12/14/14‐Helix Formation in 2:1 α/β‐Hybrid Peptides Containing Bicyclo[2.2.2]octane Ring Constraints

The highly constrained β‐amino acid ABOC induces different types of helices in β urea and 1:1 α/β amide oligomers. The latter can adopt 11/9‐ and 18/16‐helical folds depending on the chain length in solution. Short peptides alternating proteinogenic α‐amino acids and ABOC in a 2:1 α/β repeat pattern adopted an unprecedented and stable 12/14/14‐helix. The structure was established through extensive NMR, molecular dynamics, and IR studies. While the 1:1 α‐AA/ABOC helices diverged from the canonical α‐helix, the helix formed by the 9‐mer 2:1 α/β‐peptide allowed the projection of the α‐amino acid side chains in a spatial arrangement according to the α‐helix. Such a finding constitutes an important step toward the conception of functional tools that use the ABOC residue as a potent helix inducer for biological applications.     

Exploiting Aromatic Interactions for β‐Peptide Foldamer Helix Stabilization: A Significant Design Element

Tetrameric H10/12 helix stabilization was achieved by the application of aromatic side‐chains in β‐peptide oligomers by intramolecular backbone–side chain CH–π interactions. Because of the enlarged hydrophobic surface of the oligomers, a further aim was the investigation of the self‐assembly in a polar medium for the β‐peptide H10/12 helices. NMR, ECD, and molecular modeling results indicated that the oligomers formed by cis‐[1S,2S]‐ or cis‐[1R,2R]‐1‐amino‐1,2,3,4‐tetrahydronaphthalene‐2‐carboxylic acid (ATENAC) and cis‐[1R,2S]‐ or cis‐[1S,2R]‐2‐aminocyclohex‐3‐enecarboxylic acid (ACHEC) residues promote stable H10/12 helix formation with an alternating backbone configuration even at the tetrameric chain length. These results support the view that aromatic side‐chains can be applied for helical structure stabilization. Importantly, this is the first observation of a stable H10/12 helix with tetrameric chain‐length. The hydrophobically driven self‐assembly was achieved for the helix‐forming oligomers, seen as vesicles in transmission electron microscopy images. The self‐association phenomenon, which supports the helical secondary structure of these oligomers, depends on the hydrophobic surface area, because a higher number of aromatic side‐chains yielded larger vesicles. These results serve as an essential element for the design of helices relating to the H10/12 helix. Moreover, they open up a novel area for bioactive foldamer construction, while the hydrophobic area gained through the aromatic side‐chains may yield important receptor–ligand interaction surfaces, which can provide amplified binding strength.     

Controlling the Helix Handedness of ααβ‐Peptide Foldamers through Sequence Shifting

Peptide foldamers containing both cis ‐β‐aminocyclopentanecarboxylic acid and α‐amino acid residues combined in various sequence patterns (ααβ, αααβ, αβααβ, and ααβαααβ) were screened using CD and NMR spectroscopy for the tendency to form helices. ααβ‐Peptides were found to fold into an unprecedented and well‐defined 16/17/15/18/14/17‐helix. By extending the length of the sequence or shifting a fragment of the sequence from one terminus to another in ααβ‐peptides, the balance between left‐handed and right‐handed helix populations present in the solution can be controlled. Engineering of the peptide sequence could lead to compounds with either a strong propensity for the selected helix sense or a mixture of helical conformations of opposite senses.     

Theoretical Study Of β2,3‐Peptide Models

Conformational features of α,β‐disubstituted β^2,3‐dipeptide models have been studied with quantum mechanics method. Geometries were optimized with the HF/6‐31G** method, and energies were evaluated with the B3LYP/6‐31G** method. Solvent effect was evaluated with the SCIPCM method. For (2S,3S)‐β^2,3‐dipeptide model 1 , a six‐membered‐ring hydrogen bonded structure is most stable. However, the conformation corresponding to the formation of the 14‐helix is only about 1.7 kcal/mol less stable in methanol solution, indicating that the 14‐helix is favored if a (2S,3S)‐β^2,3‐polypeptide contains more than 5 residues. On the other hand, the conformation corresponding to the formation of β‐sheet is most stable for (2R,3S)‐β^2,3‐dipeptide model 2 , suggesting that this type of β‐peptides is intrinsically favored for the formation of β‐sheet secondary structure.     

