Mechanistic analysis of a suicide inactivator of histone demethylase LSD1

Lawrence M. Szewczuk, Jeffrey C. Culhane, Maojun Yang, Ananya Majumdar, Hongtao Yu, Philip A. Cole

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Abstract

Lysine-specific demethylase 1 (LSD1) is a transcriptional repressor and a flavin-dependent amine oxidase that is responsible for the removal of methyl from lysine 4 of histone H3. In this study, we characterize the mechanism and scope of LSD1 inhibition by a propargylamine-derivatized histone H3 substrate (1). Unlike aziridinyl and cyclopropylamine-derivatized histone H3 peptide substrate analogues, compound 1 appears to covalently modify and irreversibly inactivate LSD1 with high potency. Accompanying this inactivation is a spectroscopic change, which shifts the absorbance maximum to 392 nm. Spectral changes associated with the 1-LSD1 complex and reactivity to decreased pH and sodium borohydride treatment were suggestive of a structure involving a flavin-linked inhibitor conjugate between N5 of the flavin and the terminal carbon of the inhibitor. Using a 13C-labeled inhibitor, NMR analysis of the 1-flavin conjugate was consistent with this structural assignment. Kinetic analysis of the spectroscopic shift induced by 1 showed that the flavin adduct formed in a reaction with kinetic constants similar to those of the LSD1 inactivation process. Taken together, these data support a mechanism of LSD1 inactivation by 1 involving amine oxidation followed by Michael addition to the propargylic imine. We further examined the potential for a biotinylated analogue of 1 (1-Btn) to be used as a tool in affinity pulldown experiments. Using 1-Btn, it was feasible to selectively pull down spiked and endogenous LSD1 from HeLa cell nuclear extracts, setting the stage for activity-based demethylase proteomics.

Original languageEnglish (US)
Pages (from-to)6892-6902
Number of pages11
JournalBiochemistry
Volume46
Issue number23
DOIs
StatePublished - Jun 12 2007

ASJC Scopus subject areas

  • Biochemistry

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    Szewczuk, L. M., Culhane, J. C., Yang, M., Majumdar, A., Yu, H., & Cole, P. A. (2007). Mechanistic analysis of a suicide inactivator of histone demethylase LSD1. Biochemistry, 46(23), 6892-6902. https://doi.org/10.1021/bi700414b