Our recent publications from 2018 to 2024
Refereed Papers In Primary Journals
* A.C. Corresponding Author
142. Charlotte Crowe, Mark A. Nakasone, Sarah Chandler, Conner Craigon, Gajanan Sathe, Michael H. Tatham, Nikolai Makukhin, Ronald T. Hay, Alessio Ciulli
Mechanism of degrader-targeted protein ubiquitinability
-
Science Advances. Publication Date: October 11, 2024, Doi: 10.1126/sciadv.ado6492
141. Johannes Popow, William Farnaby, Andreas Gollner, Christiane Kofink, Gerhard Fischer, Melanie Wurm, David Zollman, Andre Wijaya, Nikolai Mischerikow, Carina Hasenoehrl, Polina Prokofeva, Heribert Arnhof, Silvia Arce-Solano, Sammy Bell, Georg Boeck, Emelyne Diers, Aileen B. Frost, Jake Goodwin-Tindall, Jale Karolyi-Oezguer, Shakil KhanTheresa Klawatsch, Manfred Koegl, Roland Kousek, Barbara Kratochvil, Katrin Kropatsch, Arnel A. Lauber, Ross McLennan, Sabine Olt, Daniel Peter, Oliver Petermann, Vanessa Roessler, Peggy Stolt-Bergner, Patrick Strack, Eva Strauss, Nicole Trainor, Vesna Vetma, Claire Whitworth, Siying Zhong, Jens Quant, Harald Weinstabl, Bernhard Kuster, Peter Ettmayer (Lead / Corresponding author), Alessio Ciulli (Lead / Corresponding author)
Targeting cancer with small-molecule pan-KRAS degraders
- Science. Publication Date: September 19, 2024, doi: 10.1126/science.adm8684
140. Vetma, V., Casarez-Perez, L., Eliaš, J., Stingu, A., Kombara, A., Gmaschitz, T., Braun, N., Ciftci, T., Dahmann, G., Diers, E., Gerstberger, T., Greb, P., Kidd, G., Kofink, C., Puoti, I, Spiteri, V., Trainor, N., Westermaier, Y., Whitworth, C., Ciulli, A., Farnaby, W., McAulay, K., Frost, A.B., Chessum, N., Koegl, M.
Confounding Factors in Targeted Degradation of Short-Lived Proteins
- ACS Chem. Biol. Publication Date: July 3, 2024, doi: 10.1021/acschembio.4c00152
- Pre-print first posted at BioRxiv on 22 February 2024; doi: 10.1101/2024.02.19.581012
139. Pierri, M., Liu, X., Kroupova, A., Rutter, Z., Hallatt, A.J., Ciulli, A.*
Stereochemical inversion at a 1,4-cyclohexyl PROTAC linker fine-tunes conformation and binding affinity
- Bioorg. Med. Chem. Lett. 2024, 110, Article 129861.
138. Diehl, C. J., Salerno, A., Ciulli, A.*
Ternary Complex-Templated Dynamic Combinatorial Chemistry for the Selection and Identification of Homo-PROTACs.
- Angew. Chem. Int. Ed. 2024, doi: 10.1002/anie.202319456
- Pre-print first posted at ChemRxiv on 16 December 2023; doi: 10.26434/chemrxiv-2023-tz70z
137. Yuki Hatoyama, Moutushi Islam, Adam G. Bond, Ken-Ichiro Hayashi, Alessio Ciulli, Masato T Kanemaki.
Combination of AID2 and BromoTag expands the utility of degron-based protein knockdowns
- BioRxiv 2024.03.20.586026; doi: 10.1101/2024.03.20.586026
136. Ponzo I., Solda A., Crowe C., Dahl G., Geschwindner S.*, Ciulli A.*, Rant U.*
Proximity Biosensor Assay for PROTAC Ternary Complex Analysis
- ChemRxiv. 2024; doi: 10.26434/chemrxiv-2024-8w4zb
135. Oliver Hsia, Matthias Hinterndorfer, Angus D. Cowan, Kentaro Iso, Tasuku Ishida, Ramasubramanian Sundaramoorthy, Mark A. Nakasone, Hana Imrichova, Caroline Schätz, Andrea Rukavina, Koraljka Husnjak, Martin Wegner, Alejandro Correa-Sáez, Conner Craigon, Ryan Casement, Chiara Maniaci, Andrea Testa, Manuel Kaulich, Ivan Dikic, Georg E. Winter* & Alessio Ciulli*
Targeted protein degradation via intramolecular bivalent glues
- Nature 2024 doi: 10.1038/d41573-024-00044-0
- Pre-print first posted at BioRxiv on 14 January 2023; doi: 10.1101/2023.02.14.528511; v2 updated 10/10/2023
- Highlighted in Nature Reviews Drug Discovery; doi: 10.1038/d41573-024-00044-0
- Highlighted in Cancer Discovery Research Watch; doi: 10.1158/2159-8290.CD-RW2024-040
134. Charlotte Crowe, Mark Nakasone, Sarah Chandler, Michael H. Tatham, Nikolai Makukhin, Ronald T. Hay, Alessio Ciulli*
Mechanism of degrader-targeted protein ubiquitinability
