E-Selective Ring-Closing Metathesis in α-Helical Stapled Peptides Using Carbocyclic α,α-Disubstituted α-Amino Acids.

We present an E-selective ring-closing metathesis reaction in α-helical stapled peptides at positions i and i + 4. The use of two chiral carbocyclic α,α-disubstituted α-amino acids, (1S,3S)-Ac5c3OAll and (1R,3S)-Ac5c3OAll, provides a high E-selectivity of a ≤59:1 E:Z ratio, while mixtures with E:Z ratios of 2.1-0.5:1 were produced with standard acyclic (S)-(4-pentenyl)alanine amino acids. A stapled octapeptide composed of (1S,3S)- and (1R,3S)-Ac5c3OAll amino acids showed a right-handed α-helical crystal structure.

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.

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.

Left-Handed Helix of Three-Membered Ring Amino Acid Homopeptide Interrupted by an N-H···Ethereal O-Type Hydrogen Bond.

A chiral three-membered ring Cα,α-disubstituted α-amino acid ( R, R)-Ac3cdMOM, in which the α-carbon is not a chiral center, but two side chain ß-carbons are chiral centers, was synthesized from dimethyl l-(+)-tartrate, and its homopeptides were prepared. X-ray crystallographic analysis of ( R, R)-Ac3cdMOM pentapeptide showed bent left-handed ( M) 310-helical structures with an unusual intramolecular hydrogen bond of the N-H···O (ethereal) type. The left-handedness of the bent helices was exclusively controlled by the side-chain ß-carbon chiral centers.

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.

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-foldamers having a chiral five-membered ring amino acid with two azido functional groups.

A chiral five-membered ring α,α-disubstituted α-amino acid (R,R)-Ac5c(dN3) having two azido functional groups has been designed and synthesized. The cyclic amino acid (R,R)-Ac5c(dN3) could be efficiently converted into several cyclic amino acids with various two 1,2,3-triazole functional groups. (R,R)-Ac5c(dN3) homochiral peptides (up to hexapeptide) and (R,R)-Ac5c(dN3)-containing l-Leu-based peptides were prepared, and their conversion of azido functional groups into triazole groups was completed. The preferred conformation of oligomers, before and after the "click reaction", together with the azido gauche effect of amino acid residues were studied using FT-IR absorption, CD, (1)H NMR, and X-ray crystallographic analysis. The cyclic amino acid (R,R)-Ac5c(dN3) could be used as a helical conformation controlling residue and also has a versatile functionalizing site in its oligopeptides.

Modulating the structure of phenylalanine-incorporated ascidiacyclamide through fluorination.

We designed four fluorinated Phe-incorporated ascidiacyclamide ([Phe]ASC) analogs, (cyclo(-Xxx1-oxazoline2-D-Val3-thiazole4-Ile5-oxazoline6-D-Val7-thiazole8-)), [(4-F)Phe]ASC (Xxx1: 4-fluorophenylalanine), [(3,5-F2)Phe]ASC (Xxx1: 3,5-difluorophenylalanine), [(3,4,5-F3)Phe]ASC (Xxx1: 3,4,5-trifluorophenylalanine) and [(F5)Phe]ASC (Xxx1: pentafluorophenylalanine), to modulate the π-electron density of the aromatic ring of the Phe residue. X-ray diffraction analysis, ¹H NMR and CD spectra all suggested that the interactions between the benzene ring of the Xxx1 residue and the alkyl groups of oxazoline2 contribute to the stability of the folded structure of these analogs. Substituting fluorines for the hydrogens progressively weakened those interactions through reducing the π-electron density, thereby mediating transformation from the folded to square structure. As a result, [(F5)Phe]ASC preferred the square form more than the other analogs did. Also contributing to the preference for the square form may be the hindrance of the rotation around the Cα-Cß bond by the two ortho-fluoro substituents of [(F5)Phe]ASC. These findings demonstrate that the structure of ASC can be modulated by using fluorine as an electron-withdrawing group.

Bio-imaging of hydroxyl radicals in plant cells using the fluorescent molecular probe rhodamine B hydrazide, without any pretreatment.

Rhodamine B hydrazide can be used to detect hydroxyl radicals in plant cells. RBH was easily inserted into plant cells without any pretreatment, and specifically reacted with intracellular hydroxyl radicals produced by antimycin A. RBH will be a powerful tool for detecting hydroxyl radicals in plant cells.

