Abstract
d-Alanine:d-alanine ligase (Ddl) catalyzes the ATP-driven ligation of two d-alanine (d-Ala) molecules resulting in the formation of d-alanyl:d-alanine dipeptide. Inhibition of Ddl prevents bacterial growth, which makes this enzyme an attractive and viable target for searching effective antimicrobial drugs. Current study aimed at the discovery of potent inhibitors against Strepotococcus sanguinis SK36 Ddl (SsDdl). Using comparative molecular modeling approach, models for SsDdl were constructed by MODELLER and other web servers. The model with best stereo-chemical profile was further studied for structure function relationship by performing docking with seventy nine inhibitors. The results demonstrated the model generated via MODELLER was the best among all predicted SsDdl structures. Docking analysis revealed that compounds 73 and 61, obtained from pyridopyrimidine scaffolds yielded highest GOLD scores and exhibited consistently better binding interactions. The final compounds exhibit reasonable SsDdl inhibitory activity and can be further employed to design derivatives with customized activities.
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