Methyl effects on protein-ligand binding.

Abstract:

:The effects of addition of a methyl group to a lead compound on biological activity are examined. A literature analysis of >2000 cases reveals that an activity boost of a factor of 10 or more is found with an 8% frequency, and a 100-fold boost is a 1 in 200 event. Four cases in the latter category are analyzed in depth to elucidate any unusual aspects of the protein-ligand binding, distribution of water molecules, and changes in conformational energetics. The analyses include Monte Carlo/free-energy perturbation (MC/FEP) calculations for methyl replacements in inhibitor series for p38α MAP kinase, ACK1, PTP1B, and thrombin. Methyl substitutions ortho to an aryl ring can be particularly effective at improving activity by inducing a propitious conformational change. The greatest improvements in activity arise from coupling the conformational gain with the burial of the methyl group in a hydrophobic region of the protein.

journal_name

J Med Chem

authors

Leung CS,Leung SS,Tirado-Rives J,Jorgensen WL

doi

10.1021/jm3003697

subject

Has Abstract

pub_date

2012-05-10 00:00:00

pages

4489-500

issue

9

eissn

0022-2623

issn

1520-4804

journal_volume

55

pub_type

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