{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Tabular":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063557/wp-esf_566-8hr_esf4_diann_directdia_20240506.pr_matrix_upload.tsv"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063557/esf4_7781_RPG-01-139_8hr_Slot1-25_1_2599.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063557/esf4_7784_DGY-08-151_8hr_Slot1-28_1_2603.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063557/esf4_7778_DMSO_8hr_Slot1-22_1_2594.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063557/esf4_7782_RPG-01-139_8hr_Slot1-26_1_2600.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063557/esf4_7780_RPG-01-132_8hr_Slot1-24_1_2597.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063557/esf4_7777_DMSO_8hr_Slot1-21_1_2593.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063557/esf4_7775_DMSO_8hr_Slot1-19_1_2591.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063557/esf4_7783_DGY-08-151_8hr_Slot1-27_1_2602.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063557/esf4_7779_RPG-01-132_8hr_Slot1-23_1_2596.d.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063557/esf4_7776_DMSO_8hr_Slot1-20_1_2592.d.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["eric_fischer@dfci.harvard.edu"],"submitter":["Eric Fischer"],"technology_type":["Mass Spectrometry","Data-independent acquisition"],"software":[""],"submitter_keywords":["Virus","Chemical biology","Ubiquitin","Degrader","Dengue","Capsin","Protac","Crbn"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD063557"],"tissue":["Cell Culture"],"sample_protocol":["MOLT4 cells were treated with DMSO or 5 µM test compounds (RPG-01-132 or RPG-01-139) for 8 h. Cells were harvested by centrifugation and washed with phosphate buffered saline (PBS) before snap freezing in liquid nitrogen. Cells were lysed by addition of lysis buffer (8 M Urea, 50 mM NaCl, 50 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (EPPS) pH 8.5, Protease and Phosphatase inhibitors) and homogenization by bead beating (BioSpec) for three repeats of 30 seconds at 2400 strokes/min. Bradford assay was used to determine the final protein concentration in the clarified cell lysate. 50 µg of protein for each sample was reduced, alkylated and precipitated using methanol/chloroform as previously described [1] and the resulting washed precipitated protein was allowed to air dry. Precipitated protein was resuspended in 4 M urea, 50 mM HEPES pH 7.4, followed by dilution to 1 M urea with the addition of 200 mM EPPS, pH 8. Proteins were digested with the addition of LysC (1:50; enzyme:protein) and trypsin (1:50; enzyme:protein) for 12 h at 37 °C. Sample digests were acidified with formic acid to a pH of 2-3 before desalting using C18 solid phase extraction plates (SOLA, Thermo Fisher Scientific). Desalted peptides were dried in a vacuum-centrifuged and reconstituted in 0.1% formic acid for liquid chromatography-mass spectrometry analysis.  Data were collected using a TimsTOF Pro2 (Bruker Daltonics, Bremen, Germany) coupled to a nanoElute LC pump (Bruker Daltonics, Bremen, Germany) via a CaptiveSpray nano-electrospray source. Peptides were separated on a reversed-phase C18 column (25 cm x 75 µm ID, 1.6 µM, IonOpticks, Australia) containing an integrated captive spray emitter. Peptides were separated using a 50 min gradient of 2 - 30% buffer B (acetonitrile in 0.1% formic acid) with a flow rate of 250 nL/min and column temperature maintained at 50 ºC. Data were collected using a diaPASEF acquisition method where the precursor distribution in the DDA m/z-ion mobility plane was used to design an acquisition scheme for Data-independent acquisition (DIA) data collection which included two windows in each 50 ms diaPASEF scan. Data was acquired using sixteen of these 25 Da precursor double window scans (creating 32 windows) which covered the diagonal scan line for doubly and triply charged precursors, with singly charged precursors able to be excluded by their position in the m/z-ion mobility plane. These precursor isolation windows were defined between 400 - 1200 m/z and 1/k0 of 0.7 - 1.3 V.s/cm2."