4w9e Citations

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.

OpenAccess logo J Med Chem 57 8657-63 (2014)
Related entries: 4w9c, 4w9d, 4w9f, 4w9g, 4w9h, 4w9i, 4w9j, 4w9k, 4w9l

Cited: 143 times
EuropePMC logo PMID: 25166285

Abstract

E3 ubiquitin ligases are attractive targets in the ubiquitin-proteasome system, however, the development of small-molecule ligands has been rewarded with limited success. The von Hippel-Lindau protein (pVHL) is the substrate recognition subunit of the VHL E3 ligase that targets HIF-1α for degradation. We recently reported inhibitors of the pVHL:HIF-1α interaction, however they exhibited moderate potency. Herein, we report the design and optimization, guided by X-ray crystal structures, of a ligand series with nanomolar binding affinities.

Articles - 4w9e mentioned but not cited (1)

  1. Discovery of novel inhibitors disrupting HIF-1α/von Hippel-Lindau interaction through shape-based screening and cascade docking. Xue X, Zhao NY, Yu HT, Sun Y, Kang C, Huang QB, Sun HP, Wang XL, Li NG. PeerJ 4 e2757 (2016)


Reviews citing this publication (55)

  1. Induced protein degradation: an emerging drug discovery paradigm. Lai AC, Crews CM. Nat Rev Drug Discov 16 101-114 (2017)
  2. Small-Molecule PROTACS: New Approaches to Protein Degradation. Toure M, Crews CM. Angew Chem Int Ed Engl 55 1966-1973 (2016)
  3. Targeting Transcription Factors for Cancer Treatment. Lambert M, Jambon S, Depauw S, David-Cordonnier MH. Molecules 23 E1479 (2018)
  4. Targeted Protein Degradation: from Chemical Biology to Drug Discovery. Cromm PM, Crews CM. Cell Chem Biol 24 1181-1190 (2017)
  5. Advancing targeted protein degradation for cancer therapy. Dale B, Cheng M, Park KS, Kaniskan HÜ, Xiong Y, Jin J. Nat Rev Cancer 21 638-654 (2021)
  6. Small-molecule PROTACs: An emerging and promising approach for the development of targeted therapy drugs. An S, Fu L. EBioMedicine 36 553-562 (2018)
  7. Targeting Cullin-RING E3 ubiquitin ligases for drug discovery: structure, assembly and small-molecule modulation. Bulatov E, Ciulli A. Biochem J 467 365-386 (2015)
  8. Degradation of proteins by PROTACs and other strategies. Wang Y, Jiang X, Feng F, Liu W, Sun H. Acta Pharm Sin B 10 207-238 (2020)
  9. Molecular recognition of ternary complexes: a new dimension in the structure-guided design of chemical degraders. Hughes SJ, Ciulli A. Essays Biochem 61 505-516 (2017)
  10. Cyclic and Macrocyclic Peptides as Chemical Tools To Recognise Protein Surfaces and Probe Protein-Protein Interactions. Cardote TA, Ciulli A. ChemMedChem 11 787-794 (2016)
  11. Targeted Protein Degradation by Small Molecules. Bondeson DP, Crews CM. Annu Rev Pharmacol Toxicol 57 107-123 (2017)
  12. Chemical approaches to targeted protein degradation through modulation of the ubiquitin-proteasome pathway. Collins I, Wang H, Caldwell JJ, Chopra R. Biochem J 474 1127-1147 (2017)
  13. E3 Ligase Ligands for PROTACs: How They Were Found and How to Discover New Ones. Ishida T, Ciulli A. SLAS Discov 26 484-502 (2021)
  14. PROTACs- a game-changing technology. Konstantinidou M, Li J, Zhang B, Wang Z, Shaabani S, Ter Brake F, Essa K, Dömling A. Expert Opin Drug Discov 14 1255-1268 (2019)
  15. PROTACs: past, present and future. Li K, Crews CM. Chem Soc Rev 51 5214-5236 (2022)
  16. Recognition of substrate degrons by E3 ubiquitin ligases and modulation by small-molecule mimicry strategies. Lucas X, Ciulli A. Curr Opin Struct Biol 44 101-110 (2017)
  17. Current strategies for the design of PROTAC linkers: a critical review. Troup RI, Fallan C, Baud MGJ. Explor Target Antitumor Ther 1 273-312 (2020)
  18. Targeting Protein-Protein Interactions in the HIF System. Wilkins SE, Abboud MI, Hancock RL, Schofield CJ. ChemMedChem 11 773-786 (2016)
