References
- Arturo Fernandez, R. T., Tristan Quimque, M. J., & Israel Notarte, K. (2021). Myxobacterial Depsipeptide Chondramides Interrupt SARS-CoV-2 Entry by Targeting Its Broad. Antagonistic Prospects for Anti-COVID-19 Drug Discovery. https://doi.org/10.13140/RG.2.2.20343.34728
- Báez-Santos, Y. M., St. John, S. E., & Mesecar, A. D. (2015). The SARS-coronavirus papain-like protease: Structure, function and inhibition by designed antiviral compounds. Antiviral Research, 115, 21–38. https://doi.org/10.1016/j.antiviral.2014.12.015
- Bharadwaj, S., Dubey, A., & Yadava, U. (2021). Exploration of natural compounds with anti-SARS-CoV-2 activity via inhibition of SARS-CoV-2 Mpro. Briefings in Bioinformatics, 22, 1361–1377. https://doi.org/10.1093/bib/bbaa382
- Bhardwaj, V. K., Singh, R., Das, P., & Purohit, R. (2021a). Evaluation of acridinedione analogs as potential SARS-CoV-2 main protease inhibitors and their comparison with repurposed anti-viral drugs. Computers in Biology and Medicine, 128, 104117. https://doi.org/10.1016/j.compbiomed.2020.104117
- Bhardwaj, V. K., Singh, R., & Sharma, J. (2020). Identification of bioactive molecules from tea plant as SARS-CoV-2 main protease inhibitors. Journal of Biomolecular Structure and Dynamics, 39, 3449–3458. https://doi.org/10.1080/07391102.2020.1766572
- Bhardwaj, V. K., Singh, R., Sharma, J., Rajendran, V., Purohit, R., & Kumar, S. (2021b). Bioactive molecules of tea as potential inhibitors for RNA-dependent RNA polymerase of SARS-CoV-2. Frontiers in Medicine, 8, 645. https://doi.org/10.3389/fmed.2021.684020
- Bittmann, S. (2020). COVID-19: Expression of ACE2-receptors in the brain suggest neurotropic damage. Journal of Regenerative Biology and Medicine, 2, 1–3. https://doi.org/10.37191/Mapsci-2582-385X-2(3)-027
- Chang, F.-R., Yen, C.-T., Ei-Shazly, M., Lin, W.-H., Yen, M.-H., Lin, K.-H., & Wu, Y.-C. (2012). Anti-human coronavirus (anti-HCoV) triterpenoids from the leaves of Euphorbia neriifolia. Natural Products Communications, 7(11), 1934578X1200701. https://doi.org/10.1177/1934578X1200701103
- Chen, B., Tian, E. K., & He, B. (2020). Overview of lethal human coronaviruses. Signal Transduction and Targeted Therapy, 5, 89. https://doi.org/10.1038/s41392-020-0190-2
- Chen, D., Oezguen, N., & Urvil, P. (2016). Regulation of protein-ligand binding affinity by hydrogen bond pairing. Science Advances. https://doi.org/10.1126/sciadv.1501240
- da Silva, J. K. R., Figueiredo, P. L. B., Byler, K. G., & Setzer, W. N. (2020). Essential oils as antiviral agents. Potential of essential oils to treat sars − cov − 2 infection: An in − silico investigation. International Journal of Molecular Sciences, 21(10), 3426. https://doi.org/10.3390/ijms21103426
- 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/10.1038/srep42717
- Devaux, C. A., Rolain, J. M., Colson, P., & Raoult, D. (2020). New insights on the antiviral effects of chloroquine against coronavirus: What to expect for COVID-19? International Journal of Antimicrobial Agents, 55(5), 105938. https://doi.org/10.1016/j.ijantimicag.2020.105938
- Diniz, L. R. L., Perez-Castillo, Y., Elshabrawy, H. A., Filho, C. d. S. M. B., & de Sousa, D. P. (2021). Article bioactive terpenes and their derivatives as potential SARS-CoV-2 proteases inhibitors from molecular modeling studies. Biomolecules, 11(1), 74. https://doi.org/10.3390/biom11010074
- Dresser, G. K., Spence, J. D., & Bailey, D. G. (2000). Pharmacokinetic-pharmacodynamic consequences and clinical relevance of cytochrome P450 3A4 inhibition. Clinical Pharmacokinetics, 38, 41–57. https://doi.org/10.2165/00003088-200038010-00003
