Araştırma Makalesi
BibTex RIS Kaynak Göster

Kurkuminin SARS-CoV-2 Üzerindeki Antiviral Etkileri Üzerine Moleküler Kenetlenme Analizi

Yıl 2022, Cilt: 5 Sayı: 2, 223 - 228, 31.12.2022
https://doi.org/10.55117/bufbd.1138678

Öz

Kurkumin (C21H20O6) molekülünün yapısal tercihleri Spartan06 programı kullanılarak MMFF yöntemi ile analiz edilmiş ve en kararlı geometri belirlenmiştir. Kurkuminin SARS-CoV-2 üzerindeki etkilerini değerlendirmek için, SARS-CoV-2 ana proteaz enziminin (Mpro) apo/holo formları ve spike glikoprotein ile moleküler kenetlenme çalışmaları yapılmıştır. SARS-CoV-2 proteinlerini hedefleyen kurkuminin bağlanma afiniteleri ve bağlanma modları belirlenmiştir. Kurkuminin ana proteaz enziminin (Mpro) apo ve holo formlarına ve spike glikoproteine bağlanma afiniteleri sırasıyla -7.3, -5.7 ve -7.6 kcal/mol olarak bulunmuştur. Sonuçlar, kurkuminin COVID-19 tedavisi için potansiyel bir terapötik ajan olabileceğini göstermiştir.

Teşekkür

Yayınladığınız makalemizde, ilgi ve alakanız için teşekkür ederim. Yeni makalemizi size göndermek istedik.

Kaynakça

  • [1] H. Gopinath and K. Karthikeyan, “Turmeric: A condiment, cosmetic and cure,” Indian Journal of Dermatology, Venereology and Leprology, vol. 84, no. 1, pp. 16, 2018.
  • [2] S. Hewlings and D. Kalman, “Curcumin: A Review of Its’ Effects on Human Health,” Foods, vol. 6, no. 10, pp. 92, 2017.
  • [3] J. Tabeshpour, M. Hashemzaei, and A. Sahebkar, “The regulatory role of curcumin on platelet functions,” Journal of Cellular Biochemistry, vol. 119, no. 11, pp. 8713–8722, 2018.
  • [4] A. Ali and A. C. Banerjea, “Curcumin inhibits HIV-1 by promoting Tat protein degradation,” Scientific Reports, vol. 6, no. 1, 2016.
  • [5] N. Zhang, H. Li, J. Jia, and M. He, “Anti-inflammatory effect of curcumin on mast cell-mediated allergic responses in ovalbumin-induced allergic rhinitis mouse,” Cellular Immunology, vol. 298, no. 1–2, pp. 88– 95, 2015.
  • [6] M. S. Karimian, M. Pirro, M. Majeed, and A. Sahebkar, “Curcumin as a natural regulator of monocyte chemoattractant protein-1,” Cytokine & Growth Factor Reviews, vol. 33, pp. 55–63, 2017.
  • [7] F. Zahedipour et al., “Potential effects of curcumin in the treatment of COVID ‐19 infection,” Phytotherapy Research, 2020.
  • [8] H. Noor, A. Ikram, T. Rathinavel, S. Kumarasamy, M. Nasir Iqbal, and Z. Bashir, “Immunomodulatory and anti-cytokine therapeutic potential of curcumin and its derivatives for treating COVID-19 – a computational modeling,” Journal of Biomolecular Structure and Dynamics, pp. 1–16, 2021.
  • [9] R. Jäger, R. P. Lowery, A. V. Calvanese, J. M. Joy, M. Purpura, and J. M. Wilson, “Comparative absorptionof curcumin formulations,” Nutrition Journal, vol. 13, no. 1, 2014.
  • [10] L. Sun et al., “Coronavirus Papain-like Proteases Negatively Regulate Antiviral Innate Immune Response through Disruption of STING-Mediated Signaling,” PLoS ONE, vol. 7, no. 2, pp. e30802, 2012.
  • [11] J. W. Schoggins and C. M. Rice, “Interferon-stimulated genes and their antiviral effector functions,” Current Opinion in Virology, vol. 1, no. 6, pp. 519–525, 2011.
  • [12] D. Ting et al., “Multisite Inhibitors for Enteric Coronavirus: Antiviral Cationic Carbon Dots Based on Curcumin,” ACS Applied Nano Materials, vol. 1, no. 10, pp. 5451–5459, 2018.
  • [13] Y. Imai et al., “Identification of Oxidative Stress and Toll-like Receptor 4 Signaling as a Key Pathway of Acute Lung Injury,” Cell, vol. 133, no. 2, pp. 235–249, 2008.
  • [14] S. Rong et al., “Curcumin prevents chronic alcohol-induced liver disease involving decreasing ROS generation and enhancing antioxidative capacity,” Phytomedicine, vol. 19, no. 6, pp. 545–550, 2012.
  • [15] M. Head-Gordon and et al. et al., “Advances in Methods and Algorithms in a Modern Quantum Chemistry Program Package,” ChemInform, vol. 37, no. 39, 2006.
  • [16] T. A. Halgren, “Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94,” Journal of Computational Chemistry, vol. 17, no. 5–6, pp. 553–586, 1996.
  • [17] A. Jurcik et al., “CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories,” Bioinformatics, vol. 34, no. 20, pp. 3586–3588, 2018.
  • [18] O. Trott and A. J. Olson, “AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading,” Journal of Computational Chemistry, vol. 31, no. 2, 2009.
  • [19] B. Zhang, Y. Zhao, Z. Jin, X. Liu, H. Yang, and Z. Rao, “The crystal structure of COVID-19 main protease in apo form,” 2020.
  • [20] V. Nath, A. Rohini, and V. Kumar, “Identification of Mpro inhibitors of SARS-CoV-2 using structure based computational drug repurposing,” Biocatalysis and Agricultural Biotechnology, vol. 37, pp. 102178, 2021.
  • [21] A. C. Walls, Y.-J. Park, M. A. Tortorici, A. Wall, A. T. McGuire, and D. Veesler, “Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein,” Cell, vol. 183, no. 6, pp. 1735, 2020.

