Structural-based design of HD-TAC7 PROteolysis TArgeting chimeras (PROTACs) candidate transformations to abrogate SARS-CoV-2 infection

References

• Abraham, M. J., & Gready, J. E. (2011). Optimization of parameters for molecular dynamics simulation using smooth particle‐mesh Ewald in GROMACS 4.5. Journal of Computational Chemistry, 32(9), 2031–2040. https://doi.org/10.1002/jcc.21773
   PubMed Web of Science ®Google Scholar
• 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/10.1016/j.softx.2015.06.001
   Google Scholar
• Arshia, A. H., Shadravan, S., Solhjoo, A., Sakhteman, A., & Sami, A. (2021). De novo design of novel protease inhibitor candidates in the treatment of SARS-CoV-2 using deep learning, docking, and molecular dynamic simulations. Computers in Biology and Medicine, 139, 104967. https://doi.org/10.1016/j.compbiomed.2021.104967
   PubMed Web of Science ®Google Scholar
• Banerjee, N. S., Moore, D. W., Broker, T. R., & Chow, L. T. (2018). Vorinostat, a pan-HDAC inhibitor, abrogates productive HPV-18 DNA amplification. Proceedings of the National Academy of Sciences of the United States of America, 115(47), E11138–E11147. https://doi.org/10.1073/pnas.1801156115
   PubMed Web of Science ®Google Scholar
• Berman, H. M., Bhat, T. N., Bourne, P. E., Feng, Z., Gilliland, G., Weissig, H., & Westbrook, J. (2000). The protein data bank and the challenge of structural genomics. Nature Structural Biology, 7, 957–959. https://doi.org/10.1038/80734
   PubMedGoogle Scholar
• Blanco-Melo, D., Nilsson-Payant, B. E., Liu, W.-C., Uhl, S., Hoagland, D., Møller, R., Jordan, T. X., Oishi, K., Panis, M., Sachs, D., Wang, T. T., Schwartz, R. E., Lim, J. K., Albrecht, R. A., & tenOever, B. R. (2020). Imbalanced host response to SARS-CoV-2 drives development of COVID-19. Cell, 181(5), 1036–1045.e9. https://doi.org/10.1016/j.cell.2020.04.026
   PubMed Web of Science ®Google Scholar
• Bondeson, D. P., Smith, B. E., Burslem, G. M., Buhimschi, A. D., Hines, J., Jaime-Figueroa, S., Wang, J., Hamman, B. D., Ishchenko, A., & Crews, C. M. (2018). Lessons in PROTAC design from selective degradation with a promiscuous warhead. Cell Chemical Biology, 25(1), 78–87.e5. https://doi.org/10.1016/j.chembiol.2017.09.010e5
   PubMed Web of Science ®Google Scholar
• Cao, F., de Weerd, S., Chen, D., Zwinderman, M. R., van der Wouden, P. E., & Dekker, F. J. (2020). Induced protein degradation of histone deacetylases 3 (HDAC3) by proteolysis targeting chimera (PROTAC). European Journal of Medicinal Chemistry, 208, 112800. https://doi.org/10.1016/j.ejmech.2020.112800
   PubMed Web of Science ®Google Scholar
• Chan, K. H., Zengerle, M., Testa, A., & Ciulli, A. (2018). Impact of target warhead and linkage vector on inducing protein degradation: Comparison of bromodomain and extra-terminal (BET) degraders derived from triazolodiazepine (JQ1) and tetrahydroquinoline (I-BET726) BET inhibitor scaffolds. Journal of Medicinal Chemistry, 61(2), 504–513. https://doi.org/10.1021/acs.jmedchem.6b01912
   PubMed Web of Science ®Google Scholar
• Chen, G., Wu, D., Guo, W., Cao, Y., Huang, D., Wang, H., Wang, T., Zhang, X., Chen, H., Yu, H., Zhang, X., Zhang, M., Wu, S., Song, J., Chen, T., Han, M., Li, S., Luo, X., Zhao, J., & Ning, Q. (2020). Clinical and immunological features of severe and moderate coronavirus disease 2019. The Journal of Clinical Investigation, 130(5), 2620–2629. https://doi.org/10.1172/JCI137244
