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

Research Articles

Early Access

Screening and selection of a lead phytochemical inhibitor against Nsp3 protein, from Lawsonia inermis L. through in silico approaches

DOI
https://doi.org/10.14719/pst.10092
Submitted
16 June 2025
Published
23-12-2025

Abstract

Lawsonia inermis L., a plant of immense significance as the natural source of dye “Mehendi” is rich in secondary metabolites that impart important medicinal properties. These phytochemicals offer plant-based alternatives to synthetic drugs, which are often associated with harmful side effects, reinforcing the need to explore such natural compounds. The main objective of this study is to find plant-based lead from among the phytochemicals present in Lawsonia inermis L., against Nsp3 protein. Methanolic extracts from the plant was used and a group of phytochemicals were verified and identified by ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry, which were then subjected to phytochemical screening. The shortlisted best ligands (caffeic acid and lawsone) were subjected to molecular dynamic simulations for 100 ns, where RMSD, Rg and RMSF were analysed along with the binding affinities to the protein. Lawsone and caffeic acid emerged as good candidates. Molecular dynamic simulations indicated that lawsone, a naphthoquinone, formed stable complexes with Nsp3, exhibiting favourable RMSD, RMSF and Rg values, as well as a strong binding affinity of -20.72 kcal/mol. Our analysis shows the prospective possibility of lawsone, as a potential antiviral compound. This also highlights the interactions of a naphthoquinone, against Nsp3 protein, increasing the medicinal importance of the plant. Previous studies usually reveal phenols and flavonoids to be effective antiviral agents. This study, for the very first time, reveals the potential of lawsone (naphthoquinone and the main pigment of the plant), against Nsp3 protein.

