Conformational Studies Research Articles

Instrumentation for Vibrational Circular Dichroism Spectroscopy: Method Comparison and Newer Developments.

Vibrational circular dichroism (VCD) is a widely used standard method for determination of absolute stereochemistry, and somewhat less so for biomolecule characterization and following dynamic processes. Over the last few decades, different VCD instrument designs have developed for various purposes, and reliable commercial instrumentation is now available. This review will briefly survey historical and currently used instrument designs and describe some aspects of more recently reported developments. An important factor in applying VCD to conformational studies is theoretical modeling of spectra for various structures, techniques for which are briefly surveyed.

Quantifying compliance and acceptance through public and private social conformity

Social conformity is a class of social influence whereby exposure to the attitudes and beliefs of a group causes an individual to alter their own attitudes and beliefs towards those of the group. Compliance and acceptance are varieties of social influence distinguished on the basis of the attitude change brought about. Compliance involves public, but not private conformity, while acceptance occurs when group norms are internalised and conformity is demonstrated both in public and in private. Most contemporary paradigms measuring conformity conflate compliance and acceptance, while the few studies to have addressed this issue have done so using between-subjects designs, decreasing their sensitivity. Here we present a novel task which measures compliance and acceptance on a within-subjects basis. Data from a small sample reveal that compliance and acceptance can co-occur, that compliance is increased with an increasing majority, and demonstrate the usefulness of the task for future studies of conformity.

Conformational study of the electronic interactions and nitric oxide release potential of new S‑nitrosothiols esters derivatives of ibuprofen, naproxen and phenyl acids substituted (SNO-ESTERS): Synthesis, infrared spectroscopy analysis and theoretical calculations.

The conformational study on the new S‑nitrosothiols esters (SNO-ESTERS): para-substituted (X = H, OMe, Cl and NO2) S‑nitrosothiol derivatives 2‑methyl‑2‑(sulfanyl)propyl phenylacetates (R1), 2‑(4‑isobutylphenyl)propanoate (ibuprofen, R2), and 2‑(4‑isobutylphenyl)propanoate of 2‑methyl‑2‑(nitrososulfanyl)propyl (naproxen, R3) was performed using infrared spectroscopy (IR) in solvents with increasing polarity (CCl4, CH3Cl, and CH3CN), and theoretical calculations, to determine the preferential conformer and the potential of these compounds to release nitric oxide (NO). S‑Nitrosothiols were synthesized by esterification reactions, using chlorides of the corresponding carboxylic acids, with good yields (~60%). IR results showed that these compounds presented only one conformation, and the experimental data were supported by the theoretical results obtained by density functional theory (DFT) calculations using the 6311+G (2df, 2p) basis set. The calculations revealed that all S‑nitrosothiols presented one preferential anticlinal (ac) geometric conformation, which agrees with the data obtained experimentally in CCl4. These conformers are stabilized by intramolecular hydrogen bonds. Examination of the geometry with regard to the RSNO group revealed that these compounds are preferentially in the trans (anti) conformation. The calculation of the orbital interactions using the Natural Bond Orbital (NBO) method showed that the nO(NO) → σ(SN)∗ hyper-conjugative interaction increases the SN bond length. The strong nS → π(NO)∗ interaction and electronic delocalization induces a partial π character to the SN bond. The weak σSN bond indicates strong delocalization of the electron pair in O (NO) by the nO(NO) → σ(SN)∗ interaction, thereby increasing the capacity of NO release from SNO-ESTERS.

Structural and conformational studies of the heparan sulfate mimetic PI-88.

The heparan sulfate mimetic PI-88 is a complex mixture of sulfated oligosaccharides with anti-metastatic and anti-angiogenic activity due to its potent inhibition of heparanase and heparan sulfate-dependent angiogenic growth factors. It was recently in Phase III clinical trials for postresection hepatocellular carcinoma. The major oligosaccharide constituents of PI-88 were prepared for the first time by sulfonation of individually purified phosphorylated oligosaccharides isolated from the PI-88 precursor. PI-88 and its components were subjected to detailed 1D and 2D NMR spectroscopic analysis. The spectra of the individual components greatly assisted the assignment of minor resonances in the 1H NMR spectrum of PI-88. The data also showed that the majority of the oligosaccharides in PI-88 are fully sulfated and that undersulfated species present are largely due to anomeric desulfation. The solution conformation of the phosphomannopentaose sulfate (major component) of PI-88 was then determined by a combination of molecular dynamics simulations and NOE measurements which may provide insights into its binding interactions with target proteins.

