Characterizing the structural and physicochemical properties of medicinal plants as a proposal for treating of viral malady

Fatemeh Mollaamin

Article ID: 2329
Vol 7, Issue 2, 2023

VIEWS - 411 (Abstract) 161 (PDF)

Abstract


Regarding coronavirus disease (COVID-19) pandemic, this research article wants to study some herbals as the probable therapy for this disease. Cinnamon leaves, curcuma longa (turmeric), ginger, mentha pulegium (pennyroyal), rosemary, salvia divinorum and thyme including some principal chemical compounds of cynnamil, curcumin, gingerol, pulegone, rosmarinic acid, salvinorina A and thymol, respectively, as a probable anti COVID-19 receptor have been selected. The possible roles of these medicinal plants in COVID-19 treatment have been carried out through quantum sensing methods. Formation of hydrogen bonding between principal substances selected in COVID-19 natural drugs bound to Tyrosine-Methionine-Histidine (Tyr-Met-His) or (TMH) (the database amino acids fragment) as the active area of the COVID-19 protein has been evaluated. In fact, it has been exhibited the role of oxygen, nitrogen, and hydrogen atoms in the active sites of these anti-virus medications towards hydrogen bonding in the active site if “TMH” protein. The physical and chemical attributes of nuclear magnetic resonance, vibrational frequency, the highest occupied molecular orbital energy and the lowest unoccupied molecular orbital energy, partial charges and spin density and have been accomplished using density functional theory (DFT) method and 6-311+G (2d,p) basis set by Gaussian 16 revision C.01 program toward the industry of drug design. This research has exhibited that there is a relative agreement among the results that these medicinal plants could be efficient against COVID-19 symptoms

Keywords


molecular modeling; medicinal plant; COVID-19; Tyr160-Met161-His162

Full Text:

PDF


References


1. Alomair L, Mustafa S, Jafri MS, et al. Molecular dynamics simulations to decipher the role of phosphorylation of SARS-CoV-2 nonstructural proteins (nsps) in viral replication. Viruses 2022; 14(11): 2436. doi: 10.3390/v14112436

2. Plavec Z, Domanska A, Liu X, et al. SARS-CoV-2 production, purification methods and UV Inactivation for proteomics and structural studies. Viruses 2022; 14(9): 1989. doi: 10.3390/v14091989

3. Monajjemi M, Shahriari S, Mollaamin F. Evaluation of coronavirus families & COVID-19 proteins: Molecular modeling study. Biointerface Research in Applied Chemisty 2020; 10(5): 6039–6057. doi: 10.33263/BRIAC105.60396057

4. Yarovaya OI, Shcherbakov DN, Borisevich SS, et al. Borneol ester derivatives as entry inhibitors of a wide spectrum of SARS-CoV-2 viruses. Viruses 2022; 14(6): 1295. doi:10.3390/v14061295

5. Shahriari S, Monajjemi M, Mollaamin F. Determination of proteins specification with SARS-COVID-19 based ligand designing. Journal of the Chilean Chemical Society 2022; 67(2): 5468–5476. doi: 10.4067/S0717-97072022000205468

6. Majeed A, Zhang X. On the adoption of modern technologies to fight the COVID-19 pandemic: A technical synthesis of latest developments. COVID 2023; 3(1): 90–123. doi: 10.3390/covid3010006

7. Bonaccorsi G, Pierri F, Cinelli M, et al. Economic and social consequences of human mobility restrictions under COVID-19. Proceedings of the National Academy of Sciences 2020; 117(27): 15530–15535. doi: 10.1073/pnas.2007658117

8. Barakat A, Mostafa A, Ali M, et al. Design, synthesis and in vitro evaluation of spirooxindole-based phenylsulfonyl moiety as a candidate anti-SAR-CoV-2 and MERS-CoV-2 with the implementation of combination studies. International Journal of Molecular Sciences 2022; 23(19): 11861. doi: 10.3390/ijms231911861

9. Mollaamin F, Monajjemi M. Thermodynamic research on the inhibitors of coronavirus through drug delivery method. Journal of the Chilean Chemical Society 2021; 66(2): 5195–5205. doi: 10.4067/S0717-97072021000205195

