Cyclic Conformation Research Articles

Cyclic polymers as a building block for cyclic brush polymers and gels

Cyclic polymers, as one of the oldest topological polymers, are undergoing resurgence. This is largely ascribed to the significant achievements in modern polymer chemistry. The novel ring-expansion techniques have conveniently produced varied cyclic polymers with highly topological purity and on large scales, which should facilitate their use in the near future. Beyond the monocyclic molecular conformations, the combination of controlled polymerization techniques and click chemistry have established a robust strategy for preparing cyclic polymers with more complex architectures, such as theta, eight, and tadpole shapes. This diversification in cyclic polymer composition and conformation significantly broadens interest in the cyclic polymers. However, compared to the synthesis achievements, the exploration of cyclic polymer property and application are lagging behind. Recently, we explored the ring-expansion metathesis polymerization on various functional ring-strained olefin monomers to produce cyclic functional polymers, which were then used as the building blocks to fabricate cyclic brush polymers and cyclic gel materials and will be discussed here.

Comprehensive determination of the cyclic FEE peptide chemical stability in solution

The FEE cyclic hexapeptide (cFEE) is an investigational new drug added to the insemination medium in order to improve the in vitro fertilization rate. The pharmacological activity of small peptides is highly dependent on the conservation of the amino acid sequence and of the structural conformation of the active site. To enhance the scientific knowledge required for the clinical use of cFEE, a comprehensive determination of its chemical stability in solution was realized in accelerated conditions. Degradation products have been detected and identified by liquid chromatography/Qtrap® mass spectrometry. The main degradation products highlighted during the product shelf life were produced by hydrolysis and only certain sites were involved. In most cases, the cyclic conformation was lost and regarding the major degradation pathway, the sequence representing the active site was affected.

Free Energy Surface for Brønsted Acid-Catalyzed Glucose Ring-Opening in Aqueous Solution

Car-Parrinello-based molecular dynamics coupled with metadynamics simulations were used to determine the mechanism and associated free energy surface for opening the ring structure of cyclic glucopyranose in acidic aqueous solutions. The ring-opening process is initiated by the protonation of the ring oxygen atom and the breakage of the C1-O5 bond. The barrier for this process is about 25 kcal/mol, in good agreement with experimental measurements. Moreover, the glucose cyclic conformation is found to be more stable than the open chain form. The barrier for proton-catalyzed ring-opening in aqueous solution appears to be largely solvent induced due to the high affinity of water molecules for protons.

Solution State Conformational Preferences of Dipeptides Derived from N-Aminoazetidinecarboxylic Acid: An Assessment of the Hydrazino Turn

Four model compounds and four dipeptides containing N-aminoazetidinecarboxylic acid (AAzC) and a particular stereoisomer of 2-aminocyclobutanecarboxylic acid (ACBC) were studied to establish their solution state conformational preferences, particularly regarding the ability of AAzC to induce a three-center hydrogen-bonded folding feature known as a "hydrazino turn". On the basis of IR and NMR experiments, supported by molecular modeling, the AAzC residue adopted a trans configuration amenable to the formation of a cyclic eight-membered hydrogen bond conformation in solution, in all cases studied. The implication of the heterocyclic nitrogen atom of AAzC in the trans-like structure was demonstrated via a refined (1)H-(15)N HMBC experiment giving exploitable data at natural (15)N isotopic abundance, providing unprecedented evidence for the solution state hydrazino turn conformation. The predominance of this secondary structural feature depended on the configuration of the neighboring ACBC residue in the dipeptides: while the trans-ACBC derivatives prefer the hydrazino turn, the cis-ACBC derivatives may also populate low-energy 10-membered hydrogen-bonded ring structures. X-ray diffraction analysis of three compounds confirmed the presence of a solid state hydrazino turn in two cases, with geometries similar to those deduced from the solution state studies, but in the third compound, no intramolecular hydrogen-bonding feature was in evidence.

