EUbOPEN: Enabling and Unlocking biology in the OPEN

Deliverables

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.

Publications

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

Author(s): Chaikuad A, Zhubi R, Tredup C, Knapp S.
Published in: IUCr, 2022, ISSN 2052-2525
Publisher: IUCr Journals
DOI: 10.1107/s2052252522008582

Technologies for Direct Detection of Covalent Protein–Drug Adducts

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

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

Author(s): 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
Published in: J Med Chem, 2022, ISSN 0022-2623
Publisher: American Chemical Society
DOI: 10.1021/acs.jmedchem.2c01789

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

Author(s): Sarath Ramachandran, Alessio Ciulli
Published in: Current Opinion in Structural Biology, Issue 67, 2021, Page(s) 110-119, ISSN 0959-440X
Publisher: Elsevier BV
DOI: 10.1016/j.sbi.2020.10.009

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

Author(s): 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
Published in: J Med Chem., 2021, ISSN 0022-2623
Publisher: American Chemical Society
DOI: 10.1021/acs.jmedchem.1c00868

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

Author(s): 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.
Published in: Journal of Medicinal Chemistry, 2022, ISSN 0022-2623
Publisher: American Chemical Society
DOI: 10.1021/acs.jmedchem.2c01106

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

Author(s): Kevin Haubrich; Valentina A. Spiteri; William Farnaby; Frank Sobott; Alessio Ciulli
Published in: Crossref, Issue 2, 2023, ISSN 0346-251X
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.sbi.2023.102534

Ubiquitin ligases: guardians of mammalian development

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

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

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

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

Author(s): 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
Published in: Nat Chem Biol, 2022, ISSN 1552-4450
Publisher: Nature Publishing Group
DOI: 10.1038/s41589-022-01059-7

The ethnogeographic variability of genetic factors underlying G6PD deficiency

Author(s): Koromina, M., Pandi, M. T., van der Spek, P. J., Patrinos, G. P., & Lauschke, V. M.
Published in: Pharmacological Research, 2021, ISSN 1043-6618
Publisher: Academic Press
DOI: 10.1016/j.phrs.2021.105904

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

Author(s): Yitian Zhou, Carolina Dagli Hernandez, Volker M. Lauschke
Published in: British Journal of Cancer, Issue 123/12, 2020, Page(s) 1782-1789, ISSN 0007-0920
Publisher: Nature Publishing Group
DOI: 10.1038/s41416-020-01084-0

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

Author(s): 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
Published in: Cell Discov, 2022, ISSN 2056-5968
Publisher: Nature Publishing Group
DOI: 10.1038/s41421-021-00344-4

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

Author(s): 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
Published in: Nature Chemical Biology, 2022, ISSN 1552-4450
Publisher: Nature Publishing Group
DOI: 10.1038/s41589-022-01024-4

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

Author(s): Tjaden A, Giessmann RT, Knapp S, Schröder M, Müller S.
Published in: STAR Protoc., 2022, ISSN 2666-1667
Publisher: Cell Press
DOI: 10.1016/j.xpro.2022.101791

No shortcuts to SARS-CoV-2 antivirals.

Author(s): Edwards A, Hartung IV
Published in: Science, 2021, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abj9488

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

Author(s): 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
Published in: Molecules, Issue 26/14, 2021, Page(s) 4353, ISSN 1420-3049
Publisher: 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

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

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

Author(s): Carrow I. Wells, Hassan Al-Ali, David M. Andrews, Christopher R. M. Asquith, Alison D. Axtman, Ivan Dikic, Daniel Ebner, Peter Ettmayer, Christian Fischer, Mathias Frederiksen, Robert E. Futrell, Nathanael S. Gray, Stephanie B. Hatch, Stefan Knapp, Ulrich Lücking, Michael Michaelides, Caitlin E. Mills, Susanne Müller, Dafydd Owen, Alfredo Picado, Kumar S. Saikatendu, Martin Schröder, Alexandra
Published in: International Journal of Molecular Sciences, Issue 22/2, 2021, Page(s) 566, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22020566

Post-transcriptional and Post-translational Modifications of Primary Cilia: How to Fine Tune Your Neuronal Antenna.

Author(s): Rocha C, Prinos P
Published in: Front Cell Neurosci, 2022, ISSN 1662-5102
Publisher: Frontiers Research Foundation
DOI: 10.3389/fncel.2022.809917

DFG-1 Residue Controls Inhibitor Binding Mode and Affinity, Providing a Basis for Rational Design of Kinase Inhibitor Selectivity

Author(s): Martin Schröder, Alex N. Bullock, Oleg Fedorov, Franz Bracher, Apirat Chaikuad, Stefan Knapp
Published in: Journal of Medicinal Chemistry, Issue 63/18, 2020, Page(s) 10224-10234, ISSN 0022-2623
Publisher: American Chemical Society
DOI: 10.1021/acs.jmedchem.0c00898

Genotoxicity and Epigenotoxicity of Carbazole-Derived Molecules on MCF-7 Breast Cancer Cells

Author(s): Claudio Luparello, Ilenia Cruciata, Andreas C. Joerger, Cory A. Ocasio, Rhiannon Jones, Raysa Khan Tareque, Mark C. Bagley, John Spencer, Martin Walker, Carol Austin, Tiziana Ferrara, Pietro D′Oca, Rossella Bellina, Rossella Branni, Fabio Caradonna
Published in: International Journal of Molecular Sciences, Issue 22/7, 2021, Page(s) 3410, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22073410

Autoantibodies against Four-and-a-Half-LIM Domain 1 (FHL1) in Inflammatory Myopathies: Results from an Australian Single-Center Cohort.

