A novel robust inhibitor of papain-like protease (PLpro) as a COVID-19 drug

References

• Amin, S. A., Banerjee, S., Ghosh, K., Gayen, S., & Jha, T. (2021). Protease targeted COVID-19 drug discovery and its challenges: Insight into viral main protease (Mpro) and papain-like protease (PLpro) inhibitors. Bioorganic & Medicinal Chemistry, 29, 115860–115869. https://doi.org/10.1016/j.bmc.2020.115860
   PubMedGoogle Scholar
• Anirudhan, V., Lee, H., Cheng, H., Cooper, L., & Rong, L. (2021). Targeting SARS‐CoV‐2 viral proteases as a therapeutic strategy to treat COVID‐19. Journal of Medical Virology, 93(5), 2722–2734. https://doi.org/10.1002/jmv.26814
   PubMed Web of Science ®Google Scholar
• Cheng, H. (2001). The power issue: Determination of KB or Ki from IC50: A closer look at the Cheng–Prusoff equation, the Schild plot and related power equations. Journal of Pharmacological and Toxicological Methods, 46(2), 61–71.https://doi.org/10.1016/s1056-8719(02)00166-1
   PubMed Web of Science ®Google Scholar
• Clasman, J. R., Everett, R. K., Srinivasan, K., & Mesecar, A. D. (2020). Decoupling deISGylating and deubiquitinating activities of the MERS virus papain-like protease. Antiviral Research, 174, 104661–104684. https://doi.org/10.1016/j.antiviral.2019.104661
   PubMed Web of Science ®Google Scholar
• Fernandez, M. M., Clark, D. S., & Blanch, H. W. (1991). Papain kinetics in the presence of a water‐miscible organic solvent. Biotechnology and Bioengineering, 37(10), 967–972. https://doi.org/10.1002/bit.260371011
   PubMed Web of Science ®Google Scholar
• Flores-Canales, J. C., & Kurnikova, M. (2015). Targeting electrostatic interactions in accelerated molecular dynamics with application to protein partial unfolding. Journal of Chemical Theory and Computation, 11(6), 2550–2559. https://doi.org/10.1021/ct501090y
   PubMed Web of Science ®Google Scholar
• Gao, X., Qin, B., Chen, P., Zhu, K., Hou, P., Wojdyla, J. A., Wang, M., & Cui, S. (2021). Crystal structure of SARS-CoV-2 papain-like protease. Acta Pharmaceutica Sinica. B, 11(1), 237–245. https://doi.org/10.1016/j.apsb.2020.08.014
   PubMed Web of Science ®Google Scholar
• Ghahremanian, S., Rashidi, M. M., Raeisi, K., & Toghraie, D. (2022). Molecular dynamics simulation approach for discovering potential inhibitors against SARS-CoV-2: A structural review. Journal of Molecular Liquids, 354, 118901–118914. https://doi.org/10.1016/j.molliq.2022.118901
   PubMed Web of Science ®Google Scholar
• Ghoneim, M. M., Afifi, W. M., Ibrahim, M., Elagawany, M., Khayat, M. T., Aboutaleb, M. H., & Metwaly, A. M. (2019). Biological evaluation and molecular docking study of metabolites from Salvadora Persica L. Growing in Egypt. Pharmacognosy Magazine, 15(61), 232–247. https://doi.org/10.4103/pm.pm_361_18
   Web of Science ®Google Scholar
• Ghosh, A. K., Takayama, J., Rao, K. V., Ratia, K., Chaudhuri, R., Mulhearn, D. C., Lee, H., Nichols, D. B., Baliji, S., Baker, S. C., Johnson, M. E., & Mesecar, A. D. (2010). Severe acute respiratory syndrome coronavirus papain-like novel protease inhibitors: Design, synthesis, protein − ligand X-ray structure and biological evaluation. Journal of Medicinal Chemistry, 53(13), 4968–4979. https://doi.org/10.1021/jm1004489
   PubMed Web of Science ®Google Scholar
• Harcourt, B. H., Jukneliene, D., Kanjanahaluethai, A., Bechill, J., Severson, K. M., Smith, C. M., Rota, P. A., & Baker, S. C. (2004). Identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity. Journal of Virology, 78(24), 13600–13612. https://doi.org/10.1128/JVI
