Skip to content
2000
  1. Home
  2. A-Z Publications
  3. Combinatorial Chemistry & High Throughput Screening
  4. Fast Track Articles
  5. Fast Track Article
image of A Comparative Chemoinformatics Analysis of Compounds Extracted from Nyctanthes Arbor-tristis

Abstract

Introduction

Natural products are a rich source of diverse chemical compounds with interesting therapeutic properties. There is a need for in-depth investigation of this reservoir with tools to assert the molecular diversity with respect to clinical significance. Although studies have been reported on plants such as and its medicinal importance. A comprehensive study on comparative analysis of all phyto-constituents has not been carried out.

Aim

n the present work, we have carried out a comparative study of compounds obtained from the ethanolic extracts of various parts such as calyx, corolla, leaf, and bark of the NAT plant.

Methods

The extracted compounds were characterized by LCMS and GCMS studies. This was further corroborated by the network analysis, docking, and dynamic simulation studies with validated anti-arthritic targets.

Results

The most significant observation from LCMS and GCMS was that the compounds from calyx and corolla were closer in chemical space to the anti-arthritic compounds. To further expand and explore chemical space, the common scaffolds were seeded to enumerate a virtual library. The virtual molecules were prioritized based on the drug-like, leadlike scores and docked against anti-arthritic targets to reveal identical interactions in the pocket region.

Conclusion

The comprehensive study will be of immense value to medicinal chemists for the rational synthesis of molecules as well as bioinformatics professionals for getting useful insight into identifying rich diverse molecules from plant sources.

© 2025 Bentham Science Publishers
Loading

Article metrics loading...

/content/journals/cchts/10.2174/1386207326666230417085141
2025-02-02
2025-03-28

  • From This Site

    /content/journals/cchts/10.2174/1386207326666230417085141
    dcterms_title,dcterms_subject,pub_keyword
    -contentType:Contributor -contentType:Concept -contentType:Institution
    10
    5
Loading full text...

Full text loading...

