Abstract: Therapeutic drug discovery is an extensive market in biopharmaceuticals, suffering from a 90% failure rate in late-stage development. During target validation and compound screening, there are often >10,000 candidates for evaluation, necessitating high-throughput screening methods with improved characterization data for lead discovery. Current off-target screening methods suffer from low-throughput or utilize in silico methods which often have high false-positive rates that must be biologically validated. Key unmet needs in the industry are evaluating i) off-target binding prior to expensive clinical trials; ii) on-target affinity in a high-throughput manner; iii) drug-escape due to mutational loss of affinity; and iv) possible novel targets to re-purpose drugs. Our proprietary sensor-integrated proteome on chip (SPOC) platform is poised to solve these unmet industry needs by providing the ability to screen drugs on up to 1000 targets simultaneously. SPOC is the only proteomics platform capable of delivering real-time, label-free, quantitative, qualitative, and kinetic (affinity) information for binding interactions in a single assay, at scale. SPOC utilizes simultaneous, cell-free, protein expression and capture directly from plasmid DNA onto a surface plasmon resonance (SPR) biosensor chip with up to 2500 unique proteins per chip: effectively reducing the cost of recombinant protein production and purification by 10-100x from traditional workflows, democratizing high-throughput proteomic screening. In this study, we utilized SPOC biosensor chips to screen COVID EUA monoclonal antibodies (mAbs) Bamlanivimab, Etesevimab, Tixagevimab, and Cilgavimab, alone and in combination against 10 COVID variant RBD domains, including Wuhan, Alpha, Delta, and multiple Omicron BA, BQ, and XBB lineage subvariants. Proper folding of the RBD domain was demonstrated by differential mAb binding in the presence or absence of disulfide bond enhancers. We demonstrate discrimination of the mAbs binding efficiency to each variant through the SPR-generated kinetic affinity data, providing a proof-of-concept that SPOC can be used to pro-actively screen for mutational drug escape during the drug development phase, as these clinical antibodies are known to have reduced efficacy after new COVID variants acquired certain mutations in the RBD domain. The screening panel also contained a set of 18 respiratory pathogens to assess off-target interactions for the mAb antibodies. In a second proof-of-concept study, we explored the use of SPOC biosensor chips for small molecule drug discovery by incubating our SPOC chips containing up to 1000 targets with small molecules followed by MALDI-TOF analysis to determine interacting binding partners. Overall, results indicate that SPOC can be an effective high-throughput tool for screening drug candidates in the lead discovery phase for target specificity and preempting drug escape by analyzing binding affinity to numerous mutational variants of the drug target.
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