{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T18:50:02Z","timestamp":1773773402522,"version":"3.50.1"},"posted":{"date-parts":[[2026,3,14]]},"group-title":"Molecular Biology","reference-count":75,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T00:00:00Z","timestamp":1773446400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIH","award":["5T32GM008284-33"],"award-info":[{"award-number":["5T32GM008284-33"]}]},{"name":"NIH","award":["U54AI170792"],"award-info":[{"award-number":["U54AI170792"]}]},{"DOI":"10.13039\/100000060","name":"NIAID","doi-asserted-by":"crossref","award":["U19AI171110"],"award-info":[{"award-number":["U19AI171110"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,3,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Biased Fab phage-display libraries were designed to determine whether inhibitory CDR H3 motifs from potent anti-matriptase antibodies could be transferred to target homologous serine proteases. Using reverse-binding and substrate-like H3 motifs from parental clones A11 and E2 as templates, six synthetic libraries with 10\n                  <jats:sup>10<\/jats:sup>\n                  diversity were constructed. Selection against matriptase identified sixteen inhibitors with sub-100 nM potency, representing 100,000-fold improvement over circularized H3 loops alone. Selection against TMPRSS2, a serine protease implicated in viral entry and prostate cancer with 43% sequence identity to matriptase, yielded binders with micromolar inhibitory potency. Selection against urokinase plasminogen activator (uPA, 35% identity) identified binders that adopted a substrate-like CDR H3 binding mode in our structural models. Across all reference structures, including the separately identified uPA inhibitor AB2 (PDB: 9PYF, deposited with this work), benchmarking of five co-folding methods and rigid-body docking showed that co-folding consistently achieved acceptable to high quality DockQ scores, outperforming traditional docking and capturing the recognition of key active site determinants. Ensemble predictions of mutational binding energy changes (\u0394\u0394\n                  <jats:italic>G<\/jats:italic>\n                  ) using these models identified key paratope-epitope interactions, with predictions validated through mutagenesis. This work establishes a framework integrating biased antibody libraries with computational structure prediction and analysis for targeting conserved protease epitopes.\n                <\/jats:p>","DOI":"10.64898\/2026.03.12.711446","type":"posted-content","created":{"date-parts":[[2026,3,15]],"date-time":"2026-03-15T05:15:10Z","timestamp":1773551710000},"source":"Crossref","is-referenced-by-count":0,"title":["Structural Basis of Serine Protease Inhibition by Antibodies from Biased Fab Phage-Display Libraries"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2737-8129","authenticated-orcid":false,"given":"Kyle J.","family":"Anderson","sequence":"first","affiliation":[{"name":"Biophysics Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Melody S.","family":"Lee","sequence":"additional","affiliation":[{"name":"Graduate Group in Chemistry and Chemical Biology, 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