{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T20:02:45Z","timestamp":1784750565727,"version":"3.55.0"},"reference-count":46,"publisher":"Springer Science and Business Media LLC","issue":"2","license":[{"start":{"date-parts":[[2025,1,6]],"date-time":"2025-01-06T00:00:00Z","timestamp":1736121600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,1,6]],"date-time":"2025-01-06T00:00:00Z","timestamp":1736121600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000002","name":"HHS | National Institutes of Health","doi-asserted-by":"publisher","award":["1U19AI1711401"],"award-info":[{"award-number":["1U19AI1711401"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000861","name":"Burroughs Wellcome Fund","doi-asserted-by":"publisher","award":["1017195.01"],"award-info":[{"award-number":["1017195.01"]}],"id":[{"id":"10.13039\/100000861","id-type":"DOI","asserted-by":"publisher"}]},{"name":"jack ma foundation","award":["N\/A"],"award-info":[{"award-number":["N\/A"]}]},{"DOI":"10.13039\/100023581","name":"NSF | National Science Foundation Graduate Research Fellowship Program","doi-asserted-by":"publisher","award":["DGE-2038238"],"award-info":[{"award-number":["DGE-2038238"]}],"id":[{"id":"10.13039\/100023581","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Mol Syst Biol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>With current treatments addressing only a fraction of pathogens and new viral threats constantly evolving, there is a critical need to expand our existing therapeutic arsenal. To speed the rate of discovery and better prepare against future threats, we establish a high-throughput platform capable of screening compounds against 40 diverse viral proteases simultaneously. This multiplex approach is enabled by using cellular biosensors of viral protease activity combined with DNA-barcoding technology, as well as several design innovations that increase assay sensitivity and correct for plate-to-plate variation. Among &gt;100,000 compound-target interactions explored within our initial screen, a series of broad-acting inhibitors against coronavirus proteases were uncovered and validated through orthogonal assays. A medicinal chemistry campaign was performed to improve one of the inhibitor\u2019s potency while maintaining its broad activity. This work highlights the power of multiplex screening to efficiently explore chemical space at a fraction of the time and costs of previous approaches.<\/jats:p>","DOI":"10.1038\/s44320-024-00082-1","type":"journal-article","created":{"date-parts":[[2025,1,6]],"date-time":"2025-01-06T06:42:30Z","timestamp":1736145750000},"page":"158-172","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["A multiplex method for rapidly identifying viral protease inhibitors"],"prefix":"10.1038","volume":"21","author":[{"given":"Seo Jung","family":"Hong","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1224-2114","authenticated-orcid":false,"given":"Samuel J","family":"Resnick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3733-9556","authenticated-orcid":false,"given":"Sho","family":"Iketani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ji Won","family":"Cha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8989-077X","authenticated-orcid":false,"given":"Benjamin Alexander","family":"Albert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher T","family":"Fazekas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-0892-7419","authenticated-orcid":false,"given":"Ching-Wen","family":"Chang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hengrui","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shlomi","family":"Dagan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael R","family":"Abagyan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pavla","family":"Fajtov\u00e1","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bruce","family":"Culbertson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5009-6125","authenticated-orcid":false,"given":"Brooklyn","family":"Brace","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eswar