Skip to main navigation menu Skip to main content Skip to site footer
Plant Science Today (PST)

Research Articles

Early Access

In silico ADMET profiling and PTP1B molecular docking of phytochemicals from the desert medicinal plant Pergularia tomentosa L.

DOI
https://doi.org/10.14719/pst.12116
Submitted
4 October 2025
Published
02-01-2026

Abstract

This study presents an in silico profiling of phytochemical compounds derived from Pergularia tomentosa L. against the protein tyrosine phosphatase 1B (PTP1B), a key regulator in type 2 diabetes mellitus (T2DM). With the aid of computational assessment, the phytochemicals were examined for their drug-likeness, absorption, distribution, metabolism, excretion and toxicity (ADMET) properties and molecular interactions with the target protein PTP1B. A total of 40 phytochemical compounds derived from P. tomentosa were evaluated using ADMET tools and molecular docking against PTP1B, a central enzyme involved in the negative regulation of insulin signalling and thus a critical target in T2DM. Molecular docking analysis identified six top phytochemical compounds from P. tomentosa with binding affinities ranging from -6.8 to -7.9 kcal/mol relative to the reference inhibitor and exhibiting satisfactory ADMET profiles with no major toxicity. These findings suggest that phytochemicals from P. tomentosa possess promising antidiabetic potential by potentially inhibiting PTP1B, as indicated by in silico studies.

