Macrocyclic Peptides Uncover a Novel Binding Mode for Reversible Inhibitors of LSD1

Jie Yang; Vladimir O Talibov; Stefan Peintner; Claire Rhee; Vasanthanathan Poongavanam; Matthis Geitmann; Matteo Rossi Sebastiano; Bernd Simon; Janosch Hennig; Doreen Dobritzsch; U Helena Danielson; Jan Kihlberg

doi:10.1021/acsomega.9b03493

Macrocyclic Peptides Uncover a Novel Binding Mode for Reversible Inhibitors of LSD1

ACS Omega. 2020 Feb 17;5(8):3979-3995. doi: 10.1021/acsomega.9b03493. eCollection 2020 Mar 3.

Affiliations

¹ Department of Chemistry-BMC, Uppsala University, Box 576, SE-75123 Uppsala, Sweden.
² Beactica AB, Uppsala Business Park, Virdings allé 2, SE-75450 Uppsala, Sweden.
³ Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
⁴ Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden.

Abstract

Lysine-specific demethylase 1 (LSD1) is an epigenetic enzyme which regulates the methylation of Lys4 of histone 3 (H3) and is overexpressed in certain cancers. We used structures of H3 substrate analogues bound to LSD1 to design macrocyclic peptide inhibitors of LSD1. A linear, Lys4 to Met-substituted, 11-mer (4) was identified as the shortest peptide distinctly interacting with LSD1. It was evolved into macrocycle 31, which was >40 fold more potent (K _i = 2.3 μM) than 4. Linear and macrocyclic peptides exhibited unexpected differences in structure-activity relationships for interactions with LSD1, indicating that they bind LSD1 differently. This was confirmed by the crystal structure of 31 in complex with LSD1-CoREST1, which revealed a novel binding mode at the outer rim of the LSD1 active site and without a direct interaction with FAD. NMR spectroscopy of 31 suggests that macrocyclization restricts its solution ensemble to conformations that include the one in the crystalline complex. Our results provide a solid basis for the design of optimized reversible LSD1 inhibitors.