Chemical Proteomics

NUDT5 regulates the global efficacy of nucleoside analog drugs by coordinating purine synthesis and PRPP allocation

Valerie NCK, Alam S, Hormann FM, ..., Arvidsson PI, Altun M

- - (-) - [2025-11-20; online 2025-11-20]

A generative deep learning approach to de novo antibiotic design.

Krishnan A, Anahtar MN, Valeri JA, ..., Wong F, Collins JJ

Cell 188 (21) 5962-5979.e22 [2025-10-16; online 2025-08-14]

Toward a Species Search Engine: KISSE Offers a Rigorous Statistical Framework for Bone Collagen Tandem Mass Spectrometry Data.

Gharibi H, Saei AA, Chernobrovkin AL, ..., Gaetani M, Zubarev RA

Adv Sci (Weinh) 12 (40) e03963 [2025-10-00; online 2025-08-11]

Proteome integral solubility alteration assay for monitoring antibody-antigen cell interactions

Lu W, Lundstrom SL, Hou Y, ..., Gaetani M, Zubarev RA

- - (-) - [2025-09-06; online 2025-09-06]

Diverse oncogenes use common mechanisms to drive growth of major forms of human cancer.

Kauko O, Turunen M, Pihlajamaa P, ..., Hautaniemi S, Taipale J

Sci Adv 11 (34) eadt1798 [2025-08-22; online 2025-08-20]

Thioredoxin Reductase 1 inhibition triggers ferroptosis in KRAS-independent lung cancers.

Andreani C, Bartolacci C, Melegari M, ..., Galassi R, Scaglioni PP

bioRxiv - (-) - [2025-07-30; online 2025-07-30]

Identification of a small molecule targeting EPLIN as a novel strategy for the treatment of pediatric neuroblastoma and medulloblastoma.

Lindell E, Guo J, Zhao M, ..., Sjöblom T, Zhang X

Cell Death Dis 16 (1) 554 [2025-07-23; online 2025-07-23]

Chemical Proteomics [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

High-ratiO partiaL proteolysiS with carriER proteome (HOLSER) Enables Global Structure Profiling and Site-resolved Elucidation of Ligand–Protein Interactions

Zhang X, Sokolova B, Meng Z, ..., Gaetani M, Zubarev RA

- - (-) - [2025-07-15; online 2025-07-15]

A cell-based degrader assessment platform facilitates discovery of functional NUDT5 PROTACs

Alam S, Pires MJ, Tidestav G, ..., Valerie NCK, Altun M

- - (-) - [2025-06-19; online 2025-06-19]

Above-Filter Digestion Proteomics reveals drug targets and localizes ligand binding site

Sokolova B, Gharibi H, Jafari M, ..., Saei AA, Zubarev R

- - (-) - [2025-03-13; online 2025-03-13]

Year 2024

One-Pot Time-Induced Proteome Integral Solubility Alteration Assay for Automated and Sensitive Drug-Target Identification.

Meng Z, Saei AA, Lyu H, Gaetani M, Zubarev RA

Anal. Chem. - (-) - [2024-11-20; online 2024-11-20]

Merging multi-omics with proteome integral solubility alteration unveils antibiotic mode of action.

Maity R, Zhang X, Liberati FR, ..., Aínsa JA, Sancho J

Elife 13 (-) - [2024-09-27; online 2024-09-27]

Gel-Assisted Proteome Position Integral Shift Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Caspase 3 Substrates.

Meng Z, Saei AA, Gharibi H, ..., Gaetani M, Zubarev RA

Anal. Chem. 96 (33) 13533-13541 [2024-08-20; online 2024-08-07]

Multifaceted Proteome Analysis at Solubility, Redox, and Expression Dimensions for Target Identification.

Saei AA, Lundin A, Lyu H, ..., Gygi SP, Zubarev RA

Adv Sci (Weinh) - (-) e2401502 [2024-08-09; online 2024-08-09]

A chemical inhibitor of IST1-CHMP1B interaction impairs endosomal recycling and induces noncanonical LC3 lipidation.

