Harnessing the power of computational chemical biology to address non-traditional drug targets
Welcome to the Karanicolas Lab! Our goal is to develop structure-based approaches for modulating protein function using small-molecules. We apply these new approaches in projects seeking to re-activate disabled tumor suppressors, inhibit cancer-driving RNA-binding proteins, disable key oncogenic kinases, and tune the activity of antibodies used in cancer immunotherapy.
NEWS:
Yusuf’s paper is published
PHILADELPHA (July 15, 2020) Yusuf Adeshina’s paper was published today in PNAS! It’s entitled “Machine learning classification can reduce false positives in structure-based virtual screening”; in it, Yusuf first develops a new way to train machine learning scoring functions for virtual screening, then uses the resulting model to pick out hits for testing in a prospective experiment. Amazingly, essentially all the compounds predicted by his model have biological activity, and the best are remarkably potent! Already we’ve adopted this tool for other projects in our lab, and we hope others will too. Congratulations Yusuf!!
Welcome to Max and Gabriel
PHILADELPHA (June 1, 2020) Two new undergrads are joining the Karanicolas Lab for the summer: Max Yates (of Montana State) and Gabriel Ong (of Bowdoin College). Max is part of the RosettaCommons REU program, and Gabriel is supported by Bowdoin’s internship program. Welcome to both, and here’s to a fun and productive summer!
Jake’s paper is published
PHILADELPHA (March 11, 2020) Jake Khowsathit’s paper was published today in ACS Cent Sci! It’s entitled “Computational design of an allosteric antibody switch by deletion and rescue of a complex structural constellation”, and it’s the product of many years of hard work from our team. The paper report new computational approaches developed by Andrea to design protein-ligand complexes, followed by Jake’s application of these tools and thorough wetlab characterization of the resulting designs. Congratulations Jake and Andrea!!
Nan Bai and Yusuf Adeshina earn their PhDs
LAWRENCE (December 19, 2019) Nan Bai and Yusuf Adeshina successfully defended their dissertations today - congratulations to both! Nan’s dissertation is entitled “Designing small molecule inhibitors of RNA-binding protein Musashi using new biochemical and computational approaches”, and Yusuf’s is entitled “Computational tools to address challenging targets in drug discovery: target- focused chemical libraries and structure-based machine learning”. They are the last two students from University of Kansas in the lab - the end of an era!
John Karanicolas promoted to Full Professor
PHILADELPHIA (August 21, 2019) – John Karanicolas, PhD, was recently promoted to the rank of Professor at Fox Chase Cancer Center. Reviewers highlighted the fact that his research program is among the most innovative in computer-aided drug design in the United States, and that he serves as an outstanding mentor.
Shipra Malhotra and Jake Khowsathit earn their PhDs
LAWRENCE (May 1, 2019) Shipra Malhotra and Jake Khowsathit successfully defended their dissertations today - congratulations to both! Shipra’s dissertation is entitled “Predicting the most tractable protein surfaces in the human proteome for developing new therapeutics”, and Jake’s is entitled “Using chemical biology to modulate antibody activity”. Both did an outstanding job!
John Karanicolas receives kinase-focused grant from the National Science Foundation
PHILADELPHIA (October 30, 2018) – John Karanicolas, PhD, has received a grant from the National Science Foundation to conduct deep learning to design selective kinase-targeted chemical probes. Read More
