Publications

Refereed Papers In Primary Journals

* A.C. Corresponding Author

 

Independent Research: Ciulli Group

128. 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]

 

127. Lan Phuong Vu, Ryan Casement, Adam G. Bond, Christian Steinebach, Nika Strašek, Aleša Bricelj, Andrej Perdih, Claudia J. Diehl, Gregor Schnakenburg, Izidor Sosič, Alessio Ciulli* and Michael Gütschow*

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

ChemRxiv 2023.03.07; doi: https://doi.org/10.26434/chemrxiv-2023-5gbb6

 

126. Oliver Hsia, Matthias Hinterndorfer, Angus D. Cowan, Kentaro Iso, Tasuku Ishida, Ramasubramanian Sundaramoorthy, Mark A. Nakasone, Andrea Rukavina, Koraljka Husnjak, Martin Wegner, Alejandro Correa-Sáez, Conner Craigon, Chiara Maniaci, Andrea Testa, Manuel Kaulich, Ivan Dikic, Georg E. Winter*, Alessio Ciulli*

An intramolecular bivalent degrader glues an intrinsic BRD4-DCAF16 interaction

bioRxiv 2023.02.14.528511; doi: https://doi.org/10.1101/2023.02.14.528511

 

125. Kevin Haubrich, Valentina A. Spiteri, William Farnaby, Frank Sobott, Alessio Ciulli*

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

Curr. Opin. Struct. Biol., 2023, 79, 102534

 

124. Wijaya, A.J., Farnaby, W., Ciulli, A.*

Crystallization of VHL-based PROTAC-induced ternary complexes

Methods in Enzymology 2023, 681, 241–263

 

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

 

122. Ramachandran, S., Makukhin, N., Haubrich, K., Casement, R., Nagala, M., Lynch, D., Testa, A., Bruno, E., Gitto, R., Ciulli, A.*

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

ChemRxiv. Cambridge: Cambridge Open Engage; 2022;  DOI: 10.26434/chemrxiv-2022-bvj80

 

121. 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

Nat. Commun. 2022, 13, 5969

 

120. 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

  • See front cover here

 

119. 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

 

118. 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

  • See front cover here

 

117. 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

 

116. 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

 

115. 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

Nat. Commun. 2022, 13, 2073

 

114. 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

 

113. Webb, T., Craigon, C., Ciulli, A.*

Targeting Epigenetic Modulators Using PROTAC Degraders: Current Status and Future Perspective

Bioorg. Med. Chem. Lett. 2022, 63, 128653

  • 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)

 

112. Liu, X., Ciulli, A.*

Targeted protein stabilization: DUB be good to me

Nat. Chem. Biol. 2022, 18 (4), 358-359

 

111. 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

Oncogene 2022, 41, 1647–1656

 

110. 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

 

109. 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

 

108. 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

 

107. 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

 

106. 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

 

105. 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

 

104. 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

  • 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) 

 

103. 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

 

102. Ciulli, A.*, Trainor, N.

A beginner’s guide to PROTACs and targeted protein degradation 

Biochem (Lond) 2021, 43 (5), 74–79

 

101. 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

 

100. 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

 

99. Ciulli, A.*; Wertz, I.E.*

Editorial overview: Hot targets and new modalities.

Curr. Opin. Chem. Biol. 2021, 62, A1-A3

 

98. 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

Oncogene 2021, 40, 3799-3814

 

97. 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

 

96. 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

 

95. 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

 

94. Makukhin, N., Ciulli, A.*

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

RSC Med. Chem. 2021, 12, 8-23

 

93. 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

  • See Figures here
  • Listed amongst the Most Read Articles in the journal (1-month timeframe: September 2020; 12-month timeframe: April 2021)

 

92. Bond, A.G., Testa, A., Ciulli, A.*

Stereoselective Synthesis of Allele-Specific BET Inhibitors

Org. Biomol. Chem. 2020, 18, 7533-7539

 

91. Cipriano, A., Sbardella, G.,* Ciulli, A.*

Targeting epigenetic reader domains by chemical biology

Curr. Opin. Chem. Biol. 2020, 57, 82-94

  • Read the article open access before September 18, 2020 via the Share Link here
  • See Figures here

 

90. Whitworth, C., Ciulli, A.*

Protein degraders extend their reach

Nature 2020, 584, 193-194

 

89. 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

 

88. 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

  • 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)

 

