DFT, molecular docking and molecular dynamics simulations of 2-imino-4-oxo-1,3-thiazolidine hydrochloride and its activity against Bacillus pasteurii urease

Abstract

Abstract According to reports, the bioactive thiourea derivative was prepared from the ethanol solutions of thiourea and chloro acetic acid in a 1:1 M ratio. DFT calculations of 2-Imino-4-oxo-1,3-thiazolidine hydrochloride (IOTH) were performed with the use of B3LYP and the 6-311+G(2d,p) basis set. Frontier molecular orbitals, mapped electrostatic potential (MEP) map, and nonlinear optical (NLO) properties of the IOTH were all assessed. The compound was tested for drug-likeness using Swiss ADME. Using B. pasteurii (PDB ID: 4UBP), calculations for molecular docking were then performed on the geometry-optimized structure. In order to determine the complex’s stability and the interactions between ligands and the receptor, the complex was subjected to molecular dynamics (MD) simulations. According to the results, the first hyperpolarizability value (β 0) was 7.459 × 10−24 esu. The large first hyper polarization rate theoretically supported its use in the design of NLO materials. The calculated HOMO–LUMO energy gap value of the IOTH was found to be 2.87 eV. The small HOMO–LUMO energy gap suggested that IOTH is a soft molecule with a high degree of chemical reactivity but poor kinetic stability. The molecular docking study showed that the best ligand pose energy for the IOTH was −101.35 kcal/mol whereas the standard drug (acetohydroxamic acid) was −64.29 kcal/mol. The results demonstrated that the ligand–receptor complex remained stable during the MD simulations due to high binding affinity to Bacillus pasteurii urease. The Lipinski Rule of Five was not violated in any way in the studied compound. This demonstrated that it is bioavailable. During clinical trials, the compound attrition rates would be lower, and the drug would have a better chance of being commercialized.