EUbOPEN: Enabling and Unlocking biology in the OPEN

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

300 proteins purified in year 1

1,500 proteins purified at a rate of approximately 300 per year (reported at M12, M36, M60). Expression constructs and proteins will be produced by UOXF, GUF, KI, UNIVDUN, LUMC, with contributions from EFPIA and Associated Partners where applicable.

Applied to ≥2 new chemical series in year 3

First version of platform for automated compound synthesis applied to 2 new scaffoldsyear M36 M60

Additional ten PCAs established and/or optimised (20 in total)

Ten PCAs established and/or optimised (20 in total, 10 by month 24 and additional 10 by month 48).

Family wide screening platform for kinases using NanoBRET or ABPP technology

Family wide screening platform for kinases and one new family using NanoBRET or ABPP technology M24 M60

40 CRISPR knockout cell lines in year 1

40 CRISPR knockout cell lines per year (total 160) (M12, M36, M48).

First set of community engagement events or symposium held

Community engagement events and symposia held

Deposit intermediate set of data in sustainable resources
Evaluation of Raman assays and establishment of protocols in cell culture and patient-derived tissues

Evaluation of Raman assays and establishment of protocols in cell culture and patient-derived tissues.

Data for initial CG set released

Data for each Chemogenomic set release in EUbOPEN gateway Zenodo

50 targets enabled with in vitro assays and 30 targets with cellular assays

D5.1 250 targets enabled with assays for chemical probe discovery and optimisation at a rate of approximately 50 per year and 150 targets enabled with an in-cell target engagement assay at a rate of about 30 per year (M12, M36, M60).

EUbOPEN database gateway development

EUbOPEN database gateway specification and further development

Acquisition of > 500 compounds for CGL covering >250 targets

Acquisition of CG compounds (500 compounds/year) from commercial sources, academic partners and EFPIA.

EUbOPEN database gateway specification

EUbOPEN database gateway specification and further development.

Guiding principles for global network with similar organisations

Guiding principles for global network with similar organisations.

Five aggregated, anonymized and quality assured screening data sets released to the public

Five aggregated anonymized and quality assured screening data sets released to the public on annual basis through project website and other dissemination channels

20 recombinant antibodies or binders in year 2 and 3

50 recombinant antibodies or other binders at a rate of about 10 per year reported at M12 M36 M60 Binders will be generated by KI and ReSOLUTE with donations from Pharma partners

100 protein structures in year 1

100 protein structures in year 1.

Standardized chip design and processing established

Standardized chip design and processing established.

20 CP in year 1

20 EUbOPEN-generated CPs in year 1, including EFPIA contributions and jointly generated CPs as well as contributions from other scientists outside EUbOPEN.

First version of platform for automated compound synthesis

First version of platform for automated compound synthesis M24

Additional five aggregated, anonymized and quality assured screening data sets released to the public

Five aggregated anonymized and quality assured screening data sets released to the public on annual basis through project website and other dissemination channels

First EUbOPEN website review and development

EUbOPEN website development with regular reviews and updates

Update on web-based internal database system development

Webbased internal database system implementation and development

Intermediate release of curated CG compound profiling data

Release of curated CGL profiling data

First review of data ontology

Data ontology defined by working group and regularly reviewed

Acquisition of > 2,000 compounds for CGL covering >750 new targets

Acquisition of CG compounds (500 compounds/year) from commercial sources, academic partners and EFPIA.

Web-based internal database system initial implementation

Web-based internal database system implementation and development.

LiP-MS or BioID datasets of ≥10 probe-cell interactions

LiPMS datasets of 5 probecell interactionsyear M36 M60

Agreed quality control criteria approved by JMC

Agreed quality control criteria approved by JMC.

Ten PCAs established and/or optimised (20 in total)

Ten PCAs established andor optimised 20 in total 10 by month 24 and additional 10 by month 48

>1500 novel CG compounds sourced

At least 1500 CG compounds sourced or synthesised .

600 proteins purified in year 2 and 3

1500 proteins purified at a rate of approximately 300 per year reported at M12 M36 M60 Expression constructs and proteins will be produced by UOXF GUF KI UNIVDUN LUMC with contributions from EFPIA and Associated Partners where applicable

Data ontology defined by working group

Data ontology defined by working group.

A total of fifteen aggregated, anonymized and quality assured screening data sets released to the public

Five aggregated, anonymized and quality assured screening data sets released to the public on annual basis through project website and other dissemination channels.

40 CP in year 2 and 3

40 EUbOPENgenerated CPs in year 2 and 3 to a total of 60 CPs The CPs will include EFPIA contributions and jointly generated CPs as well as contributions from other scientists outside EUbOPEN

10 recombinant antibodies or binders in year 1

50 recombinant antibodies or other binders at a rate of about 10 per year (reported at M12, M36, M60). Binders will be generated by KI and ReSOLUTE with donations from Pharma partners.

Data deposition of genome/proteome wide analysis for >60 CG compounds

Genomeproteome wide analysis of subset of CG compounds 150 in total and deposition of data in sustainable resources M24 M60

100 targets enabled with in vitro assays and 60 targets with cellular assays in year 2 and 3

D51 250 targets enabled with assays for chemical probe discovery and optimisation at a rate of approximately 50 per year and 150 targets enabled with an incell target engagement assay at a rate of about 30 per year M12 M36 M60

Steady state sample access (1-2 per week) from IBD and CRC

Steady state sample access (1-2 per week) from IBD and CRC.

Establish data publication standard and database
200 protein structures in years 2 and 3

200 protein structures in year 2 and 3

Assembly of expanded reaction toolkit and fragment set for plate-based chemistry

Assembly of expanded reaction toolkit and fragment set for platebased chemistry

New protein family sentinel selectivity panel

New protein family sentinel selectivity panel for three families

Initial protocols made openly available through portal and public databases

Protocols made openly available through portal and public databases

Partnerships with >25 international partners

Partnerships with 25 international organisations with efforts in screening assay development patientderived cell assays chemical screening chemical probe generation and compound profiling established

80 CRISPR knockout cell lines in years 2 and 3

40 CRISPR knockout cell lines per year total 160 M12 M36 M48

Online compound ordering system for the public

Online compound ordering system for the public operational.

EUbOPEN website implementation

EUbOPEN website development with regular reviews and updates (M3, M36, M60).

Define criteria for compounds of CGL

The criteria underlying the list of targets to be covered by the CGL will be defined by the JMC and TPN (M3), and surveyed in regular meetings to govern the activities of Pillar 1.

Define target list of 1,000 targets

Defined target list of 1,000 proteins covered by the CGL.

Revised target list

The target list will be revised during the project.

Distribution of additionally approved CG sets and CP

Additionally approved CGs and CPs will be assembled and released with appropriate instructions to the public.

Extended FRAGALYSIS cloud infrastructure for in silico compound design

Extended FRAGALYSIS cloud infrastructure for in silico compound design Comprehensive compound prioritisation based on commercially available compounds

Extended FRAGALYSIS cloud infrastructure for de novo compound design

FRAGALYSIS de novo compound design interface compatible with platforms for automated compound synthesis.

Distribution of approved CG sets and CP

Newly approved CGs and CPs will be assembled and released with appropriate instructions to the public.

Pubblicazioni

Comparative structural analyses of the NHL domains from the human E3 ligase TRIM-NHL family

Autori: Chaikuad A, Zhubi R, Tredup C, Knapp S.
Pubblicato in: IUCr, 2022, ISSN 2052-2525
Editore: IUCr Journals
DOI: 10.1107/s2052252522008582

A guide to selecting high-performing antibodies for STING1 (Uniprot ID: Q86WV6) for use in western blot, immunoprecipitation, and immunofluorescence

Autori: Vera Ruíz Moleón, Charles Alende, Maryam Fotouhi, Riham Ayoubi, Kathleen Southern, Carl Laflamme, null null, null null
Pubblicato in: F1000Research, Numero 13, 2025, Pagina/e 1049, ISSN 2046-1402
Editore: F1000 Research Ltd.
DOI: 10.12688/f1000research.155929.2

Technologies for Direct Detection of Covalent Protein–Drug Adducts

Autori: Elma Mons, Robbert Q. Kim, Monique P. C. Mulder
Pubblicato in: Pharmaceuticals, 2023, ISSN 1424-8247
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ph16040547

DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes

Autori: Frommelt F, Fossati A, Uliana F, Wendt F, Xue P, Heusel M, Wollscheid B, Aebersold R, Ciuffa R, Gstaiger M.
Pubblicato in: Nat Methods, 2024, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/s41592-024-02211-y

The Pan-Canadian Chemical Library: A Mechanism to Open Academic Chemistry to High-Throughput Virtual Screening

Autori: Corentin Bedart, Grace Shimokura, Frederick G. West, Tabitha E. Wood, Robert A. Batey, John J. Irwin, Matthieu Schapira
Pubblicato in: Scientific Data, Numero 11, 2024, ISSN 2052-4463
Editore: Springer Science and Business Media LLC
DOI: 10.1038/s41597-024-03443-5

Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile-Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence.

