ArticleCell chemical biology2021
An automatic pipeline for the design of irreversible derivatives identifies a potent SARS-CoV-2 M
Article in Cell chemical biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed, 86 citations in OpenAlex.
- Recent Advances in the Design of Inhibitors Targeting the Viral Entry and Replication of the SARS-CoV-2 Virus, Driven by In Silico Approaches.Molecules (Basel, Switzerland) · 2026Review
- Antiviral drug discovery and development: challenges and future directions.Signal transduction and targeted therapy · 2026Review
- Exploring Novel E3 Ligases and Neosubstrates for Molecular Glue Degraders and Therapeutic Applications in Cancer.Oncology research · 2026Review
- Exploring covalent inhibitors of SARS-CoV-2 main protease: from peptidomimetics to novel scaffolds.Journal of enzyme inhibition and medicinal chemistry · 2025Review
- The covalent docking software landscape: features and applications in drug design.Briefings in bioinformatics · 2025Review
- Optimized pipeline and designer cells for synthetic-biology-based high-throughput screening of viral protease inhibitors.Cell reports methods · 2025Article
- Computational Design of Lysine Targeting Covalent Binders Using Rosetta.Journal of chemical information and modeling · 2025Article
- Template-Based Docking Using Automated Maximum Common Substructure Identification with EnzyDock: Mechanistic and Inhibitor Docking.Journal of chemical information and modeling · 2025Article
- SuFEx Chemistry Enables Covalent Assembly of a 280-kDa 18-Subunit Pore-Forming Complex.Journal of the American Chemical Society · 2024Article
- Inhibitors of SARS-CoV-2 Main Protease (Mpro) as Anti-Coronavirus Agents.Biomolecules · 2024Review
- Preclinical evaluation of the SARS-CoV-2 MNature microbiology · 2024Article
- Scaffold Matcher: A CMA-ES based algorithm for identifying hotspot aligned peptidomimetic scaffolds.Proteins · 2024Article
- Design, Synthesis, X-ray Crystallography, and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease.ACS infectious diseases · 2024Article
- Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.Acta crystallographica. Section D, Structural biology · 2024Article
- On the origins of SARS-CoV-2 main protease inhibitors.RSC medicinal chemistry · 2024Review
- An Update on SARS-CoV-2 Clinical Trial Results-What We Can Learn for the Next Pandemic.International journal of molecular sciences · 2023Review
- Two-Step Covalent Docking with Attracting Cavities.Journal of chemical information and modeling · 2023Article
- Structure and function of SARS-CoV and SARS-CoV-2 main proteases and their inhibition: A comprehensive review.European journal of medicinal chemistry · 2023Review
- Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors.Science (New York, N.Y.) · 2023Article
- Recent Advances in SARS-CoV-2 Main Protease Inhibitors: From Nirmatrelvir to Future Perspectives.Biomolecules · 2023Review
Corrections and comments
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Authors and funding
18 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Designing covalent inhibitors is increasingly important, although it remains challenging. Here, we present covalentizer, a computational pipeline for identifying irreversible inhibitors based on structures of targets with non-covalent binders. Through covalent docking of tailored focused libraries, we identify candidates that can bind covalently to a nearby cysteine while preserving the interactions of the original molecule. We found ∼11,000 cysteines proximal to a ligand across 8,386 complexes in the PDB. Of these, the protocol identified 1,553 structures with covalent predictions. In a prospective evaluation, five out of nine predicted covalent kinase inhibitors showed half-maximal inhibitory concentration (IC
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.