held RG, Subramanian S, Marcus K, Pfuetzner RA, Esquivies L, Doyle CA, Kuriyan J, Vapalahti O, Balistreri G, Kirchhausen T, Brunger AT. Nanomolar inhibition of SARS-CoV-2 infection by an unmodified peptide targeting the prehairpin intermediate of the spike protein. Proc Natl Acad Sci U S A 2022; 119:e2210990119. [PMID: 36122200 PMCID: PMC9546559 DOI: 10.1073/pnas.2210990119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/16/2022] [Indexed: 12/02/2022] Open
Abstract
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available coronavirus disease 2019 vaccines and monoclonal antibody therapies through epitope change on the receptor binding domain of the viral spike glycoprotein. Hence, there is a specific urgent need for alternative antivirals that target processes less likely to be affected by mutation, such as the membrane fusion step of viral entry into the host cell. One such antiviral class includes peptide inhibitors, which block formation of the so-called heptad repeat 1 and 2 (HR1HR2) six-helix bundle of the SARS-CoV-2 spike (S) protein and thus interfere with viral membrane fusion. We performed structural studies of the HR1HR2 bundle, revealing an extended, well-folded N-terminal region of HR2 that interacts with the HR1 triple helix. Based on this structure, we designed an extended HR2 peptide that achieves single-digit nanomolar inhibition of SARS-CoV-2 in cell-based and virus-based assays without the need for modifications such as lipidation or chemical stapling. The peptide also strongly inhibits all major SARS-CoV-2 variants to date. This extended peptide is ∼100-fold more potent than all previously published short, unmodified HR2 peptides, and it has a very long inhibition lifetime after washout in virus infection assays, suggesting that it targets a prehairpin intermediate of the SARS-CoV-2 S protein. Together, these results suggest that regions outside the HR2 helical region may offer new opportunities for potent peptide-derived therapeutics for SARS-CoV-2 and its variants, and even more distantly related viruses, and provide further support for the prehairpin intermediate of the S protein.
Collapse
Affiliation(s)
- Kailu Yang
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Chuchu Wang
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Alex J. B. Kreutzberger
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
| | - Ravi Ojha
- Department of Virology, University of Helsinki, Helsinki 00290, Finland
| | - Suvi Kuivanen
- Department of Virology, University of Helsinki, Helsinki 00290, Finland
| | - Sergio Couoh-Cardel
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Serena Muratcioglu
- HHMI, University of California, Berkeley, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Timothy J. Eisen
- HHMI, University of California, Berkeley, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - K. Ian White
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Richard G. Held
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Subu Subramanian
- HHMI, University of California, Berkeley, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Kendra Marcus
- HHMI, University of California, Berkeley, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Richard A. Pfuetzner
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Luis Esquivies
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Catherine A. Doyle
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22903
| | - John Kuriyan
- HHMI, University of California, Berkeley, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Olli Vapalahti
- Department of Virology, University of Helsinki, Helsinki 00290, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki 00290, Finland
- Helsinki University Hospital Diagnostic Center, Clinical Microbiology, University of Helsinki, Helsinki 00290, Finland
| | | | - Tom Kirchhausen
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Axel T. Brunger
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| |
Collapse
|
14
|
Chiliveri SC, Louis JM, Best RB, Bax A. Real-time Exchange of the Lipid-bound Intermediate and Post-fusion States of the HIV-1 gp41 Ectodomain. J Mol Biol 2022; 434:167683. [PMID: 35700771 PMCID: PMC9378563 DOI: 10.1016/j.jmb.2022.167683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/03/2022] [Accepted: 06/08/2022] [Indexed: 11/17/2022]
Abstract
The envelope glycoprotein gp41 of the HIV-1 virus mediates its entry into the host cell. During this process, gp41 undergoes large conformational changes and the energy released in the remodeling events is utilized to overcome the barrier associated with fusing the viral and host membranes. Although the structural intermediates of this fusion process are attractive targets for drug development, no detailed high-resolution structural information or quantitative thermodynamic characterization are available. By measuring the dynamic equilibrium between the lipid-bound intermediate and the post-fusion six-helical bundle (6HB) states of the gp41 ectodomain in the presence of bilayer membrane mimetics, we derived both the reaction kinetics and energies associated with these two states by solution NMR spectroscopy. At equilibrium, an exchange time constant of about 12 seconds at 38 °C is observed, and the post-fusion conformation is energetically more stable than the lipid-bound state by 3.4 kcal mol-1. The temperature dependence of the kinetics indicates that the folding occurs through a high-energy transition state which may resemble a 5HB structure. The energetics and kinetics of gp41 folding in the context of membrane bilayers provide a molecular basis for an improved understanding of viral membrane fusion.
