Kalantar Masoud, Kalanther Ifthichar, Kumar Sachin, Buxton Elham Khorasani, Raeeszadeh-Sarmazdeh Maryam
Department of Chemical and Materials Engineering, University of Nevada, Reno, NV 89557, USA.
Department of Computer Science, University of Illinois, Springfield, USA.
Comput Struct Biotechnol J. 2024 Oct 10;23:3759-3770. doi: 10.1016/j.csbj.2024.10.005. eCollection 2024 Dec.
Given the crucial role of specific matrix metalloproteinases (MMPs) in the extracellular matrix, an imbalance in the regulation of activation of matrix metalloproteinase-9 (MMP-9) zymogen and inhibition of the enzyme can result in various diseases, such as cancer, neurodegenerative, and gynecological diseases. Thus, developing novel therapeutics that target MMP-9 with single-chain antibody fragments (scFvs) is a promising approach. We used fluorescent-activated cell sorting (FACS) to screen a synthetic scFv antibody library displayed on yeast for enhanced binding to MMP-9. The screened scFv mutants demonstrated improved binding to MMP-9 compared to the natural inhibitor of MMPs, tissue inhibitor of metalloproteinases (TIMPs). To identify the molecular determinants of these engineered scFv variants that affect binding to MMP-9, we used next-generation DNA sequencing and computational protein structure analysis. Additionally, a deep-learning language model was trained on the screened scFv library of variants to predict the binding affinities of scFv variants based on their CDR-H3 sequences.
鉴于特定基质金属蛋白酶（MMPs）在细胞外基质中的关键作用，基质金属蛋白酶-9（MMP-9）酶原激活调节与该酶抑制之间的失衡会导致多种疾病，如癌症、神经退行性疾病和妇科疾病。因此，开发以单链抗体片段（scFvs）靶向MMP-9的新型疗法是一种很有前景的方法。我们使用荧光激活细胞分选（FACS）来筛选展示在酵母上的合成scFv抗体文库，以增强与MMP-9的结合。与MMPs的天然抑制剂金属蛋白酶组织抑制剂（TIMPs）相比，筛选出的scFv突变体与MMP-9的结合有所改善。为了确定这些影响与MMP-9结合的工程化scFv变体的分子决定因素，我们使用了下一代DNA测序和计算蛋白质结构分析。此外，基于筛选出的scFv变体文库训练了一个深度学习语言模型，以根据其互补决定区重链3（CDR-H3）序列预测scFv变体的结合亲和力。
