Synthesis and conformational analysis of efrapeptins

The efrapeptin family of peptide antibiotics produced by the fungus Tolypocladium niveum, and the neo‐efrapeptins from the fungus Geotrichum candidumare inhibitors of F₁‐ATPase with promising antitumor, antimalaria, and insecticidal activity. They are rich in C^α‐dialkyl amino acids (Aib, Iva, Acc) and contain one β‐alanine and several pipecolic acid residues. The C‐terminus bears an unusual heterocyclic cationic cap. The efrapeptins C–G and three analogues of efrapeptin C were synthesized using α‐azido carboxylic acids as masked amino acid derivatives. All compounds display inhibitory activity toward F₁‐ATPase. The conformation in solution of the peptides was investigated with electronic CD spectroscopy, FT‐IR spectroscopy, and VCD spectroscopy. All efrapeptins and most efrapeptin analogues were shown to adopt helical conformations in solution. In the case of efrapeptin C, VCD spectra proved that a 3₁₀‐helix prevails. In addition, efrapeptin C was conformationally studied in detail with NMR and molecular modeling. Besides NOE distance restraints, residual dipolar couplings (RDC) observed upon partial alignment with stretched PDMS gels were used for the conformational analysis and confirmed the 3₁₀‐helical conformation.     

Do Valine Side Chains Have an Influence on the Folding Behavior of β‐Substituted β‐Peptides?

The influence of valine side chains on the folding/unfolding equilibrium and, in particular, on the 3₁₄‐helical propensity of β³‐peptides were investigated by means of molecular‐dynamics (MD) simulation. To that end, the valine side chains in two different β³‐peptides were substituted by leucine side chains. The resulting four peptides, of which three have never been synthesized, were simulated for 150 to 200 ns at 298 and 340 K, starting from a fully extended conformation. The simulation trajectories obtained were compared with respect to structural preferences and folding behavior. All four peptides showed a similar folding behavior and were found to predominantly adopt 3₁₄‐helical conformations, irrespective of the presence of valine side chains. No other well‐defined conformation was observed at significant population in any of the simulations. Our results imply that β³‐peptides show a structural preference for 3₁₄‐helices independent of the branching nature of the side chains, in contrast to what has been previously proposed on the basis of circular‐dichroism (CD) measurements.     

Oriented Nanoporous Host δ Phases of Syndiotactic Polystyrene as a Tool for Spectroscopic Investigation of Guest Molecules

An efficient method to align low-molecular-mass molecules by enclosing them as isolated guests of the nanoporous host δ phase of syndiotactic polystyrene oriented films, is presented. This new method is compared with the classic method consisting in the absorption of low- molecular-mass molecules as a solute of amorphous phases of highly oriented semicrystalline polymeric films. It is shown that this new molecular alignment method provides a powerful tool to study in detail several features (spectroscopic properties, molecular motions) of relevant molecules, by separating with unprecedented selectivity their anisotropic spectral responses. The reported results refer to infrared and solid-state-²H-NMR spectra.     

NMR “Crystallography” for Uniformly (13C, 15N)‐Labeled Oriented Membrane Proteins

In oriented‐sample (OS) solid‐state NMR of membrane proteins, the angular‐dependent dipolar couplings and chemical shifts provide a direct input for structure calculations. However, so far only ¹H–¹⁵N dipolar couplings and ¹⁵N chemical shifts have been routinely assessed in oriented ¹⁵N‐labeled samples. The main obstacle for extending this technique to membrane proteins of arbitrary topology has remained in the lack of additional experimental restraints. We have developed a new experimental triple‐resonance NMR technique, which was applied to uniformly doubly (¹⁵N, ¹³C)‐labeled Pf1 coat protein in magnetically aligned DMPC/DHPC bicelles. The previously inaccessible ¹H_α–¹³C_α dipolar couplings have been measured, which make it possible to determine the torsion angles between the peptide planes without assuming α‐helical structure a priori. The fitting of three angular restraints per peptide plane and filtering by Rosetta scoring functions has yielded a consensus α‐helical transmembrane structure for Pf1 protein.     

