Stable Helical Conformation Research Articles

Function Control of Anti-microRNA Oligonucleotides Using Interstrand Cross-Linked Duplexes.

MicroRNA (miRNA)-guided argonaute (Ago) controls gene expression upon binding to the 3′ UTR of mRNA. The miRNA function can be competitively inhibited by single-stranded anti-miRNA oligonucleotides (AMOs). In this study, we constructed a novel type of AMO flanked by interstrand cross-linked 2′-O-methylated RNA duplexes (CLs) that confer a stable helical conformation. Compared with other structured AMOs, AMO flanked by CLs at the 5′ and 3′ termini exhibited much higher inhibitory activity in cells. Anti-miRNA activity, nuclease resistance, and miRNA modification pattern distinctly differed according to the CL-connected positions in AMOs. Moreover, we found that the 3′-side CL improves nuclease resistance, whereas the 5′-side CL contributes to stable binding with miRNA in Ago upon interaction with the 3′ part of miRNA. These structure-function relationship analyses of AMOs provide important insights into the function control of Ago-miRNA complexes, which will be useful for basic miRNA research as well as for determining therapeutic applications of AMO.

Aromatic Hybrid Foldamer with a Hydrophilic Helical Cavity Capable of Encapsulating Glucose.

An indolocarbazole-naphthyridine hybrid oligomer capable of adopting a stable helical conformation was prepared, and its folding properties were thoroughly studied in the solid state and in solution. As a result of folding, a hydrophilic cavity was generated inside the helix wherein monosaccharides were able to be encapsulated in the order of glucose (9.6 × 104 M-1) > galactose (1.0 × 104 M-1) ≫ mannose (∼0) in 10% (v/v) DMSO/CH2Cl2.

Synthesis and Structural Analysis of Ruthenium-bound Norvaline Peptides

A series of norvaline (Nva) peptides possessing ONO-pincer ruthenium complexes, Boc-{l-[Ru(pydc)(t-Bu-terpy)]Nva}n-OMe (n = 2–6), were synthesized successfully by solution-phase peptide synthesis. Efficient coupling of equimolar amounts of N-free Ru-bound norvaline peptides, H-{l-[Ru(pydc)(t-Bu-terpy)]Nva}n-OMe, and C-free Ru-bound norvaline, Boc-l-[Ru(pydc)(t-Bu-terpy)]Nva-OH, was achieved by using the 2-chloro-4,6-dimethoxy-1,3,5-triazine-based method. Structural analysis by means of CD and NMR spectroscopy revealed the formation of stable helical conformations in peptides more than three residues.

Bright Electrochemiluminescence Tunable in the Near-Infrared of Chiral Cationic Helicene Chromophores

Cationic helicenes are ortho-fused polyaromatics which exhibit well-defined and stable helical conformations with original absorption and emission properties in the red to near-infrared spectral ranges. Herein, a selection of cationic [4] and [6]helicenes are studied for their electrochemical, fluorescence, and electrochemiluminescence (ECL) properties in acetonitrile solutions. Their photophysical and redox responses are drastically tuned by the introduction of auxochrome substituents at their periphery or the interconversion of oxygen and nitrogen atoms within the helical core. All diaza helicenes exhibit a reversible reduction process, whereas in the presence of oxygen instead of nitrogen atoms in the helical core, irreversible oxidations and a decrease of ECL intensity are observed. ECL emission was successfully produced with two sacrificial coreactants (benzoyl peroxide and tri-n-propylamine, TPrA). [4]Helicene DMQA+, [6]helicene DIAZA(Pr/Br)+, and DIAZA(Hex/Br)+ exhibit similar ECL emission waveleng...

Membrane Mediated Antimicrobial and Antitumor Activity of Cathelicidin 6: Structural Insights from Molecular Dynamics Simulation on Multi-Microsecond Scale.