Conformational study of octopamine in gas phase and effect of hydrochloride.

This work deals with the molecular modeling and vibrational spectra of all the twenty conformers of an important biomolecule octopamine which have been investigated using the DFT/B3LYP level of theory in combination with the 6-31++g(d,p) as a suitable basis set. The experimental FTIR and FTRaman spectra of octopamine neurotransmitter were recorded in the spectral region 400-4000 cm-1 and 50-4000 cm-1 respectively and correlated with the calculated spectra of the most stable conformer. The effect of hydrochloride on the important geometrical parameters of most stable conformer of octopamine was also studied. The normal coordinate analysis was performed to scale the theoretical frequencies and to calculate potential energy distributions for precise normal mode assignment. Most of the frequencies were in good agreement with experimental one. However, some have been modified. Natural bond orbital analysis was performed in order to confirm the stability of electronic structure of octopamine molecule. HOMO-LUMO analysis for all the twenty conformers was also performed to give the transition profile and to study the chemical reactivity of octopamine.

Spectroscopic techniques investigation on the interaction of glucoamylase with 1-deoxynojirimycin: Mechanistic and conformational study.

1-Deoxynojirimycin (DNJ), a representative polyhydroxylated alkaloids, is widely used in the field of antidiabetic, antitumor, and anti-HIV. The present study tried to clarify the interaction mechanism of DNJ with glucoamylase by multi-spectroscopic techniques, dynamic light scattering in combination with molecular modeling strategies from biophysics point of view. Fluorescence and UV-vis data indicated that fluorescence quenching mechanism of glucoamylase and DNJ was a dynamic manner. The association constant, binding site and thermodynamic parameters were also obtained from fluorescence spectrum at different temperatures. Synchronous fluorescence, circular dichroism and dynamic light scattering methods demonstrated that their interaction induced microenvironment changes around tryptophan residue and protein conformational alteration. The main driving force was hydrophobic interaction and hydrogen bonding. In addition, molecular docking study indicated that 1-deoxynojirimycin could bind in the catalytic domain of glucoamylase and interact with amino acid residues Arg78, Asp79, Glu203 and Glu424 by forming hydrogen bonds. Molecular dynamics simulation demonstrated that profiles of atomic fluctuation remained the rigidity of ligand binding site. This study elucidated the detailed interaction mechanism of DNJ with glucoamylase, which will be helpful for pharmaceutical companies to design new α-glucosidase inhibitor drugs based on polyhydroxylated alkaloids compound like DNJ.

Synthesis, conformational, characterization and reactivity study of 1,7-bis(4-bromophenyl)heptane-1,7-dione

In the present study, the title compound 1,7-bis(4-bromophenyl)heptane-1,7-dione (BBPHD) was synthesized according to the procedure described in literature, and its solid state crystal structure was characterized by the single crystal x-ray diffraction study. The complete crystallographic information has been reported in the present work. Physicochemical characterization by various spectral tools such as FT-IR, FT-Raman, 1H NMR, 13C NMR and UV–visible, have been performed as well and these results have been correlated with the theoretical data. The ground state geometrical optimization of the title compound has been performed using the DFT/B3LYP/6–311++G(d,p) level of theory in gas phase. Extracted molecular structure obtained by x-ray difractometry has been used as the starting molecular structure for geometrical optimizations. Computationally obtained structural and geometric parameters are in good agreement with the experimentally obtained values. The experimental FT-IR and FT-Raman spectral data were compared with the theoretical spectral data and the complete assignment of vibrational wave numbers has been done on the basis of potential energy distribution (PED). In addition, reactive properties have been addressed on the basis of frontier molecular orbital analysis, global chemical reactivity descriptors, natural bond order (NBO) analysis, nonlinear optical (NLO) properties, molecular electrostatic potential (MEP) and average local ionization energy (ALIE) surfaces. Molecular dynamics (MD) simulations have been used in order to study the influence of water to the title compound. The docked ligand forms a stable complex with feruloyl esterase inhibitor and could be considered as a lead compound for the development of new antioxidant drug.

