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Year 2023, , 665 - 670, 28.12.2023

Serpil Kaya , Sultan Erkan , Duran Karakaş

https://doi.org/10.17776/csj.1328641

Abstract

Project Number

-

References

  • [1] Chintagunta A. D., Kumar M., Sampath Kumar N. S., Jeevan Kumar S. P., Differential diagnosis and possible therapeutics for coronavirus disease 2019, In Diagnostic Strategies for COVID-19 and other Coronaviruses, (2020) 51-71.
  • [2] Islam M. T., Sarkar C., El‐Kersh D. M., Jamaddar S., Uddin S. J., Shilpi J. A., Mubarak M. S., Natural products and their derivatives against coronavirus: A review of the non‐clinical and pre‐clinical data, Phytotherapy Research, 34(10) (2020) 2471-2492.
  • [3] Ulbricht C., Basch E., Cheung L., Goldberg H., Hammerness P., Isaac R., Wortley J., An evidence-based systematic review of elderberry and elderflower (Sambucus nigra) by the Natural Standard Research Collaboration, Journal of dietary supplements, 11(1) (2014) 80-120.
  • [4] Valles J., Bonet M. A., Agelet A., Ethnobotany of Sambucus nigra L. in catalonia (Iberian Peninsula): The integral exploitation of a natural resource in mountain regions, Economic botany, 58(3) (2004) 456-469.
  • [5] Armanini D., Fiore C., Mattarello M. J., Bielenberg J., Palermo M., History of the endocrine effects of licorice, Experimental and clinical endocrinology & diabetes, 110(06) (2002) 257-261.
  • [6] Fiore C., Eisenhut M., Krausse R., Ragazzi E., Pellati D., Armanini D., Bielenberg J., Antiviral effects of Glycyrrhiza species, Phytotherapy Research: An International Journal Devoted to Pharmacological and Toxicological Evaluation of Natural Product Derivatives, 22(2) (2008) 141-148.
  • [7] Fiore C., Eisenhut M., Ragazzi E., Zanchin G., Armanini, D., A history of the therapeutic use of liquorice in Europe, Journal of ethnopharmacology, 99(3) (2005) 317-324.
  • [8] Raus K., Pleschka S., Klein P., Schoop R., Fisher P., Effect of an Echinacea-based hot drink versus oseltamivir in influenza treatment: a randomized, double-blind, double-dummy, multicenter, noninferiority clinical trial, Current Therapeutic Research, (77) (2015) 66-72.
  • [9] San Chang J., Wang K. C., Yeh C. F., Shieh D. E., Chiang L. C., Fresh ginger (Zingiber officinale) has anti-viral activity against human respiratory syncytial virus in human respiratory tract cell lines, Journal of ethnopharmacology, 145(1) (2013) 146-151.
  • [10] Ehrhardt C., Hrincius E. R., Korte V., Mazur I., Droebner K., Poetter A., Ludwig S., A polyphenol rich plant extract, CYSTUS052, exerts anti influenza virus activity in cell culture without toxic side effects or the tendency to induce viral resistance, Antiviral research, 76(1) (2007) 38-47.
  • [11] Weber N. D., Andersen D. O., North J. A., Murray B. K., Lawson L. D., Hughes B. G., In vitro virucidal effects of Allium sativum (garlic) extract and compounds, Planta medica, 58(05) (1992) 417-423.
  • [12] Xu J., Xu Z., Zheng W., A review of the antiviral role of green tea catechins, Molecules, 22(8) (2017) 1337.
  • [13] Zhuang M., Jiang H., Suzuki Y., Li X., Xiao P., Tanaka T., Hattori T., Procyanidins and butanol extract of Cinnamomi Cortex inhibit SARS-CoV infection, Antiviral research, 82(1) (2009) 73-81.
  • [14] Praditya D., Kirchhoff L., Brüning J., Rachmawati H., Steinmann J., Steinmann E., Anti-infective properties of the golden spice curcumin, Frontiers in microbiology, (10) (2019) 912.
  • [15] Wen C. C., Kuo Y. H., Jan J. T., Liang P. H., Wang S. Y., Liu H. G., Yang N. S., Specific plant terpenoids and lignoids possess potent antiviral activities against severe acute respiratory syndrome coronavirus, Journal of medicinal chemistry, 50(17) (2007) 4087-4095.
  • [16] Stahl-Biskup E., Essential oil chemistry of the genus Thymus–a global view. In Thyme (2002) 89-138, CRC Press.
  • [17] Nickavar B., Mojab F., Dolat-Abadi R., Analysis of the essential oils of two Thymus species from Iran, Food chemistry (2005) 90(4) 609-611.
  • [18] Nikolic M., Glamoclija J., Ferreira I. C., Calhelha R. C., Fernandes A., Markovic T., Sokovic M., Chemical composition, antimicrobial, antioxidant and antitumor activity of Thymus serpyllum L., Thymus algeriensis Boiss. and Reut and Thymus vulgaris L. essential oils, Industrial Crops and Products, (52) (2014) 183-190.
  • [19] Kim S., Thiessen P. A., Cheng T., Yu B., Shoemaker B. A., Wang J., Bryant S. H., Literature information in PubChem: associations between PubChem records and scientific articles, Journal of cheminformatics, 8(1) (2016) 1-15.
  • [20] Hatada R., Okuwaki K., Mochizuki Y., Handa Y., Fukuzawa K., Komeiji Y., Tanaka S., Fragment molecular orbital-based interaction analyses on COVID-19 main protease− inhibitor N3 complex (PDB ID: 6LU7), Journal of chemical information and modeling, 60(7) (2020) 3593-3602.
  • [21] Verkhivker G. M., Agajanian S., Oztas D., Gupta G., Computational analysis of protein stability and allosteric interaction networks in distinct conformational forms of the SARS-CoV-2 spike D614G mutant: Reconciling functional mechanisms through allosteric model of spike regulation. Journal of Biomolecular Structure and Dynamics, (2021) 1-18.
  • [22] Bikadi Z., Hazai E., Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock. Journal of cheminformatics, 1(1) (2009) 1-16.
  • [23] Halgren T. A., Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. Journal of computational chemistry, 17(5‐6) (1996) 490-519.
  • [24] Gasteiger J., Marsili M., Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges, Tetrahedron, 36(22) (1980) 3219-3228.
  • [25] Tang Y., Zhu W., Chen K., Jiang H., New technologies in computer-aided drug design: Toward target identification and new chemical entity discovery, Drug discovery today: technologies, 3(3) (2006) 307-313.
  • [26] Kuntz I. D., Blaney J. M., Oatley S. J., Langridge R., Ferrin T. E., A geometric approach to macromolecule-ligand interactions, Journal of molecular biology, 161(2) (1982) 269-288.
  • [27] Onodera K., Satou K., Hirota H., Evaluations of molecular docking programs for virtual screening, Journal of chemical information and modeling, 47(4) (2007) 1609-1618.
  • [28] Kaya S., Erkan S., Karakaş D., Computational design and characterization of platinum‐II complexes of some Schiff bases and investigation of their anticancer‐antibacterial properties, Applied Organometallic Chemistry, (36) (2022) e6805.
  • [29] Kaya S., Erkan S., Karakaş D. Computational investigation of molecular structures, spectroscopic properties and antitumor-antibacterial activities of some Schiff bases, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, (244) (2021) 118829.
  • [30] Erkan, S., Karakaş, D. Computational investigation of structural, nonlinear optical and anti-tumor properties of dinuclear metal carbonyls bridged by pyridyl ligands with alkyne unit, Journal of Molecular Structure, (1199) (2020) 127054.