The cathelicidin derived bovine antimicrobial peptide BMAP27 exhibits an effective microbicidal activity and moderate cytotoxicity towards erythrocytes. Irrespective of its therapeutic and multidimensional potentiality, the structural studies are still elusive. Moreover, the mechanism of BMAP27 mediated pore formation in heterogeneous lipid membrane systems is poorly explored. Here, we studied the effect of BMAP27 in model cell-membrane systems such as zwitterionic, anionic, thymocytes-like (TLM) and leukemia-like membranes (LLM) by performing molecular dynamics (MD) simulation longer than 100 μs. All-atom MD studies revealed a stable helical conformation in the presence of anionic lipids, however, significant loss of helicity was identified in TLM and zwitterionic systems. A peptide tilt (~45˚) and central kink (at residue F10) was found in anionic and LLM models, respectively, with an average membrane penetration of < 0.5 nm. Coarse-grained (CG) MD analysis on a multi-μs scale shed light on the membrane-dependent peptide and lipid organization. Stable micelle and end-to-end like oligomers were formed in zwitterionic and TLM models, respectively. In contrast, unstable oligomer formation and monomeric BMAP27 penetration were observed in anionic and LLM systems with selective anionic lipid aggregation (in LLM). Peptide penetration up to ~1.5 nm was observed in CG-MD systems with the BMAP27 C-terminal oriented towards the bilayer core. Structural inspection suggested membrane penetration by micelle/end-to-end like peptide oligomers (carpet-model like) in the zwitterionic/TLM systems, and transmembrane-mode (toroidal-pore like) in the anionic/LLM systems, respectively. Structural insights and energetic interpretation in BMAP27 mutant highlighted the role of F10 and hydrophobic residues in mediating a membrane-specific peptide interaction. Free energy profiling showed a favorable (-4.58 kcal mol-1 for LLM) and unfavorable (+0.17 kcal mol-1 for TLM) peptide insertion in anionic and neutral systems, respectively. This determination can be exploited to regulate cell-specific BMAP27 cytotoxicity for the development of potential drugs and antibiotics.

Hexagonal Lyotropic Liquid Crystal from Simple "Abiotic" Foldamers.

The motivation of foldamer chemistry is to identify novel building blocks that have the potential to imitate natural species. Peptides and peptide mimetics can form stable helical conformations and further self‐assemble into diverse aggregates in water, where it is difficult to isolate a single helix. In contrast, most “abiotic” foldamers may fold into helical structures in solution, but are difficult to assemble into tertiary ones. It remains a challenge to obtain “abiotic” species similar to peptides. In this paper, a novel foldamer scaffold, in which p‐phenyleneethynylene units are linked by chiral carbon atoms, was designed and prepared. In very dilute solutions, these oligomers were random coils. The hexamer and octamers could form a hexagonal lyotropic liquid crystal (LC) in CH2Cl2 when the concentrations reached the critical values. The microscopic observations indicated that they could assemble into the nanofibers in the LC. Interestingly, after some LC phases were diluted at room temperature, the nanofibers could be preserved. The good stabilities of the assemblies are possibly attributed to a more compact backbone and more rigid side chains.

Solid phase synthesis of oligoethylene glycol-functionalized quinolinecarboxamide foldamers with enhanced solubility properties

Abstract A series of octameric quinoline oligoamide foldamers has been synthesized consisting exclusively of monomers which display mono-, di-, tri- or tetra-ethylene glycol side-chains. These oligomers adopt stable helical conformations. New Fmoc-acid monomer precursors were first developed. The microwave assisted solid-phase synthesis (SPS) methodology for oligomer preparation is described, and it is demonstrated that small adjustments in side-chain length translate into large differences in the solubility profile of the oligomers. The impact of such modifications on foldamer preparation, handedness inversion kinetics and potential applications is also discussed.

Helix-sense-selective radical polymerization of (S)-6-acryloyl-2,2′-bisalkoxy-1,1′-binaphthyl

A series of (S)-6-acryloyl-2,2′-bisalkoxy-1,1′-binaphthyl 1 were radically polymerized to obtain polymers. The optical rotation and the circular dichroism (CD) signal intensity of the radically polymerized poly-1 were close to that of the anionically polymerized poly-1 indicating that the radically polymerized poly-1 should adopt stable preferred-handed helical conformation in solution just as the anionically polymerized poly-1.

α-Peptide-Oligourea Chimeras: Stabilization of Short α-Helices by Non-Peptide Helical Foldamers.

Short α-peptides with less than 10 residues generally display a low propensity to nucleate stable helical conformations. While various strategies to stabilize peptide helices have been previously reported, the ability of non-peptide helical foldamers to stabilize α-helices when fused to short α-peptide segments has not been investigated. Towards this end, structural investigations into a series of chimeric oligomers obtained by joining aliphatic oligoureas to the C- or N-termini of α-peptides are described. All chimeras were found to be fully helical, with as few as 2 (or 3) urea units sufficient to propagate an α-helical conformation in the fused peptide segment. The remarkable compatibility of α-peptides with oligoureas described here, along with the simplicity of the approach, highlights the potential of interfacing natural and non-peptide backbones as a means to further control the behavior of α-peptides.