References

  1. Katz L. Baltz R.H. Natural product discovery: Past, present, and future. J. Ind. Microbiol. Biotechnol. 2016 43 2-3 155 176 10.1007/s10295‑015‑1723‑5 26739136
    [Google Scholar]
  2. Romano J.D. Tatonetti N.P. Informatics and computational methods in natural product drug discovery: A review and perspectives. Front. Genet. 2019 10 368 10.3389/fgene.2019.00368 31114606
    [Google Scholar]
  3. Parekh S. Soni A. Nyctanthes arbor-tristis: Comprehensive review on its pharmacological, antioxidant, and anticancer activities. J. Appl. Biol. Biotechnol. 2020 8 01 95 104 10.7324/JABB.2020.80116
    [Google Scholar]
  4. Singh R. Hasan S.M. Verma A. Panda S.K. Nyctanthes arbor-tristis and its role in the alleviation of arthritic pain: A review. Curr. Bioact. Compd. 2020 16 8 1147 1156 10.2174/1573407216666200109105439
    [Google Scholar]
  5. Patil S.P. Proton NMR and HR-LC/MS based phytochemical analysis of methanolic fraction of Alectra parasitica A. Rich. rhizomes. Heliyon 2020 6 1 e03171 10.1016/j.heliyon.2020.e03171 31993516
    [Google Scholar]
  6. John A. Umashankar V. Krishnakumar S. Deepa P.R. Comparative modeling and molecular dynamics simulation of substrate binding in human fatty acid synthase: Enoyl reductase and β-ketoacyl reductase catalytic domains. Genomics Inform. 2015 13 1 15 24 10.5808/GI.2015.13.1.15 25873848
    [Google Scholar]
  7. Heendeniya S.N. Keerthirathna L.R. Manawadu C.K. Dissanayake I.H. Ali R. Mashhour A. Alzahrani H. Godakumbura P. Boudjelal M. Peiris D.C. Therapeutic efficacy of Nyctanthes arbor-tristis flowers to inhibit proliferation of acute and chronic primary human leukemia cells, with adipocyte differentiation and in silico analysis of interactions between survivin protein and selected secondary metabolites. Biomolecules 2020 10 2 165 10.3390/biom10020165 31973079
    [Google Scholar]
  8. Mukherjee P.K. Quality Control and Evaluation of Herbal Drugs: Evaluating Natural Products and Traditional Medicine. Elsevier 2019
    [Google Scholar]
  9. Anand U. Tudu C.K. Nandy S. Sunita K. Tripathi V. Loake G.J. Dey A. Proćków J. Ethnodermatological use of medicinal plants in India: From ayurvedic formulations to clinical perspectives – A review. J. Ethnopharmacol. 2022 284 114744 10.1016/j.jep.2021.114744 34656666
    [Google Scholar]
  10. Karthikeyan M. Nimje D. Pahujani R. Tyagi K. Bapat S. Vyas R. Pillai Padmakumar K. Chemoinformatics approach for building molecular networks from marine organisms. Comb. Chem. High Throughput Screen. 2015 18 7 673 684 10.2174/1386207318666150703112950 26138570
    [Google Scholar]
  11. Wang L. Weller C.L. Recent advances in extraction of nutraceuticals from plants. Trends Food Sci. Technol. 2006 17 6 300 312 10.1016/j.tifs.2005.12.004
    [Google Scholar]
  12. Nn A. A review on the extraction methods use in medicinal plants, principle, strength and limitation. Med. Aromat. Plants 2015 4 1 6
    [Google Scholar]
  13. Sodeifian G. Ardestani N.S. Sajadian S.A. Moghadamian K. Properties of portulaca oleracea seed oil via supercritical fluid extraction: Experimental and optimization. J. Supercrit. Fluids 2018 135 34 44 10.1016/j.supflu.2017.12.026
    [Google Scholar]
  14. Sodeifian G. Sajadian S.A. Investigation of essential oil extraction and antioxidant activity of Echinophora platyloba DC. using supercritical carbon dioxide. J. Supercrit. Fluids 2017 121 52 62 10.1016/j.supflu.2016.11.014
    [Google Scholar]
  15. Sodeifian G. Azizi J. Ghoreishi S.M. Response surface optimization of Smyrnium cordifolium Boiss (SCB) oil extraction via supercritical carbon dioxide. J. Supercrit. Fluids 2014 95 1 7 10.1016/j.supflu.2014.07.023
    [Google Scholar]
  16. Sodeifian G. Ansari K. Optimization of ferulago angulata oil extraction with supercritical carbon dioxide. J. Supercrit. Fluids 2011 57 38 43 10.1016/j.supflu.2011.02.002
