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 Chemjournal_title
Journal of medicinal chemistryauthors
Leung CS,Leung SS,Tirado-Rives J,Jorgensen WLdoi
10.1021/jm3003697subject
Has Abstractpub_date
2012-05-10 00:00:00pages
4489-500issue
9eissn
0022-2623issn
1520-4804journal_volume
55pub_type
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