Probable Conformations Research Articles

FTIR investigation of molecular mobility in glassy epoxy-amine oligomers with azo-chromophores

Molecular mobility in glassy epoxy-amine oligomer with covalently attached 4-amino-4'-nitroazobenzene NLO chromophore fragments has been studied by conformational probes method. The conformational transitions in the probes (1,2-dichloroethane and chlorocyclohexane) embedded in the oligomer have been studied in the temperature range from −160°C to +20°C. The freezing of conformational transitions has been observed by FTIR at temperature near Tf = −90°C. This value is correlated with the secondary relaxation transition temperature in the oligomer. The comparison of the activation volumes of the mobile groups in the probes with volumes of mobile groups in the oligomer allows us to conclude that there is the freezing of benzene rings mobility near ß-process temperature.

Design, synthesis and antibacterial activities of 5-(pyrazin-2-yl)-4H-1,2,4-triazole-3-thiol derivatives containing Schiff base formation as FabH inhibitory

A series of novel schiff base derivatives (H1–H20) containing pyrazine and triazole moiety have been designed and synthesized, and their biological activities were also evaluated as potential inhibitors of β-ketoacyl-acyl carrier protein synthase III (FabH). These compounds were assayed for antibacterial activity against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Bacillus subtilis and Bacillus amyloliquefaciens and selected compounds among them were tested for their Escherichia coli FabH inhibitory activity. Based on the biological data, compound H17 showed the most potent antibacterial activity with MIC values of 0.39–1.56μg/mL against the tested bacterial strains and exhibited the most potent E. coli FabH inhibitory activity with IC50 of 5.2μM, being better than the positive control Kanamycin B with IC50 of 6.3μM. Furthermore, docking simulation was performed to position compound H17 into the E. coli FabH active site to determine the probable binding conformation. This study indicated that compound H17 has demonstrated significant E. coli FabH inhibitory activity as a potential antibacterial agent and provides valuable information for the design of E. coli FabH inhibitors.

Vanillin derivatives as the selective small molecule inhibitors of FtsZ

A series of vanillin derivatives have been designed and synthesized and their biological activities were also evaluated as potential inhibitors of FtsZ. These compounds were assayed for antibacterial activity against Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, and Staphylococcus aureus. Compounds with potent antibacterial activities were tested for their FtsZ inhibitory activity. Compound 4u showed the most potent antibacterial activity with MIC of 0.28 μg/mL against E. coli strains and exhibited the most potent FtsZ inhibitory activity with polymerization IC50 of 2.1 μM. Docking simulation was performed to position compound 4u into the FtsZ active site to determine the probable binding conformation.

The effect of supercritical carbon dioxide on secondary relaxation transitions in polysulfone and polycarbonate: The method of conformational probes

The method of FT-IR spectroscopy of conformational probes was used to study the local molecular mobility of polysulfone and polycarbonate before and after treatment by supercritical carbon dioxide. The temperature and the nature of secondary relaxation transitions have been determined. The influence of the supercritical fluid treatment on the temperature of secondary relaxation transitions and the enthalpy differences of the conformations of the probes has been analyzed.

Dissecting the Effect of RNA Aptamer Binding on the Dynamics of Plasminogen Activator Inhibitor 1 Using Hydrogen/Deuterium Exchange Mass Spectrometry

RNA aptamers, selected from large synthetic libraries, are attracting increasing interest as protein ligands, with potential uses as prototype pharmaceuticals, conformational probes, and reagents for specific quantification of protein levels in biological samples. Very little is known, however, about their effects on protein conformation and dynamics. We have employed hydrogen/deuterium exchange (HDX) mass spectrometry to study the effect of RNA aptamers on the structural flexibility of the serpin plasminogen activator inhibitor-1 (PAI-1). The aptamers have characteristic effects on the biochemical properties of PAI-1. In particular, they are potent inhibitors of the structural transition of PAI-1 from the active state to the inactive, so-called latent state. This transition is one of the largest conformational changes of a folded protein domain without covalent modification. Binding of the aptamers to PAI-1 is associated with substantial and widespread protection against deuterium uptake in PAI-1. The aptamers induce protection against exchange with the solvent both in the protein-aptamer interface as well as in other specific areas. Interestingly, the aptamers induce substantial protection against exchange in α-helices B, C and I. This observation substantiates the relevance of structural instability in this region for transition to the latent state and argues for involvement of flexibility in regions not commonly associated with regulation of latency transition in serpins.

