X-ray Crystallography-Guided Design and Synthesis of Cyclopentyl Heteroaryl Carboxylic Acid-Based Inhibitors of the SARS-CoV-2 Nsp3 Macrodomain (Mac1)

  • J Med Chem. 2026 Jul 23;69(14):16570-16600. doi: 10.1021/acs.jmedchem.6c00236.
Xinyu Wang  1 ,  William T W Butler  1 ,  James R Donald  1 ,  Yuran Wang  1 ,  Alice L Shaw  1 ,  Marion Schuller  2 ,  Daren Fearon  3  4 ,  Jasmin C Aschenbrenner  3  4 ,  Peter G Marples  3  4 ,  Grant Watt  3  4 ,  Yang Lu  2 ,  Simon C C Lucas  5 ,  Silvia Bonomo  5 ,  Jennifer E Nelson  5 ,  Ivan Ahel  2 ,  Frank von Delft  3  4  6  7 ,  Peter O'Brien  1
Affiliations
  • 1. Department of Chemistry, University of York, York YO10 5DD, U.K.
  • 2. Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, U.K.
  • 3. Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot Oxfordshire, U.K.
  • 4. Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot Oxfordshire, U.K.
  • 5. Hit Discovery, Discovery Sciences, R&D, AstraZeneca, 1 Francis Crick Ave, Cambridge CB2 0AA, U.K.
  • 6. Centre for Medicines Discovery, University of Oxford, NDM Research Building, Oxford, Oxfordshire OX3 7FZ, U.K.
  • 7. Department of Biochemistry, University of Johannesburg, Johannesburg 2092, South Africa.
PMID: 42439527 DOI: 10.1021/acs.jmedchem.6c00236
Abstract

Mac1 is a conserved macrodomain enzyme in the nonstructural protein 3 (Nsp3) of SARS-CoV-2 and is part of the viral replication machinery. Mac1 is a target for small-molecule inhibitors that could ultimately enable new COVID-19 therapeutics to be developed. Here, we report the structure-guided design, synthesis, and Mac1 inhibition profiling of 25 analogues derived from a hit identified through crystallographic fragment screening. The heteroaryl group and scaffold (cis- and trans-cyclopentane and cyclopentene) were varied. Two new approaches to trans-cyclopentanes were developed: MacMillan's Ir/Ni-mediated photoredox cross-coupling of alcohols and Barluenga-Valdés' metal-free cross-coupling of sulfonyl hydrazones and boronic acids. X-ray crystal structures of 19 compounds bound to Mac1 were determined to guide the design and to rationalize the observed SAR. A new family of Mac1 inhibitors with benzothiazole or amino benzothiazoles was discovered and characterized, with IC50 values of 6-8 μM and ligand efficiency values of up to 0.40.

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