Effects of Substituting Disubstituted Amino Acids into the Amphipathic Cell Penetrating Peptide Pep-1.

Amphipathic cell-penetrating peptides based on the pep-1 sequence were synthesized by replacing the three hydrophilic glutamic acid residues with disubstituted, non-proteinogenic, hydrophobic amino acids. These substitutions facilitated maintenance of the peptides' secondary structure in a helical conformation, even in aqueous solution. Stability against enzymatic degradation was improved through the use of disubstituted amino acids. The resultant peptides exhibited high membrane permeability that remained relatively stable during prolonged incubation times. The results of this study indicate that the use of non-proteinogenic amino acids may be an effective approach to improve the cell membrane permeability for existing amphiphilic peptides.

Asymmetric 1,4-Addition Reactions Catalyzed by N-Terminal Thiourea-Modified Helical l-Leu Peptide with Cyclic Amino Acids.

N-terminal thiourea-modified l-Leu-based peptide {(3,5-diCF3 Ph)NHC(=S)-(l-Leu-l-Leu-Ac5 c)2 -OMe} with five-membered ring α,α-disubstituted α-amino acids (Ac5 c) catalyzed a highly enantioselective 1,4-addition reaction between ß-nitrostyrene and dimethyl malonate. The enantioselective reaction required only 0.5 mol % chiral peptide-catalyst in the presence of i Pr2 EtN (2.5 equiv.), and gave a 1,4-adduct with 93 % ee of an 85 % yield. As Michael acceptors, various ß-nitrostyrene derivatives such as methyl, p-fluoro, p-bromo, and p-methoxy substituents on the phenyl group, 2-furyl, 2-thiophenyl, and naphthyl ß-nitroethylenes could be applied. Furthermore, various alkyl malonates and cyclic ß-keto-esters could be used as Michael donors. It became clear that the length of the peptide chain, a right-handed helical structure, amide N-Hs, and the N-terminal thiourea moiety play crucial roles in asymmetric induction.

Synthesis of six-membered carbocyclic ring α,α-disubstituted amino acids and arginine-rich peptides to investigate the effect of ring size on the properties of the peptide.

Cell-penetrating peptides (CPPs) have been attracting attention as tools for intracellular delivery of membrane-impermeant functional molecules. Among the variety of CPPs that have been developed, many are composed of both natural and unnatural amino acids. We previously synthesized α,α-disubstituted α-amino acids (dAAs) containing a five-membered carbocyclic ring in its side chain and revealed the utility of dAAs for the development of novel CPPs. In the present study, we designed a six-membered carbocyclic ring dAA with an amino group on the ring and introduced it into arginine (Arg)-rich peptides to further investigate the value of dAAs for developing CPPs. We also assessed the effects of the size of the dAA carbocyclic ring on cellular uptake of dAA-containing peptides. The stability of the peptide's secondary structure and its membrane permeability were both greater in dAA-containing peptides than in an Arg nonapeptide. However, the number of carbon atoms in the dAA side chain ring had little effect. Nevertheless, these results show the utility of cyclic dAAs in the design of novel CPPs containing unnatural amino acids.

Effect of the powerful plasticity of the tert-butyl side chain on the conformational equilibrium of ascidiacyclamides.

Ascidiacyclamide [cyclo(-Ile1,5 -oxazoline2,6 -d-Val3,7 -thiazole4,8 -)2 ] is a cytotoxic cyclic peptide from ascidian. Through structural analyses using monosubstituted analogues (Xaa1 : Ala, 2-aminobutyric acid, Val, cyclohexylglycine, and phenylglycine), we previously demonstrated the conformational equilibrium between its square and folded forms. As the bulkiness of the Xaa1 residue side chain was reduced, spontaneous folding was promoted, and the cytotoxicity decreased accordingly. In the present study, five disubstituted analogues in which a tert-leucine residue (Tle) was incorporated at the 5-position of the abovementioned monosubstituted analogues were synthesized, after which their structures were analyzed using X-ray diffraction, circular dichroism (CD) spectral measurements, and 1 H NMR-based quantitative analysis. The side chains of the Tle and Ile residues are structural isomers of one another, and the Tle residue bearing the tert-butyl group can be expected to play a role as a building block. In fact, peptides incorporating Tle5 exhibited much less spontaneous folding than their Ile5 counterparts in both crystal and solution. Increases in enthalpy and entropy due to the tert-butyl group during the folding process resulted in increased conformational free energy (ΔG°). The powerful plasticity of the tert-butyl group would stabilize the square form relating with cytotoxicity.