Development of a Maleimide Amino Acid for Use as a Tool for Peptide Conjugation and Modification

An amino acid possessing a maleimide side chain was developed and synthesized in good yield. With a propensity to undergo the Michael addition reaction, the creation of a maleimide amino acid derivative was targeted for use as a highly functional tool for enabling peptide conjugation and structural modifications. After addressing the inherent potential side reactions of maleimides during solid phase peptide synthesis, the ability to incorporate the maleimide amino acid in an RGDS peptide sequence was demonstrated. 1H NMR and mass spectroscopic techniques enabled thorough characterization of the peptide sequence, confirming the presence of the maleimide functionality. Once characterized, the ability to use the maleimide moiety as a peptide modification tool was investigated. Specifically, it was shown that the maleimide functional group could be exploited, given the proper reaction conditions, to anchor a peptide to a surface and create a cyclic conformation from a linear sequence. Furthermore, bioactivity of the peptide containing maleimide amino acid was evaluated by studying cellular interactions with surfaces functionalized with an integrin binding sequence.

Anopheles gambiae, Anoga-HrTH hormone, free and bound structure – A nuclear magnetic resonance experiment

The spread of malaria by the female mosquito, Anopheles gambiae, is dependent, amongst other things, on its ability to fly. This in turn, is dependent on the adipokinetic hormone, Anoga-HrTH (pGlu-Leu-Thr-Phe-Thr-Pro-Ala-Trp-NH2). No crystal structure of this important neuropeptide is available and hence NMR restrained molecular dynamics was used to investigate its conformational space in aqueous solution and when bound to a membrane surface. The results showed that Anoga-HrTH has an almost cyclic conformation that is stabilized by a hydrogen bond between the C-terminus and Thr3. Upon docking of the agonist to its receptor, this H-bond is broken and the molecule adopts a more extended structure. Preliminary AKHR docking calculations give the free energy of binding to be −47.30kJ/mol. There is a close correspondence between the structure of the docked ligand and literature structure–activity studies. Information about the 3D structure and binding mode of Anoga-HrTH to its receptor is vital for the design of suitable mimetics which can act as insecticides.

Deposition of (WO3)3 nanoclusters on the MgO(001) surface: A possible way to identify the charge states of the defect centers

Periodic density functional theory calculations have been performed to study the most stable structure of the (WO(3))(3) nanocluster deposited on the MgO(001) surface with three kinds of F(S) centers (F(S)(0), F(S)(+), and F(S)(2+)). Our results indicate that the configuration of (WO(3))(3) cluster, including the cyclic conformation and the heights of three W atoms, and the oxidation states are sensitive to the charge state of the F(S) center. It is interesting that the electron-riched F(S) (0) vacancy on the MgO(001) surface can act as a promoting site to enhance the W-W interaction and the W(3)O(3) cyclic conformation is maintained, while the skeleton of cluster becomes flexible when (WO(3))(3) is adsorbed on the electron-deficient vacancy (F(S)(+) and F(S)(2+)). Accordingly, three F(S)-centers exhibit different arrangements of X-ray photoelectron spectra, the scanning tunneling microscopy images, and the vibrational spectra after depositing (WO(3))(3) cluster. Present results reveal that the (WO(3))(3) cluster may be used as a probe to identify the different F(S) centers on the MgO(001) surface.

Analogs of pancreatic polypeptide and peptide YY with a locked PP-fold structure are biologically active

Pancreatic polypeptide (PP), peptide YY (PYY) and neuropeptide Y (NPY), members of the PP-fold family share a high degree of sequence homology. Nuclear magnetic resonance (NMR) and X-ray crystallography studies have shown these peptides can adopt a tightly organized tertiary structure called the PP-fold, which has long been assumed to be the active structure of this family of peptides. To date, however, no studies have been completed with PYY and PP which confirm if the PP-fold structure is important for their physiological actions. The aim of the study was to test if PYY and PP locked into the PP-fold maintained biological activity. Therefore, we designed and produced analogs of PP and PYY in a cyclic conformation with two cysteine amino acid substitutions at the N-terminus and at position 27. These were oxidized to form a cysteine disulfide bond locking the peptides into the PP-fold structure. Studies demonstrate that the cyclic analogs have both similar in vivo activity to their parent molecules, and affinity for the Y2 and Y4 receptors. Results suggest that the proposed PP and PYY-fold is likely to be their biologically active conformation.

