References
- Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/https://doi.org/10.1016/j.softx.2015.06.001
- Adnan, M., Rasul, A., Hussain, G., Shah, M. A., Zahoor, M. K., Anwar, H., Sarfraz, I., Riaz, A., Manzoor, M., Adem, S., & Selamoglu, Z. (2020). Ginkgetin: A natural biflavone with versatile pharmacological activities. Food and Chemical Toxicology: An International Journal Published for the British Industrial Biological Research Association, 145, 111642. https://doi.org/https://doi.org/10.1016/j.fct.2020.111642
- Agudelo-Gómez, L. S., Betancur-Galvis, L., & González, M. A. (2012). Anti HHV-1 and HHV-2 activity in vitro of abietic and dehydroabietic acid derivatives. Pharmacologyonline, 1(1), 36–42.
- Alamri, M. A., Tahir Ul Qamar, M., Mirza, M. U., Bhadane, R., Alqahtani, S. M., Muneer, I., Froeyen, M., & Salo-Ahen, O. M. H. (2020). Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CL(pro). Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/https://doi.org/10.1080/07391102.2020.1782768
- Anand, K., Ziebuhr, J., Wadhwani, P., Mesters, J. R., & Hilgenfeld, R. (2003). Coronavirus main proteinase (3CLpro) structure: Basis for design of anti-SARS drugs. Science (New York, N.Y.), 300(5626), 1763–1767. https://doi.org/https://doi.org/10.1126/science.1085658
- Baby, K., Maity, S., Mehta, C. H., Suresh, A., Nayak, U. Y., & Nayak, Y. (2020). Targeting SARS-CoV-2 main protease: A computational drug repurposing study. Archives of Medical Research, 1–10. https://doi.org/https://doi.org/10.1016/j.arcmed.2020.09.013
- Beck, B. R., Shin, B., Choi, Y., Park, S., & Kang, K. (2020). Predicting commercially available antiviral drugs that may act on the novel coronavirus (SARS-CoV-2) through a drug-target interaction deep learning model. Computational and Structural Biotechnology Journal, 18, 784–790. https://doi.org/https://doi.org/10.1016/j.csbj.2020.03.025
- Berendsen, H. J. C., Postma, J. P. M., Gunsteren, W. F. v., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/https://doi.org/10.1063/1.448118
- Bharadwaj, S., Lee, K. E., Dwivedi, V. D., & Kang, S. G. (2020). Computational insights into tetracyclines as inhibitors against SARS-CoV-2 Mpro via combinatorial molecular simulation calculations. Life Sciences, 257, 118080. https://doi.org/https://doi.org/10.1016/j.lfs.2020.118080
- 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, 1–10. https://doi.org/https://doi.org/10.1080/07391102.2020.1766572
- Bhargava, S., Patel, T., Gaikwad, R., Patil, U. K., & Gayen, S. (2019). Identification of structural requirements and prediction of inhibitory activity of natural flavonoids against Zika virus through molecular docking and Monte Carlo based QSAR Simulation. Natural Product Research, 33(6), 851–857. https://doi.org/https://doi.org/10.1080/14786419.2017.1413574
- Biovia, D. S. (2017). Discovery studio modeling environment. Release.