Induction of Helical Structure by Sesamin,and Production of Oriented Helical Polymer with Liquid Crystal Magneto‐Electrochemical Polymerization

Sesamin was employed as a chiral dopant for preparing cholesteric liquid crystals with right‐handed helical architecture. Helical twisting power of sesamin is to be 13.4 μm^?1. Electrochemical polymerizations were carried out with sesamin‐induced cholesteric liquid crystal electrolyte solution for obtaining conjugated polymer films with helical structure. The film was transcribed the helical order from the liquid crystal electrolyte solution with helical structure produced by sesamin during the polymerization process. The helical axes of the macromolecular superstructure of the polymer films were oriented in a magnetic field of 4.5 T. This results demonstrated liquid crystal magneto‐electrochemical polymerization with helical structure induced by sesamin as a natural chiral compound. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55 , 1894–1899     

Delivering Structural Information on the Polar Face of Membrane‐Active Peptides: 19F‐NMR Labels with a Cationic Side Chain

Conformationally constrained non‐racemizing trifluoromethyl‐substituted lysine isosteres [(E)‐ and (Z)‐TCBLys] with charged side chains are presented as a new type of ¹⁹F‐NMR labels for peptide studies. Design of the labels, their synthesis, incorporation into peptides and experimental demonstration of their application for solid state NMR studies of membrane‐active peptides are described. A series of fluorine‐labeled analogues of the helical amphipathic antimicrobial peptide PGLa(Nle) was obtained, in which different lysine residues in the original peptide sequence were replaced, one at a time, by either (E)‐ or (Z)‐TCBLys. Antimicrobial activities of the synthesized analogues were practically the same as those of the parent peptide. The structural and orientational parameters of the helical PGLa(Nle) peptide in model bilayers, as determined using the novel labels confirmed and refined the previously known structure. (E)‐ and (Z)‐TCBLys, as a set of cationic ¹⁹F‐NMR labels, were shown to deliver structural information about the charged face of amphipathic peptides by solid state ¹⁹F‐NMR, previously inaccessible by this method.     

NMR‐Solution Structures in Methanol of an α‐Heptapeptide,of a β3/β2‐Nonapeptide,and of an all‐β3‐Icosapeptide Carrying the 20 Proteinogenic Side Chains

The NMR‐solution structure of an α‐heptapeptide with a central Aib residue was investigated in order to verify that, in contrast to β‐peptides, short α‐peptides do not form a helical structures in MeOH. Although the central Aib residue was found to induce a bend in the experimentally determined structure, no secondary structure typical for longer α‐peptides or proteins was found. A β²/β³‐nonapeptide with polar, positively charged side chains was subjected to NMR analysis in MeOH and H₂O. Whereas, in MeOH, it folds into a 10/12‐helix very similar to the structure determined for a corresponding β²/β³‐nonapeptide with only aliphatic side chains, no dominant conformation could be determined in H₂O. Finally, the NMR analysis of a β³‐icosapeptide containing the side chains of all 20 proteinogenic amino acids in MeOH is described. It revealed that this 20mer folds into a 3₁₄‐helix over its whole length forming six full turns, the longest 3₁₄‐helix found so far. Together, our findings confirm that, in contrast to α‐peptides, β‐peptides not only form helices with just six residues, but also form helices that are longer than helical sections usually observed in proteins or natural peptides. The higher helix‐forming propensity of long β‐peptides is attributed to the conformation‐stabilizing effect of the staggered ethane sections in β‐peptides which outweighs the detrimental effect of the increasing macrodipole.     