  19. Recent Developments in PROTAC-Mediated Protein Degradation: From Bench to Clinic. Hu Z, Crews CM. Chembiochem 23 e202100270 (2022)
  20. Targeting Brd4 for cancer therapy: inhibitors and degraders. Duan Y, Guan Y, Qin W, Zhai X, Yu B, Yu B, Liu H. Medchemcomm 9 1779-1802 (2018)
  21. E3 Ligase Ligands in Successful PROTACs: An Overview of Syntheses and Linker Attachment Points. Bricelj A, Steinebach C, Kuchta R, Gütschow M, Sosič I. Front Chem 9 707317 (2021)
  22. Bivalent Ligands for Protein Degradation in Drug Discovery. Scheepstra M, Hekking KFW, van Hijfte L, Folmer RHA. Comput Struct Biotechnol J 17 160-176 (2019)
  23. Next-Generation Drugs and Probes for Chromatin Biology: From Targeted Protein Degradation to Phase Separation. Cermakova K, Hodges HC. Molecules 23 E1958 (2018)
  24. Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors. Sable R, Jois S. Molecules 20 11569-11603 (2015)
  25. Targeting the Ubiquitin-Proteasome System for Cancer Therapeutics by Small-Molecule Inhibitors. LaPlante G, Zhang W. Cancers (Basel) 13 3079 (2021)
  26. Small Molecule Modulators of RING-Type E3 Ligases: MDM and Cullin Families as Targets. Bulatov E, Zagidullin A, Valiullina A, Sayarova R, Rizvanov A. Front Pharmacol 9 450 (2018)
  27. Ligandability of E3 Ligases for Targeted Protein Degradation Applications. Belcher BP, Ward CC, Nomura DK. Biochemistry 62 588-600 (2023)
  28. Chemical Protein Degradation Approach and its Application to Epigenetic Targets. Itoh Y. Chem Rec 18 1681-1700 (2018)
  29. Protein degraders enter the clinic - a new approach to cancer therapy. Chirnomas D, Hornberger KR, Crews CM. Nat Rev Clin Oncol 20 265-278 (2023)
  30. Proteolysis targeting chimeras (PROTACs) in cancer therapy. Ocaña A, Pandiella A. J Exp Clin Cancer Res 39 189 (2020)
  31. Opportunities and Challenges of Small Molecule Induced Targeted Protein Degradation. He M, Lv W, Rao Y. Front Cell Dev Biol 9 685106 (2021)
  32. Strategies to Reduce the On-Target Platelet Toxicity of Bcl-xL Inhibitors: PROTACs, SNIPERs and Prodrug-Based Approaches. Negi A, Voisin-Chiret AS. Chembiochem 23 e202100689 (2022)
  33. Bifunctional HDAC Therapeutics: One Drug to Rule Them All? Smalley JP, Cowley SM, Hodgkinson JT. Molecules 25 E4394 (2020)
  34. Discovery of small molecule ligands for the von Hippel-Lindau (VHL) E3 ligase and their use as inhibitors and PROTAC degraders. Diehl CJ, Ciulli A. Chem Soc Rev 51 8216-8257 (2022)
  35. Targeting TRIM Proteins: A Quest towards Drugging an Emerging Protein Class. D'Amico F, Mukhopadhyay R, Ovaa H, Mulder MPC. Chembiochem 22 2011-2031 (2021)
  36. Light-Controllable PROTACs for Temporospatial Control of Protein Degradation. Liu J, Peng Y, Wei W. Front Cell Dev Biol 9 678077 (2021)
  37. Targeting protein function: the expanding toolkit for conditional disruption. Campbell AE, Bennett D. Biochem J 473 2573-2589 (2016)
  38. Inhibitors, PROTACs and Molecular Glues as Diverse Therapeutic Modalities to Target Cyclin-Dependent Kinase. Rana S, Mallareddy JR, Singh S, Boghean L, Natarajan A. Cancers (Basel) 13 5506 (2021)
  39. Chemical Methods to Knock Down the Amyloid Proteins. Gao N, Chen YX, Zhao YF, Li YM. Molecules 22 E916 (2017)
  40. Chemical modulation of transcription factors. Wiedemann B, Weisner J, Rauh D. Medchemcomm 9 1249-1272 (2018)
  41. Discovery of E3 Ligase Ligands for Target Protein Degradation. Lee J, Lee Y, Jung YM, Park JH, Yoo HS, Park J. Molecules 27 6515 (2022)
  42. Enriching Proteolysis Targeting Chimeras with a Second Modality: When Two Are Better Than One. Salerno A, Seghetti F, Caciolla J, Uliassi E, Testi E, Guardigni M, Roberti M, Milelli A, Bolognesi ML. J Med Chem 65 9507-9530 (2022)
