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

Yıl 2023, Cilt: 7 Sayı: 3, 42 - 56, 03.09.2023

Handan Saraç Ahmet Demirbaş Burak Tüzün

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

Öz

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.

Anahtar Kelimeler

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

Proje Numarası

RGD-020

Kaynakça

  • [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.

Yıl 2023, Cilt: 7 Sayı: 3, 42 - 56, 03.09.2023

Handan Saraç Ahmet Demirbaş Burak Tüzün

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

Öz

Destekleyen Kurum

sivas cumhuriyet üniversity

Proje Numarası

RGD-020

Kaynakça

  • [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.
Toplam 30 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Kimya Mühendisliği
Bölüm Research Article
Yazarlar

Handan Saraç 0000-0001-7481-7978

Ahmet Demirbaş 0000-0003-2523-7322

Burak Tüzün 0000-0002-0420-2043

Proje Numarası RGD-020
Erken Görünüm Tarihi 26 Mayıs 2023
Yayımlanma Tarihi 3 Eylül 2023
Gönderilme Tarihi 2 Kasım 2022
Yayımlandığı Sayı Yıl 2023 Cilt: 7 Sayı: 3

Kaynak Göster

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). Eylül 2023;7(3):42-56. doi:10.33435/tcandtc.1198612
Chicago Saraç, Handan, Ahmet Demirbaş, ve Burak Tüzün. “Could Zingiber Officinale Plant Be Effective Against Omicron BA.2.75 of SARS-CoV-2?”. Turkish Computational and Theoretical Chemistry 7, sy. 3 (Eylül 2023): 42-56. https://doi.org/10.33435/tcandtc.1198612.
EndNote Saraç H, Demirbaş A, Tüzün B (01 Eylül 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, ve B. Tüzün, “Could Zingiber officinale plant be effective against Omicron BA.2.75 of SARS-CoV-2?”, Turkish Comp Theo Chem (TC&TC), c. 7, sy. 3, ss. 42–56, 2023, doi: 10.33435/tcandtc.1198612.
ISNAD Saraç, Handan vd. “Could Zingiber Officinale Plant Be Effective Against Omicron BA.2.75 of SARS-CoV-2?”. Turkish Computational and Theoretical Chemistry 7/3 (Eylül 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 vd. “Could Zingiber Officinale Plant Be Effective Against Omicron BA.2.75 of SARS-CoV-2?”. Turkish Computational and Theoretical Chemistry, c. 7, sy. 3, 2023, ss. 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)