Conformational Studies on Peptides of α‐Aminoxy Acids with Functionalized Side‐Chains

Peptides of homochiral α‐aminoxy acids of nonpolar side chains can form a 1.8₈‐helix. In this paper, we report the conformational studies of α‐aminoxy peptides 1 , 2 , 3 , which have functionalized side chains, in both nonpolar and polar solvents. ¹H NMR, XRD, and FTIR absorption studies confirm the presence of the eight‐membered‐ring intramolecular hydrogen bonds (the N‐O turns) in nonpolar solvents as well as in methanol. CD studies of peptides 1 , 2 , 3 in different solvents indicate that a substantial degree of helical content is retained in methanol and acidic aqueous buffers. The introduction of functionalized side chains in α‐aminoxy peptides provides opportunities for designing biologically active peptides.     

侧链间氢键的协同效应对环状多肽自组装的影响

运用密度泛函(DFT)B3LYP方法和半经验分子轨道方法AM1对四种环状多肽[-(L-Asn-Ala)4-], [-(L-Asp-Ala)4-], [-(L-Gln-Ala)4-] 和[-(L-Glu-Ala)4-]的单体、平行和反平行二聚体到十聚体进行了理论研究. 结果表明, 四种环状多肽无论以平行还是以反平行的方式聚集, 聚集体中相邻两个环状多肽的侧链之间都能形成氢键. 侧链间氢键的相互作用使得这些环状多肽在组装过程中的结构和能量变化均表现出一定的协同效应, 这种协同效应加强了多肽纳米管的稳定性, 同时对聚集模式的选取起到了决定性作用.     

cis‐Peptide Bonds: A Key for Intestinal Permeability of Peptides?

Recent structural studies on libraries of cyclic hexapeptides led to the identification of common backbone conformations that may be instrumental to the oral availability of peptides. Furthermore, the observation of differential Caco‐2 permeabilities of enantiomeric pairs of some of these peptides strongly supports the concept of conformational specificity driven uptake and also suggests a pivotal role of carrier‐mediated pathways for peptide transport, especially for scaffolds of polar nature. This work presents investigations on the Caco‐2 and PAMPA permeability profiles of 13 selected N‐methylated cyclic pentaalanine peptides derived from the basic cyclo(‐D ‐Ala‐Ala₄‐) template. These molecules generally showed moderate to low transport in intestinal epithelia with a few of them exhibiting a Caco‐2 permeability equal to or slightly higher than that of mannitol, a marker for paracellular permeability. We identified that the majority of the permeable cyclic penta‐ and hexapeptides possess an N‐methylated cis‐peptide bond, a structural feature that is also present in the orally available peptides cyclosporine A and the tri‐N‐methylated analogue of the Veber–Hirschmann peptide. Based on these observations it appears that the presence of N‐methylated cis‐peptide bonds at certain locations may promote the intestinal permeability of peptides through a suitable conformational preorganization.     

Conformational flexibility, internal hydrogen bonding, and passive membrane permeability: successful in silico prediction of the relative permeabilities of cyclic peptides

We report an atomistic physical model for the passive membrane permeability of cyclic peptides. The computational modeling was performed in advance of the experiments and did not involve the use of "training data". The model explicitly treats the conformational flexibility of the peptides by extensive conformational sampling in low (membrane) and high (water) dielectric environments. The passive membrane permeabilities of 11 cyclic peptides were obtained experimentally using a parallel artificial membrane permeability assay (PAMPA) and showed a linear correlation with the computational results with R(2) = 0.96. In general, the results support the hypothesis, already well established in the literature, that the ability to form internal hydrogen bonds is critical for passive membrane permeability and can be the distinguishing factor among closely related compounds, such as those studied here. However, we have found that the number of internal hydrogen bonds that can form in the membrane and the solvent-exposed polar surface area correlate more poorly with PAMPA permeability than our model, which quantitatively estimates the solvation free energy losses upon moving from high-dielectric water to the low-dielectric interior of a membrane.     

Triazine‐Based Sequence‐Defined Polymers with Side‐Chain Diversity and Backbone–Backbone Interaction Motifs

Sequence control in polymers, well‐known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence‐defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone–backbone interactions, including H‐bonding motifs and pi–pi interactions. This architecture is arguably biomimetic while differing from sequence‐defined polymers having peptide bonds. The synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone–backbone hydrogen‐bonding motifs, and will thus enable new macromolecules and materials with useful functions.     

