Theoretical investigations on the stability of alkali metal substituted phenylpentazole

The alkali metal (M=Li, Na, and K) para-substituted (M-1), meta-substituted (M-2) or ortho-substituted (M-3) derivatives of phenylpentazole (PhN₅) were studied using density functional theory. The substituted metals improve the energy barrier for decomposition of the N₅ ring of PhN₅ by 19.3?～?65.0 kJ/mol. M-3 has the ionic N-M bond, which is not found for M-1 and M-2. M-1 and M-2 have similar electrostatic potentials and dispersion interactions between metal and N₅ ring. The comparable intramolecular interactions of M-1 and M-2 lead to similar N₅ ring stability. Compared to M-1 and M-2, M-3 has a more negative charge on N₅ ring and stronger dispersion interaction. The stronger intramolecular interactions of M-3 result in the higher N₅ ring stability. For M-1 and M-2, different metals have slight affects on N₅ ring stability. For M-3, N₅ ring stability decreases in the order of Li > Na > K. The substituted metal lowers E _g of PhN₅.     

Theoretical investigations of the hydrolysis pathway of verdoheme to biliverdin

Conversion of iron(II) verdoheme to iron biliverdin in the presence of OH(-) was investigated using B3LYP method. Both 3-21G and 6-31G* basis sets were employed for geometry optimization calculation as well as energy stabilization estimation. Calculation at 6-31G* level was found necessary for a correct spin state estimation of the iron complexes. Two possible pathways for the conversion of iron verdoheme to iron biliverdin were considered. In one path the iron was six-coordinate while in the other it was considered to be five-coordinate. In the six-coordinated pathway, the ground state of bis imidazole iron verdoheme is singlet while that for open chain iron biliverdin it is triplet state with 4.86 kcal/mol more stable than the singlet state. The potential energy surface suggests that a spin inversion take place during the course of reaction after TS. The ring opening process in the six-coordinated pathway is in overall -2.26 kcal/mol exothermic with a kinetic barrier of 9.76 kcal/mol. In the five-coordinated pathway the reactant and product are in the ground triplet state. In this path, hydroxyl ion attacks the iron center to produce a complex, which is only 1.59 kcal/mol more stable than when OH(-) directly attacks the macrocycle. The activation barrier for the conversion of iron hydroxy species to the iron biliverdin complex by a rebound mechanism is estimated to be 32.68 kcal/mol. Large barrier for rebound mechanism, small barrier of 4.18 kcal/mol for ring opening process of the hydroxylated macrocycle, and relatively same stabilities for complexes resulted by the attack of nucleophile to the iron and macrocycle indicate that five-coordinated pathway with direct attack of nucleophile to the 5-oxo position of macrocycle might be the path for the conversion of verdoheme to biliverdin.     

A mechanistic study of aromatic hydroxylamine rearrangement in the rat

A modified crossover experiment was conducted to determine the mechanism of arylhydroxylamine rearrangement in the rat. When 1-hydroxy-1-phenyl-3-methylurea was incubated with fractionated liver homogenates or injected intraperitoneally in rats, 1-methylbenzimidazol-2-one was isolated as the major metabolite. Small amounts of the anticipated aminophenol, 1-(o-hydroxylphenyl)-3-methylurea were also isolated. Evidence is presented suggesting that hepatic isomerase-catalyzed rearrangements of hydroxylamines proceed via pathways analogous to those described for chemical model systems. Isomerization appears to be intermolecular involving the generation of a resonance-stabilized nitrenium ion capable of binding to amino acids and nucleotide bases.     

Theoretical investigations on the functionalization of carbon nanotubes

In this paper, our recent work concerning theoretical studies on the functionalization of carbon nanotubes (CNTs) is reviewed. In particular, two different aspects of the functionalization process are taken into account. On the one hand, the chemical functionalization of the sidewall is exploited as a way to develop nanostructured gas sensing devices. On the other hand, we investigated the possibility of functionalizing the sidewall with transition metal complexes, thus extending the concepts of organometallic chemistry to CNTs. Calculations were performed by applying statical and dynamical (Car-Parrinello) density functional theory methods, as well as hybrid (quantum mechanics/molecular mechanics) schemes. The structural and electronic peculiarities of the CNT model under study, due, for example to the presence of defects, were found to play a crucial role in the modelization of the functionalization process. In most cases, the use of realistic models was essential to achieve a full agreement with experiments.     