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["The diaPASEF raw file processing and controlling peptide and protein level false discovery rates, assembling proteins from peptides, and protein quantification from peptides were performed using library free analysis in DIA-NN 1.8 (Demichev et al., 2020) searched against a Swissprot human database (January 2021). Database search criteria largely followed the default settings for directDIA including: tryptic with two missed cleavages, carbamidomethylation of cysteine, and oxidation of methionine and precursor Q-value (FDR) cut-off of 0.01. Precursor quantification strategy was set to Robust LC (high accuracy) with RT-dependent cross run normalization. Proteins with low sum of abundance (<2,000 x no. of treatments) were excluded from further analysis and resulting data was filtered to only include proteins that had a minimum of 3 counts in at least 4 replicates of each independent comparison of treatment sample to the DMSO control. Proteins with missing values were imputed by random selection from a Gaussian distribution either with a mean of the non-missing values for that treatment group or with a mean equal to the median of the background (in cases when all values for a treatment group are missing) (Baek et al., 2024) using in-house scripts in the R framework (R Development Core Team, 2014). Significant changes comparing the relative protein abundance of these treatment to DMSO control comparisons were assessed by two-sided moderated t test as implemented in the limma package within the R framework (M.E. Ritchie et al., 2015, Nucleic Acids Res, 43(7):e47)."],"omics_type":["Proteomics"],"labhead":["Eric Fischer"],"instrument_platform":[""],"labhead_affiliation":["Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA., Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["eric_fischer@dfci.harvard.edu"],"publication":["41667458 Chakravarty A, Wang LN, Golden RP, Li Z, Donovan KA, Afanzar O, Zhang Y, Fischer ES, Gray NS, Yang PL. Degraders of the dengue virus capsid protein exhibit differentiated pharmacology relative to capsid inhibitors. Nat Commun. 2026 17(1):2594 10.1038/s41467-026-69263-w"],"submitter_affiliation":["Dana-Farber Cancer Institute"],"submitter_country":["United States"],"pubmed_abstract":["Due to the limited size of viral genomes, most viral proteins are multifunctional; yet most direct-acting antivirals are designed as single-function inhibitors. The dengue virus (DENV) capsid protein serves as a building block for new virions while also interacting with multiple host factors to remodel the cellular environment. Using established capsid inhibitor ST148 as a targeting ligand, we develop a DENV capsid degrader, RPG-01-132, that exhibits a broadened spectrum of activity against the four DENV serotypes and an ST148-resistant mutant virus. Using multiple approaches, we show that RPG-01-132's sub-micromolar antiviral activity is due to CRL4<sup>CRBN</sup>-dependent degradation of capsid and that this mechanism disrupts capsid-related pathways required for productive infection, including infectious virus output and capsid-mediated antagonism of the interferon response. This pharmacology is well-differentiated from ST148, which interferes with assembly of new virions, but has no demonstrated effect on the capsid's nonstructural functions. These findings demonstrate that targeted protein degradation can thus enable antiviral pharmacology not observed with conventional antiviral inhibitors and that is resilient to point mutations that reduce inhibitor potency."],"pubmed_title":["Degraders of the dengue virus capsid protein exhibit differentiated pharmacology relative to capsid inhibitors."],"pubmed_authors":["Chakravarty Antara A, Wang Lu-Ning LN, Golden Ryan P RP, Li Zhengnian Z, Donovan Katherine A KA, Afanzar Oshri O, Zhang Yupeng Y, Fischer Eric S ES, Gray Nathanael S NS, Yang Priscilla L PL"],"additional_accession":[]},"is_claimable":false,"name":"Degraders of the dengue virus capsid protein exhibit differentiated pharmacology relative to capsid inhibitors","description":"Due to the limited size of viral genomes, most viral proteins are multifunctional; yet most direct-acting antivirals are designed as single-function inhibitors. The dengue virus (DENV) capsid protein serves as a building