SARS-CoV-2 M
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
07 May 2024
07 May 2024
Historique:
received:
15
09
2023
accepted:
19
04
2024
medline:
8
5
2024
pubmed:
8
5
2024
entrez:
7
5
2024
Statut:
epublish
Résumé
The main protease (M
Identifiants
pubmed: 38714735
doi: 10.1038/s41467-024-48109-3
pii: 10.1038/s41467-024-48109-3
doi:
Substances chimiques
Disulfides
0
Coronavirus 3C Proteases
EC 3.4.22.28
Cysteine
K848JZ4886
3C-like proteinase, SARS-CoV-2
EC 3.4.22.-
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
3827Subventions
Organisme : Helmholtz Association
ID : HIR3X
Organisme : Helmholtz Association
ID : FISCOV
Organisme : Helmholtz Association
ID : FragX
Organisme : Deutsche Forschungsgemeinschaft (German Research Foundation)
ID : EXC 2056 - project ID 390715994
Organisme : Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)
ID : 05K19GU4
Organisme : Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)
ID : 05K20GUB
Informations de copyright
© 2024. The Author(s).
Références
Hu, Q. et al. The SARS-CoV-2 main protease (Mpro): structure, function, and emerging therapies for COVID-19. MedComm 3, e151 (2022).
doi: 10.1002/mco2.151
pubmed: 35845352
pmcid: 9283855
Zhang, L. et al. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved a-ketoamide inhibitors. Science 368, 409–412 (2020).
doi: 10.1126/science.abb3405
pubmed: 32198291
pmcid: 7164518
Dai, W. et al. Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease. Science 368, 1331–1335 (2020).
doi: 10.1126/science.abb4489
pubmed: 32321856
U.S. Food and Drug Administration (FDA). Coronavirus (COVID-19) update: FDA authorizes first oral antiviral for treatment of COVID-19 (Food and Drug Administration, 2021).
Ding, L., Zhang, X. X., Wei, P., Fan, K. & Lai, L. The interaction between severe acute respiratory syndrome coronavirus 3C-like proteinase and a dimeric inhibitor by capillary electrophoresis. Anal. Biochem. 343, 159–65 (2005).
doi: 10.1016/j.ab.2005.04.027
pubmed: 15935325
pmcid: 7094366
Anand, K. et al. Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra α-helical domain. EMBO J. 21, 3213–3224 (2002).
doi: 10.1093/emboj/cdf327
pubmed: 12093723
pmcid: 126080
Zhong, N. et al. C-terminal domain of SARS-CoV main protease can form a 3D domain-swapped dimer. Protein Sci. 18, 839–44 (2009).
doi: 10.1002/pro.76
pubmed: 19319935
pmcid: 2762595
Miseta, A. & Csutora, P. Relationship between the occurrence of cysteine in proteins and the complexity of organisms. Mol. Biol. Evol. 17, 1232–1239 (2000).
doi: 10.1093/oxfordjournals.molbev.a026406
pubmed: 10908643
Funk, L.-M. et al. Multiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design. Nat. Commun. 15, 411 (2024).
doi: 10.1038/s41467-023-44621-0
pubmed: 38195625
pmcid: 10776599
Davis, D. A. et al. Regulation of the dimerization and activity of SARS-CoV-2 main protease through reversible glutathionylation of cysteine 300. mBio 12, 1–21 (2021).
Kneller, D. W. et al. Room-temperature X-ray crystallography reveals the oxidation and reactivity of cysteine residues in SARS-CoV-2 3CL Mpro: insights into enzyme mechanism and drug design. IUCrJ 7, 1028–1035 (2020).
doi: 10.1107/S2052252520012634
pubmed: 33063790
pmcid: 7553146
Rabe von Pappenheim, F. et al. Widespread occurrence of covalent lysine–cysteine redox switches in proteins. Nat. Chem. Biol. 18, 368–375 (2022).
doi: 10.1038/s41589-021-00966-5
pubmed: 35165445
pmcid: 8964421
Yang, K. S. et al. A novel Y-shaped, S-O-N-O-S-bridged cross-link between three residues C22, C44, and K61 is frequently observed in the SARS-CoV-2 main protease. ACS Chem. Biol. 18, 449–455 (2022).
Tran, N. et al. The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease. Nat. Commun. 14, 5625 (2023).
doi: 10.1038/s41467-023-40023-4
pubmed: 37699927
pmcid: 10497556
Schwarz, K. B. Oxidative stress during viral infection: a review. Free Radic. Biol. Med. 21, 641–649 (1996).
doi: 10.1016/0891-5849(96)00131-1
pubmed: 8891667
Davis, D. A. et al. Regulation of HIV-1 protease activity through cysteine modification. Biochemistry 35, 2482–2488 (1996).
doi: 10.1021/bi951525k
pubmed: 8652592
Davis, D. A. et al. Reversible oxidative modification as a mechanism for regulating retroviral protease dimerization and activation. J. Virol. 77, 3319–3325 (2003).
doi: 10.1128/JVI.77.5.3319-3325.2003
pubmed: 12584357
pmcid: 149757
Daniels, S. I. et al. The initial step in human immunodeficiency virus type 1 GagProPol processing can be regulated by reversible oxidation. PLoS ONE 5, 1–9 (2010).
Cecchini, R. & Cecchini, A. L. SARS-CoV-2 infection pathogenesis is related to oxidative stress as a response to aggression. Med. Hypotheses 143, 110102 (2020).
doi: 10.1016/j.mehy.2020.110102
pubmed: 32721799
pmcid: 7357498
Reinke, P. Y. A. et al. Calpeptin is a potent cathepsin inhibitor and drug candidate for SARS-CoV-2 infections. Commun. Biol. 6, 1–13 (2023).
