اخبار و اعلانات

 آمار

تعداد نشریات285
تعداد نشریات سازمان83
تعداد شماره‌ها3,086
تعداد مقالات34,442
تعداد مشاهده مقاله48,907,050
تعداد دریافت فایل اصل مقاله79,347,554
Mahmood Janlou, Mehr Ali, Sahebjamee, Hassan, Alaei, Hamid Reza, Heidari, Mahmoud. (1403). A Virtual Study on the Active Ingredients of Zingiber officinale and Boswellia serrata as Potential Natural Inhibitors of SARS-COV-2 Main Protease Enzyme. سامانه مدیریت نشریات علمی, 14(2), 137-148. doi: 10.22034/jmpb.2024.365268.1670
Mehr Ali Mahmood Janlou; Hassan Sahebjamee; Hamid Reza Alaei; Mahmoud Heidari. "A Virtual Study on the Active Ingredients of Zingiber officinale and Boswellia serrata as Potential Natural Inhibitors of SARS-COV-2 Main Protease Enzyme". سامانه مدیریت نشریات علمی, 14, 2, 1403, 137-148. doi: 10.22034/jmpb.2024.365268.1670
Mahmood Janlou, Mehr Ali, Sahebjamee, Hassan, Alaei, Hamid Reza, Heidari, Mahmoud. (1403). 'A Virtual Study on the Active Ingredients of Zingiber officinale and Boswellia serrata as Potential Natural Inhibitors of SARS-COV-2 Main Protease Enzyme', سامانه مدیریت نشریات علمی, 14(2), pp. 137-148. doi: 10.22034/jmpb.2024.365268.1670
Mahmood Janlou, Mehr Ali, Sahebjamee, Hassan, Alaei, Hamid Reza, Heidari, Mahmoud. A Virtual Study on the Active Ingredients of Zingiber officinale and Boswellia serrata as Potential Natural Inhibitors of SARS-COV-2 Main Protease Enzyme. سامانه مدیریت نشریات علمی, 1403; 14(2): 137-148. doi: 10.22034/jmpb.2024.365268.1670

A Virtual Study on the Active Ingredients of Zingiber officinale and Boswellia serrata as Potential Natural Inhibitors of SARS-COV-2 Main Protease Enzyme

