155
Views
0
CrossRef citations to date
0
Altmetric
Research Articles

Exploration of potent antiviral phytomedicines from Lauraceae family plants against SARS-CoV-2 RNA-dependent RNA polymerase

, , , , ORCID Icon, , , , & show all
Pages 15085-15105 | Received 07 Nov 2022, Accepted 23 Feb 2023, Published online: 08 Mar 2023

References

  • Alam, A., Agrawal, G. P., Khan, S., Khalilullah, H., Saifullah, M. K., & Arshad, M. F. (2022). Towards the discovery of potential RdRp inhibitors for the treatment of COVID-19: Structure guided virtual screening, computational ADME and molecular dynamics study. Structural Chemistry, 33(5), 1569–1583. https://doi.org/10.1007/s11224-022-01976-2
  • Appleby, T. C., Perry, J. K., Murakami, E., Barauskas, O., Feng, J., Cho, A., Fox, D., Wetmore, D. R., McGrath, M. E., Ray, A. S., Sofia, M. J., Swaminathan, S., & Edwards, T. E. (2015). Structural basis for RNA replication by the hepatitis C virus polymerase. Science (New York, N.Y.), 347(6223), 771–775. https://doi.org/10.1126/science.1259210
  • Bajrai, L. H., Khateb, A. M., & Alawi, M. M. (2022). Glycosylated flavonoid compounds as potent CYP121 inhibitors of mycobacterium tuberculosis. Biomolecules, 12, 1356. https://doi.org/10.3390/biom12101356
  • Banerjee, P., Eckert, A. O., Schrey, A. K., & Preissner, R. (2018). ProTox-II: A webserver for the prediction of toxicity of chemicals. Nucleic Acids Research, 46(W1), W257–W263. https://doi.org/10.1093/nar/gky318
  • Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
  • Bharadwaj, S., Azhar, E. I., Kamal, M. A., Bajrai, L. H., Dubey, A., Jha, K., Yadava, U., Kang, S. G., & Dwivedi, V. D. (2022). SARS-CoV-2 Mpro inhibitors: Identification of anti-SARS-CoV-2 Mpro compounds from FDA approved drugs. Journal of Biomolecular Structure & Dynamics, 40(6), 2769–2784. https://doi.org/10.1080/07391102.2020.1842807
  • Bharadwaj, S., Dubey, A., Yadava, U., Mishra, S. K., Kang, S. G., & Dwivedi, V. D. (2021). Exploration of natural compounds with anti-SARS-CoV-2 activity via inhibition of SARS-CoV-2 Mpro. Briefings in Bioinformatics, 22(2), 1361–1377. https://doi.org/10.1093/bib/bbaa382
  • Bharadwaj, S., El-Kafrawy, S. A., & Alandijany, T. A. (2021). Structure-based identification of natural products as SARS-CoV-2 Mpro antagonist from Echinacea angustifolia using computational approaches. Viruses, 13, 305. https://doi.org/10.3390/v13020305
  • Bruni, R., Medici, A., & Andreotti, E. (2004). Chemical composition and biological activities of Ishpingo essential oil, a traditional Ecuadorian spice from Ocotea quixos (Lam.) Kosterm. (Lauraceae) flower calices. Food chemistry. [Internet] [cited 2022 Oct 10] https://scholar.google.com/scholar_lookup?title=Chemical+composition+and+biological+activities+of+Ishpingo+essential+oil%2C+a+traditional+Ecuadorian+spice+from+Ocotea+quixos+%28Lam.%29+Kosterm.+%28Lauraceae%29+flower+calices&author=Bruni%2C+R.&publication_year=2004.
  • Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chen, L., Crichlow, G. V., Christie, C. H., Dalenberg, K., Di Costanzo, L., Duarte, J. M., Dutta, S., Feng, Z., Ganesan, S., Goodsell, D. S., Ghosh, S., Green, R. K., Guranović, V., Guzenko, D., Hudson, B. P., … Zhuravleva, M. (2021). RCSB protein data bank: Powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. Nucleic Acids Research, 49(D1), D437–D451. https://doi.org/10.1093/nar/gkaa1038
  • Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. The Journal of Chemical Physics, 126(1), 014101. https://doi.org/10.1063/1.2408420
  • Chafekar, A., & Fielding, B. C. (2018). MERS-CoV: Understanding the latest human coronavirus threat. Viruses, 10, 93. https://doi.org/10.3390/v10020093
  • Cheng, A., Zhang, W., Xie, Y., Jiang, W., Arnold, E., Sarafianos, S. G., & Ding, J. (2005). Expression, purification, and characterization of SARS coronavirus RNA polymerase. Virology, 335(2), 165–176. https://doi.org/10.1016/j.virol.2005.02.017
  • Chin, C., Yen, K. H., & Mian, V. J. Y. (2010). Antioxidant activities of traditional medicinal plants from Lauraceae family in Sarawak. International Conference on Science and Social Research (CSSR 2010) (pp. 783–785).
  • 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, 42717. https://doi.org/10.1038/srep42717
  • Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. Journal of Chemical Physics, 98, 10089–10092. https://doi.org/10.1063/1.464397
  • DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsl Protein Crystallogr, 40, 82–92.
  • Deng, S.-Q., & Peng, H.-J. (2020). Characteristics of and public health responses to the coronavirus disease 2019 outbreak in China. Journal of Clinical Medicine, 9, 575. https://doi.org/10.3390/jcm9020575
  • Eberhardt, J., Santos-Martins, D., Tillack, A. F., & Forli, S. (2021). AutoDock Vina 1.2.0: New docking methods, expanded force field, and python bindings. Journal of Chemical Information and Modeling, 61(8), 3891–3898. https://doi.org/10.1021/acs.jcim.1c00203
  • Fährrolfes, R., Bietz, S., Flachsenberg, F., Meyder, A., Nittinger, E., Otto, T., Volkamer, A., & Rarey, M. (2017). ProteinsPlus: A web portal for structure analysis of macromolecules. Nucleic Acids Research, 45(W1), W337–W343. https://doi.org/10.1093/nar/gkx333
  • Geethangili, M., & Ding, S.-T. (2018). A review of the phytochemistry and pharmacology of Phyllanthus urinaria L. Frontiers in Pharmacology, 9, 1109.
  • Glab-Ampai, K., Kaewchim, K., & Thavorasak, T. (2022). Targeting emerging RNA viruses by engineered human superantibody to hepatitis C virus RNA-dependent RNA polymerase. Frontiers in Microbiology, 13, 926929.
  • Gong, P., & Peersen, O. B. (2010). Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase. Proceedings of the National Academy of Sciences of the United States of America, 107(52), 22505–22510. https://doi.org/10.1073/pnas.1007626107
  • Guan, W.-J., Ni, Z.-Y., Hu, Y., Liang, W.-H., Ou, C.-Q., He, J.-X., Liu, L., Shan, H., Lei, C.-L., Hui, D. S. C., Du, B., Li, L.-J., Zeng, G., Yuen, K.-Y., Chen, R.-C., Tang, C.-L., Wang, T., Chen, P.-Y., Xiang, J., … Zhong, N.-S, China Medical Treatment Expert Group for Covid-19. (2020). Clinical characteristics of coronavirus disease 2019 in China. The New England Journal of Medicine, 382(18), 1708–1720. https://doi.org/10.1056/NEJMoa2002032
  • Hardin, C., Pogorelov, T. V., & Luthey-Schulten, Z. (2002). Ab initio protein structure prediction. Current Opinion in Structural Biology, 12(2), 176–181. https://doi.org/10.1016/s0959-440x(02)00306-8
  • Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(3), 435–447. https://doi.org/10.1021/ct700301q
  • Hu, B., Guo, H., Zhou, P., & Shi, Z.-L. (2021). Characteristics of SARS-CoV-2 and COVID-19. Nature Reviews. Microbiology, 19(3), 141–154. https://doi.org/10.1038/s41579-020-00459-7
  • Huang, C., Wang, Y., Li, X., Ren, L., Zhao, J., Hu, Y., Zhang, L., Fan, G., Xu, J., Gu, X., Cheng, Z., Yu, T., Xia, J., Wei, Y., Wu, W., Xie, X., Yin, W., Li, H., Liu, M., … Cao, B. (2020). Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet (London, England), 395(10223), 497–506. https://doi.org/10.1016/S0140-6736(20)30183-5
  • Jayaram, B., Singh, T., & Mukherjee, G. (2012). Sanjeevini: A freely accessible web-server for target directed lead molecule discovery. BMC Bioinformatics, 13, S7. https://doi.org/10.1186/1471-2105-13-S17-S7
  • Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., & Bolton, E. E. (2021). PubChem in 2021: New data content and improved web interfaces. Nucleic Acids Research, 49(D1), D1388–D1395. https://doi.org/10.1093/nar/gkaa971
  • Kirchdoerfer, R. N., & Ward, A. B. (2019). Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors. Nature Communications, 10(1), 2342. https://doi.org/10.1038/s41467-019-10280-3
  • Kumar, S., Bajrai, L. H., & Faizo, A. A. (2022). Pharmacophore-model-based drug repurposing for the identification of the potential inhibitors targeting the allosteric site in dengue virus NS5 RNA-dependent RNA polymerase. Viruses, 14, 1827. https://doi.org/10.3390/v14081827
  • Kumar, S., Kumar, G. S., & Maitra, S. S. (2022). Viral informatics: Bioinformatics-based solution for managing viral infections. Briefings in Bioinformatics, 23, bbac326. https://doi.org/10.1093/bib/bbac326
  • Kumari, R., Kumar, R., & Lynn, A. (2014). g_mmpbsa—A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
  • Lipinski, C. A. (2004). Lead- and drug-like compounds: the rule-of-five revolution. Drug Discovery Today Technologies, 1(4), 337–341. https://doi.org/10.1016/j.ddtec.2004.11.007
  • Liyongo Inkoto, C., Ngiala Bongo, G., & Mutwale Kapepula, P. (2018). Microscopic features and chromatographic fingerprints of selected congolese medicinal plants: Aframomum alboviolaceum (Ridley) K. Schum, Annona senegalensis Pers. and Mondia whitei (Hook.f.) Skeels. ELSR, 4, 1–10. https://doi.org/10.31783/ELSR.2018.410110
  • MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., … Karplus, M. (1998). All-atom empirical potential for molecular modeling and dynamics studies of proteins. The Journal of Physical Chemistry B, 102(18), 3586–3616. https://doi.org/10.1021/jp973084f
  • Malik, Y. S., Kumar, N., & Sircar, S. (2020). Coronavirus disease pandemic (COVID-19): Challenges and a global perspective. Pathogens, 9, 519. https://doi.org/10.3390/pathogens9070519
  • Martí-Renom, M. A., Stuart, A. C., Fiser, A., Sánchez, R., Melo, F., & Sali, A. (2000). Comparative protein structure modeling of genes and genomes. Annual Review of Biophysics and Biomolecular Structure, 29, 291–325. https://doi.org/10.1146/annurev.biophys.29.1.291
  • McDonald, S. M. (2013). RNA synthetic mechanisms employed by diverse families of RNA viruses. Wiley Interdisciplinary Reviews. RNA, 4(4), 351–367. https://doi.org/10.1002/wrna.1164
  • Mercatelli, D., & Giorgi, F. M. (2020). Geographic and genomic distribution of SARS-CoV-2 Mutations. Frontiers in Microbiology, 11, 1800.
