Molecular insights to the anti-COVID-19 potential of α-, β- and γ-cyclodextrins

References

• Almeida, B., Domingues, C., Mascarenhas-Melo, F., Silva, I., Jarak, I., Veiga, F., & Figueiras, A. (2023). The role of cyclodextrins in COVID-19 therapy-A literature review. International Journal of Molecular Sciences, 24(3), 2974. https://doi.org/10.3390/ijms24032974
   PubMed Web of Science ®Google Scholar
• Bezerra, B. B., Silva, G., Coelho, S. V. A., Correa, I. A., Souza, M. R. M., Macedo, K. V. G., Matos, B. M., Tanuri, A., Matassoli, F. L., Costa, L. J. D., Hildreth, J. E. K., & Arruda, L. B. (2022). Hydroxypropyl-beta-cyclodextrin (HP-BCD) inhibits SARS-CoV-2 replication and virus-induced inflammatory cytokines. Antiviral Research, 205, 105373. https://doi.org/10.1016/j.antiviral.2022.105373
   PubMed Web of Science ®Google Scholar
• Bhowmick, N. A., Oft, J., Dorff, T., Pal, S., Agarwal, N., Figlin, R. A., Posadas, E. M., Freedland, S. J., & Gong, J. (2020). COVID-19 and androgen-targeted therapy for prostate cancer patients. Endocrine-Related Cancer, 27(9), R281–R292. https://doi.org/10.1530/ERC-20-0165
   PubMed Web of Science ®Google Scholar
• Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx. Methods in Molecular Biology (Clifton, N.J.), 1263, 243–250. https://doi.org/10.1007/978-1-4939-2269-7_19
   PubMedGoogle Scholar
• Davey, R. A., & Grossmann, M. (2016). Androgen receptor structure, function and biology: From bench to bedside. The Clinical Biochem. Reviews, 37(1), 3–15.
   PubMedGoogle Scholar
• Ergoren, M. C., Paolacci, S., Manara, E., Dautaj, A., Dhuli, K., Anpilogov, K., Camilleri, G., Suer, H. K., Sayan, M., Tuncel, G., Sultanoglu, N., Farronato, M., Tartaglia, G. M., Dundar, M., Farronato, G., Gunsel, I. S., Bertelli, M., & Sanlidag, T. (2020). A pilot study on the preventative potential of alpha-cyclodextrin and hydroxytyrosol against SARS-CoV-2 transmission. Acta Bio-Medica: Atenei Parmensis, 91(13-S), e2020022. https://doi.org/10.23750/abm.v91i13-S.10817
   PubMedGoogle Scholar
• Fraser, B. J., Beldar, S., Seitova, A., Hutchinson, A., Mannar, D., Li, Y., Kwon, D., Tan, R., Wilson, R. P., Leopold, K., Subramaniam, S., Halabelian, L., Arrowsmith, C. H., & Bénard, F. (2022). Structure and activity of human TMPRSS2 protease implicated in SARS-CoV-2 activation. Nature Chemical Biology, 18(9), 963–971. https://doi.org/10.1038/s41589-022-01059-7
   PubMed Web of Science ®Google Scholar
• Glowacka, I., Bertram, S., Herzog, P., Pfefferle, S., Steffen, I., Muench, M. O., Simmons, G., Hofmann, H., Kuri, T., Weber, F., Eichler, J., Drosten, C., & Pöhlmann, S. (2010). Differential downregulation of ACE2 by the spike proteins of severe acute respiratory syndrome coronavirus and human coronavirus NL63. Journal of Virology, 84(2), 1198–1205. https://doi.org/10.1128/JVI.01248-09
   PubMed Web of Science ®Google Scholar
• Hoffmann, M., Hofmann-Winkler, H., Smith, J. C., Krüger, N., Arora, P., Sørensen, L. K., Søgaard, O. S., Hasselstrøm, J. B., Winkler, M., Hempel, T., Raich, L., Olsson, S., Danov, O., Jonigk, D., Yamazoe, T., Yamatsuta, K., Mizuno, H., Ludwig, S., Noé, F., … Pöhlmann, S. (2021). Camostat mesylate inhibits SARS-CoV-2 activation by TMPRSS2-related proteases and its metabolite GBPA exerts antiviral activity. EBioMedicine, 65, 103255. https://doi.org/10.1016/j.ebiom.2021.103255
   PubMed Web of Science ®Google Scholar
• 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. e278. https://doi.org/10.1016/j.cell.2020.02.052
   PubMed Web of Science ®Google Scholar
• Hu, B., Guo, H., Zhou, P., & Shi, Z. L. (2021). Characteristics of SARS-CoV-2 and COVID-19. Nature Reviews. Microbiology, 19(3), 141–154. https://doi.org/10.1038/s41579-020-00459-7
   PubMed Web of Science ®Google Scholar
• Jansook, P., Ogawa, N., & Loftsson, T. (2018). Cyclodextrins: Structure, physicochemical properties and pharmaceutical applications. International Journal of Pharmaceutics, 535(1-2), 272–284. https://doi.org/10.1016/j.ijpharm.2017.11.018
   PubMed Web of Science ®Google Scholar
• Jicsinszky, L., Martina, K., & Cravotto, G. (2021). Cyclodextrins in the antiviral therapy. Journal of Drug Delivery Science and Technology, 64, 102589. https://doi.org/10.1016/j.jddst.2021.102589
   PubMed Web of Science ®Google Scholar
