Allosteric Inhibitor of KRas Identified Using a Barcoded Assay Microchip Platform

• Published in: Analytical chemistry (Washington) Vol. 90; no. 15; pp. 8824 - 8830
• Main Authors: McCarthy, Amy M, Kim, Jungwoo, Museth, A. Katrine, Henning, Ryan K, Heath, John E, Winson, Emma, Oh, Joseph J, Liang, Jingxin, Hong, Sunga, Heath, James R
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 07.08.2018
• Subjects: Allosteric Regulation - drug effects; Allosteric Site - drug effects; Analytical chemistry; Assaying; Bioassays; Biotinylation; Chemistry; DNA, Single-Stranded - chemistry; Drug Evaluation, Preclinical - methods; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - pharmacology; Epitopes; Genes; Humans; Immunoglobulins; Ligands; Microarray Analysis - methods; Organic chemistry; Proteins; Proto-Oncogene Proteins p21(ras) - antagonists & inhibitors; Proto-Oncogene Proteins p21(ras) - chemistry; Proto-Oncogene Proteins p21(ras) - metabolism; Reagents; Screens; Semiconductors; Streptavidin - chemistry
• DOI: 10.1021/acs.analchem.8b00706
• ISSN: 0003-2700; 1520-6882

Protein catalyzed capture agents (PCCs) are synthetic antibody surrogates that can target a wide variety of biologically relevant proteins. As a step toward developing a high-throughput PCC pipeline, we report on the preparation of a barcoded rapid assay platform for the analysis of hits from PCC library screens. The platform is constructed by first surface patterning a micrometer scale barcode composed of orthogonal ssDNA strands onto a glass slide. The slide is then partitioned into microwells, each of which contains multiple copies of the full barcode. Biotinylated candidate PCCs from a click screen are assembled onto the barcode stripes using a complementary ssDNA-encoded cysteine-modified streptavidin library. This platform was employed to evaluate candidate PCC ligands identified from an epitope targeted in situ click screen against the two conserved allosteric switch regions of the Kirsten rat sarcoma (KRas) protein. A single microchip was utilized for the simultaneous evaluation of 15 PCC candidate fractions under more than a dozen different assay conditions. The platform also permitted more than a 10-fold savings in time and a more than 100-fold reduction in biological and chemical reagents relative to traditional multiwell plate assays. The best ligand was shown to exhibit an in vitro inhibition constant (IC50) of ∼24 μM.