Deeper Insights on Cnesmone javanica Blume Leaves Extract: Chemical Profiles, Biological Attributes, Network Pharmacology and Molecular Docking
Abstract
:1. Introduction
2. Results and Discussion
2.1. Effects of CV on Anxiolytic and Antidepressant Activity
2.2. Molecular Docking
3. Materials and Methods
3.1. Preparation and Optimization of the Methanol Extract
3.2. GC–MS Analysis
3.3. Animals and Experimental Design
3.4. Anxiolytic Tests
3.4.1. Elevated Plus Maze (EPM) Test
3.4.2. Hole-Board Test (HBT)
3.5. Antidepressant Tests
3.5.1. Forced Swim Test (FST)
3.5.2. Tail Suspension Test (TST)
3.6. Statistical Analysis
3.7. In Silico Molecular Docking Study
3.7.1. Protein Preparation
3.7.2. Ligand Preparation
3.7.3. Receptor Grid Generation and Molecular Docking
3.8. Network Pharmacology and Pathway Analysis
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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SL. No. | RT (min) | Tentative Compounds | MW (amu) | PA (%) |
---|---|---|---|---|
1 | 3.991 | Cyclopentyl acetylene | 94.078 | 0.20 |
2 | 4.128 | Hydrazine, 1,1-dimethyl- | 60.069 | 0.23 |
3 | 4.329 | Ethanethioamide | 75.014 | 0.52 |
4 | 4.964 | Phenacyl thiocyanate | 177.025 | 0.84 |
5 | 5.204 | Ethenamine, N-methyl-1-(methylthio)-2-nitro- | 148.031 | 0.12 |
7 | 6.303 | Furfural | 96.021 | 0.65 |
9 | 9.055 | 2-furancarboxaldehyde, 5-methyl- | 110.037 | 0.20 |
10 | 14.216 | 4H-pyran-4-one, 2,3-dihydro-3,5-dihydroxy-6-methyl- | 144.042 | 0.26 |
11 | 14.845 | 5,6-epoxy-6-methyl-2-heptanone | 142.099 | 0.14 |
16 | 18.902 | 2-methoxy-4-vinylphenol | 150.068 | 0.54 |
17 | 22.742 | Benzofuran, 2,3-dihydro-2-methyl- | 134.073 | 0.16 |
18 | 25.214 | 2,3,5,6-tetrafluoroanisole | 180.020 | 0.26 |
19 | 25.551 and 26.627 | Megastigmatrienone | 190.136 | 0.26 and 0.34 |
20 | 26.364 | 3-hydroxy-.beta.-damascone | 208.146 | 0.20 |
23 | 29.551 | Tetradecanoic acid | 228.209 | 0.49 |
27 | 31.222 | 2-hexadecene, 2,6,10,14-tetramethyl- | 280.313 | 0.25 |
28 | 31.588 | 1,4-eicosadiene | 278.297 | 0.58 |
30 | 32.727 | 4-(2,2-dimethyl-6-methylenecyclohexyl)butanal | 194.167 | 0.20 |
31 | 32.83 | Hexadecanoic acid, methyl ester | 270.256 | 0.88 |
32 | 33.242 and 33.665 | n-hexadecanoic acid | 256.240 | 1.17 and 5.77 |
33 | 34.254 | Farnesol (E), methyl ether | 236.214 | 0.14 |
35 | 35.462 | 2,6,10,14-hexadecatetraen-1-ol, 3,7,11,15-tetramethyl-, acetate | 332.272 | 0.26 |
37 | 36.011 | 9,12-octadecadienoic acid, methyl ester | 294.256 | 0.96 |