Autori: Zhou J, Horton JR, Menna M, Fiorentino F, Ren R, Yu D, Hajian T, Vedadi M, Mazzoccanti G, Ciogli A, Weinhold E, HÃ¼ben M, Blumenthal RM, Zhang X, Mai A, Rotili D, Cheng X
Pubblicato in: J Med Chem, 2022, ISSN 0022-2623
Editore: American Chemical Society
DOI: 10.1021/acs.jmedchem.2c01789

Synthesis and functional screening of novel inhibitors targeting the HDAC6 zinc finger ubiquitin-binding domain

Autori: Silke Geurs, Eleni Staessens, Kato Bredael, Stefaan Borghgraef, Jordy De Ridder, Leentje Persoons, Steven De Jonghe, Dominique Schols, Mandeep K. Mann, Rachel J. Harding, Jorick Franceus, Tom Desmet, Kristof Van Hecke, Dorien Clarisse, Karolien De Bosscher, Matthias D'hooghe
Pubblicato in: European Journal of Medicinal Chemistry, Numero 285, 2025, Pagina/e 117208, ISSN 0223-5234
Editore: Elsevier BV
DOI: 10.1016/j.ejmech.2024.117208

Building ubiquitination machineries: E3 ligase multi-subunit assembly and substrate targeting by PROTACs and molecular glues

Autori: Sarath Ramachandran, Alessio Ciulli
Pubblicato in: Current Opinion in Structural Biology, Numero 67, 2021, Pagina/e 110-119, ISSN 0959-440X
Editore: Elsevier BV
DOI: 10.1016/j.sbi.2020.10.009

Quantitative Hydrogen–Deuterium Exchange Mass Spectrometry for Simultaneous Structural Characterization and Affinity Indexing of Single Target Drug Candidate Libraries

Autori: Esther Wolf, Oleksandra Herasymenko, Maria Kutera, Cristina Lento, Cheryl Arrowsmith, Suzanne Ackloo, Derek Wilson
Pubblicato in: Analytical Chemistry, Numero 96, 2024, Pagina/e 13015-13024, ISSN 0003-2700
Editore: American Chemical Society
DOI: 10.1021/acs.analchem.4c01001

Development of a Selective Dual Discoidin Domain Receptor (DDR)/p38 Kinase Chemical Probe.

Autori: Rohm, S., Berger, B. T., Schroder, M., Chatterjee, D., Mathea, S., Joerger, A. C., Pinkas, D. M., Bufton, J. C., Tjaden, A., Kovooru, L., Kudolo, M., Pohl, C., Bullock, A. N., Muller, S., Laufer, S. and Knapp, S
Pubblicato in: J Med Chem., 2021, ISSN 0022-2623
Editore: American Chemical Society
DOI: 10.1021/acs.jmedchem.1c00868

Serine phosphorylation facilitates protein degradation by the human mitochondrial ClpXP protease

Autori: Yue Feng, Monica M. Goncalves, Yulia Jitkova, Alexander F. A. Keszei, Yongran Yan, Chaitra Sarathy, Jonathan St-Germain, Tristan M. G. Kenney, Matthew Tcheng, Vincent Trudel, Ross S. Mancini, Rahul Upadhyay, Rose Hurren, Marcela Gronda, Matthew Schultz, Kaylen Soriano, Kaitlin Lees, Neil C. Pomroy, S. Quinn W. Currie, Gilbert G. Privé, Mark A. Reed, Andrei K. Yudin, Linda Z. Penn, Cheryl H. Arrow
Pubblicato in: Proceedings of the National Academy of Sciences, Numero 122, 2025, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2422447122

Development and Characterization of Type I, Type II, and Type III LIM-Kinase Chemical Probes

Autori: Hanke T, Mathea S, Woortman J, Salah E, Berger BT, Tumber A, Kashima R, Hata A, Kuster B, Müller S, Knapp S. J Med Chem 2022.
Pubblicato in: Journal of Medicinal Chemistry, 2022, ISSN 0022-2623
Editore: American Chemical Society
DOI: 10.1021/acs.jmedchem.2c01106

Macrocycle-based PROTACs selectively degrade cyclophilin A and inhibit HIV-1 and HCV

Autori: Lydia S. Newton, Clara Gathmann, Sophie Ridewood, Robert J. Smith, Andre J. Wijaya, Thomas W. Hornsby, Kate L. Morling, Dara Annett, Riccardo Zenezini Chiozzi, Ann-Kathrin Reuschl, Morten L. Govasli, Ying Ying Tan, Lucy G. Thorne, Clare Jolly, Konstantinos Thalassinos, Alessio Ciulli, Greg J. Towers, David L. Selwood
Pubblicato in: Nature Communications, Numero 16, 2025, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-025-56317-8

Mechanism and evolutionary origins of alanine-tail C-degron recognition by E3 ligases Pirh2 and CRL2-KLHDC10.

Autori: Patil PR, Burroughs AM, Misra M, Cerullo F, Costas-Insua C, Hung HC, Dikic I, Aravind L, Joazeiro CAP
Pubblicato in: Cell Rep, 2023, ISSN 2211-1247
Editore: Cell Press
DOI: 10.1016/j.celrep.2023.113100

Big data and benchmarking initiatives to bridge the gap from AlphaFold to drug design

Autori: Matthieu Schapira, Levon Halabelian, Cheryl H. Arrowsmith, Rachel J. Harding
Pubblicato in: Nature Chemical Biology, Numero 20, 2024, Pagina/e 937-940, ISSN 1552-4450
Editore: Nature Publishing Group
DOI: 10.1038/s41589-024-01570-z

Breaking free from the crystal lattice: Structural biology in solution to study protein degraders

Autori: Kevin Haubrich; Valentina A. Spiteri; William Farnaby; Frank Sobott; Alessio Ciulli
Pubblicato in: Crossref, Numero 2, 2023, ISSN 0346-251X
Editore: Pergamon Press Ltd.
DOI: 10.1016/j.sbi.2023.102534

Ubiquitin ligases: guardians of mammalian development

Autori: Cruz Walma, D. A., Chen, Z., Bullock, A. N. and Yamada, K. M
Pubblicato in: Nat Rev Mol Cell Biol, 2022, ISSN 1471-0072
Editore: Nature Publishing Group
DOI: 10.1038/s41580-021-00448-5

Hepatic miR-144 Drives Fumarase Activity Preventing NRF2 Activation During Obesity

Autori: Azzimato, V., Chen, P., Barreby, E., Morgantini, C., Levi, L., Vankova, A., ... & Aouadi, M.
Pubblicato in: Gastroenterology, 2021, ISSN 0016-5085
Editore: W. B. Saunders Co., Ltd.
DOI: 10.1053/j.gastro.2021.08.030

Revisiting huntingtin activity and localization signals in the context of protein structure

Autori: Ray Truant, Rachel J Harding, Kaitlyn Neuman, Tamara Maiuri
Pubblicato in: Journal of Huntington's Disease, Numero 13, 2025, Pagina/e 419-430, ISSN 1879-6397
Editore: IOS Press
DOI: 10.1177/18796397241295303

Structure and activity of human TMPRSS2 protease implicated in SARS-CoV-2 activation.

Autori: Fraser BJ, Beldar S, Seitova A, Hutchinson A, Mannar D, Li Y, Kwon D, Tan R, Wilson RP, Leopold K, Subramaniam S, Halabelian L, Arrowsmith CH, BÃ©nard F
Pubblicato in: Nat Chem Biol, 2022, ISSN 1552-4450
Editore: Nature Publishing Group
DOI: 10.1038/s41589-022-01059-7

A data science roadmap for open science organizations engaged in early-stage drug discovery

Autori: Kristina Edfeldt, Aled M. Edwards, Ola Engkvist, Judith Günther, Matthew Hartley, David G. Hulcoop, Andrew R. Leach, Brian D. Marsden, Amelie Menge, Leonie Misquitta, Susanne Müller, Dafydd R. Owen, Kristof T. Schütt, Nicholas Skelton, Andreas Steffen, Alexander Tropsha, Erik Vernet, Yanli Wang, James Wellnitz, Timothy M. Willson, Djork-Arné Clevert, Benjamin Haibe-Kains, Lovisa Holmberg Schia
Pubblicato in: Nature Communications, Numero 15, 2024, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-024-49777-x

Benchmarking Methods for PROTAC Ternary Complex Structure Prediction

Autori: Evianne Rovers, Matthieu Schapira
Pubblicato in: Journal of Chemical Information and Modeling, Numero 64, 2024, Pagina/e 6162-6173, ISSN 1549-9596
Editore: American Chemical Society
DOI: 10.1021/acs.jcim.4c00426

The ethnogeographic variability of genetic factors underlying G6PD deficiency

Autori: Koromina, M., Pandi, M. T., van der Spek, P. J., Patrinos, G. P., & Lauschke, V. M.
Pubblicato in: Pharmacological Research, 2021, ISSN 1043-6618
Editore: Academic Press
DOI: 10.1016/j.phrs.2021.105904

Small-molecule activation of OGG1 increases oxidative DNA damage repair by gaining a new function.