Author(s): Galindo-Feria AS, Horuluoglu B, Day J, Fernandes-Cerqueira C, Wigren E, Gräslund S, Proudman S, Lundberg IE, Limaye V
Published in: Rheumatology, 2022, ISSN 1462-0324
Publisher: Oxford University Press
DOI: 10.1093/rheumatology/keac003

SS148 and WZ16 inhibit the activities of nsp10-nsp16 complexes from all seven human pathogenic coronaviruses.

Author(s): Li F, Ghiabi P, Hajian T, Klima M, Li ASM, Yazdi AK, Chau I, Loppnau P, Kutera M, Seitova A, Bolotokova A, Hutchinson A, Perveen S, Boura E, Vedadi M
Published in: Biochim Biophys Acta, 2023, ISSN 0304-4165
Publisher: Elsevier BV
DOI: 10.1016/j.bbagen.2023.130319

Prediction and Validation of a Protein's Free Energy Surface Using Hydrogen Exchange and (Importantly) Its Denaturant Dependence.

Author(s): Peng X, Baxa M, Faruk N, Sachleben JR, Pintscher S, Gagnon IA, Houliston S, Arrowsmith CH, Freed KF, Rocklin GJ, Sosnick TR
Published in: J Chem Theory Comput, 2021, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.1c00960

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

Author(s): Fabian Göricke; Victoria Vu; Leanna Smith; Ulrike Scheib; Raphael Böhm; Namik Akkilic; Gerd Wohlfahrt; Jörg Weiske; Ulf Bömer; Krzysztof Brzezinka; Niels Lindner; Philip Lienau; Stefan Gradl; Hartmut Beck; Peter J. Brown; Vijayaratnam Santhakumar; Masoud Vedadi; Dalia Barsyte-Lovejoy; Cheryl H. Arrowsmith; Norbert Schmees; Kirstin Petersen
Published in: Crossref, Issue 3, 2023, ISSN 0022-2623
Publisher: American Chemical Society
DOI: 10.1021/acs.jmedchem.2c01933

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

Author(s): Mehmet Karatas, Apirat Chaikuad, Bianca Berger, Michael H. G. Kubbutat, Frank Totzke, Stefan Knapp, Conrad Kunick
Published in: Molecules, Issue 26/6, 2021, Page(s) 1611, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules26061611

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

Author(s): Laura E. Russell, Yitian Zhou, Ahmed A. Almousa, Jasleen K. Sodhi, Chukwunonso K. Nwabufo, Volker M. Lauschke
Published in: Drug Metabolism Reviews, 2021, Page(s) 1-26, ISSN 0360-2532
Publisher: Marcel Dekker Inc.
DOI: 10.1080/03602532.2021.1909613

Structure and Function of Protein Arginine Methyltransferase PRMT7.

Author(s): Halabelian L, Barsyte-Lovejoy D
Published in: Life (Basel), 2021, ISSN 2075-1729
Publisher: MDPI
DOI: 10.3390/life11080768

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

Author(s): Willems, S.; Müller, M.; Ohrndorf, J.; Heering, J.; Proschak, E.; Merk, D.
Published in: ChemMedChem, 2022, ISSN 1860-7179
Publisher: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/cmdc.202200026

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

Author(s): Sven H. Schmidt, Jui-Hung Weng, Phillip C. Aoto, Daniela Boassa, Sebastian Mathea, Steve Silletti, Junru Hu, Maximilian Wallbott, Elizabeth A. Komives, Stefan Knapp, Friedrich W. Herberg, Susan S. Taylor
Published in: Proceedings of the National Academy of Sciences, Issue 118/23, 2021, Page(s) e2100844118, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2100844118

Integrated analysis of Shank1 PDZ interactions with C-terminal and internal binding motifs

Author(s): Muhammad Ali, Mishal Mariam McAuley, Susanne Lüchow, Stefan Knapp, Andreas C. Joerger, Ylva Ivarsson
Published in: Current Research in Structural Biology, Issue 3, 2021, Page(s) 41-50, ISSN 2665-928X
Publisher: Elsevier
DOI: 10.1016/j.crstbi.2021.01.001

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

Author(s): Chen, Z., Ioris, R. M., Richardson, S., Van Ess, A. N., Vendrell, I., Kessler, B.M., Buffa, F.M., Busino, L., Clifford, S. C., Bullock, A. N. D'Angiolella, V.
Published in: Cell Death Differ., 2022, ISSN 1350-9047
Publisher: Nature Publishing Group
DOI: 10.1038/s41418-022-00983-4

Huntingtin structure is orchestrated by HAP40 and shows a polyglutamine expansion-specific interaction with exon 1.

Author(s): Harding RJ, Deme JC, Hevler JF, Tamara S, Lemak A, Cantle JP, Szewczyk MM, Begeja N, Goss S, Zuo X, Loppnau P, Seitova A, Hutchinson A, Fan L, Truant R, Schapira M, Carroll JB, Heck AJR, Lea SM, Arrowsmith CH
Published in: Commun Biol, 2021, ISSN 2399-3642
Publisher: Springer Nature
DOI: 10.1038/s42003-021-02895-4

Discovery of Nanomolar DCAF1 Small Molecule Ligands.

Author(s): Li ASM, Kimani S, Wilson B, Noureldin M, GonzÃ¡lez-Ãlvarez H, Mamai A, Hoffer L, Guilinger JP, Zhang Y, von Rechenberg M, Disch JS, Mulhern CJ, Slakman BL, Cuozzo JW, Dong A, Poda G, Mohammed M, Saraon P, Mittal M, Modh P, Rathod V, Patel B, Ackloo S, Santhakumar V, Szewczyk MM, Barsyte-Lovejoy D, Arrowsmith CH, Marcellus R, GuiÃ© MA, Keefe AD, Brown PJ, Halabelian L, Al-Awar R, Vedadi M
Published in: Journal of Medicinal Chemistry, 2023, ISSN 0022-2623
Publisher: American Chemical Society
DOI: 10.1021/acs.jmedchem.2c02132

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

Author(s): Volker M. Lauschke
Published in: Drug Metabolism Reviews, 2021, Page(s) 1-8, ISSN 0360-2532
Publisher: Marcel Dekker Inc.
DOI: 10.1080/03602532.2021.1894571

De novo design of immunoglobulin-like domains.

