Computational Analysis of the Impact of Environmental Pollutants on Arginine-Rich Catalase Enzyme

الملخص

Background: Molecular docking is a computational tool widely used to investigate protein–ligand interactions and assess the potential molecular effects of environmental pollutants. As an example, nitric acid (HNO₃) is a major component of acid rain, and it poses serious risks to enzymes (cellular signalling) and antioxidants such as catalase.

Objectives: We aimed to study how HNO₃ interacts with catalase, which is found in some bacteria and other living cells, via the development of HNO₃ as a synthetic ligand and the determination of the binding interface characterized by a binding pocket dense in arginine residues.

Methods: Using AutoDock Vina as well as downstream visualization software, we were able to map out the binding site and characterize any hydrogen bonds, salt bridges, and electrostatic interactions observed within the binding interface. Catalase from Penicillium vitale (PDB ID: 1DGB) was used as the receptor.

Results: Based upon our binding analysis, we found HNO₃ (as a synthetically developed ligand) has many polar contacts and forms strong anchors through several high-affinity polar contacts predominantly with ARG A:365 and ARG A:72. However, there are also significant areas of electrostatic repulsion between adjacent positively charged arginine residues on catalase, suggesting a mechanism of inhibition. The receptor’s stereochemistry has been validated through Ramachandran plotting, validating its requisite structure for docking studies.

Conclusion: The results further our understanding of ligand-modulated functioning via arginine-based binding domains and provide molecular support for the ligand's role as an inhibitor. The docking analysis demonstrated that nitric acid was successfully accommodated within the catalytic pocket of catalase. The best-ranked binding pose exhibited a binding affinity of -3.9 kcal/mol, indicating a favorable interaction between the ligand and the receptor. This docking pose was selected for subsequent interaction analysis because it presented the lowest predicted binding free energy together with the most stable orientation within the active site.