References

  1. 1. Goldstein BJ. Protein-tyrosine phosphatase 1B (PTP1B): A novel therapeutic target for type 2 diabetes mellitus, obesity and related states of insulin resistance. Current Drug Targets Immune Endocr Metabol Disord. 2001;1(3):265-75. https://doi.org/10.2174/1568008013341163
  2. 2. Cakan N, Kizilbash S, Kamat D. Changing spectrum of diabetes mellitus in children. Clin Pediatr. 2012;51(10):939-44. https://doi.org/10.1177/0009922812441666
  3. 3. Cao Y. Docking and pharmacophore methods in drug discovery. ChemistrySelect. 2025;10(24):e01269. https://doi.org/10.1002/slct.202501269
  4. 4. Daina A, Michielin O, Zoete V. SwissTargetPrediction: Updated data and new features for efficient prediction of protein targets of small molecules. Nucleic Acids Res. 2019;47(W1):W357-64. https://doi.org/10.1093/nar/gkz382
  5. 5. Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, et al. ChEBI: A database and ontology for chemical entities of biological interest. Nucleic Acids Res. 2007;36(Database):D344-50. https://doi.org/10.1093/nar/gkm791
  6. 6. Delibegovic M, Mody N. Protein tyrosine phosphatase 1B (PTP1B) in obesity and type 2 diabetes. Acta Med Saliniana. 2009;38(1):2-7. https://doi.org/10.5457/ams.v38i1.23
  7. 7. Dinda B, Saha S. Obesity and Diabetes. InNatural Products in Obesity and Diabetes: Therapeutic Potential and Role in Prevention and Treatment 2022 Mar 9 (pp. 1-61). Cham: Springer International Publishing. https://doi.org/10.1007/978-3-030-92196-5_1
  8. 8. Donath MY, Dinarello CA, Mandrup-Poulsen T. Targeting innate immune mediators in type 1 and type 2 diabetes. Nat Rev Immunol. 2019;19(12):734-46. https://doi.org/10.1038/s41577-019-0213-9
  9. 9. Dong J, Wang NN, Yao ZJ, Zhang L, Cheng Y, Ouyang D, et al. ADMETlab: A platform for systematic ADMET evaluation based on a comprehensively collected ADMET database. J Cheminform. 2018;10(1). https://doi.org/10.1186/s13321-018-0283-x
  10. 10. Farsani L, Latifi M, Salimi S, Karami N, Dolatabadi N. Effective characteristics on designing the information system of medicinal plants from users' perspective. J Educ Health Promot. 2020;9:245. https://doi.org/10.4103/jehp.jehp_750_19
  11. 11. Forli S, Huey R, Pique ME, Sanner MF, Goodsell DS, Olson AJ. Computational protein-ligand docking and virtual drug screening with the AutoDock suite. Nat Protoc. 2016;11(5):905-19. https://doi.org/10.1038/nprot.2016.051
  12. 12. Gfeller D, Grosdidier A, Wirth M, Daina A, Michielin O, Zoete V. SwissTargetPrediction: A web server for target prediction of bioactive small molecules. Nucleic Acids Res. 2014;42(W1):W32-8. https://doi.org/10.1093/nar/gku293
  13. 13. Gras A, Parada M, Rigat M, Vallès J, Garnatje T. Folk medicinal plant mixtures: Establishing a protocol for further studies. J Ethnopharmacol. 2018;214:244-73. https://doi.org/10.1016/j.jep.2017.12.014
  14. 14. Grosdidier A, Zoete V, Michielin O. SwissDock: A protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res. 2011;39(Suppl):W270-7. https://doi.org/10.1093/nar/gkr366
  15. 15. He S, Yang L, Ye S, Lin Y, Li X, Wang Y, et al. MPOD: Applications of integrated multi-omics database for medicinal plants. Plant Biotechnol J. 2022;20(5):797-9. https://doi.org/10.1111/pbi.13769
  16. 16. Hosseini SH, Masullo M, Cerulli A, Martucciello S, Ayyari M, Pizza C, et al. Antiproliferative cardenolides from the aerial parts of Pergularia tomentosa. J Nat Prod. 2019;82(1):74-9. https://doi.org/10.1021/acs.jnatprod.8b00630
  17. 17. Jamal S, Arora S, Scaria V. Computational analysis and predictive cheminformatics modeling of small molecule inhibitors of epigenetic modifiers. PLoS One. 2016;11(9):e0083032. https://doi.org/10.1371/journal.pone.0083032
  18. 18. Joos S, Glassen K, Musselmann B. Herbal medicine in primary healthcare in Germany: The patient's perspective. Evid Based Complement Alternat Med. 2012;2012:1-10. https://doi.org/10.1155/2012/294638
  19. 19. Kazeem MI, Davies TC. Anti-diabetic functional foods as sources of insulin secreting, insulin sensitizing and insulin mimetic agents. J Funct Foods. 2016;20:122-38. https://doi.org/10.1016/j.jff.2015.10.013
  20. 20. Kharroubi AT, Darwish HM. Diabetes mellitus: The epidemic of the century. World J Diabetes. 2015;6(6):850-67. https://doi.org/10.4239/wjd.v6.i6.850
