Classical DEL Technology

First proposed by Brenner and Lerner in 1992, DNA-Encoded Library technology is a powerful tool for drug discovery. The library consists of a collection of potential drug molecules, each attached to a unique DNA strand which functions as an identifying code. A pharmaceutically relevant target protein is attached to a solid support and treated with an aliquot of the library. After washing off non-binding compounds, the DNA tags of bound molecules are amplified with PCR and then decoded and identified via DNA sequencing.

DEL technology is an elegant approach to the “needle in a haystack” problem of finding new drugs. The approach lends itself to using combinatorial chemistry, allowing the production of very large libraries, and as it is based on compound binding, no biochemical assay is necessary for the process. While undoubtedly attractive, the first generation of DEL technology suffered from certain limitations. Issues with poor signal-to-noise ratio, and the time and expense of deep sequencing and compound resynthesis/optimization for validation limit the full potential of the method. Fortunately, DyNAbind’s proprietary technologies are leading the way to a new generation of DEL drug discovery.

DyNAbind’s Innovations

Dynamic Libraries

DyNAbind’s dynamic chemical libraries improve the low signal-to-noise ratios seen with classical DEL technology. The first-generation process typically generates many false positive hits. Moreover, hit counts cannot neccessarily be directly correlated to hit effectiveness, meaning that excessive time and resources are spent triaging the hit compounds to determine which are worth further investigation.

DyNAbind’s patented dynamic chemical library technology allows constant reshuffling of the library. While higher-affinity compounds are stabilized by binding to the target, low-affinity compound-pairs split and reshuffle to generate additional binders. The end result is a smaller number of more reliable hits, with significant boosting of the signal-to-noise ratio.[1,2]

Dynamic Reshuffling

Path-Coding Algorithm

Classical DEL technology relies on Next-Generation Sequencing (NGS) to analyze the results of each selection experiment to optimize selection conditions. Although NGS can be expensive, the real problem with the method is the time it takes for results to come back. Experiments which could otherwise be completed in days are delayed by weeks while waiting for sequencing data. Moreover, with traditional condensed DNA codes, a single error in a base read can give back a false positive hit, amplifying the volume of work to be done downstream in hit validation

DyNAbind’s patented Path-Coding algorithm takes advantage of the DNA information space to design highly diverse codes. [3] This provides a form of built-in error proofing which allows reading errors to be identified and often corrected, as well as allowing a novel, rapid method of selection condition optimization with real-time PCR.

Path Coding

Binding Profiler Validation

Once hits have been identified, they must be validated with kinetic measurements. Classically, this meant a slow and expensive process of resynthesizing all hit compounds “off-DNA.” Moreover, when using a dual-pharmacophore library, linkage between the components would also need to be optimized; an especially tedious process when faced with the hundreds of hits provided in a typical selection.

DyNAbind’s Binding Profiler technology offers a rapid, automated way to obtain kinetic parameters without off-DNA resynthesis or linker optimization. Over 300 compounds can be analyzed in a day, enabling high-throughput analysis of fragment-based hits for DEL discovery for the first time. The technology is compatible with all biosensor platforms on the market. [4]

Regenerable Sensor

1) Reddavide et. al. Angew. Chem. Int. Ed. 2015. 54 

2) Patent: DE 10 2014 213 783

3) Patent: DE 10 2014 200 446

4) Lin et. al. Anal. Chem. 2015. 87