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bioRxiv · 10.1101/2024.06.04.597476

Elucidating key determinants of engineered scFv antibody in MMP-9 binding using high throughput screening and machine learning

Kalantar, M.·Kalanther, I.·Kumar, S.·Buxton, E. K.·Raeeszadeh-Sarmazdeh, M.
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Abstract

An imbalance in matrix metalloproteinase-9 (MMP-9) regulation can lead to numerous diseases, including neurological disorders, cancer, and pre-term labor. Engineering single-chain antibody fragments (scFvs) Targeting MMP-9 to develop novel therapeutics for such diseases is desirable. We screened a synthetic scFv antibody library displayed on the yeast surface for binding improvement to MMP-9 using FACS (fluorescent-activated cell sorting). The scFv antibody clones isolated after FACS showed improvement in binding to MMP-9 compared to the endogenous inhibitor. To understand molecular determinants of binding between engineered scFv antibody variants and MMP-9, next-generation DNA sequencing, and computational protein structure analysis were used. Additionally, a deep-learning language model was trained on the synthetic library to predict the binding of scFv variants using their CDR-H3 sequences.

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Kalantar, M., Kalanther, I., Kumar, S., Buxton, E. K., Raeeszadeh-Sarmazdeh, M.. 2024-06-06. Elucidating key determinants of engineered scFv antibody in MMP-9 binding using high throughput screening and machine learning. https://doi.org/10.1101/2024.06.04.597476

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