- Du, A., Zheng, R., Disoma, C., Li, S., Chen, Z., Li, S., Liu, P., Zhou, Y., Shen, Y., Liu, S., Zhang, Y., Dong, Z., Yang, Q., Alsaadawe, M., Razzaq, A., Peng, Y., Chen, X., Hu, L., Peng, J., … Xia, Z. (2021). Epigallocatechin-3-gallate, an active ingredient of Traditional Chinese Medicines, inhibits the 3CLpro activity of SARS-CoV-2. International Journal of Biological Macromolecules, 176, 1–12. https://doi.org/10.1016/j.ijbiomac.2021.02.012
- Fabbri, L. M., Piattella, M., Caramori, G., & Ciaccia, A. (1996). Oral vs inhaled asthma therapy. Drugs, 52(Supplement 6), 20–28. https://doi.org/10.2165/00003495-199600526-00005
- Fatima, S., Gupta, P., & Sharma, S. (2019). ADMET profiling of geographically diverse phytochemical using chemoinformatic tools. Future Medicinal Chemistry, 12, 1. https://doi.org/10.4155/fmc-2019-0206
- Forli, S., Huey, R., Pique, M. E., Sanner, M. F., Goodsell, D. S., & Olson, A. J. (2016). Computational protein-ligand docking and virtual drug screening with the AutoDock suite. Nature Protocols, 11(5), 905–919. https://doi.org/10.1038/nprot.2016.051
- Gao, X., Qin, B., & Chen, P. (2021). Crystal structure of SARS-CoV-2 papain-like protease. Acta Pharmaceutica Sinica B, 11, 237–245. https://doi.org/10.1016/j.apsb.2020.08.014
- 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 (New York, N.Y.), 368(6492), 779–782. https://doi.org/10.1126/science.abb7498
- Ghosh, A. K., Brindisi, M., Shahabi, D., Chapman, M. E., & Mesecar, A. D. (2020). Drug development and medicinal chemistry efforts toward SARS-Coronavirus and Covid-19 therapeutics. Chemmedchem, 15(11), 907–932. https://doi.org/10.1002/cmdc.202000223
- Gowrishankar, S., Muthumanickam, S., Kamaladevi, A., Karthika, C., Jothi, R., Boomi, P., Maniazhagu, D., & Pandian, S. K. (2021). Promising phytochemicals of traditional Indian herbal steam inhalation therapy to combat COVID-19 – An in silico study. Food and Chemical Toxicology., 148, 111966. https://doi.org/10.1016/j.fct.2020.111966
- Hasan, M., Parvez, M. S. A., Azim, K. F., Imran, M. A. S., Raihan, T., Gulshan, A., Muhit, S., Akhand, R. N., Ahmed, S. S. U., & Uddin, M. B. (2021). Main protease inhibitors and drug surface hotspots for the treatment of COVID-19: A drug repurposing and molecular docking approach. Biomedicine & Pharmacotherapy = Biomedecine & Pharmacotherapie, 140, 111742. https://doi.org/10.1016/j.biopha.2021.111742
- Hedayat, K. M. (2009). United States Patent Application Publication: Essential Oil Diffusion. Patent US20090169487 A1
- Hill, N. S., Preston, I. R., & Roberts, K. E. (2015). Inhaled therapies for pulmonary hypertension. Respir Care, 60, 794–805. https://doi.org/10.4187/respcare.03927
- Hoffmann, M., Kleine-Weber, H., Schroeder, S., Krüger, N., Herrler, T., Erichsen, S., Schiergens, T. S., Herrler, G., Wu, N.-H., Nitsche, A., Müller, M. A., Drosten, C., & Pöhlmann, S. (2020). SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell, 181(2), 271–280.e8. https://doi.org/10.1016/j.cell.2020.02.052
- Johnson, P. H., & Quay, S. C. (2005). Advances in nasal drug delivery through tight junction technology. Expert Opinion on Drug Delivery, 2(2), 281-98. https://doi.org/10.1517/17425247.2.2.281S
- Khodadadi, E., Maroufi, P., Khodadadi, E., Esposito, I., Ganbarov, K., Espsoito, S., Yousefi, M., Zeinalzadeh, E., & Kafil, H. S. (2020). Study of combining virtual screening and antiviral treatments of the Sars-CoV-2 (Covid-19). Microbial Pathogenesis, 146, 104241. https://doi.org/10.1016/j.micpath.2020.104241
