Distinct functional and conformational states of the human lymphoid tyrosine phosphatase catalytic domain can be targeted by choice of the inhibitor chemotype

Abstract

The lymphoid tyrosine phosphatase (LYP), encoded by the PTPN22 gene, has recently been identified as a promising drug target for human autoimmunity diseases. Like the majority of protein-tyrosine phosphatases LYP can adopt two functionally distinct forms determined by the conformation of the WPD-loop. The WPD-loop plays an important role in the catalytic dephosphorylation by protein-tyrosine phosphatases. Here we investigate the binding modes of two chemotypes of small molecule LYP inhibitors with respect to both protein conformations using computational modeling. To evaluate binding in the active form, we built a LYP protein structure model of high quality. Our results suggest that the two different compound classes investigated, bind to different conformations of the LYP phosphatase domain. Binding to the closed form is facilitated by an interaction with Asp195 in the WPD-loop, presumably stabilizing the active conformation. The analysis presented here is relevant for the design of inhibitors that specifically target either the closed or the open conformation of LYP in order to achieve better selectivity over phosphatases with similar binding sites.

Fig. 1

Hypothesis: (a) thiazolidinedione type inhibitors bind to the closed, and (b) benzofuran salicylic acid inhibitors bind to the open LYP conformation

Fig. 2

Comparison of the closed-conformation LYP PTP domain model (in cyan) and the experimental structure (PDB 3brh, in green); RMSD is 0.506 Å. The PTP signature (H/V)C(X)5R(S/T) motif residues are shown as sticks and the remaining residues as ribbon. The missing residues between His196 and Asp197 (ends shown in pink) of the experimental structure are located in the WPD-loop

Fig. 3

Induced fit docking scores versus experimental pIC₅₀ values for the 17 thiazolidinedione inhibitors in the closed-conformation LYP model

Fig. 4

Best docking poses of the thiazolidinedione series of ligands in the active (closed) (a) and inactive (open) (b) LYP conformation. (a) The salicylic acid moieties interact in the catalytic site, including a hydrogen bond interaction to Asp195 in the WPD-loop in the closed conformation. (b) The docked ligands’ orientations are not consistent in the open form

Fig. 5

Best docking poses of 35 6-hydroxybenzofuran-5-carboxylic acid-derived ligands in the closed (a) and open (b) LYP conformation. Interactions outside the catalytic side include residues Lys32, Lys61, and Lys136

Fig. 6

Protein-ligand interactions between (a) closed LYP conformation and thiazolidinedione 444 and (b) open LYP conformation and compound 526