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Research Article

Phytochemicals of Cocculus hirsutus deciphered SARS-CoV-2 inhibition by targeting main proteases in molecular docking, simulation, and pharmacological analyses

ORCID Icon, , , , &
Pages 7406-7420 | Received 27 Apr 2022, Accepted 31 Aug 2022, Published online: 13 Sep 2022

References

  • Bhardwaj, V. K., Singh, R., Das, P., & Purohit, R. (2021). Evaluation of acridinedione analogs as potential SARS-CoV-2 main protease inhibitors and their comparison with repurposed anti-viral drugs. Computers in Biology and Medicine, 128, 104117. https://doi.org/10.1016/j.compbiomed.2020.104117
  • Bhardwaj, V. K., Singh, R., Sharma, J., Rajendran, V., Purohit, R., & Kumar, S. (2021). Bioactive molecules of Tea as potential inhibitors for RNA-dependent RNA polymerase of SARS-CoV-2. Frontiers in Medicine, 8, 684020. https://dx.doi.org/10.3389/fmed.2021.684020
  • Bhardwaj, V. K., Singh, R., Sharma, J., Rajendran, V., Purohit, R., & Kumar, S. (2021). Identification of bioactive molecules from tea plant as SARS-CoV-2 main protease inhibitors. Journal of Biomolecular Structure & Dynamics, 39(10), 3449–3458.
  • Chen, B., Tian, E.-K., He, B., Tian, L., Han, R., Wang, S., Xiang, Q., Zhang, S., El Arnaout, T., & Cheng, W. (2020). Overview of lethal human coronaviruses. Signal Transduction and Targeted Therapy, 5(1), 1–16. https://doi.org/10.1038/s41392-020-0190-2
  • Coelho, C., Gallo, G., Campos, C. B., Hardy, L., & Wurtele, M. (2020). Biochemical screening for SARS-CoV-2 main protease inhibitors. PloS One, 15(10), e0240079. https://doi.org/10.1371/journal.pone.0240079
  • Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42713–42717. https://doi.org/10.1038/srep42717
  • Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx. In Chemical biology (vol. 1263, pp. 243–250). Humana press. https://doi.org/10.1007/978-1-4939-2269-7_19
  • De Ruyck, J., Brysbaert, G., Blossey, R., & Lensink, M. F. (2016). Molecular docking as a popular tool in drug design, an in-silico travel. Advances and Applications in Bioinformatics and Chemistry: AABC, 9, 1–11. https://doi.org/10.2147/aabc.s105289
  • De Wet, H., Struwig, M., & Van Wyk, B. E. (2015). Taxonomic notes on the genus Cocculus (Menispermaceae) in southern Africa. South African Journal of Botany, 96, 99–104. https://doi.org/10.1016/j.sajb.2014.10.007
  • Ding, Y. G., Zhao, Y. L., Zhang, J., Zuo, Z. T., Zhang, Q. Z., & Wang, Y. Z. (2021). The traditional uses, phytochemistry, and pharmacological properties of Paris L.(Liliaceae): A review. Journal of Ethnopharmacology, 278, 114293. https://doi.org/10.1016/j.jep.2021.114293
  • Fearon, D., Powell, A., Douangamath, A., Owen, C., Wild, C., Krojer, T., Lukacik, P., Strain-Damerell, C., Walsh, M., & von Delft, F. (2020). PanDDA analysis group deposition–crystal structure of COVID-19 main protease in complex with Z219104216. Protein Data Base, 10. https://doi.org/10.2210/pdb5R82/pdb
  • Fearon, D., Powell, A., Douangamath, A., Owen, C., Wild, C., Krojer, T., Lukacik, P., Strain-Damerell, C., Walsh, M., & von Delft, F. (2020). PanDDA analysis group deposition—crystal structure of SARS-CoV-2 main protease in complex with Z1220452176. Protein Data Bank. https://doi.org/10.2210/pdb5R7Z/pdb
  • Ghasemi, F., Zomorodipour, A., Karkhane, A. A., & Khorramizadeh, M. R. (2016). In silico designing of hyper-glycosylated analogs for the human coagulation factor IX. Journal of Molecular Graphics & Modelling, 68, 39–47.
  • Goodla, L., Manubolu, M., Pathakoti, K., & Poondamalli, P. R. (2017). Preventive and curative effects of Cocculus hirsutus (Linn.) Diels leaves extract on CCl4 provoked hepatic injury in rats. Egyptian Journal of Basic and Applied Sciences, 4(4), 264–269. https://doi.org/10.1016/j.ejbas.2017.10.004
  • Hospital, A., Andrio, P., Fenollosa, C., Cicin-Sain, D., Orozco, M., & Gelpi, J. L. (2012). MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Bioinformatics (Oxford, England), 28(9), 1278–1279. https://doi.org/10.1093/bioinformatics/bts139
  • Hospital, A., Goñi, J. R., Orozco, M., & Gelpí, J. L. (2015). Molecular dynamics simulations: advances and applications. Advances and Applications in Bioinformatics and Chemistry, 8, 37.