- Chakraborty, A., Nandi, S. K., Panda, A. K., Mahapatra, P. P., Giri, S., & Biswas, A. (2018). Probing the structure-function relationship of Mycobacterium leprae HSP18 under different UV radiations. International Journal of Biological Macromolecules, 119, 604–616. https://doi.org/https://doi.org/10.1016/j.ijbiomac.2018.07.151
- Chen, J. (2016). Drug resistance mechanisms of three mutations V32I, I47V and V82I in HIV-1 protease toward inhibitors probed by molecular dynamics simulations and binding free energy predictions. RSC Advances, 6(63), 58573–58585. https://doi.org/https://doi.org/10.1039/C6RA09201B
- Chen, J., Wang, X., Zhu, T., Zhang, Q., & Zhang, J. Z. (2015). A comparative insight into amprenavir resistance of mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 protease based on thermodynamic integration and MM-PBSA methods. Journal of Chemical Information and Modeling, 55(9), 1903–1913. https://doi.org/https://doi.org/10.1021/acs.jcim.5b00173
- Chen, N., Zhou, M., Dong, X., Qu, J., Gong, F., Han, Y., Qiu, Y., Wang, J., Liu, Y., Wei, Y., Xia, J., Yu, T., Zhang, X., & Zhang, L. (2020). Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: A descriptive study. Lancet (London, England), 395(10223), 507–513. https://doi.org/https://doi.org/10.1016/S0140-6736(20)30211-7
- Chou, K. C., Wei, D. Q., & Zhong, W. Z. (2003). Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS. Biochemical and Biophysical Research Communications, 308(1), 148–151. https://doi.org/https://doi.org/10.1016/s0006-291x(03)01342-1
- Choudhury, C. (2020). Fragment tailoring strategy to design novel chemical entities as potential binders of novel corona virus main protease. Journal of Biomolecular Structure and Dynamics, 1–14. https://doi.org/https://doi.org/10.1080/07391102.2020.1771424
- Coulerie, P., Nour, M., Maciuk, A., Eydoux, C., Guillemot, J. C., Lebouvier, N., Hnawia, E., Leblanc, K., Lewin, G., Canard, B., & Figadere, B. (2013). Structure-activity relationship study of biflavonoids on the Dengue virus polymerase DENV-NS5 RdRp. Planta Medica, 79(14), 1313–1318. https://doi.org/https://doi.org/10.1055/s-0033-1350672
- Cucinotta, D., & Vanelli, M. (2020). WHO declares COVID-19 a pandemic. Acta Bio-Medica: Atenei Parmensis, 91(1), 157–160. https://doi.org/https://doi.org/10.23750/abm.v91i1.9397
- Dai, W., Zhang, B., Jiang, X. M., Su, H., Li, J., Zhao, Y., Xie, X., Jin, Z., Peng, J., Liu, F., Li, C., Li, Y., Bai, F., Wang, H., Cheng, X., Cen, X., Hu, S., Yang, X., Wang, J., … Liu, H. (2020). Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease. Science (New York, N.Y.), 368(6497), 1331–1335. https://doi.org/https://doi.org/10.1126/science.abb4489
- 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/https://doi.org/10.1038/srep42717
- Das, B. K., Pv, P., & Chakraborty, D. (2019). Computational insights into factor affecting the potency of diaryl sulfone analogs as Escherichia coli dihydropteroate synthase inhibitors. Computational Biology and Chemistry, 78, 37–52. https://doi.org/https://doi.org/10.1016/j.compbiolchem.2018.11.005
- Drosten, C., Gunther, S., Preiser, W., van der Werf, S., Brodt, H. R., Becker, S., Rabenau, H., Panning, M., Kolesnikova, L., Fouchier, R. A., Berger, A., Burguiere, A. M., Cinatl, J., Eickmann, M., Escriou, N., Grywna, K., Kramme, S., Manuguerra, J. C., Muller, S., … Doerr, H. W. (2003). Identification of a novel coronavirus in patients with severe acute respiratory syndrome. The New England Journal of Medicine, 348(20), 1967–1976. https://doi.org/https://doi.org/10.1056/NEJMoa030747
- Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/https://doi.org/10.1063/1.470117
- Fan, K., Wei, P., Feng, Q., Chen, S., Huang, C., Ma, L., Lai, B., Pei, J., Liu, Y., Chen, J., & Lai, L. (2004). Biosynthesis, purification, and substrate specificity of severe acute respiratory syndrome coronavirus 3C-like proteinase. The Journal of Biological Chemistry, 279(3), 1637–1642. https://doi.org/https://doi.org/10.1074/jbc.M310875200
- Frisch, M., Clemente, F., Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G. A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H. P., Izmaylov, A. F., Bloino, J., & Zhe, G. (2016). Gaussian 09, Revision A. 01. Gaussian, Inc.
