Systems-Based Design of Bi-Ligand Inhibitors of Oxidoreductases: Filling the Chemical Proteomic Toolbox

Genomics-driven growth in the number of enzymes of unknown function has created a need for better strategies to characterize them. Since enzyme inhibitors have traditionally served this purpose, we present here an efficient systems-based inhibitor design strategy, enabled by bioinformatic and NMR structural developments. First, we parse the oxidoreductase gene family into structural subfamilies termed pharmacofamilies, which share pharmacophore features in their cofactor binding sites. Then we identify a ligand for this site and use NMR-based binding site mapping (NMR SOLVE) to determine where to extend a combinatorial library, such that diversity elements are directed into the adjacent substrate site. The cofactor mimic is reused in the library in a manner that parallels the reuse of cofactor domains in the oxidoreductase gene family. A library designed in this manner yielded specific inhibitors for multiple oxidoreductases

Docking and homology modeling studies of proteins: estrogen receptor and dihydrodipicolinate reductase

Structure-based inhibitor design utilizes knowledge of the 3D structure of a protein receptor, often with a bound lead molecule, in an attempt to optimize affinity for the protein target. Docking plays an important role in this process by placing a molecule into the active site of the target molecule in the lowest energy conformation. So, docking can be viewed as a search or optimization method, to facilitate design of protein inhibitors. The purpose of this work is to facilitate drug design efforts to discover new chemical entities by attempting to predict and explain their binding modes. Another goal is to characterize zebrafish as a biological model system to study protein-ligand interactions involving estrogen receptors. In the first chapter of this thesis are docking studies of a newly synthesized compound with high affinity for the estrogen receptor. In these studies we tried to characterize the role of helix-12 motion and His 524 location when an agonist is bound versus an antagonist. Chapter 2 presents an analysis of the similarity of zebrafish estrogen receptor with human estrogen receptor, thereby suggesting zebrafish as a good model to study estrogen receptor-ligand interactions. These studies are relevant for use of zebrafish as a human model system and to detect endocrine disruptors. Chapter 3 presents docking studies of a cofactor mimic for oxidoreductases which . has served as a template for building a combinatorial chemistry library