A Multiple Ligand Docking Study of Phycocyanin Peptide as Antibacterial Agent: Mechanism and Inhibition against LpxC Protein Ni Putu Yunika Arindita(1), Heli Siti Halimatul Munawaroh(1*), Siti Aisyah(1), Selmi Fiqhi Khoiriah(2)
1)Department of Chemistry, Indonesia University of Education, Bandung 40154, Indonesia
2)Faculty of Mathematics and Natural Sciences, Bandung Institute of Technology, Bandung 40132, Indonesia
Abstract
The rise of antibiotic resistance has become a global health concern, necessitating the search for alternative antibacterial agents. The potential of peptide-based antibacterial agents derived from C-phycocyanin was investigated through molecular docking in light of the growing need for novel therapies to combat antibiotic-resistant bacteria. Multiple ligands docking techniques were employed to investigate the binding interactions between bioactive peptide phycocyanin (AF (Ala-Phe), AC (Ala-Cys), APG (Ala-Pro-Gly), MA (Met-Ala), PG (Pro-Gly), YF(Tyr-Phe), TF (Thr-Phe), YCL (Tyr-Cys-Leu) and ASYF (Ala-Ser-Tyr-Phe)) against the LpxC protein from Pseudomonas aeruginosa as an antibacterial target. Multiple ligand AC-AF displayed the highest affinity value of -15.4 kcal/mol, indicating its potential as an antibacterial agent compared to its native ligand BB-78485, which had an affinity value of -9.7 kcal/mol. The results of molecular docking showed favorable binding interactions between multiple ligand peptide phycocyanin and the active site residues of LpxC. Key amino acid residues involved in ligand-protein interactions were identified, including hydrogen bonding, hydrophobic interactions, electrostatic contacts and van der Waals forces. In silico ADMET evaluations of phytochemical peptide ligands revealed that all peptides except YCL and ASYF were Lipinski^s rule of five and exhibited drug-like properties.
Keywords: phycocyanin, antibacterial, peptide docking, LpxC protein
