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Halogen Bonding at the Active Sites of Human Cathepsin L and MEK1 Kinase: Efficient Interactions in Different Environments
Author(s) -
Hardegger Leo A.,
Kuhn Bernd,
Spinnler Beat,
Anselm Lilli,
Ecabert Robert,
Stihle Martine,
Gsell Bernard,
Thoma Ralf,
Diez Joachim,
Benz Jörg,
Plancher JeanMarc,
Hartmann Guido,
Isshiki Yoshiaki,
Morikami Kenji,
Shimma Nobuo,
Haap Wolfgang,
Banner David W.,
Diederich François
Publication year - 2011
Publication title -
chemmedchem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.817
H-Index - 100
eISSN - 1860-7187
pISSN - 1860-7179
DOI - 10.1002/cmdc.201100353
Subject(s) - chemistry , aryl , iodide , bromide , ligand (biochemistry) , crystallography , halogen bond , halide , halogen , stereochemistry , acceptor , crystal structure , molecule , active site , inorganic chemistry , enzyme , alkyl , organic chemistry , biochemistry , receptor , physics , condensed matter physics
In two series of small‐molecule ligands, one inhibiting human cathepsin L (hcatL) and the other MEK1 kinase, biological affinities were found to strongly increase when an aryl ring of the inhibitors is substituted with the larger halogens Cl, Br, and I, but to decrease upon F substitution. X‐ray co‐crystal structure analyses revealed that the higher halides engage in halogen bonding (XB) with a backbone CO in the S3 pocket of hcatL and in a back pocket of MEK1. While the S3 pocket is located at the surface of the enzyme, which provides a polar environment, the back pocket in MEK1 is deeply buried in the protein and is of pronounced apolar character. This study analyzes environmental effects on XB in protein–ligand complexes. It is hypothesized that energetic gains by XB are predominantly not due to water replacements but originate from direct interactions between the XB donor (C aryl X) and the XB acceptor (CO) in the correct geometry. New X‐ray co‐crystal structures in the same crystal form (space group P 2 1 2 1 2 1 ) were obtained for aryl chloride, bromide, and iodide ligands bound to hcatL. These high‐resolution structures reveal that the backbone CO group of Gly61 in most hcatL co‐crystal structures maintains water solvation while engaging in XB. An arylCF 3 ‐substituted ligand of hcatL with an unexpectedly high affinity was found to adopt the same binding geometry as the aryl halides, with the CF 3 group pointing to the CO group of Gly61 in the S3 pocket. In this case, a repulsive F 2 CF⋅⋅⋅OC contact apparently is energetically overcompensated by other favorable protein–ligand contacts established by the CF 3 group.