Chemical and bioprotective studies of Xylopia aethiopica seed extract and molecular docking of doconexent and cryptopinone as the prominent compounds
DOI:
https://doi.org/10.46481/asr.2024.3.2.186Keywords:
Xylopia aethiopica, Phytochemicals, Antioxidants, Antibacterials, Molecular dockingAbstract
Fourteen phytochemical compounds were identified in the gas chromatography/mass spectrometry (GC/MS) analysis of the petroleum ether extract of the seeds of Xylopia aethiopica. The compounds comprised of terpenoids (56.027 %), unsaturated fatty acids (30.081 %), alcohol (9.385 %) and saturated fatty acid (4.507 %). The extract showed high antioxidant activity in a dose dependent pattern at a minimum and maximum concentrations of 25 and 400 μg/ml respectively and could be compared with that of ascorbic acid used as a standard antioxidant agent. The antibacterial activity screening of the extract against five pathogenic bacteria organisms indicated that the extract possessed more antibacterial activity than gentamicin used as a standard antibacterial agent. The trend of activity was Klebsiella pneumoniae (gram-negative) > Shigella flexneri (gram-negative) > Staphylococcus epidermidis (gram-positive) > Escherichia coli (gram-negative) > Streptococcus pneumoniae (gram-positive). The presence of high amount of terpenoids in the extract of X. aethiopica could be the reason for the high antioxidant and antibacterial activities shown by the extract and also suggests why the seed extract of the plant is used in herbal medicine for the treatment of diseases and infections. All of the test compounds had negative binding affinities, according to molecular docking modelling, indicating that the compounds had been successfully docked to the receptors. The compounds showed good pharmacokinetic properties, such as high blood-brain barrier absorption, oral bioavailability, and water solubility, in the in-silico ADME and drug-likeness predictions. The findings of this study significantly increase the relevance of these compounds as promising first targets for the treatment of drug resistant bacteria. This may help pharmacologists and other medicinal chemists create and synthesize even more potent drug candidates.
Downloads
References
O. U. Igwe, “Chromatographic and spectrometric characterization of bioactive compounds from the leaves of Hyptis lanceolata Poir”, International Journal of Chemistry and Pharmaceutical Sciences 2 (2014) 547. https://oaji.net/articles/2014/292-1393078059.pdf.
O. U. Igwe & N. M. Mgbemena, “Chemical investigation and antibacterial activity of the leaves of Peperomia pellucida L. HBK (Piper-aceae)”, Asian Journal of Chemical and Pharmaceutical Research 2 (2014) 78. https://www.researchgate.net/publication/281748872.
J. P. Fetse, W. Kofie & R. K. Adosraku, “Ethnopharmacological importance of Xylopia aethiopica (Dunal) A. Rich (Annonaceae)–A Review”, British Journal of Pharmaceutical Research 11 (2016) 1. http://dx.doi.org/10.9734/BJPR/2016/24746.
X. Yin, M. A. S. C. Leon, R. Osae, L. O. Linus, L. W. Qi & R. N. Alolga, “Xylopia aethiopica seeds from two countries in West Africa exhibit differences in their proteomes, mineral content and bioactive phytochemical composition”, Molecules 24 (2019) 1979. https://doi.org/10.3390/molecules24101979.
J. J. R. Bouagnon, G. E. K. Bolou, K. B. Guédé, D. Sanga, L. R. Koffi, C. D. R. N’Guessan, Y. Konan, E. V. Adjogoua, J. D. N’Guessan, A. J. Djaman & M. Dosso, “Phytochemical study and evaluation of the antiviral activity of aqueous extracts of three medicinal plants; Xylopia aethiopica, Gliricidia sepium and Ocimum gratissimum used in Cote d’Ivoire”, African Journal of Clinical and Experimental Microbiology 23 (2022) 141. https://dx.doi.org/10.4314/ajcem.v23i2.4.
V. Lobo, A. Patil, A. Phatak A. & N. Chandra, “Free radicals, antioxidants and functional foods: impact on human health”, Pharmacognosy Reviews 4 (2010) 118. https://doi.org/10.4103/0973-7847.70902.
I. S. Young & J. V. Woodside, “Antioxidants in health and diseases”, Journal of Clinical Pathology 54 (2001) 86. https://doi.org/10.1136/jcp.54.3.176.
O. U. Igwe & D. E. Okwu, “Isolation, characterization and antioxidant activity of a furo-chromen-4-one from the seeds of Brachystegia eurycoma Harms”, International Journal of Chemical Sciences 11 (2013) 121. https://www.tsijournals.com/articles/isolation-characterization-and-antioxidantactivity-of-a-furochromen4one-from-theseeds-of-brachystegia-eurycoma-harms.pdf.