Study of brazilian structural concrete block conformity

Abstract This paper presents a study of the conformity of structural concrete blocks manufactured and used in masonry construction in Brazil. It is based on compressive strength tests, on dimensional analysis and absorption tests of over six thousand samples from three classes (A, B and C) and two modular sizes (M-15 and M-20). National results show that blocks tend to have an estimated compressive strength higher than specified, except blocks from class A. Regional results show that blocks manufactured in the northeast (NE) are consistently non-conforming, for all block classes. The study also shows that dimensional variations and absorption tests results are within code tolerances.

Sulfur doping in multivacancy graphene systems

The conformational, magnetic and electronic study of one and two sulfur atoms doping on multivacancy graphene systems, using first principles calculations is presented. The location for the addition of the sulfur atoms is ruled by the presence of pentagonal figures in the optimized multivacancy graphene system or, in case of the absence of such figures, by the concave four membered structures in the vacancy. The electronic structure and the magnetism in these systems are strongly affected by the cancellation of dangling bonds due to the inclusion of sulfur atoms. Finally, it was possible to demonstrate that the inclusion of one and even a second sulfur atoms in the multivacancy graphene systems is favorable.

Small- and large-scale galactic conformity in SDSS DR7

Galactic conformity is the phenomenon whereby galaxy properties exhibit excess correlations across distance than that expected if these properties only depended on halo mass. We perform a comprehensive study of conformity at low redshift using a galaxy group catalogue from the SDSS DR7 spectroscopic sample. We study correlations both between central galaxies and their satellites (1-halo), and between central galaxies in separate haloes (2-halo). We use the quenched fractions and the marked correlation function (MCF), to probe for conformity in three galaxy properties, $(g-r)$ colour, specific star formation rate (sSFR), and morphology. We assess the statistical significance of conformity signals with a suite of mock galaxy catalogues that have no built-in conformity, but contain the same group-finding and mass assignment errors as the real data. In the case of 1-halo conformity, quenched fractions show strong signals at all group masses. However, these signals are equally strong in mock catalogues, indicating that the conformity signal is spurious and likely entirely caused by group-finding systematics, calling into question previous claims of 1-halo conformity detection. The MCF reveals a significant detection of radial segregation within massive groups, but no evidence of conformity. In the case of 2-halo conformity, quenched fractions show no significant evidence of conformity in colour or sSFR once compared with mock catalogues, but a clear signal using morphology. In contrast, the MCF reveals a small, yet highly significant signal for all three properties in low mass groups and scales of $0.8-4\ h^{-1}\textrm{Mpc}$, possibly representing the first robust detection of 2-halo conformity.

PH-Driven Conformational Switching of Quinoxaline Cavitands in Polymer Matrices

While pH-driven interconversion of tetraquinoxaline cavitands (QxCav) from vase to kite conformation has been extensively studied both in solution and at interfaces, cavitands behavior in solid matrices is still unexplored. Therefore, the synthesis of a new class of quinoxaline cavitand based copolymers is here reported; a soluble linear poly(butyl methacrylate) (PBMA) and an insoluble cross-linked polydimethylsiloxane (PDMS), ensuring a convenient incorporation of the switchable unit, were chosen as polymer matrices. Conformational studies, performed both in solution and at the solid state, confirmed the retention of vase → kite switching behavior when moving from monomeric units to polymeric structures.

