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Cistus incanus’un Bazı Biyoaktif Moleküllerinin SARS CoV-2 ye Karşı Moleküler Doking Analizi

Yıl 2021, Cilt: 11 Sayı: 2, 522 - 532, 15.12.2021
https://doi.org/10.31466/kfbd.939421

Öz

Koronavirüs hastalığı, halen yaşanmakta olan pandemik süreçle bütün dünyayı etkilemektedir. Hastalık ile mücadele tüm dünyada, aşılama çalışmaları ile devam etmektedir. Koruyuculuk süresi ve aşıya ulaşmadaki zorluklar düşünüldüğünde, hastalık ile mücadelede başarılı olunabilmesi için, virüsün öldürülmesi ya da replikayonunun engellenmesini sağlayan ilaçlara ihtiyaç vardır. İlaç çalışmalarında fitokimyasalların virüs üzerine etkisinin incelenmesinin ardından, daha etkili moleküllerin sentezlenebilmesi için izole moleküllerin modifiye edilmesi yöntemi uygulanır. İzole edilen her bir molekülün anti-viral aktivitesinin in-vitro yöntemlerle analizi mümkün değildir ve bu sorunun üstesinden gelmek için in-silico yöntemler yardımcı olabilir. Cistus incanus daha önce pek çok virüsün denemeleri yapılarak anti-viral aktivitesi teyit edilmiş bir bitkidir. Bu çalışmada içerik analizi sonrasında Cistus incanus’da tespit edilen myricetin 3-O-hexoside, myricitrin, quercitrin ve kaempferol 3-O-rutinocide moleküllerinin papain-like protease and main protease ile etkileşimi moleküler doking yöntemleri ile analiz edilmiştir. Analizlerin sonucunda incelenen moleküller ile papain-like protease ve main protease arasında güçlü H-bağları tespit edilmiştir.

Kaynakça

  • Adhikari, B., Marasini, B. P., Rayamajhee, B., Bhattarai, B. J., Lamichhane, G., Khadayat, K., Adhikari, A., Khanal, S., and Parajuli,N. (2020). Potential roles of medicinal plants for the treatment of viral diseases focusing on COVID-19: A review. Phytotherapy Research, 35, 1298–1312.
  • Alfaro, M., Alfaro, I., & Angel, C. (2020). Identification of potential inhibitors of SARS-CoV-2 papain-like proteasefrom tropane alkaloids from Schizanthus porrigens: A moleculardocking study. Chemical Physics Letters, 761, 138068.Tallei, T. E., Tumilaar, S. G., Niode, N. J., Fatimawali, Kepel, B. J., Idroes, R., Effendi, Y., Sakib, S. A., Emran, T. B. (2020). Potential of plant bioactive compounds as SARS-CoV-2 main protease (Mpro) and spike (S) glycoprotein inhibitors: A molecular docking study". Scientifica, Article ID 6307457.
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  • Banerjee, A., Santra, D., & Maiti,S. (2020). Energetics and IC50 based epitope screening in SARS CoV-2 (COVID 19) spike protein by immune informatic analysis implicating for a suitable vaccine development. Journal of Translational Medicine, 18, 281.
  • Banerjee, R., Perera, L., and Tillekeratne, L. M. V. (2021). Potential SARS-CoV-2 main protease inhibitors. Drug Discovery Today, 26(3).
  • Barrajón-Catalán, E., Fernández-Arroyo, S., Saura, D., Guillén, E., Fernández- Gutiérrez, A., Segura-Carretero, A. (2010). Cistaceae aqueous extracts containing ellagitannins show antioxidant and antimicrobial capacity, and cyto- toxic activity against human cancer cells. Food Chemistry and Toxicology, 48. 2273–2282. doi: 10.1016/j.fct.2010.05.060.
  • Barros, L., Dueñas, M., Alves, C. T., Silva, S., Henriques, M., Santos-Buelga, C. (2013). Antifungal activity and detailed chemical characterization of Cistus ladanifer phenolic extracts. Industrial Crops and Products, 41. 41–45. doi: 10.1016/j.indcrop.2012.03.038.
  • Behl, T., Rocchetti, G., Chadha, S., Zengin, G., Bungau, S., Kumar, A., Mehta, V., Uddin, S., Khullar, G., Setia, D., Arora, S., Sinan, K. I., Ak, G., Putnik, P., Gallo,M., and Montesano, D. (2021). Phytochemicals from plant foods as potential source ofantiviral agents: an overview. Pharmaceuticals, 14, 381.
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  • Chebaibi, M., Bousta, D., Gonçalves, R. F. B., Hoummani, H., & Achour, S. (2021). Medicinal Plants Against Coronavirus (SARS-COV-2) in Morocco Via Computational Virtual Screening Approach, Research Square, DOI: https://doi.org/10.21203/rs.3.rs-679827/v1
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  • Chhetri, A., Chettri, S., Rai, P., Mishra, D. K., Sinha, B., & Brahman, D. (2021). Synthesis, characterization and computational study on potential inhibitory action of novel azo imidazole derivatives against COVID-19 main protease (Mpro: 6LU7). Journal of molecular structure, 1225, 129230.
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  • Dimas, K., Demetzos, C., Marsellos, M., Sotiriadou, R., Malamas, M., and Kokkinopoulos, D. (1998). Cytotoxic activity of labdane type diterpenes against human leukemic cell lines in vitro. Planta Medica, 64. 208–211. doi:10.1055/s- 2006-957410
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Molecular Docking Analysis of Some Bioactive Molecules of Cistus incanus Against SARS CoV-2

