Computational Modeling of the Staphylococcal Enterotoxins and Their Interaction with Natural Antitoxin Compounds

Abstract

Staphylococcus aureus is an opportunistic bacterium that produces various types of toxins, resulting in serious food poisoning. Staphylococcal enterotoxins (SEs) are heat-stable and resistant to hydrolysis by digestive enzymes, representing a potential hazard for consumers worldwide. In the present study, we used amino-acid sequences encoding SEA and SEB-like to identify their respective template structure and build the three-dimensional (3-D) models using homology modeling method. Two natural compounds, Betulin and 28-Norolean-12-en-3-one, were selected for docking study on the basis of the criteria that they satisfied the Lipinski’s Rule-of-Five. A total of 14 and 13 amino-acid residues were present in the best binding site predicted in the SEA and SEB-like, respectively, using the Computer Atlas of Surface Topology of Proteins (CASTp). Among these residues, the docking study with natural compounds Betulin and 28-Norolean-12-en-3-one revealed that GLN43 and GLY227 in the binding site of the SEA, each formed a hydrogen-bond interaction with 28-Norolean-12-en-3-one; while GLY227 residue established a hydrogen bond with Betulin. In the case of SEB-like, the docking study demonstrated that ASN87 and TYR88 residues in its binding site formed hydrogen bonds with Betulin; whereas HIS59 in the binding site formed a hydrogen-bond interaction with 28-Norolean-12-en-3-one. Our results demonstrate that the toxic effects of these two SEs can be effectively treated with antitoxins like Betulin and 28-Norolean-12-en-3-one, which could provide an effective drug therapy for this pathogen.

GC–MS analysis of phytoconstituents from Amomum nilgiricum and molecular docking interactions of bioactive serverogenin acetate with target proteins

“…The three-dimensional (3D) structures of phytocompounds were optimized for docking conformation study. The structure-based molecular docking was performed to study the protein ligand interactions of the phytocompounds with bacterial (PDB code:5iwm), fungal (PDB code:4i9p), viral (PDB code:1rev), antioxidant (PDB code:2he3) and diabetic [α-glucosidase (PDB code:5nn3), α-amylase (PDB code:i-tasser) and aldose reductase (PDB code:4ys1)] target proteins obtained from the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank ( https://www.rscb.org ) 61 using the iGEMDOCK 2.1 software ( https://gemdock.life.nctu.edu.tw/dock/igemdock.php) 62 and AutoDock program 63 .…”

Identification of Salicylic Acid Mechanism against Leaf Blight Disease in Oryza sativa by SR-FTIR Microspectroscopic and Docking Studies

“…To be more specific, PROCHECK and verify 3D checked out and verified a very simple and accurate model that correctly predicted the final structure [ 51 , 52 ]. Because there was a difference in the RMS deviation of this structure from the template structure, as well as a difference after MD simulations, our predicted form can be used safely for docking [ 53 , 54 , 55 , 56 ]. Because the PR1b sequence and structure of both proteins are conserved, the function of the respective proteins is highly likely to be the same.…”

CHIP Reverses Hyperglycemia-associated PTEN Stability in Wharton's Jelly Derived Mesenchymal Stem Cells and Promotes Its Therapeutic Potential Against Diabetes-induced Cardiac Injury

“…Later the FOXO3a structure collected from the PDB database was docked with Bim promoter sequence using GOLD 3.0.1. The binding studies of Bim promoter with FOXO3a protein predicted to nd the interaction sites of FOXO3a with the Bim promoter region [38].…”