Polymer encoding technology for single-molecule screening of small-molecule binders using nanopores

Growing health challenges, such as cancers, neurodegenerative diseases, and diabetes, are straining healthcare systems and society, necessitating expedited drug discovery. DNA-encoded libraries (DEL) utilize oligonucleotide tags to encode chemical information which can be retrieved via DNA sequencing. This innovation has transformed the drug discovery landscape by enabling highthroughput screenings of millions of compounds in a single test tube.

However, the DEL method faces intrinsic constraints, including limited compatibility with synthetic methodologies, restricted target scope, detection sensitivity, and a lack of quantitative affinity information for target-binder interactions.

Nanopore technology emerges as a versatile single-molecule parallel sensing platform. It has been commercialized for ultralong-read DNA/RNA sequencing and holds great potential in solving the challenges faced by DEL screening. However, applying off-the-shelf nanopore DNA sequencers to the DEL is technically challenging mainly owing to their limitations in reading short sequences.

With the recent advances in polymer chemistry and nanopore technology, we now aim to further accelerate the drug screening process through developing synthetic polymer encoded libraries (SPEL) tailored to nanopore technology. We will leverage the chemical stepping strategy developed by the host lab to retrieve information within compact synthetic polymer barcodes for chemical library screening and concurrently assess the affinity of a chemical binder with a given target.

The methodologies will be employed for screening and characterizing small-molecule binders for the tumor necrosis factor alpha (TNF-alpha) as a demonstration. If successfully established as a proof-of-concept system, it could potentially be adapted to the commercial nanopore sensing platform containing over 120,000 nanopores, achieving real-time parallel screening of >1 million compounds in <2 hours.