Welcome to The Esposito Research Group!

We are focused on the study of Computational Biochemistry as it relates to Computer-Aided Drug Discovery (Computer-Aided Molecular Design, Small Molecule Design) and protein structure prediction. Specific areas include Quantitative Structure-Activity Relationship (QSAR), Comparative (Homology) Modelling, and Docking and Scoring. These three areas are powerful when used individually, but their true power is exploited when they are used together to provide a complete story of the interaction of a ligand with its receptor.

There is a myriad of different methods to construct QSAR models, but the ability to construct a chemically meaningful model is important. The primary goal of a QSAR study is to determine the physical properties of "good" and "bad" binders. QSAR models can also be used to derive the physicochemical properties involved in binding. This can lead to a better understanding of the composition of the binding site and the key ligand - receptor interactions.

The construction of protein models has many different facets with the common goal of better understanding biochemical processes. Comparative modelling is the bridging of bioinformatics to molecular biology and computational biochemistry. Bioinformatics tools are not a far departure from the world of biochemistry and provide additional information useful to those investigating biochemical problems. X-ray structures of solved proteins are used in conjunction with comparative modelling methods to predict the structures of unsolved proteins of interest.

The exploration of probable ligand binding modes (conformation, orientation, location) is accomplished through simulated docking. Using the solved X-ray structures of protein or protein structures based on comparative modelling, ligands are placed into the defined binding region and energy calculations are performed to determine the most-likely binding configuration. The docking of ligands to receptors provides a starting point for further simulations and analysis; specifically, receptor-dependent QSAR and molecular dynamics to elucidate the properties of binding and the interactions between the ligand and receptor.

The use of these methodologies provides insight to the experimental results. I am currently involved in several projects with different faculty members in the department ranging from drug discovery to the exploration of fundamental wet-chemistry research.