Cyclic Conformation Research Articles

Engineered FcRn Binding Fusion Peptides Significantly Enhance the Half-Life of a Fab Domain in Cynomolgus Monkeys.

There is a rapidly growing reinvigoration of the investigation of small proteins, cyclic peptides, and mAb derived domains as biotherapies. The drugability of these structures are challenged by fast peripheral clearance properties that can reduce their potential to be realized as medicines. Engineering strategies have been of limited value because mechanistically the half-life benefit is manifested by increasing the molecular weight and/or the hydrodyanimc radius which slows the molecule's renal elimination, but can result in the inherent loss of activity and target accessibility. The present work evaluated an alternative approach using smaller peptide sequences which bind to the neonatal Fc receptor (FcRn). Results revealed, small linear and cyclic FcRn binding peptides (FcRnBPs) fused to a combination of the N- and C-termini of a Fab can significantly improve the pharmacokinetics of the protein in cynomolgus monkeys relative to the parental Fab. The linear and cyclic conformations, as well as, the number of FcRnBPs fused to the Fab both influence the clearance and the extent of pharmacokinetic benefit. FcRnBP fusion protein kinetics were also affected by a combination of post-translation modifications and non-specific binding properties. The results in this report lay some foundation in fostering the advent of newer technologies toward successfully improving the pharmacokinetics of proteins, peptides, and mAb-derived domains. Additional work in the integration of a variety of factors including the intended site of action, tissue disposition, metabolism, toxicity and pharmacokinetic, and pharmacodynamics relationship of the intended therapeutic modality are key areas for advancement of these approaches.

Intramolecular magnesium bonds in malonaldehyde-like systems: a critical view of the resonance-assisted phenomena

Through the use of high-level G4-theory calculations, we have investigated the structure, stability, and bonding of a set of Mg derivatives formed by replacing the –OH group of malonaldehyde or only the hydrogen atom of this group by a –MgH group. To give insight into the resonance-assisted phenomenon, which might be involved in the stabilization of these compounds, we also included the corresponding saturated analogs in our survey. The effect of the rigidity of the molecular framework was considered by analyzing the Mg derivatives of (Z)-4-(hydroxymethylene)cyclobut-2-enone, obtained through the same substitutions mentioned above. The effect of replacing the carbonyl group by an imino group was also contemplated. In all cases, the global minimum is a cyclic conformer stabilized through the formation of rather strong intramolecular magnesium bonds. The strength of these interactions is directly related with the intrinsic basicity of the carbonyl group (or the imino group) and the intrinsic acidity of the –MgH group, rather than with a resonance-assisted phenomenon. As a matter of fact, for all the investigated systems, the conclusion is that resonance in the cyclic conformer is directly correlated with the strength of the intramolecular magnesium bond, and not vice versa. Interestingly, the strength and characteristics of these interactions for these Mg-containing derivatives are very similar to those of the corresponding Be-containing analogs.

Computational study of phenolic compounds-water clusters

Eight molecules (phenol, o-cresol, m-cresol, p-cresol, pyrocatechol, guaiacol, syringol, and vanillin) were investigated in their one water complex clusters by quantum calculations using B3LYP/cc-pVTZ level of theory. For the first time, the structures of o-cresol, m-cresol, syringol, and vanillin with water were determined. When in contact with water, phenol, cresols, and pyrocatechol present a translinear structure while guaiacol and syringol are in cyclic configurations. It was found that vanillin and water interact via the aldehyde function and the presence of H2O does not affect the intramolecular hydrogen bond in the vanillin structure. The NBO analysis indicates that water electronegativity increases in the structures as follows: translinear < cyclic < vanillin. The HOMO-LUMO energy gap shows that the presence of water increases the hardness of guaiacol and syringol. This phenomenon is probably caused by the cyclic conformations created between water and the phenolic compound.

Dithiothreitol-Regulated Coverage of Oligonucleotide-Modified Gold Nanoparticles To Achieve Optimized Biosensor Performance.

