Nanoscale Helical Optical Force for Determining Crystal Chirality.

The deterministic control of material chirality has been a sought-after goal. As light possesses intrinsic chirality, light-matter interactions offer promising avenues for achieving non-contact, enantioselective optical induction, assembly, or sorting of chiral entities. However, experimental validations are confined to the microscale due to the limited strength of asymmetrical interactions within sub-diffraction limit ranges. In this study, a novel approach is presented to facilitate chirality modulation through chiral crystallization using a helical optical force field originating from localized nanogap surface plasmon resonance. The force field emerges near a gold trimer nanogap and is propelled by linear and angular momentum transfer from the incident light to the resonant nanogap plasmon. By employing Gaussian and Laguerre-Gaussian incident laser beams, notable enantioselectivity is achieved through low-power plasmon-induced chiral crystallization of an organic compound-ethylenediamine sulfate. The findings provide new insights into chirality transmission orchestrated by the exchange of linear and angular momentum between light and nanomaterials.

Total synthesis of the natural, medium-length, peptaibol pentadecaibin and study of the chemical features responsible for its membrane activity.

Peptaibols are naturally occurring, antimicrobial peptides endowed with well-defined helical conformations and resistance to proteolysis. Both features stem from the presence in their sequence of several, Cα -tetrasubstituted, α-aminoisobutyric acid (Aib) residues. Peptaibols interact with biological membranes, usually causing their leakage. All of the peptaibol-membrane interaction mechanisms proposed so far begin with peptide aggregation or accumulation. The long-length alamethicin, the most studied peptaibol, acts by forming pores in the membranes. Conversely, the carpet mechanism has been claimed for short-length peptaibols, such as trichogin. The mechanism of medium-length peptaibols is far less studied, and this is partly due to the difficulties of their synthesis. They are believed to perturb membrane permeability in different ways, depending on the membrane properties. The present work focuses on pentadecaibin, a recently discovered, medium-length peptaibol. In contrast to the majority of its family members, its sequence does not comprise hydroxyprolines or prolines, and its helix is not kinked. A reliable and effective synthesis procedure is described that allowed us to produce also two shorter analogs. By a combination of techniques, we were able to establish a 3D-structure-activity relationship. In particular, the membrane activity of pentadecaibin heavily depends on the presence of three consecutive Aib residues that are responsible for the clear, albeit modest, amphiphilic character of its helix. The shortest analog, devoid of two of these three Aib residues, preserves a well-defined helical conformation, but not its amphipathicity, and loses almost completely the ability to cause membrane leakage. We conclude that pentadecaibin amphiphilicity is probably needed for the peptide ability to perturb model membranes.

Synthesis, Conformational Analysis and Antitumor Activity of the Naturally Occurring Antimicrobial Medium-Length Peptaibol Pentadecaibin and Spin-Labeled Analogs Thereof.

Peptaibols are proteolysis-resistant, membrane-active peptides. Their remarkably stable helical 3D-structures are key for their bioactivity. They can insert themselves into the lipid bilayer as barrel staves, or lay on its surface like carpets, depending on both their length and the thickness of the lipid bilayer. Medium-length peptaibols are of particular interest for studying the peptide-membrane interaction because their length allows them to adopt either orientation as a function of the membrane thickness, which, in turn, might even result in an enhanced selectivity. Electron paramagnetic resonance (EPR) is the election technique used to this aim, but it requires the synthesis of spin-labeled medium-length peptaibols, which, in turn, is hampered by the poor reactivity of the Cα-tetrasubstituted residues featured in their sequences. After several years of trial and error, we are now able to give state-of-the-art advice for a successful synthesis of nitroxide-containing peptaibols, avoiding deleted sequences, side reactions and difficult purification steps. Herein, we describe our strategy and itsapplication to the synthesis of spin-labeled analogs of the recently discovered, natural, medium-length peptaibol pentadecaibin. We studied the antitumor activity of pentadecaibin and its analogs, finding potent cytotoxicity against human triple-negative breast cancer and ovarian cancer. Finally, our analysis of the peptide conformational preferences and membrane interaction proved that pentadecaibinspin-labeling does not alter the biological features of the native sequence and is suitable for further EPR studies. The nitroxide-containing pentadecaibins, and their synthetic strategy described herein, will help to shed light on the mechanism of the peptide-membrane interaction of medium-length peptaibols.

Peptaibol Analogs Show Potent Antibacterial Activity against Multidrug Resistant Opportunistic Pathogens.