Investigation of the Effect of Main Components of Wild Thyme on Covid-19 by Computational Methods

Year 2023, , 665 - 670, 28.12.2023

Serpil Kaya , Sultan Erkan , Duran Karakaş

https://doi.org/10.17776/csj.1328641

Abstract

Aromatic plant species of the genus thymus have an important role as they have therapeutic properties such as antirheumatic, antiseptic, antispasmodic, antimicrobial, cardiac, carminative, diuretic and expectorant. It is also known that such plants strengthen the immune system and help cope with infectious diseases such as colds and flu. In this study, the effects of thymol, p-cymene, -terpinene, bornyl acetate, borneol, carvacrol, thymol methyl ether, thymol acetate, which are the main components of wild thyme (thymus serpyllum L.), on Covid-19 were investigated at the molecular level. Optimizations and molecular docking were done in Docking Server with the MMFF94 method. Major components of wild thyme were docked separately against 6LU7 protein representing the first gene form of Covid-19 and 7KDL protein representing the mutated form. Docking poses and binding energies between target proteins and wild thyme components were calculated. The results were compared with favipiravir, an antiviral drug developed against influenza virus and also used in the treatment of Covid-19. It was found that the thymol molecule, one of the main components of wild thyme, has the highest biological activity against both 6LU7 and 7KDL protein chains of Covid-19.