block for new virions while also interacting with multiple host factors to remodel the cellular environment. Using established capsid inhibitor ST148 as a targeting ligand, we developed a DENV capsid degrader, RPG-01-132, that exhibits a broadened spectrum of activity against the four DENV serotypes and a known ST148-resistant virus. Using multiple approaches, we show that RPG-01-132's sub-micromolar antiviral activity is due to CRL4CRBN-dependent degradation of capsid and that this mechanism both prevents formation of virions and blocks capsid's antagonism of the interferon response. This pharmacology is well-differentiated from ST148, which prevents virion budding but has no demonstrated effect on capsid's nonstructural functions. Targeted protein degradation can thus enable improved activity spectrum and new antiviral pharmacology.","dates":{"publication":"2026-03-30","submission":"2025-05-02"},"accession":"PXD063557","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:3555","NEWT:241368","NEWT:2","NEWT:157546","NEWT:190802","NEWT:35554","NEWT:150475","NEWT:9417","NEWT:347515","NEWT:1216979","NEWT:307972","NEWT:544496","NEWT:5180","NEWT:256737","NEWT:115104","NEWT:1081927","NEWT:67825","NEWT:13076","NEWT:1249668","NEWT:317","NEWT:1736309","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:4081","NEWT:876138","NEWT:554","NEWT:98334","NEWT:237561","NEWT:10036","NEWT:7574","NEWT:1351","NEWT:7215","NEWT:272563","NEWT:507601","NCBITaxon:79857","NCBITaxon:6157","NEWT:95648","NEWT:746360","NEWT:6239","NEWT:1589","NEWT:470150","NEWT:135622","NEWT:216257","NEWT:6915","NEWT:9986","NEWT:101510","NEWT:4054","NEWT:3880","NEWT:8782","NEWT:1000589","NEWT:1902","NEWT:85962","NEWT:160488","NEWT:28104","NEWT:317447","NEWT:7955","NCBITaxon:2","NEWT:985076","NEWT:7959","NEWT:2261","NEWT:4565","NEWT:1264690","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:216595","NEWT:243230","NEWT:8355","NEWT:931281","NEWT:7029","NEWT:1283300","NEWT:334747","NCBITaxon:79824","NCBITaxon:4563","NEWT:5755","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:436486","NEWT:6287","NEWT:2242","NEWT:300641","NEWT:4784","NEWT:727","NEWT:9796","NEWT:725","NEWT:360106","NEWT:260707","NEWT:287","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1836","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:29760","NEWT:703612","NEWT:260705","NEWT:80863","NEWT:2697049","NEWT:1148","NEWT:11676","NEWT:55571","NEWT:100226","NCBITaxon:6073","NEWT:4530","NEWT:4896","NEWT:6279","NEWT:7370","NEWT:6282","NEWT:1134506","NEWT:575584","NEWT:1773","NEWT:38783","NEWT:8727","NEWT:1895","NEWT:1182590","NEWT:8726","NEWT:10090","NEWT:935293","NEWT:749200","NEWT:4120","NEWT:5693","NEWT:8724","NEWT:51511","NEWT:92867","NEWT:8723","NEWT:990346","NEWT:5334","NEWT:145953","NEWT:257309","NEWT:230741","NEWT:284812","NCBITaxon:10359","NCBITaxon:1313","NEWT:43330","NEWT:242619","NEWT:44544","NEWT:373995","NEWT:544404","NEWT:3702","NEWT:129249","NEWT:8839","NEWT:4232","NEWT:990119","NEWT:4113","NEWT:11298","NEWT:171101","NEWT:196627","NEWT:408172","NEWT:5691","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:627025","NEWT:400772","NEWT:1097677","NEWT:3708","NEWT:106592","NEWT:9913","NEWT:1432138","NEWT:10312","NEWT:4100","NEWT:1076","NEWT:6763","NEWT:803","NEWT:8030","NEWT:29722","NEWT:380394","NEWT:1692259","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:135588","NEWT:1843183","NEWT:95486","NEWT:58002","NEWT:9103","NEWT:4577","NEWT:5664","NEWT:2157","NEWT:146479","NEWT:10306","NEWT:1911079","NEWT:145943","NEWT:3635","NEWT:1480154","NEWT:235443","NEWT:1274414","NEWT:3197","NEWT:9615","NEWT:10299","NEWT:860688","NEWT:884019","NEWT:169963","NEWT:36329","NEWT:9606","NEWT:367830","NEWT:157295","NEWT:410289","NEWT:373153","NEWT:915099","NEWT:74940","NEWT:1450511","NEWT:470","NEWT:84023","NEWT:9838","NCBITaxon:9615","NEWT:1193501","NEWT:3055","NEWT:6326","NEWT:6689","NEWT:2762","NEWT:5476","NEWT:1174673","NEWT:562","NEWT:1274432","NEWT:1274426","NEWT:1423","NEWT:4932","NEWT:70448","NEWT:9825","NEWT:1274423","NEWT:3603","NEWT:698936","NEWT:2759","NEWT:3847","NEWT:39946","NEWT:9823","NEWT:9940","NEWT:573","NEWT:9031","NEWT:1274420","NEWT:7091"],"pubmed":["41667458"],"ORCID":["0000-0001-7337-6306"]}}