DNA-modified gold nanoparticles (AuNPs) are useful signal-reporters for detecting diverse molecules through various hybridization- and enzyme-based assays. However, their performance is heavily dependent on the probe DNA surface coverage, which can influence both target binding and enzymatic processing of the bound probes. Current methods used to adjust the surface coverage of DNA-modified AuNPs require the production of multiple batches of AuNPs under different conditions, which is costly and laborious. We here develop a single-step assay utilizing dithiothreitol (DTT) to fine-tune the surface coverage of DNA-modified AuNPs. DTT is superior to the commonly used surface diluent, mercaptohexanol, as it is less volatile, allowing for the rapid and reproducible controlling of surface coverage on AuNPs with only micromolar concentrations of DTT. Upon adsorption, DTT forms a dense monolayer on gold surfaces, which provides antifouling capabilities. Furthermore, surface-bound DTT adopts a cyclic conformation, which reorients DNA probes into an upright position and provides ample space to promote DNA hybridization, aptamer assembly, and nuclease digestion. We demonstrate the effects of surface coverage on AuNP-based sensors using DTT-regulated DNA-modified AuNPs. We then use these AuNPs to visually detect DNA and cocaine in colorimetric assays based on enzyme-mediated AuNP aggregation. We determine that DTT-regulated AuNPs with lower surface coverage achieve shorter reaction times and lower detection limits relative to those for assays using untreated AuNPs or DTT-regulated AuNPs with high surface coverage. Additionally, we demonstrate that our DTT-regulated AuNPs can perform cocaine detection in 50% urine without any significant matrix effects. We believe that DTT regulation of surface coverage can be broadly employed for optimizing DNA-modified AuNP performance for use in biosensors as well as drug delivery and therapeutic applications.

Using 1H and 13C NMR chemical shifts to determine cyclic peptide conformations: a combined molecular dynamics and quantum mechanics approach.

Solving conformations of cyclic peptides can provide insight into structure-activity and structure-property relationships, which can help in the design of compounds with improved bioactivity and/or ADME characteristics. The most common approaches for determining the structures of cyclic peptides are based on NMR-derived distance restraints obtained from NOESY or ROESY cross-peak intensities, and 3J-based dihedral restraints using the Karplus relationship. Unfortunately, these observables are often too weak, sparse, or degenerate to provide unequivocal, high-confidence solution structures, prompting us to investigate an alternative approach that relies only on 1H and 13C chemical shifts as experimental observables. This method, which we call conformational analysis from NMR and density-functional prediction of low-energy ensembles (CANDLE), uses molecular dynamics (MD) simulations to generate conformer families and density functional theory (DFT) calculations to predict their 1H and 13C chemical shifts. Iterative conformer searches and DFT energy calculations on a cyclic peptide-peptoid hybrid yielded Boltzmann ensembles whose predicted chemical shifts matched the experimental values better than any single conformer. For these compounds, CANDLE outperformed the classic NOE- and 3J-coupling-based approach by disambiguating similar β-turn types and also enabled the structural elucidation of the minor conformer. Through the use of chemical shifts, in conjunction with DFT and MD calculations, CANDLE can help illuminate conformational ensembles of cyclic peptides in solution.

Hydrogen-bonding behavior of various conformations of the HNO3…(CH3OH)2 ternary system.

Nine minima were found on the intermolecular potential energy surface for the ternary system HNO3(CH3OH)2 at the MP2/aug-cc-pVDZ level of theory. The cooperative effect, which is a measure of the hydrogen-bonding strength, was probed in these nine conformations of HNO3…(CH3OH)2. The results are discussed here in terms of structures, energetics, infrared vibrational frequencies, and topological parameters. The cooperative effect was observed to be an important contributor to the total interaction energies of the cyclic conformers of HNO3…(CH3OH)2, meaning that it cannot be neglected in simulations in which the pair-additive potential is applied. Graphical abstract The H-bonding behavior of various conformations of the HNO3(CH3OH)2 trimer was investigated.

