Computational insight into the Rh-mediated activation of white phosphorus

Density functional calculations on the reaction of white phosphorus with the ligand bis(diphenylphosphino)methyl (dppm) at a rhodium center are presented. The cationic transition metal fragment can react as a nucleophilic as well as an electrophilic species, driven by a simple twisting of the four-membered rings. As a consequence of the conformational controlled philicity, the insertion reaction into white phosphorus occurs with a small energy barrier. The white phosphorus tetrahedron can be chelated by two cationic transition metal fragments into an opened bicyclobutane moiety, strongly stabilized by π-stacking interactions of the phenyl groups at the two transition metal fragments. It causes a 2:1 coordination; in the first stage of the reaction two molecules of the fragment add to one molecule of white phosphorus. The resulting dicationic complex easily undergoes dissociation into a cationic monoaddition product plus one cationic transition metal fragment. The ring expansion reaction of one ligand is explained by a j-step mechanism in one intermediary product. One ligand of the transition metal fragment dissociates and facilitates, by a cascade of low-energy processes, the rearrangement of the P(4)-moiety. Under bipyramid formation a PP-bond is broken, and the free ligand finally attaches to one phosphorus atom. Overall the reaction can be divided in low-energy processes, which pass through different unstable intermediates and more high-energy processes, requiring ligand dissociation.     

Molecular insight into the T798M gatekeeper mutation-caused acquired resistance to tyrosine kinase inhibitors in ErbB2-positive breast cancer

Human epidermal growth factor receptor 2 (ErbB2) is an attractive therapeutic target for metastatic breast cancer. The kinase has been clinically observed to harbor a gatekeeper mutation T798M in its active site, which causes acquired resistance to the first-line targeted breast cancer therapy with small-molecule tyrosine kinase inhibitors. Previously, several theories have been proposed to explain the molecular mechanism of gatekeeper mutation-caused drug resistance, such as blocking of inhibitor binding and increasing of ATP affinity. In the current study, the direct binding of three wild type-selective inhibitors (Lapatinib, AEE788 and TAK-285) and two wild type-sparing inhibitors (Staurosporine and Bosutinib) to the wild-type ErbB2 and its T798M mutant are investigated in detail by using rigorous computational analysis and binding affinity assay. Substitution of the polar threonine with a bulky methionine at residue 798 can impair and improve the direct binding affinity of wild type-selective and wild type-sparing inhibitors, respectively. Hindrance effect is responsible for the affinity decrease of wild type-selective inhibitors, while additional nonbonded interactions contribute to the affinity increase of wild type-sparing inhibitors, thus conferring selectivity to the inhibitors for mutant over wild type. The binding affinity of Staurosporine and Bosutinib to ErbB2 kinase domain is improved by 11.9-fold and 2.1-fold upon T798M mutation, respectively. Structural analysis reveals that a nonbonded network of S–π contact interactions (for Staurosporine) or an S-involving halogen bond (for Bosutinib) forms with the sulfide group of mutant Met798 residue.     

A new insight into Fischer-Tropsch synthesis

Fischer-Tropsch (FT) reaction is an important synthetic route to convert CO and H(2) to fuels and chemicals in industry. To date, its reaction mechanism remains uncertain. With extensive density functional theory studies on FT reactions on Ru, we compare quantitatively several C/C coupling mechanisms that are likely to be involved. We found that a well-regarded CH(2) + CH(2)R (R = H or alkyl) mechanism possesses high reaction barriers, and a stepwise C + CR mechanism has been identified that may be relevant to FT synthesis.     

N2 provides insight into the mechanism of H-C(sp3) bond cleavage

Exchange of deuterium in d6-benzene with all C-H sites in (PNP)Ru(OTf), where PNP is N(SiMe2CH2PtBu2)2 and OTf is OSO2CF3, is rapid at 22 degrees C. Although intact planar triplet (PNP)Ru(OTf) binds N2 only very weakly, these reagents are observed to react rapidly to give a diamagnetic 1:1 adduct whose structure has one tBu C-H bond cleaved: the carbon binds to Ru but the hydrogen is on the PNP nitrogen, creating a secondary amine ligand bound to RuII. It is suggested that the benzene C-D cleavage and the N2 product of tBu C-H bond heterolysis both derive from a common intermediate, [HN(SiMe2CH2PtBu2)(SiMe2CH2PtBuCMe2CH2)] Ru(OTf); the formation energy and structure of this species are discussed on the basis of DFT results.     