87. 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

Organometallics 2020, 39 (3), 408-416

 

86. 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)

 

85. 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

 

84. Ciulli, A.*, Farnaby, W.*

Protein degradation for drug discovery. [Editorial]

Drug Discov. Today Technol. 2019 Apr 31: 1-3

 

83. 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

  • A Publisher Correction to this article was published on 02 July 2019
  • Featured in UoD and SLS News websites
  • 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)
  • Featured in a News & Views article by Daffyd Owen in Nature Chemical Biology
  • 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

 

82. Kung, W.-W., Ramachandran, S., Makukhin, N., Bruno, E., Ciulli, A.*

Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase

Nat. Commun. 2019, 10, 2534

  • 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)

 

81. 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

 

80. 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

 

79. 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.

 

78. 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

 

77. 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)

 

76. Castro, G.V, Ciulli, A.*

Spy vs. spy: selecting the best reporter for 19F NMR competition experiments

Chem. Commun. 2019, 55 (10), 1482-1485

 

75. 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

  • 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
  • Listed as 1st Most Read Article in the journal (1-month timeframe, Jan 2019)
  • Highlighted in the blog Promega Connection: "A Roadmap for PROTAC Development"
  • Find out more about VZ185 in the Chemical Probes Portal
  • Our dual Brd7/9 degrader VZ185 is available from Tocris (October 2019)
  • The inactive epimer cis-VZ185 is also available from Tocris (April 2020) 
  • Our VHL ligand "VH101, phenol" functionalized for PROTAC conjugation is available from Tocris (January 2020) 

 

74. 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

Haematologica 2019, 104 (6), e256-e259

 

73. 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 Access the recommendation on F1000Prime

 

72. 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

 

71. 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) 

 

70. 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

 

69. 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

Chem. Sci. 2018, 9, 2452-2468

 

68. Hughes, S.J., Ciulli, A.*

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

Essays Biochem. 2017, 61, 505-516

 

67. Maniaci, C., Hughes, S.J., Testa, A., Chen, W., Lamont, D.J., Rocha, S., Alessi, D.R., Romeo, R., Ciulli, A.*

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

Nat. Commun. 2017, 8, 830

  • See Figures here
  • Our VHL dimerizer/degrader CM11 and inactive epimer CMP98 are available from Tocris (April 2018)
  • Find out more about CM11 in the Chemical Probes Portal
  • Highlighted as "Promising PROTAC" in the 2020s Top Probes list of the Chemical Probes Portal 

 

66. Morreale, F.E., Testa, A., Chaugule, V.K., Bortoluzzi, A., Ciulli, A.*, Walden, H.*

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

J. Med. Chem. 2017, 60 (19), 8183-8191

 

65. Soares, P., Gadd, M.S., Frost, J., Galdeano, C., Ellis, L.C.J., Epemolu, O., Rocha, S., Read, K.D., Ciulli, A.*

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)

J. Med. Chem. 2018, 61 (2), 599-618

 

64. Khan, R., Marsh, G., Felix, R., Kemmitt, P.D., Baud, M.G.J., Ciulli, A., Spencer, J.

Gram-Scale Laboratory Synthesis of TC AC 28, a High-Affinity BET Bromodomain Ligand

ACS Omega 2017, 2 (8), 4328–4332

 

63. Cardote, T.A.F., Ciulli, A.*

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

ChemMedChem 2017, 12 (18), 1491-1496

 

62. Chan, K.-H., Zengerle, M., Testa, A., Ciulli, A.*

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

J. Med. Chem. 2018, 61 (2), 504-513

 

61. Cardote, T.A.F., Gadd, M.S., Ciulli, A.*

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

Structure 2017, 25 (6), 901-911.e3

  • See Figures here
  • Featured in the SLS News website
  • Access the coordinates of our pentameric complex crystal structure in the Protein DataBank: PDB entry code is 5N4W

 

60. Fernandez-Alonso, R., Davidson, L., Hukelmann, J., Zengerle, M., Prescott, A.R., Lamond, A., Ciulli, A., Sapkota, G.P., Findlay, G.M.