  43. Estrogen Receptor-α Targeting: PROTACs, SNIPERs, Peptide-PROTACs, Antibody Conjugated PROTACs and SNIPERs. Negi A, Kesari KK, Voisin-Chiret AS. Pharmaceutics 14 2523 (2022)
  44. Exploration of Aberrant E3 Ligases Implicated in Alzheimer's Disease and Development of Chemical Tools to Modulate Their Function. Potjewyd FM, Axtman AD. Front Cell Neurosci 15 768655 (2021)
  45. Small molecule PROTACs: an emerging technology for targeted therapy in drug discovery. Pei H, Peng Y, Zhao Q, Chen Y. RSC Adv 9 16967-16976 (2019)
  46. LISTERIN E3 Ubiquitin Ligase and Ribosome-Associated Quality Control (RQC) Mechanism. Mishra R, Bansal A, Mishra A. Mol Neurobiol 58 6593-6609 (2021)
  47. PROTAC: targeted drug strategy. Principles and limitations. Koroleva OA, Dutikova YV, Trubnikov AV, Zenov FA, Manasova EV, Shtil AA, Kurkin AV. Russ Chem Bull 71 2310-2334 (2022)
  48. Targeting the ubiquitin system by fragment-based drug discovery. Kennedy C, McPhie K, Rittinger K. Front Mol Biosci 9 1019636 (2022)
  49. Current Challenges in Small Molecule Proximity-Inducing Compound Development for Targeted Protein Degradation Using the Ubiquitin Proteasomal System. Radhakrishnan S, Hoff O, Muellner MK. Molecules 27 8119 (2022)
  50. Huntingtin Ubiquitination Mechanisms and Novel Possible Therapies to Decrease the Toxic Effects of Mutated Huntingtin. Fiorillo A, Morea V, Colotti G, Ilari A. J Pers Med 11 1309 (2021)
  51. Proteasomal Degradation of Zn-Dependent Hdacs: The E3-Ligases Implicated and the Designed Protacs That Enable Degradation. Márquez-Cantudo L, Ramos A, Coderch C, de Pascual-Teresa B. Molecules 26 5606 (2021)
  52. Recent advancements in the discovery of cereblon-based protease-targeted chimeras with potential for therapeutic intervention. Singh H, Agrawal DK. Future Med Chem 14 1403-1416 (2022)
  53. PROTAC'ing oncoproteins: targeted protein degradation for cancer therapy. Kelm JM, Pandey DS, Malin E, Kansou H, Arora S, Kumar R, Gavande NS. Mol Cancer 22 62 (2023)
  54. Treatment strategies for clear cell renal cell carcinoma: Past, present and future. Yang J, Wang K, Yang Z. Front Oncol 13 1133832 (2023)
  55. PROTACs: A novel strategy for cancer drug discovery and development. Han X, Sun Y. MedComm (2020) 4 e290 (2023)

Articles citing this publication (87)

  1. Selective Small Molecule Induced Degradation of the BET Bromodomain Protein BRD4. Zengerle M, Chan KH, Ciulli A. ACS Chem Biol 10 1770-1777 (2015)
  2. Structural basis of PROTAC cooperative recognition for selective protein degradation. Gadd MS, Testa A, Lucas X, Chan KH, Chen W, Lamont DJ, Zengerle M, Ciulli A. Nat Chem Biol 13 514-521 (2017)
  3. Lessons in PROTAC Design from Selective Degradation with a Promiscuous Warhead. Bondeson DP, Smith BE, Burslem GM, Buhimschi AD, Hines J, Jaime-Figueroa S, Wang J, Hamman BD, Ishchenko A, Crews CM. Cell Chem Biol 25 78-87.e5 (2018)
  4. A Chemoproteomic Approach to Query the Degradable Kinome Using a Multi-kinase Degrader. Huang HT, Dobrovolsky D, Paulk J, Yang G, Weisberg EL, Doctor ZM, Buckley DL, Cho JH, Ko E, Jang J, Shi K, Choi HG, Griffin JD, Li Y, Treon SP, Fischer ES, Bradner JE, Tan L, Gray NS. Cell Chem Biol 25 88-99.e6 (2018)
  5. Iterative Design and Optimization of Initially Inactive Proteolysis Targeting Chimeras (PROTACs) Identify VZ185 as a Potent, Fast, and Selective von Hippel-Lindau (VHL) Based Dual Degrader Probe of BRD9 and BRD7. Zoppi V, Hughes SJ, Maniaci C, Testa A, Gmaschitz T, Wieshofer C, Koegl M, Riching KM, Daniels DL, Spallarossa A, Ciulli A. J Med Chem 62 699-726 (2019)
  6. Potent and selective chemical probe of hypoxic signalling downstream of HIF-α hydroxylation via VHL inhibition. Frost J, Galdeano C, Soares P, Gadd MS, Grzes KM, Ellis L, Epemolu O, Shimamura S, Bantscheff M, Grandi P, Read KD, Cantrell DA, Rocha S, Ciulli A. Nat Commun 7 13312 (2016)