R","family":"Reddem","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5571-7397","authenticated-orcid":false,"given":"Farhad","family":"Forouhar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6706-4039","authenticated-orcid":false,"given":"J Fraser","family":"Glickman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James M","family":"Balkovec","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3532-3868","authenticated-orcid":false,"given":"Brent R","family":"Stockwell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lawrence","family":"Shapiro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony J","family":"O\u2019Donoghue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yosef","family":"Sabo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joel S","family":"Freundlich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David D","family":"Ho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5626-7140","authenticated-orcid":false,"given":"Alejandro","family":"Chavez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,1,6]]},"reference":[{"key":"82_CR1","doi-asserted-by":"crossref","first-page":"3647","DOI":"10.1039\/D0CS01118E","volume":"50","author":"CS Adamson","year":"2021","unstructured":"Adamson CS, Chibale K, Goss RJM, Jaspars M, Newman DJ, Dorrington RA (2021) Antiviral drug discovery: preparing for the next pandemic. Chem Soc Rev 50:3647\u20133655","journal-title":"Chem Soc Rev"},{"key":"82_CR2","doi-asserted-by":"crossref","first-page":"939","DOI":"10.4155\/fmc-2019-0307","volume":"12","author":"N Berdigaliyev","year":"2020","unstructured":"Berdigaliyev N, Aljofan M (2020) An overview of drug discovery and development. Future Med Chem 12:939\u2013947","journal-title":"Future Med Chem"},{"key":"82_CR3","doi-asserted-by":"crossref","first-page":"F1000","DOI":"10.12688\/f1000research.7665.1","volume":"5","author":"W Blair","year":"2016","unstructured":"Blair W, Cox C (2016) Current landscape of antiviral drug discovery. F1000Res 5:F1000. Faculty Rev-202","journal-title":"F1000Res"},{"key":"82_CR4","doi-asserted-by":"crossref","first-page":"1445","DOI":"10.1016\/j.chembiol.2004.08.011","volume":"11","author":"JE Blanchard","year":"2004","unstructured":"Blanchard JE, Elowe NH, Huitema C, Fortin PD, Cechetto JD, Eltis LD, Brown ED (2004) High-throughput screening identifies inhibitors of the SARS coronavirus main proteinase. Chem Biol 11:1445\u20131453","journal-title":"Chem Biol"},{"key":"82_CR5","doi-asserted-by":"crossref","first-page":"1086","DOI":"10.1074\/jbc.M205636200","volume":"278","author":"R Blanco","year":"2003","unstructured":"Blanco R, Carrasco L, Ventoso I (2003) Cell killing by HIV-1 protease. J Biol Chem 278:1086\u20131093","journal-title":"J Biol Chem"},{"key":"82_CR6","doi-asserted-by":"crossref","first-page":"1369","DOI":"10.3390\/v14071369","volume":"14","author":"C-W Chang","year":"2022","unstructured":"Chang C-W, Parsi KM, Somasundaran M, Vanderleeden E, Liu P, Cruz J, Cousineau A, Finberg RW, Kurt-Jones EA (2022) A newly engineered A549 cell line expressing ACE2 and TMPRSS2 is highly permissive to SARS-CoV-2, including the delta and omicron variants. Viruses 14:1369","journal-title":"Viruses"},{"key":"82_CR7","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1038\/s41573-023-00692-8","volume":"22","author":"A von Delft","year":"2023","unstructured":"von Delft A, Hall MD, Kwong AD, Purcell LA, Saikatendu KS, Schmitz U, Tallarico JA, Lee AA (2023) Accelerating antiviral drug discovery: lessons from COVID-19. Nat Rev Drug Discov 22:585\u2013603","journal-title":"Nat Rev Drug Discov"},{"key":"82_CR8","doi-asserted-by":"crossref","first-page":"1232","DOI":"10.1016\/j.tim.2022.07.002","volume":"30","author":"D Forni","year":"2022","unstructured":"Forni