{"doi":"10.1016/j.csbj.2024.10.005","title":"Determining key residues of engineered scFv antibody variants with improved MMP-9 binding using deep sequencing and machine learning","abstract":"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.","journal":"Computational and Structural Biotechnology Journal","year":2024,"id":477708,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9491,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1316344,"name":"Ifthichar Kalanther","orcid":null,"position":1,"is_corresponding":false},{"id":781825,"name":"Sachin Kumar","orcid":"0000-0002-3835-8935","position":2,"is_corresponding":false},{"id":1316345,"name":"Elham Khorasani Buxton","orcid":null,"position":3,"is_corresponding":false},{"id":800026,"name":"Maryam Raeeszadeh‐Sarmazdeh","orcid":"0000-0003-2946-5584","position":4,"is_corresponding":false},{"id":1236622,"name":"Masoud Kalantar","orcid":"0009-0009-9926-704X","position":0,"is_corresponding":true}],"reference_count":73,"raw_metadata":null,"created_at":"2026-07-19T02:06:37.812633Z","pmid":"39525083","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}