Development of stapled short helical peptides capable of inhibiting vitamin D receptor (VDR)-coactivator interactions.

We synthesized stapled helical leucine-based peptides (DPI-01-07) containing 2-aminoisobutyric acid and a covalent cross-linked unit as inhibitors of vitamin D receptor (VDR)-coactivator interactions. The effects of these peptides on the human VDR were examined in an inhibition assay based on the receptor cofactor assay system, and one of them, DPI-07, exhibited potent inhibitory activity (IC50: 3.2 µM).

One-handed helical screw direction of homopeptide foldamer exclusively induced by cyclic α-amino acid side-chain chiral centers.

Chiral cyclic α,α-disubstituted amino acids, (3S,4S)- and (3R,4R)-1-amino-3,4-(dialkoxy)cyclopentanecarboxylic acids ((S,S)- and (R,R)-Ac(5)c(dOR); R: methyl, methoxymethyl), were synthesized from dimethyl L-(+)- or D-(-)-tartrate, and their homochiral homoligomers were prepared by solution-phase methods. The preferred secondary structure of the (S,S)-Ac(5)c(dOMe) hexapeptide was a left-handed (M) 3(10) helix, whereas those of the (S,S)-Ac(5)c(dOMe) octa- and decapeptides were left-handed (M) α helices, both in solution and in the crystal state. The octa- and decapeptides can be well dissolved in pure water and are more α helical in water than in 2,2,2-trifluoroethanol solution. The left-handed (M) helices of the (S,S)-Ac(5)c(dOMe) homochiral homopeptides were exclusively controlled by the side-chain chiral centers, because the cyclic amino acid (S,S)-Ac(5)c(dOMe) does not have an α-carbon chiral center but has side-chain γ-carbon chiral centers.

Conformational studies on peptides containing α,α-disubstituted α-amino acids: chiral cyclic α,α-disubstituted α-amino acid as an α-helical inducer.

Four types of α,α-disubstituted amino acids {i.e., α-aminoisobutyric acid (Aib), 1-aminocyclopentanecarboxylic acid (Ac(5)c), (3S,4S)-1-amino-(3,4-dimethoxy)cyclopentanecarboxylic acid [(S,S)-Ac(5)c(dOM)] and its enantiomer (R,R)-Ac(5)c(dOM)} were introduced into l-leucine-based hexapeptides and nonapeptides. The dominant conformations of eight peptides: Cbz-(L-Leu-L-Leu-dAA)(2)-OMe [dAA = 1: Aib; 2: Ac(5)c; 3: (S,S)-Ac(5)c(dOM); 4: (R,R)-Ac(5)c(dOM)] and Boc-(L-Leu-L-Leu-dAA)(3)-OMe [dAA = 5: Aib; 6: Ac(5)c; 7: (S,S)-Ac(5)c(dOM); 8: (R,R)-Ac(5)c(dOM)], were investigated by IR, CD spectra and X-ray crystallographic analysis. The CD spectra revealed that Aib hexapeptide 1 and Ac(5)c hexapeptide 2 formed right-handed (P) 3(10)-helices, while Ac(5)c(dOM) hexapeptides 3 and 4 formed a mixture of (P) 3(10)- and α-helices. The Aib nonapeptide 5 formed a (P) 3(10)-helix, the Ac(5)c nonapeptide 6 formed a mixture of (P) 3(10)- and α-helices, and the Ac(5)c(dOM) nonapeptides 7 and 8 formed (P) α-helices. X-Ray crystallographic analysis revealed that the Aib hexapeptide 1 formed a (P) 3(10)-helix, while (S,S)-Ac(5)c(dOM) hexapeptide 3 formed a (P) α-helix. In addition, the Ac(5)c nonapeptide 6 and (R,R)-Ac(5)c(dOM) nonapeptide 8 formed (P) α-helices. The Aib and achiral Ac(5)c residues have the propensity to form 3(10)-helices in short peptides, whereas the chiral Ac(5)c(dOM) residues have a penchant for forming α-helices.

Conformations of peptides containing a chiral cyclic α, α-disubstituted α-amino acid within the sequence of Aib residues.

