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Research Articles

In-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain)

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Pages 2724-2732 | Received 20 Mar 2020, Accepted 31 Mar 2020, Published online: 18 May 2020

References

  • Adasme-Carreño, F., Muñoz-Gutierrez, C., Caballero, J., & Alzate-Morales, J. H. (2014). Performance of the MM/GBSA scoring using a binding site hydrogen bond network-based frame selection: The protein kinase case. Physical Chemistry Chemical Physics, 16(27), 14047–14058. doi:10.1039/C4CP01378F
  • Chang, C., Lo, S.-C., Wang, Y.-S., & Hou, M.-H. (2016). Recent insights into the development of therapeutics against coronavirus diseases by targeting N protein. Drug Discovery Today, 21(4), 562–572. doi:10.1016/j.drudis.2015.11.015
  • Chang, C., Sue, S.-C., Yu, T., Hsieh, C.-M., Tsai, C.-K., Chiang, Y.-C., Lee, S., Hsiao, H., Wu, W.-J., Chang, W.-L., Lin, C.-H., & Huang, T. (2006). Modular organization of SARS coronavirus nucleocapsid protein. Journal of Biomedical Science, 13(1), 59–72. doi:10.1007/s11373-005-9035-9
  • Chenavas, S., Crépin, T., Delmas, B., Ruigrok, R. W. H., & Slama-Schwok, A. (2013). Influenza virus nucleoprotein: Structure, RNA binding, oligomerization and antiviral drug target. Future Microbiology, 8(12), 1537–1545. doi:10.2217/fmb.13.128
  • Coronavirus Disease (COVID-19)—Events as they happen. (n.d.). Retrieved March 16, 2020, from https://www.who.int/emergencies/diseases/novel-coronavirus-2019/events-as-they-happen
  • Desmond, S. (n.d.). Desmond | Schrödinger. Retrieved from https://www.schrodinger.com/desmond
  • Franco, R., Oñatibia-Astibia, A., & Martínez-Pinilla, E. (2013). Health Benefits of Methylxanthines in Cacao and Chocolate. Nutrients, 5(10), 4159–4173. https://doi.org/10.3390/nu5104159
  • Huang, Q., Yu, L., Petros, A. M., Gunasekera, A., Liu, Z., Xu, N., Hajduk, P., Mack, J., Fesik, S. W., & Olejniczak, E. T. (2004). Structure of the N-Terminal RNA-Binding Domain of the SARS CoV Nucleocapsid Protein. Biochemistry, 43(20), 6059–6063. https://doi.org/10.1021/bi036155b
  • GlideScore/Docking Score doesn’t correlate with my known activities. What is wrong? | Schrödinger [Internet]. Retrieved February 21, 2020, from https://www.schrodinger.com/kb/144
  • 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. The Lancet, 395(10223), 497–506. doi:10.1016/S0140-6736(20)30183-5
  • Huang, Q., Yu, L., Petros, A. M., Gunasekera, A., Liu, Z., Xu, N., Hajduk, P., Mack, J., Fesik, S. W., & Olejniczak, E. T. (2004). Structure of the N-terminal RNA-binding domain of the SARS CoV nucleocapsid protein. Biochemistry, 43(20), 6059–6063. 10.2210/pdb1ssk/pdb
  • Jin, Y.-H., Cai, L., Cheng, Z.-S., Cheng, H., Deng, T., Fan, Y.-P., … Wang, X.-H. (2020). A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version). Military Medical Research, 7(1).
  • LigPrep, S. (n.d.). LigPrep | Schrödinger. Retrieved from https://www.schrodinger.com/ligprep
  • Lin, S. Y., Liu, C. L., Chang, Y. M., Zhao, J., Perlman, S., & Hou, M. H. (2014). Structural basis for the identification of the N-terminal domain of coronavirus nucleocapsid protein as an antiviral target. Journal of Medicinal Chemistry, 57(6), 2247–2257. doi:10.1021/jm500089r
  • Meng, X.-Y., Zhang, H.-X., Mezei, M., & Cui, M. (2011). Molecular docking: A powerful approach for structure-based drug discovery. Current Computer Aided-Drug Design, 7(2), 146–157. doi:10.2174/157340911795677602
  • Nain, Z., Sayed, S. B., Karim, M. M., Islam, M. A., & Adhikari, U. K. (2019). Energy-optimized pharmacophore coupled virtual screening in the discovery of quorum sensing inhibitors of LasR protein of Pseudomonas aeruginosa. Available from https://www.preprints.org/manuscript/201910.0074/v1
  • PDB Database. (n.d.). RCSB PDB: Homepage. Retrieved January 13, 2020, from https://www.rcsb.org/