- BioRxiv 2024.02.05.578957; doi: 10.1101/2024.02.05.578957
133. Alena Kroupova, Valentina A. Spiteri, Hirotake Furihata, Darren Darren, Sarath Ramachandran, Zoe J. Rutter, Sohini Chakraborti, Kevin Haubrich, Julie Pethe, Denzel Gonzales, Andre Wijaya, Maria Rodriguez-Rios, Dylan M. Lynch, William Farnaby, Mark A. Nakasone, David Zollman*, Alessio Ciulli*
Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders
- BioRxiv 2024.01.17.575503; doi: 10.1101/2024.01.17.575503
132. Johannes Popow, William Farnaby, Andreas Gollner, Christiane Kofink, Gerhard Fischer, Melanie Wurm, David Zollman, Andre Wijaya, Nikolai Mischerikow, Carina Hasenoehrl, Polina Prokofeva, Heribert Arnhof, Silvia Arce-Solano, Sammy Bell, Georg Boeck, Emelyne Diers, Aileen B Frost, Jake Goodwin-Tindall, Jale Karolyi-Oezguer, Shakil Khan, Theresa Klawatsch, Manfred Koegl, Roland Kousek, Barbara Kratochvil, Katrin Kropatsch, Arnel A Lauber, Ross McLennan, Sabine Olt, Daniel Peter, Oliver Petermann, Vanessa Roessler, Peggy Stolt-Bergner, Patrick Strack, Eva Strauss, Nicole Trainor, Vesna Vetma, Claire Whitworth, Siying Zhong, Jens Quant, Harald Weinstabl, Bernhard Küster, Peter Ettmayer*, Alessio Ciulli*
Targeting cancer with small molecule pan-KRAS degraders
bioRxiv 2023.10.24.563163; doi: https://doi.org/10.1101/2023.10.24.563163
131. Ciulli, A.*, O’Connor, S.*, Chung, C.-W., Hartung, I. V., Testa, A., Daniels, D. L., Heitman, L. H.*
The 17th EFMC Short Course on Medicinal Chemistry on Small Molecule Protein Degraders
- PMID: 37817354
130. Ramachandran, S., Makukhin, N., Haubrich, K., Nagala, M., Forrester, B., Lynch, D.M., Casement, R., Testa, A., Bruno, E., Gitto, R., Ciulli, A. *
Structure-based design of a phosphotyrosine-masked covalent ligand targeting the E3 ligase SOCS2
- PMID: 37816714 PMCID: PMC10564737
- Preprint version 1 DOI: 10.26434/chemrxiv-2022-bvj80
- Preprint version 2 DOI: 10.26434/chemrxiv-2022-bvj80-v2
- X-ray crystallographic atomic coordinates and structure factors are available at the PDB under accession codes 7ZLP (compound 9 soaked to SBC2), 7ZLN (compound 11 soaked to SBC2), 7ZLO (compound 12 soaked to SBC2), 7ZLR (compound 13 soaked to SBC2), 7ZLS (compound 13 co-crystallized in complex with SBC2), 7ZLM (compound MN551 co-crystallized in complex with SBC2).
129. Oliver Hsia, Matthias Hinterndorfer, Angus D. Cowan, Kentaro Iso, Tasuku Ishida, Ramasubramanian Sundaramoorthy, Mark A. Nakasone, Hana Imrichova, Caroline Schätz, Andrea Rukavina, Koraljka Husnjak, Martin Wegner, Alejandro Correa-Sáez, Conner Craigon, Ryan Casement, Chiara Maniaci, Andrea Testa, Manuel Kaulich, Ivan Dikic, Georg E. Winter*, Alessio Ciulli*
Targeted protein degradation via intramolecular bivalent glues
bioRxiv 2023.02.14.528511; doi: https://doi.org/10.1101/2023.02.14.528511
- Preprint version 1: DOI: 10.1101/2023.02.14.528511v1
- Cryo-EM density maps are deposited in the EMDB with the accession code EMD-17172 and will be released upon publication. The atomic model is deposited under Protein Data Bank ID 8OV6.
128. 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.*, Gütschow, M*
Expanding the Structural Diversity at the Phenylene Core of Ligands for the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase: Development of Highly Potent Hypoxia-Inducible Factor-1alpha (HIF-1alpha) Stabilizers
J. Med. Chem. 2023, 66 (18), 12776-12811
- PMID: 37708384 PMCID: PMC10544018
- Pre-print first posted at ChemRxiv on 07 March 2023; DOI: 10.26434/chemrxiv-2023-5gbb6
- Newer version 2 available from August 1st, 2023 at 10.26434/chemrxiv-2023-5gbb6-v2
- The coordinates and structure factors of the associated co-crystal structure of the binary complexes between VHL and inhibitors 30, 33, and 37 are available in the PDB with accession codes 8CQK, 8CQL, and 8CQE, respectively.
