Deep mutational scanning to enhance immunogenicity and map antibody responses to HIV-1

Abstract

Vaccines have proven effective against numerous viral diseases, yet the development of a successful vaccine for Human Immunodeficiency Virus (HIV-1) remains elusive. A key immunogen for vaccine design is the surface envelope glycoprotein (Env) of HIV-1, particularly gp120, which is prominently displayed on the viral surface. The formidable challenge in eliciting a potent neutralizing antibody response against HIV-1 arises from the extensive variability in the Env sequence. Beyond sequence diversity, HIV-1 employs various defense mechanisms to evade the host immune system. The gp120 subunit of the Env protein is one of the most heavily glycosylated viral proteins known, with approximately half of its molecular mass attributed to glycans. This extensive glycosylation serves to obscure vital neutralization epitopes, although some broadly neutralizing antibodies (bNAbs) target glycan-dependent epitopes to achieve virus neutralization. Moreover, the presence of lengthy, variable immunodominant loops in gp120 strategically directs the immune response away from conserved epitopes, further complicating vaccine development against HIV-1. Certain conserved epitopes are cryptic and are exposed only after gp120 binds to CD4 and eventually remain exposed to the immune system for a very short period of time. Structural characterization of gp120 is exceptionally challenging due to its high flexibility and the labile nature of the gp120:gp41 complex. Shed gp120 adopts various non-native conformations that may not be present in the native Env, leading to the elicitation of non-neutralizing antibodies. Despite these defense mechanisms, approximately 20-30% of HIV-1 patients manage to generate a broad neutralization response, with about 1% achieving high potency. While the identification of bNAbs and their corresponding epitopes has occurred, the challenge lies in inducting similar bNAbs through immunization. This underscores the complexity of inducing a robust and broadly effective immune response against HIV-1. Monomeric gp120 stands out as a potential immunogen due to its surface accessibility and immunogenicity observed in natural infections. However, initial immunization attempts using full-length monomeric gp120 proved unsuccessful in eliciting neutralizing antibodies and did not demonstrate protective efficacy in a human clinical trial. This suggests a suboptimal presentation of neutralization epitopes on monomeric gp120. Given the importance of inducing neutralizing antibodies for an effective vaccine, there is an urgent need for rational design approaches to direct the immune response towards specific epitopes targeted by known bNAbs. The primary goal of any rational immunogen design methodology for HIV-1 is to enhance the exposure of conserved neutralization epitopes while simultaneously minimizing the exposure of variable, non-neutralizing epitopes to the immune system. This can be achieved by stabilizing the immunogen, which eventually helps to minimize the exposure of non- neutralizing epitopes and focus the immune responses toward the conserved neutralizing epitopes