Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) urgently needs an effective cure. 3CL protease (3CL
pro
) ...is a highly conserved cysteine proteinase that is indispensable for coronavirus replication, providing an attractive target for developing broad-spectrum antiviral drugs. Here we describe the discovery of myricetin, a flavonoid found in many food sources, as a non-peptidomimetic and covalent inhibitor of the SARS-CoV-2 3CL
pro
. Crystal structures of the protease bound with myricetin and its derivatives unexpectedly revealed that the pyrogallol group worked as an electrophile to covalently modify the catalytic cysteine. Kinetic and selectivity characterization together with theoretical calculations comprehensively illustrated the covalent binding mechanism of myricetin with the protease and demonstrated that the pyrogallol can serve as an electrophile warhead. Structure-based optimization of myricetin led to the discovery of derivatives with good antiviral activity and the potential of oral administration. These results provide detailed mechanistic insights into the covalent mode of action by pyrogallol-containing natural products and a template for design of non-peptidomimetic covalent inhibitors against 3CL
pro
s, highlighting the potential of pyrogallol as an alternative warhead in design of targeted covalent ligands.
The pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a global crisis. Replication of SARS-CoV-2 requires the viral ...RNA-dependent RNA polymerase (RdRp) enzyme, a target of the antiviral drug remdesivir. Here we report the cryo-electron microscopy structure of the SARS-CoV-2 RdRp, both in the apo form at 2.8-angstrom resolution and in complex with a 50-base template-primer RNA and remdesivir at 2.5-angstrom resolution. The complex structure reveals that the partial double-stranded RNA template is inserted into the central channel of the RdRp, where remdesivir is covalently incorporated into the primer strand at the first replicated base pair, and terminates chain elongation. Our structures provide insights into the mechanism of viral RNA replication and a rational template for drug design to combat the viral infection.
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is the etiological agent responsible for the global COVID-19 (coronavirus disease 2019) outbreak. The main protease of SARS-CoV-2, M
, is ...a key enzyme that plays a pivotal role in mediating viral replication and transcription. We designed and synthesized two lead compounds (
and
) targeting M
Both exhibited excellent inhibitory activity and potent anti-SARS-CoV-2 infection activity. The x-ray crystal structures of SARS-CoV-2 M
in complex with
or
, both determined at a resolution of 1.5 angstroms, showed that the aldehyde groups of
and
are covalently bound to cysteine 145 of M
Both compounds showed good pharmacokinetic properties in vivo, and
also exhibited low toxicity, which suggests that these compounds are promising drug candidates.
A comprehensive characterization of the thermodynamic and kinetic profiling of ligands binding to a given target protein is crucial for the hit selection as well as the hit-to-lead-to-drug evolution. ...Isothermal titration calorimetry (ITC), widely known as an invaluable tool to measure the thermodynamic data, has recently found its way to determine the binding kinetics too. The extensive application of ITC in measurement of both thermodynamic and kinetic data manifests unique roles of ITC in drug discovery and development. This mini-review concentrates on elaborating how to gain the thermodynamic and kinetic data using ITC, highlighting the importance of these data in lead discovery and optimization, and intends to provide an overview of the technical and conceptual advances that offer unprecedented access to protein-ligand recognition by ITC measurement.
Despite being technically possible, the hydrogen production by means of electrocatalytic water splitting is still practically unreachable mainly because of the lack of inexpensive and high active ...catalysts. Herein, a novel and facile approach by melamine polymerization, exfoliation and Co2+-assisted thermal annealing is developed to fabricate Co nanoparticles embedded in bamboo-like and nitrogen-rich carbonitride nanotubes (Co@NCN). The electronic interaction between the embedded Co nanoparticles and N-rich carbonitride nanotubes could strongly promote the HER performance. The optimized Co@NCN-800 exhibits outstanding HER activity with an onset potential of −89 mV (vs RHE), a large exchange current density of 62.2 μA cm–2, and small Tafel slope of 82 mV dec–1, as well as excellent stability (5000 cycles) in acid media, demonstrating the potential for the replacement of Pt-based catalysts. Control experiments reveal that the superior performance should be ascribed to the synergistic effects between embedded Co nanoparticles and N-rich carbonitride nanotubes, which originate from the high pyridinic N content, fast charge transfer rate from Co particles to electrodes via electronic coupling, and porous and bamboo-like carbonitride nanotubes for more active sites in HER.
A novel series of peptidomimetic aldehydes was designed and synthesized to target 3C protease (3Cpro) of enterovirus 71 (EV71). Most of the compounds exhibited high antiviral activity, and among ...them, compound 18p demonstrated potent enzyme inhibitory activity and broad-spectrum antiviral activity on a panel of enteroviruses and rhinoviruses. The crystal structure of EV71 3Cpro in complex with 18p determined at a resolution of 1.2 Å revealed that 18p covalently linked to the catalytic Cys147 with an aldehyde group. In addition, these compounds also exhibited good inhibitory activity against the 3CLpro and the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), especially compound 18p (IC50 = 0.034 μM, EC50 = 0.29 μM). According to our previous work, these compounds have no reasons for concern regarding acute toxicity. Compared with AG7088, compound 18p also exhibited good pharmacokinetic properties and more potent anticoronavirus activity, making it an excellent lead for further development.