The Carbonyl⋅⋅⋅Tellurazole Chalcogen Bond as a Molecular Recognition Unit: From Model Studies to Supramolecular Organic Frameworks

In the last years, chalcogen bonding, the noncovalent interaction involving chalcogen centers, has emerged as interesting alternative to the ubiquitous hydrogen bonding in many research areas. Here, we could show by means of high‐level quantum chemical calculations that the carbonyl???tellurazole chalcogen bond is at least as strong as conventional hydrogen bonds. Using the carbonyl???tellurazole binding motif, we were able to design complex supramolecular networks in solid phase starting from tellurazole‐substituted cyclic peptides. X‐ray analyses reveal that the rigid structure of the cyclic peptides is caused by hydrogen bonds, whereas the supramolecular network is held together by chalcogen bonding. The type of the supramolecular network depends on peptide used; both linear wires and a honeycomb‐like supramolecular organic framework (SOF) were observed. The unique structure of the SOF shows two channels filled with different types of solvent mixtures that are either locked or freely movable.     

Influence of hydrogen bonds between sidechains and cooperativity on self‐assembly of the cyclopeptides

The self‐assembly of four cyclic D,L‐octapeptides, [‐(D‐Ala‐Gln)₄‐], [‐(D‐Val‐Gln)₄‐], [‐(D‐Leu‐Gln)₄‐], and [‐(D‐Phe‐Gln)₄‐], was investigated on the theory level in detail. Based on these cyclic peptides, which contain L‐Gln residues and possess C₄ symmetry, a series of oligomers were constructed according to different stacking modes as well as interaction patterns. We employed the semiempirical molecular orbital method AM1 to optimize the structures of all the oligomers, some of which were further studied using density functional method B3PW91/6‐31G to calculate the interaction energies. The studies indicate that when these cyclopeptides aggregate to form oligomers, or even nanotubes, four more hydrogen bonds could form between the sidechains of L‐Gln residues in addition to eight hydrogen bonds formed between the backbones of adjacent two cyclic peptides, a result that would clearly affect the self‐assembling process of cyclic peptides. The main effects can be summarized as follows. First, the dimers of these cyclic peptides with C₄ symmetry are more stable than those with D₄ symmetry due to their additional H‐bonds between Gln sidechains. Second, for the self‐assembly of the cyclopeptides, there is a competition between parallel and antiparallel stacking modes in lower oligomers such as dimers. However, with an increasing degree of oligomerization, energetically there is an increased possibility for the cyclic peptides to take the parallel stacking mode in assembly. Finally, the synergetic effect of weak interactions is the fundamental driving force for cyclic peptides to form stable nanotubes. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Synthesis of heptapeptides and analysis of sequence by tandem ion trap mass spectrometry

Two heptapeptides have been prepared by Fmoc methodology using Wang resin as solid support. For attachment of the first amino acid, several coupling systems were evaluated, and DIC/DMAP system could give yields of >99% and low levels of racemization. The selection of scavenger combination to deprotect side chains revealed that H₂O/p-cresol was good at scavenging trityl and 1,2-ethanedithiol was highly efficient for scavenging t-butyl. Through shortening the preactivation time to 5 min, the racemization which occurred during formation of amide bonds coupled by HBTU was minimized. The crude peptides were characterized by RP-HPLC and MS, and sequenced by MS/MS to acquire reliable amino acid sequence information.     

H-bonding cooperativity and energetics of alpha-helix formation of five 17-amino acid peptides

Five peptides, each containing 17 amino acids, have been completely geometrically optimized in their alpha-helical and beta-strand forms using a mixed DFT/AM1 procedure. B3LYP/D95** was used for the entire helical structures, while AM1 was initially used to optimize the side chains, followed by reoptimization at the DFT level. The energetic and structural results show (1) that the helices are favored over the strands by 29.5 to 37.4 kcal/mol; (2) that alkyl groups on the amino acid side chains favor helix formation even in the absence of solvent; (3) that C-H...O hydrogen bonds contribute to the relative stability of the helices that contain amino acids (val, leu and ile) with beta-hydrogens in their alkyl side chains; (4) that formation of these helices entails approximately 6.6 kcal/mol of strain within the backbone per hydrogen bond; and (5) that H-bond cooperativity is essential for the alpha-helix to become more stable than a corresponding beta-strand. This last observation strongly suggests that pairwise potentials are inadequate for modeling of peptides and proteins.     