D, Cagliani R, Clerici M, Sironi M (2022) Disease-causing human viruses: novelty and legacy. Trends Microbiol 30:1232\u20131242","journal-title":"Trends Microbiol"},{"key":"82_CR9","doi-asserted-by":"crossref","first-page":"e28479","DOI":"10.1371\/journal.pone.0028479","volume":"6","author":"M Frieman","year":"2011","unstructured":"Frieman M, Basu D, Matthews K, Taylor J, Jones G, Pickles R, Baric R, Engel DA (2011) Yeast based small molecule screen for inhibitors of SARS-CoV. PLoS ONE 6:e28479","journal-title":"PLoS ONE"},{"key":"82_CR10","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1038\/nprot.2007.13","volume":"2","author":"RD Gietz","year":"2007","unstructured":"Gietz RD, Schiestl RH (2007) High-efficiency yeast transformation using the LiAc\/SS carrier DNA\/PEG method. Nat Protoc 2:31\u201334","journal-title":"Nat Protoc"},{"key":"82_CR11","doi-asserted-by":"crossref","first-page":"770","DOI":"10.3389\/fphar.2020.00770","volume":"11","author":"IV Hinkson","year":"2020","unstructured":"Hinkson IV, Madej B, Stahlberg EA (2020) Accelerating therapeutics for opportunities in medicine: a paradigm shift in drug discovery. Front Pharmacol 11:770","journal-title":"Front Pharmacol"},{"key":"82_CR12","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1111\/j.1476-5381.2010.01127.x","volume":"162","author":"JP Hughes","year":"2011","unstructured":"Hughes JP, Rees S, Kalindjian SB, Philpott KL (2011) Principles of early drug discovery. Br J Pharmacol 162:1239\u20131249","journal-title":"Br J Pharmacol"},{"key":"82_CR13","volume":"12","author":"S Iketani","year":"2021","unstructured":"Iketani S, Forouhar F, Liu H, Hong SJ, Lin F-Y, Nair MS, Zask A, Huang Y, Xing L, Stockwell BR et al (2021) Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors. Nat Commun 12:2016","journal-title":"Nat Commun"},{"key":"82_CR14","doi-asserted-by":"crossref","first-page":"1354","DOI":"10.1016\/j.chom.2022.08.003","volume":"30","author":"S Iketani","year":"2022","unstructured":"Iketani S, Hong SJ, Sheng J, Bahari F, Culbertson B, Atanaki FF, Aditham AK, Kratz AF, Luck MI, Tian R et al (2022) Functional map of SARS-CoV-2 3CL protease reveals tolerant and immutable sites. Cell Host Microbe 30:1354\u20131362.e6","journal-title":"Cell Host Microbe"},{"key":"82_CR15","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1038\/s41586-020-2223-y","volume":"582","author":"Z Jin","year":"2020","unstructured":"Jin Z, Du X, Xu Y, Deng Y, Liu M, Zhao Y, Zhang B, Li X, Zhang L, Peng C et al (2020) Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors. Nature 582:289\u2013293","journal-title":"Nature"},{"key":"82_CR16","doi-asserted-by":"crossref","first-page":"968","DOI":"10.1038\/nature09627","volume":"468","author":"CM Johannessen","year":"2010","unstructured":"Johannessen CM, Boehm JS, Kim SY, Thomas SR, Wardwell L, Johnson LA, Emery CM, Stransky N, Cogdill AP, Barretina J et al (2010) COT drives resistance to RAF inhibition through MAP kinase pathway reactivation. Nature 468:968\u2013972","journal-title":"Nature"},{"key":"82_CR17","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1038\/nbt1358","volume":"26","author":"MW Karaman","year":"2008","unstructured":"Karaman MW, Herrgard S, Treiber DK, Gallant P, Atteridge CE, Campbell BT, Chan KW, Ciceri P, Davis MI, Edeen PT et al (2008) A quantitative analysis of kinase inhibitor selectivity. Nat Biotechnol 26:127\u2013132","journal-title":"Nat Biotechnol"},{"key":"82_CR18","doi-asserted-by":"crossref","first-page":"11754","DOI":"10.1128\/JVI.01348-12","volume":"86","author":"Y Kim","year":"2012","unstructured":"Kim Y, Lovell S, Tiew K-C, Mandadapu SR, Alliston KR, Battaile KP, Groutas WC, Chang K-O (2012) Broad-spectrum antivirals against 3C or 3C-like proteases of picornaviruses, noroviruses, and coronaviruses. J Virol 86:11754\u201311762","journal-title":"J Virol"},{"key":"82_CR19","volume":"15","author":"L-H