Binding Pocket Identification and Determination of Overlapping with Different Software Tools for V8 Protease (1QY6) from Staphylococcus aureus

Background:

Protein-ligand interactions are critical for biochemical functionality in living organisms, and determining the binding pocket characteristics of a protein is essential for designing drugs that interact with specific protein pockets. Several software tools, such as Deepsite, FTSite, CASTp, and F pocket, are available for identifying these binding pockets.

Objective:

This study aimed to determine the percentage overlap and identify the best binding pocket of V8 Protease (1QY6) from Staphylococcus aureus using different software tools.

Method:

The study retrieved the protease protein's PDB file from the Protein Data Bank and used software programs such as Deepsite, CASTp, and FTsite to identify its binding pockets. The amino acid residues that fit into each of the identified pockets were downloaded, and their unique sequence identifiers were noted. The overlap of the binding pockets identified by the software tools was determined by entering the amino acid values into Excel.

Result:

The study found that binding pocket 3 showed the most overlap between Deepsite and CASTp, indicating that Deepsite may have superior specificity and efficiency for determining binding pockets compared to other tools. The total overlap between the software tools was 19%, demonstrating the importance of using multiple tools to identify potential binding pockets.

Conclusion:

The comparison of three different software tools for identifying the binding pocket of the protease protein (1QY6) resulted in different results with no agreement among the binding pockets established by each tool. However, the study's findings suggest that binding pocket 3 of the protease protein (1QY6) may function as the best binding pocket for drug design studies targeting this protein. These findings could aid in the development of new drugs to treat infections caused by Staphylococcus aureus.