{"doi":"10.1016/j.jbc.2025.110258","title":"Directed evolution of metalloproteinase inhibitor TIMP-1 for selective inhibition of MMP-9 exploits catalytic and fibronectin domain interactions","abstract":"Matrix metalloproteinase-9 (MMP-9) is a critical enzyme involved in extracellular matrix degradation and is strongly implicated in many diseases, including triple-negative breast cancer and other poor prognosis cancers. Selective inhibition of MMP-9 is therefore a promising therapeutic strategy. However, development of MMP inhibitors has been hindered by challenges in achieving specificity, with past efforts failing in clinical trials due to off-target effects and associated toxicity. Here, we present a novel approach to overcoming these challenges by engineering tissue inhibitor of metalloproteinases-1 (TIMP-1), a natural broad-spectrum MMP inhibitor, to achieve enhanced specificity and affinity for MMP-9. We demonstrate that TIMP-1 can be strategically engineered to selectively inhibit MMP-9 through modulating interactions not only with the catalytic domain but also with the unique fibronectin (FN) domains. By leveraging yeast surface display with strategic library design, we identified TIMP-1 variants that exploit multiple surface epitopes to optimize interactions with both the catalytic and FN domains of MMP-9. Molecular dynamics simulations further suggest how modifications in the N-terminal and C-terminal domains of TIMP-1 drive these selective interactions. The top engineered TIMP-1 variant exhibited significantly improved selectivity for MMP-9 in a manner dependent upon novel interactions with the FN domains, as validated through inhibition kinetics. This variant also demonstrated potent inhibition of MMP-9-driven triple-negative breast cancer cell invasiveness, underscoring the therapeutic potential of this approach. Our study highlights the versatility of TIMP-1 as a scaffold that can be optimized for highly selective MMP inhibition, providing new avenues for the development of targeted therapies.","journal":"Journal of Biological Chemistry","year":2025,"id":516237,"datarank":0.3596842909197557,"base_score":2.3978952727983707,"endowment":2.3978952727983707,"self_citation_contribution":0.3596842909197557,"citation_network_contribution":0.0,"self_endowment_contribution":0.3596842909197557,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":10,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9538,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":332568,"name":"Matt Coban","orcid":"0000-0001-6396-6759","position":1,"is_corresponding":false},{"id":656712,"name":"Alexandra Hockla","orcid":"0009-0007-7179-5671","position":2,"is_corresponding":false},{"id":1003895,"name":"Arlinda Rezhdo","orcid":null,"position":3,"is_corresponding":false},{"id":1382063,"name":"Alexandra M. Dimesa","orcid":null,"position":4,"is_corresponding":false},{"id":800026,"name":"Maryam Raeeszadeh‐Sarmazdeh","orcid":"0000-0003-2946-5584","position":5,"is_corresponding":false},{"id":499037,"name":"James A. Van Deventer","orcid":"0000-0003-4343-6157","position":6,"is_corresponding":false},{"id":274154,"name":"Evette S. Radisky","orcid":"0000-0003-3121-109X","position":7,"is_corresponding":false},{"id":1067577,"name":"Alireza Shoari","orcid":"0000-0003-3842-2156","position":0,"is_corresponding":true}],"reference_count":69,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:48:49.486328Z","pmid":"40409544","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":[]}