Current strategies for the design of PROTAC linkers: a critical review
Open accessAbstract
PROteolysis TArgeting Chimeras (PROTACs) are heterobifunctional molecules consisting of two ligands; an “anchor” to bind to an E3 ubiquitin ligase and a “warhead” to bind to a protein of interest, connected by a chemical linker. Targeted protein degradation by PROTACs has emerged as a new modality for the knock down of a range of proteins, with the first agents now reaching clinical evaluation. It has become increasingly clear that the length and composition of the linker play critical roles on the physicochemical properties and bioactivity of PROTACs. While linker design has historically received limited attention, the PROTAC field is evolving rapidly and currently undergoing an important shift from synthetically tractable alkyl and polyethylene glycol to more sophisticated functional linkers. This promises to unlock a wealth of novel PROTAC agents with enhanced bioactivity for therapeutic intervention. Here, the authors provide a timely overview of the diverse linker classes in the published literature, along with their underlying design principles and overall influence on the properties and bioactivity of the associated PROTACs. Finally, the authors provide a critical analysis of current strategies for PROTAC assembly. The authors highlight important limitations associated with the traditional “trial and error” approach around linker design and selection, and suggest potential future avenues to further inform rational linker design and accelerate the identification of optimised PROTACs. In particular, the authors believe that advances in computational and structural methods will play an essential role to gain a better understanding of the structure and dynamics of PROTAC ternary complexes, and will be essential to address the current gaps in knowledge associated with PROTAC design.
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The composition and length of linkers can affect the efficiency of degraders.
“The composition and length of linkers can affect the efficiency of degraders40,41.”
From An HDAC4-specific PROTAC degrader achieves radiation sensitization by enhancing ferroptosis in lung cancer (2026) · cites this paper as [41]
Short linkers can be used to modulate PROTAC molecular weights and properties.
“Short linkers can be used to modulate PROTAC molecular weights67 and properties65”
From PROTAC targeted protein degraders: the past is prologue (2022) · cites this paper as [67]
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Triazoles in Medicinal Chemistry: Physicochemical Properties, Bioisosterism, and Application
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Recent developments in epigenetic cancer therapeutics: clinical advancement and emerging trends
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E3 ligase ligand chemistries: from building blocks to protein degraders
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The role of reversible and irreversible covalent chemistry in targeted protein degradation
Kiely‐Collins, H., Winter, G. E., & Bernardes, G. J. L. (2021) · Cell chemical biology · doi:10.1016/j.chembiol.2021.03.005 · Cited by 156 · see citing works
Affinity and cooperativity modulate ternary complex formation to drive targeted protein degradation
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Linker-Dependent Folding Rationalizes PROTAC Cell Permeability
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Microneedle Patch Delivery of PROTACs for Anti-Cancer Therapy
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PROTAC’ing oncoproteins: targeted protein degradation for cancer therapy
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Deep generative design with 3D pharmacophoric constraints
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Annual review of PROTAC degraders as anticancer agents in 2022
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Delivering on the promise of protein degraders
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What is in Our Kit? An Analysis of Building Blocks Used in Medicinal Chemistry Parallel Libraries
Wang, Y., Haight, I., Gupta, R., & Vasudevan, A. (2021) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.1c01139 · Cited by 103 · see citing works
Designing Soluble PROTACs: Strategies and Preliminary Guidelines
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Exploring the target scope of KEAP1 E3 ligase-based PROTACs
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Molecular Strategies to Target Protein Aggregation in Huntington’s Disease
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Degrader–Antibody Conjugates: Emerging New Modality
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Targeting the Ubiquitin-Proteasome System for Cancer Therapeutics by Small-Molecule Inhibitors
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DNA-Encoded Library Screening To Inform Design of a Ribonuclease Targeting Chimera (RiboTAC)
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Advancing targeted protein degradation for metabolic diseases therapy
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Optical control of targeted protein degradation
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Lenalidomide derivatives and proteolysis-targeting chimeras for controlling neosubstrate degradation
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Computer-Aided Drug Discovery for Undruggable Targets
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Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs
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Small-Molecule Ferritin Degrader as a Pyroptosis Inducer
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A beginner’s guide to current synthetic linker strategies towards VHL-recruiting PROTACs
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Insight into Recent Advances in Degrading Androgen Receptor for Castration-Resistant Prostate Cancer
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DNA framework-engineered chimeras platform enables selectively targeted protein degradation
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Drug design targeting active posttranslational modification protein isoforms
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Proteolysis-Targeting Chimera (PROTAC) Delivery into the Brain across the Blood-Brain Barrier
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PROTACs and Building Blocks: The 2D Chemical Space in Very Early Drug Discovery
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Impact of Linker Composition on VHL PROTAC Cell Permeability
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PROTACs bearing piperazine-containing linkers: what effect on their protonation state?