127. Liu, X. Ciulli, A.*
Proximity-Based Modalities for Biology and Medicine
ACS Cent. Sci. 2023, 9 (7), 1269–1284
- PMID: 37521793 PMCID: PMC10375889
- See Figures here
- Listed as 1st Most Read Article in the journal (1-month timeframe, Aug 2023)
126. Clara Gathmann, Lydia S Newton, Sophie Ridewood, Robert J Smith, Thomas W Hornsby, Ann-Kathrin Reuschl, Andre J Wijaya, Kate L Morling, Ying Ying Tan, Lucy G Thorne, Alessio Ciulli, Clare Jolly, Greg J Towers, David L Selwood
Synthetic PROTACs based on a depsipeptide macrocycle selectively degrade cyclophilin A and inhibit HIV-1
15 March 2023, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-2639894/v1]
125. Haubrich, K., Spiteri, V.A., Farnaby, W., Sobott, F., Ciulli, A.*
Breaking free from the crystal lattice: Structural biology in solution to study protein degraders
Curr. Opin. Struct. Biol., 2023, 79, 102534
- PMID: 36804675
- Ranked amongst Most Downloaded Articles in the journal (August 2023)
124. Wijaya, A.J., Farnaby, W., Ciulli, A.*
Crystallization of VHL-based PROTAC-induced ternary complexes
Methods in Enzymology 2023, 681, 241–263
- PMID: 36764760
123. Hanzl, A., Casement, R., Imrichova, H., Hughes, S.J., Barone, E., Testa, A., Bauer, S., Wright, J., Brand, M., Ciulli, A.*, Winter, G.E.*
Functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders
Nat. Chem. Biol. 2023, 19 (3), 323-333
- PMID: 36329119 PMCID: PMC7614256
- Pre-print posted at BioRxiv on 14 April 2022; DOI: https://doi.org/10.1101/2022.04.14.488316
- Covered in UoD News website
- Covered in CeMM News website
- Highlighted in Nature Reviews Drug Discovery
- Featured in a Spotlight article by Nico Thoma and colleagues in Trends in Pharmacological Sciences
- Atomic coordinates and structure factors for the ternary complex crystal structure VHL:AT7:Brd4-BD2 are available at the PDB under accession code 7ZNT.
122. Kofink, C., Trainor, N., Mair, B., Wöhrle, S., Wurm, M., Mischerikow, N., Roy, M., Bader, G., Greb, P., Garavel, G., Diers, E., McLennan, R., Whitworth, C., Vetma, V., Rumpel, K., Scharnweber, M., Fuchs, J.E., Gerstberger, T., Cui, Y., Gremel, G., Chetta, P., Hopf, S., Budano, N., Rinnenthal, J., Gmaschitz, G., Mayer, M., Koegl, M., Ciulli, A., Weinstabl, H., Farnaby, W.
A selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivo
- PMID: 36216795 PMCID: PMC9551036
- Pre-print posted at ChemRxiv on 1 February 2022; DOI: 10.26434/chemrxiv-2022-q63s3
- Covered in UoD News website
- Featured in a Comment article by John Harling and Chris Tinworth in Nature Communication
- X-ray co-crystal structures data have been deposited to the PDB under accession codes 7Z78 (compound 4 in complex with SMARCA2-BD), 7Z6L (VCB: compound 5: SMARCA2-BD ternary complex), 7Z77 (VCB: compound 6: SMARCA2-BD ternary complex), and 7Z76 (VCB: compound 10: SMARCA2-BD ternary complex).
121. Cipriano, A., Milite, C., Feoli, A., Viviano, M., Pepe, G., Campiglia, P., Sarno, G., Picaud, S., Imaide, S., Makukhin, N., Filippakopoulos, P., Ciulli, A., Castellano, S., Sbardella, G.
Discovery of benzo[d]imidazole-6-sulfonamides as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with Selectivity for the First Bromodomain
ChemMedChem 2022, 17 (20), e202200343
- PMID: 36040095 PMCID: PMC9826262
- See front cover here
120. Liu, X., Kalogeropulou, A., Domingos, S., Makukhin, N., Nirujogi, R., Singh, F., Shpiro, N., Saalfrank, A., Sammler, E., Ganley, I., Moreira, R., Alessi, D.*, Ciulli, A.*
Discovery of XL01126: A Potent, Fast, Cooperative, Selective, Oral bioavailable and Blood Brain Barrier Penetrant PROTAC Degrader of Leucine Rich Repeat Kinase 2 (LRRK2)
J. Am. Chem. Soc. 2022, 144 (37), 16930–16952
- PMID: 36007011 PMCID: PMC9501899
- Pre-print posted at ChemRxiv on 23 May 2022; DOI: 10.26434/chemrxiv-2022-4gzm0
- Covered in UoD Stories websites
- Listed as 3rd Most Read Article in the journal (1-month timeframe, Sept 2022)
- Listed as one of the Most Read Articles in the journal within the 12-month timeframe (July 2023)
119. Diehl, C.J., Ciulli, A.*
Discovery of small molecule ligands for the von Hippel-Lindau (VHL) E3 ligase and their use as inhibitors and PROTAC degraders.
Chem. Soc. Rev. 2022, 51, 8216-8257
- PMID: 35983982 PMCID: PMC9528729
- See front cover here
118. Rasmussen, S.V.,Jin, J.X., Bickford, L.R., Woods, A.D., Sahm, F., Crawford, K.A., Nagamori, K., Goto, H., Torres, K.E., Sidoni, A., Rudzinski, E.R., Thway, K., Jones, R.L., Ciulli, A., Wright, H., Lathara, M., Srinivasa, G., Kannan, K., Huang, P.H., Grünewald, T.G.P., Berlow, N.E., Keller, C.