A single chiral cyclic α,α-disubstituted amino acid, (3S,4S)-1-amino-(3,4-dimethoxy)cyclopentanecarboxylic acid [(S,S)-Ac(5)c(dOM)], was placed at the N-terminal or C-terminal positions of achiral α-aminoisobutyric acid (Aib) peptide segments. The IR and (1)H NMR spectra indicated that the dominant conformations of two peptides Cbz-[(S,S)-Ac(5)c(dOM)]-(Aib)(4)-OEt (1) and Cbz-(Aib)(4)-[(S,S)-Ac(5)c(dOM)]-OMe (2) in solution were helical structures. X-ray crystallographic analysis of 1 and 2 revealed that a left-handed (M) 3(10)-helical structure was present in 1 and that a right-handed (P) 3(10)-helical structure was present in 2 in their crystalline states.

Stabilized alpha-helix-catalyzed enantioselective epoxidation of alpha,beta-unsaturated ketones.

Chiral cyclic alpha-amino acid containing oligopeptide catalyzed highly enantioselective epoxidation of alpha,beta-unsaturated ketones and the alpha-helical secondary structure of the peptide catalyst were revealed by X-ray crystallographic analysis.

Controlling the helical screw sense of peptides with C-terminal L-valine.

One chiral L-valine (L-Val) was inserted into the C-terminal position of achiral peptide segments constructed from alpha-aminoisobutyric acid (Aib) and alpha,beta-dehydrophenylalanine (Delta(Z)Phe) residues. The IR, (1)H NMR and CD spectra indicated that the dominant conformations of the pentapeptide Boc-Aib-DeltaPhe-(Aib)(2)-L-Val-NH-Bn (3) and the hexapeptide Boc-Aib-DeltaPhe-(Aib)(3)-L-Val-NH-Bn (4) in solution were both right-handed (P) 3(10)-helical structures. X-ray crystallographic analyses of 3 and 4 revealed that only a right-handed (P) 3(10)-helical structure was present in their crystalline states. The conformation of 4 was also studied by molecular-mechanics calculations.

Design and synthesis of regioisomerically pure unsymmetrical xanthene derivatives for staining live cells and their photochemical properties.

We have demonstrated the synthesis of regioisomerically pure unsymmetrical xanthene derivatives consisting of three units which can be independently modified to control their physical properties. The photochemical properties of the synthetic unsymmetrical xanthene derivatives were investigated in solution by UV-vis absorption and fluorescence measurements, and their cell imaging properties were examined by confocal laser-scanning microscopy.

Pericosines, antitumour metabolites from the sea hare-derived fungus Periconia byssoides. Structures and biological activities.

Pericosines A-E 1-5 have been isolated from a strain of Periconia byssoides originally separated from the sea hare Aplysia kurodai. Among them, pericosines C 3 and E 5 were separated as enantiomeric mixtures. Their stereostructures, except for compound 1, have been elucidated or identified on the basis of spectroscopic analyses, including 1D and 2D NMR techniques, and X-ray analysis. In addition, conformation for all the compounds has been discussed. Compounds 1-3 exhibited significant growth inhibition against tumour cell lines. Pericosine A 1 also showed significant in vivo tumour inhibitory activity. In addition, compound inhibited the protein kinase EGFR and topoisomerase II.

Variation in cytostatic constituents of a sponge-derived Gymnascella dankaliensis by manipulating the carbon source.

The Halichondria sponge-derived fungus, Gymnacella dankaliensis, was cultured in two different media conditions. A modified malt extract medium containing soluble starch instead of glucose resulted in two extremely unusual steroids, dankasterones A (2) and B (3), while four additional unusual steroids, gymnasterones A (4), B (5), C (6), and D (7), were isolated from the original malt extract medium. Their stereostructures have been established on the basis of spectroscopic analyses along with X-ray crystal structure analyses, modified Mosher's method, CD exciton method, and a chemical transformation. All the steroids except for 4 exhibited significant growth inhibition against the murine P388 cancer cell line. Dankasterone A (2) also exhibited potent growth inhibition against human cancer cell lines.

Controlling 3(10)-helix and alpha-helix of short peptides in the solid state.

L-Leu hexapeptide containing alpha-aminoisobutyric acid (Aib) forms a right-handed (P) 3(10)-helix, whereas that containing cyclic alpha,alpha-disubstituted amino acid Ac(5)c(dOM) assumes a right-handed (P) alpha-helix in the solid state.