Search for novel aminoglycosides by combining fragment-based virtual screening and 3D-QSAR scoring.

ABSTRACT: Aminoglycosides are antibiotics targeting the 16S RNA A site of the bacterial ribosome. There have been many efforts directed toward design of their synthetic derivatives, however with only few successes. As RNA binders, aminoglycosides are also a difficult target for computational drug design, since most of the existing methods were developed for protein ligands. Here, we present an approach that allows for evading the problems related to still poorly developed RNA docking and scoring algorithms. It is aimed at identification of new molecular scaffolds potentially binding to the A site. The considered molecules are based on the neamine core, which is common for all aminoglycosides and provides specificity toward the binding site, linked with diverse molecular fragments via its O5 or O6 ox

SUBMITTER: Setny P 

PROVIDER: S-EPMC2772172 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature