title: In silico modeling of the type 2 IDI enzymes of Bacillus licheniformis, Pseudomonas stutzeri, Streptococcus pyogenes, and Staphylococcus aureus for virtual screening of potential inhibitors of this therapeutic target.
abstract: Isopentenyl diphosphate isomerase is an essential enzyme in those living organisms such as pathogenic strains of Streptococcus and Staphylococcus genera which rely on the Mevalonate pathway for the production of isoprenoids. The pathogens contain type 2 IDI in contrast to human that contains type 1 IDI. Therefore, the type 2 IDI may be a potential target for the therapy of some infectious diseases. In the current study, a virtual screening by docking was performed among 2000 chemicals from CoCoCo library to find a specific inhibitor for type 2 IDIs. To this end, the structures of the type 2 IDIs of Bacillus licheniformis, Pseudomonas stutzeri, Streptococcus pyogenes, and Staphylococcus aureus were molded using comparative modeling and Hidden Markov Model (HMM) based prediction. The predicted models were evaluated based on Q-mean and Prosa score. Molegro Virtual Docker with MolDock scoring function was used for measuring the binding affinity of the found inhibitor to the active site of the models. Also the inhibition effect of the compound was virtually tested on the crystallography-solved structures of the Sulfolobus shibatae and Thermus thermophilus type 2 IDIs as well as the Escherichia coli type 1 IDI. Finally, the inhibition effect of the found inhibitor was virtually tested on the human type 1 IDI. Interestingly, the results suggest that the inhibitor efficiently binds to and inhibits the bacterial IDIs especially the type 2 IDIs of pathogens while it is not inhibiting the human IDI.
authors.affiliation: Department of Molecular Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.
authors.forename: Ibrahim
authors.initials: I
authors.lastname: Torktaz
authors.forename: Hossein
authors.initials: H
authors.lastname: Shahbani Zahiri
authors.forename: Kambiz
authors.initials: K
authors.lastname: Akbari Noghabi
mesh_terms: D000595:Amino Acid Sequence; D001407:Bacillus / Q000201:enzymology; D019748:Carbon-Carbon Double Bond Isomerases / Q000737:chemistry*; D003198:Computer Simulation; D015195:Drug Design; D004791:Enzyme Inhibitors / Q000737:chemistry*; D045782:Hemiterpenes; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D008969:Molecular Sequence Data; D011487:Protein Conformation; D044223:Pseudomonas stutzeri / Q000201:enzymology; D013211:Staphylococcus aureus / Q000201:enzymology; D013297:Streptococcus pyogenes / Q000201:enzymology; D013379:Substrate Specificity
chemical_list: D004791:Enzyme Inhibitors; D045782:Hemiterpenes; D019748:Carbon-Carbon Double Bond Isomerases; C021453:isopentenyldiphosphate delta-isomerase