PUBLICATIONS

2023

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Ji, H.; Lu, X.; Zhao, S.; Wang, Q.; Liao, B.; Bauer, L. G.; Huber, K. V. M.; Luo, R.; Tian, R.; Tan, C. S. H. Target deconvolution with matrix-augmented pooling strategy reveals cell-specific drug-protein interactions. Cell Chem. Biol. 2023. DOI: https://doi.org/10.1016/j.chembiol.2023.08.002
 

Coleman, O. D.; Macdonald, J.; Thomson, B.; Ward, J. A.; Stubbs, C. J.; McAllister, T. E.; Clark, S.; Amin, S.; Cao, Y.; Abboud, M. I.; et al. Cyclic peptides target the aromatic cage of a PHD-finger reader domain to modulate epigenetic protein function. Chem. Sci. 2023. DOI: https://doi.org/10.1039/D2SC05944D

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Balıkçı, E.; Marques, A.-S. M. C.; Hansen, J. S.; Huber, K. V. M. Open resources for chemical probes and their implications for future drug discovery. Expert Opin Drug Discov 2023, 18 (5), 505-513. DOI: https://doi.org/10.1080/17460441.2023.2199979

 

Martinelli, P.; Schaaf, O.; Mantoulidis, A.; Martin, L. J.; Fuchs, J. E.; Bader, G.; Gollner, A.; Wolkerstorfer, B.; Rogers, C.; Balıkçı, E.; et al. Discovery of a Chemical Probe to Study Implications of BPTF Bromodomain Inhibition in Cellular and in vivo Experiments. ChemMedChem 2023, 18 (6), e202200686. DOI: https://doi.org/10.1002/cmdc.202200686

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Londregan, A. T.; Aitmakhanova, K.; Bennett, J.; Byrnes, L. J.; Canterbury, D. P.; Cheng, X.; Christott, T.; Clemens, J.; Coffey, S. B.; Dias, J. M.; et al. Discovery of High-Affinity Small-Molecule Binders of the Epigenetic Reader YEATS4. J Med Chem 2023, 66 (1), 460-472. https://doi.org/10.1021/acs.jmedchem.2c01421

 

2022

Ketley R.F., Battistini F., Alagia A., Mondielli C., Iehl F., Balikçi E., Huber K.V.M., Orozco M., Gullerova M., DNA double-strand break-derived RNA drives TIRR/53BP1 complex dissociation. Cell Rep. 2022 Oct 25;41(4):111526. https://doi.org/10.1016/j.celrep.2022.111526

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Rothweiler, E.M., Brennan P. E. and Huber, K. V. M., Covalent fragment-based ligand screening approaches for identification of novel ubiquitin proteasome system modulators, Biological Chemistry 403(4), pp.391-402. https://doi.org/10.1515/hsz-2021-0396

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Rothweiler, E. M.;  Stefaniak, J.;  Ward, J. A.;  Rogers, C.;  Balikci, E.; Huber, K. V. M., A chemical biology toolbox to investigate in-cell target engagement and specificity of PRMT5-inhibitors. bioRxiv 2022, 2022.01.20.477145. https://doi.org/10.1101/2022.01.20.477145

 

2021

Feyertag, F. and Huber, K.V., 2021. TP-MAP-an Integrated Software Package for the Analysis of 1D and 2D Thermal Profiling Data. bioRxiv.  https://doi.org/10.1101/2021.02.22.432361

Martin, J.G., Ward, J.A., Feyertag, F., Zhang, L., Couvertier, S., Guckian, K., Huber, K.V. and Johnson, D.S., 2021. Chemoproteomic Profiling of Covalent XPO1 Inhibitors to Assess Target Engagement and Selectivity. ChemBioChem 22, pp.2116-2123. https://doi.org/10.1002/cbic.202100038 - highlighted as VIP (Very Important Paper)

Pinto-Fernandez, A., Salio, M., Partridge, T., Chen, J., Vere, G., Greenwood, H., Olie, C.S., Damianou, A., Scott, H.C., Pegg, H.J. and Chiarenza, A., 2021. Deletion of the deISGylating enzyme USP18 enhances tumour cell antigenicity and radiosensitivity. British Journal of Cancer 124(4), pp.817-830. https://doi.org/10.1038/s41416-020-01167-y