Folding–Unfolding Equilibrium of a Methylidene‐Substituted β‐Peptide

β‐Peptides possess the ability to fold into secondary structure elements, and this property, together with resistance to biodegradation, makes these compounds interesting for pharmaceutical applications. Recently, a novel class of β‐peptides containing methylidene moieties was described. The GROMOS 53A6 force field was used to simulate the folding equilibrium of a β³‐hexapeptide with methylidene (CH₂?) groups at all six CA‐atoms. Due to the rotational barriers induced by these methylidene groups, the helical secondary‐structure elements, normally found in β³‐peptides, are disfavored in this molecule. Simulations, started from fully extended and 3₁₄‐helical conformations, showed that the molecule adopts a complete 2₈‐helix for ca. 5% of the time and partial 2₈‐helical conformations for ca. 20% of the time. Yet, as suggested by experiments, the folding equilibrium is dominated by unfolded conformations.     

Semi-Rigid Nitroxide Spin Label for Long-Range EPR Distance Measurements of Lipid Bilayer Embedded β-Peptides

β-Peptides are an interesting new class of transmembrane model peptides based on their conformationally stable and well-defined secondary structures. Herein, we present the synthesis of the paramagnetic β-amino acid β³-hTOPP (4-(3,3,5,5-tetramethyl-2,6-dioxo-4-oxylpiperazin-1-yl)-d -β³-homophenylglycine) that enables investigations of β-peptides by EPR spectroscopy. This amino acid adds to the, to date, sparse number of β-peptide spin labels. Its performance was evaluated by investigating the helical turn of a 3₁₄-helical transmembrane model β-peptide. Nanometer distances between two incorporated β³-hTOPP labels in different environments were measured by using pulsed electron/electron double resonance (PELDOR/DEER) spectroscopy. Due to the semi-rigid conformational design, the label delivers reliable distances and sharp (one-peak) distance distributions even in the lipid bilayer. The results indicate that the investigated β-peptide folds into a 3.25₁₄ helix and maintains this conformation in the lipid bilayer.     

Helix‐Forming Oligoureas: Temperature‐Dependent NMR,Structure Determination,and Circular Dichroism of a Nonamer with Functionalized Side Chains

To further investigate the degree of structural homology between γ‐peptides A and N,N′‐linked oligoureas B , we prepared oligourea nonamer 2 containing Ala, Val, Leu, Phe, Tyr and Lys side chains. Oligomer 2 was synthesized on solid support from activated monomers, i.e., from enantiomerically pure succinimidyl {2‐{[(9H‐fluoren‐9‐ylmethoxy)carbonyl]amino}ethyl}carbamates 3a – f that are further substituted at C(2) of the ethyl moiety. These precursors were conveniently prepared from N‐Fmoc‐protected β³‐amino acids with corresponding side chains. Detailed NMR studies (DQF‐COSY, TOCSY, and ROESY) in (D₅)pyridine revealed that 2 adopts a regular (P)‐2.5 helical secondary structure very similar to that previously determined for oligourea heptamer 1 and closely related to the (P)‐2.6₁₄ helix of γ‐peptides. Temperature‐dependent NMR further demonstrated the conformational homogeneity and remarkable stability of the structure of 2 in pyridine. The CD spectrum of 2 (0.2 mM ) was recorded in MeOH with the aim to gain more information about the conformation of oligoureas. In contrast to 2.6‐helical γ‐peptides, which display only a weak or no Cotton effect, oligourea 2 exhibits an intense positive Cotton effect at ca. 203 nm ([Θ]=+373000 deg cm² dmol⁻¹) that decreases only slowly upon increasing the temperature.     

