A computational prediction of SARS-CoV-2 structural protein inhibitors from Azadirachta indica (Neem)

References

• Aanouz, I., Belhassan, A., El-Khatabi, K., Lakhlifi, T., El-Ldrissi, M., & Bouachrine, M. (2020). Moroccan Medicinal plants as inhibitors against SARS-CoV-2 main protease: Computational investigations. Journal of Biomolecular Structure and Dynamics, 1–9. https://doi.org/10.1080/07391102.2020.1758790
   Google Scholar
• Abdelli, I., Hassani, F., Bekkel Brikci, S., & Ghalem, S. (2020). In silico study the inhibition of angiotensin converting enzyme 2 receptor of COVID-19 by Ammoides verticillata components harvested from Western Algeria. Journal of Biomolecular Structure and Dynamics, 1–14. https://doi.org/10.1080/07391102.2020.1763199
   Web of Science ®Google Scholar
• Akram, M., Tahir, I. M., Shah, S. M. A., Mahmood, Z., Altaf, A., Ahmad, K., Munir, N., Daniyal, M., Nasir, S., & Mehboob, H. (2018). Antiviral potential of medicinal plants against HIV, HSV, influenza, hepatitis, and coxsackievirus: A systematic review. Phytotherapy Research: PTR, 32(5), 811–822. https://doi.org/10.1002/ptr.6024
   PubMed Web of Science ®Google Scholar
• Alzohairy, M. A. (2016). Therapeutics role of Azadirachta indica (Neem) and their active constituents in diseases prevention and treatment. Evidence-Based Complementary and Alternative Medicine, 2016, 7382506. https://doi.org/10.1155/2016/7382506
   PubMed Web of Science ®Google Scholar
• Arndt, A. L., Larson, B. J., & Hogue, B. G. (2010). A conserved domain in the coronavirus membrane protein tail is important for virus assembly. Journal of Virology, 84(21), 11418–11428. https://doi.org/10.1128/JVI.01131-10
   PubMed Web of Science ®Google Scholar
• Badam, L., Joshi, S. P., & Bedekar, S. S. (1999). ‘In vitro’ antiviral activity of neem (Azadirachta indica. A. Juss) leaf extract against group B coxsackieviruses. Journal of Communicable Diseases, 31(2), 79–90.
   PubMedGoogle Scholar
• Baker, N. A., Sept, D., Joseph, S., Holst, M. J., & McCammon, J. A. (2001). Electrostatics of nanosystems: Application to microtubules and the ribosome. Proceedings of the National Academy of Sciences of the United States of America, 98(18), 10037–10041. https://doi.org/10.1073/pnas.181342398
   PubMed Web of Science ®Google Scholar
• Barrett, J. (2020). FDA issues emergency use authorization for remdesivir in COVID-19. Retrieved May 1, 2020, from https://www.drugtopics.com/covid-19/fda-issues-emergency-use-authorization-remdesivir-covid-19
   Google Scholar
• Bhardwaj, V. K., Singh, R., Sharma, J., Rajendran, V., Purohit, R., & Kumar, S. (2020). Identification of bioactive molecules from Tea plant as SARS-CoV-2 main protease inhibitors. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2020.1766572
   Google Scholar
• Bhattacharya, D., Nowotny, J., Cao, R., & Cheng, J. (2016). 3Drefine: An interactive web server for efficient protein structure refinement. Nucleic Acids Research, 44(W1), W406–W409. https://doi.org/10.1093/nar/gkw336
   PubMed Web of Science ®Google Scholar
• Boopathi, S., Poma, A. B., & Kolandaivel, P. (2020). Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment. Journal of Biomolecular Structure and Dynamics, 1–10. https://doi.org/10.1080/07391102.2020.1758788
   Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Caly, L., Druce, J. D., Catton, M. G., Jans, D. A., & Wagstaff, K. M. (2020). The FDA-approved drug ivermectin inhibits the replication of SARS-CoV-2 in vitro. Antiviral Research, 178, 104787. https://doi.org/10.1016/j.antiviral.2020.104787
   PubMed Web of Science ®Google Scholar
• Cheng, F., Li, W., Zhou, Y., Shen, J., Wu, Z., Liu, G., Lee, P. W., & Tang, Y. (2012). admetSAR: A comprehensive source and free tool for assessment of chemical ADMET properties. Journal of Chemical Information and Modeling, 52(11), 3099–3105. https://doi.org/10.1021/ci300367a
   PubMed Web of Science ®Google Scholar