Keywords

Thymus serpyllum L. Covid-19 Molecular docking

Supporting Institution

-

Project Number

-

Thanks

-

References

  • [1] Chintagunta A. D., Kumar M., Sampath Kumar N. S., Jeevan Kumar S. P., Differential diagnosis and possible therapeutics for coronavirus disease 2019, In Diagnostic Strategies for COVID-19 and other Coronaviruses, (2020) 51-71.
  • [2] Islam M. T., Sarkar C., El‐Kersh D. M., Jamaddar S., Uddin S. J., Shilpi J. A., Mubarak M. S., Natural products and their derivatives against coronavirus: A review of the non‐clinical and pre‐clinical data, Phytotherapy Research, 34(10) (2020) 2471-2492.
  • [3] Ulbricht C., Basch E., Cheung L., Goldberg H., Hammerness P., Isaac R., Wortley J., An evidence-based systematic review of elderberry and elderflower (Sambucus nigra) by the Natural Standard Research Collaboration, Journal of dietary supplements, 11(1) (2014) 80-120.
  • [4] Valles J., Bonet M. A., Agelet A., Ethnobotany of Sambucus nigra L. in catalonia (Iberian Peninsula): The integral exploitation of a natural resource in mountain regions, Economic botany, 58(3) (2004) 456-469.
  • [5] Armanini D., Fiore C., Mattarello M. J., Bielenberg J., Palermo M., History of the endocrine effects of licorice, Experimental and clinical endocrinology & diabetes, 110(06) (2002) 257-261.
  • [6] Fiore C., Eisenhut M., Krausse R., Ragazzi E., Pellati D., Armanini D., Bielenberg J., Antiviral effects of Glycyrrhiza species, Phytotherapy Research: An International Journal Devoted to Pharmacological and Toxicological Evaluation of Natural Product Derivatives, 22(2) (2008) 141-148.
  • [7] Fiore C., Eisenhut M., Ragazzi E., Zanchin G., Armanini, D., A history of the therapeutic use of liquorice in Europe, Journal of ethnopharmacology, 99(3) (2005) 317-324.
  • [8] Raus K., Pleschka S., Klein P., Schoop R., Fisher P., Effect of an Echinacea-based hot drink versus oseltamivir in influenza treatment: a randomized, double-blind, double-dummy, multicenter, noninferiority clinical trial, Current Therapeutic Research, (77) (2015) 66-72.
  • [9] San Chang J., Wang K. C., Yeh C. F., Shieh D. E., Chiang L. C., Fresh ginger (Zingiber officinale) has anti-viral activity against human respiratory syncytial virus in human respiratory tract cell lines, Journal of ethnopharmacology, 145(1) (2013) 146-151.
  • [10] Ehrhardt C., Hrincius E. R., Korte V., Mazur I., Droebner K., Poetter A., Ludwig S., A polyphenol rich plant extract, CYSTUS052, exerts anti influenza virus activity in cell culture without toxic side effects or the tendency to induce viral resistance, Antiviral research, 76(1) (2007) 38-47.
  • [11] Weber N. D., Andersen D. O., North J. A., Murray B. K., Lawson L. D., Hughes B. G., In vitro virucidal effects of Allium sativum (garlic) extract and compounds, Planta medica, 58(05) (1992) 417-423.
  • [12] Xu J., Xu Z., Zheng W., A review of the antiviral role of green tea catechins, Molecules, 22(8) (2017) 1337.
  • [13] Zhuang M., Jiang H., Suzuki Y., Li X., Xiao P., Tanaka T., Hattori T., Procyanidins and butanol extract of Cinnamomi Cortex inhibit SARS-CoV infection, Antiviral research, 82(1) (2009) 73-81.
  • [14] Praditya D., Kirchhoff L., Brüning J., Rachmawati H., Steinmann J., Steinmann E., Anti-infective properties of the golden spice curcumin, Frontiers in microbiology, (10) (2019) 912.
  • [15] Wen C. C., Kuo Y. H., Jan J. T., Liang P. H., Wang S. Y., Liu H. G., Yang N. S., Specific plant terpenoids and lignoids possess potent antiviral activities against severe acute respiratory syndrome coronavirus, Journal of medicinal chemistry, 50(17) (2007) 4087-4095.
  • [16] Stahl-Biskup E., Essential oil chemistry of the genus Thymus–a global view. In Thyme (2002) 89-138, CRC Press.