Heavy‐Atom Labeled Transmembrane β‐Peptides: Synthesis,CD‐Spectroscopy,and X‐ray Diffraction Studies in Model Lipid Multilayer

Transmembrane β‐peptides are promising candidates for the design of well‐controlled membrane anchors in lipid membranes. Here, we present the synthesis of transmembrane β‐peptides with and without tryptophan anchors, as well as a novel iodine‐labeled d ‐β³‐amino acid. By using one or more of the heavy‐atom labeled amino acids as markers, the orientation of the helical peptide was inferred based on the electron‐density profile determined by X‐ray reflectivity. The β‐peptides were synthesized through manual Fmoc‐based solid‐phase peptide synthesis (SPPS) and reconstituted in unilamellar vesicles forming a right‐handed 3₁₄‐helix secondary structure, as shown by circular dichroism spectroscopy. We then integrated the β‐peptide into solid‐supported membrane stacks and carried out X‐ray reflectivity and grazing incidence small‐angle X‐ray scattering to determine the β‐peptide orientation and its effect on the membrane bilayers. These β‐peptides adopt a well‐ordered transmembrane motif in the solid‐supported model membrane, maintaining the basic structure of the original bilayer with some distinct alterations. Notably, the helical tilt angle, which accommodates the positive hydrophobic mismatch, induces a tilt of the acyl chains. The tilted chains, in turn, lead to a membrane thinning effect.     

Validation of the GROMOS 54A7 Force Field Regarding Mixed α/β‐Peptide Molecules

A molecular‐dynamics (MD) simulation study of two heptapeptides containing α‐ and β‐amino acid residues is presented. According to NMR experiments, the two peptides differ in dominant fold when solvated in MeOH: peptide 3 adopts predominantly β‐hairpin‐like conformations, while peptide 8 adopts a 14/15‐helical fold. The MD simulations largely reproduce the experimental data. Application of NOE atom? atom distance restraining improves the agreement with experimental data, but reduces the conformational sampling. Peptide 3 shows a variety of conformations, while still agreeing with the NOE and ³J‐coupling data, whereas the conformational ensemble of peptide 8 is dominated by one helical conformation. The results confirm the suitability of the GROMOS 54A7 force field for simulation or structure refinement of mixed α/β‐peptides in MeOH.     

Mixed β2/β3‐Hexapeptides and β2/β3‐Nonapeptides Folding to (P)‐Helices with Alternating Twelve‐ and Ten‐Membered Hydrogen‐Bonded Rings

The structural properties of four mixed β‐peptides with alternating β²/β³‐ or β³/β²‐sequences have been analyzed by two‐dimensional homonuclear ¹H‐NMR‐ and CD spectroscopic measurements. All four β‐peptides fold into (P)‐helices with twelve‐ and ten‐membered H‐bonded rings (Figs. 3–6). CD Spectra (Fig. 2) of the mixed β³/β²‐hexapeptide 4a and β³/β²‐nonapeptide 5a , indicating that peptides of this type also adopt the 12/10‐helical conformation, were confirmed by NMR structural analysis. For the deprotected β³/β²‐nonapeptide 5d , NOEs not consistent with the 10/12 helix have been observed, showing that the stability of the helix decreases upon N‐terminal deprotection. From the NMR structures obtained, an idealized helical‐wheel representation was generated (Fig. 7), which will be used for the design of further 12/10 or 10/12 helices.     

Helix Nucleation by the Smallest Known α‐Helix in Water

Cyclic pentapeptides (e.g. Ac‐(cyclo‐1,5)‐[KAXAD]‐NH₂; X=Ala, 1 ; Arg, 2 ) in water adopt one α‐helical turn defined by three hydrogen bonds. NMR structure analysis reveals a slight distortion from α‐helicity at the C‐terminal aspartate caused by torsional restraints imposed by the K(i)–D(i+4) lactam bridge. To investigate this effect on helix nucleation, the more water‐soluble 2 was appended to N‐, C‐, or both termini of a palindromic peptide ARAARAARA (≤5 % helicity), resulting in 67, 92, or 100 % relative α‐helicity, as calculated from CD spectra. From the C‐terminus of peptides, 2 can nucleate at least six α‐helical turns. From the N‐terminus, imperfect alignment of the Asp5 backbone amide in 2 reduces helix nucleation, but is corrected by a second unit of 2 separated by 0–9 residues from the first. These cyclic peptides are extremely versatile helix nucleators that can be placed anywhere in 5–25 residue peptides, which correspond to most helix lengths in protein–protein interactions.     

