The severe acute respiratory syndrome coronavirus (SARS-CoV-2) is responsible for the COVID-19 pandemic that continues to negatively impact global health and the world economy and may have lingering long-term impact on people infected. Following the outbreaks of SARS-CoV in 2002?2003 and the Middle East respiratory syndrome (MERS-CoV) in 2012 this is the third instance of a global coronavirus outbreak. As part of a world-wide effort by scientists to understand the biology of SARS-CoV-2, this project involved the development of protocols for producing and purifying some of the 29 proteins encoded by the viral genome. These purified proteins are essential for determining the structure and biophysical properties of the proteins, which can then be used to investigate their biological functions, and lead to the development of interventions (such as drugs or antibodies) that can be used to treat or prevent viral infection. The collective efforts of hundreds of scientists resulted in a remarkably rapid determination of 2124 3D structures of different proteins and domains encoded by the virus genome. In many instances, the similarity between the SARS-CoV-2 protein sequences and known proteins from other viruses is sufficient to identify their functional roles. However, some of the proteins encoded by SARS-CoV-2 do not have a known function. In particular, the non-structural protein nsp3, the largest protein encoded by the SARS-CoV-2 genome, consists of 15 structural domains, and some of these do not have known functions. As the project evolved, we began to focus on these domains: the C-terminal domain Y1 and CoV-Y. Y1 is a domain conserved in all viruses of the order Nidovirales, and CoV-Y is specific to coronavirus. There are no known structures or functions for these domains in SARS-CoV-2 or any other viruses. We obtained nuclear magnetic resonance (NMR) spectra for the nsp3 CoV-Y domain, assigned the majority of the resonance to specific atoms in the protein, and used the NMR data to carry out using screens against libraries of common metabolites and small molecules representing fragments of common drugs. Based on these data, we plan to continue studies on nsp3 domains, their structures, interactions with one another, and interactions with small molecules. These studies will help complete our understanding of SARS-CoV-2 biology, and provide the basis for additional and novel therapeutic interventions.

Last Modified: 09/15/2022
Modified by: Jeffrey C Hoch