Conformational modeling of the system pollutant/three-dimensional poly (2-hydroxyethyl methacrylate) (PHEMA) in aqueous medium: a new approach

The polluted water, mixture of chemicals and dyes, discharged by various textile and paper industries, is a serious problem for the environment, peculiarly the water. Dyes are stable to light, heat and oxidizing agents and are usually biologically non-degradable, which makes them complicated environmental pollutants. To examine the removal of dye from water, a three-dimensional poly (2-hydroxyethyl methacrylate) (PHEMA) and eosin Y were used, respectively, as a dye retention support and pollutant. The study of the interaction between dye and a hydrophilic polymer networks by the conformational modeling using computer software represents the goal of the present work. Both the swelling and ultraviolet–visible spectrophotometry studies show that the pollutant was well retained by the porous polymer network PHEMA. The conformational study of the system composed of polymer network/dye shows that the interaction of the oxygen (O) and bromine (Br) of eosin Y with the hydrogen (H) of the PHEMA depends on the polymer porosity that was varied by the cross-linking rate of the three-dimensional polymer networks. The results obtained by this work can be applied to improve the retention efficiency of such material for use in wastewater application.

Structure–activity relationship and conformational studies of the natural product cyclic depsipeptides YM-254890 and FR900359

G proteins are key mediators in the signaling of G protein-coupled receptors and involved in a plethora of important physiological processes. The natural product cyclic depsipeptides YM-254890 and FR900359 are the only known selective inhibitors of the Gq protein subfamily. So far, all reported YM-254890 and FR900359 analogs show no inhibition of other G protein subtypes except the Gq, G11 and G14 proteins. Here we report the rationalization of the high potency of FR900359 and efforts towards understanding the G protein subtype selectivity by synthesis of a collection of structurally and stereochemically diverse analogs of YM-254890 using an efficient synthetic protocol. We performed the first conformational study of YM-254890 in aqueous solution by NMR spectroscopy and replica exchange molecular dynamics, which suggested that the combined contribution of residues with appropriate size, stereochemistry and conformational stability are critical for inhibitory potency. Moreover, in addition to the fit of the binding pocket, more factors should be taken into consideration for the development of compounds targeting other G proteins.

5-Hydroxy-3-(4-hydroxyphenyl)-8,8-dimethyl-6-(3-methylbut-2-enyl)pyrano[2,3-h]chromen-4-one

Natural and semi-synthetic compounds are being studied as novel phosphodiesterase 5 (PDE5) inhibitors for the treatment of erectile dysfunction, pulmonary hypertension, and lower urinary symptoms. Maclura pomifera is a source of flavonoids, one of the main classes of molecules investigated for these purposes. The extraction of the natural isoflavone osajin and its modification to obtain a semi-synthetic derivative are described in this short note. 1H and 13C-nuclear magnetic resonance spectroscopy (NMR), mass spectrometry, high-performance liquid chromatography (HPLC) and spectroscopic characterization of the title compound are also hereby provided. Two-dimensional (2D) nuclear Overhauser effect spectroscopy (NOESY) NMR, supported by in silico conformational studies, was used to achieve a complete assignment of the proton signals, assessing the correct chemical structure of the compound. Heteronuclear single quantum coherence spectroscopy (HSQC) and heteronuclear multiple bond correlation (HMBC) NMR experiments were performed to assign 13C chemical shifts. Calculated chemical properties and preliminary in silico docking suggest that this molecule might be a promising candidate as PDE5 inhibitor.

Cyclic Hexapeptide Mimics of the LEDGF Integrase Recognition Loop in Complex with HIV-1 Integrase.

The p75 splice variant of lens epithelium-derived growth factor (LEDGF) is a 75 kDa protein, which is recruited by the human immunodeficiency virus (HIV) to tether the pre-integration complex to the host chromatin and promote integration of proviral DNA into the host genome. We designed a series of small cyclic peptides that are structural mimics of the LEDGF binding domain, which interact with integrase as potential binding inhibitors. Herein we present the X-ray crystal structures, NMR studies, SPR analysis, and conformational studies of four cyclic peptides bound to the HIV-1 integrase core domain. Although the X-ray studies show that the peptides closely mimic the LEDGF binding loop, the measured affinities of the peptides are in the low millimolar range. Computational analysis using conformational searching and free energy calculations suggest that the low affinity of the peptides is due to mismatch between the low-energy solution and bound conformations.