Collapse
Affiliation(s)
- Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA. https://twitter.com/SaiChiliveri
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
15
|
Marcink TC, Kicmal T, Armbruster E, Zhang Z, Zipursky G, Golub KL, Idris M, Khao J, Drew-Bear J, McGill G, Gallagher T, Porotto M, des Georges A, Moscona A. Intermediates in SARS-CoV-2 spike-mediated cell entry. SCIENCE ADVANCES 2022; 8:eabo3153. [PMID: 35984891 PMCID: PMC9390989 DOI: 10.1126/sciadv.abo3153] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 07/07/2022] [Indexed: 05/17/2023]
Abstract
SARS-CoV-2 cell entry is completed after viral spike (S) protein-mediated membrane fusion between viral and host cell membranes. Stable prefusion and postfusion S structures have been resolved by cryo-electron microscopy and cryo-electron tomography, but the refolding intermediates on the fusion pathway are transient and have not been examined. We used an antiviral lipopeptide entry inhibitor to arrest S protein refolding and thereby capture intermediates as S proteins interact with hACE2 and fusion-activating proteases on cell-derived target membranes. Cryo-electron tomography imaged both extended and partially folded intermediate states of S2, as well as a novel late-stage conformation on the pathway to membrane fusion. The intermediates now identified in this dynamic S protein-directed fusion provide mechanistic insights that may guide the design of CoV entry inhibitors.
Collapse
Affiliation(s)
- Tara C. Marcink
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Thomas Kicmal
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - Emily Armbruster
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, USA
| | - Zhening Zhang
- Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Gillian Zipursky
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Kate L. Golub
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Mohab Idris
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | | | - Jennifer Drew-Bear
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Gael McGill
- Digizyme Inc., Brookline, MA, USA
- Center for Molecular and Cellular Dynamics, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli,” 81100 Caserta, Italy
| | - Amédée des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, USA
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, City University of New York, New York, NY, USA
| | - Anne Moscona
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| |
Collapse
|
16
|
Yang K, Wang C, Kreutzberger AJB, Ojha R, Kuivanen S, Couoh-Cardel S, Muratcioglu S, Eisen TJ, White KI, Held RG, Subramanian S, Marcus K, Pfuetzner RA, Esquivies L, Doyle CA, Kuriyan J, Vapalahti O, Balistreri G, Kirchhausen T, Brunger AT. Nanomolar inhibition of SARS-CoV-2 infection by an unmodified peptide targeting the pre-hairpin intermediate of the spike protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.11.503553. [PMID: 35982670 PMCID: PMC9387137 DOI: 10.1101/2022.08.11.503553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available COVID-19 vaccines and monoclonal antibody therapies through epitope change on the receptor binding domain of the viral spike glycoprotein. Hence, there is a specific urgent need for alternative antivirals that target processes less likely to be affected by mutation, such as the membrane fusion step of viral entry into the host cell. One such antiviral class includes peptide inhibitors which block formation of the so-called HR1HR2 six-helix bundle of the SARS-CoV-2 spike (S) protein and thus interfere with viral membrane fusion. Here we performed structural studies of the HR1HR2 bundle, revealing an extended, well-folded N-terminal region of HR2 that interacts with the HR1 triple helix. Based on this structure, we designed an extended HR2 peptide that achieves single-digit nanomolar inhibition of SARS-CoV-2 in cell-based fusion, VSV-SARS-CoV-2 chimera, and authentic SARS-CoV-2 infection assays without the need for modifications such as lipidation or chemical stapling. The peptide also strongly inhibits all major SARS-CoV-2 variants to date. This extended peptide is ~100-fold more potent than all previously published short, unmodified HR2 peptides, and it has a very long inhibition lifetime after washout in virus infection assays, suggesting that it targets a pre-hairpin intermediate of the SARS-CoV-2 S protein. Together, these results suggest that regions outside the HR2 helical region may offer new opportunities for potent peptide-derived therapeutics for SARS-CoV-2 and its variants, and even more distantly related viruses, and provide further support for the pre-hairpin intermediate of the S protein. Significance Statement SARS-CoV-2 infection requires fusion of viral and host membranes, mediated by the viral spike glycoprotein (S). Due to the importance of viral membrane fusion, S has been a popular target for developing vaccines and therapeutics. We discovered a simple peptide that inhibits infection by all major variants of SARS-CoV-2 with nanomolar efficacies. In marked contrast, widely used shorter peptides that lack a key N-terminal extension are about 100 x less potent than this peptide. Our results suggest that a simple peptide with a suitable sequence can be a potent and cost-effective therapeutic against COVID-19 and they provide new insights at the virus entry mechanism.
