Redesigning Arenicin-1, an Antimicrobial Peptide from the Marine Polychaeta Arenicola marina, by Strand Rearrangement or Branching, Substitution of Specific Residues, and Backbone Linearization or Cyclization

Abstract

Arenicin-1, a β-sheet antimicrobial peptide isolated from the marine polychaeta Arenicola marina coelomocytes, has a potent, broad-spectrum microbicidal activity and also shows significant toxicity towards mammalian cells. Several variants were rationally designed to elucidate the role of structural features such as cyclization, a certain symmetry of the residue arrangement, or the presence of specific residues in the sequence, in its membranolytic activity and the consequent effect on microbicidal efficacy and toxicity. The effect of variations on the structure was probed using molecular dynamics simulations, which indicated a significant stability of the β-hairpin scaffold and showed that modifying residue symmetry and β-strand arrangement affected both the twist and the kink present in the native structure. In vitro assays against a panel of Gram-negative and Gram-positive bacteria, including drug-resistant clinical isolates, showed that inversion of the residue arrangement improved the activity against Gram-negative strains but decreased it towards Gram-positive ones. Variants with increased symmetry were somewhat less active, whereas both backbone-cyclized and linear versions of the peptides, as well as variants with R→K and W→F replacement, showed antimicrobial activity comparable with that of the native peptide. All these variants permeabilized both the outer and the inner membranes of Escherichia coli, suggesting that a membranolytic mechanism of action was maintained. Our results indicate that the arenicin scaffold can support a considerable degree of variation while maintaining useful biological properties and can thus serve as a template for the elaboration of novel anti-infective agents.

Antimicrobial Peptide Arenicin-1 Derivative Ar-1-(C/A) as Complement System Modulator

“…According to this analysis, Ar-1-(C/A) adopts a predominantly antiparallel β-sheet structure with a considerable right twist in aqueous solution. The experimentally observed propensity of Ar-1-(C/A) to form a β-hairpin structure even without the disulfide bond supports the previous molecular dynamics simulations showing the rapid folding of linear Ar-1 with alkylated cysteines into its native conformation [ 29 ]. Indeed, the average content of β-sheet structures in Ar-1-(C/A) is lower than in wild-type arenicins, where disulfide bonds restrict the conformational space and confer additional stability to the β-hairpin.…”

Antimicrobial Peptides: Classification, Design, Application and Research Progress in Multiple Fields

“…The synthesis of disulfide bonds often complicates the development of synthetic peptides. The circularisation of the main chain of arenicin-1 molecule resulted in increased activity against drug-resistant clinical isolates but caused no substantial effect on cytotoxicity (Orlov et al, 2019). The HDPs tachyplesins I, II, and III and their cyclic analogs cTI, cTII, and cTIII, respectively, have similar structures and activities and can resist bacterial and cancer cells.…”

Caprine Bactenecins as Promising Tools for Developing New Antimicrobial and Antitumor Drugs

“…Modifications that maintained a comparable length to the native peptide did not result in a significant difference in activity. Two variants which showed a slight improvement in the geometric mean of MICs (GMIC), used as the general assessment value (Orlov et al, 2019), were ChBac3.4(Н-), with the histidine deletion, and RFR-ChBac3.4(1-14)-NH 2 , the truncated analogue with an additional N-terminal RFR triplet, albeit no more than a 2-fold reduction was sometimes observed. Comparing the effect of C-terminal amidation, the fluctuations of individual MICs between amidated and non-amidated variants were generally minor, so there is no evidence suggesting that this particular feature plays a relevant role in the antimicrobial action, considering either the ChBac3.4 or ChBac3.4-1 series.…”