Research Article
BibTex RIS Cite

SARS-CoV-2 Ana Proteazın (Mpro) potansiyel inhibitörleri olarak rutin, luteolin ve mirisetin: Sanal bir tarama çalışması

Year 2022, Volume: 4 Issue: 2, 171 - 192, 31.12.2022

Abstract

COVID-19 pandemisi 17 Kasım 2019'da Çin'de ortaya çıktı. 22 Aralık 2021 itibariyle ilk vaka görüldükten sonra 276.879.062 vaka gözlemlendi ve toplam 5.374.615 ölüm bildirildi (Johns Hopkins Üniversitesi, 2021). COVID-19'un pandemi olarak tanınmasının ardından tüm dünyada aşı geliştirme seferberliği başladı. Aşı geliştirme çalışmaları devam ederken, tedavi için önerilen ancak en etkili sonuçları olmayan bazı ilaçlar var. İlaç tasarımı, geliştirme ve test prosedürleri zaman alıcı olduğundan, mevcut ilaç veri tabanları yardımıyla sanal tarama çalışmaları inisiyatif almakta ve bu noktada zamandan tasarruf sağlamaktadır. Ayrıca, ilaç yeniden kullanım stratejileri, bu tür hastalıklar için yeni potansiyel ajanları zaman açısından kritik bir şekilde tanımlamayı vaat ediyor. Burada, SARS-CoV-2'nin COVID-19 ana proteazlarından (6W63) biri üzerindeki üç flavonoid, rutin, luteolin ve mirisetin'in kenetlenme profillerini ortaya çıkarmak için yapı tabanlı sanal tarama yöntemini rapor ediyoruz.