Li","year":"2024","unstructured":"Li L-H, Chiu W, Huang Y-A, Rasulova M, Vercruysse T, Thibaut HJ, Ter Horst S, Rocha-Pereira J, Vanhoof G, Borrenberghs D et al (2024) Multiplexed multicolor antiviral assay amenable for high-throughput research. Nat Commun 15:42","journal-title":"Nat Commun"},{"key":"82_CR20","doi-asserted-by":"crossref","first-page":"2517","DOI":"10.1042\/BCJ20210244","volume":"478","author":"CT Lim","year":"2021","unstructured":"Lim CT, Tan KW, Wu M, Ulferts R, Armstrong LA, Ozono E, Drury LS, Milligan JC, Zeisner TU, Zeng J et al (2021) Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of Nsp3 papain-like protease. Biochem J 478:2517\u20132531","journal-title":"Biochem J"},{"key":"82_CR21","volume":"13","author":"H Liu","year":"2022","unstructured":"Liu H, Iketani S, Zask A, Khanizeman N, Bednarova E, Forouhar F, Fowler B, Hong SJ, Mohri H, Nair MS et al (2022) Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19. Nat Commun 13:1891","journal-title":"Nat Commun"},{"key":"82_CR22","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1021\/acscentsci.1c00519","volume":"7","author":"C Ma","year":"2021","unstructured":"Ma C, Sacco MD, Xia Z, Lambrinidis G, Townsend JA, Hu Y, Meng X, Szeto T, Ba M, Zhang X et al (2021) Discovery of SARS-CoV-2 papain-like protease inhibitors through a combination of high-throughput screening and a FlipGFP-based reporter assay. ACS Cent Sci 7:1245\u20131260","journal-title":"ACS Cent Sci"},{"key":"82_CR23","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1038\/nchembio.1938","volume":"11","author":"S M\u00fcller","year":"2015","unstructured":"M\u00fcller S, Chaikuad A, Gray NS, Knapp S (2015) The ins and outs of selective kinase inhibitor development. Nat Chem Biol 11:818\u2013821","journal-title":"Nat Chem Biol"},{"key":"82_CR24","unstructured":"NIAID Emerging Infectious Diseases\/Pathogens. NIAID: National Institute of Allergy and Infectious Diseases (2018)"},{"key":"82_CR25","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1042\/BJ20120509","volume":"447","author":"M Ogura","year":"2012","unstructured":"Ogura M, Yamaki J, Homma MK, Homma Y (2012) Mitochondrial c-Src regulates cell survival through phosphorylation of respiratory chain components. Biochem J 447:281\u2013289","journal-title":"Biochem J"},{"key":"82_CR26","doi-asserted-by":"crossref","first-page":"982","DOI":"10.1038\/nchembio.2436","volume":"13","author":"JS Piotrowski","year":"2017","unstructured":"Piotrowski JS, Li SC, Deshpande R, Simpkins SW, Nelson J, Yashiroda Y, Barber JM, Safizadeh H, Wilson E, Okada H et al (2017) Functional annotation of chemical libraries across diverse biological processes. Nat Chem Biol 13:982\u2013993","journal-title":"Nat Chem Biol"},{"key":"82_CR27","doi-asserted-by":"crossref","first-page":"16119","DOI":"10.1073\/pnas.0805240105","volume":"105","author":"K Ratia","year":"2008","unstructured":"Ratia K, Pegan S, Takayama J, Sleeman K, Coughlin M, Baliji S, Chaudhuri R, Fu W, Prabhakar BS, Johnson ME et al (2008) A noncovalent class of papain-like protease\/deubiquitinase inhibitors blocks SARS virus replication. Proc Natl Acad Sci USA 105:16119\u201316124","journal-title":"Proc Natl Acad Sci USA"},{"key":"82_CR28","doi-asserted-by":"publisher","unstructured":"Resnick SJ, Qamar S, Sheng J, Huang LH, Nixon-Abell J, Melore S, Chung CW, Li X, Wang J, Zhang N et al (2022) A multiplex platform to identify mechanisms and modulators of proteotoxicity in neurodegeneration. Preprint at bioRxiv 2022.09.19.508444 https:\/\/doi.org\/10.1101\/2022.09.19.508444","DOI":"10.1101\/2022.09.19.508444"},{"key":"82_CR29","doi-asserted-by":"crossref","DOI":"10.1038\/srep01046","volume":"3","author":"S van Rijn","year":"2013","unstructured":"van Rijn S, Nilsson J, Noske DP, Vandertop WP, Tannous BA, W\u00fcrdinger T (2013) Functional multiplex reporter assay using tagged Gaussia luciferase. Sci Rep 