   PubMed Web of Science ®Google Scholar
• Chua, R. L., Lukassen, S., Trump, S., Hennig, B. P., Wendisch, D., Pott, F., Debnath, O., Thürmann, L., Kurth, F., Völker, M. T., Kazmierski, J., Timmermann, B., Twardziok, S., Schneider, S., Machleidt, F., Müller-Redetzky, H., Maier, M., Krannich, A., Schmidt, S., … Eils, R. (2020). COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis. Nature Biotechnology, 38(8), 970–979. https://doi.org/10.1038/s41587-020-0602-4
   PubMed Web of Science ®Google Scholar
• Churcher, I. (2018). Protac-induced protein degradation in drug discovery: Breaking the rules or just making new ones? Journal of Medicinal Chemistry, 61(2), 444–452. https://doi.org/10.1021/acs.jmedchem.7b01272
   PubMed Web of Science ®Google Scholar
• Clark, M., Cramer, R. D., & Van Opdenbosch, N. (1989). Validation of the general purpose tripos 5.2 force field. Journal of Computational Chemistry, 10(8), 982–1012. https://doi.org/10.1002/jcc.540100804
   Web of Science ®Google Scholar
• Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by docking with pyrx. Methods in Molecular Biology (Clifton, NJ), 1263, 243–250. https://doi.org/10.1007/978-1-4939-2269-7_19
   PubMedGoogle Scholar
• Desantis, J., Mercorelli, B., Celegato, M., Croci, F., Bazzacco, A., Baroni, M., Siragusa, L., Cruciani, G., Loregian, A., & Goracci, L. (2021). Indomethacin-based PROTACs as pan-coronavirus antiviral agents. European Journal of Medicinal Chemistry, 226, 113814. https://doi.org/10.1016/j.ejmech.2021.113814
   PubMed Web of Science ®Google Scholar
• Diao, B., Wang, C., Tan, Y., Chen, X., Liu, Y., Ning, L., Chen, L., Li, M., Liu, Y., Wang, G., Yuan, Z., Feng, Z., Zhang, Y., Wu, Y., & Chen, Y. (2020). Reduction and functional exhaustion of T cells in patients with coronavirus disease 2019 (COVID-19). Frontiers in Immunology, 11, 827. https://doi.org/10.3389/fimmu.2020.00827
   PubMed Web of Science ®Google Scholar
• Doss, C. G. P., Rajith, B., Chakraborty, C., NagaSundaram, N., Ali, S. K., & Zhu, H. (2014). Structural signature of the G719S-T790M double mutation in the EGFR kinase domain and its response to inhibitors. Scientific Reports, 4(1), 1–7. https://doi.org/10.1038/srep05868
   Google Scholar
• Drummond, M. L., & Williams, C. I. (2019). In silico modeling of PROTAC-mediated ternary complexes: Validation and application. Journal of Chemical Information and Modeling, 59(4), 1634–1644. https://doi.org/10.1021/acs.jcim.8b00872
   PubMed Web of Science ®Google Scholar
• Emsley, P., & Cowtan, K. (2004). Coot: Model-building tools for molecular graphics. Acta Crystallographica Section D, Biological Crystallography, 60(Pt 12 Pt 1), 2126–2132. https://doi.org/10.1107/S0907444904019158
   PubMedGoogle Scholar
• Fakhar, M., Zahid, S., Rashid., & S., Najumuddin. (2022). Structural basis of Klotho binding to VEGFR2 and TRPC1 and repurposing calcium channel blockers as TRPC1 antagonists for the treatment of age-related cardiac hypertrophy. Archives of Biochemistry and Biophysics, 719, 109171. https://doi.org/10.1016/j.abb.2022.109171
   PubMed Web of Science ®Google Scholar
• Feuston, B. P., Miller, M. D., Culberson, J. C., Nachbar, R. B., & Kearsley, S. K. (2001). Comparison of knowledge-based and distance geometry approaches for generation of molecular conformations. Journal of Chemical Information and Computer Sciences, 41(3), 754–763. https://doi.org/10.1021/ci000464g
   PubMedGoogle Scholar