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Oral Absorption of Middle-to-Large Molecules and Its Improvement, with a Focus on New Modality Drugs
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Application and challenges of nitrogen heterocycles in PROTAC linker
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Lessons learned in linking PROTACs from discovery to the clinic
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Radioactive ADME Demonstrates ARV-110’s High Druggability Despite Low Oral Bioavailability
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Tau degradation in Alzheimer's disease: Mechanisms and therapeutic opportunities
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Discovery of novel BTK PROTACs with improved metabolic stability via linker rigidification strategy
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Options to Improve the Action of PROTACs in Cancer: Development of Controlled Delivery Nanoparticles
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Towards design of drugs and delivery systems with the Martini coarse-grained model
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DiffPROTACs is a deep learning-based generator for proteolysis targeting chimeras
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ByeTAC: Bypassing E-Ligase-Targeting Chimeras for Direct Proteasome Degradation
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Designing HDAC-PROTACs: Lessons Learned So Far
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Fragment Linker Prediction Using the Deep Encoder-Decoder Network for PROTACs Drug Design
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PROTAC: targeted drug strategy. Principles and limitations
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Targeting PRMT5 through PROTAC for the treatment of triple-negative breast cancer
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Targeted degradation of extracellular proteins: state of the art and diversity of degrader designs
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PROTACs: Current Trends in Protein Degradation by Proteolysis-Targeting Chimeras
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Selective Wee1 degradation by PROTAC degraders recruiting VHL and CRBN E3 ubiquitin ligases
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What influences the activity of Degrader−Antibody conjugates (DACs)
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IMHB-Mediated Chameleonicity in Drug Design: A Focus on Structurally Related PROTACs
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Target protein degradation by protacs: A budding cancer treatment strategy
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The efflux pump ABCC1/MRP1 constitutively restricts PROTAC sensitivity in cancer cells
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PROTACs in the Management of Prostate Cancer
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Current strategies for improving limitations of proteolysis targeting chimeras
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A comprehensive review of emerging approaches in machine learning for de novo PROTAC design
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Protacs in cancer therapy: mechanisms, design, clinical trials, and future directions
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Discovery of Highly Potent and Efficient CBP/p300 Degraders with Strong In Vivo Antitumor Activity
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Rational Design and Optimization of a Potent IDO1 Proteolysis Targeting Chimera (PROTAC)
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Discovery and Characterization of RP03707: A Highly Potent and Selective KRAS G12D PROTAC
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PROTAC Technology as a New Tool for Modern Pharmacotherapy
Kubryń, N., Fijałkowski, Ł., Nowaczyk, J., Jamil, A., & Nowaczyk, A. (2025) · Molecules · doi:10.3390/molecules30102123 · Cited by 28 · see citing works
Cross, J. M., Coulson, M. E., Smalley, J. P., Pytel, W. A., Ismail, O., Trory, J. S., Cowley, S. M., & Hodgkinson, J. T. (2022) · RSC Medicinal Chemistry · doi:10.1039/d2md00199c · Cited by 27 · see citing works
Computer aided drug design in the development of proteolysis targeting chimeras
Tunjic, T. M., Weber, N., & Brunsteiner, M. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.02.042 · Cited by 27 · see citing works
Reversible Assembly of Proteolysis Targeting Chimeras
Gui, W., Giardina, S. F., Balzarini, M., Barany, F., & Kodadek, T. J. (2023) · ACS Chemical Biology · doi:10.1021/acschembio.3c00199 · Cited by 27 · see citing works
- Authors
- Troup, R. I., Fallan, C., & Baud, M. G. J.
- Affiliations
- University of Southampton (GB)
- AstraZeneca (United Kingdom) (GB)
- Corresponding author
- Fallan, Charlene
- Baud, Matthias G. J.
- Venue
- Exploration of Targeted Anti-tumor Therapy
- Publisher
- Open Exploration Publishing
- Published
- 2020-10-11
- Volume
- 1
- Issue
- 5
- Pages
- 273-312
- ISSN
- 2692-3114 (ISSN-L)
- PMC
- PMC9400730
- OpenAlex
- W3093395956
- Cited by
- 424
- References
- 183
- Citations by year
- 2026: 91 · 2025: 102 · 2024: 96 · 2023: 66 · 2022: 48 · 2021: 19 · 2020: 1 · 2014: 1
- FWCI
- 3.28
- Type
- journal article
- Language
- en
- Open access
- diamond
- doi.org
- Locations
- Exploration of Targeted Anti-tumor Therapy (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- ePrints Soton (University of Southampton) (acceptedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- AstraZeneca
- Engineering and Physical Sciences Research Council (EP/R513325/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Keywords
- PROTACs, linker design, targeted protein degradation, E3 ubiquitin ligase, heterobifunctional molecules, ternary complex structure, rational drug design, polyethylene glycol linker, alkyl linkers
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