Peptides, repetitive synthesis

The term iterative hbrary deconvolution describes a process consisting of repetitive synthesis, screening, and selection steps, during which all mixture positions of the hbrary (see also Section 4.3.7.3.2.1) are successively defined, resulting in the identification of individual peptides with the desired bioactivify.P At each step of this iterative process, the number of peptides per mixture is reduced by a factor equal to the number of amino adds in the mixture position that was defined at that step. At the final step of the process, individual peptides are synthesized and tested. For a hexapeptide library with two defined and four mixture positions, the iterative deconvolution consists of four cycles of synthesis, screening, and selection (see Table 2).P 1... 

One common example of repetitive synthetic strategy comes from the field of natural products. The preparation of oligo- and polypeptides is a repeating sequence of protection and activation of the reactants, followed by the addition of a new amino acid. In 1963, one of the highlights in repetitive synthesis was the automation of peptide production by Merrifield8 (Figure 1). In the literature, authors often speak of a protein machine since it is now possible to build up peptides mechanically without the preparative help of a chemist. 

Some six hundred structures of naturally occurring carbogenic molecules appe on the pages which follow, together with the name of each compound and references to the original literature of successful chemical synthesis. Thus, Part Three of this book is effectively a key to the literature of chemical synthesis as applied to the complex molecules of nature. The survey does not include oligomeric or polymeric structures, such as peptides, proteins, carbohydrates and polynucleotides, which fall outside the scope of this book because they can be assembled by repetitive procedures. 

Peptide synthesis was amenable to solid-phase techniques since the process was repetitive. The C-terminal amino acid is attached to polymeric surface and the peptide chain is assembled via a two-step process coupling of the incoming amino acid that has the alpha-amino group protected... 

HC Beyerman, EWB De Leer, J Floor. On the repetitive excess mixed anhydride method for the synthesis of peptides. Synthesis of the sequence 1-10 of human growth hormone. Rec Trav Chim Pays-Bas 92, 481, 1973. 

The sections presented above provide an account of the separate topics into which translation can be divided. These act as an introduction to the current section, in which a description of the individual reactions in peptide synthesis is presented in a single diagram, i.e. a diagram that encapsulates the whole process (Figure 20.22). An analysis of each separate reaction provides a simple explanation of the interactions that are required in a sequential manner to form the various complexes in the pathway, the activities of which result in the synthesis of, initially, a dipeptide but then a growing peptide. The repetition of the formation of the complexes for each amino acid results in the synthesis of the final peptide, as dictated by the base sequence in the mRNA. 

During peptide synthesis, the reactions catalysed by the various aminoacyl-tRNA synthetases must occur repetitively for each amino acid. Simplicity in regulation is provided by the fact that all these different synthetases are saturated with their respective amino acids, that is, the values of all the synthetases for their respective amino acids must be much lower than the concentrations of the amino acids, so that the enzyme activity is regulated solely by the changes in concentration of the co-substrates, i.e. the free tRNAs. This property, together with external regulation at steps 2 and 7, provides a relatively simple mecha-... 

Peptidomimetics is an active branch of patterned synthesis. A notable family of tumor-avid peptides was derived from synthesis patterned on neurotensin, a peptide constituted of 13-amino acids. These synthetic peptides bind to the NT receptors expressed by many forms of cancer, which may serve to map the tumor, delivering radionuclides in situ (Waibel 2000). Molecules that, like the peptides, are constituted of repetitive blocks, are much simpler to synthesize than those composed of non-repetitive units. Given the powerful bioactivity, and improved stability on systemic administration, synthetic peptides may become rewarding it as it has been estimated, one in two men, and one in three women, will get cancer in their lifetime. 

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. 

Marti et alJ4"1 have used a similar approach involving Fmoc-protection. However, they have demonstrated that it is possible to use Fmoc-protected diazo ketones derived from a-amino acids together with a peptide on a solid support with a free N-terminus in a silver-promoted Amdt-Eistert procedure. Hence, homologation and peptide coupling are achieved in one step. This approach has led to the synthesis of a-peptides containing one (l3-amino acid (Scheme 19) and also, if the homologation procedure is used repetitively, to p3-peptides. 

Polypeptide formation involves a repetition of the process involved in peptide synthesis. 

At the conclusion of the initiation process, the ribosome is poised to translate the reading frame associated with the initiator codon. The translation of the contiguous codons in mRNA is accomplished by the sequential repetition of three reactions with each amino acid. These three reactions of elongation are similar in both prokaryotic and eukaryotic systems two of them require nonribosomal proteins known as elongation factors (EF). Interestingly, the actual formation of the peptide bond does not require a factor and is the only reaction of protein synthesis catalyzed by the ribosome itself. 

Solid-phase methodology was established in 1963 in pioneering work conducted by Merrifield in the area of peptide synthesis [19]. Interest in this synthetic strategy continues unabated to this day, particularly in connection with the production of new active components for drugs, since the repetitive amide bond formation performed in automated synthesisers lends itself ideally to the construction of extensive substance libraries by combinatorial chemistry [20]. 

The repetitive nature of oligomeric synthesis has enabled the rapid implementation of solid-phase and automated methods for DNA [20,21,85,86] and peptide combinatorial libraries. Using these systems for the synthesis of single compounds or mixtures of compounds, multiple reaction vessels numbering 8 [45], 15 [80], 20 [59], 24 [50], 25 [57,58], 36 [53-55,77-79], 48 [26,39-41], or 96 [42-44] can be manipulated. Only a few of these systems enable automated resin mixing and splitting within the instrument to generate mixtures of compounds [53,59,78,87,88],... 

The synthesis continues with repetition ofthese two steps until the peptide chain is complete. The peptide is cleaved from the resin, usually with HF in pyridine or CF3SO2OH in CF3CO2H and given a final purification from small amounts of peptides of the wrong sequence by chromatography, usually HPLC. 

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