Analogues of tentoxin: Tools for mechanistic investigations

Tentoxin[cyclo-(MeAla¹-Leu²-MePhe³-Gly⁴] is a metabolite isolated from a phytopathogenic fungusAlternaria alternata, which induces chlorosis of many plants. This potentialnatural herbicide binds specifically to the soluble part CF₁of the chloroplastic coupling factor, which is a proton ATP-synthase. Theeffect of the toxin is concentration dependent: at low concentration it is apowerful inhibitor, while at higher concentration, it stimulates the enzyme.We synthesized tentoxin and we designed new analogues in order to vary thehydrophobicity on the side chain and to study the structure activityrelationships. Comparative activities suggest that it is possible toseparate inhibitory and activating effects using tentoxin analogues, showingsome evidence for the existence of two binding sites with different affinityconstant.     

Analogues of tentoxin: Tools for mechanistic investigations

Summary Tentoxin [cyclo-(MeAla¹-Leu²-MeΔPhe³-Gly⁴] is a metabolite isolated from a phytopathogenic fungusAlternaria alternata, which induces chlorosis of many plants. This potential natural herbicide binds specifically to the soluble part CF₁ of the chloroplastic coupling factor, which is a proton ATP-synthase. The effect of the toxin is concentration dependent: at low concentration it is a powerful inhibitor, while at higher concentration, it stimulates the enzyme. We synthesized tentoxin and we designed new analogues in order to vary the hydrophobicity on the side chain and to study the structure activity relationships. Comparative activities suggest that it is possible to separate inhibitory and activating effects using tentoxin analogues, showing some evidence for the existence of two binding sites with different affinity constant.     

A mechanistic investigation on the formation and rearrangement of silaspiropentane: A theoretical study

The formation of silaspiropentane from addition of singlet silacyclopropylidene 1 and silacyclopropylidenoid 8 to ethylene has been investigated separately at the B3LYP, X3LYP, WB97XD, and M05–2X theories using the 6–31+G(d,p) basis set. The silacycloproylidenoid addition follows a stepwise route. In contrast, a concerted mechanism occurs for silacyclopropylidene addition. Moreover, the intramolecular rearrangements of silaspiropentane 9 to methylenesilacyclobutane 11 and 2-silaallene?+?ethylene 12 have been studied extensively. The required energy barrier for the isomerization of 9 to 10 was determined to be 44.0 kcal mol^?1 at the B3LYP/6–31+G(d,p) level. After formation of 10, the rearrangement to methylenesilacyclobutane 12 is highly exergonic by ?15.9 kcal mol^?1, which makes this reaction promising. However, the conversion of 9 to 11 is calculated to be quite endergonic, by 26.5 kcal mol^?1.     

Kinetic and mechanistic investigations on reductions of aflatoxins by lactic acid

The kinetics of reduction of AFB(1) to AFB(2) and AFG(1) to AFG(2) by lactic acid has been investigated in dilute aqueous acidic solutions (pH 3.35-4.50) as a function of the concentrations of lactic acid, AFB(1), AFG(1) and hydrogen ion at 37 degrees C. The rate of the reaction was found to be first order with respect to the concentrations of lactic acid and aflatoxins and independent on hydrogen ion concentration. The experimental results are interpreted in terms of mechanisms involving an initial formation of transient oxonium intermediate, which tends to polarize the olefinic (C=C) carbon, which in turn causes the hydride abstraction from alpha-carbon atom of lactic acid in rate determining step. The proposed mechanisms involve an overall transfer of two protons and two electrons from lactic acid to AFB(1) and AFG(1) to give the corresponding reduced less toxic products AFB(2) and AFG(2) and the oxidised product pyruvic acid.     

Assays for mechanistic investigations of protein/histone acetyltransferases

Protein/histone acetyltransferases (PATs/HATs) have been implicated in a number of cellular functions including gene regulation, DNA synthesis, and repair. This paper reviews methods that can be used to quantitatively determine the activity and ultimately the catalytic/kinetic mechanism of PAT/HATs in vitro. Two methods will be described in detail. The first method is a filter-binding assay that measures the transfer of radiolabeled acetate from acetyl-CoA to protein. The second method is a continuous, spectroscopic, enzyme-coupled assay that links the PAT/HAT reaction to the reduction of NAD+ by pyruvate or alpha-ketoglutarate dehydrogenase. Both methods are highly applicable in determining steady-state reaction rates, and obtaining the kinetic constants Vmax, Km, and V/K from substrate saturation curves. We describe a new application of the filter-binding assay to determine the kinetic parameters for HATs using low concentrations of nucleosomal substrates.     