Author(s): Chidyausiku TM, Mendes SR, Klima JC, Nadal M, Eckhard U, Roel-Touris J, Houliston S, Guevara T, Haddox HK, Moyer A, Arrowsmith CH, Gomis-RÃ¼th FX, Baker D, Marcos E
Published in: Nat Commun, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-33004-6

Covalent Proximity Scanning of a Distal Cysteine to Target PI3Kα

Author(s): Chiara Borsari, Erhan Keles, Jacob A. McPhail, Alexander Schaefer, Rohitha Sriramaratnam, Wojciech Goch, Thorsten Schaefer, Martina De Pascale, Wojciech Bal, Matthias Gstaiger, John E. Burke, and Matthias P. Wymann
Published in: Journal of the American Chemical Society, 2022, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.1c13568

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

Author(s): Rovers E, Liu L, Schapira M
Published in: Computational and Structural Biotechnology Journal, 2022, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2022.11.010

Nurr1 Modulation Mediates Neuroprotective Effects of Statins

Author(s): Sabine Willems, Julian A. Marschner, Whitney Kilu, Giuseppe Faudone, Romy Busch, Silke Duensing-Kropp, Jan Heering, Daniel Merk
Published in: Adv. Sci, 2022, ISSN 2198-3844
Publisher: Willey-VCH
DOI: 10.1002/advs.202104640

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

Author(s): Tasuku Ishida, Alessio Ciulli
Published in: SLAS DISCOVERY: Advancing the Science of Drug Discovery, Issue 26/4, 2021, Page(s) 484-502, ISSN 2472-5552
Publisher: SAGE Journals
DOI: 10.1177/2472555220965528

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

Author(s): Alessio Reggio, Viviana Buonomo, Rayene Berkane, Ramachandra M Bhaskara, Mariana Tellechea, Ivana Peluso, Elena Polishchuk, Giorgia Di Lorenzo, Carmine Cirillo, Marianna Esposito, Adeela Hussain, Antje K Huebner, Christian A Hübner, Carmine Settembre, Gerhard Hummer, Paolo Grumati, Alexandra Stolz
Published in: EMBO reports, 2021, ISSN 1469-221X
Publisher: Nature Publishing Group
DOI: 10.15252/embr.202052289

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

Author(s): Muller, S., Ackloo, S., Al Chawaf, A., Al-Lazikani, B., Antolin, A., Baell, J. B., Beck, H., Beedie, S., Betz, U. A. K., Bezerra, G. A., Brennan, P. E., Brown, D., Brown, P. J., Bullock, A. N., Carter, A. J., Chaikuad, A., Chaineau, M., Ciulli, A., Collins, I., Dreher, J., Drewry, D., Edfeldt, K., Edwards, A. M., Egner, U., Frye, S. V., Fuchs, S. M., Hall, M. D., Hartung, I. V., Hillisch, A., Hitc
Published in: RSC Medicinal Chemistry, 2022, ISSN 2046-2069
Publisher: Royal Society of Chemistry
DOI: 10.1039/d1md00228g

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

Author(s): Lukas Grätz, Maria Kowalski-Jahn, Magdalena M. Scharf, Pawel Kozielewicz, Michael Jahn, Julien Bous, Nevin A. Lambert, David E. Gloriam & Gunnar Schulte
Published in: Nature Communications, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-40213-0

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

Author(s): Liu Y, Iqbal A, Li W, Ni Z, Wang Y, Ramprasad J, Abraham KJ, Zhang M, Zhao DY, Qin S, Loppnau P, Jiang H, Guo X, Brown PJ, Zhen X, Xu G, Mekhail K, Ji X, Bedford MT, Greenblatt JF, Min J
Published in: Nat Commun, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-33229-5

Enzymatic nucleosome acetylation selectively affects activity of histone methyltransferases in vitro

Author(s): Trush, Viacheslav V.; Feller, Christian; Li, Alice Shi Ming; Allali-Hassani, Abdellah; Szewczyk, Magdalena M.; Chau, Irene; Eram, Mohammad S.; Jiang, Boya; Luu, Raymond; Zhang, Fangfei; Barsyte-Lovejoy, Dalia; Aebersold, Ruedi; Arrowsmith, Cheryl H.; Vedadi, Masoud
Published in: Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, 1865 (5), Issue 1, 2022, ISSN 1874-9399
Publisher: Elsevier BV
DOI: 10.1016/j.bbagrm.2022.194845

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

Author(s): Lihua Liu, Evianne Rovers, Matthieu Schapira
Published in: Database, 2022, ISSN 1758-0463
Publisher: Oxford University Press
DOI: 10.1093/database/baac088

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

Author(s): Isigkeit, L.; Chaikuad, A.; Merk, D
Published in: Molecules, 2022, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules27082513

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

Author(s): Sonia Youhanna, Volker M. Lauschke
Published in: Journal of Pharmaceutical Sciences, Issue 110/1, 2021, Page(s) 50-65, ISSN 0022-3549
Publisher: John Wiley & Sons Inc.
DOI: 10.1016/j.xphs.2020.07.001

Longitudinal assessment of reactivity and affinity profile of anti-Jo1 autoantibodies to distinct HisRS domains and a splice variant in a cohort of patients with myositis and anti-synthetase syndrome

