Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2
Abstract
The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small-molecule inhibitors of Mac1 have great therapeutic potential, at the outset of the COVID-19 pandemic, there were no well-validated inhibitors for this protein nor, indeed, the macrodomain enzyme family, making this target a pharmacological orphan. Here, we report the structure-based discovery and development of several different chemical scaffolds exhibiting low- to sub-micromolar affinity for Mac1 through iterations of computer-aided design, structural characterization by ultra-high-resolution protein crystallography, and binding evaluation. Potent scaffolds were designed with in silico fragment linkage and by ultra-large library docking of over 450 million molecules. Both techniques leverage the computational exploration of tangible chemical space and are applicable to other pharmacological orphans. Overall, 160 ligands in 119 different scaffolds were discovered, and 153 Mac1-ligand complex crystal structures were determined, typically to 1 Å resolution or better. Our analyses discovered selective and cell-permeable molecules, unexpected ligand-mediated conformational changes within the active site, and key inhibitor motifs that will template future drug development against Mac1.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Jan 04, 2023
- Source ID
- 10.1073/pnas.2212931120
Entities
People
- Adam R Renslo
- Alan Ashworth
- Brian K. Shoichet
- Daren Fearon
- Dmytro S. Radchenko
- Frank von Delft
- Galen J Correy
- Ivan Ahel
- James S Fraser
- Jason E Gestwicki
- Jenny Taylor
- John J Irwin
- Marion Schuller
- Matteo P Ferla
- Moira M Rachman
- Morgan E. Diolaiti
- R. Jeffrey Neitz
- Siyi Wang
- Stefan Gahbauer
- Taiasean Wu
- Yagmur U. Doruk
- Yurii S. Moroz
Organizations
- Diamond Light Source
- Division of Biological Infrastructure
- Enamine Ltd
- National Institute for Health and Care Research
- National Institute of Allergy and Infectious Diseases
- National Institute of General Medical Sciences
- Taras Shevchenko National University of Kyiv
- University of California, San Francisco
- University of Johannesburg
- University of Oxford