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A semiempirical approach to ligand-binding affinities: Dependence on the Hamiltonian and corrections

✍ Scribed by Paulius Mikulskis; Samuel Genheden; Karin Wichmann; Ulf Ryde

Publisher
John Wiley and Sons
Year
2012
Tongue
English
Weight
927 KB
Volume
33
Category
Article
ISSN
0192-8651

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✦ Synopsis

Abstract

We present a combination of semiempirical quantum‐mechanical (SQM) calculations in the conductor‐like screening model with the MM/GBSA (molecular‐mechanics with generalized Born and surface‐area solvation) method for ligand‐binding affinity calculations. We test three SQM Hamiltonians, AM1, RM1, and PM6, as well as hydrogen‐bond corrections and two different dispersion corrections. As test cases, we use the binding of seven biotin analogues to avidin, nine inhibitors to factor Xa, and nine phenol‐derivatives to ferritin. The results vary somewhat for the three test cases, but a dispersion correction is mandatory to reproduce experimental estimates. On average, AM1 with the DH2 hydrogen‐bond and dispersion corrections gives the best results, which are similar to those of standard MM/GBSA calculations for the same systems. The total time consumption is only 1.3–1.6 times larger than for MM/GBSA. © 2012 Wiley Periodicals, Inc.

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