Solid-supported synthesis of a peptide beta-turn mimetic

[structure: see text]The solid-supported synthesis of a bicyclic diketopiperazine, a potential peptide beta-turn mimetic, is described. The Ugi reaction between the resin ester of alpha-N-Boc-diaminopropionic acid (an amine input), alpha-bromo acid, aldehyde, and isocyanide is the key step in the proposed protocol.     

Stereoselective synthesis of novel dipeptide beta-turn mimetics targeting melanocortin peptide receptors

[reaction: see text] The novel dipeptide beta-turn mimetic, 4,8-disubstituted azabicyclo[4.3.0]nonane amino acid ester (15), has been synthesized to serve as a peptide mimetic of the dipeptide Phe-Arg, which contains two important pharmacophore elements in melanotropin peptides. Introduction of side-chain functionality at C-8 was achieved by using beta-functionalized pyroglutamate (8) as a synthetic precursor. The side chain at C-4 was introduced by bromination of dehydroamino acid intermediate (10) followed by Suzuki cross-coupling.     

A minimal peptide scaffold for beta-turn display: optimizing a strand position in disulfide-cyclized beta-hairpins.

Phage display of peptide libraries has become a powerful tool for the evolution of novel ligands that bind virtually any protein target. However, the rules governing conformational preferences in natural peptides are poorly understood, and consequently, structure-activity relationships in these molecules can be difficult to define. In an effort to simplify this process, we have investigated the structural stability of 10-residue, disulfide-constrained beta-hairpins and assessed their suitability as scaffolds for beta-turn display. Using disulfide formation as a probe, relative free energies of folding were measured for 19 peptides that differ at a one strand position. A tryptophan substitution promotes folding to a remarkable degree. NMR analysis confirms that the measured energies correlate well with the degree of beta-hairpin structure in the disulfide-cyclized peptides. Reexamination of a subset of the strand substitutions in peptides with different turn sequences reveals linear free energy relationships, indicating that turns and strand-strand interactions make independent, additive contributions to hairpin stability. Significantly, the tryptophan strand substitution is highly stabilizing with all turns tested, and peptides that display model turns or the less stable C'-C' ' turn of CD4 on this tryptophan "stem" are highly structured beta-hairpins in water. Thus, we have developed a small, structured beta-turn scaffold, containing only natural L-amino acids, that may be used to display peptide libraries of limited conformational diversity on phage.     

Reversible photocontrol of peptide conformation with a rhodopsin-like photoswitch

Reversible photocontrol of biomolecules requires chromophores that can efficiently undergo large conformational changes upon exposure to wavelengths of light that are compatible with living systems. We designed a benzylidene-pyrroline chromophore that mimics the Schiff base of rhodopsin and can be used to introduce light-switchable intramolecular cross-links in peptides and proteins. This new class of photoswitch undergoes an ~10 ? change in end-to-end distance upon isomerization and can be used to control the conformation of a target peptide efficiently and reversibly using, alternately, violet (400 nm) and blue (446 nm) light.     

Bidirectional photocontrol of peptide conformation with a bridged azobenzene derivative

It goes both ways: A thiol-reactive cross-linker based on a bridged azobenzene derivative permits photoreversible control of peptide conformation on irradiation with violet (407?nm) and green (500-550?nm) light (see picture) through isomerization of the cross-linker. The large separation of the absorbance bands of the cis (yellow) and trans (red) isomers enables complete bidirectional photoswitching.     

Solid-supported synthesis of putative peptide beta-turn mimetics via Ugi reaction for diketopiperazine formation

The scope and limitations of the solid-supported synthesis of a bicyclic diketopiperazine, an internal, putative peptide beta-turn mimetic, are presented. The 4CC multicomponent Ugi reaction of alpha-N-Boc-diaminopropionic acid resin ester (an amine input), optically active alpha-bromoacid, aldehyde, and isocyanide is the key step in the proposed synthetic protocol. Application of cyclitive cleavage as the final step led to desired products in high purity.     