The Miraculous CD Spectra (and Secondary Structures?) of β‐Peptides as They Grow Longer,Preliminary Communication

The recently improved conditions for solid‐phase synthesis of β³‐peptides by the Fmoc strategy were used to synthesize a β‐tetracosapeptide ( 4 , Scheme) composed of eight different β‐amino acid residues; 11 of the 24 residues carry functionalized proteinogenic side chains (namely those of Glu, Lys, Ser, and Tyr). The highly H₂O‐soluble β‐tetracosapeptide was identified by ¹H‐NMR spectroscopy (in MeOH), analytical HPL chromatography, and ESI‐mass spectrometry (Fig. 1). The expected 3₁₄‐helical secondary structure of the new β‐peptide was designed to have one hydrophobic and two hydrophilic faces, and to be compared with other β‐peptides ( 1 – 3 ), two of which are also of amphipathic character in this secondary structure (Fig. 2). In the absence of NMR‐structural proof, the CD spectra of the four β‐peptides were compared (Figs. 3 and 4). The β‐tetracosapeptide exhibits an unprecedented CD pattern (in MeOH and in H₂O solution) that may arise from a new type of secondary structure or from an unordered conformation.     

The Propensity of α‐Aminoisobutyric Acid (=2‐Methylalanine; Aib) to Induce Helical Secondary Structure in an α‐Heptapeptide: A Computational Study

We present a molecular‐dynamics simulation study of an α‐heptapeptide containing an α‐aminoisobutyric acid (=2‐methylalanine; Aib) residue, Val¹‐Ala²‐Leu³‐Aib⁴‐Ile⁵‐Met⁶‐Phe⁷, and a quantum‐mechanical (QM) study of simplified models to investigate the propensity of the Aib residue to induce 3₁₀/α‐helical conformation. For comparison, we have also performed simulations of three analogues of the peptide with the Aib residue being replaced by L ‐Ala, D ‐Ala, and Gly, respectively, which provide information on the subtitution effect at C(α) (two Me groups for Aib, one for L ‐Ala and D ‐Ala, and zero for Gly). Our simulations suggest that, in MeOH, the heptapeptide hardly folds into canonical helical conformations, but appears to populate multiple conformations, i.e., C₇ and 3₁₀‐helical ones, which is in agreement with results from the QM calculations and NMR experiments. The populations of these conformations depend on the polarity of the solvent. Our study confirms that a short peptide, though with the presence of an Aib residue in the middle of the chain, does not have to fold to an α‐helical secondary structure. To generate a helical conformation for a linear peptide, several Aib residues should be present in the peptide, either sequentially or alternatively, to enhance the propensity of Aib‐containing peptides towards the helical conformation. A correction of a few of the published NMR data is reported.     

Efficient Access to Enantiopure γ4‐Amino Acids with Proteinogenic Side‐Chains and Structural Investigation of γ4‐Asn and γ4‐Ser in Hybrid Peptide Helices

