The development of dimetallic metal complexes into functional and selective recognition agents for monophosphorylated peptides is described. The development of dimetallic metal complexes into functional and selective phosphopeptide recognition agents is described. Scaffold functionalization was conducted to assess whether binding affinity for phosphate monoesters could be modulated. A protocol for the facile synthesis of symmetric and asymmetric pyridine-functionalized bis-dipicolylamine (BDPA) scaffolds was thus first optimized. Zn(II) complexes were screened for the ability to bind to various phosphate monoesters of biological relevance using isothermal titration calorimetry (ITC). An expanded family of compounds was then screened using a variety of biophysicial and biological techniques for the ability to bind to disrupt Stat3 dimer both in biophysical assays and in whole cells. Several compounds displayed the ability to potently disrupt Stat3 dimer formation at low micromolar doses. Moreover, one compound emerged as having potent anti-cancer activity against MDA468, a solid breast cancer tumor line. Efforts were subsequently redirected towards the development of Zn(II)-BDPA receptors which mimicked the pY, pY+X recognition motif displayed by human SH2 domains. A family of ditopic biphenyl-based receptors, computationally predicted to adopt this binding mode, were synthesized and screened against a family of high-profile pY-containing phosphopeptides. The reported family of mimetics displayed a wide variance in cytotoxicity against common cancer cell lines, supporting our structure-activity hypothesis. Selectivity observed in our fluorescence intensity assay did not hold in a cellular context. We next pursued the development of selective receptors for phosphopeptides containing pS instead of pY. A diverse family of Zn(II)-BDPA receptors featuring a 2’ substituted benzothiazole core were synthesized, and their binding affinities toward model phosphopeptides assessed. A central conclusion of this project is that development of potent, selective receptors for anionic and hydrophobic peptides will likely be possible only by using receptors with cationic or hydrophobic pendants, and by maximizing phosphopeptide-specific interactions. Lastly, investigations into the use of bowl-type receptors as phosphopeptide recognition agents are presented. Synthesis of a prototype bowl receptor and early efforts to characterize the receptor’s binding preferences using ITC are reported. Progress-to-date in the development of a FRET system, which will be used to measure the receptor’s affinity for different dephosphorylation motifs, is also reported.

Thesis (Ph. D.)--Ohio State University, 2009. / Title from first page of PDF file. Includes vita. Includes bibliographical references (p. 113-117).

Thesis (Ph. D.)--University of Texas at Austin, 2003. / Vita. Includes bibliographical references. Available also from UMI Company.

Thesis (Ph. D.)--University of Hong Kong, 1999. / Includes bibliographical references (leaves 226-247).

The failure of the pharmaceutical industry to increase the delivery of new drugs into the market is driving a re-assessment of practices and methods in drug discovery and development. In particular alternative strategies are being pursued to find therapeutics that are more selective, including small molecules that target protein-protein interactions. However, success depends on improving our understanding of the recognition of small molecules by interfaces in order to develop better methods for maximising their affinity and selectivity, whilst trying to confer an appropriate therapeutic profile. This thesis starts with the description of the creation of TIMBAL, a database that holds small molecules disrupting protein-protein interactions. The thesis then focuses on the analysis of these molecules and their interactions in a medicinal chemistry and structural biology context. TIMBAL molecules are profiled against other sets of molecules (drugs, drug-like and screening compounds) in terms of molecular properties. Using the structural databases in the Blundell group, the atomic detail of the interaction patterns of TIMBAL molecules with their protein targets are compared with other molecules interacting with proteins, comprising natural molecules, small peptides, synthetic small molecules (including drug-like and drugs) and other proteins. The structural features and composition of the binding sites of these complexes are also analysed. Keeping in mind that current drug candidates are somewhat too lipophilic to succeed, these interaction profiles are defined in terms of polar and apolar contacts, with the aim of migrating natural patterns into the design of new therapeutics.

No description available.

The development of suitable models to study and quantify the strengths of noncovalent interactions is a major goal of our group. With this goal in mind, we have synthesized octasubstituted diarylacetylenes (tolanes) as potential model systems to measure intramolecular noncovalent interactions. The Stille cross-coupling reaction allowed synthesis of both arylacetylenes and tolanes from aryl iodides. The Stille reaction is usually slow for electron rich aryl iodides (such as these aryl iodides that are substituted resorcinol derivatives). However, these crowded penta-substituted aryl iodides underwent the Stille coupling reactions (typically 2-3 hours) at a significantly faster rate than the Stille couplings of the un-crowded tri-substituted aryl iodides (typically 24 hours). DFT calculations on 1,3-dimethoxy-2-iodobenzene (as a model system) indicate that this rate difference is mainly due to a decrease in the reduction potential of the crowded penta-substituted aryl iodides (~ 0.4 eV lower) relative to the tri-substituted aryl iodides. The successful synthesis of the targeted crowded symmetrical tetra ester produced a mixture of atropomers, which separated into two components with similar NMR and MS data. HF calculations on 4,4',6,6'-tetra-tert-butyl-1,1',3,3'-tetramethoxydiphenylacetylene (as a model system) showed that there are five possible atropomeric conformations. We separated the component which showed a green fluorescence when irradiated with UV (254 nm) light and grew a suitable single crystal. The X-ray crystal structure revealed that this component is the syn-syn_anti atropomer. The remaining atropomers, which show blue fluorescence when irradiated with UV (254 nm) light, were not successfully separated. Comparison of the observed UV spectrum of the green-fluorescent atropomer (syn-syn_anti) with a calculated (ZINDO) UV spectrum of diphenylacetylene, with an interplanar angle of 0° between the arene rings, showed that the observed and calculated spectra closely matched. The calculated (ZINDO) UV spectrum of diphenylacetylene, with an interplanar angle of 60° between the arene rings, closely matched the observed spectrum for the blue-fluorescent component (mixture of atropomers). The combination of experimental and computational methods demonstrated the stereochemical complexities of the crowded symmetrical tetra ester. / Ph. D.

published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

The creation of small molecule libraries for binding into the NS1A protein of influenza A viruses and the development of an indicator displacement assay for the differentiation of fatty acids are reported herein. Using Mitsunobu chemistry, a variety of structures based on hydroquinone, resorcinol and 2,7-dihydroxynaphthalene cores were synthesized. Both polar and non-polar functional groups were added to diversify the cores to help understand which molecule binds best to the protein. Because of poor protein binding, the focus of the project moved to a new lead compound, epigallocatechin-3-gallate (EGCG). EGCG showed promise in computational studies and efforts towards the synthesis of the epigallocatechin core were undertaken. Using a fluorescent indicator displacement assay (IDA), a sensing system for fatty acids was developed. The system consisted of bovine, rabbit, and human serum albumins as host molecules, while the fluorescent indicators were fluorescein, 2-anthracene carboxylic acid, and 1-anilino-8-naphthalene sulfonic acid. Fatty acids were able to be differentiated from one another based on their carbon chain length and the degree of unsaturation. The IDA was then subjected to a complex mixture of fatty acids, in the form of edible oils. The oils (extra virgin olive, hazelnut, peanut, sunflower and canola) with different fatty acid profiles were able to be differentiated from each other using principal component analysis. / text

No description available.