An Ornithine-Free Gramicidin S Analogue Using Norleucine, Cyclo(Val-Nle-Leu-D-Phe-Pro)2, Forms Helically Aligned ß-Sheets.

The structure of an ornithine (Orn)-free Gramicidin S (GS) analogue, cyclo(Val-Nle-Leu-D-Phe-Pro)2 (NGS), was studied. Its circular dichroism (CD) spectrum showed that NGS has a structure similar to GS, though the value of [θ] indicated smaller ß-turn and sheet populations. This is probably because the Nle side chain could not form intramolecular hydrogen bonds stabilizing the sheet structure. The chemical shift perturbation of αH and JNH-αH were similar in GS and NGS. Three independent NGS molecules formed intramolecular ß-sheet structures in crystal. The turn structures of D-Phe-Pro moieties were classed as type II' ß-turns, but one part was unclassed. The molecules were arranged in a twisting manner, which resulted in the formation of a helical sheet. Similar structural characteristics were observed previously in a Leu-type, Orn-free GS analogue and in GS trifluoroacetic acid salt.

X-ray Crystallographic Structure of α-Helical Peptide Stabilized by Hydrocarbon Stapling at i,i + 1 Positions.

Hydrocarbon stapling is a useful tool for stabilizing the secondary structure of peptides. Among several methods, hydrocarbon stapling at i,i + 1 positions was not extensively studied, and their secondary structures are not clarified. In this study, we investigate i,i + 1 hydrocarbon stapling between cis-4-allyloxy-l-proline and various olefin-tethered amino acids. Depending on the ring size of the stapled side chains and structure of the olefin-tethered amino acids, E- or Z-selectivities were observed during the ring-closing metathesis reaction (E/Z was up to 8.5:1 for 17-14-membered rings and up to 1:20 for 13-membered rings). We performed X-ray crystallographic analysis of hydrocarbon stapled peptide at i,i + 1 positions. The X-ray crystallographic structure suggested that the i,i + 1 staple stabilizes the peptide secondary structure to the right-handed α-helix. These findings are especially important for short oligopeptides because the employed stapling method uses two minimal amino acid residues adjacent to each other.

Incorporation of ß-amino acids into ascidiacyclamides: Effects on conformation, cytotoxicity and interaction with copper (II) ion.

Seven ascidiacyclamide [cyclo(-Ile-oxazoline-d-Val-thiazole-)2 ] (ASC) analogues incorporating the ß-amino acids ßIle, ßoxazoline, and/or d-ßVal were synthesized. We then investigated the effects of the position and number of incorporated ß-amino acids on the structure, cytotoxicity, and copper binding by these seven analogues. The structural analyses revealed that both ßIle and d-ßVal favor a gauche-type θ torsion angles, while ßoxazoline favors a trans-type θ torsion angle. Expansion of the macrocycle by incorporation of ßIle or d-ßVal readily induced molecular folding. On the other hand, the incorporation of two ßoxazoline residues strongly extended the peptide conformation, and the incorporation of one was sufficient for the moderate restriction important for conformational equilibrium and cytotoxicity. Despite expansion of the macrocycles, the structure-cytotoxicity relationships were largely maintained. In studies of complexation of the analogues with Cu (II) ion, the position and number of incorporated ß-amino acids had a large impact on the structure of the metal complex and may contribute to its stabilization.

Ascidiacyclamides containing oxazoline and thiazole motifs assume square conformations and show high cytotoxicity.

Four cyclic octapeptides were designed from ascidiacyclamide [cyclo(-Ile-Oxz-D-Val- Thz-)2 ] (ASC, 1) to investigate the effects of oxazoline (Oxz) and thiazole (Thz) rings on the structures and cytotoxicities of the peptides. cyclo(-Ile-Thz-D-Val-Oxz-)2 (2) had the same number of Oxz and Thz rings as ASC, but the ring positions were switched. cyclo(-Ile-Oxz-D-Val-Thz-Ile-Thz-D-Val-Thz-) (3) and cyclo(-Ile-Thz-D-Val-Oxz-Ile-Thz-D-Val-Thz-) (4) contained one Oxz and three Thz rings within the molecule. All Oxz rings were substituted with Thz in cyclo(-Ile-Thz-D-Val-Thz-)2 (5). These analogues had new Oxz and Thz blocks forming the 24-membered ring. Based on CD spectra and X-ray diffraction analyses, the structures of all four analogues were classified as square ASC forms. But the structures of 2 and 5 differed from the original square form of 1, and they showed no cytotoxicity. The structure of 3 was very similar to that of 1, and 3 showed 10 times greater cytotoxicity than 1. Although no definite structure of 4 was obtained, it showed three times greater cytotoxicity than 1. It appears that the position and number of Oxz residues are essential determinants in the structure-cytotoxicity relationship of ASC analogues.