39 | 36.143 | 9,12,15-octadecatrienoic acid, methyl ester | 292.240 | 1.86 |
40 | 36.372 | Phytol | 296.308 | 4.35 |
42 | 36.595 | Octadecanoic acid, methyl ester | 298.287 | 0.68 |
43 | 36.984 | 9,12,15-octadecatrienoic acid | 278.225 | 10.44 |
44 | 37.356 | Octadecanoic acid | 284.272 | 1.46 |
45 | 40.503 | Longipinane | 206.203 | 0.49 |
46 | 40.646 | Curan-17-oic acid, 2,16-didehydro-20-hydroxy-19-oxo-, methyl ester | 354.158 | 0.42 |
47 | 40.88 | (+)-(Z)-longipinane | 206.203 | 0.54 |
48 | 41.241 | Hexanedioic acid, bis(2-ethylhexyl) ester | 370.308 | 7.89 |
49 | 43.598 | Phthalic acid, 2-ethylhexyl tetradecyl ester | 474.371 | 5.23 |
50 | 48.531 | Squalene | 410.391 | 6.31 |
51 | 50.219 | Cyclopropanemethanol, alpha, 2-dimethyl-2-(4-methyl-3-pentenyl)-, [1.alpha.(R*),2.alpha.]- | 182.167 | 0.34 |
52 | 50.396 | 2H-1-benzopyran-6-ol, 3,4-dihydro-2,8-dimethyl-2-(4,8,12-trimethyltridecyl)-, [2R-[2R*(4R*,8R*)]]- | 402.350 | 1.30 |
53 | 50.877 | 2,6,10,15,19,23-hexamethyl-tetracosa-2,10,14,18,22-pentaene-6,7-diol | 444.397 | 0.18 |
54 | 51.455 | Chola-5,22-dien-3-ol, (3.beta.,22Z)- | 342.292 | 0.30 |
55 | 51.764 | β-tocopherol | 416.365 | 0.36 |
56 | 51.981 | γ-tocopherol | 416.365 | 2.12 |
57 | 53.183 and 57.417 | DL-α-tocopherol | 430.381 | 23.53 and 3.72 |
58 | 53.457 | 7-(1,3-dimethylbuta-1,3-dienyl)-1,6,6-trimethyl-3,8-dioxatricyclo[5.1.0.0(2,4)]octane | 234.162 | 0.55 |
59 | 54.373 | Campesterol | 400.371 | 0.75 |
60 | 54.825 | 1H-indole-2-carboxylic acid, 6-(4-ethoxyphenyl)-3-methyl-4-oxo-4,5,6,7-tetrahydro-, isopropyl ester | 355.178 | 0.60 |
61 | 55.62 | β-sitosterol | 414.386 | 9.07 |
62 | 55.843 | Androst-5,15-dien-3ol acetate | 314.225 | 1.89 |
Compound Name | Docking Scores | |
---|---|---|
4UUJ | 5I6X | |
Cyclopentyl acetylene | −3.285 | −4.557 |
Hydrazine, 1,1-dimethyl- | −3.474 | −3.568 |
Ethanethioamide | −3.088 | −5.163 |
Phenacyl thiocyanate | −3.475 | −5.666 |
Ethenamine, N-methyl-1-(methylthio)-2-nitro- | −2.092 | −2.195 |
Furfural | −4.077 | −5.300 |
2-furancarboxaldehyde, 5-methyl- | −4.244 | −5.998 |
4H-pyran-4-one, 2,3-dihydro-3,5-dihydroxy-6-methyl- | −4.887 | −5.312 |
5,6-epoxy-6-methyl-2-heptanone | −2.828 | −4.659 |
2-methoxy-4-vinylphenol | −3.817 | −4.860 |
Benzofuran, 2,3-dihydro-2-methyl- | −3.491 | −6.541 |
2,3,5,6-tetrafluoroanisole | −3.633 | −6.911 |
Megastigmatrienone | −3.480 | −5.691 |
3-hydroxy-beta-damascone | −3.896 | −6.060 |
Tetradecanoic acid | +2.287 | −0.427 |
2-hexadecene, 2,6,10,14-tetramethyl- | +0.384 | −1.286 |
1,4-Eicosadiene | +2.442 | 0.337 |