• 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 M(pro) from SARS-CoV-2 and discovery of its inhibitors. Nature, 582(7811), 289–293. https://doi.org/10.1038/s41586-020-2223-y
   PubMed Web of Science ®Google Scholar
• Kalra, R. S., Kumar, V., Dhanjal, J. K., Garg, S., Li, X., Kaul, S. C., Sundar, D., & Wadhwa, R. (2021). COVID19-inhibitory activity of withanolides involves targeting of the host cell surface receptor ACE2: Insights from computational and biochemical assays. Journal of Biomolecular Structure & Dynamics, 40(17), 7885–7898. https://doi.org/10.1080/07391102.2021.1902858
   PubMed Web of Science ®Google Scholar
• Kumar, V., Dhanjal, J. K., Bhargava, P., Kaul, A., Wang, J., Zhang, H., Kaul, S. C., Wadhwa, R., & Sundar, D. (2022). Withanone and withaferin-A are predicted to interact with transmembrane protease serine 2 (TMPRSS2) and block entry of SARS-CoV-2 into cells. Journal of Biomolecular Structure & Dynamics, 40(1), 1–13. https://doi.org/10.1080/07391102.2020.1775704
   PubMed Web of Science ®Google Scholar
• Kumar, V., Dhanjal, J. K., Kaul, S. C., Wadhwa, R., & Sundar, D. (2021). 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 & Dynamics, 39(11), 3842–3854. https://doi.org/10.1080/07391102.2020.1772108
   PubMed Web of Science ®Google Scholar
• Kurkov, S. V., & Loftsson, T. (2013). Cyclodextrins. International Journal of Pharmaceutics, 453(1), 167–180. https://doi.org/10.1016/j.ijpharm.2012.06.055
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Lim, C. H., Rasti, B., Sulistyo, J., & Hamid, M. A. (2021). Comprehensive study on transglycosylation of CGTase from various sources. Heliyon, 7(2), e06305. https://doi.org/10.1016/j.heliyon.2021.e06305
   PubMed Web of Science ®Google Scholar
• Malik, V., Kumar, V., Kaul, S. C., Wadhwa, R., & Sundar, D. (2021). Potential of withaferin-A, withanone and caffeic acid phenethyl ester as ATP-competitive inhibitors of BRAF: A bioinformatics study. Current Research in Structural Biology, 3, 301–311. https://doi.org/10.1016/j.crstbi.2021.11.004
   PubMedGoogle Scholar
• Meyerowitz, E. A., Richterman, A., Gandhi, R. T., & Sax, P. E. (2021). Transmission of SARS-CoV-2: A review of viral, host, and environmental factors. Annals of Internal Medicine, 174(1), 69–79. https://doi.org/10.7326/M20-5008
   PubMed Web of Science ®Google Scholar
• Nguyen, D. D., Gao, K., Chen, J., Wang, R., & Wei, G. W. (2020). Unveiling the molecular mechanism of SARS-CoV-2 main protease inhibition from 137 crystal structures using algebraic topology and deep learning. Chemical Science, 11(44), 12036–12046. https://doi.org/10.1039/d0sc04641h
   PubMed Web of Science ®Google Scholar
• Ni, W., Yang, X., Yang, D., Bao, J., Li, R., Xiao, Y., Hou, C., Wang, H., Liu, J., Yang, D., Xu, Y., Cao, Z., & Gao, Z. (2020). Role of angiotensin-converting enzyme 2 (ACE2) in COVID-19. Critical Care (London, England), 24(1), 422. https://doi.org/10.1186/s13054-020-03120-0
   PubMed Web of Science ®Google Scholar
• Paolacci, S., Ceccarini, M. R., Codini, M., Manara, E., Tezzele, S., Percio, M., Capodicasa, N., Kroni, D., Dundar, M., Ergoren, M. C., Sanlidag, T., Beccari, T., Farronato, M., Farronato, G., Tartaglia, G. M., & Bertelli, M. (2020). Pilot study for the evaluation of safety profile of a potential inhibitor of SARS-CoV-2 endocytosis. Acta Bio-Medica: Atenei Parmensis, 91(13-S), e2020009. https://doi.org/10.23750/abm.v91i13-S.10583
   PubMedGoogle Scholar
• Phan, T. (2020). Novel coronavirus: From discovery to clinical diagnostics. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 79, 104211. https://doi.org/10.1016/j.meegid.2020.104211
   PubMed Web of Science ®Google Scholar
• Pillaiyar, T., Manickam, M., Namasivayam, V., Hayashi, Y., & Jung, S. H. (2016). An overview of severe acute respiratory syndrome-coronavirus (SARS-CoV) 3CL protease inhibitors: Peptidomimetics and small molecule chemotherapy. Journal of Medicinal Chemistry, 59(14), 6595–6628. https://doi.org/10.1021/acs.jmedchem.5b01461
   PubMed Web of Science ®Google Scholar
• Protein Preparation Wizard, Epik, Impact, Prime, LigPrep, Glide, Schrödinger, LLC, New York, NY. 2020. Desmond Molecular Dynamics System, D. E. Shaw Research, New York, NY, 2020. Maestro-Desmond Interoperability Tools, Schrödinger, New York, NY, 2020., Schrödinger Release 2020–3.