Molecular Docking Analysis on the Antiviral Effects of Curcumin on SARS-CoV-2

Yıl 2022, Cilt: 5 Sayı: 2, 223 - 228, 31.12.2022
https://doi.org/10.55117/bufbd.1138678

Öz

The structural preferences of curcumin (C21H20O6) molecule were analyzed by
MMFF method using Spartan06 program and the most stable geometry was
determined. To evaluate the effects of curcumin on SARS-CoV-2, the molecular
docking studies have been done on the spike glycoprotein and the apo/holo forms of
the SARS-CoV-2 major protease enzyme (Mpro). The binding affinities and binding
modes of curcumin targeted to the SARS-CoV-2 proteins were determined. It was
discovered that curcumin had binding affinities of -7.3, -5.7, and -7.6 kcal/mol to the
apo and holo forms of the major protease enzyme (Mpro) and spike glycoprotein,
respectively. The findings suggested that curcumin could be a useful therapeutic
agent for COVID-19 treatment.

Kaynakça

  • [1] H. Gopinath and K. Karthikeyan, “Turmeric: A condiment, cosmetic and cure,” Indian Journal of Dermatology, Venereology and Leprology, vol. 84, no. 1, pp. 16, 2018.
  • [2] S. Hewlings and D. Kalman, “Curcumin: A Review of Its’ Effects on Human Health,” Foods, vol. 6, no. 10, pp. 92, 2017.
  • [3] J. Tabeshpour, M. Hashemzaei, and A. Sahebkar, “The regulatory role of curcumin on platelet functions,” Journal of Cellular Biochemistry, vol. 119, no. 11, pp. 8713–8722, 2018.
  • [4] A. Ali and A. C. Banerjea, “Curcumin inhibits HIV-1 by promoting Tat protein degradation,” Scientific Reports, vol. 6, no. 1, 2016.
  • [5] N. Zhang, H. Li, J. Jia, and M. He, “Anti-inflammatory effect of curcumin on mast cell-mediated allergic responses in ovalbumin-induced allergic rhinitis mouse,” Cellular Immunology, vol. 298, no. 1–2, pp. 88– 95, 2015.
  • [6] M. S. Karimian, M. Pirro, M. Majeed, and A. Sahebkar, “Curcumin as a natural regulator of monocyte chemoattractant protein-1,” Cytokine & Growth Factor Reviews, vol. 33, pp. 55–63, 2017.
  • [7] F. Zahedipour et al., “Potential effects of curcumin in the treatment of COVID ‐19 infection,” Phytotherapy Research, 2020.
  • [8] H. Noor, A. Ikram, T. Rathinavel, S. Kumarasamy, M. Nasir Iqbal, and Z. Bashir, “Immunomodulatory and anti-cytokine therapeutic potential of curcumin and its derivatives for treating COVID-19 – a computational modeling,” Journal of Biomolecular Structure and Dynamics, pp. 1–16, 2021.
  • [9] R. Jäger, R. P. Lowery, A. V. Calvanese, J. M. Joy, M. Purpura, and J. M. Wilson, “Comparative absorptionof curcumin formulations,” Nutrition Journal, vol. 13, no. 1, 2014.
  • [10] L. Sun et al., “Coronavirus Papain-like Proteases Negatively Regulate Antiviral Innate Immune Response through Disruption of STING-Mediated Signaling,” PLoS ONE, vol. 7, no. 2, pp. e30802, 2012.
  • [11] J. W. Schoggins and C. M. Rice, “Interferon-stimulated genes and their antiviral effector functions,” Current Opinion in Virology, vol. 1, no. 6, pp. 519–525, 2011.
  • [12] D. Ting et al., “Multisite Inhibitors for Enteric Coronavirus: Antiviral Cationic Carbon Dots Based on Curcumin,” ACS Applied Nano Materials, vol. 1, no. 10, pp. 5451–5459, 2018.
  • [13] Y. Imai et al., “Identification of Oxidative Stress and Toll-like Receptor 4 Signaling as a Key Pathway of Acute Lung Injury,” Cell, vol. 133, no. 2, pp. 235–249, 2008.
  • [14] S. Rong et al., “Curcumin prevents chronic alcohol-induced liver disease involving decreasing ROS generation and enhancing antioxidative capacity,” Phytomedicine, vol. 19, no. 6, pp. 545–550, 2012.
  • [15] M. Head-Gordon and et al. et al., “Advances in Methods and Algorithms in a Modern Quantum Chemistry Program Package,” ChemInform, vol. 37, no. 39, 2006.
  • [16] T. A. Halgren, “Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94,” Journal of Computational Chemistry, vol. 17, no. 5–6, pp. 553–586, 1996.
  • [17] A. Jurcik et al., “CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories,” Bioinformatics, vol. 34, no. 20, pp. 3586–3588, 2018.
  • [18] O. Trott and A. J. Olson, “AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading,” Journal of Computational Chemistry, vol. 31, no. 2, 2009.
  • [19] B. Zhang, Y. Zhao, Z. Jin, X. Liu, H. Yang, and Z. Rao, “The crystal structure of COVID-19 main protease in apo form,” 2020.
  • [20] V. Nath, A. Rohini, and V. Kumar, “Identification of Mpro inhibitors of SARS-CoV-2 using structure based computational drug repurposing,” Biocatalysis and Agricultural Biotechnology, vol. 37, pp. 102178, 2021.
  • [21] A. C. Walls, Y.-J. Park, M. A. Tortorici, A. Wall, A. T. McGuire, and D. Veesler, “Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein,” Cell, vol. 183, no. 6, pp. 1735, 2020.
Toplam 21 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Metroloji,Uygulamalı ve Endüstriyel Fizik
Bölüm Araştırma Makaleleri
Yazarlar