Establishing effective simulation protocols for β‐ and α/β‐peptides. III. Molecular mechanical model for acyclic β‐amino acids

All‐atom molecular mechanics (MM) force field parameters are developed for the backbone of acyclic β‐amino acid using an improved version of the multiobjective evolutionary algorithm (MOEA). The MM model is benchmarked using β³‐homo‐Alanine (β³‐hAla) diamide in water with SCC‐DFTB/MM simulations as the reference. Satisfactory agreements are found between the MM and SCC‐DFTB/MM results regarding the distribution of key dihedral angles for the β³‐hAla diamide in water. The MM model is further applied to a β‐hepta‐peptide in methanol solution. The calculated NOE values and ³J coupling constants averaged over different trajectories are consistent with experimental data. By contrast, simulations using parameters directly transferred from the CHARMM22 force field for proteins lead to much worse agreement, which highlights the importance of careful parameterization for non‐natural peptides, for which the improved MOEA is particularly useful. Finally, as an initial application of the new force field parameters, the behaviors of a short random copolymer consisting of β amino acids in bulk solution and membrane/water interface are studied using a generalized Born implicit solvent model (GBSW). Results for four selected sequences show that segregation of hydrophobic and cationic groups occur easily at the membrane/solution interface for all sequences. The sequence that features alternating short blocks exhibits signs of lower stability at the interface compared to other sequences. These results confirm the hypothesis in recent experimental studies that β‐amino‐acid based random copolymers can develop a high degree of amphiphilicity without regular three‐dimensional structure. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Phosphoryl group differentiating α‐amino acids from β‐ and γ‐amino acids in prebiotic peptide formation

In recent years β‐amino acids have increased their importance enormously in defining secondary structures of β‐peptides. Interest in β‐amino acids raises the question: Why and how did nature choose α‐amino acids for the central role in life? In this article we present experimental results of MS and ³¹P NMR methods on the chemical behavior of N‐phosphorylated α‐alanine, β‐alanine, and γ‐amino butyric acid in different solvents. N‐Phosphoryl α‐alanine can self‐assemble to N‐phosphopeptides either in water or in organic solvents, while no assembly was observed for β‐ or γ‐amino acids. An intramolecular carboxylic–phosphoric mixed anhydride (IMCPA) is the key structure responsible for their chemical behaviors. Relative energies and solvent effects of three isomers of IMCPA derived from α‐alanine (2a–c), with five‐membered ring, and five isomers of IMCPA derived from β‐alanine (4a–e), with six‐membered ring, were calculated with density functional theory at the B3LYP/6‐31G** level. The lower relative energy (3.2 kcal/mol in water) of 2b and lower energy barrier for its formation (16.7 kcal/mol in water) are responsible for the peptide formation from N‐phosphoryl α‐alanine. Both experimental and theoretical studies indicate that the structural difference among α‐, β‐, and γ‐amino acids can be recognized by formation of IMCPA after N‐phosphorylation. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 232–241, 2003     