  21. 21. Lahmar I, Radeva G, Marinkova D, Velitchkova M, Belghith H, Ben Abdallah F, et al. Immobilization and topochemical mechanism of a new β-amylase extracted from Pergularia tomentosa. Process Biochem. 2018;64:143-51. https://doi.org/10.1016/j.procbio.2017.09.007
  22. 22. Larsen CM, Faulenbach M, Vaag A, Ehses JA, Donath MY, Mandrup-Poulsen T. Sustained effects of interleukin-1 receptor antagonist treatment in type 2 diabetes. Diabetes Care. 2009;32(9):1663-8. https://doi.org/10.2337/dc09-0533
  23. 23. Lee J, Noh S, Lim S, Kim B. Plant extracts for type 2 diabetes: From traditional medicine to modern drug discovery. Antioxidants. 2021;10(1):81. https://doi.org/10.3390/antiox10010081
  24. 24. Li GQ, Kam A, Wong KH, Zhou X, Omar EA, Alqahtani A, et al. Herbal medicines for the management of diabetes. In: Advances in Experimental Medicine and Biology. New York: Springer; 2012. p. 396-413. https://doi.org/10.1007/978-1-4614-5441-0_28
  25. 25. Li X, Watanabe K, Kimura I. Gut microbiota dysbiosis drives and implies novel therapeutic strategies for diabetes mellitus and related metabolic diseases. Front Immunol. 2017;8:1882. https://doi.org/10.3389/fimmu.2017.01882
  26. 26. Maheshwari N, Karthikeyan C, Trivedi P, Moorthy NSHN. Recent advances in protein tyrosine phosphatase 1B targeted drug discovery for type II diabetes and obesity. Curr Drug Targets. 2018;19(5):551-75. https://doi.org/10.2174/1389450118666170222143739
  27. 27. Mahmud S, Paul GK, Biswas S, Kazi T, Mahbub S, Mita MA, et al. phytochemdb: A platform for virtual screening and computer-aided drug designing. Database. 2022;2022. https://doi.org/10.1093/database/baac002
  28. 28. Maran S, Yeo WWY, Lim SHE, Lai KS. Plant secondary metabolites for tackling antimicrobial resistance: A pharmacological perspective. In: Antimicrobial Resistance. Singapore: Springer; 2022. p. 153-73. https://doi.org/10.1007/978-981-16-3120-7_6
  29. 29. Masullo M, Hossaini H, Cerulli A, Martucciello S, Ayyari M, Pizza C, et al. Further insights in the antiproliferative activity of cardenolides from the aerial parts of Pergularia tomentosa. Planta Med. 2019. https://doi.org/10.1055/s-0039-3400039
  30. 30. Mohanraj K, Karthikeyan BS, Vivek-Ananth RP, Chand RPB, Aparna SR, Mangalapandi P, et al. IMPPAT: A curated database of Indian medicinal plants, phytochemistry and therapeutics. Sci Rep. 2018;8(1). https://doi.org/10.1038/s41598-018-22631-z
  31. 31. Mumtaz A, Ashfaq UA, Ul Qamar MT, Anwar F, Gulzar F, Ali MA, et al. MPD3: A useful medicinal plants database for drug designing. Nat Prod Res. 2016;31(11):1228-36. https://doi.org/10.1080/14786419.2016.1233409
  32. 32. Naaz S, Balramnavar VM, Kaur A. Medicinal plant databases: Analyzing strengths, weaknesses and innovations for future improvements. Life Sci Res Commun. 2024;1(1):31-41. https://doi.org/10.5530/lsrc.1.1.8
  33. 33. Nandi S, Saxena M. Potential inhibitors of protein tyrosine phosphatase (PTP1B) enzyme: Promising target for type II diabetes mellitus. Curr Top Med Chem. 2020;20(29):2692-707. https://doi.org/10.2174/1568026620999200904121432
  34. 34. Nguyen-Vo TH, Nguyen L, Do N, Nguyen TN, Trinh K, Cao H, et al. Plant metabolite databases: From herbal medicines to modern drug discovery. J Chem Inf Model. 2019;60(3):1101-10. https://doi.org/10.1021/acs.jcim.9b00826
  35. 35. Ningthoujam SS, Talukdar AD, Potsangbam KS, Choudhury MD. Challenges in developing medicinal plant databases for sharing ethnopharmacological knowledge. J Ethnopharmacol. 2012;141(1):9-32. https://doi.org/10.1016/j.jep.2012.02.042
  36. 36. O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: An open chemical toolbox. J Cheminform. 2011;3(1). https://doi.org/10.1186/1758-2946-3-33
  37. 37. Ochwang'i DO, Kimwele CN, Oduma JA, Gathumbi PK, Mbaria JM, Kiama SG. Medicinal plants used in treatment and management of cancer in Kakamega County, Kenya. J Ethnopharmacol. 2014;151(3):1040-55. https://doi.org/10.1016/j.jep.2013.11.051
  38. 38. Ojo OA, Ibrahim HS, Rotimi DE, Ogunlakin AD, Ojo AB. Diabetes mellitus: From molecular mechanism to pathophysiology and pharmacology. Med Novel Technol Devices. 2023;19:100247. https://doi.org/10.1016/j.medntd.2023.100247
  39. 39. Othman MS, Obeidat ST, Aleid GM, Abdel-Daim MM, Habotta OA, Schwartz L, et al. Pergularia tomentosa coupled with selenium nanoparticles salvaged lead acetate-induced redox imbalance, inflammation, apoptosis and neurotransmission disruption in rat brain. Open Chem. 2022;20(1):1313-26. https://doi.org/10.1515/chem-2022-0246
