A High-Throughput Biocatalytic Platform for Screening Isomeric Kainoid Natural Products

Random mutagenesis generates large, diverse enzyme libraries, however high-throughput screening is challenging when transformations yield isomeric small molecule products. We developed a matrix-assisted laser desorption/ionization-trapped ion mobility spectrometry-mass spectrometry (MALDI-TIMS-MS) platform for rapid, label-free screening of libraries of kainoid synthases, Fe/αKG-dependent cyclases that produce the isomeric neurotransmitters kainic acid (KA) and kainic acid lactone (KAL). This platform achieves near-baseline separation of KA and KAL directly from microbial biomass, with parallel reaction monitoring-PASEF (PRM-PASEF) enhancing signal-to-noise for isomeric product ratio analysis. Using this workflow, we screened a 318-variant DsKabC/GfKabC DNA shuffle library in under 30 minutes, identifying seven variants with improved KAL conversion. Two variants showed a near-complete shift toward KAL production with greater substrate consumption, while retaining favorable expression profiles compared to GfKabC. These results establish MALDI-TIMS-MS as a generalizable platform for high-throughput isomeric product screening and provides new kainoid synthase variants to probe structure-function relationships for further development as biocatalysts. Importantly, this screening approach can be broadly applied to interrogate enzyme variants acting on small molecules, delivering rapid and accurate quantitative insights without reliance on chromatography, enzyme purification, or substrate derivatization.