Mackinnon, S.R., Krojer, T., Foster, W.R., Diaz-Saez, L., Tang, M., Huber, K.V., von Delft, F., Lai, K., Brennan, P.E., Arruda Bezerra, G. and Yue, W.W., 2021. Fragment Screening Reveals Starting Points for Rational Design of Galactokinase 1 Inhibitors to Treat Classic Galactosemia. ACS Chemical Biology 16(4), pp.586-595. https://doi.org/10.1021/acschembio.0c00498

2020

Ward, J.A., Pinto-Fernandez, A., Cornelissen, L., Bonham, S., Díaz-Sáez, L., Riant, O., Huber, K.V., Kessler, B.M., Feron, O. and Tate, E.W., 2020. Re-evaluating the mechanism of action of α, β-unsaturated carbonyl DUB inhibitors b-AP15 and VLX1570: a paradigmatic example of unspecific protein cross-linking with Michael acceptor motif-containing drugs. Journal of Medicinal Chemistry 63 (7), pp.3756-3762.  https://doi.org/10.1021/acs.jmedchem.0c00144

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Stefaniak, J., Galan, S.R. and Huber, K.V., 2020. Assays to Characterize the Cellular Pharmacology of a Chemical Probe. The Discovery and Utility of Chemical Probes in Target Discovery (pp. 247-275). 
https://pubs.rsc.org/en/content/ebook/978-1-78801-589-9

Stefaniak, J. and Huber, K.V., 2020. Importance of Quantifying Drug-Target Engagement in Cells. ACS Medicinal Chemistry Letters 11 (4), pp.403-406. https://doi.org/10.1021/acsmedchemlett.9b00570

Wells, C.I., Vasta, J.D., Corona, C.R., Wilkinson, J., Zimprich, C.A., Ingold, M.R., Pickett, J.E., Drewry, D.H., Pugh, K.M., Schwinn, M.K. and Hwang, B.B., 2020. Quantifying CDK inhibitor selectivity in live cells. Nature Communications 11 (1), pp.1-11.
https://doi.org/10.1038/s41467-020-16559-0
 

Robers, M. B.,  Friedman-Ohana, R.,  Huber, K. V. M.,  Kilpatrick, L.,  Vasta, J. D.,  Berger, B.-T.,  Chaudhry, C.,  Hill, S.,  Müller, S.,  Knapp, S., Wood, K. V., 2020. Quantifying Target Occupancy of Small Molecules Within Living Cells. Annual Review of Biochemistry 89 (1), pp. 557-581. https://doi.org/10.1146/annurev-biochem-011420-092302

 

Kidd, S.L., Fowler, E., Reinhardt, T., Compton, T., Mateu, N., Newman, H., Bellini, D., Talon, R., McLoughlin, J., Krojer, T. and Aimon, A., 2020. Demonstration of the utility of DOS-derived fragment libraries for rapid hit derivatisation in a multidirectional fashion. Chemical Science 11(39), pp.10792-10801. https://doi.org/10.1039/D0SC01232G

Khan Tareque, R., Hassell‐Hart, S., Krojer, T., Bradley, A., Velupillai, S., Talon, R., Fairhead, M., Day, I.J., Bala, K., Felix, R. and Kemmitt, P.D., 2020. Deliberately Losing Control of C− H Activation Processes in the Design of Small‐Molecule‐Fragment Arrays Targeting Peroxisomal Metabolism. ChemMedChem 15(24), pp.2513-2520. 
https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cmdc.202000543

2019

Vazquez‐Rodriguez, S., Wright, M., Rogers, C.M., Cribbs, A.P., Velupillai, S., Philpott, M., Lee, H., Dunford, J.E., Huber, K.V., Robers, M.B. and Vasta, J.D., 2019. Design, synthesis and characterization of covalent KDM5 inhibitors. Angewandte Chemie International Edition 58(2), pp.515-519. https://doi.org/10.1002/cmdc.202000543

Resnick, E., Bradley, A., Gan, J., Douangamath, A., Krojer, T., Sethi, R., Geurink, P.P., Aimon, A., Amitai, G., Bellini, D. and Bennett, J., 2019. Rapid covalent-probe discovery by electrophile-fragment screening. Journal of the American Chemical Society 141(22), pp.8951-8968. https://pubs.acs.org/doi/10.1021/jacs.9b02822

Scheer, S., Ackloo, S., Medina, T.S., Schapira, M., Li, F., Ward, J.A., Lewis, A.M., Northrop, J.P., Richardson, P.L., Kaniskan, H.Ü. and Shen, Y., 2019. A chemical biology toolbox to study protein methyltransferases and epigenetic signaling. Nature Communications 10(1), pp.1-14. https://doi.org/10.1038/s41467-018-07905-4