O. U. Igwe & H. C. Akabuike, “Free radical scavenging activity, phytochemistry and antimicrobial properties of Tetrapleura tetraptera Seeds”, International Research Journal of Chemistry and Chemical Sciences 3 (2016) 037. https://www.researchgate.net/publication/309802656.
O. U. Igwe & P. U. Onuoha, “Potentials of Citrulluslanatus seeds as antioxidant and antimicrobial agents and a probe of their phytochemicals”, International Journal of Chemical, Material and Environmental Research 3 (2016) 62. https://www.researchgate.net/publication/307975511.
O. U. Igwe & I. P. Ugwunnaji, “Phytochemistry, antioxidant and antimicrobial studies of endosperm tissues of Cocos nucifera L.”, International Journal of Chemical, Material and Environmental Research 3 (2016) 78. https://www.researchgate.net/publication/311901554.
I. E. Otuokere, O. U. Akoh, J. O. Echeme, F. C. Nwadire, C. I. Nwankwo, J. N. Egbucha & K Ammasai, “GC-MS analysis and molecular docking studies to identify potential SARS-CoV-2 nonstructural protein inhibitors from Icacina trichantha Oliv Tubers”, Tropical Journal of Natural Product Research 6 (2022a) 1342. https://doi.org/10.26538/tjnpr/v6i8.29.
O. U. Igwe & J. O. Echeme, “Isolation, characterization and antibacterial activity of 4-(4-phenyl-1,4-dihydronaphthalen-1-yl) pentenoic acid from the stem bark of Brachystegia eurycoma Harms”, International Journal of Drug Development and Research 5 (2013) 335. https://www.itmedicalteam.pl/articles/isolation-characterization-and-antibacterial-activity-of-44phenyl14dihydronaphthalen1yl-pentenoic-acid-from-the-stem-bar-101464.html.
O. U. Igwe, “Quantitative estimation of ascorbic acid levels in citrus fruits at variable temperatures and physicochemical properties”, International Journal of Chemical and Biochemical Sciences 5 (2014b) 67. https://www.iscientific.org/wp-content/uploads/2018/02/12-IJCBS-14-05-05.pdf.
C. Almeida, L. Cerqueira, N. F. Azevedo & M. J. Vieira, “Detection of Salmonella enterica serovar Enteritidis using real time PCR, immunocapture assay, PNA FISH and standard culture methods in different types of food samples”, International Journal of Food Microbiology 161 (2013) 16. https://doi.org/10.1016/j.ijfoodmicro.2012.11.014.
CLC bio, Molecular Molegro Viewer 2.5, CLC bio company, 2012. https://www.researchgate.net/profile/Yoshinobu-Ishikawa/post/Can-I-fix-part-of-the-ligand- to-interact-with-the-protein-receptor-while-leave-the-rest-flexible-for-docking.
S. Dallakyan & A. J. Olson, “Small-molecule library screening by docking with PyRx”, Methods in Molecular Biology 1263 (2015) 243. http://dx.doi.org/10.1007/978-1-4939-2269-7 19
M. F. Adasme, K. L. Linnemann, S. N. Bolz, F. Kaiser, S. Salentin, V. J. Haupt & M. Schroeder, “PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA”, Nucleic Acids Research 49 (2021) 530. https://doi.org/10.1093/nar/gkab294.
A. Daina, O. Michielin & V. Zoete, “SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules”, Sci Rep 7 (2017) 42717. https://doi.org/10.1038/srep42717.
O. U. Igwe & T. Abii, “Characterization of bioactive sesquiterpenes, organic acids and their derivatives from the leaves of Psidium guajava Linn”, International Research Journal of Pure and Applied Chemistry 4 (2014) 456. http://dx.doi.org/10.9734/IRJPAC/2014/8592.
I. E. Otuokere, O. U. Akoh, F. C. Nwadire, C. I. Nwankwo, J. N. Egbucha, C. Wisdom & O. A. Okwudiri, “GC-MS profiling and in silico studies to identify potential SARS-CoV-2 nonstructural protein inhibitors from Psidium guajava”, African Scientific Reports 1 (2022) 173. https://doi.org/10.46481/asr.2022.1.3.52.
C. I. Nwankwo, T. N. Omeh, O. D. Omodamiro, I. E. Otuokere, P. O. Alaebo, O. C. Atasie & G. A. Ekwuribe, “Phenolics of Abelmoschus esculentus Pods: HPLC identification and in silico studies to identify potential anti-inflammatory agents”, Tropical Journal of Natural Product Research 6 (2022) 1311. https://doi.org/10.26538/tjnpr/v6i8.25.