Collapse
|
17
|
Raghunath G, Chen YC, Marin M, Wu H, Melikyan GB. SERINC5-Mediated Restriction of HIV-1 Infectivity Correlates with Resistance to Cholesterol Extraction but Not with Lipid Order of Viral Membrane. Viruses 2022; 14:v14081636. [PMID: 35893701 PMCID: PMC9332783 DOI: 10.3390/v14081636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/19/2022] [Accepted: 07/23/2022] [Indexed: 12/13/2022] Open
Abstract
Serine incorporator 5 (SER5) is a protein that upon incorporation into virions inhibits HIV-1 infectivity by interfering with the ability of the Env glycoprotein to promote viral fusion. The mechanisms by which SER5 antagonizes HIV-1 fusion are not well understood. A recent study of SER5's structure revealed a lipid-binding pocket, suggesting the ability to sequester lipids. This finding, along with the well-documented modulation of HIV-1 infectivity by viral lipids, especially cholesterol, prompted our examination of SER5's effect on the general lipid order of the HIV-1 membrane. Pseudoviruses bearing the SER5-sensitive HXB2-Env and containing SER5 or SER2, a control protein that lacks antiviral activity, were analyzed using two distinct lipid-order probes. We show that SER5 incorporation does not noticeably affect the lipid order of pseudoviruses. Although viral cholesterol extraction reduces HIV-1 infectivity, SER5+ viruses are less sensitive to cholesterol extraction than the control samples. In contrast, the virus' sensitivity to cholesterol oxidation was not affected by SER5 incorporation. The hydrolytic release of sphingomyelin-sequestered cholesterol had a minimal impact on the apparent resistance to cholesterol extraction. Based on these results, we propose that a subpopulation of more stable Env glycoproteins responsible for the residual infectivity of SER5+ viruses is less sensitive to the cholesterol content of the viral membrane.
Collapse
Affiliation(s)
- Gokul Raghunath
- Department of Pediatrics, Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA 30322, USA; (G.R.); (Y.-C.C.); (M.M.); (H.W.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Yen-Cheng Chen
- Department of Pediatrics, Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA 30322, USA; (G.R.); (Y.-C.C.); (M.M.); (H.W.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Mariana Marin
- Department of Pediatrics, Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA 30322, USA; (G.R.); (Y.-C.C.); (M.M.); (H.W.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Hui Wu
- Department of Pediatrics, Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA 30322, USA; (G.R.); (Y.-C.C.); (M.M.); (H.W.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Gregory B. Melikyan
- Department of Pediatrics, Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA 30322, USA; (G.R.); (Y.-C.C.); (M.M.); (H.W.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
- Correspondence:
| |
Collapse
|
18
|
Yang K, Wang C, White KI, Pfuetzner RA, Esquivies L, Brunger AT. Structural conservation among variants of the SARS-CoV-2 spike postfusion bundle. Proc Natl Acad Sci U S A 2022; 119:e2119467119. [PMID: 35363556 PMCID: PMC9169775 DOI: 10.1073/pnas.2119467119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/22/2022] [Indexed: 01/10/2023] Open
Abstract
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available COVID-19 vaccines and monoclonal antibody therapies due to structural and dynamic changes of the viral spike glycoprotein (S). The heptad repeat 1 (HR1) and heptad repeat 2 (HR2) domains of S drive virus–host membrane fusion by assembly into a six-helix bundle, resulting in delivery of viral RNA into the host cell. We surveyed mutations of currently reported SARS-CoV-2 variants and selected eight mutations, including Q954H, N969K, and L981F from the Omicron variant, in the postfusion HR1HR2 bundle for functional and structural studies. We designed a molecular scaffold to determine cryogenic electron microscopy (cryo-EM) structures of HR1HR2 at 2.2–3.8 Å resolution by linking the trimeric N termini of four HR1 fragments to four trimeric C termini of the Dps4 dodecamer from Nostoc punctiforme. This molecular scaffold enables efficient sample preparation and structure determination of the HR1HR2 bundle and its mutants by single-particle cryo-EM. Our structure of the wild-type HR1HR2 bundle resolves uncertainties in previously determined structures. The mutant structures reveal side-chain positions of the mutations and their primarily local effects on the interactions between HR1 and HR2. These mutations do not alter the global architecture of the postfusion HR1HR2 bundle, suggesting that the interfaces between HR1 and HR2 are good targets for developing antiviral inhibitors that should be efficacious against all known variants of SARS-CoV-2 to date. We also note that this work paves the way for similar studies in more distantly related viruses.