Theoretical and experimental evidence of the photonitration pathway of phenol and 4-chlorophenol: a mechanistic study of environmental significance

Light-induced nitration pathways of phenols are important processes for the transformation of pesticide-derived secondary pollutants into toxic derivatives in surface waters and for the formation of phytotoxic compounds in the atmosphere. Moreover, phenols can be used as ˙NO(2) probes in irradiated aqueous solutions. This paper shows that the nitration of 4-chlorophenol (4CP) into 2-nitro-4-chlorophenol (NCP) in the presence of irradiated nitrate and nitrite in aqueous solution involves the radical ˙NO(2). The experimental data allow exclusion of an alternative nitration pathway by ˙OH + ˙NO(2). Quantum mechanical calculations suggest that the nitration of both phenol and 4CP involves, as a first pathway, the abstraction of the phenolic hydrogen by ˙NO(2), which yields HNO(2) and the corresponding phenoxy radical. Reaction of phenoxyl with another ˙NO(2) follows to finally produce the corresponding nitrated phenol. Such a pathway also correctly predicts that 4CP undergoes nitration more easily than phenol, because the ring Cl atom increases the acidity of the phenolic hydrogen of 4CP. This favours the H-abstraction process to give the corresponding phenoxy radical. In contrast, an alternative nitration pathway that involves ˙NO(2) addition to the ring followed by H-abstraction by oxygen (or by ˙NO(2) or ˙OH) is energetically unfavoured and erroneously predicts faster nitration for phenol than for 4CP.     

Structural and mechanistic investigations of photosystem II through computational methods

The advent of oxygenic photosynthesis through water oxidation by photosystem II (PSII) transformed the planet, ultimately allowing the evolution of aerobic respiration and an explosion of ecological diversity. The importance of this enzyme to life on Earth has ironically been paralleled by the elusiveness of a detailed understanding of its precise catalytic mechanism. Computational investigations have in recent years provided more and more insights into the structural and mechanistic details that underlie the workings of PSII. This review will present an overview of some of these studies, focusing on those that have aimed at elucidating the mechanism of water oxidation at the CaMn? cluster in PSII, and those exploring the features of the structure and dynamics of this enzyme that enable it to catalyse this energetically demanding reaction. This article is part of a Special Issue entitled: Photosystem II.     

Inhibitory and mechanistic investigations of oxo-lipids with human lipoxygenase isozymes

Oxo-lipids, a large family of oxidized human lipoxygenase (hLOX) products, are of increasing interest to researchers due to their involvement in different inflammatory responses in the cell. Oxo-lipids are unique because they contain electrophilic sites that can potentially form covalent bonds through a Michael addition mechanism with nucleophilic residues in protein active sites and thus increase inhibitor potency. Due to the resemblance of oxo-lipids to LOX substrates, the inhibitor potency of 4 different oxo-lipids; 5-oxo-6,8,11,14-(E,Z,Z,Z)-eicosatetraenoic acid (5-oxo-ETE), 15-oxo-5,8,11,13-(Z,Z,Z,E)-eicosatetraenoic acid (15-oxo-ETE), 12-oxo-5,8,10,14-(Z,Z,E,Z)-eicosatetraenoic acid (12-oxo-ETE), and 13-oxo-9,11-(Z,E)-octadecadienoic acid (13-oxo-ODE) were determined against a library of LOX isozymes; leukocyte 5-lipoxygenase (h5-LOX), human reticulocyte 15-lipoxygenase-1 (h15-LOX-1), human platelet 12-lipoxygenase (h12-LOX), human epithelial 15-lipoxygenase-2 (h15-LOX-2), soybean 15-lipoxygenase-1 (s15-LOX-1), and rabbit reticulocyte 15-LOX (r15-LOX). 15-Oxo-ETE exhibited the highest potency against h12-LOX, with an IC₅₀ = 1 ± 0.1 μM and was highly selective. Steady state inhibition kinetic experiments determined 15-oxo-ETE to be a mixed inhibitor against h12-LOX, with a K_ic value of 0.087 ± 0.008 μM and a K_iu value of 2.10 ± 0.8 μM. Time-dependent studies demonstrated irreversible inhibition with 12-oxo-ETE and h15-LOX-1, however, the concentration of 12-oxo-ETE required (K_i = 36.8 ± 13.2 μM) and the time frame (k₂ = 0.0019 ± 0.00032 s⁻¹) were not biologically relevant. These data are the first observations that oxo-lipids can inhibit LOX isozymes and may be another mechanism in which LOX products regulate LOX activity.     