• Furlan, A., Monzani, V., Reznikov, L. L., Leoni, F., Fossati, G., Modena, D., Mascagni, P., & Dinarello, C. A. (2011). Pharmacokinetics, safety and inducible cytokine responses during a phase 1 trial of the oral histone deacetylase inhibitor ITF2357 (Givinostat). Molecular Medicine (Cambridge, MA), 17(5–6), 353–362. https://doi.org/10.2119/molmed.2011.00020
   PubMed Web of Science ®Google Scholar
• Gamage, A. M., Tan, K. S., Chan, W. O. Y., Liu, J., Tan, C. W., Ong, Y. K., Thong, M., Andiappan, A. K., Anderson, D. E., Wang, D. Y., & Wang, L. F. (2020). Infection of human nasal epithelial cells with SARS-CoV-2 and a 382-Nt deletion isolate lacking ORF8 reveals similar viral kinetics and host transcriptional profiles. PLoS Pathogens, 16(12), e10009130. https://doi.org/10.1371/journal.ppat.1009130
   Web of Science ®Google Scholar
• Gao, S., Huang, T., Song, L., Xu, S., Cheng, Y., Cherukupalli, S., Kang, D., Zhao, T., Sun, L., Zhang, J., Zhan, P., & Liu, X. (2022). Medicinal chemistry strategies towards the development of effective SARS-CoV-2 inhibitors. Acta Pharmaceutica Sinica B, 12(2), 581–599. https://doi.org/10.1016/j.apsb.2021.08.027
   PubMed Web of Science ®Google Scholar
• Ghiboub, M., Zhao, J., Li Yim, A. Y. F., Schilderink, R., Verseijden, C., van Hamersveld, P. H. P., Duarte, J. M., Hakvoort, T. B. M., Admiraal, I., Harker, N. R., Tough, D. F., Henneman, P., de Winther, M. P. J., & de Jonge, W. J. (2020). HDAC3 mediates the inflammatory response and LPS tolerance in human monocytes and macrophages. Frontiers in Immunology, 11, 550769. https://doi.org/10.3389/fimmu.2020.550769
   PubMed Web of Science ®Google Scholar
• Gordon, J. C., Myers, J. B., Folta, T., Shoja, V., Heath, L. S., & Onufriev, A. (2005). H++: A server for estimating pkas and adding missing hydrogens to macromolecules. Nucleic Acids Research, 33, W368–371. https://doi.org/10.1093/nar/gki464
   PubMed Web of Science ®Google Scholar
• Grabiec, A. M., Krausz, S., de Jager, W., Burakowski, T., Groot, D., Sanders, M. E., Prakken, B. J., Maslinski, W., Eldering, E., Tak, P. P., & Reedquist, K. A. (2010). Histone deacetylase inhibitors suppress inflammatory activation of rheumatoid arthritis patient synovial macrophages and tissue. Journal of Immunology (Baltimore, MD: 1950), 184(5), 2718–2728. https://doi.org/10.4049/jimmunol.0901467
   PubMed Web of Science ®Google Scholar
• Guenther, M. G., Barak, O. R. R., & Lazar, M. A. (2001). The SMRT and N-CoR corepressors are activating cofactors for histone deacetylase 3. Molecular and Cellular Biology, 21(18), 6091–6101. https://doi.org/10.1128/MCB.21.18.6091-6101.2001
   PubMed Web of Science ®Google Scholar
• Guenther, M. G., Lane, W. S., Fischle, W., Verdin, E., Lazar, M. A., & Shiekhattar, R. (2000). A core SMRT corepressor complex containing HDAC3 and TBL1, a WD40-repeat protein linked to deafness. Genes & Development, 14(9), 1048–1057. https://doi.org/10.1101/gad.14.9.1048
   PubMed Web of Science ®Google Scholar
• Gul, M., Navid, A., & Rashid, S. (2023). Structural basis of constitutive c-Src kinase activity due to R175L and W118A mutations. Journal of Biomolecular Structure and Dynamics, 41(2), 634–645. https://doi.org/10.1080/07391102.2021.2010600
   PubMed Web of Science ®Google Scholar
• Halgren, T. A. (1996). Merck molecular force field. Ii. Mmff94 van der Waals and electrostatic parameters for intermolecular interactions. Journal of Computational Chemistry, 17(5–6), 520–552. https://doi.org/10.1002/(SICI)1096-987X(199604)17:5/6 < 520::AID-JCC2 > 3.0.CO;2-W