Collapse
Affiliation(s)
- Kailu Yang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Chuchu Wang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - K. Ian White
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Richard A. Pfuetzner
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Luis Esquivies
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| |
Collapse
|
19
|
Carlon-Andres I, Malinauskas T, Padilla-Parra S. Structure dynamics of HIV-1 Env trimers on native virions engaged with living T cells. Commun Biol 2021; 4:1228. [PMID: 34707229 PMCID: PMC8551276 DOI: 10.1038/s42003-021-02658-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 09/09/2021] [Indexed: 11/29/2022] Open
Abstract
The HIV-1 envelope glycoprotein (Env) mediates viral entry into the host cell. Although the highly dynamic nature of Env intramolecular conformations has been shown with single molecule spectroscopy in vitro, the bona fide Env intra- and intermolecular mechanics when engaged with live T cells remains unknown. We used two photon fast fluorescence lifetime imaging detection of single-molecule Förster Resonance Energy Transfer occurring between fluorescent labels on HIV-1 Env on native virions. Our observations reveal Env dynamics at two levels: transitions between different intramolecular conformations and intermolecular interactions between Env within the viral membrane. Furthermore, we show that three broad neutralizing anti-Env antibodies directed to different epitopes restrict Env intramolecular dynamics and interactions between adjacent Env molecules when engaged with living T cells. Importantly, our results show that Env-Env interactions depend on efficient virus maturation, and that is disrupted upon binding of Env to CD4 or by neutralizing antibodies. Thus, this study illuminates how different intramolecular conformations and distribution of Env molecules mediate HIV-1 Env-T cell interactions in real time and therefore might control immune evasion.
Collapse
Affiliation(s)
- Irene Carlon-Andres
- Department of Infectious Diseases, King's College London, Faculty of Life Sciences & Medicine, London, United Kingdom.
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom.
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
| | - Tomas Malinauskas
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Sergi Padilla-Parra
- Department of Infectious Diseases, King's College London, Faculty of Life Sciences & Medicine, London, United Kingdom.
- Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom.
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
| |
Collapse
|
20
|
Chiliveri SC, Louis JM, Ghirlando R, Bax A. Transient lipid-bound states of spike protein heptad repeats provide insights into SARS-CoV-2 membrane fusion. SCIENCE ADVANCES 2021; 7:eabk2226. [PMID: 34623907 PMCID: PMC8500521 DOI: 10.1126/sciadv.abk2226] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Entry of SARS-CoV-2 into a host cell is mediated by spike, a class I viral fusion protein responsible for merging the viral and host cell membranes. Recent studies have revealed atomic-resolution models for both the postfusion 6-helix bundle (6HB) and the prefusion state of spike. However, a mechanistic understanding of the molecular basis for the intervening structural transition, important for the design of fusion inhibitors, has remained elusive. Using nuclear magnetic resonance spectroscopy and other biophysical methods, we demonstrate the presence of α-helical, membrane-bound, intermediate states of spike’s heptad repeat (HR1 and HR2) domains that are embedded at the lipid-water interface while in a slow dynamic equilibrium with the postfusion 6HB state. These results support a model where the HR domains lower the large energy barrier associated with membrane fusion by destabilizing the host and viral membranes, while 6HB formation actively drives their fusion by forcing physical proximity.
