Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors. (August 2021)

• Record Type: Journal Article
• Authors: Brosey, Chris A.; Houl, Jerry H.; Katsonis, Panagiotis; Balapiti-Modarage, Lakshitha P.F.; Bommagani, Shobanbabu; Arvai, Andy; Moiani, Davide; Bacolla, Albino; Link, Todd; Warden, Leslie S.; Lichtarge, Olivier; Jones, Darin E.; Ahmed, Zamal; Tainer, John A.
• Is Part Of: Progress in biophysics and molecular biology. Volume 163(2021)
• Page Start: 171
• Page End: 186
• Publication Date: 2021-08
• Subjects: SARS-CoV-2 Nsp3 macrodomain -- Poly(ADP-Ribose) glycohydrolase (PARG) -- PARG inhibitor (PARGi) -- Evolutionary trace (ET) -- In silico screening -- Drug discovery; Severe Acute Respiratory Syndrome (SARS) -- nonstructural protein 3 (Nsp3) -- 2-(N-morpholino)ethanesulfonic acid (MES) -- poly(ADP-ribose) glycohydrolase (PARG) -- poly(ADP-ribose) polymerase (PARP) -- evolutionary trace (ET) -- multiple sequence alignment (MSA) -- microscale thermophoresis (MST); Biophysics -- Periodicals; Biochemistry -- Periodicals; Biophysics -- Periodicals; Molecular Biology -- Periodicals; Biophysique -- Périodiques; Biochimie -- Périodiques; 571.4
• DOI: 10.1016/j.pbiomolbio.2021.02.002
• Languages: English
• ISSNs: 0079-6107

Abstract

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. Highlights: Sequence and evolutionary analyses show CoV-2 macrodomain 1 (Mac1) shares active site homology with human PARG macrodomain. Virtual screening of CoV-2 Mac1 with JA2131 PARGi reveals morpholine and phenyl fragments targeting the distal ribose site. Scaffold optimization of VHTS PARGi fragments yields PARG-345 and PARG-329, which engage the full CoV-2 Mac1 active site. Rationale PARGi scaffold optimization is a strategy to target CoV-2 Mac1 efficiently with pre-existing inhibitor libraries.