Total synthesis of five proline-enriched cyclic heptapeptides from the marine sponge Stylissa carteri

The total synthesis of five naturally occurring cyclic proline-enriched heptapeptides from the marine sponge Stylissa carteri was reported. The five cyclic heptapeptides were synthesized by applying a two-step solid-phase/solution synthesis strategy. The linear heptapeptides were assembled by standard Fmoc chemistry on 2-chlorotrityl chloride resin, cleaved off-resin with acetic acid/trifluoroethanol/dichloromethane to keep side-chain protecting groups intact, and subsequently cyclization was achieved by a solution method. The final products were purified by a preparative RP-HPLC system, and their structures were characterized by HR-QTOF-MS NMR. The spectral data of synthetic peptides were found to be identical to that reported for the natural products.     

Ring-closing metathesis of olefinic peptides: design, synthesis, and structural characterization of macrocyclic helical peptides

Heptapeptides containing residues with terminal olefin-derivatized side chains (3 and 4) have been treated with ruthenium alkylidene 1 and undergone facile ring-closing olefin metathesis (RCM) to give 21- and 23-membered macrocyclic peptides (5 and 6). The primary structures of peptides 3 and 4 were based upon a previously studied heptapeptide (2), which was shown to adopt a predominantly 3(10)-helical conformation in CDCl(3) solution and an alpha-helical conformation in the solid state. Circular dichroism, IR, and solution-phase (1)H NMR studies strongly suggested that acyclic precursors 3 and 4 and the fully saturated macrocyclic products 7 and 8 also adopted helical conformations in apolar organic solvents. Single-crystal X-ray diffraction of cyclic peptide 8 showed it to exist as a right-handed 3(10)-helix up to the fifth residue. Solution-phase NMR structures of both acyclic peptide 4 and cyclic peptide 8 in CD(2)Cl(2) indicated that the acyclic diene assumes a loosely 3(10)-helical conformation, which is considerably rigidified upon macrocyclization. The relative ease of introducing carbon-carbon bonds into peptide secondary structures by RCM and the predicted metabolic stability of these bonds renders olefin metathesis an exceptional methodology for the synthesis of rigidified peptide architectures.     

Molecular dynamics study of the solvation of an alpha-helical transmembrane peptide by DMSO

A 10-ns molecular dynamics study of the solvation of a hydrophobic transmembrane helical peptide in dimethyl sulfoxide (DMSO) is presented. The objective is to analyze how this aprotic polar solvent is able to solvate three groups of amino acid residues (i.e., polar, apolar, and charged) that are located in a stable helical region of a transmembrane peptide. The 25-residue peptide (sMTM7) used mimics the cytoplasmic proton hemichannel domain of the seventh transmembrane segment (TM7) from subunit a of H(+)-V-ATPase from Saccharomyces cerevisiae. The three-dimensional structure of peptide sMTM7 in DMSO has been previously solved by NMR spectroscopy. The radial and spatial distributions of the DMSO molecules surrounding the peptide as well as the number of hydrogen bonds between DMSO and the side chains of the amino acid residues involved are extracted from the molecular dynamics simulations. Analysis of the molecular dynamics trajectories shows that the amino acid side chains are fully embedded in DMSO. Polar and positively charged amino acid side chains have dipole-dipole interactions with the oxygen atom of DMSO and form hydrogen bonds. Apolar residues become solvated by DMSO through the formation of a hydrophobic pocket in which the methyl groups of DMSO are pointing toward the hydrophobic side chains of the residues involved. The dual solvation properties of DMSO cause it to be a good membrane-mimicking solvent for transmembrane peptides that do not unfold due to the presence of DMSO.     

