Characterizing Epitope Binding Regions of Entire Antibody Panels by Combining Experimental and Computational Analysis of Antibody: Antigen Binding Competition

Vaccines and immunotherapies depend on the ability of antibodies to sensitively and specifically recognize particular antigens and specific epitopes on those antigens. As such, detailed characterization of antibody-antigen binding provides important information to guide development. Due to the time and expense required, high-resolution structural characterization techniques are typically used sparingly and late in a development process. Here, we show that antibody-antigen binding can be characterized early in a process for whole panels of antibodies by combining experimental and computational analyses of competition between monoclonal antibodies for binding to an antigen. Experimental "epitope binning" of monoclonal antibodies uses high-throughput surface plasmon resonance to reveal which antibodies compete, while a new complementary computational analysis that we call "dock binning" evaluates antibody-antigen docking models to identify why and where they might compete, in terms of possible binding sites on the antigen. Experimental and computational characterization of the identified antigenic hotspots then enables the refinement of the competitors and their associated epitope binding regions on the antigen. While not performed at atomic resolution, this approach allows for the group-level identification of functionally related monoclonal antibodies (i.e., communities) and identification of their general binding regions on the antigen. By leveraging extensive epitope characterization data that can be readily generated both experimentally and computationally, researchers can gain broad insights into the basis for antibody-antigen recognition in wide-ranging vaccine and immunotherapy discovery and development programs.

Properties of a herpes simplex virus multiple immediate-early gene-deleted recombinant as a vaccine vector

Herpes simplex virus (HSV) recombinants induce durable immune responses in rhesus macaques and mice and have induced partial protection in rhesus macaques against mucosal challenge with virulent simian immunodeficiency virus (SIV). In this study, we evaluated the properties of a new generation HSV vaccine vector, an HSV-1 multiple immediate-early (IE) gene deletion mutant virus, d106, which contains deletions in the ICP4, ICP27, ICP22, and ICP47 genes. Because several of the HSV IE genes have been implicated in immune evasion, inactivation of the genes encoding these proteins was expected to result in enhanced immunogenicity. The d106 virus expresses few HSV gene products and shows minimal cytopathic effect in cultured cells. When d106 was inoculated into mice, viral DNA accumulated at high levels in draining lymph nodes, consistent with an ability to transduce dendritic cells and activate their maturation and movement to lymph nodes. A d106 recombinant expressing Escherichia coli beta-galactosidase induced durable beta-gal-specific IgG and CD8(+) T cell responses in naive and HSV-immune mice. Finally, d106-based recombinants have been constructed that express simian immunodeficiency virus (SIV) gag, env, or a rev-tat-nef fusion protein for several days in cultured cells. Thus, d106 shows many of the properties desirable in a vaccine vector: limited expression of HSV gene products and cytopathogenicity, high level expression of transgenes, ability to induce durable immune responses, and an ability to transduce dendritic cells and induce their maturation and migration to lymph nodes.

Degradation of Quillaja saponaria Molina saponins: loss of the protective effects of a herpes simplex virus 1 subunit vaccine

Quillaja saponins (Q. saponins) are readily hydrolyzed at neutral pH to yield degraded deacylated saponins (DS-saponins). Degradation of Q. saponins resulted in some reduction of their capacity to elicit IgG1, IgG2a and IgG2b isotypes against the highly immunogenic envelope glycoprotein D (gD) from herpes simplex virus, type 1 (HSV-1). Addition to gD of a dose of DS-saponins tenfold higher than the original Q. saponins dose stimulated lower IgG2a and IgG2b titers than those obtained with gD alone or combined with native saponins. However, the IgG1 response was somewhat similar in all the groups. In contrast, Q. saponins' deacylation resulted in a significant reduction in both the production of HSV-1 neutralizing antibodies and survival rates after viral challenge. Vaccination with gD alone did not protect mice against a lethal challenge with HSV-1, while the addition of Q. saponins to gD resulted in protection against HSV-1. Vaccines containing partially deacylated saponins yielded lower survival rates, while vaccines containing DS-saponins did not protect mice against HSV-1. Increasing the dose of DS-saponins tenfold resulted in a marginal increase in protection. These results show that degradation of Q. saponins during storage can have a deleterious effect on vaccines' efficacies.