Synthesis, and antibacterial activity of novel 4,5-dihydro-1H-pyrazole derivatives as DNA gyrase inhibitors

A series of novel 4,5-dihydropyrazole derivatives (4a-4t), containing the dinitrobenzotrifluoride moiety, as DNA gyrase inhibitors were designed and synthesized. Based on the preliminary results, compounds 4d, 4f and 4t with potent inhibitory activity in bacterial growth may be wonderful antibacterial agents; among them, compound 4t displayed the most potent activity with minimum inhibitory concentration (MIC) values of 3.125, 0.39, 0.39 and 0.39 μg mL(-1) against Bacillus subtilis, Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli respectively, which was comparable with penicillin and kanamycin B with corresponding MIC values of 3.125, 3.125, 0.39, 0.39 μg mL(-1) and 1.562, 1.562, 1.562, 1.562 μg mL(-1), respectively. In particular, compound 4d showed the most potent anti-Gram-positive bacterial activity with a MIC value of 0.39 μg mL(-1) against the tested Gram-positive bacterial strains and exhibited the most potent B. subtilis DNA gyrase and S. aureus DNA gyrase inhibitory activity with an IC50 of 0.125 μg mL(-1). Docking simulation was performed to insert compound 4d into the S. aureus DNA gyrase active site to determine the probable binding conformation.

The role of ECL2 in CGRP receptor activation: a combined modelling and experimental approach

The calcitonin gene-related peptide (CGRP) receptor is a complex of a calcitonin receptor-like receptor (CLR), which is a family B G-protein-coupled receptor (GPCR) and receptor activity modifying protein 1. The role of the second extracellular loop (ECL2) of CLR in binding CGRP and coupling to Gs was investigated using a combination of mutagenesis and modelling. An alanine scan of residues 271–294 of CLR showed that the ability of CGRP to produce cAMP was impaired by point mutations at 13 residues; most of these also impaired the response to adrenomedullin (AM). These data were used to select probable ECL2-modelled conformations that are involved in agonist binding, allowing the identification of the likely contacts between the peptide and receptor. The implications of the most likely structures for receptor activation are discussed.

Conformational analysis of arylphosphine selenides

We have carried out the conformational analysis by the methods of dipole moments and quantum chemistry [DFT B3PW91/6-31G(d), B3PW91/6-311++G(3df, 3pd)] of bis[(4-chlorophenyl)ethyl]phosphine selenide (I) and bis-[(4-tert-butylphenyl)ethyl]phosphine selenide (II), which are promising initial materials for the synthesis of various organophosphoselenium compounds. Their structural formulas are presented in the scheme. The coeffi cients of the calculation equations and the experimental dipole moments of phosphine selenides I, II are compiled in Table 1. The most probable conformers of compounds I, II according to the quantum-chemical calculations are given below (hydrogen atoms are not shown). The energies, theoretical dipole moments and those computed using the vector-additive scheme for the conformational isomers of compounds I, II are presented in Table 2. In phosphine selenide I according to the data of B3PW91/6-31G(d) the energy minimum corresponds to conformer IА possessing a symmetric structure. However the calculation in an extended basis indicates the energy prevalence of conformer IB. Taking into consideration that the dipole moment values of conformer IB calculated in both bases is in better agreement with the experimental fi nding than those of conformer IA the results of B3PW91/6-311++G(3df,3pd) concerning the energy preference of conformer IB apparently should be regarded Table 1. Coeffi cients of calculation equations and experimental dipole moments of compounds I, II