- Fritz, D., Venturi, C. R., Cargnin, S., Schripsema, J., Roehe, P. M., Montanha, J. A., & von Poser, G. L. (2007). Herpes virus inhibitory substances from Hypericum connatum Lam., a plant used in southern Brazil to treat oral lesions. Journal of Ethnopharmacology, 113(3), 517–520. https://doi.org/https://doi.org/10.1016/j.jep.2007.07.013
- Ghosh, R., Chakraborty, A., Biswas, A., & Chowdhuri, S. (2020a). Evaluation of green tea polyphenols as novel corona virus (SARS CoV-2) main protease (Mpro) inhibitors - an in silico docking and molecular dynamics simulation study. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/https://doi.org/10.1080/07391102.2020.1779818
- Ghosh, R., Chakraborty, A., Biswas, A., & Chowdhuri, S. (2020b). Identification of polyphenols from Broussonetia papyrifera as SARS CoV-2 main protease inhibitors using in silico docking and molecular dynamics simulation approaches. Journal of Biomolecular Structure and Dynamics, 1–14. https://doi.org/https://doi.org/10.1080/07391102.2020.1802347
- Gorla, U. S., Rao, G. K., Kulandaivelu, U. S., Alavala, R. R., & Panda, S. P. (2020). Lead finding from selected flavonoids with antiviral (SARS-CoV-2) potentials against COVID-19: An in-silico evaluation. Combinatorial Chemistry & High Throughput Screening. https://doi.org/https://doi.org/10.2174/1386207323999200818162706
- Gurung, A. B., Ali, M. A., Lee, J., Farah, M. A., & Al-Anazi, K. M. (2020). Unravelling lead antiviral phytochemicals for the inhibition of SARS-CoV-2 Mpro enzyme through in silico approach. Life Sciences, 255, 117831. https://doi.org/https://doi.org/10.1016/j.lfs.2020.117831
- Hage-Melim, L., Federico, L. B., de Oliveira, N. K. S., Francisco, V. C. C., Correia, L. C., de Lima, H. B., Gomes, S. Q., Barcelos, M. P., Francischini, I. A. G., & da Silva, C. (2020). Virtual screening, ADME/Tox predictions and the drug repurposing concept for future use of old drugs against the COVID-19. Life Sciences, 256, 117963. https://doi.org/https://doi.org/10.1016/j.lfs.2020.117963
- Hakmi, M., Bouricha, E. M., Kandoussi, I., Harti, J. E., & Ibrahimi, A. (2020). Repurposing of known anti-virals as potential inhibitors for SARS-CoV-2 main protease using molecular docking analysis. Bioinformation, 16(4), 301–306. https://doi.org/https://doi.org/10.6026/97320630016301
- Hayashi, K., Hayashi, T., & Morita, N. (1992). Mechanism of action of the antiherpesvirus biflavone ginkgetin. Antimicrobial Agents and Chemotherapy, 36(9), 1890–1893. https://doi.org/https://doi.org/10.1128/aac.36.9.1890
- Hegyi, A., & Ziebuhr, J. (2002). Conservation of substrate specificities among coronavirus main proteases. The Journal of General Virology, 83(Pt 3), 595–599. https://doi.org/https://doi.org/10.1099/0022-1317-83-3-595
- Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/https://doi.org/10.1002/(sici)1096-987x(199709)18:12 < 1463::aid-jcc4 > 3.0.co;2-h
- Hilgenfeld, R. (2014). From SARS to MERS: Crystallographic studies on coronaviral proteases enable antiviral drug design. The FEBS Journal, 281(18), 4085–4096. https://doi.org/https://doi.org/10.1111/febs.12936
- Hou, T., Wang, J., Li, Y., & Wang, W. (2011). Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling, 51(1), 69–82. https://doi.org/https://doi.org/10.1021/ci100275a
