Bioactive natural peptides

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. 

Dairy proteins are rich in nutrients and occupy a unique place of importance in food and human nutrition because of their wide acceptance in the world. Milk proteins are important in the diet because of the many health benefits associated with their consumption. The proteins have long been recognized as natural sources of health enhancing bioactive peptides because of their stmctural and physicochemical components as recently reviewed by Livney (2010). 

The above examples illustrate the versatility and overlapping substrate specificities of peptidases, but they also serve to explain the difficulties faced by medicinal chemists who try to design bioactive peptides that have improved pharmacokinetic properties. Clearly, general predictive rules and a global understanding of the in vivo fate of peptides are not in sight, but the sections below will show that medicinal chemists have developed various successful strategies of a rather empirical nature [7][181-188],... 

The potential utility of peptides as therapeutic agents with clinical applications is limited as a consequence of intrinsic peptide properties such as metabolic instability or poor transmembrane mobility. Hence, the design and synthesis of meta-bolically stable peptide analogs that can either mimic or block the bioactivity of natural peptides or enzymes is an important area of medicinal chemistry research. Numerous structural modifications to peptides have been examined in pursuit of molecules with more desirable properties [1-3]. These modified structures, peptidomimetics, are nonpeptide molecules that imitate the desired properties of the natural substances. 

The simplest approach to isosteric replacement of one or both sulfur atoms of the cystine disulfide with a methylene or ethylene moiety is given for natural bioactive peptides when one cysteine residue is located in the N-terminal sequence position and the related amino group or peptide extension is not involved in the bioactivity. This allows for direct side chain to backbone (N-terminus) cyclization via amide bonds with suitable 5-carboxyalkyl derivatives of the second cysteine residue, or with the oo-carboxy group of aminodicarboxylic adds containing an alkyl side chain that mimics the Ca to Ca spacer in cystine. Thereby, the length and degree of branching of the sulfide or alkyl spacer can additionally be varied. 

Table 1 Amino Acid Sequences of Known Naturally Occurring Bioactive Peptides Sulfated at Tyrosine...

Cyclic hexapeptides can be considered as the classical and the most prominent representatives among cyclic peptides. Natural products are numerous and widespread (see Scheme 11), e.g. segetalin A,[278] bouvardin/279280 RA-IIlJ281-283 or pneumocandin B0,[284 286] and this type of ring structure has frequently been used to stabilize conformational preferences of bioactive portions of larger peptides or even proteins. 

In natural bioactive peptides the modes of cyclization described previously may be prevented either by the lack of suitable side-chain functionalities for lactamization or because these as well as the amino and carboxy termini are crucially involved in the bioactivity itself, and thus cannot be modified. In order to overcome these potential limitations, the concept of backbone cyclization has been proposed.129 According to this, the cyclization is performed by a covalent interconnection of two backbone amides by artificial spacers or of one backbone amide by a correctly functionalized spacer with side-chain functions or with the N- and C-terminus of the peptide (Scheme 21). This type of strategy significantly increases the diversity of possible ring structures (see Scheme 22) and of their related libraries (see Section 6.8.4). Its potential for enhancing the stability of the related peptide derivatives toward proteolytic digestion,[417 419 potency,141942" and selectivity,11417-419 is well-established. 

Synthetic cyclic peptides are of eminent interest not only as replicates or analogues of natural products or as conformationally restricted bioactive peptides and peptide or protein fragments, but may also serve for specific purposes as listed in the following sections. 

Figure 3.1 Peptidomimetic chemistry attempts to produce a non-peptidic drug to mimic a bioactive peptide. In Step A, the smallest bioactive fragment of the larger peptide is identified in Step B, a process such as an alanine scan is used to identify which of the amino acids are important for bioactivity in Step C, individual amino acids have their configuration changed from the naturally occurring L-configuration to the unnatural D-configuration (in an attempt to make the peptide less naturally peptidic ) in Step D, individual amino acids are replaced with atypical unnatural amino acids and amino acid mimics in Step E the peptide is cychzed to constrain it con-formationally finally, in Step F, fragments of the cyclic peptide are replaced with bioisosteres in an attempt to make a non-peptidic organic molecule.

In addition to endogenous heterocycles, there are also medically important exogenous heterocycles. Nature is a great source of molecular diversity, especially for bioactive molecules. Nature provides a rich source of peptidic (penicillin), lipid (terpenes), and other (alkaloid) heterocyclic natural products. These compounds are produced in plants or nonhuman animals, but may exert profound biological effects when administered to humans. 

The discovery of a multitude of naturally occurring, bioactive peptides has generated a rich source of pharmacophores from which medicinal chemists are developing new useful therapeutic drugs. After binding to an enzyme, or a membrane receptor, peptide-based inhibitors, neurotransmitters, immunomodulators, and hormones influence cell-to-cell communications and control a variety of vital functions such as metabolism, immune defense, digestion, respiration, sensitivity to pain, reproduction, and behavior. 

The following protocols can be used for the isolation and structural characterization of any natural bioactive peptides from the immune system of invertebrates. The different procedures that will be detailed below refer to the identification and primary structure determination of the Drosophila immune-induced peptides (19,20,23,27,30) and of bioactive peptides from the immune system of other Diptera (17,21,24,31). These approaches were also successfully used for the discovery of bioactive peptides from crustaceans, arachnids, and mollusks. These methods should be considered as a guideline and not as the exact procedure to follow (see Note 3). The suggested procedures will be reported following the normal order of execution, (1) induction of the immune response by an experimental infection, (2) collection of the immunocompetent cells (hemocytes), tissues (epithelia, trachea, salivary glands, etc.)... 

Experimental infections, tissue collection, extraction conditions, purification procedures, and strategies for determining the primary structure of the natural bioactive peptides should be adapted to the animal model (size, rarity, possibility to conduct molecular biology investigations, availability of EST, and genomic databases, etc.) considered and to the complexity of the bioactive peptide. 

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