Peptide bioactive conformation

This effect is particularly well documented for y - and -amino acid residues [217, 218] which in several natural products (bleomycin A2 [219], calyculins [220]) have been shown to play a substantial role in the pre-organization of the whole molecule into its bioactive conformation. For example, changes in the substitution pattern of the y-amino acid linker in bleomycin A2 result in reduced DNA cleavage efficiency [219]. In the case of y-peptides, changing the relative configuration like or unlike of y " -amino acids has been used as a strategy to generate different local conformations (Fig. 2.34) suitable either for the construction of helices [201] or turns ]202-204]. 

In preparation for use as a surrogate vaccine, these peptides were synthesized as conjugates to tetanus toxoid, and in this form also competed with the 0-antigen polysaccharide for binding [104]. Whether these peptides will function as effective immunogenic mimics will likely depend on their propensity to adopt the bioactive conformation in solution. A certain amount... 

Conformational analysis can be performed using a variety of methods.1161 Most important are X-ray analysis and NMR spectroscopic techniques, which allow detailed insights into the topology of the peptides. NMR combined with molecular dynamic calculations provides the spatial structure of the peptide, but also its dynamics in solution.13643491 Additional information can be obtained from FTIR,15,4521 CD,151,53-551 or Raman spectroscopy. 56,571 The results derived from such conformational analysis of cyclic peptides have a considerable impact on the study of the bioactive conformations of peptides and on the design of cyclic peptides as proteinomimetics.124,58,59,6301... 

Bioactive sequences of up to six amino acid residues known to assume (1- or "/-turns in the bioactive conformation are suitable for such libraries. If the sequence is short, residues have to be added in a manner to retain the desired physicochemical properties of the peptide (e.g., to short polar active sequences hydrophobic residues are preferentially added and vice versa). The choice of the scaffold depends on the number of structure-inducing amino acids such as Gly or Pro present in the native sequence. In absence of such residues scaffolds (1) or (4) (Scheme 24) are selected, whereas if Gly or Pro is present alternative scaffolds can be considered. Then the components of the four stereoisomeric sublibraries of Scheme 26 (or their equivalents if other scaffolds are chosen) are synthesized according to procedures described in the preceding sections. 

For the cycloscan, conformational libraries are synthesized by cyclization of continuous or noncontinuous bioactive epitopes and not by their insertion into a scaffold. Originally, the concept of cycloscan was introduced for the generation of backbone-cyclized peptide libraries 467 however, cycloscan can also be applied to other modes of cyclization. In this approach all components of each sublibrary bear the identical sequence, and differ from each other in distinct parameters that affect their conformation, but do not alter their connectivity, and hence their potential bioactivity. This is achieved by gradually introducing discrete conformational perturbations, which allow an efficient screening of the conformational space of the parent peptide. The majority of the components of such libraries should be inactive, because they do not overlap the bioactive conformation. However, the peptide that does fit the bioactive conformation should be very potent and have all the pharmacological advantages of cyclic peptides. 

Amino-acid abbreviations are spelled out in Appendix V. Through a series of structure-activity relationship studies, the bioactive conformation and peptide sequences that produce undesirable biologic responses were identihed. Also identified were sequences susceptible to proteolysis, and a working-model compound that eliminated these sequences was proposed (Figure 4.6). This allowed the rational design of optimized somatostatin analogues with desirable biologic characteristics and activity and increased stability. 

The above examples of peptide scaffold- or nonpeptide template-based peptidomimetic agonists or antagonists illustrate various strategies to elaborate bioactive conformation and/or pharmacophore models of peptide ligands at their receptors. In many cases, receptor subtype selectivity has also been achieved by systematic structural modifications of prototypic leads of peptidomimetics. Thus, although the 3D structures of G-protein-coupled receptors (GPCRs) remain as elusive (except for models constructed from homology-based low-... 

In a separate study, compounds 10A and 10B were incorporated into the gastrin peptide sequence, replacing the Tyr12-Gly13, to provide a potent analogue. 60 These data were used to imply an Alan-Trp14 p-turn in the bioactive conformation of gastrin. 

It has been suggested that y-turns are present in the solution structures of several peptides, and furthermore implicated in their bioactive conformations 101 including brady-kinin, 111 substance P,1121 cyclic somatostatin analogues, 131 cyclolinopeptide, 141 and the 6-opioid receptor bound conformation of enkephalin. 151 Yet, despite the fact that y-tums are frequently hypothesized to represent important features of secondary structure 161 based upon computational,1171 IR absorption,1181 NMR spectroscopic,119 201 and X-ray diffraction crystallographic determinations,1211 verification of the role of this predicted secondary structural element remains a difficult, but nonetheless critical step. 

Approaches Used to Stabilize Bioactive Conformations at Peptides by Metal Coordination I 41... 

BIOACTIVE CONFORMATION OF CONFORMATIONALLY CONSTRAINED DELTA PEPTIDE LIGANDS... 

Conformational analyses of JOM-13 and [L-Ala3]DPDPE have proven to be critical for the determination of the bioactive conformation of enkephalin-like peptides at the delta receptor. H-NMR studies of JOM-13 in aqueous solution revealed that this tetrapeptide exists in two distinct conformations on the NMR time scale as evidenced by two sets of resonances [63]. Large differences in the observed chemical shifts and coupling constants for the D-Cys2 residue in the two conformers suggested that the major differences between the two NMR conformers reside in the disulfide portion of the molecule however, a paucity of conformationally informative nuclear Overhauser enhancement (NOE) interactions precluded the development of a detailed structural model from the NMR studies. In order to develop such a model a thorough conformational analysis of JOM-13 was undertaken, in which the NMR data were complemented by x-ray diffraction results and by molecular mechanics calculations [64]. The results indicate that the 11-... 

To eliminate the remaining uncertainty regarding the bioactive conformations of DPDPE and JOM-13, the conformation of the Phe3,4 side chain, Phe in these peptides was replaced by (3-MePhe (all four isomers). The results [70,71] clearly suggested that both peptides bind to the delta receptor... 

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