Yıl 2021, Cilt: 11 Sayı: 2, 522 - 532, 15.12.2021
https://doi.org/10.31466/kfbd.939421

Öz

Coronavirus disease affects all the world with the pandemic way that we are still living. The fight against the disease continues with vaccination all over the world. Considering the protection time and the difficulties in attaining the vaccine, in order to be successful in fighting against the disease, we need drugs that enable to kill or hinder replication of the viruses. In drug studies, after analyzing the effect of phytochemicals on the viruses, isolated phytochemical is modified in order to synthesize a more effective molecule. It is not possible to analyze the anti-viral activity of each isolated molecule by in-vitro methods, and in-silico methods can help to overcome this problem. Cistus incanus is a plant whose anti-viral activity has been confirmed by previous trials on many viruses. In this study, the interaction of myricetin 3-O-hexoside, myricitrin, quercitrin and kaempferol 3-O-rutinocide which were detected in the Cistus incanus, were analyzed by molecular docking methods with papain-like protease and main protease crystal. Strong H-bonds were detected between the investigated molecules and papain-like protease and main protease.

Kaynakça

  • Adhikari, B., Marasini, B. P., Rayamajhee, B., Bhattarai, B. J., Lamichhane, G., Khadayat, K., Adhikari, A., Khanal, S., and Parajuli,N. (2020). Potential roles of medicinal plants for the treatment of viral diseases focusing on COVID-19: A review. Phytotherapy Research, 35, 1298–1312.
  • Alfaro, M., Alfaro, I., & Angel, C. (2020). Identification of potential inhibitors of SARS-CoV-2 papain-like proteasefrom tropane alkaloids from Schizanthus porrigens: A moleculardocking study. Chemical Physics Letters, 761, 138068.Tallei, T. E., Tumilaar, S. G., Niode, N. J., Fatimawali, Kepel, B. J., Idroes, R., Effendi, Y., Sakib, S. A., Emran, T. B. (2020). Potential of plant bioactive compounds as SARS-CoV-2 main protease (Mpro) and spike (S) glycoprotein inhibitors: A molecular docking study". Scientifica, Article ID 6307457.
  • Ali, A. M., and Kunugi, H. (2021). Propolis, bee honey, and their components protect against coronavirus disease 2019 (COVID-19): A Review of in silico, in vitro, and clinical studies”, Molecules, 26, 1232.
  • Antonio, A. S., Wiedemann, L. S. M., and Veiga-Junior, V. F. (2020). Natural products' role against COVID-19. RSC Advances, 10, 23379.
  • Attaguile, G., Russo, A., Campisi, A., Savoca, F., Acquaviva, R., Ragusa, N, and Vanella, A. (2000). Antioxidant activity and protective effect on DNA cleavage of extracts from Cistus incanus L. and Cistus monspeliensis L. Cell Biology and Toxicology, 16, 83 - 90.
  • Banerjee, A., Santra, D., & Maiti,S. (2020). Energetics and IC50 based epitope screening in SARS CoV-2 (COVID 19) spike protein by immune informatic analysis implicating for a suitable vaccine development. Journal of Translational Medicine, 18, 281.
  • Banerjee, R., Perera, L., and Tillekeratne, L. M. V. (2021). Potential SARS-CoV-2 main protease inhibitors. Drug Discovery Today, 26(3).
