Energetic and Structural Effects in Protein-Ligand Interactions

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With the support of an award from the Organic and Macromolecular Program, Professor Stephen Martin has recognized a critical challenge in molecular recognition which is understanding how to design small molecules that bind tightly to proteins. Toward this end, understanding how introducing specific structural changes into a ligand affects the relative binding affinity of the modified ligand is of paramount importance. The task is rendered more complicated because enthalpy/entropy compensation invariably attends such structural variations. The group recently discovered that introducing conformational constraints in small molecules does not necessarily lead to more favorable binding entropies, a finding that is opposite to the putative effects of ligand preorganization. They thus suggest that variations in ligand structure will have differential consequences upon protein flexibility and dynamics that will be manifested in compensating changes in binding enthalpies and entropies that may enhance, attenuate, or override the anticipated effects of making structural modifications to a small molecule. In order to evaluate this hypothesis, a multidisciplinary approach has been adopted to investigate how selected variations in ligand structure affect energetics, structure and dynamics in protein-ligand interactions. Specifically, they will prepare constrained and flexible phosphotyrosine-derived ligands that will bind to the Grb2 SH2 domain. They will also prepare analogs having varying ratios of polar and nonpolar surface areas to probe hydrophobic effects. They will then use isothermal titration calorimetry to determine binding of various ligands to the Grb2 SH2 domain. Selected complexes will be characterized by x-ray crystallography to study the detailed interactions between the ligands and the domain. Analysis of the experimental data will enable use to correlate variations in ligand structure with changes in energetics, structure and protein flexibility and to probe the origin of enthalpy/entropy compensation in protein-ligand interactions. The broader impact of the proposed activity is that participating graduate and undergraduate students, especially undergraduate women and Latinos, will gain knowledge and learn experimental techniques in an interdisciplinary project at the forefront of biomolecular recognition. This training will enable them to pursue careers at the critical interface of organic chemistry, molecular biology and biophysics. Presenting the findings in the undergraduate classroom and a local high school will help stimulate even more students to pursue careers in science. Additionally, the results of these investigations will contribute to developing a core of knowledge that will enhance our understanding of protein-ligand interactions and facilitate the structure-based design of small molecules having high affinities for protein targets. Insights thus derived will better enable medicinal chemists to optimize ligand binding affinities as they transform leads into selective and potent therapeutic agents to treat diseases.