This summer, I will be working on a pseudo-Chemical Genomics project. Chad Myers’ lab group here at UMN has been working on making chemical genetic profiles, which means they’ve been able to run large libraries of compounds with different gene deletion libraries and, by comparing those with previously known genetic interaction profiles, can determine the modes of actions of many of these compounds (i.e. their function and likely genes that encode for the protein they’re targeting). For example, a compound from an oncology database might be shown to be involved with DNA Repair and Replication. For more information on this project, you can go to the lab website.
After this process, each compound can be annotated with its function on their chemical genomics database. These compounds are consequently associated with a list of proteins that are potential targets. My project will be trying to match each compound with its exact target protein from that list.
Docking is commonly used for computer aided drug design (CADD) and involves taking huge libraries of potential drug targets, or ligands, and “docking” them into a target protein. For example, the general idea is that if a pharmaceutical company or research group knows that protein X causes disease Y, it will dock each compound from a library into protein X knowing that if they can find the compound that binds to protein X and inhibits its function, that compound would likely be a successful drug candidate for disease Y.
My project will be using this docking software in a unique way from this standard use by instead using it to sample proteins that have been determined to be possible targets of the ligand via chemical genomics, and try to determine which protein is the most likely target. Through this project, I hope to learn how to work with big data and databases, become familiar with docking and pharmaceutical software, experience what computer science research is like, and hopefully contribute to this field which has the potential to help find new drug candidates.