A Complete Configurational Ensemble Approach to Expand Lsd1/Corest Druggability

Abstract

Lysine specific demethylase-1 (LSD1/KDM1A) in complex with the corepressor protein CoREST is a promising target for epigenetic drugs yet no therapeutics targeting LSD1/CoREST are currently available. Extended molecular dynamics (MD) simulations have indicated that LSD1/CoREST nanoscale clamp dynamics are regulated by substrate binding and highlighted key hinge points of this large-scale motion as well as the relevance of local residue dynamics. Prompted by the urgent need for new molecular probes and inhibitors to understand LSD1/CoREST interactions with small-molecules, peptides, protein partners, and chromatin, we undertake here a complete configurational ensemble approach to expand LSD1/CoREST druggability. The independent algorithms FTMap and SiteMap and a newly developed Druggable Site Visualizer (DSV) software tool were used to predict and inspect favorable binding sites on an ensemble of structures generated by MD simulation. We found that three hinge points revealed by MD simulations are new potential targets for the discovery of molecular probes to block association of LSD1/CoREST with chromatin or protein partners. A fourth region was also predicted from simulated configurational ensembles and was experimentally validated to have strong binding propensity for a small peptide. This prediction would be prevented when using only the X-ray structures available (including the X-ray structure bound to the same peptide), which underscores the relevance of protein conformational dynamics in protein interactions. A fifth region was also highlighted corresponding to a small pocket on the AOD domain. This study sets the basis for future virtual screening campaigns targeting the five novel regions reported herein and for the design of LSD1/CoREST mutants to probe LSD1/CoREST binding with chromatin and various protein partners. The newly developed computational methods are being further validated on various protein receptors and have shown promising preliminary results.