   Web of Science ®Google Scholar
• Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeersch, T., Zurek, E., & Hutchison, G. R. (2012). Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. Journal of Cheminformatics, 4(1), 17. https://doi.org/10.1186/1758-2946-4-17
   PubMed Web of Science ®Google Scholar
• Honig, B., & Nicholls, A. (1995). Classical electrostatics in biology and chemistry. Science (New York, NY), 268(5214), 1144–1149. https://doi.org/10.1126/science.7761829
   Google Scholar
• Ishizuka, T., & Lazar, M. A. (2005). The nuclear receptor corepressor deacetylase activating domain is essential for repression by thyroid hormone receptor. Molecular Endocrinology (Baltimore, MD), 19(6), 1443–1451. https://doi.org/10.1210/me.2005-0009
   PubMedGoogle Scholar
• Jose, R. J., & Manuel, A. (2020). COVID-19 cytokine storm: The interplay between inflammation and coagulation. The Lancet Respiratory Medicine, 8(6), e46–e47. https://doi.org/10.1016/S2213-2600(20)30216-2
   PubMed Web of Science ®Google Scholar
• Karki, R., Sharma, B. R., Tuladhar, S., Williams, E. P., Zalduondo, L., Samir, P., Zheng, M., Sundaram, B., Banoth, B., Malireddi, R. K. S., Schreiner, P., Neale, G., Vogel, P., Webby, R., Jonsson, C. B., & Kanneganti, T.-D. (2021). Synergism of TNF-α and IFN-γ triggers inflammatory cell death, tissue damage, and mortality in SARS-CoV-2 infection and cytokine shock syndromes. Cell, 184(1), 149–168.e17. https://doi.org/10.1016/j.cell.2020.11.025
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., & Lynn, A, Open Source Drug Discovery Consortium. (2014). g_mmpbsa A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Labute, P. (2010). LowModeMD implicit low-mode velocity filtering applied to conformational search of macrocycles and protein loops. Journal of Chemical Information and Modeling, 50(5), 792–800. https://doi.org/10.1021/ci900508k
   PubMed Web of Science ®Google Scholar
• Lai, A. C., & Crews, C. M. (2017). Induced protein degradation: An emerging drug discovery paradigm. Nature Reviews. Drug Discovery, 16(2), 101–114. https://doi.org/10.1038/nrd.2016.211
   PubMed Web of Science ®Google Scholar
• Leoni, F., Zaliani, A., Bertolini, G., Porro, G., Pagani, P., Pozzi, P., Donà, G., Fossati, G., Sozzani, S., Azam, T., Bufler, P., Fantuzzi, G., Goncharov, I., Kim, S. H., Pomerantz, B. J., Reznikov, L. L., Siegmund, B., Dinarello, C. A., & Mascagni, P. (2002). The antitumor histone deacetylase inhibitor suberoylanilide hydroxamic acid exhibits antiinflammatory properties via suppression of cytokines. Proceedings of the National Academy of Sciences of the United States of America, 99(5), 2995–3000. https://doi.org/10.1073/pnas.052702999
   PubMed Web of Science ®Google Scholar
• Li, W., Elhassan, R. M., Hou, X., & Fang, H. (2021). Recent advances in small molecule PROTACs for the treatment of cancer. Current Medicinal Chemistry, 28(24), 4893–4909. https://doi.org/10.2174/0929867327666201117141611
   PubMed Web of Science ®Google Scholar
• Liu, K., Zou, R., Cui, W., Li, M., Wang, X., Dong, J., Li, H., Li, H., Wang, P., Shao, X., Su, W., Chan, H. C. S., Li, H., & Yuan, S. (2020). Clinical HDAC inhibitors are effective drugs to prevent the entry of SARS-Cov2. ACS Pharmacology & Translational Science, 3(6), 1361–1370. https://doi.org/10.1021/acsptsci.0c00163