Knyazeva A, Li S, Corkery DP, ..., Waldmann H, Wu YW

Proc. Natl. Acad. Sci. U.S.A. 121 (17) e2317680121 [2024-04-23; online 2024-04-18]

Chemical Proteomics [Collaborative] Cryo-EM [Service]

Dual molecule targeting HDAC6 leads to intratumoral CD4+ cytotoxic lymphocytes recruitment through MHC-II upregulation on lung cancer cells.

Ducellier S, Demeules M, Letribot B, ..., Nascimento M, Apcher S

J Immunother Cancer 12 (4) - [2024-04-11; online 2024-04-11]

Ultralight Ultrafast Enzymes.

Zhang X, Meng Z, Beusch CM, ..., Gaetani M, Zubarev RA

Angew. Chem. Int. Ed. Engl. 63 (3) e202316488 [2024-01-15; online 2023-12-07]

Distinct molecular targets of ProEGCG from EGCG and superior inhibition of angiogenesis signaling pathways for treatment of endometriosis.

Hung SW, Gaetani M, Li Y, ..., Zubarev RA, Wang CC

J Pharm Anal 14 (1) 100-114 [2024-01-00; online 2023-09-11]

Year 2023

Chemogenetic inhibition of IST1-CHMP1B interaction impairs endosomal recycling and promotes unconventional LC3 lipidation at stalled endosomes

Knyazeva A, Li S, Corkery DP, ..., Waldmann H, Wu YW

- - (-) - [2023-08-28; online 2023-08-28]

Proteome integral solubility alteration high-throughput proteomics assay identifies Collectin-12 as a non-apoptotic microglial caspase-3 substrate.

Grabert K, Engskog-Vlachos P, Škandík M, ..., Joseph B, Cheray M

Cell Death Dis 14 (3) 192 [2023-03-11; online 2023-03-11]

NCF1-dependent production of ROS protects against lupus by regulating plasmacytoid dendritic cell development and functions.

Luo H, Urbonaviciute V, Saei AA, ..., Zubarev RA, Holmdahl R

JCI Insight - (-) - [2023-02-28; online 2023-02-28]

Year 2022

DAR 16-II Primes Endothelial Cells for Angiogenesis Improving Bone Ingrowth in 3D-Printed BCP Scaffolds and Regeneration of Critically Sized Bone Defects.

Alfayez E, Veschini L, Dettin M, ..., Coward T, Di Silvio L

Biomolecules 12 (11) 1619 [2022-11-02; online 2022-11-02]

Proteomics-Compatible Fourier Transform Isotopic Ratio Mass Spectrometry of Polypeptides.

Gharibi H, Chernobrovkin AL, Saei AA, ..., Makarov AA, Zubarev RA

Anal. Chem. 94 (43) 15048-15056 [2022-11-01; online 2022-10-17]

Proteome Integral Solubility Alteration (PISA) for High-Throughput Ligand Target Deconvolution with Increased Statistical Significance and Reduced Sample Amount.

Gaetani M, Zubarev RA

Methods Mol. Biol. 2554 (-) 91-106 [2022-10-01; online 2022-10-01]

Mapping the GALNT1 substrate landscape with versatile proteomics tools

Saei AA, Lundström SL, Lyu H, ..., Gygi SP, Zubarev RA

- - (-) - [2022-08-24; online 2022-08-24]

Ultrafast and selective labeling of endogenous proteins using affinity-based benzotriazole chemistry.

Xin X, Zhang Y, Gaetani M, ..., Corkery DP, Wu Y

Chem. Sci. 13 (24) 7240-7246 [2022-06-22; online 2022-05-30] Open Access

Hepatocyte Thorns, A Novel Drug-Induced Stress Response in Human and Mouse Liver Spheroids.

