DrugE3CRL's: Probing Druggability of Multisubunit Complexes: E3 Cullin RING Ligases (ERC Starting Grant)

2024

Stereochemical inversion at a 1,4-cyclohexyl PROTAC linker fine-tunes conformation and binding affinity

Pierri, M., Liu, X., Kroupova, A., Rutter, Z., Hallatt, A. J. & Ciulli, A. (Lead / Corresponding author), 15 Sept 2024, In: Bioorganic & Medicinal Chemistry Letters. 110, 6 p., 129861.

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

Diehl, C. J., Salerno, A. & Ciulli, A. (Lead / Corresponding author), 17 Jun 2024, In: Angewandte Chemie International Edition. 63, 25, e202319456.

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2023

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

Haubrich, K., Spiteri, V., Farnaby, W., Sobott, F. & Ciulli, A. (Lead / Corresponding author), Apr 2023, In: Current Opinion in Structural Biology. 79, 9 p., 102534.

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4 Citations (Scopus)

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Expanding the Structural Diversity at the Phenylene Core of Ligands for the von Hippel-Lindau E3 Ubiquitin Ligase: Development of Highly Potent Hypoxia-Inducible Factor-1α Stabilizers

Vu, L. P., Diehl, C. J., Casement, R., Bond, A. G., Steinebach, C., Strašek, N., Bricelj, A., Perdih, A., Schnakenburg, G., Sosič, I., Ciulli, A. (Lead / Corresponding author) & Gütschow, M. (Lead / Corresponding author), 28 Sept 2023, In: Journal of Medicinal Chemistry. 66, 18, p. 12776-12811 36 p.

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2 Citations (Scopus)

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Functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders

Hanzl, A., Casement, R., Imrichova, H., Hughes, S. J., Barone, E., Testa, A., Bauer, S., Wright, J., Brand, M., Ciulli, A. (Lead / Corresponding author) & Winter, G. E. (Lead / Corresponding author), Mar 2023, In: Nature Chemical Biology. 19, p. 323-333 11 p.

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41 Citations (Scopus)

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Structure-based design of a phosphotyrosine-masked covalent ligand targeting the E3 ligase SOCS2

Ramachandran, S., Makukhin, N., Haubrich, K., Nagala, M., Forrester, B., Lynch, D. M., Casement, R., Testa, A., Bruno, E., Gitto, R. & Ciulli, A. (Lead / Corresponding author), 10 Oct 2023, In: Nature Communications. 14, 17 p., 6345.

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6 Citations (Scopus)

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2022

Development of NanoLuc-targeting protein degraders and a universal reporter system to benchmark tag-targeted degradation platforms

Grohmann, C., Magtoto, C. M., Walker, J. R., Chua, N. K., Gabrielyan, A., Hall, M., Cobbold, S. A., Mieruszynski, S., Brzozowski, M., Simpson, D. S., Dong, H., Dorizzi, B., Jacobsen, A. V., Morrish, E., Silke, N., Murphy, J. M., Heath, J. K., Testa, A., Maniaci, C. & Ciulli, A. & 3 others, Lessene, G., Silke, J. & Feltham, R. (Lead / Corresponding author), 19 Apr 2022, In: Nature Communications. 13, p. 1-13 13 p., 2073.

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13 Citations (Scopus)

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Discovery of small molecule ligands for the von Hippel-Lindau (VHL) E3 ligase and their use as inhibitors and PROTAC degraders

Diehl, C. J. & Ciulli, A. (Lead / Corresponding author), 19 Aug 2022, In: Chemical Society Reviews. 51, 19, p. 8216-8257 42 p.

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62 Citations (Scopus)

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2021

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

Ramachandran, S. & Ciulli, A. (Lead / Corresponding author), Apr 2021, In: Current Opinion in Structural Biology. 67, p. 110-119 10 p.

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33 Citations (Scopus)

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Development of BromoTag: A “Bump-&-Hole”-PROTAC system to induce potent, rapid, and selective degradation of tagged target proteins

Bond, A. G., Craigon, C., Chan, K. H., Testa, A., Karapetsas, A., Fasimoye, R., Macartney, T., Blow, J. J., Alessi, D. R. & Ciulli, A. (Lead / Corresponding author), 28 Oct 2021, In: Journal of Medicinal Chemistry. 64, 20, p. 15477-15502 26 p.

