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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,...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier Masson SAS.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9528019/ https://www.ncbi.nlm.nih.gov/pubmed/36209629 http://dx.doi.org/10.1016/j.ejmech.2022.114803 |
Sumario: | 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 IC(50) values less than 12 μM and the strongest one inhibited SARS-CoV-2 3CL protease with an IC(50) 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. |
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