Alpha-gamma hybrid peptides that contain the conformationally constrained gabapentin residue: characterization of mimetics of chain reversals

The crystal structures of four dipeptides that contain the stereochemically constrained gamma-amino acid residue gabapentin (1-(aminomethyl)cyclohexaneacetic acid Gpn) are described. The molecular conformation of Piv-Pro-Gpn-OH (1), reveals a beta-turn mimetic conformation, stabilized by a ten atom C[bond]H...O hydrogen bond between the Piv CO group and the pro S hydrogen of the Gpn CH(2)[bond]CO group. The peptides Boc-Gly-Gpn-OH (2), Boc-Aib-Gpn-OH (3), and Boc-Aib-Gpn-OMe (4) form compact, folded structures, in which a distinct reversal of polypeptide chain direction is observed. In all cases, the Gpn residue adopts a gauche,gauche (g,g) conformation about the C(gamma)[bond]C(beta) (theta(1)) and C(beta)[bond]C(alpha) (theta(2)) bonds. Two distinct Gpn conformational families are observed. In peptides 1 and 3, the average backbone torsion angle values for the Gpn residue are phi=98 degrees, theta(1)=-62 degrees, theta(2)=-73 degrees, and psi=79 degrees, while in peptide 2 and 4 the average values are phi=-103 degrees, theta(1)=-46 degrees, theta(2)=-49 degrees, and psi=-92 degrees. In the case of 1 and 3, an intramolecular nine-membered O[bond]H...O hydrogen bond is formed between the C[double bond]O of the preceding residue and the terminal carboxylic acid OH group. All four alpha-gamma dipeptide sequences yield compact folded backbone conformations; this suggests that the Gpn residue may be employed successfully in the design of novel folded structures.     

A new triferrocenyl-tris(hydroxymethyl)aminomethane derivative as a highly sensitive electrochemical marker of biomolecules: application to the labelling of PNA monomers and their electrochemical characterization

We have designed and synthesised a new organometallic molecule containing three ferrocene groups for use as a highly sensitive electrochemical marker in biological assays. This trisferrocene derivative was conjugated to different PNA monomers, and the electrochemical activities of the conjugates were extensively investigated in organic solvents, in view of their potential diagnostic applications. The results showed that the introduction of a trisferrocene unit on the PNA monomer triples the current signal in comparison with the monoferrocene-labelled one. Despite their greater molecular complexity, trisferrocene-conjugated PNA monomers are even more electrochemically active than the reference ferrocene. By using differential pulse voltammetry (DPV), the detection limit can reach 10(-8) M in acetonitrile solution. These results are a good premise for the use of the trisferrocene unit as an effective electrochemical probe for biomolecules.     

The synthesis,structural characterization and biological evaluation of N‐(ferrocenylmethyl amino acid) fluorinated benzene‐carboxamide derivatives as potential anticancer agents

A series of N‐(ferrocenylmethyl amino acid) fluorinated benzene‐carboxamide derivatives 4b , 4c , 4d , 4e , 4f , 4g , 4h , 4i and 5b , 5c , 5d , 5e , 5f , 5g , 5h , 5i have been synthesized by coupling ferrocenylmethyl amine 3 with various substituted N‐(fluorobenzoyl) amino acid derivatives using the standard N‐(3‐dimethylaminopropyl)‐N′‐ethylcarbodiimide hydrochloride, 1‐hydroxybenzotriazole protocol. The amino acids employed in this study were glycine and L‐alanine. All of the compounds were fully characterized using a combination of ¹H NMR, ¹³C NMR, ¹⁹F NMR, distortionless enhancement by polarization transfer (DEPT)‐135, ¹H–¹H correlation spectroscopy (COSY) and ¹H–¹³C COSY (heteronuclear multiple‐quantum correlation) spectroscopy. The compounds were biologically evaluated on the oestrogen‐positive MCF‐7 breast cancer cell line. Compounds 4g , 4i , 5h and 5i exhibited cytotoxic effects on the MCF‐7 breast cancer cell line. N‐(Ferrocenylmethyl‐L‐alanine)‐3,4,5‐trifluorobenzene‐carboxamide ( 5h ) was the most active compound, with an IC₅₀ value of 2.84 μm . Compounds 4i , 5h and 5i had lower IC₅₀ values than that found for the clinically employed anticancer drug cisplatin (IC₅₀ = 16.3 μm against MCF‐7). Guanine oxidation studies confirmed that 5h was capable of generating oxidative damage via a reactive oxygen species‐mediated mechanism. Copyright © 2013 John Wiley & Sons, Ltd.     