Supporting Institution

Ege üniversitesi

References

  • Abdul-Hammed, M., Adedotun, I. O., Olajide, M., Irabor, C. O., Afolabi, T. I., Gbadebo, I. O., … Ramasami, P. (2021). Virtual screening, ADMET profiling, PASS prediction, and bioactivity studies of potential inhibitory roles of alkaloids, phytosterols, and flavonoids against COVID-19 main protease (M-pro). Natural Product Research.
  • Agrawal, P K, Agrawal, C., & Blunden, G. (2021). Pharmacological Significance of Hesperidin and Hesperetin, Two Citrus Flavonoids, as Promising Antiviral Compounds for Prophylaxis Against and Combating COVID-19. Natural Product Communications, 16(10).
  • Agrawal, Pawan K., Agrawal, C., & Blunden, G. (2021). Rutin: A Potential Antiviral for Repurposing as a SARS-CoV-2 Main Protease (Mpro) Inhibitor. Natural Product Communications, 16(4). https://doi.org/10.1177/1934578X21991723
  • Alhadrami, H. A., Sayed, A. M., Hassan, H. M., Youssif, K. A., Gaber, Y., Moatasim, Y., … Gamaleldin, N. M. (2021). Cnicin as an Anti-SARS-CoV-2: An Integrated In Silico and In Vitro Approach for the Rapid Identification of Potential COVID-19 Therapeutics. Antibiotics-Basel, 10(5).
  • Ali, A. M., & 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(5).
  • Allam, A. E., Assaf, H. K., Hassan, H. A., Shimizu, K., & Elshaier, Y. A. M. M. (2020). Anin silicoperception for newly isolated flavonoids from peach fruit as privileged avenue for a countermeasure outbreak of COVID-19. Rsc Advances, 10(50), 29983–29998.
  • Babaeekhou, L., Ghane, M., & Abbas-Mohammadi, M. (2021). In silico targeting SARS-CoV-2 spike protein and main protease by biochemical compounds. Biologia, 76(11), 3547–3565.
  • Batool, F., Mughal, E. U., Zia, K., Sadiq, A., Naeem, N., Javid, A., … Saeed, M. (2020). Synthetic flavonoids as potential antiviral agents against SARS-CoV-2 main protease. Journal of Biomolecular Structure & Dynamics.
  • Bhati, S., Kaushik, V., & Singh, J. (2021). Rational design of flavonoid based potential inhibitors targeting SARS-CoV 3CL protease for the treatment of COVID-19. Journal of Molecular Structure, 1237.
  • Bhowmik, D., Nandi, R., Prakash, A., & Kumar, D. (2021). Evaluation of flavonoids as 2019-nCoV cell entry inhibitor through molecular docking and pharmacological analysis. Heliyon, 7(3).
  • Biagioli, M., Marchiano, S., Roselli, R., Di Giorgio, C., Bellini, R., Bordoni, M., … Fiorucci, S. (2021). Discovery of a AHR pelargonidin agonist that counter-regulates Ace2 expression and attenuates ACE2-SARS-CoV-2 interaction. Biochemical Pharmacology, 188.
  • Bolelli, K., Ertan-Bolelli, T., Unsalan, O., & Altunayar-Unsalan, C. (2021). Fenoterol and dobutamine as SARS-CoV-2 main protease inhibitors: A virtual screening study. Journal of Molecular Structure, 1228(xxxx), 129449. https://doi.org/10.1016/j.molstruc.2020.129449
  • Chan, J. F. W., Yuan, S., Kok, K. H., To, K. K. W., Chu, H., Yang, J., … Yuen, K. Y. (2020). A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. The Lancet, 395(10223), 514–523. https://doi.org/10.1016/S0140-6736(20)30154-9
  • Chapman, R. L., & Andurkar, S. V. (2021). A review of natural products, their effects on SARS-CoV-2 and their utility as lead compounds in the discovery of drugs for the treatment of COVID-19. Medicinal Chemistry Research.
  • Chen, C. N., Lin, C. P. C., Huang, K. K., Chen, W. C., Hsieh, H. P., Liang, P. H., & Hsu, J. T. A. (2005). Inhibition of SARS-CoV 3C-like protease activity by theaflavin-3,3′- digallate (TF3). Evidence-Based Complementary and Alternative Medicine, 2(2), 209–215. https://doi.org/10.1093/ecam/neh081
  • Chen, N., Zhou, M., Dong, X., Qu, J., Gong, F., Han, Y., … Zhang, L. (2020). Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. The Lancet, 395(10223), 507–513. https://doi.org/10.1016/S0140-6736(20)30211-7
  • da Silva, F. M. A., da Silva, K. P. A., de Oliveira, L. P. M., Costa, E. V, Koolen, H. H. F., Pinheiro, M. L. B., … de Souza, A. D. L. (2020). Flavonoid glycosides and their putative human metabolites as potential inhibitors of the SARS-CoV-2 main protease (Mpro) and RNA-dependent RNA polymerase (RdRp). Memorias Do Instituto Oswaldo Cruz, 115.
  • Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx. Methods in Molecular Biology, 1263(January 2015), 243–250. https://doi.org/10.1007/978-1-4939-2269-7_19
  • Das, P., Majumder, R., Mandal, M., & Basak, P. (2021). In-Silico approach for identification of effective and stable inhibitors for COVID-19 main protease (M-pro) from flavonoid based phytochemical constituents ofCalendula officinalis. Journal of Biomolecular Structure & Dynamics, 39(16), 6265–6280.
  • Dubey, K., & Dubey, R. (2020). Computation screening of narcissoside a glycosyloxyflavone for potential novel coronavirus 2019 (COVID-19) inhibitor. Biomedical Journal, 43(4), 363–367. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7233213/pdf/main.pdf
  • Dubey, R., & Dubey, K. (2021). Molecular Docking Studies of Bioactive Nicotiflorin against 6W63 Novel Coronavirus 2019 (COVID-19). Combinatorial Chemistry & High Throughput Screening, 24(6), 874–878.
  • Ebada, S. S., Al-Jawabri, N. A., Youssef, F. S., El-Kashef, D. H., Knedel, T. O., Albohy, A., … Proksch, P. (2020). Anti-inflammatory, antiallergic and COVID-19 protease inhibitory activities of phytochemicals from the Jordanian hawksbeard: identification, structure-activity relationships, molecular modeling and impact on its folk medicinal uses. Rsc Advances, 10(62), 38128–38141.
  • Fadaka, A. O., Sibuyi, N. R. S., Martin, D. R., Klein, A., Madiehe, A., & Meyer, M. (2021). Development of Effective Therapeutic Molecule from Natural Sources against Coronavirus Protease. International Journal of Molecular Sciences, 22(17).
  • Fakhar, Z., Faramarzi, B., Pacifico, S., & Faramarzi, S. (2021). Anthocyanin derivatives as potent inhibitors of SARS-CoV-2 main protease: An in-silico perspective of therapeutic targets against COVID-19 pandemic. Journal of Biomolecular Structure & Dynamics, 39(16), 6171–6183.
  • Fayed, M. A. A., El-Behairy, M. F., Abdallah, I. A., Abdel-Bar, H. M., Elimam, H., Mostafa, A., … Elshaier, Y. A. M. M. (2021). Structure- and Ligand-Based in silico Studies towards the Repurposing of Marine Bioactive Compounds to Target SARS-CoV-2. Arabian Journal of Chemistry, 14(4).
  • Glaab, E., Manoharan, G. B., & Abankwa, D. (2021). Pharmacophore Model for SARS-CoV-2 3CLpro Small-Molecule Inhibitors and in Vitro Experimental Validation of Computationally Screened Inhibitors. Journal of Chemical Information and Modeling, 61(8), 4082–4096. Retrieved from https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.1c00258
  • Gogoi, N., Chowdhury, P., Goswami, A. K., Das, A., Chetia, D., & Gogoi, B. (2021). Computational guided identification of a citrus flavonoid as potential inhibitor of SARS-CoV-2 main protease. Molecular Diversity, 25(3), 1745–1759. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7685905/pdf/11030_2020_Article_10150.pdf
  • Gomez, C. R., Espinoza, I., Faruke, F. S., Hasan, M., Rahman, K. M., Walker, L. A., & Muhammad, I. (2021). Therapeutic Intervention of COVID-19 by Natural Products: A Population-Specific Survey Directed Approach. Molecules, 26(4).
  • Goris, T., Perez-Valero, A., Martinez, I., Yi, D., Fernandez-Calleja, L., San Leon, D., … Nogales, J. (2021). Repositioning microbial biotechnology against COVID-19: the case of microbial production of flavonoids. Microbial Biotechnology, 14(1), 94–110. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7675739/pdf/MBT2-14-94.pdf
  • Gorla, U. S., Rao, G. K., Kulandaivelu, U. S., Alavala, R. R., & Panda, S. P. (2021). Lead Finding from Selected Flavonoids with Antiviral (SARS-CoV-2) Potentials Against COVID-19: An In-silico Evaluation. Combinatorial Chemistry & High Throughput Screening, 24(6), 879–890.
  • Guler, H. I., Sal, F. A. Y., Can, Z., Kara, Y., Yildiz, O., Belduz, A. O., … Kolayli, S. (2021). Targeting CoV-2 spike RBD and ACE-2 interaction with flavonoids of Anatolian propolis by in silico and in vitro studies in terms of possible COVID-19 therapeutics. Turkish Journal of Biology, 45(4), 530–548. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8576337/pdf/turkjbio-45-530.pdf
  • Guler, H. I., Tatar, G., Yildiz, O., Belduz, A. O., & Kolayli, S. (2021). Investigation of potential inhibitor properties of ethanolic propolis extracts against ACE-II receptors for COVID-19 treatment by molecular docking study. Archives of Microbiology, 203(6), 3557–3564. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8098016/pdf/203_2021_Article_2351.pdf
  • Gurung, A. B., Ali, M. A., Lee, J., Abul Farah, M., Al-Anazi, K. M., & Al-Hemaid, F. (2021). Identification of SARS-CoV-2 inhibitors from extracts of Houttuynia cordata Thunb. Saudi Journal of Biological Sciences, 28(12), 7517–7527.
  • Hassan, A. R., Sanad, I. M., Allam, A. E., Abouelela, M. E., Sayed, A. M., Emam, S. S., … Shimizu, K. (2021). Chemical constituents from Limonium tubiflorum and their in silico evaluation as potential antiviral agents against SARS-CoV-2. Rsc Advances, 11(51), 32346–32357.
  • Hiremath, S., Kumar, H. D. V, Nandan, M., Mantesh, M., Shankarappa, K. S., Venkataravanappa, V., … Reddy, C. N. L. (2021). In silico docking analysis revealed the potential of phytochemicals present in Phyllanthus amarus and Andrographis paniculata, used in Ayurveda medicine in inhibiting SARS-CoV-2. 3 Biotech, 11(2).