New classes of antibacterial drugs are urgently needed to address the global issue of antibiotic resistance. In this context, peptaibols are promising membrane-active peptides since they are not involved in innate immunity and their antimicrobial activity does not involve specific cellular targets, therefore reducing the chance of bacterial resistance development. Trichogin GA IV is a nonhemolytic, natural, short-length peptaibol active against Gram-positive bacteria and resistant to proteolysis. In this work, we report on the antibacterial activity of cationic trichogin analogs. Several peptides appear non-hemolytic and strongly active against many clinically relevant bacterial species, including antibiotic-resistant clinical isolates, such as Staphylococcus aureus, Acinetobacter baumannii, and extensively drug-resistant Pseudomonas aeruginosa, against which there are only a limited number of antibiotics under development. Our results further highlight how the modification of natural peptides is a valuable strategy for obtaining improved antibacterial agents with potential therapeutic applications.

Crystal Structure and NMR of an α,δ-Peptide Foldamer Helix Shows Side-Chains are Well Placed for Bifunctional Catalysis: Application as a Minimalist Aldolase Mimic.

We report the first NMR and X-ray diffraction (XRD) structures of an unusual 13/11-helix (alternating i, i+1 {NH-O=C} and i, i+3 {C=O-H-N} H-bonds) formed by a heteromeric 1 : 1 sequence of α- and δ-amino acids, and demonstrate the application of this framework towards catalysis. Whilst intramolecular hydrogen bonds (IMHBs) are the clear driver of helix formation in this system, we also observe an apolar interaction between the ethyl residue of one δ-amino acid and the cyclohexyl group of the next δ-residue in the sequence that seems to stabilize one type of helix over another. To the best of our knowledge this type of additional stabilization leading to a specific helical preference has not been observed before. Critically, the helix type realized places the α-residue functionalities in positions proximal enough to engage in bifunctional catalysis as demonstrated in the application of our system as a minimalist aldolase mimic.

Directing the Self-Assembly of Aromatic Foldamer Helices using Acridine Appendages and Metal Coordination.

Folded molecules provide complex interaction interfaces amenable to sophisticated self-assembly motifs. Because of their high conformational stability, aromatic foldamers constitute suitable candidates for the rational elaboration of self-assembled architectures. Several multiturn helical aromatic oligoamides have been synthesized that possess arrays of acridine appendages pointing in one or two directions. The acridine units were shown to direct self-assembly in the solid state via aromatic stacking leading to recurrent helix-helix association patterns under the form of discrete dimers or extended arrays. In the presence of Pd(II), metal coordination of the acridine units overwhelms other forces and generates new metal-mediated multihelical self-assemblies, including macrocycles. These observations demonstrate simple access to different types of foldamer-containing architectures, ranging from discrete objects to 1D and, by extension, 2D and 3D arrays.

Generalizing the Aromatic δ-Amino Acid Foldamer Helix.

A series of aromatic oligoamide foldamer sequences containing different proportions of three δ-amino acids derived from quinoline, pyridine, and benzene and possessing varying flexibility, for example due to methylene bridges, were synthesized. Crystallographic structures of two key sequences and 1 H NMR data in water concur to show that a canonical aromatic helix fold prevails in almost all cases and that helix stability critically depends on the ratio between rigid and flexible units. Notwithstanding subtle variations of curvature, i. e. the numbers of units per turn, the aromatic δ-peptide helix is therefore shown to be general and tolerant of a great number of sp3 centers. We also demonstrate canonical helical folding upon alternating two monomers that do not promote folding when taken separately: folding occurs with two methylenes between every other unit, not with one methylene between every unit. These findings highlight that a fine-tuning of helix handedness inversion kinetics, curvature, and side chain positioning in aromatic δ-peptidic foldamers can be realized by systematically combining different yet compatible δ-amino acids.

Effect of pendant stereostructure on backbone conformation and enantioseparation ability of helical polyacetylene-based chiral stationary phases.

