Binding Modes of Peptidomimetics Designed to Inhibit STAT3

Abstract

STAT3 is a transcription factor that has been found to be constitutively activated in a number of human cancers. Dimerization of STAT3 via its SH2 domain and the subsequent translocation of the dimer to the nucleus leads to transcription of anti-apoptotic genes. Prevention of the dimerization is thus an attractive strategy for inhibiting the activity of STAT3. Phosphotyrosine-based peptidomimetic inhibitors, which mimic pTyr-Xaa-Yaa-Gln motif and have strong to weak binding affinities, have been previously investigated. It is well-known that structures of protein-inhibitor complexes are important for understanding the binding interactions and designing stronger inhibitors. Experimental structures of inhibitors bound to the SH2 domain of STAT3 are, however, unavailable. In this paper we describe a computational study that combined molecular docking and molecular dynamics to model structures of 12 peptidomimetic inhibitors bound to the SH2 domain of STAT3. A detailed analysis of the modeled structures was performed to evaluate the characteristics of the binding interactions. We also estimated the binding affinities of the inhibitors by combining MMPB/GBSA-based energies and entropic cost of binding. The estimated affinities correlate strongly with the experimentally obtained affinities. Modeling results show binding modes that are consistent with limited previous modeling studies on binding interactions involving the SH2 domain and phosphotyrosine(pTyr)-based inhibitors. We also discovered a stable novel binding mode that involves deformation of two loops of the SH2 domain that subsequently bury the C-terminal end of one of the stronger inhibitors. The novel binding mode could prove useful for developing more potent inhibitors aimed at preventing dimerization of cancer target protein STAT3.

Targeting the Src Homology 2 (SH2) Domain of Signal Transducer and Activator of Transcription 6 (STAT6) with Cell-Permeable, Phosphatase-Stable Phosphopeptide Mimics Potently Inhibits Tyr641 Phosphorylation and Transcriptional Activity

“…Interactions between the C=O of the pY+1 residue and the NH of Glu638 (analogous to Gln590) were also seen in computed models of phosphopeptides bound to STAT3. 36,41 The aryl group of the cinnamate and the C-terminal iodophenyl group “sandwich” the side chain of Gln590, which extends away from the protein surface (Figures 3A,B,D). Not surprisingly, there were several hydrophobic interactions with the SH2 domain of STAT6, which are depicted as orange surfaces in Figure 3A and which are summarized in the interaction diagram in Figure 3C.…”

Novel synthetic (E)-2-methoxy-4-(3-(4-methoxyphenyl) prop-1-en-1-yl) phenol inhibits arthritis by targeting signal transducer and activator of transcription 3

“…It is well known that MR products exhibit potent anti-inflammatory and antioxidant activities29303132. We previously identified BHPB, a tyrosine-fructose MR product as a STAT3 inhibitor, which has potential therapeutic properties against multiple diseases including RA15161718192021222333.…”

DINC 2.0: A New Protein–Peptide Docking Webserver Using an Incremental Approach

“…In recent years, there has been a growing interest in the use of peptides as protein inhibitors, given their natural role as binders and regulators in a variety of pathways [6,7]. However, even small peptides and peptidomimetics (i.e., synthetic peptide-based inhibitors [8]) are too large and too flexible for most available molecular docking methods [9]. Note that peptide-docking is a growing field of research and that other tools have been recently proposed [7].…”

“…However, this experiment also highlighted the limitations of the original implementation: indeed, good reproductions were only observed for drug-like ligands with up to 16 DoFs. In another study, our group investigated the use of peptidomimetics as inhibitors of the Src Homology 2 (SH2) [11] domain of STAT3, a transcription factor that was found to be constitutively activated in a number of human cancers [8]. Since no structural information was available on potential SH2 inhibitors, we used DINC to predict the binding modes of a group of previously experimentally-identified peptidomimetic inhibitors with up to 22 DoFs.…”

“…Besides predicting binding modes that were in agreement with data from previous studies, we were able to differentiate between strong and weak binders using predicted free-energies and conformational analysis through molecular dynamics simulations. In addition, DINC predicted a yet unknown alternative binding mode to SH2, leading to new opportunities for developing stronger inhibitors [8]. …”