Pridgeon CS, Bolhuis DP, Milosavljević F, ..., Jukić MM, Ingelman-Sundberg M

Cells 11 (10) - [2022-05-10; online 2022-05-10]

The antimicrobial drug pyrimethamine inhibits STAT3 transcriptional activity by targeting the enzyme dihydrofolate reductase.

Heppler LN, Attarha S, Persaud R, ..., Page BDG, Frank DA

J. Biol. Chem. 298 (2) 101531 [2022-02-00; online 2021-12-23] Open Access

Proteome Integral Solubility Alteration (PISA) Assay in Mammalian Cells for Deep, High-Confidence, and High-Throughput Target Deconvolution

Zhang X, Lytovchenko O, Lundström S, Zubarev R, Gaetani M

BIO-PROTOCOL 12 (22) - [2022-00-00; online 2022-00-00]

Proteome Integral Solubility Alteration (PISA) for High-Throughput Ligand Target Deconvolution with Increased Statistical Significance and Reduced Sample Amount (Book chapter)

Year 2021

Gaetani_M_and_Zubarev_RA

Methods in Molecular Biology in press (-) - [2021-12-09]

An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation.

Sabatier P, Beusch CM, Saei AA, ..., Rodin S, Zubarev RA

Nat Commun 12 (1) 6558 [2021-11-12; online 2021-11-12] Open Access

System-wide identification and prioritization of enzyme substrates by thermal analysis.

Saei AA, Beusch CM, Sabatier P, ..., Schüler H, Zubarev RA

Nat Commun 12 (1) 1296 [2021-02-26; online 2021-02-26] Open Access

Year 2020

Capillary leakage provides nutrients and antioxidants for rapid pneumococcal proliferation in influenza-infected lower airways.

Sender V, Hentrich K, Pathak A, ..., Normark S, Henriques-Normark B

Proc. Natl. Acad. Sci. U.S.A. 117 (49) 31386-31397 [2020-12-08; online 2020-11-23]

Bioinformatics Support for Computational Resources [Service] Chemical Proteomics [Collaborative]

Lysine-specific demethylase 1A restricts ex vivo propagation of human HSCs and is a target of UM171.

Subramaniam A, Žemaitis K, Talkhoncheh MS, ..., Zubarev RA, Larsson J

Blood 136 (19) 2151-2161 [2020-11-05; online 2020-06-26]

Bioinformatics Support for Computational Resources [Service] Chemical Proteomics [Collaborative]

Thermal Proteome Profiling Identifies Oxidative-Dependent Inhibition of the Transcription of Major Oncogenes as a New Therapeutic Mechanism for Select Anticancer Compounds.

Peuget S, Zhu J, Sanz G, ..., Zubarev R, Selivanova G

Cancer Res. 80 (7) 1538-1550 [2020-04-01; online 2020-02-04]

Year 2019

ProTargetMiner as a proteome signature library of anticancer molecules for functional discovery

Saei AA, Beusch CM, Chernobrovkin A, ..., Végvári Á, Zubarev RA

Nat Commun 10 (1) 5715 [2019-12-00; online 2019-12-16]

Proteome Integral Solubility Alteration: A High-Throughput Proteomics Assay for Target Deconvolution.

Gaetani M, Sabatier P, Saei AA, ..., Lundström SL, Zubarev RA

J. Proteome Res. 18 (11) 4027-4037 [2019-11-01; online 2019-10-14]

Functional Identification of Target by Expression Proteomics (FITExP)

Gaetani M, Zubarev RA

- - (-) 257-266 [2019-08-13; online 2019-07-26]

SpotLight Proteomics-A IgG-Enrichment Phenotype Profiling Approach with Clinical Implications.

Lundström SL, Heyder T, Wiklundh E, ..., Grunewald J, Zubarev RA

Int J Mol Sci 20 (9) 2157 [2019-05-01; online 2019-05-01]

Year 2018

Small-molecule inhibitor of OGG1 suppresses proinflammatory gene expression and inflammation.