Functional genomic analysis of epithelioid sarcoma reveals distinct proximal and distal subtype biology
Clin. Transl. Med. 2022, 12 (7), e961
- PMID: 35839307 PMCID: PMC9286527
117. Gollner, A., Köster, M., Nicklin, P., Trieselmann, T., Klein, E., Vlach, J., Heine, C., Grundl, M., Ramharter, J., Wyatt, D., Chaturvedi, M., Ciulli, A., Carter, K.C., Müller, S., Bischoff, D., Ettmayer, P., Haaksma, E., Mack, J., McConnell, D., Stenkamp, D., Weinstabl, H., Zentgraf, M., Wood, C.R., Montel, F.
OpnMe.com: a digital initiative for sharing tools with the biomedical research community
Nat. Rev. Drug Discov. 2022, 21, 475-476
- PMID: 35459938
116. 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., Lessene, G., Silke, J., Feltham, R.
Development of NanoLuc-targeting protein degraders and a universal reporter system to benchmark tag-targeted degradation platforms
- PMID: 35440107 PMCID: PMC9019100
115. Cowan, A.D., Ciulli, A.*
Driving E3 Ligase Substrate Specificity for Targeted Protein Degradation: Lessons from Nature and the Laboratory
Annu. Rev. Biochem., 2022, 91, 295-319
- PMID: 35320687
114. Webb, T., Craigon, C., Ciulli, A.*
Targeting Epigenetic Modulators Using PROTAC Degraders: Current Status and Future Perspective
Bioorg. Med. Chem. Lett. 2022, 63, 128653
- PMID: 35257896
- See Figures here
- Read the article open access before April 29, 2022 via the personalized Share Link
- Listed amongst the top Most Downloaded Articles in the Journal of the last 90 days (Sept 2022)
113. Liu, X., Ciulli, A.*
Targeted protein stabilization: DUB be good to me
Nat. Chem. Biol. 2022, 18 (4), 358-359
- PMID: 37039823
- News & Views article on Henning et al. Nat. Chem. Biol. 2022
- Read the article Open Access as SharedIt version here
- See Figure and links here
112. Bharathy, N., Cleary, M.M., Kim, J-A., Nagamori, K., Crawford, K.A., Wang, E., Saha, D., Settelmeyer, T.P., Purohit, R., Skopelitis, D., Chang, K., Doran, J.A., Kirschbaum, C.W., Bharathy, S., Crews, D.W., Randolph, M.E., Karnezis, A.N., Hudson-Price, L., Dhawan, J., Michalek, J.E., Ciulli, A.,* Vakoc, C.R. & Keller, C.*
SMARCA4 biology in alveolar rhabdomyosarcoma
111. Tarantelli, C., Cannas, E., Ekeh, H., Moscatello, C., Gaudio, E., Cascione, L., Napoli, S., Rech, C., Testa, A., Maniaci, C., Rinaldi, A., Zucca, E., Stathis, A., Ciulli, A., Bertoni, F.
The bromodomain and extra-terminal domain degrader MZ1 exhibits preclinical anti-tumoral activity in diffuse large B-cell lymphoma of the activated B cell-like type
Explor. Target Antitumor Ther. 2021, 2, 586–601
- PMID: 36046113 PMCID: PMC9400774
110. Klein, V.G., Bond, A.G., Craigon, C., Lokey, R.S.*, Ciulli, A.*
Amide-to-ester substitution as a strategy for optimizing PROTAC permeability and cellular activity
J. Med. Chem. 2021, 64 (24), 18082–18101
- PMID: 34881891 PMCID: PMC8713283
- Pre-print posted at ChemRxiv on 5 July 2021; DOI: 10.33774/chemrxiv-2021-47tqn
- See Figures here
- Listed as 2nd Most Read Article in the journal (1-month timeframe, Jan 2022)
- Featured as Literature Spotlight in the monthly EFMC MedChemBioWatch newsletter (February 2022)
109. Müller, S., Ackloo, S., Al Chawaf, A., Al-Lazikani, B., Antolin, A., Baell, J.B., Beck, H., Beedie, S., Betz, U.A.K., Arruda Bezerra, G., 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., Hitchcock, S.H., Homan, E., Kannan, N., Kiefer, J.R., Knapp, S., Kostic, M., Kubicek, S., Leach, A.R., Lindemann, S., Marsden, B.D., Matsui, H., Meier, J.L., Merk, D., Michel, M., Morgan, M.R., Mueller-Fahrnow, A., Owen, D.R., Perry, B.G., Rosenberg, S.H., Singh Saikatendu, K., Schapira, M., Scholten, C., Sharma, S., Simeonov, A., Sundström, M., Superti-Furga, G., Todd, M.H., Tredup, C., Vedadi, M., von Delft, F., Willson, T.M., Winter, G.E., Workman, P., Arrowsmith, C.H.
Target 2035 – update on the quest for a probe for every protein
RSC Med. Chem. 2022, 13, 13-21
- PMID: 35211674 PMCID: PMC8792830
- Selected as the inside front cover of the issue.