Radical‐initiated polymerization of β‐methyl‐α‐methylene‐γ‐butyrolactone

β‐Methyl‐α‐methylene‐γ‐butyrolactone (MMBL) was synthesized and then was polymerized in an N,N‐dimethylformamide (DMF) solution with 2,2‐azobisisobutyronitrile (AIBN) initiation. The homopolymer of MMBL was soluble in DMF and acetonitrile. MMBL was homopolymerized without competing depolymerization from 50 to 70 °C. The rate of polymerization (R_p) for MMBL followed the kinetic expression R_p = [AIBN]^0.54[MMBL]^1.04. The overall activation energy was calculated to be 86.9 kJ/mol, k_p/k_t^1/2 was equal to 0.050 (where k_p is the rate constant for propagation and k_t is the rate constant for termination), and the rate of initiation was 2.17 × 10^?8 mol L^?1 s^?1. The free energy of activation, the activation enthalpy, and the activation entropy were 106.0, 84.1, and 0.0658 kJ mol^?1, respectively, for homopolymerization. The initiation efficiency was approximately 1. Styrene and MMBL were copolymerized in DMF solutions at 60 °C with AIBN as the initiator. The reactivity ratios (r₁ = 0.22 and r₂ = 0.73) for this copolymerization were calculated with the Kelen–Tudos method. The general reactivity parameter Q and the polarity parameter e for MMBL were calculated to be 1.54 and 0.55, respectively. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 1759–1777, 2003     

Synthesis of new optically active α,α′,β‐trisubstituted‐β‐lactones as monomers for stereoregular biopolyesters

Various optically active (4R)‐alkyloxycarbonyl‐3,3‐dialkyl‐2‐oxetanones as monomers were synthesized from L‐(S)‐malic acid in six steps to prepare a new family of stereopolyesters for biomedical applications. The synthesis began with an esterification followed of a dialkylation in the aim to introduce hydrophobic groups as methyl or reactive group as allyl. Then, a saponification has permitted to obtain the corresponding diacids that reacted with appropriate alcohols to furnish different monoesters. The last and most important step was activation of hydroxyl group of monoesters with the asymmetric carbon configuration inversion according to the Mitsunobu reaction. Thus, this reaction has provided lactones from monoesters with 100% enantiomeric excess which was confirmed by ¹H NMR and by the synthesis of corresponding isotactic and semicrystalline homopolyesters. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 2586–2597     

The effect of amino acid backbone length on molecular packing: crystalline tartrates of glycine, β‐alanine, γ‐aminobutyric acid (GABA) and dl‐α‐aminobutyric acid (AABA)

We report a novel 1:1 cocrystal of β‐alanine with dl ‐tartaric acid, C₃H₇NO₂·C₄H₆O₆, (II), and three new molecular salts of dl ‐tartaric acid with β‐alanine {3‐azaniumylpropanoic acid–3‐azaniumylpropanoate dl ‐tartaric acid–dl ‐tartrate, [H(C₃H₇NO₂)₂]⁺·[H(C₄H₅O₆)₂]⁻, (III)}, γ‐aminobutyric acid [3‐carboxypropanaminium dl ‐tartrate, C₄H₁₀NO₂⁺·C₄H₅O₆⁻, (IV)] and dl ‐α‐aminobutyric acid {dl ‐2‐azaniumylbutanoic acid–dl ‐2‐azaniumylbutanoate dl ‐tartaric acid–dl ‐tartrate, [H(C₄H₉NO₂)₂]⁺·[H(C₄H₅O₆)₂]⁻, (V)}. The crystal structures of binary crystals of dl ‐tartaric acid with glycine, (I), β‐alanine, (II) and (III), GABA, (IV), and dl ‐AABA, (V), have similar molecular packing and crystallographic motifs. The shortest amino acid (i.e. glycine) forms a cocrystal, (I), with dl ‐tartaric acid, whereas the larger amino acids form molecular salts, viz. (IV) and (V). β‐Alanine is the only amino acid capable of forming both a cocrystal [i.e. (II)] and a molecular salt [i.e. (III)] with dl ‐tartaric acid. The cocrystals of glycine and β‐alanine with dl ‐tartaric acid, i.e. (I) and (II), respectively, contain chains of amino acid zwitterions, similar to the structure of pure glycine. In the structures of the molecular salts of amino acids, the amino acid cations form isolated dimers [of β‐alanine in (III), GABA in (IV) and dl ‐AABA in (V)], which are linked by strong O—H…O hydrogen bonds. Moreover, the three crystal structures comprise different types of dimeric cations, i.e. (A…A)⁺ in (III) and (V), and A⁺…A⁺ in (IV). Molecular salts (IV) and (V) are the first examples of molecular salts of GABA and dl ‐AABA that contain dimers of amino acid cations. The geometry of each investigated amino acid (except dl ‐AABA) correlates with the melting point of its mixed crystal.     

