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New Putative Antimicrobial Candidates: In silico Design of Fish-Derived Antibacterial Peptide-Motifs
Antimicrobial resistance remains a great threat to global health. In response to the World Health Organizations’ global call for action, nature has been explored for novel and safe antimicrobial candidates. To date, fish have gained recognition as potential source of safe, broad spectrum and effecti...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7744477/ https://www.ncbi.nlm.nih.gov/pubmed/33344436 http://dx.doi.org/10.3389/fbioe.2020.604041 |
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author | Okella, Hedmon Georrge, John J. Ochwo, Sylvester Ndekezi, Christian Koffi, Kevin Tindo Aber, Jacqueline Ajayi, Clement Olusoji Fofana, Fatoumata Gnine Ikiriza, Hilda Mtewa, Andrew G. Nkamwesiga, Joseph Bassogog, Christian Bernard Bakwo Kato, Charles Drago Ogwang, Patrick Engeu |
author_facet | Okella, Hedmon Georrge, John J. Ochwo, Sylvester Ndekezi, Christian Koffi, Kevin Tindo Aber, Jacqueline Ajayi, Clement Olusoji Fofana, Fatoumata Gnine Ikiriza, Hilda Mtewa, Andrew G. Nkamwesiga, Joseph Bassogog, Christian Bernard Bakwo Kato, Charles Drago Ogwang, Patrick Engeu |
author_sort | Okella, Hedmon |
collection | PubMed |
description | Antimicrobial resistance remains a great threat to global health. In response to the World Health Organizations’ global call for action, nature has been explored for novel and safe antimicrobial candidates. To date, fish have gained recognition as potential source of safe, broad spectrum and effective antimicrobial therapeutics. The use of computational methods to design antimicrobial candidates of industrial application has however, been lagging behind. To fill the gap and contribute to the current fish-derived antimicrobial peptide repertoire, this study used Support Vector Machines algorithm to fish out fish-antimicrobial peptide-motif candidates encrypted in 127 peptides submitted at the Antimicrobial Peptide Database (APD3), steered by their physico-chemical characteristics (i.e., positive net charge, hydrophobicity, stability, molecular weight and sequence length). The best two novel antimicrobial peptide-motifs (A15_B, A15_E) with the lowest instability index (−28.25, −22.49, respectively) and highest isoelectric point (pI) index (10.48 for each) were selected for further analysis. Their 3D structures were predicted using I-TASSER and PEP-FOLD servers while ProSA, PROCHECK, and ANOLEA were used to validate them. The models predicted by I-TASSER were found to be better than those predicted by PEP-FOLD upon validation. Two I-TASSER models with the lowest c-score of −0.10 and −0.30 for A15_B and A15_E peptide-motifs, respectively, were selected for docking against known bacterial-antimicrobial target-proteins retrieved from protein databank (PDB). Carbapenam-3-carboxylate synthase (PDB ID; 4oj8) yielded the lowest docking energy (−8.80 and −7.80 Kcal/mol) against motif A15_B and A15_E, respectively, using AutoDock VINA. Further, in addition to Carbapenam-3-carboxylate synthase, these peptides (A15_B and A15_E) were found to as well bind to membrane protein (PDB ID: 1by3) and Carbapenem synthetase (PDB: 1q15) when ClusPro and HPEPDOCK tools were used. The membrane protein yielded docking energy scores (DES): −290.094, −270.751; coefficient weight (CW): −763.6, 763.3 for A15_B and A15_E) whereas, Carbapenem synthetase (PDB: 1q15) had a DES of −236.802, −262.75 and a CW of −819.7, −829.7 for peptides A15_B and A15_E, respectively. Motif A15_B of amino acid positions 2–19 in Pleurocidin exhibited the strongest in silico antimicrobial potentials. This segment could be a good biological candidate of great application in pharmaceutical industries as an antimicrobial drug candidate. |
format | Online Article Text |