Author(s): Notarnicola A, Preger C, Lundström SL, Renard N, Wigren E, Van Gompel E, Galindo-Feria AS, Persson H, Fathi M, Grunewald J, Jakobsson PJ, Gräslund S, Lundberg IE, Fernandes-Cerqueira C
Published in: Arthritis research and therapy, 2022, ISSN 1478-6362
Publisher: Springer Nature
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Target 2035 – an update on private sector contributions

Author(s): 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
Published in: RSC Medicinal Chemistry, 2022, ISSN 2040-2503
Publisher: Royal Society of Chemistry
DOI: 10.1039/d2md00441k

Recent developments in in vitro and in vivo models for improved translation of preclinical pharmacokinetics and pharmacodynamics data

Author(s): Jaydeep Yadav, Mehdi El Hassani, Jasleen Sodhi, Volker M. Lauschke, Jessica H. Hartman & Laura E. Russell
Published in: Drug Metabolism Reviews, 2021, ISSN 0360-2532
Publisher: Marcel Dekker Inc.
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Assessing reversible and irreversible binding effects of kinase covalent inhibitors through ADP-Glo assays.

Author(s): 37. Schröder M, Chaikuad A.
Published in: Star Protocols, 2021, ISSN 2666-1667
Publisher: Elsevier
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The human pseudouridine synthase PUS7 recognizes RNA with an extended multi-domain binding surface.

Author(s): Guegueniat J, Halabelian L, Zeng H, Dong A, Li Y, Wu H, Arrowsmith CH, Kothe U
Published in: Nucleic Acids Res, 2021, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab934

Human resident liver myeloid cells protect against metabolic stress in obesity

Author(s): 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
Published in: Nature Metabolism, 2023, ISSN 2522-5812
Publisher: Nature
DOI: 10.1038/s42255-023-00834-7

Assembly and Application of a Low Budget Photoreactor**

Author(s): Olov Wallner, Kirill Mamonov, Florian Ortis, Dana Michel, Maurice Michel
Published in: Chemistry–Methods, Issue 1/5, 2021, Page(s) 240-244, ISSN 2628-9725
Publisher: Wiley-VCH GmbH
DOI: 10.1002/cmtd.202100022

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

Author(s): Lesbon JCC, Garnica TK, Xavier PLP, Rochetti AL, Reis RM, Müller S, Fukumasu H.
Published in: International Journal of Molecular Sciences, 2022, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
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Calcium/calmodulin-dependent protein kinase kinase 2 regulates hepatic fuel metabolism

Author(s): 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.
Published in: Mol Metab, 2022, ISSN 2212-8778
Publisher: Elsevier GmbH
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Chemical Toolkit for PARK7: Potent, Selective, and High-Throughput

Author(s): Yuqing Jia, Robbert Q. Kim, Raymond Kooij, Huib Ovaa, Aysegul Sapmaz*, and Paul P. Geurink*
Published in: J Med Chem, 2022, ISSN 0022-2623
Publisher: American Chemical Society
DOI: 10.1021/acs.jmedchem.2c01113

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

Author(s): Aurino M. Kemas, Sonia Youhanna, Reza Zandi Shafagh, Volker M. Lauschke
Published in: The FASEB Journal, Issue 35/3, 2021, ISSN 0892-6638
Publisher: Federation of American Societies for Experimental Biology
DOI: 10.1096/fj.202001989rr

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

Author(s): Erdogdu U, Dolgikh N, Laszig S, Särchen V, Meister MT, Wanior M, Knapp S, Boedicker C
Published in: Neoplasia, 2022, ISSN 1522-8002
Publisher: Elsevier BV
DOI: 10.1016/j.neo.2021.11.012

Detection of antibodies against the huntingtin protein in human plasma.

Author(s): Denis HL, Alpaugh M, Alvarez CP, Fenyi A, Barker RA, Chouinard S, Arrowsmith CH, Melki R, Labib R, Harding RJ, Cicchetti F
Published in: Cell Mol Life Sci, 2023, ISSN 1420-682X
Publisher: Birkhauser Verlag
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Rare genetic variability in human drug target genes modulates drug response and can guide precision medicine

Author(s): Zhou, Y., Arribas, G. H., Turku, A., Jürgenson, T., Mkrtchian, S., Krebs, K., ... & Lauschke, V. M.
Published in: Science Advances, 2021, ISSN 2375-2548
Publisher: American Association for the Advancement of Science
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A Chemical Toolbox for Labeling and Degrading Engineered Cas Proteins

Author(s): Gama-Brambila RA, Chen J, Dabiri Y, Tascher G, Němec V, Münch C, Song G, Knapp S, Cheng X.
Published in: JACS Au, 2021, ISSN 2691-3704
Publisher: American Chemical Society
DOI: 10.1021/jacsau.1c00007

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

Author(s): 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
Published in: Adv Sci (Weinh), 2022, ISSN 2198-3844
Publisher: John Wiley and Sons
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Amide-to-ester substitution as a strategy for optimizing PROTAC permeability and cellular activity

Author(s): Victoria G. Klein; Adam G. Bond; Conner Craigon; R. Scott Lokey; Alessio Ciulli
Published in: Journal of Medicinal Chemistry, Issue 2, 2021, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/acs.jmedchem.1c01496

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

Author(s): Nicole Wesch, Frank Löhr, Natalia Rogova, Volker Dötsch, Vladimir V. Rogov
Published in: International Journal of Molecular Sciences, Issue 22/14, 2021, Page(s) 7390, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
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The MYC oncoprotein directly interacts with its chromatin cofactor PNUTS to recruit PP1 phosphatase.