Abstract 2996: Insulator dysfunction and epigenetic oncogene activation in SDH-deficient gastrointestinal stromal tumor

Abstract Metabolic lesions with profound effects on epigenetic regulation are widely implicated in cancer, yet the mechanistic links between this epigenetic dysregulation and tumorigenesis remain unclear. Succinate dehydrogenase (SDH) deficiency, responsible for a subset of gastrointestinal stromal tumors (GISTs), causes accumulation of the metabolite succinate and DNA hypermethylation. We identified convergent mechanisms involving altered chromosomal conformation and pseudo-hypoxia that mediate the tumorigenic effects of SDH deficiency in GIST. To investigate epigenetic alterations in this disease, we created epigenetic maps of 14 clinical GIST specimens; including KIT and PDGFRA mutant, and SDH-deficient tumors. We characterized the landscapes of enhancers, genetic regulatory elements which can drive gene expression, through histone H3 lysine 27 acetylation chromatin immunoprecipitation sequencing (ChIP-seq). We characterized both the DNA methylation and CTCF occupancy of insulators, elements which help control chromatin conformation and restrict enhancer-gene interactions, through hybrid selection bisulfite sequencing and CTCF ChIP-seq, respectively. Analyzing these data, we uncovered thousands of putative insulators where DNA methylation replaced CTCF binding in SDH-deficient GISTs. One of the strongest disrupted insulators protected the receptor tyrosine kinase and known driver of GIST, c-KIT, from a nearby superenhancer. Chromatin conformation studies confirmed an SDH-deficient-specific interaction of this superenhancer with the KIT gene. CRISPR-mediated excision of the insulator in an SDH-intact GIST model resulted in enhancer interaction and KIT upregulation. Immunohistochemical studies confirm strong expression of c-KIT in SDH-deficient GIST clinical samples. SDH deficiency has also been reported to cause pseudohypoxia in tumors. We confirmed that the enhancer landscape of SDH-deficient tumors had a signature of pseudohypoxia. Additionally, following pseudohypoxia induction in a SDH-intact GIST model, the c-KIT ligand Stem Cell Factor (SCF/KITLG) was upregulated 12-fold. While activating KIT mutations drive the majority (~75%) of GIST tumors and are mutually exclusive with SDH deficiency, we show that a primary consequence of SDH loss is in fact induction of KIT signaling. Our findings demonstrate how metabolic lesions can provide alternate epigenetic mechanisms to activate classic tumorigenic pathways in the absence of canonical genetic mutations. Citation Format: William A. Flavahan, Yotam Drier, Sarah E. Johnstone, Daniel R. Tarjan, Esmat Hegazi, Ewa T. Sicinska, Matthew L. Hemming, Chandrajit P. Raut, Jason L. Hornick, George D. Demetri, Bradley E. Bernstein. Insulator dysfunction and epigenetic oncogene activation in SDH-deficient gastrointestinal stromal tumor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2996.

Abstract 5361: Spatial genome organization as a framework for somatic alterations in human cancer

Abstract Genomic material within the nucleus is folded into successive layers in order to package and organize the long string of linear DNA. This hierarchical level of folding is closely associated with transcriptional regulation and DNA replication. Recent chromosome conformation studies have revealed that mammalian chromosomes are structured into tissue-invariant topologically associating domains (TADs) where the DNA within a given domain interacts more frequently together than with regions in other domains. Genes within the same TADs represent similar expression and histone-modification profiles. Therefore, regions separating different TADs (boundaries) have important roles in reinforcing the stability of these domain-wide features. Indeed, TAD boundary disruptions in human genetic disorders or human cancers lead to misregulation of certain genes, due to de novo enhancer exposure to promoters. Here, to understand effects and distributions of somatic structural variations across TADs, we utilized single nucleotide variations and genomic rearrangements from 2658 high-coverage whole genome sequencing data across various cancer types with paired normal samples. Our analysis revealed that deletions between repressed and active TADs result in up-regulation of genes on the repressed end of the deletions, whereas active domain genes remain unaffected. Interestingly, we further identified a strong correlation between the mutational distributions in human cancers and the spatial organization of the genome. Transcriptionally active TADs contain less mutation burden compared to inactive TADs, as a result regional mutation rates are drastically different around the boundaries delineating epigenetically distinct domains. However, mutation rates remain similar around the boundaries for samples with the DNA mismatch repair deficiency. Taken together, our analyses reveal new insights about genome architecture, aberrant gene expression and mutational distributions in human cancers. Citation Format: Kadir C. Akdemir, Andrew Futreal. Spatial genome organization as a framework for somatic alterations in human cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5361.

