TERÅ beads is an end-to-end DEL*-based platform to boost the performance of oligonucleotide therapeutics by deep-learning the effects of chemical modifications

It all starts with a bead

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High Throughput
Combinatorial Chemistry

The first step of the TERÅ beads (topologically encoded, RNA-active) platform is to create a vast number of therapeutic RNA molecules with unique patterns of chemical modifications.

During the synthesis of the therapeutic RNA molecules, we also create DNA barcodes on each bead that record the pattern of these RNA modifications, making them accessible to high throughput sequencing.

To synthesize these molecules in a cost-effective manner, we subject millions of beads to a split-pool process.

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Split I

The beads are split at random into different synthesis columns.

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Coupling of RNA
and DNA using
orthogonal chemistry

Our patent-pending orthogonal chemistry coupling simultaneously synthesizes the modified RNA oligo and the DNA barcode.

In the illustration, the left column uses 2′-F Uridine as the first base of the therapeutic RNA oligo and a DNA pyrimidine nucleotide to signify the addition of the 2’F-U modification. The right column uses 2′-OMe Uridine for the RNA oligo and DNA purine nucleosides to signify the 2′-OMe modification of the RNA.

The process can support a wide repertoire of chemical modifications in the nucleobase, sugar ring, and phosphate backbone.

Pool I

After synthesis, the beads from all columns are pooled, creating a mixture of beads.

In the illustration, we have a mixture of two types of beads: those with 2’F-Uridine and those 2′-OMe-Uridine. Each of these beads is labelled with a DNA nucleotide according to the chemical modification.

Split II

We subject the mixture of beads to an additional split. Again, in each synthesis column, we use the orthogonal chemistry to extend the therapeutic RNA oligo by an additional modified nucleoside and to record the identity of the modification by coupling the proper nucleoside to the DNA barcode in a distinct reaction.

In the illustration, the left column couples 2′-F-Cytidine and the right column couples 2′-OMe-Cytidine. Again, a coupling of DNA pyridine nucleoside signifies the left column and the coupling of a purine DNA nucleoside signifies the right column.

Pool II

After two split-pool cycles, we have four types of beads.

Each synthesis path creates a distinct pattern of chemical modification for the RNA oligonucleotides on the bead and a unique sequence on the DNA barcode that records the synthesis path of the bead.

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Split-Pool #3
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The final product:
Bead DEL for
chemically modified
RNA molecules

At the end of the process, each bead holds therapeutic
RNA oligos with a unique chemical pattern and DNA
barcodes that record the identity of these modifications.

We repeat the split-pool process multiple times to create variability in desired positions along the therapeutic RNA molecules.
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How it works

Using the split-pool process, we create millions of TERÅ beads, each with a unique type of chemically modified RNA oligo and a DNA barcode that records the modifications.
We incubate the beads with cells, so that each cell sees only a single bead. We then release the modified RNA oligos and DNA barcodes from the beads. These molecules enter the cells and the RNA oligos exert their effect on the cells. We measure this effect in each cell using a high throughput assay.
We sequence the cells to reveal the identity of the DNA barcodes and decode the pattern of chemical modifications and associate it with the effect of the therapeutic RNA oligo on the cell. Using the vast data that we collect, we train a deep learning framework to decipher the structure-activity relationship (SAR) of the RNA modifications. The output of this process can be used for additional build-measure-learn rounds to refine the SAR and further optimize the RNA therapeutic.
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Build
Measure
Learn

How it works

  • Build

    Using the split-pool process, we create millions of TERÅ beads, each with a unique type of chemically modified RNA oligo and a DNA barcode that records the modifications.
  • Measure

    We incubate the beads with cells, so that each cell sees only a single bead. We then release the modified RNA oligos and DNA barcodes from the beads. These molecules enter the cells and the RNA oligos exert their effect on the cells. We measure this effect in each cell using a high throughput assay.
  • Learn

    We sequence the cells to reveal the identity of the DNA barcodes and decode the pattern of chemical modifications and associate it with the effect of the therapeutic RNA oligo on the cell. Using the vast data that we collect, we train a deep learning framework to decipher the structure-activity relationship (SAR) of the RNA modifications. The output of this process can be used for additional build-measure-learn rounds to refine the SAR and further optimize the RNA therapeutic.
work_circle
Build
Measure
Learn

In vivo validation

The TERÅ platform allows us to refine our hypothesis space and to only advance to in vivo testing those RNA oligonucleotides that are backed by sufficient evidence from the in-cellulo assay.

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We know how to
overclock any molecule

RNAi triggers, ASOs, gRNA, and even short mRNA — if it can be chemically synthesized, the revolutionary TERÅ® platform can find the optimal pattern for chemical modifications. These modifications can increase the duration of effect of the therapeutic molecule, tune its bioavailability, reduce immunogenicity, and mitigate off-target effects.