  • Hu, X. P., Cai, X., Song, X., Li, C. Y., Zhao, J., Luo, W. L., … He, Z. D. (2020). Possible SARS-coronavirus 2 inhibitor revealed by simulated molecular docking to viral main protease and host toll-like receptor. Future Virology, 15(6), 359–368.
  • Huang, C., Wang, Y., Li, X., Ren, L., Zhao, J., Hu, Y., … Cao, B. (2020). Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. The Lancet, 395(10223), 497–506. https://doi.org/10.1016/S0140-6736(20)30183-5
  • Huang, F., Zhang, C., Liu, Q., Zhao, Y., Zhang, Y., Qin, Y., … Jiang, C. (2020). Identification of amitriptyline HCl, flavin adenine dinucleotide, azacitidine and calcitriol as repurposing drugs for influenza A H5N1 virus-induced lung injury. PLoS Pathogens, 16(3), 1–16. https://doi.org/10.1371/journal.ppat.1008341
  • Ibrahim, M. A. A., Abdelrahman, A. H. M., Atia, M. A. M., Mohamed, T. A., Moustafa, M. F., Hakami, A. R., … Hegazy, M. E. F. (2021). Blue Biotechnology: Computational Screening of Sarcophyton Cembranoid Diterpenes for SARS-CoV-2 Main Protease Inhibition. Marine Drugs, 19(7).
  • Ibrahim, M. A. A., Mohamed, E. A. R., Abdelrahman, A. H. M., Allemailem, K. S., Moustafa, M. F., Shawky, A. M., … Atia, M. A. M. (2021). Rutin and flavone analogs as prospective SARS-CoV-2 main protease inhibitors: In silico drug discovery study. Journal of Molecular Graphics & Modelling, 105.
  • Irfan, A., Imran, M., Khalid, N., Hussain, R., Basra, M. A. R., Khaliq, T., … Assiri, M. A. (2021). Isolation of phytochemicals from Malva neglecta Wallr and their quantum chemical, molecular docking exploration as active drugs against COVID-19. Journal of Saudi Chemical Society, 25(12).
  • Istifli, E. S., Netz, P. A., Tepe, A. S., Husunet, M. T., Sarikurkcu, C., & Tepe, B. (2020). In silico analysis of the interactions of certain flavonoids with the receptor-binding domain of 2019 novel coronavirus and cellular proteases and their pharmacokinetic properties. Journal of Biomolecular Structure & Dynamics.
  • Jain, A. S., Sushma, P., Dharmashekar, C., Beelagi, M. S., Prasad, S. K., Shivamallu, C., … Prasad, K. S. (2021). In silico evaluation of flavonoids as effective antiviral agents on the spike glycoprotein of SARS-CoV-2. Saudi Journal of Biological Sciences, 28(1), 1040–1051. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7783825/pdf/main.pdf
  • Jalmakhanbetova, R. I., Suleimen, Y. M., Oyama, M., Elkaeed, E. B., Eissa, I. H., Suleimen, R. N., … Ishmuratova, M. Y. (2021). Isolation and in Silico Anti-COVID-19 Main Protease (Mpro) Activities of Flavonoids and a Sesquiterpene Lactone from Artemisia sublessingiana. Journal of Chemistry, 2021. https://doi.org/10.1155/2021/5547013
  • Jannat, K., Paul, A. K., Bondhon, T. A., Hasan, A., Nawaz, M., Jahan, R., … Rahmatullah, M. (2021). Nanotechnology Applications of Flavonoids for Viral Diseases. Pharmaceutics, 13(11).
  • Jiménez-Avalos, G., Vargas-Ruiz, A. P., Delgado-Pease, N. E., Olivos-Ramirez, G. E., Sheen, P., Fernández-Díaz, M., … Ygnacio-Aguirre, F. (2021). Comprehensive virtual screening of 4.8 k flavonoids reveals novel insights into allosteric inhibition of SARS-CoV-2 MPRO. Scientific Reports, 11(1), 1–19. https://doi.org/10.1038/s41598-021-94951-6
  • Jo, S, Kim, S., Kim, D. Y., Kim, M. S., & Shin, D. H. (2020). Flavonoids with inhibitory activity against SARS-CoV-2 3CLpro. Journal of Enzyme Inhibition and Medicinal Chemistry, 35(1), 1539–1544. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7470085/pdf/IENZ_35_1801672.pdf
  • Jo, Seri, Kim, S., Shin, D. H., & Kim, M. S. (2020). Inhibition of SARS-CoV 3CL protease by flavonoids. Journal of Enzyme Inhibition and Medicinal Chemistry, 35(1), 145–151. https://doi.org/10.1080/14756366.2019.1690480
  • Johns Hopkins. (2021). Covid 19 Map Channelnewsasis. Retrieved from https://coronavirus.jhu.edu/map.html
  • Johns Hopkins University. (n.d.). COVID-19 Dashboard by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU).
  • Karim, S. S. A., & Karim, Q. A. (2021). Omicron SARS-CoV-2 variant: a new chapter in the COVID-19 pandemic. The Lancet, 398(10317), 2126–2128. https://doi.org/10.1016/s0140-6736(21)02758-6
  • Khursheed, A., Jain, V., Rasool, A., Rather, M. A., Malik, N. A., & Shalla, A. H. (2021). Molecular scaffolds from mother nature as possible lead compounds in drug design and discovery against coronaviruses: A landscape analysis of published literature and molecular docking studies. Microbial Pathogenesis, 157.
  • Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., … Bryant, S. H. (2016). PubChem substance and compound databases. Nucleic Acids Research, 44(D1), D1202–D1213. https://doi.org/10.1093/nar/gkv951
  • Kumar, B., Zaidi, S., Haque, S., Dasgupta, N., Hussain, A., Pramodh, S., … Mishra, B. N. (2021). In Silico Studies Reveal Antiviral Effects of Traditional Indian Spices on COVID-19. Current Pharmaceutical Design, 27(32), 3462–3475. Retrieved from https://www.eurekaselect.net/article/112631
  • Lee, Y. G., Kang, K. W., Hong, W., Kim, Y. H., Oh, J. T., Park, D. W., … Kang, S. C. (2021). Potent antiviral activity of Agrimonia pilosa, Galla rhois, and their components against SARS-CoV-2. Bioorganic & Medicinal Chemistry, 45.
  • Li, L. Y., Ma, L. Y., Hu, Y., Li, X. X., Yu, M., Shang, H., & Zou, Z. M. (2022). Natural biflavones are potent inhibitors against SARS-CoV-2 papain-like protease. Phytochemistry, 193.
  • Liao, Q., Chen, Z. Y., Tao, Y. L., Zhang, B. B., Wu, X. J., Yang, L., … Wang, Z. T. (2021). An integrated method for optimized identification of effective natural inhibitors against SARS-CoV-2 3CLpro. Scientific Reports, 11(1).
  • Lin, Y., Shi, R., Wang, X., & Shen, H.-M. (2008). Luteolin, a Flavonoid with Potential for Cancer Prevention and Therapy. Current Cancer Drug Targets, 8(7), 634–646. https://doi.org/10.2174/156800908786241050
  • Liskova, A., Samec, M., Koklesova, L., Samuel, S. M., Zhai, K. V, Al-Ishaq, R. K., … Kubatka, P. (2021). Flavonoids against the SARS-CoV-2 induced inflammatory storm. Biomedicine & Pharmacotherapy, 138.
  • Ma, L. L., Liu, H. M., Liu, X. M., Yuan, X. Y., Xu, C., Wang, F., … Zhang, D. K. (2021). Screening S protein-ACE2 blockers from natural products: Strategies and advances in the discovery of potential inhibitors of COVID-19. European Journal of Medicinal Chemistry, 226.
  • Maddah, M., Bahramsoltani, R., Yekta, N. H., Rahimi, R., Aliabadi, R., & Pourfath, M. (2021). Proposing high-affinity inhibitors from Glycyrrhiza glabra L. against SARS-CoV-2 infection: virtual screening and computational analysis. New Journal of Chemistry, 45(35), 15977–15995.
  • Maiti, S., & Banerjee, A. (2021). Epigallocatechin gallate and theaflavin gallate interaction inSARS-CoV-2 spike-protein central channel with reference to the hydroxychloroquine interaction: Bioinformatics and molecular docking study. Drug Development Research, 82(1), 86–96. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7436314/pdf/DDR-9999-na.pdf
  • Majumder, R., & Mandal, M. (2020). Screening of plant-based natural compounds as a potential COVID-19 main protease inhibitor: anin silicodocking and molecular dynamics simulation approach. Journal of Biomolecular Structure & Dynamics.
  • Mandour, Y. M., Zlotos, D. P., & Salem, M. A. (2020). A multi-stage virtual screening of FDA-approved drugs reveals potential inhibitors of SARS-CoV-2 main protease. Journal of Biomolecular Structure & Dynamics.
  • Mangiavacchi, F., Botwina, P., Menichetti, E., Bagnoli, L., Rosati, O., Marini, F., … Santi, C. (2021). Seleno-Functionalization of Quercetin Improves the Non-Covalent Inhibition of M-pro and Its Antiviral Activity in Cells against SARS-CoV-2. International Journal of Molecular Sciences, 22(13).
  • Maroli, N., Bhasuran, B., Natarajan, J., & Kolandaivel, P. (2020). The potential role of procyanidin as a therapeutic agent against SARS-CoV-2: a text mining, molecular docking and molecular dynamics simulation approach. Journal of Biomolecular Structure & Dynamics.
  • Mathpal, S., Sharma, P., Joshi, T., Joshi, T., Pande, V., & Chandra, S. (2021). Screening of potential bio-molecules from Moringa olifera against SARS-CoV-2 main protease using computational approaches. Journal of Biomolecular Structure & Dynamics.
  • Mohapatra, P. K., Chopdar, K. S., Dash, G. C., Mohanty, A. K., & Raval, M. K. (2021). In silico screening and covalent binding of phytochemicals of Ocimum sanctum against SARS-CoV-2 (COVID 19) main protease. Journal of Biomolecular Structure & Dynamics.
  • Moradkhani, S., Farmani, A., Saidijam, M., & Taherkhani, A. (2021). COVID-19: docking-based virtual screening and molecular dynamics study to identify potential SARS-CoV-2 spike protein inhibitors from plant-based phenolic compounds. Acta Virologica, 65(3), 288–302.
  • Mosquera-Yuqui, F., Lopez-Guerra, N., & Moncayo-Palacio, E. A. (2020). Targeting the 3CLpro and RdRp of SARS-CoV-2 with phytochemicals from medicinal plants of the Andean Region: molecular docking and molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics.
  • Neves, K. O. G., Ramos, A. S., Bruginski, E. R. D., Souza, A. D. L., Nunomura, R. D. S., Campos, F. R., … Machado, M. B. (2021). Lisboaeflavanonol A: A new flavonoid glycoside obtained from Amazonian Eugenia lisboae. Phytochemistry Letters, 43, 65–69.
