6PX9

Crystal structure of procaspase-8 in complex with covalent small molecule inhibitor 63-R

Summary for 6PX9

• Entry DOI: 10.2210/pdb6px9/pdb
• Descriptor: Caspase-8, N-{(3R)-1-[4-(morpholin-4-yl)benzene-1-carbonyl]piperidin-3-yl}-N-phenylacetamide (3 entities in total)
• Functional Keywords: zymogen, procaspase, covalent inhibitor, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 6
• Total formula weight: 187585.13

Authors

Xu, J.H.,Wolan, D.W. (deposition date: 2019-07-25, release date: 2020-01-29, Last modification date: 2024-11-06)

Primary citation

Xu, J.H.,Eberhardt, J.,Hill-Payne, B.,Gonzalez-Paez, G.E.,Castellon, J.O.,Cravatt, B.F.,Forli, S.,Wolan, D.W.,Backus, K.M.
Integrative X-ray Structure and Molecular Modeling for the Rationalization of Procaspase-8 Inhibitor Potency and Selectivity.
Acs Chem.Biol., 15:575-586, 2020

PubMed Abstract: Caspases are a critical class of proteases involved in regulating programmed cell death and other biological processes. Selective inhibitors of individual caspases, however, are lacking, due in large part to the high structural similarity found in the active sites of these enzymes. We recently discovered a small-molecule inhibitor, , that covalently binds the zymogen, or inactive precursor (pro-form), of caspase-8, but not other caspases, pointing to an untapped potential of procaspases as targets for chemical probes. Realizing this goal would benefit from a structural understanding of how small molecules bind to and inhibit caspase zymogens. There have, however, been very few reported procaspase structures. Here, we employ X-ray crystallography to elucidate a procaspase-8 crystal structure in complex with , which reveals large conformational changes in active-site loops that accommodate the intramolecular cleavage events required for protease activation. Combining these structural insights with molecular modeling and mutagenesis-based biochemical assays, we elucidate key interactions required for inhibition of procaspase-8. Our findings inform the mechanism of caspase activation and its disruption by small molecules and, more generally, have implications for the development of small molecule inhibitors and/or activators that target alternative (e.g., inactive precursor) protein states to ultimately expand the druggable proteome.

PubMed: 31927936
DOI: 10.1021/acschembio.0c00019

Experimental method

X-RAY DIFFRACTION (2.88 Å)