Aug 2026· Cell Reports· Vol 45 8, pp.
117760
· 0 citations· 71 references
Medicine
TL;DR
Describing the genetic, structural, functional, and epitope features of 25 BD-directed nAbs isolated from HCV-infected individuals or immunized macaques underscores BD as a promising target for rational HCV vaccine design.
Abstract
The bridging domain (BD) region on hepatitis C virus (HCV) E1E2 glycoprotein complex is a conserved, E1-dependent conformational site of vulnerability formed by E2 residues 646-704. Given its importance for rational vaccine design, here, we characterized the genetic, structural, functional, and epitope features of 25 BD-directed nAbs isolated from HCV-infected individuals or immunized macaques. These antibodies derive from diverse B cell lineages but frequently display recurrent CDRH3 motifs and recognize overlapping epitopes spanning antigenic regions AR4 and AR5, with variable engagement of the E2 back layer (BL) region. A crystal structure of the macaque nAb RM3-26 bound to E2 core domain reveals a BL-directed binding mode analogous to the human nAb hcab40. Importantly, BD-directed nAbs achieve broad neutralization with minimal somatic hypermutation at contact residues and act additively with neutralizing face-directed antibodies. Together, these findings underscore BD as a promising target for rational HCV vaccine design.
A major goal for hepatitis C virus (HCV) vaccine development is to elicit broadly neutralizing antibodies (bNAbs) against the E1E2 glycoprotein complex located on the viral surface. Inducing HCV bNAbs requires engagement of their germline B cell precursors. HCV glycoproteins usually do not bind and activate inferred germline precursors of bNAbs (igl-bNAbs), possibly because most circulating strains contain non-conserved isolate-specific residues, even in bNAb epitopes. Here, we generated stabilized native-like soluble E1E2 (sE1E2) antigens based on a consensus sequence of HCV (HepCon) to limit the exposure of antigenically rare residues. The antigenicity and glycosylation profiles show that HepCon sE1E2 resembles a native-like E1E2 heterodimer. HepCon sE1E2 induced cross-reactive neutralizing antibody responses as a soluble protein immunogen and as membrane-anchored mRNA-delivered immunogen in animals. Importantly, HepCon sE1E2 engages multiple igl-bNAbs against two major epitopes: antigenic region 3 (AR3), which is targeted by igl-bNAbs derived from the widely expressed human VH1-69 B cell gene, and antigenic region 4 (AR4), which is only present on native-like E1E2. Nanoparticles with HepCon sE1E2 efficiently activated B cell lines expressing AR3 and AR4 igl-bNAb B cell receptors in vitro. Finally, using HepCon sE1E2 we elucidated the atomic contacts of an AR3 igl-bNAb by cryo-electron microscopy. Thus, HepCon sE1E2 is a promising candidate for germline-targeting vaccination strategies.
Fabian Mulder, F. Cannac, Joan Capella-Pujol et al.· bioRxiv· 0 citations
Hepatitis C virus (HCV) affects 47 million people and causes 239,000 deaths annually, yet no vaccine is on the horizon. Generating a stable native-like mimic of the envelope complex E1E2, the only target for known neutralizing antibodies, is an important aim for HCV vaccine development. Starting from a recombinant E1E2 design that utilizes a leucine zipper for proper folding, we used an iterative structure-based design approach to engineer antigens with at least 100-fold stronger binding to conformational antibodies and increased thermal stability. These new E1E2 designs facilitate production of native-like E1E2 antigens based on strains from different HCV genotypes and enable the generation of a recombinant E1E2 antigen design that lacks the immunogenic leucine zipper. A cryo-EM structure of one of the stabilized E1E2 antigens in complex with neutralizing antibody AT1211 provides atomic-level insights into an atypical epitope on the E2 subunit. Finally, immunogenicity studies in rabbits with adjuvanted E1E2 proteins show that immunogen stabilization alone does do not enhance serum neutralization breadth, but that removing the leucine zipper does increase homologous serum neutralization. The hepatitis C virus E1E2 glycoprotein is the only target of neutralizing antibodies. Here, the authors used structure-based design to generate soluble antigens that resemble the viral E1E2 heterodimer.
