{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T18:45:21Z","timestamp":1768502721055,"version":"3.49.0"},"posted":{"date-parts":[[2023,2,27]]},"group-title":"Synthetic Biology","reference-count":37,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,2,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Chemical control of protein activity is a powerful tool for scientific study, synthetic biology, and cell therapy; however, for broad use, effective chemical inducer systems must minimally crosstalk with endogenous processes and exhibit desirable drug delivery properties. Accordingly, the drug-controllable proteolytic activity of hepatitis C\n                  <jats:italic>cis-<\/jats:italic>\n                  protease NS3 and its associated antiviral drugs have been used to regulate protein activity and gene modulation. These tools advantageously exploit non-eukaryotic\/prokaryotic proteins and clinically approved inhibitors. Here we expand the toolkit by utilizing catalytically inactive NS3 protease as a high affinity binder to genetically encoded, antiviral peptides. Through our approach, we create NS3-peptide complexes that can be displaced by FDA-approved drugs to modulate transcription, cell signaling, split-protein complementation. With our developed system, we discover a new mechanism to allosterically regulate Cre recombinase. Allosteric Cre regulation with NS3 ligands enables orthogonal recombination tools in eukaryotic cells and functions in divergent organisms to control prokaryotic recombinase activity.\n                <\/jats:p>","DOI":"10.1101\/2023.02.27.530290","type":"posted-content","created":{"date-parts":[[2023,2,27]],"date-time":"2023-02-27T21:35:13Z","timestamp":1677533713000},"source":"Crossref","is-referenced-by-count":0,"title":["Controlled protein activities with viral proteases, antiviral peptides, and antiviral drugs"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7129-5913","authenticated-orcid":false,"given":"Elliot P.","family":"Tague","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeffrey B.","family":"McMahan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nathan","family":"Tague","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9261-8216","authenticated-orcid":false,"given":"Mary J.","family":"Dunlop","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3508-1915","authenticated-orcid":false,"given":"John T.","family":"Ngo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2023030803300732000_2023.02.27.530290v1.1","first-page":"1794","article-title":"Controlling signal transduction with synthetic ligands","volume":"262","year":"1993","journal-title":"Tanpakushitsu Kakusan Koso"},{"key":"2023030803300732000_2023.02.27.530290v1.2","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1080\/19336934.2016.1168552","article-title":"Regulated protein depletion by the auxin-inducible degradation system in Drosophila melanogaster","volume":"10","year":"2016","journal-title":"Fly (Austin)"},{"key":"2023030803300732000_2023.02.27.530290v1.3","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1038\/nchembio.2529","article-title":"Human antibody-based chemically induced dimerizers for cell therapeutic applications","volume":"14","year":"2018","journal-title":"Nat. Chem. Biol"},{"key":"2023030803300732000_2023.02.27.530290v1.4","doi-asserted-by":"publisher","DOI":"10.1126\/scisignal.2001902"},{"key":"2023030803300732000_2023.02.27.530290v1.5","doi-asserted-by":"publisher","DOI":"10.1038\/nchembio.922"},{"key":"2023030803300732000_2023.02.27.530290v1.6","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1928"},{"key":"2023030803300732000_2023.02.27.530290v1.7","doi-asserted-by":"crossref","unstructured":"Matsuda, T. & Cepko, C. L. Controlled expression of transgenes introduced by in vivo electroporation. PNAS 104, (2006).","DOI":"10.1073\/pnas.0610155104"},{"key":"2023030803300732000_2023.02.27.530290v1.8","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/s41592-018-0042-y","article-title":"Chemogenetic control of gene expression and cell signaling with antiviral drugs","volume":"15","year":"2018","journal-title":"Nat. Methods"},{"key":"2023030803300732000_2023.02.27.530290v1.9","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-018-0041-z"},{"key":"2023030803300732000_2023.02.27.530290v1.10","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg291"},{"key":"2023030803300732000_2023.02.27.530290v1.11","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M112.393843"},{"key":"2023030803300732000_2023.02.27.530290v1.12","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1038\/nmeth.4222","article-title":"Optogenetic control with a photocleavable protein, Phocl","volume":"14","year":"2017","journal-title":"Nat. Methods"},{"key":"2023030803300732000_2023.02.27.530290v1.13","first-page":"8","article-title":"A Chemically Disrupted Proximity System for Controlling Dynamic Cellular Processes","volume":"141","year":"2019","journal-title":"J. Am. Chem. Soc"},{"key":"2023030803300732000_2023.02.27.530290v1.14","doi-asserted-by":"crossref","first-page":"1209","DOI":"10.1038\/s41587-019-0242-8","article-title":"Multi-input