108. Laveglia, V., Giachetti, A., Cerofolini, L., Haubrich, K., Fragai, M., Ciulli, A., Rosato, A.
Automated Determination of Nuclear Magnetic Resonance Chemical Shift Perturbations in Ligand Screening Experiments: The PICASSO Web Server
J. Chem. Inf. Model. 2021, 61 (12), 5726–5733
- PMID: 34843238 PMCID: PMC8715503
107. 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.*
Trivalent PROTACs enhance protein degradation via combined avidity and cooperativity
Nat. Chem. Biol. 2021, 17 (11), 1157–1167
- PMID: 34675414 PMCID: PMC7611906
- Pre-print posted at ChemRxiv on 12 November 2020; DOI: 10.26434/chemrxiv.13218695.v1
- See Figures here
- Covered in UoD and SLS News websites
- Covered as joint Dundee-Promega Press Release in BusinessWire
- Read the article Open Access as SharedIt version here
- Highlighted in Blog Promega Connections
- Featured in Chemical & Engineering News
- Featured in Biocentury
- Recommended in Faculty Opinions
- Featured in BiopharmaTrend
- Our trivalent PROTAC degrader SIM1 is available from Tocris (September 2021)
- The non-degrading epimer cis-SIM1 is also available from Tocris (November 2021)
106. Riching, K.M., Vasta, J.D., Hughes, S.J., Zoppi, V., Maniaci, C., Testa, A., Urh, M., Ciulli, A.*, Daniels, D.L.*
Translating PROTAC chemical series optimization into functional outcomes underlying BRD7 and BRD9 protein degradation
Curr. Res. Chem. Biol., 2021, 1, 100009
- 2nd Most Downloaded Article in the journal (April 2022)
105. Bond, A.G., Craigon, C., Chan, K.-H., Testa, A., Karapetsas, A., Fasimoye, R., Macartney, T., Blow, J.J., Alessi, D.R., Ciulli, A.*
Development of BromoTag: A “Bump-and-Hole”–PROTAC System to Induce Potent, Rapid, and Selective Degradation of Tagged Target Proteins
J. Med. Chem. 2021, 64 (20), 15477–15502
- PMID: 34652918 PMCID: PMC8558867
- See Figures here
- Featured in UoD and SLS News websites
- Listed amongst the Most Read Articles in the journal (1-month timeframe, November 2021)
- Highlighted in SynFacts
- Our BromoTag-specific bumped-PROTAC degrader AGB1 is available from Tocris (April 2022)
- The non-degrading epimer cis-AGB1 is also available from Tocris (April 2022)
- A second BromoTag-specific bumped-PROTAC degrader AGB3 is also available from Tocris (November 2022)
104. Castro, G.V, Ciulli, A.*
Estimating the cooperativity of PROTAC-induced ternary complexes using 19F NMR displacement assay
RSC Med. Chem. 2021, 12, 1765-1770
- PMID: 34778777 PMCID: PMC8528210
- Pre-print posted at ChemRxiv on 21 June 2021; DOI: 10.33774/chemrxiv-2021-zj19k
- See Figures here
- Correction published (Web): December 20, 2021. DOI: 10.1039/D1MD90045E (Correction)
103. Ciulli, A.*, Trainor, N.
A beginner’s guide to PROTACs and targeted protein degradation
Biochem (Lond) 2021, 43 (5), 74–79
102. Frost, J.; Rocha, S.*; Ciulli, A.*
Von Hippel-Lindau (VHL) small molecule inhibitor binding increases stability and intracellular levels of VHL protein
J. Biol. Chem. 2021, 297 (2), 100910
- PMID: 34174286 PMCID: PMC8313594
- Pre-print posted at BioRxiv on 12 April 2021; DOI: 10.1101/2021.04.12.439487
- See Figures here
- Julianty Frost is recipient of one of the 2022 JBC Herbert Tabor Early Career Investigator Awards, recognizing first authors of exceptional JBC papers that appeared in the preceding year
101. Ciulli, A.; Hamann, L.; Jahnke, W.; Kalgutkar, A.S.; Magauer, T.; Ritter, T.; Steadman, V.; Williams, S.D.; Winter, G.; Hoegenauer, K.; Krawinkler, K.H.; Stepan, A.F.
The 2nd Alpine Winter Conference on Medicinal and Synthetic Chemistry.
ChemMedChem 2021, 16 (15), 2417-2413
- PMID: 34114371
100. Ciulli, A.*; Wertz, I.E.*
Editorial overview: Hot targets and new modalities.
Curr. Opin. Chem. Biol. 2021, 62, A1-A3
- PMID: 34116929
99. Pietrobono, S.; 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.
Targeting non-canonical activation of GLI1 by the SOX2-BRD4 transcriptional complex improves the efficacy of HEDGEHOG pathway inhibition in melanoma
