Interaction of Pelargonium sidoides Compounds with Lactoferrin and SARS-CoV-2: Insights from Molecular Simulations
Abstract
:1. Introduction
2. Materials and Methods
2.1. Molecular Docking of the PEL Compounds
2.2. Molecular Dynamics of the Best Docking Complexes
2.3. Molecular Dynamics of the SARS-CoV-2 Membrane–PEL Compounds Interaction
2.4. Trajectory Analysis
3. Results
3.1. Prediction of PEL Compounds Toxicity
3.2. Interaction of PEL Compounds with the Bovine Lactoferrin
3.3. Interaction of PEL Compounds with the SARS-CoV-2 Protease (3CLpro)
3.4. Interaction of PEL Compounds with the SARS-CoV-2 Spike Glycoprotein
3.5. Interaction of PEL Compounds with the SARS-CoV-2 RdRp Polymerase
3.6. Interaction of PEL Compounds with the SARS-CoV-2 Membrane
4. Discussion
5. 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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Compound | Interaction Energy (kcal/mol ± SD) |
---|---|
Epigallocatechin-3-gallate | −8.1 (0.3) |
Taxifolin-3-glucoside | −7.9 (0.2) |
Gallocatechin | −7.7 (0.2) |
Artelin | −7.7 (0.2) |
Pentagalloylglucose | −7.6 (0.4) |
Vitexin | −7.6 (0.3) |
Isoorientin | −7.5 (0.2) |
Isovitexin | −7.3 (0.2) |
Orientin | −7.2 (0.3) |
Magnolioside | −7.2 (0.3) |
Quercetin | −7.1 (0.2) |
6-8-dihydroxy-7-methoxycoumarin | −7.0 (0.3) |
7-acetoxy-5-6-dimethoxycoumarin | −6.8 (0.2) |
Dimethoxycoumarin | −6.4 (0.3) |
Fraxetin | −6.4 (0.2) |
6-7-8-trihydroxycoumarin | −6.2 (0.4) |
Isofraxoside | −6.2 (0.2) |
Umckalin | −6.2 (0.2) |
Scopoletin | −6.0 (0.2) |
5-6-7-trimethoxycoumarin | −6.0 (0.2) |
Caffeic acid | −5.7 (0.3) |
Ferulic acid | −5.7 (0.2) |
Vanillic acid | −5.4 (0.3) |
Gallic acid | −5.3 (0.2) |
Apocynin | −5.3 (0.2) |
Homovanillic acid | −5.3 (0.1) |
Dihydroxybenzoic acid | −4.7 (0.2) |
Compound | Interaction Energy (kcal/mol ± SD) |
---|---|
Taxifolin-3-glucoside | −39.1 (4.5) |
Isoorientin | −33.7 (3.6) |
Gallocatechin | −30.8 (2.8) |
Artelin | −30.0 (3.4) |
Vitexin | −24.6 (4.8) |
Epigallocatechin-3-gallate | −21.3 (2.5) |
Pentagalloyl glucose | −16.6 (4.2) |
Compound | Interaction Energy (kcal/mol ± SD) |
---|---|
Vitexin | −8.7 (0.3) |
Pentagalloylglucose | −8.3 (0.4) |
Quercetin | −8.1 (0.2) |
Magnolioside | −8.0 (0.3) |
Isovitexin | −8.0 (0.2) |
Artelin | −8.0 (0.2) |
Isoorientin | −8.0 (0.2) |
Orientin | −7.4 (0.3) |
Taxifolin-3-glucoside | −7.4 (0.1) |
Epigallocatechin-3-gallate | −7.3 (0.3) |
Gallocatechin | −7.3 (0.2) |
Isofraxoside | −7.2 (0.2) |
Fraxetin | −6.9 (0.2) |
7-acetoxy-5-6-dimethoxycoumarin | −6.7 (0.2) |
Dimethoxycoumarin | −6.4 (0.3) |
6-8-dihydroxy-7-methoxycoumarin | −6.2 (0.3) |
Dihydroxybenzoic acid | −6.2 (0.2) |
Scopoletin | −5.9 (0.2) |
6-7-8-trihydroxycoumarin | −5.7 (0.4) |
Caffeic acid | −5.7 (0.3) |
5-6-7-trimethoxycoumarin | −5.7 (0.2) |
Umckalin | −5.7 (0.2) |
Ferulic acid | −5.6 (0.2) |
Gallic acid | −5.6 (0.2) |
Vanillic acid | −5.3 (0.3) |
Apocynin | −5.3 (0.2) |
Homovanillic acid | −4.6 (0.1) |
Compound | Interaction Energy (kcal/mol ± SD) |
---|---|
Vitexin | −29.87 (3.40) |
Pentagalloyl-glucose | −25.74 (5.99) |
Magnolioside | −25.44 (4.05) |
Isoorientin | −23.14 (3.95) |
Artelin | −21.76 (5.59) |
Quercetin | −15.21 (2.69) |
Isovitexin | −15.08 (3.59) |
Compound | Interaction Energy (kcal/mol ± SD) |
---|---|
Pentagalloylglucose | −10.4 (0.3) |
Vitexin | −9.5 (0.2) |
6-8-Dihydroxy-7-methoxycoumarin | −9.3 (0.3) |
Quercetin | −9.3 (0.2) |
Taxifolin-3-glucoside | −9.1 (0.1) |
Isofraxoside | −8.7 (0.2) |
Isovitexin | −8.6 (0.2) |
Gallocatechin | −8.6 (0.2) |
Isoorientin | −8.5 (0.2) |