α‐Peptide–Oligourea Chimeras: Stabilization of Short α‐Helices by Non‐Peptide Helical Foldamers

AbstractShort α‐peptides with less than 10 residues generally display a low propensity to nucleate stable helical conformations. While various strategies to stabilize peptide helices have been previously reported, the ability of non‐peptide helical foldamers to stabilize α‐helices when fused to short α‐peptide segments has not been investigated. Towards this end, structural investigations into a series of chimeric oligomers obtained by joining aliphatic oligoureas to the C‐ or N‐termini of α‐peptides are described. All chimeras were found to be fully helical, with as few as 2 (or 3) urea units sufficient to propagate an α‐helical conformation in the fused peptide segment. The remarkable compatibility of α‐peptides with oligoureas described here, along with the simplicity of the approach, highlights the potential of interfacing natural and non‐peptide backbones as a means to further control the behavior of α‐peptides.

Polypeptide-b-Poly(Phenyl Isocyanide) Hybrid Rod-Rod Copolymers: One-Pot Synthesis, Self-Assembly, and Cell Imaging.

Hybrid rod-rod diblock copolymers, poly(γ-benzyl L-glutamate)-poly(4-cyano-benzoic acid 2-isopropyl-5-methyl-cyclohexyl ester) (PBLG-PPI), with determined chirality are facilely synthesized through sequential copolymerization of γ-benzyl-L-glutamate N-carboxyanhydride (BLG-NCA) and phenyl isocyanide monomers bearing chiral menthyl pendants using a Ni(cod)(bpy) complex as the catalyst in one-pot. Circular dichroism and absorption spectra reveal that each block of the block copolymers possesses a stable helical conformation with controlled helicity in solution due to the induction of chiral pendants. The two diastereomeric polymers self-assemble into helical nanofibrils with opposite handedness due to the different chiral induction of the L- and D-menthyl pendants, confirmed by transmission electron microscopy (TEM). Deprotection of the benzyl groups of the PBLG segment affords biocompatible amphiphilic diblock copolymers, poly(L-glutamic acid)-poly(4-cyano-benzoic acid 2-isopropyl-5-methyl-cyclohexyl ester) (PLGA-PPI), that can self-assemble into well-defined micelles by cosolvent induced aggregation. Very interestingly, a chiral rhodamine chromophores RhB(D) can be selectively encapsulated into the chiral polymeric micelles, which is efficiently internalized into living cells when directly monitored with a confocal microscope. This contribution will be useful for developing novel rod-rod biocompatible hybrid block copolymers with a controlled helicity, and may also provide unique chiral materials for potential bio-medical applications.

Optically Active Helical Poly[(S)‐3‐vinyl‐2,2′‐dihydroxy‐1,1′‐binaphthyl]: New Ligand for Asymmetric Addition of Diethylzinc to Aryl Aldehyde

AbstractPoly[(S)‐3‐vinyl‐2,2′‐dihydroxy‐1,1′‐binaphthyl] (L*) was obtained by taking off the protecting groups of poly[(S)‐3‐vinyl‐2,2′‐bis(methoxymethoxy)‐1,1′‐binaphthyl] (poly‐1). L* was proved to keep a stable helical conformation in solution. The application of helical L* in the asymmetric addition of diethylzinc to aldehydes has been studied. The catalytic system employing 10 mol% of L* and 150 mol% of Ti(OiPr)4 was found to promote the addition of diethylzinc to a wide range of aromatic aldehydes, giving up to 99% enantiomeric excess (ee) and up to 93% yield of the corresponding secondary alcohol at 0°C. The chiral polymer can be easily recovered and reused without loss of catalytic activity as well as enantioselectivity.

Mechanism of stabilization of helix secondary structure by constrained Cα-tetrasubstituted α-amino acids.

The theoretical basis behind the ability of constrained Cα-tetrasubstituted amino acids (CTAAs) to induce stable helical conformations has been studied through Replica Exchange Molecular Dynamics Potential of Mean Force Quantum Theory of Atoms In Molecules calculations on Ac-l-Ala-CTAA-l-Ala-Aib-l-Ala-NHMe peptide models. We found that the origin of helix stabilization by CTAAs can be ascribed to at least two complementary mechanisms limiting the backbone conformational freedom: steric hindrance predominantly in the (+x,+y,-z) sector of a right-handed 3D Cartesian space, where the z axis coincides with the helical axis and the Cα of the CTAA lies on the +y axis (0,+y,0), and the establishment of additional and relatively strong C-H···O interactions involving the CTAA.

