Publications

Refereed Papers In Primary Journals

* A.C. Corresponding Author

 

Independent Research: Ciulli Group

 

91. Makukhin, N., Ciulli A.*

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

RSC Med. Chem., 2020, Advance Article DOI: 10.1039/D0MD00272K (Review Article)

 

90. 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

 

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

Stereoselective Synthesis of Allele-Specific BET Inhibitors

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

 

88. 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

 

87. Whitworth, C., Ciulli, A.*

Protein degraders extend their reach

Nature, 2020584, 193-194

 

86. 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

 

85. 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.

 

84. 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

 

83. 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)

 

82. 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

 

81. Ciulli, A.*, Farnaby, W.*

Protein degradation for drug discovery. [Editorial]

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

 

80. 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. 201915, 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!
  • Our VHL ligand "VH101, phenol" functionalized for PROTAC conjugation is available from Tocris (January 2020)

 

79. 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)

 

78. 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

 

77. 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

 

76. 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.

 

75. 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

 

74. 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)

 

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

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

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

 

72. 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"
  • 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) 

 

71. 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

 

70. 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

 

69. 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

 

68. 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) 

 

67. 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

 

66. 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

 

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

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

Essays in Biochemistry 2017, 61, 505-516

 

64. 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)  

 

63. 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

 

62. 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

 

61. 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

 

60. 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

 

59. 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

 

58. 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

 

57. 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

 

56. 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

 

55. 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. 2017174 (14), 2209-2224

 

54. 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

 

53. 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

 

52. 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

 

51. 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

 

50. 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)

 

49. Ciulli, A.*

Target validation: Switching domains

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

 

48. 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

 

47. 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

 

46. 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

 

45. 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

 

44. 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

 

43. 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

 

42. 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!

 

41. 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

 

40. 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

 

39. 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

 

38. 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

 

37. 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

 

36. 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 J. Med. Chem. (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

 

35. 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

 

34. 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)

 

33. 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. 201356 (24), 10183-10187

 

32. 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

 

31. 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

 

30. 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.

 

29. 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) 

 

28. 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

27. 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

 

26. 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

 

25. 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

 

24. 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

 

23. 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

                                    

22. 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

 

21. 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

 

20. 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

 

19. 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

 

18. Ciulli, A., Abell, C. 

Fragment-based approaches to enzyme inhibition.

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

 

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

Coenzyme biosynthesis: enzyme mechanism, structure and inhibition.

Nat. Prod. Rep. 2007, 24, 1009–1026

 

16. 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

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

Nucleophile selectivity of chorismate-utilizing enzymes.

ChemBioChem 2007, 8, 622–624

 

14. 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

 

13. 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

 

12. 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

 

11. 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

 

10. Ciulli, A.,* Abell, C. 

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

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

 

9. 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

8. 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

 

7. 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

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

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