Investigation of the Interactions of β‐Peptides with DNA Duplexes by Circular Dichroism Spectroscopy

The interaction of β‐peptides with the DNA duplexes of dA₂₀dT₂₀ and a GCN4‐binding CRE sequence was examined. To gauge the factors that govern these interactions, two β‐pentadecapeptides, 1 and 2 , a β‐dodecapeptide, 3 , three β‐decapeptides, 4 – 6 , three β‐heptapeptides, 7 – 9 , and β‐octaarginine 10 were designed and synthesized. The β‐peptides were conceived to adopt a β‐peptide 3₁₄ helix, in which the side chains at position i and i + 3 are aligned vertically along one side of the helix. The side chains of Lys, Asn, and Arg were positioned such that potential H‐bonding sites were created for a helical conformation to interact with the base pairs of DNA. CD Analysis showed that β‐peptides 1, 2 , and 10 interacted with dA₂₀dT₂₀. In addition, β‐peptides 1 and 2 showed significant interaction with a DNA‐duplex 20mer containing the ATF/CREB recognition sequence for the regulatory protein GCN4. It is impossible, at this stage of the investigation, to make a safe proposal about the actual nature of the interaction of the structures(s) of the complexes, the formation of which is suggested by the CD spectra reported herein.     

Multi-stage collisionally-activated decomposition in an ion trap for identification of sequences, structures and bn --> bn-1 fragmentation pathways of protonated cyclic peptides

Cyclic penta-, hexa- and heptapeptides have been designed, synthesized and their fragmentations induced by multistage tandem mass spectrometry have been studied. Under low-energy collisionally activated decomposition (CAD), the protonated cyclic peptides mainly dissociate via ring opening pathways and the corresponding bn --> bn-1 pathways to form several sets of b ions as oxazolone rings (and b1 ions as aziridinone rings). Through repeated observation of these b ions in multistep CAD experiments, accurate sequencing and head-to-tail ring structure of cyclic peptides can be determined. The mistaken assignments of these b ions can be avoided by this sequencing method. Semiempirical molecular orbital calculations have been utilized to provide insight into the proposed dissociation mechanism. In addition, for cyclic peptides that include an Asn residue, the nitrogen of the Asn side chain is observed to be preferentially protonated, which can induce a unique ring-opening pathway with a loss of ammonia that competes with the conventional ring opening pathway.     

Enantiomeric Cyclic Peptides with Different Caco‐2 Permeability Suggest Carrier‐Mediated Transport

Recently, oral absorption of cyclic hexapeptides was improved by N‐methylation of their backbone amides. However, the number and position of N‐methylations or of solvent exposed NHs did not correlate to intestinal permeability, measured in a Caco‐2 model. In this study, we investigate enantiomeric pairs of three polar and two lipophilic peptides to demonstrate the participation of carrier‐mediated transporters. As expected, all the enantiomeric peptides exhibited identical lipophilicity (logD_7.4) and passive transcellular permeability determined by the parallel artificial membrane permeability assay (PAMPA). However, the enantiomeric polar peptides exhibited different Caco‐2 permeability (P_app) in both directions a–b and b–a. The same trend was observed for one of the lipophilic peptide, whereas the second lipophilic enantiomer pair showed identical Caco‐2 permeability (within the errors). These findings provide the first evidence for the involvement of carrier‐mediated transport for peptides, especially for those of polar nature.     

Molecular Dynamics Simulation of Ester‐Linked Hen Egg White Lysozyme Reveals the Effect of Missing Backbone Hydrogen Bond Donors on the Protein Structure

The three‐dimensional structure of a protein is stabilized by a number of different atomic interactions. One of these is hydrogen bonding. Its influence on the spatial structure of the hen egg white lysozyme is investigated by replacing peptide bonds (except those of the two proline residues) by ester bonds. Molecular dynamics simulations of native and ester‐linked lysozyme are compared with the native crystal structure and with NOE distance bounds derived from solution NMR experiments. The ester‐linked protein shows a slight compaction while losing its native structure. However, it does not unfold completely. The structure remains compact due to its hydrophobic core and a changed network of hydrogen bonds involving side chains.     

Chemistry of aqueous silica nanoparticle surfaces and the mechanism of selective peptide adsorption

