Unprotected side chains

A second method of activating the acid for esterification (see Section 7.6) is as the mixed anhydride. The mixed-anhydride reaction had been employed decades ago for preparing activated esters. However, it was never adopted because of its unreliability and the modest yields obtained. The method was fine-tuned (Figure 7.12), after reliable information on the properties of mixed anhydrides was acquired (see Section 2.8). Tertiary amine is required for esterification of the mixed anhydride to occur. The method is generally applicable, except for derivatives of asparagine, glutamine, and serine with unprotected side chains. The base also prevents decomposition that occurs when the activated derivative is a Boc-amino acid (see... 

The acylated peptides (Myr)GCX-Bimane 31 a-e (X = G, L, R, T, V), which are found in certain nonreceptor tyrosine kinases and ct-subunits of several heterotrimeric G-proteins, were synthesized in solution using common solution-phase peptide synthesis with X-myristoylglycine as a building block. These model peptides were used for acylation studies with palmitoyl-CoA in phospholipid vesicles at physiological pH. For such uncatalyzed spontaneous reactions only a modest molar excess of acyl donor species (2.5 1) was necessary. Unprotected side chains of threonine or serine are not interfering with this S-acylation (Scheme 14). 

The first synthesis of peptide aldehydes involved amino acid residues with no side-chain functional groups. Subsequently, peptide aldehydes with a number of side-chain functional groups have been synthesized. Protecting groups utilized include Arg(N02), Lys(Z), Asp(OCy), Asp(OtBu), Glu(OtBu), Ser(Z), Thr(tBu), and Cys(Z). 311 1319 20 It should be noted that many unprotected side-chain functional groups will react with the aldehyde functional group and this is discussed in Section 15.1.1.1. 3,5,11,21 ... 

As mentioned above, in the case of glutamine or asparagine residues the side-chain amide groups have to be protected or alternatively, preformed and purified active esters have to be used. When unprotected side-chain threonine derivatives are activated, a partial (3-elimination to a-aminocrotonic acid has been reported,f l whereas arginine, either unprotected and protonated or as co-tosyl derivative may cyclize to a 6-lactam during activa-tion.f l... 

The incorporation of unprotected side-chain derivatives of Asn and Gin derivatives has also been investigated using HATU. In the SPPS of AGP no cyano derivatives of Asn and Gin were detected, however, the incorporation of Asn was not complete, possibly due to the low solubility of Fmoc-Asn-OH in DMF.P l Due to this low solubility of Fmoc-Asn-OH and the unfavorable effects of unprotected side chains on the aggregation behavior of the growing peptide chain, the use of side-chain protection is reconunended (Section 2.3.3).f l For reasons still not clear, even side-chain protection of Asn does not fully eliminate deficiencies in phosphonium- or uronium-mediated couplings. Thus, the incorporation of Fmoc-Asn(Trt)-OH is more satisfactory if one equivalent of HOAt is present during HATU-mediated couplings.P ... 

Hydrolyzing enzymes, especially proteases, constitute an alternative to chemical synthesis. The principal advantages are the use of unprotected side chain amino acids (except cysteine), racemization-free couplings (especially in fragment couplings) and the specificity of the involved enzyme. As a consequence, the number of synthetic steps is drastically reduced and the procedures are environmentally safe. 

The N-terminal residue should be incorporated as an IV-Boc derivative, or the N-terminal amino group can be capped by treating the resin with di-t-butyl-dicarbonate (5 eq) in DMF for 30 min. The former method is preferred when the peptide contains residues with unprotected side-chain hydroxyl functionalities. 

Scheme 1 Cartoon of a peptide ligation. The substrates combine chemoselectively to form a backbone amide bond in the presence of unprotected side chains, under water-compatible conditions, and without reagents or catalysts...

Takeo and Lei showed that it was indeed possible to use our methods for a-ketoacid and hydroxylamine synthesis to prepare several cyclic peptide namral products [34, 35]. No post-cyclization manipulatimis other than purification were required. The ability to perform the cyclization on unprotected side chains may... 

Nevertheless, the use of chloroacetic acid is superior to the other acids, when using unprotected side-chain heterocycles [253]. This is due to the irreversible alkylation reaction that can occur with nucleophiles in the side chains. The lowered reactivity of the chloride can be enhanced by previous addition of, e.g., KI, which enables the generation of 15-mers in > 80% aver-... 

In this chapter, we will focus on Ser/Thr phosphorylation. Tyr phosphorylation is described in Ottinger et al. [15, 16]. The chapter describes a novel and general methodology for the solid-phase synthesis of phosphopeptides, featuring direct incorporation of Mx-Fmoc-phospho-l-Tyr, with an unprotected side chain. This technique obviated the formation of peptide by-products containing Tyr H-phosphonate. 

Unoptimized initial work in peptide coupling with BOP had already shown high yields and short reaction times, even with bulky amino acids (eq 2) and little if no side reactions with some sensitive amino acids bearing unprotected side chain functional groups. ... 

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