Phytochemical Analysis, In Vitro Biological Activities, and Computer-Aided Analysis of Potentilla nepalensis Hook Compounds as Potential Melanoma Inhibitors Based on Molecular Docking, MD Simulations, and ADMET
Abstract
:1. Introduction
2. Results
2.1. Quantification of Total Phenolic and Flavonoid Content
2.2. In Vitro Antioxidant Activity
2.3. Cytotoxic Activity of Roots and Shoots of P. nepalensis
2.4. Identification of Major Phytocompounds of Methanolic and n-Hexane Extracts of Roots and Shoots of P. nepalensis via GC-MS Profiling
2.5. Molecular Docking Analysis
2.6. MD Simulations Study
2.7. Assessment of Drug Likeness and Toxicity Prediction
3. Discussion
4. Materials and Methods
4.1. Chemicals and Reagents
4.2. Collection and Identification of Plant Material
4.3. Preparation of Extracts of Roots and Shoots of P. nepalensis
4.4. Spectrophotometric Quantification of Total Phenolic (TPC) and Flavonoid Content (TFC)
4.5. In Vitro Antioxidant Potential Using DPPH Radical Scavenging Assay
4.6. In Vitro Cytotoxic Activity of P. nepalensis Roots and Shoots
4.7. GC-MS Profiling of Root and Shoot Extracts of P. nepalensis to Identify Major Phytocompounds
4.8. Ligand Preparation
4.9. Retrieval and Preparation of Target Proteins
4.10. Molecular Docking
4.11. Molecular Dynamics Simulations
4.12. Evaluation of Drug-Likeness and ADME/Toxicity Properties
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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Plant Part | Solvent Used | TPC (mg g−1 GAE) | TFC (mg g−1 RE) | DPPH Activity IC50 (µg mL−1) |
---|---|---|---|---|
Roots | Methanol | 21.21 ± 0.54 | 4.24 ± 0.17 | 23.5 ± 0.92 |
Shoots | Methanol | 15.68 ± 2.79 | 2.58 ± 0.1 | 12.83 ± 0.35 |
Roots | n-Hexane | 0.90 ± 0.19 | 0.06 ± 0.03 | 65.69 ± 0.77 |
Shoots | n-Hexane | 1.59 ± 0.13 | 0.49 ± 0.06 | 74.93 ± 1.01 |
Ascorbic Acid | Methanol | - | - | 5.86 ± 0.13 |
RT (min) | Area% | Name of Phytocompound | Molecular Formula | Bioactivity Reported | References |
---|---|---|---|---|---|
28.61 | 12.64 | Tetradecanoic acid, 10,13-dimethyl-, methyl ester | C17H34O2 | - | - |
31.32 | 10.58 | Heptadecanoic acid, 16-methyl-, methyl ester | C19H38O2 | Effective against skin cancer | [21] |
27.15 | 6.44 | 1,1,1,5,7,7,7-Heptamethyl-3,3-bis (trimethyl siloxy) tetrasiloxane | C13H40O5Si6 | Anti-quorum sensing | [22,23] |
29.26 | 6.34 | Phthalic acid, butyl hept-4-yl ester | C19H28O4 | - | - |
29.35 | 5.87 | 1,1,1,3,5,5,7,7,7-Nonamethyl-3-(trimethyl siloxy) tetrasiloxane | C12H36O4Si5 | - | - |
24.68 | 4.95 | Norepinephrine, (R)-, 4TMS derivative | C20H43NO3Si4 | - | - |
31.02 | 4.63 | 2-Isopropyl-6-phenylnicotinonitrile | C15H14N2 | - | - |
33.35 | 4.56 | Cyclononasiloxane, octadecamethyl | C18H54O9Si9 | antifungal, antibacterial and/or antiviral properties | [24,25] |
39.03 | 4.23 | Oxalic acid, 2TMS derivative | C8H18O4Si2 | - | - |
23.47 | 3.8 | 2-Tetradecanol | C14H30O | Ingredient in cosmetics such as cold creams for its emollient properties | [26] |