Collapse
Affiliation(s)
- Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Corresponding author. (S.C.C.); (A.B.)
| | - John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Corresponding author. (S.C.C.); (A.B.)
| |
Collapse
|
21
|
Murakami T, Ono A. Roles of Virion-Incorporated CD162 (PSGL-1), CD43, and CD44 in HIV-1 Infection of T Cells. Viruses 2021; 13:v13101935. [PMID: 34696365 PMCID: PMC8541244 DOI: 10.3390/v13101935] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
Nascent HIV-1 particles incorporate the viral envelope glycoprotein and multiple host transmembrane proteins during assembly at the plasma membrane. At least some of these host transmembrane proteins on the surface of virions are reported as pro-viral factors that enhance virus attachment to target cells or facilitate trans-infection of CD4+ T cells via interactions with non-T cells. In addition to the pro-viral factors, anti-viral transmembrane proteins are incorporated into progeny virions. These virion-incorporated transmembrane proteins inhibit HIV-1 entry at the point of attachment and fusion. In infected polarized CD4+ T cells, HIV-1 Gag localizes to a rear-end protrusion known as the uropod. Regardless of cell polarization, Gag colocalizes with and promotes the virion incorporation of a subset of uropod-directed host transmembrane proteins, including CD162, CD43, and CD44. Until recently, the functions of these virion-incorporated proteins had not been clear. Here, we review the recent findings about the roles played by virion-incorporated CD162, CD43, and CD44 in HIV-1 spread to CD4+ T cells.
Collapse
|
22
|
Li S. Cryo-electron tomography of enveloped viruses. Trends Biochem Sci 2021; 47:173-186. [PMID: 34511334 DOI: 10.1016/j.tibs.2021.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Viruses are macromolecular machineries that hijack cellular metabolism for replication. Enveloped viruses comprise a large variety of RNA and DNA viruses, many of which are notorious human or animal pathogens. Despite their importance, the presence of lipid bilayers in their assembly has made most enveloped viruses too pleomorphic to be reconstructed as a whole by traditional structural biology methods. Furthermore, structural biology of the viral lifecycle was hindered by the sample thickness. Here, I review the recent advances in the applications of cryo-electron tomography (cryo-ET) on enveloped viral structures and intracellular viral activities.
Collapse
Affiliation(s)
- Sai Li
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
23
|
HIV-1 entry: Duels between Env and host antiviral transmembrane proteins on the surface of virus particles. Curr Opin Virol 2021; 50:59-68. [PMID: 34390925 DOI: 10.1016/j.coviro.2021.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 12/18/2022]
Abstract
Human Immunodeficiency Virus type-1 (HIV-1) is the causative agent of AIDS. Its entry step is mediated by the envelope glycoprotein (Env). During the entry process, Env vastly changes its conformation. While non-liganded Env tends to have a closed structure, receptor-binding of Env opens its conformation, which leads to virus-cell membrane fusion. Single-molecule fluorescence resonance energy transfer (smFRET) imaging allows observation of these conformational changes on the virion surface. Nascent HIV-1 particles incorporate multiple host transmembrane proteins, some of which inhibit the entry process. The Env structure or its dynamics may determine the effectiveness of these antiviral mechanisms. Here, we review recent findings about the Env conformation changes on virus particles and inhibition of Env activities by virion-incorporated host transmembrane proteins.
Collapse
|
24
|
Rubio AA, Filsinger Interrante MV, Bell BN, Brown CL, Bruun TUJ, LaBranche CC, Montefiori DC, Kim PS. A Derivative of the D5 Monoclonal Antibody That Targets the gp41 N-Heptad Repeat of HIV-1 with Broad Tier-2-Neutralizing Activity. J Virol 2021; 95:e0235020. [PMID: 33980592 PMCID: PMC8274607 DOI: 10.1128/jvi.02350-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/30/2021] [Indexed: 01/11/2023] Open
Abstract
HIV-1 infection is initiated by the viral glycoprotein Env, which, after interaction with cellular coreceptors, adopts a transient conformation known as the prehairpin intermediate (PHI). The N-heptad repeat (NHR) is a highly conserved region of gp41 exposed in the PHI; it is the target of the FDA-approved drug enfuvirtide and of neutralizing monoclonal antibodies (mAbs). However, to date, these mAbs have only been weakly effective against tier-1 HIV-1 strains, which are most sensitive to neutralizing antibodies. Here, we engineered and tested 11 IgG variants of D5, an anti-NHR mAb, by recombining previously described mutations in four of D5's six antibody complementarity-determining regions. One variant, D5_AR, demonstrated 6-fold enhancement in the 50% inhibitory dose (ID50) against lentivirus pseudotyped with HXB2 Env. D5_AR exhibited weak cross-clade neutralizing activity against a diverse set of tier-2 HIV-1 viruses, which are less sensitive to neutralizing antibodies than tier-1 viruses and are the target of current antibody-based vaccine efforts. In addition, the neutralization potency of D5_AR IgG was greatly enhanced in target