Autori: Michel M, Benítez-Buelga C, Calvo PA, Hanna BMF, Mortusewicz O, Masuyer G, Davies J, Wallner O, Sanjiv K, Albers JJ, Castañeda-Zegarra S, Jemth AS, Visnes T, Sastre-Perona A, Danda AN, Homan EJ, Marimuthu K, Zhenjun Z, Chi CN, Sarno A, Wiita E, von Nicolai C, Komor AJ, Rajagopal V, Müller S, Hank EC, Varga M, Scaletti ER, Pandey M, Karsten S, Haslene-Hox H, Loevenich S, Marttila P, Rasti A, Mam
Pubblicato in: Science, 2023, ISSN 0036-8075
Editore: American Association for the Advancement of Science
DOI: 10.1126/science.abf8980

Population-scale predictions of DPD and TPMT phenotypes using a quantitative pharmacogene-specific ensemble classifier

Autori: Yitian Zhou, Carolina Dagli Hernandez, Volker M. Lauschke
Pubblicato in: British Journal of Cancer, Numero 123/12, 2020, Pagina/e 1782-1789, ISSN 0007-0920
Editore: Nature Publishing Group
DOI: 10.1038/s41416-020-01084-0

ATPase activity profiling of three human DExD/H-box RNA helicases

Autori: Fengling Li, U Hang Chan, Julia Garcia Perez, Hong Zeng, Irene Chau, Yanjun Li, Almagul Seitova, Levon Halabelian
Pubblicato in: SLAS Discovery, Numero 32, 2025, Pagina/e 100229, ISSN 2472-5552
Editore: Elsevier BV
DOI: 10.1016/j.slasd.2025.100229

A guide to selecting high-performing antibodies for Huntingtin (UniProt ID: P42858) for use in western blot, immunoprecipitation, and immunofluorescence

Autori: Rebeka Fanti, Riham Ayoubi, Charles Alende, Maryam Fotouhi, Sara González Bolívar, Renu Chandrasekaran, Kathleen Southern, Aled M. Edwards, Rachel J. Harding, Carl Laflamme, null null, null null
Pubblicato in: F1000Research, Numero 13, 2025, Pagina/e 922, ISSN 2046-1402
Editore: F1000 Research Ltd.
DOI: 10.12688/f1000research.153670.2

Harnessing CD3 diversity to optimize CAR T cells.

Autori: Velasco Cárdenas RM, Brandl SM, Meléndez AV, Schlaak AE, Buschky A, Peters T, Beier F, Serrels B, Taromi S, Raute K, Hauri S, Gstaiger M, Lassmann S, Huppa JB, Boerries M, Andrieux G, Bengsch B, Schamel WW, Minguet S.
Pubblicato in: Nat Immunol., 2024, ISSN 1529-2908
Editore: Nature Publishing Group
DOI: 10.1038/s41590-023-01658-z

Histone lysine methacrylation is a dynamic post-translational modification regulated by HAT1 and SIRT2

Autori: Delaney K, Tan M, Zhu Z, Gao J, Dai L, Kim S, Ding J, He M, Halabelian L, Yang L, Nagarajan P, Parthun MR, Lee S, Khochbin S, Zheng YG, Zhao Y
Pubblicato in: Cell Discov, 2022, ISSN 2056-5968
Editore: Nature Publishing Group
DOI: 10.1038/s41421-021-00344-4

PRMT inhibition induces a viral mimicry response in triple-negative breast cancer.

Autori: Wu Q, Nie DY, Ba-Alawi W, Ji Y, Zhang Z, Cruickshank J, Haight J, Ciamponi FE, Chen J, Duan S, Shen Y, Liu J, Marhon SA, Mehdipour P, Szewczyk MM, Dogan-Artun N, Chen W, Zhang LX, Deblois G, Prinos P, Massirer KB, Barsyte-Lovejoy D, Jin J, De Carvalho DD, Haibe-Kains B, Wang X, Cescon DW, Lupien M, Arrowsmith CH
Pubblicato in: Nature Chemical Biology, 2022, ISSN 1552-4450
Editore: Nature Publishing Group
DOI: 10.1038/s41589-022-01024-4

Crystal structures of DCAF1-PROTAC-WDR5 ternary complexes provide insight into DCAF1 substrate specificity

Autori: Mark F. Mabanglo, Brian Wilson, Mahmoud Noureldin, Serah W. Kimani, Ahmed Mamai, Chiara Krausser, Héctor González-Álvarez, Smriti Srivastava, Mohammed Mohammed, Laurent Hoffer, Manuel Chan, Jamie Avrumutsoae, Alice Shi Ming Li, Taraneh Hajian, Sarah Tucker, Stuart Green, Magdalena Szewczyk, Dalia Barsyte-Lovejoy, Vijayaratnam Santhakumar, Suzanne Ackloo, Peter Loppnau, Yanjun Li, Almagul Seito
Pubblicato in: Nature Communications, Numero 15, 2024, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-024-54500-x

Proteomic workflows for deep phenotypic profiling of 3D organotypic liver models

Autori: Stefania Koutsilieri, Evgeniya Mickols, Ákos Végvári, Volker M Lauschke
Pubblicato in: Biotechnol J, 2023, ISSN 1860-6768
Editore: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/biot.202300684

High-content live-cell multiplex screen for chemogenomic compound annotation based on nuclear morphology

Autori: Tjaden A, Giessmann RT, Knapp S, Schröder M, Müller S.
Pubblicato in: STAR Protoc., 2022, ISSN 2666-1667
Editore: Cell Press
DOI: 10.1016/j.xpro.2022.101791

The novel adrenergic agonist ATR-127 targets skeletal muscle and brown adipose tissue to tackle diabesity and steatohepatitis

Autori: Emanuela Talamonti, Jelena Davegardh, Anastasia Kalinovich, Sten M.M. van Beek, Nodi Dehvari, Carina Halleskog, Hamza M. Bokhari, Dana S. Hutchinson, Seungmin Ham, Laura J. Humphrys, Nicola C. Dijon, Aikaterini Motso, Anna Sandstrom, Evelyn Zacharewicz, Ilga Mutule, Edgars Suna, Jana Spura, Karolina Ditrychova, Leigh A. Stoddart, Nicholas D. Holliday, Shane C. Wright, Volker M. Lauschke, Soren Nie
Pubblicato in: Molecular Metabolism, Numero 85, 2024, Pagina/e 101931, ISSN 2212-8778
Editore: Elsevier GmbH
DOI: 10.1016/j.molmet.2024.101931

"CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13"

Autori: Oleksandra Herasymenko, Madhushika Silva, Abd Al-Aziz A. Abu-Saleh, Ayaz Ahmad, Jesus Alvarado-Huayhuaz, Oscar E. A. Arce, Roly J. Armstrong, Cheryl Arrowsmith, Kelly E. Bachta, Hartmut Beck, Denes Berta, Mateusz K. Bieniek, Vincent Blay, Albina Bolotokova, Philip E. Bourne, Marko Breznik, Peter J. Brown, Aaron D. G. Campbell, Emanuele Carosati, Irene Chau, Daniel J. Cole, Ben Cree, Wim Dehaen, Ka
Pubblicato in: Journal of Chemical Information and Modeling, Numero 65, 2025, Pagina/e 6884-6898, ISSN 1549-9596
Editore: American Chemical Society
DOI: 10.1021/acs.jcim.5c00535

No shortcuts to SARS-CoV-2 antivirals.

