PJB-2021-621
In silico modeling and docking of salicylic acid revealing the sod like activity of an antimicrobial seed vicilin of Capsicum annuum L. var. Grossum
Nermeen Kainat, Ahsan Saeed, Arslan Ali, Binish Khaliq, Sohaib Mehmood, Muhammad Qamar Saeed, Rana Khalid Iqbal, Sobia Khalid and Ahmed Akrem
Abstract
This work is presenting a thorough in-silico modeling and salicylic acid docking in the predicted structure of Capsicum annuum var. grossum (bell pepper) seed vicilin along with antimicrobial activities. The Capsicum annuum var. grossum vicilin (CagV) was purified by ammonium sulfate precipitation (60%) followed by anion exchange chromatography and gel filtration. SDS-PAGE showed an intact 50 kDa band of CagV under both non-reduced and reduced conditions. LC-MS/MS analysis produced one fragment (14 residues) which showed 100% sequence homology with already reported vicilin of Capsicum annuum var. grossum in the NCBI database. The primary sequence of this highly homologous C. annuum var. grossum vicilin (NCBI Accession ID: KAF3621967.1) along with crystallographic coordinates of PDB ID: 5YJS were used for prediction of the in-silico model. The predicted cartoon model (PCagV) showed an intact copper-binding extended loop having polar residues as well as the presence of non-mutated sites (Gly-Phe-Gly). Low Root Mean Square Deviation (RMSD) values indicated high structural homology of PCagV with 5YJS, 6L4C, and 6L4M vicilins. Additionally, the docking experiment confirmed the binding of salicylic acid to the C-terminal localized binding pocket of PCagV. Numerous hydrogen bonds and hydrophobic interactions took part in stabilizing the ligand binding. Purified CagV (15 μg) showed strong antibacterial activity against pathogenic bacterial stains. Similarly, CagV (60 µg) exhibited strong mycelial inhibition of phytopathogenic fungi. Thus, it is concluded that CagV is an effective antibacterial and antifungal agent
To Cite this article:
Kainat, N., A. Saeed, A. Ali, B. Khaliq, S. Mehmood, M.Q. Saeed, R.K. Iqbal, S.Khalid and A. Akrem. 2023. In silico modeling and docking of salicylic acid revealing the sod like activity of an antimicrobial seed vicilin of Capsicum annuum L. var. Grossum. Pak. J. Bot., 55(5): DOI: http://dx.doi.org/10.30848/PJB2023-5(35)
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