Synthesis and Chiroptical Properties of Helical Polyallenes Bearing Chiral Amide Pendants

Two allene derivatives, l- and d-N-(1-(octylamino)-1-oxopropan-2-yl)-4-(propa-1,2-dien-1-yloxy)benzamide (l-1 and d-1), bearing chiral amide pendants were designed and synthesized. Living polymerizations of l-1 and d-1 with allylnickel complex as a catalyst afforded poly-l-1m and poly-d-1m with controlled molecular weights and narrow molecular weight distributions. These polymers were found to possess a stable helical conformation with a preferred handedness in aprotic solvents on the basis of their circular dichroism (CD) spectra and specific rotation as well as computer simulation. The helical conformation of the polymers was revealed to be stabilized by elongation of the repeating unit until the degree of the polymerization reaches 80. The slightly influence of temperature on the CD spectra of poly-l-1100 in CHCl3 indicated the helical conformation was quite stable at least in the range of 0–55 °C. Although poly-l-1100 showed similar CD spectra in different aprotic solvents, remarkable decrease was observed upon the addition of protic solvents such as methanol due to the weakened hydrogen bonding interactions between the adjacent repeating units. The poly-l-1100 behaves as a pH-responsive property; the helical structure of the main chain can be transformed to random coil by addition of trifluoroacetic acid to the THF solution which again switches back to helical conformation by neutralization with triethylamine. It was confirmed that the copolymerization of l-1 and d-1 obeyed the majority rule as supported by the nonlinear correlation between the enantiomeric excess of monomer 1 with the CD intensities of the generated copolymers. Atomic force microscope (AFM) and scanning electron microscope (SEM) studies revealed poly-l-1100 self-assembled into well-defined helical fibrils with distinct handedness.

Gas-phase helical peptides mimic solution-phase behavior.

In solution, α-helices are stabilized at the termini by a variety of different capping interactions. Study of these interactions in the gas phase provides a unique means to explore the intrinsic properties that cause this stabilization. Evidence of helical and globular conformations is presented here for gas-phase, doubly charged peptides of sequence XAnK, wherein X is D, N, Q, or L. The relative abundance of the helical conformation is found to vary as a function of peptide length and the identity of the first amino acid, consistent with solution phase studies that have looked at the identity of the first amino acid. The N-terminal, b ion fragments of the doubly charged precursor peptides are shown to form helical and globular conformations. The stability of the helical fragments is examined as a function of fragment length, N-terminal amino acid, precursor conformation, and the activation energy used to generate the fragment. At lower collision energies, helical b ions preferentially form, particularly from helical precursors. The abundance of the helical b ion population is observed to dramatically decrease for NAn and DAn b ions smaller than the b10; simulations suggest this feature is due to the b10 having two complete turns of the helix, while the b9 and smaller ions have only a partial second turn, suggesting the b10 is the lower limit for stable helical conformations in b ions. Use of higher collision energies promotes the formation of globular structures in the b ions. This characteristic is attributed to increased conformational dynamics and subsequently improved proton transfer kinetics from the b ion's C-terminal oxazolone ring to the N-terminus.

Aromatic triazole foldamers induced by C-H···X (X = F, Cl) intramolecular hydrogen bonding.

Aryl-triazole oligomers based on isobutyl 4-fluorobenzoate and isobutyl 4-chlorobenzoate were designed and synthesized. Crystal structure and (1)H-(1)H NOESY experiments demonstrate that the oligomers adopt stable helical conformation, which are induced by C(5)-H···X-C (X = F, Cl) intramolecular hydrogen bonding between triazole protons and halogen atoms. The stabilities of the folded conformations are confirmed by DFT calculations, which show that each C(5)-H···F-C planar interaction lowers the energy by ~3 kcal mol(-1) on average, and by ~1 kcal mol(-1) when C(5)-H···Cl-C bridges are formed. The hydrogen-bonding networks are disrupted in competitive hydrogen-bonding media such as DMSO, generating the unfolded oligomers.

Conformational Analysis of the Frog Skin Peptide, Plasticin-L1 and its Effects on the Production of Proinflammatory Cytokines by Macrophages

