In silico identification and validation of triarylchromones as potential inhibitor against main protease of severe acute respiratory syndrome coronavirus 2

References

• Akaji, K., Konno, H. (2020). Design and evaluation of anti-SARS-coronavirus agents based on molecular interactions with the viral protease. Molecules, 25(17), 3920. https://doi.org/10.3390/molecules25173920
   PubMed Web of Science ®Google Scholar
• Ali, A., & Vijayan, R. (2020). Dynamics of the ACE2–SARS-CoV-2/SARS-CoV spike protein interface reveal unique mechanisms. Science Reports, 10, 14214. https://doi.org/10.1038/s41598-020-71188-3
   PubMed Web of Science ®Google Scholar
• Astuti, I., & Ysrafil (2020). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): An overview of viral structure and host response. Diabetes & Metabolic Syndrome, 14(4), 407–412. https://doi.org/10.1016/j.dsx.2020.04.020
   PubMed Web of Science ®Google Scholar
• Aucoin, M., & Cooley, K. (2020). The effect of quercetin on the prevention or treatment of COVID-19 and other respiratory tract infections in humans: A rapid review. Advanced & Integrated Medicine, 7(4), 247–251. https://doi.org/10.1016/j.aimed.2020.07.007
   PubMed Web of Science ®Google Scholar
• Cao, B., & Yang. Y. (2020). A trial of lopinavir–ritonavir in adults hospitalized with severe Covid-19. New England Journal of Medicine, 382, 1787–1799. https://doi.org/10.1056/NEJMoa2001282
   PubMed Web of Science ®Google Scholar
• Chaccour, C., Abizanda, G., Irigoyen-Barrio, Á., et al. (2020). Nebulized ivermectin for COVID-19 and other respiratory diseases, a proof of concept, dose-ranging study in rats. Scientific Reports, 10, 17073. https://doi.org/10.1038/s41598-020-74084-y
   PubMed Web of Science ®Google Scholar
• Chandel, V., Raj, S., Rathi, B., & Kumar, D. (2020). In silico identification of potent FDA approved drugs against coronavirus covid-19 main protease: A drug repurposing approach. Chemical Biology Letters, 7(3), 166–175.
   Web of Science ®Google Scholar
• Chandel, V., Srivastava, M., Srivastava, A., Asthana, S., & Kumar, D. (2020). In-silico interactions of active phytochemicals with c-Myc EGFR and ERBB2 oncoproteins. Chemical Biology Letters, 7(1), 47–54.
   Web of Science ®Google Scholar
• Choi, H., Min, M., et al. (2016). Unraveling innate substrate control in site-selective palladium-catalyzed C–H heterocycle functionalization. Chemical Sciences, 7, 3900–3909. https://doi.org/10.1039/c5sc04590h
   Web of Science ®Google Scholar
• Coelho, C., Gallo, G., Campos, C. B., Hardy, L., & WüRtele, M. (2020). PLoS One, 15(10), e0240079. https://doi.org/10.1371/journal.pone.0240079
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin O., & Vincent, Z. (2007) SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7, 1–13. https://doi.org/10.1038/srep42717
   Google Scholar
• Derosa, G., Maffioli, P., D'Angelo, A., & Di Pieero, F. (2020). Drugs against coronavirus COVID-19 main protease: A drug repurposing approach. Chemical Phytotherapy & Research, 35,1230–1236. https://doi.org/10.1002/ptr.6887
   PubMed Web of Science ®Google Scholar
• Ferner, R. E., & Aronson, J. K. (2020). Chloroquine and hydroxychloroquine in covid-19. British Medical Journal, 369, m1432. https://doi.org/10.1136/bmj.m1432
   PubMedGoogle Scholar
• Focosi, D., Anderson, A. O., Tang, J. W., & Tuccori, M. (2020). Convalescent plasma therapy for COVID-19: State of the art. Clinical Microbiology & Review, 33(4), e00072-20. https://doi.org/10.1128/CMR.00072-20
   PubMed Web of Science ®Google Scholar
• Gaspar, A., Matos, M. J., Garrido, J., Uriarte, E., & Borges, F. (2014). Chromone: A valid scaffold in medicinal chemistry. Chemical Review, 114(9), 4960–4992. https://doi.org/10.1021/cr400265z
