URSP Student Jihyun Lee Uses Molecular Modeling and Docking to study Caspase 1

My name is Jihyun Lee. I am a senior majoring in biochemistry and planning to pursue a pharmacy. I have always been fascinated with how drugs interact with the cells and also curious about why some of them sometimes work and sometimes do not. This further led me to want to learn more about my field of study through experience and go deeper into understanding biochemistry on the molecular level. Last semester, when I found that Michael Girgis who was my organic chemistry II lab instructor had his own ongoing research project on Organic synthesis, I often visited him to ask volunteer to participate in his outstanding research. After a number of persistent visits, I got to learn about part of the ongoing research in Michael’s group on Caspase 3 enzyme, which is associated with apoptosis (programmed cell death). This was the first time computational molecular modeling and docking were introduced to me.

My project for this semester is focused on Caspase 1 as one of enzymes responsible for inflammatory process and finding the best conformation of its potent inhibitor. On a weekly basis, I conduct docking using a software called AutoDock and saving the best 10 conformations in appropriate file format in order to open in Chimera or Ligplot software for further analysis of intermolecular interactions.

Through this research experience in this semester, I learned that molecular modeling and docking experiments are the most efficient and through step in the drug discovery process. Furthermore, studying the docking conformations can help me understand the nature of the intermolecular interactions between the different compounds to the binding site of the enzyme.