Clinically significant antibiotic resistance has evolved against virtually every antibiotic deployed. Yet the development of new classes of antibiotics has lagged far behind our growing need for such drugs. Antimicrobial peptides (AMPs) have emerged as novel therapeutics hailed for their bactericidal and immunomodulatory properties. However, the process of optimizing antimicrobial peptide stability, using large peptide libraries is both tedious and expensive. The intent of this study is to analyze computationally the stability of anti-bacterial peptides (ABPs), particularly gram positive and to discover a potential template from a pool of ABPs for therapeutic use. Consequently we highlighted that MiAMP1 appears advantageous over the other ABPs with respect to stability, and may provide a convenient platform for the development of anti-bacterial therapeutic peptide.

Ramanathan K

Department of Biotechnology

School of Bio Sciences and Technology

Vellore Campus

Sethumadhavan R.

Vellore Institute of Technology (VIT) is a private university located in&nbsp;Tamil Nadu, India. Founded in 1984, as Vellore Engineering College, the institution offers 20 undergraduate, 34 postgraduate, four integrated and four research programs. It has campuses in Vellore, Amravati, Bhopal and Chennai.

VIT is one of the top ranked private universities in India according to NIRF, THE and QS Rankings.&nbsp;Govt. of India has recognized&nbsp;VIT, Vellore as an&nbsp;Institution of Eminence. This has allowed VIT to take independent quality initiatives and move up in world ranking.

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VIT University

Interdisciplinary Sciences: Computational Life Sciences

The native structure of Antimicrobial peptides is stabilized by a large number of individually weak forces; a complete understanding of folding implies the need to evaluate the contribution of each of these, including nonconventional hydrogen bonds. In this work, we have analyzed the influence of C-H...O interactions in the structural stability of Antimicrobial peptides by comparison with conventional hydrogen bond. There are a number of amino acid residues that can form hydrogen bonds via their side chains in addition to their peptide group. Perhaps highest contribution in this category is polar residue (Cys) and charged residues such as Lys and Arg. A total of 2513 C-H...O interactions were found in a data set of 53 Antimicrobial peptides. Among the 2513 nonconventional interactions observed in the data set, 40% of interactions are bonded to alpha carbon. This is consistent with the fact that the hydrogens are more acidic than others. Most prominent were side-chain to main-chain C-H...O interactions (SM-C-H...O). 92% of the stabilizing centers in the Antimicrobial peptides were found to be involved in C-H...O interactions. These interactions are mainly formed by short range contacts. Moreover, the study shows that, there is an average of more than one C-H...O interactions observed for every single residue in the Antimicrobial peptides data set. It is concluded that the C-H...O interaction can, indeed, be categorized as a true stabilizing force like hydrogen bond in Antimicrobial peptides.

Contribution of unconventional C-H…O bonds to the structural stability of Antimicrobial peptides

A computational analysis on the C – H … π interactions in a group of 53 antimicrobial peptides was investigated. A total of 162 C – H … π interactions were observed. Side-chain to side-chain C – H … π interactions are the predominant type of interactions in antimicrobial peptides data set. There was an average of one significant C – H … π interaction for every 7 residues in the antimicrobial peptides investigated. Long-range C – H … π interactions are the predominant type of interactions. The secondary structure preference, solvent accessibility and stabilization centers of these of C – H … π interacting residues were estimated. It is likely that the C – H … π interactions contribute significantly to the overall stability of antimicrobial peptides. These interactions were observed after a molecular dynamics study on these set of antimicrobial peptides using CHARMM force field.

Journal of Theoretical and Computational Chemistry

EXPLORING THE ROLE OF C–H … π INTERACTIONS ON THE STRUCTURAL STABILITY OF ANTIMICROBIAL PEPTIDES

ChemInform

ChemInform Abstract: The CH/π Interaction. Implications in Molecular Recognition

Nucleic Acids Research

APD2: the updated antimicrobial peptide database and its application in peptide design

Open Life Sciences

Antimicrobial peptides: an overview of a promising class of therapeutics

Identifying therapeutic template by evaluating the structural stability of gram positive anti-bacterial peptides-a computational approach

Journal	Data powered by TypesetInterdisciplinary Sciences: Computational Life Sciences
Publisher	Data powered by TypesetSpringer Science and Business Media LLC
ISSN	1913-2751
Open Access	0