The vicinal F-C-C-F moiety as a tool for influencing peptide conformation

Diastereoisomers of bis(amino acid amides) of 2,3-difluorosuccinic acid have been prepared and the erythro- and threo-isomers display very different conformations.     

Synthesis of a novel cis-proline-derived cyclic type VI beta-turn mimic via ring-closing metathesis

A cis-proline derived cyclic mimic of a type VI beta-turn is synthesized via a ring-closing metathesis reaction. The solution NMR conformational study indicates that the major conformer of the cyclic peptide adopts a type VIa beta-turn in CDCl(3) and a type VIb beta-turn in DMSO-d(6).     

A novel di-triazole based peptide as a highly sensitive and selective fluorescent chemosensor for Zn2+ ions

A di-triazole based peptide has been synthesised by copper catalyzed Huisgen cycloaddition. Fluorescence intensity is enhanced selectively in the presence of Zn(2+), which is ascribed to reversal of photoelectron transfer. Compound 7 was found to self-assemble in the presence of Zn(ClO(4))(2) in an exclusive 2:1 ratio, which is supported by (1)H NMR titration and mass spectral data. The fluorescence intensity of 7 shows a subsequent ON-OFF phenomenon upon repetitive and alternate addition of Zn(ClO(4))(2) and HClO(4).     

A novel conformation optimization model and algorithm for structure-based drug design

In this paper, we present a multi-scale optimization model and an entropy-based genetic algorithm for molecular docking. In this model, we introduce to the refined docking design a concept of residue groups based on induced-fit and adopt a combination of conformations in different scales. A new iteration scheme, in conjunction with multi-population evolution strategy, entropy-based searching technique with narrowing down space and the quasi-exact penalty function, is developed to address the optimization problem for molecular docking. A new docking program that accounts for protein flexibility has also been developed. The docking results indicate that the method can be efficiently employed in structure-based drug design.     

Prediction of peptide conformation using a scale-transformed entropy sampling algorithm

An algorithm for predicting the lowest energy structure of a peptide has been developed. High-energy barriers on an energy surface can be easily overcome by logarithmically transforming the energy space. For efficient optimizations, the energy space is searched using a scale-transformed entropy sampling method, and conformations specific to a primary structure of the peptide are sampled with large weights. The efficiency of the present method is demonstrated by calculations on cholecystokinin octapeptide (CCK-8).     

Callynormine A, a new marine cyclic peptide of a novel class

[structure: see text] A novel cyclic peptide, callynormine A, was isolated from the Kenyan marine sponge Callyspongia abnormis and its structure elucidated by interpretation of its NMR data and X-ray diffraction analysis. Callynormine A represents a new class of heterodetic cyclic peptides (designated endiamino peptides) possessing an alpha-amido-beta-aminoacrylamide cyclization functionality.     

Synthesis of novel polyethers in a geometrically precise conformation

[reaction: see text] A convergent design for the preparation of a polyoxyethylene-based channel molecule is presented, and the synthesis of the key unit 2 required for the projected construction is described. The essential elements of the design included face to face oriented macrorings spaced by rigid trans-fused oxanes. The strategy combines conformational predictability of C-linked oxanyl systems and ring-closing metathesis for the synthesis of crown ethers with engineerable ion-binding abilities.     

A novel fluorescent probe with a large stokes shift for cysteine based on dicyanoisophorone

In this work, a dicyanoisophorone-based turn-on fluorescent probe, DCIP, for highly selective and sensitive detection of cysteine was designed based on nucleophilic substitution mechanism. Moreover, compared with typical cysteine probes, DCIP showed great selectivity and sensitivity for cysteine over other amino acids including the similar structured homocysteine (Hcy) and glutathione (GSH). Further, the detection limit toward cysteine was calculated to be as low as 0.70?μM. In addition, the utility of DCIP as a bioanalytical molecular tool was demonstrated by fluorescence imaging of biothiols in living cells.     

A novel scoop-shaped conformation of C-methylcalix[4]resorcinarene in a bilayer structure

A new scoop-shaped conformation of C-methylcalix[4]resorcinarene has been identified; it is a hybrid of the previously observed crown- and flattened cone conformations.