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However, it remains challenging to obtain non\u2010proteinogenic sequences that carry out a specific task. Here we develop a platform to discover functional non\u2010standard proteins and illustrate its utility by generating a family of bioactive proteins whose hydrophobic cores are built using fluorinated amino acids (fAAs). Starting from the protein chymotrypsin inhibitor 2 (CI2), we use genetic code reprogramming, combinatorial mutagenesis and mRNA display\u2010based in vitro selection to discover fluorinated mutant sequences with optimised inhibitory activity. Using microwave\u2010assisted solid\u2010phase peptide synthesis, we perform preparative chemical synthesis of 14 selected proteins, which contain up to eight fAAs\u2014or 19 fluorine atoms. All are nanomolar inhibitors of chymotrypsin; several hits are more active than the wildtype, and possess thermostabilities of up to 70\u00b0C. Crystal structures reveal that these proteins maintain native\u2010like folds, with fluorine atoms forming close and epistatically coupled packing contacts within the core. This work demonstrates how to generate functional protein sequences with multiple interacting npAAs, namely neoproteins, and thereby provides a framework for exploring the use of unnatural building blocks in protein design.<\/jats:p>","DOI":"10.1002\/anie.5293145","type":"journal-article","created":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T03:13:26Z","timestamp":1789528406000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["In Vitro Selection of Functional Neoproteins Containing Highly Fluorinated Cores"],"prefix":"10.1002","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1672-2756","authenticated-orcid":false,"given":"Adam","family":"Beattie","sequence":"first","affiliation":[{"name":"Department of Chemistry Graduate School of Science The University of Tokyo  Bunkyo\u2010ku Tokyo 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