Peterson, Alexander A.Rangwala, Aziz M.Thakur, Manish K.Ward, Patrick S.Hung, ChristieOuthwaite, Ian R.Chan, Alix I.Usanov, Dmitry L.Mootha, Vamsi K.Seeliger, Markus A.Liu, David2023-07-272022-09-26Peterson, Alexander A., Aziz M. Rangwala, Manish K. Thakur, Patrick S. Ward, Christie Hung, Ian R. Outhwaite, Alix I. Chan et al. "Discovery and molecular basis of subtype-selective cyclophilin inhibitors." Nat Chem Biol 18, no. 11 (2022): 1184-1195. DOI: 10.1038/s41589-022-01116-11552-44501552-4469https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37376634AbstractAlthough 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.en-USCell BiologyMolecular BiologyJournal Article2023-07-2710.1038/s41589-022-01116-1