10. Sardar T, Nadim SS, Rana S, Chattopadhyay J. Assessment of lockdown effect in some states and overall India: A predictive mathematical study on COVID-19 outbreak. Chaos, Solitons & Fractals 2020; 139: 110078. doi: 10.1016/j.chaos.2020.110078

11. Mollaamin F, Shahriari S, Monajjemi M. Treating omicron BA.4 & BA.5 via herbal antioxidant asafoetida: A DFT study of carbon nanocarrier in drug delivery. Journal of the Chilean Chemical Society 2023; 68(1): 5781–5786. doi: 10.4067/S0717-97072023000105781

12. Zeng F, Huang Y, Guo Y, et al. Association of inflammatory markers with the severity of COVID-19: A meta-analysis. International Journal of Infectious Diseases 2020; 96: 467–474. doi: 10.1016/j.ijid.2020.05.055

13. Mollaamin F. Physicochemical investigation of anti-COVID19 drugs using several medicinal plants. Journal of the Chilean Chemical Society 2022; 67(2): 5537–5546. doi: 10.4067/S0717-97072022000205537

14. Jamal QMS. Antiviral potential of plants against COVID-19 during outbreaks—An update. International Journal of Molecular Sciences 2022; 23(21): 13564. doi: 10.3390/ijms232113564

15. Remali J, Aizat WM. A review on plant bioactive compounds and their modes of action against coronavirus infection. Frontiers in Pharmacology 2021; 11: 589044. doi: 10.3389/fphar.2020.589044

16. Mollaamin F, Monajjemi M. Application of DFT/TD-DFT frameworks in the drug delivery mechanism: Investigation of chelated bisphosphonate with transition metal cations in bone treatment. Chemistry 2023; 5(1): 365–380. doi: 10.3390/chemistry5010027

17. Capell T, Twyman RM, Armario-Najera V, et al. Potential applications of plant biotechnology against SARS-CoV-2. Trends in Plant Science 2020; 25(7): 635–643. doi: 10.1016/j.tplants.2020.04.009

18. Mollaamin F. Function of anti-CoV structure using INH [1-6]-Tyr160-Met161-His162 complex. Biointerface Research in Applied Chemistry 2021; 11(6): 14433–14450. doi: 10.33263/BRIAC116.1443314450

19. Bibi S, Khan MS, El-Kafrawy SA, et al. Virtual screening and molecular dynamics simulation analysis of Forsythoside A as a plant-derived inhibitor of SARS-CoV-2 3CLpro. Saudi Pharmaceutical Journal 2022; 30(7): 979–1002. doi: 10.1016/j.jsps.2022.05.003

20. Ćavar Zeljković S, Schadich E, Džubák P, et al. Antiviral activity of selected lamiaceae essential oils and their monoterpenes against SARS-Cov-2. Frontiers in Pharmacology 2022; 13: 893634. doi: 10.3389/fphar.2022.893634

21. Mollaamin F, Monajjemi M, Mohammadi S. Physicochemical characterization of antiviral phytochemicals of artemisia annua plant as therapeutic potential against coronavirus disease: In silico-drug delivery by density functional theory benchmark. Journal of Biological Regulators and Homeostatic Agents 2023; 37(7): 3629–3639. doi: 10.23812/j.biol.regul.homeost.agents.20233707.358

22. Maurya VK, Kumar S, Prasad AK, et al. Structure-based drug designing for potential antiviral activity of selected natural products from ayurveda against SARS-CoV-2 spike glycoprotein and its cellular receptor. VirusDisease 2020; 31: 179–193. doi: 10.1007/s13337-020-00598-8

23. Kosakowska O, Bączek K, Przybył JL, et al. Morphological and chemical traits as quality determinants of common Thyme (Thymus vulgaris L.), on the example of ‘standard winter’ cultivar. Agronomy 2020; 10(6): 909. doi: 10.3390/agronomy10060909