4-(2,2-dimethyl-6-methylenecyclohexyl)butanal | −2.474 | −4.984 |
Hexadecanoic acid, methyl ester | +1.833 | −0.370 |
n-hexadecanoic acid | +1.793 | −1.049 |
Farnesol (E), methyl ether | +0.176 | −3.018 |
2,6,10,14-hexadecatetraen-1-ol, 3,7,11,15-tetramethyl-, acetate | −2.332 | −6.588 |
9,12-octadecadienoic acid, methyl ester | +0.840 | −2.495 |
9,12,15-octadecatrienoic acid, methyl ester | +0.046 | −1.589 |
Phytol | −0.678 | −4.012 |
Octadecanoic acid, methyl ester | +1.018 | −1.84 |
9,12,15-octadecatrienoic acid | −0.123 | −1.99 |
Octadecanoic acid | +1.519 | −1.663 |
Longipinane | − | −5.889 |
Curan-17-oic acid, 2,16-didehydro-20-hydroxy-19-oxo-, methyl ester | −3.243 | −5.678 |
Hexanedioic acid, bis(2-ethylhexyl) ester | −2.807 | −5.211 |
Phthalic acid, 2-ethylhexyl tetradecyl ester | −1.001 | −5.789 |
Squalene | −2.206 | −5.270 |
Cyclopropanemethanol, .alpha.,2-dimethyl-2-(4-methyl-3-pentenyl)-, [1.alpha.(R*),2.alpha.]- | −3.075 | −4.684 |
2H-1-benzopyran-6-ol, 3,4-dihydro-2,8-dimethyl-2-(4,8,12-trimethyltridecyl)-, [2R-[2R*(4R*,8R*)]]- | −3.741 | −9.303 |
2,6,10,15,19,23-hexamethyl-tetracosa-2,10,14,18,22-pentaene-6,7-diol | −3.467 | −6.719 |
Chola-5,22-dien-3-ol, (3.beta.,22Z)- | −3.054 | −5.988 |
β-tocopherol | −3.344 | −7.609 |
γ-tocopherol | −3.680 | −8.384 |
DL-α-tocopherol | −4.041 | −8.285 |
7-(1,3-dimethylbuta-1,3-dienyl)-1,6,6-trimethyl-3,8-dioxatricyclo[5.1.0.0(2,4)]octane | − | −6.085 |
Campesterol | −2.303 | −7.242 |
1H-indole-2-carboxylic acid, 6-(4-ethoxyphenyl)-3-methyl-4-oxo-4,5,6,7-tetrahydro-, isopropyl ester | −3.832 | −5.753 |
β -sitosterol | −2.626 | −7.361 |
Androst-5,15-dien-3-ol acetate | −2.530 | −5.591 |
Standard (diazepam/paroxetine) | −3.475 | −8.978 |
Compounds | Docking Score (4UUJ) | Hydrogen Bond Interactions | Hydrophobic Bond Interactions | Attractive Charges |
---|---|---|---|---|
Phenacyl thiocyanate | −3.475 | Arg64 | Pro63, Arg64 | − |
γ-tocopherol | −3.68 | Asp32, Asn92 | Gly30, Pro63, Trp67, Leu81 | Arg64 |
DL-α-tocopherol | −4.041 | Ser31, Arg100 | Tyr62, Pro63, Arg64, Leu66, Leu81, Arg100 | − |
Furfural | −4.077 | Lys49, Tyr104 | Tyr50, Glu53, Asp102 | − |
2-furancarboxaldehyde, 5-methyl- | −4.244 | Lys49, Tyr104 | Tyr50, Asp102 | − |
4H-Pyran-4-one, 2,3-dihydro-3,5-dihydroxy-6-methyl- | −4.887 | Lys49, Glu53, Asp102, Tyr104 | Lys49 | − |
1H-indole-2-carboxylic acid, 6-(4-ethoxyphenyl)-3-methyl-4-oxo-4,5,6,7-tetrahydro-, isopropyl ester | −3.832 | Asp102, Tyr104 | Tyr50, Glu53, Pro63 | − |