  7. Homo-PROTACs: bivalent small-molecule dimerizers of the VHL E3 ubiquitin ligase to induce self-degradation. Maniaci C, Hughes SJ, Testa A, Chen W, Lamont DJ, Rocha S, Alessi DR, Romeo R, Ciulli A. Nat Commun 8 830 (2017)
  8. Protein Degradation by In-Cell Self-Assembly of Proteolysis Targeting Chimeras. Lebraud H, Wright DJ, Johnson CN, Heightman TD. ACS Cent Sci 2 927-934 (2016)
  9. Impact of Target Warhead and Linkage Vector on Inducing Protein Degradation: Comparison of Bromodomain and Extra-Terminal (BET) Degraders Derived from Triazolodiazepine (JQ1) and Tetrahydroquinoline (I-BET726) BET Inhibitor Scaffolds. Chan KH, Zengerle M, Testa A, Ciulli A. J Med Chem 61 504-513 (2018)
  10. Reversible Spatiotemporal Control of Induced Protein Degradation by Bistable PhotoPROTACs. Pfaff P, Samarasinghe KTG, Crews CM, Carreira EM. ACS Cent Sci 5 1682-1690 (2019)
  11. Mapping the Degradable Kinome Provides a Resource for Expedited Degrader Development. Donovan KA, Ferguson FM, Bushman JW, Eleuteri NA, Bhunia D, Ryu S, Tan L, Shi K, Yue H, Liu X, Dobrovolsky D, Jiang B, Wang J, Hao M, You I, Teng M, Liang Y, Hatcher J, Li Z, Manz TD, Groendyke B, Hu W, Nam Y, Sengupta S, Cho H, Shin I, Agius MP, Ghobrial IM, Ma MW, Che J, Buhrlage SJ, Sim T, Gray NS, Fischer ES. Cell 183 1714-1731.e10 (2020)
  12. Crystal Structure of the Cul2-Rbx1-EloBC-VHL Ubiquitin Ligase Complex. Cardote TAF, Gadd MS, Ciulli A. Structure 25 901-911.e3 (2017)
  13. Structure-Based Discovery of SD-36 as a Potent, Selective, and Efficacious PROTAC Degrader of STAT3 Protein. Zhou H, Bai L, Xu R, Zhao Y, Chen J, McEachern D, Chinnaswamy K, Wen B, Dai L, Kumar P, Yang CY, Liu Z, Wang M, Liu L, Meagher JL, Yi H, Sun D, Stuckey JA, Wang S. J Med Chem 62 11280-11300 (2019)
  14. Group-Based Optimization of Potent and Cell-Active Inhibitors of the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase: Structure-Activity Relationships Leading to the Chemical Probe (2S,4R)-1-((S)-2-(1-Cyanocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (VH298). Soares P, Gadd MS, Frost J, Galdeano C, Ellis L, Epemolu O, Rocha S, Read KD, Ciulli A. J Med Chem 61 599-618 (2018)
  15. Extended pharmacodynamic responses observed upon PROTAC-mediated degradation of RIPK2. Mares A, Miah AH, Smith IED, Rackham M, Thawani AR, Cryan J, Haile PA, Votta BJ, Beal AM, Capriotti C, Reilly MA, Fisher DT, Zinn N, Bantscheff M, MacDonald TT, Vossenkamper A, Dace P, Churcher I, Benowitz AB, Watt G, Denyer J, Scott-Stevens P, Harling JD. Commun Biol 3 140 (2020)
  16. 3-Fluoro-4-hydroxyprolines: Synthesis, Conformational Analysis, and Stereoselective Recognition by the VHL E3 Ubiquitin Ligase for Targeted Protein Degradation. Testa A, Lucas X, Castro GV, Chan KH, Wright JE, Runcie AC, Gadd MS, Harrison WTA, Ko EJ, Fletcher D, Ciulli A. J Am Chem Soc 140 9299-9313 (2018)
  17. Cereblon versus VHL: Hijacking E3 ligases against each other using PROTACs. Girardini M, Maniaci C, Hughes SJ, Testa A, Ciulli A. Bioorg Med Chem 27 2466-2479 (2019)
  18. TF-PROTACs Enable Targeted Degradation of Transcription Factors. Liu J, Chen H, Kaniskan HÜ, Xie L, Chen X, Jin J, Wei W. J Am Chem Soc 143 8902-8910 (2021)
  19. Systematic exploration of different E3 ubiquitin ligases: an approach towards potent and selective CDK6 degraders. Steinebach C, Ng YLD, Sosič I, Lee CS, Chen S, Lindner S, Vu LP, Bricelj A, Haschemi R, Monschke M, Steinwarz E, Wagner KG, Bendas G, Luo J, Gütschow M, Krönke J. Chem Sci 11 3474-3486 (2020)
  20. Developing degraders: principles and perspectives on design and chemical space. Maple HJ, Clayden N, Baron A, Stacey C, Felix R. Medchemcomm 10 1755-1764 (2019)
