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This thesis presents new spherical harmonic (SH) approaches for ligand-based high-throughput virtual screening (HTVS). If it is assumed that small drug molecules may be adequately superposed and distinguished by co-locating their centers of mass and by performing rotational correlations of their shapes, then to a good approximation each molecule may be represented very compactly using a two dimensional (2D) SH surface envelope. Of course, this assumes that the true molecular surface is star-like, or single-valued, with respect to radial rays projecting from the selected origin. However, this often holds to a very good approximation for small globular molecules. Even when this is not the case, it is nonetheless reasonable to suppose that similar molecules should give similar radial projections and, therefore, that they should share very similar SH representations. Following this premise, a new program called “SpotLight” was developed. The results obtained with this software show that SH-based global shape matching provides a powerful new way to perform HTVS. SH surface representations are increasingly being applied to a broad range of object recognition and registration tasks, and have also been used to model protein-ligand shape complementarity. Most current shape similarity techniques search for global similarities, and may therefore miss finding active compounds with different overall shapes and sizes but which share similar substructures or surface features. Existing molecular fragment matching algorithms can identify common covalent substructures but they are not well suited for performing scaffold-hopping shape-based database searches. This thesis introduces a novel SH fragment-based shape matching approach that can exploit knowledge of structures of existing protein-ligand complexes to perform virtual screening using as queries SH surface fragments derived from crystallographic ligand binding surfaces.

In order to provide scalable, efficient and selective routes towards pharmaceutically relevant compounds, we have focused on improving the economical viability and practicality of strained-silane Lewis acid activation. Towards these goals, the Leighton group has developed a new mode of anion catalysis to activate silane Lewis acids. Weakly coordinating anions have been used to access hyper-coordinate silicon species with unprecedented levels of reactivity, which have facilitated previously unattainable complex fragment couplings. A highly enantioselective and efficient method for anion catalyzed nucleophilic addition to aldehydes has enabled the synthesis of rationally designed, structurally simplified D-ring modified analogs of spongistatin 1. The completion of a step-economical route towards extremely potent, linker-handle equipped spongistatin 1 analogs and their application to targeted drug delivery will be discussed.

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Thesis (Ph.D.) -- University of Rhode Island, 2007 / Typescript. Includes bibliographical references (leaves 73-82).

Thesis (Ph.D.)--Aberdeen University, 2009. / Title from web page (viewed on July 8, 2009). Includes bibliographical references.

Thesis (M.S. in Management of Technology)--Vanderbilt University, May 2006. / Title from title screen. Includes bibliographical references.