Bifunctional chemical probes inducing protein–protein interactions

ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering

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Phthalimide conjugation as a strategy for in vivo target protein degradation

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The Myeloma Drug Lenalidomide Promotes the Cereblon-Dependent Destruction of Ikaros Proteins

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Ubiquitin ligases: structure, function, and regulation

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Induced protein degradation: an emerging drug discovery paradigm

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Catalytic in vivo protein knockdown by small-molecule PROTACs

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Structural basis of PROTAC cooperative recognition for selective protein degradation

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Structure of the DDB1–CRBN E3 ubiquitin ligase in complex with thalidomide

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Hijacking the E3 Ubiquitin Ligase Cereblon to Efficiently Target BRD4

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Small molecules, big targets: drug discovery faces the protein–protein interaction challenge

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The dTAG system for immediate and target-specific protein degradation

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mTOR kinase structure, mechanism and regulation

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Small-Molecule Inhibitors of Protein-Protein Interactions: Progressing toward the Reality

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Selective Small Molecule Induced Degradation of the BET Bromodomain Protein BRD4

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Structure of the FKBP12-Rapamycin Complex Interacting with Binding Domain of Human FRAP

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Lessons in PROTAC Design from Selective Degradation with a Promiscuous Warhead

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Lenalidomide induces ubiquitination and degradation of CK1α in del(5q) MDS

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Controlling Signal Transduction with Synthetic Ligands

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X-ray structure of calcineurin inhibited by the immunophilin-immunosuppressant FKBP12-FK506 complex

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PROteolysis TArgeting Chimeras (PROTACs) — Past, present and future

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Anticancer sulfonamides target splicing by inducing RBM39 degradation via recruitment to DCAF15

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A novel cereblon modulator recruits GSPT1 to the CRL4CRBN ubiquitin ligase

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Structural basis of lenalidomide-induced CK1α degradation by the CRL4CRBN ubiquitin ligase

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Plasticity in binding confers selectivity in ligand-induced protein degradation

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Characterization of the FKBP·Rapamycin·FRB Ternary Complex

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Targeting the von Hippel-Lindau E3 ubiquitin ligase using small molecules to disrupt the VHL/HIF-1α interaction

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BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design

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Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN

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Structure of the human Cereblon-DDB1-lenalidomide complex reveals basis for responsiveness to thalidomide analogs

Chamberlain, P. P., Lopez-Girona, A., Miller, K., Carmel, G., Pagarigan, B., Chie-Leon, B., Rychak, E., Corral, L. G., Ren, Y. J., Wang, M., et al. (2014) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2874 · Cited by 531 · see citing works

Differential PROTAC substrate specificity dictated by orientation of recruited E3 ligase

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Thalidomide promotes degradation of SALL4, a transcription factor implicated in Duane Radial Ray syndrome

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HaloPROTACS: Use of Small Molecule PROTACs to Induce Degradation of HaloTag Fusion Proteins

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Electrophilic PROTACs that degrade nuclear proteins by engaging DCAF16

Zhang, X., Crowley, V. M., Wucherpfennig, T. G., Dix, M. M., & Cravatt, B. F. (2019) · Nature Chemical Biology · doi:10.1038/s41589-019-0279-5 · Cited by 487 · see citing works

Chemically induced proximity in biology and medicine

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A Comprehensive Mathematical Model for Three-Body Binding Equilibria

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BET Bromodomain Proteins Function as Master Transcription Elongation Factors Independent of CDK9 Recruitment

Winter, G. E., Mayer, A., Buckley, D. L., Erb, M. A., Roderick, J. E., Vittori, S., Reyes, J. M., di Iulio, J., Souza, A., Ott, C. J., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.06.004 · Cited by 465 · see citing works

Harnessing the anti-cancer natural product nimbolide for targeted protein degradation

Spradlin, J. N., Hu, X., Ward, C. C., Brittain, S. M., Jones, M. D., Ou, L., To, M., Proudfoot, A., Ornelas, E., Woldegiorgis, M., et al. (2019) · Nature Chemical Biology · doi:10.1038/s41589-019-0304-8 · Cited by 432 · see citing works

Drugging the undruggables: exploring the ubiquitin system for drug development

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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

Galdeano, C., Gadd, M. S., Soares, P., Scaffidi, S., Molle, I. V., Birced, I., Hewitt, S. H., Dias, D. M. G., & Ciulli, A. (2014) · Journal of Medicinal Chemistry · doi:10.1021/jm5011258 · Cited by 424 · see citing works

Proteolysis targeting chimeras (PROTACs) in ‘beyond rule-of-five’ chemical space: Recent progress and future challenges