Tessellate &amp; Montage: Molecular analytics of cyclic conformations

The conformations and shapes of macromolecular structures in biological and synthetic materials often define the macroscopic functions of the systems. Tessellate and Montage provide a standardized toolset for rapid reporting of large datasets allowing comparisons of cyclic molecule conformations (ring pucker) from structural databases and simulation trajectory data. This facilitates an understanding of the dynamic transition between common conformations and the flexible range in a ring that underlies molecular behaviour and recognition properties.

Targeting cancer-specific glycans by cyclic peptide lectinomimics.

The transformation from normal to malignant phenotype in human cancers is associated with aberrant cell-surface glycosylation. Thus, targeting glycosylation changes in cancer is likely to provide not only better insight into the roles of carbohydrates in biological systems, but also facilitate the development of new molecular probes for bioanalytical and biomedical applications. In the reported study, we have synthesized lectinomimics based on odorranalectin 1; the smallest lectin-like cyclic peptide isolated from the frog Odorrana grahami skin, and assessed the ability of these peptides to bind specific carbohydrates on molecular and cellular levels. In addition, we have shown that the disulfide bond found in 1 can be replaced with a lactam bridge. However, the orientation of the lactam bridge, peptides 2 and 3, influenced cyclic peptide's conformation and thus these peptides' ability to bind carbohydrates. Naturally occurring 1 and its analog 3 that adopt similar conformation in water bind preferentially L-fucose, and to a lesser degree D-galactose and N-acetyl-D-galactosamine, typically found within the mucin O-glycan core structures. In cell-based assays, peptides 1 and 3 showed a similar binding profile to Aleuria aurantia lectin and these two peptides inhibited the migration of metastatic breast cancer cell lines in a Transwell assay. Altogether, the reported data demonstrate the feasibility of designing lectinomimics based on cyclic peptides.

Vibrational spectroscopy of the mass-selected tetrahydrofurfuryl alcohol monomers and its dimers in gas phase using IR depletion and VUV single photon ionization

Tetrahydrofurfuryl alcohol (THFA, C5H10O2) is a close chemical analog of the sugar rings present in the phosphate-deoxyribose backbone structure of the nucleic acids. In present report, the infrared (IR) spectra of the size-selected THFA monomer and its dimer have been investigated in a pulsed supersonic jet using infrared-vacuum ultraviolet (VUV) ionization. Herein, the laser light at 118nm wavelength served as the source of “soft” ionization in a time-of-flight mass spectrometer. The IR features for the monomers located at 3622cm−1 can be assigned to the intramolecular hydrogen bonding stretch vibrations mainly referring to A and C conformers. Compared with the monomer, however, characteristic peaks for the dimer centered at 3415 and 3453cm−1, red shifted 207 and 169cm−1, respectively, were associated with the intermolecular hydrogen bonding stretch vibrations. Combined with the quantum-chemical calculations, the dimer in the gas phase preferred cyclic AC conformer stabled by forming two strong intermolecular hydrogen bonds, which shown the high hydrogen bond selectivity in the cluster. The conclusions drawn from the role played in the conformational flexibility by the hydroxyl and ether groups may be extended to other biomolecules.

Classification of ligand molecules in PDB with graph match-based structural superposition.

The fast heuristic graph match algorithm for small molecules, COMPLIG, was improved by adding a structural superposition process to verify the atom-atom matching. The modified method was used to classify the small molecule ligands in the Protein Data Bank (PDB) by their three-dimensional structures, and 16,660 types of ligands in the PDB were classified into 7561 clusters. In contrast, a classification by a previous method (without structure superposition) generated 3371 clusters from the same ligand set. The characteristic feature in the current classification system is the increased number of singleton clusters, which contained only one ligand molecule in a cluster. Inspections of the singletons in the current classification system but not in the previous one implied that the major factors for the isolation were differences in chirality, cyclic conformations, separation of substructures, and bond length. Comparisons between current and previous classification systems revealed that the superposition-based classification was effective in clustering functionally related ligands, such as drugs targeted to specific biological processes, owing to the strictness of the atom-atom matching.