chemical control of protein dimerization for programming graded cellular responses","volume":"37","year":"2019","journal-title":"Nat. Biotechnol"},{"key":"2023030803300732000_2023.02.27.530290v1.15","doi-asserted-by":"crossref","first-page":"1294","DOI":"10.1016\/j.ccell.2022.08.008","article-title":"High-performance multiplex drug-gated CAR circuits","volume":"40","year":"2022","journal-title":"Cancer Cell"},{"key":"2023030803300732000_2023.02.27.530290v1.16","doi-asserted-by":"crossref","first-page":"6208","DOI":"10.1128\/jvi.71.8.6208-6213.1997","article-title":"Probing the substrate specificity of hepatitis C virus NS3 serine protease by using synthetic peptides","volume":"71","year":"1997","journal-title":"J Virol"},{"key":"2023030803300732000_2023.02.27.530290v1.17","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0408824102"},{"key":"2023030803300732000_2023.02.27.530290v1.18","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0508531102"},{"key":"2023030803300732000_2023.02.27.530290v1.19","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1016\/j.jmb.2016.11.031","article-title":"Large-Scale Structure-Based Prediction and Identification of Novel Protease Substrates Using Computational Protein Design","volume":"429","year":"2017","journal-title":"J. Mol. Biol"},{"key":"2023030803300732000_2023.02.27.530290v1.20","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3312"},{"key":"2023030803300732000_2023.02.27.530290v1.21","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.01.012"},{"key":"2023030803300732000_2023.02.27.530290v1.22","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.01.011"},{"key":"2023030803300732000_2023.02.27.530290v1.23","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0404041101"},{"key":"2023030803300732000_2023.02.27.530290v1.24","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.50.3.899-909.2006"},{"key":"2023030803300732000_2023.02.27.530290v1.25","doi-asserted-by":"publisher","DOI":"10.1038\/nchembio.492"},{"key":"2023030803300732000_2023.02.27.530290v1.26","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-09078-0"},{"key":"2023030803300732000_2023.02.27.530290v1.27","doi-asserted-by":"publisher","DOI":"10.1021\/bi0272306"},{"key":"2023030803300732000_2023.02.27.530290v1.28","doi-asserted-by":"crossref","unstructured":"Serre, M. C. et al. The Carboxy-Terminal \u03b1N Helix of the Archaeal XerA Tyrosine Recombinase Is a Molecular Switch to Control Site-Specific Recombination. PLoS One 8, (2013).","DOI":"10.1371\/journal.pone.0063010"},{"key":"2023030803300732000_2023.02.27.530290v1.29","first-page":"202011448","article-title":"DNA binding induces a cis-to-trans switch in Cre recombinase to enable intasome assembly","volume":"117","year":"2020","journal-title":"Proc. Natl. Acad. Sci"},{"key":"2023030803300732000_2023.02.27.530290v1.30","doi-asserted-by":"publisher","DOI":"10.1038\/37925"},{"key":"2023030803300732000_2023.02.27.530290v1.31","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1998.2149"},{"key":"2023030803300732000_2023.02.27.530290v1.32","doi-asserted-by":"crossref","unstructured":"Eroshenko, N. & Church, G. M. Mutants of Cre recombinase with improved accuracy. Nat. Commun. 4, (2013).","DOI":"10.1038\/ncomms3509"},{"key":"2023030803300732000_2023.02.27.530290v1.33","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.62047"},{"key":"2023030803300732000_2023.02.27.530290v1.34","doi-asserted-by":"crossref","unstructured":"Dickinson, B. C. , Packer, M. S. , Badran, A. H. & Liu, D. R. A system for the continuous directed evolution of proteases rapidly reveals drug-resistance mutations. Nat. Commun. 5, (2014).","DOI":"10.1038\/ncomms6352"},{"key":"2023030803300732000_2023.02.27.530290v1.35","doi-asserted-by":"crossref","first-page":"15996","DOI":"10.1021\/jacs.5b10290","article-title":"A Panel of Protease-Responsive RNA Polymerases Respond to Biochemical Signals by Production of Defined RNA Outputs in Live Cells","volume":"137","year":"2015","journal-title":"J. Am. Chem. Soc"},{"key":"2023030803300732000_2023.02.27.530290v1.36","doi-asserted-by":"crossref","unstructured":"de Wispelaere, M. et al. Small molecule degraders of the hepatitis C virus protease reduce susceptibility to resistance mutations. Nat. Commun. 10, (2019).","DOI":"10.1038\/s41467-019-11429-w"},{"key":"2023030803300732000_2023.02.27.530290v1.37","first-page":"15","article-title":"BglBrick vectors and datasheets: A synthetic biology platform for gene expression","volume":"5","year":"2011","journal-title":"J. Biol. Eng"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2023.02.27.530290","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T04:19:19Z","timestamp":1768450759000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2023.02.27.530290"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,2,27]]},"references-count":37,"URL":"https:\/\/doi.org\/10.1101\/2023.02.27.530290","relation":{"is-preprint-of":[{"id-type":"doi","id":"10.1021\/acschembio.3c00138","asserted-by":"subject"}]},"subject":[],"published":{"date-parts":[[2023,2,27]]},"subtype":"preprint"}}