A nucleosome sliding assay platform to screen inhibitors of SWI/SNF chromatin remodeling complexes

Period of Performance: 06/01/2017 - 05/31/2018


Phase 1 SBIR

Recipient Firm

Epicypher, Inc.
Durham, NC 27713
Principal Investigator


PROJECT SUMMARY In this proposal, EpiCypher Inc. will develop the first commercially available assay to monitor nucleosome remodeling, a major current focus for rational drug discovery that is starved of HTS tools. Nucleosomes are the basic units of chromatin, made up of ~147 bp DNA tightly wrapped around an octamer of histone proteins. Chromatin remodeling complexes utilize ATP to disrupt DNA- histone interactions and reposition nucleosomes, thus regulating DNA access. Aberrant nucleosome organization can severely disrupt gene expression, DNA repair and cellular differentiation, and is associated with cancer and disorders including schizophrenia, chronic inflammation, and intellectual disability. The profound role of remodeling complexes in tumorigenesis and cancer progression represents a new target class for epigenetic drug discovery rapidly gathering attention from our commercial partners. Of particular therapeutic interest are the SWI/SNF family of chromatin remodeling complexes, with 20% of all human cancers harboring a subunit mutation. SWI/SNF complexes are comprised of a remodeling ATPase (SMARCA2 [BRM] or SMARCA4 [BRG1]), three core proteins, and an additional four to eight accessory proteins (varying by cell type) that direct genomic localization of the complex and stimulate catalysis. The catalytic ATPase domains of SWI/SNF complexes have been identified in multiple studies as rational targets for therapeutic development. However, chromatin remodeling assays amenable to high throughput screening are currently lacking, a problem EpiCypher will address through this proposal. We will assess the feasibility of using recombinant nucleosomes (rNucs) homogenously assembled on sliding DNA sequences as a high- throughput, biologically relevant screening platform to identify compounds that directly inhibit chromatin remodeling. In Aim 1, EpiCypher will develop an innovative rNuc- based nucleosome sliding assay, which capitalizes on a unique DNA template that can be radiolabeled after SWI/SNF repositions the histone octamer to expose a Dam methylation site (GATC). In Aim 2, we will validate the sliding rNuc substrates by assaying chromatin remodeler activity with the isolated SMARCA4 enzyme. In Phase II, we will focus on commercial production of this high- throughput sliding rNuc screening platform for the identification of inhibitors that target the SWI/SNF chromatin remodeling family. This highly innovative research program will enable therapeutic development toward chromatin remodeling complexes, a major class of drug targets that currently lack adequate screening tools.