Böttcher, J., Dilworth, D., Reiser, U., Neumüller, R.A., Schleicher, M., Petronczki, M., Zeeb, M., Mischerikow, N., Allali-Hassani, A., Szewczyk, M.M. and Li, F., 2019. Fragment-based discovery of a chemical probe for the PWWP1 domain of NSD3. Nature Chemical Biology 15(8), pp.822-829. https://doi.org/10.1038/s41589-019-0310-x

Fagan, V., Johansson, C., Gileadi, C., Monteiro, O., Dunford, J.E., Nibhani, R., Philpott, M., Malzahn, J., Wells, G., Faram, R. and Cribbs, A.P., 2019. A chemical probe for tudor domain protein Spindlin1 to investigate chromatin function. Journal of Medicinal Chemistry 62(20), pp.9008-9025. https://doi.org/10.1021/acs.jmedchem.9b00562

Artarini, A., Meyer, M., Shin, Y.J., Huber, K., Hilz, N., Bracher, F., Eros, D., Orfi, L., Keri, G., Goedert, S. and Neuenschwander, M., 2019. Regulation of influenza A virus mRNA splicing by CLK1. Antiviral Research 168, pp.187-196. 
https://doi.org/10.1016/j.antiviral.2019.06.003


2018

Stefaniak, J., Lewis, A.M., Conole, D., Galan, S.R., Bataille, C.J., Wynne, G.M., Castaldi, M.P., Lundbäck, T., Russell, A.J. and Huber, K.V., 2018. Chemical instability and promiscuity of arylmethylidenepyrazolinone-based MDMX Inhibitors. ACS Chemical Biology 13(10), pp.2849-2854. https://pubs.acs.org/doi/10.1021/acschembio.8b00665

Vasta, J.D., Corona, C.R., Wilkinson, J., Zimprich, C.A., Hartnett, J.R., Ingold, M.R., Zimmerman, K., Machleidt, T., Kirkland, T.A., Huwiler, K.G. and Ohana, R.F., 2018. Quantitative, wide-spectrum kinase profiling in live cells for assessing the effect of cellular ATP on target engagement. Cell Chemical Biology 25(2), pp.206-214. https://doi.org/10.1016/j.chembiol.2017.10.010

Moustakim, M., Christott, T., Monteiro, O.P., Bennett, J., Giroud, C., Ward, J., Rogers, C.M., Smith, P., Panagakou, I., Díaz‐Sáez, L. and Felce, S.L., 2018. Discovery of an MLLT1/3 YEATS domain chemical probe. Angewandte Chemie International Edition 57(50), pp.16302-16307. https://doi.org/10.1002/anie.201810617

Rahm, F., Viklund, J., Trésaugues, L., Ellermann, M., Giese, A., Ericsson, U., Forsblom, R., Ginman, T., Günther, J., Hallberg, K. and Lindström, J., 2018. Creation of a novel class of potent and selective MutT homologue 1 (MTH1) inhibitors using fragment-based screening and structure-based drug design. Journal of Medicinal Chemistry 61(6), pp.2533-2551.  
https://doi.org/10.1021/acs.jmedchem.7b01884

Hrdinka, M., Schlicher, L., Dai, B., Pinkas, D.M., Bufton, J.C., Picaud, S., Ward, J.A., Rogers, C., Suebsuwong, C., Nikhar, S. and Cuny, G.D., 2018. Small molecule inhibitors reveal an indispensable scaffolding role of RIPK 2 in NOD 2 signaling. The EMBO Journal 37(17), p.e99372. https://doi.org/10.15252/embj.201899372


2017

Huber, K.V., 2017. Shining a light. Nature chemical biology, 13(2), pp.133-134. https://doi.org/10.1038/nchembio.2295

Bataille, C.J., Brennan, M.B., Byrne, S., Davies, S.G., Durbin, M., Fedorov, O., Huber, K.V., Jones, A.M., Knapp, S., Liu, G. and Nadali, A., 2017. Thiazolidine derivatives as potent and selective inhibitors of the PIM kinase family. Bioorganic & Medicinal Chemistry 25(9), pp.2657-2665. https://doi.org/10.1016/j.bmc.2017.02.056