  • Miller, B. R., McGee, T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA.py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3321. https://doi.org/10.1021/ct300418h
  • Min, J. S., Kwon, S., & Jin, Y.-H. (2021). SARS-CoV-2 RdRp inhibitors selected from a cell-based SARS-CoV-2 RdRp activity assay system. Biomedicines, 9, 996. https://doi.org/10.3390/biomedicines9080996
  • Mishra, A., & Rathore, A. S. (2022). RNA dependent RNA polymerase (RdRp) as a drug target for SARS-CoV2. Journal of Biomolecular Structure & Dynamics, 40(13), 6039–6051. https://doi.org/10.1080/07391102.2021.1875886
  • Molecular complexes at a glance: Automated generation of two-dimensional complex diagrams – PubMed. (2022 October 10). [Internet]. https://pubmed.ncbi.nlm.nih.gov/16632493/.
  • Mpiana, P. T., Ngbolua, K.-T.-N., Tshibangu, D. S. T., Kilembe, J. T., Gbolo, B. Z., Mwanangombo, D. T., Inkoto, C. L., Lengbiye, E. M., Mbadiko, C. M., Matondo, A., Bongo, G. N., & Tshilanda, D. D. (2020). Identification of potential inhibitors of SARS-CoV-2 main protease from Aloe vera compounds: A molecular docking study. Chemical Physics Letters, 754, 137751. https://doi.org/10.1016/j.cplett.2020.137751
  • Mukherjee, S., & Zhang, Y. (2011). Protein-protein complex structure predictions by multimeric threading and template recombination. Structure (London, England: 1993), 19(7), 955–966. https://doi.org/10.1016/j.str.2011.04.006
  • O’Boyle, N. M., Banck, M., & James, C. A. (2011). Open babel: An open chemical toolbox. Journal of Cheminformatics, 3, 33. https://doi.org/10.1186/1758-2946-3-33
  • Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52, 7182–7190. https://doi.org/10.1063/1.328693
  • ProteinsPlus: Interactive analysis of protein–ligand binding interfaces | Nucleic Acids Research | Oxford Academic. (2022 October 10). [Internet]. https://academic.oup.com/nar/article/48/W1/W48/5820880.
  • R Core Team. (2017). R: A language and environment for statistical computing. https://www.R-project.org/.
  • Sanders, J. M., Monogue, M. L., Jodlowski, T. Z., & Cutrell, J. B. (2020). Pharmacologic treatments for coronavirus disease 2019 (COVID-19): A review. JAMA, 323(18), 1824–1836. https://doi.org/10.1001/jama.2020.6019
  • Sawicki, S. G., Sawicki, D. L., & Siddell, S. G. (2007). A contemporary view of coronavirus transcription. Journal of Virology, 81(1), 20–29. https://doi.org/10.1128/JVI.01358-06
  • Singh, N. A., Kumar, P., Jyoti, & Kumar, N. (2021). Spices and herbs: Potential antiviral preventives and immunity boosters during COVID-19. Phytotherapy Research: PTR, 35(5), 2745–2757. https://doi.org/10.1002/ptr.7019
  • Snijder, E. J., Decroly, E., & Ziebuhr, J. (2016). Chapter three – The nonstructural proteins directing coronavirus RNA synthesis and processing. In Ziebuhr J (Ed.), Advances in virus research [Internet] (pp. 59–126). Academic Press. [cited 2022 Oct 10]. Available from: https://www.sciencedirect.com/science/article/pii/S0065352716300471.
  • Spiteri, G., Fielding, J., & Diercke, M. (2020). First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020. Euro Surveill, 25, 2000178.
  • Subissi, L., Posthuma, C. C., Collet, A., Zevenhoven-Dobbe, J. C., Gorbalenya, A. E., Decroly, E., Snijder, E. J., Canard, B., & Imbert, I. (2014). One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities. Proceedings of the National Academy of Sciences of the United States of America, 111(37), E3900–E3909. https://doi.org/10.1073/pnas.1323705111
  • Swain, S. S., Panda, S. K., & Luyten, W. (2021). Phytochemicals against SARS-CoV as potential drug leads. Biomedical Journal, 44(1), 74–85. https://doi.org/10.1016/j.bj.2020.12.002
  • Trott, O., & 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, 455–461.
