Targeting the Nalidixic Acid Binding Site on Human Serum Albumin Through Computational Approach: A Re-Investigation

Nalidixic acid (NA) is a quinolone drug used to treat urinary tract infections. It inhibits bacterial gyrase-DNA complex formation, an essential step for DNA supercoiling during bacterial replication. Due to the medical application of this drug, it would be interesting to get insight into its binding mechanism with human serum albumin (HSA), the primary carrier protein in blood circulation. Two reports of NA binding to HSA were published using molecular docking approaches. The first report revealed that the preferred binding site of NA was Site II of serum albumins, while the recent finding predicted Site I of bovine serum albumin (BSA) as the preferred site. Given the high sequence homology between these albumins, it is presumed that the binding preference of this drug should be the same in these proteins. To re-investigate this phenomenon, the interaction of NA with HSA was conducted using AutoDockTool 4.0. The molecular docking results revealed that NA binding preference was at Site I, involving Lys 199 in HSA, due to the formation of more significant contacts. Hence, it is concluded that any variable or parameters in the software should be wisely standardized to minimize the controversial results using different programs.