Theoretical investigations of prostatic acid phosphatase

The phosphotyrosyl protein phosphatase activity of prostatic acid phosphatase (PAP) has been well established. It has also been suggested that PAP partly regulates the activity of growth factor receptors by dephosphorylating the autophosphorylysable tyrosines in them. We studied the binding of the peptides from epidermal growth factor receptor (EGFR) and its homolog (ErbB-2), corresponding to their autophosphorylation sites, to PAP using theoretical modeling and molecular dynamics (MD) simulation methods. Nine different peptides, each with a phosphotyrosine residue, were docked on human PAP. The binding energies of these peptide-PAP complexes were calculated theoretically and compared to experimentally obtained affinities. The peptide Ace--DNLpYYWD--NH2 from ErbB-2(1197-1203) showed the most favorable free energy of binding when estimated theoretically. The results demonstrate that the presence of another tyrosine residue proximate to C-terminal of autophosphorylysable Tyr enhances the binding affinity considerably. The presence of a bulky group instead prevents the binding, as is observed in case of peptide Ace--NLYpYWDQ--NH2 which failed to bind, both in theoretical calculations and experiments. Thus we demonstarted that PAP could potentially bind to EGFR and Erbb-2 and dephosphorylate them. Thus it could be involved in the regulation of the function of such receptors. In addition, complexes of a peptide from AngiotensinII and phosphotyrosine(pY) with human PAP were also modeled. The effects of different protonation states of the titratable active site residues on ligand (pY) binding have also been investigated. For a favorable binding His12 and Asp258 should be neutral, His257 should be positively charged and the phosphate group of the ligand should be in PO(4) (3-) state. Furthermore, the analysis of protein motion as observed during simulations suggests the loop-loop contact in the PAP dimer to be of importance in cooperativity.     

Recent investigations into the lipoxygenase pathway of plants

The plant lipoxygenase (LOX) pathway is in many respects the equivalent of the 'arachidonic acid cascade' in animals. The LOX-catalyzed dioxygenation of the plant fatty acids, linoleic and linolenic acids, is followed by metabolism of the resulting fatty acid hydroperoxides by other enzymes. Although the physiological functions of the end-products do not appear to be fully defined at this time, hormonal and anti-fungal activities have been reported.     

Analysis of mechanistic pathway models in drug discovery: p38 pathway

Mechanistic models of signal transduction have emerged as valuable tools for untangling complex signaling networks and gaining detailed insight into pathway dynamics. The natural extension of these tools is for the design of therapeutic strategies. We have generated a novel computational model of lipopolysaccharide-induced p38 signaling in the context of TNF-alpha production in inflammatory disease. Using experimental measurement of protein levels and phospho-protein time courses, populations of model parameters were estimated. With a collection of parameter sets, reflecting virtual diversity, we step through analysis of the p38 signaling pathway model to answer specific drug discovery questions regarding target prioritization, inhibitor simulation, model robustness and co-drugging. We demonstrate that target selection cannot be assessed independently from inhibitor mechanism of action and is also linked with robustness to cellular variability. Finally, we assert that in the face of parameter uncertainty one can still uncover consistent findings that can guide drug discovery efforts.     