  • [17] Nickavar B., Mojab F., Dolat-Abadi R., Analysis of the essential oils of two Thymus species from Iran, Food chemistry (2005) 90(4) 609-611.
  • [18] Nikolic M., Glamoclija J., Ferreira I. C., Calhelha R. C., Fernandes A., Markovic T., Sokovic M., Chemical composition, antimicrobial, antioxidant and antitumor activity of Thymus serpyllum L., Thymus algeriensis Boiss. and Reut and Thymus vulgaris L. essential oils, Industrial Crops and Products, (52) (2014) 183-190.
  • [19] Kim S., Thiessen P. A., Cheng T., Yu B., Shoemaker B. A., Wang J., Bryant S. H., Literature information in PubChem: associations between PubChem records and scientific articles, Journal of cheminformatics, 8(1) (2016) 1-15.
  • [20] Hatada R., Okuwaki K., Mochizuki Y., Handa Y., Fukuzawa K., Komeiji Y., Tanaka S., Fragment molecular orbital-based interaction analyses on COVID-19 main protease− inhibitor N3 complex (PDB ID: 6LU7), Journal of chemical information and modeling, 60(7) (2020) 3593-3602.
  • [21] Verkhivker G. M., Agajanian S., Oztas D., Gupta G., Computational analysis of protein stability and allosteric interaction networks in distinct conformational forms of the SARS-CoV-2 spike D614G mutant: Reconciling functional mechanisms through allosteric model of spike regulation. Journal of Biomolecular Structure and Dynamics, (2021) 1-18.
  • [22] Bikadi Z., Hazai E., Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock. Journal of cheminformatics, 1(1) (2009) 1-16.
  • [23] Halgren T. A., Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. Journal of computational chemistry, 17(5‐6) (1996) 490-519.
  • [24] Gasteiger J., Marsili M., Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges, Tetrahedron, 36(22) (1980) 3219-3228.
  • [25] Tang Y., Zhu W., Chen K., Jiang H., New technologies in computer-aided drug design: Toward target identification and new chemical entity discovery, Drug discovery today: technologies, 3(3) (2006) 307-313.
  • [26] Kuntz I. D., Blaney J. M., Oatley S. J., Langridge R., Ferrin T. E., A geometric approach to macromolecule-ligand interactions, Journal of molecular biology, 161(2) (1982) 269-288.
  • [27] Onodera K., Satou K., Hirota H., Evaluations of molecular docking programs for virtual screening, Journal of chemical information and modeling, 47(4) (2007) 1609-1618.
  • [28] Kaya S., Erkan S., Karakaş D., Computational design and characterization of platinum‐II complexes of some Schiff bases and investigation of their anticancer‐antibacterial properties, Applied Organometallic Chemistry, (36) (2022) e6805.
  • [29] Kaya S., Erkan S., Karakaş D. Computational investigation of molecular structures, spectroscopic properties and antitumor-antibacterial activities of some Schiff bases, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, (244) (2021) 118829.
  • [30] Erkan, S., Karakaş, D. Computational investigation of structural, nonlinear optical and anti-tumor properties of dinuclear metal carbonyls bridged by pyridyl ligands with alkyne unit, Journal of Molecular Structure, (1199) (2020) 127054.
There are 30 citations in total.

Details

Primary Language English
Subjects Bioinorganic Chemistry
Journal Section Natural Sciences
Authors

Serpil Kaya 0000-0003-3360-4735

Sultan Erkan 0000-0001-6744-929X

Duran Karakaş 0000-0002-6770-3726

Project Number -
Publication Date December 28, 2023
Submission Date July 17, 2023
Acceptance Date November 8, 2023
Published in Issue Year 2023

Cite

APA Kaya, S., Erkan, S., & Karakaş, D. (2023). Investigation of the Effect of Main Components of Wild Thyme on Covid-19 by Computational Methods. Cumhuriyet Science Journal, 44(4), 665-670. https://doi.org/10.17776/csj.1328641