    [Google Scholar]
  17. Zhou T. Xiao X. Li G. Microwave accelerated selective Soxhlet extraction for the determination of organophosphorus and carbamate pesticides in ginseng with gas chromatography/mass spectrometry. Anal. Chem. 2012 84 13 5816 5822 10.1021/ac301274r 22686368
    [Google Scholar]
  18. Lavenburg V.M. Rosentrater K.A. Jung S. Extraction methods of oils and phytochemicals from seeds and their environmental and economic impacts. Processes 2021 9 10 1839 10.3390/pr9101839
    [Google Scholar]
  19. Abubakar A. Haque M. Preparation of medicinal plants: Basic extraction and fractionation procedures for experimental purposes. J. Pharm. Bioallied Sci. 2020 12 1 1 10 10.4103/jpbs.JPBS_175_19 32801594
    [Google Scholar]
  20. Virot M. Tomao V. Colnagui G. Visinoni F. Chemat F. New microwave-integrated Soxhlet extraction. J. Chromatogr. A 2007 1174 1-2 138 144 10.1016/j.chroma.2007.09.067 17942103
    [Google Scholar]
  21. Baümler E.R. Carrín M.E. Carelli A.A. Extraction of sunflower oil using ethanol as solvent. J. Food Eng. 2016 178 190 197 10.1016/j.jfoodeng.2016.01.020
    [Google Scholar]
  22. Basheer S.N. Sharma D.K. Phytochemical composition, gc-ms analysis of nigella sativum and eugenia caryophyllus and its antimicrobial efficacy compared with 2.5% sodium hypochlorite and 2% chlorhexidine against enterococcus faecalis and candida albicans-an in vitro study. Tob. Regul. Sci. 2021 7 7449 7465
    [Google Scholar]
  23. Shannon P. Markiel A. Ozier O. Baliga N.S. Wang J.T. Ramage D. Amin N. Schwikowski B. Ideker T. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 2003 13 11 2498 2504 10.1101/gr.1239303 14597658
    [Google Scholar]
  24. Molecular Operating Environment (MOE), 2022.02 Chemical Computing Group ULC 1010 Sherbooke St. West, Suite #910, Montreal, QC, Canada, H3A 2R7 2022
    [Google Scholar]
  25. 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 1 42717 10.1038/srep42717 28256516
    [Google Scholar]
  26. Maunz A. Gütlein M. Rautenberg M. Vorgrimmler D. Gebele D. Helma C. lazar: A modular predictive toxicology framework. Front. Pharmacol. 2013 4 38 10.3389/fphar.2013.00038 23761761
    [Google Scholar]
  27. Trott O. Olson A.J. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 2010 31 2 455 461 19499576
    [Google Scholar]
  28. Jejurikar B.L. Rohane S.H. Drug designing in discovery studio. Asian J. Res. Chem 2021 14 135 138
    [Google Scholar]
  29. Schrödinger L. Schrödinger Suite 2016-2 Protein Preparation Wizard: Maestro, Version 10.2. New York Schrödinger 2016
    [Google Scholar]
  30. Rutz A. Sorokina M. Galgonek J. Mietchen D. Willighagen E. Gaudry A. Graham J.G. Stephan R. Page R. Vondrášek J. The LOTUS initiative for open natural products research: Knowledge management through wikidata. BioRxiv 2021 10.1101/2021.02.28.433265
    [Google Scholar]
  31. Sorokina M. Merseburger P. Rajan K. Yirik M.A. Steinbeck C. COCONUT online: Collection of open natural products database. J. Cheminform. 2021 13 1 2 10.1186/s13321‑020‑00478‑9 33423696
    [Google Scholar]
  32. Jaadi Z. A Step-by-Step Explanation of Principal Component Analysis (PCA) 2021
    [Google Scholar]
  33. Wishart D.S. Feunang Y.D. Guo A.C. Lo E.J. Marcu A. Grant J.R. Sajed T. Johnson D. Li C. Sayeeda Z. Assempour N. Iynkkaran I. Liu Y. Maciejewski A. Gale N. Wilson A. Chin L. Cummings R. Le D. Pon A. Knox C. Wilson M. DrugBank 5.0: A major update to the DrugBank database for 2018. Nucleic Acids Res. 2018 46 D1 D1074 D1082 10.1093/nar/gkx1037 29126136
    [Google Scholar]
  34. Kiela P.R. Ghishan F.K. Physiology of intestinal absorption and secretion. Best Pract. Res. Clin. Gastroenterol. 2016 30 2 145 159 10.1016/j.bpg.2016.02.007 27086882
    [Google Scholar]