Autori: Edwards A, Hartung IV
Pubblicato in: Science, 2021, ISSN 0036-8075
Editore: American Association for the Advancement of Science
DOI: 10.1126/science.abj9488

Targeting MYC effector functions in pancreatic cancer by inhibiting the ATPase RUVBL1/2

Autori: Markus Vogt, Nevenka Dudvarski Stankovic, Yiliam Cruz Garcia, Julia Hofstetter, Katharina Schneider, Filiz Kuybu, Theresa Hauck, Bikash Adhikari, Anton Hamann, Yamila Rocca, Lara Grysczyk, Benedikt Martin, Anneli Gebhardt-Wolf, Armin Wiegering, Markus Diefenbacher, Georg Gasteiger, Stefan Knapp, Dieter Saur, Martin Eilers, Mathias Rosenfeldt, Florian Erhard, Seychelle M Vos, Elmar Wolf
Pubblicato in: Gut, Numero 73, 2024, Pagina/e 1509-1528, ISSN 0017-5749
Editore: BMJ Publishing Group
DOI: 10.1136/gutjnl-2023-331519

Chemogenomics for steroid hormone receptors (NR3)

Autori: Espen Schallmayer, Laura Isigkeit, Lewis Elson, Susanne Müller, Stefan Knapp, Julian A. Marschner, Daniel Merk
Pubblicato in: Communications Chemistry, Numero 8, 2025, ISSN 2399-3669
Editore: Springer Science and Business Media LLC
DOI: 10.1038/s42004-025-01427-z

Crystal Structure-Guided Design of Bisubstrate Inhibitors and Photoluminescent Probes for Protein Kinases of the PIM Family

Autori: Olivier E. Nonga, Darja Lavogina, Erki Enkvist, Katrin Kestav, Apirat Chaikuad, Sarah E. Dixon-Clarke, Alex N. Bullock, Sergei Kopanchuk, Taavi Ivan, Ramesh Ekambaram, Kaido Viht, Stefan Knapp, Asko Uri
Pubblicato in: Molecules, Numero 26/14, 2021, Pagina/e 4353, ISSN 1420-3049
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules26144353

Mutation in Abl kinase with altered drug-binding kinetics indicates a novel mechanism of imatinib resistance

Autori: Lyczek A, Berger BT, Rangwala AM, Paung Y, Tom J, Philipose H, Guo J, Albanese SK, Robers MB, Knapp S, Chodera JD, Seeliger MA.
Pubblicato in: Proc Natl Acad Sci U S A, 2021, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2111451118

RNF8 ubiquitylation of XRN2 facilitates R-loop resolution and restrains genomic instability in BRCA1 mutant cells

Autori: Rehna Krishnan, Mariah Lapierre, Brandon Gautreau, Kevin C J Nixon, Samah El Ghamrasni, Parasvi S Patel, Jun Hao, V Talya Yerlici, Kiran Kumar Naidu Guturi, Jonathan St-Germain, Francesca Mateo, Amine Saad, Arash Algouneh, Rebecca Earnshaw, Duan Shili, Alma Seitova, Joshua Miller, Negin Khosraviani, Adam Penn, Brandon Ho, Otto Sanchez, M Prakash Hande, Jean-Yves Masson, Grant W Brown, Moulay Alaou
Pubblicato in: Nucleic Acids Res, 2023, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkad733

The Kinase Chemogenomic Set (KCGS): An Open Science Resource for Kinase Vulnerability Identification

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Discovery and Characterization of BAY-805, a Potent and Selective Inhibitor of Ubiquitin-Specific Protease USP21

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Editorial: The next generation of tools and technologies for studying human neurons in a dish

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7-(2-Anilinopyrimidin-4-yl)-1-benzazepin-2-ones Designed by a “Cut and Glue” Strategy Are Dual Aurora A/VEGF-R Kinase Inhibitors

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Pharmacogenomics in the era of next generation sequencing – from byte to bedside

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Structure Activity of β-Amidomethyl Vinyl Sulfones as Covalent Inhibitors of Chikungunya nsP2 Cysteine Protease with Antialphavirus Activity

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Scaffold hopping from amodiaquine to novel Nurr1 agonist chemotypes via microscale analogue libraries.

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Conformation and dynamics of the kinase domain drive subcellular location and activation of LRRK2

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Disease-associated KBTBD4 mutations in medulloblastoma elicit neomorphic ubiquitylation activity to promote CoREST degradation

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Discovery of Nanomolar DCAF1 Small Molecule Ligands.

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Mutation in the Common Docking Domain Affects MAP Kinase ERK2 Catalysis and Stability

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Toxicogenomics of drug induced liver injury – from mechanistic understanding to early prediction.

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De novo design of immunoglobulin-like domains.

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Covalent Proximity Scanning of a Distal Cysteine to Target PI3Kα

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ProxyBind: A compendium of binding sites for proximity-induced pharmacology.

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Nurr1 Modulation Mediates Neuroprotective Effects of Statins

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A chemical screen identifies PRMT5 as a therapeutic vulnerability for paclitaxel-resistant triple-negative breast cancer

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"CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson’s Disease Associated Protein"

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E3 Ligase Ligands for PROTACs: How They Were Found and How to Discover New Ones

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Octyl itaconate enhances VSVΔ51 oncolytic virotherapy by multitarget inhibition of antiviral and inflammatory pathways

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Discovery of 3-Amino-1-pyrazole-Based Kinase Inhibitors to Illuminate the Understudied PCTAIRE Family.

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Role of FAM134 paralogues in endoplasmic reticulum remodeling, ER‐phagy, and Collagen quality control

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Structural variation of the coding and non-coding human pharmacogenome

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Target 2035 - update on the quest for a probe for every protein.

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Pathway selectivity in Frizzleds is achieved by conserved micro-switches defining pathway-determining, active conformations

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A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II.

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Synthesis of 5-Benzylamino and 5-Alkylamino-Substituted Pyrimido[4,5-c]quinoline Derivatives as CSNK2A Inhibitors with Antiviral Activity

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ChemRAP uncovers specific mRNA translation regulation via RNA 5' phospho-methylation

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A Target Class Ligandability Evaluation of WD40 Repeat-Containing Proteins

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Enzymatic nucleosome acetylation selectively affects activity of histone methyltransferases in vitro

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Rational Design of PROTAC Linkers Featuring Ferrocene as a Molecular Hinge to Enable Dynamic Conformational Changes

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DiscoveryofPotentandExquisitelySelectiveInhibitorsofKinaseCK1withTunableIsoformSelectivity

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ChemBioPort: an online portal to navigate the structure, function and chemical inhibition of the human proteome

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A Consensus Compound/Bioactivity Dataset for Data-Driven Drug Design and Chemogenomics

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The Past, Present and Future of Intestinal In Vitro Cell Systems for Drug Absorption Studies

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Target 2035 – an update on private sector contributions

Autori: Suzanne Ackloo, * a Albert A. Antolin, b Jose Manuel Bartolome, c Hartmut Beck, d Alex Bullock, e Ulrich A. K. Betz, f Jark Böttcher, g Peter J. Brown, h Menorca Chaturvedi, i Alisa Crisp,j Danette Daniels, k Jan Dreher, d Kristina Edfeldt, l Aled M. Edwards, a Ursula Egner, m Jon Elkins, e Christian Fischer, n Tine Glendorf, o Steven Goldberg, p Ingo V. Hartung, q Alexander Hillisch, d Evert Hom
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Recent developments in in vitro and in vivo models for improved translation of preclinical pharmacokinetics and pharmacodynamics data

Autori: Jaydeep Yadav, Mehdi El Hassani, Jasleen Sodhi, Volker M. Lauschke, Jessica H. Hartman & Laura E. Russell
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Atg8 family proteins, LIR/AIM motifs and other interaction modes

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Altered desensitization and internalization patterns of rodent versus human glucose‐dependent insulinotropic polypeptide (GIP) receptors. An important drug discovery challenge

Autori: Lærke Smidt Gasbjerg, Rasmus Syberg Rasmussen, Adrian Dragan, Peter Lindquist, Josefine Ulrikke Melchiorsen, Tomasz Maciej Stepniewski, Sine Schiellerup, Esther Karen Tordrup, Sarina Gadgaard, Hüsün Sheyma Kizilkaya, Sabine Willems, Yi Zhong, Yi Wang, Shane C. Wright, Volker M. Lauschke, Bolette Hartmann, Jens Juul Holst, Jana Selent, Mette Marie Rosenkilde
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Covalent Targeting Leads to the Development of a LIMK1 Isoform-Selective Inhibitor

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Chemogenomics for NR1 nuclear hormone receptors

Autori: Laura Isigkeit, Espen Schallmayer, Romy Busch, Lorene Brunello, Amelie Menge, Lewis Elson, Susanne Müller, Stefan Knapp, Alexandra Stolz, Julian A. Marschner, Daniel Merk
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The human pseudouridine synthase PUS7 recognizes RNA with an extended multi-domain binding surface.

Autori: Guegueniat J, Halabelian L, Zeng H, Dong A, Li Y, Wu H, Arrowsmith CH, Kothe U
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The pro-drug C13 activates AMPK by two distinct mechanisms

Autori: Jordana B. Freemantle, Dinesh Shah, Dylan M. Lynch, Alessio Ciulli, Harinder S. Hundal, D. Grahame Hardie
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Modulation of tau tubulin kinases (TTBK1 and TTBK2) impacts ciliogenesis.