2-methoxy-4-vinylphenol | −3.817 | Lys49, Asp102 | Tyr50, Glu53 | − |
Benzofuran, 2,3-dihydro-2-methyl- | −3.491 | Arg64 | Tyr50, Pro63, Arg64 | − |
2,3,5,6-tetrafluoroanisole | −3.633 | Lys49, Tyr104 | Lys49, Tyr50, Glu53 | − |
Megastigmatrienone | −3.480 | Lys49, Tyr104 | Tyr50, Pro63, Arg64 | − |
3-hydroxy-.beta.-damascone | −3.896 | Lys49, Asp102 | Tyr50, Pro63, Arg64 | − |
2H-1-benzopyran-6-ol, 3,4-dihydro-2,8-dimethyl-2-(4,8,12-trimethyltridecyl)-, [2R-[2R*(4R*,8R*)]]- | −3.741 | Asp32, Asn92 | Gly30, Pro63, Trp67, Leu81 | Arg64 |
Standard (diazepam) | −3.475 | Lys49, Tyr104 | Tyr50, Glu53, Asp102 | − |
Compounds | Docking Score (5I6X) | Hydrogen Bond Interactions | Hydrophobic Bond Interactions | Attractive Charges |
---|---|---|---|---|
2-furancarboxaldehyde, 5-methyl- | −5.998 | Asn177 | Ala169, Ile172, Ala173, Phe341 | − |
Benzofuran, 2,3-dihydro-2-methyl- | −6.541 | − | Ala169, Ile172,Ala173, Tyr176, Ser438, Ser439, Leu443 | − |
2,3,5,6-tetrafluoroanisole | −6.911 | − | Ala169, Ile172,Ala173, Tyr176, Ser439, Leu443 | − |
3-hydroxy-.beta.-damascone | −6.060 | Tyr175, Thr497 | Tyr95, Ile172, Tyr176, Phe335, Phe341, Val501 | − |
2,6,10,14-hexadecatetraen-1-ol, 3,7,11,15-tetramethyl-, acetate | −6.588 | Arg104 | Tyr95, Ile172,Ala173, Tyr176, Phe335, Phe341, Val501 | − |
2H-1-benzopyran-6-ol, 3,4-dihydro-2,8-dimethyl-2-(4,8,12-trimethyltridecyl)-, [2R-[2R*(4R*,8R*)]]- | −9.303 | Ser439 | Tyr95, Ala169, Ile172,Ala173, Tyr176, Phe335, Phe341, Val501 | − |
2,6,10,15,19,23-hexamethyl-tetracosa-2,10,14,18,22-pentaene-6,7-diol | −6.719 | Asp98, Gly100 | Leu99, Trp103, Ile172, Tyr176, Ile179, Phe335, Phe341, Pro403, Val501 | − |
Chola-5,22-dien-3-ol, (3.beta.,22Z)- | −5.988 | Glu494 | Ile172, Tyr176, Phe335, Glu493 | − |
β-tocopherol | −7.609 | Arg104 | Tyr95,Arg104, Ile172, Ala173, Phe335, Phe341, Val501 | − |
γ-tocopherol | −8.384 | Asn177 | Tyr95, Ala169, Ile172,Ala173, Tyr176, Phe335, Phe341, Gly442, Leu443, Val501 | − |
DL-α-tocopherol | −8.285 | Asn177 | Tyr95, Ala169, Ile172,Ala173, Tyr176, Phe335, Phe341, Gly442, Leu443, Val501 | − |
Campesterol | −7.242 | Arg104, Glu494 | Ile172, Tyr176, Phe335, Phe341 | − |
β-sitosterol | −7.361 | Arg104, Glu494 | Ile172, Tyr176, Phe335, Phe341 | − |
Paroxetine (standard) | −8.978 | Tyr95, Ala96 | Tyr95, Asp98, Ala169, Ile172, Ala173, Tyr176, Ser336, Phe341, Ser438, Ser439 | − |
Pathway ID | Pathway Description | Gene Count | False Discovery Rate | Genes |
---|---|---|---|---|