I. G. Asuquo, M. Solangi, K. M. Khan, S. Chigurupati, I. E. Otuokere, F. K. Ekuma, U. Salar, G. S. Felemban, A. U. Rehman, A Wadood & M. Taha, “Design, synthesis and bioevaluation of indolin-2-ones as potential antidiabetic agents”, Future Medicinal Chemistry 15 (2023) 0184. https://doi.org/10.4155/fmc-2022-0184.
F. J. Amaku, I. E. Otuokere, V. O. Ikpeazu, K. K. Igwe, “Using the pharmacophoric features of Azithromycin to design potential SARS-CoV-2 inhibitor”, Communication in Physical Sciences 5 (2020) 518. http://dx.doi.org/10.24018/ejers.2020.5.9.2057.
I. E. Otuokere, J. G. Ohwimu, K. C. Amadi, C. O. Alisaa, F. C. Nwadire, O. U. Igwe, A. A. Okoyeagu & C. M. Ngwu, “Synthesis, characterization and molecular docking studies of Mn (II) complex of sulfathiazole”, Journal of the Nigerian Society of Physical Sciences 1 (2019) 95. https://doi.org/10.46481/jnsps.2019.20.
I. E. Otuokere, J. G. Ohwimu, K. C. Amadi, O. U. Igwe & F. C. Nwadire, “Synthesis, characterization and molecular docking studies of Co(II) metal complex of sulfathiazole”, Bulletin of the Chemical Society of Ethiopia 34 (2020) 83. https://doi.org/10.4314/bcse.v34i1.8.
C. A. Lipinski, F. Lombardo, B. W. Dominy, P. J. Feeney, “In vitro models for selection of development candidates experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings” Adv Drug Deliv. Rev. 23 (2012) 3. https://doi.org/10.1016/s0169-409x(00)00129-0
T. J. Ritchie, S. J. F. Macdonald, S. Peace, S. D. Pickett & C. N. Luscombe, “Increasing small molecule drug developability in suboptimal chemical space”, MedChemComm 4 (2013) 673. https://doi.org/10.1039/c3md00003f.
G. Ottaviani, “What is modulating solubility in simulated intestinal fluids?”, European Journal of Pharmaceutical Science 41 (2010) 452. https://doi.org/10.1016/j.ejps.2010.07.012.
K. T. Savjani, A. K. Gajjar & J. K. Savjani, “Drug solubility: importance and enhancement techniques”, ISRM Pharmaceutical 2012 (2012) 195727. https://pubmed.ncbi.nlm.nih.gov/22830056/.
J. S. Delaney, “ESOL: estimating aqueous solubility directly from molecular structure” Journal of Chemical Information and Modeling 44 (2004) 1000. https://doi.org/10.1021/ci034243x.
Y. C. Martin, “A bioavailability score”, Journal of Medicinal Chemistry 48 (2005) 3164. https://doi.org/10.1021/jm0492002.
R. A. B. Van Waterschoot & A. H. Schinkel, “A critical analysis of the interplay between cytochrome P450 3A and P-glycoprotein: recent insights from knockout and transgenic mice”, Pharmacological Reviews 63 (2011) 390. https://doi.org/10.1124/pr.110.002584.
P. F. Hollenberg, “Characteristics and common properties of inhibitors, inducers, and activators of CYP enzymes”, Drug Metabolism Reviews 34 (2002) 17. https://doi.org/10.1081/dmr-120001387.
J. Kirchmair, H. G. Andreas, L. Dieter, K. Jens, T. Bernard, D. W. Ian, C. G. Robert & S. Gisbert, “Predicting drug metabolism: experiment and/or computation?”, Nature Reviews Drug Discovery 14 (2015) 387. https://doi.org/10.1038/nrd4581.
H. Veith, N. Southall, R. Huang, T. James, D. Fayne, N. Artemenko, M. Shen, J. Inglese, C. P. Austin, D. G. Lloyd & D. S. Auld, “Comprehensive characterization of cytochrome P450 isozyme selectivity across chemical libraries”, Nature Biotechnology 27 (2009) 1050. https://doi.org/10.1038/nbt.1581.
R. O. Potts & R. H. Guy, “Predicting skin permeability”, Pharm. Res. 9 (1992) 663. https://doi.org/10.1023/a:1015810312465.
T. J. Ritchie, P. Ertl & R. Lewis, “The graphical representation of ADME-related molecule properties for medicinal chemists”, Drug Discovery Today 16 (2011) 65. https://doi.org/10.1016/j.drudis.2010.11.002.
F. Lovering, J. Bikker & C. Humblet, “Escape from flatland: increasing saturation as an approach to improving clinical success”, Journal of Medicinal Chemistry 52 (2009) 6752. https://doi.org/10.1021/jm901241e.
Additional Files
Published
License
Copyright (c) 2024 O. U. Igwe, C. C. Oru, I. E. Otuokere
This work is licensed under a Creative Commons Attribution 4.0 International License.