Label-free and ultrasensitive microRNA detection based on novel molecular beacon binding readout and target recycling amplification

A label-free and high-sensitive microRNA (miRNA) detection approach by coupling a metal ion-meditated conformational molecular beacon (MB), using novel fluorescent Ag nanocluster (AgNCs) as fluorophore, with endonuclease-assisted target recycling amplification was developed. The assay comprised an Hg2+ ion-meditated conformational MB probe and an assistant probe that do not hybridize with each other at a specific temperature and can be annealed to each other in the presence of the target to form a Y-shape junction structure and released Hg2+. The target-MB hybridization event with the help of assistant probe can readily be read out based on the efficient fluorescence quenching of AgNCs by released Hg2+, while the Y-shape junction structure consisting of the probe MB, assistant probe and target miRNA could be recognized by the endonuclease Nt.BbvCI. The MB probe was then effectively cleaved by the endonuclease, and the regenerated assistant probe and the target further attended another cleavage cycle to implement the signal amplification. The competition displacing interaction between the target and the Hg2+ endows the biosensor with high sequence discrimination capability, while the high signal-to-noise ratio and target recycling amplification allows the biosensor to detect the target with high sensitivity. Under the optimal conditions, the concentration of target miRNA could be conveniently read out with a linear range from 10pM to 1fM. The proposed approach, avoiding any laborious label, possessing high sensitivity and selectivity, provided significant potential applications in future clinical analysis.

Allostery and Substrate Channeling in the Tryptophan Synthase Bienzyme Complex: Evidence for Two Subunit Conformations and Four Quaternary States

The allosteric regulation of substrate channeling in tryptophan synthase involves ligand-mediated allosteric signaling that switches the α- and β-subunits between open (low activity) and closed (high activity) conformations. This switching prevents the escape of the common intermediate, indole, and synchronizes the α- and β-catalytic cycles. (19)F NMR studies of bound α-site substrate analogues, N-(4'-trifluoromethoxybenzoyl)-2-aminoethyl phosphate (F6) and N-(4'-trifluoromethoxybenzenesulfonyl)-2-aminoethyl phosphate (F9), were found to be sensitive NMR probes of β-subunit conformation. Both the internal and external aldimine F6 complexes gave a single bound peak at the same chemical shift, while α-aminoacrylate and quinonoid F6 complexes all gave a different bound peak shifted by +1.07 ppm. The F9 complexes exhibited similar behavior, but with a corresponding shift of -0.12 ppm. X-ray crystal structures show the F6 and F9 CF3 groups located at the α-β subunit interface and report changes in both the ligand conformation and the surrounding protein microenvironment. Ab initio computational modeling suggests that the change in (19)F chemical shift results primarily from changes in the α-site ligand conformation. Structures of α-aminoacrylate F6 and F9 complexes and quinonoid F6 and F9 complexes show the α- and β-subunits have closed conformations wherein access of ligands into the α- and β-sites from solution is blocked. Internal and external aldimine structures show the α- and β-subunits with closed and open global conformations, respectively. These results establish that β-subunits exist in two global conformational states, designated open, where the β-sites are freely accessible to substrates, and closed, where the β-site portal into solution is blocked. Switching between these conformations is critically important for the αβ-catalytic cycle.