  21. Insights into Cullin-RING E3 ubiquitin ligase recruitment: structure of the VHL-EloBC-Cul2 complex. Nguyen HC, Yang H, Fribourgh JL, Wolfe LS, Xiong Y. Structure 23 441-449 (2015)
  22. Cancer Selective Target Degradation by Folate-Caged PROTACs. Liu J, Chen H, Liu Y, Shen Y, Meng F, Kaniskan HÜ, Jin J, Wei W. J Am Chem Soc 143 7380-7387 (2021)
  23. Design and Characterization of SGK3-PROTAC1, an Isoform Specific SGK3 Kinase PROTAC Degrader. Tovell H, Testa A, Zhou H, Shpiro N, Crafter C, Ciulli A, Alessi DR. ACS Chem Biol 14 2024-2034 (2019)
  24. PROTAC-mediated crosstalk between E3 ligases. Steinebach C, Kehm H, Lindner S, Vu LP, Köpff S, López Mármol Á, Weiler C, Wagner KG, Reichenzeller M, Krönke J, Gütschow M. Chem Commun (Camb) 55 1821-1824 (2019)
  25. PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes. Zaidman D, Prilusky J, London N. J Chem Inf Model 60 4894-4903 (2020)
  26. Rapid and Reversible Knockdown of Endogenously Tagged Endosomal Proteins via an Optimized HaloPROTAC Degrader. Tovell H, Testa A, Maniaci C, Zhou H, Prescott AR, Macartney T, Ciulli A, Alessi DR. ACS Chem Biol 14 882-892 (2019)
  27. A small molecule HIF-1α stabilizer that accelerates diabetic wound healing. Li G, Ko CN, Li D, Yang C, Wang W, Yang GJ, Di Primo C, Wong VKW, Xiang Y, Lin L, Ma DL, Leung CH. Nat Commun 12 3363 (2021)
  28. Demonstrating In-Cell Target Engagement Using a Pirin Protein Degradation Probe (CCT367766). Chessum NEA, Sharp SY, Caldwell JJ, Pasqua AE, Wilding B, Colombano G, Collins I, Ozer B, Richards M, Rowlands M, Stubbs M, Burke R, McAndrew PC, Clarke PA, Workman P, Cheeseman MD, Jones K. J Med Chem 61 918-933 (2018)
  29. Design, synthesis and biological evaluation of Proteolysis Targeting Chimeras (PROTACs) as a BTK degraders with improved pharmacokinetic properties. Jaime-Figueroa S, Buhimschi AD, Toure M, Hines J, Crews CM. Bioorg Med Chem Lett 30 126877 (2020)
  30. Development of Selective Histone Deacetylase 6 (HDAC6) Degraders Recruiting Von Hippel-Lindau (VHL) E3 Ubiquitin Ligase. Yang K, Wu H, Zhang Z, Leisten ED, Nie X, Liu B, Wen Z, Zhang J, Cunningham MD, Tang W. ACS Med Chem Lett 11 575-581 (2020)
  31. Uncoupling of PARP1 trapping and inhibition using selective PARP1 degradation. Wang S, Han L, Han J, Li P, Ding Q, Zhang QJ, Liu ZP, Chen C, Yu Y. Nat Chem Biol 15 1223-1231 (2019)
  32. Understanding and Improving the Membrane Permeability of VH032-Based PROTACs. Klein VG, Townsend CE, Testa A, Zengerle M, Maniaci C, Hughes SJ, Chan KH, Ciulli A, Lokey RS. ACS Med Chem Lett 11 1732-1738 (2020)
  33. Trivalent PROTACs enhance protein degradation via combined avidity and cooperativity. Imaide S, Riching KM, Makukhin N, Vetma V, Whitworth C, Hughes SJ, Trainor N, Mahan SD, Murphy N, Cowan AD, Chan KH, Craigon C, Testa A, Maniaci C, Urh M, Daniels DL, Ciulli A. Nat Chem Biol 17 1157-1167 (2021)
  34. Ligand deconstruction: Why some fragment binding positions are conserved and others are not. Kozakov D, Hall DR, Jehle S, Luo L, Ochiana SO, Jones EV, Pollastri M, Allen KN, Whitty A, Vajda S. Proc Natl Acad Sci U S A 112 E2585-94 (2015)
  35. Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta. Bai N, Miller SA, Andrianov GV, Yates M, Kirubakaran P, Karanicolas J. J Chem Inf Model 61 1368-1382 (2021)
  36. A novel strategy to block mitotic progression for targeted therapy. Chi JJ, Li H, Zhou Z, Izquierdo-Ferrer J, Xue Y, Wavelet CM, Schiltz GE, Zhang B, Cristofanilli M, Lu X, Bahar I, Wan Y. EBioMedicine 49 40-54 (2019)
  37. Identification of New Small-Molecule Inducers of Estrogen-related Receptor α (ERRα) Degradation. Peng L, Zhang Z, Lei C, Li S, Zhang Z, Ren X, Chang Y, Zhang Y, Xu Y, Ding K. ACS Med Chem Lett 10 767-772 (2019)
  38. Amide-to-Ester Substitution as a Strategy for Optimizing PROTAC Permeability and Cellular Activity. Klein VG, Bond AG, Craigon C, Lokey RS, Ciulli A. J Med Chem 64 18082-18101 (2021)