Scope
GTPs (green tea polyphenols) exert anti‐CRC (colorectal cancer) activity. The intestinal microbiota and intestinal colonization by bacteria of oral origin has been implicated in colorectal ...carcinogenesis. GT modulates the composition of mouse gut microbiota harmonious with anticancer activity. Therefore, the effect of green tea liquid (GTL) consumption on the gut and oral microbiome is investigated in healthy volunteers (n = 12).
Methods and results
16S sequencing and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis of both fecal and saliva samples (collected before intervention, after 2 weeks of GTL (400 mL per day) and after a washout period of one week) in healthy volunteers show changes in microbial diversity and core microbiota and difference in clear classification (partial least squares‐discriminant analysis PLS‐DA). An irreversible, increased FIR:BAC (Firmicutes to Bacteroidetes ratio), elevated SCFA producing genera, and reduction of bacterial LPS synthesis in feces are discovered in response to GTL. GTL alters the salivary microbiota and reduces the functional pathways abundance relevance to carcinogenesis. Similar bacterial networks in fecal and salivary microbiota datasets comprising putative oral bacteria are found and GTL reduces the fecal levels of Fusobacterium. Interestingly, both Lachnospiraceae and B/E (Bifidobacterium to Enterobacteriacea ratio—markers of colonization resistance CR) are negatively associated with the presence of oral‐like bacterial networks in the feces.
Conclusion
These results suggest that GTL consumption causes both oral and gut microbiome alterations.
Green tea (GT) polyphenols exert anticancer activity. The intestinal microbiota and intestinal colonization by bacteria of oral origin has been implicated in colorectal carcinogenesis. GT modulates the composition of mouse gut microbiota harmonious with anticancer activity. Therefore, the effect of GT liquid consumption on the human microbiome is investigated. This study provides evidence that green tea liquid consumption alters the human oral and gut microbiome harmonious with anti‐cancer activity.
Nonoxidative dehydrogenation of low-cost alkanes provides a promising route to produce valuable olefins. Herein, we hydrothermally synthesized various non-noble-metal-based, environment-friendly, and ...Al-free Co@MFI catalysts without the assistance of any additional coordination agents. The Co2+ species were successfully incorporated into well-crystallized MFI to form a stable and atomically dispersed −Coδ+–Oδ−– structure. The Co@MFI catalyst could show a stably high activity for ethane dehydrogenation with equilibrium-approached conversions at 600 °C and at the same time gave an extremely high selectivity to ethylene (∼99%), which is owed to the relatively unreducible −Co–O– species and its appropriate chemical state at the right reaction-temperature window. However, the Co@MFI catalyst showed equilibrium-deviated conversions at lower temperatures (such as 550 °C) and a suppressed activity in the H2O or CO2 co-feeding tests. Then, with characterizations, density functional theory calculations, and abundant experiments over different catalysts, including impregnated Co/MFI and amorphous Co@MFI, this study has impressively demonstrated that the chemical state of Coδ+ species manipulates the conversion–selectivity trade-off relationship in the conversion of alkanes. It is suggested that Co with a lower valence like Co0 promotes both C–C and C–H bond scissions of alkanes into coke and CH4, while Co with a higher one shows a decreased activity or even inactivity for alkane dehydrogenation. In this study, the possible causes for the success in the synthesis of the ligand-unassisted Co@MFI catalyst, the catalyst deactivation modes and the strategies for improving catalyst stability were also demonstrated in detail. This work not only contributes a performance-advanced Co-based catalyst for alkane dehydrogenation but also provides new insights into incorporation of a metal into zeolites.
Abstract
The persistent pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants accentuates the great demand for ...developing effective therapeutic agents. Here, we report the development of an orally bioavailable SARS-CoV-2 3C-like protease (3CL
pro
) inhibitor, namely simnotrelvir, and its preclinical evaluation, which lay the foundation for clinical trials studies as well as the conditional approval of simnotrelvir in combination with ritonavir for the treatment of COVID-19. The structure-based optimization of boceprevir, an approved HCV protease inhibitor, leads to identification of simnotrelvir that covalently inhibits SARS-CoV-2 3CL
pro
with an enthalpy-driven thermodynamic binding signature. Multiple enzymatic assays reveal that simnotrelvir is a potent pan-CoV 3CL
pro
inhibitor but has high selectivity. It effectively blocks replications of SARS-CoV-2 variants in cell-based assays and exhibits good pharmacokinetic and safety profiles in male and female rats and monkeys, leading to robust oral efficacy in a male mouse model of SARS-CoV-2 Delta infection in which it not only significantly reduces lung viral loads but also eliminates the virus from brains. The discovery of simnotrelvir thereby highlights the utility of structure-based development of marked protease inhibitors for providing a small molecule therapeutic effectively combatting human coronaviruses.
The papain-like protease (PL
) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a critical role in the proteolytic processing of viral polyproteins and the dysregulation of the ...host immune response, providing a promising therapeutic target. Here, we report the structure-guide design of novel peptidomimetic inhibitors covalently targeting SARS-CoV-2 PL
. The resulting inhibitors demonstrate submicromolar potency in the enzymatic assay (IC
= 0.23 μM) and significant inhibition of SARS-CoV-2 PL
in the HEK293T cells using a cell-based protease assay (EC
= 3.61 μM). Moreover, an X-ray crystal structure of SARS-CoV-2 PL
in complex with compound
confirms the covalent binding of the inhibitor to the catalytic residue cysteine 111 (C111) and emphasizes the importance of interactions with tyrosine 268 (Y268). Together, our findings reveal a new scaffold of SARS-CoV-2 PL
inhibitors and provide an attractive starting point for further optimization.
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