Visnes T, Cázares-Körner A, Hao W, ..., Boldogh I, Helleday T

Science 362 (6416) 834-839 [2018-11-16; online 2018-11-18]

Bioinformatics Support for Computational Resources [Service] Chemical Biology Consortium Sweden [Collaborative] Chemical Proteomics [Collaborative] Drug Discovery and Development [Service] Protein Science Facility (PSF) [Service]

STAT3 differential scanning fluorimetry and differential scanning light scattering assays: Addressing a missing link in the characterization of STAT3 inhibitor interactions.

Desroses M, Busker S, Astorga-Wells J, ..., Grandér D, Page BDG

Journal of Pharmaceutical and Biomedical Analysis 160 (-) 80-88 [2018-10-25; online 2018-07-17]

Chemical Proteomics [Collaborative] Protein Science Facility (PSF) [Service]

Year 2017

New Promises of Chemical Proteomics for Drug Development

Gaetani M, Zubarev RA

Novel Approaches in Drug Designing & Development 2 (1) 555579 [2017-06-27]

SpotLight Proteomics: uncovering the hidden blood proteome improves diagnostic power of proteomics.

Lundström SL, Zhang B, Rutishauser D, Aarsland D, Zubarev RA

Sci Rep 7 (-) 41929 [2017-02-07; online 2017-02-07]

Year 2016

Human IgM Antibodies to Malondialdehyde Conjugated With Albumin Are Negatively Associated With Cardiovascular Disease Among 60-Year-Olds.

Thiagarajan D, Frostegård AG, Singh S, ..., Lundström SL, Frostegård J

J Am Heart Assoc 5 (12) - [2016-12-20; online 2016-12-20]

Validation and development of MTH1 inhibitors for treatment of cancer.

Warpman Berglund U, Sanjiv K, Gad H, ..., Scobie M, Helleday T

Ann. Oncol. 27 (12) 2275-2283 [2016-12-00; online 2016-11-08]

Advanced Mass Spectrometry Proteomics [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Chemical Biology Consortium Sweden [Collaborative] Chemical Proteomics [Service] Clinical Proteomics Mass spectrometry [Collaborative] Drug Discovery and Development [Collaborative]

Application of amide hydrogen/deuterium exchange mass spectrometry for epitope mapping in human cystatin C.

Prądzińska M, Behrendt I, Astorga-Wells J, ..., Rodziewicz-Motowidło S, Czaplewska P

Amino Acids 48 (12) 2809-2820 [2016-12-00; online 2016-08-29]

Advanced Mass Spectrometry Proteomics [Collaborative] Chemical Proteomics [Collaborative]

Functional and Structural Characterization of a Novel HLA-DRB1*04:01-Restricted α-Enolase T Cell Epitope in Rheumatoid Arthritis.

Gerstner C, Dubnovitsky A, Sandin C, ..., Achour A, Malmström V

Front Immunol 7 (-) 494 [2016-11-14; online 2016-11-14]

Chemical Proteomics [Service]

Isolation and characterization of autoantibodies against human cystatin C.

Prądzińska M, Behrendt I, Spodzieja M, ..., Macur K, Czaplewska P

Amino Acids 48 (11) 2501-2518 [2016-11-00; online 2016-06-08]

Advanced Mass Spectrometry Proteomics [Collaborative] Chemical Proteomics [Collaborative]

Establishing a Proteomics-Based Monocyte Assay To Assess Differential Innate Immune Activation Responses.

Tarasova NK, Ytterberg AJ, Lundberg K, ..., Harris RA, Zubarev RA

J. Proteome Res. 15 (7) 2337-2345 [2016-07-01; online 2016-06-03]

Advanced Mass Spectrometry Proteomics [Collaborative] Chemical Proteomics [Technology development]

DeMix-Q: Quantification-Centered Data Processing Workflow.

Zhang B, Käll L, Zubarev RA

Mol. Cell Proteomics 15 (4) 1467-1478 [2016-04-00; online 2016-01-04]

Year 2015