Helical Structures of Cyclopentene-based α,α-Disubstituted α-Amino Acid Homopeptides.

The cyclopentene-based α,α-disubstituted α-amino acid Ac5c= and its homopeptides, up to nonapeptides, were synthesized. The side-chain cyclopentene was expected to become symmetric, the Cα-carbon to be puckered, and other Cß, Cß', Cγ, Cγ'-carbons to be coplanar. As expected, side-chain cyclopentene conformations became symmetric and Cα-carbons were puckered. Conformational studies using FT-IR absorption, 1H NMR spectra, and X-ray crystallographic analyses revealed that Ac5c= homopeptides did not form a planar conformation, but assumed a 310-helical structure, similar to cyclopentane-based α,α-disupstituted α-amino acid homopeptides.

Diastereomeric Right- and Left-Handed Helical Structures with Fourteen (R)-Chiral Centers.

The relationship between chiral centers and the helical-screw control of their peptides has already been reported, but it has yet to be elucidated in detail. A chiral four-membered ring α,α-disubstituted α-amino acid with a (R,R)-butane-2,3-diol acetal moiety at the γ-position, but no α-chiral carbon, was synthesized. X-ray crystallographic analysis unambiguously revealed that its homo-chiral heptapeptide formed right-handed (P) and left-handed (M) 310 -helical structures at a ratio of 1:1. They appeared to be enantiomeric at the peptide backbone, but diastereomeric with fourteen (R)-configuration chiral centers. Conformational analyses of homopeptides in solution also indicated that diastereomeric (P) and (M) helices existed at approximately equal amounts, with a slight preference toward right-handedness, and they quickly interchanged at room temperature. The circumstances of chiral centers are important for the control of their helical-screw direction.

Low pH-triggering changes in peptide secondary structures.

We developed a novel methodology using cyclic α,α-disubstituted α-amino acids (dAAs) with an acetal-side chain to control peptide secondary structures. The introduction of cyclic dAAs into peptides contributed to the stabilization of peptide secondary structures as a helix, while an acidic treatment of peptides resulted in a marked conformational change.

Conformational properties of ascydiacyclamide analogues with cyclic α-amino acids instead of oxazoline residues.

Ascidiacyclamide [ASC, cyclo(-Ile-oxazoline-d-Val-thiazole-)2] is a cyclic octapeptide isolated from tunicates. We designed ASC analogues [cyclo(-Ile-Xxx-d-Val-thiazole-)2] in which Pro or a homologue was substituted for oxazoline: [Pro]ASC (Xxx: proline), [Aze]ASC (Xxx: (S)-Azetidine-2-carboxylic acid), [Pip]ASC (Xxx: (S)-Piperidine-2-carboxylic acid) and [ΔPro]ASC (Xxx: (S)-3-pyrroline-2-carboxylic acid) to explore their potential to serve as substitutes for the oxazoline ring. The conformations of these analogues were examined using X-ray diffraction, 1H NMR and CD spectroscopy. In both the crystal and solution states, the conformations of [Pro]ASC, [Aze]ASC and [ΔPro]ASC were novel square structures having two trans imide bonds and stabilized by two intramolecular hydrogen bonds. The crystal structure of [Pip]ASC was a folded conformation with cis and trans imide bonds. Three isomers (cc, ct and tt) were present in a solution of [Pip]ASC. From crystal structures, the degree of puckering in the side chains of Pro and its homologues was estimated to be in the order Pip > Pro > Aze > ΔPro. [Pro]ASC and [Pip]ASC showed strong cytotoxicity, but [Aze]ASC and [ΔPro]ASC showed no cytotoxicity. Among the four analogues, there is consistency between the prolyl ring puckering and cytotoxicity, but not between the peptide backbone structure and cytotoxicity.

Conformational studies on peptides having dipropylglycine (Dpg) or 1-aminocycloheptanecarboxylic acid (Ac7 c) within the sequence of l-leucine (Leu) residues.

