Determinants of ligand binding to cAMP-dependent protein kinase.
Protein kinases are essential for the regulation of cellular growth and metabolism. Since their dysfunction leads to debilitating diseases, they represent key targets for pharmaceutical research. The rational design of kinase inhibitors requires an understanding of the determinants of ligand binding to these proteins. In the present study, a theoretical model based on continuum electrostatics and a surface-area-dependent nonpolar term is used to calculate binding affinities of balanol derivatives, H-series inhibitors, and ATP analogues toward the catalytic subunit of cAMP-dependent protein kinase (cAPK or protein kinase A). The calculations reproduce most of the experimental trends and provide insight into the driving forces responsible for binding. Nonpolar interactions are found to govern protein-ligand affinity. Hydrogen bonds represent a negligible contribution, because hydrogen bond formation in the complex requires the desolvation of the interacting partners. However, the binding affinity is decreased if hydrogen-bonding groups of the ligand remain unsatisfied in the complex. The disposition of hydrogen-bonding groups in the ligand is therefore crucial for binding specificity. These observations should be valuable guides in the design of potent and specific kinase inhibitors.
Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla 92093-0365, USA. phunenbe@ucsd.edu
P H
PH
Hünenberger
V
V
Helms
N
N
Narayana
S S
SS
Taylor
J A
JA
McCammon
D000255:Adenosine Triphosphate / Q000737:chemistry; D001381:Azepines / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D017868:Cyclic AMP-Dependent Protein Kinases / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism*; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000378:metabolism; D006160:Guanosine Triphosphate / Q000737:chemistry; D062385:Hydroxybenzoates / Q000737:chemistry / Q000378:metabolism; D007293:Inosine Triphosphate / Q000737:chemistry; D008024:Ligands; D008432:Mathematical Computing; D008956:Models, Chemical; D012997:Solvents; D055672:Static Electricity; D013816:Thermodynamics
D001381:Azepines; D004791:Enzyme Inhibitors; D062385:Hydroxybenzoates; D008024:Ligands; D012997:Solvents; D007293:Inosine Triphosphate; C036863:magnesium ITP; C036852:magnesium GTP; C015405:ophiocordin; D006160:Guanosine Triphosphate; D000255:Adenosine Triphosphate; D017868:Cyclic AMP-Dependent Protein Kinases