  • Ngwa, W., Kumar, R., Thompson, D., Lyerly, W., Moore, R., Reid, T., … Toyang, N. (2020). against COVID-19. 1–10.
  • O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel. Journal of Cheminformatics, 3(33), 1–14.
  • Owis, A. I., El-Hawary, M. S., El Amir, D., Aly, O., Abdelmohsen, U. R., & Kamel, M. S. (2020). Molecular docking reveals the potential of Salvadora persica flavonoids to inhibit COVID-19 virus main protease. Rsc Advances, 10(33), 19570–19575.
  • Owis, A. I., El-Hawary, M. S., El Amir, D., Refaat, H., Alaaeldin, E., Aly, O. M., … Kamel, M. S. (2021). Flavonoids of Salvadora persica L. (meswak) and its liposomal formulation as a potential inhibitor of SARS-CoV-2. Rsc Advances, 11(22), 13537–13544.
  • Potshangbam, A. M., Nongdam, P., Kumar, A. K., & Rathore, R. S. (2021). Phenylbenzopyrone of Flavonoids as a Potential Scaffold to Prevent SARS-CoV-2 Replication by Inhibiting its M-PRO Main Protease. Current Pharmaceutical Biotechnology, 22(15), 2054–2070. Retrieved from https://www.eurekaselect.net/article/113711
  • Prasansuklab, A., Theerasri, A., Rangsinth, P., Sillapachaiyaporn, C., Chuchawankul, S., & Tencomnao, T. (2021). Anti-COVID-19 drug candidates: A review on potential biological activities of natural products in the management of new coronavirus infection. Journal of Traditional and Complementary Medicine, 11(2), 144–157.
  • Puttaswamy, H., Gowtham, H. G., Ojha, M. D., Yadav, A., Choudhir, G., Raguraman, V., … Chauhan, L. (2020). In silico studies evidenced the role of structurally diverse plant secondary metabolites in reducing SARS-CoV-2 pathogenesis. Scientific Reports, 10(1).
  • Rahman, F., Tabrez, S., Ali, R., Alqahtani, A. S., Ahmed, M. Z., & Rub, A. (2021). Molecular docking analysis of rutin reveals possible inhibition of SARS-CoV-2 vital proteins. Journal of Traditional and Complementary Medicine, 11(2), 173–179.
  • Rakshit, M., Muduli, S., Srivastav, P. P., & Mishra, S. (2021). Pomegranate peel polyphenols prophylaxis against SARS-CoV-2 main protease by in-silico docking and molecular dynamics study. Journal of Biomolecular Structure & Dynamics.
  • Rameshkumar, M. R., Indu, P., Arunagirinathan, N., Venkatadri, B., El-Serehy, H. A., & Ahmad, A. (2021). Computational selection of flavonoid compounds as inhibitors against SARS-CoV-2 main protease, RNA-dependent RNA polymerase and spike proteins: A molecular docking study. Saudi Journal of Biological Sciences, 28(1), 448–458. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7581406/pdf/main.pdf
  • Rehman, M. T., AlAjmi, M. F., & Hussain, A. (2021). Natural Compounds as Inhibitors of SARS-CoV-2 Main Protease (3CLpro): A Mo-lecular Docking and Simulation Approach to Combat COVID-19. Current Pharmaceutical Design, 27(33), 3577–3589. Retrieved from https://www.eurekaselect.net/article/111556
  • Rizzuti, B., Grande, F., Conforti, F., Jimenez-Alesanco, A., Ceballos-Laita, L., Ortega-Alarcon, D., … Velazquez-Campoy, A. (2021). Rutin Is a Low Micromolar Inhibitor of SARS-CoV-2 Main Protease 3CLpro: Implications for Drug Design of Quercetin Analogs. Biomedicines, 9(4).
  • Rottier, P. J. M. (1995). The Coronavirus Membrane Glycoprotein. The Coronaviridae, 115–139. https://doi.org/10.1007/978-1-4899-1531-3_6
  • Rudrapal, M., Issahaku, A. R., Agoni, C., Bendale, A. R., Nagar, A., Soliman, M. E. S., & Lokwani, D. (2021). In silico screening of phytopolyphenolics for the identification of bioactive compounds as novel protease inhibitors effective against SARS-CoV-2. Journal of Biomolecular Structure & Dynamics.
  • Samy, M. N., Attia, E. Z., Shoman, M. E., Khalil, H. E., Sugimoto, S., Matsunami, K., & Fahim, J. R. (2021). Phytochemical investigation of Amphilophium paniculatum; an underexploredBignoniaceae species as a source of SARS-CoV-2 M-pro inhibitory metabolites: Isolation, identification, and molecular docking study. South African Journal of Botany, 141, 421–430.
  • Sen, D., Bhaumik, S., Debnath, P., & Debnath, S. (2021). Potentiality of Moringa oleifera against SARS-CoV-2: identified by a rational computer aided drug design method. Journal of Biomolecular Structure & Dynamics.
  • Shaldam, M. A., Yahya, G., Mohamed, N. H., Abdel-Daim, M. M., & Al Naggar, Y. (2021). In silico screening of potent bioactive compounds from honeybee products against COVID-19 target enzymes. Environmental Science and Pollution Research, 28(30), 40507–40514. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8088405/pdf/11356_2021_Article_14195.pdf
  • Shu, Y., & McCauley, J. (2017). GISAID: Global initiative on sharing all influenza data – from vision to reality. Eurosurveillance, 22(13), 2–4. https://doi.org/10.2807/1560-7917.ES.2017.22.13.30494
  • Singh, J., Malik, D., & Raina, A. (2020). Computational investigation for identification of potential phytochemicals and antiviral drugs as potential inhibitors for RNA-dependent RNA polymerase of COVID-19. Journal of Biomolecular Structure & Dynamics.
  • Singh, A. V. (2021). Potential of amentoflavone with antiviral properties in COVID-19 treatment. Asian Biomedicine, 15(4), 153–159.
  • Song, X., Tan, L., Wang, M., Ren, C., Guo, C., Yang, B., … Pei, J. (2021). Myricetin: A review of the most recent research. Biomedicine and Pharmacotherapy, 134, 111017. https://doi.org/10.1016/j.biopha.2020.111017
  • Tyrrell, D. A., & Bynoe, M. L. (1966). Cultivation of viruses from a high proportion of patients with colds. https://doi.org/10.1016/s0140-6736(66)92364-6
  • Vijayakumar, B. G., Ramesh, D., Joji, A., Prakasan, J. J., & Kannan, T. (2020). In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2. European Journal of Pharmacology, 886.
  • Wang, D., Hu, B., Hu, C., Zhu, F., Liu, X., Zhang, J., … Peng, Z. (2020). Clinical Characteristics of 138 Hospitalized Patients with 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China. JAMA - Journal of the American Medical Association, 323(11), 1061–1069. https://doi.org/10.1001/jama.2020.1585
  • Wang, J., Ge, W., Peng, X., Yuan, L. X., He, S. B., & Fu, X. Y. (2021). Investigating the active compounds and mechanism of HuaShi XuanFei formula for prevention and treatment of COVID-19 based on network pharmacology and molecular docking analysis. Molecular Diversity.
  • Xiao, T., Cui, M. Q., Zheng, C. J., Wang, M., Sun, R. H., Gao, D. D., … Zhou, H. G. (2021). Myricetin Inhibits SARS-CoV-2 Viral Replication by Targeting M-pro and Ameliorates Pulmonary Inflammation. Frontiers in Pharmacology, 12.
  • Xiao, T., Cui, M. Q., Zheng, C. J., Zhang, P. P., Ren, S. F., Bao, J. L., … Yang, C. (2021). Both Baicalein and Gallocatechin Gallate Effectively Inhibit SARS-CoV-2 Replication by Targeting M-pro and Sepsis in Mice. Inflammation.
  • Xiong, Y., Zhu, G. H., Zhang, Y. N., Hu, Q., Wang, H. N., Yu, H. N., … Ge, G. B. (2021). Flavonoids in Ampelopsis grossedentata as covalent inhibitors of SARS-CoV-2 3CL(pro): Inhibition potentials, covalent binding sites and inhibitory mechanisms. International Journal of Biological Macromolecules, 187, 976–987. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8322037/pdf/main.pdf
  • Xu, Z. R., Yang, L. X., Zhang, X. H., Zhang, Q. L., Yang, Z. B., Liu, Y. H., … Liu, W. K. (2020). Discovery of Potential Flavonoid Inhibitors Against COVID-19 3CL Proteinase Based on Virtual Screening Strategy. Frontiers in Molecular Biosciences, 7.
  • Xu, Z., Yang, L., Zhang, X., Zhang, Q., Yang, Z., Liu, Y., … Liu, W. (2020). Discovery of Potential Flavonoid Inhibitors Against COVID-19 3CL Proteinase Based on Virtual Screening Strategy. Frontiers in Molecular Biosciences, 7(September), 1–8. https://doi.org/10.3389/fmolb.2020.556481
  • Yosri, N., Abd El-Wahed, A. A., Ghonaim, R., Khattab, O. M., Sabry, A., Ibrahim, M. A. A., … El-Seedi, H. R. (2021). Anti-Viral and Immunomodulatory Properties of Propolis: Chemical Diversity, Pharmacological Properties, Preclinical and Clinical Applications, and In Silico Potential against SARS-CoV-2. Foods, 10(8).
  • Yu, R., Chen, L., Lan, R., Shen, R., & Li, P. (2020). Computational screening of antagonists against the SARS-CoV-2 (COVID-19) coronavirus by molecular docking. International Journal of Antimicrobial Agents, 56(2).
  • Zaki, A. A., Al-Karmalawy, A. A., El-Amier, Y. A., & Ashour, A. (2020). Molecular docking reveals the potential of Cleome amblyocarpa isolated compounds to inhibit COVID-19 virus main protease. New Journal of Chemistry, 44(39), 16752–16758.
  • Zhang, Y., Yao, Y. F., Yang, Y. F., & Wu, H. Z. (2021). Investigation of Anti-SARS, MERS, and COVID-19 Effect of Jinhua Qinggan Granules Based on a Network Pharmacology and Molecular Docking Approach. Natural Product Communications, 16(5).
  • Zhou, P., Yang, X. Lou, Wang, X. G., Hu, B., Zhang, L., Zhang, W., … Shi, Z. L. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270–273. https://doi.org/10.1038/s41586-020-2012-7
  • Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., … Tan, W. (2020). A Novel Coronavirus from Patients with Pneumonia in China, 2019. New England Journal of Medicine, 382(8), 727–733. https://doi.org/10.1056/nejmoa2001017
  • Zhu, Y., & Xie, D. Y. (2020). Docking Characterization and in vitro Inhibitory Activity of Flavan-3-ols and Dimeric Proanthocyanidins Against the Main Protease Activity of SARS-Cov-2. Frontiers in Plant Science, 11.