  • Phucho, I. T., Nongpiur, A., Tumtin, S., Nongrum, R., Nongkhlaw, R. L. (2009). Recent progress in the chemistry of dihydropyrimidinones. Rasayan J Chem, 2(3), 662–676.
  • Prajapat, M., Sarma, P., Shekhar, N., Avti, P., Sinha, S., Kaur, H., Kumar, S., Bhattacharyya, A., Kumar, H., Bansal, S., & Medhi, B. (2020). Drug targets for corona virus: A systematic review. Indian Journal of Pharmacology, 52(1), 56–65. doi:10.4103/ijp.IJP_115_20
  • Saikatendu, K. S., Joseph, J. S., Subramanian, V., Neuman, B. W., Buchmeier, M. J., Stevens, R. C., & Kuhn, P. (2007). Ribonucleocapsid formation of severe acute respiratory syndrome coronavirus through molecular action of the N-terminal domain of N protein. Journal of Virology, 81(8), 3913–3921. doi:10.1128/JVI.02236-06
  • Sarma, P., Prajapat, M., Avti, P., Kaur, H., Kumar, S., & Medhi, B. (2020). Therapeutic options for the treatment of 2019-novel coronavirus: An evidence-based approach. Indian Journal of Pharmacology, 52(1), 1–5. doi:10.4103/ijp.IJP_119_20
  • Seley-Radtke, K. L., & Yates, M. K. (2018). The evolution of nucleoside analogue antivirals: A review for chemists and non-chemists. Part 1: Early structural modifications to the nucleoside scaffold. Antiviral Research, 154, 66–86. doi:10.1016/j.antiviral.2018.04.004
  • Singh, K. D., & Muthusamy, K. (2013). Molecular modeling, quantum polarized ligand docking and structure-based 3D-QSAR analysis of the imidazole series as dual AT(1) and ET(A) receptor antagonists. Acta Pharmacologica Sinica, 34(12), 1592–1606. 10.1038/aps.2013.129
  • Sharma, V., Chitranshi, N., & Agarwal, A. K. (2014). Significance and biological importance of pyrimidine in the microbial world. International Journal of Medicinal Chemistry, 2014, p. e202784. Available from https://www.hindawi.com/journals/ijmc/2014/202784/
  • Skulnick, H. I., Weed, S. D., Eidson, E. E., Renis, H. E., Wierenga, W., & Stringfellow, D. A. (1985). Pyrimidinones. 1. 2-amino-5-halo-6-aryl-4(3H)-pyrimidinones. Interferon-inducing antiviral agents. Journal of Medicinal Chemistry, 28(12), 1864–1869. doi:10.1021/jm00150a018
  • SwissADME. (n.d.). Retrieved March 18, 2020, from http://www.swissadme.ch/
  • Tripathi, K. (2013). Essentials of medical pharmacology (17th ed.). JAYPEE.
  • Wang, C., Horby, P. W., Hayden, F. G., & Gao, G. F. (2020). A novel coronavirus outbreak of global health concern. The Lancet, 395(10223), 470–473. doi:10.1016/S0140-6736(20)30185-9
  • What do all the Prime MM-GBSA energy properties mean? | Schrödinger. (n.d.). Retrieved February 22, 2020, from https://www.schrodinger.com/kb/1875
  • Wierenga, W. (1985). Antiviral and other bioactivities of pyrimidinones. Pharmacology & Therapeutics, 30(1), 67–89. doi:10.1016/0163-7258(85)90048-8
  • Yamazaki, Z., & Tagaya, I. (1980). Antiviral Effects of Atropine and Caffeine. Journal of General Virology, 50(2), 429–431. https://doi.org/10.1099/0022-1317-50-2-429
  • Zhavoronkov, A., Aladinskiy, V., Zhebrak, A., Zagribelnyy, B., Terentiev, V., Bezrukov, D. S., Polykovskiy, D., Shayakhmetov, R., Filimonov, A., Orekhov, P., Yan, Y., Popova, O., Vanhaelen, Q., Aliper, A., & Ivanenkov, Y. (2020). Potential 2019-nCoV 3C-like protease inhibitors designed using generative deep learning approaches. 10.26434/chemrxiv.11829102.v1
  • Zheng, Z., Li, J., Sun, J., Song, T., Wei, C., Zhang, Y., Rao, G., Chen, G., Li, D., Yang, G., Han, B., Wei, S., Cao, C., & Zhong, H. (2011). Inhibition of HBV replication by theophylline. Antiviral Research, 89(2), 149–155. doi:10.1016/j.antiviral.2010.12.004
  • Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., Niu, P., Zhan, F., Ma, X., Wang, D., Xu, W., Wu, G., Gao, G. F., & Tan, W. (2020). A novel coronavirus from patients with pneumonia in China, 2019. New England Journal of Medicine, 382(8), 727–733. doi:10.1056/NEJMoa2001017

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