A new approach to understanding structure, functions and classificasion of GABA-benzodiazepine receptor complex, a molecular target for creation of new anticonvulsants on the base of inhibitory amino acids

The GABA molecule was shown to the methods of quantum mechanic characteristics and molecular geometry has three conformational states: linear (GABA-1 conformer), cyclic (GABA-2 comformer) and bucket-like (GABA-3 conformer). The play different functions in the brain neurons: cyclic and bucket-like conformers play role of endogenous transmitters, and linear conformer participates in neuronal metabolism. The theoretical conformational analysis shows there are two types of GABA receptors in the CNS neurons: GABA-2 receptors, agonists of which are cyclic conformer of GABA, glycine and β-alanine and antagonists are bemegride, pentilentetrazol and strychnine; and GABA-3 receptors, agonists of which is bucket-like conformer of GABA and antagonists are picrotoxin and bicuculline. Anticonvulsive and other behavioral effects of derivatives of barbituric acid, benzazepine, benzodiazepine, gidantoine, succinimide and oxasolidindione are realized probably via GABA-2 receptors to switch on them the following functional centers of their structure are nessesary: α, γ and [δ-ε] for barbitirates; β, [δ-ε] and γ for carbamazepine; β and [δ-ε] for benzodiazepine derivatives, gabapentine and vigabatrine; α, β, γ and [δ-ε] for gidantoine and oxasolidindione derivatives; α, β, γ for succinimide derivatives. The power of any behavioral effect of anticonvulsants and inhibitory amino acids depends on power, location and numbers of hydrogen bounds developed between active centers of pharmacophore of anticonvulsant or inhibitory amino acids and active centers of functional skeleton of GABA-2 receptor complex, these properties determine absense of nootropic activity in anticonvulsive drugs and presense of them in inhibitory amino acids. It is concluded there are perspectives of synthesis of conpounds, pharmacophore of which should be like as cyclic conformer of GABA, glycine and β-alanine on their quantum mechanic characteristics and molecular geometry

Mechanistic investigation of the uncatalyzed esterification reaction of acetic acid and acid halides with methanol: a DFT study.

Implementation of catalysts to drive reactions from reactants to products remains a burden to synthetic and organic chemists. In spite of investigations into the kinetics and mechanism of catalyzed esterification reactions, less effort has been made to explore the possibility of an uncatalyzed esterification process. Therefore, a comprehensive mechanistic perspective for the uncatalyzed mechanism at the molecular level is presented. Herein, we describe the non-catalyzed esterification reaction of acetic acid and its halide derivatives (XAc, where X= OH, F, Cl, Br, I) with methanol (MeOH) through a concerted process. The reaction in vacuum and methanol was performed using the density functional theory (DFT) method at M06-2X level with def2-TZVP basis set after a careful literature survey and computations. Esterification through cyclic 4- or 6-membered transition state structures in one- or two-step concerted mechanisms were investigated. The present study outlines the possible cyclic geometry conformations that may occur during experiments at simple ratio of reactants. The free energy of activation for acetic acid and acetyl chloride are 36 kcal mol(-1) and 21 kcal mol(-1), respectively. These are in good agreement with available experimental results from the literature. The selected quantum chemical descriptors proved to be useful tools in chemical reactivity prediction for the reaction mechanism. This quantum mechanics study can serve as a necessary step towards revisiting uncatalyzed reaction mechanisms in some classical organic reactions.

Rationally Designed Peptide Interface for Potential Modulated Cell Adhesion and Migration

Conformational changes of peptides are critically important in the control of their biological activities. Here, a quaternary ammonium group‐terminated RGD‐containing peptide (RGD‐NMe3) is designed, which may undergo reversible conformational switch upon different electrochemical potentials. Potential responsive peptide interfaces are constructed on gold substrates with RGD‐NMe3 in a tetra (ethylene glycol) background. It is demonstrated that by applying positive and negative potentials, the RGD peptide can be reversibly switched between linear and cyclic conformation, which can be used in reversible controlling of cell adhesion/migration on the interface. Furthermore, by combining microfluidics, adhesion of the cells in specific areas on the surface and subsequent directional migration of the cells can be controlled. It is believed that this straightforward potential modulation mechanism for peptide conformation control may find a wide use in design responsive peptide interfaces.