Brd4-Brd2 isoform switching coordinates pluripotent exit and Smad2-dependent lineage specification

EMBO Reports 2017, 18 (7), 1108-1122

 

59. Morreale, F.E., Bortoluzzi, A., Chaugule, V.K., Arkinson, C., Walden, H.*, Ciulli, A.*

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

J. Med. Chem. 2017, 60 (9), 4093-4098

 

58. Ryan, A., Polycarpou, E., Lack, N.A., Evangelopoulos, D., Sieg, C., Halman, A., Bhakta, S., Eleftheriadou, O., McHugh, T.D., Keany, S., Lowe, E.D., Ballet, R., Abuhammad, A., Jacobs, W.R. Jr, Ciulli, A., Sim, E.

Investigation of the mycobacterial enzyme HsaD as a potential novel target for anti-tubercular agents using a fragment-based drug design approach

Br. J. Pharmacol. 2017, 174 (14), 2209-2224

 

57. Bortoluzzi, A., Amato, A., Lucas, X., Blank, M., Ciulli, A.*

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

Biochem. J. 2017, 474 (10), 1633-1651

  • See Figures here
  • Access the coordinates of our domain-peptide complex crystal structure in the Protein Data Bank: PDB entry code is 5T8R

 

56. Gadd, M.S., Testa, A., Lucas, X., Chan, K.-H., Chen, W., Lamont, D.J., Zengerle, M., Ciulli, A.*

Structural basis of PROTAC cooperative recognition for selective protein degradation

Nat. Chem. Biol. 2017, 13 (5), 514-521

 

55. De Schutter, J.W., Morrison, J.P., Morrison, M.J., Ciulli, A., Imperiali, B.

Targeting Bacillosamine Biosynthesis in Bacterial Pathogens: Development of Inhibitors to a Bacterial Amino-Sugar Acetyltransferase from Campylobacter jejuni

J. Med. Chem. 2017, 60 (5), 2099-2118

 

54. Lucas, X., Ciulli, A.*

Recognition of substrate degrons by E3 ubiquitin ligases and modulation by small-molecule mimicry strategies

Curr. Opin. Struct. Biol. 2017, 44, 101-110

 

53. Frost, J., Galdeano, C., Soares, P., Gadd, M.S., Epemolu, O., Grzes, K., Ellis, L., Shimamura, S., Bantscheff, M., Grandi, P., Read, K.D., Cantrell, D.A., Rocha, S., Ciulli, A.*

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

Nat. Commun. 2016, 7, 13312

  • See Figures here
  • Featured in the UoD and SLS News websites
  • Highlighted in Drug Discovery Today and Phys.org
  • Access the coordinates of our protein-ligand co-crystal structure in the Protein DataBank: PDB entry code is 5LLI
  • FInd out more about VH298 in the Chemical Probes Portal
  • Our VHL inhibitor VH298 and inactive epimer cis-VH298 are available from Tocris (from April 2017)

 

52. Ciulli, A.*

Target validation: Switching domains

Nat. Chem. Biol. 2016, 12 (9), 659-660

 

51. Runcie, A.C., Chan, K.-H., Zengerle, M., Ciulli, A.*

Chemical genetics approaches for selective intervention in epigenetics

Curr. Opin. Chem. Biol. 2016, 33, 186-194

 

50. Galdeano, C., Ciulli, A.*

Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology

Future Med. Chem. 2016, 8 (13), 1655-1680

 

49. Dias, D.M., Furtado, J., Wasielewski, E., Cruz, R., Costello, B., Cole, L., Faria, T.Q., Baaske, P., Brito, R.M., Ciulli, A., Simões, I., Macedo-Ribeiro, S., Faro, C., Geraldes, C.F., Castanheira, P.

Biophysical characterization of laforin-carbohydrate interaction

Biochem. J. 2016, 473 (3), 335-345

 

48. Cardote, T.A.F., Ciulli, A.*

Cyclic and Macrocyclic Peptides as Chemical Tools To Recognise Protein Surfaces and Probe Protein-Protein Interactions

ChemMedChem 2016, 11 (8), 787-794

 

47. Baud, M.G., Lin-Shiao, E., Zengerle, M., Tallant, C., Ciulli, A.*

New Synthetic Routes to Triazolo-Benzodiazepine Analogues: Expanding the Scope of the Bump-and-Hole Approach for Selective BET Bromodomain Inhibition

J. Med. Chem. 2016, 59 (4), 1492-1500

 

46. Gadd, M.S., Bulatov, E., Ciulli, A.*

Serendipitous SAD Solution for DMSO-Soaked SOCS2-ElonginC-ElonginB Crystals Using Covalently Incorporated Dimethylarsenic: Insights into Substrate Receptor Conformational Flexibility in Cullin RING Ligases

