Hydrogen bond geometry in DNA-minor groove binding drug complexes

Abstract

The geometry of the hydrogen bonding interaction between DNA and minor-groove binding drugs has been analyzed from a sample of 22 crystal structures of DNA-drug complexes, retrieved from the Nucleic Acid Database. Seventy-seven interactions between the drugs and acceptor groups in the nucleotide bases can be classified as hydrogen bonds. Their geometry departs significantly from linearity since, in most instances, the interactions can be described as three-center or multiple hydrogen bonds. Results also show that there is no preference for hydrogen bonds involving positively charged groups in the drugs. Relationships between hydrogen bond geometry and positioning of the drug along the minor groove are also discussed. The information presented may be useful in the design of new specific minor groove binding drugs.