Plasticin-L1 (GLVNGLLSSVLGGGQGGGGLLGGIL) is a conformationally flexible glycine/leucine-rich peptide originally isolated from norepinephrine-stimulated skin secretions of the South-American Santa Fe frog Leptodactylus laticeps (Leptodactylidae). A nuclear magnetic resonance (NMR)/molecular dynamics (MD) characterization of plasticin-L1 in the presence of dodecylphosphocholine (DPC) and DPC/sodium dodecylsulphate (SDS) micelles as membrane-mimetic models showed that the peptide has affinity for both neutral and anionic membranes. The peptide adopts a stable helical conformation at the N-terminal region and a more disordered helix at the C-terminal region, separated by an unstructured loop wherein the highest number of glycines is localized. In both micelle environments, plasticin-L1 slowly inserts between the detergent head groups, but always remains localized at the micelle/water interface. Plasticin-L1 lacks direct antimicrobial activity but stimulates cytokine production by macrophages. Incubation with plasticin-L1 (20 µg/mL) significantly (P < 0.05) increased the production of the proinflammatory cytokines IL-1β, IL-12 IL-23 and TNF-α from unstimulated peritoneal macrophages from both C57BL/6 and BALB/C mice. The peptide also increased IL-6 production by unstimulated (P < 0.01) and lipopolysaccharide-stimulated (P < 0.01) macrophages, while the effects on production of the anti-inflammatory cytokine IL-10 were not significant. These findings suggest that plasticin-L1 may play an immunomodulatory role in vivo by stimulating cytokine production from frog skin macrophages in response to microbial pathogens. This peptide may represent a template for the design of peptides with therapeutic applications as immunostimulatory agents.

Helical structures of unnatural peptides for biological applications

Many important biological functions involve the recognition of helical domains of natural proteins. A number of strategies have been developed to mimic natural helices in proteins. Unnatural peptides are constructed with incorporation of artificial building blocks other than α-amino acid residues, and could adopt stable helical conformations. These nontraditional helical oligomers have been explored to mimic biological functions involved with helical domains of natural proteins. This review provides representative examples of the mimicry of natural peptide helices with unnatural ones and related biological applications.

Conformational Analysis of the Frog Skin Peptide, Plasticin-L1, and Its Effects on Production of Proinflammatory Cytokines by Macrophages

Plasticin-L1 (GLVNGLLSSVLGGGQGGGGLLGGIL) is a conformationally flexible glycine/leucine-rich peptide originally isolated from norepinephrine-stimulated skin secretions of the South-American Santa Fe frog Leptodactylus laticeps (Leptodactylidae). A nuclear magnetic resonance/molecular dynamics characterization of plasticin-L1 in the presence of dodecylphosphocholine (DPC) and DPC/sodium dodecylsulphate micelles as membrane-mimetic models showed that the peptide has affinity for both neutral and anionic membranes. The peptide adopts a stable helical conformation at the N-terminal region and a more disordered helix at the C-terminal region, separated by an unstructured loop wherein the highest number of glycines is localized. In both micelle environments, plasticin-L1 slowly inserts between the detergent head groups but always remains localized at the micelle/water interface. Plasticin-L1 lacks direct antimicrobial activity but stimulates cytokine production by macrophages. Incubation with plasticin-L1 (20 μg/mL) significantly (P < 0.05) increased the production of the proinflammatory cytokines IL-1β, IL-12, IL-23, and TNF-α from unstimulated peritoneal macrophages from both C57BL/6 and BALB/C mice. The peptide also increased IL-6 production by unstimulated (P < 0.01) and lipopolysaccharide-stimulated (P < 0.01) macrophages, whereas the effects on production of the anti-inflammatory cytokine IL-10 were not significant. These findings suggest that plasticin-L1 may play an immunomodulatory role in vivo by stimulating cytokine production from frog skin macrophages in response to microbial pathogens. This peptide may represent a template for the design of peptides with therapeutic applications as immunostimulatory agents.

Remarkable Structure Effects on Chiroptical Properties of Polyisocyanides Carrying Proline Pendants

Chiral polymers with simple chemical structures and high helical conformation stabilities are important for their applications as chiral supports and asymmetrical catalysts. We report herein the synthesis of a series of aliphatic polyisocyanides carrying proline pendants of different chiralities, and an investigation of the effects of the chemical structures of these pendants on the chiroptical properties of the polymers. The configuration of the chiral center at the 4-position of the proline pendants was changed from S to R to check its effect on the handedness of the helical conformation. To examine the effects of steric hindrance on the stabilities of the helical conformation for these aliphatic representatives, proline pendants with various substituents at both the carboxyl and amine terminals were designed. To further examine the steric effects of the proline pendants, aromatic counterparts were also prepared. In the latter case, the effects of hydrogen bonds between pendant units on the enhancement and stabilities of the helical conformation were investigated by switching from the ester to an amide linkage. The Cotton effects and signal intensities of both aliphatic and aromatic polyisocyanides from circular dichroism spectroscopy were compared based on the bulkiness of the pendant groups, solvent polarities, and solution temperatures. It was found that highly stable helical conformations of polyisocyanides could be imposed by small bulky monoproline pendants.