A Designed Three‐Stranded β‐Sheet in an α/β Hybrid Peptide

The incorporation of β‐amino acid residues into the antiparallel β‐strand segments of a multi‐stranded β‐sheet peptide is demonstrated for a 19‐residue peptide, Boc‐LV^βFV^DPGL^βFVVL^DPGLVL^βFVV‐OMe (BBH19). Two centrally positioned ^DPro–Gly segments facilitate formation of a stable three‐stranded β‐sheet, in which β‐phenylalanine (^βPhe) residues occur at facing positions 3, 8 and 17. Structure determination in methanol solution is accomplished by using NMR‐derived restraints obtained from NOEs, temperature dependence of amide NH chemical shifts, rates of H/D exchange of amide protons and vicinal coupling constants. The data are consistent with a conformationally well‐defined three‐stranded β‐sheet structure in solution. Cross‐strand interactions between ^βPhe3/^βPhe17 and ^βPhe3/Val15 residues define orientations of these side‐chains. The observation of close contact distances between the side‐chains on the N‐ and C‐terminal strands of the three‐stranded β‐sheet provides strong support for the designed structure. Evidence is presented for multiple side‐chain conformations from an analysis of NOE data. An unusual observation of the disappearance of the Gly NH resonances upon prolonged storage in methanol is rationalised on the basis of a slow aggregation step, resulting in stacking of three‐stranded β‐sheet structures, which in turn influences the conformational interconversion between type I′ and type II′ β‐turns at the two ^DPro–Gly segments. Experimental evidence for these processes is presented. The decapeptide fragment Boc‐LV^βFV^DPGL^βFVV‐OMe (BBH10), which has been previously characterized as a type I′ β‐turn nucleated hairpin, is shown to favour a type II′ β‐turn conformation in solution, supporting the occurrence of conformational interconversion at the turn segments in these hairpin and sheet structures.     

Cyclic peptides containing a δ-sugar amino acid—synthesis and evaluation as artificial receptors

An Fmoc-protected δ-sugar amino acid, prepared by oxidation of a glucosamine derivative, was coupled to three different tripeptide tert-butyl esters (H-Tyr-Tyr-Tyr-O^tBu, H-Tyr-Glu(OBzl)-Tyr-O^tBu and H-Tyr-Arg(Mtr)-Tyr-O^tBu) and the resulting sugar amino acid/amino acid hybrids were transformed into dimers that were subsequently cyclized to give three C₂-symmetric macrocycles. The macrocycles were deprotected and their binding properties towards p-nitrophenyl glycosides, nucleotides, and purines were examined. Of the ligands screened, only some of the purines showed weak, but significant, binding.     

Supramolecular helical fluid columns from self-assembly of homomeric dipeptides

Herein, we demonstrate that with the widespread theme of residue patterning and stereochemical restraints of self-complimenting proteinogenic amino acids, a new and rich class of homomeric dipeptides exhibiting two-dimensional fluid aggregates with hierarchical ordering can be obtained. In particular, a simple way of achieving a class of functional dipeptides, wherein the first and the second residues chosen are L-/D-alanines and L-/D-leucines, has been accomplished. The supramolecules synthesized can be regarded as intermediates between polycatenars and taper-shaped amphiphiles because they possess two lipophilic segments interlinked by a peptide unit (spacer). Two pairs of enantiomers and their respective diastereomers derived from these amino acids are evidenced to self-organize into a helical columnar phase through hydrogen bonding by means of FTIR, UV/Vis, and chiroptical circular dichroism (CD) spectral analyses as well as by optical, calorimetric, electrical switching, and X-ray studies. The CD and X-ray studies have revealed that the form chirality (handedness) and the magnitude of out-of-plane fluctuations of the lattice planes of the fluid supramolecular columnar structures are solely directed by the stereochemistry encoded in the spacer. Of special significance, the less frequently found oblique helical columnar phase formed by a pair of enantiomers derived from L-/D-alanines, unlike those derived from other amino acids, exhibit ferroelectric behavior; the measured spontaneous polarization is as high as 440 nC cm(-2). Besides, all these supramolecules form stable organogels in ethanol and the CD and SEM studies on a representative gel suggest the presence of helical structures.     