Autori: Bashore FM, Marquez AB, Chaikuad A, Howell S, Dunn AS, Beltran AA, Smith JL, Drewry DH, Beltran AS, Axtman AD.
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Human resident liver myeloid cells protect against metabolic stress in obesity

Autori: Emelie Barreby, Benedikt Strunz, Sebastian Nock, Léa Naudet, Joanne X. Shen, Helene Johansson, Isabella Sönnerborg, Junjie Ma, Egon Urgard, Laura J. Pallett, Yizhou Hu, Achilleas Fardellas, Valerio Azzimato, Ana Vankova, Laura Levi, Cecilia Morgantini, Mala K. Maini, Per Stål, Stephan P. Rosshart, Jonathan M. Coquet, Greg Nowak, Erik Näslund, Volker M. Lauschke, Ewa Ellis, Niklas K. Björkstr
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Compound Absorption in Polymer Devices Impairs the Translatability of Preclinical Safety Assessments

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Optimization of 3-Cyano-7-cyclopropylamino-pyrazolo[1,5- a]pyrimidines toward the Development of an In Vivo Chemical Probe for CSNK2A

Autori: Xuan Yang , Han Wee Ong , Rebekah J Dickmander, Jeffery L Smith, Jason W Brown, William Tao, Edcon Chang, Nathaniel J Moorman , Alison D Axtman, Timothy M Willson
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Assembly and Application of a Low Budget Photoreactor**

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Characterization of genetic variants of GIPR reveals a contribution of β-arrestin to metabolic phenotypes

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A Screening of Epigenetic Therapeutic Targets for Non-Small Cell Lung Cancer Reveals PADI4 and KDM6B as Promising Candidates

Autori: Lesbon JCC, Garnica TK, Xavier PLP, Rochetti AL, Reis RM, Müller S, Fukumasu H.
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The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks

Autori: Christian Kramer, John Chodera, Kelly L. Damm-Ganamet, Michael K. Gilson, Judith Günther, Uta Lessel, Richard A. Lewis, David Mobley, Eva Nittinger, Adam Pecina, Matthieu Schapira, W. Patrick Walters
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Calcium/calmodulin-dependent protein kinase kinase 2 regulates hepatic fuel metabolism

Autori: Stork BA, Dean A, Ortiz AR, Saha P, Putluri N, Planas-Silva MD, Mahmud I, Rajapakshe K, Coarfa C, Knapp S, Lorenzi PL, Kemp BE, Turk BE, Scott JW, Means AR, York B.
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Use of Aldehyde–Alkyne–Amine Couplings to Generate Medicinal Chemistry-Relevant Linkers

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Chemical Toolkit for PARK7: Potent, Selective, and High-Throughput

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Insulin‐dependent glucose consumption dynamics in 3D primary human liver cultures measured by a sensitive and specific glucose sensor with nanoliter input volume

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Selective BH3 mimetics synergize with BET inhibition to induce mitochondrial apoptosis in rhabdomyosarcoma cells

Autori: Erdogdu U, Dolgikh N, Laszig S, Särchen V, Meister MT, Wanior M, Knapp S, Boedicker C
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Discovery of a novel inhibitor of macropinocytosis with antiviral activity

Autori: Bartlomiej Porebski, Wanda Christ, Alba Corman, Martin Haraldsson, Myriam Barz, Louise Lidemalm, Maria Häggblad, Juliana Ilmain, Shane C. Wright, Matilde Murga, Jan Schlegel, Malin Jarvius, Maris Lapins, Erdinc Sezgin, Gira Bhabha, Volker M. Lauschke, Jordi Carreras-Puigvert, Miguel Lafarga, Jonas Klingström, Daniela Hühn, Oscar Fernandez-Capetillo
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Opportunities and Challenges of Population Pharmacogenomics

Autori: Yitian Zhou, Yoomi Park, Mahamadou D. Camara, Volker M. Lauschke
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Detection of antibodies against the huntingtin protein in human plasma.

Autori: Denis HL, Alpaugh M, Alvarez CP, Fenyi A, Barker RA, Chouinard S, Arrowsmith CH, Melki R, Labib R, Harding RJ, Cicchetti F
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Scaling of an antibody validation procedure enables quantification of antibody performance in major research applications

Autori: Ayoubi R, Ryan J, Biddle MS, Alshafie W, Fotouhi M, Bolivar SG, Ruiz Moleon V, Eckmann P, Worrall D, McDowell I, Southern K, Reintsch W, Durcan TM, Brown C, Bandrowski A, Virk H, Edwards AM, McPherson P, Laflamme C.
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Development of PROTAC Degrader Drugs for Cancer

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Discovery and Characterization of a Chemical Probe Targeting the Zinc-Finger Ubiquitin-Binding Domain of HDAC6

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A high-throughput approach to identify BRCA1-downregulating compounds to enhance PARP inhibitor sensitivity

Autori: Erin Sellars, Margarita Savguira, Jie Wu, Sabrina Cancelliere, Mark Jen, Rehna Krishnan, Anne Hakem, Dalia Barsyte-Lovejoy, Razqallah Hakem, Steven A. Narod, Joanne Kotsopoulos, Leonardo Salmena
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Structure-Reactivity Studies of 2-Sulfonylpyrimidines Allow Selective Protein Arylation.

Autori: Pichon MM, Drelinkiewicz D, Lozano D, Moraru R, Hayward LJ, Jones M, McCoy MA, Allstrum-Graves S, Balourdas DI, Joerger AC, Whitby RJ, Goldup SM, Wells N, Langley GJ, Herniman JM, Baud MGJ.
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Structure-Based Development of Isoform Selective Inhibitors ofCasein Kinase 1ε vs. Casein Kinase 1δ

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The identification of high-performing antibodies for transmembrane protein 106B (TMEM106B) for use in Western blot, immunoprecipitation, and immunofluorescence.

Autori: 3. Riham Ayoubi, Maryam Fotouhi, Kathleen Southern, Ritika Bhajiawala, Rebeka Fanti, Panagiotis Prinos, Peter S. McPherson, Carl Laflamme, NeuroSGC/YCharOS/EDDU collaborative group, ABIF Consortium.
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Discovery and characterization of a specific inhibitor of serine-threonine kinase cyclin-dependent kinase-like 5 (CDKL5) demonstrates role in hippocampal CA1 physiology

Autori: Anna Castano, Margaux Silvestre, Carrow I Wells, Jennifer L Sanderson, Carla A Ferrer, Han Wee Ong, Yi Lang, William Richardson, Josie A Silvaroli, Frances M Bashore, Jeffery L Smith, Isabelle M Genereux, Kelvin Dempster, David H Drewry, Navlot S Pabla, Alex N Bullock, Tim A Benke, Sila K Ultanir, and Alison D Axtman
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Rare genetic variability in human drug target genes modulates drug response and can guide precision medicine

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Discovery of CHD1 Antagonists for PTEN-Deficient Prostate Cancer

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A Chemical Toolbox for Labeling and Degrading Engineered Cas Proteins

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The co-crystal structure of Cbl-b and a small-molecule inhibitor reveals the mechanism of Cbl-b inhibition.

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Cdyl Deficiency Brakes Neuronal Excitability and Nociception through Promoting Kcnb1 Transcription in Peripheral Sensory Neurons.

Autori: Sun ZW, Waybright JM, Beldar S, Chen L, Foley CA, Norris-Drouin JL, Lyu TJ, Dong A, Min J, Wang YP, James LI, Wang Y
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GPCR Function in Autophagy Control: A Systematic Approach of Chemical Intervention

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Wnt/β-catenin and NFκB signaling synergize to trigger growth factor-free regeneration of adult primary human hepatocytes

Autori: Nuria Oliva-Vilarnau, Christian M Beusch , Pierre Sabatier, Eirini Sakaraki, Amelie Tjaden, Lukas Graetz, Florian A Büttner, Debra Dorotea , My Nguyen , Filip Bergqvist, Yvonne Sundström, Susanne Müller, Roman A Zubarev, Gunnar Schulte, Claudia Tredu, Roberto Gramignoli , Uwe J F Tietge , Volker M Lauschke
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Amide-to-ester substitution as a strategy for optimizing PROTAC permeability and cellular activity

Autori: Victoria G. Klein; Adam G. Bond; Conner Craigon; R. Scott Lokey; Alessio Ciulli
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DARPins detect the formation of hetero-tetramers of p63 and p73 in epithelial tissues and in squamous cell carcinoma.

Autori: Strubel A, Münick P, Hartmann O, Chaikuad A, Dreier B, Schaefer JV, Gebel J, Osterburg C, Tuppi M, Schäfer B, Buck V, Rosenfeldt M, Knapp S, Plückthun A, Diefenbacher ME, Dötsch V.
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Identification and evaluation of small-molecule inhibitors against the dNTPase SAMHD1 via a comprehensive screening funnel

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A Concerted Action of UBA5 C-Terminal Unstructured Regions Is Important for Transfer of Activated UFM1 to UFC1

Autori: Nicole Wesch, Frank Löhr, Natalia Rogova, Volker Dötsch, Vladimir V. Rogov
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Tracking the PROTAC degradation pathway in living cells highlights the importance of ternary complex measurement for PROTAC optimization.

