De novo peptides as potential antimicrobial agents

Abstract

The phenomenon of antimicrobial resistance threatens our ability to treat common infections. The clinical pipeline for new antimicrobials is pretty much dry and hence, there is a need for the development of new antimicrobial agents with low toxicities to help fight resistant microorganisms. This work aimed to design antimicrobial peptides with low toxicities using a database filtering technology and evaluate their bioactivities. The physicochemical properties of the designed peptides were explored with molecular dynamics (MD) simulations. Microbroth dilution and hemolytic assays were used to assess the peptides' antimicrobial activity and toxicity. The activity of combinations of the peptides and some standard antibiotics was tested by the checkerboard method. In general, the designed peptides had a charge of +2, chain length of 13, and hydrophobicity of 61%. The predicted secondary structures of the peptides were either extended conformations or alpha-helices, and these structures were found to fluctuate during the MD simulations, where coils, bends, and helices dominated. , of the peptides, BRG003, BRG004 and BRG002 had the greatest aggregation propensities, whereas BRG001, BRG005, and BRG006 exhibited lower aggregation propensities. The minimum inhibitory concentration (MIC) of the peptides ranged from 0.015 to >1.879 μM, with BRGP-001 exhibiting high activity against MRSA with an MIC of 15 nM. BRGP-005 and BRGP-006 exhibited synergistic effects against Escherichia coli^R when used in combination with erythromycin. At the minimum hemolytic concentration, the percentage of lysed erythrocytes was lower for all the peptides in comparison to the reference peptide, indicating low hemolytic activity. The study revealed the importance of peptide self-association in the antimicrobial activity of the peptides. These peptides provide a basis for the design of potent antimicrobial peptides that can further be developed for use in antimicrobial therapy.

Keywords: Antimicrobial peptides; Database filtering technology; Hemolytic activity; Molecular dynamics; Peptide design.

Fig. 1

(a)Amino acid composition of the peptides from the antimicrobial peptide database, (b)percent hydrophobicities of the peptide from the antimicrobial peptide database (APD) and (c) secondary structures of the designed peptides as predicted by the iTASSER server.

Fig. 2

Plots of amino acid residue and A3D score predicted with the AGGRESCAN3D web server for (a) BRGP-001, (b) BRGP-002, (c) BRGP-003, (d) BRGP-004, (e) BRGP-005, (f) BRGP-006 and (g) BRGP-007. A higher score indicates a higher aggregation propensity and hence, a darker red colour. Soluble residues are coloured in gradients of blue. A lower score corresponds to higher solubility and hence, darker blue colour. Residues with A3D scores equal to or close to zero do not influence aggregation and are coloured in white.

Fig. 3

(a) Root mean square deviation (RMSD), (b) Root mean square fluctuations (RMSF), (c) Radius of gyration and (d) Solvent accessible surface area obtained from the molecular simulations of the peptides.

Fig. 4

Ramachandran plots for BRGP-001 (a), BRGP-002 (b), BRGP-003 (c), BRGP-004 (d), BRGP-005 (e), BRGP-006 (f) and BRGP-007 (g) obtained from the molecular simulations.

Fig. 5

Secondary structure patterns for (a) BRGP-001, (b) BRGP-002, (c) BRGP-003, (d) BRGP-004, (e) BRGP-005, (f) BRGP-006 and (g) BRGP-007 predicted from DSSP after molecular dynamics simulations.

Fig. 6

The free energy surface for (a) BRGP-001, (b) BRGP-002, (c) BRGP-003, (d) BRGP-004, (e) BRGP-005, (f) BRGP-006 and (g) BRGP-007 computed using the RMSD and radius of gyration as order parameters. The different intensities of the FES represent the energy state of the peptides with different conformational structures.