Joan Capella-Pujol, Fabian Mulder, F. Cannac et al.· Nature Communications· 1 citation
Hepatitis C virus (HCV) remains a major global health challenge despite the availability of highly effective antiviral therapies, underscoring the need for a broadly protective vaccine. The envelope glycoprotein E2 is the principal target of neutralizing antibodies, yet the full repertoire of vulnerable epitopes and mechanisms of antibody-mediated neutralization remains incompletely understood. Here, we exploited the unique binding properties of camelid nanobodies to probe the antigenic landscape of HCV E2 beyond the immunodominant human antibody response. We isolated a diverse panel of E2-specific nanobodies, including broadly neutralizing antibodies with high-affinity cross-reactivity toward genetically diverse HCV isolates. By combining cross-neutralization assays, competition binding experiments, and high-resolution hydrogen–deuterium exchange mass spectrometry (HDX-MS), we identified three mechanistically distinct classes of neutralizing epitopes. While one class targets the canonical E2 neutralization face, a second class recognizes antigenic region 1 (AR1), independently validating and extending recent evidence that this region represents a functional site of viral vulnerability. These findings demonstrate that broadly neutralizing antibody responses extend beyond the canonical neutralization face and establish a broader framework for understanding HCV neutralization. More broadly, our study illustrates how alternative antibody repertoires can reveal functionally important antigenic surfaces that are underrepresented in conventional human antibody responses, providing new opportunities for the rational design of next-generation HCV vaccine immunogens.
Two human-derived monoclonal antibodies are characterized that recognize conserved epitopes on the SARS-CoV-2 RBD and retain activity across antigenically distinct variants, and conserved, mutationally constrained epitopes may serve as targets for vaccines designed to elicit antibody responses resilient to ongoing SARS-CoV-2 evolution and future sarbecovirus emergence.
M. Abernathy, William B. Foreman, Jasmyn A. Lopez et al.· bioRxiv· 0 citations
Functional cure of chronic hepatitis B virus (HBV) infection remains a significant challenge, making viral-entry-blocking antibodies a promising antiviral strategy. Here, we developed a structure-guided computational workflow for affinity-enhancing candidate mutations at the interface between the humanized neutralizing antibody HzKR127 and the HBV preS1 peptide epitope. Based on the crystal structure of the HzKR127–preS1 complex, we performed single-site saturation mutagenesis across the paratope, evaluating variants with a consensus effect score integrated from seven computational models. Benchmarking against published alanine scanning data showed that our consensus score effectively identified major-affinity-loss residues, achieving ROC AUC values of 0.81 and 0.84 for residue-level and site-level predictions, respectively. Mutational profiling revealed distinct asymmetric mutational responses, with broad intolerance on the preS1 side and localized favorable substitutions within antibody CDRs. Multilevel prioritization identified 26 antibody-side candidates, 17 of which showed improved HADDOCK refinement scores compared to the wild type. In particular, the H:D97W/F/Y substitutions presented the strongest structural rationale for enhancing improved interfacial packing through aromatic hydrophobic contacts with preS1 Phe10. These findings provide a prioritized list of candidates for experimental validation and a practical framework for the rational optimization of antibodies targeting functionally constrained viral epitopes.
Wen-Qing Chen, Yuan-Zhong Tu, Kai Wang et al.· Current Issues in Molecular...· 0 citations
Dengue virus (DENV) envelope protein domain III (EDIII) is a premier target for vaccine design because EDIII-specific antibodies can potently neutralize DENV with a low propensity for inducing antibody-dependent enhancement (ADE). We previously identified a cross-reactive antibody, R3N_2D3, which targets the EDIII AG-strand epitope and neutralizes all four DENV serotypes with low ADE, a desirable combination of activities among anti-DENV antibodies. In this study, we expanded this AG-strand-targeting antibody panel by identifying four additional anti-EDIII antibodies from our dengue-immune single-chain variable fragment (scFv)-phage libraries. Despite variations in their binding footprints, these new antibodies converged on key residues within the AG-strand epitope. When expressed as full IgG1, these candidates showed potent cross-neutralization with subnanomolar focus reduction neutralization titers (FRNT50 values) and consistently low ADE compared to the prototypical fusion-loop antibody 4G2 when tested in an in vitro U937 monocytic cell model. Collectively, these findings demonstrate that the AG-strand epitope can elicit broadly protective antibodies with reduced ADE risk, highlighting its potential as a strategic epitope for pan-DENV vaccine development.
Napon Nilchan, Anunyaporn Phungsom, Mongkhonphan Tantiwatcharakunthon et al.· ACS Omega· 0 citations
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