Author(s): Wei Y, Redel C, Ahlner A, Lemak A, Johansson-Ã…khe I, Houliston S, Kenney TMG, Tamachi A, Morad V, Duan S, Andrews DW, Wallner B, Sunnerhagen M, Arrowsmith CH, Penn LZ
Published in: Nucleic Acids Res, 2022, ISSN 0305-1048
Publisher: Oxford University Press
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The Structure-Based Design of SARS-CoV-2 nsp14 Methyltransferase Ligands Yields Nanomolar Inhibitors.

Author(s): Otava T, Å Ã¡la M, Li F, FanfrlÃ-k J, Devkota K, Perveen S, Chau I, Pakarian P, Hobza P, Vedadi M, Boura E, Nencka R
Published in: ACS Infect Dis, 2021, ISSN 2373-8227
Publisher: American Chemical Society
DOI: 10.1021/acsinfecdis.1c00131

Discovery of a Chemical Probe to Study Implications of BPTF Bromodomain Inhibition in Cellular and in vivo Experiments

Author(s): Martinelli P., Schaaf O., Mantoulidis A., Martin L., Fuchs JE., Bader G., Gollner A., Wolkerstorfer B., Rogers C., Balıkçı E., Lipp J., Mischerikow N., Doebel S., Gerstberger T., Sommergruber W., Huber KVM., Böttcher J.
Published in: ChemMedChem, 2023, ISSN 1860-7179
Publisher: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/cmdc.202200686

In vitro and ex vivo modeling of enteric bacterial infections

Author(s): Taebnia, N., Römling, U., Lauschke, V.M
Published in: Gut Microbes, 2022, ISSN 1949-0976
Publisher: Landes Bioscience
DOI: 10.1080/19490976.2022.2158034

Single tracer-based protocol for broad-spectrum kinase profiling in live cells with NanoBRET

Author(s): Robers MB, Wilkinson JM, Vasta JD, Berger LM, Berger BT, Knapp S.
Published in: Star Protoc, 2021, ISSN 2666-1667
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Structure and Inhibitor Binding Characterization of Oncogenic MLLT1 Mutants

Author(s): Xiaomin Ni, Allyn T. Londregan, Dafydd R. Owen, Stefan Knapp, Apirat Chaikuad
Published in: ACS Chemical Biology, Issue 16/4, 2021, Page(s) 571-578, ISSN 1554-8929
Publisher: American Chemical Society
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Exploiting vulnerabilities of SWI/SNF chromatin remodelling complexes for cancer therapy

Author(s): Marek Wanior, Andreas Krämer, Stefan Knapp, Andreas C. Joerger
Published in: Oncogene, 2021, ISSN 0950-9232
Publisher: Nature Publishing Group
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Arginine ADP-Ribosylation: Chemical Synthesis of Post-Translationally Modified Ubiquitin Proteins

Author(s): Voorneveld J, Kloet MS, Wijngaarden S, Kim RQ, Moutsiopoulou A, Verdegaal M, Misra M, Đikić I, van der Marel GA, Overkleeft HS, Filippov DV, van der Heden van Noort GJ
Published in: Journal of the AMerican Chemical Societyf, 2022, ISSN 0002-7863
Publisher: American Chemical Society
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Sequence and structural variations determining the recruitment of WNK kinases to the KLHL3 E3 ligase.

Author(s): Chen, Z., Zhang, J., Murillo-de-Ozores, A. R., Castaneda-Bueno, M., D'Amico, F., Heilig, R., Manning, C. E., Sorrell, F. J., D'Angiolella, V., Fischer, R., Mulder, M. P. C., Gamba, G., Alessi, D. R. and Bullock, A. N.
Published in: Biochem J., 2022, ISSN 0264-6021
Publisher: Portland Press, Ltd.
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A chemical probe targeting the PWWP domain alters NSD2 nucleolar localization.

Author(s): Dilworth D, Hanley RP, Ferreira de Freitas R, Allali-Hassani A, Zhou M, Mehta N, Marunde MR, Ackloo S, Carvalho Machado RA, Khalili Yazdi A, Owens DDG, Vu V, Nie DY, Alqazzaz M, Marcon E, Li F, Chau I, Bolotokova A, Qin S, Lei M, Liu Y, Szewczyk MM, Dong A, Kazemzadeh S, Abramyan T, Popova IK, Hall NW, Meiners MJ, Cheek MA, Gibson E, Kireev D, Greenblatt JF, Keogh MC, Min J, Brown PJ, Vedadi M, Ar
Published in: Nat Chem Biol, 2021, ISSN 1552-4450
Publisher: Nature Publishing Group
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Cellular shape reinforces niche to stem cell signaling in the small intestine

Author(s): Pentinmikko N, Lozano R, Scharaw S, Andersson S, Englund JI, Castillo-Azofeifa D, Gallagher A, Broberg M, Song KY, Sola Carvajal A,Speidel AT, Sundstrom M, Allbritton N, Stevens MM ,Klein OD , Teixeira A ,Katajisto P
Published in: Science Advances, 2022, ISSN 2375-2548
Publisher: AAAS
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Current Advances in CETSA

Author(s): Tolvanen, TA
Published in: Frontiers in Molecular Biosciences, 2022, ISSN 2296-889X
Publisher: Frontiers Media S.A
DOI: 10.3389/fmolb.2022.866764

PRMT5 regulates ATF4 transcript splicing and oxidative stress response.

Author(s): Szewczyk MM, Luciani GM, Vu V, Murison A, Dilworth D, Barghout SH, Lupien M, Arrowsmith CH, Minden MD, Barsyte-Lovejoy D
Published in: Redox Biol, 2022, ISSN 2213-2317
Publisher: Elsevier BV
DOI: 10.1016/j.redox.2022.102282

Structural and functional characterization of ubiquitin variant inhibitors for the JAMM-family deubiquitinases STAMBP and STAMBPL1.

