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Peptide-Membrane Docking and Molecular Dynamic Simulation of In Silico Detected Antimicrobial Peptides from Portulaca oleracea’s Transcriptome

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Abstract

The main issue with clinical infections is multidrug resistance to traditional antibiotics. As they are essential to innate immunity, shielding hosts from pathogenic microbes, traditional herbal remedies are an excellent supplier of antimicrobial peptides (AMPs), vital parts of defensive systems. Nevertheless, little is known about the bioactive peptide components of most ethnobotanical species. Our goal in this study was to find new, likely AMPs from Portulaca oleracea (P. oleracea) using in silico studies. The P. oleracea transcriptome was gained from Sequence Read Archive (SRA) and quality controlled, then adapters and other low-quality reads were trimmed. Afterward, de novo assembled and translated open reading frames (ORFs) were determined. Next, the ORFs were filtered based on AMP physiochemical criteria and deep learning methods. Finally, the five selected putative AMPs docked with E. coli and S. aureus membranes that showed penetration in bilayers. In this step, PO2 was chosen as a candidate AMP to analyze with molecular dynamics (MD) simulations. Our data demonstrated that PO2 is more stable in E. coli than in S. aureus. Moreover, these predicted AMPs can be good candidates for in vitro and in vivo analysis.

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The data generated or analyzed during this study are included in the manuscript and its supplementary information files.

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Acknowledgements

We thank the Engineering and Medical Physics Department for providing the computational server in bioinformatics analysis.

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Authors and Affiliations

  1. Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran

    Behnam Hasannejad-Asl, Farkhondeh Pooresmaeil & Azam Bolhassani

  2. Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran

    Behnam Hasannejad-Asl

  3. Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran

    Salimeh Heydari

  4. Department of Biology, Faculty of Science, University of Yazd, Yazd, Iran

    Fahime Azod

  5. Department of Medical Biotechnology, School of Allied Medicine, Iran , University of Medical Science, Tehran, Iran

    Farkhondeh Pooresmaeil

  6. Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran

    Ali Esmaeili

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Contributions

BHA performed study design, in silico analysis, validation, and writing—original draft; SH, FA, FP, and AE performed in silico analysis and literature review; AB performed supervision, conceptualization, and manuscript review. All authors read and approved the final manuscript.

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Correspondence to Azam Bolhassani.

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Supplementary Information

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12602_2024_10261_MOESM1_ESM.jpg

Supplementary file1 (JPG 270 KB): Figure S1: Quality control of reads: (a and c) related to “Per base sequence content” analysis of forward and reverse reads before trimming, respectively; (b and d) related to “Per base sequence content” analysis of forward and reverse reads after trimming, respectively

12602_2024_10261_MOESM2_ESM.jpg

Supplementary file2 (JPG 25 KB): Figure S2: 3-D model of PO10 putative AMP: The residues at 10–14 positions (as shown in red color) make a coil structure and result in the rotation of helical structure

Supplementary file3 (MP4 6805 KB): Supplementary Video 1: PO2 movement along z-direction in E. coli (left side video) and S. aureus (right side video) systems: In both systems, the membrane and ions are depicted as spheres, while PO2 is represented as a new cartoon drawing method in red color.

Supplementary file4 (DOCX 14 KB)

Supplementary file5 (DOCX 13 KB)

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Hasannejad-Asl, B., Heydari, S., Azod, F. et al. Peptide-Membrane Docking and Molecular Dynamic Simulation of In Silico Detected Antimicrobial Peptides from Portulaca oleracea’s Transcriptome. Probiotics & Antimicro. Prot. (2024). https://doi.org/10.1007/s12602-024-10261-z

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