Six proline-derived acetylene monomers bearing either two stereocenters (S-mR, S-mS, R-mS, Rac-mS and S-mRac) or one stereocenter (S-mBn) were obtained from commercially available N-(tert-butoxycarbonyl)-prolinal. Under the catalysis of Rh-diene complex, they were converted to the corresponding optically active helical polymers, S-pR, S-pS, R-pS, Rac-pS, S-pRac, and S-pBn. The correlations between configuration and position of stereocenters in pendants with the polymer conformation as well as chiral resolution performance were systematically explored by a combination of nuclear magnetic resonance (NMR), Raman, UV-Vis absorption, electronic/vibration circular dichroism spectroscopies, high-performance liquid chromatography (HPLC), and computational simulation. The configuration of the stereocenter adjacent to polymer mainchain determined the sense of helical conformation and the elution order of analytes, while that of the remote one affected the arrangement of pendants and the scope of analytes that could be discriminated. Among 18 aromatic analytes selected, S-pR could discriminate 10, while S-pS recognized 12. The racemization of adjacent or remote stereocenters greatly reduced the scope of analytes that could be resolved. Based on computer simulations, S-pS had larger recognition space than S-pR, favoring the steric fit with the racemates containing axial chirality. The strength and number of intermolecular hydrogen bondings between enantiomers and CSPs predominantly determined the chiral discrimination.

Differential Peptide Multi-Macrocyclizations at the Surface of a Helical Foldamer Template.

Hybrid sequences comprising a peptide with several Cys residues and an aromatic foldamer helix with several chloroacetamide functions at its surface were synthesized. Such products may in principle form numerous macromulticyclic thioether products by intramolecularly combining all Cys residues and all chloroacetamide functions. However, we show that the reactive sites on the structurally defined helix can be placed at such locations that the peptide selectively stitches itself to form a series of different macrocycles within mostly one preferred product. Reactions were monitored by HPLC and products with two, three or four macrocycles were identified using LC-MS and NMR. The series of selective macrocyclizations define a sort of reaction trail where reaction sites otherwise identical are involved successively because of their precise positioning in space. The trails can be predicted to a large extent based on structural considerations and the assumption that smaller macrocycles form faster.

Accelerated Mechanochemistry in Helical Polymers.

Polymer chains, if long enough, are known to undergo bond scission when mechanically stressed. While the mechanochemical response of random coils is well understood, biopolymers and some key synthetic chains adopt well-defined secondary structures such as helices. To understand covalent mechanochemistry in such structures, poly(γ-benzyl glutamates) are prepared while regulating the feed-monomer chirality, producing chains with similar molecular weights and backbone chemistry but different helicities. Such chains are stressed in solution and their mechanochemistry rates compared by following molecular weight change and using a rhodamine mechanochromophore. Results reveal that while helicity itself is not affected by the covalent bond scissions, chains with higher helicity undergo faster mechanochemistry. Considering that the polymers tested differ only in conformation, these results indicate that helix-induced chain rigidity improves the efficiency of mechanical energy transduction.

Synthesis of Alternating Polyisocyanate Copolymers by Anionic Polymerization for Mimicking Amphiphilic Helical Peptides.

The amphiphilic conformation of α-helical peptides has important biological functions, such as ion transport, antifreeze, and innate immunity, which can be mimicked by alternating polyisocyanate copolymers. We synthesized poly(allyl isocyanate-alt-(S)-(-)-α-methylbenzyl isocyanate (P(AIC-alt-SMBIC)) and ammonium-containing P(AIC-alt-SMBIC) (N-P(AIC-alt-SMBIC)), ensuring the amphiphilic helical conformation. The benzyl group of SMBIC plays an important role in alternating copolymerization with its steric and electron-withdrawing effects, while AIC provides an alkene group capable of introducing a customized functional group. The P(AIC-alt-SMBIC) with predominantly alternating sequence was acquired at fSMBIC /fAIC =8 with a controlled molecular weight and narrow dispersity. N-P(AIC-alt-SMBIC)s were synthesized from thiol-ene radical addition with P(AIC-alt-SMBIC).

Discrete Stacked Dimers of Aromatic Oligoamide Helices.

Tight binding was observed between the C-terminal cross section of aromatic oligoamide helices in aqueous solution, leading to the formation of discrete head-to-head dimers in slow exchange on the NMR timescale with the corresponding monomers. The nature and structure of the dimers was evidenced by 2D NOESY and DOSY spectroscopy, mass spectrometry and X-ray crystallography. The binding interface involves a large hydrophobic aromatic surface and hydrogen bonding. Dimerization requires that helices have the same handedness and the presence of a C-terminal carboxy function. The protonation state of the carboxy group plays a crucial role, resulting in pH dependence of the association. Dimerization is also influenced by neighboring side chains and can be programmed to selectively produce heteromeric aggregates.

Nuclear magnetic resonance studies on conformation and stability of mastoparan in methanol.

