ArticleJournal of chemical theory and computation2022
Testing Affordable Strategies for the Computational Study of Reactivity in Cysteine Proteases: The Case of SARS-CoV-2 3CL Protease Inhibition.
Article in Journal of chemical theory and computation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 25 citations in OpenAlex.
- Methods for the establishment of enzymatic mechanisms - from QM to ML.Chemical science · 2026Review
- A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats.The journal of physical chemistry letters · 2025Review
- CHARMM-GUIJournal of chemical theory and computation · 2025Article
- Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development.ACS omega · 2024Review
- Unraveling the catalytic mechanism of SARS-CoV-2 papain-like protease with allosteric modulation of C270 mutation using multiscale computational approaches.Chemical science · 2023Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cysteine proteases are an important target for the development of inhibitors that could be used as drugs to regulate the activity of these kinds of enzymes involved in many diseases, including COVID-19. For this reason, it is important to have methodological tools that allow a detailed study of their activity and inhibition, combining computational efficiency and accuracy. We here explore the performance of different quantum mechanics/molecular mechanics methods to explore the inhibition reaction mechanism of the SARS-CoV-2 3CL protease with a hydroxymethyl ketone derivative. We selected two density functional theory (DFT) functionals (B3LYP and M06-2X), two semiempirical Hamiltonians (AM1d and PM6), and two tight-binding DFT methods (DFTB3 and GFN2-xTB) to explore the free energy landscape associated with this reaction. We show that it is possible to obtain an accurate description combining molecular dynamics simulations performed using tight-binding DFT methods and single-point energy corrections at a higher QM description. The use of a computational strategy that provides reliable results at a reasonable computational cost could assist the in silico screening of possible candidates during the design of new drugs directed against cysteine proteases.
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Registered trials
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