THE ABUNDANCE OF C 3 H 2 AND OTHER SMALL HYDROCARBONS IN THE DIFFUSE INTERSTELLAR MEDIUM

Hydrocarbons are ubiquitous in the interstellar medium, observed in diverse environments ranging from diffuse to molecular dark clouds and strong photon-dominated regions near HII regions. Recently, two broad diffuse interstellar bands (DIBs) at 4881{\AA} and 5450{\AA} were attributed to the linear version of propynylidene l-C3H2, a species whose more stable cyclic conformer c-C3H2 has been widely observed in the diffuse interstellar medium at radio wavelengths. This attribution has already been criticized on the basis of indirect plausibility arguments because the required column densities are quite large, N(l-C3H2)/EB-V = 4 \times 1014 cm-2 mag-1. Here we present new measurements of N(l-C3H2) based on simultaneous 18-21 GHz VLA absorption profiles of cyclic and linear C3H2 taken along sightlines toward extragalactic radiocontinuum background sources with foreground Galactic reddening EB-V = 0.1 - 1.6 mag. We find that N(l-C3H2)/N(c-C3H2) ? 1/15 - 1/40 and N(l-C3H2)/EB-V ? 2 \pm 1 \times 1011 cm-2 mag-1, so that the column densities of l-C3H2 needed to explain the diffuse interstellar bands are some three orders of magnitude higher than what is observed. We also find N(C4H)/EB-V < 1.3 \times 1013 cm-2 mag-1 and N(C4H-)/EB-V < 1 \times 1011 cm-2 mag-1 (3?). Using available data for CH and C2H we compare the abundances of small hydrocarbons in diffuse and dark clouds as a guide to their ability to contribute as DIB carriers over a wide range of conditions in the interstellar medium.

Lead Finder docking and virtual screening evaluation with Astex and DUD test sets

Lead Finder is a molecular docking software. Sampling uses an original implementation of the genetic algorithm that involves a number of additional optimization procedures. Lead Finder's scoring functions employ a set of semi-empiric molecular mechanics functionals that have been parameterized independently for docking, binding energy predictions and rank-ordering for virtual screening. Sampling and scoring both utilize a staged approach, moving from fast but less accurate algorithm versions to computationally more intensive but more accurate versions. Lead Finder includes tools for the preparation of full atom protein and ligand models. In this exercise, Lead Finder achieved 72.9% docking success rate on the Astex test set when the original author-prepared full atom models were used, and 74.1% success rate when the structures were prepared by Lead Finder. The major cause of docking failures were scoring errors resulting from the use of imperfect solvation models. In many cases, docking errors could be corrected by the proper protonation and the use of correct cyclic conformations of ligands. In virtual screening experiments on the DUD test set the early enrichment factor of several tens was achieved on average. However, the area under the ROC curve ("AUC ROC") ranged from 0.70 to 0.74 depending on the screening protocol used, and the separation from the null model was not perfect-0.12-0.15 units of AUC ROC. We assume that effective virtual screening in the whole range of enrichment curve and not just at the early enrichment stages requires more accurate solvation modeling and accounting for the protein backbone flexibility.

Conformationally Controlled Mechanistic Aspects of BACE 1 Inhibitors

This study highlights conformationally controlled mechanistic aspects of peptide inhibitors for BACE 1. Peptide inhibitors with reduced molecular weight tend to have cyclic conformation leading to reduced interactions with catalytic motif. Conformation plays a major role in determining potency of peptide inhibitors. An attempt has been made at designing lead compound with reduced molecular weight along with proper conformation suitable for active site and retention of specificity analogous to natural substrate. Reduced molecular weight should hopefully lead to enhanced bioavailability.