Relationship between Dynamic Planarization Processes and Exciton Delocalization in Cyclic Oligothiophenes.

In cyclic molecular structures, while the effect of conformational disorder on exciton delocalization is well understood, the impact of dynamic planarization processes remains unclear due to a lack of detailed investigation on the associated exciton dynamics. Thus, we have investigated the exciton delocalization of π-conjugated linear and cyclic oligothiophenes in the course of dynamic planarization processes by time-resolved fluorescence spectra measurements and theoretical calculations. Especially, through a comparative analysis of linear and cyclic oligothiophenes, we found that the evolution of 0-0 and 0-1 vibronic bands is strongly related to the conformations of cyclic molecular systems, reflecting the extent of exciton delocalization. Collectively, we believe that our findings are applicable to various π-conjugated organic materials and will provide new insights into the relationship between exciton delocalization and cyclic molecular conformation.

Steric group enforced aromatic cyclic trimer conformer in tripodal molecules

A family of tripodal molecules (1–6) with/without steric ethyl groups at the central benzene scaffold and with furan/thiophene/pyridyl groups at the 2-position of the benzimidazolyl unit was synthesised.

L-Arabinose (pyranose and furanose rings)-branched poly(vinyl alcohol): Enzymatic synthesis of the sugar esters followed by free radical polymerization

Herein this study reports the successful synthesis of a new poly(vinyl alcohol) (PVA), containing L-arabinose (L-arabinopyranose and arabinofuranose isomers) branched in only two steps: (1) production of polymerizable monomers of L-arabinose isomers (pyranose and furanose forms) through enzymatic synthesis using alkaline protease from Bacillus subtilis as catalyst and two substrates: L-arabinose and Divinyl Adipate (DVA) in N,N-dimethylformamide (DMF); (2) radical polymerization of the monomers, using an initiator system consisting of potassium persulfate and hydrogen peroxide in water. The transesterification of DVA with L-arabinose was monitored via qualitative analysis by TLC, confirming the formation of the vinyl sugar ester. The acylation occurred on the two different cyclic conformations of the L-arabinose which coexist in equilibrium: (α/β) arabinofuranose and (α/β) arabinopyranose. The acylation positions and the chemical structure of the 5-O-vinyl adipoyl L-arabinofuranose and 4-O-vinyl adipolyl L-arabinopyranose formed were determined by 13C NMR. The surface activity of the L-arabinose esters mixture (monomers) was compared with a commercial product based on phenol formaldehyde polyoxyalkylene polyamine, largely used as surfactant in many industries. FTIR spectroscopy of the sugar ester monomers and the respective polymer were compared revealing the disappearance of the vinyl group in the polymer spectrum. The polymer number-average molar mass (Mn) and the weight-average molar mass (Mw) were determined by gel permeation chromatography (GPC) presenting the following results: 2.9×104Da and 7.2×104Da, respectively, and polydispersity (Mw/Mn) equal to 2.48.

Radiolabeling and biological evaluation of the GX1 and RGD-GX1 peptide sequence for angiogenesis targeting

IntroductionAiming to develop a novel 99mTc-labeled imaging agent, for angiogenesis and tumor receptors, two peptides obtained from phage display library, namely GX1 and the heterodimer RGD-GX1, were synthesized in a cyclic conformation. They were radiolabeled with 99mTc, employing the HYNIC chelator, for radiochemical evaluation and biological properties. MethodsRadiolabeling, radiochemical control, plasma protein binding, and partition coefficient were assessed for both radioconjugates. Biodistribution in healthy Balb/c mice was carried out, in order to evaluate the biological behaviour of the radiocomplexes. ResultsThe conjugates displayed a rather similar pharmacokinetic profile. They were prepared with high radiochemical purity (>96%), and both were hydrophilic (log P of −2.25 and −2.51 respectively). Preferential renal excretion was observed. Kidney uptake (42.31±5.35 %ID/g) for 99mTc-HYNIC-E-[c(RGDfk)-c(GX1)], 1h post-injection was about three times higher than the uptake of 99mTc-HYNIC-PEG4-c(GX1) (11.92±4.77%ID/g). Total blood, bone and muscle values revealed a slightly slower clearance for the RGD-GX1 radiocomplex. ConclusionThe high radiochemical purity achieved, and the similar in vivo profile observed for both radioconjugates, make them potential candidates for radiopharmaceuticals for tumor imaging. Further investigations of binding affinity, and uptake of GX1 and RGD-GX1 peptides in tumor models, are warranted.