Edmondson, S. D., Yang, B., & Fallan, C. (2019) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2019.04.030 · Cited by 422 · see citing works

Delineating the role of cooperativity in the design of potent PROTACs for BTK

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Selective degradation of splicing factor CAPERα by anticancer sulfonamides

Uehara, T., Minoshima, Y., Sagane, K., Sugi, N. H., Mitsuhashi, K. O., Yamamoto, N., Kamiyama, H., Takahashi, K., Kotake, Y., Uesugi, M., et al. (2017) · Nature Chemical Biology · doi:10.1038/nchembio.2363 · Cited by 396 · see citing works

SPR-measured dissociation kinetics of PROTAC ternary complexes influence target degradation rate

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Small-molecule PROTACs: An emerging and promising approach for the development of targeted therapy drugs

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SALL4 mediates teratogenicity as a thalidomide-dependent cereblon substrate

Matyskiela, M. E., Couto, S., Zheng, X., Lu, G., Hui, J., Stamp, K., Drew, C., Ren, Y., Wang, M., Carpenter, A., et al. (2018) · Nature Chemical Biology · doi:10.1038/s41589-018-0129-x · Cited by 338 · see citing works

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, S. J., Maniaci, C., Testa, A., Gmaschitz, T., Wieshofer, C., Koegl, M., Riching, K. M., Daniels, D. L., Spallarossa, A., et al. (2019) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.8b01413 · Cited by 336 · see citing works

Covalent Ligand Screening Uncovers a RNF4 E3 Ligase Recruiter for Targeted Protein Degradation Applications

Ward, C. C., Kleinman, J. I., Brittain, S. M., Lee, P. S., Chung, C. Y. S., Kim, K., Petri, Y., Thomas, J. R., Tallarico, J. A., McKenna, J. M., et al. (2019) · ACS Chemical Biology · doi:10.1021/acschembio.8b01083 · Cited by 336 · see citing works

Quantitative Live-Cell Kinetic Degradation and Mechanistic Profiling of PROTAC Mode of Action

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Inhibitors of protein–protein interactions (PPIs): an analysis of scaffold choices and buried surface area

Xu, R., & Gestwicki, J. E. (2018) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2018.06.004 · Cited by 262 · see citing works

Interfacial inhibitors: targeting macromolecular complexes

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Homolog-Selective Degradation as a Strategy to Probe the Function of CDK6 in AML

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

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

Hughes, S. J., & Ciulli, A. (2017) · Essays in Biochemistry · doi:10.1042/ebc20170041 · Cited by 240 · see citing works

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, K.-H., Zengerle, M., Testa, A., & Ciulli, A. (2017) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.6b01912 · Cited by 222 · see citing works

Prospective discovery of small molecule enhancers of an E3 ligase-substrate interaction

Simonetta, K. R., Taygerly, J., Boyle, K., Basham, S. E., Padovani, C., Lou, Y., Cummins, T. J., Yung, S. L., von Soly, S. K., Kayser, F., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09358-9 · Cited by 217 · see citing works

Small Molecule Targeted Recruitment of a Nuclease to RNA

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<i>In Silico</i> Modeling of PROTAC-Mediated Ternary Complexes: Validation and Application

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BET protein proteolysis targeting chimera (PROTAC) exerts potent lethal activity against mantle cell lymphoma cells

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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 (2 S ,4 R )-1-(( S )-2-(1-Cyanocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy- N -(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (VH298)

Soares, P., Gadd, M. S., Frost, J., Galdeano, C., Ellis, L. C. J., Epemolu, O., Rocha, S., Read, K. D., & Ciulli, A. (2017) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.7b00675 · Cited by 180 · see citing works

Prime time for PROTACs

Deshaies, R. J. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1887 · Cited by 162 · see citing works

Stabilization of protein-protein interactions in drug discovery

Andrei, S. A., Sijbesma, E., Hann, M. M., Davis, J., O’Mahony, G., Perry, M. W. D., Karawajczyk, A., Eickhoff, J., Brunsveld, L., Doveston, R. G., et al. (2017) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2017.1346608 · Cited by 162 · see citing works

Homo-PROTACs for the Chemical Knockdown of Cereblon

Steinebach, C., Lindner, S., Udeshi, N. D., Mani, D. R., Kehm, H., Köpff, S., Carr, S. A., Gütschow, M., & Krönke, J. (2018) · ACS Chemical Biology · doi:10.1021/acschembio.8b00693 · Cited by 160 · see citing works

Design and characterization of bivalent BET inhibitors

Tanaka, M., Roberts, J. M., Seo, H., Souza, A., Paulk, J., Scott, T. G., DeAngelo, S. L., Dhe‐Paganon, S., & Bradner, J. E. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2209 · Cited by 157 · see citing works