   PubMed Web of Science ®Google Scholar
• Hegazy, M. M., Metwaly, A. M., Mostafa, A. E., Radwan, M. M., Mehany, A. B. M., Ahmed, E., Enany, S., Magdeldin, S., Afifi, W. M., & ElSohly, M. A. (2021). Biological and chemical evaluation of some African plants belonging to Kalanchoe species: Antitrypanosomal, cytotoxic, antitopoisomerase I activities and chemical profiling using ultra-performance liquid chromatography/quadrupole-time-of-flight mass spectrometer. Pharmacognosy Magazine, 17(73), 6–16. https://doi.org/10.4103/pm.pm_232_20
   Web of Science ®Google Scholar
• Hong, H., Zheng, Y., Song, S., Zhang, Y., Zhang, C., Liu, J., & Luo, Y. (2020). Identification and characterization of DPP-IV inhibitory peptides from silver carp swim bladder hydrolysates. Food Bioscience, 38, 100748–100756. https://doi.org/10.1016/j.fbio.2020.100748
   Web of Science ®Google Scholar
• Ibezim, A., Onuku, R. S., Ibezim, A., Ntie-Kang, F., Nwodo, N. J., & Adikwu, M. U. (2021). Structure-based virtual screening and molecular dynamics simulation studies to discover new SARS-CoV-2 main protease inhibitors. Scientific African, 14, e00970.https://doi.org/10.1080/07391102.2021.1891969
   PubMedGoogle Scholar
• Jiang, H., Yang, P., & Zhang, J. (2022). Potential Inhibitors Targeting Papain-Like Protease of SARS-CoV-2: Two Birds With One Stone. Frontiers in Chemistry, 10, 822785–822792. https://doi.org/10.3389/fchem.2022.822785
   PubMed Web of Science ®Google Scholar
• 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., van der 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), e106275. https://doi.org/10.15252/embj.2020106275
   PubMed Web of Science ®Google Scholar
• Lee, H., Lei, H., Santarsiero, B. D., Gatuz, J. L., Cao, S., Rice, A. J., Patel, K., Szypulinski, M. Z., Ojeda, I., Ghosh, A. K., & Johnson, M. E. (2015). Inhibitor recognition specificity of MERS-CoV papain-like protease may differ from that of SARS-CoV. ACS Chemical Biology, 10(6), 1456–1465. https://doi.org/10.1021/cb500917m
   PubMed Web of Science ®Google Scholar
• Li, L., Ma, L., Hu, Y., Li, X., Yu, M., Shang, H., & Zou, Z. (2022). Natural biflavones are potent inhibitors against SARS-CoV-2 papain-like protease. Phytochemistry, 193, 112984. https://doi.org/10.1016/j.phytochem.2021.112984
   PubMed Web of Science ®Google Scholar
• Liu, S., Höldrich, M., Sievers-Engler, A., Horak, J., & Lämmerhofer, M. (2017). Papain-functionalized gold nanoparticles as heterogeneous biocatalyst for bioanalysis and biopharmaceuticals analysis. Analytica Chimica Acta, 963, 33–43. https://doi.org/10.1016/j.aca.2017.02.009
   PubMed Web of Science ®Google Scholar
• Martonák, R., Laio, A., & Parrinello, M. (2003). Predicting crystal structures: The Parrinello-Rahman method revisited. Physical Review Letters, 90(7), 075503. https://doi.org/10.1103/PhysRevLett.90.075503
   PubMed Web of Science ®Google Scholar
• Metwaly, A. M., Ghoneim, M. M., Eissa, I. H., Elsehemy, I. A., Mostafa, A. E., Hegazy, M. M., Afifi, W. M., & Dou, D. (2021). Traditional ancient Egyptian medicine: A review. Saudi Journal of Biological Sciences, 28(10), 5823–5832. https://doi.org/10.1016/j.sjbs.2021.06.044
   PubMed Web of Science ®Google Scholar
• Metwaly, A. M., Ghoneim, M. M., & Musa, A. (2015). Two new antileishmanial diketopiperazine alkaloids from the endophytic fungus Trichosporum sp. Derpharmachemica, 7, 322–337.
