Rapid Assessment of Chemical Complementarity of Ligands for Protein Design

Rapid Assessment of Chemical Complementarity of Ligands for Protein Design | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Rapid Assessment of Chemical Complementarity of Ligands for Protein Design Derek Woolfson, Rokas Petrenas, Katarzyna Ożga, Joel Chubb, Andrey Romanyuk, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7592160/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Computational protein design is delivering de novo structures rapidly and reliably. This opens new frontiers for functional design, for instance, for binding small molecules tightly and specifically. However, achieving predictable and tuneable binding is challenging. Here we introduce a rapid physics-based method to generate isosteric and chemically complementary binding pockets for small-molecule targets in de novo proteins. We test this by constructing and characterizing binding proteins for several synthetic and natural chromophores. By evaluating only single-digit numbers of designs, the pipeline delivers stable proteins with pre-organised binding sites confirmed by X-ray crystallography, which bind the targets with micromolar affinities or better. To illustrate the scope and applications of this approach, we incorporate selective and coupled chromophore-binding sites in a two-domain de novo protein enabling controlled energy transfer between the two sites, and we develop a small de novo binding protein that can be used in live mammalian cells to visualise sub-cellular structures. Biological sciences/Chemical biology/Protein design Physical sciences/Chemistry/Chemical biology/Protein design Full Text Additional Declarations There is NO Competing Interest. Supplementary Files RASSCCoLNatureChemBiolDec2025SI.pdf RASSCCoL_NatureChemBiol_Dec2025_SI Cite Share Download PDF Status: Under Review Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7592160","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":557748104,"identity":"83a3cfc1-afcd-47b2-9cf6-7242ab4ab334","order_by":0,"name":"Derek 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