Synthesis,and Helix or Hairpin‐Turn Secondary Structures of ‘Mixed’ α/β‐Peptides Consisting of Residues with Proteinogenic Side Chains and of 2‐Amino‐2‐methylpropanoic Acid (Aib)

Twelve peptides, 1 – 12 , have been synthesized, which consist of alternating sequences of α‐ and β‐amino acid residues carrying either proteinogenic side chains or geminal dimethyl groups (Aib). Two peptides, 13 and 14 , containing 2‐methyl‐3‐aminobutanoic acid residues or a ‘random mix’ of α‐, β²‐, and β³‐amino acid moieties were also prepared. The new compounds were fully characterized by CD (Figs. 1 and 2), and ¹H‐ and ¹³C‐NMR spectroscopy, and high‐resolution mass spectrometry (HR‐MS). In two cases, 3 and 14 , we discovered novel types of turn structures with nine‐ and ten‐membered H‐bonded rings forming the actual turns. In two other cases, 8 and 11 , we found 14/15‐helices, which had been previously disclosed in mixed α/β‐peptides containing unusual β‐amino acids with non‐proteinogenic side chains. The helices are formed by peptides containing the amino acid moiety Aib in every other position, and their backbones are primarily not held together by H‐bonds, but by the intrinsic conformations of the containing amino acid building blocks. The structures offer new possibilities of mimicking peptide–protein and protein–protein interactions (PPI).     

Improved treatment of cyclic β‐amino acids and successful prediction of β‐peptide secondary structure using a modified force field: AMBER*C

We added parameters to the AMBER* force field to model cyclic β‐amino acid derivatives more accurately within the commonly used MacroModel program. In an effort to generate an improved treatment of cyclohexane and cyclopentane conformational preferences, carbon–carbon torsional parameters were modified and incorporated into a force field we call AMBER*C. Simulation of trans‐2‐aminocyclohexanecarboxylic acid (trans‐ACHC) and trans‐2‐aminocyclopentanecarboxylic acid (trans‐ACPC) derivatives using AMBER*C produces more realistic energy differences between (pseudo)diaxial and (pseudo)diequatorial conformations than does simulation using AMBER*. AMBER*C molecular dynamics simulations more accurately reproduce the experimental hydrogen‐bonding tendencies of simple diamide derivatives of trans‐ACHC and trans‐ACPC than do simulations using the AMBER* force field. More importantly, this modified force field allows accurate qualitative prediction of the helical secondary structures adopted by β‐amino acid homo‐oligomers. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 763–773, 2000     

Studies on the Mass Spectra of N‐Aryl α,β‐Unsaturated γ‐Lactams

The mass spectra of a series of N‐aryl α,β‐unsaturated γ‐lactams were studied. Besides the molecular ion, the three characteristic fragments such as [M⁺‐29], [M⁺‐55], and [M⁺‐82] were commonly found in a series of N‐Aryl α,β‐unsaturated γ‐lactams in EI/MS. Further more the mechanism for the interpretation of these fragments is also de scribed.     

