HIV-1 and SARS-CoV-2 immunogen design

Abstract

Human Immunodeficiency Virus (HIV-1) is the aetiologic agent of AIDS. Presently there are ~38 million HIV-1 infected individuals worldwide and ~1 million deaths in 2019. Since its discovery, the quest for vaccine candidate for HIV-1 is alive, yet no effective vaccine exists till date. HIV-1 viral displayed Envelope (Env) protein is the primary viral target of the humoral immune system and is thus an obvious vaccine candidate. The historic RV144 HIV-1 clinical trial resulted in a modest efficacy of the gp120 clade B/E vaccine candidate and renewed hope in finding a HIV-1 vaccine. However, monomeric gp120 does not induce protective antibodies and native-like trimeric Env was hypothesized to be a better candidate to induce broadly neutralizing antibodies. The recent structure of the BG505SOSIP.664 gp140 ectodomain reinvigorated interest in rational immunogen design. Chapter 1 outlines the HIV-1 virus, organisation, and structures of the Env ectodomain gp140, gp120, gp41 and various strategies to elicit neutralizing antibodies. Chapter 2 provides proof of principle of a method involving a computational sequence and structure guided Rosetta mutational scanning approach PROSS, to generate high yielding variants of the Env derivative gp140 without altering the trimeric structure and antigenicity. Chapter 3 utilizes the approach of cyclic permutation to rationally design trimeric gp120 derivatives that display a native V1V2 apex and retain binding to quaternary epitope directed bNAbs such as PGT145 and PGDM1400. Further, a nanoparticle display of the cyclic permutant was carried out to improve the immunogenicity of these potentially attractive vaccine candidates. Chapter 4 utilizes a structure guided approach to derive stable Env ectodomain variants by a cyclic permutation design strategy and describes an approach to engineer disulfides at the trimer Apex to covalently link the trimers for obtaining dynamically stable Env variants. HIV-1 Env displays conserved epitopes that are targeted by broadly neutralizing antibodies. CD4 binding site (CD4bs) antibodies are amongst the most potent. These CD4bs in humans are observed to be produced from a highly restricted set of germline sequences of the antibody repertoire. Chapter 5 attempts to utilize a structure guided approach to computationally design antibodies derived from novel germlines that are predicted to be energetically stable. Functional and biochemical characterization of these antibodies is reported Chapter 5. With the ongoing COVID-19 pandemic we attempted to develop a vaccine candidate utilizing a structure guided approach in Chapter 6. The Receptor binding domain (RBD) of the Spike protein of SARS-CoV-2 has been observed to be the primary target of the most potent neutralizing antibodies. Hence in Chapter 6 we designed an RBD subunit vaccine candidate to combat COVID-19. The designed RBD derivative is highly thermotolerant and also immunogenic and produces neutralizing antibodies comparable to several candidates currently being tested in the clinic.