Tryptophan 375 stabilizes the outer-domain core of gp120 for HIV vaccine immunogen design

The enormous diversity of HIV-1 is a significant impediment in selecting envelopes (Envs) that can be suitable for designing vaccine immunogens. While tremendous progress has been made in developing soluble, trimeric, native-like Env proteins, those that have elicited neutralizing antibodies (Abs) in animal models are relatively few. A strategy of selecting naturally occurring Envs suitable for immunogen design by studying the correlation between efficient cleavage on the cell surface and their selective binding to broadly neutralizing Abs (bNAbs) and not to non-neutralizing Abs (non-NAbs), properties essential in immunogens, may be useful. Here we discuss some of the challenges of developing an efficacious HIV-1 vaccine and the work done in generating soluble immunogens. We also discuss the study of naturally occurring, membrane-bound, efficiently cleaved (naturally more sensitive to furin) Envs and how they may positively add to the repertoire of HIV-1 Envs that can be used for vaccine immunogen design. However, even with such Envs, the challenges of developing well-folded, native-like trimers as soluble proteins or using other immunogen strategies such as virus-like particles with desirable antigenic properties remain, and are formidable. In spite of the progress that has been made in the HIV-1 vaccine field, an immunogen that elicits neutralizing Abs with significant breadth and potency in vaccines has still not been developed. Efficiently cleaved Envs may increase the number of available Envs suitable for immunogen design and should be studied further.

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Range of CD4-Bound Conformations of HIV-1 gp120, as Defined Using Conditional CD4-Induced Antibodies

Journal of Virology ◽

10.1128/jvi.03206-15 ◽

2016 ◽

Vol 90 (9) ◽

pp. 4481-4493 ◽

Cited By ~ 7

Author(s):

Gilad Kaplan ◽

Anna Roitburd-Berman ◽

George K. Lewis ◽

Jonathan M. Gershoni

Keyword(s):

Conformational Changes ◽

Conformational Transitions ◽

Atomic Structures ◽

Outer Domain ◽

Gp120 Core ◽

Immunogen Design ◽

Monomeric Gp120 ◽

Antibody Specificities ◽

Hiv Envelope ◽

Hiv 1

ABSTRACTThe HIV envelope binds cellular CD4 and undergoes a range of conformational changes that lead to membrane fusion and delivery of the viral nucleocapsid into the cellular cytoplasm. This binding to CD4 reveals cryptic and highly conserved epitopes, the molecular nature of which is still not fully understood. The atomic structures of CD4 complexed with gp120 core molecules (a form of gp120 in which the V1, V2, and V3 loops and N and C termini have been truncated) have indicated that a hallmark feature of the CD4-bound conformation is the bridging sheet minidomain. Variations in the orientation of the bridging sheet hairpins have been revealed when CD4-liganded gp120 was compared to CD4-unliganded trimeric envelope structures. Hence, there appears to be a number of conformational transitions possible in HIV-1 monomeric gp120 that are affected by CD4 binding. The spectrum of CD4-bound conformations has been interrogated in this study by using a well-characterized panel of conditional, CD4-induced (CD4i) monoclonal antibodies (MAbs) that bind HIV-1 gp120 and its mutations under various conditions. Two distinct CD4i epitopes of the outer domain were studied: the first comprises the bridging sheet, while the second contains elements of the V2 loop. Furthermore, we show that the unliganded extended monomeric core of gp120 (coree) assumes an intermediate CD4i conformation in solution that further undergoes detectable rearrangements upon association with CD4. These discoveries impact both accepted paradigms concerning gp120 structure and the field of HIV immunogen design.IMPORTANCEElucidation of the conformational transitions that the HIV-1 envelope protein undergoes during the course of entry into CD4+cells is fundamental to our understanding of HIV biology. The binding of CD4 triggers a range of gp120 structural rearrangements that could present targets for future drug design and development of preventive vaccines. Here we have systematically interrogated and scrutinized these conformational transitions using a panel of antibody probes that share a specific preference for the CD4i conformations. These have been employed to study a collection of gp120 mutations and truncations. Through these analyses, we propose 4 distinct sequential steps in CD4i transitions of gp120 conformations, each defined by antibody specificities and structural requirements of the HIV envelope monomer. As a result, we not only provide new insights into this dynamic process but also define probes to further investigate HIV infection.

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Structure of a germline-like human antibody defines a neutralizing epitope on the SARS-CoV-2 spike NTD

10.1101/2021.07.08.451649 ◽

2021 ◽

Author(s):

Clara Gilda Altomare ◽

Daniel Cole Adelsberg ◽

Juan Manuel Carreno ◽

Iden Avery Sapse ◽

Fatima Amanat ◽

...

Keyword(s):

Arms Race ◽

Human Antibody ◽

Neutralizing Epitope ◽

Vaccine Immunogen ◽

Direct Competition ◽

High Resolution Structure ◽

Immunogen Design ◽

Insight Into ◽

Resolution Structure

Structural characterization of infection- and vaccination-elicited antibodies in complex with antigen provides insight into the evolutionary arms race between the host and the pathogen and informs rational vaccine immunogen design. We isolated a germline-like monoclonal antibody (mAb) from plasmablasts activated upon mRNA vaccination against SARS-CoV-2 and determined its structure in complex with the spike glycoprotein by cryo-EM. We show that the mAb engages a previously uncharacterized neutralizing epitope on the spike N-terminal domain (NTD). The high-resolution structure reveals details of the intermolecular interactions and shows that the mAb inserts its HCDR3 loop into a hydrophobic NTD cavity previously shown to bind a heme metabolite, biliverdin. We demonstrate direct competition with biliverdin and that - because of the conserved nature of the epitope - the mAb maintains binding to viral variants B.1.1.7 and B.1.351. Our study illustrates the feasibility of targeting the NTD to achieve broad neutralization against SARS-CoV-2 variants.

