Insilico Analysis And Molecular Docking Studies Of Potential Compounds From Crateva Magna (Lour.) DC. Using POAP
Keywords:
POAP, Binding affinity, GNU parallel pipeline, Drug design, Binding pocket prediction, Crateva magna (Lour. )DC
Abstract
In silico analysis provides an accelerated screening method to identify potential bioactive compounds in plant extracts. Though Crateva magna’s application in traditional medicine is well documented, the bioactivity of its secondary metabolites are not extensive. Gas Chromatography-Mass Spectroscopy (GC-MS) analysis of methanolic extracts of root, bark, flower and leaves of Crateva magna revealed numerous compounds. Virtual screening was performed using POAP against 57 proteins encompassing antimicrobial targets and those implicated in human diseases. Evaluation of docked complexes with scores above -9.6 revealed ligands interacts strongly with 10 protein targets. Leaf extract based compound, Butane, 1,4-bis(9,10-dihydro-9-methylanthracen-10-yl)-, a reported bioherbicide showed strong affinity to multiple targets of Staphylococcus aureus, SARS Cov2 and opportunistic Candida albicans. Isoquinoline, 1-[(3,5- dibenzyloxy)benzyl]-1,2,3,4- tetrahydro-6-methoxy- interacted strongly with diabetic protein targets in addition to antimicrobial proteins. The multitude of novel bioactive compounds detected in Crateva magna by GC-MS followed by virtual screening would pave the way for identifying potential drug candidates.
References
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4. Bopana, N., & Saxena, S. (2008). Crataeva nurvala: A Valuable Medicinal Plant. Journal of Herbs, Spices & Medicinal Plants, 14(1–2), 107–127. https://doi.org/10.1080/10496470802341532
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8. Durdagi, S., Tahir Ul Qamar, M., Salmas, R. E., Tariq, Q., Anwar, F., & Ashfaq, U. A. (2018). Investigating the molecular mechanism of staphylococcal DNA gyrase inhibitors: A combined ligand-based and structure-based resources pipeline. Journal of Molecular Graphics & Modelling, 85, 122–129. https://doi.org/10.1016/j.jmgm.2018.07.010
9. Fan, S., Chang, J., Zong, Y., Hu, G., & Jia, J. (2018). GC-MS Analysis of the Composition of the Essential Oil from Dendranthema indicum Var. Aromaticum Using Three Extraction Methods and Two Columns. Molecules (Basel, Switzerland), 23(3), 576. https://doi.org/10.3390/molecules23030576
10. Gimeno, A., Ojeda-Montes, M., Tomás-Hernández, S., Cereto-Massagué, A., Beltrán-Debón, R., Mulero, M., Pujadas, G., & Garcia-Vallvé, S. (2019). The Light and Dark Sides of Virtual Screening: What Is There to Know? International Journal of Molecular Sciences, 20(6), 1375. https://doi.org/10.3390/ijms20061375
11. Hebbar, D. R., & Nalini, M. S. (2020). GC-MS Characterization of Antioxidative Compounds from the Stem Bark and Flower Extracts of Schefflera Species, from Western Ghats. Der Pharmacia Lettre, 12(7), 51–60.
12. Jabra-Rizk, M. A., Kong, E. F., Tsui, C., Nguyen, M. H., Clancy, C. J., Fidel, P. L., & Noverr, M. (2016). Candida albicans Pathogenesis: Fitting within the Host-Microbe Damage Response Framework. Infection and Immunity, 84(10), 2724–2739. https://doi.org/10.1128/IAI.00469-16
13. Jeoung, N. H. (2015). Pyruvate Dehydrogenase Kinases: Therapeutic Targets for Diabetes and Cancers. Diabetes & Metabolism Journal, 39(3), 188. https://doi.org/10.4093/dmj.2015.39.3.188
14. Jeoung, N. H., Rahimi, Y., Wu, P., Lee, W. N. P., & Harris, R. A. (2012). Fasting induces ketoacidosis and hypothermia in PDHK2/PDHK4-double-knockout mice. The Biochemical Journal, 443(3), 829–839. https://doi.org/10.1042/BJ20112197
15. Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., Zhang, B., Li, X., Zhang, L., Peng, C., Duan, Y., Yu, J., Wang, L., Yang, K., Liu, F., Jiang, R., Yang, X., You, T., Liu, X., … Yang, H. (2020). Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature, 582(7811), 289–293. https://doi.org/10.1038/s41586-020-2223-y
16. Joy, C., & Cyriac, M. C. (2022). Phytochemicals as Potential Drug Candidates for SARS Cov-2: An RDRp Based In-Silico Drug Designing. Proceedings of the Conference BioSangam 2022: Emerging Trends in Biotechnology (BIOSANGAM 2022), 58–69. https://doi.org/10.2991/978-94-6463-020-6_7
17. Juszczak, Zovko-Končić, & Tomczyk. (2019). Recent Trends in the Application of Chromatographic Techniques in the Analysis of Luteolin and Its Derivatives. Biomolecules, 9(11), 731. https://doi.org/10.3390/biom9110731
18. Kumar, A., Kumari, P., & somasundaram, T. (2014). Gas Chromatography-Mass Spectrum (GC-MS) Analysis of Bioactive Components of the Methanol Extract of Halophyte, Sesuvium portulacastrum L. International Journal of Advances in Pharmacy, Biology and Chemistry, 3(3), 766–772.