PLoS ONE June 29, 2015; 10(6):e013218

 

45. Zengerle, M., Chan, K.-H., Ciulli, A.*

Selective small molecules induced degradation of the BET bromodomain protein BRD4

ACS Chem. Biol. 2015, 10 (8), 1770-1777

  • See Figures here
  • Featured in the UoD and CLS News websites 
  • Featured in BBC News
  • Listed amongst Most Read Articles in ACS Chem. Biol. (1 and 12 months frameworks)
  • Find out more about MZ1 in the Chemical Probes Portal
  • Our Brd4 degrader PROTAC MZ1 and the inactive epimer cis-MZ1 are available from Tocris (from April 2017)
  • MZ1 (and cis-MZ1) are available from Boehringer Ingelheim's OpnMe Portal: order for free, no strings attached!

 

44. Bulatov, E., Ciulli, A.*

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

Biochem. J. 2015, 467 (3), 365-386

 

43. Tallant, C., Valentini, E. Fedorov, O., Overvoorde, L., Ferguson, F.M., Filippakopoulos, P., Svergun, D.I., Knapp, S., Ciulli, A.*

Molecular basis of histone tail recognition by human TIP5 PHD finger and Bromodomain of the chromatin remodelling complex NoRC

Structure 2015, 23 (1), 80-92

 

42. Bulatov, E., Martin, E.M., Chatterjee, S., Knebel, A., Shimamura, S., Konijnenberg, A., Johnson, C., Zinn, N., Grandi, P., Sobott, F., Ciulli, A.*

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)

J. Biol. Chem. 2015, 290 (7), 4178-4191

 

41. Baud, M.G., Lin-Shiao, E., Cardote, T., Tallant, C., Pschibul, A., Chan, K.H., Zengerle, M., Garcia, J.R., Kwan, T.T., Ferguson, F.M., Ciulli, A.*

A bump-and-hole approach to engineer controlled selectivity of BET bromodomain chemical probes

Science 2014, 346 (6209), 638-641

 

40. Ferguson, F.M., Dias, D.M., Rodrigues, J.P., Wienk, H., Boelens, R., Bonvin, A.M., Abell C., Ciulli A.*

Binding Hotspots of BAZ2B Bromodomain: Histone Interaction Revealed by Solution NMR Driven Docking

Biochemistry 2014, 53 (42), 6706-6716

  •  See Figures here

 

39. Galdeano, C., Gadd, M.S., Soares, P., Scaffidi, S., Van Molle, I., Birced, I., Hewitt, S., Dias, D.M., Ciulli A.* 

Structure-Guided Design and Optimization of Small Molecules Targeting the Protein-Protein Interaction between the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (HIF) Alpha Subunit with In Vitro Nanomolar Affinities

J. Med. Chem. 2014, 57 (20), 8657-8663

  • See Figures here
  • Top Most Read Article in the journal (12 months timeframe)
  • Our VHL ligand VH032-amide and its inactive epimer cis-VH032, as well as various functionalized versions e.g. VHL-ligand plus linkers are available from Tocris

 

38. Dias, D.M., Ciulli, A.* 

NMR approaches in structure-based lead discovery: Recent developments and new frontiers for targeting multi-protein complexes

Prog. Biophys. Mol. Biol. 2014, 116 (2-3), 101-112

 

37. Dias, D.M., Van Molle, I., Baud, M.G.J., Galdeano, C., Geraldes, C.F.G.C., Ciulli, A.* 

Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein-Protein Interactions?

ACS Med. Chem. Lett. 2014, 5 (1), 23-28

  • See Figures here
  • Highlighted in Practical Fragments
  • 4th Most-Read Article in ACS Med. Chem. Lett. (Nov-Dec 2013)

 

36. Ferguson, F.M., Fedorov, O., Chaikuad, A., Philpott, M., Muniz, J., Felletar, I., von Delft, F., Heightman, T.D., Knapp, S., Abell, C., Ciulli, A.* 

Targeting Low-Druggability Bromodomains: Fragment Based Screening and Inhibitor Design Against the BAZ2B Bromodomain

J. Med. Chem. 2013, 56 (24), 10183-10187

 