A conformational analysis of peptides having dipropylglycine (Dpg) or 1-aminocycloheptanecarboxylic acid (Ac7 c) within l-leucine (Leu) residues was conducted in solution and in a crystal state. Dpg and Ac7 c had similar structures with acyclic and cyclic side chains, respectively. FTIR, 1 H NMR, and CD spectra measurements revealed that the preferred conformations of Dpg- and Ac7 c-containing l-Leu peptides in solution were similar; both had a right-handed (P) 310 -helix. The Dpg-containing octapeptide adopted a right-handed (P) α-helix in the crystal state. Dpg and Ac7 c homopeptides had planar and helical structures as their preferred conformations, respectively; however, Dpg- and Ac7 c-containing l-Leu peptides adopted similar structures in solution. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 210-218, 2016.

The side-chain hydroxy groups of a cyclic α,α-disubstituted α-amino acid promote oligopeptide 310 -helix packing in the crystalline state.

A single chiral cyclic α,α-disubstituted amino acid with side-chain methoxymethyl (MOM) protecting groups, (3S,4S)-1-amino-(3,4-dimethoxymethoxy)cyclopentanecarboxylic acid [(S, S)-Ac5 c(dOMOM) ], or side-chain hydroxy groups, (3S,4S)-1-amino-(3,4-dihydroxy)cyclopentanecarboxylic acid [(S, S)-Ac5 c(dOH) ], was attached to the N-terminal or C-terminal position of α-aminoisobutyric acid (Aib) tetrapeptide segments; i.e., we designed and synthesized four pentapeptides, Cbz-[(S, S)-Ac5 c(dOMOM) ]-(Aib)4 -OEt (1), Cbz-[(S, S)-Ac5 c(dOH) ]-(Aib)4 -OEt (2), Cbz-(Aib)4 -[(S, S)-Ac5 c(dOMOM) ]-OMe (3), and Cbz-(Aib)4 -[(S, S)-Ac5 c(dOH) ]-OMe (4). We then analyzed the peptides' structures in the crystalline state. The four peptides all folded into 310 -helical structures; 1 formed a left-handed (M) 310 -helix, 2 formed a mixture of right-handed (P) and (M) 310 -helices, 3 formed a mixture of (P) and (M) 310 -helices, and 4 formed a (P) 310 -helix, respectively. In packing mode, the molecules of peptides 1 and 3, which both possessed an Ac5 c(dOMOM) residue, were connected by intermolecular hydrogen bonds along the peptide backbone (NH···O type). On the other hand, the packing of peptides 2 and 4, which both contained an Ac5 c(dOH) residue, was based on intermolecular hydrogen bonds derived from both the peptide backbone and the side-chain hydroxy groups of the amino acid Ac5 c(dOH) (OH···O type). © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 757-768, 2016.

Synthesis of chiral five-membered carbocyclic ring amino acids with an acetal moiety and helical conformations of its homo-chiral homopeptides.

Chiral five-membered carbocyclic ring amino acids bearing various diol acetal moieties were synthesized starting from l-malic acid, and homo-chiral homopeptides composed of cyclic amino acid (S)-Ac5 c(3EG) bearing an ethylene glycol acetal, up to an octapeptide, were prepared. A conformational analysis revealed that (S)-Ac5 c(3EG) homopeptides formed helical structures. (S)-Ac5 c(3EG) homopeptides, up to hexapeptides, formed helical structures without controlling the helical screw direction, while (S)-Ac5 c(3EG) hepta- and octapeptides formed helical structures with a preference for the left-handed (M) helical-screw direction. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 555-562, 2016.

Helical-Peptide-Catalyzed Enantioselective Michael Addition Reactions and Their Mechanistic Insights.

Helical peptide foldamer catalyzed Michael addition reactions of nitroalkane or dialkyl malonate to α,ß-unsaturated ketones are reported along with the mechanistic considerations of the enantio-induction. A wide variety of α,ß-unsaturated ketones, including ß-aryl, ß-alkyl enones, and cyclic enones, were found to be catalyzed by the helical peptide to give Michael adducts with high enantioselectivities (up to 99%). On the basis of X-ray crystallographic analysis and depsipeptide study, the amide protons, N(2)-H and N(3)-H, at the N terminus in the α-helical peptide catalyst were crucial for activating Michael donors, while the N-terminal primary amine activated Michael acceptors through the formation of iminium ion intermediates.