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47 Citations (Scopus)

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

Ishida, T. & Ciulli, A. (Lead / Corresponding author), 1 Apr 2021, In: SLAS Discovery. 26, 4, p. 484-502 19 p.

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171 Citations (Scopus)

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Estimating the cooperativity of PROTAC-induced ternary complexes using ¹⁹F NMR displacement assay

de Castro, G. V. & Ciulli, A. (Lead / Corresponding author), Oct 2021, In: RSC Medicinal Chemistry. 12, p. 1765-1770 6 p.

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10 Citations (Scopus)

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Mechanistic and Structural Features of PROTAC Ternary Complexes

Casement, R., Bond, A., Craigon, C. & Ciulli, A. (Lead / Corresponding author), 2021, Targeted Protein Degradation: Methods and Protocols. Cacace, A. M., Hickey, C. M. & Békés, M. (eds.). 1 ed. New York: Humana Press, p. 79-113 35 p. (Methods in Molecular Biology; vol. 2365).

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33 Citations (Scopus)

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Recent advances in synthetic and medicinal chemistry of phosphotyrosine and phosphonate-based phosphotyrosine analogues

Makukhin, N. & Ciulli, A. (Lead / Corresponding author), Jan 2021, In: RSC Medicinal Chemistry. 12, 1, p. 8-23 16 p.

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17 Citations (Scopus)

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Targeting non-canonical activation of GLI1 by the SOX2-BRD4 transcriptional complex improves the efficacy of HEDGEHOG pathway inhibition in melanoma

Pietrobono, S. (Lead / Corresponding author), Gaudio, E., Gagliardi, S., Zitani, M., Carrassa, L., Migliorini, F., Petricci, E., Manetti, F., Makukhin, N., Bond, A. G., Paradise, B. D., Ciulli, A., Fernandez-Zapico, M. E., Bertoni, F. & Stecca, B. (Lead / Corresponding author), 3 Jun 2021, In: Oncogene. 40, p. 3799-3814 16 p.

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28 Citations (Scopus)

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Trivalent PROTACs enhance protein degradation via combined avidity and cooperativity

Imaide, S., Riching, K. M., Makukhin, N., Vetma, V., Whitworth, C., Hughes, S. J., Trainor, N., Mahan, S. D., Murphy, N., Cowan, A., Chan, K.-H., Craigon, C., Test, A., Maniai, C., Urh, M., Daniels, D. L. & Ciulli, A. (Lead / Corresponding author), Nov 2021, In: Nature Chemical Biology. 17, 11, p. 1157-1167 11 p.

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121 Citations (Scopus)

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Von Hippel-Lindau (VHL) small molecule inhibitor binding increases stability and intracellular levels of VHL protein

Frost, J., Rocha, S. (Lead / Corresponding author) & Ciulli, A. (Lead / Corresponding author), Aug 2021, In: Journal of Biological Chemistry. 297, 2, 12 p., 100910.

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16 Citations (Scopus)

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2020

Inducible Degradation of Target Proteins through a Tractable Affinity-Directed Protein Missile System

Simpson, L. M., Macartney, T. J., Nardin, A., Fulcher, L. J., Röth, S., Testa, A., Maniaci, C., Ciulli, A., Ganley, I. G. & Sapkota, G. P. (Lead / Corresponding author), 17 Sept 2020, In: Cell Chemical Biology. 27, 9, p. 1164-1180.e5 17 p.

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42 Citations (Scopus)

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Stereoselective synthesis of allele-specific BET inhibitors

Bond, A., Testa, A. & Ciulli, A. (Lead / Corresponding author), 14 Oct 2020, In: Organic and Biomolecular Chemistry. 18, 38, p. 7533-7539 7 p.

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4 Citations (Scopus)

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Structure-Based Design of a Macrocyclic PROTAC

Testa, A., Hughes, S. J., Lucas, X., Wright, J. E. & Ciulli, A. (Lead / Corresponding author), 20 Jan 2020, In: Angewandte Chemie International Edition. 59, 4, p. 1727-1734 8 p.

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157 Citations (Scopus)

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2019

Bifunctional chemical probes inducing protein-protein interactions

Maniaci, C. & Ciulli, A. (Lead / Corresponding author), Oct 2019, In: Current Opinion in Chemical Biology. 52, p. 145-156 12 p.