   Google Scholar
• 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/10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• Narayanan, A., Narwal, M., Majowicz, S. A., Varricchio, C., Toner, S. A., Ballatore, C., Brancale, A., Murakami, K. S., Jose, J and., et.al. (2022). Identification of SARS-CoV-2 inibition targeting Mpro and PLpro using in-cell-protease assay. Communications Biology, 5(1), 169. https://doi.org/10.1038/s42003-022-03090-9
   PubMed Web of Science ®Google Scholar
• Novinec, M., & Lenarčič, B. (2013). Papain-like peptidases: Structure, function, and evolution. Biomolecular Concepts, 4(3), 287–308. https://doi.org/10.1515/bmc-2012-0054
   PubMedGoogle Scholar
• Park, J.-Y., Jeong, H. J., Kim, J. H., Kim, Y. M., Park, S.-J., Kim, D., Park, K. H., Lee, W. S., & Ryu, Y. B. (2012). Diarylheptanoids from Alnus japonica inhibit papain-like protease of severe acute respiratory syndrome coronavirus. Biological and Pharmaceutical Bulletin, 35(11), 2036–2042. https://doi.org/10.1248/bpb.b12-00623
   PubMed Web of Science ®Google Scholar
• Park, J.-Y., Ko, J.-A., Kim, D. W., Kim, Y. M., Kwon, H.-J., Jeong, H. J., Kim, C. Y., Park, K. H., Lee, W. S., & Ryu, Y. B. (2016). Chalcones isolated from Angelica keiskei inhibit cysteine proteases of SARS-CoV. Journal of Enzyme Inhibition and Medicinal Chemistry, 31(1), 23–30. https://doi.org/10.3109/14756366.2014.1003215
   PubMed Web of Science ®Google Scholar
• Park, J.-Y., Yuk, H. J., Ryu, H. W., Lim, S. H., Kim, K. S., Park, K. H., Ryu, Y. B., & Lee, W. S. (2017). Evaluation of polyphenols from Broussonetia papyrifera as coronavirus protease inhibitors. Journal of Enzyme Inhibition and Medicinal Chemistry, 32(1), 504–515. https://doi.org/10.1080/14756366.2016.1265519
   PubMed Web of Science ®Google Scholar
• Petushkova, A. I., & Zamyatnin, A. A. Jr, (2020). Papain-like proteases as coronaviral drug targets: Current inhibitors, opportunities, and limitations. Pharmaceuticals, 13(10), 277–286. https://doi.org/10.3390/ph13100277
   Web of Science ®Google Scholar
• Rawlings, N. D., Barrett, A. J., Thomas, P. D., Huang, X., Bateman, A., & Finn, R. D. (2012). The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. Nucleic Acids Research, 40(Database issue), D343–D350. https://doi.org/10.1093/nar/gkr987
   PubMedGoogle Scholar
• Rut, W., Lv, Z., Zmudzinski, M., Patchett, S., Nayak, D., Snipas, S. J., El Oualid, F., Huang, T. T., Bekes, M., & Drag, M. (2020). Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti–COVID-19 drug design. Science Advances, 6, 4596–4607. https://doi.org/10.1126/sciadv.abd4596
   Web of Science ®Google Scholar
• Sanders, B. C., Pokhrel, S., Labbe, A. D., Mathews, I. I., Cooper, C. J., Davidson, R. B., Phillips, G., Weiss, K. L., Zhang, Q., O'Neill, H., Kaur, M., Schmidt, J. G., Reichard, W., Surendranathan, S., Parvathareddy, J., Phillips, L., Rainville, C., Sterner, D. E., Kumaran, D., … Parks, J. M. (2023). Potent and selective covalent inhibitors of the papain-like protease from SARS-CoV-2. Nature Communications, 14(1), 1733–1745.https://doi.org/10.21203/rs.3.rs-906621/v1