  • Ibrahim, M. A., Abdelrahman, A. H., Hussien, T. A., Badr, E. A., Mohamed, T. A., El-Seedi, H. R., Pare, P. W., Efferth, T., & Hegazy, M.-E. F. (2020). In silico drug discovery of major metabolites from spices as SARS-CoV-2 main protease inhibitors. Computers in Biology and Medicine, 126, 104046. https://dx.doi.org/10.1016/2Fj.compbiomed.2020.104046
  • Ibrahim, M. A., Mohamed, E. A., Abdelrahman, A. H., Allemailem, K. S., Moustafa, M. F., Shawky, A. M., Mahzari, A., Hakami, A. R., Abdeljawaad, K. A., & Atia, M. A. (2021). Rutin and flavone analogs as prospective SARS-CoV-2 main protease inhibitors: In silico drug discovery study. Journal of Molecular Graphics & Modelling, 105, 107904. https://doi.org/10.1016/j.jmgm.2021.107904
  • Jacobson, M. P., Pincus, D. L., Rapp, C. S., Day, T. J., Honig, B., Shaw, D. E., & Friesner, R. A. (2004). A hierarchical approach to all-atom protein loop prediction. Proteins, 55(2), 351–367. https://doi.org/10.1002/prot.10613
  • Jha, A., Verma, S., & Kumar, A. (2020). Identification of potential inhibitors targeted for strengthening search of anti-leishmanial therapeutics. Biologia, 75(3), 437–445. https://doi.org/10.2478/s11756-019-00360-6
  • Kashiwada, Y., Aoshima, A., Ikeshiro, Y., Chen, Y. P., Furukawa, H., Itoigawa, M., Fujioka, T., Mihashi, K., Cosentino, L. M., Morris-Natschke, S. L., & Lee, K. H. (2005). Anti-HIV benzylisoquinoline alkaloids and flavonoids from the leaves of Nelumbo nucifera, and structure–activity correlations with related alkaloids. Bioorganic & Medicinal Chemistry, 13(2), 443–448. https://doi.org/10.1016/j.bmc.2004.10.020
  • Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., Wang, J., Yu, B., Zhang, J., & Bryant, S. H. (2016). PubChem Substance and Compound databases. Nucleic Acids Research, 44(D1), D1202–13. https://doi.org/10.1093/nar/gkv951. Epub 2015 Sep 22
  • Kufareva, I., & Abagyan, R. (2011). Methods of protein structure comparison. In Homology modeling (pp. 231–257). Humana Press. https://doi.org/10.1007/978-1-61779-588-6_10
  • Kumar, A. N., & Murugan, K. (2011). Antimalarial and antivectoral activities of traditionally used indigenous medicinal plants. Advances in Environmental Biology, 5(2), 407–413.
  • Lin, X., Li, X., & Lin, X. (2020). A review on applications of computational methods in drug screening and design. Molecules, 25(6), 1375. https://doi.org/10.3390/molecules25061375
  • Liu, M., Wang, T., Zhou, Y., Zhao, Y., Zhang, Y., & Li, J. (2020). Potential role of ACE2 in coronavirus disease 2019 (COVID-19) prevention and management. Journal of Translational Internal Medicine, 8(1), 9–19. https://dx.doi.org/10.2478/2Fjtim-2020-0003
  • Liu, X., Zhang, B., Jin, Z., Yang, H., & Rao, Z. (2020). The crystal structure of COVID-19 main protease in complex with an inhibitor N3. Protein Data Bank, 10. https://doi.org/10.2210/pdb6LU7/pdb
  • Lobanov, M. I., Bogatyreva, N. S., & Galzitskaia, O. V. (2008). Radius of gyration is indicator of compactness of protein structure. Molekuliarnaia Biologiia, 42(4), 701–706.
  • Lokhande, K. B., Doiphode, S., Vyas, R., & Swamy, K. V. (2021). Molecular docking and simulation studies on SARS-CoV-2 Mpro reveals Mitoxantrone, Leucovorin, Birinapant, and Dynasore as potent drugs against COVID-19. Journal of Biomolecular Structure & Dynamics, 39(18), 7294–7305.