   PubMedGoogle Scholar
• Liu, Y., Liang, C., Xin, L., Ren, X., Tian, L., Ju, X., Li, H., Wang, Y., Zhao, Q., Liu, H., Cao, W., Xie, X., Zhang, D., Wang, Y., & Jian, Y. (2020). The development of coronavirus 3C-like protease (3CLpro) inhibitors from 2010 to 2020. European Journal of Medicinal Chemistry, 206, 112711. https://doi.org/10.3390/molecules25245932
   PubMed Web of Science ®Google Scholar
• Mehta, P., McAuley, D. F., Brown, M., Sanchez, E., Tattersall, R. S., & Manson, J. J, HLH Across Speciality Collaboration, UK. (2020). COVID-19: Consider cytokine storm syndromes and immunosuppression. Lancet (London, England), 395(10229), 1033–1034. https://doi.org/10.1016/S0140-6736(20)30628-0
   PubMed Web of Science ®Google Scholar
• Meng, E. C., Pettersen, E. F., Couch, G. S., Huang, C. C., & Ferrin, T. E. (2006). Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinformatics, 7(1), 1–10. https://doi.org/10.1186/1471-2105-7-339
   PubMedGoogle Scholar
• Netea, M. G., Joosten, L. A. B., Latz, E., Mills, K. H. G., Natoli, G., Stunnenberg, H. G., O’Neill, L. A. J., & Xavier, R. J. (2016). Trained immunity: A program of innate immune memory in health and disease. Science (New York, NY), 352(6284), aaf1098. https://doi.org/10.1126/science.aaf1098
   Google Scholar
• Noor, Z., Afzal, N., & Rashid, S. (2015). Exploration of novel inhibitors for class I histone deacetylase isoforms by QSAR modeling and molecular dynamics simulation assays. PLoS One, 10(10), e0139588. https://doi.org/10.1371/journal.pone.0143155
   PubMed Web of Science ®Google Scholar
• Oberoi, J., Fairall, L., Watson, P. J., Yang, J.-C., Czimmerer, Z., Kampmann, T., Goult, B. T., Greenwood, J. A., Gooch, J. T., Kallenberger, B. C., Nagy, L., Neuhaus, D., & Schwabe, J. W. R. (2011). Structural basis for the assembly of the SMRT/NCoR core transcriptional repression machinery. Nature Structural & Molecular Biology, 18(2), 177–184. https://doi.org/10.1038/nsmb.1983
   PubMed Web of Science ®Google Scholar
• O’Boyle, N. M., Vandermeersch, T., Flynn, C. J., Maguire, A. R., & Hutchison, G. R. (2011). Confab-Systematic generation of diverse low-energy conformers. Journal of Cheminformatics, 3(1), 1–9. https://doi.org/10.1186/1758-2946-3-8
   PubMed Web of Science ®Google Scholar
• Paiva, S. L., & Crews, C. M. (2019). Targeted protein degradation: Elements of PROTAC design. Current Opinion in Chemical Biology, 50, 111–119. https://doi.org/10.1016/j.cbpa.2019.02.022
   PubMed Web of Science ®Google Scholar
• Park, A., & Iwasaki, A. (2020). Type I and type III interferons – induction, signaling, evasion, and application to combat COVID-19. Cell Host & Microbe, 27(6), 870–878. https://doi.org/10.1016/j.chom.2020.05.008
   PubMed Web of Science ®Google Scholar
• Pedersen, S. F., & Ho, Y. C. (2020). SARS-CoV-2: A storm is raging. The Journal of Clinical Investigation, 130(5), 2202–2205. https://doi.org/10.1172/JCI137647
   PubMed Web of Science ®Google Scholar
• Perico, L., Benigni, A., Casiraghi, F., Ng, L. F. P., Renia, L., & Remuzzi, G. (2021). Immunity, endothelial injury and complement-induced coagulopathy in COVID-19. Nature Reviews. Nephrology, 17(1), 46–64. https://doi.org/10.1038/s41581-020-00357-4
   PubMed Web of Science ®Google Scholar
• Pitt, B., Sutton, N. R., Wang, Z., Goonewardena, S. N., & Holinstat, M. (2021). Potential repurposing of the HDAC inhibitor valproic acid for patients with COVID-19. European Journal of Pharmacology, 898, 173988. https://doi.org/10.1016/j.ejphar.2021.173988
