Dataset Information

Computational modelling of the antimicrobial peptides Cruzioseptin-4 extracted from the frog Cruziohyla calcarifer and Pictuseptin-1 extracted from the frog Boana picturata.

ABSTRACT: A computational study of the peptides Cruzioseptin-4 and Pictuseptin-1, identified in Cruziohyla calcarifer and Boana picturata respectively, has been carried out. The studies on Cruzioseptin-4 show that it is a cationic peptide with a chain of 23 amino acids that possess 52.17% of hydrophobic amino acids and a charge of + 1.2 at pH 7. Similarly, Pictuseptin-1 is a 22 amino acids peptide with a charge of + 3 at pH 7 and 45.45% of hydrophobic amino acids. Furthermore, the predominant secondary structure for both peptides is alpha-helical. The physicochemical properties were predicted using PepCalc and Bio-Synthesis; secondary structures using Jpred4 and PredictProtein; while molecular docking was performed using Autodock Vina. Geometry optimization of the peptides was done using the ONIOM hybrid method with the HF/6-31G basis set implemented in the Gaussian 09 program. Finally, the molecular docking study indicates that the viable mechanism of action for both peptides is through a targeted attack on the cell membrane of pathogens via electrostatic interactions with different membrane components, leading to cell lysis.

SUBMITTER: Rengifo-Lema MJ

PROVIDER: S-EPMC10899591 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature

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Computational modelling of the antimicrobial peptides Cruzioseptin-4 extracted from the frog Cruziohyla calcarifer and Pictuseptin-1 extracted from the frog Boana picturata.

Rengifo-Lema María José MJ Proaño-Bolaños Carolina C Cuesta Sebastián S Meneses Lorena L

Scientific reports 20240227 1

A computational study of the peptides Cruzioseptin-4 and Pictuseptin-1, identified in Cruziohyla calcarifer and Boana picturata respectively, has been carried out. The studies on Cruzioseptin-4 show that it is a cationic peptide with a chain of 23 amino acids that possess 52.17% of hydrophobic amino acids and a charge of + 1.2 at pH 7. Similarly, Pictuseptin-1 is a 22 amino acids peptide with a charge of + 3 at pH 7 and 45.45% of hydrophobic amino acids. Furthermore, the predominant secondary st ...[more]

PMID: 38413681

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Project description:Increases in the prevalence of multiply resistant microbes have necessitated the search for new molecules with antimicrobial properties. One noteworthy avenue in this search is inspired by the presence of native antimicrobial peptides in the skin of amphibians. Having the second highest diversity of frogs worldwide, Colombian anurans represent an extensive natural reservoir that could be tapped in this search. Among this diversity, species such as Boana pugnax (the Chirique-Flusse Treefrog) are particularly notable, in that they thrive in a diversity of marginal habitats, utilize both aquatic and arboreal habitats, and are members of one of few genera that are known to mount a robust immunological response against the fungus Batrachochytrium dendrobatidis, which has decimated the population of frogs worldwide. To search for molecules with potential antimicrobial activity, we have assembled and annotated a reference transcriptome from the skin of four wild captured B. pugnax from Antioquia, Colombia. Analysis of potential antimicrobial and immunological components was performed using ontology analyses, we identified several antimicrobial chemokines with particularly strong potential for exhibiting broadscale antimicrobial activities, as well as several genes related to rapid alteration of transcriptional (KRAB zinc finger protein) and phosphorylation (MAPK) responses to exogenous stressors. We also found eight families of transmembrane transport proteins, including sodium, potassium and voltage-dependent calcium channels, which will be invaluable in future studies aimed at more precisely defining the diversity and function of cationic antimicrobial peptides with alpha-helical structures. These data highlight the utility of frogs such as Boana pugnax in the search of new antimicrobial molecules. Moreover, the molecular datasets presented here allow us to expand our knowledge of this species and illustrate the importance of preserving the vast potential of Colombian biodiversity for the identification of useful biomolecules.

Project description:Antimicrobial peptides (AMPs), produced by a wide range of organisms, have attracted attention due to their potential use as novel antibiotics. The majority of these peptides are cationic and are thought to function by permeabilizing the bacterial membrane, either by making pores or by dissolving it ('carpet' model). A key hypothesis in the literature is that antimicrobial and hemolytic activity correlate with binding affinity to anionic and zwitterionic membranes, respectively. Here we test this hypothesis by using binding free energy data collected from the literature and theoretical binding energies calculated from implicit membrane models for 53 helical AMPs. We indeed find a correlation between binding energy and biological activity, depending on membrane anionic content: antibacterial activity correlates best with transfer energy to membranes with anionic lipid fraction higher than 30% and hemolytic activity correlates best with transfer energy to a 10% anionic membrane. However, the correlations are weak, with correlation coefficient up to 0.4. Weak correlations of the biological activities have also been found with other physical descriptors of the peptides, such as surface area occupation, which correlates significantly with antibacterial activity; insertion depth, which correlates significantly with hemolytic activity; and structural fluctuation, which correlates significantly with both activities. The membrane surface coverage by many peptides at the MIC is estimated to be much lower than would be required for the 'carpet' mechanism. Those peptides that are active at low surface coverage tend to be those identified in the literature as pore-forming. The transfer energy from planar membrane to cylindrical and toroidal pores was also calculated for these peptides. The transfer energy to toroidal pores is negative in almost all cases while that to cylindrical pores is more favorable in neutral than in anionic membranes. The transfer energy to pores correlates with the deviation from predictions of the 'carpet' model.

Dataset Information

Computational modelling of the antimicrobial peptides Cruzioseptin-4 extracted from the frog Cruziohyla calcarifer and Pictuseptin-1 extracted from the frog Boana picturata.

Publications

Computational modelling of the antimicrobial peptides Cruzioseptin-4 extracted from the frog Cruziohyla calcarifer and Pictuseptin-1 extracted from the frog Boana picturata.

Similar Datasets

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