  35. Martin Y.C. A bioavailability score. J. Med. Chem. 2005 48 9 3164 3170 10.1021/jm0492002 15857122
    [Google Scholar]
  36. Price G. Patel D.A. Drug Bioavailability. StatPearls StatPearls Publishing 2021
    [Google Scholar]
  37. Arnott J.A. Planey S.L. The influence of lipophilicity in drug discovery and design. Expert Opin. Drug Discov. 2012 7 10 863 875 10.1517/17460441.2012.714363 22992175
    [Google Scholar]
  38. Sodeifian G. Razmimanesh F. Diffusional interaction behavior of NSAIDs in lipid bilayer membrane using molecular dynamics (MD) simulation: Aspirin and Ibuprofen. J. Biomol. Struct. Dyn. 2019 37 7 1666 1684 10.1080/07391102.2018.1464956 29695194
    [Google Scholar]
  39. Singh S. Bani Baker Q. Singh D.B. Molecular docking and molecular dynamics simulation. Academic Press. Singh D.B. Pathak R.K.B.TB. 2022 291 304
    [Google Scholar]
  40. Kopustinskiene D.M. Jakstas V. Savickas A. Bernatoniene J. Flavonoids as anticancer agents. Nutrients 2020 12 2 457 10.3390/nu12020457 32059369
    [Google Scholar]
  41. Xie Y. Yang W. Tang F. Chen X. Ren L. Antibacterial activities of flavonoids: Structure-activity relationship and mechanism. Curr. Med. Chem. 2014 22 1 132 149 10.2174/0929867321666140916113443 25245513
    [Google Scholar]
  42. Ginwala R. Bhavsar R. Chigbu D.I. Jain P. Khan Z.K. Potential role of flavonoids in treating chronic inflammatory diseases with a special focus on the anti-inflammatory activity of apigenin. Antioxidants 2019 8 2 35 10.3390/antiox8020035 30764536
    [Google Scholar]
  43. Choy K.W. Murugan D. Leong X.F. Abas R. Alias A. Mustafa M.R. Flavonoids as natural anti-inflammatory agents targeting nuclear factor-kappa b (nfκb) signaling in cardiovascular diseases: A mini review. Front. Pharmacol. 2019 10 1295 10.3389/fphar.2019.01295 31749703
    [Google Scholar]
  44. Olivieri D. Ciaccia A. Marangio E. Marsico S. Todisco T. Del Vita M. Role of bromhexine in exacerbations of bronchiectasis. Double-blind randomized multicenter study versus placebo. Respiration 1991 58 3-4 117 121 10.1159/000195910 1745841
    [Google Scholar]
  45. Kapugi M. Cunningham K. Corticosteroids. Orthop. Nurs. 2019 38 5 336 339 10.1097/NOR.0000000000000595 31568125
    [Google Scholar]
  46. Ingawale D.K. Mandlik S.K. New insights into the novel anti-inflammatory mode of action of glucocorticoids. Immunopharmacol. Immunotoxicol. 2020 42 2 59 73 10.1080/08923973.2020.1728765 32070175
    [Google Scholar]
  47. Trevino C.M. Geier T. Morris R. Cronn S. deRoon-Cassini T. Relationship between decreased cortisol and development of chronic pain in traumatically injured. J. Surg. Res. 2022 270 286 292 10.1016/j.jss.2021.08.040 34717262
    [Google Scholar]
  48. Siafis S. Deste G. Ceraso A. Mussoni C. Vita A. Hasanagic S. Schneider-Thoma J. Papazisis G. Davis J.M. Leucht S. Antipsychotic drugs v. barbiturates or benzodiazepines used as active placebos for schizophrenia: A systematic review and meta-analysis. Psychol. Med. 2020 50 15 2622 2633 10.1017/S003329171900285X 31625485
    [Google Scholar]
/content/journals/cchts/10.2174/1386207326666230417085141
Loading
A Comparative Chemoinformatics Analysis of Compounds Extracted from Nyctanthes Arbor-tristis
Bentham Science Publishers ; https://doi.org/10.2174/1386207326666230417085141
/content/journals/cchts/10.2174/1386207326666230417085141
/content/journals/cchts/10.2174/1386207326666230417085141
Loading

Data & Media loading...

Supplements

Supplementary material is available on the publisher's website along with the published article.

file format download Download

  • Article Type:     Research Article
Keywords: virtual screening ; molecular docking ; chemoinformatics ; molecular dynamics ; Nyctanthes arbor-tristis ; natural products

Most Cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error
Please enter a valid_number test