Journal of Medicinal plants and By-products
مقاله 5، دوره 14، شماره 2، خرداد و تیر 2025، صفحه 137-148    اصل مقاله (1.43 M)
نوع مقاله: Research Paper
شناسه دیجیتال (DOI): 10.22034/jmpb.2024.365268.1670
نویسندگان
Mehr Ali Mahmood Janlou* 1، 2؛ Hassan Sahebjamee3؛ Hamid Reza Alaei4؛ Mahmoud Heidari5
1Department of Biophysics, Faculty of Biological Sciences, Gorgan Branch, Islamic Azad University, Gorgan, Iran
2Medicinal Plants Research Center, Gorgan Branch, Islamic Azad University, Gorgan, Iran
3Department of Biophysics, Faculty of Biological Science, Varamin-Pishva Branch, Islamic Azad University, Varamin, I.R. Iran
4Department of Physics, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran
5Department of Biology, Faculty of Science, Gorgan Branch, Islamic Azad University, Gorgan, Iran
چکیده
SARS-CoV-2 is one of the most important novel coronaviruses and was recognized as a major global concern due to the declaration of the pandemic in March 2020. Researchers have attempted to develop antiviral agents against coronavirus, and the Mpro protein may be an effective drug target. To identify potential hit molecules for clinical use, we analyzed the inhibitory effects of phytochemical compounds from ginger and kundur and seven FDA-approved drugs against Mpro. Employing molecular docking and scoring functions, three top phytochemical compounds, gingerone A, astelbin, and L-(-)-catechin, and three reported antiviral drugs, chloroquine, ritonavir, and remdesivir, showed higher interaction profiles. According to the toxicity and ADME properties, L-(−)-catechin and remdesivir were selected for further analysis via MD simulations. The MD results supported by standard analysis (e.g., RMSD, RMSF, Rg, and SASA) revealed that L-(-)-catechin had a greater impact on the Mpro structure than remdesivir. Proteinligand energy calculations via the MM/PBSA method also supported the molecular docking data. Interestingly, our docking studies revealed that L-(-)-catechin has different interactions with Cys145 and His41, which may disrupt the formation of the Cys-His dyad, which is crucial for Mpro protease activity. We believe that due to the significant effect of L-(−)-catechin on the Mpro protein, this compound can be evaluated as a candidate molecule in drug development studies against SARS-CoV-2.
کلیدواژه‌ها
SARS-COV-2 main protease؛ Kundur؛ Ginger؛ Docking؛ MD simulation
مراجع
  1. Gorbalenya A.E., Baker S.C., Baric R.S., de Groot R.J., Drosten C., Gulyaeva A.A., Haagmans B.L., Lauber C., Leontovich A.M., Neuman B.W., Penzar D., Perlman S., Poon L.L.M., Samborskiy D. V., Sidorov I. A., Sola I., Ziebuhr J. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nature Microbiology. 2020;5(4):536–544.
  2. Krammer F. SARS-CoV-2 vaccines in development. Nature. 2020;586(7830):516–527. https://doi.org/10.1038/s41586-020-2798-3
  3. Wardeh M., Baylis M., Blagrove M.S.C. Predicting mammalian hosts in which novel coronaviruses can be generated. Nature Communications. 2021;12(1):780.
  4. Ahmad S., Usman Mirza M., Yean Kee L., Nazir M., Abdul Rahman N., Trant J. F., Abdullah I. Fragment‐based in silico design of SARS‐CoV‐2 main protease inhibitors. Chem Biology Drug Design. 2021;98(4):604-619.
  5. Zhang L., Lin D., Sun X., Curth U., Drosten C., Sauerhering L., Becker S., Rox K., Hilgenfeld R. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved a-ketoamide inhibitors. Sci. 2020;368(6489):409–412.
  6. Hilgenfeld R. From SARS to MERS: crystallographic studies on coronaviral proteases enable antiviral drug design. The FEBS J. 2014;281(18):4085–4096.
  7. Jia Z., Lan X., Lu K., Meng X., Jing W., Jia S., Zhao K., Dai Y. Synthesis, molecular docking, and binding Gibbs free energy calculation of -nitrostyrene derivatives: Potential inhibitors of SARS-CoV-2 3CL protease. J Molecular Structure. 2023;1284:135409.
  8. Mandal A., Jha A.K., Hazra B. Plant Products as Inhibitors of Coronavirus 3CL Protease. Frontiers in Pharmacol. 2021;12(4):1–16.
  9. Jin Z., Du X., Xu Y., Deng Y., Liu M., Zhao Y., Zhang B., Li X., Zhang L., Peng C., Duan Y., Yu J., Wang L., Yang K., Liu F., Jiang R., Yang X., You T., Liu X., … Yang H. Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature. 2020;582(7811):289–293.
  10. Citarella A., Scala A., Piperno A., Micale N. Sars-cov-2 mpro: A potential target for peptidomimetics and small-molecule inhibitors. Biomolecules. 2021;11(4):607.
  11. Ramajayam R., Tan K.-P., Liang P.-H. Recent development of 3C and 3CL protease inhibitors for anti-coronavirus and anti-picornavirus drug discovery. Biochemical Society Transactions. 2011;39(5):1371–1375.
  12. Dong L., Hu S., Gao J. Discovering drugs to treat coronavirus disease 2019 (COVID-19). Drug Discoveries & Therapeutics. 2020;14(1):58–60.
  13. Kumar D.C.V., Chethan B.S., Shalini V., Rangappa K.S., Lokanath N.K. Structural elucidation and in-silico evaluation of 1, 2, 4-triazole derivative as potent Omicron variant of SARS-CoV-2 spike protein inhibitor with pharmacokinetics ADMET and drug-likeness predictions. J Molecular Structure. 2024;12(97):136976.
  14. Ni L., Zhou L., Zhou M., Zhao J., Wang D.W. Combination of western medicine and Chinese traditional patent medicine in treating a family case of COVID-19. Frontiers of Med. 2020;14(2):210–214.
  15. Wang M., Cao R., Zhang L., Yang X., Liu J., Xu M., Shi Z., Hu Z., Zhong W., Xiao G. Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res. 2020;30(3):269–271.
  16. Mirza M.U., Froeyen M. Structural elucidation of SARS-CoV-2 vital proteins: Computational methods reveal potential drug candidates against main protease, Nsp12 polymerase and Nsp13 helicase. J Pharmaceutical Analysis. 2020;10(4):320–328.
  17. Bellanger R.A., Seeger C.M., Smith H.E. Safety of complementary and alternative medicine (CAM) treatments and practices. In Side Effects of Drugs Annual. 2018;40:609–619.
  18. Jahan R., Paul A. K., Bondhon T. A., Hasan A., Jannat K., Mahboob T., Nissapatorn V., Pereira M. de L., Wiart C., Wilairatana P., Rahmatullah, M. Zingiber officinale: Ayurvedic Uses of the Plant and In Silico Binding Studies of Selected Phytochemicals With Mpro of SARS-CoV-2. Natural Prod Communications. 2021;16(10).
  19. Ayub M.A., Hanif M.A., Sarfraz R.A., Shahid M. Biological activity of boswellia serrata roxb. Oleo gum resin essential oil: Effects of extraction by supercritical carbon dioxide and traditional methods. Int J Food Properties. 2018;21(1):808–820.
  20. Roy N.K., Parama D., Banik K., Bordoloi D., Devi A.K., Thakur K.K., Padmavathi G., Shakibaei M., Fan L., Sethi G., Kunnumakkara A. B. An update on pharmacological potential of boswellic acids against chronic diseases. Int J Molecular Sci. 2019;20(17). https://doi.org/10.3390/ijms20174101
  21. Sultana A., Raheman K. Boswellia serrata Roxb. a traditional herb with versatile pharmacological activity: a review. Int J Pharmaceutical Sci Res. 2013;4(6):2106-2117.