4918 | Thyroid hormone synthesis | 5 | 6.98E-07 | GPX1,GPX2,GSR,PRKACA,PRKCA |
4726 | Serotonergic synapse | 4 | 0.000247 | CASP3,PRKACA,PRKCA,PTGS2 |
480 | Glutathione metabolism | 3 | 0.000821 | GPX1,GPX2,GSR |
590 | Arachidonic acid metabolism | 3 | 0.00119 | GPX1,GPX2,PTGS2 |
4723 | Retrograde endocannabinoid signaling | 3 | 0.00373 | PRKACA,PRKCA,PTGS2 |
5146 | Amoebiasis | 3 | 0.00394 | CASP3,PRKACA,PRKCA |
5200 | Pathways in cancer | 4 | 0.00488 | CASP3,PPARG,PRKCA,PTGS2 |
5206 | MicroRNAs in cancer | 3 | 0.00759 | CASP3,PRKCA,PTGS2 |
4921 | Oxytocin signaling pathway | 3 | 0.00808 | PRKACA,PRKCA,PTGS2 |
5016 | Huntington’s disease | 3 | 0.0121 | CASP3,GPX1,PPARG |
4913 | Ovarian steroidogenesis | 2 | 0.0155 | PRKACA,PTGS2 |
4961 | Endocrine and other factor-regulated calcium reabsorption | 2 | 0.0155 | PRKACA,PRKCA |
5014 | Amyotrophic lateral sclerosis (ALS) | 2 | 0.0155 | CASP3,GPX1 |
5110 | Vibrio cholerae infection | 2 | 0.0155 | PRKACA,PRKCA |
5205 | Proteoglycans in cancer | 3 | 0.0155 | CASP3,PRKACA,PRKCA |
4010 | MAPK signaling pathway | 3 | 0.0184 | CASP3,PRKACA,PRKCA |
4370 | VEGF signaling pathway | 2 | 0.0184 | PRKCA,PTGS2 |
4720 | Long-term potentiation | 2 | 0.0196 | PRKACA,PRKCA |
5031 | Amphetamine addiction | 2 | 0.0198 | PRKACA,PRKCA |
4971 | Gastric acid secretion | 2 | 0.0218 | PRKACA,PRKCA |
4210 | Apoptosis | 2 | 0.0248 | CASP3,PRKACA |
4540 | Gap junction | 2 | 0.0248 | PRKACA,PRKCA |
4727 | GABAergic synapse | 2 | 0.0248 | PRKACA,PRKCA |
4911 | Insulin secretion | 2 | 0.0248 | PRKACA,PRKCA |
4912 | GnRH signaling pathway | 2 | 0.0248 | PRKACA,PRKCA |
4970 | Salivary secretion | 2 | 0.0248 | PRKACA,PRKCA |
5032 | Morphine addiction | 2 | 0.0248 | PRKACA,PRKCA |
4713 | Circadian entrainment | 2 | 0.0256 | PRKACA,PRKCA |
4750 | Inflammatory mediator regulation of TRP channels | 2 | 0.0269 | PRKACA,PRKCA |
4916 | Melanogenesis | 2 | 0.0271 | PRKACA,PRKCA |
4668 | TNF signaling pathway | 2 | 0.0314 | CASP3,PTGS2 |
4725 | Cholinergic synapse | 2 | 0.0314 | PRKACA,PRKCA |
4724 | Glutamatergic synapse | 2 | 0.0316 | PRKACA,PRKCA |
4270 | Vascular smooth muscle contraction | 2 | 0.0331 | PRKACA,PRKCA |
4919 | Thyroid hormone signaling pathway | 2 | 0.0331 | PRKACA,PRKCA |
4650 | Natural-killer-cell-mediated cytotoxicity | 2 | 0.0362 | CASP3,PRKCA |
4728 | Dopaminergic synapse | 2 | 0.0362 | PRKACA,PRKCA |
4310 | Wnt signaling pathway | 2 | 0.0416 | PRKACA,PRKCA |
5012 | Parkinson’s disease | 2 | 0.0418 | CASP3,PRKACA |
5161 | Hepatitis B | 2 | 0.0418 | CASP3,PRKCA |