Author(s): Guo Y, Liu Q, Mallette E, Caba C, Hou F, Fux J, LaPlante G, Dong A, Zhang Q, Zheng H, Tong Y, Zhang W
Published in: J Biol Chem, 2021, ISSN 0021-9258
Publisher: American Society for Biochemistry and Molecular Biology Inc.
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Chemical Starting Matter for HNF4α Ligand Discovery and Chemogenomics

Author(s): Isabelle Meijer, Sabine Willems, Xiaomin Ni, Jan Heering, Apirat Chaikuad, Daniel Merk
Published in: International Journal of Molecular Sciences, Issue 21/21, 2020, Page(s) 7895, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
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Human MettL3-MettL14 RNA adenine methyltransferase complex is active on double-stranded DNA containing lesions.

Author(s): Yu D, Horton JR, Yang J, Hajian T, Vedadi M, Sagum CA, Bedford MT, Blumenthal RM, Zhang X, Cheng X
Published in: Nucleic Acids Res, 2021, ISSN 0305-1048
Publisher: Oxford University Press
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Stopping pandemics before they start: Lessons learned from SARS-CoV-2

Author(s): Edwards AM, Baric RS, Saphire EO, Ulmer JB
Published in: Science, 2022, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
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A pro-Fluorescent Ubiquitin-based Probe to Monitor Cysteine-based E3 Ligase Activity

Author(s): David Pérez Berrocal, Thimmalapura Vishwanatha, Daniel Horn Ghetko, Josephine Bosch, laura hehl, Sebastian Kostrhon, Mohit Misra, Ivan Dikic, Paul geurink, hans van dam, Brenda Schulman, Monique Priscilla Catharina Mulder
Published in: Angewandte, 2023, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202303319

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

Author(s): Yitian Zhou, Volker M. Lauschke
Published in: Clinical Pharmacology & Therapeutics, 2021, ISSN 0009-9236
Publisher: Nature Publishing Group
DOI: 10.1002/cpt.2289

Binding Adaptation of GS-441524Diversifies Macro Domains and Down-regulates SARS-CoV-2 de-MARylationCapacity

Author(s): Tsika AC, Gallo A, Fourkiotis NK, Argyriou AI, Sreeramulu S, Löhr F, Rogov VV, Richter C, Linhard V, Gande SL, Altincekic N, Krishnathas R, Elamri I, Schwalbe H, Wollenhaupt J, Weiss MS, Spyroulias GA.
Published in: JMB, 2022, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2022.167720

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

Author(s): Leyre Pernaute-Lau, Ayola Akim Adegnika, Yitian Zhou, Jeannot F. Zinsou, Jose Pedro Gil, Sanjeev Krishna, Peter G. Kremsner, Volker M. Lauschke, Thirumalaisamy P. Velavan
Published in: Antimicrobial Agents and Chemotherapy, Issue 65/7, 2021, ISSN 0066-4804
Publisher: American Society for Microbiology
DOI: 10.1128/aac.00275-21

Open resources for chemical probes and their implications for future drug discovery

Author(s): Balıkçı E., Marques A-SMC., Hansen JS., Huber KVM.
Published in: Expert Opinion on Drug Discovery, 2023, ISSN 1746-0441
Publisher: Informa Healthcare
DOI: 10.1080/17460441.2023.2199979

Automated Determination of Nuclear Magnetic Resonance Chemical Shift Perturbations in Ligand Screening Experiments: The PICASSO Web Server

Author(s): Laveglia, V., Giachetti, A., Cerofolini, L., Haubrich, K., Fragai, M., Ciulli, A., Rosato, A.
Published in: Journal of Chemical Information and Modeling, 2021, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.1c00871

Discovery of Conformationally Constrained ALK2 Inhibitors

Author(s): Héctor González-Álvarez; Deeba Ensan; Tao Xin; Jong Fu Wong; Carlos A. Zepeda-Velázquez; Julien Cros; Melissa N. Sweeney; Laurent Hoffer; Taira Kiyota; Brian J. Wilson; Ahmed Aman; Owen Roberts; Methvin B. Isaac; Alex N. Bullock; David Smil; Rima Al-awar
Published in: Crossref, Issue 45, 2024, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/acs.jmedchem.3c02308

Image-Based Annotation of Chemogenomic Libraries for Phenotypic Screening

Author(s): Tjaden A, Chaikuad A, Kowarz E, Marschalek R, Knapp S, Schröder M, Müller S.
Published in: Molecules, 2022, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules27041439

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

Author(s): 9. Weng JH, Aoto PC, Lorenz R, Wu J, Schmidt SH, Manschwetus JT, Kaila-Sharma P, Silletti S, Mathea S, Chatterjee D, Knapp S, Herberg FW, Taylor SS.
Published in: PLoS Biol, 2022, ISSN 1544-9173
Publisher: Public Library of Science
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Bioengineered Pancreas–Liver Crosstalk in a Microfluidic Coculture Chip Identifies Human Metabolic Response Signatures in Prediabetic Hyperglycemia

Author(s): Zandi Shafagh, R., Youhanna, S., Keulen, J., Shen, J.X., Taebnia, N., Preiss, L.C., Klein, K., Büttner, F., Bergqvist, M., van der Wijngaart, W., Lauschke, V.M
Published in: Advanced Science, 2022, ISSN 2198-3844
Publisher: Wiley-VCH
DOI: 10.1002/advs.202203368

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

Author(s): Monika Raab, Marcel Rak, Roberta Tesch, Khayal Gasimli, Sven Becker, Stefan Knapp, Klaus Strebhardt, Mourad Sanhaji
Published in: Cancers, Issue 13/15, 2021, Page(s) 3658, ISSN 2072-6694
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers13153658

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

Author(s): Ann-Sofie Jemth1, Emma Rose Scaletti, Evert Homan, Pål Stenmark, Thomas Helleday, and Maurice Michel
Published in: JBC, 2022, ISSN 0021-9258
Publisher: American Society for Biochemistry and Molecular Biology Inc.
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PRMT7 ablation stimulates anti-tumor immunity and sensitizes melanoma to immune checkpoint blockade.

