*The seminar will be in English, the event is open to the public.

Abstract 
High Performance Computing is becoming an essential tool in assisting fast and cost-efficient lead discovery and optimization. The application of rational, structure-based drug design is proven to be more efficient than the traditional way of drug discovery since it aims to understand the molecular basis of a disease and utilizes the knowledge of the three-dimensional structure of the biological target in the process. In this talk, we focus on the principles and applications of methodologies applied to computer-aided drug design.

We discuss Molecular Dynamics (MD) simulations to discover allosteric pockets in proteins, Virtual Screening to discover novel small molecule inhibitors of protein function and Free Energy Perturbation calculations to optimize the binding affinity of small molecule inhibitors. We examine different procedures ranging from the initial stages of the process that include receptor and library pre-processing, to docking, scoring and post-processing of top-scoring hits and how HPC resources have been used to achieve the desired results.

About the Speaker
Zoe Cournia graduated from the Chemistry Department in the University of Athens and subsequently pursued doctoral studies in the University of Heidelberg, Germany, with Dr. Jeremy Smith in the field of computational biophysical chemistry. For her thesis she used a combination of Molecular Dynamics (MD) simulations, Quantum Chemical, and Neutron Scattering calculations to provide insights into why cholesterol is evolutionary preferred for mammalian plasma membranes. Cournia then joined Dr. Bill Jorgensen's lab in the Department of Chemistry, Yale University to perform post-doctoral studies in computer-aided drug design - focusing on the design and discovery of novel anti-cancer agents and prediction of pharmacological properties using computational techniques. In the same lab, Dr. Cournia also worked on the discovery of novel and selective inhibitors of the parasitic Leishmania Major and Ancylostoma Ceylanicum MIF orthologs.

Dr. Cournia served as a co-President of the Yale Pharmaceutical and Biotechnology Society during 2007-2008, became a Lecturer in Yale College in 2009 and in 2009 was honored with the "Women of Innovation Award" from the Connecticut Technology Council. Since October 2009 she is a member of BRFAA, where as a researcher (Lecturer Level) she works on targeting the mutated cancerous PI3Kα protein with small molecule inhibitors, inhibition of the c-Myc-Max interaction with small molecule inhibitors, and the design of small molecule agonists for the RXRalpha-Nurr1 heterodimer as a means to treat Parkinson's disease. For these studies the Cournia lab employs a combination of MD simulations, virtual screening, de novo drug design, free energy perturbation calculations, pharmacological property prediction and Monte Carlo simulations.

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This event is part of the CyI Seminar Series.  View all CyI events.