DFTr Studies of Five‐ and Six‐Residue Cyclic‐β(1→4) Cellulosic Molecules

Density functional (DFT) conformational in vacuo studies of cellobiose have shown that ϕ(H) -anti conformations are low in energy relative to the syn forms, while the ψ(H) -anti forms are higher in energy. Further, as the cellulosic fragments became larger than a disaccharide and new hydrogen bonding interactions between multiple residues become available, stable low energy ϕ(H) -anti, and ψ(H) -anti cellulosic structures became possible. To test the stability of cyclic anti-conformations, a number of β-linked five- and six-residue molecules were created and then energy optimized in solvent (water, n-heptane) using the implicit solvation method COSMO at the B3LYP level of theory. The created symmetric cyclic structures were without distortion. Upon optimization some cyclic conformations were found to be of low energy when compared with linear five- and six-residue chains, after correcting the energy for the exclusion of a water molecule upon cyclization. It was also obvious from the hydrogen bonding network formed above and below the plane of the cyclic structure that these structures could exhibit strong synergistic tendencies. The conformational energy preferences for clockwise "c" and counter-clockwise "r" hydroxyl groups and preference for the hydroxymethyl rotamers is described. Because these structures contain energetically unfavorable flipped conformations in water, that is, dihedral angles of ∼180°/0° or ∼0°/180° in ϕ(H) /ψ(H) , it is clear that the synthesis of these compounds will be challenging.

Formation of cyclic structure at amino-terminus of glucagon-like peptide-1 exhibited a prolonged half-life in vivo

The multiple physiological characterizations of glucagon-like peptide-1 (GLP-1) make it a promising drug candidate for the therapy of type 2 diabetes. However, the biological half-life of GLP-1 is short in vivo due to degradation by dipeptidyl peptidase-IV (DPP-IV) and renal clearance. The stabilization of GLP-1 is critical for its utility in drug development. In this study, several GLP-1 mutants containing an N-terminal cyclic conformation were prepared in that the existence of cyclic conformation is predicted to increase the stabilization of GLP-1 in vivo. In this study, the binding capacities of the mutants were determined, the stabilities of the mutants were investigated and the physiological functions of the mutants were compared with those of wild-type GLP-1 in animals. The results indicated that the mutant (GLP1N8) remarkably raised the half-life in vivo; it also showed better glucose tolerance and higher HbA1c reduction than GLP-1 and exendin-4 in rodents. These results suggest that the GLP-1 analog (GLP1N8) which contains an N-terminal cyclic structure might be utilized as possible potent anti-diabetic drugs in the treatment of type 2 diabetes mellitus.

Design, synthesis and structural analysis of mixed α/β-peptides that adopt stable cyclic hairpin-like conformations

The strategic replacement of four α-amino acid residues of a cyclo-(ααααα)2 peptide by β-, β2- or β3-amino acids residues provided a series of novel 2:1 α/β-mixed peptides that were designed to adopt cyclic hairpin-like structures. It was shown that conformationally stable cyclo-(αβαβα)2 isomers can be obtained using both enantiomers of the central two basic α-amino acid residues, a known α-amino acid turn sequence and several combinations of facing β-amino acid residues with no side chain or a hydrophobic side chain having specific regio- and stereochemistry. The X-ray analysis of two derivatives provides molecular details of the intra-molecular hydrogen bonding interaction, dihedral angles of the backbone and side chain positioning of the novel cyclic hairpin-like structures. One of these isomers forms an unprecedented hexagon-shaped nano-channel assembly in the crystal structure. Well-defined cyclic hairpin-like structures as described here and derivatives that can be readily designed based on this research can be used as scaffolds onto which functional groups can be grafted in a spatially controlled manner and as β-hairpin mimics with specific biological properties.

Optical Properties of a Visible Push–Pull Chromophore Covalently Bound to Carbohydrates: Solution and Gas-Phase Spectroscopy Combined to Theoretical Investigations