  • Barrajón-Catalán, E., Fernández-Arroyo, S., Saura, D., Guillén, E., Fernández- Gutiérrez, A., Segura-Carretero, A. (2010). Cistaceae aqueous extracts containing ellagitannins show antioxidant and antimicrobial capacity, and cyto- toxic activity against human cancer cells. Food Chemistry and Toxicology, 48. 2273–2282. doi: 10.1016/j.fct.2010.05.060.
  • Barros, L., Dueñas, M., Alves, C. T., Silva, S., Henriques, M., Santos-Buelga, C. (2013). Antifungal activity and detailed chemical characterization of Cistus ladanifer phenolic extracts. Industrial Crops and Products, 41. 41–45. doi: 10.1016/j.indcrop.2012.03.038.
  • Behl, T., Rocchetti, G., Chadha, S., Zengin, G., Bungau, S., Kumar, A., Mehta, V., Uddin, S., Khullar, G., Setia, D., Arora, S., Sinan, K. I., Ak, G., Putnik, P., Gallo,M., and Montesano, D. (2021). Phytochemicals from plant foods as potential source ofantiviral agents: an overview. Pharmaceuticals, 14, 381.
  • Bhushan, I., Sharmaa, M., Mehtaa, M., Badyala, S., Sharmab, V., Sharmab, I., Singha, S., Sistlac, H. (2020). Bioactive compounds and probiotics-a ray of hope in COVID-19 management. Food Science and Human Wellness, 10, 131-140.
  • Bouamama, H., Villard, J., Benharref, A., and Jana, M. (1999). Antibacterial and antifungal activities of Cistusincanus and C. monspeliensis leaf extracts. Thérapie 54, 731–733.
  • Capasso, C., Nocentini, A., & Supuran, C. T. (2021) Protease inhibitors targeting the main protease and papain-like protease of coronaviruses. Expert Opinion on Therapeutic Patents, 31(4), 309-324
  • Carbonell-Capella, J. M., Buniowska, M., Esteve, M.J. (2015). Effect of Stevia rebaudiana addition on bioaccessibility of bioactive compounds and antioxidant activity of beverages based on exotic fruits mixed with oat following simulated human digestion. Food Chemistry, 184, 122-130. https://doi.org/10.1016/j.foodchem.2015.03.095.
  • Chebaibi, M., Bousta, D., Gonçalves, R. F. B., Hoummani, H., & Achour, S. (2021). Medicinal Plants Against Coronavirus (SARS-COV-2) in Morocco Via Computational Virtual Screening Approach, Research Square, DOI: https://doi.org/10.21203/rs.3.rs-679827/v1
  • Chen, j., Gao, K., Wang, R., and Wei, G. W. (2021). Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies. Chemical Science, DOI: 10.1039/D1SC01203G (Edge Article)
  • Chhetri, A., Chettri, S., Rai, P., Mishra, D. K., Sinha, B., & Brahman, D. (2021). Synthesis, characterization and computational study on potential inhibitory action of novel azo imidazole derivatives against COVID-19 main protease (Mpro: 6LU7). Journal of molecular structure, 1225, 129230.
  • Chinou, F., Demefzos, C., Harvala, C., Roussakis, C., and Verbist, J. F. (1994). Cytotoxic and antibacterial labdane-type diterpenes from the aerial parts of Cistus incanus subsp. Creticus. Planta Medica, 60 (1), 34–36.
  • Contreras-Puentes, N., and Alvíz-Amador, A. (2020). Virtual screening of natural metabolites and antiviral drugswith potential inhibitory activity against 3CL-PRO and PL-PRO. Biomedical and Pharmacology Journal, 13(2), 933-941.