cells expressing FcγRI, with ID50 values of <0.1 μg/ml; this immunoglobulin receptor is expressed on macrophages and dendritic cells, which are implicated in the early stages of HIV-1 infection of mucosal surfaces. D5 and D5_AR have equivalent neutralization potency in IgG, Fab, and single-chain variable-fragment (scFv) formats, indicating that neutralization is not impacted by steric hindrance. Taken together, these results provide support for vaccine strategies that target the PHI by eliciting antibodies against the gp41 NHR and support investigation of anti-NHR mAbs in nonhuman primate passive immunization studies. IMPORTANCE Despite advances in antiretroviral therapy, HIV remains a global epidemic and has claimed more than 32 million lives. Accordingly, developing an effective HIV vaccine remains an urgent public health need. The gp41 N-heptad repeat (NHR) of the HIV-1 prehairpin intermediate (PHI) is highly conserved (>90%) and is inhibited by the FDA-approved drug enfuvirtide, making it an attractive vaccine target. However, to date, anti-NHR antibodies have not been potent. Here, we engineered D5_AR, a more potent variant of the anti-NHR antibody D5, and established its ability to inhibit HIV-1 strains that are more difficult to neutralize and are more representative of circulating strains (tier-2 strains). The neutralizing activity of D5_AR was greatly potentiated in cells expressing FcγRI; FcγRI is expressed on cells that are implicated at the earliest stages of sexual HIV-1 transmission. Taken together, these results bolster efforts to target the gp41 NHR and the PHI for vaccine development.
Collapse
Affiliation(s)
- Adonis A. Rubio
- Stanford ChEM-H, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University School of Humanities & Sciences, Stanford, California, USA
| | - Maria V. Filsinger Interrante
- Stanford ChEM-H, Stanford University, Stanford, California, USA
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, California, USA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin N. Bell
- Stanford ChEM-H, Stanford University, Stanford, California, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, USA
| | - Clayton L. Brown
- Stanford ChEM-H, Stanford University, Stanford, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Theodora U. J. Bruun
- Stanford ChEM-H, Stanford University, Stanford, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Celia C. LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - David C. Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Peter S. Kim
- Stanford ChEM-H, Stanford University, Stanford, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| |
Collapse
|
25
|
Bennett AL, Henderson R. HIV-1 Envelope Conformation, Allostery, and Dynamics. Viruses 2021; 13:852. [PMID: 34067073 PMCID: PMC8150877 DOI: 10.3390/v13050852] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/28/2021] [Accepted: 05/04/2021] [Indexed: 11/16/2022] Open
Abstract
The HIV-1 envelope glycoprotein (Env) mediates host cell fusion and is the primary target for HIV-1 vaccine design. The Env undergoes a series of functionally important conformational rearrangements upon engagement of its host cell receptor, CD4. As the sole target for broadly neutralizing antibodies, our understanding of these transitions plays a critical role in vaccine immunogen design. Here, we review available experimental data interrogating the HIV-1 Env conformation and detail computational efforts aimed at delineating the series of conformational changes connecting these rearrangements. These studies have provided a structural mapping of prefusion closed, open, and transition intermediate structures, the allosteric elements controlling rearrangements, and state-to-state transition dynamics. The combination of these investigations and innovations in molecular modeling set the stage for advanced studies examining rearrangements at greater spatial and temporal resolution.
Collapse
Affiliation(s)
| | - Rory Henderson
- Duke Human Vaccine Institute, Durham, NC 27710, USA;
- Department of Medicine, Duke University, Durham, NC 27710, USA
| |
Collapse
|
26
|
HIV-1 Entry and Membrane Fusion Inhibitors. Viruses 2021; 13:v13050735. [PMID: 33922579 PMCID: PMC8146413 DOI: 10.3390/v13050735] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/13/2021] [Accepted: 04/21/2021] [Indexed: 12/14/2022] Open
Abstract
HIV-1 (human immunodeficiency virus type 1) infection begins with the attachment of the virion to a host cell by its envelope glycoprotein (Env), which subsequently induces fusion of viral and cell membranes to allow viral entry. Upon binding to primary receptor CD4 and coreceptor (e.g., chemokine receptor CCR5 or CXCR4), Env undergoes large conformational changes and unleashes its fusogenic potential to drive the membrane fusion. The structural biology of HIV-1 Env and its complexes with the cellular receptors not only has advanced our knowledge of the molecular mechanism of how HIV-1 enters the host cells but also provided a structural basis for the rational design of fusion inhibitors as potential antiviral therapeutics. In this review, we summarize our latest understanding of the HIV-1 membrane fusion process and discuss related therapeutic strategies to block viral entry.