References

  1. 1. Kala CP, Dhyani PP, Sajwan BS. Developing the medicinal plants sector in northern India: challenges and opportunities. J Ethnobiol Ethnomed. 2006;2:32. https://doi.org/10.1186/1746-4269-2-32
  2. 2. Fokunang CN, Ndikum V, Tabi OY, Jiofack RB, Ngameni B, Guedje NM, et al. Traditional medicine: past, present and future research and development prospects and integration in the national health system of Cameroon. Afr J Tradit Complement Altern Med. 2011;8(3):284-95. https://doi.org/10.4314/ajtcam.v8i3.65276
  3. 3. Alzaabi MM, Hamdy R, Ashmawy NS, Hamoda AM, Alkhayat F, Khademi NN, et al. Flavonoids are promising safe therapy against COVID-19. Phytochem Rev. 2022;21(1):291-312.https://doi.org/10.1007/s11101-021-09759-z
  4. 4. Ravishankar B, Shukla VJ. Indian systems of medicine: a brief profile. Afr J Tradit Complement Altern Med. 2007;4(3):319-37. https://doi.org/10.4314/ajtcam.v4i3.31226
  5. 5. Viale M, Vicol M. Conserving traditional wisdom in a commodified landscape: unpacking brand Ayurveda. J Ayurveda Integr Med. 2023;14(1):100667. https://doi.org/10.1016/j.jaim.2022.100667
  6. 6. Kumar S, Dobos GJ, Rampp T. The significance of Ayurvedic medicinal plants. Evid Based Complement Alternat Med. 2016;22(3):494-501. https://doi.org/10.1177/2156587216671392
  7. 7. Kudlu C. Keeping the doctor in the loop: Ayurvedic pharmaceuticals in Kerala. Anthropol Med. 2016;23(3):275-94. https://doi.org/10.1080/13648470.2016.1181520
  8. 8. Chaudhary G, Goyal S, Poonia P. Lawsonia inermis Linnaeus: a phytopharmacological review. Int J Pharm Sci Drug Res. 2010;2(2):91-8. https://doi.org/10.25004/IJPSDR.2010.020202
  9. 9. Adiga A, Gandhi A, Pradeep P, Hegde L. Comprehensive review on Madayantika (Lawsonia inermis L.). J Ayurveda Integr Med Sci. 2022;7(10):204-10.
  10. 10. Badoni Semwal R, Semwal DK, Combrinck S, Cartwright-Jones C, Viljoen A. Lawsonia inermis L. (henna): ethnobotanical, phytochemical and pharmacological aspects. J Ethnopharmacol. 2014;155(1):80-103. https://doi.org/10.1016/j.jep.2014.05.042
  11. 11. Singh D, Luqman S. Lawsonia inermis (L.): a perspective on anticancer potential of mehndi/henna. Biomed Res Ther. 2014;1(4):112-20. https://doi.org/10.7603/s40730-014-0018-1
  12. 12. Ponugoti M. A pharmacological and toxicological review of Lawsonia inermis. Int J Pharm Sci Res. 2018;9(3):902-15.
  13. 13. Tungmunnithum D, Thongboonyou A, Pholboon A, Yangsabai A. Flavonoids and other phenolic compounds from medicinal plants for pharmaceutical and medical aspects: an overview. Medicines (Basel). 2018;5(3):93. https://doi.org/10.3390/medicines5030093
  14. 14. Ekor M. The growing use of herbal medicines: issues relating to adverse reactions and challenges in monitoring safety. Front Pharmacol. 2014;4:177. https://doi.org/10.3389/fphar.2013.00177
  15. 15. Das D, Mallick B, Sinha S, Ganguli S, Samanta D, Banerjee R, et al. Unearthing the inhibitory potential of phytochemicals from Lawsonia inermis L. and some drugs against dengue virus protein NS1: an in silico approach. J Biomol Struct Dyn. 2023;29:1-18. https://doi.org/10.1080/07391102.2023.2298730
  16. 16. Dhamanti I, Suwantika AA, Adlia A, Yamani LN, Yakub F. Adverse reactions of COVID-19 vaccines: a scoping review of observational studies. Int J Gen Med. 2023;16:609-18. https://doi.org/10.2147/IJGM.S400458
  17. 17. Rabail R, Ahmed W, Ilyas M, Rajoka MSR, Hassoun A, Khalid AR, et al. The side effects and adverse clinical cases reported after COVID-19 immunization. Vaccines. 2022;10(4):488. https://doi.org/10.3390/vaccines10040488
  18. 18. El Sayed KA. Natural products as antiviral agents. Stud Nat Prod Chem. 2000;24:473-572. https://doi.org/10.1016/S1572-5995(00)80051-4
  19. 19. Badshah SL, Faisal S, Muhammad A, Poulson BG, Emwas AH, Jaremko M. Antiviral activities of flavonoids. Biomed Pharmacother. 2021;140:111596. https://doi.org/10.1016/j.biopha.2021.111596
  20. 20. Ben-Shabat S, Yarmolinsky L, Porat D, Dahan A. Antiviral effect of phytochemicals from medicinal plants: applications and drug delivery strategies. Drug Deliv Transl Res. 2020;10(2):354-67. https://doi.org/10.1007/s13346-019-00691-6
  21. 21. Loaiza-Cano V, Monsalve-Escudero LM, da Silva Maia Bezerra Filho C, Martinez-Gutierrez M, De Sousa DP. Antiviral role of phenolic compounds against dengue virus: a review. Biomolecules. 2020;11(1):11. https://doi.org/10.3390/biom11010011