Chiral discrimination of β‐3‐homo‐amino acids using the kinetic method

Chiral discrimination of seven enantiomeric pairs of β‐3‐homo‐amino acids was studied by using the kinetic method and trimeric metal‐bound complexes, with natural and unnatural α‐amino acids as chiral reference compounds and divalent metal ions (Cu²⁺ and Ni²⁺) as the center ions. The β‐3‐homo‐amino acids were selected for this study because, first of all, chiral discrimination of β‐amino acids has not been extensively studied by mass spectrometry. Moreover, these β‐3‐homo‐amino acids studied have different aromatic side chains. Thus, the emphasis was to study the effect of the side chain (electron density of the phenyl ring, as well as the difference between phenyl and benzyl side chains) for the chiral discrimination. The results showed that by the proper choice of a metal ion and a chiral reference compound, all seven enantiomeric pairs of β‐3‐homo‐amino acids could be differentiated. Moreover, it was noted that the β‐3‐homo‐amino acids with benzyl side chains provided higher enantioselectivity than the corresponding phenyl ones. However, increasing or decreasing the electron density of the aromatic ring by different substituents in both the phenyl and benzyl side chains had practically no role for chiral discrimination of β‐3‐homo‐amino acids studied. When copper was used as the central metal, the phenyl side chain containing reference molecules (S)‐2‐amino‐2‐phenylacetic acid (L ‐Phg) and (S)‐2‐amino‐2‐(4‐hydroxyphenyl)‐acetic acid (L ‐4′‐OHPhg) gave rise to an additional copper‐reduced dimeric fragment ion, [Cu^I(ref)(A)]⁺. The inclusion of this ion improved noticeably the enantioselectivity values obtained. Copyright © 2010 John Wiley & Sons, Ltd.     

Microwave‐Assisted Synthesis of β‐Lactams and Cyclo‐β‐dipeptides

Different cyclo‐β‐dipeptides were prepared from corresponding N‐substituted β‐alanine derivatives under mild conditions using PhPOCl₂ as activating agent in benzene and Et₃N as base. To evaluate β³‐substituent influence, the amino acids 7 – 26 were synthesized, and a β‐lactam formation reaction was carried out instead of cyclo‐β‐dipeptide formation. The crystal structures of three derivatives of cyclo‐β‐peptides and one β‐lactam are presented.     

Helical‐Ribbon Formation by a β‐Amino Acid Modified Amyloid β‐Peptide Fragment

An addition to the family : The introduction of β‐amino acid residues into a modified amyloid β peptide fragment resulted in well‐defined helical nanoribbons (see cryo‐TEM image) comprising β strands mainly oriented perpendicular to the ribbon axis. The nanoribbons order into a flow‐aligning nematic phase at higher concentration. The β‐strand nanoribbon structure is an addition to the known set of secondary structures adopted by β‐peptides.

     

Synthesis of Phenanthrene Derivatives through the Reaction of an α,α‐Dicyanoolefin with α,β‐Unsaturated Carbonyl Compounds

Phenanthrene derivatives were prepared by reacting an α,α‐dicyanoolefin with different α,β‐unsaturated carbonyl compounds resulting from Wittig reaction of ninhydrin and phosphanylidene or condensation of barbituric acid and an aldehyde. The easy procedure, mild and metal‐catalyst free, reaction conditions, good yields, and no need for chromatographic purifications are important features of this protocol. The structures of the product of type 3 and 5 were corroborated spectroscopically (IR, ¹H‐ and ¹³C‐NMR, and EI‐MS). A plausible mechanism for this type of reaction is proposed (Scheme 1).     

A rare occurrence of a β‐turn in an amyloid βA4 peptide

The fragment β(25–35) of the amyloid β‐peptide, like its parent βA4, has shown neurotrophic and late neurotoxic activities in cultured cells. The 3D structure of this important peptide was examined by ¹H and ¹³C 2D‐NMR and MD simulations in DMSO‐d₆ and water. The NMR parameters of chemical shift, ³J(N,Hα) coupling constants, temperature coefficients of NH chemical shifts and the pattern of intra and inter‐residue NOEs were used to deduce the structures. In DMSO‐d₆, the peptide was found to take up a type I β‐turn around the C‐terminal residues Ile⁸–Gly⁹–Leu¹⁰–Met¹¹, whereas in water at pH 5.5, it adopts a random coil conformation. This is only the second report of a β‐turn in the β‐amyloid class of peptides. The solution structures generated using restrained molecular dynamics were refined by MARDIGRAS to an R factor of 0.33 in the case of DMSO‐d₆ and to 0.56 for water. Copyright © 2002 John Wiley & Sons, Ltd.     

Norbornane Mimics of Distorted β‐D‐Glucopyranosides – Inhibitors of β‐D‐Glucopyranosidases?