3:1046","journal-title":"Sci Rep"},{"key":"82_CR30","doi-asserted-by":"crossref","first-page":"e0004589","DOI":"10.1371\/journal.pntd.0004589","volume":"10","author":"PK Russell","year":"2016","unstructured":"Russell PK (2016) The Zika pandemic - a perfect storm? PLoS Negl Trop Dis 10:e0004589","journal-title":"PLoS Negl Trop Dis"},{"key":"82_CR31","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-019-13651-y","volume":"10","author":"A Sarrion-Perdigones","year":"2019","unstructured":"Sarrion-Perdigones A, Chang L, Gonzalez Y, Gallego-Flores T, Young DW, Venken KJT (2019) Examining multiple cellular pathways at once using multiplex hextuple luciferase assaying. Nat Commun 10:5710","journal-title":"Nat Commun"},{"key":"82_CR32","doi-asserted-by":"crossref","first-page":"945","DOI":"10.15252\/msb.20177834","volume":"13","author":"B Schmierer","year":"2017","unstructured":"Schmierer B, Botla SK, Zhang J, Turunen M, Kivioja T, Taipale J (2017) CRISPR\/Cas9 screening using unique molecular identifiers. Mol Syst Biol 13:945","journal-title":"Mol Syst Biol"},{"key":"82_CR33","doi-asserted-by":"crossref","first-page":"2396","DOI":"10.1016\/j.celrep.2017.08.040","volume":"20","author":"FEM Scholte","year":"2017","unstructured":"Scholte FEM, Zivcec M, Dzimianski JV, Deaton MK, Spengler JR, Welch SR, Nichol ST, Pegan SD, Spiropoulou CF, Bergeron \u00c9 (2017) Crimean-Congo hemorrhagic fever virus suppresses innate immune responses via a ubiquitin and ISG15 specific protease. Cell Rep 20:2396\u20132407","journal-title":"Cell Rep"},{"key":"82_CR34","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1038\/s41586-020-2601-5","volume":"587","author":"D Shin","year":"2020","unstructured":"Shin D, Mukherjee R, Grewe D, Bojkova D, Baek K, Bhattacharya A, Schulz L, Widera M, Mehdipour AR, Tascher G et al (2020) Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature 587:657\u2013662","journal-title":"Nature"},{"key":"82_CR35","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/s41579-020-00468-6","volume":"19","author":"P V\u2019kovski","year":"2021","unstructured":"V\u2019kovski P, Kratzel A, Steiner S, Stalder H, Thiel V (2021) Coronavirus biology and replication: implications for SARS-CoV-2. Nat Rev Microbiol 19:155\u2013170","journal-title":"Nat Rev Microbiol"},{"key":"82_CR36","volume":"236","author":"L Wang","year":"2022","unstructured":"Wang L, Liu M, Zu Y, Yao H, Wu C, Zhang R, Ma W, Lu H, Xi S, Liu Y et al (2022) Optimization of NAMPT activators to achieve in vivo neuroprotective efficacy. Eur J Med Chem 236:114260","journal-title":"Eur J Med Chem"},{"key":"82_CR37","doi-asserted-by":"crossref","first-page":"2864","DOI":"10.1098\/rstb.2011.0354","volume":"367","author":"M Woolhouse","year":"2012","unstructured":"Woolhouse M, Scott F, Hudson Z, Howey R, Chase-Topping M (2012) Human viruses: discovery and emergence. Philos Trans R Soc Lond B Biol Sci 367:2864\u20132871","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"82_CR38","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/s41586-020-2008-3","volume":"579","author":"F Wu","year":"2020","unstructured":"Wu F, Zhao S, Yu B, Chen Y-M, Wang W, Song Z-G, Hu Y, Tao Z-W, Tian J-H, Pei Y-Y et al (2020) A new coronavirus associated with human respiratory disease in China. Nature 579:265\u2013269","journal-title":"Nature"},{"key":"82_CR39","first-page":"e02168","volume":"11","author":"C Ye","year":"2020","unstructured":"Ye C, Chiem K, Park J-G, Oladunni F, Platt RN, Anderson T, Almazan F, de la Torre JC, Martinez-Sobrido L (2020) Rescue of SARS-CoV-2 from a single bacterial artificial chromosome. mBio 11:e02168\u201320","journal-title":"mBio"},{"key":"82_CR40","doi-asserted-by":"crossref","first-page":"jcs253237","DOI":"10.1242\/jcs.253237","volume":"134","author":"J Yi","year":"2021","unstructured":"Yi J, Peng J, Yang W, Zhu G, Ren J, Li D, Zheng H (2021) Picornavirus 3C - a protease ensuring virus replication