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Research Abstracts Online
January 2008 - March 2009

Mayo Clinic College of Medicine
Department of Molecular Pharmacology and Experimental Therapeutics

PI: Yuan-Ping Pang, Associate Fellow

Structure-based Drug Design

This project’s goal is to develop and apply computational methods for determining three-dimensional models of drug targets from genomes and identifying drug candidates from chemical databases. Previous work has culminated in the cationic dummy atom approach for molecular dynamics simulations of metalloproteins such as the zinc endopeptidase of botulinum neurotoxin serotype A and a group of improved, dimeric analogs of therapeutic agents. With high-productivity computing, the researchers intend to predict three-dimensional protein structures as drug targets from genomic information by using multiple molecular dynamics simulations and the group’s new protein simulation method, and to predict viable drug candidates from millions of unique chemical structures by using massive parallel docking. 

During this period, the researchers have used the supercomputers to test the practicality of their methods in identification and optimization of small-molecule reactivators of human acetylcholinesterase and small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A, protein kinase C, insect acetylcholinesterases, and ribosome inactivating proteins. Successful completion of these projects will lead to computational approaches that complement experimental approaches in drug discovery and development, and ultimately result in therapeutics for treating cancers, infectious diseases, and other medical problems.

Group Members

Paramita Dasgupta, Research Associate
James R. Thompson, Faculty Collaborator