Epigallocatechin-3-gallate | −8.3 (0.3) |
Artelin | −8.2 (0.2) |
Magnolioside | −8.0 (0.1) |
Orientin | −7.4 (0.3) |
Fraxetin | −7.4 (0.2) |
Scopoletin | −7.0 (0.2) |
7-acetoxy-5-6-dimethoxycoumarin | −6.8 (0.2) |
Umckalin | −6.8 (0.2) |
Caffeic acid | −6.6 (0.3) |
5-6-7-trimethoxycoumarin | −6.6 (0.2) |
Ferulic acid | −6.4(0.2) |
Dimethoxycoumarin | −6.4 (0.3) |
Homovanillic acid | −6.1 (0.1) |
Gallic acid | −5.7(0.2) |
6-7-8-trihydroxycoumarin | −5.7 (0.4) |
Vanillic acid | −5.6 (0.3) |
Apocynin | −5.3 (0.2) |
Dihydroxybenzoic acid | −5.2 (0.2) |
Compound | Interaction Energy (kcal/mol ± SD) |
---|---|
Taxifolin-3-glucoside | −43.2 (5.8) |
Pentagalloylglucose | −38.7 (5.5) |
Magnolioside | −32.2 (4.2) |
Isovitexin | −26.3 (4.7) |
Epigallocatechin-3-gallate | −25.8 (3.4) |
Gallocatechin | −24.7 (3.9) |
Isofraxoside | −23.3 (4.7) |
Isoorientin | −20.9 (6.8) |
6-8-dihydroxy-7-methoxycoumarin | −19.4 (4.5) |
Quercetin | −19.3 (4.5) |
Vitexin | −18.9 (6.1) |
Compound | Interaction Energy (kcal/mol ± SD) |
---|---|
Pentagalloyl glucose | −9.0 (0.5) |
Vitexin | −7.4 (0.1) |
Taxifolin-3-glucoside | −7.4 (0.1) |
Magnolioside | −7.3 (0.2) |
Isovitexin | −7.3 (0.2) |
Isoorientin | −7.3 (0.3) |
Quercetin | −7.2 (0.2) |
Isofraxoside | −7.2 (0.2) |
Epigallocatechin-3-gallate | −6.9 (0.3) |
Gallocatechin | −6.9 (0.2) |
Orientin | −6.8 (0.1) |
Artelin | −6.4 (0.2) |
6-8-dihydroxy-7-methoxycoumarin | −6.2 (0.3) |
Fraxetin | −6.0 (0.1) |
7-acetoxy-5-6-dimethoxycoumarin | −5.9 (0.2) |
Gallic acid | −5.9 (0.2) |
Caffeic acid | −5.8 (0.4) |
Scopoletin | −5.8 (0.1) |
6-7-8-trihydroxycoumarin | −5.7 (0.3) |
Vanillic acid | −5.7 (0.3) |
Umckalin | −5.7 (0.2) |
Ferulic acid | −5.6 (0.2) |
Dimethoxycoumarin | −5.5 (0.3) |
Apocynin | −5.5 (0.2) |
Dihydroxybenzoic acid | −5.4 (0.3) |
5-6-7-trimethoxycoumarin | −5.4 (0.1) |
Homovanillic acid | −5.4 (0.1) |
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Iacovelli, F.; Costanza, G.; Romeo, A.; Cosio, T.; Lanna, C.; Bagnulo, A.; Di Maio, U.; Sbardella, A.; Gaziano, R.; Grelli, S.; et al. Interaction of Pelargonium sidoides Compounds with Lactoferrin and SARS-CoV-2: Insights from Molecular Simulations. Int. J. Environ. Res. Public Health 2022, 19, 5254. https://doi.org/10.3390/ijerph19095254
Iacovelli F, Costanza G, Romeo A, Cosio T, Lanna C, Bagnulo A, Di Maio U, Sbardella A, Gaziano R, Grelli S, et al. Interaction of Pelargonium sidoides Compounds with Lactoferrin and SARS-CoV-2: Insights from Molecular Simulations. International Journal of Environmental Research and Public Health. 2022; 19(9):5254. https://doi.org/10.3390/ijerph19095254
Chicago/Turabian StyleIacovelli, Federico, Gaetana Costanza, Alice Romeo, Terenzio Cosio, Caterina Lanna, Antonino Bagnulo, Umberto Di Maio, Alice Sbardella, Roberta Gaziano, Sandro Grelli, and et al. 2022. "Interaction of Pelargonium sidoides Compounds with Lactoferrin and SARS-CoV-2: Insights from Molecular Simulations" International Journal of Environmental Research and Public Health 19, no. 9: 5254. https://doi.org/10.3390/ijerph19095254
APA StyleIacovelli, F., Costanza, G., Romeo, A., Cosio, T., Lanna, C., Bagnulo, A., Di Maio, U., Sbardella, A., Gaziano, R., Grelli, S., Squillaci, E., Miani, A., Piscitelli, P., Bianchi, L., Falconi, M., & Campione, E. (2022). Interaction of Pelargonium sidoides Compounds with Lactoferrin and SARS-CoV-2: Insights from Molecular Simulations. International Journal of Environmental Research and Public Health, 19(9), 5254. https://doi.org/10.3390/ijerph19095254