  • Ma, C., Sacco, M. D., Hurst, B., Townsend, J. A., Hu, Y., Szeto, T., Zhang, X., Tarbet, B., Marty, M. T., Chen, Y., & Wang, J. (2020). Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease. Cell Research, 30(8), 678–692. https://doi.org/10.1038/s41422-020-0356-z
  • Marquez, S., Prado-Vivar, B., Guadalupe, J. J., Gutierrez Granja, B., Jibaja, M., Tobar, M., Mora, F., Gaviria, J., Garcia, M., Ligna, E., Espinosa, F., Reyes, J., Barragan, V., Rojas-Silva, P., Trueba, G., Grunauer, M., & Cardenas, P. (2020). Genome sequencing of the first SARS-CoV-2 reported from patients with COVID-19 in Ecuador. MedRxiv. https://doi.org/10.1101/2020.06.11.20128330
  • Marya, B. H., & Bothara, S. (2011). Ethnopharmacological properties of Cocculus hirsutus (L.) Diels-a review. International Journal of Pharmaceutical Sciences Review and Research, 7(1), 108–112.
  • Meena, M. K., Singh, N., & Patni, V. (2014). Determination of bioactive components of the leaves of Cocculus hirsutus (L.) Diels using GC-MS analysis. International Journal of Pharmacy and Pharmaceutical Sciences, 6, 327–329.
  • Panigrahy, S. K., Kumar, A., & Bhatt, R. (2020). Hedychium coronarium rhizomes: promising antidiabetic and natural inhibitor of α-amylase and α-glucosidase. Journal of Dietary Supplements, 17(1), 81–87. https://doi.org/10.1080/19390211.2018.1483462
  • Pattar, S. V., Adhoni, S. A., Kamanavalli, C. M., & Kumbar, S. S. (2020). In silico molecular docking studies and MM/GBSA analysis of coumarin-carbonodithioate hybrid derivatives divulge the anticancer potential against breast cancer. Beni-Suef University Journal of Basic and Applied Sciences, 9(1), 1–10. https://doi.org/10.1186/s43088-020-00059-7
  • Pavlova, N. I., Savinova, O. V., Nikolaeva, S. N., Boreko, E. I., & Flekhter, O. B. (2003). Antiviral activity of betulin, betulinic and betulonic acids against some enveloped and non-enveloped viruses. Fitoterapia, 74(5), 489–492. https://doi.org/10.1016/S0367-326X(03)00123-0
  • Qiao, J., Li, Y.-S., Zeng, R., Liu, F.-L., Luo, R.-H., Huang, C., Wang, Y.-F., Zhang, J., Quan, B., Shen, C., Mao, X., Liu, X., Sun, W., Yang, W., Ni, X., Wang, K., Xu, L., Duan, Z.-L., Zou, Q.-C., … Yang, S. (2021). SARS-CoV-2 Mpro inhibitors with antiviral activity in a transgenic mouse model. Science (New York, NY), 371(6536), 1374–1378. https://doi.org/10.1126/science.abf1611
  • Rowaiye, A. B., Olubiyi, J., Bur, D., Uzochukwu, I. C., Akpa, A., & Esimone, C. O. (2021). In silico screening and molecular dynamic simulation studies of potential small molecule immuno-modulators of the KIR2DS2 receptor. Journal of Phytomedicine and Therapeutics, 20(1), 542–567. https://doi.org/10.4314/jopat.v20i1.8
  • Sacco, M. D., Ma, C., Lagarias, P., Gao, A., Townsend, J. A., Meng, X., Dube, P., Zhang, X., Hu, Y., Kitamura, N., Hurst, B., Tarbet, B., Marty, M. T., Kolocouris, A., Xiang, Y., Chen, Y., & Wang, J. (2020). Structure and inhibition of the SARS-CoV-2 main protease reveal strategy for developing dual inhibitors against M(pro) and cathepsin L. Science Advances, 6(50), eabe0751. https://dx.doi.org/10.1101/2F2020.07.27.223727
  • Seth, S., Batra, J., & Srinivasan, S. (2020). COVID-19: Targeting proteases in viral invasion and host immune response. Frontiers in Molecular Biosciences, 7, 215. https://doi.org/10.3389/fmolb.2020.00215
  • Sharma, J., Bhardwaj, V. K., Singh, R., Rajendran, V., Purohit, R., & Kumar, S. (2021). An in-silico evaluation of different bioactive molecules of tea for their inhibition potency against non-structural protein-15 of SARS-CoV-2. Food Chemistry, 346, 128933. https://dx.doi.org/10.1016/j.foodchem.2020.128933
  • Shukla, R., Rajpoot, R. K., Poddar, A., Ahuja, R., Beesetti, H., Shanmugam, R. K., Chaturvedi, S., Nayyar, K., Singh, D., Singamaneni, V., Gupta, P., Gupta, A. P., Gairola, S., Kumar, P., Bedi, Y. S., Jain, T., Vashishta, B., Patil, R., Madan, H., … Khanna, N. (2021). Cocculus hirsutus-derived phytopharmaceutical drug has potent anti-dengue activity. Frontiers in Microbiology, 12, 746110. https://doi.org/10.3389/fmicb.2021.746110
