Hydrogen-bonding patterns of minor groove-binder-DNA complexes reveal criteria for discovery of new scaffolds.
Minor groove-binding ligands are able to control gene expression and are of great interest for therapeutic applications. We extracted hydrogen-bonding geometries from all available structures of minor groove-binder-DNA complexes of two noncovalent binding modes, namely 1:1 (including hairpin and cyclic ligands) and 2:1 ligand/DNA binding. Positions of the ligand atoms involved in hydrogen bonding deviate from idealized hydrogen bond geometries and do not exploit the possibilities indicated by water molecules. Therefore, we suggest the inclusion of shape-based descriptors rather than hydrogen-bond patterns in virtual screening protocols for the identification of innovative minor groove-binding scaffolds.
Spitzer
Gudrun M
GM
Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria. gudrun.spitzer@uibk.ac.at
Wellenzohn
Bernd
B
Markt
Patrick
P
Kirchmair
Johannes
J
Langer
Thierry
T
Liedl
Klaus R
KR
D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D030541:Databases, Genetic; D015870:Gene Expression / Q000187:drug effects; D006860:Hydrogen Bonding; D008024:Ligands; D009690:Nucleic Acid Conformation; D012984:Software; D014867:Water / Q000737:chemistry
D008024:Ligands; D014867:Water; D004247:DNA