Rutin, luteolin, and myricetin as potential inhibitors of SARS-CoV-2 Main Protease (Mpro): A virtual screening study

Year 2022, Volume: 4 Issue: 2, 171 - 192, 31.12.2022

Abstract

The COVID-19 pandemic appeared in China on November 17, 2019. As of 22 December 2021, after the first case was seen, 276,879,062 cases were observed and 5,374,615 total deaths were reported (Johns Hopkins University, 2021). After the recognition of COVID-19 as pandemic, a mobilization for vaccine development started all over the world. While the vaccine development studies continue, there are some drugs recommended for the treatment but not with the most effective results. Since drug design, development and testing procedures are time consuming, virtual screening studies with the help of existing drug databases take the initiative and save time at this point. Moreover, drug repurposing strategies promise to identify new potential agents for such diseases in a time-critical manner. Here, we report structure-based virtual screening method to reveal the docking profiles of three flavonoids, rutin, luteolin, and myricetin on one of the COVID-19 main protease (6W63) of SARS-CoV-2.

References

  • Abdul-Hammed, M., Adedotun, I. O., Olajide, M., Irabor, C. O., Afolabi, T. I., Gbadebo, I. O., … Ramasami, P. (2021). Virtual screening, ADMET profiling, PASS prediction, and bioactivity studies of potential inhibitory roles of alkaloids, phytosterols, and flavonoids against COVID-19 main protease (M-pro). Natural Product Research.
  • Agrawal, P K, Agrawal, C., & Blunden, G. (2021). Pharmacological Significance of Hesperidin and Hesperetin, Two Citrus Flavonoids, as Promising Antiviral Compounds for Prophylaxis Against and Combating COVID-19. Natural Product Communications, 16(10).
  • Agrawal, Pawan K., Agrawal, C., & Blunden, G. (2021). Rutin: A Potential Antiviral for Repurposing as a SARS-CoV-2 Main Protease (Mpro) Inhibitor. Natural Product Communications, 16(4). https://doi.org/10.1177/1934578X21991723
  • Alhadrami, H. A., Sayed, A. M., Hassan, H. M., Youssif, K. A., Gaber, Y., Moatasim, Y., … Gamaleldin, N. M. (2021). Cnicin as an Anti-SARS-CoV-2: An Integrated In Silico and In Vitro Approach for the Rapid Identification of Potential COVID-19 Therapeutics. Antibiotics-Basel, 10(5).
  • Ali, A. M., & 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(5).
  • Allam, A. E., Assaf, H. K., Hassan, H. A., Shimizu, K., & Elshaier, Y. A. M. M. (2020). Anin silicoperception for newly isolated flavonoids from peach fruit as privileged avenue for a countermeasure outbreak of COVID-19. Rsc Advances, 10(50), 29983–29998.
  • Babaeekhou, L., Ghane, M., & Abbas-Mohammadi, M. (2021). In silico targeting SARS-CoV-2 spike protein and main protease by biochemical compounds. Biologia, 76(11), 3547–3565.
  • Batool, F., Mughal, E. U., Zia, K., Sadiq, A., Naeem, N., Javid, A., … Saeed, M. (2020). Synthetic flavonoids as potential antiviral agents against SARS-CoV-2 main protease. Journal of Biomolecular Structure & Dynamics.
  • Bhati, S., Kaushik, V., & Singh, J. (2021). Rational design of flavonoid based potential inhibitors targeting SARS-CoV 3CL protease for the treatment of COVID-19. Journal of Molecular Structure, 1237.
  • Bhowmik, D., Nandi, R., Prakash, A., & Kumar, D. (2021). Evaluation of flavonoids as 2019-nCoV cell entry inhibitor through molecular docking and pharmacological analysis. Heliyon, 7(3).
  • Biagioli, M., Marchiano, S., Roselli, R., Di Giorgio, C., Bellini, R., Bordoni, M., … Fiorucci, S. (2021). Discovery of a AHR pelargonidin agonist that counter-regulates Ace2 expression and attenuates ACE2-SARS-CoV-2 interaction. Biochemical Pharmacology, 188.
  • Bolelli, K., Ertan-Bolelli, T., Unsalan, O., & Altunayar-Unsalan, C. (2021). Fenoterol and dobutamine as SARS-CoV-2 main protease inhibitors: A virtual screening study. Journal of Molecular Structure, 1228(xxxx), 129449. https://doi.org/10.1016/j.molstruc.2020.129449
  • Chan, J. F. W., Yuan, S., Kok, K. H., To, K. K. W., Chu, H., Yang, J., … Yuen, K. Y. (2020). A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. The Lancet, 395(10223), 514–523. https://doi.org/10.1016/S0140-6736(20)30154-9
  • Chapman, R. L., & Andurkar, S. V. (2021). A review of natural products, their effects on SARS-CoV-2 and their utility as lead compounds in the discovery of drugs for the treatment of COVID-19. Medicinal Chemistry Research.
  • Chen, C. N., Lin, C. P. C., Huang, K. K., Chen, W. C., Hsieh, H. P., Liang, P. H., & Hsu, J. T. A. (2005). Inhibition of SARS-CoV 3C-like protease activity by theaflavin-3,3′- digallate (TF3). Evidence-Based Complementary and Alternative Medicine, 2(2), 209–215. https://doi.org/10.1093/ecam/neh081
  • Chen, N., Zhou, M., Dong, X., Qu, J., Gong, F., Han, Y., … Zhang, L. (2020). Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. The Lancet, 395(10223), 507–513. https://doi.org/10.1016/S0140-6736(20)30211-7
  • da Silva, F. M. A., da Silva, K. P. A., de Oliveira, L. P. M., Costa, E. V, Koolen, H. H. F., Pinheiro, M. L. B., … de Souza, A. D. L. (2020). Flavonoid glycosides and their putative human metabolites as potential inhibitors of the SARS-CoV-2 main protease (Mpro) and RNA-dependent RNA polymerase (RdRp). Memorias Do Instituto Oswaldo Cruz, 115.
  • Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx. Methods in Molecular Biology, 1263(January 2015), 243–250. https://doi.org/10.1007/978-1-4939-2269-7_19
  • Das, P., Majumder, R., Mandal, M., & Basak, P. (2021). In-Silico approach for identification of effective and stable inhibitors for COVID-19 main protease (M-pro) from flavonoid based phytochemical constituents ofCalendula officinalis. Journal of Biomolecular Structure & Dynamics, 39(16), 6265–6280.
  • Dubey, K., & Dubey, R. (2020). Computation screening of narcissoside a glycosyloxyflavone for potential novel coronavirus 2019 (COVID-19) inhibitor. Biomedical Journal, 43(4), 363–367. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7233213/pdf/main.pdf
  • Dubey, R., & Dubey, K. (2021). Molecular Docking Studies of Bioactive Nicotiflorin against 6W63 Novel Coronavirus 2019 (COVID-19). Combinatorial Chemistry & High Throughput Screening, 24(6), 874–878.
  • Ebada, S. S., Al-Jawabri, N. A., Youssef, F. S., El-Kashef, D. H., Knedel, T. O., Albohy, A., … Proksch, P. (2020). Anti-inflammatory, antiallergic and COVID-19 protease inhibitory activities of phytochemicals from the Jordanian hawksbeard: identification, structure-activity relationships, molecular modeling and impact on its folk medicinal uses. Rsc Advances, 10(62), 38128–38141.
  • Fadaka, A. O., Sibuyi, N. R. S., Martin, D. R., Klein, A., Madiehe, A., & Meyer, M. (2021). Development of Effective Therapeutic Molecule from Natural Sources against Coronavirus Protease. International Journal of Molecular Sciences, 22(17).
  • Fakhar, Z., Faramarzi, B., Pacifico, S., & Faramarzi, S. (2021). Anthocyanin derivatives as potent inhibitors of SARS-CoV-2 main protease: An in-silico perspective of therapeutic targets against COVID-19 pandemic. Journal of Biomolecular Structure & Dynamics, 39(16), 6171–6183.
  • Fayed, M. A. A., El-Behairy, M. F., Abdallah, I. A., Abdel-Bar, H. M., Elimam, H., Mostafa, A., … Elshaier, Y. A. M. M. (2021). Structure- and Ligand-Based in silico Studies towards the Repurposing of Marine Bioactive Compounds to Target SARS-CoV-2. Arabian Journal of Chemistry, 14(4).