Barrila, J., Gabelli, S. B., Bacha, U., Amzel, L. M. & Freire, E. Mutation of Asn28 disrupts the dimerization and enzymatic activity of SARS 3CLpro. Biochemistry 49, 4308–4317 (2010).
doi: 10.1021/bi1002585
pubmed: 20420403
Silvestrini, L. et al. The dimer-monomer equilibrium of SARS-CoV-2 main protease is affected by small molecule inhibitors. Sci. Rep. 11, 1–16 (2021).
Caleman, C., Junior, F. J., Grånäs, O. & Martin, A. V. A perspective on molecular structure and bonding-breaking in radiation damage in serial femtosecond crystallography. Crystals 10, 1–16 (2020).
Chapman, H. N., Caleman, C. & Timneanu, N. Diffraction before destruction. Philos. Trans. R. Soc. B Biol. Sci. 369, 1–13 (2014).
Nass, K. Radiation damage in protein crystallography at X-ray free-electron lasers. Acta Crystallogr. D Struct. Biol. 75, 211–218 (2019).
doi: 10.1107/S2059798319000317
pubmed: 30821709
pmcid: 6400258
Ulrich, K. & Jakob, U. The role of thiols in antioxidant systems. Free Radic. Biol. Med. https://doi.org/10.1016/j.freeradbiomed.2019.05.035 (2019).
Han, H. et al. The XBI BioLab for life science experiments at the European XFEL. J. Synchrotron Radiat. 54, 7–21 (2021).
Günther, S. et al. X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science 372, 642–646 (2021).
doi: 10.1126/science.abf7945
pubmed: 33811162
pmcid: 8224385
Mancuso, A. P. et al. The single particles, clusters and biomolecules and serial femtosecond crystallography instrument of the European XFEL: initial installation. J. Synchrotron Radiat. 26, 660–676 (2019).
doi: 10.1107/S1600577519003308
pubmed: 31074429
pmcid: 6510195
Henrich, B. et al. The adaptive gain integrating pixel detector AGIPD a detector for the European XFEL. Nucl. Instrum. Methods Phys. Res. A 633, 1–4 (2011).
doi: 10.1016/j.nima.2010.06.107
Fangohr, H. et al. Data analysis support in Karabo at European XFEL. In 16th International Conference on Accelerator and Large Experimental Control Systems 245–252 (Joint Accelerator Conferences Website, 2018).
Oberthuer, D. et al. Double-flow focused liquid injector for efficient serial femtosecond crystallography. Sci. Rep. 7, 1–12 (2017). 2017 7:1.
Knoška, J. et al. Ultracompact 3D microfluidics for time-resolved structural biology. Nat. Commun. 11, 657 (2020).
doi: 10.1038/s41467-020-14434-6
pubmed: 32005876
pmcid: 6994545
Vakili, M. et al. 3D printed devices and infrastructure for liquid sample delivery at the European XFEL. J. Synchrotron Radiat. 29, 331–346 (2022).
Burkhardt, A. et al. Status of the crystallography beamlines at PETRA III. Eur. Phys. J. Plus 131, 1–9 (2016).
Mariani, V. et al. OnDA: online data analysis and feedback for serial X-ray imaging. J. Appl. Crystallogr. 49, 1073–1080 (2016).
doi: 10.1107/S1600576716007469
pubmed: 27275150
pmcid: 4886993
Yefanov, O. et al. Accurate determination of segmented X-ray detector geometry. Opt. Express 23, 28459–28470 (2015).
doi: 10.1364/OE.23.028459
pubmed: 26561117
pmcid: 4646514
Barty, A. et al. Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data. J. Appl. Crystallogr. 47, 1118–1131 (2014).
doi: 10.1107/S1600576714007626
pubmed: 24904246
pmcid: 4038800
White, T. A. et al. CrystFEL: a software suite for snapshot serial crystallography. J. Appl. Crystallogr. 45, 335–341 (2012).
doi: 10.1107/S0021889812002312
Leslie, A. G. W. & Powell, H. R. Processing diffraction data with mosflm. Evol. Methods Macromol. Crystallogr. 245, 41–51 (2007).
doi: 10.1007/978-1-4020-6316-9_4
Gevorkov, Y. et al. XGANDALF - extended gradient descent algorithm for lattice finding. Acta Crystallogr. A Found. Adv. 75, 694–704 (2019).
doi: 10.1107/S2053273319010593
pubmed: 31475914
pmcid: 6718201
Kabsch, W. XDS. Acta Crystallogr. D Biol. Crystallogr. 66, 125–132 (2010).
doi: 10.1107/S0907444909047337
pubmed: 20124692
pmcid: 2815665
Karplus, P. A. & Diederichs, K. Linking crystallographic model and data quality. Science 336, 1030–1033 (2012).
doi: 10.1126/science.1218231
pubmed: 22628654
pmcid: 3457925
Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774–797 (2007).
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).
doi: 10.1107/S0907444910007493
pubmed: 20383002
pmcid: 2852313
Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D Struct. Biol. 75, 861–877 (2019).
doi: 10.1107/S2059798319011471
pubmed: 31588918
pmcid: 6778852
Juers, D. H. & Ruffin, J. MAP-CHANNELS: a computation tool to aid in the visualization and characterization of solvent channels in macromolecular crystals. J. Appl. Crystallogr. 47, 2105–2108 (2014).
doi: 10.1107/S160057671402281X
pubmed: 25484846
pmcid: 4248570
Delano, W. L. The PyMOL molecular graphics system. CCP4 Newslett. 40, 1–9 (2002).