Studying the interaction of 1QVL as an antibacterial peptide with DNA gyrase enzyme
Studying the interaction of 1QVL as an antibacterial peptide with DNA gyrase enzyme
Forouzan Daka,1,*Mahan Ebadpour,2Fatemeh Shams Moattar,3
1. Department of Microbiology, Faculty of Basic Sciences, Lahijan Branch, Islamic Azad University, Lahijan, Iran. 2. Department of Microbiology, Faculty of Basic Sciences, Lahijan Branch, Islamic Azad University, Lahijan, Iran. 3. Department of Microbiology, Faculty of Basic Sciences, Lahijan Branch, Islamic Azad University, Lahijan, Iran.
Introduction: In recent decades, peptide antibacterial products have attracted much attention.
Antimicrobial peptides (AMPs) are small peptides that are produced by different organisms
through ribosomal translation of mRNA or non-ribosomal pathways. These peptides are short
amino acid sequences with less than 50 amino acids. They have low molecular weight and high
thermal stability. AMPs are effective alternatives instead of antibiotics and have a good inhibitory
effect on pathogenic bacteria. Antimicrobial peptides can inhibit the key enzymes of
microorganisms. Bacterial DNA gyrase is a type II topoisomerase. This enzyme is heterotetramer
and consists of two subunits GyrA (containing a tyrosine residue in the active site responsible for
breaking and rejoining to dsDNA) and GyrB (containing the ATPase in the active site and
providing the energy required for supercoiling DNA). This enzyme is essential for
microorganisms. This enzyme plays an important role in controlling the topological state of DNA,
in cellular processes such as replication and transcription. Therefore DNA gyrase is a good
intracellular target for antibacterial agents, and its inhibition causes bacterial death. This study
aims to Study the interaction of 1QVL as an antibacterial peptide with DNA gyrase enzyme.
Methods: In this study, Discovery software version 3.5 was installed on a 5-core windows
operating system to perform molecular docking. The 3D structure of the ligand and DNA gyrase
with the identifier codes 1QVL and 1kzn were extracted from the website https://www.rcsb.org/
and downloaded in pdb format to be displayed in Discovery software. This protein initially existed
in an impure form (along with water molecules and other unnecessary molecules such as the
default ligand). Only the main chain of the protein structure is needed to perform the autodock
steps. In this way, the crystal water molecules, ligand, and hetatm were removed from this
structure and the protein was used for the molecular docking process. In the last step, molecular
docking was performed.
Results: This research aimed to investigate the interaction of 1QVL as an antibacterial peptide
with DNA gyrase. In this section, the ligand-protein complex with a docking score of -226.36 was
obtained from the docking process and analyzed by Discovery software. The ligand-protein
complex has five hydrogen bonds which contain A:ARG1:NH1 – A:GLU131:OE2, A:ARG1:NH2
– A:GLU131:OE1, A:ARG1:NH2 – A: GLU131:OE2, A:TRP3:NE1 – A:THR62:OG1,
A:ARG5:NH1 - A:THR163:O. Also, DNA gyrase bonds to TRP3 and TRP4 in 1QVL by
pi_Cation and pi_Sigma interactions.
Conclusion: the studied antibacterial peptide is capable of inhibiting the replication by interacting
with the DNA gyrase enzyme. In addition, more laboratory investigations in the future can increase
the credibility of this study.