   PubMed Web of Science ®Google Scholar
• Poli, V., Pui-Yan Ma, V., Di Gioia, M., Broggi, A., Benamar, M., Chen, Q., Mazitschek, R., Haggarty, S. J., Chatila, T. A., Karp, J. M., & Zanoni, I. (2021). Zinc-dependent histone deacetylases drive neutrophil extracellular trap formation and potentiate local and systemic inflammation. iScience, 24(11), 103256. https://doi.org/10.1016/j.isci.2021.103256
   PubMed Web of Science ®Google Scholar
• Ripamonti, C., Spadotto, V., Pozzi, P., Stevenazzi, A., Vergani, B., Marchini, M., Sandrone, G., Bonetti, E., Mazzarella, L., Minucci, S., Steinkühler, C., & Fossati, G. (2022). HDAC inhibition as potential therapeutic strategy to restore the deregulated immune response in severe COVID-19. Frontiers in Immunology, 13, 841716. https://doi.org/10.3389/fimmu.2022.841716
   PubMed Web of Science ®Google Scholar
• Saeed, S., Quintin, J., Kerstens, H. H. D., Rao, N. A., Aghajanirefah, A., Matarese, F., Cheng, S.-C., Ratter, J., Berentsen, K., van der Ent, M. A., Sharifi, N., Janssen-Megens, E. M., Ter Huurne, M., Mandoli, A., van Schaik, T., Ng, A., Burden, F., Downes, K., Frontini, M., … Stunnenberg, H. G. (2014). Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity. Science (New York, NY), 345(6204), 1251086. https://doi.org/10.1126/science.1251086
   Google Scholar
• Saha, B., & Parks, R. J. (2019). Histone deacetylase inhibitor suberoylanilide hydroxamic acid suppresses human adenovirus gene expression and replication. Journal of Virology, 93(12), e00088–19. https://doi.org/10.1128/JVI.00088-19
   PubMed Web of Science ®Google Scholar
• Schapira, M., Calabrese, M. F., Bullock, A. N., & Crews, C. M. (2019). Targeted protein degradation: Expanding the toolbox. Nature Reviews Drug Discovery, 18(12), 949–963. https://doi.org/10.1038/s41573-019-0047-y
   PubMed Web of Science ®Google Scholar
• Schator, D., Gomez-Valero, L., Buchrieser, C., & Rolando, M. (2021). Patho-epigenetics: Histone deacetylases as targets of pathogens and therapeutics. microLife, 2, uqai013. https://doi.org/10.1093/femsml/uqab013
   Google Scholar
• Shin, S. A., Joo, B. J., Lee, J. S., Ryu, G., Han, M., Kim, W. Y., Park, H. H., Lee, J. H., & Lee, C. S. (2020). Phytochemicals as anti-inflammatory agents in animal models of prevalent inflammatory diseases. Molecules, 25(24), 5932. https://doi.org/10.3390/molecules25245932
   PubMed Web of Science ®Google Scholar
• Sindhu, T., & Srinivasan, P. (2015). Exploring the binding properties of agonists interacting with human TGR5 using structural modeling, molecular docking and dynamics simulations. RSC Advances, 5(19), 14202–14213. https://doi.org/10.1080/07391102.2021.2010600
   Web of Science ®Google Scholar
• Takahashi, Y., Hayakawa, A., Sano, R., Fukuda, H., Harada, M., Kubo, R., Okawa, T., & Kominato, Y. (2021). Histone deacetylase inhibitors suppress ACE2 and ABO simultaneously, suggesting a preventive potential against COVID-19. Scientific Reports, 11(1), 3379. https://doi.org/10.1038/s41598-021-82970-2
   PubMed Web of Science ®Google Scholar
• Takeuchi, O., & Akira, S. (2010). Pattern recognition receptors and inflammation. Cell, 140(6), 805–820. https://doi.org/10.1016/j.cell.2010.01.022
   PubMed Web of Science ®Google Scholar