  • Tshilanda, D. D., Onyamboko, D. N., Babady-Bila, P., Ngbolua, K.-T.-N., Tshibangu, D. S., Dia Fita Dibwe, E., & Mpiana, P. T. (2015). Anti-sickling activity of ursolic acid isolated from the leaves of Ocimum gratissimum L. (Lamiaceae). Natural Products and Bioprospecting, 5(4), 215–221. https://doi.org/10.1007/s13659-015-0070-6
  • Uengwetwanit, T., Chutiwitoonchai, N., Wichapong, K., & Karoonuthaisiri, N. (2022). Identification of novel SARS-CoV-2 RNA dependent RNA polymerase (RdRp) inhibitors: From in silico screening to experimentally validated inhibitory activity. Computational and Structural Biotechnology Journal, 20, 882–890. https://doi.org/10.1016/j.csbj.2022.02.001
  • Valdés-Tresanco, M. S., Valdés-Tresanco, M. E., Valiente, P. A., & Moreno, E. (2021). gmx_MMPBSA: A new tool to perform end-state free energy calculations with GROMACS. Journal of Chemical Theory and Computation, 17(10), 6281–6291. https://doi.org/10.1021/acs.jctc.1c00645
  • Vanommeslaeghe, K., Raman, E. P., & MacKerell, A. D. (2012). Automation of the CHARMM General Force Field (CGenFF) II: Assignment of bonded parameters and partial atomic charges. Journal of Chemical Information and Modeling, 52(12), 3155–3168. https://doi.org/10.1021/ci3003649
  • Walls, A. C., Park, Y.-J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020). Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell, 181(2), 281–292.e6. https://doi.org/10.1016/j.cell.2020.02.058
  • Wang, C., Horby, P. W., Hayden, F. G., & Gao, G. F. (2020). A novel coronavirus outbreak of global health concern. Lancet (London, England), 395(10223), 470–473. https://doi.org/10.1016/S0140-6736(20)30185-9
  • Wang, L., Wang, Y., Ye, D., et al. (2020). Review of the 2019 novel coronavirus (SARS-CoV-2) based on current evidence. International Journal of Antimicrobial Agents, 55, 105948. https://doi.org/10.1016/j.ijantimicag.2020.105948
  • WHO supports scientifically-proven traditional medicine. (2022 October 10) WHO | Regional Office for Africa. [Internet]. https://www.afro.who.int/news/who-supports-scientifically-proven-traditional-medicine.
  • Xu, Y., Gnanasekaran, R., & Leitner, D. M. (2012). Analysis of water and hydrogen bond dynamics at the surface of an antifreeze protein. Journal of Atomic and Molecular Physics, 2012, e125071. https://doi.org/10.1155/2012/125071
  • Yin, W., Mao, C., Luan, X., Shen, D.-D., Shen, Q., Su, H., Wang, X., Zhou, F., Zhao, W., Gao, M., Chang, S., Xie, Y.-C., Tian, G., Jiang, H.-W., Tao, S.-C., Shen, J., Jiang, Y., Jiang, H., Xu, Y., … Xu, H. E. (2020). Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir. Science (New York, N.Y.), 368(6498), 1499–1504. https://doi.org/10.1126/science.abc1560
  • Zhu, W., Chen, C. Z., Gorshkov, K., Xu, M., Lo, D. C., & Zheng, W. (2020). RNA-dependent rna polymerase as a target for COVID-19 drug discovery. SLAS Discovery: Advancing Life Sciences R & D, 25(10), 1141–1151. https://doi.org/10.1177/2472555220942123
  • Zhu, Z., Lian, X., Su, X., Wu, W., Marraro, G. A., & Zeng, Y. (2020). From SARS and MERS to COVID-19: A brief summary and comparison of severe acute respiratory infections caused by three highly pathogenic human coronaviruses. Respiratory Research, 21(1), 224. https://doi.org/10.1186/s12931-020-01479-w

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.