An integrated chemical biology approach provides insight into cdk2 functional redundancy and inhibitor sensitivity

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Highlights? Demonstration that Cdk2 is rate-limiting for DNA replication due to insufficient Cdk1 activity ? A simple bioinformatic approach to design inhibitor resistant mutations in kinases ? Demonstration of distinct binding modes and selectivity of Cdk inhibitors ? Identification of kinetic and structural mechanisms of inhibitor resistance     

Synthesis of potential prodrug systems for reductive activation. Prodrugs for anti-angiogenic isoflavones and VEGF receptor tyrosine kinase inhibitory oxindoles

A number of potential prodrug systems for reductive activation have been investigated. The prodrug systems chosen for the study were the 2-nitrophenylacetyl, 3-methyl-3-(3,6-dimethyl-1,4-benzoquinon-2-yl)butanoyl and 4-nitrobenzyl groups, readily attached to acidic OH or NH groups in drug molecules, and released upon bioreductive activation. The drug molecules studied were the naturally occurring isoflavone biochanin A, an inhibitor of VEGF-induced angiogenesis, and the pyrrolylmethylidenyl oxindole SU5416 (semaxanib) and its 6-hydroxy derivative, inhibitors of VEGF receptor tyrosine kinase. Following coupling the prodrug system to the drug, the compounds were evaluated chemically and biologically. Under chemical reducing conditions, the 3-methyl-3-(3,6-dimethyl-1,4-benzoquinon-2-yl)butanoic acid based prodrugs appear to fragment the most efficiently, followed by the 2-nitrophenylacetate esters with the 4-nitrobenzyl ethers being the least efficient. The potentially pro-anti-angiogenic compounds were also assayed for their ability to block VEGF-induced angiogenesis in HUVECS in comparison to the free agents. Control compounds that cannot be activated under bioreductive conditions are less potent than the free drug, whereas many of the potential prodrugs not only exhibit a dose response, but appear at least equipotent with the free drug.     

Ambiguous origin: two sides of an ephrin receptor tyrosine kinase

The assembly of a functional receptor tyrosine kinase via expressed protein ligation using receptor segments produced in two different organisms by Singla et al. (2011) provides a tool for monitoring the order of tyrosine phosphorylation events upon ligand activation.     

A theoretical insight into the photophysics of psoralen

Psoralen photophysics has been studied on quantum chemistry grounds using the multiconfigurational second-order perturbation method CASPT2. Absorption and emission spectra of the system have been rationalized by computing the energies and properties of the low-lying singlet and triplet excited states. The S1 pipi* state has been determined to be responsible of the lowest absorption and fluorescence bands and to initially carry the population in the photophysical processes related to the phototherapeutic properties of psoralen derivatives. The low-lying T1 pipi* state is, on the other hand, protagonist of the phosphorescence, and its prevalent role in the reactivity of psoralen is suggested to be related to the elongation of the pyrone ring C3-C4 bond, where the spin density is distributed on both carbon atoms. Analysis of energy gaps and spin-orbit coupling elements indicates that the efficient photophysical process leading to the population of the lowest triplet state does not take place at the Franck-Condon region but along the S1 relaxation path.     

3D-QSAR and receptor modeling of tyrosine kinase inhibitors with flexible atom receptor model (FLARM)

A set of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors was investigated with the aim of developing 3D-QSAR models using the Flexible Atom Receptor Model (FLARM) method. Some 3D-QSAR models were built with high correlation coefficients, and the FLARM method predicted the biological activities of compounds in test set well. The FLARM method also gave the pseudoreceptor model, which indicates the possible interactions between the receptor and the ligand. The possible interactions include two hydrogen bonds, one hydrophobic interaction, and one sulfur-aromatic interaction, which are in accord with those in the pharmacophore model given by the scientists at Novartis. This shows that the FLARM method can bridge 3D-QSAR and receptor modeling in computer-aided drug design. Pharmacophore can be obtained according to these results, and 3D searching can then be done with databases to find the lead compound of EGFR tyrosine kinase inhibitors.     

A new insight into the vibrational analysis of pyridine

A new proposal of vibrational assignment for pyridine is reported. Infrared spectra for the liquid and gas phases as well as Raman spectra for the liquid have been recorded and analyzed for -d(0), -d(5) and, for the first time to our knowledge, for 15N isotopomers as well. The proposal of assignment has been assessed by the calculation of a number of force fields, theoretical (ab initio, density functional theory) approaches as well as by a set of simple valence internal coordinates force constants transferred from benzene using the pure vibrational force field approximation. In all cases, the root mean square (rms) for the wavenumbers turn out to be lower than the best obtained so far, i.e. 6.6 cm(-1), as stated by Wiberg et al.     

A deeper insight into direct trifluoromethoxylation with trifluoromethyl triflate

Commercially available fluorides (silver fluoride and n-tetrabutylammonium triphenyldifluorosilicate), combined with TFMT, allow a simple generation, in situ, of silver and n-tetrabutylammonium trifluoromethoxides which were able to react with electrophilic substrates. Silver trifluoromethoxide, which is usually more efficient than n-tetrabutylammonium trifluoromethoxide, converts, under mild conditions, primary aliphatic bromides and iodides, as well as primary and secondary benzylic or allylic bromides to the corresponding trifluoromethoxylated compounds. Several trifluoromethyl ethers, which could be valuable building-blocks, were prepared in such a way.     

Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora

Enzymatic cleavage of the glycosidic bond yields products in which the anomeric configuration is either retained or inverted. Each mechanism reflects the dispositions of the enzyme functional groups; a facet of which is essentially conserved in 113 glycoside hydrolase (GH) families. We show that family GH97 has diverged significantly, as it contains both inverting and retaining alpha-glycosidases. This reflects evolution of the active center; a glutamate acts as a general base in inverting members, exemplified by Bacteroides thetaiotaomicron alpha-glucosidase BtGH97a, whereas an aspartate likely acts as a nucleophile in retaining members. The structure of BtGH97a and its complexes with inhibitors, coupled to kinetic analysis of active-site variants, reveals an unusual calcium ion dependence. 1H NMR analysis shows an inversion mechanism for BtGH97a, whereas another GH97 enzyme from B. thetaiotaomicron, BtGH97b, functions as a retaining alpha-galactosidase.     

A [3Cu:2S] cluster provides insight into the assembly and function of the CuZ site of nitrous oxide reductase

Nitrous oxide reductase (N₂OR) is the only known enzyme reducing environmentally critical nitrous oxide (N₂O) to dinitrogen (N₂) as the final step of bacterial denitrification. The assembly process of its unique catalytic [4Cu:2S] cluster Cu_Z remains scarcely understood. Here we report on a mutagenesis study of all seven histidine ligands coordinating this copper center, followed by spectroscopic and structural characterization and based on an established, functional expression system for Pseudomonas stutzeri N₂OR in Escherichia coli. While no copper ion was found in the Cu_Z binding site of variants H129A, H130A, H178A, H326A, H433A and H494A, the H382A variant carried a catalytically inactive [3Cu:2S] center, in which one sulfur ligand, S_Z2, had relocated to form a weak hydrogen bond to the sidechain of the nearby lysine residue K454. This link provides sufficient stability to avoid the loss of the sulfide anion. The UV-vis spectra of this cluster are strikingly similar to those of the active enzyme, implying that the flexibility of S_Z2 may have been observed before, but not recognized. The sulfide shift changes the metal coordination in Cu_Z and is thus of high mechanistic interest.

Variants of all seven histidine ligands of the [4Cu:2S] active site of nitrous oxide reductase mostly result in loss of the metal site. However, a H382A variant retains a [3Cu:2S] cluster that hints towards a structural flexibility also present in the intact site.     

An insight into the changes in the thermal analysis curves of boehmite with mechanical activation

This study deals with the changes in the thermal transformation behaviour of boehmite with mechanical activation (MA), carried out in planetary mill. Observed changes in the TG-DTG–DTA curves are: shifting of the desorption of physically adsorbed water to higher temperature, decrease in the γ-Al₂O₃ transformation temperature and its peak area, formation of α-Al₂O₃, not observed for unmilled boehmite upto 1,200 °C, for milling time ≥60 min. Reasons for such changes are explored on the basis of physicochemical changes occurring as a result of high energy milling. Structural degradation is found to increase with increase in milling time. As a consequence of structural changes, Al–OH bonds get stronger, whereas the hydrogen bonds get weaker. Stronger Al–OH bonding and enhanced surface energy increase water affinity and delays its removal. Decreased hydrogen bond strength, easy exit of dehydroxylation product (water) and displacement of Al to tetrahedral positions make the γ-Al₂O₃ transformation easier. Ease of removal of residual hydroxyls from small crystallite transition alumina from MA boehmite, as a result of shorter diffusion path, ensures α-Al₂O₃ transformation at lower temperature.     

Enantioselective capillary electrophoresis provides insight into the phase II metabolism of ketamine and its metabolites in vivo and in vitro

Glucuronidation catalyzed by uridine‐5′‐diphospho‐glucuronosyl‐transferases (UGTs) is the most important reaction in phase II metabolism of drugs and other compounds. O‐glucuronidation is more common than N‐glucuronidation. The anesthetic, analgesic and antidepressive drug ketamine is metabolized in phase I by cytochrome P450 enzymes to norketamine, hydroxynorketamine (HNK) diastereomers and dehydronorketamine (DHNK). Equine urine samples collected two hours after ketamine injection were treated with β‐glucuronidase and analyzed with three enantioselective capillary electrophoresis assays. Concentrations of HNK diastereomers and norketamine were significantly higher in comparison to untreated urine and an increase of ketamine and DHNK levels was found in selected but not all samples. This suggests that O‐glucuronides of HNK and N‐glucuronides of the other compounds are formed in equines. N‐glucuronidation of norketamine was studied in vitro with liver microsomes of different species and the single human enzyme UGT1A4. With equine liver microsomes (ELM) a stereoselective N‐glucuronidation of norketamine was found that compares well to the results obtained with urines collected after ketamine administration. No reaction was observed with canine liver microsomes, human liver microsomes and UGT1A4. Incubation of ketamine and DHNK with ELM did not reveal any glucuronidation. Enantioselective CE is suitable to provide insight into the phase II metabolism of ketamine and its metabolites.     