  • Glaab, E., Manoharan, G. B., & Abankwa, D. (2021). Pharmacophore Model for SARS-CoV-2 3CLpro Small-Molecule Inhibitors and in Vitro Experimental Validation of Computationally Screened Inhibitors. Journal of Chemical Information and Modeling, 61(8), 4082–4096. Retrieved from https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.1c00258
  • Gogoi, N., Chowdhury, P., Goswami, A. K., Das, A., Chetia, D., & Gogoi, B. (2021). Computational guided identification of a citrus flavonoid as potential inhibitor of SARS-CoV-2 main protease. Molecular Diversity, 25(3), 1745–1759. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7685905/pdf/11030_2020_Article_10150.pdf
  • Gomez, C. R., Espinoza, I., Faruke, F. S., Hasan, M., Rahman, K. M., Walker, L. A., & Muhammad, I. (2021). Therapeutic Intervention of COVID-19 by Natural Products: A Population-Specific Survey Directed Approach. Molecules, 26(4).
  • Goris, T., Perez-Valero, A., Martinez, I., Yi, D., Fernandez-Calleja, L., San Leon, D., … Nogales, J. (2021). Repositioning microbial biotechnology against COVID-19: the case of microbial production of flavonoids. Microbial Biotechnology, 14(1), 94–110. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7675739/pdf/MBT2-14-94.pdf
  • Gorla, U. S., Rao, G. K., Kulandaivelu, U. S., Alavala, R. R., & Panda, S. P. (2021). Lead Finding from Selected Flavonoids with Antiviral (SARS-CoV-2) Potentials Against COVID-19: An In-silico Evaluation. Combinatorial Chemistry & High Throughput Screening, 24(6), 879–890.
  • Guler, H. I., Sal, F. A. Y., Can, Z., Kara, Y., Yildiz, O., Belduz, A. O., … Kolayli, S. (2021). Targeting CoV-2 spike RBD and ACE-2 interaction with flavonoids of Anatolian propolis by in silico and in vitro studies in terms of possible COVID-19 therapeutics. Turkish Journal of Biology, 45(4), 530–548. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8576337/pdf/turkjbio-45-530.pdf
  • Guler, H. I., Tatar, G., Yildiz, O., Belduz, A. O., & Kolayli, S. (2021). Investigation of potential inhibitor properties of ethanolic propolis extracts against ACE-II receptors for COVID-19 treatment by molecular docking study. Archives of Microbiology, 203(6), 3557–3564. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8098016/pdf/203_2021_Article_2351.pdf
  • Gurung, A. B., Ali, M. A., Lee, J., Abul Farah, M., Al-Anazi, K. M., & Al-Hemaid, F. (2021). Identification of SARS-CoV-2 inhibitors from extracts of Houttuynia cordata Thunb. Saudi Journal of Biological Sciences, 28(12), 7517–7527.
  • Hassan, A. R., Sanad, I. M., Allam, A. E., Abouelela, M. E., Sayed, A. M., Emam, S. S., … Shimizu, K. (2021). Chemical constituents from Limonium tubiflorum and their in silico evaluation as potential antiviral agents against SARS-CoV-2. Rsc Advances, 11(51), 32346–32357.
  • Hiremath, S., Kumar, H. D. V, Nandan, M., Mantesh, M., Shankarappa, K. S., Venkataravanappa, V., … Reddy, C. N. L. (2021). In silico docking analysis revealed the potential of phytochemicals present in Phyllanthus amarus and Andrographis paniculata, used in Ayurveda medicine in inhibiting SARS-CoV-2. 3 Biotech, 11(2).
  • Hu, X. P., Cai, X., Song, X., Li, C. Y., Zhao, J., Luo, W. L., … He, Z. D. (2020). Possible SARS-coronavirus 2 inhibitor revealed by simulated molecular docking to viral main protease and host toll-like receptor. Future Virology, 15(6), 359–368.
  • Huang, C., Wang, Y., Li, X., Ren, L., Zhao, J., Hu, Y., … Cao, B. (2020). Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. The Lancet, 395(10223), 497–506. https://doi.org/10.1016/S0140-6736(20)30183-5
  • Huang, F., Zhang, C., Liu, Q., Zhao, Y., Zhang, Y., Qin, Y., … Jiang, C. (2020). Identification of amitriptyline HCl, flavin adenine dinucleotide, azacitidine and calcitriol as repurposing drugs for influenza A H5N1 virus-induced lung injury. PLoS Pathogens, 16(3), 1–16. https://doi.org/10.1371/journal.ppat.1008341
  • Ibrahim, M. A. A., Abdelrahman, A. H. M., Atia, M. A. M., Mohamed, T. A., Moustafa, M. F., Hakami, A. R., … Hegazy, M. E. F. (2021). Blue Biotechnology: Computational Screening of Sarcophyton Cembranoid Diterpenes for SARS-CoV-2 Main Protease Inhibition. Marine Drugs, 19(7).
  • Ibrahim, M. A. A., Mohamed, E. A. R., Abdelrahman, A. H. M., Allemailem, K. S., Moustafa, M. F., Shawky, A. M., … Atia, M. A. M. (2021). Rutin and flavone analogs as prospective SARS-CoV-2 main protease inhibitors: In silico drug discovery study. Journal of Molecular Graphics & Modelling, 105.
  • Irfan, A., Imran, M., Khalid, N., Hussain, R., Basra, M. A. R., Khaliq, T., … Assiri, M. A. (2021). Isolation of phytochemicals from Malva neglecta Wallr and their quantum chemical, molecular docking exploration as active drugs against COVID-19. Journal of Saudi Chemical Society, 25(12).
  • Istifli, E. S., Netz, P. A., Tepe, A. S., Husunet, M. T., Sarikurkcu, C., & Tepe, B. (2020). In silico analysis of the interactions of certain flavonoids with the receptor-binding domain of 2019 novel coronavirus and cellular proteases and their pharmacokinetic properties. Journal of Biomolecular Structure & Dynamics.
  • Jain, A. S., Sushma, P., Dharmashekar, C., Beelagi, M. S., Prasad, S. K., Shivamallu, C., … Prasad, K. S. (2021). In silico evaluation of flavonoids as effective antiviral agents on the spike glycoprotein of SARS-CoV-2. Saudi Journal of Biological Sciences, 28(1), 1040–1051. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7783825/pdf/main.pdf
  • Jalmakhanbetova, R. I., Suleimen, Y. M., Oyama, M., Elkaeed, E. B., Eissa, I. H., Suleimen, R. N., … Ishmuratova, M. Y. (2021). Isolation and in Silico Anti-COVID-19 Main Protease (Mpro) Activities of Flavonoids and a Sesquiterpene Lactone from Artemisia sublessingiana. Journal of Chemistry, 2021. https://doi.org/10.1155/2021/5547013
  • Jannat, K., Paul, A. K., Bondhon, T. A., Hasan, A., Nawaz, M., Jahan, R., … Rahmatullah, M. (2021). Nanotechnology Applications of Flavonoids for Viral Diseases. Pharmaceutics, 13(11).
  • Jiménez-Avalos, G., Vargas-Ruiz, A. P., Delgado-Pease, N. E., Olivos-Ramirez, G. E., Sheen, P., Fernández-Díaz, M., … Ygnacio-Aguirre, F. (2021). Comprehensive virtual screening of 4.8 k flavonoids reveals novel insights into allosteric inhibition of SARS-CoV-2 MPRO. Scientific Reports, 11(1), 1–19. https://doi.org/10.1038/s41598-021-94951-6
  • Jo, S, Kim, S., Kim, D. Y., Kim, M. S., & Shin, D. H. (2020). Flavonoids with inhibitory activity against SARS-CoV-2 3CLpro. Journal of Enzyme Inhibition and Medicinal Chemistry, 35(1), 1539–1544. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7470085/pdf/IENZ_35_1801672.pdf
  • Jo, Seri, Kim, S., Shin, D. H., & Kim, M. S. (2020). Inhibition of SARS-CoV 3CL protease by flavonoids. Journal of Enzyme Inhibition and Medicinal Chemistry, 35(1), 145–151. https://doi.org/10.1080/14756366.2019.1690480
  • Johns Hopkins. (2021). Covid 19 Map Channelnewsasis. Retrieved from https://coronavirus.jhu.edu/map.html
  • Johns Hopkins University. (n.d.). COVID-19 Dashboard by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU).
  • Karim, S. S. A., & Karim, Q. A. (2021). Omicron SARS-CoV-2 variant: a new chapter in the COVID-19 pandemic. The Lancet, 398(10317), 2126–2128. https://doi.org/10.1016/s0140-6736(21)02758-6
  • Khursheed, A., Jain, V., Rasool, A., Rather, M. A., Malik, N. A., & Shalla, A. H. (2021). Molecular scaffolds from mother nature as possible lead compounds in drug design and discovery against coronaviruses: A landscape analysis of published literature and molecular docking studies. Microbial Pathogenesis, 157.
  • Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., … Bryant, S. H. (2016). PubChem substance and compound databases. Nucleic Acids Research, 44(D1), D1202–D1213. https://doi.org/10.1093/nar/gkv951
  • Kumar, B., Zaidi, S., Haque, S., Dasgupta, N., Hussain, A., Pramodh, S., … Mishra, B. N. (2021). In Silico Studies Reveal Antiviral Effects of Traditional Indian Spices on COVID-19. Current Pharmaceutical Design, 27(32), 3462–3475. Retrieved from https://www.eurekaselect.net/article/112631
  • Lee, Y. G., Kang, K. W., Hong, W., Kim, Y. H., Oh, J. T., Park, D. W., … Kang, S. C. (2021). Potent antiviral activity of Agrimonia pilosa, Galla rhois, and their components against SARS-CoV-2. Bioorganic & Medicinal Chemistry, 45.
  • Li, L. Y., Ma, L. Y., Hu, Y., Li, X. X., Yu, M., Shang, H., & Zou, Z. M. (2022). Natural biflavones are potent inhibitors against SARS-CoV-2 papain-like protease. Phytochemistry, 193.
  • Liao, Q., Chen, Z. Y., Tao, Y. L., Zhang, B. B., Wu, X. J., Yang, L., … Wang, Z. T. (2021). An integrated method for optimized identification of effective natural inhibitors against SARS-CoV-2 3CLpro. Scientific Reports, 11(1).
  • Lin, Y., Shi, R., Wang, X., & Shen, H.-M. (2008). Luteolin, a Flavonoid with Potential for Cancer Prevention and Therapy. Current Cancer Drug Targets, 8(7), 634–646. https://doi.org/10.2174/156800908786241050
  • Liskova, A., Samec, M., Koklesova, L., Samuel, S. M., Zhai, K. V, Al-Ishaq, R. K., … Kubatka, P. (2021). Flavonoids against the SARS-CoV-2 induced inflammatory storm. Biomedicine & Pharmacotherapy, 138.
  • Ma, L. L., Liu, H. M., Liu, X. M., Yuan, X. Y., Xu, C., Wang, F., … Zhang, D. K. (2021). Screening S protein-ACE2 blockers from natural products: Strategies and advances in the discovery of potential inhibitors of COVID-19. European Journal of Medicinal Chemistry, 226.
  • Maddah, M., Bahramsoltani, R., Yekta, N. H., Rahimi, R., Aliabadi, R., & Pourfath, M. (2021). Proposing high-affinity inhibitors from Glycyrrhiza glabra L. against SARS-CoV-2 infection: virtual screening and computational analysis. New Journal of Chemistry, 45(35), 15977–15995.
  • Maiti, S., & Banerjee, A. (2021). Epigallocatechin gallate and theaflavin gallate interaction inSARS-CoV-2 spike-protein central channel with reference to the hydroxychloroquine interaction: Bioinformatics and molecular docking study. Drug Development Research, 82(1), 86–96. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7436314/pdf/DDR-9999-na.pdf
  • Majumder, R., & Mandal, M. (2020). Screening of plant-based natural compounds as a potential COVID-19 main protease inhibitor: anin silicodocking and molecular dynamics simulation approach. Journal of Biomolecular Structure & Dynamics.
  • Mandour, Y. M., Zlotos, D. P., & Salem, M. A. (2020). A multi-stage virtual screening of FDA-approved drugs reveals potential inhibitors of SARS-CoV-2 main protease. Journal of Biomolecular Structure & Dynamics.
  • Mangiavacchi, F., Botwina, P., Menichetti, E., Bagnoli, L., Rosati, O., Marini, F., … Santi, C. (2021). Seleno-Functionalization of Quercetin Improves the Non-Covalent Inhibition of M-pro and Its Antiviral Activity in Cells against SARS-CoV-2. International Journal of Molecular Sciences, 22(13).
  • Maroli, N., Bhasuran, B., Natarajan, J., & Kolandaivel, P. (2020). The potential role of procyanidin as a therapeutic agent against SARS-CoV-2: a text mining, molecular docking and molecular dynamics simulation approach. Journal of Biomolecular Structure & Dynamics.
  • Mathpal, S., Sharma, P., Joshi, T., Joshi, T., Pande, V., & Chandra, S. (2021). Screening of potential bio-molecules from Moringa olifera against SARS-CoV-2 main protease using computational approaches. Journal of Biomolecular Structure & Dynamics.
  • Mohapatra, P. K., Chopdar, K. S., Dash, G. C., Mohanty, A. K., & Raval, M. K. (2021). In silico screening and covalent binding of phytochemicals of Ocimum sanctum against SARS-CoV-2 (COVID 19) main protease. Journal of Biomolecular Structure & Dynamics.
  • Moradkhani, S., Farmani, A., Saidijam, M., & Taherkhani, A. (2021). COVID-19: docking-based virtual screening and molecular dynamics study to identify potential SARS-CoV-2 spike protein inhibitors from plant-based phenolic compounds. Acta Virologica, 65(3), 288–302.
  • Mosquera-Yuqui, F., Lopez-Guerra, N., & Moncayo-Palacio, E. A. (2020). Targeting the 3CLpro and RdRp of SARS-CoV-2 with phytochemicals from medicinal plants of the Andean Region: molecular docking and molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics.
  • Neves, K. O. G., Ramos, A. S., Bruginski, E. R. D., Souza, A. D. L., Nunomura, R. D. S., Campos, F. R., … Machado, M. B. (2021). Lisboaeflavanonol A: A new flavonoid glycoside obtained from Amazonian Eugenia lisboae. Phytochemistry Letters, 43, 65–69.
  • Ngwa, W., Kumar, R., Thompson, D., Lyerly, W., Moore, R., Reid, T., … Toyang, N. (2020). against COVID-19. 1–10.
  • O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel. Journal of Cheminformatics, 3(33), 1–14.
  • Owis, A. I., El-Hawary, M. S., El Amir, D., Aly, O., Abdelmohsen, U. R., & Kamel, M. S. (2020). Molecular docking reveals the potential of Salvadora persica flavonoids to inhibit COVID-19 virus main protease. Rsc Advances, 10(33), 19570–19575.
  • Owis, A. I., El-Hawary, M. S., El Amir, D., Refaat, H., Alaaeldin, E., Aly, O. M., … Kamel, M. S. (2021). Flavonoids of Salvadora persica L. (meswak) and its liposomal formulation as a potential inhibitor of SARS-CoV-2. Rsc Advances, 11(22), 13537–13544.
  • Potshangbam, A. M., Nongdam, P., Kumar, A. K., & Rathore, R. S. (2021). Phenylbenzopyrone of Flavonoids as a Potential Scaffold to Prevent SARS-CoV-2 Replication by Inhibiting its M-PRO Main Protease. Current Pharmaceutical Biotechnology, 22(15), 2054–2070. Retrieved from https://www.eurekaselect.net/article/113711
  • Prasansuklab, A., Theerasri, A., Rangsinth, P., Sillapachaiyaporn, C., Chuchawankul, S., & Tencomnao, T. (2021). Anti-COVID-19 drug candidates: A review on potential biological activities of natural products in the management of new coronavirus infection. Journal of Traditional and Complementary Medicine, 11(2), 144–157.
  • Puttaswamy, H., Gowtham, H. G., Ojha, M. D., Yadav, A., Choudhir, G., Raguraman, V., … Chauhan, L. (2020). In silico studies evidenced the role of structurally diverse plant secondary metabolites in reducing SARS-CoV-2 pathogenesis. Scientific Reports, 10(1).
  • Rahman, F., Tabrez, S., Ali, R., Alqahtani, A. S., Ahmed, M. Z., & Rub, A. (2021). Molecular docking analysis of rutin reveals possible inhibition of SARS-CoV-2 vital proteins. Journal of Traditional and Complementary Medicine, 11(2), 173–179.
  • Rakshit, M., Muduli, S., Srivastav, P. P., & Mishra, S. (2021). Pomegranate peel polyphenols prophylaxis against SARS-CoV-2 main protease by in-silico docking and molecular dynamics study. Journal of Biomolecular Structure & Dynamics.
  • Rameshkumar, M. R., Indu, P., Arunagirinathan, N., Venkatadri, B., El-Serehy, H. A., & Ahmad, A. (2021). Computational selection of flavonoid compounds as inhibitors against SARS-CoV-2 main protease, RNA-dependent RNA polymerase and spike proteins: A molecular docking study. Saudi Journal of Biological Sciences, 28(1), 448–458. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7581406/pdf/main.pdf