• DeDiego, M. L., Alvarez, E., Almazán, F., Rejas, M. T., Lamirande, E., Roberts, A., Shieh, W.-J., Zaki, S. R., Subbarao, K., & Enjuanes, L. (2007). A severe acute respiratory syndrome coronavirus that lacks the E gene is attenuated in vitro and in vivo. Journal of Virology, 81(4), 1701–1713. https://doi.org/10.1128/JVI.01467-06
   PubMed Web of Science ®Google Scholar
• Ekhteiari Salmas, R., Unlu, A., Bektaş, M., Yurtsever, M., Mestanoglu, M., & Durdagi, S. (2017). Virtual screening of small molecules databases for discovery of novel PARP-1 inhibitors: Combination of in silico and in vitro studies. Journal of Biomolecular Structure & Dynamics, 35(9), 1899–1915. https://doi.org/10.1080/07391102.2016.1199328
   PubMed Web of Science ®Google Scholar
• Elfiky, A. A. (2020). SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: An in silico perspective. Journal of Biomolecular Structure and Dynamics, 1–9. https://doi.org/10.1080/07391102.2020.1761882
   Web of Science ®Google Scholar
• Enmozhi, S. K., Raja, K., Sebastine, I., & Joseph, J. (2020). Andrographolide as a potential inhibitor of SARS-CoV-2 main protease: An in silico approach. Journal of Biomolecular Structure and Dynamics, 1–7. https://doi.org/10.1080/07391102.2020.1760136
   Google Scholar
• Eswar, N., Webb, B., Marti-Renom, M. A., Madhusudhan, M. S., Eramian, D., Shen, M.-Y., Pieper, U., & Sali, A. (2006). Comparative protein structure modeling using Modeller. Current Protocols in Bioinformatics, 15, 5.6.1–5.6.30. https://doi.org/10.1002/0471250953.bi0506s15
   Google Scholar
• Gao, Y., Yan, L., Huang, Y., Liu, F., Zhao, Y., Cao, L., Wang, T., Sun, Q., Ming, Z., Zhang, L., Ge, J., Zheng, L., Zhang, Y., Wang, H., Zhu, Y., Zhu, C., Hu, T., Hua, T., Zhang, B., … Rao, Z. (2020). Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science, 368(6492), 779–782. https://doi.org/10.1126/science.abb7498
   PubMed Web of Science ®Google Scholar
• Hendaus, M. A. (2020). Remdesivir in the treatment of Coronavirus Disease 2019 (COVID-19): A simplified summary. Journal of Biomolecular Structure and Dynamics, 1–10. https://doi.org/10.1080/07391102.2020.1767691
   Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J., & Fraaije, J. G. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12 < 1463::AID-JCC4 > 3.0.CO;2-H
   Web of Science ®Google Scholar
• Jimenez-Guardeno, J. M., Nieto-Torres, J. L., DeDiego, M. L., Regla-Nava, J. A., Fernandez-Delgado, R., Castano-Rodriguez, C., & Enjuanes, L. (2014). The PDZ-binding motif of severe acute respiratory syndrome coronavirus envelope protein is a determinant of viral pathogenesis. PLoS Pathogens, 10(8), e1004320. https://doi.org/10.1371/journal.ppat.1004320
   PubMed Web of Science ®Google Scholar
• Kawata, M., & Nagashima, U. (2001). Particle mesh Ewald method for three-dimensional systems with two-dimensional periodicity. Chemical Physics Letters, 340(1-2), 165–172. https://doi.org/10.1016/S0009-2614(01)00393-1
   Web of Science ®Google Scholar
• Khan, S. A., Zia, K., Ashraf, S., Uddin, R., & Ul-Haq, Z. (2020). Identification of chymotrypsin-like protease inhibitors of SARS-CoV-2 via integrated computational approach. Journal of Biomolecular Structure and Dynamics, 1–10. https://doi.org/10.1080/07391102.2020.1751298
   Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Kuo, L., Hurst-Hess, K. R., Koetzner, C. A., & Masters, P. S. (2016). Analyses of coronavirus assembly interactions with interspecies membrane and nucleocapsid protein chimeras. Journal of Virology, 90(9), 4357–4368. https://doi.org/10.1128/JVI.03212-15
   PubMed Web of Science ®Google Scholar
• Martoňák, R., Laio, A., & Parrinello, M. (2003). Predicting crystal structures: The Parrinello-Rahman method revisited. Physical Review Letters, 90(7), 075503. https://doi.org/10.1103/PhysRevLett.90.075503
   PubMed Web of Science ®Google Scholar
