7TGS image
Entry Detail
PDB ID:
7TGS
Keywords:
Title:
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor JOMBt
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2022-01-09
Release Date:
2022-08-24
Method Details:
Experimental Method:
Resolution:
1.75 Å
R-Value Free:
0.18
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Mutations:K175I
Chain IDs:A (auth: X)
Chain Length:164
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Discovery and molecular basis of subtype-selective cyclophilin inhibitors.
Nat.Chem.Biol. 18 1184 1195 (2022)
PMID: 36163383 DOI: 10.1038/s41589-022-01116-1

Abstact

Although cyclophilins are attractive targets for probing biology and therapeutic intervention, no subtype-selective cyclophilin inhibitors have been described. We discovered novel cyclophilin inhibitors from the in vitro selection of a DNA-templated library of 256,000 drug-like macrocycles for cyclophilin D (CypD) affinity. Iterated macrocycle engineering guided by ten X-ray co-crystal structures yielded potent and selective inhibitors (half maximal inhibitory concentration (IC50) = 10 nM) that bind the active site of CypD and also make novel interactions with non-conserved residues in the S2 pocket, an adjacent exo-site. The resulting macrocycles inhibit CypD activity with 21- to >10,000-fold selectivity over other cyclophilins and inhibit mitochondrial permeability transition pore opening in isolated mitochondria. We further exploited S2 pocket interactions to develop the first cyclophilin E (CypE)-selective inhibitor, which forms a reversible covalent bond with a CypE S2 pocket lysine, and exhibits 30- to >4,000-fold selectivity over other cyclophilins. These findings reveal a strategy to generate isoform-selective small-molecule cyclophilin modulators, advancing their suitability as targets for biological investigation and therapeutic development.

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