RT (min) | Area% | Name of Phytocompound | Molecular Formula | Bioactivity Reported | Reference |
---|---|---|---|---|---|
28.61 | 11.82 | Hexadecanoic acid, methyl ester | C17H34O2 | Antimicrobial | [27] |
31.36 | 8.58 | 1,1,1,5,7,7,7-Heptamethyl-3,3-bis(trimethylsiloxy)tetrasiloxane | C13H40O5Si6 | Anti-quorum sensing | [22,23] |
29.35 | 5.54 | Oxalic acid, 2TMS derivative | C8H18O4Si2 | - | - |
24.68 | 5.4 | Cyclooctasiloxane, hexadecamethyl- | C16H48O8Si8 | - | - |
36.11 | 5.11 | 3-Ethyl-7-hydroxyphthalide | C10H10O3 | Antioxidant | [28] |
29.26 | 4.7 | Phthalic acid, butyl hex-3-yl ester | C18H26O4 | Antimicrobial, insecticidal activity | [29] |
33.35 | 4.36 | 1,1,1,3,5,5,7,7,7-Nonamethyl-3-(trimethylsiloxy)tetrasiloxane | C12H36O4Si5 | - | - |
31.02 | 4.09 | 1-Hexyl-1-nitrocyclohexane | C12H23NO2 | Antimicrobial and anti-inflammatory | [30] |
22.44 | 3.71 | Isobutyl 4-hydroxybenzoate | C11H14O3 | Antimicrobial activity | [31] |
39.04 | 3.55 | Octanoic acid, 5-(acetyloxy)-, methyl ester | C11H20O4 | - | - |
RT (min) | Area% | Name of Phytocompound | Molecular Formula | Bioactivity Reported | Reference |
---|---|---|---|---|---|
44.85 | 22.9 | Trichloromethyl 9-anthracenecarbodithioate | C16H9Cl3S2 | - | - |
20.01 | 17.71 | Heptane, 3,3-dimethyl- | C9H20 | - | - |
23.59 | 12.28 | Hexadecane | C16H34 | Antifungal, Antibacterial, antioxidant activity | [32] |
39 | 7.01 | 1,1,1,5,7,7,7-Heptamethyl-3, 3-bis(trimethylsiloxy)tetrasiloxane | C13H40O5Si6 | Anti-quorum sensing | [22,23] |
15.8 | 5.57 | Dodecane | C12H26 | Antifungal activity | [32] |
26.76 | 4.99 | Eicosane | C20H42 | Antimicrobial activity against clinical pathogens | [33] |
29.34 | 4.79 | 1,1,1,3,5,5,7,7,7-Nonamethyl-3-(trimethylsiloxy) tetrasiloxane | C12H36O4Si5 | - | [34] |
33.33 | 4.68 | Propanoic acid, 2-oxo-3-(trimethylsilyl)-, trimethylsilyl ester | C9H20O3Si2 | - | - |
43.52 | 4.3 | 1,1,1,3,5,7,7,7-Octamethyl-3,5-bis(trimethylsiloxy) tetrasiloxane | C14H42O5Si6 | - | [35] |
11 | 2 | 2,4,6,9-Dehydroadamantane | C10H12 | - | - |
RT (min) | Area% | Name of Phytocompound | Molecular Formula | Bioactivity Reported | Reference |
---|---|---|---|---|---|
25.03 | 23.19 | Benzene, 1,3,5-tri-tert-butyl- | C18H30 | - | - |
32.79 | 23.19 | 1,1,1,3,5,5,5-Heptamethyltrisiloxane | C7H22O2Si3 | Anti-inflammatory and antimicrobial properties | [36] |
46.46 | 17.32 | 4H-1-Benzopyran-2-carboxylic acid, 5-amino-6-hydroxy-4-oxo-, ethyl ester | C12H11NO5 | - | - |
42.15 | 10.13 | 1-Propene, 3-methoxy- | C4H8O | - | - |
29.24 | 8.05 | Phthalic acid, butyl hept-4-yl ester | C19H28O4 | - | [29] |
20 | 3.14 | Heptane, 3,3-dimethyl- | C9H20 | - | - |
36.59 | 2.71 | N- (Methyl sulfonyl)-N, O-bis (trimethyl silyl) hydroxylamine | C7H21NO3SSi2 | - | - |
28.6 | 2.3 | Dodecanoic acid, 2-methyl- | C13H26O2 | - | - |
38.8 | 2.27 | 2-Acetyl-3-ethylpyrazine | C8H10N2O | - | - |
