The pterin binding site of dihydropteroate synthase (DHPS): In silico screening and in vitro antibacterial activity of existing drugs

Abstract

Antimicrobial resistance has rendered the sulfonamide class of antibiotics obsolete. An additional binding site on the dihydropteroate synthase (DHPS) enzyme, i.e., the pterin binding site, has been shown to be a valid alternative to the well-known para-aminobenzoic acid binding site. The aim of this study was to identify compounds that may bind to the pterin binding site using a computational approach. Different computer docking/scoring combinations were firstly validated using the root mean square deviation, enrichment factor (EF10%) and the area under the receiver operating characteristic curve (ROC-AUC) as three validation metrics. The most promising docking/scoring combination was used to screen an online database of existing drugs (DrugBank) to identify potential inhibitors of pterin binding. The minimum inhibitory concentration of these drugs was determined against Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonasaeruginosa, Escherichia coli and Klebsiellaaerogenes.The LigandFit/LigScore 1 combination was the most promising (EF10%: 6.3, ROC-AUC: 0.87 ± 0.058) and identified 79 existing drugs as potential inhibitors of pterin binding. Of these drugs, 26 were screened for in vitro antibacterial activity of which amiloride, citric acid, diazolidinyl urea, imidurea, riboflavin, diflunisal, nitrofurantion, sapropterin, zidovudine and N-carbamyl-L-glutamic had antibacterial activity against at least one bacterium. The antibacterial activity of some of these drugs are known, whereas the antibacterial activity for N-carbamyl-L-glutamic acid and sapropterin is novel. The docking results as well as the in vitro activity are indicators that the pterin binding site was the target, however additional DHPS enzyme assays must be carried out to conclusively substantiate these findings.