Discovery of New Inhibitors of D-Alanine:D-Alanine Ligase by Structure-Based Virtual Screening

The terminal dipeptide, D-Ala-D-Ala, of the peptidoglycan precursor UDPMurNAc-pentapetide is a crucial building block involved in peptidoglycan cross-linking. It is synthesized in the bacterial cytoplasm by the enzyme D-alanine:D-alanine ligase (Ddl). Structure-based virtual screening of the NCI diversity set of almost 2000 compounds was performed with a Dd1B isoform from Escherichia coli using the computational tool AutoDock 4.0. The 130 best-ranked compounds from this screen were tested in an in vitro assay for their inhibition of E. coli DdlB. Three compounds were identified that inhibit the enzyme with K-i values in micromolar range. Two of these also have promising antibacterial activities against Gram-positive and Gram-negative bacteria.