26.76 | 1.87 | Eicosane | C20H42 | Antimicrobial activity against food-borne pathogens | [33] |
Sr. No. | Phytocompounds | PubChem ID | PDB ID: 5K5N | |
---|---|---|---|---|
Binding Energy (Kcal/mol) | Interacting Amino Acids | |||
1 | Trichloromethyl 9-anthracenecarbodithioate | 613595 | −8.9 | Val A:70, Ala A:83, Lys A:85, Tyr A:134, Leu A:188, Cys A:199 |
2 | 4H-1-Benzopyran-2-carboxylic acid, 5-amino-6-hydroxy-4-oxo-, ethyl ester | 619354 | −7.4 | Val A:70, Ala A:83, Met A:101, Val A:110, Leu A:130, Leu A:132, Val A:135, Leu A:188, Cys A:199, Asp A:200 |
3 | Benzene, 1,3,5-tri-tert-butyl- | 15089 | −7.1 | Ile A:62, Phe A:67, Val A:70, Leu A:132, Cys A:199 |
4 | Heptane, 3,3-dimethyl- | 520991 | −4.6 | Val A:70, Ala A:83, Lys A:85, A:132, Tyr A:134, Leu A:188, Cys A:199 |
5 | Hexadecane | 11006 | −5.1 | Ile A:62, Val A:70, Ala A:83, Lys A:85, Leu A:132, Tyr A:134, Leu A:188, Cys A:199 |
6 | 1,1,1,3,5,5,5-Heptamethyltrisiloxane | 6327366 | −3.6 | - |
7 | 1-Propene, 3-methoxy- | 69392 | −2.8 | Tyr A71, Ile A: 84 |
8 | Encorafenib (drug) | 50922675 | −8.6 | Gly A:65, Phe A:67, Lys A:183, Asp A:200 |
Compound | cLogP | nrot | MW | HBD | HBA | Lipinski Rule | Hepato-Toxicity | Immuno-Genicity | Carcino-Genicity | Cyto- Toxicity | LD50 (mg/kg) |
---|---|---|---|---|---|---|---|---|---|---|---|
Trichloromethyl 9-anthracenecarbodithioate | 3.29 | 3 | 371.73 | 0 | 0 | Yes | No | No | Yes | No | 493 mg/kg (Class IV) |
4H-1-Benzopyran-2-carboxylic acid, 5-amino-6-hydroxy-4-oxo-, ethyl ester | 1.89 | 3 | 249.22 | 2 | 5 | Yes | No | No | No | No | 100 mg/kg (Class III) |
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Sharma, S.; Kumar, V.; Yaseen, M.; S. Abouzied, A.; Arshad, A.; Bhat, M.A.; Naglah, A.M.; Patel, C.N.; Sivakumar, P.K.; Sourirajan, A.; et al. Phytochemical Analysis, In Vitro Biological Activities, and Computer-Aided Analysis of Potentilla nepalensis Hook Compounds as Potential Melanoma Inhibitors Based on Molecular Docking, MD Simulations, and ADMET. Molecules 2023, 28, 5108. https://doi.org/10.3390/molecules28135108
Sharma S, Kumar V, Yaseen M, S. Abouzied A, Arshad A, Bhat MA, Naglah AM, Patel CN, Sivakumar PK, Sourirajan A, et al. Phytochemical Analysis, In Vitro Biological Activities, and Computer-Aided Analysis of Potentilla nepalensis Hook Compounds as Potential Melanoma Inhibitors Based on Molecular Docking, MD Simulations, and ADMET. Molecules. 2023; 28(13):5108. https://doi.org/10.3390/molecules28135108
Chicago/Turabian StyleSharma, Subhash, Vikas Kumar, Muhammad Yaseen, Amr S. Abouzied, Abgeena Arshad, Mashooq Ahmad Bhat, Ahmed M. Naglah, Chirag N. Patel, Prasanth Kumar Sivakumar, Anuradha Sourirajan, and et al. 2023. "Phytochemical Analysis, In Vitro Biological Activities, and Computer-Aided Analysis of Potentilla nepalensis Hook Compounds as Potential Melanoma Inhibitors Based on Molecular Docking, MD Simulations, and ADMET" Molecules 28, no. 13: 5108. https://doi.org/10.3390/molecules28135108