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Structural Basis and Mode of Action for Two Broadly Neutralizing Antibodies Against SARS-CoV-2 Emerging Variants of Concern

10.1101/2021.08.02.454546 ◽

2021 ◽

Author(s):

Walther Mothes ◽

Wenwei Li ◽

Yaozong Chen ◽

Jeremie Prevost ◽

Irfan Ullah ◽

...

Keyword(s):

Immune Responses ◽

Mode Of Action ◽

Neutralizing Antibodies ◽

Structural Basis ◽

Receptor Binding Domain ◽

Broadly Neutralizing Antibodies ◽

Vaccine Immunogen ◽

Immunogen Design

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 beta-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.

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Preclinical Development of a Fusion Peptide Conjugate as an HIV Vaccine Immunogen

Scientific Reports ◽

10.1038/s41598-020-59711-y ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 4

Author(s):

Li Ou ◽

◽

Wing-Pui Kong ◽

Gwo-Yu Chuang ◽

Mridul Ghosh ◽

...

Keyword(s):

Fusion Peptide ◽

Hiv Vaccine ◽

Vaccine Immunogen ◽

Preclinical Development

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Structural topology defines protective CD8+ T cell epitopes in the HIV proteome

Science ◽

10.1126/science.aav5095 ◽

2019 ◽

Vol 364 (6439) ◽

pp. 480-484 ◽

Cited By ~ 27

Author(s):

Gaurav D. Gaiha ◽

Elizabeth J. Rossin ◽

Jonathan Urbach ◽

Christian Landeros ◽

David R. Collins ◽

...

Keyword(s):

T Cell ◽

Human Leukocyte ◽

Hiv Vaccine ◽

Amino Acid Residues ◽

T Cell Epitopes ◽

Structural Topology ◽

Leukocyte Antigen ◽

Immunogen Design ◽

Mechanistic Basis ◽

Protein Structure Data

Mutationally constrained epitopes of variable pathogens represent promising targets for vaccine design but are not reliably identified by sequence conservation. In this study, we employed structure-based network analysis, which applies network theory to HIV protein structure data to quantitate the topological importance of individual amino acid residues. Mutation of residues at important network positions disproportionately impaired viral replication and occurred with high frequency in epitopes presented by protective human leukocyte antigen (HLA) class I alleles. Moreover, CD8+ T cell targeting of highly networked epitopes distinguished individuals who naturally control HIV, even in the absence of protective HLA alleles. This approach thereby provides a mechanistic basis for immune control and a means to identify CD8+ T cell epitopes of topological importance for rational immunogen design, including a T cell–based HIV vaccine.

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Murine Antibody Responses to Cleaved Soluble HIV-1 Envelope Trimers Are Highly Restricted in Specificity

Journal of Virology ◽

10.1128/jvi.01653-15 ◽

2015 ◽

Vol 89 (20) ◽

pp. 10383-10398 ◽

Cited By ~ 86

Author(s):

Joyce K. Hu ◽

Jordan C. Crampton ◽

Albert Cupo ◽

Thomas Ketas ◽

Marit J. van Gils ◽

...

Keyword(s):

Neutralizing Antibodies ◽

First Generation ◽

Hiv Vaccine ◽

Antibody Responses ◽

Tier 2 ◽

Efficacy Trials ◽

Follicular Helper ◽

Immunogen Design ◽

Hiv Envelope ◽

Hiv 1

ABSTRACTGenerating neutralizing antibodies (nAbs) is a major goal of many current HIV-1 vaccine efforts. To be of practical value, these nAbs must be both potent and cross-reactive in order to be capable of preventing the transmission of the highly diverse and generally neutralization resistant (Tier-2) HIV-1 strains that are in circulation. The HIV-1 envelope glycoprotein (Env) spike is the only target for nAbs. To explore whether Tier-2 nAbs can be induced by Env proteins, we immunized conventional mice with soluble BG505 SOSIP.664 trimers that mimic the native Env spike. Here, we report that it is extremely difficult for murine B cells to recognize the Env epitopes necessary for inducing Tier-2 nAbs. Thus, while trimer-immunized mice raised Env-binding IgG Abs and had high-quality T follicular helper (Tfh) cell and germinal center (GC) responses, they did not make BG505.T332N nAbs. Epitope mapping studies showed that Ab responses in mice were specific to areas near the base of the soluble trimer. These areas are not well shielded by glycans and likely are occluded on virions, which is consistent with the lack of BG505.T332N nAbs. These data inform immunogen design and suggest that it is useful to obscure nonneutralizing epitopes presented on the base of soluble Env trimers and that the glycan shield of well-formed HIV Env trimers is virtually impenetrable for murine B cell receptors (BCRs).IMPORTANCEHuman HIV vaccine efficacy trials have not generated meaningful neutralizing antibodies to circulating HIV strains. One possible hindrance has been the lack of immunogens that properly mimic the native conformation of the HIV envelope trimer protein. Here, we tested the first generation of soluble, native-like envelope trimer immunogens in a conventional mouse model. We attempted to generate neutralizing antibodies to neutralization-resistant circulating HIV strains. Various vaccine strategies failed to induce neutralizing antibodies to a neutralization-resistant HIV strain. Further analysis revealed that mouse antibodies targeted areas near the bottom of the soluble envelope trimers. These areas are not easily accessible on the HIV virion due to occlusion by the viral membrane and may have resulted from an absence of glycan shielding. Our results suggest that obscuring the bottom of soluble envelope trimers is a useful strategy to reduce antibody responses to epitopes that are not useful for virus neutralization.

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