ModulatoryATPbinding to the E2 state of maize plasma membrane H+‐ATPase indicated by the kinetics of vanadate inhibition

P-type ATPases, as major consumers of cellular ATP in eukaryotic cells, are characterized by the formation of a phosphorylated enzyme intermediate (E2P), a process that is allosterically coupled to translocation of cations against an electrochemical gradient. The catalytic cycle comprises binding of Mg-ATP at the nucleotide-binding domain, phosphorylation of the E1 state (E1), conformational transition to the E2P state, and dephosphorylation through the actuator domain and re-establishment of the E1 state. Recently, it has been suggested that, for several P-type ATPases, Mg-ATP binds to the phosphorylated enzyme, thereby accelerating the transition to the E1 state, before then becoming the enzyme's catalytic substrate. Here, we provide evidence supporting this viewpoint. We employed kinetic models based on steady-state kinetics in the presence and absence of the reversible inhibitor orthovanadate. Vanadate is generally considered to be a conformational probe that specifically binds to the E2 state, arresting the enzyme in a state analogous to the E2P state. Hydrolytic H(+) -ATPase activities were measured in inside-out plasma membrane vesicles isolated from roots and shoots of maize plants. For root enzymes, kinetic models of vanadate inhibition that allow simultaneous binding of Mg-ATP and vanadate to the same enzyme state were most plausible. For shoot enzymes, application of the competitive inhibitor Mg-free ATP attenuated vanadate inhibition, which is consistent with a model in which either Mg-free ATP or Mg-ATP is bound to the enzyme when vanadate binds. Therefore, data from roots and shoots indicate that binding of ATP species before transition to the E1 state plays an important role in the catalytic cycle of plant plasma membrane H(+) -ATPase.

ChemInform Abstract: Organic Stereochemistry. Part 6. The Conformation Factor in Molecular Pharmacology

AbstractReview: ca. 40 refs.

Exploration of the six tryptophan residues of Escherichia coli cystathionine β-lyase as probes of enzyme conformational change

Cystathionine β-lyase (CBL) catalyzes the hydrolysis of l-cystathionine (l-Cth), producing l-homocysteine (l-Hcys), pyruvate and ammonia, in the second step of the transsulfuration pathway of bacteria and plants. A series of 17 site-directed variants of Escherichia coli CBL (eCBL) was constructed to probe the contributions of the six tryptophan residues (W131, W188, W230, W276, W300 and W340) to the fluorescence spectrum of eCBL and to assess their mutability and utility as conformational probes. The effects of these Trp→Phe substitutions on kcat and Kml-Cth are less than 2-fold, with the exception of the 8-fold increase in Kml-Cth observed for eCBL-W340F. The midpoint of thermal denaturation, as monitored by circular dichroism spectroscopy, is reduced 4.7°C by the W188F substitution while the targeted replacement of the other five tryptophans alter Tm by less than 1.7°C. The fluorescence spectrum of eCBL is dominated by W230 and the contribution of W340, situated in the active site, is minor. The observed 5-fold increase in the 336nm fluorescence emission of W188 between 0 and 2M urea, suggests a conformational change at the domain interface. Residues W188 and W340, conserved in proteobacterial CBL enzymes, are situated at the core of the domain interface that forms the active-site cleft. The results of this study suggest that W188 is a useful probe of subtle conformational changes at the domain interface and active site.

Design and Synthesis of Fluoroacylshikonin as an Anticancer Agent

A series of shikonin derivatives, selectively acylated by various fluorinated carboxylic acids at the side chain of shikonin, were synthesized and their anticancer activity evaluated, in which eight compounds are reported for the first time. Among all the compounds tested, compound showed the most potent anticancer activity against B16-F10 (malignant melanoma cells), MG63 (human osteosarcoma cells), and A549 (lung cancer cells) with IC50 0.39 ± 0.01, 0.72 ± 0.04 and 0.58 ± 0.02 µmol/L. Docking simulation of compound was carried out to position into a tubulin active site to determine the probable binding conformation. All the results suggested that compound may be a potential anticancer agent.