Characterization of a putative sensory [FeFe]-hydrogenase provides new insight into the role of the active site architecture

[FeFe]-hydrogenases are known for their high rates of hydrogen turnover, and are intensively studied in the context of biotechnological applications. Evolution has generated a plethora of different subclasses with widely different characteristics. The M2e subclass is phylogenetically distinct from previously characterized members of this enzyme family and its biological role is unknown. It features significant differences in domain- and active site architecture, and is most closely related to the putative sensory [FeFe]-hydrogenases. Here we report the first comprehensive biochemical and spectroscopical characterization of an M2e enzyme, derived from Thermoanaerobacter mathranii. As compared to other [FeFe]-hydrogenases characterized to-date, this enzyme displays an increased H₂ affinity, higher activation enthalpies for H⁺/H₂ interconversion, and unusual reactivity towards known hydrogenase inhibitors. These properties are related to differences in active site architecture between the M2e [FeFe]-hydrogenase and “prototypical” [FeFe]-hydrogenases. Thus, this study provides new insight into the role of this subclass in hydrogen metabolism and the influence of the active site pocket on the chemistry of the H-cluster.

Characterization of a group D putative sensory [FeFe]-hydrogenase reveals how the active site can be tuned to decrease CO inhibition and increase stability of a reduced H-cluster while retaining the ability to catalyze H⁺/H₂ interconversion.     

A concise synthesis of a novel antiangiogenic tyrosine kinase inhibitor

An efficient synthesis of the potent KDR inhibitor 3-[5-[[4-(methylsulfonyl)-1-piperazinyl]methyl]-1H-indole-2-yl]quinolin-2(1H)-one (1) is described. The process features a noncryogenic indole boronation and a dicyclohexylamine-mediated Suzuki coupling.     

A novel insight into the inductive effect in silicon chemistry

A revision of quantitative literature data for the reactivity of organosilicon compounds in light of conceptions stemmed from organic chemistry has been carried out. It has been found that in structure-reactivity analysis for organosilicon compounds, differently of carbon compounds, the inductive effect of substituents, at least in nucleophilic displacement reactions at silicon, must be expressed by two terms involving that for electronegativity. A protocol for the correlation analysis in organosilicon chemistry is now available.     

Identification of a molecular recognition role for the activation loop phosphotyrosine of the SRC tyrosine kinase

A human cDNA phage display library screen, using a phosphopeptide designed to mimic the activation loop phosphotyrosine of the Src tyrosine kinase, has identified the N-terminal SH2 domain of the p85 regulatory subunit of phosphatidyl inositol-3 kinase (PI3K) as an interacting recognition domain. Activation loop phosphorylation is known to play a conformational role in kinase activation, but is largely not thought to play a role in protein/protein recognition. Affinity chromatography and biochemical evaluation in mouse fibroblast cells has confirmed the dependence of this interaction on both the Src activation loop phosphotyrosine and the N-terminal SH2 domain of PI3K.     

Allosteric inhibition abrogates dysregulated LFA-1 activation: Structural insight into mechanisms of diminished immunologic disease

Lymphocyte Function Associated antigen-1(LFA-1) has been implicated severely in the pathophysiology of inflammatory and autoimmune diseases. Its active and inactive conformations correlate with its diseased and non-diseased state respectively. This is determined by its degree of affinity for its intrinsic ligand (ICAM) at the active site and accompanying synergistic coordination at the α7 helix. This potentiates the role of inhibitors in disrupting this interaction allosterically. Herein, we present a first account of the structural dynamics which characterizes the inhibitory effect of a novel LFA-1 antagonist, Lifitegrast (SAR1118), upon binding to the I-domain allosteric site (IDAS) using molecular dynamics simulation. Findings from this study revealed that the inhibitor stabilized the closed conformation and reversed the open conformation to a low ICAM-affinity state (closed) as evidenced by the upward movement of the α7 helix and corresponding transitions at the active site. This in both cases favors the formation of the non-disease inactive form. Upon allosteric modulation, the inhibitor significantly restored protein stability, enhanced compactness and decreased residual fluctuation as crucial to its potency in the amelioration of immunological and inflammatory diseases which agrees with experimental studies. These findings could therefore serve as the basis for the exploration of the allosteric domain and its active site affinity modulation to aid the design of more specific and selective inhibitors.