   PubMed Web of Science ®Google Scholar
• Gavriatopoulou, M., Korompoki, E., Fotiou, D., Ntanasis-Stathopoulos, I., Psaltopoulou, T., Kastritis, E., Terpos, E., & Dimopoulos, M. A. (2020) Organ-specific manifestations of COVID-19 infection. Clinical & Experimental Medicine, 20(4), 493–506. https://doi.org/10.1007/s10238-020-00648-x
   PubMed Web of Science ®Google Scholar
• Guy, R. K., DiPaola, R. S., Romanelli, F., & Dutch, R. E. (2020). Rapid repurposing of drugs for COVID-19. Science, 368(6493), 829–830. https://doi.org/10.1126/science.abb9332
   PubMed Web of Science ®Google Scholar
• Harrison, C. (2020). Coronavirus puts drug repurposing on the fast track. Nature Biotechnology, 38(4), 379–381. https://doi.org/10.1038/d41587-020-00003-1
   PubMed Web of Science ®Google Scholar
• https://covid19.who.int/. (2020)
   Google Scholar
• https://www.nature.com/articles/d41586-020-03248-7. (2020)
   Google Scholar
• https://www.pfizer.com/news/press-release/press-release-detail/pfizer-and-biontech-announce-vaccine-candidate-against. (2020)
   Google Scholar
• Huang, Chaolin, Wang, Yeming, Li, Xingwang, Ren, Lili, Zhao, Jianping, Hu, Yi, Zhang, Li, Fan, Guohui, Xu, Jiuyang, Gu, Xiaoying, Cheng, Zhenshun, Yu, Ting, Xia, Jiaan, Wei, Yuan, Wu, Wenjuan, Xie, Xuelei, Yin, Wen, Li, Hui, Liu, Min, Xiao, Yan, Gao, Hong, Cao, Bin, et al., (2020). Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China, Lancet, 395( 10223), 497–506. https://doi.org/10.1016/S0140-6736(20)30183-5
   PubMed Web of Science ®Google Scholar
• Huang, Y., Yang, C., Xu, X. F., et al. (2020). Structural and functional properties of SARS-CoV-2 spike protein: Potential antivirus drug development for COVID-19. Acta Pharmacology Sinica, 41, 1141–1149. https://doi.org/10.1038/s41401-020-0485-4
   Google Scholar
• Jackson, L. A., Anderson, E. J., et al. (2020). An mRNA vaccine against SARS-CoV-2 – Preliminary report. New England Journal of Medicine, 383,1920–193. https://doi.org/10.1056/NEJMoa2022483
   PubMed Web of Science ®Google Scholar
• Keri, R. S., Budagumpi, S., Pai, R. K., & Balakrishna, R. G. (2014). European Journal of Medicinal Chemistry, 78, 340–374. https://doi.org/10.1016/j.ejmech.2014.03.047
   PubMed Web of Science ®Google Scholar
• Kim, K. H., Lee, H. S., Kim, S. H., & Kim, J. N. (2012). Palladium-catalyzed oxidative arylation of chromones via a double C–H activation: An expedient approach to flavones. Tetrahedron Letters, 53(22), 2761–2764. https://doi.org/10.1016/j.tetlet.2012.03.100
   Web of Science ®Google Scholar
• Krammer, F. (2020). SARS-CoV-2 vaccines in development. Nature, 586, 516–527. https://doi.org/10.1016/j.immuni.2020.03.007
   PubMed Web of Science ®Google Scholar
• Kumar, A., Singh, A. K., & Tripathi, G. (2020). Phytochemicals as potential curative agents against viral infection: A review. Current Organic Chemistry, 24( 20), 2356–2366. https://doi.org/10.2174/1385272824999200910093524
   Web of Science ®Google Scholar
• Lammers, T., Sofias, A. M., van der Meel, R., et al. (2020). Dexamethasone nanomedicines for COVID-19. Nature Nanotechnology, 15, 622–624. https://doi.org/10.1038/s41565-020-0752-z
   PubMed Web of Science ®Google Scholar
• Morris, G., Huey, R., Lindstrom, W., et al. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computer Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• Morris, M., Huey R., & Olson, A. J. (2008). Using Autodock for receptor ligand docking. Current Protocols Bioinformatics, 30(16), 2785–2791. https://doi.org/10.1002/0471250953.bi0814s24
   Google Scholar