  • Dimas, K., Demetzos, C., Marsellos, M., Sotiriadou, R., Malamas, M., and Kokkinopoulos, D. (1998). Cytotoxic activity of labdane type diterpenes against human leukemic cell lines in vitro. Planta Medica, 64. 208–211. doi:10.1055/s- 2006-957410
  • Dimas, K., Papadaki, M., Tsimplouli, C., Hatziantoniou, S., Alevizopoulos, K., Pantazis, P. (2006). Labd-14-ene-8,13-diol (sclareol) induces cell cycle arrest and apoptosis in human breast cancer cells and enhances the activity of anti-cancer drugs. Biomedicine & Pharmacotherapy,60. 127–133. doi: 10.1016/j.biopha.2006.01.003
  • Dimcheva, V., and Karsheva, M. (2017). Antioxidant activity and polyphenolic content of the bulgarian wild herb Cistus incanus L. stored under different conditions. Journal of Chemical Technology and Metallurgy, 52 (5). 781-790.
  • Droebner, K., Ehrhardt, C., Poetter, A., Ludwig, S., and Planz, O. (2007). CYSTUS052, a polyphenol-rich plant extract, exerts anti-influenza virus activity in mice. Antiviral Research, 76. 1–10. doi:10.1016/j.antiviral.2007.04.001
  • Ehrhardt, C., Hrincius, E. R., Korte, V., Mazur, I., Droebner, K., Poetter, A. (2007). 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. 38–47. doi:10.1016/j.antiviral.2007.05.002
  • Freitas, B. T., Durie, I. A., Murray, J., Longo, J. E., Miller, H. C., Crich, D., Hogan,R. J., Tripp, R. A., and Pegan, S. D. (2020). Characterization and noncovalent inhibition of the deubiquitinase and deisgylase activity of sars-cov-2 papain-like protease. ACS Infectious Diseases, 6(8), 2099–2109.
  • Furukawa, N. W., Brooks, J. T., and Sobel, J. (2020). Evidence supporting transmission of severe acute respiratory syndrome coronavirus 2 while presymptomatic or asymptomatic. Emerging Infectious Diseases Journal, 26(7), e201595.
  • Gao, X., Qin, B., Chen, P., Zhu, K., Hou, P., Wojdyla, J. A., Wang, M., and Cui, S. (2021). Crystal structure of SARS-CoV-2 papain-like protease. Acta Pharmaceutica Sinica B, 11(1), 237-245.
  • Gori, A., Ferrini, F., Marzano, M. C., Tattini, M., Centritto, M., Baratto, M. C., Pogni R., and Brunetti, C. (2016). Characterisation and antioxidant activity of crude extract and polyphenolic rich fractions from C. incanus leaves. International Journal of Moleculer Science, 17, 1344.
  • Hannig, C., Spitzmüller, B., Al-Ahmand, A., Hannig, M. (2008). Effects of Cistus-tea on bacterial colonization and enzyme activities of the in-situ pellicle. Journal of Dentistry, 36. 540–545.
  • Hatziantoniou, S., Dimas, K., Georgopoulos, A., Sotiriadou, N., and Demetzos, C. (2006). Cytotoxic and anti-tumor activity of liposome-incorporated sclareol against cancer cell lines and human colon cancer xenografts. Pharmacoogical Research, 53. 80–87. doi:10.1016/j.phrs.2005.09.008
  • Holt, P. A., Chaire, J. B., and Trent, J. O. (2008). Molecular docking of intercalators and groove-binders to nucleic acids using autodock and surflex. Journal of Chemical Information and Modeling, 48(8), 1602–1615.
