Unexpected Hydrolytic Instability of N-Acylated Amino Acid Amides and Peptides

Abstract

Remote amide bonds in simple N-acyl amino acid amide or peptide derivatives 1 can be surprisingly unstable hydrolytically, affording, in solution, variable amounts of 3 under mild acidic conditions, such as trifluoroacetic acid/water mixtures at room temperature. This observation has important implications for the synthesis of this class of compounds, which includes N-terminal-acylated peptides. We describe the factors contributing to this instability and how to predict and control it. The instability is a function of the remote acyl group, R2CO, four bonds away from the site of hydrolysis. Electron-rich acyl R2 groups accelerate this reaction. In the case of acyl groups derived from substituted aromatic carboxylic acids, the acceleration is predictable from the substituent’s Hammett σ value. N-Acyl dipeptides are also hydrolyzed under typical cleavage conditions. This suggests that unwanted peptide truncation may occur during synthesis or prolonged standing in solution when dipeptides or longer peptides are acylated on the N-terminus with electron-rich aromatic groups. When amide hydrolysis is an undesired secondary reaction, as can be the case in the trifluoroacetic acid-catalyzed cleavage of amino acid amide or peptide derivatives 1 from solid-phase resins, conditions are provided to minimize that hydrolysis.

Scanning Electron Microscopic Evidence of Spontaneous Heteropeptide Formation in Abiotic Solutions of Selected α‐Amino Acid Pairs

“…). Numerous reports on the lack of peptide stability in abiotic solutions refer to their decay (e.g., hydrolysis) rather than to their spontaneous formation (the latter process being the leitmotif of our own investigations), and they tend to ascribe such phenomena to basically external stimuli, such as pH, temperature, the chemical nature of the solvents, etc …”

Surface-enhanced Raman scattering investigation of targeted delivery and controlled release of gemcitabine

“…Recent studies indicate that strength of amide bonds depends on the kind of groups on both sides of the bond, which may cause the so-called "bond-twisting", which decreases amide bond stability and makes it prone to acidolysis. 56,57 In addition to that, DNA 8,58 and enzymes that have the ability to promote cleaving the amide bonds will contribute to the drug release. The amide bond cleavage allows the GEM to diffuse away from the AuNPs unmasking the MBA Raman signal.…”

Documenting and harnessing the biological potential of molecules in Distributed Drug Discovery (D3) virtual catalogs

“…However, two major factors often limit their utility: (i) Member compounds and analogs may be difficult to synthesize or (ii) there is no inherent probability of biological activity. To the first issue, we have created large virtual catalogs of N ‐acyl α‐amino acids and their methyl ester and primary amide derivatives based on reproducible procedures and demonstrated student syntheses of individual catalog members 1 2, and, presented here for the first time, 3 (Figure ).…”