Cereblon versus VHL: Hijacking E3 ligases against each other using PROTACs

Girardini, M., Maniaci, C., Hughes, S. J., Testa, A., & Ciulli, A. (2019) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2019.02.048 · Cited by 157 · see citing works

Rapid and Reversible Knockdown of Endogenously Tagged Endosomal Proteins via an Optimized HaloPROTAC Degrader

Tovell, H., Testa, A., Maniaci, C., Zhou, H., Prescott, A. R., Macartney, T., Ciulli, A., & Alessi, D. R. (2019) · ACS Chemical Biology · doi:10.1021/acschembio.8b01016 · Cited by 146 · see citing works

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, G. V., Chan, K.-H., Wright, J. E., Runcie, A. C., Gadd, M. S., Harrison, W. T. A., Ko, E. J., Fletcher, D., et al. (2018) · Journal of the American Chemical Society · doi:10.1021/jacs.8b05807 · Cited by 144 · see citing works

Potent and selective bivalent inhibitors of BET bromodomains

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Bivalent Ligands for Protein Degradation in Drug Discovery

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A small-molecule inhibitor of the aberrant transcription factor CBFβ-SMMHC delays leukemia in mice

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Site-Directed Fragment-Based Screening for the Discovery of Protein–Protein Interaction Stabilizers

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Discovery of Chemical Inhibitors of Human Bromodomains

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Cereblon modulators: Low molecular weight inducers of protein degradation

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PROTAC-mediated crosstalk between E3 ligases

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

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Optimization of a Series of Bivalent Triazolopyridazine Based Bromodomain and Extraterminal Inhibitors: The Discovery of (3R)-4-[2-[4-[1-(3-Methoxy-[1,2,4]triazolo[4,3-b]pyridazin-6-yl)-4-piperidyl]phenoxy]ethyl]-1,3-dimethyl-piperazin-2-one (AZD5153)

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On-Demand Targeting: Investigating Biology with Proximity-Directed Chemistry

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Cooperative binding mitigates the high-dose hook effect

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Targeted protein degradation in vivo with Proteolysis Targeting Chimeras: Current status and future considerations

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New molecular and therapeutic insights into canine diffuse large B-cell lymphoma elucidates the role of the dog as a model for human disease

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Meisoindigo Acts as a Molecular Glue to Target PKMYT1 for Degradation in Chronic Myeloid Leukemia Therapy

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Trivalent PROTACs Enhance Protein Degradation Through Cooperativity and AvidityPreprint

Imaide, S., Riching, K. M., Vetma, V., Whitworth, C., Hughes, S. J., Trainor, N. B., Mahan, S. D., Murphy, N., Chan, K.-H., Testa, A., et al. (2020) · ChemRxiv · doi:10.26434/chemrxiv.13218695.v1 · Cited by 3 · see citing works

How Feasible Is Docking of PROTACs to POI-E3L Complexes? Testing Physics-Based and ML-Based Docking Tools

Jiménez-Boi, R., Miñán, R., Pallara, C., Lozoya, E., Guallar, V., Molina, A., & Soliva, R. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c01581 · Cited by 2 · see citing works

Evolving CRBN ligands enhance the drug-like properties of protein degraders

Ji, X.-Q., Wang, L., & Dai, X. (2026) · Journal of Enzyme Inhibition and Medicinal Chemistry · doi:10.1080/14756366.2026.2700038 · Cited by 2 · see citing works

Discovery of an Antiviral PROTAC Targeting the SARS-CoV-2 Main Protease Using an Allosteric WarheadPreprint

Veeck, C., Laube, L., Werner, A., Diederich, W. E., & Becker, S. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.03.652023 · Cited by 2 · see citing works

Searching for EGF Fragments Recreating the Outer Sphere of the Growth Factor Involved in Receptor Interactions

Czerczak-Kwiatkowska, K., Kaminska, M., Frączyk, J., Majsterek, I., & Kolesińska, B. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25031470 · Cited by 1 · see citing works

From Tethered to Freestanding Stabilizers of 14‐3‐3 Protein‐Protein Interactions through Fragment Linking

Visser, E. J., Jaishankar, P., Sijbesma, E., Pennings, M. A. M., Vandenboorn, E., Guillory, X., Neitz, R. J., Morrow, J. K., Dutta, S., Renslo, A. R., et al. (2023) · Angewandte Chemie · doi:10.1002/ange.202308004 · Cited by 1 · see citing works

Protac synthesized on the basis of azaflavonoid derivatives possesses favorable anti-hepatocellular carcinoma activity

