Application of molecular modeling to drug discovery and functional genomics

Molecular modeling can accelerate and guide drug design and contribute to the understanding of the biochemical functions of gene products. This thesis applies molecular modeling to facilitate the drug design for human African trypanosomiasis and develops a new modeling technique for protein biochemical function annotations. A special technique employed in this work is the prediction of the individual amino acids in protein structures that are involved in ligand interactions; these predicted local interaction sites are used for drug discovery and for the prediction of the biochemical function of proteins of unknown function.;Chapter 2 applies molecular modeling to the structure based drug design for human African trypanosomiasis (HAT) at the Aurora kinase -1 target. HAT is a vector borne disease caused by several species of trypanosomes, affecting thousands of people every year. This disease is fatal if untreated. Current therapeutic interventions are unsatisfactory, all with limited efficacy or life-threatening side effects. In humans, Aurora kinase is an important target for cancer therapies. Its homologue from the pathogenic Trypanosoma brucei, Aurora kinase -1 (TbAUK1), is a validated target for therapeutic intervention for trypanosomiasis, providing an opportunity to repurpose human Aurora kinase inhibitors for the development of TbAUK1 inhibitors. We conducted comparative modeling of TbAUK1 and docking studies to help design and prioritize inhibitors based on a series of analogs of the pyrrolopyrazole inhibitor danusertib, currently in clinical trials for cancer. The TbAUK1 model has provided further structure-based insights for design of inhibitor affinity and selectivity. New inhibitors designed using the TbAUK1 homology model showed sub-micromolar inhibition in the T. brucei proliferation assay with 25-fold selectivity over human cells.;Chapter 3 describes the application of molecular modeling techniques to investigate other targets for Trypanosomiasis treatment, Trypanosoma brucei phosphodiesterase B1 (TbrPDEB1) and Trypanosoma brucei phosphodiesterase B2 (TbrPDEB2). Homology modeling and docking studies for the inhibitors that are repurposed from human phosphodiesterase 4 (PDE-4) inhibitors help to rationalize the structure-activity relationships for the piclamilast series analogs. The comparison of TbrPDEB1, TbrPDEB2 and human PDE-4 has provided insight for the next generation ligand design.;Chapter 4 describes molecular modeling techniques applied to the development of protein function annotation methodology for structural genomics proteins. The Protein Structure Initiative (PSI) has led to significant growth in the number of protein structures. So far, over 11,000 structural genomics (SG) proteins have been deposited in the PDB and most of these SG proteins are of unknown or uncertain function. To bridge the biochemical functions and structures of the proteins, we developed a computational method to facilitate the classification and identification of the function of proteins using the 3D structures as input. A new methodology, Structurally Aligned Local Sites of Activity (SALSA) has been developed for this purpose. This method utilizes two previously developed computational active site predictors, POOL and THEMATICS. As a proof of concept, the enzymes in the concanavalin-A like lectins/glucanases superfamily have been classified according to their biochemical function. The proteins in this superfamily have a similar fold, consisting of a sandwich of 12-14 antiparallel beta strands in two curved sheets. Based on the computationally predicted active site residues and a local structural alignment, the enzymes in this superfamily have been successfully sorted into six functional subgroups and information about the function of SG proteins also has been provided. One SG protein has been found to be correctly annotated and four SG proteins are likely to belong to new functional subgroups.