id | pubmed-7744477 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-77444772020-12-18 New Putative Antimicrobial Candidates: In silico Design of Fish-Derived Antibacterial Peptide-Motifs Okella, Hedmon Georrge, John J. Ochwo, Sylvester Ndekezi, Christian Koffi, Kevin Tindo Aber, Jacqueline Ajayi, Clement Olusoji Fofana, Fatoumata Gnine Ikiriza, Hilda Mtewa, Andrew G. Nkamwesiga, Joseph Bassogog, Christian Bernard Bakwo Kato, Charles Drago Ogwang, Patrick Engeu Front Bioeng Biotechnol Bioengineering and Biotechnology Antimicrobial resistance remains a great threat to global health. In response to the World Health Organizations’ global call for action, nature has been explored for novel and safe antimicrobial candidates. To date, fish have gained recognition as potential source of safe, broad spectrum and effective antimicrobial therapeutics. The use of computational methods to design antimicrobial candidates of industrial application has however, been lagging behind. To fill the gap and contribute to the current fish-derived antimicrobial peptide repertoire, this study used Support Vector Machines algorithm to fish out fish-antimicrobial peptide-motif candidates encrypted in 127 peptides submitted at the Antimicrobial Peptide Database (APD3), steered by their physico-chemical characteristics (i.e., positive net charge, hydrophobicity, stability, molecular weight and sequence length). The best two novel antimicrobial peptide-motifs (A15_B, A15_E) with the lowest instability index (−28.25, −22.49, respectively) and highest isoelectric point (pI) index (10.48 for each) were selected for further analysis. Their 3D structures were predicted using I-TASSER and PEP-FOLD servers while ProSA, PROCHECK, and ANOLEA were used to validate them. The models predicted by I-TASSER were found to be better than those predicted by PEP-FOLD upon validation. Two I-TASSER models with the lowest c-score of −0.10 and −0.30 for A15_B and A15_E peptide-motifs, respectively, were selected for docking against known bacterial-antimicrobial target-proteins retrieved from protein databank (PDB). Carbapenam-3-carboxylate synthase (PDB ID; 4oj8) yielded the lowest docking energy (−8.80 and −7.80 Kcal/mol) against motif A15_B and A15_E, respectively, using AutoDock VINA. Further, in addition to Carbapenam-3-carboxylate synthase, these peptides (A15_B and A15_E) were found to as well bind to membrane protein (PDB ID: 1by3) and Carbapenem synthetase (PDB: 1q15) when ClusPro and HPEPDOCK tools were used. The membrane protein yielded docking energy scores (DES): −290.094, −270.751; coefficient weight (CW): −763.6, 763.3 for A15_B and A15_E) whereas, Carbapenem synthetase (PDB: 1q15) had a DES of −236.802, −262.75 and a CW of −819.7, −829.7 for peptides A15_B and A15_E, respectively. Motif A15_B of amino acid positions 2–19 in Pleurocidin exhibited the strongest in silico antimicrobial potentials. This segment could be a good biological candidate of great application in pharmaceutical industries as an antimicrobial drug candidate. Frontiers Media S.A. 2020-12-03 /pmc/articles/PMC7744477/ /pubmed/33344436 http://dx.doi.org/10.3389/fbioe.2020.604041 Text en Copyright © 2020 Okella, Georrge, Ochwo, Ndekezi, Koffi, Aber, Ajayi, Fofana, Ikiriza, Mtewa, Nkamwesiga, Bassogog, Kato and Ogwang. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Bioengineering and Biotechnology Okella, Hedmon Georrge, John J. Ochwo, Sylvester Ndekezi, Christian Koffi, Kevin Tindo Aber, Jacqueline Ajayi, Clement Olusoji Fofana, Fatoumata Gnine Ikiriza, Hilda Mtewa, Andrew G. Nkamwesiga, Joseph Bassogog, Christian Bernard Bakwo Kato, Charles Drago Ogwang, Patrick Engeu New Putative Antimicrobial Candidates: In silico Design of Fish-Derived Antibacterial Peptide-Motifs |
title | New Putative Antimicrobial Candidates: In silico Design of Fish-Derived Antibacterial Peptide-Motifs |
title_full | New Putative Antimicrobial Candidates: In silico Design of Fish-Derived Antibacterial Peptide-Motifs |
title_fullStr | New Putative Antimicrobial Candidates: In silico Design of Fish-Derived Antibacterial Peptide-Motifs |
title_full_unstemmed | New Putative Antimicrobial Candidates: In silico Design of Fish-Derived Antibacterial Peptide-Motifs |
title_short | New Putative Antimicrobial Candidates: In silico Design of Fish-Derived Antibacterial Peptide-Motifs |
title_sort | new putative antimicrobial candidates: in silico design of fish-derived antibacterial peptide-motifs |
topic | Bioengineering and Biotechnology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7744477/ https://www.ncbi.nlm.nih.gov/pubmed/33344436 http://dx.doi.org/10.3389/fbioe.2020.604041 |
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