Mastoparan is a small peptide composed of 14 amino acid residues found in wasp venom. It penetrates into cytoplasm through the cell membranes and then binds to a G protein to stimulate the release of histamine. Conformation and its thermal stability of mastoparan from Vespula lewisi (MP) in methanol are investigated by using proton nuclear magnetic resonance (NMR) spectroscopy. On the basis of data on NOESY cross peaks, spin-spin coupling constants between an amide proton (NH) and an α-proton, NH chemical shift analyses, and temperature dependence of integrated intensity of NH resonance lines, we found that MP forms the helix between the 5th and 12th residues at low temperatures and the helix segment is maintained even at 54°C. This conformation is similar to that of MP bound to detergent micelles, and hence, methanol is considered to be appropriate as a membrane mimetic for MP. In connection with the function of the venom peptide, significance of high stability of the helical conformation is discussed.

Dutch Resolution of a configurationally stable [5]helquat.

Synthesis and nontrivial optical resolution of a helicene-like dication, helquat 1, has been accomplished. Starting with gram scale of the racemic helquat 1 sample, Dutch Resolution using family of 3 tartrate anions was key to achieve successful separation of M and P helical enantiomers of 1. Hundreds of milligrams of each enantiomer of this configurationally stable C2 -symmetric helquat have been obtained. Racemization barrier of 1 has been determined. To our knowledge this is the first report on Dutch Resolution performed with a helicene-like compound. Moreover, there are no literature precedents for Dutch Resolution of chiral quaternary ammonium cations.

N-terminal diproline and charge group effects on the stabilization of helical conformation in alanine-based short peptides: CD studies with water and methanol as solvent.

Protein folding problem remains a formidable challenge as main chain, side chain and solvent interactions remain entangled and have been difficult to resolve. Alanine-based short peptides are promising models to dissect protein folding initiation and propagation structurally as well as energetically. The effect of N-terminal diproline and charged side chains is assessed on the stabilization of helical conformation in alanine-based short peptides using circular dichroism (CD) with water and methanol as solvent. A1 (Ac-Pro-Pro-Ala-Lys-Ala-Lys-Ala-Lys-Ala-NH2 ) is designed to assess the effect of N-terminal homochiral diproline and lysine side chains to induce helical conformation. A2 (Ac-Pro-Pro-Glu-Glu-Ala-Ala-Lys-Lys-Ala-NH2 ) and A3 (Ac-dPro-Pro-Glu-Glu-Ala-Ala-Lys-Lys-Ala-NH2 ) with N-terminal homochiral and heterochiral diproline, respectively, are designed to assess the effect of Glu...Lys (i, i + 4) salt bridge interactions on the stabilization of helical conformation. The CD spectra of A1, A2 and A3 in water manifest different amplitudes of the observed polyproline II (PPII) signals, which indicate different conformational distributions of the polypeptide structure. The strong effect of solvent substitution from water to methanol is observed for the peptides, and CD spectra in methanol evidence A2 and A3 as helical folds. Temperature-dependent CD spectra of A1 and A2 in water depict an isodichroic point reflecting coexistence of two conformations, PPII and ß-strand conformation, which is consistent with the previous studies. The results illuminate the effect of N-terminal diproline and charged side chains in dictating the preferences for extended-ß, semi-extended PPII and helical conformation in alanine-based short peptides. The results of the present study will enhance our understanding on stabilization of helical conformation in short peptides and hence aid in the design of novel peptides with helical structures. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

Metal-Coordination-Assisted Folding and Guest Binding in Helical Aromatic Oligoamide Molecular Capsules.

The development of foldamer-based receptors is driven by the design of monomers with specific properties. Herein, we introduce a pyridazine-pyridine-pyridazine diacid monomer and its incorporation into helical aromatic oligoamide foldamer containers. This monomer codes for a wide helix diameter and can sequester metal ions on the inner wall of the helix cavity. Crystallographic studies and NMR titrations show that part of the metal coordination sphere remains available and may then promote the binding of a guest within the cavity. In addition to metal coordination, binding of the guest is assisted by cooperative interactions with the helix host, thereby resulting in significant enhancements depending on the foldamer sequence, and in slow guest capture and release on the NMR time scale. In the absence of metal ions, the pyridazine-pyridine-pyridazine monomer promotes an extended conformation of the foldamer that results in aggregation, including the formation of an intertwined duplex.

Crystal structure of DPF3b in complex with an acetylated histone peptide.