Hybrid peptides: expanding the beta turn in peptide hairpins by the insertion of beta-, gamma-, and delta-residues

The beta turn segment in designed peptide hairpins has been expanded by the insertion of beta-, gamma- and delta-amino acids at the i+2 position. The model octapeptides Boc-Leu-Phe-Val-DPro-Ac6c-Leu-Phe-Val-OMe (1), Boc-Leu-Phe-Val-DPro-beta3-Ac6c-Leu-Phe-Val-OMe (2), and Boc-Leu-Phe-Val-DPro-Gpn-Leu-Phe-Val-OMe (3) have been shown to adopt beta hairpin conformations in methanol by the observation of key diagnostic nuclear Overhauser effects. Boc-Leu-Val-Val-DPro-delta-Ava-Leu-Val-Val-OMe (4) adopts a beta hairpin conformation in crystals; this is stabilized by three cross-strand hydrogen bonds as demonstrated by X-ray diffraction. The canonical C10 turn in an alpha-alpha segment is expanded to C11, C12, and C13 turns in alpha-beta, alpha-gamma, and alpha-delta segments, respectively. The crystal structures of Piv-LPro-beta3-Ac6c-NHMe (5) and Boc-Ac6c-Gpn-Ac6c-OMe (6) reveal intramolecularly hydrogen-bonded C11 and C12 conformations, respectively. Computer modeling of octapeptide sequences that contain centrally positioned hybrid-turn segments, by using turn parameters derived from the structures of peptides 5 and 6, establishes the stereochemical acceptability of the beta hairpins in the cases of peptides 2 and 3. Accommodation of omega-amino acids into the turn segments is achieved by the adoption of gauche conformations around the backbone C--C bonds.     

A cyclic hexapeptide comprising alternating alpha-aminoxy and alpha-amino acids is a selective chloride ion receptor

In nonpolar solvents, the cyclic hexapeptide 2, which comprises alternating D-alpha-amino and D-alpha-aminoxy acids, adopts a C3-symmetric conformation with alternating eight (N--O turns)- and seven (gamma turns)-membered-ring hydrogen bonds. A series of anion-binding studies has suggested that 2 can function as an effective anion receptor that not only displays a high selectivity for chloride ions, but also the capability to extract chloride ions from aqueous solutions into organic phases.     

4-Amino-1-oxyl-2,2,6,6-tetramethylpiperidine-3-carboxylic acid (β-TOAC), the first spin-labelled, cyclic, chiral β-amino acid resolved in an enantiomerically pure state

Amination of 3-carboxymethyl-1-oxyl-2,2,6,6-tetramethyl-4-piperidone with (R)-α-methylbenzylamine, NaBH₃CN reduction of the resulting enamine and removal of the chiral auxiliary from the separated diastereoisomers, led to enantiomerically pure (3S,4S) and (3R,4R) methyl 4-amino-1-oxyl-2,2,6,6-tetramethylpiperidine-3-carboxylates.     

Synthesis and structural studies of peptides containing a glucose-derived furanoid sugar amino acid

Conformational analysis of peptides containing a glucose-derived furanoid sugar amino acid (Gaa) by detailed NMR and constrained MD studies revealed that peptides with repeating Gaa-Leu-Val units had conformational signatures very similar to those of linear homooligomers of Gaa.     

Di-oxanipecotic acids as more stable turn motifs than di-nipecotic acids

The folded structures of peptidomimetics containing dimers of oxanipecotic acid (Oxa) in loop segments were characterized and compared with those of the corresponding nipecotic acid (Nip)-based ones. According to structural studies using FT-IR and NMR spectroscopies, di-oxanipecotic acid adopted more stable turn conformations than di-nipecotic acid, and for tetramers, L,(S)-Oxa,(S)-Oxa,L and L,(S)-Oxa,(R)-Oxa,L formed hairpin-like structures but only L,(R)-Nip,(S)-Nip,L promoted the stable folded conformations.     

Development and validation of force-field parameters for molecular simulations of peptides and proteins containing open-shell residues

Parameters suitable for extending the AMBER force field for nucleic acids and proteins to open-shell derivatives of amino acid residues are proposed and tested. Two new atom types (radical carbon [CE] and hydrogen directly bonded to it [HE]) are introduced, whose parameters have been determined by a best fitting of quantum-mechanical computations of the simplest analogue of glycine radical (GlyR) in a peptide. The new force field is able to fit the reference results concerning both the structural parameters and the relative stabilities of the different conformers. It has been next applied to a conformational study of the distortions induced by extraction of the glycine H^α atom in an initially helical structure of a dodecamer of alanine including a central glycine residue. Our results show that the helical structure corresponds to a local energy minimum, but deeper minima are found which correspond to a fully planar GlyR residue included in a distorted helical sequence. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1720–1728, 1997