Peptides, derivatives stability

The influence of backbone flexibility was seen, for example, when the stability of the linear tetrapeptide 6.70 was compared to that of a cyclic hexa-peptide derivative of the same sequence [91]. Indeed, the cyclic peptide was approximately one order of magnitude more stable than the linear peptide in the pH range of 2-7. The results at higher pH values were inconclusive since the stability of the cyclic peptide decreased dramatically due to the degradation of a disulfide bond absent in the linear peptide. 

Robust peptide-derived approaches aim to identify a small drug-like molecule to mimic the peptide interactions. The primary peptide molecule is considered in these approaches as a tool compound to demonstrate that small molecules can compete with a given interaction. A variety of chemical, 3D structural and molecular modeling approaches are used to validate the essential 3D pharmacophore model which in turn is the basis for the design of the mimics. The chemical approaches include in addition to N- and C-terminal truncations a variety of positional scanning methods. Using alanine scans one can identify the key pharmacophore points D-amino-acid or proline scans allow stabilization of (i-turn structures cyclic scans bias the peptide or portions of the peptide in a particular conformation (a-helix, (i-turn and so on) other scans, like N-methyl-amino-acid scans and amide-bond-replacement (depsi-peptides) scans aim to improve the ADME properties." ... 

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. 

Figure 14.8. Thermograms for the volatilization of peptide-derived compounds in freeze-dried rhizodeposits leached from a soil cropped with maize after a daytime and a nighttime growth period and thermogram for the volatilization of L-glutamic acid. Reprinted from Leinweber, P., Jandl, G., Baum, C., Eckhardt, K.-U., and Kandeler, E. (2008). Stability and composition of soil organic matter control respiration and soil enzyme activities. Soil Biology and Biochemistry 40,1496-1505, with permission from Elsevier.

Interestingly, a series of homo-peptides derived from the C -didehydro a-amino acid with the shortest side chain (C -didehydroalanine or AAla, 6) was shown unambiguously to overwhelmingly adopt a multiple, consecutive, fully extended conformation (29). These peptide molecules are essentially flat, including the amino acid side chains, and form completely planar sheets (Fig. 5). This uncommon peptide 3-D structure is stabilized by two types of intramolecular H-bonds, Nj-H- Oi=Ci (typical of the 2.05-helix) and Oi=Ci (characteris-... 

Several factors affect the volatility and stability of a peptide derivative, not least of these being the number and nature of the constituent amino acids. Heterocyclic and aromatic amino acids reduce volatility while those containing sulphur tend to decrease the thermal stability. Small naturally occurring peptides which are not derived from proteins often contain only aliphatic amino acids which lack functional groups in the side chains. Peptides of this type of up to about ten amino acids, after conversion to suitable derivatives, are amenable to analysis by mass spectrometry, e.g. [164]. A variety of derivatives has been reported and include N-trifluoroacetyl peptide esters [136,165], N-acetyl peptide esters [166-168], aromatic N-acyl peptide esters [169-172], and per-methylated N-acyl peptides [173]. The principal modes of the electron impact induced fragmentation of these peptide derivatives are well established and have been summarised in recent reviews [174,175]. Although the spectra of the permethylated derivatives [176] are perhaps the simplest and easiest to interpret and are now frequently used, the N-acyl peptide esters have been widely and successfully employed. 

Capillary gas chromatography with optically active stationary phases became a well-established technique for stereochemical analysis after the pioneering work of Gil-Av and his associates in the mid-1960s (2). Thermal stability of the initially low-molecular-weight amino add and peptide derivatives was greatly improved after the introduction of chiral polysUox-anes by Frank, Nicholson, and Bayer (Chirasil-val [1], 1977) (3) and of... 

Hanessian studied the solution structure of tetra-, hexa-, and octa-y-peptide analogues of the sequence (-Ala-Val-).236 All three of these y4-peptides derived from L-amino acids adopted stable right-handed helical conformations in solution. The helical parameters were identical to those found by the Seebach group 2.6 residues per turn stabilized by S(14) H-bonds. Temperature-dependent chemical shifts suggested that these intrastrand interactions are strong. As also noted by Seebach, CD did not reveal a pattern diagnostic of secondary structure. The obvious but important lesson from these reports is that CD cannot be used alone as a means of screening for secondary structure. 

Insects and arachnoids produce well-known amyloids. Silk and spider webs, like P-keratin, also differ from amyloids in being fibrous P-sheet proteins composed of peptide strands that are parallel, rather than perpendicular, to the direction of the fibril axis. For the process of silk formation by spiders, it has been proposed that fibrils in the silk gland have an initial cross-P structure (Kenney et al. 2002 Table 3) that, when stretched, assume parallel P-structures. However, X-ray diffraction for a peptide derived from the central domain of the A class of chorion proteins, derived frovaAntheraea polyphemus eggshells, displayed P-sheets perpendicular to the fibril axis, the same cross-P structure that occurs in amyloid proteins (Iconomidou et al. 2000 Table 3). The stability and strength of the amyloid fibres provides mechanical and biological protection for the oocyte and developing embryo from a variety of environmental and predatory hazards. 

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