Li, J., Casteels, T., Frogne, T., Ingvorsen, C., Honore, C., Courtney, M., Huber, K.V., Schmitner, N., Kimmel, R.A., Romanov, R.A. and Sturtzel, C., 2017. Artemisinins target GABAA receptor signaling and impair α cell identity. Cell 168(1-2), pp.86-100. https://doi.org/10.1016/j.cell.2016.11.010

Moustakim, M., Clark, P.G., Trulli, L., Fuentes de Arriba, A.L., Ehebauer, M.T., Chaikuad, A., Murphy, E.J., Mendez‐Johnson, J., Daniels, D., Hou, C.F.D. and Lin, Y.H., 2017. Discovery of a PCAF bromodomain chemical probe. Angewandte Chemie 129(3), pp.845-849. https://doi.org/10.1002/anie.201610816

Fernández-Montalván, A.E., Berger, M., Kuropka, B., Koo, S.J., Badock, V., Weiske, J., Puetter, V., Holton, S.J., Stöckigt, D., Ter Laak, A. and Centrella, P.A., 2017. Isoform-selective ATAD2 chemical probe with novel chemical structure and unusual mode of action. ACS Chemical Biology 12(11), pp.2730-2736. https://doi.org/10.1021/acschembio.7b00708

Vladimer, G.I., Snijder, B., Krall, N., Bigenzahn, J.W., Huber, K.V., Lardeau, C.H., Sanjiv, K., Ringler, A., Berglund, U.W., Sabler, M. and de la Fuente, O.L., 2017. Global survey of the immunomodulatory potential of common drugs. Nature Chemical Biology 13(6), p.681. https://doi.org/10.1038/nchembio.2360

Bouché, L., Christ, C.D., Siegel, S., Fernández-Montalván, A.E., Holton, S.J., Fedorov, O., Ter Laak, A., Sugawara, T., Stöckigt, D., Tallant, C. and Bennett, J., 2017. Benzoisoquinolinediones as potent and selective inhibitors of BRPF2 and TAF1/TAF1L bromodomains. Journal of Medicinal Chemistry 60(9), pp.4002-4022. https://doi.org/10.1021/acs.jmedchem.7b00306

2016

Huber, K.V. and Superti-Furga, G., 2016. Profiling of small molecules by chemical proteomics, Proteomics in Systems Biology (pp. 211-218). Humana Press, New York, NY. https://link.springer.com/protocol/10.1007%2F978-1-4939-3341-9_15

Martins, R., Maier, J., Gorki, A.D., Huber, K.V., Sharif, O., Starkl, P., Saluzzo, S., Quattrone, F., Gawish, R., Lakovits, K. and Aichinger, M.C., 2016. Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. Nature Immunology 17(12), pp.1361-1372. https://www.nature.com/articles/ni.3590

Sdelci, S., Lardeau, C.H., Tallant, C., Klepsch, F., Klaiber, B., Bennett, J., Rathert, P., Schuster, M., Penz, T., Fedorov, O. and Superti-Furga, G., 2016. Mapping the chemical chromatin reactivation landscape identifies BRD4-TAF1 cross-talk. Nature Chemical Biology 12(7), p.504. https://doi.org/10.1038/nchembio.2080

2015

Arrowsmith, C.H., Audia, J.E., Austin, C., Baell, J., Bennett, J., Blagg, J., Bountra, C., Brennan, P.E., Brown, P.J., Bunnage, M.E. and Buser-Doepner, C., 2015. The promise and peril of chemical probes. Nature Chemical Biology 11(8), pp.536-541.
https://doi.org/10.1038/nchembio.1867

Rebsamen, M., Pochini, L., Stasyk, T., de Araújo, M.E., Galluccio, M., Kandasamy, R.K., Snijder, B., Fauster, A., Rudashevskaya, E.L., Bruckner, M. and Scorzoni, S., 2015. SLC38A9 is a component of the lysosomal amino acid sensing machinery that controls mTORC1. Nature 519(7544), pp.477-481. https://doi.org/10.1038/nature14107

Grebien, F., Vedadi, M., Getlik, M., Giambruno, R., Grover, A., Avellino, R., Skucha, A., Vittori, S., Kuznetsova, E., Smil, D. and Barsyte-Lovejoy, D., 2015. Pharmacological targeting of the Wdr5-MLL interaction in C/EBPα N-terminal leukemia. Nature Chemical Biology 11(8), pp.571-578. https://doi.org/10.1038/nchembio.1859

