Inhibiting peptidylarginine deiminases (PAD1-4) by targeting a Ca2+ dependent allosteric binding site
Peptidylarginine deiminases (PAD1-4) are calcium dependent enzymes responsible for protein citrullination, a post-translational modification converting arginine residues to citrulline. Elevated levels of citrullinated proteins have been associated with rheumatoid arthritis, neurodegenerative diseases, and cancers. Though highly selective PAD4 inhibitors have been described, inhibitors to the broader family currently are limited to covalent substrate analogs. Herein, we describe an allosteric binding pocket common to PAD1-4 suitable for the identification of potent, non-covalent enzyme inhibitors. A ligand-based virtual screen is utilized to identify a PAD4 inhibitor for which surface plasmon resonance confirms target binding but non-competitively with a known PAD4 ligand. We further show through co-crystal structure analysis that the ligand binds PAD4 at an allosteric pocket resulting in stabilization of a catalytically inactive, calcium-deficient enzyme conformation. A ligand designed based on this site potently inhibits all four PAD isozymes and prevents protein citrullination in neutrophils with a broader protein repertoire than observed with a PAD4-selective inhibitor.
Authors
- Fabien Vincent (ORCID: https://orcid.org/0000-0002-8782-0225)
- Shenping Liu (ORCID: https://orcid.org/0000-0001-9400-3007)
- Paul Balbo
- Simeon Ramsey
- John M. Curto (ORCID: https://orcid.org/0000-0001-9033-5952)
- Kimberly F. Fennell (ORCID: https://orcid.org/0000-0002-1687-5237)
- Mark E. Schnute (ORCID: https://orcid.org/0000-0003-3075-4578)
- John I. Trujillo (ORCID: https://orcid.org/0000-0003-2303-0256)
- Jennifer E. Davoren (ORCID: https://orcid.org/0000-0002-7312-0666)
- Frank Lovering (ORCID: https://orcid.org/0000-0002-9515-8200)
- Parag V. Sahasrabudhe (ORCID: https://orcid.org/0000-0002-8442-637X)
- Jeffrey W. Pelker
- Stephen W. Wright (ORCID: https://orcid.org/0000-0002-9785-5077)
- Jeanne S. Chang (ORCID: https://orcid.org/0000-0002-8043-8621)
- Kentaro Futatsugi (ORCID: https://orcid.org/0000-0003-3137-9212)
- Susan E. Drozda
- Steve Kortum
- Katherine L. Lee (ORCID: https://orcid.org/0000-0003-0155-290X)
- Mary Ellen Banker
- Leslie Dakin
- F.F. Vajdos (ORCID: https://orcid.org/0000-0002-8256-2087)
- J. Perry Hall (ORCID: https://orcid.org/0000-0002-0316-847X)
- Xing Li (ORCID: https://orcid.org/0000-0002-9056-7996)
- Jennifer Nicki (ORCID: https://orcid.org/0000-0002-5440-2991)
- Won Young Choi
- Weidong Ding
Institutions
- Pfizer (United States) (US)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-05-16
- DOI
- https://doi.org/10.1038/s41467-025-59919-4
- Citations
- 8
- Primary Topic
- Galectins and Cancer Biology
- Type
- article
- Field-Weighted Citation Impact
- 6.38
Funders
- U.S. Department of Energy
- Industrial Macromolecular Crystallography Association Collaborative Access Team
- Office of Science
- Argonne National Laboratory