  • 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, X., Bai, F., Liu, H., Liu, X., Guddat, L. W., Xu, W., Xiao, G., Qin, C., Shi, Z., Jiang, H., Rao, Z., Yang, H. & Yang, H. (2020). Structure of M pro from SARS-CoV-2 and discovery of its inhibitors. Nature, 582(7811), 289-293.
  • Kalusa,U., Grigorova, A., Kadeckib, O., Jansenc, J. P., Kiesewettera, H., Radtkea, H. (2009). Cistus incanus (CYSTUS052) for treating patients with infection of the upper respiratory tract a prospective, randomized, placebo-controlled clinical study. Antiviral Research, 84. 267–271.
  • Kandeel, M., and Al-Nazawi, M. (2020). Virtual screening and repurposing of FDA approved drugs against COVID-19 main protease. Life Sciences Volume, 251, 117627.
  • Li, D., Luan, J., and Zhang, L. (2021). Molecular docking of potential SARS-CoV-2 papain-like proteaseinhibitors. Biochemical and Biophysical Research Communications, 538, 72-79.
  • Liang, C., Hui, N., Liu,Y., Qiao, G., Li, J., Tian, L., Ju, X., Jia, M., Liu, H., Cao, W., Yu, P., Li, H., & Ren, X. (2021). Insights into forsythia honeysuckle (Lianhuaqingwen) capsules: A Chinese herbal medicine repurposed for COVID-19 pandemic. Phytomedicine Plus, 1, 100027.
  • Lipsitch, M., and Dean, N. E. (2020). Understanding COVID-19 vaccine efficacy. Science, 370, 6518, 763-765.
  • Maiti, B. K. (2020). Can papain-like protease inhibitors halt SARS-CoV-2 replication?. ACS Pharmacology & Translational Science, 3(5), 1017-1019.
  • Osipiuk, J., Jedrzejczak, R., Tesar, C., Endres, M., Stols, L., Babnigg, G., Kim, Y., Michalska, K., Joachimiak, A. The crystal structure of papain-like protease of SARS CoV-2. Center for Structural Genomics of Infectious Diseases (CSGID), To be published.
  • Papaefthimiou, D., Papanikolaou, A., Falara, V., Givanoudi, S., Kostas, S., and Kanellis, A. K. (2014) . Genus Cistus: a model for exploring labdane type diterpenes’ biosynthesis and a natural source of high value products with biological, aromatic, and pharmacological properties. Frontiers in Chemistry, 2(35). doi: 10.3389/fchem.2014.00035
  • Peiris, J. S. M., Guan, Y., and Yuen, K. Y. (2004). Severe acute respiratory syndrome. Nature Medicine, 10, 88–97.
  • Rebensburg, S., Helfer, M., Schneider, M., Koppensteiner, H., Eberle, J., Schindler, M., ... & Brack-Werner, R. (2016). Potent in vitro antiviral activity of Cistus incanus extract against HIV and Filoviruses targets viral envelope proteins. Scientific Reports, 6(1), 1-15.
  • Reddy. M. P., Makhal, P., and Rao, K. V. (2021). Potential herbal drugs and phytochemicals to minimize the risk of COVID-19: A review. Journal of Pharmacognosy and Phytochemistry, 10(1), 670-675.
  • Refat, M. S., Bakare, S. B., Altalhi, T. A., Alam, K., & Al-Hazmi, G. H. (2021). Synthesis and spectroscopic interpretations of Co (II), Ni (II) and Cu (II) decxycholate complexes with molecular docking of COVId-19 protease. Polish Journal of Chemical Technology, 23(2), 54-59.
  • Saakre, M., Mathew D., and Ravisankar, V. (2021). Perspectives on plant flavonoid quercetin-based drugs for novel SARS-CoV-2. Beni-Suef University Journal of Basic and Applied Sciences.
