Discovery and molecular basis of subtype-selective cyclophilin inhibitors

  • Nat Chem Biol. 2022 Sep 26. doi: 10.1038/s41589-022-01116-1.
Alexander A Peterson  #  1  2  3 ,  Aziz M Rangwala  #  4 ,  Manish K Thakur  4 ,  Patrick S Ward  5  6  7 ,  Christie Hung  1  2  3 ,  Ian R Outhwaite  4 ,  Alix I Chan  1  2  3 ,  Dmitry L Usanov  1  2  3 ,  Vamsi K Mootha  5  6  7 ,  Markus A Seeliger  8 ,  David R Liu  9  10  11
Affiliations
  • 1. Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • 2. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
  • 3. Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
  • 4. Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA.
  • 5. Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • 6. Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA, USA.
  • 7. Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
  • 8. Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA. [email protected].
  • 9. Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA. [email protected].
  • 10. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. [email protected].
  • 11. Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA. [email protected].
  • # Contributed equally.
PMID: 36163383 DOI: 10.1038/s41589-022-01116-1
Abstract

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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