MP01:Abdelkarim:ChemicalNaniteHDAC3NCoR2
From LabAutopedia
The development and implementation of chemical nanites to probe HDAC3/NCoR2 interface
Hazem Abdelkarim,1 Michael Brunsteiner,1 Bai He,1 Raghupathi Neelarapu,1 Yong Soo Choi,1 Subash Velaparthi,1 Richard van Breemen,1 Sylvie Y. Blond,2 Pavel A. Petukhov1*
1Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, IL 60612.
2UMRS-940, Institut Universitaire d’Hématologie (IUH) Saint Louis, Institut de Génétique Moléculaire, 27 rue Juliette Dodu, 75010 Paris, France.
Histone deacetylases (HDACs) are a family of enzymes involved in the regulation of gene transcription through deacetylation of lysine side chains in histones and other proteins. HDACs isoforms, in particular HDAC3, have emerged as a viable drug targets for multiple therapeutic applications including oncological, neurological, immunological, and inflammatory diseases. The design of selective inhibitors of particular HDAC isoforms is deemed necessary to enhance potency and reduce toxicity of currently available inhibitors and to broaden the scope of applications of HDAC inhibitors in diseases other than cancer. As most of HDAC isoforms assemble with other proteins to form unique functional complexes, the structures of these complexes might hold the key for successful rational design of isoform selective HDAC inhibitors. In mammalian cells, HDAC3, a member of the class I HDAC family, is found as part of a large protein complex with Nuclear Receptor Co-repressor 2 (NCoR2). Direct interactions with the deacetylase activating domain (DAD), a segment of approximately 80 amino acids in NCoR2, is required and sufficient for HADC3 activation. Despite the progress in HDAC drug discovery, both ligand-based (LBDD) and structure-based drug design (SBDD) approaches are limited in their applicability in targeting of HDAC3/NCoR2 complex because high resolution three-dimensional structures are known only for four (HDAC2, HDAC4, HDAC7, and HDAC8) out of 11 human HDAC isoforms. The need of new tools that can characterize the HDAC3-NCoR2 interface with respect to NCoR2 position and directionality, distance to the catalytic site of HDAC3, and accessibility to inhibitors is high. We hypothesized that it would be possible to map HDAC3-NCoR2 complex by photo-affinity probes/nanites (PAPs) that can cross-link to HDAC3 only or to HDAC3 and NCoR2. Inspired by the BEProFL approach, an in house drug discovery tool for mapping HDACs surfaces for selective inhibitors, we designed and synthesized novel potent photoreactive HDAC3 inhibitors. Using these photoreactive chemical probes, which we call chemical nanites, we performed a set of in vitro biological experiments and in silico analysis to build an experimentally based homology model of the complex. We demonstrated that NCoR2 binds in the vicinity of the rim of the catalytic site of HDAC3 where it can be reached by the HDAC inhibitor surface binding group. This study has established a new drug discovery tool that can help in the SBDD of new HDAC inhibitor and a robust chemical biology tool that can advance our understanding of the biology of HDACs within their functional physiological complexes. Currently, we are actively engaged on development of a novel assay for identification of disruptors of the HDAC3-NCoR2 interface based on the HDAC3/NCoR2 complex structural model.
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