35. Thomas, J.C., Matak-Vinkovic, D., Van Molle, I., Ciulli, A.* 

Multimeric Complexes among Ankyrin-Repeat and SOCS-box Protein 9 (ASB9), ElonginBC, and Cullin 5: Insights into the Structure and Assembly of ECS-type Cullin-RING E3 Ubiquitin Ligases

Biochemistry 2013, 52 (31), 5236-5246

 

34. Van Molle, I., Thomann, A., Buckley, D.L., So, E.C., Lang, S., Crews, C.M., Ciulli, A.* 

Dissecting Fragment-Based Lead Discovery at the von-Hippel Lindau Protein : Hypoxia Inducible Factor 1α Protein-Protein Interface

Chem. Biol. 2012, 19, 1300-1312

 

33. Buckley, D.L., Gustafson, J.L., Van Molle, I., Roth, A.G., Tae, H.S., Gareiss, P.C., Jorgensen, W.L., Ciulli, A., Crews, C.M.

Small Molecules Inhibitors of the Interaction Between the E3 Ligase VHL and HIF1α

Angew. Chem. Int. Ed. 2012, 51, 11463-11467

  • Selected as a "Hot paper" by the Editors of Angew. Chem. and Angew. Chem. Int. Ed.

 

32. Buckley, D.L., Van Molle, I., Gareiss, P.C., Tae, H.S., Michel, J., Noblin, D.J., Jorgensen, W.L., Ciulli, A.,* Crews, C.M.*

Targeting the von Hippel-Lindau E3 Ubiquitin Ligase Using Small Molecules to Disrupt the VHL/HIF-1α Interaction

J. Am. Chem. Soc. 2012, 134, 4465–4468

  • Highlighted in PPI-Net.org
  • Highlighted in Lou, K.-J. SciBX 5(20)
  • The fluorescent FAM-labeled 10-mer HIF-1α peptide (FAM-DALA-Hyp-YIPD) first used in this paper to develop a VHL-HIF displacement FP assay is now available on Tocris (October 2020) 

 

31. Philpott, M., Yang, J., Tumber, T., Fedorov, O., Uttarkar, S., Filippakopoulos, P., Picaud, S., Keates, T., Felletar, I., Ciulli, A., Knapp, S., Heightman, T.D.

Bromodomain-peptide displacement assays for interactome mapping and inhibitor discovery

Mol. Biosyst. 2011, 7, 2899–2908

  • Top Most-Accessed Article in August 2011

 

 

Postdoctoral Studies: Prof. Chris Abell and Prof. Tom L. Blundell

30. Macaulay, K.M., Heath, G.A., Ciulli, A., Murphy, A.M., Abell, C., Carr, J.P., Smith, A.G.

The biochemical properties of the two Arabidopsis thaliana isochorismate synthases.

Biochem. J. 2017, 474 (10), 1579-1590

 

29. Hung, A.W., Silvestre, H.L., Wen, S., George, G.P.C., Boland, J., Blundell, T.L., Ciulli, A., Abell, C.

Optimization of Inhibitors of Mycobacterium tuberculosis Pantothenate Synthetase Based on Group Efficiency Analysis

ChemMedChem 2016, 11(1), 38-42

  • Selected as a "Very Important Paper" (VIP) by the Editors of ChemMedChem

 

28. Silvestre, H.L., Blundell, T.L., Abell, C., Ciulli, A.*

Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery.

Proc. Natl. Acad. Sci. U.S.A. 2013, 110 (32), 12984-12989

 

27. Hudson, S.A., McLean, K.J., Surade, S., Yang, Y.-Q., Leys, D., Ciulli, A., Munro, A.W., Abell, C.

Application of fragment screening and merging to the discovery of inhibitors of the Mycobacterium tuberculosis cytochrome P450 CYP121.

Angew. Chem. Int. Ed. 2012, 51, 9311–9316

 

26. Dias, M.V.B., Snee, W.C., Bromfield, K.M., Payne, R.J., Palaninathan, S.K., Ciulli, A., Howard, N.I., Abell, C., Sacchettini, J.C., Blundell, T.L.

Structural investigation of inhibitor designs targeting 3-dehydroquinate dehydratase from the shikimate pathway of Mycobacterium tuberculosis.

Biochem. J. 2011, 436 (3), 729–39

                                    

25. Śledź, P., Silvestre, H.L., Hung, A.W., Ciulli, A., Blundell, T.L., Abell, C.

