endo-BCN-PEG2-PFP ester
Endo-BCN-PEG2-PFP ester is a bifunctional PROTAC linker reagent designed for chemoselective conjugation and subsequent assembly of targeted protein degraders. Structurally, it combines an endo-bicyclononyne (BCN) strained-alkyne handle with a short, two–ethylene glycol unit polyethylene glycol (PEG2) spacer and a pentafluorophenyl (PFP) ester activated for acyl transfer. In PROTAC workflows, the BCN group enables rapid strain-promoted azide–alkyne cycloaddition with azide-bearing ligands or biomolecular partners, while the PFP ester provides a reactive electrophile to form stable amide or related linkages with primary amines. This dual functionality supports modular synthesis, allowing researchers to tether ligands to E3-recruiting or target-binding moieties with controlled spacing and improved solubility. The reagent is valuable for constructing well-defined conjugates that can be evaluated in targeted degradation experiments, including optimization of linker length and conjugation chemistry for efficient ternary complex formation.
Structure of 1421932-53-7
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* For research and manufacturing use only. Not for human or clinical use.
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Endo-BCN-PEG2-PFP ester is a PEG-based, BCN (bicyclononyne) functionalized linker designed for efficient PROTAC assembly and subsequent bioorthogonal conjugation. Its PEG spacer supports favorable solubility and linker flexibility, while the PFP ester enables robust acyl transfer to nucleophilic groups on targeting ligands. This combination supports modular synthesis workflows; the detailed structural and reactivity considerations are provided below.
Structure: The linker contains a BCN moiety for strain-promoted cycloaddition, connected through a short polyethylene glycol spacer to a pentafluorophenyl ester. It features ether linkages in the PEG segment and an activated carboxylate derived from the PFP leaving group, providing amphiphilic, water-compatible behavior.
Reactivity: The PFP ester is suitable for acylation reactions with nucleophiles such as amines or other appropriate functional groups under mild, base-assisted conditions commonly used for ester-to-amide or ester-to-derivative formation. The BCN group enables catalyst-free, strain-promoted cycloaddition with complementary partners, typically proceeding in aqueous or mixed solvent systems. For PROTAC construction, this supports sequential coupling of the targeting ligand followed by bioorthogonal conjugation, with solvent choice guided by nucleophile solubility and stability of the ester.
* Our calculator is based on the following equation:
Concentration (start) x Volume (start) = Concentration (final) x Volume (final)
It is commonly abbreviated as: C1V1 = C2V2
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