The use of visible absorbing and fluorescent tags for sensing and structural analysis of carbohydrates is a promising route in a variety of medical, diagnostic, and therapeutic contexts. Here we report an easy method for covalent attachment of nonfluorescent push-pull chromophores based on the 4-cyano-5-dicyanomethylene-2-oxo-3-pyrroline ring to carbohydrate moieties. The impact of sugar grafting on the optical properties of the push-pull chromophore in the gas phase and in solution was investigated by absorption and action spectroscopy and theoretical methods. The labeled sugars efficiently absorb photons in the visible range, as demonstrated by their intense photodissociation in a quadrupole ion trap. A strong blue shift (-70 nm) of the gas-phase photodissociation intensity maximum is observed upon sugar grafting, whereas no such effect is visible on the solution absorption spectra. Molecular dynamics simulations of labeled maltose in the gas phase describe strong interactions between the sulfonated chromophore and the carbohydrate, which lead to cyclic conformations. These are not observed in the simulations with explicit solvation. Time-dependent density functional theory (TD-DFT) calculations on model molecules permit us to attribute the observed shift to the formation of such cyclic conformations and to the displacement of the negative charge relative to the aromatic moiety of the chromophore.

Ultrasound molecular imaging of arterial thrombi with novel microbubbles modified by cyclic RGD in vitro and in vivo

Despite immense potential, ultrasound molecular imaging (UMI) of arterial thrombi remains very challenging because the high-shear arterial flow limits binding of site-targeted microbubbles to the thrombi. The linear Arg-Gly-Asp (RGD) peptides have been successfully applied to evaluate venous, atrial, and arteriolar thrombi, but have thus far failed in the detection of arterial thrombi. Cyclic RGD (Arg-Gly-Asp-D-Phe-Cys) is a cyclic conformation of linear RGD peptides, which has much higher binding-affinity and selectivity for binding to the glycoprotein (GP) IIb/IIIa receptor than its linear counterpart and thus is likely to be an optimal targeted molecular probe for ultrasound molecular imaging of arterial thrombi. In this study, we sought to assess the feasibility of a novel microbubble conjugated with cyclic RGD (Mb-cyclic RGD) in UMI of arterial thrombi in vitro and in vivo . As expected, Mb-cyclic RGD had greater GP IIb/IIIa-targeted binding capability in all shear stress conditions. In addition, the shear stress at half-maximal detachment of Mb-cyclic RGD was 5.7-fold higher than that of microbubbles with non-specific peptide (Mb-CON) (p<0.05). Mb-cyclic RGD enhanced the echogenicity of the platelet-rich thrombus in vitro whereas Mb-CON did not produce enhancement. In the in vivo setting, optimal signal enhancement of the abdominal aortic thrombus was displayed with Mb-cyclic RGD in all cases. Mean video intensity of the abdominal aortic thrombi with Mb-cyclic RGD was 3.2-fold higher than that with Mb-CON (p<0.05). The novel Mb-cyclic RGD facilitated excellent visualisation of arterial thrombi using UMI and showed great promise for clinical applications.

Milestoning with transition memory

Milestoning is a method used to calculate the kinetics and thermodynamics of molecular processes occurring on time scales that are not accessible to brute force molecular dynamics (MD). In milestoning, the conformation space of the system is sectioned by hypersurfaces (milestones), an ensemble of trajectories is initialized on each milestone, and MD simulations are performed to calculate transitions between milestones. The transition probabilities and transition time distributions are then used to model the dynamics of the system with a Markov renewal process, wherein a long trajectory of the system is approximated as a succession of independent transitions between milestones. This approximation is justified if the transition probabilities and transition times are statistically independent. In practice, this amounts to a requirement that milestones are spaced such that trajectories lose position and velocity memory between subsequent transitions. Unfortunately, limiting the number of milestones limits both the resolution at which a system's properties can be analyzed, and the computational speedup achieved by the method. We propose a generalized milestoning procedure, milestoning with transition memory (MTM), which accounts for memory of previous transitions made by the system. When a reaction coordinate is used to define the milestones, the MTM procedure can be carried out at no significant additional expense as compared to conventional milestoning. To test MTM, we have applied its version that allows for the memory of the previous step to the toy model of a polymer chain undergoing Langevin dynamics in solution. We have computed the mean first passage time for the chain to attain a cyclic conformation and found that the number of milestones that can be used, without incurring significant errors in the first passage time is at least 8 times that permitted by conventional milestoning. We further demonstrate that, unlike conventional milestoning, MTM permits milestones to be spaced such that trajectories do not have enough time to lose their velocity memory between successively crossed milestones.