• Menachery, V. D., Yount, B. L., Debbink, K., Agnihothram, S., Gralinski, L. E., Plante, J. A., Graham, R. L., Scobey, T., Ge, X.-Y., Donaldson, E. F., Randell, S. H., Lanzavecchia, A., Marasco, W. A., Shi, Z.-L., & Baric, R. S. (2015). A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence. Nature Medicine, 21(12), 1508–1513. https://doi.org/10.1038/nm.3985
   PubMed Web of Science ®Google Scholar
• Mohanraj, K., Karthikeyan, B. S., Vivek-Ananth, R. P., Chand, R. P. B., Aparna, S. R., Mangalapandi, P., & Samal, A. (2018). IMPPAT: A curated database of Indian Medicinal Plants, Phytochemistry and Therapeutics. Scientific Reports, 8(1), 4329. https://doi.org/10.1038/s41598-018-22631-z
   PubMed Web of Science ®Google Scholar
• Mortola, E., & Roy, P. (2004). Efficient assembly and release of SARS coronavirus-like particles by a heterologous expression system. FEBS Letters, 576(1-2), 174–178. https://doi.org/10.1016/j.febslet.2004.09.009
   PubMed Web of Science ®Google Scholar
• Nieto-Torres, J. L., DeDiego, M. L., Verdiá-Báguena, C., Jimenez-Guardeño, J. M., Regla-Nava, J. A., Fernandez-Delgado, R., Castaño-Rodriguez, C., Alcaraz, A., Torres, J., Aguilella, V. M., & Enjuanes, L. (2014). Severe acute respiratory syndrome coronavirus envelope protein ion channel activity promotes virus fitness and pathogenesis. PLoS Pathogens, 10(5), e1004077. https://doi.org/10.1371/journal.ppat.1004077
   PubMed Web of Science ®Google Scholar
• Oostenbrink, C., Villa, A., Mark, A. E., & Van Gunsteren, W. F. (2004). A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. Journal of Computational Chemistry, 25(13), 1656–1676. https://doi.org/10.1002/jcc.20090
   PubMed Web of Science ®Google Scholar
• Patridge, E., Gareiss, P., Kinch, M. S., & Hoyer, D. (2016). An analysis of FDA-approved drugs: Natural products and their derivatives. Drug Discovery Today, 21(2), 204–207. https://doi.org/10.1016/j.drudis.2015.01.009
   PubMed Web of Science ®Google Scholar
• Perrier, A., Bonnin, A., Desmarets, L., Danneels, A., Goffard, A., Rouillé, Y., Dubuisson, J., & Belouzard, S. (2019). The C-terminal domain of the MERS coronavirus M protein contains a trans-Golgi network localization signal. The Journal of Biological Chemistry, 294(39), 14406–14421. https://doi.org/10.1074/jbc.RA119.008964
   PubMed Web of Science ®Google Scholar
• Pervushin, K., Tan, E., Parthasarathy, K., Lin, X., Jiang, F. L., Yu, D., Vararattanavech, A., Soong, T. W., Liu, D. X., & Torres, J. (2009). Structure and inhibition of the SARS coronavirus envelope protein ion channel. PLoS Pathogens, 5(7), e1000511. https://doi.org/10.1371/journal.ppat.1000511
   PubMed Web of Science ®Google Scholar
• Rajkumari, J., Borkotoky, S., Murali, A., Suchiang, K., Mohanty, S. K., & Busi, S. (2018). Attenuation of quorum sensing controlled virulence factors and biofilm formation in Pseudomonas aeruginosa by pentacyclic triterpenes, betulin and betulinic acid. Microbial Pathogenesis, 118, 48–60. https://doi.org/10.1016/j.micpath.2018.03.012
   PubMed Web of Science ®Google Scholar
• Roy, A., Kucukural, A., & Zhang, Y. (2010). I-TASSER: A unified platform for automated protein structure and function prediction. Nature Protocols, 5(4), 725–738. https://doi.org/10.1038/nprot.2010.5
   PubMed Web of Science ®Google Scholar
• Sarkar, L., Putchala, R. K., Safiriyu, A. A., & Sarma, J. D. (2020). Azadirachta indica A. Juss ameliorates mouse hepatitis virus-induced neuroinflammatory demyelination by modulating cell-to-cell fusion in an experimental animal model of multiple sclerosis. Frontiers in Cellular Neuroscience, 14, 116. https://doi.org/10.3389/fncel.2020.00116
   PubMed Web of Science ®Google Scholar
• Schoeman, D., & Fielding, B. C. (2019). Coronavirus envelope protein: Current knowledge. Virology Journal, 16(1), 69. https://doi.org/10.1186/s12985-019-1182-0
   PubMed Web of Science ®Google Scholar
• Schüttelkopf, A. W., & van Aalten, D. M. F. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica Section D Biological Crystallography, 60(Pt 8), 1355–1363. https://doi.org/10.1107/S0907444904011679
   PubMedGoogle Scholar