4261 | Adrenergic signaling in cardiomyocytes | 2 | 0.0420 | PRKACA,PRKCA |
Pathway ID | Pathway Description | Gene Count | False Discovery Rate | Genes |
---|---|---|---|---|
GO.0009743 | Response to carbohydrate | 5 | 0.00163 | CASP3,GPX1,PRKACA,PRKCA,PTGS2 |
GO.0006979 | Response to oxidative stress | 5 | 0.0121 | CASP3,GPX1,GPX2,GSR,PTGS2 |
GO.0009746 | Response to hexose | 4 | 0.0121 | CASP3,GPX1,PRKACA,PTGS2 |
GO.0055114 | Oxidation-reduction process | 7 | 0.0121 | GPX1,GPX2,GSR,PPARG,PRKACA,PRKCA,PTGS2 |
GO.1901700 | Response to oxygen-containing compound | 8 | 0.0121 | CASP3,GPX1,GPX2,GSR,PPARG,PRKACA,PRKCA,PTGS2 |
GO.0000302 | Response to reactive oxygen species | 4 | 0.0203 | CASP3,GPX1,GPX2,GSR |
GO.0043627 | Response to estrogen | 4 | 0.0298 | CASP3,GPX1,PPARG,PTGS2 |
Pathway ID | Pathway Description | Gene Count | False Discovery Rate | Genes |
---|---|---|---|---|
GO.0016209 | Antioxidant activity | 4 | 0.000881 | GPX1,GPX2,GSR,PTGS2 |
GO.0004601 | Peroxidase activity | 3 | 0.00499 | GPX1,GPX2,PTGS2 |
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Obaidullah, A.J.; Alanazi, M.M.; Alsaif, N.A.; Mahdi, W.A.; Fantoukh, O.I.; Tareq, A.M.; Sami, S.A.; Alqahtani, A.M.; Emran, T.B. Deeper Insights on Cnesmone javanica Blume Leaves Extract: Chemical Profiles, Biological Attributes, Network Pharmacology and Molecular Docking. Plants 2021, 10, 728. https://doi.org/10.3390/plants10040728
Obaidullah AJ, Alanazi MM, Alsaif NA, Mahdi WA, Fantoukh OI, Tareq AM, Sami SA, Alqahtani AM, Emran TB. Deeper Insights on Cnesmone javanica Blume Leaves Extract: Chemical Profiles, Biological Attributes, Network Pharmacology and Molecular Docking. Plants. 2021; 10(4):728. https://doi.org/10.3390/plants10040728
Chicago/Turabian StyleObaidullah, Ahmad J., Mohammed M. Alanazi, Nawaf A. Alsaif, Wael A. Mahdi, Omer I. Fantoukh, Abu Montakim Tareq, Saad Ahmed Sami, Ali M. Alqahtani, and Talha Bin Emran. 2021. "Deeper Insights on Cnesmone javanica Blume Leaves Extract: Chemical Profiles, Biological Attributes, Network Pharmacology and Molecular Docking" Plants 10, no. 4: 728. https://doi.org/10.3390/plants10040728
APA StyleObaidullah, A. J., Alanazi, M. M., Alsaif, N. A., Mahdi, W. A., Fantoukh, O. I., Tareq, A. M., Sami, S. A., Alqahtani, A. M., & Emran, T. B. (2021). Deeper Insights on Cnesmone javanica Blume Leaves Extract: Chemical Profiles, Biological Attributes, Network Pharmacology and Molecular Docking. Plants, 10(4), 728. https://doi.org/10.3390/plants10040728