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74 Citations (Scopus)

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Cereblon versus VHL: Hijacking E3 ligases against each other using PROTACs

Girardini, M., Maniaci, C., Hughes, S. J., Testa, A. & Ciulli, A. (Lead / Corresponding author), 15 Jun 2019, In: Bioorganic & Medicinal Chemistry. 27, 12, p. 2466-2479 14 p.

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95 Citations (Scopus)

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Design and Characterization of SGK3-PROTAC1, an Isoform Specific SGK3 Kinase PROTAC Degrader

Tovell, H., Testa, A., Zhou, H., Shpiro, N., Crafter, C., Ciulli, A. (Lead / Corresponding author) & Alessi, D. (Lead / Corresponding author), 20 Sept 2019, In: ACS Chemical Biology. 14, 9, p. 2024-2034 11 p.

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72 Citations (Scopus)

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Iterative design and optimization of initially inactive Proteolysis Targeting Chimeras (PROTACs) identify VZ185 as a potent, fast and selective von Hippel-Lindau (VHL)-based dual degrader probe of BRD9 and BRD7

Zoppi, V., Hughes, S. J., Maniaci, C., Testa, A., Gmaschitz, T., Wieshofer, C., Koegl, M., Riching, K. M., Daniels, D. L., Spallarossa, A. & Ciulli, A. (Lead / Corresponding author), 24 Jan 2019, In: Journal of Medicinal Chemistry. 62, 2, p. 699-726 28 p.

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234 Citations (Scopus)

605 Downloads (Pure)

Rapid and reversible knockdown of endogenously tagged endosomal proteins via an optimized HaloPROTAC degrader

Tovell, H., Testa, A., Maniaci, C., Zhou, H., Prescott, A., Macartney, T., Ciulli, A. (Lead / Corresponding author) & Alessi, D. (Lead / Corresponding author), 17 May 2019, In: ACS Chemical Biology. 14, 5, p. 882-892 11 p.

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85 Citations (Scopus)

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RNA-seq analysis of PHD and VHL inhibitors reveals differences and similarities to the hypoxia response

Frost, J., Ciulli, A. (Lead / Corresponding author) & Rocha, S. (Lead / Corresponding author), 29 Jan 2019, In: Wellcome Open Research. 4, p. 1-17 17 p., 17.

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11 Citations (Scopus)

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SPR-measured dissociation kinetics of PROTAC ternary complexes influence target degradation rate

Roy, M., Winkler, S., Hughes, S. J., Whitworth, C., Galant, M., Farnaby, W., Rumpel, K. & Ciulli, A. (Lead / Corresponding author), 15 Mar 2019, In: ACS Chemical Biology. 14, 3, p. 361-368 8 p.

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204 Citations (Scopus)

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Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase

Kung, W.-W., Ramachandran, S., Makukhin, N., Bruno, E. & Ciulli, A. (Lead / Corresponding author), 10 Jun 2019, In: Nature Communications. 10, 1, p. 1-14 14 p., 2534.

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25 Citations (Scopus)

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2018

3-Fluoro-4-hydroxyprolines: Synthesis, conformational analysis and stereoselective recognition by the VHL E3 ubiquitin ligase for targeted protein degradation

Testa, A., Lucas, X., Castro, G., Chan, K. H., Wright, J., Runcie, A., Gadd, M., Harrison, W. T. A., Ko, E. J., Fletcher, D. & Ciulli, A. (Lead / Corresponding author), 25 Jul 2018, In: Journal of the American Chemical Society. 140, 29, p. 9299-9313 15 p.

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103 Citations (Scopus)

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Group-based optimization of potent and cell-active inhibitors of the von Hippel-Lindau (VHL) E3 ubiquitin ligase: structure-activity relationships leading to the chemical probe (2S,4R)-1-((S)-2-(1-cyanocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (VH298)

Soares, P., Gadd, M., Frost, J., Galdeano, C., Ellis, L., Epemolu, R., Rocha, S., Read, K. & Ciulli, A. (Lead / Corresponding author), 25 Jan 2018, In: Journal of Medicinal Chemistry. 61, p. 599-618 19 p.