3D-QSAR and Docking studies of N-hydroxy 1,8-naphthyridine 2-one analogues as Ribonuclease H Inhibitors

Three-dimensional quantitative structure activity relationship (3D-QSAR) studies were performed for a series of ribonuclease H inhibitors using comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and docking studies. A large set of 33 different aromatic/ heterocyclic N-hydroxy 1,8- naphthyridine 2-one analogs as Ribonuclease H inhibitors wher chosen for the present study. The naphthyridine ring of the n-hydroxy 1,8-naphthyridine 2-one gives the class of compounds which has the ability to chelate metal cations Mn2+ present in RNase H active. The conventional ligand-based 3D-QSAR studies were performed based on the low energy conformations employing database alignment rule. The ligand-based model gave q2 values 0.663 and 0.512 and r2 values 0.997 and 0.999 for CoMFA and CoMSIA respectively and the predictive ability of the model was also evaluated. The predicted r2 values were 0.660 and 0.650 for CoMFA and CoMSIA, respectively. Docking studies were employed to bind the inhibitors into the active site to determine the probable binding conformation. N-hydroxy 1,8-naphthyridine 2-one binds an RNA:DNA substrate, the RT/RNA:DNA structure (PDB code: 1HYS) was superimposed on our RT/N-Hydroxy 1,8-Naphthyridine 2-one (3QLH) structure (residues Val442 to Asp443, Glu478, and Asp549). Present study indicates that the CoMFA and CoMSIA models along with molecular docking could be reliable to establish a suitable molecular model which may be used in the design of novel ribonuclease H inhibitors as leads. Keywords: N-hydroxy 1, 8-naphthyridine 2-one, Ribonuclease H inhibitors, 1HYS, Docking, CoMFA, CoMSIA.

Reinterpreting the Action of ATP Analogs on KATP Channels

Neuroendocrine-type K(ATP) channels, (SUR1/Kir6.2)4, couple the transmembrane flux of K(+), and thus membrane potential, with cellular metabolism in various cell types including insulin-secreting β-cells. Mutant channels with reduced activity are a cause of congenital hyperinsulinism, whereas hyperactive channels are a cause of neonatal diabetes. A current regulatory model proposes that ATP hydrolysis is required to switch SUR1 into post-hydrolytic conformations able to antagonize the inhibitory action of nucleotide binding at the Kir6.2 pore, thus coupling enzymatic and channel activities. Alterations in SUR1 ATPase activity are proposed to contribute to neonatal diabetes and type 2 diabetes risk. The regulatory model is partly based on the reduced ability of ATP analogs such as adenosine 5'-(β,γ-imino)triphosphate (AMP-PNP) and adenosine 5'-O-(thiotriphosphate) (ATPγS) to stimulate channel activity, presumably by reducing hydrolysis. This study uses a substitution at the catalytic glutamate, SUR(1E1507Q), with a significantly increased affinity for ATP, to probe the action of these ATP analogs on conformational switching. ATPγS, a slowly hydrolyzable analog, switches SUR1 conformations, albeit with reduced affinity. Nonhydrolyzable AMP-PNP and adenosine 5'-(β,γ-methylenetriphosphate) (AMP-PCP) alone fail to switch SUR1, but do reverse ATP-induced switching. AMP-PCP displaces 8-azido-[(32)P]ATP from the noncanonical NBD1 of SUR1. This is consistent with structural data on an asymmetric bacterial ABC protein that shows that AMP-PNP binds selectively to the noncanonical NBD to prevent conformational switching. The results imply that MgAMP-PNP and MgAMP-PCP (AMP-PxP) fail to activate K(ATP) channels because they do not support NBD dimerization and conformational switching, rather than by limiting enzymatic activity.

Organic Stereochemistry. Part 6

AbstractFollowing the previous Part on the mechanisms of chiral recognition in pharmacology, the road was open to cover one aspect of stereoselectivity that had been evoked in Part 5 but not discussed explicitly, namely the pharmacological significance of the conformational behavior of active molecules. There, we saw how ligands and binding sites adapt to each other, but these results were not related explicitly to the conformational behavior of the ligand. The focus of the present Part is to use a few well‐known drugs, examine their conformational behavior, compare the 3D geometry of probable conformers with rigid analogs acting at the same receptor, and reflect on the concept of ‘active conformation’.