  • Rehman, M. T., AlAjmi, M. F., & Hussain, A. (2021). Natural Compounds as Inhibitors of SARS-CoV-2 Main Protease (3CLpro): A Mo-lecular Docking and Simulation Approach to Combat COVID-19. Current Pharmaceutical Design, 27(33), 3577–3589. Retrieved from https://www.eurekaselect.net/article/111556
  • Rizzuti, B., Grande, F., Conforti, F., Jimenez-Alesanco, A., Ceballos-Laita, L., Ortega-Alarcon, D., … Velazquez-Campoy, A. (2021). Rutin Is a Low Micromolar Inhibitor of SARS-CoV-2 Main Protease 3CLpro: Implications for Drug Design of Quercetin Analogs. Biomedicines, 9(4).
  • Rottier, P. J. M. (1995). The Coronavirus Membrane Glycoprotein. The Coronaviridae, 115–139. https://doi.org/10.1007/978-1-4899-1531-3_6
  • Rudrapal, M., Issahaku, A. R., Agoni, C., Bendale, A. R., Nagar, A., Soliman, M. E. S., & Lokwani, D. (2021). In silico screening of phytopolyphenolics for the identification of bioactive compounds as novel protease inhibitors effective against SARS-CoV-2. Journal of Biomolecular Structure & Dynamics.
  • Samy, M. N., Attia, E. Z., Shoman, M. E., Khalil, H. E., Sugimoto, S., Matsunami, K., & Fahim, J. R. (2021). Phytochemical investigation of Amphilophium paniculatum; an underexploredBignoniaceae species as a source of SARS-CoV-2 M-pro inhibitory metabolites: Isolation, identification, and molecular docking study. South African Journal of Botany, 141, 421–430.
  • Sen, D., Bhaumik, S., Debnath, P., & Debnath, S. (2021). Potentiality of Moringa oleifera against SARS-CoV-2: identified by a rational computer aided drug design method. Journal of Biomolecular Structure & Dynamics.
  • Shaldam, M. A., Yahya, G., Mohamed, N. H., Abdel-Daim, M. M., & Al Naggar, Y. (2021). In silico screening of potent bioactive compounds from honeybee products against COVID-19 target enzymes. Environmental Science and Pollution Research, 28(30), 40507–40514. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8088405/pdf/11356_2021_Article_14195.pdf
  • Shu, Y., & McCauley, J. (2017). GISAID: Global initiative on sharing all influenza data – from vision to reality. Eurosurveillance, 22(13), 2–4. https://doi.org/10.2807/1560-7917.ES.2017.22.13.30494
  • Singh, J., Malik, D., & Raina, A. (2020). Computational investigation for identification of potential phytochemicals and antiviral drugs as potential inhibitors for RNA-dependent RNA polymerase of COVID-19. Journal of Biomolecular Structure & Dynamics.
  • Singh, A. V. (2021). Potential of amentoflavone with antiviral properties in COVID-19 treatment. Asian Biomedicine, 15(4), 153–159.
  • Song, X., Tan, L., Wang, M., Ren, C., Guo, C., Yang, B., … Pei, J. (2021). Myricetin: A review of the most recent research. Biomedicine and Pharmacotherapy, 134, 111017. https://doi.org/10.1016/j.biopha.2020.111017
  • Tyrrell, D. A., & Bynoe, M. L. (1966). Cultivation of viruses from a high proportion of patients with colds. https://doi.org/10.1016/s0140-6736(66)92364-6
  • Vijayakumar, B. G., Ramesh, D., Joji, A., Prakasan, J. J., & Kannan, T. (2020). In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2. European Journal of Pharmacology, 886.
  • Wang, D., Hu, B., Hu, C., Zhu, F., Liu, X., Zhang, J., … Peng, Z. (2020). Clinical Characteristics of 138 Hospitalized Patients with 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China. JAMA - Journal of the American Medical Association, 323(11), 1061–1069. https://doi.org/10.1001/jama.2020.1585
  • Wang, J., Ge, W., Peng, X., Yuan, L. X., He, S. B., & Fu, X. Y. (2021). Investigating the active compounds and mechanism of HuaShi XuanFei formula for prevention and treatment of COVID-19 based on network pharmacology and molecular docking analysis. Molecular Diversity.
  • Xiao, T., Cui, M. Q., Zheng, C. J., Wang, M., Sun, R. H., Gao, D. D., … Zhou, H. G. (2021). Myricetin Inhibits SARS-CoV-2 Viral Replication by Targeting M-pro and Ameliorates Pulmonary Inflammation. Frontiers in Pharmacology, 12.
  • Xiao, T., Cui, M. Q., Zheng, C. J., Zhang, P. P., Ren, S. F., Bao, J. L., … Yang, C. (2021). Both Baicalein and Gallocatechin Gallate Effectively Inhibit SARS-CoV-2 Replication by Targeting M-pro and Sepsis in Mice. Inflammation.
  • Xiong, Y., Zhu, G. H., Zhang, Y. N., Hu, Q., Wang, H. N., Yu, H. N., … Ge, G. B. (2021). Flavonoids in Ampelopsis grossedentata as covalent inhibitors of SARS-CoV-2 3CL(pro): Inhibition potentials, covalent binding sites and inhibitory mechanisms. International Journal of Biological Macromolecules, 187, 976–987. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8322037/pdf/main.pdf
  • Xu, Z. R., Yang, L. X., Zhang, X. H., Zhang, Q. L., Yang, Z. B., Liu, Y. H., … Liu, W. K. (2020). Discovery of Potential Flavonoid Inhibitors Against COVID-19 3CL Proteinase Based on Virtual Screening Strategy. Frontiers in Molecular Biosciences, 7.
  • Xu, Z., Yang, L., Zhang, X., Zhang, Q., Yang, Z., Liu, Y., … Liu, W. (2020). Discovery of Potential Flavonoid Inhibitors Against COVID-19 3CL Proteinase Based on Virtual Screening Strategy. Frontiers in Molecular Biosciences, 7(September), 1–8. https://doi.org/10.3389/fmolb.2020.556481
  • Yosri, N., Abd El-Wahed, A. A., Ghonaim, R., Khattab, O. M., Sabry, A., Ibrahim, M. A. A., … El-Seedi, H. R. (2021). Anti-Viral and Immunomodulatory Properties of Propolis: Chemical Diversity, Pharmacological Properties, Preclinical and Clinical Applications, and In Silico Potential against SARS-CoV-2. Foods, 10(8).
  • Yu, R., Chen, L., Lan, R., Shen, R., & Li, P. (2020). Computational screening of antagonists against the SARS-CoV-2 (COVID-19) coronavirus by molecular docking. International Journal of Antimicrobial Agents, 56(2).
  • Zaki, A. A., Al-Karmalawy, A. A., El-Amier, Y. A., & Ashour, A. (2020). Molecular docking reveals the potential of Cleome amblyocarpa isolated compounds to inhibit COVID-19 virus main protease. New Journal of Chemistry, 44(39), 16752–16758.
  • Zhang, Y., Yao, Y. F., Yang, Y. F., & Wu, H. Z. (2021). Investigation of Anti-SARS, MERS, and COVID-19 Effect of Jinhua Qinggan Granules Based on a Network Pharmacology and Molecular Docking Approach. Natural Product Communications, 16(5).
  • Zhou, P., Yang, X. Lou, Wang, X. G., Hu, B., Zhang, L., Zhang, W., … Shi, Z. L. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270–273. https://doi.org/10.1038/s41586-020-2012-7
  • Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., … Tan, W. (2020). A Novel Coronavirus from Patients with Pneumonia in China, 2019. New England Journal of Medicine, 382(8), 727–733. https://doi.org/10.1056/nejmoa2001017
  • Zhu, Y., & Xie, D. Y. (2020). Docking Characterization and in vitro Inhibitory Activity of Flavan-3-ols and Dimeric Proanthocyanidins Against the Main Protease Activity of SARS-Cov-2. Frontiers in Plant Science, 11.
There are 108 citations in total.

Details

Primary Language English
Subjects Atomic, Molecular and Optical Physics, Nonlinear Optics and Spectroscopy
Journal Section Articles
Authors

Tayfun Gençsoy 0000-0001-7893-280X

Naim Peker 0000-0002-6446-1258

Hasan Tugra Yavas 0000-0002-6604-8731

Ozan Ünsalan 0000-0001-5736-7530

Early Pub Date December 25, 2022
Publication Date December 31, 2022
Submission Date December 27, 2021
Acceptance Date September 3, 2022
Published in Issue Year 2022 Volume: 4 Issue: 2

Cite

APA Gençsoy, T., Peker, N., Yavas, H. T., Ünsalan, O. (2022). Rutin, luteolin, and myricetin as potential inhibitors of SARS-CoV-2 Main Protease (Mpro): A virtual screening study. Journal of Spectroscopy and Molecular Sciences, 4(2), 171-192.