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107 Citations (Scopus)

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Impact of target warhead and linkage vector on inducing protein degradation: comparison of Bromodomain and Extra-Terminal (BET) degraders derived from triazolodiazepine (JQ1) and tetrahydroquinoline (I-BET726) BET inhibitor scaffolds

Chan, K. H., Zengerle, M., Testa, A. & Ciulli, A. (Lead / Corresponding author), 25 Jan 2018, In: Journal of Medicinal Chemistry. 61, 2, p. 504-513 10 p.

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161 Citations (Scopus)

344 Downloads (Pure)

Optimization of a “Bump-and-Hole” Approach to Allele-Selective BET Bromodomain Inhibition

Runcie, A., Zengerle, M., Chan, K. H., Testa, A., Van Beurden, L., Baud, M., Epemolu, R., Ellis, L., Read, K., Coulthard, V., Brien, A. & Ciulli, A. (Lead / Corresponding author), 7 Mar 2018, In: Chemical Science. 9, 9, p. 2452-2468 17 p., 2452.

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34 Citations (Scopus)

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Surface probing by fragment-based screening and computational methods identifies ligandable pockets on the von Hippel-Lindau (VHL) E3 ubiquitin ligase

Lucas, X., van Molle, I. & Ciulli, A. (Lead / Corresponding author), 23 Aug 2018, In: Journal of Medicinal Chemistry. 61, 16, p. 7387-7393 7 p.

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23 Citations (Scopus)

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Targeting ligandable pockets on PHD zinc finger domains by a fragment-based approach

Amato, A., Lucas, X., Bortoluzzi, A., Wright, D. & Ciulli, A. (Lead / Corresponding author), 20 Apr 2018, In: ACS Chemical Biology. 13, 4, p. 915-921 7 p.

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24 Citations (Scopus)

248 Downloads (Pure)

Thioamide substitution to probe the hydroxyproline recognition of VHL ligands

Soares, P., Lucas, X. & Ciulli, A. (Lead / Corresponding author), 15 Jul 2018, In: Bioorganic & Medicinal Chemistry. 26, 11, p. 2992-2995 4 p.

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16 Citations (Scopus)

207 Downloads (Pure)

2017

Allosteric targeting of the Fanconi anemia ubiquitin-conjugating enzyme Ube2T by fragment screening

Morreale, F., Bortoluzzi, A., Chaugule, V., Arkinson, C., Walden, H. & Ciulli, A. (Lead / Corresponding author), 11 May 2017, In: Journal of Medicinal Chemistry. 60, 9, p. 4093-4098 6 p.

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25 Citations (Scopus)

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BRD4-BRD2 isoform switching coordinates pluripotent exit and Smad2-dependent lineage specification

Fernandez-Alonso, R., Davidson, L., Hukelmann, J., Zengerle, M., Prescott, A. R., Lamond, A., Ciulli, A., Sapkota, G. P. & Findlay, G. M. (Lead / Corresponding author), Jun 2017, In: EMBO Reports. 18, 6, p. 859-1037 178 p., e201643534.

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21 Citations (Scopus)

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Crystal Structure of the Cul2-Rbx1-EloBC-VHL Ubiquitin Ligase Complex

Cardote, T. A. F., Gadd, M. S. & Ciulli, A. (Lead / Corresponding author), 6 Jun 2017, In: Structure. 25, 6, p. 901-911.e3 14 p.

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96 Citations (Scopus)

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Homo-PROTACs: bivalent small-molecule dimerizers of the VHL E3 ubiquitin ligase to induce self-degradation

Maniaci, C., Hughes, S. J., Testa, A., Chen, W., Lamont, D. J., Rocha, S., Alessi, D. R., Romeo, R. & Ciulli, A. (Lead / Corresponding author), 10 Oct 2017, In: Nature Communications. 8, p. 1-14 14 p., 830.

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186 Citations (Scopus)

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Mind the metal: a fragment library-derived zinc impurity binds the E2 ubiquitin-conjugating enzyme Ube2T and induces structural rearrangements

Morreale, F., Testa, A., Chaugule, V., Bortoluzzi, A., Ciulli, A. & Walden, H. (Lead / Corresponding author), 12 Oct 2017, In: Journal of Medicinal Chemistry. 60, 19, p. 8183-8191 9 p.

