ArticleChemMedChem2019
DUckCov: a Dynamic Undocking-Based Virtual Screening Protocol for Covalent Binders.
Article in ChemMedChem, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 24 citations in OpenAlex.
- Effective virtual screening strategy toward JAK3 covalent inhibitors: combining multi‑conformational consensus calculation with covalent docking.Molecular diversity · 2026Article
- Discovery of Covalent Ligands with AlphaFold3.Journal of the American Chemical Society · 2026Article
- De novo covalent drug generation with enhanced drug-likeness and safety.Communications biology · 2026Article
- The covalent docking software landscape: features and applications in drug design.Briefings in bioinformatics · 2025Review
- Modeling receptor flexibility in the structure-based design of KRASJournal of computer-aided molecular design · 2022Article
- CovPDB: a high-resolution coverage of the covalent protein-ligand interactome.Nucleic acids research · 2022Article
- An automatic pipeline for the design of irreversible derivatives identifies a potent SARS-CoV-2 MCell chemical biology · 2021Article
- Fragment-based covalent ligand discovery.RSC chemical biology · 2021Review
- Discovery of fragments inducing conformational effects in dynamic proteins using a second-harmonic generation biosensor.RSC advances · 2021Article
- Structure-based inhibitor design of mutant RAS proteins-a paradigm shift.Cancer metastasis reviews · 2020Review
- Selective and Effective: Current Progress in Computational Structure-Based Drug Discovery of Targeted Covalent Inhibitors.Trends in pharmacological sciences · 2020Review
- DUckCov: a Dynamic Undocking-Based Virtual Screening Protocol for Covalent Binders.ChemMedChem · 2019Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Thanks to recent guidelines, the design of safe and effective covalent drugs has gained significant interest. Other than targeting non-conserved nucleophilic residues, optimizing the noncovalent binding framework is important to improve potency and selectivity of covalent binders toward the desired target. Significant efforts have been made in extending the computational toolkits to include a covalent mechanism of protein targeting, like in the development of covalent docking methods for binding mode prediction. To highlight the value of the noncovalent complex in the covalent binding process, here we describe a new protocol using tethered and constrained docking in combination with Dynamic Undocking (DUck) as a tool to privilege strong protein binders for the identification of novel covalent inhibitors. At the end of the protocol, dedicated covalent docking methods were used to rank and select the virtual hits based on the predicted binding mode. By validating the method on JAK3 and KRas, we demonstrate how this fast iterative protocol can be applied to explore a wide chemical space and identify potent targeted covalent inhibitors.
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