- PMID: 33958721 PMCID: PMC8175236
98. Farnaby, W.; Koegl, M.; McConnell, D.B.; Ciulli, A.
Transforming targeted cancer therapy with PROTACs: A forward-looking perspective
Curr. Opin. Pharmacol. 2021, 57, 175-183
- PMID: 33799000
- See more info here
- 2nd Most Downloaded Article in the journal in the last 3 months (August 2021)
97. Ramachandran, S.; Ciulli, A.*
Building ubiquitination machineries: E3 ligase multi-subunit assembly and substrate targeting by PROTACs and molecular glues
Curr. Opin. Struct. Biol. 2021, 67, 110-119
- PMID: 33271439
- See Figures here
- Top Most Downloaded Article in the journal (April 2021)
96. Ishida, T., Ciulli, A.*
E3 Ligase Ligands for PROTACs: How They Were Found and How to Discover New Ones
SLAS Discov. 2021, 26 (4), 484-502
- PMID: 33143537 PMCID: PMC8013866
- See Figures here
- Most Read article in the journal in the last 6 months (August 2021)
- Honored with the 2021 SLAS Discovery Readers Choice Award, reflecting popularity among readers throughout 2021
- Top amongst SLAS Discovery’s Editor’s Top 10 for 2021. Read the full Editorial here
- Mentioned in SLAS ELN article: “Art of the Review: SLAS Journals Authors Offer Expert Interpretation of Life Science Literature”. Read the full article here
95. Makukhin, N., Ciulli, A.*
Recent advances in synthetic and medicinal chemistry of phosphotyrosine and phosphonate- based phosphotyrosine analogues
- PMID: 34041480 PMCID: PMC8130623
- See Figures here
94. Klein, V.G., Townsend, C.E., Testa, A., Zengerle, M., Maniaci, C., Hughes, S.J., Chan, K.-H., Ciulli, A., Lokey, R.S.
Understanding and improving the membrane permeability of VH032-based PROTACs
ACS Med. Chem. Lett. 2020, 11 (9), 1732-1738
- PMID: 32939229 PMCID: PMC7488288
- See Figures here
- Listed amongst the Most Read Articles in the journal (1-month timeframe: September 2020; 12-month timeframe: April 2021)
93. Bond, A.G., Testa, A., Ciulli, A.*
Stereoselective Synthesis of Allele-Specific BET Inhibitors
Org. Biomol. Chem. 2020, 18, 7533-7539
- PMID: 3275671
- Pre-print posted at ChemRxiv on 18 May 2020; https://doi.org/10.26434/chemrxiv.12317354.v1
- See Figures here
- Selected as the front cover of the issue. Read more about it here
92. Cipriano, A., Sbardella, G.,* Ciulli, A.*
Targeting epigenetic reader domains by chemical biology
Curr. Opin. Chem. Biol. 2020, 57, 82-94
- PMID: 32739717
- Read the article open access before September 18, 2020 via the Share Link here
- See Figures here
91. Whitworth, C., Ciulli, A.*
Protein degraders extend their reach
- PMID: 32728153
- See Figure here
- News & Views article on Banik et al. Nature 2020, DOI: 10.1038/s41586-020-2545-9
90. 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.
Inducible Degradation of Target Proteins through a Tractable Affinity-Directed Protein Missile System
Cell Chem. Biol. 2020, 27 (9), 1164-1180.e5
- PMID: 32668203 PMCID: PMC7505680
- See Figures here
- Highlighted in Nature Chemical Biology
89. Testa, A., Hughes, S.J., Lucas, X., Wright, J.E., Ciulli, A.*
Structure-Based Design of a Macrocyclic PROTAC
Angew. Chem. Int. Ed. 2020, 59, 1727-1734
- PMID: 31746102 PMCID: PMC7004083
- Pre-print posted at ChemRxiv on 22 July 2019; DOI: 10.26434/chemrxiv.8967941.v1
- Selected as a “Hot paper” by the Editors of Angew. Chem. and Angew. Chem. Int. Ed.
- See Figures here.
- The coordinates and structure factors of the associated co-crystal structure of the ternary complex between VHL, Brd4-BD2 and macroPROTAC-1 is available in the PDB with accession code 6SIS.
- Listed amongst the Most Accessed in the journal for the period 02/2020 to 01/2021 (April 2021)
88. Hassell-Hart, S., Runcie, A.C., Krojer, T., Doyle, J., Lineham, E., Ocasio, C.A., Neto, B.A.D., Fedorov, O., Marsh, G., Maple, H., Felix, R., Banks, R., Ciulli, A., Picaud, S., Filippakopoulos, P., von Delft, F., Brennan, P., Stewart, H.J.S., Chevassut, T.J., Walker, M., Austin, C., Morley, S., Spencer, J.