 

  1. Wang J., Prinz R.A., Liu X., Xu X. In vitro and in vivo antiviral activity of gingerenone a on influenza a virus is mediated by targeting janus kinase 2. Viruses. 2020;12(10):1–18. https://doi.org/10.3390/v12101141
  2. Abd El-Wahab A., El-Adawi H., El-Demellawy M. In vitro study of the antiviral activity of Zingiber officinale. Planta Medica. 2009; 75(09)-PF7.
  3. Rahmani A.H., Al Shabrmi F.M., Aly S.M. Active ingredients of ginger as potential candidates in the prevention and treatment of diseases via modulation of biological activities. Int J Physiol Pathophysiol and Pharmacol. 2014;6(2):125–136.
  4. Zaini N.A.M., Anwar F., Hamid A.A., Saari N. Kundur [Benincasa hispida (Thunb.) Cogn.]: A potential source for valuable nutrients and functional foods. Food Res Int. 2011;44(7):2368–2376.
  5. O’Boyle N.M., Banck M., James C.A., Morley C., Vandermeersch T., Hutchison G. R. Open Babel: An Open chemical toolbox. Journal of Cheminformatics. 2011;3(10):33. https://doi.org/10.1186/1758-2946-3-33
  6. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., Ferrin T.E. UCSF Chimera - A visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605–1612.
  7. Goodsell D.S. Computational docking of biomolecular complexes with autodock. Cold Spring Harbor Protocols. 2009; 4(5). https://doi.org/10.1101/pdb.prot5200
  8. Abraham M.J., Murtola T., Schulz R., Páll S., Smith J.C., Hess B., Lindah E. Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015;1(2):19–25.
  9. Hess B., Kutzner C., Van Der Spoel D., Lindahl E. GRGMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory and Comput. 2008;4(3):435–447.
  10. Van Der Spoel D., Lindahl E., Hess B., Groenhof G., Mark AE., Berendsen HJC. GROMACS: Fast, flexible, and free. J Comput Chem. 2005;26(16):1701–1718.
  11. https://doi.org/10.1002/jcc.20291
  12. Schüttelkopf A.W., Van Aalten D.M.F. PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica Section D: Biological Crystallography. 2004;60(8):1355–1363.
  13. Darden T., York D., Pedersen L. Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems. The Journal of Chemical Physics . 1993;98(12):10089–10092.
  14. Homeyer N., Gohlke H. Free energy calculations by the Molecular Mechanics Poisson-Boltzmann Surface Area method. Molecular Informatics. 2012;31(2):114–122.
  15. Aier I., Varadwaj P. K., Raj U. Structural insights into conformational stability of both wild-type and mutant EZH2 receptor. Scientific Reports. 2016;6(7):1–10.
  16. Gaur R., Thakur J.P., Yadav D.K., Kapkoti D.S., Verma R.K., Gupta N., Khan F., Saikia D., Bhakuni R.S. Synthesis, antitubercular activity, and molecular modeling studies of analogues of isoliquiritigenin and liquiritigenin, bioactive components from Glycyrrhiza glabra. Med Chem Res. 2015;24(9):3494–3503.
  17. Ponnan P., Gupta S., Chopra M., Tandon R., Baghel A.S., Gupta G., Prasad A.K., Rastogi R.C., Bose M., Raj H.G. 2D-QSAR, Docking Studies, and In Silico ADMET Prediction of Polyphenolic Acetates as Substrates for Protein Acetyltransferase Function of Glutamine Synthetase of Mycobacterium tuberculosis . ISRN Structural Biology. 2013;(11):1–12.
  18. Mahase E. Covid-19: US approves remdesivir despite WHO trial showing lack of efficacy. British Med J Publishing Group. 2020;371:m4120. http:// doi:
  19. Halsey G, Remdesivir Gets FDA" OK" for COVID-19 Treatment in Hepatic Disease Across Stages. Patient Care (Online). 2023.
  20. Garibaldi B.T., Wang K., Robinson M.L., Zeger S.L., Bandeen-Roche K., Wang M.C., Alexander G.C., Gupta A., Bollinger R., Xu Y. Comparison of time to clinical improvement with vs without remdesivir treatment in hospitalized patients with COVID-19. JAMA Network Open. 2021; 4(3):e213071.
  21. Singh R., Bhardwaj V.K., Das P., Purohit R. A computational approach for rational discovery of inhibitors for non-structural protein 1 of SARS-CoV-2. Computers in Biol Med. 2021;135:104555.
آمار
تعداد مشاهده مقاله: 434
تعداد دریافت فایل اصل مقاله: 303


counter
سامانه مدیریت نشریات علمی. طراحی و پیاده سازی از سیناوب