Published January 30, 2023 | Version v1
Dataset Open

High-throughput crystallography for rapid early-stage fragment growth from crude arrays by low-cost robotics


Data to support the paper - High-throughput crystallography for rapid early-stage fragment growth from crude arrays by low-cost robotics. Data includes a summary of X-ray and LCMS results for the reactions executed on the OpenTrons, output reports and summaries from MSCheck (semi-automated LCMS analyzer tool) and the Python scripts used to execute single and multistep chemistry on the OpenTrons.


We demonstrate that a simple workflow of array synthesis, combining low-cost robotics with analytic techniques to deconvolute crude reaction mixtures, is an effective way to collect structural data on a binding site.  Starting from the high information content of the crystallographic fragment screens on PHIP(2) (second bromodomain of the pleckstrin homology domain interacting protein), a collection of more than 1800 compounds was enumerated. Several thousand Crude Reaction Mixtures (CRMs) were synthesized on one robotic platform, an OpenTrons OT-1 liquid handler, using reaction sequences of up to 5 chemical steps. Analysis via MScheck, an algorithm-based system for finding a m/z in a CRM, significantly shortened product identification protocol times. 957 usable X-ray diffraction datasets were acquired, which resolved as 22 reaction products binding to the protein, 19 with conserved poses relative to the original fragment and 3 with a new, unexpected binding pose. The 22 crystallographic hit compounds were subsequently tested with peptide displacement alpha-screen assay and time-resolved grating-coupled interferometry-based biosensor assays, which confirmed one molecule with an IC50 = 34 μM and KD = 50 μM, from an inactive fragment.  The procedures described are entirely formulaic and engineerable and the method is eminently scalable. We anticipate that this cheap, low solvent-use approach will yield vast amounts of data, enabling rapid SAR landscape exploration around fragments, leading to faster fragment to lead times.


MSCheck - semi-automated QC analyser results and