Hybrid peptides composed of α‐ and β‐amino acids have recently emerged as new class of peptide foldamers. Comparatively, γ‐ and hybrid γ‐peptides composed of γ⁴‐amino acids are less studied than their β‐counterparts. However, recent investigations reveal that γ⁴‐amino acids have a higher propensity to fold into ordered helical structures. As amino acid side‐chain functional groups play a crucial role in the biological context, the objective of this study was to investigate efficient synthesis of γ⁴‐residues with functional proteinogenic side‐chains and their structural analysis in hybrid‐peptide sequences. Here, the efficient and enantiopure synthesis of various N‐ and C‐terminal free‐γ⁴‐residues, starting from the benzyl esters (COOBzl) of N‐Cbz‐protected (E)‐α,β‐unsaturated γ‐amino acids through multiple hydrogenolysis and double‐bond reduction in a single‐pot catalytic hydrogenation is reported. The crystal conformations of eight unprotected γ⁴‐amino acids (γ⁴‐Val, γ⁴‐Leu, γ⁴‐Ile, γ⁴‐Thr(OtBu), γ⁴‐Tyr, γ⁴‐Asp(OtBu), γ⁴‐Glu(OtBu), and γ‐Aib) reveals that these amino acids adopted a helix favoring gauche conformations along the central C^γ? C^β bond. To study the behavior of γ⁴‐residues with functional side chains in peptide sequences, two short hybrid γ‐peptides P1 (Ac‐Aib‐γ⁴‐Asn‐Aib‐γ⁴‐Leu‐Aib‐γ⁴‐Leu‐CONH₂) and P2 (Ac‐Aib‐γ⁴‐Ser‐Aib‐γ⁴‐Val‐Aib‐γ⁴‐Val‐CONH₂) were designed, synthesized on solid phase, and their 12‐helical conformation in single crystals were studied. Remarkably, the γ⁴‐Asn residue in P1 facilitates the tetrameric helical aggregations through interhelical H bonding between the side‐chain amide groups. Furthermore, the hydroxyl side‐chain of γ⁴‐Ser in P2 is involved in the interhelical H bonding with the backbone amide group. In addition, the analysis of 87 γ⁴‐residues in peptide single‐crystals reveal that the γ⁴‐residues in 12‐helices are more ordered as compared with the 10/12‐ and 12/14‐helices.     

NMR spectra of chiral smectic liquid crystals differing in helical parameters

Chiral liquid crystals with three-ring rigid core were examined. The method based on the selectively reflected light was used to determine the helical pitch. The helical twist sense was worked out using the polarimetry method. ¹H and ¹³C NMR measurements were performed. The influence of three molecular structure parameters: the type of chiral centre, the length of non-chiral chain and substitution of benzene ring by fluorine atoms, on helical pitch, handedness of helical structure and values of chemical shift in proton and carbon spectra was determined. The change of the length of non-chiral terminal chain has the most significant influence on the temperature dependence of helical pitch. All tested parameters have the biggest influence on the values of chemical shift of atoms in the chiral centre.     

Can Helical Peptides Unwind One Turn at a Time? ‐ Controlled Conformational Transitions in α,β2,3‐Hybrid Peptides

Unfolding of helical trans‐β^2,3‐hybrid peptides with (α–β)_nα composition, when executed by increasing solvent polarity or temperature, proceeded in a systematic manner with the turns unwinding sequentially; C‐terminal region of these peptides were first to unwind and the process propagated towards N terminus with more and more β residues equilibrating from the gauche to the anti rotameric state across C_α?C_β. This is evidenced by clear change in their C_βH signal splitting, ³J_CαH–CβH values, and sequential disappearance of i,i+2 NOEs.     

Introducing the Petasis Reaction for Late‐Stage Multicomponent Diversification,Labeling, and Stapling of Peptides

For the first time, the Petasis (borono‐Mannich) reaction is employed for the multicomponent labeling and stapling of peptides. The report includes the solid‐phase derivatization of peptides at the N‐terminus, Lys, and N^?‐MeLys side‐chains by an on‐resin Petasis reaction with variation of the carbonyl and boronic acid components. Peptides were simultaneously functionalized with aryl/vinyl substituents bearing fluorescent/affinity tags and oxo components such as dihydroxyacetone, glyceraldehyde, glyoxylic acid, and aldoses, thus encompassing a powerful complexity‐generating approach without changing the charge of the peptides. The multicomponent stapling was conducted in solution by linking N^?‐MeLys or Orn side‐chains, positioned at i, i+7 and i, i+4, with aryl tethers, while hydroxy carbonyl moieties were introduced as exocyclic fragments. The good efficiency and diversity oriented character of these methods show prospects for peptide drug discovery and chemical biology.