Structure-Based Identification of High-Affinity scFv Antibody Targeting YKL-40 as a Biomarker for Early Alzheimer’s Disease Detection

Alzheimer’s disease (AD) is a neurological disease where the brain shrinks due to the death of brain cells. Common symptoms of this disease include problems with memory and cognitive tasks. Patients suffering from this disease have elevated levels of the protein YKL-40, which is a secreted glycoprotein produced by inflammatory cells. A single-chain fragment variable (scFv) is a small unit of an antibody that is genetically engineered to bind to an antigen. We hypothesize that the scFv 5yd3 will bind to the YKL-40 protein and can be used to detect YKL-40 protein in the cerebrospinal fluid of AD patients. By obtaining the amino acid sequence of YKL-40 from the UniProt database, we were able to utilize it to create a 3D structure of YKL-40 using AlphaFold3, a machine learning based method. Next, we conducted a series of molecular docking experiments, in which we used 10 different scFv and attempted to bind them to YKL-40. These docking results were further compared to the predicted binding site obtained from P2rank and ScanNet web server. Finally, after receiving the results from the molecular docking, we analyzed the strength of those bonds through PLIP and PRODIGY. Following our analysis, scFv 9b6t was selected as a suitable candidate for detecting YKL-40 protein. In future studies, we will be performing amino acid mutations to enhance the antibody binding affinity. This current research will pave the way for future detection of AD, and possibly even treatment.