NSP13 Helicase crystal structure and XChem fragment screen

To contribute towards the development of novel anti-viral therapeutics targeting the current and future emerging coronavirus threats the Gileadi lab at the University of Oxford together with the XChem team at Diamond Light Source have teamed up to perform a crystallographic fragment screen against SARS-CoV-2 NSP13 helicase.

NSP13 is a large 67 kDa protein that utilizes the energy of nucleotide triphosphate hydrolysis to catalyze the unwinding of double stranded DNA or RNA in a 5’ to 3’ direction. NSP13 is a Upf1-like helicase from Superfamily 1B, that contains 5 domains: a N-terminal Zinc binding domain that coordinates 3 structural Zinc ions; a helical “stalk” domain; a beta-barrel 1B domain; and two “RecA like” helicase subdomains 1A and 2A that contain the residues responsible for nucleotide binding and hydrolysis.

Whilst its precise role in the viral life cycle is not currently well-defined, it is believed to act in concert with the replication-transcription complex (NSP7/NSP8₂/NSP12), conceivably involved in either disrupting downstream RNA secondary structures or template switching, and playing an essential role in the life cycle of SARS-CoV-2.

Previously, crystal structures of NSP13 were solved for MERS-CoV and the highly related SARS-CoV, to 3.0 Å and 2.8 Å respectively. These indicated that the protein may be crystallizable, although the resolution of these structures would have been too low to reliably detect fragment binders in a X-ray Fragment screen.

We began lab work on this project in mid-April and by using previous structures to define domain boundaries, were rapidly able to obtain a new crystal form for the full-length protein that is reproducible and diffracts routinely to around 2.0 Å. We deposited the SARS-CoV-2Nnsp13 structure in the pdb (6ZSL).

Potential sites of inhibition of NSP13 include the nucleotide binding pocket, the DNA/RNA binding pocket, and putative allosteric pockets that might block domain movements that are required as part of the NSP13 catalytic cycle. Initial druggability analysis indicates both nucleotide and DNA/RNA binding pockets as being druggable, and amongst the most well conserved pockets in the entire SARS-CoV-2 genome.