   Google Scholar
• Ravaioli, S., Tebaldi, M., Fonzi, E., Angeli, D., Mazza, M., Nicolini, F., Lucchesi, A., Fanini, F., Pirini, F., Tumedei, M. M., Cerchione, C., Viale, P., Sambri, V., Martinelli, G., & Bravaccini, S. (2020). ACE2 and TMPRSS2 potential involvement in genetic susceptibility to SARS-COV-2 in cancer patients. Cell Transplantation, 29, 963689720968749. https://doi.org/10.1177/0963689720968749
   PubMed Web of Science ®Google Scholar
• Roos, K., Wu, C., Damm, W., Reboul, M., Stevenson, J. M., Lu, C., Dahlgren, M. K., Mondal, S., Chen, W., Wang, L., Abel, R., Friesner, R. A., & Harder, E. D. (2019). OPLS3e: Extending force field coverage for drug-like small molecules. Journal of Chemical Theory and Computation, 15(3), 1863–1874. https://doi.org/10.1021/acs.jctc.8b01026
   PubMed Web of Science ®Google Scholar
• Rosenbaum, A. I., & Maxfield, F. R. (2011). Niemann-pick type C disease: Molecular mechanisms and potential therapeutic approaches. Journal of Neurochemistry, 116(5), 789–795. https://doi.org/10.1111/j.1471-4159.2010.06976.x
   PubMed Web of Science ®Google Scholar
• Schrödinger, L.N.Y., NY, USA. (2020). Academic version of Desmond integrated with Schrödinger Maestro (1st ed.).
   Google Scholar
• Szente, L., Singhal, A., Domokos, A., & Song, B. (2018). Cyclodextrins: Assessing the impact of cavity size, occupancy, and substitutions on cytotoxicity and cholesterol homeostasis. Molecules (Basel, Switzerland), 23(5), 1228. https://doi.org/10.3390/molecules23051228
   PubMed Web of Science ®Google Scholar
• Towler, P., Staker, B., Prasad, S. G., Menon, S., Tang, J., Parsons, T., Ryan, D., Fisher, M., Williams, D., Dales, N. A., Patane, M. A., & Pantoliano, M. W. (2004). ACE2 X-ray structures reveal a large hinge-bending motion important for inhibitor binding and catalysis. The Journal of Biological Chemistry, 279(17), 17996–18007. https://doi.org/10.1074/jbc.M311191200
   PubMed Web of Science ®Google Scholar
• Wang, Z., Wang, X., Li, Y., Lei, T., Wang, E., Li, D., Kang, Y., Zhu, F., & Hou, T. (2019). farPPI: A webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods. Bioinformatics (Oxford, England), 35(10), 1777–1779. https://doi.org/10.1093/bioinformatics/bty879
   PubMed Web of Science ®Google Scholar
• Wüpper, S., Lüersen, K., & Rimbach, G. (2021). Cyclodextrins, natural compounds, and plant bioactives-A nutritional perspective. Biomolecules, 11(3), 401. https://doi.org/10.3390/biom11030401
   PubMed Web of Science ®Google Scholar
• Yao, Y., Wang, H., & Liu, Z. (2020). Expression of ACE2 in airways: Implication for COVID-19 risk and disease management in patients with chronic inflammatory respiratory diseases. Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunology, 50(12), 1313–1324. https://doi.org/10.1111/cea.13746
   PubMed Web of Science ®Google Scholar
• Zang, R., Gomez Castro, M. F., McCune, B. T., Zeng, Q., Rothlauf, P. W., Sonnek, N. M., Liu, Z., Brulois, K. F., Wang, X., Greenberg, H. B., Diamond, M. S., Ciorba, M. A., Whelan, S. P. J., & Ding, S. (2020). TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes. Science Immunology, 5(47), eabc3582. https://doi.org/10.1126/sciimmunol.abc3582
   PubMed Web of Science ®Google Scholar
• Zanganeh, S., Goodarzi, N., Doroudian, M., & Movahed, E. (2022). Potential COVID-19 therapeutic approaches targeting angiotensin-converting enzyme 2; An updated review. Reviews in Medical Virology, 32(4), e2321. https://doi.org/10.1002/rmv.2321
   PubMed Web of Science ®Google Scholar
• Zhou, L., Xu, Z., Castiglione, G. M., Soiberman, U. S., Eberhart, C. G., Duh,., & E., J. (2020). ACE2 and TMPRSS2 are expressed on the human ocular surface, suggesting susceptibility to SARS-CoV-2 infection. The Ocular Surface, 18(4), 537–544. https://doi.org/10.1016/j.jtos.2020.06.007
   PubMed Web of Science ®Google Scholar