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Could Zingiber officinale plant be effective against Omicron BA.2.75 of SARS-CoV-2?

Year 2023, Volume: 7 Issue: 3, 42 - 56, 03.09.2023

Handan Saraç Ahmet Demirbaş Burak Tüzün

https://doi.org/10.33435/tcandtc.1198612

Abstract

Zingiber officinale plant was examined in this study. The chemicals found in this plant were identified using the GC-MS method. The activities of the determined chemical molecules against the SARS-CoV-2 Omicron variant were compared. We focused to determine whether Zingiber officinale plant would be an inhibitor against Omicron of SARS-CoV-2 in silico. As a result of theoretical calculations, Zingiber officinale plant was found to contain many chemicals as a result of GC-MS analysis. These chemicals were detected one by one and their activity values were calculated for the SARS-CoV-2 virus. As a result, molecules with high activity were detected. ADME/T properties were investigated in order to examine the drug properties of molecules with high activity. According to ADME/T results, these five molecules examined are suitable for use in human metabolism as drug molecules.

Keywords

Zingiber officinale SARS-CoV-2 omicron molecular docking ADME/T

Project Number

RGD-020

References

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  • [15] B. Tüzün, K. Sayin, H. Ataseven, Could Momordica Charantia Be Effective In The Treatment of COVID19?. Cumhuriyet Science Journal, 43(2) (2022) 211-220.
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  • [19] Q. Geng, K. Shi, G. Ye, W. Zhang, H. Aihara, F. Li, Structural Basis for Human Receptor Recognition by SARS-CoV-2 Omicron Variant BA. 1. Journal of Virology, 96(8) (2022) e00249-22.
  • [20] W. Yin, Y. Xu, P. Xu, X. Cao, C. Wu, C. Gu, ... & H. E. Xu, Structures of the Omicron Spike trimer with ACE2 and an anti-Omicron antibody. Science, 375(6584) (2022) 1048-1053.
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  • [28] A. Mermer, M. V. Bulbul, S. M. Kalender, I. Keskin, B. Tuzun, O. E. Eyupoglu, Benzotriazole-oxadiazole hybrid Compounds: Synthesis, anticancer Activity, molecular docking and ADME profiling studies. Journal of Molecular Liquids, 359 (2022) 119264.
  • [29] H. Yalazan, B. Tüzün, D. Akkaya, B. Barut, H. Kantekin, S. Yıldırmış, Quinoline‐fused both non‐peripheral and peripheral ZnII and MgII phthalocyanines: Anti‐cholinesterase, anti‐α‐glucosidase, DNA nuclease, antioxidant activities, and in silico studies. Applied Organometallic Chemistry, (2022) e6696.
  • [30] M. S. Çelik, Ş. A. Çetinus, A. F. Yenidünya, S. Çetinkaya, B. Tüzün, Biosorption of Rhodamine B dye from aqueous solution by Rhus coriaria L. plant: Equilibrium, kinetic, thermodynamic and DFT calculations. Journal of Molecular Structure, 1272 (2023) 134158.