   PubMed Web of Science ®Google Scholar
• Thomsen, R., & Christensen, M. H. (2006). MolDock: a new technique for high-accuracy molecular docking. Journal of Medicinal Chemistry, 49(11), 3315–3321. https://doi.org/10.1021/jm051197e
   PubMed Web of Science ®Google Scholar
• Tsuge, H., Nishimura, T., Tada, Y., Asao, T., Turk, D., Turk, V., & Katunuma, N. (1999). Inhibition mechanism of cathepsin L-specific inhibitors based on the crystal structure of papain–CLIK148 complex. Biochemical and Biophysical Research Communications, 266(2), 411–416. https://doi.org/10.1006/bbrc.1999.1830
   PubMed Web of Science ®Google Scholar
• Turk, V., Stoka, V., Vasiljeva, O., Renko, M., Sun, T., Turk, B., & Turk, D. (2012). Cysteine cathepsins: From structure, function and regulation to new frontiers. Biochimica et Biophysica Acta, 1824(1), 68–88. https://doi.org/10.1016/j.bbapap.2011.10.002
   PubMed Web of Science ®Google Scholar
• Valdés-Tresanco, M. S., Valdés-Tresanco, M. E., Valiente, P. A., & Moreno, E. (2021). gmx_MMPBSA: A new tool to perform end-state free energy calculations with GROMACS. Journal of Chemical Theory and Computation, 17(10), 6281–6291. https://doi.org/10.1021/acs.jctc.1c00645
   PubMed Web of Science ®Google Scholar
• Xian, M., Chen, X., Liu, Z., Wang, K., & Wang, P. G. (2000). Inhibition of papain by S-nitrosothiols: Formation of mixed disulfides. The Journal of Biological Chemistry, 275(27), 20467–20473. https://doi.org/10.1074/jbc.M001054200
   PubMed Web of Science ®Google Scholar
• Zamani Amirzakaria, J., Malboobi, M. A., Marashi, S.-A., & Lohrasebi, T. (2021). In silico prediction of enzymatic reactions catalyzed by acid phosphatases. Journal of Biomolecular Structure & Dynamics, 39(11), 3900–3911. https://doi.org/10.1080/07391102.2020.1785943
   PubMed Web of Science ®Google Scholar
• Zamani, A., Hajimoradloo, A., Madani, R., & Farhangi, M. (2009). Assessment of digestive enzymes activity during the fry development of Rainbow Trout, Oncorhynchus mykiss: From hatching to primary stages after yolk sac absorption. Journal of Fish Biology, 75(4), 932–937. https://doi.org/10.1111/j.1095-8649.2009.02348.x
   PubMed Web of Science ®Google Scholar
• Zhanzhaxina, A., Suleimen, Y., Metwaly, A. M., Eissa, I. H., Elkaeed, E. B., Suleimen, R., Ishmuratova, M., Akatan, K., & Luyten, W. (2021). In vitro and in silico cytotoxic and antibacterial activities of a diterpene from cousinia alata schrenk. Journal of Chemistry, 2021, 1–11. https://doi.org/10.1155/2021/5542455
   Web of Science ®Google Scholar
• Zhao, Y., Du, X., Duan, Y., Pan, X., Sun, Y., You, T., Han, L., Jin, Z., Shang, W., Yu, J., Guo, H., Liu, Q., Wu, Y., Peng, C., Wang, J., Zhu, C., Yang, X., Yang, K., Lei, Y., … Yang, H. (2021). High-throughput screening identifies established drugs as SARS-CoV-2 PLpro inhibitors. Protein & Cell, 12(11), 877–888. https://doi.org/10.1007/s13238-021-00836-9
   PubMed Web of Science ®Google Scholar