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The MYC oncoprotein directly interacts with its chromatin cofactor PNUTS to recruit PP1 phosphatase.

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Small Molecule Screen Identifies Non-catalytic USP3 Chemical Handle.

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The Structure-Based Design of SARS-CoV-2 nsp14 Methyltransferase Ligands Yields Nanomolar Inhibitors.

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Probe my Pathway (PmP): a portal to explore the chemical coverage of the human Reactome

Autori: Haejin Angela Kwak, Lihua Liu, Matthieu Schapira
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Discovery of a Chemical Probe to Study Implications of BPTF Bromodomain Inhibition in Cellular and in vivo Experiments

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Mechanism of degrader-targeted protein ubiquitinability

Autori: Charlotte Crowe, Mark A. Nakasone, Sarah Chandler, Conner Craigon, Gajanan Sathe, Michael H. Tatham, Nikolai Makukhin, Ronald T. Hay, Alessio Ciulli
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Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells

Autori: Martin P. Schwalm, Krishna Saxena, Susanne Müller, Stefan Knapp
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In vitro and ex vivo modeling of enteric bacterial infections

Autori: Taebnia, N., Römling, U., Lauschke, V.M
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Single tracer-based protocol for broad-spectrum kinase profiling in live cells with NanoBRET

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Ternary Complex‐Templated Dynamic Combinatorial Chemistry for the Selection and Identification of Homo‐PROTACs

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Inhibiting EZH2 targets atypical teratoid rhabdoid tumor by triggering viral mimicry via both RNA and DNA sensing pathways

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Synthesis and Biological Evaluation of 2-Substituted Quinazolin-4(3)-Ones with Antiproliferative Activities

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"Functionally active modulators targeting the LRRK2 WD40 repeat domain identified by FRASE-bot in CACHE Challenge #1"

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Unravelling the druggability and immunological roles of the SOCS-family proteins

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LOPAC library screening identifies suramin as a TRIM21 binder with a unique binding mode revealed by crystal structure

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Structural Chemistry of Helicase Inhibition

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PRMT5 regulates ATF4 transcript splicing and oxidative stress response.

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Pharmacogenomics Beyond Single Common Genetic Variants: The Way Forward

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The PB1 and the ZZ domain of the autophagy receptor p62/SQSTM1 regulate the interaction of p62/SQSTM1 with the autophagosome protein LC3B

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Discovery of potent Plasmodium falciparum protein kinase 6 (PfPK6) inhibitors with a type II inhibitor pharmacophore.

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From N-0385 to N-0920: Unveiling a Host-Directed Protease Inhibitor with Picomolar Antiviral Efficacy against Prevalent SARS-CoV-2 Variants

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Inhibition of bromodomain and extra-terminal proteins targets constitutively active NFκB and STAT signaling in lymphoma and influences the expression of the antiapoptotic proteins BCL2A1 and c-MYC

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Novel biochemical, structural, and systems insights into inflammatory signaling revealed by contextual interaction proteomics.

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Chemical Starting Matter for HNF4α Ligand Discovery and Chemogenomics

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Human MettL3-MettL14 RNA adenine methyltransferase complex is active on double-stranded DNA containing lesions.

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Discovery of a Potent and Selective CDKL5/GSK3 Chemical Probe That Is Neuroprotective

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PRMT5 promotes full-length HTT expression by repressing multiple proximal intronic polyadenylation sites

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Stopping pandemics before they start: Lessons learned from SARS-CoV-2

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Potent and selective SETDB1 covalent negative allosteric modulator reduces methyltransferase activity in cells

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A pro-Fluorescent Ubiquitin-based Probe to Monitor Cysteine-based E3 Ligase Activity

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Computational tools to assess the functional consequences of rare and noncoding pharmacogenetic variability

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Hepatic Inhibition of ANGPTL3 Mimics the Molecular Hallmarks of Hypothyroidism

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Phenomics‐Based Discovery of Novel Orthosteric Choline Kinase Inhibitors

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Chemogenomic Screening in a Patient‐Derived 3D Fatty Liver Disease Model Reveals the CHRM1‐TRPM8 Axis as a Novel Module for Targeted Intervention

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Pharmacogene Sequencing of a Gabonese Population with Severe Plasmodium falciparum Malaria Reveals Multiple Novel Variants with Putative Relevance for Antimalarial Treatment

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Emerging structure-based computational methods to screen the exploding accessible chemical space

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Discovery of Nedd4 auto-ubiquitination inhibitors

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A guide to selecting high-performing antibodies for TAF15 (UniProt ID: Q92804) for use in western blot, immunoprecipitation, and immunofluorescence

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A chemical probe to modulate human GID4 Pro/N-degron interactions

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Targeting the Alternative Vitamin E Metabolite Binding Site Enables Noncanonical PPARγ Modulation

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GLP-1R signaling neighborhoods associate with the susceptibility to adverse drug reactions of incretin mimetics.

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Toward effective Atg8-based ATTECs: Approaches and perspectives

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The Transcriptional Repressor Orphan Nuclear Receptor TLX Is Responsive to Caffeine and Istradefylline

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Colorectal cancer organoid-stroma biobank allows subtype-specific assessment of individualized therapy responses.

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Image-Based Annotation of Chemogenomic Libraries for Phenotypic Screening

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Organocatalytic Switches of DNA Glycosylase OGG1 Catalyze a Highly Efficient AP‐Lyase Function

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Deep Annotation of Donated Chemical Probes (DCP) in Organotypic Human Liver Cultures and Patient-Derived Organoids from Tumor and Normal Colorectum

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Poly ADP-ribose signaling is dysregulated in Huntington disease

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Discovery of a 53BP1 Small Molecule Antagonist Using a Focused DNA-Encoded Library Screen

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LRRK2 dynamics analysis identifies allosteric control of the crosstalk between its catalytic domains

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Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders

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A covalent chemical probe for Chikungunya nsP2 cysteine protease with antialphaviral activity and proteome-wide selectivity

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Bioengineered Pancreas–Liver Crosstalk in a Microfluidic Coculture Chip Identifies Human Metabolic Response Signatures in Prediabetic Hyperglycemia

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The Small-Molecule Inhibitor MRIA9 Reveals Novel Insights into the Cell Cycle Roles of SIK2 in Ovarian Cancer Cells

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Discovery of a Potent, Selective, and Cell-Active SPIN1 Inhibitor

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Chemical coverage of human biological pathways

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Nudix hydrolase 18 catalyzes the hydrolysis of active triphosphate metabolites of the antivirals remdesivir, ribavirin, and molnupiravir

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PRMT7 ablation stimulates anti-tumor immunity and sensitizes melanoma to immune checkpoint blockade.

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The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods

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Phosphorylation-linked complex profiling identifies assemblies required for Hippo signal integration

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Discovery of a Novel Class of Covalent Dual Inhibitors Targeting the Protein Kinases BMX and BTK

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A patent review of von Hippel-Lindau (VHL)-recruiting chemical matter: E3 ligase ligands for PROTACs and targeted protein degradation (2019–present)

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Two FAM134B isoforms differentially regulate ER dynamics during myogenesis

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Toward target 2035: EUbOPEN - a public–private partnership to enable & unlock biology in the open

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Non-alcoholic fatty liver disease - opportunities for personalized treatment and drug development

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Kinetic characterization of human mRNA guanine-N7 methyltransferase

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Reprogramming Transcription Factors Oct4 and Sox2 Induce a BRD-Dependent Immunosuppressive Transcriptome in GBM-Propagating Cells.

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A Toolbox for the Generation of Chemical Probes for Baculovirus IAP Repeat Containing Proteins

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PSW-Designer: An Open-Source Computational Platform for the Design and Virtual Screening of Photopharmacological Ligands

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RAS and PP2A activities converge on epigenetic gene regulation.

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3D Adipose Tissue Culture Links the Organotypic Microenvironment to Improved Adipogenesis

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The Chemical Probes Portal: an expert review-based public resource to empower chemical probe assessment, selection and use

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PharmVar GeneFocus: CYP2B6

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Discovery of XL01126: A Potent, Fast, Cooperative, Selective, Oral bioavailable and Blood Brain Barrier Penetrant PROTAC Degrader of Leucine Rich Repeat Kinase 2 (LRRK2)

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3D microperfusion of mesoscale human microphysiological liver models improves functionality and recapitulates hepatic zonation

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Organotypic human ex vivo models for coronavirus disease 2019 research and drug development

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Development of Peptide Displacement Assays to Screen for Antagonists of DDB1 Interactions

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Huntingtin is an RNA binding protein and participates in NEAT1 -mediated paraspeckles

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Antecedent chromatin organization determines cGAS recruitment to ruptured micronuclei.

