Deep Learning-based Protein Design of HIV-1 Env GP120 Core Immunogens for CD4 Binding Site Germline Targeting

PROJECT SUMMARY/ABSTRACT This research proposal aims to develop new immunogens for an HIV-1 vaccine by utilizing advanced protein design techniques and deep learning methods. Conventional structure-guided approaches have limitations in achieving desired structural characteristics. Therefore, this study proposes using RFdiffusion, ProteinMPNN, and AlphaFold2, to generate new germline-targeting gp120 cores based on the pre-fusion native-like structure of the HIV-1 strain 426c. The designed immunogens prioritize maintaining the structural integrity of the pre-fusion gp120 while removing the bridging sheet and re-designing specific regions to maintain the pre-fusion native-like backbone structure. In addition, particular attention is directed towards masking off-target epitopes. In vitro characterization will be performed to evaluate the binding characteristics of these immunogens with germline, broadly neutralizing, and non-neutralizing antibodies. Subsequently, transgenic mice expressing human germline VRC01-class BCRs will be utilized to assess the immunogenicity of selected immunogens presented on nanoparticles and analyze their impact on germinal center B cell responses and memory B cell repertoire. Monoclonal antibodies (mAbs) obtained from immunized animals will be structurally characterized, shedding light on antibody maturation pathways influenced by the immunogen structure. Additionally, this research plan aims to expand the immunogen repertoire by designing gp120 cores based from diverse HIV-1 clades/strains. Furthermore, to enhance immunogenicity, membrane-bound and nanoparticles delivery through self-amplifying mRNA will be explored. The ultimate objective of this research is to gain valuable insights into novel antigen design techniques and their application in HIV-1 vaccine strategies for broadly neutralizing antibodies development. The findings from this study will contribute to the development of immunogens that closely resemble the pre-fusion gp120 state, potentially leading to enhanced B-cell responses capable of generating broadly neutralizing antibody lineages. By addressing the complex features of the HIV-1 Env protein and advancing immunogen design strategies, this research aims to make significant contributions towards the development of an effective HIV-1 vaccine.