Computational investigations of enzyme catalysis, design, and conformational aspects of drug-target interactions

In Chapter 1, the active conformation of the epothilone class of anti-tumor compounds was investigated. A new method was developed to determine the active conformations of drugs, named conformational panning. It involves correlating the energies of candidate active conformations relative to the global minima with experimentally known potencies in a series of analogues. The conformation discovered by this method fits the density data obtained by electron crystallography experiments on the epothilone-target complex better than the previously proposed conformer. This new conformation may be used in the future to help design more potent compounds.;The reaction cycle of the serine esterase enzyme butyrylcholinesterase was modeled quantum mechanically in Chapter 2. A combination of quantum and molecular mechanical techniques were employed to investigate the degree of active site reorganization these enzymes undergo during the course of catalyzing their multi-step reaction. It is shown that the active site reorganizes as little as possible. This expands our understanding of enzyme catalysis, as motions are often seen as beneficial, and provides methods for the future design of enzyme active sites to catalyze multi-step reactions without natural precedent.;Chapter 3 is a perspective on the potential use of covalent interactions in drug-target binding. These interactions can ensure potency early in the stages of drug development, and are not necessarily subject to the off-target toxicities with which they have been previously associated.;The goal of the project in Chapter 4 was to create transition state force fields to be used during computational enzyme design. The model system studied was the acetate base-catalyzed Kemp elimination of a benzisoxazole. Quantum mechanical energies of perturbed geometries were fitted to a force field equation for distances, angles, and dihedrals, and the effects of modifying the function were investigated.;In Chapter 5 the phosphate-transfer reaction of uridine-cytidine kinase was modeled using a combined quantum mechanical/molecular mechanical potential. The activation energy agrees well with the experimental barrier, and the transition structure may be used to help design substrates to be phosphorylated by this enzyme as probes for the UCK2 enzyme acting as a positron emission tomography (PET) reporter enzyme.