- Kim, S., Chen, J., & Cheng, T. (2021). PubChem in 2021: New data content and improved web interfaces. Nucleic Acids Research, 49, D1388–D1395. https://doi.org/10.1093/nar/gkaa971
- Klemm, T., Ebert, G., Calleja, D. J., Allison, C. C., Richardson, L. W., Bernardini, J. P., Lu, B. G., Kuchel, N. W., Grohmann, C., Shibata, Y., Gan, Z. Y., Cooney, J. P., Doerflinger, M., Au, A. E., Blackmore, T. R., Heden van Noort, G. J., Geurink, P. P., Ovaa, H., Newman, J., … Komander, D. (2020). Mechanism and inhibition of the papain‐like protease, PLpro, of SARS‐CoV‐2. The EMBO Journal, 39(18). https://doi.org/10.15252/embj.2020106275
- Knapp, B., Ospina, L., & Deane, C. M. (2018). Avoiding false positive conclusions in molecular simulation: The importance of replicas. Journal of Chemical Theory and Computation, 14, 6127–6138. https://doi.org/10.1021/acs.jctc.8b00391
- Kollman, P. A., Massova, I., & Reyes, C. (2000). Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts of Chemical Research, 33, 889–897. https://doi.org/10.1021/ar000033j
- Kumari, R., Kumar, R., & Lynn, A. (2014a). G-mmpbsa -A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54, 1951–1962. https://doi.org/10.1021/ci500020m
- Kumari, S., Pundhir, S., Priya, P., Jeena, G., Punetha, A., Chawla, K., Firdos Jafaree, Z., Mondal, S., & Yadav, G. (2014b). EssOilDB: A database of essential oils reflecting terpene composition and variability in the plant kingdom. Database (Oxford), 2014, bau120. https://doi.org/10.1093/database/bau120
- Lan, J., Ge, J., Yu, J., Shan, S., Zhou, H., Fan, S., Zhang, Q., Shi, X., Wang, Q., Zhang, L., & Wang, X. (2020). Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature, 581(7807), 215–220. https://doi.org/10.1038/s41586-020-2180-5
- Li, Y. C., Bai, W. Z., & Hashikawa, T. (2020). The neuroinvasive potential of SARS-CoV2 may play a role in the respiratory failure of COVID-19 patients. Journal of Medical Virology, 92(6), 552-555. https://doi.org/10.1002/jmv.25728
- Martínez, L. (2015). Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis. PLoS One, 10(3), e0119264. https://doi.org/10.1371/journal.pone.0119264
- Mesecarr, A. D. (2020). A taxonomically-driven approach to development of potent, broad-spectrum inhibitors of coronavirus main protease including SARS-CoV-2 (COVID-19). https://doi.org/10.2210/pdb6w63/pdb
- Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). Software news and updates AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
- Oran, D. P., & Topol, E. J. (2020). Prevalence of Asymptomatic SARS-CoV-2 Infection: A Narrative Review. Annals of Internal Medicine, 173, 362–367. https://doi.org/10.7326/M20-3012
- Osipiuk, J., Jedrzejczak, R., & Tesar, C. (2020). The crystal structure of papain-like protease of SARS CoV-2. https://doi.org/10.2210/pdb6w9c/pdb
- Panikar, S., Shoba, G., & Arun, M. (2021). Essential oils as an effective alternative for the treatment of COVID-19: Molecular interaction analysis of protease (Mpro) with pharmacokinetics and toxicological properties. Journal of Infection and Public Health, 14, 601–610. https://doi.org/10.1016/j.jiph.2020.12.037
- Pence, H. E., & Williams, A. (2010). Chemspider: An online chemical information resource. Journal of Chemical Education, 87(11), 1123–1124. https://doi.org/10.1021/ed100697w
- Pires, D. E. V., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58, 4066–4072. https://doi.org/10.1021/acs.jmedchem.5b00104
