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Reinventing the small molecule toolbox: from proteins to RNA

Dark Matter Blog

The bulk of my nearly three decades of experience up to that point was with drugging protein targets using a variety of modalities, but principally small molecules. Each yielded some insights; for example, fragment screening gave good hits, but advancing them against the conformational dynamism of RNA was problematic.

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Target-directed cancer: protein-ligand interactions  

Drug Target Review

The mission of the CCDD is to discover novel small-molecule therapeutics for the treatment of cancer and progress them to hypothesis testing phase 1 clinical trials. In terms of compound libraries, we have a high-throughput screening library of about 200,000 ligands. We can screen with many different formats and modalities.

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Silly Things Large Language Models Do With Molecules

Practical Cheminformatics

Testing Claude’s Molecule Generation Ability To test the molecule generation ability of Claude, a general-purpose LLM from Anthropic, I prompted it to generate analogs for hits from fragment screens. These fragment hits are small molecules with between 11 and 21 heavy atoms.

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Biophysical Technologies

Sygnature Discovery

Our in-house SPR equipment comprises: 2x Biacore TM 8K+ 3x Biacore TM 8K 1x Biacore TM T200 This covers mM binders, such as fragments, through to sub pM interactions (such as late stage small molecules or very high affinity biological interactions, Tollenaere et al 2023 [link] ).

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Biophysics

Sygnature Discovery

Small Molecule Binding Assays · Fragment Screening · HTS Hit Validation · Virtual Screen Hit Confirmation · DEL Screening Hit Validation · Affinity/Kinetic Determination (lead identification/lead optimisation) 2.

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Open-source Electrophilic Fragment Screening Platform to Identify Chemical Starting Points for UCHL1 Covalent Inhibitors

Covalent Modifiers

Marto SLAS Discovery, 2024 [link] Target-based screening of covalent fragment libraries with mass spectrometry has emerged as a powerful strategy to identify chemical starting points for small molecule inhibitors or find new binding pockets on proteins of interest.