Identification of natural peptides from “PlantPepDB” database as anti-SARS-CoV-2 agents: A protein-protein docking approach
Background: A global pandemic owing to COVID-19 infection has created havoc in the entire world. The etiological agent responsible for this viral outbreak is classified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Still, there's no specific drug or preventive medication to t...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-05-01
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| Series: | Phytomedicine Plus |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2667031323000428 |
| _version_ | 1797829465872531456 |
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| author | Priyanka Bhandu Himanshu Verma Baddipadige Raju Gera Narendra Shalki Choudhary Manmeet Singh Pankaj Kumar Singh Om Silakari |
| author_facet | Priyanka Bhandu Himanshu Verma Baddipadige Raju Gera Narendra Shalki Choudhary Manmeet Singh Pankaj Kumar Singh Om Silakari |
| author_sort | Priyanka Bhandu |
| collection | DOAJ |
| description | Background: A global pandemic owing to COVID-19 infection has created havoc in the entire world. The etiological agent responsible for this viral outbreak is classified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Still, there's no specific drug or preventive medication to treat SARS-CoV-2. This study was designed to demonstrate the efficacy of some anti-viral peptides obtained from a plant database i.e., PlantPepDB as potential ACE-2-Spike (S) protein complex neutralizers using a structure-based drug designing approach. Method: A total of 83 anti-viral plant peptides were screened from a peptide database i.e. PlantPepDB based on their reported anti-viral activities against various viral strains. In order to screen peptides that may potentially interfere with ACE-2 and S complex formation, molecular docking studies were conducted using the flare module of Cresset software and subsequently, analysed the crucial interactions between the peptides and S complexes and ACE-2/S complex. Herein, the interactions and docking scores obtained for ACE-2/S complex were considered as references. The S-peptides complexes which displayed superior interactions and docking scores than reference complex i.e., ACE2-S were considered as final hits. The Molecular dynamics studies were conducted for a period of 30 ns for each of the final hit/S complex to understand the interaction stability and binding mechanism of designed peptides. Results: The molecular docking results revealed that five peptides including Cycloviolacin Y3, Cycloviolacin Y1, White cloud bean defensin, Putative defensin 3.1, and Defensin D1 showed superior docking scores (i.e. -1372.5 kJ/mol to -1232.6 kJ/mol) when docked at the ACE2 binding site of S-protein than score obtained for the complex of ACE-2 and S protein i.e. -1183.4 kJ/mol. Moreover, these top five peptides manifested key interactions required to prevent the binding of S protein with ACE2. The molecular dynamics simulation study revealed that two of these five peptides i.e. Cycloviolacin Y3 and Cycloviolacin Y1 displayed minimal RMSD fluctuations. Conclusions: The current structure-based drug-designing approach shows the possible role of anti-viral plant peptides as potential molecules to be explored at the initial stage of viral pathogenesis. |
| first_indexed | 2024-04-09T13:21:46Z |
| format | Article |
| id | doaj.art-1c401530e25b472886c23f84f724a011 |
| institution | Directory Open Access Journal |
| issn | 2667-0313 |
| language | English |
| last_indexed | 2024-04-09T13:21:46Z |
| publishDate | 2023-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Phytomedicine Plus |
| spelling | doaj.art-1c401530e25b472886c23f84f724a0112023-05-11T04:24:56ZengElsevierPhytomedicine Plus2667-03132023-05-0132100446Identification of natural peptides from “PlantPepDB” database as anti-SARS-CoV-2 agents: A protein-protein docking approachPriyanka Bhandu0Himanshu Verma1Baddipadige Raju2Gera Narendra3Shalki Choudhary4Manmeet Singh5Pankaj Kumar Singh6Om Silakari7Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, IndiaMolecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, IndiaMolecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, IndiaMolecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, IndiaMolecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, IndiaMolecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, IndiaFaculty of Medicine, Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, FI-20014, FinlandCorresponding author.; Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, IndiaBackground: A global pandemic owing to COVID-19 infection has created havoc in the entire world. The etiological agent responsible for this viral outbreak is classified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Still, there's no specific drug or preventive medication to treat SARS-CoV-2. This study was designed to demonstrate the efficacy of some anti-viral peptides obtained from a plant database i.e., PlantPepDB as potential ACE-2-Spike (S) protein complex neutralizers using a structure-based drug designing approach. Method: A total of 83 anti-viral plant peptides were screened from a peptide database i.e. PlantPepDB based on their reported anti-viral activities against various viral strains. In order to screen peptides that may potentially interfere with ACE-2 and S complex formation, molecular docking studies were conducted using the flare module of Cresset software and subsequently, analysed the crucial interactions between the peptides and S complexes and ACE-2/S complex. Herein, the interactions and docking scores obtained for ACE-2/S complex were considered as references. The S-peptides complexes which displayed superior interactions and docking scores than reference complex i.e., ACE2-S were considered as final hits. The Molecular dynamics studies were conducted for a period of 30 ns for each of the final hit/S complex to understand the interaction stability and binding mechanism of designed peptides. Results: The molecular docking results revealed that five peptides including Cycloviolacin Y3, Cycloviolacin Y1, White cloud bean defensin, Putative defensin 3.1, and Defensin D1 showed superior docking scores (i.e. -1372.5 kJ/mol to -1232.6 kJ/mol) when docked at the ACE2 binding site of S-protein than score obtained for the complex of ACE-2 and S protein i.e. -1183.4 kJ/mol. Moreover, these top five peptides manifested key interactions required to prevent the binding of S protein with ACE2. The molecular dynamics simulation study revealed that two of these five peptides i.e. Cycloviolacin Y3 and Cycloviolacin Y1 displayed minimal RMSD fluctuations. Conclusions: The current structure-based drug-designing approach shows the possible role of anti-viral plant peptides as potential molecules to be explored at the initial stage of viral pathogenesis.http://www.sciencedirect.com/science/article/pii/S2667031323000428SARS-CoV-2Protein-protein dockingPlant peptides, Anti-viral peptides |
| spellingShingle | Priyanka Bhandu Himanshu Verma Baddipadige Raju Gera Narendra Shalki Choudhary Manmeet Singh Pankaj Kumar Singh Om Silakari Identification of natural peptides from “PlantPepDB” database as anti-SARS-CoV-2 agents: A protein-protein docking approach Phytomedicine Plus SARS-CoV-2 Protein-protein docking Plant peptides, Anti-viral peptides |
| title | Identification of natural peptides from “PlantPepDB” database as anti-SARS-CoV-2 agents: A protein-protein docking approach |
| title_full | Identification of natural peptides from “PlantPepDB” database as anti-SARS-CoV-2 agents: A protein-protein docking approach |
| title_fullStr | Identification of natural peptides from “PlantPepDB” database as anti-SARS-CoV-2 agents: A protein-protein docking approach |
| title_full_unstemmed | Identification of natural peptides from “PlantPepDB” database as anti-SARS-CoV-2 agents: A protein-protein docking approach |
| title_short | Identification of natural peptides from “PlantPepDB” database as anti-SARS-CoV-2 agents: A protein-protein docking approach |
| title_sort | identification of natural peptides from plantpepdb database as anti sars cov 2 agents a protein protein docking approach |
| topic | SARS-CoV-2 Protein-protein docking Plant peptides, Anti-viral peptides |
| url | http://www.sciencedirect.com/science/article/pii/S2667031323000428 |
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