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Design, Synthesis, and Evaluation of WD-Repeat-Containing Protein 5 (WDR5) Degraders

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The genetic landscape of major drug metabolizing cytochrome P450 genes—an updated analysis of population-scale sequencing data

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Practice guidance documents for the diagnosis and management of non-alcoholic fatty liver disease—recent updates and open questions

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Trivalent PROTACs enhance protein degradation via combined avidity and cooperativity

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Population pharmacogenomics: an update on ethnogeographic differences and opportunities for precision public health

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Aurora Kinase A Is Involved in Controlling the Localization of Aquaporin-2 in Renal Principal Cells

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Critical assessment of LC3/GABARAP ligands used for degrader development and ligandability of LC3/GABARAP binding pockets

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Development of Inhibitors, Probes, and PROTAC Provides a Complete Toolbox to Study PARK7 in the Living Cell

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Nucelotide Binding, Evolutionary Insights and Interaction Partners of the Pseudokinase Unc-51-like Kinase 4

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ALK2 Receptor Kinase Association with FKBP12.6 Is Structurally Conserved with the ALK2-FKBP12 Complex

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Calcium measurements in enzymatically dissociated or mechanically microdissected mouse primary skeletal muscle fibers

Autori: Youhanna S, Bruton J, Jardemark K, Westerblad H, Lauschke VM
Pubblicato in: STAR protocols, 2023, ISSN 2666-1667
Editore: Cell Press
DOI: 10.1016/j.xpro.2023.102260

Targeting TRIM Proteins: A Quest towards Drugging an Emerging Protein Class

Autori: Francesca D'Amico, Rishov Mukhopadhyay, Huib Ovaa, Monique P. C. Mulder
Pubblicato in: ChemBioChem, 2021, ISSN 1439-4227
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.202000787

Phosphorylation of the DNA repair scaffold SLX4drives folding of the SAP domain and activation of theMUS81-EME1 endonucleas

Autori: Payliss BJ, Tse YWE, Reichheld SE, Lemak A, Yun HY, Houliston S, Patel A, Arrowsmith CH, Sharpe S, Wyatt HDM
Pubblicato in: Cell Reports, 2022, ISSN 2211-1247
Editore: Cell Press
DOI: 10.1016/j.celrep.2022.111537

Autoinhibition of ubiquitin-specific protease 8: Insights into domain interactions and mechanisms of regulation

Autori: Cody Caba, Megan Black, Yujue Liu, Ashley A. DaDalt, Josh Mallare, Lixin Fan, Rachel J. Harding, Yun-Xing Wang, Panayiotis O. Vacratsis, Rui Huang, Zhihao Zhuang, Yufeng Tong
Pubblicato in: Journal of Biological Chemistry, Numero 300, 2025, Pagina/e 107727, ISSN 0021-9258
Editore: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.jbc.2024.107727

The use of a multi-metric readout screen to identify EHMT2/G9a-inhibition as a modulator of cancer-associated fibroblast activation state

Autori: Nila C. Wu, Rene Quevedo, Michelle Nurse, Kebria Hezaveh, Haijiao Liu, Fumao Sun, Julien Muffat, Yu Sun, Craig A. Simmons, Tracy L. McGaha, Panagiotis Prinos, Cheryl H. Arrowsmith, Laurie Ailles, Elisa D'Arcangelo, Alison P. McGuigan
Pubblicato in: Biomaterials, Numero 314, 2024, Pagina/e 122879, ISSN 0142-9612
Editore: Pergamon Press Ltd.
DOI: 10.1016/j.biomaterials.2024.122879

JAK inhibition reduces SARS-CoV-2 liver infectivity and modulates inflammatory responses to reduce morbidity and mortality

Autori: Justin Stebbing, Ginés Sánchez Nievas, Marco Falcone, Sonia Youhanna, Peter Richardson, Silvia Ottaviani, Joanne X. Shen, Christian Sommerauer, Giusy Tiseo, Lorenzo Ghiadoni, Agostino Virdis, Fabio Monzani, Luis Romero Rizos, Francesco Forfori, Almudena Avendaño Céspedes, Salvatore De Marco, Laura Carrozzi, Fabio Lena, Pedro Manuel Sánchez-Jurado, Leonardo Gianluca Lacerenza, Nencioni Cesira,
Pubblicato in: Science Advances, Numero 7/1, 2021, Pagina/e eabe4724, ISSN 2375-2548
Editore: Science
DOI: 10.1126/sciadv.abe4724

CACHE (Critical Assessment of Computational Hit-finding Experiments): A public–private partnership benchmarking initiative to enable the development of computational methods for hit-finding

Autori: Ackloo S, Al-awar R, Amaro RE, Arrowsmith CH, Azevedo H, Batey RA, et al.
Pubblicato in: Nat Rev Chem, 2022, ISSN 1755-4330
Editore: Nature Publishing Group
DOI: 10.1038/s41570-022-00363-z

Interplay between β-propeller subunits WDR26 and muskelin regulates the CTLH E3 ligase supramolecular complex

Autori: Matthew E. R. Maitland, Gabriel Onea, Dominic D. G. Owens, Brianna C. Gonga-Cavé, Xu Wang, Cheryl H. Arrowsmith, Dalia Barsyte-Lovejoy, Gilles A. Lajoie, Caroline Schild-Poulter
Pubblicato in: Communications Biology, Numero 7, 2024, Pagina/e Communications Biology, ISSN 2399-3642
Editore: Springer Science and Business Media LLC
DOI: 10.1038/s42003-024-07371-3

Leveraging Dual-Ligase Recruitment to Enhance Protein Degradation via a Heterotrivalent Proteolysis Targeting Chimera

Autori: Adam G. Bond, Miquel Muñoz i Ordoño, Celia M. Bisbach, Conner Craigon, Nikolai Makukhin, Elizabeth A. Caine, Manjula Nagala, Marjeta Urh, Georg E. Winter, Kristin M. Riching, Alessio Ciulli
Pubblicato in: Journal of the American Chemical Society, Numero 146, 2024, Pagina/e 33675-33711, ISSN 0002-7863
Editore: American Chemical Society
DOI: 10.1021/jacs.4c11556

Crimean-Congo haemorrhagic fever virus uses LDLR to bind and enter host cells.

Autori: Monteil VM, Wright SC, Dyczynski M, Kellner MJ, Appelberg S, Platzer SW, Ibrahim A, Kwon H, Pittarokoilis I, Mirandola M, Michlits G, Devignot S, Elder E, Abdurahman S, Bereczky S, Bagci B, Youhanna S, Aastrup T, Lauschke VM, Salata C, Elaldi N, Weber F, Monserrat N, Hawman DW, Feldmann H, Horn M, Penninger JM, Mirazimi A.
Pubblicato in: Nat Microbiol., 2024, ISSN 2058-5276
Editore: Nature
DOI: 10.1038/s41564-024-01672-3

Structural basis of the TAM domain of BAZ2A in binding toDNA or RNA independent of methylation status

Autori: Chen S, Zhou M, Dong A, Loppnau P, Wang M, Min J, Liu K
Pubblicato in: J Biol Chem, 2021, ISSN 0021-9258
Editore: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.jbc.2021.101351

PRMT1 inhibition perturbs RNA metabolism and induces DNA damage in clear cell renal cell carcinoma

Autori: Joseph Walton, Angel S. N. Ng, Karen Arevalo, Anthony Apostoli, Jalna Meens, Christina Karamboulas, Jonathan St-Germain, Panagiotis Prinos, Julia Dmytryshyn, Eric Chen, Cheryl H. Arrowsmith, Brian Raught, Laurie Ailles
Pubblicato in: Nature Communications, Numero 15, 2024, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-024-52507-y

Cellular Validation of a Chemically Improved Inhibitor Identifies Monoubiquitination on OTUB2

Autori: Jin Gan, Jelle de Vries, Jimmy J. L. L. Akkermans, Yassene Mohammed, Rayman T. N. Tjokrodirijo, Arnoud H. de Ru, Robbert Q. Kim, David A. Vargas, Vito Pol, Rudi Fasan, Peter A. van Veelen, Jacques Neefjes, Hans van Dam, Huib Ovaa, Aysegul Sapmaz,* and Paul P. Geurink*
Pubblicato in: ACS Chem. Biol., 2023, ISSN 0002-7863
Editore: American Chemical Society
DOI: 10.1021/acschembio.3c00227

JAK Inhibitors — More Than Just Glucocorticoids

Autori: Justin Stebbing, Volker M. Lauschke
Pubblicato in: New England Journal of Medicine, Numero 385/5, 2021, Pagina/e 463-465, ISSN 0028-4793
Editore: Massachusetts Medical Society
DOI: 10.1056/nejme2108667