Synthesis and Biological Investigation of (+)-JD1, an Organometallic BET Bromodomain Inhibitor
87. Tovell, H., Testa, A., Zhou, H., Shpiro, N., Crafter, C., Ciulli, A.*, Alessi, D.R.*
Design and characterization of SGK3-PROTAC1, an isoform specific SGK3 kinase PROTAC degrader
ACS Chem. Biol. 2019, 14 (9), 2024-2034
- See Figures here
- Ranked Top amongst the Most Read Articles in the journal (1-month timeframe, Sept-Oct 2019)
86. Maniaci, C., Ciulli, A.*
Bifunctional chemical probes inducing protein-protein interactions
Curr. Opin. Chem. Biol. 2019, 52, 145-156
- Read the article open access until 2nd October 2019 via the Share Link here
- See Figures here
- Ranked amongst Most Popular Articles in the journal
85. Ciulli, A.*, Farnaby, W.*
Protein degradation for drug discovery. [Editorial]
Drug Discov. Today Technol. 2019 Apr 31: 1-3
84. Farnaby W, Koegl M, Roy MJ, Whitworth C, Diers E, Trainor N, Zollman D, Steurer S, Karolyi-Oezguer J, Riedmueller C, Gmaschitz T, Wachter J, Dank C, Galant M, Sharps B, Rumpel K, Traxler E, Gerstberger T, Schnitzer R, Petermann O, Greb P, Weinstabl H, Bader G, Zoephel A, Weiss-Puxbaum A, Ehrenhöfer-Wölfer K, Wöhrle S, Boehmelt G, Rinnenthal J, Arnhof H, Wiechens N, Wu MY, Owen-Hughes T, Ettmayer P, Pearson M, McConnell DB*, Ciulli A.*
BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design
Nat. Chem. Biol. 2019, 15 (7), 672-680
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A Publisher Correction to this article was published on 02 July 2019
- Highlighted in EurekAlert, the Medical News, and mentioned by BioWorld
- Read the article Open Access as SharedIt version here
- See Figures here
- The coordinates and structure factors of our co-crystal structures are available in the PDB. Accession codes of ternary complexes VCB:PROTAC1:SMARCA2 bromodomain (PDB 6HAY), VCB:PROTAC2:SMARCA2 bromodomain (PDB 6HAX), and VCB:PROTAC2:SMARCA4 bromodomain (PDB 6HR2), as well as a binary complex between SMARCA2 bromodomain and SMARCA-BD ligand (PDB 6HAZ)
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Featured in a News & Views article by Daffyd Owen in Nature Chemical Biology
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Featured in Cancer Discovery Research Watch
- Featured in Biocentury Innovation
- Highlighted in SynFacts
- Check out Darryl McConnell’s video on Structure-Based SMARCA2 PROTAC Design here.
- Our SMARCA2/4 degrader ACBI1 (and cis-ACBI1) are available from Boehringer Ingelheim’s OpnMe Portal: order for free, no strings attached! (Update July 2021: in vivo DMPK data are now available online)
- Our VHL ligand “VH101, phenol” functionalized for PROTAC conjugation is available from Tocris (January 2020)
- Find out more about ACBI1 in the Chemical Probes Portal
83. Kung, W.-W., Ramachandran, S., Makukhin, N., Bruno, E., Ciulli, A.*
Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase
- Pre-print posted at bioRxiv 470187; 14 November 2018 doi: https://doi.org/10.1101/470187
- Featured in SLS News
- Read the SharedIt version here
- The coordinates and structure factors of our co-crystal structures are available in the PDB. Accession codes of SOCS2:ElonginC:ElonginB in complex with EpoR (PDB 6I4X) and GHR peptides (PDBs 6I5J and 6I5N)
82. Tovell, H., Testa, A., Maniaci, C., Zhou, H., Prescott, A.R., Macartney, T., Ciulli, A.*, Alessi, D.R.*
Rapid and reversible knockdown of endogenously tagged endosomal proteins via an optimized HaloPROTAC degrader
ACS Chem. Biol. 2019, 14 (5), 882-892
- Featured in the SLS and MRC-PPU News websites
- Ranked Top amongst the Most Read Articles in the journal (1-month timeframe, May 2019)
- See Figures here
81. Girardini, M., Maniaci, C., Hughes, S.J., Testa, A., Ciulli, A.*
Cereblon vs VHL: Hijacking E3 Ligases Against Each Other Using PROTACs
Bioorg. Med. Chem. 2019, 27 (12), 2466-2479
- Pre-print posted at ChemRxiv on 11 February 2019; doi: https://doi.org/10.26434/chemrxiv.7698185.v1
- Listed amongst the top Most Downloaded Bioorganic & Medicinal Chemistry Articles of the last 90 days (Apr 2019)
- See Figures here
- Our VHL ligand “VH101, phenol” functionalized for PROTAC conjugation is available from Tocris (January 2020)
- Our CRBN degrader PROTAC 14a is available from Tocris (October 2020)
80. Popow, J., Arnhof, H., Bader, G., Berger, H., Ciulli, A., Covini, D., Dank, C., Gmaschitz, T., Greb, P., Karolyi-Özguer, J., Koegl, M., McConnell, D.B., Pearson, M., Rieger, M., Rinnenthal, J., Roessler, V., Schrenk, A., Spina, M., Steurer, S., Trainor, N., Traxler, E., Wieshofer, C., Zoephel, A., Ettmayer, P.
Highly Selective PTK2 Proteolysis Targeting Chimeras to Probe Focal Adhesion Kinase Scaffolding Functions
J. Med. Chem. 2019, 62 (5), 2508-2520
- PTK2 PROTACs BI-0319 (VHL-based) and BI-3663 (CRBN-based) are available for free from the OpnMe Portal.