19. Lee & Kim. (2019). In-Silico Molecular Binding Prediction for Human Drug Targets Using Deep Neural Multi-Task Learning. Genes, 10(11), 906. https://doi.org/10.3390/genes10110906
20. Li, P., L. Snyder, G., & E. Vanover, K. (2016). Dopamine Targeting Drugs for the Treatment of Schizophrenia: Past, Present and Future. Current Topics in Medicinal Chemistry, 16(29), 3385–3403. https://doi.org/10.2174/1568026616666160608084834
21. Loganayaki, N., & Manian, S. (2012). Evaluation of Indian sacred tree Crataeva magna (Lour.) DC. for antioxidant activity and inhibition of key enzymes relevant to hyperglycemia. Journal of Bioscience and Bioengineering, 113(3), 378–380. https://doi.org/10.1016/j.jbiosc.2011.10.020
22. Lu, I.-L., Mahindroo, N., Liang, P.-H., Peng, Y.-H., Kuo, C.-J., Tsai, K.-C., Hsieh, H.-P., Chao, Y.-S., & Wu, S.-Y. (2006). Structure-Based Drug Design and Structural Biology Study of Novel Nonpeptide Inhibitors of Severe Acute Respiratory Syndrome Coronavirus Main Protease. Journal of Medicinal Chemistry, 49(17), 5154–5161. https://doi.org/10.1021/jm060207o
23. Michelakis, E. D., Sutendra, G., Dromparis, P., Webster, L., Haromy, A., Niven, E., Maguire, C., Gammer, T.-L., Mackey, J. R., Fulton, D., Abdulkarim, B., McMurtry, M. S., & Petruk, K. C. (2010). Metabolic Modulation of Glioblastoma with Dichloroacetate. Science Translational Medicine, 2(31). https://doi.org/10.1126/scitranslmed.3000677
24. Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
25. Oberacher, H., Whitley, G., & Berger, B. (2013). Evaluation of the sensitivity of the ‘Wiley registry of tandem mass spectral data, MSforID’ with MS/MS data of the ‘NIST/NIH/EPA mass spectral library.’ Journal of Mass Spectrometry, 48(4), 487–496. https://doi.org/10.1002/jms.3184
26. Paulsen, J. L., Bendel, S. D., & Anderson, A. C. (2011). Crystal Structures of Candida albicans Dihydrofolate Reductase Bound to Propargyl‐Linked Antifolates Reveal the Flexibility of Active Site Loop Residues Critical for Ligand Potency and Selectivity. Chemical Biology & Drug Design, 78(4), 505–512. https://doi.org/10.1111/j.1747-0285.2011.01169.x
27. Peng, K., Pan, Y., Li, J., Khan, Z., Fan, M., Yin, H., Tong, C., Zhao, Y., Liang, G., & Zheng, C. (2016). 11β-Hydroxysteroid Dehydrogenase Type 1(11β-HSD1) mediates insulin resistance through JNK activation in adipocytes. Scientific Reports, 6(1), 37160. https://doi.org/10.1038/srep37160
28. Poongattil,S., Thomas, J. & Cheruthazhakkat, S. High-performance thin-layer chromatography profiling of Crateva magna (Lour.) DC. from different parts of South India. (2024). JPC-J Planar Chromat . https://doi.org/10.1007/s00764-024-00294-z
29. Prabhat, D., Ranjan, S., Mekap.S, & Pani, S. (2010). Phytochemical and Pharmacological Screening of the Plant Crateva Magna Against Alloxan Induced Diabetes in Rats. Journal of Pharmaceutical Sciences and Research, 2.