Author(s): Srour N, Villarreal OD, Hardikar S, Yu Z, Preston S, Miller WH, Szewczyk MM, Barsyte-Lovejoy D, Xu H, Chen T, Del RincÃ³n SV, Richard S
Published in: Cell Rep, 2022, ISSN 2211-1247
Publisher: Cell Press
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The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods

Author(s): Barbara Zdrazil; Eloy Felix; Fiona Hunter; Emma J Manners; James Blackshaw; Sybilla Corbett; Marleen de Veij; Harris Ioannidis; David Mendez Lopez; Juan F Mosquera; Maria Paula Magarinos; Nicolas Bosc; Ricardo Arcila; Tevfik Kizilören; Anna Gaulton; A Patrícia Bento; Melissa F Adasme; Peter Monecke; Gregory A Landrum; Andrew R Leach
Published in: Nucleic Acids Research, 52 (D1), Issue 36, 2023, ISSN 0305-1048
Publisher: Oxford University Press
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Phosphorylation-linked complex profiling identifies assemblies required for Hippo signal integration

Author(s): Federico Uliana, Rodolfo Ciuffa, Ranjan Mishra, Andrea Fossati, Fabian Frommelt, Sabrina Keller, Martin Mehnert, Eivind Salmorin Birkeland, Frank van Drogen, Nevena Srejic, Matthias Peter, Nicolas Tapon, Ruedi Aebersold, Matthias Gstaiger
Published in: Molecular Systems Biology, Issue EMBO press, 2023, ISSN 1744-4292
Publisher: Nature Publishing Group
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Discovery of a Novel Class of Covalent Dual Inhibitors Targeting the Protein Kinases BMX and BTK

Author(s): Michael Forster, Xiaojun Julia Liang, Martin Schröder, Stefan Gerstenecker, Apirat Chaikuad, Stefan Knapp, Stefan Laufer, Matthias Gehringer
Published in: International Journal of Molecular Sciences, Issue 21/23, 2020, Page(s) 9269, ISSN 1422-0067
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Reprogramming Transcription Factors Oct4 and Sox2 Induce a BRD-Dependent Immunosuppressive Transcriptome in GBM-Propagating Cells.

Author(s): Ma T, Hu C, Lal B, Zhou W, Ma Y, Ying M, Prinos P, QuiÃ±ones-Hinojosa A, Lim M, Laterra J, Li Y
Published in: Cancer Res, 2021, ISSN 0008-5472
Publisher: American Association for Cancer Research
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A Toolbox for the Generation of Chemical Probes for Baculovirus IAP Repeat Containing Proteins

Author(s): Schwalm MP, Berger LM, Meuter MN, Vasta JD, Corona CR, Röhm S, Berger BT, Farges F, Beinert SM, Preuss F, Morasch V, Rogov VV, Mathea S, Saxena K, Robers MB, Müller S, Knapp S.
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Publisher: Frontiers Media
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RAS and PP2A activities converge on epigenetic gene regulation.

Author(s): Aakula A, Sharma M, Tabaro F, NÃ¤tkin R, Kamila J, Honkanen H, Schapira M, Arrowsmith C, Nykter M, Westermarck J
Published in: Life Sci Alliance, 2023, ISSN 2575-1077
Publisher: Life Science Alliance LLC
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Trends in kinase drug discovery: targets, indications and inhibitor design.

Author(s): 39. Attwood MM, Fabbro D, Sokolov AV, Knapp S, Schiöth HB
Published in: Nat Rev Drug Discov, 2021, ISSN 1474-1776
Publisher: Nature Publishing Group
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3D Adipose Tissue Culture Links the Organotypic Microenvironment to Improved Adipogenesis

Author(s): Joanne X. Shen, Morgane Couchet, Jérémy Dufau, Thais de Castro Barbosa, Maximilian H. Ulbrich, Martin Helmstädter, Aurino M. Kemas, Reza Zandi Shafagh, Marie‐Adeline Marques, Jacob B. Hansen, Niklas Mejhert, Dominique Langin, Mikael Rydén, Volker M. Lauschke
Published in: Advanced Science, 2021, Page(s) 2100106, ISSN 2198-3844
Publisher: Advanced Science
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The Chemical Probes Portal: an expert review-based public resource to empower chemical probe assessment, selection and use

Author(s): Antolin AA, Sanfelice D, Crisp A, Villasclaras Fernandez E, Mica IL, Chen Y, Collins I, Edwards A, Müller S, Al-Lazikani B, Workman P.
Published in: Nucleic Acids Research, 2022, ISSN 0305-1048
Publisher: Oxford University Press
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PharmVar GeneFocus: CYP2B6

Author(s): Zeruesenay Desta, Ahmed El‐Boraie, Li Gong, Andrew A Somogyi, Volker M. Lauschke, Collet Dandara, Kathrin Klein, Neil A. Miller, Teri E. Klein, Rachel F. Tyndale, Michelle Whirl‐Carrillo, Andrea Gaedigk
Published in: Clinical Pharmacology & Therapeutics, 2021, ISSN 0009-9236
Publisher: Nature Publishing Group
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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)

Author(s): Xingui Liu; Alexia Kalogeropulou; Sofia Domingos; Nikolai Makukhin; Raja Nirujogi; Francois Singh; Natalia Shpiro; Anton Saalfrank; Esther Sammler; Ian Ganley; Rui Moreira; Dario Alessi; Alessio Ciulli
Published in: Crossref, Issue 4, 2022, ISSN 0002-7863
Publisher: American Chemical Society
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Organotypic human ex vivo models for coronavirus disease 2019 research and drug development

Author(s): Sonia Youhanna, Shane C. Wright, Volker M. Lauschke
Published in: Current Opinion in Pharmacology, Issue 59, 2021, Page(s) 11-18, ISSN 1471-4892
Publisher: Elsevier BV
DOI: 10.1016/j.coph.2021.04.006

Dissecting the stability determinants of a challenging de novo protein fold using massively parallel design and experimentation.