Year 2023, Volume: 7 Issue: 3, 42 - 56, 03.09.2023

Handan Saraç Ahmet Demirbaş Burak Tüzün

https://doi.org/10.33435/tcandtc.1198612

Abstract

Supporting Institution

sivas cumhuriyet üniversity

Project Number

RGD-020

References

  • [1] M. Boozari, H. Hosseinzadeh, Natural products for COVID‐19 prevention and treatment regarding to previous coronavirus infections and novel studies. Phytotherapy Research, 35(2) (2021) 864-876.
  • [2] N. Gangal, V. Nagle, Y. Pawar, S. Dasgupta, Reconsidering traditional medicinal plants to combat COVID-19. AIJR Preprints, 34 (2020) 1-6.
  • [3] J.N.M. Kanyinda, Coronavirus (COVID-19): a protocol for prevention and treatment (Covalyse®). European Journal of Medical and Health Sciences, (2020) 2(3).
  • [4] M. Mesri, S.S.E. Saber, M. Godazi, A.R. Shirdel, R. Montazer, H.R., Koohestani, ... & N. Azizi, The effects of combination of Zingiber officinale and Echinacea on alleviation of clinical symptoms and hospitalization rate of suspected COVID-19 outpatients: a randomized controlled trial. Journal of Complementary and Integrative Medicine, 18(4) (2021) 775-781.
  • [5] D. S. N. B. K. Prasanth, M. Murahari, V. Chandramohan, G. Bhavya, A. Lakshmana Rao, S.P. Panda, ... T. Jaswitha, In-silico strategies of some selected phytoconstituents from Melissa officinalis as SARS CoV-2 main protease and spike protein (COVID-19) inhibitors. Molecular Simulation, 47(6) (2021) 457-470.
  • [6] S. Banerjee, H.I. Mullick, J. Banerjee, A. Ghosh, Zingiber officinale:‘a natural gold’. Int J Pharmaceutical Bio-Sci, 2 (2011) 283-94.
  • [7] K. Ghafoor, F. Al Juhaimi, M.M. Özcan, N. Uslu, E.E. Babiker, I.A.M. Ahmed, Total phenolics, total carotenoids, individual phenolics and antioxidant activity of ginger (Zingiber officinale) rhizome as affected by drying methods. Lwt, 126 (2020) 109354.
  • [8] A. M. A. Ali, M. E. M. El-Nour, S. M. Yagi, Total phenolic and flavonoid contents and antioxidant activity of ginger (Zingiber officinale Rosc.) rhizome, callus and callus treated with some elicitors. Journal of genetic engineering and biotechnology, 16(2) (2018) 677-682.
  • [9] Q. Q. Mao, X. Y. Xu, S. Y. Cao, R. Y. Gan, H. Corke, T. Beta, H. B. Li, Bioactive compounds and bioactivities of ginger (Zingiber officinale Roscoe). Foods, 8(6) (2019) 185.
  • [10] M. H. Shahrajabian, W. Sun, Q. Cheng, Clinical aspects and health benefits of ginger (Zingiber officinale) in both traditional Chinese medicine and modern industry. Acta agriculturae scandinavica, section b—Soil & Plant Science, 69(6) (2019) 546-556.
  • [11] A. P. Shirin, P. Jamuna, Chemical composition and antioxidant properties of ginger root (Zingiber officinale). Journal of Medicinal Plants Research, 4(24) (2010) 2674-2679.
  • [12] M. Haridas, V. Sasidhar, P. Nath, J. Abhithaj, A. Sabu, P. Rammanohar, Compounds of Citrus medica and Zingiber officinale for COVID-19 inhibition: in silico evidence for cues from Ayurveda. Future journal of pharmaceutical sciences, 7(1) (2021) 1-9.
  • [13] I. Kravchenko, L. Eberle, M. Nesterkina, A. Kobernik, Anti-inflammatory and analgesic activity of ointment based on dense ginger extract (Zingiber officinale). Journal of Herbmed Pharmacology, 8(2) (2019) 126-132.
  • [14] A. Poustforoosh, H. Hashemipour, B. Tüzün, M. Azadpour, S. Faramarz, A. Pardakhty, ... & M.H. Nematollahi, The Impact of D614G Mutation of SARS-COV-2 on the Efficacy of Anti-viral Drugs: A Comparative Molecular Docking and Molecular Dynamics Study. Current microbiology, 79(8) (2022) 1-12.
  • [15] B. Tüzün, K. Sayin, H. Ataseven, Could Momordica Charantia Be Effective In The Treatment of COVID19?. Cumhuriyet Science Journal, 43(2) (2022) 211-220.
  • [16] H. Karataş, B. Tüzün, Z. Kökbudak, Could pyrimidine derivative be effective against Omicron of SARS-CoV-2?. Bratislava Medical Journal-Bratislavske Lekarske Listy, 123(7) (2022) 505-513.
  • [17] A. Aktaş, B. Tüzün, R. Aslan, K. Sayin, H. Ataseven, New anti-viral drugs for the treatment of COVID-19 instead of favipiravir. Journal of Biomolecular Structure and Dynamics, 39(18) (2021) 7263-7273.
  • [18] D. Ni, K. Lau, P. Turelli, C. Raclot, B. Beckert, S. Nazarov, ... & D. Trono, Structural analysis of the Spike of the Omicron SARS-COV-2 variant by cryo-EM and implications for immune evasion. bioRxiv (2021).
  • [19] Q. Geng, K. Shi, G. Ye, W. Zhang, H. Aihara, F. Li, Structural Basis for Human Receptor Recognition by SARS-CoV-2 Omicron Variant BA. 1. Journal of Virology, 96(8) (2022) e00249-22.
  • [20] W. Yin, Y. Xu, P. Xu, X. Cao, C. Wu, C. Gu, ... & H. E. Xu, Structures of the Omicron Spike trimer with ACE2 and an anti-Omicron antibody. Science, 375(6584) (2022) 1048-1053.
  • [21] Schrödinger Release 2021-3: Maestro, Schrödinger, LLC, New York, NY, 2021.
  • [22] Schrödinger Release 2019-4: Protein Preparation Wizard; Epik, Schrödinger, LLC, New York, NY, 2016; Impact, Schrödinger, LLC, New York, NY, 2016; Prime, Schrödinger, LLC, New York, NY, 2019.
  • [23] Schrödinger Release 2021-3: LigPrep, Schrödinger, LLC, New York, NY, 2021.
  • [24] A. Poustforoosh, H. Hashemipour, B. Tüzün, A. Pardakhty, M. Mehrabani, & M. H. Nematollahi, Evaluation of potential anti-RNA-dependent RNA polymerase (RdRP) drugs against the newly emerged model of COVID-19 RdRP using computational methods. Biophysical chemistry, 272 (2021) 106564.
  • [25] Schrödinger Release 2021-3: QikProp, Schrödinger, LLC, New York, NY, 2021.
  • [26] H. Kekeçmuhammed, M. Tapera, B. Tüzün, S. Akkoç, Y. Zorlu, E. Sarıpınar, Synthesis, Molecular Docking and Antiproliferative Activity Studies of a Thiazole‐Based Compound Linked to Hydrazone Moiety. ChemistrySelect, 7(26) (2022) e202201502.
  • [27] M. Tapera, H. Kekeçmuhammed, B. Tüzün, E. Sarıpınar, Ü. M. Koçyiğit, E. Yıldırım, ... & Y. Zorlu, Synthesis, carbonic anhydrase inhibitory activity, anticancer activity and molecular docking studies of new imidazolyl hydrazone derivatives. Journal of Molecular Structure, 1269 (2022) 133816.
  • [28] A. Mermer, M. V. Bulbul, S. M. Kalender, I. Keskin, B. Tuzun, O. E. Eyupoglu, Benzotriazole-oxadiazole hybrid Compounds: Synthesis, anticancer Activity, molecular docking and ADME profiling studies. Journal of Molecular Liquids, 359 (2022) 119264.
  • [29] H. Yalazan, B. Tüzün, D. Akkaya, B. Barut, H. Kantekin, S. Yıldırmış, Quinoline‐fused both non‐peripheral and peripheral ZnII and MgII phthalocyanines: Anti‐cholinesterase, anti‐α‐glucosidase, DNA nuclease, antioxidant activities, and in silico studies. Applied Organometallic Chemistry, (2022) e6696.
  • [30] M. S. Çelik, Ş. A. Çetinus, A. F. Yenidünya, S. Çetinkaya, B. Tüzün, Biosorption of Rhodamine B dye from aqueous solution by Rhus coriaria L. plant: Equilibrium, kinetic, thermodynamic and DFT calculations. Journal of Molecular Structure, 1272 (2023) 134158.
There are 30 citations in total.