- Hsu, M. F., Kuo, C. J., Chang, K. T., Chang, H. C., Chou, C. C., Ko, T. P., Shr, H. L., Chang, G. G., Wang, A. H., & Liang, P. H. (2005). Mechanism of the maturation process of SARS-CoV 3CL protease. The Journal of Biological Chemistry, 280(35), 31257–31266. https://doi.org/https://doi.org/10.1074/jbc.M502577200
- Islam, M. T., & Mubarak, M. S. (2020). Diterpenes and their derivatives as promising agents against dengue virus and dengue vectors: A literature-based review. Phytotherapy Research: PTR, 34(4), 674–684. https://doi.org/https://doi.org/10.1002/ptr.6562
- Jimenez-Alberto, A., Ribas-Aparicio, R. M., Aparicio-Ozores, G., & Castelan-Vega, J. A. (2020). Virtual screening of approved drugs as potential SARS-CoV-2 main protease inhibitors. Computational Biology and Chemistry, 88, 107325. https://doi.org/https://doi.org/10.1016/j.compbiolchem.2020.107325
- 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 SARS-CoV-2 and discovery of its inhibitors. Nature, 582(7811), 289–293. https://doi.org/https://doi.org/10.1038/s41586-020-2223-y
- Jin, Z., Zhao, Y., Sun, Y., Zhang, B., Wang, H., Wu, Y., Zhu, Y., Zhu, C., Hu, T., Du, X., Duan, Y., Yu, J., Yang, X., Yang, X., Yang, K., Liu, X., Guddat, L. W., Xiao, G., Zhang, L., Yang, H., & Rao, Z. (2020). Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug carmofur. Nature Structural & Molecular Biology, 27(6), 529–532. https://doi.org/https://doi.org/10.1038/s41594-020-0440-6
- Joshi, T., Joshi, T., Sharma, P., Mathpal, S., Pundir, H., Bhatt, V., & Chandra, S. (2020). In silico screening of natural compounds against COVID-19 by targeting Mpro and ACE2 using molecular docking. European Review for Medical and Pharmacological Sciences, 24(8), 4529–4536. https://doi.org/https://doi.org/10.26355/eurrev_202004_21036
- Joshi, T., Sharma, P., Joshi, T., Pundir, H., Mathpal, S., & Chandra, S. (2020). Structure-based screening of novel lichen compounds against SARS Coronavirus main protease (Mpro) as potentials inhibitors of COVID-19. Molecular Diversity, 1–19. https://doi.org/https://doi.org/10.1007/s11030-020-10118-x
- Kandeel, M., & Al-Nazawi, M. (2020). Virtual screening and repurposing of FDA approved drugs against COVID-19 main protease. Life Sciences, 251, 117627. https://doi.org/https://doi.org/10.1016/j.lfs.2020.117627
- Kim, Y., Liu, H., Galasiti Kankanamalage, A. C., Weerasekara, S., Hua, D. H., Groutas, W. C., Chang, K. O., & Pedersen, N. C. (2016). Reversal of the progression of fatal coronavirus infection in cats by a broad-spectrum coronavirus protease inhibitor. PLoS Pathogens, 12(3), e1005531. https://doi.org/https://doi.org/10.1371/journal.ppat.1005531
- Kumar, V., Dhanjal, J. K., Kaul, S. C., Wadhwa, R., & Sundar, D. (2020). Withanone and caffeic acid phenethyl ester are predicted to interact with main protease (M(pro)) of SARS-CoV-2 and inhibit its activity. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/https://doi.org/10.1080/07391102.2020.1772108
- Lee, W. P., Lan, K. L., Liao, S. X., Huang, Y. H., Hou, M. C., & Lan, K. H. (2018). Inhibitory effects of amentoflavone and orobol on daclatasvir-induced resistance-associated variants of Hepatitis C Virus. The American Journal of Chinese Medicine, 46(4), 835–852. https://doi.org/https://doi.org/10.1142/S0192415X18500441