Author(s): Kim TE, Tsuboyama K, Houliston S, Martell CM, Phoumyvong CM, Lemak A, Haddox HK, Arrowsmith CH, Rocklin GJ
Published in: Proc Natl Acad Sci U S A, 2022, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2122676119

Antecedent chromatin organization determines cGAS recruitment to ruptured micronuclei.

Author(s): MacDonald KM, Nicholson-Puthenveedu S, Tageldein MM, Khasnis S, Arrowsmith CH, Harding SM
Published in: Nat Commun, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-36195-8

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

Author(s): Anja Dölle, Bikash Adhikari, Andreas Krämer, Janik Weckesser, Nicola Berner, Lena-Marie Berger, Mathias Diebold, Magdalena M. Szewczyk, Dalia Barsyte-Lovejoy, Cheryl H. Arrowsmith, Jakob Gebel, Frank Löhr, Volker Dötsch, Martin Eilers, Stephanie Heinzlmeir, Bernhard Kuster, Christoph Sotriffer, Elmar Wolf, Stefan Knapp
Published in: Journal of Medicinal Chemistry, 2021, ISSN 0022-2623
Publisher: American Chemical Society
DOI: 10.1021/acs.jmedchem.1c00146

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

Author(s): Zhou, Y., Lauschke, V.M.
Published in: The Pharmacogenomics Journal, 2022, ISSN 1470-269X
Publisher: Nature Publishing Group
DOI: 10.1038/s41397-022-00288-2

3D human liver spheroids for translational pharmacology and toxicology

Author(s): Magnus Ingelman‐Sundberg, Volker M. Lauschke
Published in: Basic & Clinical Pharmacology & Toxicology, 2021, ISSN 1742-7835
Publisher: Nordic Pharmacological Society
DOI: 10.1111/bcpt.13587

Trivalent PROTACs enhance protein degradation via combined avidity and cooperativity

Author(s): Imaide, S., Riching, K.M., Makukhin, N., Vetma, V., Whitworth, C., Hughes, S.J., Trainor, N., Mahan, S.D., Murphy, N., Cowan, A.D., Chan, K.-H., Craigon, C., Testa, A., Maniaci, C., Urh, M., Daniels, D.L.; Ciulli, A.
Published in: Nature Chemical Biology, 2021, ISSN 1552-4450
Publisher: Nature Publishing Group
DOI: 10.1038/s41589-021-00878-4

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

Author(s): Zhou, Y. & Lauschke, V. M.
Published in: Human Genetics, 2021, ISSN 0340-6717
Publisher: Springer Verlag
DOI: 10.1007/s00439-021-02385-x

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

Author(s): Baltzer S, Bulatov T, Schmied C, Krämer A, Berger BT, Oder A, Walker-Gray R, Kuschke C, Zühlke K, Eichhorst J, Lehmann M, Knapp S, Weston J, von Kries JP, Süssmuth RD, Klussmann E.
Published in: Int J Mol Sci, 2022, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23020763

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

Author(s): Preuss, F.; Knapp,S.; Chatterjee,D.; Mathea,S.; Shrestha,S.; St-Germain,J.; Saha, S.; Kannan, N.; Raught,B.; Rottapel, R.
Published in: Structure, 2020, ISSN 0969-2126
Publisher: Cell Press
DOI: 10.1016/j.str.2020.07.016

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

Author(s): Eleanor Williams, Elise Riesebos, Georgina Kerr, Alex N. Bullock
Published in: Biomedicines, Issue 9/2, 2021, Page(s) 129, ISSN 2227-9059
Publisher: MDPI
DOI: 10.3390/biomedicines9020129

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

Author(s): Francesca D'Amico, Rishov Mukhopadhyay, Huib Ovaa, Monique P. C. Mulder
Published in: ChemBioChem, 2021, ISSN 1439-4227
Publisher: 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

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

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

Author(s): 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,
Published in: Science Advances, Issue 7/1, 2021, Page(s) eabe4724, ISSN 2375-2548
Publisher: 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

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

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

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

JAK Inhibitors — More Than Just Glucocorticoids

Author(s): Justin Stebbing, Volker M. Lauschke
Published in: New England Journal of Medicine, Issue 385/5, 2021, Page(s) 463-465, ISSN 0028-4793
Publisher: Massachusetts Medical Society
DOI: 10.1056/nejme2108667

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

Author(s): Ketley RF., Battistini F., Alagia A., Mondielli C., Iehl F., Balikçi E., Huber KVM., Orozco M., Gullerova M.
Published in: Cell Reports, 2022, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2022.111526

Development of potent dual BET/HDAC inhibitors<i>via</i>pharmacophore merging and structure-guided optimization

Author(s): 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
Published in: Crossref, Issue 5, 2023, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.07.18.547334

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

Author(s): Shane C. Wright, Volker M. Lauschke
Published in: The Journal of Physiology, 2023
Publisher: Wiley-Blackwell
DOI: 10.1113/jp284526

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