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18 Citations (Scopus)

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Molecular recognition of ternary complexes: a new dimension in the structure-guided design of chemical degraders

Hughes, S. J. & Ciulli, A. (Lead / Corresponding author), 8 Nov 2017, In: Essays in Biochemistry. 61, 5, p. 505-516 12 p.

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154 Citations (Scopus)

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Structural Basis of Molecular Recognition of Helical Histone H3 Tail by PHD Finger Domains

Bortoluzzi, A., Amato, A., Lucas, X., Blank, M. & Ciulli, A. (Lead / Corresponding author), 4 May 2017, In: Biochemical Journal. 474, 10, p. 1633-1651 19 p.

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26 Citations (Scopus)

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Structural basis of PROTAC cooperative recognition for selective protein degradation

Gadd, M., Testa, A., Lucas, X., Chan, K. H., Chen, W., Lamont, D., Zengerle, M. & Ciulli, A. (Lead / Corresponding author), May 2017, In: Nature Chemical Biology. 13, 5, p. 514-521 11 p.

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759 Citations (Scopus)

618 Downloads (Pure)

Structure-guided design of peptides as tools to probe the protein-protein interaction between Cullin-2 and Elongin BC substrate adaptor in Cullin RING E3 ubiquitin ligases

Cardote, T. & Ciulli, A. (Lead / Corresponding author), 21 Sept 2017, In: ChemMedChem. 12, 18, p. 1491-1496 6 p.

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8 Citations (Scopus)

212 Downloads (Pure)

2016

Chemical genetics approaches for selective intervention in epigenetics

Runcie, A. C., Chan, K. H., Zengerle, M. & Ciulli, A. (Lead / Corresponding author), Aug 2016, In: Current Opinion in Chemical Biology. 33, p. 186-194 9 p.

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22 Citations (Scopus)

265 Downloads (Pure)

Potent and selective chemical probe of hypoxic signaling downstream of HIF-α hydroxylation via VHL inhibition

Frost, J., Galdeano, C., Soares, P., Gadd, M. S., Grzes, K. M., Ellis, L., Epemolu, O., Shimamura, S., Bantscheff, M., Grandi, P., Read, K. D., Cantrell, D. A., Rocha, S. & Ciulli, A. (Lead / Corresponding author), 4 Nov 2016, In: Nature Communications. 7, p. 1-12 12 p., 13312.

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160 Citations (Scopus)

300 Downloads (Pure)

2015

Biophysical studies on interactions and assembly of full-size E3 ubiquitin ligase: suppressor of cytokine signaling 2 (SOCS2):ElonginBC:Cullin5:RING-box protein 2 (Rbx2)

Bulatov, E., Martin, E. M., Chatterjee, S., Knebel, A., Shimamura, S., Konijnenberg, A., Johnson, C., Zinn, N., Grandi, P., Sobott, F. & Ciulli, A. (Lead / Corresponding author), 13 Feb 2015, In: Journal of Biological Chemistry. 290, 7, p. 4178-4191 14 p.

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25 Citations (Scopus)

Selective small molecule induced degradation of the BET bromodomain protein BRD4

Zengerle, M., Chan, K.-H. & Ciulli, A. (Lead / Corresponding author), 21 Aug 2015, In: ACS Chemical Biology. 10, 8, p. 1770-1777 8 p.

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731 Citations (Scopus)

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Serendipitous SAD solution for DMSO-soaked SOCS2-ElonginC-ElonginB crystals using covalently incorporated Dimethylarsenic: insights into substrate receptor conformational flexibility in Cullin RING Llgases

Gadd, M. S., Bulatov, E. & Ciulli, A. (Lead / Corresponding author), 29 Jun 2015, In: PLoS ONE. 10, 6, 14 p., e0131218.

Research output: Contribution to journal › Article › peer-review

19 Citations (Scopus)

Targeting Cullin-RING E3 ubiquitin ligases for drug discovery: structure, assembly and small-molecule modulation

Bulatov, E. & Ciulli, A. (Lead / Corresponding author), 1 May 2015, In: Biochemical Journal. 467, 3, p. 365-386 22 p.

Research output: Contribution to journal › Article › peer-review

175 Citations (Scopus)

DrugE3CRL's: Probing Druggability of Multisubunit Complexes: E3 Cullin RING Ligases (ERC Starting Grant)

Research output

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