24. Bendif H, Peron G, Miara MD, et al. Total phytochemical analysis of Thymus munbyanus subsp. coloratus from Algeria by HS-SPME-GC-MS, NMR and HPLC-MSn studies. Journal of Pharmaceutical and Biomedical Analysis 2020; 186: 113330. doi: 10.1016/j.jpba.2020.113330

25. Elbe H, Yigitturk G, Cavusoglu T, et al. Apoptotic effects of thymol, a novel monoterpene phenol, on different types of cancer. Bratislava Medical Journal/Bratislavske Lekarske Listy 2020; 121(2): 122–128. doi: 10.4149/BLL_2020_016

26. Kowalczyk A, Przychodna M, Sopata S, et al. Thymol and Thyme essential oil—New insights into selected therapeutic applications. Molecules 2020; 25(18): 4125. doi: 10.3390/molecules25184125

27. Kiyama R. Nutritional implications of ginger: Chemistry, biological activities and signaling pathways. The Journal of Nutritional Biochemistry 2020; 86: 108486. doi: 10.1016/j.jnutbio.2020.108486

28. Mao QQ, Xu XY, Cao SY, et al. Bioactive compounds and bioactivities of ginger (Zingiber officinale Roscoe). Foods 2019; 8(6): 185. doi: 10.3390/foods8060185

29. Ghosh D. A cinnamon-derived procyanidin type—A compound: A potential candidate molecule against coronaviruses including COVID-19. Journal of Ayurveda Case Reports 2020; 3(4): 122–126. doi: 10.4103/jacr.jacr_89_20

30. Lucas K, Fröhlich-Nowoisky J, Oppitz N, Ackermann M. Cinnamon and hop extracts as potential immunomodulators for severe COVID-19 cases. Frontiers in Plant Science 2021; 12: 589783. doi: 10.3389/fpls.2021.589783

31. Prasanth DSNBK, Murahari M, Chandramohan V, et al. In silico identification of potential inhibitors from Cinnamon against main protease and spike glycoprotein of SARS CoV-2. Journal of Biomolecular Structure and Dynamics 2020; 39(13): 4618–4632. doi: 10.1080/07391102.2020.1779129

32. de Oliveira JR, Camargo SEA, de Oliveira LD. Rosmarinus officinalis L. (rosemary) as therapeutic and prophylactic agent. Journal of Biomedical Science 2019; 26(1): 5. doi: 10.1186/s12929-019-0499-8

33. Nieto G, Ros G, Castillo J. Antioxidant and antimicrobial properties of rosemary (Rosmarinus officinalis, L.): A Review. Medicines 2018; 5(3): 98. doi: 10.3390/medicines5030098

34. Mollaamin F, Monajjemi M. Carbon nanotubes as biosensors for releasing conjugated bisphosphonates—Metal ions in bone tissue: Targeted drug delivery through the DFT method. C 2023; 9(2): 61. doi: 10.3390/c9020061

35. Akbulut S. Medicinal plants preferences for the treatment of COVID-19 symptoms in Central and Eastern Anatolia. Kastamonu University Journal of Forestry Faculty 2021; 21(3): 196–207. doi: 10.17475/kastorman.1048372

36. Dhama K, Natesan S, Yatoo MI, et al. Plant-based vaccines and antibodies to combat COVID-19: Current status and prospects. Human Vaccines & Immunotherapeutics 2020; 16(12): 2913–2920. doi: 10.1080/21645515.2020.1842034

37. Nawrot-Hadzik I, Zmudzinski M, Matkowski A, et al. Reynoutria rhizomes as a natural source of SARS-CoV-2 Mpro inhibitors—Molecular docking and in vitro study. Pharmaceuticals 2021; 14(8): 742. doi: 10.3390/ph14080742

38. Dwarka D, Agoni C, Mellem JJ, et al. Identification of potential SARS-CoV-2 inhibitors from South African medicinal plant extracts using molecular modelling approaches. South African Journal of Botany 2020; 133: 273–284. doi: 10.1016/j.sajb.2020.07.035

39. Kulkarni SA, Nagarajan SK, Ramesh V, et al. Computational evaluation of major components from plant essential oils as potent inhibitors of SARS-CoV-2 spike protein. Journal of Molecular Structure 2020; 1221: 128823. doi: 10.1016/j.molstruc.2020.128823

