In Silico Identification and Evaluation of Natural Products as Potential Tumor Necrosis Factor Function Inhibitors Using Advanced Enalos Asclepios KNIME Nodes
Abstract
:1. Introduction
2. Results
2.1. Computer-Aided Drug Design (CADD)
2.1.1. Initial Search and Filtering
2.1.2. Molecular Docking Simulations Using Enalos Asclepios KNIME rxDock Node
2.2. Pharmacological Testing
2.3. Molecular Dynamics and Free Energy Calculations
Molecular Dynamics Simulations with Enalos Asclepios KNIME MD-Simulation Node, Free Energy Calculations with MM-GBSA Method
3. Discussion
4. Material and Methods
4.1. Cheminformatics Modeling—Computer Aided Drug Design (CADD)
4.1.1. Enalos+ Similarity KNIME Node
4.1.2. Molecular Modeling
4.1.3. Enalos Asclepios KNIME Workflow
4.1.4. Molecular Docking with Enalos Asclepios KNIME Workflow
4.1.5. Molecular Dynamics
4.1.6. MM-GBSA Method
4.1.7. Absolute Binding Free Energies Calculation
4.2. Pharmacological Testing
4.2.1. Cell Lines
4.2.2. Mice
4.2.3. Chemokine Level Assay
4.2.4. Natural Products
4.2.5. Statistical Analysis
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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Average kcal/mol | Std.Dev | Average kcal/mol | Std.Dev | Average kcal/mol | Std.Dev | Average kcal/mol | Std.Dev | Average kcal/mol | Std.Dev | Average kcal/mol | Std.Dev | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Miyabenol A | Nepalensinol B | Flexuosol A | Kobophenol A | Ampelopsin H | SPD304 | |||||||
EvDW | −44.514 | 6.56 | −62.4408 | 3.1846 | −31.391 | 6.848 | −46.87 | 3.6866 | −45.9798 | 3.461 | −43.9821 | 2.5799 |
EEL | −15.963 | 6.307 | −22.2184 | 5.5841 | −19.287 | 10.104 | −18.6796 | 6.4461 | −13.0541 | 4.7604 | −111.752 | 5.2156 |
EGB | 45.629 | 6.965 | 56.5623 | 4.9438 | 39.683 | 9.983 | 50.9639 | 6.0277 | 45.0963 | 6.6032 | 144.1032 | 5.9402 |
ΔGGAS | −60.484 | 9.413 | −84.712 | 6.0403 | −50.661 | 11.583 | −65.5466 | 7.5489 | −59.0364 | 6.6642 | −155.734 | 6.5496 |
ΔGSOLV | 39.698 | 6.587 | 49.2238 | 4.8589 | 35.445 | 9.584 | 44.7208 | 5.8006 | 39.3336 | 6.47 | 139.36 | 5.8403 |
ΔGTOTAL | −20.786 | 4.184 | −35.4882 | 3.3524 | −15.216 | 7.09 | −20.8258 | 3.7012 | −19.7027 | 2.6903 | −16.3744 | 2.8002 |
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Papadopoulou, D.; Drakopoulos, A.; Lagarias, P.; Melagraki, G.; Kollias, G.; Afantitis, A. In Silico Identification and Evaluation of Natural Products as Potential Tumor Necrosis Factor Function Inhibitors Using Advanced Enalos Asclepios KNIME Nodes. Int. J. Mol. Sci. 2021, 22, 10220. https://doi.org/10.3390/ijms221910220
Papadopoulou D, Drakopoulos A, Lagarias P, Melagraki G, Kollias G, Afantitis A. In Silico Identification and Evaluation of Natural Products as Potential Tumor Necrosis Factor Function Inhibitors Using Advanced Enalos Asclepios KNIME Nodes. International Journal of Molecular Sciences. 2021; 22(19):10220. https://doi.org/10.3390/ijms221910220
Chicago/Turabian StylePapadopoulou, Dimitra, Antonios Drakopoulos, Panagiotis Lagarias, Georgia Melagraki, George Kollias, and Antreas Afantitis. 2021. "In Silico Identification and Evaluation of Natural Products as Potential Tumor Necrosis Factor Function Inhibitors Using Advanced Enalos Asclepios KNIME Nodes" International Journal of Molecular Sciences 22, no. 19: 10220. https://doi.org/10.3390/ijms221910220