Optimization of the Interligand Overhauser Effect for fragment linking: application to inhibitor discovery against Mycobacterium tuberculosis pantothenate synthetase.

J. Am. Chem. Soc. 2010, 132, 4544–4545

 

24. Scott, D.E., Dawes, G.J., Ando, M., Abell, C.*, Ciulli, A.* 

A fragment-based approach to probing adenosine recognition sites using dynamic combinatorial chemistry.

ChemBioChem 2009, 10, 2772–2779

 

23. Hung, A.W., Silvestre, H.L., Wen, S., Ciulli, A., Blundell, T.L., Abell, C. 

Application of fragment growing and fragment linking to the discovery of inhibitors of Mycobacterium tuberculosis pantothenate synthetase.

Angew. Chem. Int. Ed. 2009, 48, 8452–8456

 

22. Ciulli, A.*, Scott, D.E., Ando, M., Reyes, F., Saldanha, S.A., Tuck, K.L., Chirgadze, D.Y., Blundell, T.L., Abell, C.*

Inhibition of Mycobacterium tuberculosis pantothenate synthetase by analogues of the reaction intermediate.

ChemBioChem 2008, 9, 2606–2611

 

21. Ciulli, A., Abell, C. 

Fragment-based approaches to enzyme inhibition.

Curr. Opin. Biotech. 2007, 18 (6), 489–496

 

20. Scott, D.E., Ciulli, A., Abell, C. 

Coenzyme biosynthesis: enzyme mechanism, structure and inhibition.

Nat. Prod. Rep. 2007, 24, 1009–1026

 

19. Ciulli, A., Blundell, T.L., Abell, C.

Fragment-based approaches to inhibitor discovery: targeting cofactor-binding sites and protein-protein interactions

Drugs of the Future 2007, 32, 13-14 Suppl A

 

 

PhD Studies: Prof. Chris Abell

18. Kerbarh, O., Ciulli, A., Chirgadze, D.Y., Blundell, T.L., Abell, C. 

Nucleophile selectivity of chorismate-utilizing enzymes.

ChemBioChem 2007, 8, 622–624

 

17. Ciulli, A., Chirgadze, D.Y., Smith, A.G., Blundell, T.L., Abell, C. 

Crystal structure of ketopantoate reductase in a ternary complex with NADP+ and pantoate bound: substrate recognition, conformational change and cooperativity.

J. Biol. Chem. 2007, 282, 8487–8497

 

16. Ciulli, A., Lobley, C.M.C., Tuck, K.L., Smith, A.G., Blundell, T.L., Abell, C. 

pH tuneable binding of 2'-phospho-ADP-ribose to ketopantoate reductase: a structural and calorimetric study.

Acta Cryst. D63 2007, 171–178

 

15. Ciulli, A., Williams, G., Smith, A.G., Blundell, T.L., Abell, C. 

Probing hot spots at protein-ligand binding sites: a fragment-based approach using biophysical methods.

J. Med. Chem. 2006, 49, 4992–5000

  • Highlighted twice in the Faculty of 1000 Biology Access the recommendation on F1000Prime
  • Highlighted in the Microcal Autumn 2007 Newsletter
  • Listed 13th Most-Accessed Article in Jul–Sept 2006

 

14. Kerbarh, O., Ciulli, A., Howard, N.I., Abell, C.

Salicylate biosynthesis: over-expression, purification and characterization of Irp9, a bifunctional salicylate synthase from Yersinia enterocolitica.

J. Bacteriol. 2005, 187, 5061–5066

 

13. Ciulli, A.,* Abell, C. 

Biophysical tools to monitor enzyme-ligand interactions of enzymes involved in vitamin biosynthesis.

Biochem. Soc. Trans. 2005, 33, 767–771

 

12. Lobley, C.M.C., Ciulli, A., Whitney, H.M., Williams, G., Smith, A.G., Abell, C., Blundell, T.L. 

The crystal structure of Escherichia coli ketopantoate reductase with NADP+ bound.

Biochemistry 2005, 44, 8930–8939

 

 

Pre-PhD Studies

11. Banci, L., Bertini, I., Ciulli, A., Fragai, M., Luchinat, C., Terni, B. 

Expression and high yield production of the catalytic domain of matrix metalloproteinase 12 and of an active mutant with increased solubility.

