Non-natural peptide

Scheme 9 Examples of non-natural peptides synthesized via the direct introduction of side chains onto small peptides...

Figure 3 Designer transcriptional activation domains, (a) Sequences of both natural and non-natural peptidic activation domains. Although little sequence homology exists, all domains are amphipathic and thought to interact with target proteins through helix formation, (b) Structures of nonpeptidic transcriptional activation domains.

Ways have been found, in the laboratory, of broadening the specificity of some enzymes (particularly the proteinases, but also certain lipases that can be used in laboratory peptide synthesis see Chapter 7), for example by employing organic solvents, so that these enzymes catalyse some of the reactions of non-protein amino acid derivatives and some of the reactions of peptides that incorporate unusual amino acids. It has proved possible to involve D-enantiomers of the coded amino acids and d- and L-isomers of non-protein amino acids in peptide synthesis, to generate non-natural peptides. 

Non-natural peptides involved in the stabilization of the MFIC class I molecules can be considered as the starting point for the discovery of new immune modulators such as antitumor vaccines and T-cell receptor agonists or antagonists [44-48]. In this context, poly-N-acylated amines (PAAs) as a new class of synthetic oligomers were developed and tested as ligands for the murine class I molecule H-2Kb [49]. Based on the natural cytotoxic T-cell epitope SIINFEKL, non-peptidic structural elements were introduced in the C-ter-minal part of the ligand including the anchor positions 5 (Phe) and 8 (Leu) (Fig. 7.7). 

Regardless of the method used to construct the main pseudodipeptidic backbone, separation of different diastereoisomers has been achieved in several cases by selective crystallization at dipeptide [74, 91], tripeptide [74, 92, 93], or even tetrapeptide level [94]. The isomer corresponding to the natural peptide is usually crystallized out selectively nevertheless, in some tripeptides it has been reported that non-natural peptide isomers are prone to selective crystallization in less polar solvents (Et20 or CHCI3), probably caused by differences in the intramolecular hydrogen bonding in these media (Scheme 16) [92, 93]. 

This compound is a cyclic, non-natural peptide with a thiolactone unit and a representative of the group of cyclic peptide inhibitors of staphylococcal virulence. Thiolactone peptides are expected to act as anti-bacterial therapeutics by a highly specific mechanism, as outlined in the following sections. 

Because of their ease of synthesis and their structural similarity to peptides, many laboratories have used peptoids as the basis for combinatorial drug discovery. Peptoids were among the first non-natural compounds used to establish the basic principles and practical methods of combinatorial discovery [17]. Typically, diverse libraries of relatively short peptoids (< 10 residues) are synthesized by the mix-and-split method and then screened for biological activity. Individual active compounds can then be identified by iterative re-synthesis, sequencing of compounds on individual beads, or indirect deduction by the preparation of positional scanning libraries. 

The well-defined helical structure associated with appropriately substituted peptoid oligomers (Section 1.6) can be employed to fashion compounds that closely mimic the stracture and function of certain bioactive peptides. There are many examples of small helical peptides (<100 residues) whose mimicry by non-natural ohgomers could potentially yield valuable therapeutic and bioactive compounds. This section describes peptoids that have been rationaUy designed as mimics of antibacterial peptides, lung surfactant proteins, and coUagen proteins. Mimics of HIV-Tat protein, although relevant to this discussion, were described previously in this chapter (Sections 1.3.2 and 1.4.1). 

Patch, J.A. and Barron, A.E. Mimicry of bioactive peptides by non-natural, sequence-specific peptidomimetic oligomers. Curr. Opin. Chem. Biol. 2002, 6, 872-877. 

However, most natural peptides are composed of L-form a-amino acids and because of the ubiquitous prevalence of peptidases they have limited biostability, and consequently low bioavailability. Thus, a novel field of peptidomimetics has emerged in drug discovery, in attempts to design non-peptide compounds mimicking the pharmacophore and thus the activity of the original peptide. 

The strategy of introducing non-natural aminoacids into the oxytocin peptide skeleton in order to make antagonists has also been exploited by Havaas et al. [51], who replaced the proline at the 7-position with sarcosine and modified the tyrosine residue at the 2-position to introduce further conformational constraint. A representative example is shown, (13), with a... 

Solid-phase peptide synthesis offers a fast and convenient route for many peptides when isotope-enriched compounds are not required. Classical synthesis additionally permits the use of non-natural amino acids and allows site-specific isotope labeling. Although Fmoc protected 15N-labeled amino adds are commercially available, the cost of such synthesis is usually prohibitive, and the peptides from chemical synthesis require perdeuterated detergents and unfortunately exclude investigation of internal dynamics through measurement of 15N relaxation. 

Based on our current understanding of ribosomal protein synthesis, several strategies have been developed to incorporate amino acids other than the 20 standard proteinogenic amino acids into a peptide using the ribosomal machinery . This allows for the design of peptides with novel properties. On the one hand, such a system can be used to synthesize nonstandard peptides that are important pharmaceuticals. In nature, such peptides are produced by nonribosomal peptide synthetases, which operate in complex pathways. On the other hand, non-natural residues are a useful tool in biochemistry and biophysics to study proteins. For example, incorporation of non-natural residues by the ribosome allows for site-specific labeling of proteins with spin labels for electron paramagnetic resonance spectroscopy, with... 

Finally, it should be considered that additional non-natural functional groups, which are often incorporated in the lipidated peptides for biological studies such as fluorophores or photoactive groups, typically lead to additional restrictions for the synthesis protocols. 

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