A. Demet Demirag 0000-0002-9609-9150

Sefa Çelik 0000-0001-6216-1297

Ayşen Özel 0000-0002-8680-8830

Sevim Akyüz 0000-0003-3313-6927

Erken Görünüm Tarihi 28 Aralık 2022
Yayımlanma Tarihi 31 Aralık 2022
Yayımlandığı Sayı Yıl 2022 Cilt: 5 Sayı: 2

Kaynak Göster

APA Demirag, A. D., Çelik, S., Özel, A., Akyüz, S. (2022). Molecular Docking Analysis on the Antiviral Effects of Curcumin on SARS-CoV-2. Bayburt Üniversitesi Fen Bilimleri Dergisi, 5(2), 223-228. https://doi.org/10.55117/bufbd.1138678
AMA Demirag AD, Çelik S, Özel A, Akyüz S. Molecular Docking Analysis on the Antiviral Effects of Curcumin on SARS-CoV-2. Bayburt Üniversitesi Fen Bilimleri Dergisi. Aralık 2022;5(2):223-228. doi:10.55117/bufbd.1138678
Chicago Demirag, A. Demet, Sefa Çelik, Ayşen Özel, ve Sevim Akyüz. “Molecular Docking Analysis on the Antiviral Effects of Curcumin on SARS-CoV-2”. Bayburt Üniversitesi Fen Bilimleri Dergisi 5, sy. 2 (Aralık 2022): 223-28. https://doi.org/10.55117/bufbd.1138678.
EndNote Demirag AD, Çelik S, Özel A, Akyüz S (01 Aralık 2022) Molecular Docking Analysis on the Antiviral Effects of Curcumin on SARS-CoV-2. Bayburt Üniversitesi Fen Bilimleri Dergisi 5 2 223–228.
IEEE A. D. Demirag, S. Çelik, A. Özel, ve S. Akyüz, “Molecular Docking Analysis on the Antiviral Effects of Curcumin on SARS-CoV-2”, Bayburt Üniversitesi Fen Bilimleri Dergisi, c. 5, sy. 2, ss. 223–228, 2022, doi: 10.55117/bufbd.1138678.
ISNAD Demirag, A. Demet vd. “Molecular Docking Analysis on the Antiviral Effects of Curcumin on SARS-CoV-2”. Bayburt Üniversitesi Fen Bilimleri Dergisi 5/2 (Aralık 2022), 223-228. https://doi.org/10.55117/bufbd.1138678.
JAMA Demirag AD, Çelik S, Özel A, Akyüz S. Molecular Docking Analysis on the Antiviral Effects of Curcumin on SARS-CoV-2. Bayburt Üniversitesi Fen Bilimleri Dergisi. 2022;5:223–228.
MLA Demirag, A. Demet vd. “Molecular Docking Analysis on the Antiviral Effects of Curcumin on SARS-CoV-2”. Bayburt Üniversitesi Fen Bilimleri Dergisi, c. 5, sy. 2, 2022, ss. 223-8, doi:10.55117/bufbd.1138678.
Vancouver Demirag AD, Çelik S, Özel A, Akyüz S. Molecular Docking Analysis on the Antiviral Effects of Curcumin on SARS-CoV-2. Bayburt Üniversitesi Fen Bilimleri Dergisi. 2022;5(2):223-8.

Taranılan Dizinler