  40. 40. Papadopoulou-Marketou N, Paschou SA, Marketos N, Adamidi S, Adamidis S, Kanaka-Gantenbein C. Diabetic nephropathy in type 1 diabetes. Minerva Med. 2018;109(3):268-78. https://doi.org/10.23736/S0026-4806.17.05496-9
  41. 41. Patel D, Prasad S, Kumar R, Hemalatha S. An overview on antidiabetic medicinal plants having insulin mimetic property. Asian Pac J Trop Biomed. 2012;2(4):320-30. https://doi.org/10.1016/S2221-1691(12)60032-X
  42. 42. Pinney SE. Intrauterine growth retardation: A developmental model of type 2 diabetes. Drug Discov Today Dis Models. 2013;10(2):e71-7. https://doi.org/10.1016/j.ddmod.2013.01.003
  43. 43. Prabhakar PK, Sivakumar PM. Protein tyrosine phosphatase 1B inhibitors: A novel therapeutic strategy for the management of type 2 diabetes mellitus. Curr Pharm Des. 2019;25(23):2526-39. https://doi.org/10.2174/1381612825666190716102901
  44. 44. Rheinheimer J, de Souza BM, Cardoso NS, Bauer AC, Crispim D. Current role of the NLRP3 inflammasome on obesity and insulin resistance: A systematic review. Metabolism. 2017;74:1-9. https://doi.org/10.1016/j.metabol.2017.06.002
  45. 45. Rondinone CM, Trevillyan JM, Clampit J, Gum RJ, Berg C, Kroeger P, et al. Protein tyrosine phosphatase 1B reduction regulates adiposity and expression of genes involved in lipogenesis. Diabetes. 2002;51(8):2405-11. https://doi.org/10.2337/diabetes.51.8.2405
  46. 46. Rudra S, Kalra A, Kumar A, Joe W. Utilization of alternative systems of medicine as health care services in India: Evidence on AYUSH care from NSS 2014. PLoS One. 2017;12(5):e0176916. https://doi.org/10.1371/journal.pone.0176916
  47. 47. Saeed M, Naaz S, Tasleem M, Alshammari N, Kaur A, Alam MJ, et al. Bridging tradition and innovation: The Hail desert plant database for drug discovery. Indian J Pharm Educ Res. 2024;58(2S):S623-30. https://doi.org/10.5530/ijper.58.2s.66
  48. 48. Segueni K, Chouikh A, Tlili ML. Phytochemical profile, antioxidant and anti-inflammatory activities of crude latex (Pergularia tomentosa L.) in Algerian Sahara. Not Sci Biol. 2023;15(4):11772. https://doi.org/10.55779/nsb15411772
  49. 49. Sircana A, Framarin L, Leone N, Berrutti M, Castellino F, Parente R, et al. Altered gut microbiota in type 2 diabetes: Just a coincidence? Curr Diab Rep. 2018;18(10). https://doi.org/10.1007/s11892-018-1057-6
  50. 50. Starostina EG. Psychological aspects of diet therapy in type 2 diabetes mellitus. Obes Metab. 2008;5(2):7-10. https://doi.org/10.14341/omet200827-10
  51. 51. Tiwari RK, Ahmad A, Khan AF, Al-Keridis LA, Saeed M, Alshammari N, et al. Ethanolic extract of Artemisia vulgaris leaf promotes apoptotic cell death in non-small-cell lung carcinoma A549 cells through inhibition of the Wnt signaling pathway. Metabolites. 2023;13(4):480. https://doi.org/10.3390/metabo13040480
  52. 52. Trott O, Olson AJ. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. J Comput Chem. 2009;31(2):455-61. https://doi.org/10.1002/jcc.21334
  53. 53. Vivek-Ananth RP, Mohanraj K, Sahoo AK, Samal A. IMPPAT 2.0: An enhanced and expanded phytochemical atlas of Indian medicinal plants. ACS Omega. 2023;8(9):8827-45. https://doi.org/10.1021/acsomega.3c00156
  54. 54. Wang L, Jiang B, Wu N, Wang S, Shi D. Natural and semisynthetic protein tyrosine phosphatase 1B (PTP1B) inhibitors as anti-diabetic agents. ChemInform. 2015;46(31). https://doi.org/10.1002/chin.201531307
  55. 55. Williams AJ, Pence HE. The future of chemical information is now. Chem Int. 2017;39(3):9-14. https://doi.org/10.1515/ci-2017-0304
  56. 56. Winiwarter S, Ahlberg E, Watson E, Oprisiu I, Mogemark M, Noeske T, et al. In silico ADME in drug design: Enhancing the impact. ADMET DMPK. 2018;6(1):15-32. https://doi.org/10.5599/admet.6.1.470
  57. 57. Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, et al. HMDB: A knowledgebase for the human metabolome. Nucleic Acids Res. 2009;37(Database):D603-10. https://doi.org/10.1093/nar/gkn810
  58. 58. Msomi NZ, Simelane MBC. Herbal medicine. In: Herbal Medicine. IntechOpen; 2019.
  59. 59. Zhang S, Mathews CE. Correction to: Metabolic abnormalities in the pathogenesis of type 1 diabetes. Curr Diab Rep. 2018;18(10). https://doi.org/10.1007/s11892-018-1068-3

Downloads

Download data is not yet available.