- Rolf, D. (2004). United States Patent Application Publication: Inhalation Antiviral Patch, US 2004/0071757
- Sayampanathan, A. A., Heng, C. S., & Pin, P. H. (2021). Infectivity of asymptomatic versus symptomatic COVID-19. Lancet, 397, 93–94. https://doi.org/10.1016/S0140-6736(20)32651-9
- Schwede, T., Kopp, J., Guex, N., & Peitsch, M. C. (2003). SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Research, 31, 3381–3385. https://doi.org/10.1093/nar/gkg520
- Shah, B., Modi, P., & Sagar, S. R. (2020). In silico studies on therapeutic agents for COVID-19: Drug repurposing approach. Life Sciences, 252, 117652. https://doi.org/10.1016/j.lfs.2020.117652
- Sharma, A., Sharma, S., Gupta, M., Fatima, S., Saini, R., & Agarwal, S. M. (2018a). Pharmacokinetic profiling of anticancer phytocompounds using computational approach. Phytochemical Analysis, 29(6), 559–568. https://doi.org/10.1002/pca.2767
- Sharma, S., Gupta, M., Sharma, A., & Agarwal, S. M. (2018b). Oral Bioavailability of Naturally Occurring Anticancer Phytomolecules. Letters in Drug Design & Discovery, 15(11), 1180–1188. https://doi.org/10.2174/1570180815666180109161014
- Shawan, M. M. A. K., Halder, S. K., & Hasan, M. A. (2021). Luteolin and abyssinone II as potential inhibitors of SARS-CoV-2: An in silico molecular modeling approach in battling the COVID-19 outbreak. Bulletin of the National Research Centre, 45(1). https://doi.org/10.1186/s42269-020-00479-6
- Shin, D., Mukherjee, R., Grewe, D., Bojkova, D., Baek, K., Bhattacharya, A., Schulz, L., Widera, M., Mehdipour, A. R., Tascher, G., Geurink, P. P., Wilhelm, A., van der Heden van Noort, G. J., Ovaa, H., Müller, S., Knobeloch, K.-P., Rajalingam, K., Schulman, B. A., Cinatl, J., … Dikic, I. (2020). Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature, 587(7835), 657–662. https://doi.org/10.1038/s41586-020-2601-5
- Singh, R., Bhardwaj, V. K., Sharma, J., Kumar, D., & Purohit, R. (2021). Identification of potential plant bioactive as SARS-CoV-2 Spike protein and human ACE2 fusion inhibitors. Computers in Biology and Medicine, 136, 104631. https://doi.org/10.1016/j.compbiomed.2021.104631
- Sungnak, W., Huang, N., Bécavin, C., Berg, M., Queen, R., Litvinukova, M., Talavera-López, C., Maatz, H., Reichart, D., Sampaziotis, F., Worlock, K. B., Yoshida, M., Barnes, J. L., & HCA Lung Biological Network (2020). SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nature Medicine, 26(5), 681–687. https://doi.org/10.1038/s41591-020-0868-6
- Trott, O., & Olson, A. J. (2009). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31, 455–461. https://doi.org/10.1002/jcc.21334
- Tworowski, D., Gorohovski, A., & Mukherjee, S. (2021). COVID19 Drug Repository: Text-mining the literature in search of putative COVID19 therapeutics. Nucleic Acids Research, 49, D1113–D1121. https://doi.org/10.1093/nar/gkaa969
- van de Waterbeemd, H., & Gifford, E. (2003). ADMET in silico modelling: Towards prediction paradise? Nature Reviews. Drug Discovery, 2(3), 192–204. https://doi.org/10.1038/nrd1032
- Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C.-L., Abiona, O., Graham, B. S., & McLellan, J. S. (2020). Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science, 367(6483), 1260–1263. https://doi.org/10.1126/science.aax0902
- Yan, L., Zhang, Y., Ge, J., Zheng, L., Gao, Y., Wang, T., Jia, Z., Wang, H., Huang, Y., Li, M., Wang, Q., Rao, Z., & Lou, Z. (2020). Architecture of a SARS-CoV-2 mini replication and transcription complex. Nature Communications, 11(1), 5874. https://doi.org/10.1038/s41467-020-19770-1