Sun, G., Li, Y., Wang, Z., Xu, X., Xiang, Y., Teng, F., Zhao, L., Liu, J., Liu, Z., Xiang, C., et al. (2025) · Bioorganic Chemistry · doi:10.1016/j.bioorg.2025.108687 · Cited by 1 · see citing works

Structural and Biophysical Principles of Degrader Ternary Complexes

Zollman, D., & Ciulli, A. (2020) · Royal Society of Chemistry eBooks · doi:10.1039/9781839160691-00014 · Cited by 3 · see citing works

Trivalent PROTACs Enhance Protein Degradation Through Cooperativity and AvidityPreprint

Imaide, S., Riching, K. M., Vetma, V., Whitworth, C., Hughes, S. J., Trainor, N. B., Mahan, S. D., Murphy, N., Chan, K.-H., Testa, A., et al. (2020) · ChemRxiv · doi:10.26434/chemrxiv.13218695 · Cited by 1 · see citing works

Inhibitor fluorination pattern tunes chemically induced protein dimerizationPreprint

Schwegler, E., Harder, J.-M., Preuss, M. D., Guhl, C., Zhang, S., Wagner, A., Bader, N., Stallforth, P., Lakemeyer, M., Schindelin, H., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.23.666362 · Cited by 1 · see citing works

VHL ligand binding increases intracellular level of VHLPreprint

Frost, J., Rocha, S., & Ciulli, A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.12.439487

Early identification of cooperative fragments for protein-protein interaction stabilizationPreprint

de Vink, P. J., Cossar, P. J., Somsen, B. A., Ottmann, C., & Brunsveld, L. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.23.481635

Protein Degradation Technology

高, 杰. (2022) · Hans Journal of Medicinal Chemistry · doi:10.12677/hjmce.2022.101003

Structure of TBK1 and Small Molecule Inhibitors

张, 敏. (2022) · Journal of Organic Chemistry Research · doi:10.12677/jocr.2022.101002

A geometric and topological analysis of the binding behavior of Intrinsically Disordered Proteins

Upadhyay, A., & Ekenna, C. (2022) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm55620.2022.9995019

Application of Surface Plasmon Resonance in the Characterization of Protein–Protein Interactions

Xie, Y., & Xu, J. (2025) · doi:10.1002/9783527845828.ch6

Induced ubiquitination of the partially disordered Estrogen Receptor alpha protein via a 14-3-3-directed molecular glue-based PROTAC designPreprint

Verhoef, C. J. A., Crowe, C., Nakasone, M. A., Basté, A. D. L. C., Harzing, T., Span, N. A. S., Sathe, G. J., Iso, K., Ottmann, C., Brunsveld, L., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.17.688825

Targeting Protein Tyrosine Phosphatases via PROteolysis-TArgeting Chimeras (PROTACs): Current Developments and Prospects

Maccari, R. (2025) · Molecules · doi:10.3390/molecules30224449

Applications of Precise Chemistry in Drug Discovery★

Liu, R., Zuo, Y., Zhang, Y., & Zhang, J. (2025) · Chinese Journal of Organic Chemistry · doi:10.6023/cjoc20205031

BindingDB Entry 50015456: Development of BromoTag: A "Bump-and-Hole"-PROTAC System to Induce Potent, Rapid, and Selective Degradation of Tagged Target Proteins.

BindingDB (2023) · Discovery Research Portal (University of Dundee) · doi:10.7270/q23n27b7

Chemical Control Over Protein-Protein Interactions: Beyond Inhibitors

Gestwicki, J. E., & Marinec, P. S. (2007) · Combinatorial Chemistry & High Throughput Screening · doi:10.2174/138620707782507296 · Cited by 54 · see citing works

Design and Applications of Bifunctional Small Molecules: Why Two Heads Are Better Than One

Corson, T. W., Aberle, N. S., & Crews, C. M. (2008) · ACS Chemical Biology · doi:10.1021/cb8001792 · Cited by 166 · see citing works

Targeted protein degradation via intramolecular bivalent glues

Hsia, O., Hinterndorfer, M., Cowan, A. D., Iso, K., Ishida, T., Sundaramoorthy, R., Nakasone, M. A., Imrichova, H., Schätz, C., Rukavina, A., et al. (2024) · Nature · doi:10.1038/s41586-024-07089-6 · Cited by 222 · see citing works

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

Hughes, S. J., & Ciulli, A. (2017) · Essays in Biochemistry · doi:10.1042/ebc20170041 · Cited by 240 · see citing works

Harnessing Covalent Chemical Probes: From Inhibition to Induced Proximity Modalities

Henning, N. J. (2022) · eScholarship (California Digital Library)