The racemic gluco‐configured norbornanes 4 and 16 were prepared and tested as inhibitors of β‐glucosidases. The known alcohol 5 was deprotected to provide the triol 6 . Silylation (→ 7 ), monobenzoylation (→ 8 / 9 ), and oxidation provided the regioisomeric ketones 10 and 11 . Reduction of 10 gave the desired endo‐alcohol 13 , albeit in low yield, while reduction of the isomeric ketone 11 provided mostly the altro‐configured endo‐alcohol 12 . The alcohol 13 was desilylated to 14 . Debenzoylation to 15 followed by hydrogenolytic deprotection gave the amino triol 4 that was reductively aminated to the benzylamine 16 . The amino triols 4 and 16 proved weak inhibitors of the β‐glucosidase from Caldocellum saccharolyticum ( 4 : IC₅₀ = 5.6 mm; 16 : IC₅₀ = 3.3 mm) and from sweet almonds ( 16 : IC₅₀ = 5.5 mm) . A comparison of 4 with the manno‐configured norbornane 3 shows that 3 is a better inhibitor of snail β‐mannosidase than 4 is of β‐glucosidases, in keeping with earlier results suggesting that these β‐glycosidases enforce a different conformational itinerary.     

Comparative α‐Helicity of Cyclic Pentapeptides in Water

Helix‐constrained polypeptides have attracted great interest for modulating protein–protein interactions (PPI). It is not known which are the most effective helix‐inducing strategies for designing PPI agonists/antagonists. Cyclization linkers (X₁–X₅) were compared here, using circular dichroism and 2D NMR spectroscopy, for α‐helix induction in simple model pentapeptides, Ac‐cyclo(1,5)‐[X₁‐Ala‐Ala‐Ala‐X₅]‐NH₂, in water. In this very stringent test of helix induction, a Lys1→Asp5 lactam linker conferred greatest α‐helicity, hydrocarbon and triazole linkers induced a mix of α‐ and 3₁₀‐helicity, while thio‐ and dithioether linkers produced less helicity. The lactam‐linked cyclic pentapeptide was also the most effective α‐helix nucleator attached to a 13‐residue model peptide.     

Syntheses,and Crystal Structures of Indium Complexes with η2‐Piperidinyldithiocarbamate and η2‐Pyridine‐2‐Thionate Containing Ligands: Structures of [In(η2‐S2CNC5H10)3] and [In(η2‐pyS)3]

The η²‐thio‐indium complexes [In(η²‐thio)₃] (thio = S₂CNC₅H₁₀, 2 ; SNC₄H₄, (pyridine‐2‐thionate, pyS, 3 ) and [In(η²‐pyS)₂(η²‐acac)], 4 , (acac: acetylacetonate) are prepared by reacting the tris(η²‐acac)indium complex [In(η²‐acac)₃], 1 with HS₂CNC₅H₁₀, pySH, and pySH with ratios of 1:3, 1:3, and 1:2 in dichloromethane at room temperature, respectively. All of these complexes are identified by spectroscopic methods and complexes 2 and 3 are determined by single‐crystal X‐ray diffraction. Crystal data for 2 : space group, C2/c with a = 13.5489(8) Å, b = 12.1821(7) Å, c = 16.0893(10) Å, β = 101.654(1)°, V = 2600.9(3) ų, and Z = 4. The structure was refined to R = 0.033 and Rw = 0.086; Crystal data for 3 : space group, P2₁ with a = 8.8064 (6) Å, b = 11.7047 (8) Å, c = 9.4046 (7) Å, β = 114.78 (1)°, V = 880.13(11) ų, and Z = 2. The structure was refined to R = 0.030 and Rw = 0.061. The geometry around the metal atom of the two complexes is a trigonal prismatic coordination. The piperidinyldithiocarbamate and pyridine‐2‐thionate ligands, respectively, coordinate to the indium metal center through the two sulfur atoms and one sulfur and one nitrogen atoms, respectively. The short C‐N bond length in the range of 1.322(4)–1.381(6) Å in 2 and C‐S bond length in the range of 1.715(2)–1.753(6) Å in 2 and 3 , respectively, indicate considerable partial double bond character.