On the potential pharmacophore for the structure-based inhibitor design against phosphatases

Among carboxylic acid derivatives, aurintricarboxylic acid (ATA) has been recognized as a binder of the largest affinity and specificity to protein tyrosine phosphatases (PTPs), particularly to the Yersinia PTP (YopH). It is well rationalized that the binding of ATA to the active site (403-Cys-Arg-Ala-Gly-Val-Gly-Arg-Thr-410) of YopH is affected by the conformational dynamics of the proximal WPD loop (352-Gly-Asn-Trp-Pro-Asp-Gln-Thr-Ala-Val-Ser-361). The helix α4 spanning loop L4 (384-Glu-Ser-Lys-Gly-Ser-Ser-Ala-Val-Ala-392) was experimentally observed as a potential second binding site in YopH structure. The association of L4 with the conformational flexibility of the WPD loop was related to the stability of the WPD loop in the closed, active conformation. Thus, the proposed cooperativity between the WPD loop and L4 in substrate recognition is herein characterized by the Hill coefficient of the log(f/1-f)-log[ligand concentration] binding isotherm, where f denotes the fraction of YopH receptors occupied by ATA. Observed positive cooperativity suggests L4 as an allosteric site in YopH structure. Although there is no YopH homology in Staphylococcus aureus, the off-target effects of ATA can not be precluded. Considering the ability of ATA to bind to the Staphylococcus aureus serine/threonine phosphatase STP1 directly, the specificity factor indicates a roughly 100-fold preference for YopH over STP1. This work assists in conceiving ATA structure as a pharmacophore for designing novel inhibitors capable of achieving specificity against phosphatases.