Cyclic and acyclic fructose conformers in the gas phase: a large-scale second-order perturbation theory study.

We performed large-scale second-order perturbation theory gas-phase calculations to study about five hundred structures of D-fructose. The two lowest energy fructose structures identified are β-pyranoses possessing (2)C5 chair, with ΔG(298 K) of 6 kJ/mol, differing in orientation of the equatorially positioned hydroxymethyl group, gt and g'g, where the gt rotamer is the global minimum, consistent with the recent microwave spectroscopy study. We have found that interconversions from the fructose global minimum to the second and third most stable β-pyranose rotamers involve the energy barriers of ca. 30 kJ/mol. Among numerous fructofuranose conformers discovered (about 250), a pair of the ((3)T2) α- and (E3) β-anomers are energetically most preferred and lie at least 12 kJ/mol above the global minimum. We also found that the fructose open-chain structures lie significantly higher in energy than the most stable cyclic species. The commonly used M06-2X density functional performs well compared to MP2 and G4 theory at identifying the low-energy fructose minima, including the global one, and at reproducing their intramolecular H-bond geometric parameters. The lowest-energy gas-phase pyranose and furanose structures of fructose benefit from stabilization due to the cooperative or quasi-linear H-bonding and both endo and exo anomeric effects.

An electrochemically switched smart surface for peptide immobilization and conformation control.

We report an electrochemically switched smart surface for controlled peptide immobilization and conformation control. This dynamic surface is based on self-assembled monolayers (SAMs) containing surface-bound trimethoxybenzene moieties, which can undergo electrochemically modulated surface activation to be stepwisely converted to two catechol derivatives. This new smart surface can be used to realize stepwise immobilization of a peptide, and more importantly, to control peptide conformation on a surface. We demonstrate herein that with one electrochemical activation step, a linear peptide containing an RGD sequence can be attached onto the SAMs. With the subsequence activation step, the attached linear RGD peptide can be converted into cyclic conformation. The SAMs bounded with linear and cyclic RGD exhibit different adhesion behaviors to fibroblasts cells. The reaction procedure can be well-monitored by cyclic voltammetry (CV), electrochemical surface enhanced Raman microscopy (EC-SERS), and X-ray photoelectron spectroscopy (XPS). It is believed this robust smart surface can find wide applications in surface immobilization of bioactive moieties.

On the photostability of the disulfide bond: An electronic or a structural property?

Photostability is an essential property of molecular building blocks of nature. Disulfides are central in the structure determination of proteins, which is in striking contradiction to the result that the S–S bond is a photochemically labile structural entity that cleaves to form free radicals upon light exposure. In an earlier contribution we hypothesized that the key to the photostability of some disulfides may be found in a cyclic structural arrangement. Here we provide further evidence to support this hypothesis by showing that straight chain disulfides undergo ultrafast S–S dissociation on a sub 50fs timescale without further ado. In a cyclic motif resembling the cysteine–disulfide bond in proteins, light can perturb the S–S bond to generate short-lived diradicaloid species, but the sulfur atoms are conformationally restricted by the ring that prevents the sulfur atoms from flying apart. Conversely, in a straight chain conformation, light perturbation results in two separated RS· radicals because there is no restoring force to counteract the repulsive motion of the sulfur atoms. For the cyclic conformation this restoring force is provided by the cyclic framework, and thus the photostability of disulfide-bonds must be ascribed a cyclic structural arrangement.