Antiviral Action against SARS-CoV-2 of a Synthetic Peptide Based on a Novel Defensin Present in the Transcriptome of the Fire Salamander (Salamandra salamandra)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Transcriptome Assembly and Identification of Transcript Sequence by Homology
2.2. Sequence Alignment and Phylogenetic Analysis
2.3. In Silico Studies
2.3.1. Docking
2.3.2. Molecular Dynamics Simulations
2.3.3. Electronic Structure Calculations
2.4. Synthesis and Characterization of Peptide
2.5. In Vitro Synthetic SS-I Viability Evaluation
2.6. In Vitro Vero-CCL-81 Cell-Based SARS-CoV-2 Infection Assay
2.7. Hemolysis Assay
3. Results and Discussion
3.1. Identification and Characterization of the Defensin SS-I
3.2. Interactions between SS-I with ACE2 and SARS-CoV-2 Spike Protein (S1)
3.3. In Vitro Cytotoxic and Hemolytic Activity of Synthetic SS-I and SARS-CoV-2 Infection Assay
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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ACE2-PEP-S2 | SPIKE-PEP-S2 | ||||
---|---|---|---|---|---|
H-Bonds | |||||
Donor | Acceptor | Occupancy | Donor | Acceptor | Occupancy |
Ala16-PEP | Asp30-ACE2 | 93.72% | Arg42-PEP | Glu484-SPIKE | 97.74% |
Thr15-PEP | Asp30-ACE2 | 93.28% | Thr500-SPIKE | Asp31-PEP | 30.33% |
Lys26-ACE2 | Asp31-PEP | 65.47% | Phe1-PEP | Asn501-SPIKE | 22.97% |
Gly5-PEP | Ala387-ACE2 | 64.17% | Arg42-PEP | Gly482-SPIKE | 20.09% |
Arg42-PEP | Glu37-ACE2 | 62.71% | Phe1-PEP | Gln498-SPIKE | 19.83% |
Arg14-PEP | Asp30-ACE2 | 62.67% | Asn450-SPIKE | Met44-PEP | 19.13% |
Trp4-PEP | Gln388-ACE2 | 36.05% | Asn39-PEP | Glu484-SPIKE | 17.19% |
Lys353-ACE2 | Leu43-PEP | 27.77% | Gln498-SPIKE | Asp31-PEP | 14.91% |
Tyr33-PEP | Asp30-ACE2 | 15.81% | Asn501-SPIKE | Phe1-PEP | 14.73% |
Trp4-PEP | Ala387-ACE2 | 15.35% | Tyr33-PEP | Gln498-SPIKE | 12.20% |
Thr15-PEP | Gly446-SPIKE | 11.32% | |||
Asn39-PEP | Glu484-SPIKE | 10.58% | |||
Salt Bridges | |||||
Residues | Occupancy | Residues | Occupancy | ||
Asp31-PEP/Lys26-ACE2 | 82.18% | Glu484-SPIKE/Arg42-PEP | 93.90% | ||
Asp30-ACE2/Arg14-PEP | 68.21% | ||||
Glu37-ACE2/Arg42-PEP | 61.13% |
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Barros, A.L.A.N.; Silva, V.C.; Ribeiro-Junior, A.F.; Cardoso, M.G.; Costa, S.R.; Moraes, C.B.; Barbosa, C.G.; Coleone, A.P.; Simões, R.P.; Cabral, W.F.; et al. Antiviral Action against SARS-CoV-2 of a Synthetic Peptide Based on a Novel Defensin Present in the Transcriptome of the Fire Salamander (Salamandra salamandra). Pharmaceutics 2024, 16, 190. https://doi.org/10.3390/pharmaceutics16020190
Barros ALAN, Silva VC, Ribeiro-Junior AF, Cardoso MG, Costa SR, Moraes CB, Barbosa CG, Coleone AP, Simões RP, Cabral WF, et al. Antiviral Action against SARS-CoV-2 of a Synthetic Peptide Based on a Novel Defensin Present in the Transcriptome of the Fire Salamander (Salamandra salamandra). Pharmaceutics. 2024; 16(2):190. https://doi.org/10.3390/pharmaceutics16020190
Chicago/Turabian StyleBarros, Ana Luisa A. N., Vladimir C. Silva, Atvaldo F. Ribeiro-Junior, Miguel G. Cardoso, Samuel R. Costa, Carolina B. Moraes, Cecília G. Barbosa, Alex P. Coleone, Rafael P. Simões, Wanessa F. Cabral, and et al. 2024. "Antiviral Action against SARS-CoV-2 of a Synthetic Peptide Based on a Novel Defensin Present in the Transcriptome of the Fire Salamander (Salamandra salamandra)" Pharmaceutics 16, no. 2: 190. https://doi.org/10.3390/pharmaceutics16020190