• Surya, W., Li, Y., & Torres, J. (2018). Structural model of the SARS coronavirus E channel in LMPG micelles. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1860(6), 1309–1317. https://doi.org/10.1016/j.bbamem.2018.02.017
   PubMed Web of Science ®Google Scholar
• Teoh, K.-T., Siu, Y.-L., Chan, W.-L., Schlüter, M. A., Liu, C.-J., Peiris, J. S. M., Bruzzone, R., Margolis, B., & Nal, B. (2010). The SARS coronavirus E protein interacts with PALS1 and alters tight junction formation and epithelial morphogenesis. Molecular Biology of the Cell, 21(22), 3838–3852. https://doi.org/10.1091/mbc.E10-04-0338
   PubMed Web of Science ®Google Scholar
• Thomford, N. E., Senthebane, D. A., Rowe, A., Munro, D., Seele, P., Maroyi, A., & Dzobo, K. (2018). Natural products for drug discovery in the 21st century: Innovations for novel drug discovery. International Journal of Molecular Sciences., 19(6), 1578. https://doi.org/10.3390/ijms19061578
   Google Scholar
• Tiwari, V., Darmani, N. A., Yue, B. Y., & Shukla, D. (2010). In vitro antiviral activity of neem (Azardirachta indica L.) bark extract against herpes simplex virus type-1 infection. Phytotherapy Research: PTR, 24(8), 1132–1140. https://doi.org/10.1002/ptr.3085
   PubMed Web of Science ®Google Scholar
• Torres, J., Maheswari, U., Parthasarathy, K., Ng, L., Liu, D. X., & Gong, X. (2007). Conductance and amantadine binding of a pore formed by a lysine-flanked transmembrane domain of SARS coronavirus envelope protein. Protein Science, 16(9), 2065–2071. https://doi.org/10.1110/ps.062730007
   PubMed Web of Science ®Google Scholar
• Torres, J., Parthasarathy, K., Lin, X., Saravanan, R., Kukol, A., & Liu, D. X. (2006). Model of a putative pore: The pentameric alpha-helical bundle of SARS coronavirus E protein in lipid bilayers. Biophysical Journal, 91(3), 938–947. https://doi.org/10.1529/biophysj.105.080119
   PubMed Web of Science ®Google Scholar
• 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(2), 455–461. https://doi.org/10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Verdia-Baguena, C., Nieto-Torres, J. L., Alcaraz, A., DeDiego, M. L., Torres, J., Aguilella, V. M., & Enjuanes, L. (2012). Coronavirus E protein forms ion channels with functionally and structurally-involved membrane lipids. Virology, 432(2), 485–494. https://doi.org/10.1016/j.virol.2012.07.005
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Wang, Y., Zhang, D., Du, G., Du, R., Zhao, J., Jin, Y., Fu, S., Gao, L., Cheng, Z., Lu, Q., Hu, Y., Luo, G., Wang, K., Lu, Y., Li, H., Wang, S., Ruan, S., Yang, C., Mei, C., … Wang, C. (2020). Remdesivir in adults with severe COVID-19: A randomised, double-blind, placebo-controlled, multicentre trial. The Lancet, 395(10236), 1569–1578. https://doi.org/10.1016/S0140-6736(20)31022-9
   PubMed Web of Science ®Google Scholar
• Wani, M. C., Taylor, H. L., Wall, M. E., Coggon, P., & McPhail, A. T. (1971). Plant antitumor agents. VI. The isolation and structure of taxol, a novel antileukemic and antitumor agent from Taxus brevifolia. Journal of the American Chemical Society, 93(9), 2325–2327. https://doi.org/10.1021/ja00738a045
   PubMed Web of Science ®Google Scholar
• Wu, C., Liu, Y., Yang, Y., Zhang, P., Zhong, W., Wang, Y., Wang, Q., Xu, Y., Li, M., Li, X., Zheng, M., Chen, L., & Li, H. (2020). Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharmaceutica Sinica B. https://doi.org/10.1016/j.apsb.2020.02.008
   Google Scholar
• Yang, Y., Xiong, Z., Zhang, S., Yan, Y., Nguyen, J., Ng, B., Lu, H., Brendese, J., Yang, F., Wang, H., & Yang, X.-F. (2005). Bcl-xL inhibits T-cell apoptosis induced by expression of SARS coronavirus E protein in the absence of growth factors. The Biochemical Journal, 392(Pt 1), 135–143. https://doi.org/10.1042/BJ20050698
   PubMed Web of Science ®Google Scholar
• 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 α-ketoamide inhibitors. Science, 368(6489), 409–412. https://doi.org/10.1126/science.abb3405
   PubMed Web of Science ®Google Scholar