Huber, K.V., Olek, K.M., Müller, A.C., Tan, C.S.H., Bennett, K.L., Colinge, J. and Superti-Furga, G., 2015. Proteome-wide drug and metabolite interaction mapping by thermal-stability profiling. Nature Methods 12(11), pp.1055-1057.
https://doi.org/10.1038/nmeth.3590

Babak, M.V., Meier, S.M., Huber, K.V., Reynisson, J., Legin, A.A., Jakupec, M.A., Roller, A., Stukalov, A., Gridling, M., Bennett, K.L. and Colinge, J., 2015. Target profiling of an antimetastatic RAPTA agent by chemical proteomics: relevance to the mode of action. Chemical Science 6(4), pp.2449-2456.https://doi.org/10.1039/C4SC03905J

2014

Huber, K.V., Salah, E., Radic, B., Gridling, M., Elkins, J.M., Stukalov, A., Jemth, A.S., Göktürk, C., Sanjiv, K., Strömberg, K. and Pham, T., 2014. Stereospecific targeting of MTH1 by (S)-crizotinib as an anticancer strategy. Nature 508(7495), pp.222-227.
https://doi.org/10.1038/nature13194

Winter, G.E., Radic, B., Mayor-Ruiz, C., Blomen, V.A., Trefzer, C., Kandasamy, R.K., Huber, K.V., Gridling, M., Chen, D., Klampfl, T. and Kralovics, R., 2014. The solute carrier SLC35F2 enables YM155-mediated DNA damage toxicity. Nature Chemical Biology 10(9), pp.768-773. https://doi.org/10.1038/nchembio.1590

Kern, S., Agarwal, S., Huber, K., Gehring, A.P., Strödke, B., Wirth, C.C., Brügl, T., Abodo, L.O., Dandekar, T., Doerig, C. and Fischer, R., 2014. Inhibition of the SR protein-phosphorylating CLK kinases of Plasmodium falciparum impairs blood stage replication and malaria transmission. PloS One 9(9), p.e105732. https://doi.org/10.1371/journal.pone.0105732

2013

Weirauch, U., Beckmann, N., Thomas, M., Grünweller, A., Huber, K., Bracher, F., Hartmann, R.K. and Aigner, A., 2013. Functional role and therapeutic potential of the pim-1 kinase in colon carcinoma. Neoplasia, 15(7), pp.783-IN28.
https://doi.org/10.1593/neo.13172

Emir, H., Albrecht-Schgoer, K., Huber, K., Grebien, F., Eisenwort, G., Schgoer, W., Kaun, C., Herndlhofer, S., Theurl, M., Cerny-Reiterer, S. and Hoermann, G., 2013. Nilotinib exerts direct pro-atherogenic and anti-angiogenic effects on vascular endothelial cells: a potential explanation for drug-induced vasculopathy in CML. https://doi.org/10.1038/leu.2017.245

2012 

Huber, K., Brault, L., Fedorov, O., Gasser, C., Filippakopoulos, P., Bullock, A.N., Fabbro, D., Trappe, J., Schwaller, J., Knapp, S. and Bracher, F., 2012. 7, 8-Dichloro-1-oxo-β-carbolines as a versatile scaffold for the development of potent and selective kinase inhibitors with unusual binding modes. Journal of Medicinal Chemistry 55(1), pp.403-413. https://doi.org/10.1021/jm201286z

2011

Fedorov, O., Huber, K., Eisenreich, A., Filippakopoulos, P., King, O., Bullock, A.N., Szklarczyk, D., Jensen, L.J., Fabbro, D., Trappe, J. and Rauch, U., 2011. Specific CLK inhibitors from a novel chemotype for regulation of alternative splicing. Chemistry & Biology 18(1), pp.67-76. https://doi.org/10.1016/j.chembiol.2010.11.009

Huber, K. and Superti-Furga, G., 2011. After the grape rush: sirtuins as epigenetic drug targets in neurodegenerative disorders. Bioorganic & Medicinal Chemistry 19(12), pp.3616-3624. https://doi.org/10.1016/j.bmc.2011.01.018

2010

Brault, L., Gasser, C., Bracher, F., Huber, K., Knapp, S. and Schwaller, J., 2010. PIM serine/threonine kinases in the pathogenesis and therapy of hematologic malignancies and solid cancers. haematologica 95(6), p.1004. https://doi.org/10.3324/haematol.2009.017079