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Biomolecular ligand design : enhancing binding affinity and specificity utilizing electrostatic charge optimization and packing techniques

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dc.contributor.advisor Bruce Tidor. en_US Sherman, B. Woody (Brian Woody), 1977- en_US
dc.contributor.other Massachusetts Institute of Technology. Dept. of Chemistry. en_US 2005-06-02T18:27:51Z 2005-06-02T18:27:51Z 2004 en_US 2004 en_US
dc.description Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2004. en_US
dc.description Vita. en_US
dc.description Includes bibliographical references (p. 257-281). en_US
dc.description.abstract Theory and methods to design ligands with enhanced binding affinity and specificity for use as biological therapeutics were developed. These methods involve electrostatic charge optimization techniques and packing considerations. First, a detailed investigation of a transition state analog (TSA) binding to the E. coli chorismate mutase enzyme was performed. This study included an electrostatic component analysis of both the ligand and receptor to understands the determinants of binding as well as an optimization of the TSA charges that revealed that the system was well optimized for binding. In another study, a method was developed to predict potential affinity-enhancing modifications to a protein therapeutic. An antibody raised against the VLA-1 [alpha]-1 [beta]-1 integrin was used in this study and several mutation predictions arose that were computed to enhance binding affinity to the target. The set of predictions could be classified into four groups based on their physical characteristics within the system. The residues making long range electrostatic interactions were found to have the highest percentage of computed affinity-enhanced binders. Finally, an extension to the affinity charge optimization theory was implemented that accounted for broad and narrow specificity of binding. An application to the protease of HIV was performed to explore the determinants of specificity. General principles were found in a narrow specificity study with HIV protease as a target and the human aspartyl proteases pepsin and cathepsin D as decoys that may help to elucidate principles for designing more selective inhibitors. en_US
dc.description.abstract (cont. ) In a broad specificity study with wild type HIV protease and several escape mutant proteases, we found common features on the protease that could be targeted to create a new generation of HIV protease inhibitors that are not as susceptible to viral resistance as the current therapeutics. en_US
dc.description.statementofresponsibility by B. Woody Sherman. en_US
dc.format.extent 284 p. en_US
dc.format.extent 11812808 bytes
dc.format.extent 11812609 bytes
dc.format.mimetype application/pdf
dc.format.mimetype application/pdf
dc.language.iso eng en_US
dc.publisher Massachusetts Institute of Technology en_US
dc.rights M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. en_US
dc.subject Chemistry. en_US
dc.title Biomolecular ligand design : enhancing binding affinity and specificity utilizing electrostatic charge optimization and packing techniques en_US
dc.type Thesis en_US Ph.D. en_US
dc.contributor.department Massachusetts Institute of Technology. Dept. of Chemistry. en_US
dc.identifier.oclc 56481200 en_US

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