  39. Research Support, Non-U.S. Gov't Drugging the undruggable: targeting challenging E3 ligases for personalized medicine. Galdeano C. Future Med Chem 9 347-350 (2017)
  40. A suite of mathematical solutions to describe ternary complex formation and their application to targeted protein degradation by heterobifunctional ligands. Han B. J Biol Chem 295 15280-15291 (2020)
  41. Discovery of the first potent proteolysis targeting chimera (PROTAC) degrader of indoleamine 2,3-dioxygenase 1. Hu M, Zhou W, Wang Y, Yao D, Ye T, Yao Y, Chen B, Liu G, Yang X, Wang W, Xie Y. Acta Pharm Sin B 10 1943-1953 (2020)
  42. Disordered region of cereblon is required for efficient degradation by proteolysis-targeting chimera. Kim K, Lee DH, Park S, Jo SH, Ku B, Park SG, Park BC, Jeon YU, Ahn S, Kang CH, Hwang D, Chae S, Ha JD, Kim S, Hwang JY, Kim JH. Sci Rep 9 19654 (2019)
  43. Hypoxia inducible factor (HIF) as a model for studying inhibition of protein-protein interactions. Burslem GM, Kyle HF, Nelson A, Edwards TA, Wilson AJ. Chem Sci 8 4188-4202 (2017)
  44. Practical synthesis of a phthalimide-based Cereblon ligand to enable PROTAC development. Lohbeck J, Miller AK. Bioorg Med Chem Lett 26 5260-5262 (2016)
  45. Pharmacological difference between degrader and inhibitor against oncogenic BCR-ABL kinase. Shibata N, Shimokawa K, Nagai K, Ohoka N, Hattori T, Miyamoto N, Ujikawa O, Sameshima T, Nara H, Cho N, Naito M. Sci Rep 8 13549 (2018)
  46. Pred-binding: large-scale protein-ligand binding affinity prediction. Shar PA, Tao W, Gao S, Huang C, Li B, Zhang W, Shahen M, Zheng C, Bai Y, Wang Y. J Enzyme Inhib Med Chem 31 1443-1450 (2016)
  47. Discovery of a Novel BCL-XL PROTAC Degrader with Enhanced BCL-2 Inhibition. Pal P, Thummuri D, Lv D, Liu X, Zhang P, Hu W, Poddar SK, Hua N, Khan S, Yuan Y, Zhang X, Zhou D, Zheng G. J Med Chem 64 14230-14246 (2021)
  48. Surface Probing by Fragment-Based Screening and Computational Methods Identifies Ligandable Pockets on the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase. Lucas X, Van Molle I, Ciulli A. J Med Chem 61 7387-7393 (2018)
  49. Synthesis of 7-benzylguanosine cap-analogue conjugates for eIF4E targeted degradation. Kaur T, Menon A, Garner AL. Eur J Med Chem 166 339-350 (2019)
  50. Design, Synthesis, and Characterization of Brequinar Conjugates as Probes to Study DHODH Inhibition. Madak JT, Cuthbertson CR, Chen W, Showalter HD, Neamati N. Chemistry 23 13875-13878 (2017)
  51. Functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders. Hanzl A, Casement R, Imrichova H, Hughes SJ, Barone E, Testa A, Bauer S, Wright J, Brand M, Ciulli A, Winter GE. Nat Chem Biol 19 323-333 (2023)
  52. Selective Degradation of Polo-like Kinase 1 by a Hydrophobically Tagged Inhibitor of the Polo-Box Domain. Rubner S, Scharow A, Schubert S, Berg T. Angew Chem Int Ed Engl 57 17043-17047 (2018)
  53. Spy vs. spy: selecting the best reporter for 19F NMR competition experiments. de Castro GV, Ciulli A. Chem Commun (Camb) 55 1482-1485 (2019)
  54. Development of BromoTag: A "Bump-and-Hole"-PROTAC System to Induce Potent, Rapid, and Selective Degradation of Tagged Target Proteins. Bond AG, Craigon C, Chan KH, Testa A, Karapetsas A, Fasimoye R, Macartney T, Blow JJ, Alessi DR, Ciulli A. J Med Chem 64 15477-15502 (2021)
  55. Development of a PDEδ-Targeting PROTACs that Impair Lipid Metabolism. Winzker M, Friese A, Koch U, Janning P, Ziegler S, Waldmann H. Angew Chem Int Ed Engl 59 5595-5601 (2020)
  56. Discovery of Potent, Selective, and In Vivo Efficacious AKT Kinase Protein Degraders via Structure-Activity Relationship Studies. Yu X, Xu J, Shen Y, Cahuzac KM, Park KS, Dale B, Liu J, Parsons RE, Jin J. J Med Chem 65 3644-3666 (2022)