  22. 22. Montenegro-Landívar MF, Tapia-Quirós P, Vecino X, Reig M, Valderrama C, Granados M, et al. Polyphenols and their potential role to fight viral diseases: an overview. Sci Total Environ. 2021;801:149719. https://doi.org/10.1016/j.scitotenv.2021.149719
  23. 23. Khalil A, Tazeddinova D. The upshot of polyphenolic compounds on immunity amid COVID-19 pandemic and other emerging communicable diseases: an appraisal. Nat Prod Bioprospect. 2020;10(6):411-29. https://doi.org/10.1007/s13659-020-00271-z
  24. 24. Batiha GE, Teibo JO, Shaheen HM, Babalola BA, Teibo TKA, Al-Kuraishy HM, et al. Therapeutic potential of Lawsonia inermis Linn: a comprehensive overview. Naunyn Schmiedebergs Arch Pharmacol. 2024;397(6):3525-40. https://doi.org/10.1007/s00210-023-02735-8
  25. 25. Armstrong LA, Lange SM, Dee Cesare V, Matthews SP, Nirujogi RS, Cole I, et al. Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies. PLoS One. 2021;16(7):e0253364. https://doi.org/10.1371/journal.pone.0253364
  26. 26. Angelini MM, Akhlaghpour M, Neuman BW, Buchmeier MJ. Severe acute respiratory syndrome coronavirus non-structural proteins 3, 4 and 6 induce double-membrane vesicles. mBio. 2013;4(4):e00524-13. https://doi.org/10.1128/mBio.00524-13
  27. 27. Lei J, Kusov Y, Hilgenfeld R. Nsp3 of coronaviruses: structures and functions of a large multi-domain protein. Antiv Res. 2018;149:58-74. https://doi.org/10.1016/j.antiviral.2017.11.001
  28. 28. Bills C, Xie X, Shi P. The multiple roles of nsp6 in the molecular pathogenesis of SARS-CoV-2. Antivir Res. 2023;213:105590. https://doi.org/10.1016/j.antiviral.2023.105590
  29. 29. Osipiuk J, Azizi SA, Dvorkin S, Endres M, Jedrzejczak R, Jones KA, et al. Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. Nat Commun. 2021;12(1):743. https://doi.org/10.1038/s41467-021-21060-3
  30. 30. Majiya H, Galstyan A. Potential of a methanolic extract of Lawsonia inermis (L.) leaf as an alternative sanitiser in the time of COVID-19 pandemic and beyond. J Herb Med. 2023;38:100633. https://doi.org/10.1016/j.hermed.2023.100633
  31. 31. Jamal QMS. Antiviral potential of plants against COVID-19 during outbreaks-an update. Int J Mol Sci. 2022;23(21):13564. https://doi.org/10.3390/ijms232113564
  32. 32. Li Y, Pustovalova Y, Shi W, Gorbatyuk O, Sreeramulu S, Schwalbe H, et al. Crystal structure of the CoV-Y domain of SARS-CoV-2 non-structural protein 3. Sci Rep. 2023;13:2890. https://doi.org/10.1038/s41598-023-30045-9
  33. 33. Golwala DK, Vaidya SK, Patel TB, Patel DS, Dholwani KK. Phytochemical and antioxidant activities of methanolic extract of Lawsonia inermis L. bark. Curr Issues Pharm Med Sci. 2020;33(3):132-8. https://doi.org/10.2478/cipms-2020-0024
  34. 34. Paul D, Surendran S, Chandrakala P, Satheeshkumar N. An assessment of the impact of green tea extract on palbociclib pharmacokinetics using a validated UHPLC-QTOF-MS method. Biomed Chromatogr. 2019;33(4):e4469.https://doi.org/10.1002/bmc.4469
  35. 35. Das D, Samanta D, Banerjee R, Sinha S, Mallick B, Ganguli S, et al. Insights into the phytochemical potential of Lawsonia inermis L. for future small molecule based therapeutic applications. Int Res J Plant Sci. 2020;11:1-7.
  36. 36. Shim H, Kim H, Allen JE, Wulff H. Pose classification using three-dimensional atomic structure-based neural networks applied to ion channel-ligand docking. J Chem Inf Model. 2022;62(10):2301-15. https://doi.org/10.1021/acs.jcim.1c01510
  37. 37. Bultum LE, Tolossa GB, Lee D. Combining empirical knowledge, in silico molecular docking and ADMET profiling to identify therapeutic phytochemicals from Brucea antidysentrica for acute myeloid leukemia. PLoS One. 2022;17(7):e0270050. https://doi.org/10.1371/journal.pone.0270050
  38. 38. 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. https://doi.org/10.1038/srep42717
  39. 39. Sączewski J, Popenda Ł, Fedorowicz J. In silico SwissADME analysis of antibacterial NHC-silver acetates and halides complexes. Appl Sci. 2024;14(19):8865. https://doi.org/10.3390/app14198865
  40. 40. Shruti Y, Prabhudev SM, Channamma M, Hanamanth JK, Singh KC. Drug likeliness, bioavailability, virtual screening and docking studies of some sulphonamide derivatives. WJPR. 2023;12(13):1094-1107.
