Doderlin: Isolation and Characterization of a Broad-Spectrum Antimicrobial Peptide from Lactobacillus acidophilus

In silico prospection of receptors associated with the biological activity of U1-SCTRX-lg1a: an antimicrobial peptide isolated from the venom of Loxosceles gaucho

The emergence of antibiotic-resistant pathogens generates impairment to human health. U1-SCTRX-lg1a is a peptide isolated from a phospholipase D extracted from the spider venom of Loxosceles gaucho with antimicrobial activity against Gram-negative bacteria (between 1.15 and 4.6 μM). The aim of this study was to suggest potential receptors associated with the antimicrobial activity of U1-SCTRX-lg1a using in silico bioinformatics tools. The search for potential targets of U1-SCRTX-lg1a was performed using the PharmMapper server. Molecular docking between U1-SCRTX-lg1a and the receptor was performed using PatchDock software. The prediction of ligand sites for each receptor was conducted using the PDBSum server. Chimera 1.6 software was used to perform molecular dynamics simulations only for the best dock score receptor. In addition, U1-SCRTX-lg1a and native ligand interactions were compared using AutoDock Vina software. Finally, predicted interactions were compared with the ligand site previously described in the literature. The bioprospecting of U1-SCRTX-lg1a resulted in the identification of three hundred (300) diverse targets (Table S1), forty-nine (49) of which were intracellular proteins originating from Gram-negative microorganisms (Table S2). Docking results indicate Scores (10,702 to 6066), Areas (1498.70 to 728.40) and ACEs (417.90 to - 152.8) values. Among these, NAD + NH3-dependent synthetase (PDB ID: 1wxi) showed a dock score of 9742, area of 1223.6 and ACE of 38.38 in addition to presenting a Normalized Fit score of 8812 on PharmMapper server. Analysis of the interaction of ligands and receptors suggests that the peptide derived from brown spider venom can interact with residues SER48 and THR160. Furthermore, the C terminus (- 7.0 score) has greater affinity for the receptor than the N terminus (- 7.7 score). The molecular dynamics assay shown that free energy value for the protein complex of - 214,890.21 kJ/mol, whereas with rigid docking, this value was - 29.952.8 sugerindo that after the molecular dynamics simulation, the complex exhibits a more favorable energy value compared to the previous state. The in silico bioprospecting of receptors suggests that U1-SCRTX-lg1a may interfere with NAD + production in Escherichia coli, a Gram-negative bacterium, altering the homeostasis of the microorganism and impairing growth.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-024-00190-8.

Membrane-Active Peptides and Their Potential Biomedical Application

Membrane-active peptides (MAPs) possess unique properties that make them valuable tools for studying membrane structure and function and promising candidates for therapeutic applications. This review paper provides an overview of the fundamental aspects of MAPs, focusing on their membrane interaction mechanisms and potential applications. MAPs exhibit various structural features, including amphipathic structures and specific amino acid residues, enabling selective interaction with multiple membranes. Their mechanisms of action involve disrupting lipid bilayers through different pathways, depending on peptide properties and membrane composition. The therapeutic potential of MAPs is significant. They have demonstrated antimicrobial activity against bacteria and fungi, making them promising alternatives to conventional antibiotics. MAPs can selectively target cancer cells and induce apoptosis, opening new avenues in cancer therapeutics. Additionally, MAPs serve as drug delivery vectors, facilitating the transport of therapeutic cargoes across cell membranes. They represent a fascinating class of biomolecules with significant potential in basic research and clinical applications. Understanding their mechanisms of action and designing peptides with enhanced selectivity and efficacy will further expand their utility in diverse fields. Exploring MAPs holds promise for developing novel therapeutic strategies against infections, cancer, and drug delivery challenges.

In silico bioprospecting of receptors for Doderlin: an antimicrobial peptide isolated from Lactobacillus acidophilus

The emergence of resistant bacteria strains against traditional antibiotics and treatments increases each year. Doderlin is a cationic and amphiphilic peptide active against gram-positive, negative and yeast stains. The aim of the present work was prospect potentials receptors associated of antimicrobial activity of Doderlin using in silico bioinformatics tools. To search for potential targets of Doderlin, PharmMapper software was used. Molecular docking between Doderlin and the receptor was performed by PatchDock. Additional interaction and ligand site prediction for each receptor was performed by I-TASSER software. Those PDB Id, 1XDJ (score: 11,746), 1JMH (score: 11,046), 1YR3 (score: 10,578), 1NG3 (score: 10,082) showed highest dock score. Doderlin was found to predicted/real sites co-localize with 1XDJ and 1JMH, enzymes accountable for nitrogenic bases synthesis. The resulting receptor bioprospecting is highly correlated and suggests that Doderlin might act by interfering with DNA metabolism/production of bacteria, altering microorganism homeostasis and growth impairment.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-023-00149-1.