J. Mol. Cat. A: Chem. 2003, 204-205, 401–408

 

10. Bashall, A., Ciulli, A., Harron, E.A., Lawson, G.T., McPartlin, M., Mosquera, M.E.G., Wright, D.S. 

Effects of meta-substitution on aggregation in the cubanes [SnNR]4{R = [2-Me-5-MeOC6H3], [2,5-(MeO)2C6H3] and [3,5-(MeO)2C6H3]}.

J. Chem. Soc. Dalton Trans. 2002, 6, 1046–1050

 

 

Book Chapters

9. Ciulli, A.,* Hsia, O.

PROTAC Degraders: Mechanism, Recent Advances, and Future Challenges, In: 'Protein Homeostasis in Drug Discovery: A Chemical Biology Perspective'

M. Kostic and L. H. Jones, Ed., John Wiley & Sons. 2023, pp. 317-356. ISBN: 978-1-119-77418-1

DOI: 10.1002/9781119774198.ch9

 

8. Bartoschik, T., Zoephel, A., Rumpel, K., Ciulli, A., Heffern, C.

MST and TRIC Technology to Reliably Study PROTAC Binary and Ternary Binding in Drug Development, In: 'Targeted Protein Degradation'. Methods in Molecular Biology, vol 2365. 

Cacace A.M., Hickey C.M., Békés M. (eds) Humana, New York, NY, 2021. ISBN: 978-1-0716-1664-2

Methods Mol Biol. 2021, vol. 2365, pp. 115-133

  • See Figures here
 

7. Casement R., Bond A., Craigon C., Ciulli A.*

Mechanistic and Structural Features of PROTAC Ternary Complexes, In: 'Targeted Protein Degradation'. Methods in Molecular Biology, vol 2365. 

Cacace A.M., Hickey C.M., Békés M. (eds) Humana, New York, NY, 2021. ISBN: 978-1-0716-1664-2

Methods Mol Biol. 2021, vol. 2365, pp. 79-113

  • See Figures here
 
 

6. Zollman, D., Ciulli, A.* 

Structural and Biophysical Principles of Degrader Ternary Complexes, in: ‘Protein Degradation with New Chemical Modalities: Successful Strategies in Drug Discovery and Chemical Biology’.

H. Weinmann and C. Crews, Ed., Royal Society of Chemistry, Cambridge, UK, 2020, pp. 14–54. ISBN: 978-1-78801-686-5

DOI: 10.1039/9781839160691-00014

 

5. Bortoluzzi, A., Ciulli, A.*

Protein-Based NMR Methods Applied to Drug Discovery, in: ‘Applied Biophysics in Drug Discovery’.

D. Huddler and E. R. Zartler, Ed., John Wiley & Sons. 2017, pp. 153-173. ISBN: 978-1-119-09948-2

DOI: 10.1002/9781119099512.ch9

 

4. Ciulli, A.*

Biophysical Screening for the Discovery of Small-Molecule Ligands, in: ‘Protein-Ligand Interactions - Methods and Applications, 2nd Ed.’.

T. Daviter and M. Williams, Ed., Springer Protocols, Humana Press, 2013. ISBN: 978-1-62703-397-8 

Methods Mol Biol. 2013, vol. 1008, pp. 357-388

 

3. Śledź, P., Abell, C., Ciulli, A.*

Ligand‐Observed NMR in Fragment‐Based Approaches, in: ‘NMR of Biomolecules: Towards Mechanistic Systems Biology’.

I. Bertini, K. McGreevy and G. Parigi, Ed., Wiley, 2012, pp. 265–280. ISBN: 978-3-527-32850-5

DOI: 10.1002/9783527644506.ch15

 

2. Heikkila, T.J., Surade, S., Silvestre, H.L., Dias, M.V., Ciulli, A., Bromfield, K.M., Scott, D.E., Howard, N.I, Wen, S., Wei, A.H., Osborne, D.M., Abell, C., Blundell, T.L.

Fragment-based drug discovery in academia: Experiences from a tuberculosis programme, in: Proceedings of the NATO International School of Crystallography, 40th Course ‘From Molecules to Medicine: Structure of Biological Macromolecules and Its Relevance in Combating New Diseases and Bioterrorism’.

J. L. Sussman and P. Spadon, Ed., Springer, 2009, pp. 21–36. ISBN: 978-9-048-12338-4

DOI: 10.1007/978-90-481-2339-1_3

 

1. Ciulli, A., Blundell, T.L., Abell, C. 

Discovery and extrapolation of fragment structures towards drug design, in: ‘Computational and Structural Approaches to Drug Discovery – Ligand-Protein Interactions’.