DNA double-strand break-derived RNA drives TIRR/53BP1 complex dissociation

Autori: Ketley RF., Battistini F., Alagia A., Mondielli C., Iehl F., Balikçi E., Huber KVM., Orozco M., Gullerova M.
Pubblicato in: Cell Reports, 2022, ISSN 2211-1247
Editore: Cell Press
DOI: 10.1016/j.celrep.2022.111526

Development of potent dual BET/HDAC inhibitorsviapharmacophore merging and structure-guided optimization

Autori: Nicolas Bauer; Dimitrios-Ilias Balourdas; Joel R. Schneider; Xin Zhang; Lena M. Berger; Benedict-Tilman Berger; Nick A. Klopp; Jens T. Siveke; Stefan Knapp; Andreas C. Joerger
Pubblicato in: Crossref, Numero 5, 2023, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.07.18.547334

Potent and Selective SETDB1 Covalent Negative Allosteric Modulator Reduces Methyltransferase Activity in Cells

Autori: Mélanie Uguen, Devan J. Shell, Madhushika Silva, Yu Deng, Fengling Li, Magdalena M. Szewczyk, Ka Yang, Yani Zhao, Michael A. Stashko, Jacqueline L. Norris-Drouin, Jarod M. Waybright, Serap Beldar, Justin M. Rectenwald, Angie L. Mordant, Thomas S. Webb, Laura E. Herring, Cheryl H. Arrowsmith, Suzanne Ackloo, Steven P. Gygi, Robert K. McGinty, Dalia Barsyte-Lovejoy, Pengda Liu, Levon Halabelian, Li
Pubblicato in: Biorxiv, 2025, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.09.27.615363

Editorial: Beyond protein degradation and lysine modification: novel insights into non-canonical ubiquitination

Autori: Aysegul Sapmaz, Jin Gan, Darragh P. O’Brien, Adán Pinto-Fernández
Pubblicato in: Frontiers in Molecular Biosciences, Numero 11, 2024, ISSN 2296-889X
Editore: Frontiers Media SA
DOI: 10.3389/fmolb.2024.1461356

Enantioselective Protein Affinity Selection Mass Spectrometry (E-ASMS)

Autori: Xiaoyun Wang, Jianxian Sun, Shabbir Ahmad, Diwen Yang, Fengling Li, U Hang Chan, Hong Zeng, Conrad V. Simoben, Stuart R. Green, Madhushika Silva, Scott Houliston, Aiping Dong, Albina Bolotokova, Elisa Gibson, Maria Kutera, Pegah Ghiabi, Ivan Kondratov, Tetiana Matviyuk, Alexander Chuprina, Danai Mavridi, Christopher Lenz, Andreas C. Joerger, Benjamin D. Brown, Richard B. Heath, Wyatt W. Yue, Lucy
Pubblicato in: BioRXiv, 2025, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.01.17.633682

Systematic comparison of dCas9-based DNA methylation epimodifiers over time indicates efficient on-target and widespread off-target effects

Autori: Majid Pahlevan Kakhki, Fatemeh Rangani, Ewoud Ewing, Chiara Starvaggi Cucuzza, Galina Zheleznyakova, Maria Kalomoiri, Tejaswi Venkata S. Badam, Ruxandra Covacu, Ioanna Andreou, Maria Needhamsen, Lara Kular, Maja Jagodic
Pubblicato in: Biorxiv, 2025, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.03.15.641804

High-throughput protein target mapping enables accelerated bioactivity discovery for ToxCast and PFAS compounds

Autori: Diwen Yang, Xiaoyun Wang, Jiabao Liu, Yufeng Gong, Pranav Nair, Jianxian Sun, Xing Qian, Claire Cui, Hong Zeng, Aiping Dong, Rachel J. Harding, Nicola Burgess-Brown, Tyler S. Beyett, Datong Song, Henry Krause, Miriam L. Diamond, Derek L. Bolhuis, Nicholas G. Brown, Cheryl H. Arrowsmith, Aled M. Edwards, Levon Halabelian, Hui Peng
Pubblicato in: bioRxiv, 2025, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.03.20.644436

Discovery of a cell-active chikungunya virus nsP2 protease inhibitor using a covalent fragment-based screening approach

Autori: Eric M. Merten, John D. Sears, Tina M. Leisner, Paul B. Hardy, Anirban Ghoshal, Mohammad Anwar Hossain, Kesatebrhan Haile Asressu, Peter J. Brown, Michael A. Stashko, Laura Herring, Angie L. Mordant, Thomas S. Webb, Christine A. Mills, Natalie K. Barker, Zachary J. Streblow, Sumera Perveen, Cheryl Arrowsmith, Jamie J. Arnold, Craig E Cameron, Daniel N. Streblow, Nathaniel J. Moorman, Mark Heise, T
Pubblicato in: Biorxiv, 2024, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.03.22.586341

Large-scale discovery, analysis, and design of protein energy landscapes

Autori: Állan J. R. Ferrari, Sugyan M. Dixit, Jane Thibeault, Mario Garcia, Scott Houliston, Robert W. Ludwig, Pascal Notin, Claire M. Phoumyvong, Cydney M. Martell, Michelle D. Jung, Kotaro Tsuboyama, Lauren Carter, Cheryl H. Arrowsmith, Miklos Guttman, Gabriel J. Rocklin
Pubblicato in: bioRxiv, 2025, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.03.20.644235

k-Nearest Neighbour Adaptive Sampling (kNN-AS), a Simple Tool to Efficiently Explore Conformational Space

Autori: Evianne Rovers, Anvith Thudi, Chris Maddison, Matthieu Schapira
Pubblicato in: bioRxiv, Numero bioRxiv, 2025, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.03.05.641673

Recruitment of FBXO22 for Targeted Degradation of NSD2

Autori: avid Y. Nie, John R. Tabor, Jianping Li, Maria Kutera, Jonathan St-Germain, Ronan P. Hanley, Esther Wolf, Ethan Paulakonis, Tristan M.G. Kenney, Shili Duan, Suman Shrestha, Dominic D.G. Owens, Ailing Pon, Magdalena Szewczyk, Anthony Joseph Lamberto, Michael Menes, Fengling Li, Dalia Barsyte-Lovejoy, Nicholas G. Brown, Anthony M. Barsotti, Andrew W. Stamford, Jon L. Collins, Derek J. Wilson, Brian
Pubblicato in: Biorxiv, 2024, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.11.01.564830

A Covalent Chemical Probe for Chikungunya nsP2 Cysteine Protease with Antialphaviral Activity and Proteome-wide Selectivity

Autori: Timothy Willson, Anirban Ghoshal, Edwin Tse, Mohammad Anwar Hossain, Kesatebrhan Haile Asressu, Eric Merten, John Sears, Stefanie Howell, Sumers Perveen, Jane Burdick, Noah Morales, Sabian Martinez, Isabella Law, Davenport Bennett, Thomas Morrison, Zachary Strebblow, Daniel Streblow, Angie Mordant, Thomas Webb, Aurora Cabrera, Laura Herring, Cheryl Arrowsmith, Kenneth Pearce, Nathaniel Moorman, Ma
Pubblicato in: Research Square, 2024, ISSN 2693-5015
Editore: Research Sqare
DOI: 10.21203/rs.3.rs-5363451/v1

Probing the mechanism of Cbl-b inhibition by a small molecule inhibitor

Autori: Serah Kimani, Sumera Perveen, Magdalena Szewezyk, Hong Zeng, Aiping Dong, Fengling Li, Pegah Ghiabi, Yanjun Li, Irene Chau, Cheryl Arrowsmith, Dalia Barsyte-Lovejoy, Vijayaratnam Santhakumar*, Masoud Vedadi, Levon Halabelian*
Pubblicato in: Biorxiv, 2023, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.05.05.539612

Structure Activity of β-Amidomethyl Vinyl Sulfones as Covalent Inhibitors ofChikungunyansP2 Cysteine Protease with Anti-alphavirus Activity

Autori: Anirban Ghoshal, Kesatebrhan Haile Asressu, Mohammad Anwar Hossain, Peter J. Brown, Eric M. Merten, John D. Sears, Sumera Perveen, Kenneth H. Pearce, Konstantin I. Popov, Nathaniel J. Moorman, Mark T. Heise, Timothy M. Willson
Pubblicato in: Biorxiv, 2024, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.06.12.598722

Rewiring of catecholamine-induced calcium signalling is an early event in non-alcoholic fatty liver disease

Autori: Shane C. Wright, Volker M. Lauschke
Pubblicato in: The Journal of Physiology, 2023
Editore: Wiley-Blackwell
DOI: 10.1113/jp284526

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