作者: Rox, Katharina ; Jochmans, Dirk ; Arisetti, Nanaji ; Neyts, Johan ; Zhang, Kaixuan ; Metzen, Alina ; Göhl, Matthias ; Cooper, Mark S. ; Akula, Ravi Kumar ; Karadogan, Burhan ; Brönstrup, Mark ; Marsh, Graham P. ; Hilgenfeld, Rolf ; Röske, Judith ; El Kilani, Haifa ; Maple, Hannah J.

The main protease M^pro is a clinically validated target to treat infections by the coronavirus SARS-CoV-2. Among the first reported M^pro inhibitors was the peptidomimetic α-ketoamide 13b, whose cocrystal structure with M^pro paved the way for multiple lead-finding studies. We established structure-activity relationships for the 13b series by modifying residues at the P1', P3, and P4 sites. Guided by cocrystal structures, we reduced the P1' substituent size to better fill the pocket and added a fluorine substituent to the pyridone ring, enabling a new hydrogen bond with Gln189 in P3. Among 22 novel analogues, 6d and 12d inhibited M^pro with IC₅₀s of 110 nM and 40 nM, improving the potency of 13b by up to 9.5-fold. Compound 6d had pronounced antiviral activity with an EC₅₀ of 1.6 μM and was stable in plasma and microsomes. The study illustrates the potential of structure-based design to systematically improve peptidomimetic α-ketoamides.

2025-02-01·Journal of Ethnopharmacology

Uncovering the naturally occurring covalent inhibitors of SARS-CoV-2 Mpro from the Chinese medicine sappanwood and deciphering their synergistic anti-Mpro effects

Article

作者: Zheng, Shui-Lian ; Pan, Zong-Fu ; Ge, Guang-Bo ; Hu, Xiao-Ping ; Zhang, Yi-Wen ; Zhu, Guang-Hao ; Hu, Qing ; Song, Fei-Feng ; Zhang, Ya-Ni ; Chen, Peng-Cheng ; Shen, Nong-Er ; Huang, Ping ; Liu, Wei

ETHNOPHARMACOLOGICAL RELEVANCEThe Chinese medicine sappanwood is primarily sourced from the dried heartwood of the medicinal plant Caesalpinia sappan Linn., which has been found with a variety of valuable properties including anti-inflammatory, anti-oxidant, and anti-viral effects. Preliminary investigations have demonstrated that sappanwood showed strong anti-SARS-CoV-2 M^pro effects, but the key constituents responsible for SARS-CoV-2 M^pro inhibition and their anti-M^pro mechanisms have not been uncovered.AIM OF THE STUDYThis study aims to uncover the naturally occurring covalent inhibitors of SARS-CoV-2 M^pro from the sappanwood extract (SWE), to characterize the anti-M^pro mechanisms of the newly identified inhibitors in SWE, as well as to elucidate their synergistic anti-M^pro mechanisms.MATERIALS AND METHODSThe proteolytic activity of SARS-CoV-2 M^pro was monitored using a fluorescence-based biochemical assay. Comprehensive phytochemical profiling of SWE was conducted by UHPLC-Q-Exactive Orbitrap HRMS. The nanoLC-MS/MS-based chemoproteomic profiling was employed to characterize the phytochemical-modified peptides of SARS-CoV-2 M^pro. Inactivation kinetics, surface plasmon resonance, and molecular dynamics (MD) simulations were utilized to investigate the binding affinity and binding modes of the newly identified SARS-CoV-2 M^pro inhibitors.RESULTSSWE was found with strong anti-M^pro effect in both dose- and time-dependent manners. Twenty-three constituents in SWE were subsequently identified by utilizing UHPLC-Q-Exactive Orbitrap HRMS, while chemoproteomic profiling revealed that 14 constituents in SWE could covalently modify SARS-CoV-2 M^pro. The anti-SARS-CoV-2 M^pro effects of these newly identified M^pro binders were then tested one by one. The results showed that most of the tested phytochemicals in SWE exhibited time-dependent inhibition on SARS-CoV-2 M^pro, while hematoxylin, brazilin, sappanchalcone, and protosappanin B were identified as the potent time-dependent inhibitors against SARS-CoV-2 M^pro. Furthermore, the combination of hematoxylin and protosappanin B could synergistically block the formation of catalytic active M^pro dimers and then significantly inhibit the catalytic activity of M^pro. MD simulations provided further insight into the synergistic effects between two identified natural M^pro inhibitors (hematoxylin and protosappanin B).CONCLUSIONSThe naturally occurring covalent inhibitors of SARS-CoV-2 M^pro from the SWE were identified using an integrated approach. Among all identified covalent inhibitors of SARS-CoV-2 M^pro, hematoxylin, brazilin, sappanchalcone, and protosappanin B emerged as the efficacious M^pro inactivators, which offers powerful evidence to support the anti-coronavirus effects of the Chinese medicine sappanwood.

2024-12-31·Journal of Enzyme Inhibition and Medicinal Chemistry

Development of potent and effective SARS-CoV-2 main protease inhibitors based on maleimide analogs for the potential treatment of COVID-19

Article

作者: Ciupak, Olga ; Rak, Janusz ; Demkowicz, Sebastian ; Flis, Damian ; Biernacki, Karol ; Budka, Justyna ; Daśko, Mateusz ; Czaja, Anna ; Inkielewicz-Stępniak, Iwona ; Rachon, Janusz

In the present work, we report a new series of potent SARS-CoV-2 Main Protease (Mpro) inhibitors based on maleimide derivatives. The inhibitory activities were tested in an enzymatic assay using recombinant Mpro (3CL Protease from coronavirus SARS-CoV-2). Within the set of new Mpro inhibitors, 6e demonstrated the highest activity in the enzymatic assay with an IC₅₀ value of 8.52 ± 0.44 µM. The IC₅₀ value for Nirmatrelvir (PF-07321332, used as a reference) was 0.84 ± 0.37 µM. The cytotoxic properties were determined in the MTT assay using MRC-5 and HEK-293 cell lines. In the course of the investigation, we found that the newly obtained maleimide derivatives are not substantially cytotoxic (IC₅₀ values for most compounds were above 200 µM).

100 项与 SARS-CoV-2 Mpro inhibitors(Universität zu Lübeck) 相关的药物交易

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