• Portelli, S., Olshansky, M., & Rodrigues, C. H. M., et al. (2020). Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource. Nature Genetics, 52, 999–1001. https://doi.org/10.1038/s41588-020-0693-3
   PubMed Web of Science ®Google Scholar
• Preeti, P., Jitendra, S. R., Aroni, C., Abhijeet, K., Rajni, K., Amresh, P., & Shashikant, R. (2020). Targeting SARS-CoV-2 spike protein of COVID-19 with naturally occurring phytochemicals: An in silico study for drug development. Journal of Biomolecular Structure & Dynamics, 1–15. https://doi.org/10.1080/07391102.2020.1796811
   Google Scholar
• Rane, J. S., Pandey, P., Chatterjee, A., Khan, R., Kumar, A., Prakash, A., & Ray, S. (2020). Targeting virus–host interaction by novel pyrimidine derivative: An in silico approach towards discovery of potential drug against COVID-19. Journal of Biomolecular Structure & Dynamics. https://doi.org/10.1080/07391102.2020.1794969
   Google Scholar
• Rao, M. L. N., & Kumar, A. (2014). Pd-catalyzed atom-economic couplings of triarylbismuth reagents with 2-bromo- and 2,6-dibromochromones and synthesis of medicinally important fisetin. Tetrahedron Letters, 55(42), 5764–5770. https://doi.org/10.1002/ejoc.201201314
   Web of Science ®Google Scholar
• Rashmi, T., Mitul, S., Preeti, J., Ramendra, P. P., Shailendra, A, Dhruv, K., & Samuel, R. (2020). Development of potential proteasome inhibitors against Mycobacterium tuberculosis. Journal of Biomolecular Structure & Dynamics, 19, 1–15. https://doi.org/10.1080/07391102.2020.1835722
   Google Scholar
• Rauf, M. A., Zubair, S., & Azhar, A. (2015). Ligand docking and binding site analysis with pymol and autodock/vina. International Journal of Basic & Applied Sciences, 4(2), 168. https://doi.org/10.14419/ijbas.v4i2.4123
   Google Scholar
• Reis, J., Gaspar, A., Milhazes, N., & Borges, F. (2017) Chromone as a privileged scaffold in drug discovery: Recent advances. Journal of Medicinal Chemistry, 60, 7941–7957. https://doi.org/10.1021/acs.jmedchem.6b01720
   PubMed Web of Science ®Google Scholar
• Rohit, S., Niraj, K. J., Rohan, K., Saurabh, K. J., Ankur, S., Dhruv, K., et al. (2020) Deciphering the SSR incidences across viral members of Coronaviridae family. Chemical Biology & Interaction, 331(109226). https://doi.org/10.1016/j.cbi.2020.109226
   Google Scholar
• Schrödinger Release 2020-1: Maestro, Schrödinger, LLC, New York, NY, 2020.
   Google Scholar
• Schrödinger Release 2020-1: Prime, Schrödinger, LLC, New York, NY, 2020.
   Google Scholar
• Schrödinger Release 2020-1: Protein Preparation Wizard; Epik, Schrödinger, LLC, New York, NY, 2016; Impact, Schrödinger, LLC, New York, NY, 2016; Prime, Schrödinger, LLC, New York, NY, 2020
   Google Scholar
• Serafin, M. B., Bottega, A., Foletto, V. S., da Rosa, T. F, Hörner. A., & Hörner, R. (2020). Drug repositioning is an alternative for the treatment of coronavirus COVID-19. International Journal of Antimicrobial Agents, 55(6), 105969. https://doi.org/10.1016/j.ijantimicag.2020.105969
   PubMed Web of Science ®Google Scholar
• Seri, J., Suwon, K., Dae Y.K., Mi-Sun, K., & Dong H. S. (2020) Flavonoids with inhibitory activity against SARS-CoV-2 3CLpro. Journal of Enzyme Inhibitors & Medicinal Chemistry, 35(1), 1539–1544. https://doi.org/10.1080/14756366.2020.1801672
   PubMed Web of Science ®Google Scholar
• Straughn, A. R., & Kakar, S. S. (2020). Withaferin A: A potential therapeutic agent against COVID-19 infection. Journal of Ovarian Research, 13, 79. https://doi.org/10.1186/s13048-020-00684-x
   PubMed Web of Science ®Google Scholar
• Sumit, K., Prem, P. S., Uma, S., Dhruv, K., et al. (2020) Discovery of new hydroxyethylamine analogs against 3CLpro protein target of SARS-CoV-2: Molecular docking, molecular dynamics simulation, and structure–activity relationship studies. Journal of Chemistry & Information Model. 60(12), 5754–5770. https://doi.org/10.1021/acs.jcim.0c00326
