Characterization of Nα-Fmoc-protected dipeptide isomers by electrospray ionization tandem mass spectrometry (ESI-MS(n)): effect of protecting group on fragmentation of dipeptides.

A series of positional isomeric pairs of Fmoc-protected dipeptides, Fmoc-Gly-Xxx-OY/Fmoc-Xxx-Gly-OY (Xxx=Ala, Val, Leu, Phe) and Fmoc-Ala-Xxx-OY/Fmoc-Xxx-Ala-OY (Xxx=Leu, Phe) (Fmoc=[(9-fluorenylmethyl)oxy]carbonyl) and Y=CH(3)/H), have been characterized and differentiated by both positive and negative ion electrospray ionization ion-trap tandem mass spectrometry (ESI-IT-MS(n)). In contrast to the behavior of reported unprotected dipeptide isomers which mainly produce y(1)(+) and/or a(1)(+) ions, the protonated Fmoc-Xxx-Gly-OY, Fmoc-Ala-Xxx-OY and Fmoc-Xxx-Ala-OY yield significant b(1)(+) ions. These ions are formed, presumably with stable protonated aziridinone structures. However, the peptides with Gly- at the N-terminus do not form b(1)(+) ions. The [M+H](+) ions of all the peptides undergo a McLafferty-type rearrangement followed by loss of CO(2) to form [M+H-Fmoc+H](+). The MS(3) collision-induced dissociation (CID) of these ions helps distinguish the pairs of isomeric dipeptides studied in this work. Further, negative ion MS(3) CID has also been found to be useful for differentiating these isomeric peptide acids. The MS(3) of [M-H-Fmoc+H](-) of isomeric peptide acids produce c(1)(-), z(1)(-) and y(1)(-) ions. Thus the present study of Fmoc-protected peptides provides additional information on mass spectral characterization of the dipeptides and distinguishes the positional isomers.

New and simple synthesis of acid azides, ureas and carbamates from carboxylic acids: application of peptide coupling agents EDC and HBTU.

Conversion of carboxylic acids into acid azides using peptide coupling agents, EDC and HBTU is described. The procedure is efficient, practical and applicable to a diverse range of carboxylic acids including N-protected amino acids. Using the same reagents, one-pot synthesis of ureas, dipeptidyl urea esters and carbamates from acids has also been achieved.

N-urethane-protected amino alkyl isothiocyanates: synthesis, isolation, characterization, and application to the synthesis of thioureidopeptides.

Synthetically useful N-Fmoc amino-alkyl isothiocyanates have been described, starting from protected amino acids. These compounds have been synthesized in excellent yields by thiocarbonylation of the monoprotected 1,2-diamines with CS2/TEA/p-TsCl, isolated as stable solids, and completely characterized. The procedure has been extended to the synthesis of amino alkyl isothiocyanates from Boc- and Z-protected amino acids as well. The utility of these isothiocyanates for peptidomimetics synthesis has been demonstrated by employing them in the preparation of a series of dithioureidopeptide esters. Boc-Gly-OH and Boc-Phe-OH derived isothiocyanates 9a and 9c have been obtained as single crystals and their structures solved through X-ray diffraction. They belong to the orthorhombic crystal system, and have a single molecule in the asymmetric unit (Z' = 1). 9a crystallizes in the centrosymmetric space group Pbca, while 9c crystallizes in the noncentrosymmetric space group P2(1)2(1)2(1).

Synthesis of oligopeptides through O-acyl isopeptide method.

The O-acyl isopeptide method has recently gained attention as an efficient protocol for the synthesis of 'difficult sequence' peptides. Herein, synthesis of three oligopeptides of different length, a pentapeptide Gly-Leu-Leu-Ser-Val, a heptapeptide fragment 285-291 of transmembrane (M7-24-T40) Ala-Val-Leu-Ser-Leu-Pro-Leu and a decapeptide, Gly-Leu-Leu-Ser-Val-Leu-Gly-Ser-Val-Ala were demonstrated in solution phase by employing O-acyl isopeptide method. The peptides were established through an efficient pH triggered intramolecular O→N acyl migration under physiological conditions. The reactions were clean and complete in appreciable length of time.

Click chemistry aided synthesis of 1,4-substituted 1,2,3-triazole based N-Fmoc protected epsilon-amino acids: isolation, characterization and synthesis of novel triazole based unnatural amino acids.

A new class of 1,4-substituted 1,2,3-triazole-based unnatural amino acids is demonstrated by employing click reaction between N-Fmoc amino alkyl azides and propiolic acid. The resulting unnatural amino acids were isolated and then subjected to Fmoc deprotection to isolate 1,2,3-triazole based amino acids as stable solids. These new class of molecules were also used for chain extension from both N- and C-terminals to synthesize dipeptidomimetics bearing 1,2,3-triazole moiety in the backbone.

An efficient conversion of the carboxylic group of N-Fmoc alpha-amino acids/peptide acids into N-formamides employing isocyanates as key intermediates.

Reaction of 96% formic acid with isocyanates derived from N-Fmoc alpha-amino acids/peptide acids catalyzed by DMAP has yielded a new class of stable formamides as crystalline solids which have been characterized by IR, 1H NMR, 13C NMR, and mass spectroscopy. Conversion of the side chain carboxylic acid of N-Fmoc-5-oxazolidinones of Asp/Glu into the N-formyl group also has been accomplished. The reaction is simple, mild, and high yielding.