Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors

Prog Biophys Mol Biol. 2021 Aug;163:171-186. doi: 10.1016/j.pbiomolbio.2021.02.002. Epub 2021 Feb 23.

Abstract

Arrival of the novel SARS-CoV-2 has launched a worldwide effort to identify both pre-approved and novel therapeutics targeting the viral proteome, highlighting the urgent need for efficient drug discovery strategies. Even with effective vaccines, infection is possible, and at-risk populations would benefit from effective drug compounds that reduce the lethality and lasting damage of COVID-19 infection. The CoV-2 MacroD-like macrodomain (Mac1) is implicated in viral pathogenicity by disrupting host innate immunity through its mono (ADP-ribosyl) hydrolase activity, making it a prime target for antiviral therapy. We therefore solved the structure of CoV-2 Mac1 from non-structural protein 3 (Nsp3) and applied structural and sequence-based genetic tracing, including newly determined A. pompejana MacroD2 and GDAP2 amino acid sequences, to compare and contrast CoV-2 Mac1 with the functionally related human DNA-damage signaling factor poly (ADP-ribose) glycohydrolase (PARG). Previously, identified targetable features of the PARG active site allowed us to develop a pharmacologically useful PARG inhibitor (PARGi). Here, we developed a focused chemical library and determined 6 novel PARGi X-ray crystal structures for comparative analysis. We applied this knowledge to discovery of CoV-2 Mac1 inhibitors by combining computation and structural analysis to identify PARGi fragments with potential to bind the distal-ribose and adenosyl pockets of the CoV-2 Mac1 active site. Scaffold development of these PARGi fragments has yielded two novel compounds, PARG-345 and PARG-329, that crystallize within the Mac1 active site, providing critical structure-activity data and a pathway for inhibitor optimization. The reported structural findings demonstrate ways to harness our PARGi synthesis and characterization pipeline to develop CoV-2 Mac1 inhibitors targeting the ADP-ribose active site. Together, these structural and computational analyses reveal a path for accelerating development of antiviral therapeutics from pre-existing drug optimization pipelines.

Keywords: Drug discovery; Evolutionary trace (ET); In silico screening; PARG inhibitor (PARGi); Poly(ADP-Ribose) glycohydrolase (PARG); SARS-CoV-2 Nsp3 macrodomain.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Antiviral Agents / chemistry*
  • Antiviral Agents / pharmacology
  • COVID-19 / drug therapy
  • Catalytic Domain
  • Coronavirus Papain-Like Proteases / metabolism*
  • Crystallography, X-Ray
  • Drug Discovery
  • Enzyme Inhibitors / chemistry*
  • Enzyme Inhibitors / pharmacology
  • Glycoside Hydrolases / antagonists & inhibitors*
  • Humans
  • Models, Molecular
  • Protein Domains
  • SARS-CoV-2 / drug effects
  • SARS-CoV-2 / metabolism
  • Small Molecule Libraries / chemistry*
  • Small Molecule Libraries / pharmacology
  • Structure-Activity Relationship
  • Xanthines / chemistry*
  • Xanthines / pharmacology

Substances

  • Antiviral Agents
  • Enzyme Inhibitors
  • Small Molecule Libraries
  • Xanthines
  • methylxanthine
  • Glycoside Hydrolases
  • poly ADP-ribose glycohydrolase
  • Coronavirus Papain-Like Proteases
  • papain-like protease, SARS-CoV-2