  • Singh, N., Kumar, A., Gupta, P., Chand, K., Samant, M., Maurya, R., & Dube, A. (2008). Evaluation of antileishmanial potential of Tinospora sinensis against experimental visceral leishmaniasis. Parasitology Research, 102(3), 561–565. https://doi.org/10.1007/s00436-007-0822-2
  • Singh, R., Bhardwaj, V. K., & Purohit, R. (2021). Potential of turmeric-derived compounds against RNA‐dependent RNA polymerase of SARS‐CoV‐2: An in-silico approach. Computers in Biology and Medicine, 139, 104965. https://dx.doi.org/10.1016/j.compbiomed.2021.104965
  • Singh, R., Bhardwaj, V. K., Das, P., & Purohit, R. (2021). A computational approach for rational discovery of inhibitors for non-structural protein 1 of SARS-CoV-2. Computers in Biology and Medicine, 135, 104555. https://dx.doi.org/10.1016/j.compbiomed.2021.104555
  • Singh, R., Bhardwaj, V. K., Das, P., Bhattacherjee, D., Zyryanov, G. V., & Purohit, R. (2022). Benchmarking the ability of novel compounds to inhibit SARS-CoV-2 main protease using steered molecular dynamics simulations. Computers in Biology and Medicine, 146, 105572. https://doi.org/10.1016/j.compbiomed.2022.105572
  • Singh, R., Bhardwaj, V. K., Sharma, J., Kumar, D., & Purohit, R. (2021). Identification of potential plant bioactive as SARS-CoV-2 Spike protein and human ACE2 fusion inhibitors. Computers in Biology and Medicine, 136, 104631. https://dx.doi.org/10.1016/j.compbiomed.2021.104631
  • Singh, R., Bhardwaj, V. K., Sharma, J., Purohit, R., & Kumar, S. (2022). In-silico evaluation of bioactive compounds from tea as potential SARS-CoV-2 nonstructural protein 16 inhibitors. Journal of Traditional and Complementary Medicine, 12(1), 35–43. https://dx.doi.org/10.1016/j.jtcme.2021.05.005
  • Su, S., Wong, G., Shi, W., Liu, J., Lai, A. C. K., Zhou, J., Liu, W., Bi, Y., & Gao, G. F. (2016). Epidemiology, genetic recombination, and pathogenesis of coronaviruses. Trends in Microbiology, 24(6), 490–502. https://doi.org/10.1016/j.tim.2016.03.003
  • Sun, Z., Liu, Q., Qu, G., Feng, Y., & Reetz, M. T. (2019). Utility of B-factors in protein science: interpreting rigidity, flexibility, and internal motion and engineering thermostability. Chemical Reviews, 119(3), 1626–1665.
  • Umar, A. B., Uzairu, A., Shallangwa, G. A., & Uba, S. (2020). In silico evaluation of some 4-(quinolin-2-yl) pyrimidin-2-amine derivatives as potent V600E-BRAF inhibitors with pharmacokinetics ADMET and drug-likeness predictions. Future Journal of Pharmaceutical Sciences, 6(1), 1–10. https://doi.org/10.1186/s43094-020-00084-4
  • Vuong, W., Khan, M. B., Fischer, C., Arutyunova, E., Lamer, T., Shields, J., Saffran, H. A., McKay, R. T., van Belkum, M. J., Joyce, M. A., Young, H. S., Tyrrell, D. L., Vederas, J. C., & Lemieux, M. J. (2020). Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication. Nature Communications, 11(1), 1–8. https://doi.org/10.1038/s41467-020-18096-2
  • Yi, F., Li, L., Xu, L. J., Meng, H., Dong, Y. M., Liu, H. B., & Xiao, P. G. (2018). In silico approach in reveal traditional medicine plants pharmacological material basis. Chinese Medical Journal, 13(1), 1–20. https://doi.org/10.1186/s13020-018-0190-0
  • Zanello, P. R., Koishi, A. C., Rezende Júnior, C. D. O., Oliveira, L. A., Pereira, A. A., de Almeida, M. V., Duarte dos Santos, C. N., & Bordignon, J. (2015). Quinic acid derivatives inhibit dengue virus replication in vitro. Virology Journal, 12(1), 1–13. https://doi.org/10.1186/s12985-015-0443-9
  • Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., Becker, S., Rox, K., & Hilgenfeld, R. (2020). Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors. Science (New York, NY), 368(6489), 409–412. https://doi.org/10.1126/science.abb3405

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