References
- Amawi, H., Abu Deiab, G. A. I., A Aljabali, A. A., Dua, K., & Tambuwala, M. M. (2020). COVID-19 pandemic: An overview of epidemiology, parthenogenesis, diagnostics and potential vaccines and therapeutics. Therapeutic Delivery, 11(4), 245–268. https://doi.org/https://doi.org/10.4155/tde-2020-0035
- Aneja, R., Vangapandu, S. N., Lopus, M., Viswesarappa, V. G., Dhiman, N., Verma, A., Chandra, R., Panda, D., & Joshi, H. C. (2006). Synthesis of microtubule-interfering halogenated noscapine analogs that perturb mitosis in cancer cells followed by cell death. Biochemical Pharmacology, 72(4), 415–426. https://doi.org/https://doi.org/10.1016/j.bcp.2006.05.004
- Beigel, J. H., Tomashek, K. M., Dodd, L. E., Mehta, A. K., Zingman, B. S., Kalil, A. C., & Lopez de Castilla, D. (2020). Remdesivir for the treatment of Covid-19—preliminary report. New England Journal of Medicine. https://doi.org/https://doi.org/10.1056/NEJMoa2007764
- Chaudhary, M., Kumar, N., Baldi, A., Chandra, R., Babu, M. A., & Madan, J. (2020). 4-Bromo-4’-chloro pyrazoline analog of curcumin augmented anticancer activity against human cervical cancer, HeLa cells: In silico-guided analysis, synthesis, and in vitro cytotoxicity. Journal of Biomolecular Structure and Dynamics, 38(5), 1335–1353. https://doi.org/https://doi.org/10.1080/07391102.2019.1604266
- Chen, K., He, P., Zhang, S., & Li, P. (2016). Synthesis of aryl trimethylstannanes from aryl halides: An efficient photochemical method. Chemical Communications (Cambridge, England), 52(58), 9125–9128. https://doi.org/https://doi.org/10.1039/C6CC01135G
- Chen, Y., Liu, Q., & Guo, D. (2020). Emerging coronaviruses: Genome structure, replication, and pathogenesis. Journal of Medical Virology, 92(4), 418–423. https://doi.org/https://doi.org/10.1002/jmv.25681
- Cheng, F. (2019). In silico oncology drug repositioning and polypharmacology. In Krasnitz A. (Ed.), Cancer Bioinformatics. Methods in Molecular Biology, vol. 1878. New York, NY: Humana Press. https://doi.org/https://doi.org/10.1007/978-1-4939-8868-6_15
- Cheng, F., Hong, H., Yang, S., & Wei, Y. (2017). Individualized network-based drug repositioning infrastructure for precision oncology in the panomics era. Briefings in Bioinformatics, 18(4), 682–697. https://doi.org/https://doi.org/10.1093/bib/bbw051
- Cheng, F., Murray, J. L., & Rubin, D. H. (2016). Drug repurposing: New treatments for zika virus infection? Trends in Molecular Medicine, 22(11), 919–921. https://doi.org/https://doi.org/10.1016/j.molmed.2016.09.006
- Colson, P., Rolain, J. M., Lagier, J. C., Brouqui, P., & Raoult, D. (2020). Chloroquine and hydroxychloroquine as available weapons to fight COVID-19. International Journal of Antimicrobial Agents, 55(4), 105932. https://doi.org/https://doi.org/10.1016/j.ijantimicag.2020.105932
- Coomes, E. A., & Haghbayan, H. (2020). Favipiravir, an antiviral for COVID-19. Journal of Antimicrobial Chemotherapy, 75(7), 2013–2014. ? https://doi.org/https://doi.org/10.1093/jac/dkaa171
- Ebrahimi, S. A. (2020). Noscapine, a possible drug candidate for attenuation of cytokine release associated with SARS‐CoV‐2. Drug Development Research. https://doi.org/https://doi.org/10.1002/ddr.21676
- Ebrahimi, S. A., Zareie, M. R., Rostami, P., & Mahmoudian, M. (2003). Interaction of noscapine with the bradykinin mediation of the cough response. Acta Physiologica Hungarica, 90(2), 147–155. https://doi.org/https://doi.org/10.1556/APhysiol.90.2003.2.7
- Fung, T. S., & Liu, D. X. (2019). Human coronavirus: Host-pathogen interaction. Annual Review of Microbiology, 73, 529–557. https://doi.org/https://doi.org/10.1146/annurev-micro-020518-115759
- Gao, J., Tian, Z., & Yang, X. (2020). Breakthrough: Chloroquine phosphate has shown apparent efficacy in treatment of COVID-19 associated pneumonia in clinical studies. Bioscience Trends, 14(1), 72–73. https://doi.org/https://doi.org/10.5582/bst.2020.01047
- Graham, R. L., Donaldson, E. F., & Baric, R. S. (2013). A decade after SARS: Strategies for controlling emerging coronaviruses. Nature Reviews. Microbiology, 11(12), 836–848. https://doi.org/https://doi.org/10.1038/nrmicro3143
- Grant, B. J., Rodrigues, A. P., ElSawy, K. M., McCammon, J. A., & Caves, L. S. (2006). Bio3d: An R package for the comparative analysis of protein structures. Bioinformatics, 22(21), 2695–2696. https://doi.org/https://doi.org/10.1093/bioinformatics/btl461
- Grosdidier, A., Zoete, V., & Michielin, O. (2011). SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Research, 39(Web Server issue), W270–W277. https://doi.org/https://doi.org/10.1093/nar/gkr366
- Jin, Z., Du, X., Xu, Y., Deng, Y., Liu, M., Zhao, Y., Zhang, B., Li, X., Zhang, L., Peng, C., Duan, Y., Yu, J., Wang, L., Yang, K., Liu, F., Jiang, R., Yang, X., You, T., Liu, X., & Yang, H. (2020). Structure of Mpro from COVID19 virus and discovery of its inhibitors. Nature, 582(7811), 289–293.