- Lin, Y. M., Anderson, H., Flavin, M. T., Pai, Y. H., Mata-Greenwood, E., Pengsuparp, T., Pezzuto, J. M., Schinazi, R. F., Hughes, S. H., & Chen, F. C. (1997). In vitro anti-HIV activity of biflavonoids isolated from Rhus succedanea and Garcinia multiflora. Journal of Natural Products, 60(9), 884–888. https://doi.org/https://doi.org/10.1021/np9700275
- Lin, Y. M., Flavin, M. T., Schure, R., Chen, F. C., Sidwell, R., Barnard, D. L., Huffman, J. H., & Kern, E. R. (1999). Antiviral activities of biflavonoids. Planta Medica, 65(2), 120–125. https://doi.org/https://doi.org/10.1055/s-1999-13971
- Ma, S. C., But, P. P., Ooi, V. E., He, Y. H., Lee, S. H., Lee, S. F., & Lin, R. C. (2001). Antiviral amentoflavone from Selaginella sinensis. Biological & Pharmaceutical Bulletin, 24(3), 311–312. https://doi.org/https://doi.org/10.1248/bpb.24.311
- Macchiagodena, M., Pagliai, M., & Procacci, P. (2020). Identification of potential binders of the main protease 3CLpro of the COVID-19 via structure-based ligand design and molecular modeling . Chemical Physics Letters, 750, 137489. https://doi.org/https://doi.org/10.1016/j.cplett.2020.137489
- Mazzini, S., Musso, L., Dallavalle, S., & Artali, R. (2020). Putative SARS-CoV-2 M(pro) inhibitors from an in-house library of natural and nature-inspired products: A virtual screening and molecular docking study. Molecules, 25(16), 3745. https://doi.org/https://doi.org/10.3390/molecules25163745
- Miki, K., Nagai, T., Suzuki, K., Tsujimura, R., Koyama, K., Kinoshita, K., Furuhata, K., Yamada, H., & Takahashi, K. (2007). Anti-influenza virus activity of biflavonoids. Bioorganic & Medicinal Chemistry, 17(3), 772–775. https://doi.org/https://doi.org/10.1016/j.bmcl.2006.10.075
- Mirza, M. U., & Froeyen, M. (2020). Structural elucidation of SARS-CoV-2 vital proteins: Computational methods reveal potential drug candidates against main protease, Nsp12 polymerase and Nsp13 helicase. Journal of Pharmaceutical Analysis, 10(4), 320–328. https://doi.org/https://doi.org/10.1016/j.jpha.2020.04.008
- Mittal, L., Kumari, A., Srivastava, M., Singh, M., & Asthana, S. (2020). Identification of potential molecules against COVID-19 main protease through structure-guided virtual screening approach. Journal of Biomolecular Structure and Dynamics, 1–19. https://doi.org/https://doi.org/10.1080/07391102.2020.1768151
- Miyamoto, S., & Kollman, P. A. (1992). Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models. Journal of Computational Chemistry, 13(8), 952–962. https://doi.org/https://doi.org/10.1002/jcc.540130805
- Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/https://doi.org/10.1002/jcc.21256
- Morris, G. M., Huey, R., & Olson, A. J. (2008). Using AutoDock for ligand-receptor docking. Current Protocols in Bioinformatics, 24(1), 8–14. https://doi.org/https://doi.org/10.1002/0471250953.bi0814s24
- Muramatsu, T., Takemoto, C., Kim, Y. T., Wang, H., Nishii, W., Terada, T., Shirouzu, M., & Yokoyama, S. (2016). SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel subsite cooperativity. Proceedings of the National Academy of Sciences of the United States of America, 113(46), 12997–13002. https://doi.org/https://doi.org/10.1073/pnas.1601327113