Conformational Study and Chiroptical Properties of Chiral Dimethyl-Ethylenedithio-Tetrathiafulvalene (DM-EDT-TTF).

The enantiopure dimethyl-ethylenedithio-tetrathiafulvalene (DM-EDT-TTF) donor exists as biaxial (ax, ax) and biequatorial (eq, eq) conformers in equilibrium. DFT calculations combined with free energy surface (FES) analysis establish that the (ax, ax) form is more stable by ∼0.7 kcal·mol-1 than the (eq, eq) one and that the inter-conversion process involves a sequential conformational change through a boat type (ax, eq) conformer with an activation energy of ∼3 kcal.mol-1. TD-DFT calculations show similar, but opposite in sign, CD bands for the two conformers. A Boltzmann type average of the two CD curves, corresponding to a ratio of three (ax, ax) for one (eq, eq) conformers in equilibrium in solution, provides an excellent agreement with the experimental curve.

Second-Generation Synthesis of (+)-Fastigiatine Inspired by Conformational Studies.

(+)-Fastigiatine is a complex alkaloid isolated from the alpine club moss Lycopodium fastigatum, most commonly found in New Zealand. It has been the subject of two successful synthetic campaigns. A second-generation route toward fastigiatine was developed to resolve two problematic steps from our initial synthesis. Selective reduction and protection of the C13 ketone improved the yield and reliability of the dibromocarbene ring expansion step. In the prior synthesis, cuprate addition to the C10 enone generated a 1:1 mixture of isomers in an advanced intermediate. Protection of the C13 alcohol with a large silyl group changed the conformational preference of the enone and led to a more selective conjugate addition to produce the desired β-epimer at C10. MacMillan's decarboxylative photoredox addition method proved to be more practical than the prior aminomethyl cuprate addition chemistry. The second-generation synthesis is longer than the original but improves the selectivity and reproducibility of the overall route.

Structural, vibrational, UV–vis, quantum-chemical properties, molecular docking and anti-cancer activity study of annomontine and N-hydroxyannomontine β-carboline alkaloids: A combined experimental and DFT approach

A theoretical and experimental DFT study of the vibrational, structural and quantum properties of annomontine (1) and N-hydroxyannomontine (2) alkaloids using the B3LYP exchange-correlation functional with 6-311G (2d, p) basis set is presented. The theoretical geometry optimization data of the two structures were compared with the X-ray data of (1) in the associated literature and a conformational study is presented for both molecules, providing a good comprehension of the conformational stability. In addition, natural bond orbitals (NBOs), HOMO-LUMO energy gap and mapped molecular electrostatic potential surface (MEPS) calculations were also performed at the same calculation approach. The calculated UV spectra agreed well with the measured experimental data, with transitions assigned. The comparative IR studies confirmed the intramolecular hydrogen bonds of the conformations and the intermolecular hydrogen bonds of dimeric forms and also revealed several characteristic vibrations for the structures. Molecular docking studies with DNA Topoisomerase II-DNA complex showed binding free energies of −11.5 and −10.6 kcal/mol for 2 and 1 respectively, while for amsacrine, used for the treatment of leukemia, and doxorubicin, used for the treatment of breast cancer, bladder cancer, Kaposi's sarcoma, and acute lymphocytic leukemia, the presented binding free energies values are −10.0 and −9.9 kcal/mol respectively, revealing good bind affinities of the tested alkaloids with the complex. In vitro cytotoxicity assay revealed an expressive antitumor activity of N-hydroxyannomontine against human hepatocellular carcinoma cell line HepG2.