- Kim, D. E., Min, J. S., Jang, M. S., Lee, J. Y., Shin, Y. S., Park, C. M., Song, J. H., Kim, H. R., Kim, S., Jin, Y. H., & Kwon, S. (2019). Natural Bis-benzylisoquinoline alkaloids-tetrandrine, fangchinoline, and cepharanthine, inhibit human coronavirus OC43 infection of MRC-5 human lung cells. Biomolecules, 9(11), 696. https://doi.org/https://doi.org/10.3390/biom9110696
- Kumar, D., Kumari, K., Jayraj, A., Kumar, V., Kumar, V., Dass, S., Chandra, R., & Singh, P. (2020). Understanding the binding affinity of Noscapine with protease of COVID-19 using MD simulation at different temperature. Journal of Biomolecular Structure and Dynamics, 1–14. https://doi.org/https://doi.org/10.1080/07391102.2020.1752310
- Kumar, N., Sood, D., Sharma, N., & Chandra, R. (2020). Multiepitope subunit vaccine to evoke immune response against acute encephalitis. Journal of Chemical Information and Modeling, 60(1), 421–433. https://doi.org/https://doi.org/10.1021/acs.jcim.9b01051
- Kumar, N., Sood, D., Tomar, R., & Chandra, R. (2019). Antimicrobial peptide designing and optimization employing large-scale flexibility analysis of protein-peptide fragments. ACS Omega, 4(25), 21370–21380. https://doi.org/https://doi.org/10.1021/acsomega.9b03035
- Kumar, N., Tomar, R., Pandey, A., Tomar, V., Singh, V. K., & Chandra, R. (2018). Preclinical evaluation and molecular docking of 1, 3-benzodioxole propargyl ether derivatives as novel inhibitor for combating the histone deacetylase enzyme in cancer. Artificial Cells, Nanomedicine, and Biotechnology, 46(6), 1288–1299. https://doi.org/https://doi.org/10.1080/21691401.2017.1369423
- Laskowski, R. A., & Swindells, M. B. (2011). LigPlot+: Multiple ligand-protein interaction diagrams for drug discovery. Journal of Chemical Information and Modeling, 51(10), 2778–2786. https://doi.org/https://doi.org/10.1021/ci200227u
- Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. https://doi.org/https://doi.org/10.1107/S0021889892009944
- Li, G., & De Clercq, E. (2020). Therapeutic options for the 2019 novel coronavirus (2019-nCoV). Nature Reviews. Drug Discovery, 19(3), 149–150. https://doi.org/https://doi.org/10.1038/d41573-020-00016-0
- Liu, C., Zhou, Q., Li, Y., Garner, L. V., Watkins, S. P., Carter, L. J., Smoot, J., Gregg, A. C., Daniels, A. D., Jervey, S., & Albaiu, D. (2020). Research and development on therapeutic agents and vaccines for COVID-19 and related human coronavirus diseases. ACS Central Science, 6(3), 315–331. https://doi.org/https://doi.org/10.1021/acscentsci.0c00272
- Macindoe, G., Mavridis, L., Venkatraman, V., Devignes, M. D., & Ritchie, D. W. (2010). HexServer: An FFT-based protein docking server powered by graphics processors. Nucleic Acids Research, 38(Web Server issue), W445–W449. https://doi.org/https://doi.org/10.1093/nar/gkq311
- Magagnoli, J., Narendran, S., Pereira, F., Cummings, T., Hardin, J. W., Sutton, S. S., & Ambati, J. (2020). Outcomes of hydroxychloroquine usage in United States veterans hospitalized with Covid-19. Med. https://doi.org/https://doi.org/10.1016/j.medj.2020.06.001
- Martin, K. W., & Ernst, E. (2003). Antiviral agents from plants and herbs: A systematic review. Antiviral Therapy, 8(2), 77–90.