Histone acetylation plays an important role in chromatin dynamics and is associated with active gene transcription. This modification is written by acetyltransferases, erased by histone deacetylases and read out by bromodomain containing proteins, and others such as tandem PHD fingers of DPF3b. Here we report the high resolution crystal structure of the tandem PHD fingers of DPF3b in complex with an H3K14ac peptide. In the complex structure, the histone peptide adopts an α-helical conformation, unlike previously observed by NMR, but similar to a previously reported MOZ-H3K14ac complex structure. Our crystal structure adds to existing evidence that points to the α-helix as a natural conformation of histone tails as they interact with histone-associated proteins.

Glycosaminoglycan and DNA Binding Induced Intra- and Intermolecular Exciton Coupling of the bis-4-Aminoquinoline Surfen.

Despite the diverse biological activities of the glycosaminoglycan (GAG) antagonist surfen, the molecular details of its interaction with biomacromolecules remain poorly understood. Therefore, heparin and DNA binding properties of surfen were studied by circular dichroism (CD) and UV absorption spectroscopy methods. High-affinity (Ka ~ 10(7) M(-1)) association of surfen to the chiral heparin chain gives rise to a characteristic biphasic CD pattern due to the conformational twist of the aminoquinoline moieties around the central urea bridge. At higher drug loading, intermolecular stacking of surfen molecules alters the induced CD profile and also provokes strong UV hypochromism. In contrast to the right-handed heparin template, binding of surfen to the left-helicity chondroitin sulfate chains produces inverted CD pattern. Large UV hypochromism as well as polyphasic induced ellipticity bands indicate that surfen intercalates between the base pairs of calf-thymus DNA. Extensive CD spectroscopic changes observed at higher drug binding ratios refer to cooperative binding interactions between the intercalated drug molecules. The inherent conformational flexibility of surfen demonstrated here for the first time is important in its binding to distinct macromolecular targets and should be considered for rational drug design of novel GAG antagonists.

Helix stability of oligoglycine, oligoalanine, and oligo-ß-alanine dodecamers reflected by hydrogen-bond persistence.

Helices are important structural/recognition elements in proteins and peptides. Stability and conformational differences between helices composed of α- and ß-amino acids as scaffolds for mimicry of helix recognition has become a theme in medicinal chemistry. Furthermore, helices formed by ß-amino acids are experimentally more stable than those formed by α-amino acids. This is paradoxical because the larger sizes of the hydrogen-bonding rings required by the extra methylene groups should lead to entropic destabilization. In this study, molecular dynamics simulations using the second-generation force field, AMOEBA (Ponder, J.W., et al., Current status of the AMOEBA polarizable force field. J Phys Chem B, 2010. 114(8): p. 2549-64.) explored the stability and hydrogen-bonding patterns of capped oligo-ß-alanine, oligoalanine, and oligoglycine dodecamers in water. The MD simulations showed that oligo-ß-alanine has strong acceptor+2 hydrogen bonds, but surprisingly did not contain a large content of 3(12) -helical structures, possibly due to the sparse distribution of the 3(12) -helical structure and other structures with acceptor+2 hydrogen bonds. On the other hand, despite its backbone flexibility, the ß-alanine dodecamer had more stable and persistent <3.0 Å hydrogen bonds. Its structure was dominated more by multicentered hydrogen bonds than either oligoglycine or oligoalanine helices. The 3(1) (PII) helical structure, prevalent in oligoglycine and oligoalanine, does not appear to be stable in oligo-ß-alanine indicating its competition with other structures (stacking structure as indicated by MD analyses). These differences are among the factors that shape helical structural preferences and the relative stabilities of these three oligopeptides.

Crystal structure of N-(tert-but-oxy-carbon-yl)glycyl-(Z)-ß-bromo-dehydro-alanine methyl ester [Boc-Gly-(ß-Br)((Z))ΔAla-OMe].

The title compound, C11H17BrN2O5, is a de-hydro-amino acid with a C=C bond between the α- and ß-C atoms. The amino acid residues are linked trans to each other and there are no strong intra-molecular hydrogen bonds. The torsion angles indicate a non-helical conformation of the mol-ecule. The dipeptide folding is influenced by an inter-molecular N-H⋯O hydrogen bond and also minimizes steric repulsion. In the crystal, mol-ecules are linked by strong N-H⋯O hydrogen bonds, generating (001) sheets. The sheets are linked by weak C-H⋯O and C-H⋯Br bonds and short Br⋯Br [3.4149 (3) Å] inter-actions.