  57. Targeting Triple-Negative Breast Cancer by a Novel Proteolysis Targeting Chimera Degrader of Enhancer of Zeste Homolog 2. Dale B, Anderson C, Park KS, Kaniskan HÜ, Ma A, Shen Y, Zhang C, Xie L, Chen X, Yu X, Jin J. ACS Pharmacol Transl Sci 5 491-507 (2022)
  58. The CUL5 ubiquitin ligase complex mediates resistance to CDK9 and MCL1 inhibitors in lung cancer cells. Kabir S, Cidado J, Andersen C, Dick C, Lin PC, Mitros T, Ma H, Baik SH, Belmonte MA, Drew L, Corn JE. Elife 8 e44288 (2019)
  59. LDL suppresses angiogenesis through disruption of the HIF pathway via NF-κB inhibition which is reversed by the proteasome inhibitor BSc2118. Yao G, Zhang Q, Doeppner TR, Niu F, Li Q, Yang Y, Kuckelkorn U, Hagemann N, Li W, Hermann DM, Dai Y, Zhou W, Jin F. Oncotarget 6 30251-30262 (2015)
  60. RNA-seq analysis of PHD and VHL inhibitors reveals differences and similarities to the hypoxia response. Frost J, Ciulli A, Rocha S. Wellcome Open Res 4 17 (2019)
  61. Serendipitous SAD Solution for DMSO-Soaked SOCS2-ElonginC-ElonginB Crystals Using Covalently Incorporated Dimethylarsenic: Insights into Substrate Receptor Conformational Flexibility in Cullin RING Ligases. Gadd MS, Bulatov E, Ciulli A. PLoS One 10 e0131218 (2015)
  62. Identifying transcriptional programs underlying cancer drug response with TraCe-seq. Chang MT, Shanahan F, Nguyen TTT, Staben ST, Gazzard L, Yamazoe S, Wertz IE, Piskol R, Yang YA, Modrusan Z, Haley B, Evangelista M, Malek S, Foster SA, Ye X. Nat Biotechnol 40 86-93 (2022)
  63. Von Hippel-Lindau (VHL) small-molecule inhibitor binding increases stability and intracellular levels of VHL protein. Frost J, Rocha S, Ciulli A. J Biol Chem 297 100910 (2021)
  64. Affinity-Based Fluorescence Polarization Assay for High-Throughput Screening of Prolyl Hydroxylase 2 Inhibitors. Lei Y, Hu T, Wu X, Wu Y, Bao Q, Zhang L, Xia H, Sun H, You Q, Zhang X. ACS Med Chem Lett 6 1236-1240 (2015)
  65. Thioamide substitution to probe the hydroxyproline recognition of VHL ligands. Soares P, Lucas X, Ciulli A. Bioorg Med Chem 26 2992-2995 (2018)
  66. VHL-recruiting PROTAC attenuates renal fibrosis and preserves renal function via simultaneous degradation of Smad3 and stabilization of HIF-2α. Yang J, Ruan Y, Wang D, Fan J, Luo N, Chen H, Li X, Chen W, Wang X. Cell Biosci 12 203 (2022)
  67. Developing HDAC4-Selective Protein Degraders To Investigate the Role of HDAC4 in Huntington's Disease Pathology. Macabuag N, Esmieu W, Breccia P, Jarvis R, Blackaby W, Lazari O, Urbonas L, Eznarriaga M, Williams R, Strijbosch A, Van de Bospoort R, Matthews K, Clissold C, Ladduwahetty T, Vater H, Heaphy P, Stafford DG, Wang HJ, Mangette JE, McAllister G, Beaumont V, Vogt TF, Wilkinson HA, Doherty EM, Dominguez C. J Med Chem 65 12445-12459 (2022)
  68. Development of BODIPY FL VH032 as a High-Affinity and Selective von Hippel-Lindau E3 Ligase Fluorescent Probe and Its Application in a Time-Resolved Fluorescence Resonance Energy-Transfer Assay. Lin W, Li Y, Yang L, Chen T. ACS Omega 6 680-695 (2021)
  69. Discovery of a First-in-Class Degrader for Nuclear Receptor Binding SET Domain Protein 2 (NSD2) and Ikaros/Aiolos. Meng F, Xu C, Park KS, Kaniskan HÜ, Wang GG, Jin J. J Med Chem 65 10611-10625 (2022)
  70. Focused grid-based resampling for protein docking and mapping. Mamonov AB, Moghadasi M, Mirzaei H, Zarbafian S, Grove LE, Bohnuud T, Vakili P, Ch Paschalidis I, Vajda S, Kozakov D. J Comput Chem 37 961-970 (2016)
  71. General Stepwise Approach to Optimize a TR-FRET Assay for Characterizing the BRD/PROTAC/CRBN Ternary Complex. Lin W, Chen T. ACS Pharmacol Transl Sci 4 941-952 (2021)