- McGibbon, R. T., Beauchamp, K. A., Harrigan, M. P., Klein, C., Swails, J. M., Hernandez, C. X., Schwantes, C. R., Wang, L. P., Lane, T. J., & Pande, V. S. (2015). MDTraj: A modern open library for the analysis of molecular dynamics trajectories. Biophysical Journal, 109(8), 1528–1532. https://doi.org/https://doi.org/10.1016/j.bpj.2015.08.015
- Mengist, H. M., Fan, X., & Jin, T. (2020). Designing of improved drugs for COVID-19: Crystal structure of SARS-CoV-2 main protease M pro. Signal Transduction and Targeted Therapy, 5(1), 1–2. https://doi.org/https://doi.org/10.1038/s41392-020-0178-y
- Morris, A. L., MacArthur, M. W., Hutchinson, E. G., & Thornton, J. M. (1992). Stereochemical quality of protein structure coordinates. Proteins: Structure, Function, and Genetics, 12(4), 345–364. https://doi.org/https://doi.org/10.1002/prot.340120407
- Patrì, A., & Fabbrocini, G. (2020). Hydroxychloroquine and ivermectin: A synergistic combination for COVID-19 chemoprophylaxis and treatment? Journal of the American Academy of Dermatology, 82(6), e221https://doi.org/https://doi.org/10.1016/j.jaad.2020.04.017
- Paules, C. I., Marston, H. D., & Fauci, A. S. (2020). Coronavirus infections—More than just the common cold. JAMA, 323(8), 707–708. https://doi.org/https://doi.org/10.1001/jama.2020.0757
- Ren, L.-L., Wang, Y.-M., Wu, Z.-Q., Xiang, Z.-C., Guo, L., Xu, T., Jiang, Y.-Z., Xiong, Y., Li, Y.-J., Li, X.-W., Li, H., Fan, G.-H., Gu, X.-Y., Xiao, Y., Gao, H., Xu, J.-Y., Yang, F., Wang, X.-M., Wu, C., … Wang, J.-W. (2020). Identification of a novel coronavirus causing severe pneumonia in human: A descriptive study. Chinese Medical Journal, 133(9), 1015–1024. https://doi.org/https://doi.org/10.1097/CM9.0000000000000722
- Salentin, S., Schreiber, S., Haupt, V. J., Adasme, M. F., & Schroeder, M. (2015). PLIP: Fully automated protein–ligand interaction profiler. Nucleic Acids Research, 43(W1), W443–W447. https://doi.org/https://doi.org/10.1093/nar/gkv315
- Singh, A., Kumar, N., Sood, D., Singh, S., Awasthi, A., Tomar, V., & Chandra, R. (2019). Designing of a novel indoline scaffold based antibacterial compound and pharmacological evaluation using chemoinformatics approach. Current Topics in Medicinal Chemistry, 18(23), 2056–2065. https://doi.org/https://doi.org/10.2174/1568026619666181129125524
- Singh, V. K., Kumar, N., Kalsan, M., Saini, A., & Chandra, R. (2016). A novel peptide thrombopoietin mimetic designing and optimization using computational approach. Frontiers in Bioengineering and Biotechnology, 4, 69. https://doi.org/https://doi.org/10.3389/fbioe.2016.00069
- Sood, D., Kumar, N., Rathee, G., Singh, A., Tomar, V., & Chandra, R. (2018). Mechanistic interaction study of bromo-noscapine with bovine serum albumin employing spectroscopic and chemoinformatics approaches. Scientific Reports, 8(1), 1–11. https://doi.org/https://doi.org/10.1038/s41598-018-35384-6
- Sood, D., Kumar, N., Singh, A., Sakharkar, M. K., Tomar, V., & Chandra, R. (2018). Antibacterial and pharmacological evaluation of fluoroquinolones: A chemoinformatics Approach. Genomics & Informatics, 16(3), 44–51. https://doi.org/https://doi.org/10.5808/GI.2018.16.3.44
- Vriend, G. (1990). WHAT IF: A molecular modeling and drug design program. Journal of Molecular Graphics, 8(1), 52–56. https://doi.org/https://doi.org/10.1016/0263-7855(90)80070-V
- World Health Organization. (2020). Coronavirus disease (COVID-19) pandemic. https://www.who.int/emergencies/diseases/novel-coronavirus-2019
- Xue, X., Yu, H., Yang, H., Xue, F., Wu, Z., Shen, W., Li, J., Zhou, Z., Ding, Y., Zhao, Q., Zhang, X. C., Liao, M., Bartlam, M., & Rao, Z. (2008). Structures of two coronavirus main proteases: implications for substrate binding and antiviral drug design. Journal of Virology, 82(5), 2515–2527. https://doi.org/https://doi.org/10.1128/JVI.02114-07
- Yang, J. F., Wang, F., Chen, Y. Z., Hao, G. F., & Yang, G. F. (2019). LARMD: Integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor. Briefings in Bioinformatics, bbz141. https://doi.org/https://doi.org/10.1093/bib/bbz141
- Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., & 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.
- Zhou, Y., Hou, Y., Shen, J., Huang, Y., Martin, W., & Cheng, F. (2020). Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2. Cell Discovery, 6(1), 14–18. https://doi.org/https://doi.org/10.1038/s41421-020-0153-3
- 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., Phil, D., & Tan, W. (2020). A novel coronavirus from patients with pneumonia in China, 2019. The New England Journal of Medicine, 382(8), 727–733. https://doi.org/https://doi.org/10.1056/NEJMoa2001017