40. Shree P, Mishra P, Selvaraj C, et al. Targeting COVID-19 (SARS-CoV-2) main protease through active phytochemicals of ayurvedic medicinal plants—Withania somnifera (Ashwagandha), Tinospora cordifolia (Giloy) and Ocimum sanctum (Tulsi)—A molecular docking study. Journal of Biomolecular Structure and Dynamics. 2020; 40(1): 190–203. doi: 10.1080/07391102.2020.1810778

41. Nawrot J, Gornowicz-Porowska J, Budzianowski J, et al. Medicinal herbs in the relief of neurological, cardiovascular, and respiratory symptoms after COVID-19 infection A literature review. Cells 2022; 11(12): 1897. doi: 10.3390/cells11121897

42. Choe J, Yong PH, Ng ZX. The efficacy of traditional medicinal plants in modulating the main protease of SARS-CoV-2 and cytokine storm. Chemistry & Biodiversity 2022; 19(11): e202200655. doi: 10.1002/cbdv.202200655

43. Frisch MJ, Trucks GW, Schlegel HB, et al. Gaussian 16, revision C.01, Gaussian, Inc., Wallingford CT, 2016. Available online: https://gaussian.com/ (accessed on 30 August 2023).

44. Perdew JP, Burke K, Ernzerhof M. Generalized gradient approximation made simple. Physical Review Letters 1996; 77(18): 3865. doi: 10.1103/PhysRevLett.77.3865

45. Bakhshi K, Mollaamin F, Monajjemi M. Exchange and correlation effect of hydrogen chemisorption on nano V(100) surface: A DFT study by generalized gradient approximation (GGA). Journal of Computational and Theoretical Nanoscience 2011; 8(4): 763–768. doi: 10.1166/jctn.2011.1750

46. Mahdavian L, Monajjemi M. Alcohol sensors based on SWNT as chemical sensors: Monte Carlo and Langevin dynamics simulation. Microelectronics Journal 2010; 41(2–3): 142–149. doi: 10.1016/j.mejo.2010.01.011

47. Mollaamin F, Shahriari S, Monajjemi M. Drug design of medicinal plants as a treatment of Omicron Variant (COVID-19 Variant B.1.1.529). Journal of the Chilean Chemical Society 2022; 67(3): 5562–5570. doi: 10.4067/S0717-97072022000305562

48. Monajjemi M, Noei M, Mollaamin F. Design of fMet-tRNA and calculation of its bonding properties by quantum mechanics. Nucleosides, Nucleotides & Nucleic Acids 2010; 29(9): 676–683. doi: 10.1080/15257771003781642

49. Mollaamin F, Monajjemi M. Harmonic linear combination and normal mode analysis of semiconductor nanotubes vibrations. Journal of Computational and Theoretical Nanoscience 2015; 12(6): 1030–1039. doi: 10.1166/jctn.2015.3846

50. Khaleghian M, Zahmatkesh M, Mollaamin F, Monajjemi M. Investigation of solvent effects on armchair single-walled carbon nanotubes: A QM/MD study. Fullerenes, Nanotubes and Carbon Nanostructures 2011; 19(4): 251–261. doi: 10.1080/15363831003721757

51. Sarasia EM, Afsharnezhad S, Honarparvar B, et al. Theoretical study of solvent effect on NMR shielding tensors of luciferin derivatives. Physics and Chemistry of Liquids 2011; 49(5): 561–571. doi: 10.1080/00319101003698992

52. Ghalandari B, Monajjemi M, Mollaamin F. Theoretical investigation of carbon nanotube binding to DNA in view of drug delivery. Journal of Computational and Theoretical Nanoscience 2011; 8(7): 1212–1219. doi: 10.1166/jctn.2011.1801

53. Tahan A, Mollaamin F, Monajjemi M. Thermochemistry and NBO analysis of peptide bond: Investigation of basis sets and binding energy. Russian Journal of Physical Chemistry A 2009; 83(4): 587–597. doi: 10.1134/S003602440904013X