Conformational transformation of ascidiacyclamide analogues induced by incorporating enantiomers of phenylalanine, 1-naphthylalanine or 2-naphthylalanine.

We designed five ascidiacyclamide analogues [cyclo(-Xxx(1) -oxazoline(2) -d-Val(3) -thiazole(4) -l-Ile(5) -oxazoline(6) -d-Val(7) -thiazole(8) -)] incorporating l-1-naphthylalanine (l-1Nal), l-2-naphthylalanine (l-2Nal), d-phenylalanine (d-Phe), d-1-naphthylalanine (d-1Nal) or d-2-naphthylalanine (d-2Nal) into the Xxx(1) position of the peptide. The conformations of these analogues were then examined using (1) H NMR, CD spectroscopy, and X-ray diffraction. These analyses suggested that d-enantiomer-incorporated ASCs [(d-Phe), (d-1Nal), and (d-2Nal)ASC] transformed from the folded to the open structure in solution more easily than l-enantiomer-incorporated ASCs [(l-Phe), (l-1Nal), and (l-2Nal)ASC]. Structural comparison of the two analogues containing isomeric naphthyl groups showed that the 1-naphthyl isomer induced a more stable open structure than the 2-naphthyl isomer. In particular, [d-1Nal]ASC showed the most significant transformation from the folded to the open structure in solution, and exhibited the strongest cytotoxicity toward HL-60 cells.

A dimer model of human calcitonin13-32 forms an α-helical structure and robustly aggregates in 50% aqueous 2,2,2-trifluoroethanol solution.

Determining the cause of human calcitonin (hCT) aggregation could be of help in the effort to utilize hCT for treatment of hypercalcemia. Here we report that a dimer model of hCT13-32 aggregated to a greater degree than native hCT under aqueous 2,2,2-trifluoroethanol conditions. Analyses using circular dichroism spectroscopy, thioflavine-T binding assays and atomic force microscopy suggest that the α-helical portion of hCT is important for initiation of the aggregation process, which yields long fibrils. Dimerization, which stabilizes the ß-sheet structure of hCT, enhances aggregation potency. Dimerization of hCT stabilizes the α-helix under aqueous TFE conditions, leading to the long fibril formation. Up to now, there have been no reports of using a dimer model to investigate the properties of hCT aggregation. Our findings could potentially serve as the basis for development of novel hCT derivatives that could be utilized for treatment of hypercalcemia, as well as for development of novel therapeutics for other ailments caused by amyloid peptides. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

Topological Study of the Structures of Heterochiral Peptides Containing Equal Amounts of l-Leu and d-Leu.

We designed and synthesized two dodecapeptides, Boc-(l-Leu-l-Leu-Aib-d-Leu-d-Leu-Aib)2-OMe (5) and Boc-l-Leu-l-Leu-Aib-(d-Leu-d-Leu-Aib)2-l-Leu-l-Leu-Aib-OMe (6), that contain equal amounts of l-Leu, d-Leu, and achiral Aib residues. The conformations of peptides 5 and 6 in the crystalline state were studied using X-ray crystallographic analysis. Peptide 5 formed a left-handed (M) α-helical structure, whereas peptide 6 was composed of a combination of fused (M) α-helical and right-handed (P) 310-helical structures. In solution, roughly equivalent amounts of (P) and (M) helices were present in 5, whereas the (M) α-helix was present in 6 as its dominant conformation.

Effects of D-Leu residues on the helical secondary structures of L-Leu-based nonapeptides.

The influence of D-Leu residues on the helical structures of L-Leu-based-nonapeptides was investigated. Specifically, the preferred conformations of four diastereomeric nonapeptides, Boc-(L-Leu-L-Leu-Aib)3-OMe (1); Boc-(L-Leu-L-Leu-Aib)2-L-Leu-D-Leu-Aib-OMe (2), which contained one D-Leu residue; Boc-L-Leu-D-Leu-Aib-L-Leu-L-Leu-Aib-L-Leu-D-Leu-Aib-OMe (3), which contained two D-Leu residues; and Boc-(L-Leu-D-Leu-Aib)3-OMe (4), were analyzed in solution and in the crystalline state. Peptide 1 formed a right-handed (P) 310-helix in solution. Peptides 2 and 3 both formed (P) 310-helices in solution and (P) α-helices in the crystalline state. Peptide 4 formed a (P) α-helix both in solution and in the crystalline state.