Aminooxy-PEG3-methyl ester

Name: Aminooxy-PEG3-methyl ester
Brand: BOC Sciences
Rating: 5 (1 reviews)

CAS No.: 2086689-03-2

Cat No.: BP-501095 4.5

Aminooxy-PEG3-methyl ester is a short, functionalized polyethylene glycol linker bearing an aminooxy (–ONH2) reactive handle and a methyl ester at the terminus. The aminooxy group enables chemoselective oxime ligation with aldehyde-bearing partners under mild conditions, making it a versatile bridge for assembling PROTAC conjugates or other targeted degradation constructs. In PROTAC design, the linker’s PEG character provides aqueous solubility and conformational flexibility, helping to reduce steric constraints between the ligand-binding modules while maintaining productive geometry for ternary complex formation. The methyl ester can serve as a masked carboxyl functionality for subsequent derivatization or hydrolysis to generate a carboxylate for coupling strategies, depending on the synthetic route. This product is valuable for researchers who need reliable, modular attachment chemistry and improved handling properties when building and optimizing targeted protein degradation molecules.

Structure of 2086689-03-2

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Category

PROTAC Linker

Molecular Formula

C₁₀H₂₁NO₆

Molecular Weight

251.28

* For research and manufacturing use only. Not for human or clinical use.

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Please store the product under the recommended conditions in the Certificate of Analysis.

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Room temperature in continental US; may vary elsewhere.

IUPACName

methyl 3-[2-[2-(2-aminooxyethoxy)ethoxy]ethoxy]propanoate

InChI Key

KYJYDNKATOCUIR-UHFFFAOYSA-N

InChI

InChI=1S/C10H21NO6/c1-13-10(12)2-3-14-4-5-15-6-7-16-8-9-17-11/h2-9,11H2,1H3

SMILES

COC(=O)CCOCCOCCOCCON

1. Preparation of methyl ester precursors of biologically active agents

Yunfan Zou, Marcela Rojas-Pierce, Natasha Raikhel, Michael Pirrung Biotechniques. 2008 Mar;44(3):377-84.doi: 10.2144/000112704.

This method enables scientists to easily convert biologically active carboxylic acids into their methyl esters ("pro-drugs" generally having improved ability to penetrate cell membranes) using only equipment commonly found in a biology laboratory. An ion-exchange resin is used to convert the acid into its salt, which is thereby sequestered on the resin. The addition of methyl iodide converts the salt to the ester, which has no affinity for the resin and is readily eluted. Evaporation of the liquid phase provides the pure methyl ester. The preparation in good chemical yields of methyl esters of bioactive agents in excellent purity and 10-20 mg quantities can be achieved using this method. The method can be completed in 1 day.

2. Systematic evaluation of methyl ester bioisosteres in the context of developing alkenyldiarylmethanes (ADAMs) as non-nucleoside reverse transcriptase inhibitors (NNRTIs) for anti-HIV-1 chemotherapy

Ayako Hoshi, Takeshi Sakamoto, Jun Takayama, Meiyan Xuan, Mari Okazaki, Tracy L Hartman, Robert W Buckheit Jr, Christophe Pannecouque, Mark Cushman Bioorg Med Chem. 2016 Jul 1;24(13):3006-3022.doi: 10.1016/j.bmc.2016.05.010.Epub 2016 May 24.

The alkenyldiarylmethanes (ADAMs) are a class of non-nucleoside reverse transcriptase inhibitors (NNRTIs) targeting HIV-1. Four chemically and metabolically stabilized ADAMs incorporating N-methoxyimidoyl halide replacements of the methyl esters of the lead compound were previously reported. In this study, twenty-five new ADAMs were synthesized in order to investigate the biological consequences of installing nine different methyl ester bioisosteres at three different locations. Attempts to define a universal rank order of methyl ester bioisosteres and discover the 'best' one in terms of inhibitory activity versus HIV-1 reverse transcriptase (RT) led to the realization that the potencies are critically dependent on the surrounding structure at each location, and therefore the definition of universal rank order is impossible. This investigation produced several new non-nucleoside reverse transcriptase inhibitors in which all three of the three methyl esters of the lead compound were replaced by methyl ester bioisosteres, resulting in compounds that are more potent as HIV-1 RT inhibitors and antiviral agents than the lead compound itself and are expected to also be more metabolically stable than the lead compound.

Aminooxy-PEG3-methyl ester is a PEG-based PROTAC linker designed to enable efficient formation of stable oxime linkages with aldehyde-bearing or carbonyl-containing warheads. Its aminooxy functionality provides selective chemoselective conjugation, while the PEG spacer supports favorable solubility and conformational flexibility in bifunctional degraders. This product is particularly useful in targeted protein degradation workflows, where modular assembly and robust linker chemistry are essential; detailed structure and reactivity considerations are provided below.

Structure: The linker contains an aminooxy group capable of oxime formation, a short poly(ethylene glycol) chain that enhances hydrophilicity, and a methyl ester that serves as a functional handle. It features ether linkages within the PEG backbone and an ester carbonyl, enabling controlled chemical reactivity.

Reactivity: PROTAC construction commonly proceeds via oxime ligation between the aminooxy group and an aldehyde or suitably activated carbonyl on the targeting module, typically under mildly acidic to neutral conditions to promote condensation while preserving sensitive functionalities. The PEG segment generally tolerates common organic solvents used in bioconjugation, and the methyl ester can be retained or further transformed depending on the desired coupling strategy.

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* 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