Publications

Refereed Papers In Primary Journals

* A.C. Corresponding Author

 

Independent Research: Ciulli Group

 

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 Apr 12. doi: 10.1021/acschembio.8b01016. [Epub ahead of print]

 

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., Article in Press; DOI: 10.1016/j.bmc.2019.02.048; Publication Date (Web): February 22, 2019

 

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.

 

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"  

 

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 December 2018 : haematol.2018.207027; Doi:10.3324/haematol.2018.207027

 

70. Wei-Wei Kung, Sarath Ramachandran, Nikolai Makukhin, Elvira Bruno, Alessio Ciulli*

Structural insights into substrate recognition by the SOCS2 E3 ubiquitin ligase

bioRxiv 470187; 14 November 2018 doi: https://doi.org/10.1101/470187

 

69. 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

 

68. 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

 

67. 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) 

 

66. 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

 

65. 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.

 

64. 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.

 

63. 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)  

 

62. 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.

 

61. 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.

 

60. 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.

 

59. 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.

 

58. 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.

 

57. 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.

 

56. 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.

 

55. 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.

 

54. 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.

 

53. 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.

 

52. 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.

 

51. 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.

 

50. 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.

 

49. 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 cisVH298 are available from Tocris (from April 2017)

 

48. Ciulli, A.*

Target validation: Switching domains.

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

 

47. 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.

 

46. 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), 186-194.

 

45. 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.

 

44. 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.

 

43. 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.

 

42. 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.

 

41. 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 cisMZ1 are available from Tocris (from April 2017)

 

40. 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.

 

39. 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.

 

38. 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.

 

37. 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.

 

36. 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

 

35. 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.

 

34. 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.

 

33. 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)

 

32. 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.

 

31. 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.

 

30. 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.

 

29. 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.

 

28. 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.

 

27. 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 & Prof. Tom L. Blundell

26. 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.

 

25. 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

 

24. 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.

 

23. 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.

 

22. 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.

                                    

21. Śledź, P., Silvestre, H.L., Hung, A.W., Ciulli, A., Blundell, T.L., and 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.

 

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

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

ChemBioChem 2009, 10, 2772–2779.

 

19. Hung, A.W., Silvestre, H.L., Wen, S., Ciulli, A., Blundell, T.L., and 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.

 

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

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

ChemBioChem 2008, 9, 2606–2611.

 

17. Ciulli, A., & Abell, C. 

Fragment-based approaches to enzyme inhibition.

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

 

16. Scott, D.E., Ciulli, A., and Abell, C. 

Coenzyme biosynthesis: enzyme mechanism, structure and inhibition.

Nat. Prod. Rep. 2007, 24, 1009–1026.     

 

15. Ciulli, A., Blundell, T.L., and 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

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

Nucleophile selectivity of chorismate-utilizing enzymes.

ChemBioChem 2007, 8, 622–624.

 

13. Ciulli, A., Chirgadze, D.Y., Smith, A.G., Blundell, T.L., and 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.

 

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

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

Acta Cryst. D63 2007, 171–178.

 

11. Ciulli, A., Williams, G., Smith, A.G., Blundell, T.L., and 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

 

10. Kerbarh, O., Ciulli, A., Howard, N.I., and Abell, C.

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

J. Bacteriol. 2005, 187, 5061–5066.

 

9. Ciulli, A.*, & Abell, C. 

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

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

 

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

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

Biochemistry 2005, 44, 8930–8939.

 

 

Pre-PhD Studies

7. Banci, L., Bertini, I., Ciulli, A., Fragai, M., Luchinat, C., and 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.

 

6. Bashall, A., Ciulli, A., Harron, E.A., Lawson, G.T., McPartlin, M., Mosquera, M.E.G., and 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

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

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

D. Huddler and E. Zartler, Ed., John Wiles & 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. and 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., and 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., and 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, 2008, pp. 293–318. ISBN: 978-1-84755-796-4.

DOI: 10.1039/9781847557964-00291

 

 

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Patents

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