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Investigation of structural stability and functionality of homodimeric gramicidin towards peptide‐based drug: a molecular simulation approach
Author(s) -
Ganesan Pavithrra,
Ramalingam Rajasekaran
Publication year - 2019
Publication title -
journal of cellular biochemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.028
H-Index - 165
eISSN - 1097-4644
pISSN - 0730-2312
DOI - 10.1002/jcb.27765
Subject(s) - gramicidin , gramicidin s , peptide , antimicrobial peptides , antimicrobial , cyclic peptide , chemistry , intramolecular force , multiple drug resistance , biophysics , combinatorial chemistry , membrane , antibiotics , stereochemistry , biochemistry , biology , organic chemistry
Increasing death rates due to antibiotic resistance deteriorate the existing treatment measures. Antimicrobial peptides have turned into the emerging cure for multidrug resistance. However, the stability and functionality determine an antimicrobial peptide as a drug. Analyses of the homodimeric β‐helical peptide, gramicidin have suggested the significant role of gramicidin‐A, gramicidin‐B, and gramicidin‐C as antimicrobial compounds, but the structural basis for understanding the stability and functionality is insufficient to resolve multidrug resistance. To identify the best template among gramicidin types as a therapeutic product, we combined a detailed comparative static analysis and dynamic analysis along with conformational free energy and secondary structure prediction. We observed that the high intramolecular interactions and the geometrical features favored gramicidin‐A among other types of gramicidin. Our analyses further revealed that the secondary structure of gramicidin‐A showed β sheets with coils along the conformations without any disruption, thereby enhanced its membrane interactions in terms of binding free energy. In conclusion, gramicidin‐A has definitely showed enhanced structural stability and functionality; this could be considered the best template for a potential therapeutic product.