   Google Scholar
• Tregoning, J. S., Brown, E. S., Cheeseman, H. M., et al. (2020) Vaccines for COVID-19. Clinical & Experimental Immunology, 202(2), 162–192. https://doi.org/10.1111/cei.13517
   PubMed Web of Science ®Google Scholar
• V’kovski, P., Kratzel, A., Steiner, S., et al. (2020) Coronavirus biology and replication: Implications for SARS-CoV-2. Nature Review of Microbiology, 19, 155–170. https://doi.org/10.1038/s41579-020-00468-6
   PubMed Web of Science ®Google Scholar
• Vaishali, C., Prem Prakash, S., Sibi, R., Ramesh, C., Rathi, B., & Kumar, D. (2020). Structure-based drug repurposing for targeting Nsp9 replicase and spike proteins of severe acute respiratory syndrome coronavirus 2. Journal of Biomolecular Structure & Dynamics, 24, 1–14. https://doi.org/10.1080/07391102.2020.1811773
   Google Scholar
• Verma, S., Twilley, D., Esmear, T., Oosthuizen, C. B., Reid, A.-M., Nel, M., & Lall, N. (2020) Anti-SARS-CoV natural products with the potential to inhibit SARS-CoV-2 (COVID-19). Frontiers in Pharmacology, 11, 561334. https://doi.org/10.3389/fphar.2020.561334
   PubMed Web of Science ®Google Scholar
• Vincet, J-L., & Taccone, F. S. (2020). Understanding pathways to death in patients with COVID-19. Lancet, 8(5), 430–432. https://doi.org/10.1016/S2213-2600(20)30165-X
   Web of Science ®Google Scholar
• Vivek, P., Garima, T., Dhruv, K., Abhijeet, K., & Pawan, K.D. (2020). Novel 3,4-diarylpyrazole as prospective anti-cancerous agents. Heliyon, 6(7), e04397. https://doi.org/10.1016/j.heliyon.2020.e04397
   PubMed Web of Science ®Google Scholar
• Walsh, E. E., Frenck, R. W., et al. (2020). Safety and immunogenicity of two RNA-based COVID-19 vaccine candidates. New England Journal of Medicine. 383, 2439–2450. https://doi.org/10.1056/NEJMoa2027906
   Google Scholar
• Wang, Y., Zhang, D., et al. (2020). Remdesivir in adults with severe COVID-19: A randomised, double-blind, placebo-controlled, multicentre trial. Lancet, 395, 1569–78. https://doi.org/10.1016/S0140-6736(20)31022-9
   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, 10(5), 766–788. https://doi.org/10.1016/j.apsb.2020.02.008
   PubMed Web of Science ®Google Scholar
• Yang, Y., Xiao, Z., Ye, K., et al. (2020) SARS-CoV-2: Characteristics and current advances in research. Virology Journal, 17, 117. https://doi.org/10.1186/s12985-020-01369-z
   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
• Zhao, C., Qin, G., Niu, J., Wang, Z., Wang, C., Ren, J., & Qu, X. (2021). Targeting RNA G‐quadruplex in SARS‐CoV‐2: A promising therapeutic target for COVID‐19? Angewandte Chemie International Edition, 60( 1), 432–439. https://doi.org/10.1002/anie.202011419
   PubMed Web of Science ®Google Scholar
• Zheng, J. (2020) SARS-CoV-2: An emerging coronavirus that causes a global threat. International Journal of Biological Science, 16(10), 1678–1685. https://doi.org/10.7150/ijbs.45053
   PubMed Web of Science ®Google Scholar
• Zhu, N., Zhang, D., Wang W., et al. (2020). A novel coronavirus from patients with pneumonia in China, 2019. New England Journal of Medicine, 382, 727–733. https://doi.org/10.1056/NEJMoa2001017
   PubMed Web of Science ®Google Scholar
• Zhu, W., Xu, M., Chen, C. Z, Guo, H., Shen, M., Hu, X., Shinn, P., Klumpp-Thomas, C., Michael S. G., & Zheng, W. (2020) Identification of SARS-CoV-2 3CL protease inhibitors by a quantitative high-throughput screening. ACS Pharmacology & Translational Science, 3(5), 1008–1016. https://doi.org/10.1101/2020.07.17.207019
   PubMedGoogle Scholar