  41. 41. Stefaniu A, Pirvu LC. In silico study approach on a series of 50 polyphenolic compounds in plants; a comparison on the bioavailability and bioactivity data. Molecules. 2022;27(4):1413. https://doi.org/10.3390/molecules27041413
  42. 42. Guan L, Yang H, Cai Y, Sun L, Di P, Li W, et al. ADMET-score - a comprehensive scoring function for evaluation of chemical drug likeness. Med Chem Commun. 2018;10(1):148-57. https://doi.org/10.1039/C8MD00472B
  43. 43. Cheng F, Li W, Liu G, Tang Y. In silico ADMET prediction: recent advances, current challenges and future trends. Curr Top Med Chem. 2013;13(11):1273-89. https://doi.org/10.2174/15680266113139990033
  44. 44. 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
  45. 45. Karplus M, McCammon J. Molecular dynamics simulations of biomolecules. Nat Struct Mol Biol. 2002;9(9):646-52. https://doi.org/10.1038/nsb0902-646
  46. 46. Hospital A, Goni JR, Orozco M, Gelpi JL. Molecular dynamics simulations: advances and applications. Adv Appl Bioinform Chem. 2015;8:37-47. https://doi.org/10.2147/AABC.S70333
  47. 47. Kutzner C, Kniep C, Cherian A, Nordström L, Grubmüller H, de Groot BL, et al. GROMACS in the cloud: a global supercomputer to speed up alchemical drug design. J Chem Inf Model. 2022;62(7):1691-711. https://doi.org/10.1021/acs.jcim.2c00044
  48. 48. Teijlingen AHWA, Swanson Lau KHA, Tuttle T. Constant pH coarse-grained molecular dynamics with stochastic charge neutralization. J Phys Chem Lett. 2022;13(18):4046-51. https://doi.org/10.1021/acs.jpclett.2c00544
  49. 49. Nettey-Oppong EE, Muhammad R, Ali A, Jeong HW, Seok YS, Kim SW, et al. The impact of temperature and pressure on the structural stability of solvated solid-state conformations of Bombyx mori silk fibroins: insights from molecular dynamics simulations. Materials. 2024;17(23):5686. https://doi.org/10.3390/ma17235686
  50. 50. Kumari R, Kumar R, Lynn A. g_mmpbsa - a GROMACS tool for high-throughput MM-PBSA calculations. J Chem Inf Model. 2014;54(7):1951-62. https://doi.org/10.1021/ci500020m
  51. 51. Oláh J, Szénási T, Lehotzky A, Norris V, Ovádi J. Challenges in discovering drugs that target the protein-protein interactions of disordered proteins. Int J Mol Sci. 2022;23(3):1550.https://doi.org/10.3390/ijms23031550
  52. 52. Borhani DW, Shaw DE. The future of molecular dynamics simulations in drug discovery. J Comput Aided Mol Des. 2012;26(1):15-26. https://doi.org/10.1007/s10822-011-9517-y
  53. 53. Hassan AM, Gattan HS, Faizo AA, Alruhaili MH, Alharbi AS, Bajrai LH, et al. Evaluating the binding potential and stability of drug-like compounds with the monkeypox virus VP39 protein using molecular dynamics simulations and free energy analysis. Pharmaceuticals. 2024;17(12):1617. https://doi.org/10.3390/ph17121617
  54. 54. Li Z, Gu J, Zhuang H, Kang L, Zhao X, Guo Q. Adaptive molecular docking method based on information entropy genetic algorithm. Appl Soft Comput. 2015;26:299-302. https://doi.org/10.1016/j.asoc.2014.10.008
  55. 55. Lobanov MY, Bogatyreva NS, Galzitskaya OV. Radius of gyration as an indicator of protein structure compactness. Mol Biol (Mosk). 2008;42(4):623-28. https://doi.org/10.1134/S0026893308040195
  56. 56. Ahmed MC, Crehuet R, Lindorff-Larsen K. Computing, analysing and comparing the radius of gyration and hydrodynamic radius in conformational ensembles of intrinsically disordered proteins. Methods Mol Biol. 2020;2141:429-45. https://doi.org/10.1007/978-1-0716-0524-0_21
  57. 57. Sawant S, Patil R, Khawate M, Zambre V, Shilimkar V, Jagtap S. Computational assessment of select antiviral phytochemicals as potential SARS-CoV-2 main protease inhibitors: molecular dynamics guided ensemble docking and extended molecular dynamics. In Silico Pharmacol. 2021;9(1):44. https://doi.org/10.1007/s40203-021-00107-9
  58. 58. Pradhan R, Dandawate P, Vyas A, Padhye S, Biersack B, Schobert R, et al. From body art to anticancer activities: perspectives on medicinal properties of henna. Curr Drug Targets. 2012;13(14):1777-98. https://doi.org/10.2174/138945012804545588
  59. 59. Kumar S, Sharma PP, Upadhyay C, Kempaiah P, Rathi B, Poonam N. Multi-targeting approach for Nsp3, Nsp9, Nsp12 and Nsp15 proteins of SARS-CoV-2 by diosmin as illustrated by molecular docking and molecular dynamics simulation methodologies. Methods. 2021;195:44-56. https://doi.org/10.1016/j.ymeth.2021.02.017