54. Mollaamin F, Shahriari S, Monajjemi M. Monkeypox disease treatment by tecovirimat adsorbed onto single-walled carbon nanotube through drug delivery method. Journal of the Chilean Chemical Society 2023; 68(1): 5796–5801. doi: 10.4067/S0717-97072023000105796

55. Mollaamin F, Monajjemi M. Molecular modelling framework of metal-organic clusters for conserving surfaces: Langmuir sorption through the TD-DFT/ONIOM approach. Molecular Simulation 2023; 49(4): 365–376. doi: 10.1080/08927022.2022.2159996

56. Shahriari S, Mollaamin F, Monajjemi M. Increasing the performance of {[(1-x-y) LiCo0.3Cu0.7] (Al and Mg doped)] O2}, xLi2MnO3, yLiCoO2 composites as cathode material in lithium-ion battery: Synthesis and characterization. Micromachines 2023; 14(2): 241. doi: 10.3390/mi14020241

57. McArdle S, Mayorov A, Shan X, et al. Digital quantum simulation of molecular vibrations. Chemical Science 2019; 10(22): 5725–5735. doi: 10.1039/C9SC01313j

58. Monajjemi M, Baie MT, Mollaamin F. Interaction between threonine and cadmium cation in [Cd(Thr)n]2+ (n = 1–3) complexes: Density functional calculations. Russian Chemical Bulletin 2010; 59: 886–889. doi: 10.1007/s11172-010-0181-5

59. Zadeh MAA, Lari H, Kharghanian L, et al. Density functional theory study and anti-cancer properties of shyshaq plant: In view point of nano biotechnology. Journal of Computational and Theoretical Nanoscience 2015; 12(11): 4358–4367. doi: 10.1166/jctn.2015.4366

60. Mollaamin F. Computational methods in the drug delivery of carbon nanocarriers onto several compounds in Sarraceniaceae medicinal plant as monkeypox therapy. Computation 2023; 11(4): 84. doi: 10.3390/computation11040084

61. Hatada R, Okuwaki K, Mochizuki Y, et al. Fragment molecular orbital based interaction analyses on COVID-19 main protease-inhibitor N3 complex (PDB ID: 6LU7). Journal of Chemical Information and Modeling 2020; 60(7): 3593–3602. doi: 10.1021/acs.jcim.0c00283

62. Peele KA, Chandrasai P, Srihansa T, et al. Molecular docking and dynamic simulations for antiviral compounds against SARS-CoV-2: A computational study. Informatics in Medicine Unlocked 2020; 19: 100345. doi: 10.1016/j.imu.2020.100345

63. Qiao Z, Zhang H, Ji HF, Chen Q. Computational view toward the inhibition of SARS-CoV-2 spike glycoprotein and the 3CL protease. Computation 2020; 8(2): 53. doi: 10.3390/computation8020053

64. Liang J, Pitsillou E, Karagiannis C, et al. Interaction of the prototypical α-ketoamide inhibitor with the SARS-CoV-2 main protease active site in silico: Molecular dynamic simulations highlight the stability of the ligand-protein complex. Computational Biology and Chemistry 2020; 87: 107292. doi: 10.1016/j.compbiolchem.2020.107292

65. Zheng Q, Yan C, Lv N, et al. Natural products for Omicron BA.1, BA.1.1 and BA.2 therapy: Application of medicinal plants for drug delivery: A DFT & QM/MM simulation. Journal of Biological Regulators and Homeostatic Agents 2023; 37(6): 3403–3416. doi: 10.23812/j.biol.regul.homeost.agents.20233706.337

66. Monajjemi M, Mollaamin F, Shojaei S. An overview on coronaviruses family from past to COVID-19: Introduce some inhibitors as antiviruses from Gillan’s plants. Biointerface Research in Applied Chemistry 2020; 10(3): 5575–5585. doi: 10.33263/BRIAC103.575585

67. Sharma A, Tiwari V, Sowdhamini R. Computational search for potential COVID-19 drugs from FDA-approved drugs and small molecules of natural origin identifies several anti-virals and plant products. Journal of Biosciences 2020; 45(1): 100. doi: 10.1007/s12038-020-00069-8