• Teodori, L., Sestili, P., Madiai, V., Coppari, S., Fraternale, D., Rocchi, M. B. L., Ramakrishna, S., & Albertini, M. C. (2020). MicroRNAs bioinformatics analyses identifying HDAC pathway as a putative target for existing anti‐COVID‐19 therapeutics. Frontiers in Pharmacology, 11, 582003. https://doi.org/10.3389/fphar.2020.582003
   PubMed Web of Science ®Google Scholar
• Tisoncik, J. R., Korth, M. J., Simmons, C. P., Farrar, J., Martin, T. R., & Katze, M. G. (2012). Into the eye of the cytokine storm. Microbiology and Molecular Biology Reviews, 76(1), 16–32. https://doi.org/10.1128/mmbr.05015-11
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). Autodock vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• van Aalten, D. M. F., Bywater, R., Findlay, J. B. C., Hendlich, M., Hooft, R. W. W., & Vriend, G. (1996). Prodrg, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. Journal of Computer-Aided Molecular Design, 10(3), 255–262. https://doi.org/10.1007/BF00355047
   PubMed Web of Science ®Google Scholar
• Vankadari, N., & Wilce, J. A. (2020). Emerging COVID-19 coronavirus: Glycan shield and structure prediction of spike glycoprotein and its interaction with human CD26. Emerging Microbes & Infections, 9(1), 601–604. https://doi.org/10.1080/22221751.2020.1739565
   PubMed Web of Science ®Google Scholar
• Villagra, A., Sotomayor, E. M., & Seto, E. (2010). Histone deacetylases and the immunological network: Implications in cancer and inflammation. Oncogene, 29(2), 157–173. https://doi.org/10.1038/onc.2009.334
   PubMed Web of Science ®Google Scholar
• Vincent, J. L. (2021). COVID-19: It’s all about sepsis. Future Microbiology, 16, 131–133. https://doi.org/10.2217/fmb-2020-0312
   PubMed Web of Science ®Google Scholar
• von Knethen, A., & Brüne, B. (2019). Histone deacetylation inhibitors as therapy concept in sepsis. International Journal of Molecular Sciences, 20(2), 346. https://doi.org/10.3390/ijms20020346
   PubMed Web of Science ®Google Scholar
• Watson, P. J., Fairall, L., Santos, G. M., & Schwabe, J. W. (2012). Structure of HDAC3 bound to co-repressor and inositol tetraphosphate. Nature, 481(7381), 335–340. https://doi.org/10.1038/nature10728
   PubMed Web of Science ®Google Scholar
• Weng, G., Shen, C., Cao, D., Gao, J., Dong, X., He, Q., Yang, B., Li, D., Wu, J., & Hou, T. (2021). PROTAC-DB: An online database of PROTACs. Nucleic Acids Research, 49(D1), D1381–D1387. https://doi.org/10.1093/nar/gkaa807
   PubMed Web of Science ®Google Scholar
• Winter, G. E., Buckley, D. L., Paulk, J., Roberts, J. M., Souza, A., Dhe-Paganon, S., & Bradner, J. E. (2015). Phthalimide conjugation as a strategy for in vivo target protein degradation. Science (New York, NY), 348(6241), 1376–1381. https://doi.org/10.1126/science.aab1433
   Google Scholar
• Wu, Z., & McGoogan, J. M. (2020). Characteristics of and important lessons from the coronavirus disease 2019 (COVID-19) outbreak in China. JAMA, 323(13), 1239–1242. https://doi.org/10.1001/jama.2020.2648
   PubMed Web of Science ®Google Scholar
• Yan, K., Cao, Q., Reilly, C. M., Young, N. L., Garcia, B. A., & Mishra, N. (2011). Histone Deacetylase 9 Deficiency Protects Against Effector T Cell-Mediated Systemic Autoimmunity. The Journal of Biological Chemistry, 286(33), 28833–28843. https://doi.org/10.1074/jbc.M111.233932
   PubMed Web of Science ®Google Scholar
• Yang, K., Song, Y., Xie, H., Wu, H., Wu, Y. T., Leisten, E. D., & Tang, W. (2018). Development of the first small molecule histone deacetylase 6 (HDAC6) degraders. Bioorganic & Medicinal Chemistry Letters, 28(14), 2493–2497. https://doi.org/10.1016/j.bmcl.2018.05.057