Control over selective recognition of biomolecules on inorganic nanoparticles is a major challenge for the synthesis of new catalysts, functional carriers for therapeutics, and assembly of renewable biobased materials. We found low sequence similarity among sequences of peptides strongly attracted to amorphous silica nanoparticles of various size (15-450 nm) using combinatorial phage display methods. Characterization of the surface by acid base titrations and zeta potential measurements revealed that the acidity of the silica particles increased with larger particle size, corresponding to between 5% and 20% ionization of silanol groups at pH 7. The wide range of surface ionization results in the attraction of increasingly basic peptides to increasingly acidic nanoparticles, along with major changes in the aqueous interfacial layer as seen in molecular dynamics simulation. We identified the mechanism of peptide adsorption using binding assays, zeta potential measurements, IR spectra, and molecular simulations of the purified peptides (without phage) in contact with uniformly sized silica particles. Positively charged peptides are strongly attracted to anionic silica surfaces by ion pairing of protonated N-termini, Lys side chains, and Arg side chains with negatively charged siloxide groups. Further, attraction of the peptides to the surface involves hydrogen bonds between polar groups in the peptide with silanol and siloxide groups on the silica surface, as well as ion-dipole, dipole-dipole, and van-der-Waals interactions. Electrostatic attraction between peptides and particle surfaces is supported by neutralization of zeta potentials, an inverse correlation between the required peptide concentration for measurable adsorption and the peptide pI, and proximity of cationic groups to the surface in the computation. The importance of hydrogen bonds and polar interactions is supported by adsorption of noncationic peptides containing Ser, His, and Asp residues, including the formation of multilayers. We also demonstrate tuning of interfacial interactions using mutant peptides with an excellent correlation between adsorption measurements, zeta potentials, computed adsorption energies, and the proposed binding mechanism. Follow-on questions about the relation between peptide adsorption on silica nanoparticles and mineralization of silica from peptide-stabilized precursors are raised.     

Hydrogen‐bonded networks in 1‐(4‐methoxyphenyl)‐2,2‐dimethylpropan‐1‐ol

The asymmetric unit of the title compound, C₁₂H₁₈O₂, contains two independent molecules. They differ only slightly in conformation but form completely different intermolecular hydrogen‐bonded arrays. One molecule exhibits disorder in the hydroxy group region, but this does not influence the formation of hydrogen bonds. The bulky tert‐butyl group on one side of the carbinol C atom and the benzene ring on the other side promote the formation of discrete dimeric motifs via hydrogen‐bridged hydroxy groups. Dimers are further joined by strong hydroxy–methoxy O—H...O bonds to form chains with dangling alcohol groups. Weaker intermolecular C—H...O interactions mediate the formation of a two‐dimensional network.     

The self‐assembled of cyclic D,L‐α‐peptide systems: Insights into the structure and energetics

Cyclic D,L ‐α‐peptides are able to self‐assemble to nanotubes, although the inherent reason of the stability of this kind of nanotube as well as the intrinsic driving force of self‐assembly of the cyclic D ,L ‐α‐peptides still remain elusive. In this work, using several computational approaches, we investigated the structural and energy characteristics of a series of cyclo[(‐L ‐Phe‐D ‐Ala‐)₄] and cyclo[(‐L ‐Ala‐D ‐Ala‐)₄] oligomers. The results reveal that the thermodynamic stability, cooperativity, and self‐assembly patterns of cyclic D ,L ‐α‐peptide nanotubes are mainly determined by the interactions between cross‐strand side chains instead of those between backbones. For cyclo[(‐L ‐Phe‐D ‐Ala‐)₄] oligomers, the steric interaction between cross‐strand side chains, especially the electrostatic repulsion between the phenyls in Phe residues, brings anticooperative effect into parallel stacking mode, which is responsible for the preference of self‐assembling nanotube in antiparallel vs. parallel stacking orientation. Based on our results, a novel self‐assembling mechanism is put forward—it is the L ‐L antiparallel dimer of cyclo[(‐L ‐Phe‐D ‐Ala‐)₄], instead of the commonly presumed monomer, that acts as the basic building block in self assembly. It explains why these cyclic peptides uniquely self‐assemble to form antiparallel nanotubes. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

A planar cyclic hexamer of water molecules in dichlorido(2,4,6‐tri‐2‐pyridyl‐1,3,5‐triazine)cadmium(II) trihydrate

In the title compound, [CdCl₂(C₁₈H₁₂N₆)]·3H₂O, the Cd atom has a distorted square‐pyramidal coordination geometry. The solvent water molecules are hydrogen bonded to each other to form planar cyclic water hexamers, which, together with other hydrogen bonds, interlink the Cd complex molecules to give one‐dimensional supramolecular ribbons that extend along the [111] direction. The chains are assembled into two‐dimensional layers parallel to (111) by π–π stacking interactions. Furthermore, interlayer π–π stacking interactions and weak C—H...Cl hydrogen bonds complete the formation of a three‐dimensional framework.