Docking and cheminformatic analysis of protein-ligand interactions: Cytochromes P450 (2D6 and P450cam) and estrogen receptors from human and zebrafish

In this thesis is presented our analysis of protein-ligand interactions and development of cheminformatic tools to help in the design of protein inhibitors more effectively, either as drug leads or as reagents for studying protein function. We did cheminformtic studies characterizing the binding of potential drug candidates to the CYP2D6 enzyme, and developed a 3D QSAR descriptor in the Heme-Based Coordinate System , to help in visualizing the docking orientations in CYP binding sites. Likelihood of a molecule being a drug was found to be inversely correlated with affinity for CYP2D6. In P450cam we proposed a new two step mechanism for substrate entry into the active site pocket, based on docking. We also did docking studies of endocrine disruptors into our homology modeled zebrafish estrogen receptors (as a model for human estrogen receptors) and found their binding preferences to be the same as humans. Finally we did cheminformatic studies in the new field of fragment-based drug discovery, including fragment analysis of existing drugs and did docking studies. Although different drug classes contained different ring fragments, some common trends were observed. In particular, over half of all drugs had ring nitrogens as potential hydrogen-bond donors or acceptors. To complete this work, computational tools were used, by developing chemistry softwares or writing in house programs. Also we applied fluorescence based assays to validate our in silico studies