Vibrational and vibronic spectra of tryptamine conformers

Conformation-specific ionization-detected stimulated Raman spectra, including both Raman loss and Raman gain lines, along with visible-visible-ultraviolet hole-burning spectra of tryptamine (TRA) conformers have been measured simultaneously, with the aim of obtaining new data for identifying them. The slightly different orientations of the ethylamine side chain relative to the indole lead to unique spectral signatures, pointing to the presence of seven TRA conformers in the molecular beam. Comparison of ionization-loss stimulated Raman spectra to computationally scaled harmonic Raman spectra, especially in the alkyl C-H and amine N-H stretch regions together with the retrieved information on the stabilities of the TRA conformers assisted their characterization and structural identification. The prospects and limitations of using these spectroscopic methods as potential conformational probes of flexible molecules are discussed.

PH-Controlled Nanoaggregation in Amphiphilic Polymer Co-networks

Domain formation and control in pH-responsive amphiphilic polymer co-networks are studied theoretically. Two different molecular architectures of the polymer network are considered, depending on whether the pH-sensitive motif is borne by the hydrophobic or the hydrophilic monomer. When the hydrophobic polymer contains acidic groups, such chains form nanometric aggregates at acidic conditions, but they are found in a swollen state at alkaline pH. At intermediate pH, the nanoaggregation behavior of the hydrophobic polymer depends critically on the environment salt concentration. Moreover, our results indicate the presence of microphase separation into domains of swollen and aggregated hydrophobic chains. If the hydrophilic polymer is the ionizable component of the network, the nanoaggregation of hydrophobic monomers is weakly dependent on the pH and salt concentration, and except at very low volume fraction, the aggregate is the most probable conformation of the network in the entire range of pH and salt concentration studied. The two different hydrogels display quantitatively similar swelling transition and apparent pKa, but at the nanoscale, their behavior is qualitatively different. The spatial distribution of electric charge on the network as well as the local density of the different chemical species within the hydrogel can be controlled, as a function of pH and salt concentration, by the molecular architecture of the polymer network. These findings have relevance for applications in biomaterials and nanotechnology, in particular, in the design of oral delivery devices for the administration of hydrophobic drugs.

Theoretical and Experimental Spectroscopic Analysis of Cyano-Substituted Styrylpyridine Compounds

A combined theoretical and experimental study on the structure, infrared, UV-Vis and 1H NMR data of trans-2-(m-cyanostyryl)pyridine, trans-2-[3-methyl-(m-cyanostyryl)] pyridine and trans-4-(m-cyanostyryl)pyridine is presented. The synthesis was carried out with an efficient Knoevenagel condensation using green chemistry conditions. Theoretical geometry optimizations and their IR spectra were carried out using the Density Functional Theory (DFT) in both gas and solution phases. For theoretical UV-Vis and 1H NMR spectra, the Time-Dependent DFT (TD-DFT) and the Gauge-Including Atomic Orbital (GIAO) methods were used, respectively. The theoretical characterization matched the experimental measurements, showing a good correlation. The effect of cyano- and methyl-substituents, as well as of the N-atom position in the pyridine ring on the UV-Vis, IR and NMR spectra, was evaluated. The UV-Vis results showed no significant effect due to electron-withdrawing cyano- and electron-donating methyl-substituents. The N-atom position, however, caused a slight change in the maximum absorption wavelengths. The IR normal modes were assigned for the cyano- and methyl-groups. 1H NMR spectra showed the typical doublet signals due to protons in the trans position of a double bond. The theoretical characterization was visibly useful to assign accurately the signals in IR and 1H NMR spectra, as well as to identify the most probable conformation that could be present in the formation of the styrylpyridine-like compounds.