79. Roy, M.J., Winkler, S., Hughes, S.J., Whitworth, C., Galant, M., Farnaby, W., Rumpel, K., Ciulli, A.*
SPR-measured dissociation kinetics of PROTAC ternary complexes influence target degradation rate
ACS Chem. Biol. 2019, 14 (3), 361-368
- Pre-print posted at bioRxiv 451948; 25 October 2018 doi: https://doi.org/10.1101/451948
- Selected to be featured in ACS Editors’ Choice based on recommendation by ACS journals’ editors
- See Figures here
- Ranked Top amongst the Most Read Articles in the journal (1-month timeframe, Mar-Apr 2019)
- Highlighted in Derek Lowe’s blog In the Pipeline
- Featured in Cytiva’s web article/application note “Characterizing PROTAC ternary complex formation
78. Frost, J., Ciulli, A.*, Rocha, S.*
RNA-seq analysis of PHD and VHL inhibitors reveals differences and similarities to the hypoxia response. [version 1; referees: 2 approved]
Wellcome Open Res. 2019, 4:17 (https://doi.org/10.12688/wellcomeopenres.15044.1)
77. Castro, G.V, Ciulli, A.*
Spy vs. spy: selecting the best reporter for 19F NMR competition experiments
Chem. Commun. 2019, 55 (10), 1482-1485
- See Figures here
- Our fluorinated VHL “spy-molecule” ligands are now available from the Merck Sigma-Aldrich catalogue: Fluorinated VHL spy molecule 1, Fluorinated VHL Spy Molecule 2 and Fluorinated VHL Spy Molecule 4
76. Zoppi, V., Hughes, S.J., Maniaci, C., Testa, A., Gmaschitz, T., Wieshofer, C., Koegl, M., Riching, K., Daniels, D.L., Spallarossa, A., and Ciulli, A.*
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
J. Med. Chem. 2019, 62 (2), 699-726
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See Figures here
-
The coordinates and structure factors of the associated co-crystal structure of human BRD9 bromodomain in complex with PROTAC 5 is available in the PDB with accession code 6HM0
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Listed as 1st Most Read Article in the journal (1-month timeframe, Jan 2019)
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Highlighted in the blog Promega Connection: “A Roadmap for PROTAC Development”
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Find out more about VZ185 in the Chemical Probes Portal
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Our dual Brd7/9 degrader VZ185 is available from Tocris (October 2019)
- The inactive epimer cis-VZ185 is also available from Tocris (April 2020)
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Our VHL ligand “VH101, phenol” functionalized for PROTAC conjugation is available from Tocris (January 2020)
75. Aresu, L., Ferraresso, S., Marconato, L., Cascione, L., Napoli, S., Gaudio, E., Kwee, I., Tarantelli, C., Testa, A., Maniaci, C., Ciulli, A., Hillmann, P., Bohnacker, T., Wymann, M.P., Comazzi, S., Milan, M., Riondato, F., Dalla Rovere, G., Giantin, M., Giannuzzi, D., Bertoni, F.
New Molecular And Therapeutic Insights Into Canine Diffuse Large B Cell Lymphoma Elucidates The Role Of The Dog As A Model For Human Disease
74. Lucas, X., Van Molle, I., Ciulli, A.*
Surface probing by fragment-based screening and computational methods identifies ligandable pockets on the von Hippel-Lindau (VHL) E3 ubiquitin ligase
J. Med. Chem. 2018, 61 (16), 7387-7393
- See Figures here
- The coordinates and structure factors of our co-crystal structures are available in the PDB. Accession codes of VCB in complex with MB235 (PDB 6GMN), MB756 (PDB 6GMQ), MB1200 (PDB 6GMX), and VCBH in complex with MB756 (PDB 6GMR)
- Listed amongst the Most Read Articles in the journal (Aug 2018)
- Highlighted in the Faculty of 1000 Prime
73. Testa, A., Lucas, X., Castro, G.V., Chan, K.-H., Wright, J.E., Runcie, A.C., Gadd, M.S., Harrison, W.T.A., Ko, E.-J., Fletcher, D., Ciulli, A.*
3-Fluoro-4-hydroxyprolines: Synthesis, conformational analysis and stereoselective recognition by the VHL E3 ubiquitin ligase for targeted protein degradation
J. Am. Chem. Soc. 2018, 140 (29), 9299-9313
- See Figures here
- The coordinates and structure factors of our co-crystal structures are available in the PDB, with accession codes: 6GFX, 6GFY and 6GFZ
- Addition/Correction published (Web): April 24, 2019. DOI: 10.1021/jacs.9b03833
72. Soares, P., Lucas, X., Ciulli, A.*
Thioamide substitution to probe the hydroxyproline recognition of VHL ligands
Bioorg. Med. Chem. 2018, 26 (11), 2992-2995
- See Figures here
- The article is a contribution to the journal’s Special Issue for the 2018 Tetrahedron Young Investigators Award for Matthew Fuchter
- The coordinates and structure factors of our co-crystal structures are available in the Protein DataBank, with accession codes: 6FMI, 6FMJ, and 6FMK
- 4th Most Downloaded Article in the journal (June 2018)
71. Amato, A., Lucas, X., Bortoluzzi, A., Wright, D., Ciulli, A.*
Targeting ligandable pockets on plant homeodomain (PHD) zinc finger domains by a fragment-based approach
ACS Chem. Biol. 2018, 13 (4), 915-921
- See Figures here
- The coordinates and structure factors of our co-crystal structures are available in the Protein DataBank, with accession codes: 6FHU, 6FKP, 6FI0, 6FAP, 6FHQ, and 6FI1
70. Runcie, A.C., Zengerle, M., Chan, K.-H., Testa, A., van Beurden, L., Baud, M.G.J., Epemolu, O., Ellis, L.C.J., Read, K.D., Coulthard, V., Brien, A. and Ciulli, A.*
Optimization of a “bump-and-hole” approach to allele-selective BET bromodomain inhibition