   PubMed Web of Science ®Google Scholar
• Yang, K., Wu, H., Zhang, Z., Leisten, E. D., Nie, X., Liu, B., Wen, Z., Zhang, J., Cunningham, M. D., & Tang, W. (2020). Development of selective histone deacetylase 6 (HDAC6) degraders recruiting von Hippel–Lindau (VHL) E3 ubiquitin ligase. ACS Medicinal Chemistry Letters, 11(4), 575–581. https://doi.org/10.1021/acsmedchemlett.0c00046
   PubMed Web of Science ®Google Scholar
• Yang, X., Yu, Y., Xu, J., Shu, H., Xia, J., Liu, H., Wu, Y., Zhang, L., Yu, Z., Fang, M., Yu, T., Wang, Y., Pan, S., Zou, X., Yuan, S., & Shang, Y. (2020). Clinical course and outcomes of critically Ill patients with SARS-CoV-2 pneumonia in Wuhan, China: A single-centered, retrospective, observational study. The Lancet Respiratory Medicine, 8(5), . 75–481. https://doi.org/10.1016/S2213-2600(20)30079-5
   Web of Science ®Google Scholar
• Yang, Y., Shen, C., Li, J., Yuan, J., Wei, J., Huang, F., Wang, F., Li, G., Li, Y., Xing, L., Peng, L., Yang, M., Cao, M., Zheng, H., Wu, W., Zou, R., Li, D., Xu, Z., Wang, H., … Liu, Y. (2020). Plasma IP-10 and MCP-3 levels are highly associated with disease severity and predict the progression of COVID-19. The Journal of Allergy and Clinical Immunology, 146(1), 119–127.e4. https://doi.org/10.1016/j.jaci.2020.04.027
   PubMed Web of Science ®Google Scholar
• You, S. H., Liao, X., Weiss, R. E., & Lazar, M. A. (2010). The interaction between nuclear receptor corepressor and histone deacetylase 3 regulates both positive and negative thyroid hormone action in vivo. Molecular Endocrinology (Baltimore, MD), 24(7), 1359–1367. https://doi.org/10.1210/me.2009-0501
   PubMedGoogle Scholar
• Zahid, S., Basharat, S., Fakhar, M., & Rashid, S. (2022). Molecular dynamics and structural analysis of the binding of COP1 E3 ubiquitin ligase to β-catenin and TRIB pseudokinases. Proteins, 90(4), 993–1004. https://doi.org/10.1002/prot.26292
   PubMed Web of Science ®Google Scholar
• Zahid, S., Gul, M., Shafique, S., & Rashid, S. (2022). E2UbcH5B-derived peptide ligands target HECT E3-E2 binding site and block the Ub-dependent SARS-CoV-2 egression: A computational study. Computers in Biology and Medicine, 146, 105660. https://doi.org/10.1016/j.compbiomed.2022.105660
   PubMed Web of Science ®Google Scholar
• Zhang, H., Penninger, J. M., Li, Y., Zhong, N., & Slutsky, A. S. (2020). Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: Molecular mechanisms and potential therapeutic target. Intensive Care Medicine, 46(4), 586–590. https://doi.org/10.1007/s00134-020-05985-9
   PubMed Web of Science ®Google Scholar
• Zhong, H., May, M. J., Jimi, E., & Ghosh, S. (2002). The phosphorylation status of nuclear NF-κB determines its association with CBP/p300 or HDAC-1. Molecular Cell, 9(3), 625–636. https://doi.org/10.1016/s1097-2765(02)00477-x
   PubMed Web of Science ®Google Scholar
• Ziegler, C. G. K., Allon, S. J., Nyquist, S. K., Mbano, I. M., Miao, V. N., Tzouanas, C. N., Cao, Y., Yousif, A. S., Bals, J., Hauser, B. M., Feldman, J., Muus, C., Wadsworth, M. H., Kazer, S. W., Hughes, T. K., Doran, B., Gatter, G. J., Vukovic, M., Taliaferro, F., … Ordovas-Montanes. (2020). SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues. Cell, 181(5), 1016–1035.e19. https://doi.org/10.1016/j.cell.2020.04.035
   PubMed Web of Science ®Google Scholar