Propargyl-PEG2-N-bis(PEG2)
Propargyl-PEG2-N-bis(PEG2) is a branched trifunctional polyethylene glycol (PEG) linker featuring one terminal propargyl group for copper-catalyzed azide–alkyne cycloaddition (CuAAC) and two PEG2 arms terminated with hydroxyl groups. Structurally, it behaves as a flexible, hydrophilic spacer whose short PEG chain length and branching can reduce nonspecific interactions while maintaining effective reach between the two conjugation partners in a PROTAC construct. In targeted protein degradation designs, the propargyl handle enables site-selective attachment to an azide-bearing warhead or E3 ligase ligand, while the two terminal hydroxyl groups provide additional sites for activation or derivatization and the PEG2 branching modulates conformational freedom, which can influence ternary complex formation and degradation potency. This linker is therefore valuable for systematically optimizing PROTAC geometry, improving aqueous handling, and enabling modular assembly of degradation molecules for mechanistic and structure–activity studies.
Structure of 2100306-62-3
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Propargyl-PEG2-N-bis(PEG2) is a polyethylene glycol–based PROTAC linker designed to provide aqueous solubility, conformational flexibility, and a chemically addressable handle for modular assembly. Its PEG-rich scaffold helps tune linker length and hydrophilicity while supporting efficient conjugation to ligands used for targeted protein degradation. The structure and reactivity considerations that govern PROTAC synthesis and subsequent coupling strategies are described in detail below.
Structure: This linker features a PEG oligomer core bearing a terminal propargyl functionality and an N-substituted bis(PEG) motif. Ether linkages dominate the backbone, providing hydrophilicity and flexible conformations. The propargyl group contains a carbon–carbon triple bond suitable for bioorthogonal coupling chemistry, while the N-linked PEG substituents enhance solvation.
Reactivity: The propargyl handle is well suited for copper-catalyzed azide–alkyne cycloaddition or related alkyne-driven conjugation approaches to connect PROTAC ligands bearing azide groups. Typical assembly is performed under conditions that maintain PEG stability and preserve ligand integrity, using appropriate copper sources, ligands, and aqueous or mixed solvents. Mechanistically, the alkyne participates in cycloaddition to form a stable triazole linkage, enabling modular PROTAC construction.
* 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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