Details

Primary Language English
Subjects Chemical Engineering
Journal Section Research Article
Authors

Handan Saraç 0000-0001-7481-7978

Ahmet Demirbaş 0000-0003-2523-7322

Burak Tüzün 0000-0002-0420-2043

Project Number RGD-020
Early Pub Date May 26, 2023
Publication Date September 3, 2023
Submission Date November 2, 2022
Published in Issue Year 2023 Volume: 7 Issue: 3

Cite

APA Saraç, H., Demirbaş, A., & Tüzün, B. (2023). Could Zingiber officinale plant be effective against Omicron BA.2.75 of SARS-CoV-2?. Turkish Computational and Theoretical Chemistry, 7(3), 42-56. https://doi.org/10.33435/tcandtc.1198612
AMA Saraç H, Demirbaş A, Tüzün B. Could Zingiber officinale plant be effective against Omicron BA.2.75 of SARS-CoV-2?. Turkish Comp Theo Chem (TC&TC). September 2023;7(3):42-56. doi:10.33435/tcandtc.1198612
Chicago Saraç, Handan, Ahmet Demirbaş, and Burak Tüzün. “Could Zingiber Officinale Plant Be Effective Against Omicron BA.2.75 of SARS-CoV-2?”. Turkish Computational and Theoretical Chemistry 7, no. 3 (September 2023): 42-56. https://doi.org/10.33435/tcandtc.1198612.
EndNote Saraç H, Demirbaş A, Tüzün B (September 1, 2023) Could Zingiber officinale plant be effective against Omicron BA.2.75 of SARS-CoV-2?. Turkish Computational and Theoretical Chemistry 7 3 42–56.
IEEE H. Saraç, A. Demirbaş, and B. Tüzün, “Could Zingiber officinale plant be effective against Omicron BA.2.75 of SARS-CoV-2?”, Turkish Comp Theo Chem (TC&TC), vol. 7, no. 3, pp. 42–56, 2023, doi: 10.33435/tcandtc.1198612.
ISNAD Saraç, Handan et al. “Could Zingiber Officinale Plant Be Effective Against Omicron BA.2.75 of SARS-CoV-2?”. Turkish Computational and Theoretical Chemistry 7/3 (September 2023), 42-56. https://doi.org/10.33435/tcandtc.1198612.
JAMA Saraç H, Demirbaş A, Tüzün B. Could Zingiber officinale plant be effective against Omicron BA.2.75 of SARS-CoV-2?. Turkish Comp Theo Chem (TC&TC). 2023;7:42–56.
MLA Saraç, Handan et al. “Could Zingiber Officinale Plant Be Effective Against Omicron BA.2.75 of SARS-CoV-2?”. Turkish Computational and Theoretical Chemistry, vol. 7, no. 3, 2023, pp. 42-56, doi:10.33435/tcandtc.1198612.
Vancouver Saraç H, Demirbaş A, Tüzün B. Could Zingiber officinale plant be effective against Omicron BA.2.75 of SARS-CoV-2?. Turkish Comp Theo Chem (TC&TC). 2023;7(3):42-56.

Journal Full Title: Turkish Computational and Theoretical Chemistry


Journal Abbreviated Title: Turkish Comp Theo Chem (TC&TC)