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  Home > JCE Print > Journal of Chemical Education > Issues > 2002  > September  >
In the Laboratory
Entropy Loss of Hydroxyl Groups of Balanol upon Binding to Protein Kinase A
Gergely Gidofalvi
Department of Chemistry, San Diego State University, San Diego, CA 92182

Chung F. Wong
Department of Pharmacology and the Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093-0365

J. Andrew McCammon
Department of Chemistry and Biochemistry, Department of Pharmacology and the Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093

Cover
September 2002
Vol. 79 No. 9
p. 1122
Abstract
This article describes a short project for an undergraduate to learn several techniques for computer-aided drug design. The project involves estimating the loss of the rotational entropy of the hydroxyl groups of balanol upon its binding to the enzyme protein kinase A (PKA), as the entropy loss can significantly influence PKA–balanol binding affinity. This work employs semiempirical quantum mechanical techniques for estimating the potential energy curves for the rotation of the hydroxyl groups of balanol in vacuum and in PKA, and solves the Poisson equation to correct the potential energy curves for hydration effects. Statistical mechanical principles are then applied to estimate the desired entropy loss from the potential energy curves. The analysis examines the influence of hydration effects on the rotational preference of the hydroxyl groups and the significance of the rotational entropy in determining binding affinity.
More Information
*  Citation
 Gidofalvi, Gergely; Wong, Chung F.; McCammon, J. Andrew. J. Chem. Educ. 2002 79 1122.
*  Keywords
 Computational Chemistry; Drugs / Pharmaceuticals; Medicinal Chemistry; Molecular Recognition; Undergraduate Research
*  History
 Created:
Last Updated:		 August 12, 2002
March 16, 2005
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