ArticleNature communications2021
Exploring protein hotspots by optimized fragment pharmacophores.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Screening assay to monitor mono-ADP-ribosylhydrolase activity of viral macrodomains in cells.Communications biology · 2026Article
- Antiviral drug discovery and development: challenges and future directions.Signal transduction and targeted therapy · 2026Review
- Developments and challenges in hit progression within fragment-based drug discovery.Nature communications · 2026Review
- Untangling the Complexity of Binding Across Biomolecular Interfaces with Interaction Network Models.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Solvent-Site Prediction for Fragment Docking and Its Implication on Fragment-Based Drug Discovery.Journal of chemical information and modeling · 2025Article
- Combined crystallographic fragment screening and deep mutational scanning enable discovery of Zika virus NS2B-NS3 protease inhibitors.Nature communications · 2025Article
- High-throughput crystallographic fragment screening of Zika virus NS3 Helicase.bioRxiv : the preprint server for biology · 2025Article
- Crystallographic Fragment Screening of the Dengue Virus Polymerase Reveals Multiple Binding Sites for the Development of Non-nucleoside Antiflavivirals.Journal of medicinal chemistry · 2025Article
- E-FTMap: A Protein Structure Based Pharmacophore Identification Server for Guiding Fragment Expansion.Journal of molecular biology · 2025Article
- A Small-Molecule Drug for the Self-Checking of Mitophagy.Angewandte Chemie (International ed. in English) · 2025Article
- Identifying novel chemical matter against the Chikungunya virus nsP3 macrodomain through crystallographic fragment screening.bioRxiv : the preprint server for biology · 2024Article
- Mapping protein binding sites by photoreactive fragment pharmacophores.Communications chemistry · 2024Article
- On the relevance of query definition in the performance of 3D ligand-based virtual screening.Journal of computer-aided molecular design · 2024Article
- Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites.Journal of chemical information and modeling · 2024Article
- Pinobanksin from peony seed husk: A flavonoid with the potential to inhibit the proliferation of SH-SY5Y.Food science & nutrition · 2024Article
- Review
- An Update on the Current State of SARS-CoV-2 Mac1 Inhibitors.Pathogens (Basel, Switzerland) · 2023Review
- ACFIS 2.0: an improved web-server for fragment-based drug discovery via a dynamic screening strategy.Nucleic acids research · 2023Article
- Ultrafast Fragment Screening Using Photo-Hyperpolarized (CIDNP) NMR.Journal of the American Chemical Society · 2023Article
- Emerging approaches to CDK inhibitor development, a structural perspective.RSC chemical biology · 2023Article
Corrections and comments
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Authors and funding
19 authors.
Funding
Abstract
Fragment-based drug design has introduced a bottom-up process for drug development, with improved sampling of chemical space and increased effectiveness in early drug discovery. Here, we combine the use of pharmacophores, the most general concept of representing drug-target interactions with the theory of protein hotspots, to develop a design protocol for fragment libraries. The SpotXplorer approach compiles small fragment libraries that maximize the coverage of experimentally confirmed binding pharmacophores at the most preferred hotspots. The efficiency of this approach is demonstrated with a pilot library of 96 fragment-sized compounds (SpotXplorer0) that is validated on popular target classes and emerging drug targets. Biochemical screening against a set of GPCRs and proteases retrieves compounds containing an average of 70% of known pharmacophores for these targets. More importantly, SpotXplorer0 screening identifies confirmed hits against recently established challenging targets such as the histone methyltransferase SETD2, the main protease (3CLPro) and the NSP3 macrodomain of SARS-CoV-2.
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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.