  60. 60. Roy A, Khan A, Ahmad I, Alghamdi S, Rajab BS, Babalghith AO, et al. Flavonoids a bioactive compound from medicinal plants and its therapeutic applications. Biomed Res Int. 2022;2022:5445291. https://doi.org/10.1155/2022/5445291
  61. 61. Lozza L, Moura-Alves P, Domaszewska T, Lage Crespo C, Streata I, Kreuchwig A, et al. The henna pigment Lawsonia inermis (L.) pigment Lawsone activates the aryl hydrocarbon receptor and impacts skin homeostasis. Sci Rep. 2019;9(1):10878. https://doi.org/10.1038/s41598-019-47350-x
  62. 62. Xiang S, Li Y, Khan SN, Zhang W, Yuan G, Cui J. Exploiting the anticancer, antimicrobial and antiviral potential of naphthoquinone derivatives: recent advances and future prospects. Pharmaceuticals. 2025;18(3):350. https://doi.org/10.3390/ph18030350
  63. 63. Widhalm JR, Rhodes D. Biosynthesis and molecular actions of specialized 1,4-naphthoquinone natural products produced by horticultural plants. Hortic Res. 2016;3:16046. https://doi.org/10.1038/hortres.2016.46
  64. 64. Yadav S, Sharma A, Nayik GA, Cooper R, Bhardwaj G, Sohal HS, et al. Review of shikonin and derivatives: isolation, chemistry, biosynthesis, pharmacology and toxicology. Front Pharmacol. 2022;13:905755. https://doi.org/10.3389/fphar.2022.905755
  65. 65. Giongo V, Falanga A, De Melo CPP, da Silva GB, Bellavita R, De-Simone SG, et al. Antiviral potential of naphthoquinone derivatives encapsulated within liposomes. Molecules. 2021;26(21):6440. https://doi.org/10.3390/molecules26216440
  66. 66. Tandon VK, Yadav DB, Singh RV, Vaish M, Chaturvedi AK, Shukla PK. Synthesis and biological evaluation of novel 1,4-naphthoquinone derivatives as antibacterial and antiviral agents. Bioorg Med Chem Lett. 2005;15(14):3463-6. https://doi.org/10.1016/j.bmcl.2005.04.075
  67. 67. Moraes VT, Caires FJ, Da Silva-Neto PV, Mendonça JN, Fraga-Silva TFC, Fontanezi BB, et al. Naphthoquinone derivatives as potential immunomodulators: prospective for COVID-19 treatment. RSC Adv. 2024;14(10):6532-41. https://doi.org/10.1039/D3RA08173G
  68. 68. Vasić V, Momić T, Petković M, Krstić D. Na+, K+-ATPase as the target enzyme for organic and inorganic compounds. Sensors. 2008;8(12):8321-60. https://doi.org/10.3390/s8128321
  69. 69. De Souza E Souza KF, Rabelo VWH, Abreu PA, Santos CCC, Abreu Do Amaral E Silva N, De Luna D, et al. Synthetic naphthoquinone inhibits herpes simplex virus type-1 replication targeting Na+, K+ ATPase. ACS Omega. 2024;9(34):36835-46. https://doi.org/10.1021/acsomega.4c05904
  70. 70. Verma S, Newar J, Manoswini M, Dhal AK, Ghatak A. Interactions of the Nsp3 proteins of CHIKV with the human host protein NAP1 plays a significant role in viral pathogenesis - an in silico study. Hum Genet. 2023;36:201182. https://doi.org/10.1016/j.humgen.2023.201182
  71. 71. Tuan NA, Khanh PN, Ha NX, Binh TC, Khanh ND, Oanh TT. Compounds isolated from Lawsonia inermis L. collected in Vietnam and evaluation of their potential activity against the main protease of SARS-CoV-2 using in silico molecular docking and molecular dynamic simulation. Nat Prod Commun. 2022;17(10):1-14. https://doi.org/10.1177/1934578X221125161
  72. 72. Halder SK, Sultana I, Shuvo MN, Shil A, Himel MK, Hasan MA, et al. In silico identification and analysis of potentially bioactive antiviral phytochemicals against SARS-CoV-2: a molecular docking and dynamics simulation approach. Biomed Res Int. 2023;2023:5469258. https://doi.org/10.1155/2023/5469258
  73. 73. Ilyas M, Muhammad S, Iqbal J, Amin S, Al-Sehemi AG, Algarni H, et al. In-sighting isatin derivatives as potential antiviral agents against NSP3 of COVID-19. Chem Pap. 2022;76(10):6271-85. https://doi.org/10.1007/s11696-022-02298-7
  74. 74. Joshi R, Gaikwad H, Soge B, Alshammari A, Albekairi NA, Kabra A, et al. Exploring pyrazolines as potential inhibitors of NSP3-macrodomain of SARS-CoV-2: synthesis and in silico analysis. Sci Rep. 2025;15(1). https://doi.org/10.1038/s41598-024-81711-5
  75. 75. Roshni J, Vaishali R, Ganesh KS, Dharani N, Alzahrani KJ, Banjer HJ, et al. Multi-target potential of Indian phytochemicals against SARS-CoV-2: a docking, molecular dynamics and MM-GBSA approach extended to Omicron B.1.1.529. J Infect Public Health. 2022;15(6):662-9. https://doi.org/10.1016/j.jiph.2022.05.002

Downloads

Download data is not yet available.