R. M. Stroud and J. Finer-Moore, Ed., Royal Society of Chemistry, London, UK, 2008, pp. 293–318. ISBN: 978-1-84755-796-4

DOI: 10.1039/9781847557964-00291

 

 

PubMed Link

PubMed list of publications

 
 
 

Google Scholar Link

Google Scholar Profile

 

 

Patents

12. Protein degrader

Ciulli, Alessio; Bond, Adam George; Craigon, Connor George; Chan, Kwok-Ho; Testa, Andrea; Alessi, Dario 

PCT Int. Appl. (23/09/2022), WO 2023/047121

 

11. Improved small molecules

Ciulli, Alessio; Testa, Andrea; Maniaci, Chiara; Makukhin, Nikolai; Imaide, Satomi; Daniels, Danette; Riching, Kristin 

PCT Int. Appl. (19/10/2021), WO 2022/101603

 

10. Proteolysis targeting chimera (Protacs) as degraders of SMARCA2 and/or SMARCA4

Ciulli, Alessio; Dank, Christian; Diers, Emelyne; Farnaby, William; Roy, Michael; Steurer, Steffen; Trainor, Nicole

PCT Int. Appl. (23/04/2020), WO 2020/078933

 

9. Bifunctional molecules for targeting USP14

Testa, Andrea; Hughes, Scott J.; Butcher, Steven P.; Ciulli, Alessio

PCT Int. Appl. (19/12/2019), WO 2019/238886

 

8. Bifunctional molecules for targeting RPN11

Ciulli, Alessio; Testa, Andrea; Hughes, Scott J.; Butcher, Steven P.

PCT Int. Appl. (19/12/2019), WO 2019/238817

 

7. Bifunctional molecules for targeting UCHL5

Ciulli, Alessio; Testa, Andrea; Hughes, Scott J.; Butcher, Steven P.

PCT Int. Appl. (19/12/2019), WO 2019/238816

 

6. Small molecules

Ciulli, Alessio; Maniaci, Chiara; Hughes, Scott J.; Testa, Andrea

PCT Int. Appl. (18/10/2018), WO 2018/189554

 

5. Fluorohydroxyproline derivatives useful in the preparation of proteolysis targeting chimeras

Ciulli, Alessio; Testa, Andrea

PCT Int. Appl. (22/03/2018), WO 2018/051107

 

4. Derivatives of 1-[(cyclopentyl or 2-pyrrolidinyl)carbonylaminomethyl]-4-(1,3-thiazol-5-yl) benzene which are useful for the treatment of proliferative, autoimmune or inflammatory diseases

Ciulli, Alessio; Zengerle, Michael; Chan, Kwok-Ho

PCT Int. Appl. (22/09/2016), WO 2016/146985

 

3. Enzyme Functional Probes

Shiao, Enrique, L.; Baud, Matthias, G. J.; Ciulli, Alessio; Chan, Kwok-Ho; Zengerle, Michael

PCT Int. Appl. (04/06/2015), WO 2015/079259

 

2. Compounds and Methods for the Inhibition of VCB E3 Ubiquitin Ligase. 

Crews, Craig, M.; Buckley, Dennis; Ciulli, Alessio; Jorgensen, William; Gareiss, Peter, C.; Van Molle, Inge; Gustafson, Jeffrey; Tae, Hyun-Seop; Michel, Julien; Hoyer, Dentin, W.; Roth, Anke, G.; Harling, John, D.; Smith, Ian Edward, D.; Miah, Afjal, H.; Campos, Sebastien, A.; Le, Joelle

PCT Int. Appl. (18/07/2013), WO 2013/106646

 

1. Compounds & Methods for the Enhanced Degradation of Targeted Proteins & Other Polypeptides by an E3 Ubiquitin Ligase.

Crews, Craig, M.; Buckley, Dennis; Ciulli, Alessio; Jorgensen, William; Gareiss, Peter, C.; Van Molle, Inge; Gustafson, Jeffrey; Tae, Hyun-Seop; Michel, Julien; Hoyer, Dentin, W.; Roth, Anke, G.; Harling, John, D.; Smith, Ian Edward, D.; Miah, Afjal, H.; Campos, Sebastien, A.; Le, Joelle

PCT Int. Appl. (18/07/2013), WO 2013/106643