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https://doi.org/10.5562/cca4168

A View of the Inhibition Specificity of Aurintricarboxylic Acid Toward Protein Tyrosine Phosphatases: Implications for Structure-Based Phosphatase Inhibitor Design

Petar M. Mitrasinovic orcid.org/0000-0002-0987-4893 ; Center for Biophysical and Chemical Research, Belgrade Institute of Science and Technology, 11060 Belgrade, Serbia *

* Dopisni autor.

Prilozi: cca4168_supplement.pdf

Sažetak

Protein tyrosine phosphatases (PTPs) play a vital role in intracellular signaling pathways associated with cell transformation, growth, and proliferation. Among various carboxylic acid derivatives, aurintricarboxylic acid (ATA) has been identified as the binder with the highest affinity for Yersinia PTP (YopH). Herein, the underlying specificity of ATA, as a competitive inhibitor of several PTPs (YopH, PTP1B, TCPTP, HePTP, CD45, VHR, and Cdc25A), is explored. By observing each PTP as a primary target receptor and the rest of them as simultaneous secondary receptors, the specificity factor, as a function of free ligand concentration ([ATA]), shows at lower [ATA] (between 10–11 and 10–9 M) a 23 to 500-fold specificity in favor of YopH versus the other PTPs, indicating that the ATA-YopH interaction is the most specific. Near [ATA] = 10–8 M, the specificity factor ≈ 1 is associated with equal occupancy of the primary receptor YopH and the set of secondary receptors. When observing YopH as a primary receptor relative to every other single PTP as a secondary receptor at [ATA] ϵ (10–11, 10–9 M), the specificity to YopH is larger nearly 6, 25, 25, 40, 100, and 120 times than that to PTP1B, HePTP, CD45, TCPTP, Cdc25A, and VHR, respectively. The relative contribution to the binding free energy of each individual YopH residue located in the active site (403-Cys-Arg-Ala-Gly-Val-Gly-Arg-Thr-410) and in the proximal WPD loop (352-Gly-Asn-Trp-Pro-Asp-Gln-Thr-Ala-Val-Ser-361) was estimated using alanine scanning mutagenesis. The so-called "hot spots" of binding affinity that dominate the interaction are mostly Trp354 and Thr358. Although YopH has no homolog in Staphylococcus aureus, off-target effects of ATA cannot be ruled out. 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. Whereas the biggest issue for identifying phosphatase inhibitors is the lack of specificity, this work helps to conceptualize the ATA structure as a pharmacophore for designing new inhibitors capable of achieving specificity against phosphatases. Based on a two-layer QM/MM (SCC-DFTB-D/AMBER) approach, the conformational relationship between the L7 loop (384-Glu-Ser-Lys-Gly-Ser-Ser-Ala-Val-Ala-392) and the WPD loop in substrate (pTyr) recognition was characterized by constructing a binding isotherm log(f/1-f)-log[substrate concentration], where f denotes the fraction of the YopH receptors occupied by the substrate. The observed positive association suggests that L7 is an allosteric site in the YopH structure.

Ključne riječi

aurintricarboxylic acid; inhibitor; pharmacophore; phosphatase; specificity

Hrčak ID:

341092

URI

https://hrcak.srce.hr/341092

Datum izdavanja:

14.12.2025.

Posjeta: 907 *