Collapse
|
27
|
Caillat C, Guilligay D, Torralba J, Friedrich N, Nieva JL, Trkola A, Chipot CJ, Dehez FL, Weissenhorn W. Structure of HIV-1 gp41 with its membrane anchors targeted by neutralizing antibodies. eLife 2021; 10:65005. [PMID: 33871352 PMCID: PMC8084527 DOI: 10.7554/elife.65005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 04/18/2021] [Indexed: 12/19/2022] Open
Abstract
The HIV-1 gp120/gp41 trimer undergoes a series of conformational changes in order to catalyze gp41-induced fusion of viral and cellular membranes. Here, we present the crystal structure of gp41 locked in a fusion intermediate state by an MPER-specific neutralizing antibody. The structure illustrates the conformational plasticity of the six membrane anchors arranged asymmetrically with the fusion peptides and the transmembrane regions pointing into different directions. Hinge regions located adjacent to the fusion peptide and the transmembrane region facilitate the conformational flexibility that allows high-affinity binding of broadly neutralizing anti-MPER antibodies. Molecular dynamics simulation of the MPER Ab-stabilized gp41 conformation reveals a possible transition pathway into the final post-fusion conformation with the central fusion peptides forming a hydrophobic core with flanking transmembrane regions. This suggests that MPER-specific broadly neutralizing antibodies can block final steps of refolding of the fusion peptide and the transmembrane region, which is required for completing membrane fusion.
Collapse
Affiliation(s)
- Christophe Caillat
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Delphine Guilligay
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Johana Torralba
- Instituto Biofisika (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Nikolas Friedrich
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jose L Nieva
- Instituto Biofisika (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Christophe J Chipot
- Laboratoire de Physique et Chimie Théoriques (LPCT), University of Lorraine, Vandoeuvre-lès-Nancy, France.,Laboratoire International Associé, CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-lès-Nancy, France.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
| | - François L Dehez
- Laboratoire de Physique et Chimie Théoriques (LPCT), University of Lorraine, Vandoeuvre-lès-Nancy, France.,Laboratoire International Associé, CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-lès-Nancy, France
| | - Winfried Weissenhorn
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| |
Collapse
|
28
|
Lu M. Single-Molecule FRET Imaging of Virus Spike-Host Interactions. Viruses 2021; 13:v13020332. [PMID: 33669922 PMCID: PMC7924862 DOI: 10.3390/v13020332] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/18/2021] [Accepted: 02/18/2021] [Indexed: 02/07/2023] Open
Abstract
As a major surface glycoprotein of enveloped viruses, the virus spike protein is a primary target for vaccines and anti-viral treatments. Current vaccines aiming at controlling the COVID-19 pandemic are mostly directed against the SARS-CoV-2 spike protein. To promote virus entry and facilitate immune evasion, spikes must be dynamic. Interactions with host receptors and coreceptors trigger a cascade of conformational changes/structural rearrangements in spikes, which bring virus and host membranes in proximity for membrane fusion required for virus entry. Spike-mediated viral membrane fusion is a dynamic, multi-step process, and understanding the structure–function-dynamics paradigm of virus spikes is essential to elucidate viral membrane fusion, with the ultimate goal of interventions. However, our understanding of this process primarily relies on individual structural snapshots of endpoints. How these endpoints are connected in a time-resolved manner, and the order and frequency of conformational events underlying virus entry, remain largely elusive. Single-molecule Förster resonance energy transfer (smFRET) has provided a powerful platform to connect structure–function in motion, revealing dynamic aspects of spikes for several viruses: SARS-CoV-2, HIV-1, influenza, and Ebola. This review focuses on how smFRET imaging has advanced our understanding of virus spikes’ dynamic nature, receptor-binding events, and mechanism of antibody neutralization, thereby informing therapeutic interventions.
Collapse
Affiliation(s)
- Maolin Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| |
Collapse
|