Density functional theory and molecular dynamics investigations on substituted banana-shaped compounds

Density functional theory (DFT) calculations and molecular dynamics (MD) simulations on the atomic level were performed on three different substituted banana-shaped compounds derived from 1,3-phenylene bis[4-(4-n-hexyloxyphenyliminomethyl)benzoate] (P-6-O-PIMB). The DFT studies were carried out on the isolated molecules, and in the MD simulations clusters were treated with up to 64 monomers. The effect of polar substituents, such as chlorine and the nitro group, on the central 1,3-phenylene unit of banana-shaped compounds was investigated. In particular, flexibility, polarity, electrostatic potential (ESP) group charge distributions, B-factors, bending angles and molecular lengths were considered. The MD results were analysed by trajectories of significant torsion angles as well as order parameters such as radial atom pair distribution functions g(r), orientational correlation functions g(o), diffusion coefficients (D) and root mean square deviations (RMSD) values. The g(r) and g(o) values show that a certain long range order is generated by the introduction of a NO₂ group in the 2-position of the central 1,3-phenylene ring. In contrast, the chlorination at the 4 and 6 positions of the central 1,3-phenylene unit decreases the long range order tendency by its perturbation effect on the conformations in such molecules. Moreover, g(r) and g(o) values, as well as diffusion coefficients, show that in the NO₂ substituted compound the formation of microphase areas is preferred. Finally, the aggregation effect in such compounds was studied in a systematic way by a comparison of the conformational properties of the isolated molecules and the monomers in the clusters. Figure Molecular dynamics (MD) simulations on the aggregation behaviour of substituted banana-shaped compounds Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Theoretical mechanistic study of the reaction of the methylidyne radical with methylacetylene

A detailed doublet potential energy surface for the reaction of CH with CH₃CCH is investigated at the B3LYP/6-311G(d,p) and G3B3 (single-point) levels. Various possible reaction pathways are probed. It is shown that the reaction is initiated by the addition of CH to the terminal C atom of CH₃CCH, forming CH₃CCHCH 1 (1a,1b). Starting from 1 (1a,1b), the most feasible pathway is the ring closure of 1a to CH₃–cCCHCH 2 followed by dissociation to P ₃ (CH₃–cCCCH+H), or a 2,3 H shift in 1a to form CH₃CHCCH 3 followed by C–H bond cleavage to form P ₅ (CH₂CHCCH+H), or a 1,2 H-shift in 1 (1a, 1b) to form CH₃CCCH₂ 4 followed by C–H bond fission to form P ₆ (CH₂CCCH₂+H). Much less competitively, 1 (1a,1b) can undergo 3,4 H shift to form CH₂CHCHCH 5. Subsequently, 5 can undergo either C–H bond cleavage to form P ₅ (CH₂CHCCH+H) or C–C bond cleavage to generate P ₇ (C₂H₂+C₂H₃). Our calculated results may represent the first mechanistic study of the CH + CH₃CCH reaction, and may thus lead to a deeper understanding of the title reaction.     

Theoretical and NMR investigations on the conformations of ( − )-meptazinol hydrochloride in solution

( ? )-Meptazinol is an analgesic with an additional acetylcholinesterase (AChE) inhibitory activity. In order to investigate the formation mechanism of its biological conformation observed in AChE-bis( ? )-meptazinol complex, two different and naturally stable conformers of ( ? )-meptazinol hydrochloride in solution were determined and identified by nuclear magnetic resonance (NMR) and molecular dynamic simulations. Moreover, ab initio calculations and NMR evidence showed the difficulties in conformer interconversion. In combination with the results of conformational comparison, it was proposed that the pharmacophoric conformer of ( ? )-meptazinol might come from the conformer with less favourable energy rather than the conformer with the lowest energy.     

GLUT,SGLT, and SWEET: Structural and mechanistic investigations of the glucose transporters

Glucose is the primary fuel to life on earth. Cellular uptake of glucose is a fundamental process for metabolism, growth, and homeostasis. Three families of secondary glucose transporters have been identified in human, including the major facilitator superfamily glucose facilitators GLUTs, the sodium‐driven glucose symporters SGLTs, and the recently identified SWEETs. Structures of representative members or their prokaryotic homologs of all three families were obtained. This review focuses on the recent advances in the structural elucidation of the glucose transporters and the mechanistic insights derived from these structures, including the molecular basis for substrate recognition, alternating access, and stoichiometric coupling of co‐transport.     

Using mechanistic Bayesian networks to identify downstream targets of the Sonic Hedgehog pathway

Background  

The topology of a biological pathway provides clues as to how a pathway operates, but rationally using this topology information with observed gene expression data remains a challenge.