Visual Scanometric Detection of DNA through Silver Enhancement Regulated by Gold‐Nanoparticle Aggregation with a Molecular Beacon as the Trigger

A convenient and label-free scanometric approach for DNA assay was designed by integrating a metal-ion-mediated conformational molecular beacon (MB) and silver-signal amplification regulated by gold-nanoparticle (AuNP) aggregation. The strategy was based on displacing the interaction between the target DNA sequence and a competitor Hg(2+) ion with a link DNA sequence. In the absence of the target DNA sequence, a link DNA sequence interacted with the Hg(2+) ions, thus forming an inactive cyclic conformation of the MB. This result led to the poor aggregation of polyadenosine-functionalized AuNPs (A-AuNP). In the presence of a target DNA sequence with a stronger affinity than that of the competitor, hybridization between the link DNA and target DNA sequences turned on the trigger. The polythymidine end of the resulting linear duplex structure could react with A-AuNP, thus leading to a cross-linking aggregation. This aggregation weakened AuNP-catalyzed silver enhancement on a spot substrate. Further, by using scanometric detection, the concentration of the target DNA sequence could be conveniently read out within a linear range from 1.0 to 30 nM. Interestingly, in the same amount of Hg(2+) ions, one-base mismatched DNA showed only 22% of the relative gray-scale intensity for the target DNA sequence at the same concentration, thus indicating good specificity. The designed approach, with the help of the ion-mediated conformational MB, was simple, cost effective, adaptable, and convenient and provided significant potential applications in clinical analysis.

Identification of peptide sequences that target to the brain using in vivo phage display

Phage display technology could provide a rapid means for the discovery of novel peptides. To find peptide ligands specific for the brain vascular receptors, we performed a modified phage display method. Phages were recovered from mice brain parenchyma after administrated with a random 7-mer peptide library intravenously. A longer circulation time was arranged according to the biodistributive brain/blood ratios of phage particles. Following sequential rounds of isolation, a number of phages were sequenced and a peptide sequence (CTSTSAPYC, denoted as PepC7) was identified. Clone 7-1, which encodes PepC7, exhibited translocation efficiency about 41-fold higher than the random library phage. Immunofluorescence analysis revealed that Clone 7-1 had a significant superiority on transport efficiency into the brain compared with native M13 phage. Clone 7-1 was inhibited from homing to the brain in a dose-dependent fashion when cyclic peptides of the same sequence were present in a competition assay. Interestingly, the linear peptide (ATSTSAPYA, Pep7) and a scrambled control peptide PepSC7 (CSPATSYTC) did not compete with the phage at the same tested concentration (0.2-200pg). Labeled by Cy5.5, PepC7 exhibited significant brain-targeting capability in in vivo optical imaging analysis. The cyclic conformation of PepC7 formed by disulfide bond, and the correct structure itself play a critical role in maintaining the selectivity and affinity for the brain. In conclusion, PepC7 is a promising brain-target motif never been reported before and it could be applied to targeted drug delivery into the brain.

Overshooting effect of poly(dimethylaminoethyl methacrylate) hydrogels

AbstractAn overshooting effect was observed during the swelling procedure of poly(dimethylaminoethyl methacrylate) (PDMAEMA) gel for the first time. The effects of the temperature, ionic strength, and pH on the overshooting effect of the PDMAEMA gel were investigated. We found that the overshooting effect of the gel could not be eliminated by changing the temperature; however, the overshooting effect was indiscernible in high‐concentration NaCl solutions (&gt;0.2 mol/L) and basic (pH 11.9) and acidic solutions (pH = 2.1). The overshooting effect of the PDMAEMA gel was attributed to the dynamic conformational changes of the side chains of dimethylaminoethyl methacrylate (DMAEMA) units during the swelling of the gels. In the presence of NaCl or NaOH, the stretching of the macromolecular chains of the gels was disrupted. While in acidic solution, the protonation of tertiary amino groups in the DMAEMA units made the side chains of the DMAEMA units change from the cyclic conformation to the stretched one; this was analyzed with the aid of Fourier transform infrared spectroscopy. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2011