Structural basis to identify a target site in Shiga-toxin for the inhibitor discovery against growth of Shiga toxin-producing E. coli

Abstract

Background: Certain peptides that can bind to Shiga toxin 2 (Stx2) have been reported to treat Shiga toxin-producing E. coli (STEC) infections. However, their mechanisms of action remain unknown. We used the PEP-FOLD server to predict the 3-D structure of the five peptides that have been used against STEC growth. The modelled structures were docked with Stx2 using ClusPro server. The physiochemical properties of therapeutic peptides were computed using the ‘peptides’ package of the RStudio and ProtParam tool. Results:Of these five therapeutic peptides, one tetravalent peptide (TVP) was shortlisted based on its interaction with the active sites of Stx2. The structure of stx2-TVP complex was evaluated using the ERRAT, iMODS, and Procheck servers. The 3D refined model of TVP was generated using Galaxyserver and evaluated using ERRAT, ANOLEA, and QMEAN. PyMOL was used to visualize the docking complexes. The current study demonstrated that blocking Y77-E259 and Y114-E167 interactions is required to inhibit STEC growth. Of the five therapeutic peptides used in this study, only MAPPPRRRRA (TVP) blocked the interaction between Y77 and E259 residues of the A1 subunit of Stx2, making it active and ultimately leading to STEC cell death. However, all therapeutic peptides showed strong polar interactions with Y77 and E259, but they did not block the Y77-E259 or Y114-E167 interactions. We also demonstrated that helix-loop-helix formation near the ribosome-binding site of Stx2 might lead to the differential gene expression regulated by Stx2. The 3D refined model of TVP showed a positive G-factor, high QMEAN score, low MolProbity score, and low energy zones in the ANOLEA profile compared to original TVP. Moreover, the low radius of gyration in the refined TVP during the molecular simulation suggests that it is more compact than the original TVP. However, the low antigenicity of TVP makes it an unsuitable drug candidate. We also evaluated three antibiotics that have been used as active ingredients in FDA-approved peptides. Only Oritavancin diphosphate showed strong polar interactions with Y77-E259 and also had the highest binding affinity. Conclusions: This study identified a new target (Y77-E259) for inhibitor discovery against STEC growth.