- Nandi, S. K., Chakraborty, A., Panda, A. K., & Biswas, A. (2016). Conformational perturbation, hydrophobic interactions and oligomeric association are responsible for the enhanced chaperone function of Mycobacterium leprae HSP18 under pre-thermal condition. RSC Advances, 6(67), 62146–62156. https://doi.org/https://doi.org/10.1039/C6RA00167J
- Odhar, H. A., Ahjel, S. W., Albeer, A., Hashim, A. F., Rayshan, A. M., & Humadi, S. S. (2020). Molecular docking and dynamics simulation of FDA approved drugs with the main protease from 2019 novel coronavirus. Bioinformation, 16(3), 236–244. https://doi.org/https://doi.org/10.6026/97320630016236
- 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/https://doi.org/10.1002/jcc.20090
- Orhan, I. E., & Senol Deniz, F. S. (2020). Natural products as potential leads against Coronaviruses: Could they be encouraging structural models against SARS-CoV-2? Natural Products and Bioprospecting, 10(4), 171–186. https://doi.org/https://doi.org/10.1007/s13659-020-00250-4
- Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/https://doi.org/10.1063/1.328693
- Pathak, R. K., Baunthiyal, M., Taj, G., & Kumar, A. (2014). Virtual screening of natural inhibitors to the predicted HBx protein structure of Hepatitis B Virus using molecular docking for identification of potential lead molecules for liver cancer. Bioinformation, 10(7), 428–435. https://doi.org/https://doi.org/10.6026/97320630010428
- Pires, D. E., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. https://doi.org/https://doi.org/10.1021/acs.jmedchem.5b00104
- Ramaiah, R., & Suresh, P. C. (2013). Molecular docking studies of phytochemical compounds with viral proteases. International Journal of Pharmaceutical Sciences and Research, 4(1), 475.
- 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
- Roa-Linares, V. C., Brand, Y. M., Agudelo-Gomez, L. S., Tangarife-Castano, V., Betancur-Galvis, L. A., Gallego-Gomez, J. C., & Gonzalez, M. A. (2016). Anti-herpetic and anti-dengue activity of abietane ferruginol analogues synthesized from (+)-dehydroabietylamine. European Journal of Medicinal Chemistry, 108, 79–88. https://doi.org/https://doi.org/10.1016/j.ejmech.2015.11.009
- Rota, P. A., Oberste, M. S., Monroe, S. S., Nix, W. A., Campagnoli, R., Icenogle, J. P., Penaranda, S., Bankamp, B., Maher, K., Chen, M. H., Tong, S., Tamin, A., Lowe, L., Frace, M., DeRisi, J. L., Chen, Q., Wang, D., Erdman, D. D., Peret, T. C., … Bellini, W. J. (2003). Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science (New York, N.Y.), 300(5624), 1394–1399. https://doi.org/https://doi.org/10.1126/science.1085952
- Ryu, Y. B., Jeong, H. J., Kim, J. H., Kim, Y. M., Park, J. Y., Kim, D., Nguyen, T. T., Park, S. J., Chang, J. S., Park, K. H., Rho, M. C., & Lee, W. S. (2010). Biflavonoids from Torreya nucifera displaying SARS-CoV 3CL(pro) inhibition. Bioorganic & Medicinal Chemistry, 18(22), 7940–7947. https://doi.org/https://doi.org/10.1016/j.bmc.2010.09.035
- Sayed, A. M., Khattab, A. R., AboulMagd, A. M., Hassan, H. M., Rateb, M. E., Zaid, H., & Abdelmohsen, U. R. (2020). Nature as a treasure trove of potential anti-SARS-CoV drug leads: A structural/mechanistic rationale. RSC Advances, 10(34), 19790–19802. https://doi.org/https://doi.org/10.1039/D0RA04199H