  72. Structure-Guided Design of Peptides as Tools to Probe the Protein-Protein Interaction between Cullin-2 and Elongin BC Substrate Adaptor in Cullin RING E3 Ubiquitin Ligases. Cardote TAF, Ciulli A. ChemMedChem 12 1491-1496 (2017)
  73. Hypoxia deactivates epigenetic feedbacks via enzyme-derived clicking proteolysis-targeting chimeras. Do TC, Lau JW, Sun C, Liu S, Kha KT, Lim ST, Oon YY, Kwan YP, Ma JJ, Mu Y, Liu X, Carney TJ, Wang X, Xing B. Sci Adv 8 eabq2216 (2022)
  74. Targeted MDM2 Degradation Reveals a New Vulnerability for p53-Inactivated Triple-Negative Breast Cancer. Adams CM, Mitra R, Xiao Y, Michener P, Palazzo J, Chao A, Gour J, Cassel J, Salvino JM, Eischen CM. Cancer Discov 13 1210-1229 (2023)
  75. Dissecting Transcription Factor-Target Interaction in Bovine Coronavirus Infection. Morenikeji OB, Strutton E, Wallace M, Bernard K, Yip E, Thomas BN. Microorganisms 8 E1323 (2020)
  76. Native mass spectrometry and gas-phase fragmentation provide rapid and in-depth topological characterization of a PROTAC ternary complex. Song JH, Wagner ND, Yan J, Li J, Huang RY, Balog AJ, Newitt JA, Chen G, Gross ML. Cell Chem Biol 28 1528-1538.e4 (2021)
  77. Detection of translational noncrystallographic symmetry in Patterson functions. Caballero I, Sammito MD, Afonine PV, Usón I, Read RJ, McCoy AJ. Acta Crystallogr D Struct Biol 77 131-141 (2021)
  78. Exploring Degradation of Mutant and Wild-Type Epidermal Growth Factor Receptors Induced by Proteolysis-Targeting Chimeras. Yu X, Cheng M, Lu K, Shen Y, Zhong Y, Liu J, Xiong Y, Jin J. J Med Chem 65 8416-8443 (2022)
  79. Heterobifunctional Ligase Recruiters Enable pan-Degradation of Inhibitor of Apoptosis Proteins. Ng YLD, Bricelj A, Jansen JA, Murgai A, Peter K, Donovan KA, Gütschow M, Krönke J, Steinebach C, Sosič I. J Med Chem 66 4703-4733 (2023)
  80. Affinity and cooperativity modulate ternary complex formation to drive targeted protein degradation. Wurz RP, Rui H, Dellamaggiore K, Ghimire-Rijal S, Choi K, Smither K, Amegadzie A, Chen N, Li X, Banerjee A, Chen Q, Mohl D, Vaish A. Nat Commun 14 4177 (2023)
  81. An MDM2 degrader for treatment of acute leukemias. Marcellino BK, Yang X, Ümit Kaniskan H, Brady C, Chen H, Chen K, Qiu X, Clementelli C, Herschbein L, Li Z, Elghaity-Beckley S, Arandela J, Kelly B, Hoffman R, Liu J, Xiong Y, Jin J, Shih AH. Leukemia 37 370-378 (2023)
  82. Discovery of the First Lactate Dehydrogenase Proteolysis Targeting Chimera Degrader for the Treatment of Pancreatic Cancer. Sun N, Kabir M, Lee Y, Xie L, Hu X, Velez J, Chen X, Kaniskan HÜ, Jin J. J Med Chem 66 596-610 (2023)
  83. DNA-encoded library-enabled discovery of proximity-inducing small molecules. Mason JW, Chow YT, Hudson L, Tutter A, Michaud G, Westphal MV, Shu W, Ma X, Tan ZY, Coley CW, Clemons PA, Bonazzi S, Berst F, Briner K, Liu S, Zécri FJ, Schreiber SL. Nat Chem Biol (2023)
  84. Expanding the Structural Diversity at the Phenylene Core of Ligands for the von Hippel-Lindau E3 Ubiquitin Ligase: Development of Highly Potent Hypoxia-Inducible Factor-1α Stabilizers. Vu LP, Diehl CJ, Casement R, Bond AG, Steinebach C, Strašek N, Bricelj A, Perdih A, Schnakenburg G, Sosič I, Ciulli A, Gütschow M. J Med Chem 66 12776-12811 (2023)
  85. PROTAC targeting cyclophilin A controls virus-induced cytokine storm. Li H, Yang W, Li H, Bai X, Zhang H, Fan W, Liu W, Sun L. iScience 26 107535 (2023)
  86. QSAR modeling and in silico design of small-molecule inhibitors targeting the interaction between E3 ligase VHL and HIF-1α. Pan J, Zhang Y, Ran T, Xu A, Qiao X, Yin L, Zhou W, Zhu L, Zhao J, Lu T, Chen Y, Jiang Y. Mol Divers 21 719-739 (2017)
  87. Uncovering the Kinetic Characteristics and Degradation Preference of PROTAC Systems with Advanced Theoretical Analyses. Tang R, Wang Z, Xiang S, Wang L, Yu Y, Wang Q, Deng Q, Hou T, Sun H. JACS Au 3 1775-1789 (2023)