  • Shawky, E., Nada, A. A., and Ibrahim, R. S. (2020). Potential role of medicinal plants and their constituents in the mitigation of SARS-CoV-2: identifying related therapeutic targets using network pharmacology and molecular docking analyses. RSC Advances, 10, 27961.
  • Sherif, Y. E., Sayed, A. H., & Lotfy, M. (2021). Antiviral Effect of Curcuminoids and Curcumin Derivatives Against Coronavirus (Sars-Cov-2) Predicted Using Molecular Docking Approach. Egyptian Academic Journal of Biological Sciences. C, Physiology and Molecular Biology, 13(2), 47-62.
  • Shin, D., Mukherjee, R., Grewe, D., Bojkova, D., Baek, K., Bhattacharya,A., Schulz, L., Widera, M., Mehdipour, A. R., Tascher, G., Geurink, P. P., Wilhelm, A., Noort, G. J. H., Ovaa, H., Müller, S., Knobeloch, K. P., Rajalingam, K., Schulman,B. A., Cinatl, J., Hummer, G., Ciesek, S. & Dikic, I. (2020). Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity, Nature volume, 587, 657–662.
  • Simeray, J., Chaumont, J. P., Bevalot, F. & Vaquette, I. (1982). Les propietes antifongiques des Cistae¨es et plus particulie¨rement de Cistus Laurifolius L.: role des tanins non hydrolysables. Fitoterapia, 53(43). 8.
  • Sisakht, M., Mahmoodzadeh, A., & Darabian, M. (2021). Plant‐derived chemicals as potential inhibitors of SARS‐CoV‐2 main protease (6LU7), a virtual screening study. Phytotherapy Research, 35(6), 3262-3274.
  • Skori´c, M., Todorovi´c, S., Gligorijevi´c, N., Jankovi´c, R., Živkovi´c, S., Risti´c, M. (2012). Cytotoxic activity of ethanol extracts of in vitro grown Cistus creticus subsp. creticus L. on human cancer cell lines. Industrial and Crops Products. 38. 153–159. doi: 10.1016/j.indcrop.2012.01.017
  • Su, W., Chen, P., Yang, Z., Zhong, N., Ma, Q., Zeng, X., Zhang, J., Wang, Y., & Li, P. (2021). Network pharmacology integrated molecular docking reveals the potential of hypericum japonicum thunb. ex murray against COVID-19. Biotechnology & Biotechnological Equipment, 35(1), 453–461.
  • Trott, O., and Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455-461.
  • Wittpahl, G., Kölling-Speer, I., Basche, S., Herrmann, E., Hannig, M., Speer, K., & Hannig, C. (2015). The polyphenolic composition of Cistus incanus herbal tea and its antibacterial and anti-adherent activity against Streptococcus mutans. Planta Medica, 81(18), 1727-1735.
  • Wua, C., Liu, Y., Yang, Y., Zhang, P., Zhong, W., Wang, Y., Wang, Q., Xu,Y., Li,Xingzhou Li, M., Zheng, M., Chen, L., & Li, H. (2020). Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharmaceutica Sinica B, 10(5), 766-788.
Toplam 55 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Bölüm Makaleler
Yazarlar

Sakine Kübra Çelik Bu kişi benim 0000-0002-1554-185X

Elvan Üstün 0000-0002-0587-7261

Yayımlanma Tarihi 15 Aralık 2021
Yayımlandığı Sayı Yıl 2021 Cilt: 11 Sayı: 2

Kaynak Göster

APA Çelik, S. K., & Üstün, E. (2021). Molecular Docking Analysis of Some Bioactive Molecules of Cistus incanus Against SARS CoV-2. Karadeniz Fen Bilimleri Dergisi, 11(2), 522-532. https://doi.org/10.31466/kfbd.939421