Computational analysis of Salmalia malabarica (Bombax ceiba) for the management of ulcerative colitis

Savita Bhosale; Prashant G. Jadar; Sunil S. Jalalpure; Vishal S. Patil; Kashinath Hiremath

doi:10.7324/JAPS.2024.161733

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Abstract

Bombax ceiba leaf petiole is used as an enema in the management of ulcerative colitis, but its molecular mechanisms are yet to be established. The current study employed gene set enrichment, network pharmacology, and molecular docking studies to infer the phytocompounds from B. ceiba responsible for the modulation of therapeutic targets of UC First, data of phytocompounds present in the leaf petiole were retrieved from the literature and public phytocompounds databases and their druggability and toxicity prediction was performed by MolSoft and AdverPred online servers, respectively. Furthermore, phytocompounds probable proteins were predicted by SwissTargetPrediction, and targets of UC were retrieved from the GeneCards database. A set of genes molecular pathways were identified by the STRING, Kyoto Encyclopedia of Genes and Genomics database, and pathways involved in UC were sorted and their network between compounds, targets, and pathways was constructed by the Cytoscape software. Molecular docking of hub-gene and targets was performed by the POAP pipeline. Out of 10 compounds, 7 (showed druggability in which Rutin scored the highest druglikeness score of 0.91. A total of 2830 genes were identified for UC, of which 39 matched with targets of phytocompounds (total of 297). These 39 targets were involved in 125 pathways, of which 14 were associated with UC mainly VEGF, IL-17, Neurotrophin, JAK-STAT, cAMP, TNF, TGF-beta, and NF-kappa B, MAPK, PI3K-Akt signaling pathway. Among the predicted targets, MAPK3, TNF, and PTGS2 were identified as a hub gene. Rutin scored the lowest binding energy of −7.9 kcal/mol and possessed 22 interactions with PTGS2 and Astragalin and Isoquercitrin were the next lead hit against PTGS2. It has been concluded that the use of B. ceiba leaf petiole could be a valuable source against UC.

Keyword: Bombax ceiba molecular docking network pharmacology ulcerative colitis

Citation:

Bhosale S, Jadar PG, Jalalpure SS, Patil VS, Hiremath K. Computational analysis of Salmalia malabarica (Bombax ceiba) for the management of ulcerative colitis. J Appl Pharm Sci. 2024. Online First. http://doi.org/10.7324/JAPS.2024.161733

Copyright: © The Author(s). This is an open-access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Reference

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2. Gracie DJ, Ford AC. IBS-like symptoms in patients with ulcerative colitis. Clin Exp Gastroenterol. 2015; 19:101-9. https://doi.org/10.2147/CEG.S58153
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9. Ford AC, Khan KJ, Achkar JP, Moayyedi P. Efficacy of oral vs. topical, or combined oral and topical 5-aminosalicylates, in ulcerative colitis: systematic review and meta-analysis. Am J Gastroenterol. 2012;107(2):167-76. https://doi.org/10.1038/ajg.2011.410
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14. Jain A, Katewa SS. Medicinal plant diversity of Sitamata wildlife sanctuary, Rajasthan, India. J Ethnopharmacol 2005;102:143-57. https://doi.org/10.1016/j.jep.2005.05.047
15. Lagunin AS. Ivanov A. Rudik D. Filimonov V. Poroikov. DIGEP-Pred: web service for in silico prediction of drug-induced gene expression profiles based on structural formula. Bioinformatics. 2013;29:2062-3. https://doi.org/10.1093/bioinformatics/btt322
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19. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498-504. https://doi.org/10.1101/gr.1239303
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21. Biradar P, Patil V, Joshi H, Khanal P. Mallapur S. Experimental validation and network pharmacology evaluation to decipher the mechanism of action of Erythrina variegata L. bark against scopolamine-induced memory impairment in rats. Adv Tradit Med. 2020;22:1-14. https://doi.org/10.1007/s13596-020-00524-9
22. Patil RS, Khatib NA, Patil VS, Suryawanshi SS. Chlorogenic acid may be a potent inhibitor of dimeric SARS-CoV-2 main protease 3CLpro: an in silico study. Tradit Med Res. 2021;6:20. https://doi.org/10.53388/TMR20201208211
23. Enogieru AB, Haylett W, Hiss D, Ekpo O. Inhibition of γH2AX, COX-2 and regulation of antioxidant enzymes in MPP+-exposed SH-SY5Y cells pre-treated with rutin. Metab Brain Dis. 2021;36(7):2119-30. https://doi.org/10.1007/s11011-021-00746-z
24. Choi S, Lim TG, Hwang MK, Kim YA, Kim J, Kang NJ, et al. Rutin inhibits B[a]PDE-induced cyclooxygenase-2 expression by targeting EGFR kinase activity. Biochem Pharmacol. 2013;86(10):1468-75. https://doi.org/10.1016/j.bcp.2013.08.066
25. Moutinho MS, Aragao S, Carmo D, Casaca F, Silva S, Ribeiro J, et al. Curcumin and rutin down-regulate cyclooxygenase-2 and reduce tumor-associated inflammation in HPV16-transgenic mice. Anticancer Res. 2018;38(3):1461-6. https://doi.org/10.21873/anticanres.12371

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Bhosale S [PubMed] [Google Scholar ]

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1. Strober W, Fuss I, Mannon P. The fundamental basis of inflammatory bowel disease. J Clin Invest. 2007;117(3):514-21. https://doi.org/10.1172/JCI30587

2. Gracie DJ, Ford AC. IBS-like symptoms in patients with ulcerative colitis. Clin Exp Gastroenterol. 2015; 19:101-9. https://doi.org/10.2147/CEG.S58153

