Modern Biotechnology relies heavily on high-throughput processing of proteins to identify useful variants, such as target-specific antibodies or peptides, stable enzymes or membrane proteins. Conceptually, high-throughput processing can be achieved i) via screening, where candidate molecules are processed separated from each other in individual vials in parallel (e.g. ELISA) or ii) via selection, where entire libraries are processed as ensembles in the same vial (e.g phage display). Selections typically exhibit a much higher throughput than screens and they require less hands-on time and no expensive robots. However, only screens allow for direct characterization of individual molecules, and they are not biased by the genotype-phenotype linkage, which is required for selections to date.
NestLink is a novel technology that combines the benefits of screens and selections. It enables processing of thousands of library members as an ensemble, while still allowing for characterization of individual candidate molecules within the processed pool of proteins. This is achieved by an engineered collection of genetically fused barcoding peptides, termed flycodes, and a combination of state-of-the-art mass spectrometry and deepsequencing. Hence, NestLink is a novel protein selection principle that operates in the absence of a genotype-phenotype linkage. This paradigm-shift enables novel protein engineering applications, which we are currently exploring.
Thus far, we have demonstrated that NestLink enables identification of binders against integral membrane proteins embedded in living cells with high efficiency. Further, we showed that it is able to characterize thousands of off-rates in vitro at once and that it can be used to deep-mine camelid immune repertoires for target-binding antibodies. Our current projects explore its applicability in vivo, with an eye on its potential utility to reduce the number of animal trials required for biomolecular drug development. One focus is the identification of synthetic shuttle proteins with unique biodistribution properties and therapeutic potential.
The NestLink technology is pre-published on BioRxiv: https://www.biorxiv.org/content/early/2018/03/23/287813