Investigating the effect of Ciprofloxacin on rhodopsin protein structure using the molecular docking calculation method

Abstract

Introduction: Ciprofloxacin antibiotic is used in the treatment of retinal toxicity or retinopathy. The present study aimed to assess the effect of ciprofloxacin on rhodopsin protein structure and the stability or instability of this protein in the presence of this medicine. The type of drug and protein binding is effective in the elimination or interaction of the medicine with the target tissues. Material & Methods: Thermodynamic components can be obtained in the interactions between rhodopsin protein and ciprofloxacin using docking software. Docking studies were performed by AutoDock 4.2 software. Pymol, Ligplot, and VMD graphic software packeages were used to observe the docking performed. Findings: Based on the results obtained from docking studies, the most important bond involved in the binding of ciprofloxacin drug with rhodopsin protein is hydrophobic bonds and hydrogen bonds. The estimate of Gibbs free energies (kcal/mol) for the best docking model is equal to -6.5. This model with the lowest level of binding energy has the greatest tendency to bind to rhodopsin amino acids, and negative values of ΔG° are indicative of a spontaneous process. Discussion & Conclusion: Based on the docking results, the A position of the rhodopsin protein is a suitable place for ciprofloxacin to bind to this protein, and the complex of ciprofloxacin with the rhodopsin protein can cause rhodopsin to regenerate so that it can start the process of seeing normally. In fact, the strong hydrogen bond between the nitrogen atom in the ciprofloxacin structure and the amino acid arginine plays a key role in stabilizing the complex.

Keywords

• binding constant
• binding free energy
• ciprofloxacin
• molecular docking
• rhodopsin