3. Feagan BG, Rutgeerts P, Sands BE, Hanauer S, Colombel JF, Sandborn WJ, et al. Vedolizumab as induction and maintenance therapy for ulcerative colitis. N Engl J Med. 2013;369(8):699-710. https://doi.org/10.1056/NEJMoa1215734

4. Lockhart-Mummery HE, Morson BC. Crohn's disease (regional enteritis) of the large intestine and its distinction from ulcerative colitis. Gut. 1960;1(2):87-105. https://doi.org/10.1136/gut.1.2.87

5. Peeters M, Joossens S, Vermeire S, Vlietinck R, Bossuyt X, Rutgeerts P. Diagnostic value of anti-Saccharomyces cerevisiae and antineutrophil cytoplasmic autoantibodies in inflammatory bowel disease. Am J Gastroenterol. 2001;96(3):730-4. https://doi.org/10.1111/j.1572-0241.2001.03613.x

6. Danese S, Fiorino G, Peyrin-Biroulet L. Positioning therapies in ulcerative colitis. Clin Gastroenterol Hepatol. 2020;18(6):1280-90. https://doi.org/10.1016/j.cgh.2020.01.017

7. Loftus Jr EV. Clinical epidemiology of inflammatory bowel disease: incidence, prevalence, and environmental influences. Gastroenterology. 2004;126(6):1504-17. https://doi.org/10.1053/j.gastro.2004.01.063

8. Yang H, McElree C, Roth MP, Shanahan F, Targan SR, Rotter JI. Familial empirical risks for inflammatory bowel disease: differences between Jews and non-Jews. Gut. 1993;34:517-24. https://doi.org/10.1136/gut.34.4.517

9. Ford AC, Khan KJ, Achkar JP, Moayyedi P. Efficacy of oral vs. topical, or combined oral and topical 5-aminosalicylates, in ulcerative colitis: systematic review and meta-analysis. Am J Gastroenterol. 2012;107(2):167-76. https://doi.org/10.1038/ajg.2011.410

10. Carter MJ, Lobo AJ, Travis SP. Guidelines for the management of inflammatory bowel disease in adults. Gut. 2004;53:1-6. https://doi.org/10.1136/gut.2004.043372

11. Feagan BG, MacDonald JK. Oral 5-aminosalicylic acid for induction of remission in ulcerative colitis. Cochrane Database Syst Rev. 2012;10:CD000543. https://doi.org/10.1002/14651858.CD000543.pub3

12. Parrotta JA. Healing plants of peninsular India. Wallingford, UK: CABI publishing; 2001. https://doi.org/10.1079/9780851995014.0000

13. Chaudhary PH, Khadabadi SS. Bombax ceiba Linn.: pharmacognosy, ethnobotany and phyto-pharmacology. Phcog Commun. 2012;2(3):2-9. https://doi.org/10.5530/pc.2012.3.2

14. Jain A, Katewa SS. Medicinal plant diversity of Sitamata wildlife sanctuary, Rajasthan, India. J Ethnopharmacol 2005;102:143-57. https://doi.org/10.1016/j.jep.2005.05.047

15. Lagunin AS. Ivanov A. Rudik D. Filimonov V. Poroikov. DIGEP-Pred: web service for in silico prediction of drug-induced gene expression profiles based on structural formula. Bioinformatics. 2013;29:2062-3. https://doi.org/10.1093/bioinformatics/btt322

16. Lipinski. C.A, Lead- and drug-like compounds: the rule-of-five revolution, Drug Discov Today Technol. 2004;1:337-41. https://doi.org/10.1016/j.ddtec.2004.11.007

17. Daina A, Michielin O, Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep. 2017;7:42717. https://doi.org/10.1038/srep42717

18. Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, et al. The string database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res. 2017;45. https://doi.org/10.1093/nar/gkw937

19. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498-504. https://doi.org/10.1101/gr.1239303

20. Samdani A, Vetrivel U. POAP: A GNU parallel based multithreaded pipeline of open babel and Auto-Dock suite for boosted high throughput virtual screening. Comput Biol Chem. 2018;74:39-48. https://doi.org/10.1016/j.compbiolchem.2018.02.012

21. Biradar P, Patil V, Joshi H, Khanal P. Mallapur S. Experimental validation and network pharmacology evaluation to decipher the mechanism of action of Erythrina variegata L. bark against scopolamine-induced memory impairment in rats. Adv Tradit Med. 2020;22:1-14. https://doi.org/10.1007/s13596-020-00524-9

22. Patil RS, Khatib NA, Patil VS, Suryawanshi SS. Chlorogenic acid may be a potent inhibitor of dimeric SARS-CoV-2 main protease 3CLpro: an in silico study. Tradit Med Res. 2021;6:20. https://doi.org/10.53388/TMR20201208211

23. Enogieru AB, Haylett W, Hiss D, Ekpo O. Inhibition of γH2AX, COX-2 and regulation of antioxidant enzymes in MPP+-exposed SH-SY5Y cells pre-treated with rutin. Metab Brain Dis. 2021;36(7):2119-30. https://doi.org/10.1007/s11011-021-00746-z

24. Choi S, Lim TG, Hwang MK, Kim YA, Kim J, Kang NJ, et al. Rutin inhibits B[a]PDE-induced cyclooxygenase-2 expression by targeting EGFR kinase activity. Biochem Pharmacol. 2013;86(10):1468-75. https://doi.org/10.1016/j.bcp.2013.08.066

25. Moutinho MS, Aragao S, Carmo D, Casaca F, Silva S, Ribeiro J, et al. Curcumin and rutin down-regulate cyclooxygenase-2 and reduce tumor-associated inflammation in HPV16-transgenic mice. Anticancer Res. 2018;38(3):1461-6. https://doi.org/10.21873/anticanres.12371