Proteomic Barcoding Platform for Macromolecular Screening and Delivery

Engineered macromolecules offer compelling means for
the therapy
of conventionally undruggable interactions in human disease. However,
their efficacy is limited by barriers to tissue and intracellular
delivery. Inspired by recent advances in molecular barcoding and evolution,
we developed BarcodeBabel, a generalized method for the design of
libraries of peptide barcodes suitable for high-throughput mass spectrometry
proteomics. Combined with PeptideBabel, a Monte Carlo sampling algorithm
for the design of peptides with evolvable physicochemical properties
and sequence complexity, we developed a barcoded library of cell penetrating
peptides (CPPs) with distinct physicochemical features. Using quantitative
targeted mass spectrometry, we identified CPPS with improved nuclear
and cytoplasmic delivery exceeding hundreds of millions of molecules
per human cell while maintaining minimal membrane disruption and negligible
toxicity in vitro. These studies provide a proof of concept for peptide
barcoding as a homogeneous high-throughput method for macromolecular
screening and delivery. BarcodeBabel and PeptideBabel are available
open-source from https://github.com/kentsisresearchgroup/.