Practical_Fragments
@PracticalFrag
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A blog founded by Teddy Zartler and run by Dan Erlanson for Fragment-based Drug Discovery devotees to discuss non-confidential issues regarding fragments.
Joined February 2019
Cooler simulations, refined docking: Thermal Titration Molecular Dynamics(TTMD) protocol modified for fragments correctly identifies binding modes.@StefanoMoro1965 @JCIM_JCTC.
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Nice #fragment-to-lead story for KEAP1-NRF2 protein-protein interaction, starring crystallographic screening, structure-based design, and multiple assays to fill the Kelch pocket.@angew_chem.
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"Unexpectedly high occurrence of wrong ligands." Roche team examines > 200 high quality ligand-bound structures for fatty-acid binding proteins to gain lots of useful data, including sources of error.@ActaCrystD.
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Researchers inhibit two Mycobacterium tuberculosis enzymes with one compound using fragment screens and linking/merging to inhibit bacterial cholesterol metabolism.@mads_chem @ACSPublications.
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Stay clear of fake biology! The Chemical Probe Portal can alert astute researchers to artifacts. Ten years, >1170 compounds, and counting!.@Cancer_Cell.
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An AI aggregator alert for artifact avoidance shows its work. With MEGAN, forewarned is forearmed:.@angew_chem.
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High-throughput crystallography raise an urgent question of how to host data. Proposals from several luminaries, including head of the Protein Data Bank.@NatureComms @ManfredSWeiss @nsakaii @DiamondLightSou @proteindatabank.
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Covalent inhibitors are characterized by a ratio of two constants. @bharath_IGC explains that considering both, and how one affects the other, could help advance hits on difficult targets:.@JMedChem @CR_UK @ACSBioMed.
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Upcoming fragment meet-ups: An updated list of conferences for the rest of 2025 and into 2026.@CHI_Healthtech @FBLDconference @novalix_pharma.
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Agonists and inverse agonists for metabolic/diabetes target HNF4 (hepatocyte nuclear factor 4) using cell-based optimization of fragments.@ACSPublications.
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Finding ligands for RNA: the enthalpy, the entropy, & the limited benefits of positivity.@ACSPublications.
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Careful, meticulous work on SARS-CoV-2 RNA finds hits, and suggests just how tough these targets could be.@angew_chem.
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Promising pockets on RNA: small-molecule binding sites found computationally with fpocketR and validated by experimental fragment screening. Complex RNA structures more likely to be ligandable than simpler ones.
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Unknown rings are bioactive - researchers sought out previously unmade fragments and matched them with likely protein targets to find tiny actives. Within chemical space, little gems remain to be mined .@ACSPublications @unibern.
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High-throughput crystallography of >1000 crude reaction mixtures screened against oncology target PHIP(2) takes fragment with no activity to mid-micromolar inhibitor.@FrankvonDelft @philbiggin @DiamondLightSou @BiochemOxford @angew_chem @GrosjeanHarold.
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A macrocyle that prefers active KRAS.Fragment screens against active form of cancer target #KRAS lead to macrocycles that exploit a new pocket near the switch I-II pocket.@CRUKScotland @JMedChem @Novartis.
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NMR for FBLD gets a boost via a clever new pulse sequence. Focusing on ligand protons reveals bound structure for KRAS hits.@stem_univie @ETH_en @ETH_DCHAB @nmr900@ETH@J_A_C_S.
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Protein-detect NMR without isotopic labeling.ECHOS-ID technique from @abbvie sheds burdensome requirement but still finds weak binders.@ACSMedChemLett.
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This year's CHI Drug Discovery Chemistry in San Diego featured a wealth of improved techniques for covalent and non-covalent fragment screens, success stories, and enabling chemistries.@CHI_Healthtech.
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Probing the cysteinome: 47 hinge-binding fragments crossed with 47 protein kinases yields potential drug starting points plus some general wisdom.@uni_tue @angew_chem.
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