- Schuttelkopf, A. W., & van Aalten, D. M. (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/https://doi.org/10.1107/S0907444904011679
- Tripathi, M. K., Singh, P., Sharma, S., Singh, T. P., Ethayathulla, A. S., & Kaur, P. (2020). Identification of bioactive molecule from Withania somnifera (Ashwagandha) as SARS-CoV-2 main protease inhibitor. Journal of Biomolecular Structure and Dynamics, 1–14. https://doi.org/https://doi.org/10.1080/07391102.2020.1790425
- 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. https://doi.org/https://doi.org/10.1016/j.cell.2020.02.058
- Wen, C.-C., Kuo, Y.-H., Jan, J.-T., Liang, P.-H., Wang, S.-Y., Liu, H.-G., Lee, C.-K., Chang, S.-T., Kuo, C.-J., Lee, S.-S., Hou, C.-C., Hsiao, P.-W., Chien, S.-C., Shyur, L.-F., & Yang, N.-S. (2007). Specific plant terpenoids and lignoids possess potent antiviral activities against severe acute respiratory syndrome coronavirus. Journal of Medicinal Chemistry, 50(17), 4087–4095. https://doi.org/https://doi.org/10.1021/jm070295s
- Wilsky, S., Sobotta, K., Wiesener, N., Pilas, J., Althof, N., Munder, T., Wutzler, P., & Henke, A. (2012). Inhibition of fatty acid synthase by amentoflavone reduces coxsackievirus B3 replication. Archives of Virology, 157(2), 259–269. https://doi.org/https://doi.org/10.1007/s00705-011-1164-z
- 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, H., Xie, W., Xue, X., Yang, K., Ma, J., Liang, W., Zhao, Q., Zhou, Z., Pei, D., Ziebuhr, J., Hilgenfeld, R., Yuen, K. Y., Wong, L., Gao, G., Chen, S., Chen, Z., Ma, D., Bartlam, M., & Rao, Z. (2005). Design of wide-spectrum inhibitors targeting coronavirus main proteases. PLoS Biology, 3(10), e324. https://doi.org/https://doi.org/10.1371/journal.pbio.0030324
- Zaki, A. M., van Boheemen, S., Bestebroer, T. M., Osterhaus, A. D., & Fouchier, R. A. (2012). Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. New England Journal of Medicine, 367(19), 1814–1820. https://doi.org/https://doi.org/10.1056/NEJMoa1211721
- Zhang, J., & Wang, Y. (2020). Bilobetin, a novel small molecule inhibitor targeting influenza virus polymerase acidic (PA) endonuclease was screened from plant extracts. Natural Product Research, 1–4. https://doi.org/https://doi.org/10.1080/14786419.2020.1808636
- 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 (New York, N.Y.), 368(6489), 409–412. https://doi.org/https://doi.org/10.1126/science.abb3405
- Zhao, W., Zhong, Z., Xie, X., Yu, Q., & Liu, J. (2020). Relation between chest CT findings and clinical conditions of Coronavirus Disease (COVID-19) pneumonia: A multicenter study. AJR. American Journal of Roentgenology, 214(5), 1072–1077. https://doi.org/https://doi.org/10.2214/AJR.20.22976
- Zhou, P., Yang, X. L., Wang, X. G., Hu, B., Zhang, L., Zhang, W., Si, H. R., Zhu, Y., Li, B., Huang, C. L., Chen, H. D., Chen, J., Luo, Y., Guo, H., Jiang, R. D., Liu, M. Q., Chen, Y., Shen, X. R., Wang, X., … Shi, Z. L. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270–273. https://doi.org/https://doi.org/10.1038/s41586-020-2012-7
- 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. The New England Journal of Medicine, 382(8), 727–733. https://doi.org/https://doi.org/10.1056/NEJMoa2001017