Deciphering APOBEC Inhibition: Unraveling Structural Dynamics via Viral Protein and Nanobody Interactions

University Of Minnesota, Minneapolis MN

Investigators

Abstract

Deciphering APOBEC Inhibition: Unraveling Structural Dynamics via Viral Protein and Nanobody Interactions ABSTRACT This research delves into the intricate structural dynamics of APOBEC3A (A3A) and APOBEC3B (A3B) enzymes, key players in the delicate balance between host defense mechanisms and genomic stability. While these enzymes play pivotal roles in defending against viruses and maintaining genomic integrity, their involvement in cancer mutagenesis makes them a double-edged sword, necessitating the development of inhibitors. This project's primary objective is to overcome the impediment of limited structural information, which has been hampering the rational design of inhibitors for A3A and A3B. Aim 1 of this project focuses on elucidating the structures of A3A and A3B when bound to viral inhibitors, specifically, Macacine γ-herpesvirus 11 (McHV-11) and Kaposi sarcoma-associated herpesvirus (KSHV) ribonucleotide reductases (RNRs). Utilizing cryo-electron microscopy (cryo-EM), this aim seeks to unravel the molecular intricacies of APOBEC inhibition evolved through host-virus arms races, potentially paving the way for targeted therapeutics by comprehensively understanding the host-virus interaction. Aim 2 expands the investigation to novel alpaca-derived nanobodies exhibiting inhibitory activity against A3A and A3B. Employing a tailored approach and introducing a large protein scaffold to enhance imaging resolution, this aim seeks to uncover unique mechanisms of APOBEC3 inhibition. By mapping the A3-nanobody binding interface, this study intends to engineer these nanobodies for improved binding, with the ultimate goal of creating potent and specific A3-targeting degraders. This proposal seeks to bridge existing knowledge gaps regarding the structures and inhibition mechanisms of A3A and A3B. By advancing our understanding of these crucial enzymes, this project aims to facilitate the rational design of A3A/B inhibitors, which will mitigate their mutagenic effects in cancer cells to slow tumor evolution and enhance the efficacy of cancer treatments.