Discovery of novel SARS-CoV-2 3CL protease covalent inhibitors using deep learning-based screen.

SARS-CoV-2 3CL protease is one of the key targets for drug development against COVID-19. Most known SARS-CoV-2 3CL protease inhibitors act by covalently binding to the active site cysteine. Yet, computational screens against this enzyme were mainly focused on non-covalent inhibitor discovery. Here, we developed a deep learning-based stepwise strategy for selective covalent inhibitor screen. We used a deep learning framework that integrated a directed message passing neural network with a feed-forward neural network to construct two different classifiers for either covalent or non-covalent inhibition activity prediction. These two classifiers were trained on the covalent and non-covalent 3CL protease inhibitors dataset, respectively, which achieved high prediction accuracy. We then successively applied the covalent inhibitor model and the non-covalent inhibitor model to screen a chemical library containing compounds with covalent warheads of cysteine. We experimentally tested the inhibition activity of 32 top-ranking compounds and 12 of them were active, among which 6 showed IC50 values less than 12 µM and the strongest one inhibited SARS-CoV-2 3CL protease with an IC50 of 1.4 µM. Further investigation demonstrated that 5 of the 6 active compounds showed typical covalent inhibition behavior with time-dependent activity. These new covalent inhibitors provide novel scaffolds for developing highly active SARS-CoV-2 3CL covalent inhibitors.

Discovery of 2-(furan-2-ylmethylene)hydrazine-1-carbothioamide derivatives as novel inhibitors of SARS-CoV-2 main protease.

The COVID-19 posed a serious threat to human life and health, and SARS-CoV-2 Mpro has been considered as an attractive drug target for the treatment of COVID-19. Herein, we report 2-(furan-2-ylmethylene)hydrazine-1-carbothioamide derivatives as novel inhibitors of SARS-CoV-2 Mpro developed by in-house library screening and biological evaluation. Similarity search led to the identification of compound F8-S43 with the enzymatic IC50 value of 10.76 µM. Further structure-based drug design and synthetic optimization uncovered compounds F8-B6 and F8-B22 as novel non-peptidomimetic inhibitors of Mpro with IC50 values of 1.57 µM and 1.55 µM, respectively. Moreover, enzymatic kinetic assay and mass spectrometry demonstrated that F8-B6 was a reversible covalent inhibitor of Mpro. Besides, F8-B6 showed low cytotoxicity with CC50 values of more than 100 µM in Vero and MDCK cells. Overall, these novel SARS-CoV-2 Mpro non-peptidomimetic inhibitors provide a useful starting point for further structural optimization.

Homeostasis of gut microbiota protects against polychlorinated biphenyl 126-induced metabolic dysfunction in liver of mice.

Polychlorinated biphenyls (PCBs) exposure is closely associated with the prevalence of metabolic diseases, including fatty liver and dyslipidemia. Emerging literature suggests that disturbance of gut microbiota is related to PCB126-induced metabolic disorders. However, the causal role of dysbiosis in PCB126-induced fatty liver is still unknown. To clarify the role of the gut microbiome in the detoxification of PCB126 in intestine or PCB126-induced toxicity in liver, mice were administrated with drinking water containing antibiotics (ampicillin, vancomycin, neomycin, and metronidazole) or Inulin. We showed that PCB126 resulted in significant hepatic lipid accumulation, inflammation, and fibrosis. PCB126, Antibiotics, and Inulin significantly affected the structure and shifted community membership of gut microbiome. 7 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways at level 2 and 39 KEGG pathways at level 3 were significantly affected. Antibiotics alleviated PCB126-induced fibrosis in the liver but increased inflammation. Inulin treatment ameliorated both inflammation and fibrosis in the liver of PCB126-treated mice. Neither Antibiotics nor Inulin had significant effect on PCB126-induced hepatic steatosis. The more specific intervention of gut microbiota is needed to alleviate PCB126-induced fatty liver. These data demonstrate that homeostasis of gut microbiota is critical for the defense against PCB126 toxicity and dysbiosis plays a fundamental role in the development of inflammation and fibrosis in liver of PCB126-treated mice.