68. Wang S. Efficiently calculating anharmonic frequencies of molecular vibration by molecular dynamics trajectory analysis. ACS Omega 2019; 4(5): 9271–9283. doi: 10.1021/acsomega.8b03364

69. Mollaamin F, Monajjemi M, Salemi S, Baei MT. A dielectric effect on normal mode analysis and symmetry of BNNT nanotube. Fullerenes, Nanotubes and Carbon Nanostructures 2011; 19(3): 182–196. doi: 10.1080/15363831003782932

70. Ni W, Li G, Zhao J, et al. Use of Monte Carlo simulation to evaluate the efficacy of tigecycline and minocycline for the treatment of pneumonia due to carbapenemase-producing Klebsiella pneumonia. Infectious Diseases 2018; 50(7): 507–513. doi: 10.1080/23744235.2018.1423703

71. Mollaamin F, Monajjemi M. Transition metal (X = Mn, Fe, Co, Ni, Cu, Zn)-doped graphene as gas sensor for CO2 and NO2 detection: A molecular modeling framework by DFT perspective. Journal of Molecular Modeling 2023; 29(4): 119. doi: 10.1007/s00894-023-05526-3

72. Aji GK, Hatou K, Morimoto T. Modeling the dynamic response of plant growth to root zone temperature in hydroponic chili pepper plant using neural networks. Agriculture 2020; 10(6): 234. doi: 10.3390/agriculture10060234

73. Wang J. Fast identification of possible drug treatment of coronavirus disease-19 (COVID-19) through computational drug repurposing study. Journal of Chemical Information and Modeling 2020; 60(6): 3277–3286. doi: 10.1021/acs.jcim.0c00179

74. Khalili Hadad B , Mollaamin F, Monajjemi M. Biophysical chemistry of macrocycles for drug delivery: A theoretical study. Russian Chemical Bulletin 2011; 60: 238–241. doi: 10.1007/s11172-011-0039-5

75. Mollaamin F, Ilkhani A, Sakhaei N, et al. Thermodynamic and solvent effect on dynamic structures of nano bilayer-cell membrane: Hydrogen bonding study. Journal of Computational and Theoretical Nanoscience 2015; 12(10): 3148–3154. doi: 10.1166/jctn.2015.4092

76. Monajjemi M, Khaleghian M, Tadayonpour N, Mollaamin F. The effect of different solvents and temperatures on stability of single-walled carbon nanotube: A QM/MD study. International Journal of Nanoscience 2010; 9(5): 517–529. doi: 10.1142/S0219581X10007071

77. Ng ZX, Koick YTT, Yong PH. Comparative analyses on radical scavenging and cytotoxic activity of phenolic and flavonoid content from selected medicinal plants. Natural Product Research 2021; 35(23): 5271–5276. doi: 10.1080/14786419.2020.1749617

78. Ho KL, Yong PH, Wang CW, et al. Peperomia pellucida (L.) Kunth and eye diseases: A review on phytochemistry, pharmacology and toxicology. Journal of Integrative Medicine 2022; 20(4): 292–304. doi: 10.1016/j.joim.2022.02.002

79. Ho KL, Tan CG, Yong PH, et al. Extraction of phytochemicals with health benefit from Peperomia pellucida (L.) Kunth through liquid-liquid partitioning. Journal of Applied Research on Medicinal and Aromatic Plants 2022; 30: 100392. doi: 10.1016/j.jarmap.2022.100392

80. Ho KL, Ng ZX, Wang CW, et al. Comparative analysis of in vitro enzyme inhibitory activities and phytochemicals from platycladus orientalis (L.) franco via solvent partitioning method. Applied Biochemistry Biotechnology 2022; 194: 3621–3644. doi: 10.1007/s12010-022-03921-9




DOI: https://doi.org/10.24294/ti.v7.i2.2329

Refbacks

  • There are currently no refbacks.


Copyright (c) 2023 Fatemeh Mollaamin

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

This site is licensed under a Creative Commons Attribution 4.0 International License.