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

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.

(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.