and subverting host responses. J Cell Sci 134:jcs253237","journal-title":"J Cell Sci"},{"key":"82_CR41","first-page":"17","volume":"14","author":"Y Zang","year":"2023","unstructured":"Zang Y, Su M, Wang Q, Cheng X, Zhang W, Zhao Y, Chen T, Jiang Y, Shen Q, Du J et al (2023) High-throughput screening of SARS-CoV-2 main and papain-like protease inhibitors. Protein Cell 14:17\u201327","journal-title":"Protein Cell"},{"key":"82_CR42","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1016\/bs.enz.2021.09.004","volume":"50","author":"J Zephyr","year":"2021","unstructured":"Zephyr J, Kurt Yilmaz N, Schiffer CA (2021) Viral proteases: structure, mechanism and inhibition. Enzymes 50:301\u2013333","journal-title":"Enzymes"},{"key":"82_CR43","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1177\/108705719900400206","volume":"4","author":"JH Zhang","year":"1999","unstructured":"Zhang JH, Chung TD, Oldenburg KR (1999) A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J Biomol Screen 4:67\u201373","journal-title":"J Biomol Screen"},{"key":"82_CR44","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1038\/s41586-020-2012-7","volume":"579","author":"P Zhou","year":"2020","unstructured":"Zhou P, Yang X-L, Wang X-G, Hu B, Zhang L, Zhang W, Si H-R, Zhu Y, Li B, Huang C-L et al (2020) A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579:270\u2013273","journal-title":"Nature"},{"key":"82_CR45","volume":"20","author":"S Zhu","year":"2019","unstructured":"Zhu S, Cao Z, Liu Z, He Y, Wang Y, Yuan P, Li W, Tian F, Bao Y, Wei W (2019) Guide RNAs with embedded barcodes boost CRISPR-pooled screens. Genome Biol 20:20","journal-title":"Genome Biol"},{"key":"82_CR46","doi-asserted-by":"crossref","first-page":"1008","DOI":"10.1021\/acsptsci.0c00108","volume":"3","author":"W Zhu","year":"2020","unstructured":"Zhu W, Xu M, Chen CZ, Guo H, Shen M, Hu X, Shinn P, Klumpp-Thomas C, Michael SG, Zheng W (2020) Identification of SARS-CoV-2 3CL protease inhibitors by a quantitative high-throughput screening. ACS Pharmacol Transl Sci 3:1008\u20131016","journal-title":"ACS Pharmacol Transl Sci"}],"container-title":["Molecular Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1038\/s44320-024-00082-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1038\/s44320-024-00082-1","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1038\/s44320-024-00082-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,17]],"date-time":"2026-05-17T23:48:00Z","timestamp":1779061680000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1038\/s44320-024-00082-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,6]]},"references-count":46,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2025,2,3]]}},"alternative-id":["82"],"URL":"https:\/\/doi.org\/10.1038\/s44320-024-00082-1","relation":{},"ISSN":["1744-4292"],"issn-type":[{"value":"1744-4292","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,1,6]]},"assertion":[{"value":"12 May 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 November 2024","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 December 2024","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 January 2025","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"AC, SJH, and SJR have submitted a patent related to the design and implementation of multiplex small molecule screens. BRS is an inventor on patents and patent applications involving small molecules, holds equity in and serves as a consultant to Exarta Therapeutics and ProJenX Inc., holds equity in Sonata Therapeutics, and serves as a consultant to Weatherwax Biotechnologies Corporation and Akin Gump Strauss Hauer & Feld LLP.\u00a0DDH\u00a0is a co-founder of TaiMed Biologics and RenBio, consultant to WuXi Biologics, Brii Biosciences, Apexigen, and Veru Inc., and board director for Vicarious Surgical.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Disclosure and competing interests statement"}}]}}