Production of histone modifying enzymes and identification of chemical probes for epigenetic discovery Genomic function is the major factor in the most common diseases. Genomic function is regulated by the posttranslational methylation and acetylation state of histones. Histones are proteins found in cell nuclei that create nucleosomes into which DNA is structured. Enzymes that modify histones represent important potential drug targets for indications like cancers, neurodegenerative disorders, cardiovascular, and metabolic diseases. Enzymes that catalyze these modifications include numerous histone methyltransferases and demethylases ("MT's" &"DMT's"). Additionally, proteins that recognize or "read" these histone modifications contain bromodomains, chromodomains, etc. and are also considered epigenetic factors. If medicine is to move beyond conventional drug targets that represent symptomatic treatment only, then validation of these epigenetic enzymes and factors as drug targets remains a top priority for drug discovery. Chemical epigenetic inhibitors represent a powerful opportunity here. However, histone methylation is a relatively new discovery space, and the likely structures of MT or DMT inhibitors are not yet known. Few small molecule inhibitors are available, either for laboratory research or for lead development. Therefore, there is a significant and urgent need to develop assays and to identify new chemical probes for these targets. Small molecule probes would serve a valuable role in scientific investigations and serve as medicinal chemistry scaffolds for lead development. In this proposal, we will deploy a wide-field high throughput screening (HTS) approach by testing more than 1400 privileged scaffolds that include most FDA approved drugs and clinical trial agents against over 30 histone modifying enzymes, including HMTs and histone demethylases (HDMTs). Our preliminary studies have already demonstrated very positive results by identifying and confirming hits against a handful of selected HMTs. Wide-field HTS with known orally active and relatively safe compounds offers a number of advantages for chemical probe discovery: (1) any newly identified active compound will have a known scientific pharmacology to support new applications;(2) these probes have the potential to enable "drug rescue" or "drug repurposing";(3) for compounds already on the market, the new epigenetic activity information will help to provide enhanced understanding of their effectiveness or toxicity at the epigenetic level where no data was available;(4) for the compounds that are currently in clinical trials or have failed i late stage clinical trials, the new information will provide guidance to modify these compounds for better directed therapeutic effectiveness, and (5) this data will help establish a general chemo-epigenomic database. Having a publicly available library of epigenetic inhibitors is essential to moving ahead in this area.
It has been recognized for decades that the majority of common diseases have a genetic underpinning. More recently, it has been found that genetic function can be regulated by epigenetic factors that modify the functions of certain genes. While direct medical intervention in genomic structure has proven to be far more difficult than researchers had hoped, manipulation of epigenetic factors is seen as a much more fertile opportunity for treating diseases at their base level of causality. Chief among epigenetic factors are histones, using their posttranslational methylation and acetylation to regulate the epigenetic program of the genome. Histone modifying enzymes represent important drug targets for indications like cancers, neurodegenerative disorders, and metabolic diseases. Enzymes that catalyze these modifications include numerous histone methyltransferases and demethylases (MT's/DMT's). Additionally, proteins that recognize these histone modifications are also considered epigenetic factors. Validation of these epigenetic enzymes and factors as drug targets remains a top priority for drug discovery, if science is to move past mere symptomatic treatment. Chemical epigenetics represents a powerful approach to the discovery and validation of new targets. While the successful structures of chemical inhibitors of classic drug targets such as kinases or proteases are well established, little if anything is known about what an inhibitor of MT's or DMT's should look like. It is essential that inhibitors be found that can serv as probes to define the inhibition responses of these new drug targets. Reaction Biology Corporation (RBC) is a successful SBIR applicant with a proven track record of commercialization in producing methyltransferase proteins and creating radiolabeled assays for them. In this proposal, we build on the success of our grants to date, identifying epigenetic chemical probes by assaying proven and public small molecule collections. Probes identified will have a great potential value both as research tools and potential therapeutic agents.