In silico Analyses and Characterization of an Antimicrobial Peptide ‘Sapecin B’ Reveals its Molecular Interaction with Bacterial Peptidoglycan

Sumbal Habib1, Hina Ghaffar1, Amna Mughal1, Nasar-Ur-Rehman Khan2, Imran Shahzad1, Hafiz Muhammad Abdullah1, Ghausia Aziz1, Hafiza Kehfulvara1 and Aqsa Parvaiz3*

1Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad. 2Department of Plant Pathology, University of Agriculture Faisalabad. 3Department of Biochemistry and Biotechnology, The Women University Multan

Abstract

The antibiotics have been used to cure different bacterial diseases for a long time. But the rapidly increasing bacterial resistance against conventional antibiotics has made their use less suitable. Hence, antimicrobial peptides (AMPs) have emerged to be used as an alternative to treat microbial infections. The mechanism of action of antimicrobial peptides includes attraction and binding of AMPs to bacterial cell membrane. The bacterial cell membranes are anionic while the AMPs are cationic in nature. So, there is electrostatic force of attraction that attracts them towards each other, creating pores in the membrane that resulting in destruction of lipid bilayer. The aim of present study was to develop novel protein against antibiotics resistance bacteria. In the present study, an antimicrobial peptide (Sapecin B) was studied. Homology modeling was carried out using SWISS MODEL, Phyre-2 and evaluation of models was done by RAMPAGE server that helped to identify the best model. The structure of peptidoglycan taken from online database PubChem was used as a ligand. Then, the physiochemical properties were checked by online tool Protparam. The study showed that molecular weight of protein was 10040.92 having 88 amino acids, stability index value equal to 40 and the total number of atoms was 1428. The model was then refined to make it ready for docking purpose which was carried out using MOE, Rosetta and Patchdock. According to MOE, the results showed that peptidoglycan had bonding with some of the residues of Sapecin B protein i.e., Lys 87, Val 89 and Cys84. According to Rosetta, the result showed that the protein had shown best docking results with lowest interface_delta score as well as the transform action ratio was also less than 1. According to PatchDock, there exist hydrogen bonding between protein residue and ligand with a length of 2.41. The length higher than 2 was considered best for interaction. So it was considered that there existed strong interaction between AMPs with their ligand.