30. Premila, M. (1995). Premila MS, Ayurvedic Herbs: A Clinical Guide to the Healing Plants of Traditional Indian Medicine, In: Plants for urinary tract disorders, 5th Edn, 1995, pp. 157-160. (5th ed.).
31. Ren, Y., Li, L., Wan, L., Huang, Y., & Cao, S. (2022). Glucokinase as an emerging anti-diabetes target and recent progress in the development of its agonists. Journal of Enzyme Inhibition and Medicinal Chemistry, 37(1), 606–615. https://doi.org/10.1080/14756366.2021.2025362
32. Russell, C. W., Richards, A. C., Chang, A. S., & Mulvey, M. A. (2017). The Rhomboid Protease GlpG Promotes the Persistence of Extraintestinal Pathogenic Escherichia coli within the Gut. Infection and Immunity, 85(6), e00866-16. https://doi.org/10.1128/IAI.00866-16
33. Samdani, A., & Vetrivel, U. (2018). POAP: A GNU parallel based multithreaded pipeline of open babel and AutoDock suite for boosted high throughput virtual screening. Computational Biology and Chemistry, 74, 39–48. https://doi.org/10.1016/j.compbiolchem.2018.02.012
34. Sameen, S., Khalid, Z., & Malik, S. I. (2013). Role of pyruvate dehydrogenase kinases (PDK’s) and their respective microRNA’s in human ovarian cancer. Global Journal of Molecular Evolution and Genomics, 1(1), 56–62.
35. Sethi, V., Jain, M., & Thakur, R. (1978). Chemical constituents of Crataeva religiosa. Plant Med, 34, 223–224.
36. Shaker, B., Ahmad, S., Lee, J., Jung, C., & Na, D. (2021). In silico methods and tools for drug discovery. Computers in Biology and Medicine, 137, 104851. https://doi.org/10.1016/j.compbiomed.2021.104851
37. Sharma, P., Singh, S., Sharma, N., Singla, D., Guarve, K., & Grewal, A. S. (2022). Targeting human Glucokinase for the treatment of type 2 diabetes: An overview of allosteric Glucokinase activators. Journal of Diabetes & Metabolic Disorders, 21(1), 1129–1137. https://doi.org/10.1007/s40200-022-01019-x
38. Singh, G., Soni, H., Tandon, S., Kumar, V., Babu, G., Gupta, V., & Chaudhuri (Chattopadhyay), P. (2022). Identification of natural DHFR inhibitors in MRSA strains: Structure-based drug design study. Results in Chemistry, 4, 100292. https://doi.org/10.1016/j.rechem.2022.100292
39. Staniszewska, M., Bondaryk, M., Piłat, J., Siennicka, K., Magda, U., & Kurzatkowski, W. (2012). [Virulence factors of Candida albicans]. Przeglad Epidemiologiczny, 66(4), 629–633.
40. Sun, H., Zhu, A., Zhou, X., & Wang, F. (2017). Suppression of pyruvate dehydrogenase kinase-2 re-sensitizes paclitaxel-resistant human lung cancer cells to paclitaxel. Oncotarget, 8(32), 52642–52650. https://doi.org/10.18632/oncotarget.16991
41. Trott, O., & Olson, A. J. (2009). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, NA-NA. https://doi.org/10.1002/jcc.21334
42. Vidal-Limon, A., Aguilar-Toalá, J. E., & Liceaga, A. M. (2022). Integration of Molecular Docking Analysis and Molecular Dynamics Simulations for Studying Food Proteins and Bioactive Peptides. Journal of Agricultural and Food Chemistry, 70(4), 934–943. https://doi.org/10.1021/acs.jafc.1c06110
43. Vijayakumari, B., Sasikala, V., Radha, S. R., & Rameshwar, H. Y. (2016). In silico analysis of aqueous root extract of Rotula aquatica Lour for docking analysis of the compound 3-O-acetyl-11-keto-β-boswellic acid contents. SpringerPlus, 5(1), 1486. https://doi.org/10.1186/s40064-016-3134-0
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Published
2024-07-17
How to Cite
Shinsy Poongattil, Jibu Thomas, & Christy Joy. (2024). Insilico Analysis And Molecular Docking Studies Of Potential Compounds From Crateva Magna (Lour.) DC. Using POAP. Revista Electronica De Veterinaria, 25(1S), 298-313. https://doi.org/10.69980/redvet.v25i1S.648
Section
Articles
