Peptide libraries, synthesis

For linear peptide library synthesis, cysteine is usually excluded to avoid undesired formation of disulfide bonds. 

Besides classical resin beads, other polymeric carriers were also used for the synthesis ofpeptide libraries in various formats. Poly aery late-grafted polypropylene pins were used for the synthesis of the first combinatorial chemical library [1,2], This type of support continues to be heavily used in multiple peptide [27] and non-peptide [28] library synthesis. Cellulose paper, originally used by Frank et al. as a solid-phase support for oligodeoxy-ribonucleotide synthesis [29], has also been used as the support for multiple SPOT synthesis of peptide libraries [30,31], Polystyrene-grafted polyethylene film (PS-PE) may also be used in combinatorial peptide library synthesis [32], The specific feature of the membrane type of carrier is its dividability. This feature has been used for the synthesis of libraries with a nonstatistical distribution of library members, where no compound is missing and none is represented more than once [33],... 

Positional scanning, or 1-D indexing, was reported as a deconvolutive technique by Houghten and coworkers [35] and subsequently applied extensively to solid-phase peptide library synthesis. An example of solid-phase small organic molecule 2-D indexed library synthesis and deconvolution was reported by Berk et al. [36]. Description of this strategy, called spatially arrayed mixture (SpAM), and a comparison with classical positional scanning, are shown in Figure 8.9. 

The principal differences between the various methods of peptide library synthesis are (i) the solid support used, (ii) the means of incorporating amino acid mixtures, (iii) the state in which the libraries are screened (support-bound vs in solution), and (iv) the manner in which individual active peptides are identified within the library. 

The principal difference between the synthesis of individual peptides and peptide libraries is that mixtures of amino acids, rather than individual amino acids, are incorporated into selected or all positions of the sequence of peptide libraries. However, all current peptide chemistry strategies can be used for the synthesis of peptide libraries. In general, library synthesis requires greater emphasis on simplicity and reproducibility of the synthesis process. Although soluble supports have also been used for peptide library synthesis,the majority of methods used to synthesize peptide combinatorial libraries utilize Merrifield s concept of solid-phase synthesis,which is based on the sequential assembly of peptides after covalent attachment of the C-terminal amino acid to a polymeric solid support. This enables the excess of reagents to be removed by simple wash and filtration processes, and avoids the... 

In order to overcome the synthesis bottleneck in drug discovery, the concept of preparing many compounds at one time (parallel synthesis) rather than one compound at a time (serial synthesis) was bom. In its simplest form, this distinction constitutes the definition of combinatorial chemistry. The origin of the concept has been ascribed (1) to Furka and others as early as 1982. Early applications of parallel synthesis methods were primarily in the area of peptide library synthesis and have been extensively reviewed (2,3). In the early 1990s, however, application to small drug-like molecules was reported (4) and the explosion in combinatorial chemistry activity began. 

Then there is focussed library synthesis, FLS. In its broadest sense this involves synthesis of a larger number of compounds than TOS, often using solid-phase chemistry (Box 1), but where all the products are still quite similar. FLS allows more exhaustive exploration than TOS of a relatively small volume of biological chemical structure space. Peptide library synthesis can be considered one of the first examples of this category because an underlying polypeptide backbone, which is the same for all members of the library, is elaborated with variable side-chains. Taking its lead from peptides and oligo-nucleotides, much effort has been directed over the last decade towards library synthesis with substrates bound to solid supports, to facilitate... 

More recently, Somfai and coworkers have reported on the efficient coupling of a set of carboxylic acids suitable as potential scaffolds for peptide synthesis to a polymer-bound hydrazide linker [24]. Indole-like scaffolds were selected for this small library synthesis as these structures are found in numerous natural products showing interesting activities. The best results were obtained using 2-(7-aza-l H-benzo-triazol-l-yl)-l,l,3,3-tetramethyluronium hexafluoride (HATU) and N,N-diisopropyl-ethylamine (DIEA) in N,N-dimethylformamide as a solvent. Heating the reaction mixtures at 180 °C for 10 min furnished the desired products in high yields (Scheme 7.4). In this application, no Fmoc protection of the indole nitrogen is required. 

The first example describes the synthesis of a pyrimidine derivative. Starting from a, 3-unsaturated ketones (see Schemes 1, 8), a library of different heterocycles was prepared in research (Felder and Marzinzik 1998). In preparation for any large-scale synthesis, the availability of starting materials is always considered (Lee and Robinson 1995). For this work, we had to replace Rink amide resin B (Rink 1987), which was used by our colleagues in research for the synthesis of pyrimidine 1 due to its unavailability in large quantities (see Fig. 1). It was replaced with the Rink amide acetamido resin 4, which is well established in peptide amide synthesis (Bernatowicz et al. 1989) and easily accessible. 

While parallel synthesis of arrays of glycopeptides is readily achieved by implementation of the building-block approach (Scheme 14.1, Strategy 2),101 glycopeptide library synthesis in a combinatorial manner via the split-mix method has yet to prove routine. The difficulty lies in the structural analysis of the vast number of compounds generated in picomolar quantities on a single bead. Whereas peptides on... 

Scheme 14.1 Strategies for glycopeptide library synthesis Strategy 1 chemical or enzymatic glycosylation of peptide or glycopeptide Strategy 2 the building-block approach. While enzymes have not yet been used in the solid-phase synthesis of glycopeptide libraries, several resin-bound glycopeptides have been glycosylated enzymatically.36,114...

Riche EL, Erickson BW, Cho MJ. Novel long-circulating liposomes containing peptide library-lipid conjugates synthesis and in vivo behavior. J Drug Target 2004 12 355. 

At first, combinatorial chemistry focused on peptide and nucleotide libraries synthesis, but because poor pharmacokinetical properties cause poor oral availability of this kind of molecule, there is increasing interest in the development of new methods to prepare small, drug-tike molecules which obey lipinski s mle of five [303]. Heterocyclic compounds can offer a high degree of structural diversity and have proven to be useful as therapeutic agents. For these, there are recent advances in the preparation of heterocycles on solid supports [304]. The examples reported in this section are organized by their ring size. 

A library containing several million beads can be screened in a single afternoon. Furthermore, the library is reusable, as it may be washed in 8 M guanidine hydrochloride and then re-screened using a different probe. This split synthesis approach displays the ability to generate peptide libraries of incredible variety, variety that can be further expanded by incorporation of, for example, D-amino acids or rarely occurring amino acids. 

Houghten and co-workers[145] introduced a method for combinatorial synthesis of a per-alkylated peptide library using nonspecific N-alkylation. The peptides were synthesized by SMPS methodology 146 in combination with repetitive amide N-alkylation on the solid support after each coupling step. Peptides were synthesized on MBHA-PSty resin using Fmoc chemistry. After Fmoc deprotection the a-amino group was protected by Trt to prevent N -alkylation and to allow only amide alkylation. The on-resin amide alkylation was achieved by amide proton abstraction using LiOtBu in THF followed by nonfunctionalized alkyl and aryl halides in DMSO. 

Solid-phase peptide synthesis has become widely used for the preparation of peptides built from a-amino acids of varying sizes and complexity, and also in the recent synthetic approaches to peptide libraries. It has been recognized that the use of solid-phase protocols for the synthesis of (3-peptides is likely to make them more attractive lead compounds in drug discovery. Although still at an early stage, work has begun to develop suitable protocols for automated (3-peptide synthesis. 

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