High-throughput (HTE) reaction QC

This workflow is based on Reaction Analysis (LCMS) and has the same principles. But can be much more complicated because of sheer volume of data.

High-throughput Experimentation (HTE) is done when we want to quickly run many reactions.

Types of HTE

Reaction Screening (with purification)

At the beginning of a drug-discovery project, we have a lot of possible candidates to start exploring. But we don’t know:

  • if the reactions are easy to run

  • which of the thousands possibilities will actually interact with the target protein

It’s too tedious and too expensive to run reactions one at a time and large scale. Instead, we can scout for possible simple candidates:

  1. Select dozens/hundreds/thousands of reactions that ideally can be run in similar conditions (reagents, solvents, temperature, etc)

  2. Run them at very small scale (as small as possible)

  3. Run a Reaction Analysis (LCMS) to identify which of the reactions look successful

  4. Run purification to get isolate pure products

  5. Run bioassays to check if they have any bio activity (interact with the target protein)

This way we quickly and cheaply identify which reactions and compounds to further concentrate on.

Direct-to-biology

A lot of bioassays are sensitive to the conditions - acids, bases, reagents. They won’t succeed if the conditions are wrong. That’s why we must purify and get the isolated drug-like product.

But some assays aren’t that sensitive. So some companies try to optimize Reaction Screening even more - they skip a purification step and send a more or less crude (not purified) mixture for the bioassay. This way the slowest step in the process (purification) can be skipped.

So the workflow looks like this:

  1. We select the candidate reactions and conditions that don’t harm the bioassay too much

  2. After the synthesis, run QC to check which reactions have the product

  3. Run a "light" purification e.g. with Solid Phase Extraction (SPE). This acts like chromatography, but faster and not as good at separation. We get crude mixtures with fewer components.

  4. And send that mixture to the bioassay

Reaction Conditions screening

Suppose we have a reaction to run, but we don’t know the perfect conditions to maximize the yield or to minimize the spending (reagents, time, steps). This is the time for condition screening: we mix the same reactants in many reactions with many different conditions.

This can be done either during the Early Drug Discovery or at later stages when it’s time to think about larger quantities.

This workflow is characterized by small number of possible compounds but large number of reactions. They are easier to analyze than the Reaction Screening when we have many reactions and many different reactants/products.

Peaksel capabilities

  • Peaksel is highly optimized for HTE. Almost anything you can do with a single injection, can be applied to the whole batch: peak editing, detector alignment, extraction of chromatograms on Mass Spec or UV, doing advanced mass spec. All these can be done very quickly even in large batches: a typical reintegration takes just couple of seconds for a 1536 experiment.

  • Batch-level visualizations allow QC peak picking and other metrics. See High Throughput Experimentation: speed up analysis with visualizations.

  • Once the necessary visualizations are set up, they can be re-used using the templates.

  • If automation is required (which is often the case), Peaksel API & SDK can be used for programmatic processing and data export.

  • It’s possible to create and export batch-level reports with custom calculations.

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