N-α-Benzyl-N-ε-Boc-L-lysine methyl ester hydrochloride is a protected lysine derivative featuring an Nα-benzyl group and an Nε-tert-butoxycarbonyl (Boc) protecting group on the ε-amino side chain, with the α-carboxyl group converted to a methyl ester and the overall salt present as a hydrochloride. The molecule contains the benzyl-protected α-amino nitrogen and a Boc-protected ε-amino functionality, while the methyl ester masks the carboxylate and the hydrochloride counterion is associated with the protonated amine sites, consistent with an L-lysine stereochemical framework as indicated in the name. In peptide chemistry and related synthetic workflows, this compound functions as a stepwise amino acid building block where the orthogonal Nα and Nε protections help control chemoselective deprotection and coupling, and the methyl ester form supports controlled handling of the carboxyl functionality during intermediate preparation and downstream derivatization.
CAT No: CP01428
N-α-Benzyl-N-ε-Boc-L-lysine methyl ester hydrochloride is a protected lysine derivative featuring an L-lysine backbone with a methyl ester at the carboxyl terminus and two orthogonally protected amine functionalities: an N-α benzyl group and an N-ε Boc carbamate. The hydrochloride salt form improves handling of the basic amines while maintaining compatibility with peptide coupling and selective deprotection sequences. The molecule bears a stereogenic center at the lysine α-carbon, enabling stereochemically defined incorporation into peptide chains and chiral intermediate synthesis. The benzyl and Boc protecting groups provide controlled reactivity, allowing selective activation of the remaining functional group for derivatization, peptide bond formation, or downstream conversion into free amino acid building blocks.
1. Peptide Synthesis
N-α-Benzyl-N-ε-Boc-L-lysine methyl ester hydrochloride supports peptide building block preparation in solid-phase or solution-phase peptide synthesis workflows where orthogonal amine protection is required. The methyl ester C-terminus and the protected N-α and N-ε nitrogens enable controlled peptide coupling chemistry while preventing undesired side reactions from the lysine side-chain amine. Selective deprotection strategies, such as benzyl removal and Boc cleavage under standard conditions, can generate lysine residues with defined N- and side-chain functionality for subsequent coupling cycles. The resulting protected lysine unit can be used to construct peptides, peptide fragments, and sequence-defined analogs that retain stereochemical fidelity at the α-carbon.
2. Side-Chain Functionalization
N-α-Benzyl-N-ε-Boc-L-lysine methyl ester hydrochloride is suitable for side-chain functionalization and protected amino acid derivatization where the ε-amino group must be masked during early synthetic steps. The Boc carbamate on the lysine side chain allows controlled unmasking to reveal a primary amine for acylation, sulfonylation, alkylation, or attachment of solubilizing handles for chemical biology probes. The benzyl-protected N-α position helps maintain selectivity by reducing competing reactivity during side-chain modification and enables later regeneration of a coupling-ready amino group. Downstream targets can include modified lysine-containing peptides, peptidomimetics, and linker-bearing intermediates used for conjugation chemistry and scaffold diversification.
3. Chiral Amino Acid Intermediate
N-α-Benzyl-N-ε-Boc-L-lysine methyl ester hydrochloride functions as a chiral amino acid intermediate for stereodefined synthesis of lysine-derived motifs used in fine chemical and process-oriented manufacturing routes. The L-configuration at the α-carbon is preserved through protection of both amino termini and esterification, allowing the compound to serve as a controllable precursor for converting into free amino acids, activated esters, or protected derivatives. The hydrochloride salt form can facilitate reproducible handling of the amine-containing intermediate during scale-up, while orthogonal protecting groups support stepwise transformations without racemization-prone conditions. The compound can be employed to generate downstream chiral building blocks for peptide coupling, medicinal chemistry intermediates, and industrial chemical manufacturing of amino acid-based specialty reagents.
4. Bioconjugation Chemistry
N-α-Benzyl-N-ε-Boc-L-lysine methyl ester hydrochloride can be applied to bioconjugation reagent development where lysine's ε-amino functionality is introduced in a protected, controlled manner. The Boc-protected side chain can be selectively deprotected to provide a primary amine handle for forming amide or urea linkages with activated esters, isocyanates, or carbonyl electrophiles used in labeling and conjugation strategies. The methyl ester and protected N-α group help maintain structural integrity during linker installation, enabling the preparation of lysine-containing conjugation building blocks that can be further transformed into peptide or polymer-bound constructs. Lysine-derived conjugates prepared from this intermediate can support analytical labeling, affinity probe construction, and biomolecule modification workflows that rely on defined attachment points.
5. Pharmaceutical Manufacturing
N-α-Benzyl-N-ε-Boc-L-lysine methyl ester hydrochloride is relevant to pharmaceutical manufacturing and industrial peptide intermediate preparation where orthogonally protected lysine units are required for reliable synthesis planning. The protected amines and ester functionality allow incorporation into protected peptide sequences and controlled intermediate generation, supporting manufacturing routes that depend on predictable deprotection order and minimized impurity formation from unprotected nucleophiles. The hydrochloride salt form can improve process handling of the amine-containing intermediate, which is often advantageous in bulk chemical operations and intermediate isolation steps. The compound can be used to produce lysine-containing protected intermediates for downstream API-related peptides, peptidomimetic scaffolds, and stereochemically defined building blocks used in applied product development.
6. Analytical Standards
N-α-Benzyl-N-ε-Boc-L-lysine methyl ester hydrochloride can serve as an analytical reference material for method development and characterization of lysine-protected species in peptide chemistry. The combination of benzyl and Boc protection, along with the methyl ester and defined L-stereochemistry, provides a chemically distinct signature for chromatographic and spectrometric identification of protected lysine intermediates and deprotection outcomes. The presence of the hydrochloride salt can also support reproducible sample preparation for analytical workflows that monitor amine-containing compounds and ester stability. Analytical use can extend to verifying the identity of peptide building blocks, tracking side-chain protection state, and supporting impurity profiling during amino acid derivative synthesis and peptide manufacturing process development.
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