Structure of Rhizobium sp. 4-9 histamine dehydrogenase and analysis of the electron transfer pathway to an abiological electron acceptor

Histamine dehydrogenase from the gram-negative bacterium Rhizobium sp. 4-9 (HaDHR) is a member of a small family of dehydrogenases containing a covalently attached FMN, and the only member so far identified to date that does not exhibit substrate inhibition. In this study, we present the 2.1 Å resolution crystal structure of HaDHR. This new structure allowed for the identification of the internal electron transfer pathway to abiological ferrocene-based mediators. Alanine 437 was identified as the exit point of electrons from the Fe₄S₄ cluster. The enzyme was modified with a Ser436Cys mutation to facilitate covalent attachment of a ferrocene moiety. When modified with Fc-maleimide, this new construct demonstrated direct electron transfer from the enzyme to a gold electrode in a histamine concentration-dependent manner without the need for any additional electron mediators.

Facile assembly of 1,5-diazocan-2-ones via cyclization of tethered sulfonamides to cyclopropenes

The sulfonamide moiety was evaluated as an activating and stabilizing functional group in the metal-templated strain release-driven intramolecular nucleophilic addition of amines to cyclopropenes to generate 1,5-diazocan-2-ones.

Cyclopropene-Templated Assembly of Medium Cycles via Ru-Catalyzed Ring-Closing Metathesis

An expeditious click-click cyclize strategy for the assembly of medium-sized heterocyclic rings is described. The sequence involves the reaction of cycloprop-2-ene carboxylic acids with unsaturated amines to furnish amides, which are further subjected to a Cu-catalyzed directed carbomagnesiation and a ring-closing olefin metathesis reaction. This methodology allows for the efficient preparation of lactams with ring sizes up to 10.

Lactate as a biomarker for sleep

STUDY OBJECTIVES

An ideal biomarker for sleep should change rapidly with sleep onset, remain at a detectably differential level throughout the sleep period, and exhibit a rapid change with waking. Currently, no molecular marker has been identified that exhibits all three properties. This study examined three substances (lactate, glucose, and glutamate) for suitability as a sleep biomarker.

DESIGN

Using amperometric biosensor technology in conjunction with electroencephalograph (EEG) and electromyograph (EMG) monitoring, extracellular concentrations of lactate and glucose (Cohort 1) as well as lactate and glutamate (Cohort 2) were recorded over multiple sleep/wake cycles.

PATIENTS OR PARTICIPANTS

There were 12 C57Bl/6J male mice (3-5 mo old).

INTERVENTIONS

Sleep and waking transitions were identified using EEG recordings. Extracellular concentrations of lactate, glucose, and glutamate were evaluated before and during transition events as well as during extended sleep and during a 6-h sleep deprivation period.

MEASUREMENTS AND RESULTS

Rapid and sustained increases in cortical lactate concentration (approximately 15 μM/min) were immediately observed upon waking and during rapid eye movement sleep. Elevated lactate concentration was also maintained throughout a 6-h period of continuous waking. A persistent and sustained decline in lactate concentration was measured during nonrapid eye movement sleep. Glutamate exhibited similar patterns, but with a much slower rise and decline (approximately 0.03 μM/min). Glucose concentration changes did not demonstrate a clear correlation with either sleep or wake.

CONCLUSIONS

These findings indicate that extracellular lactate concentration is a reliable sleep/wake biomarker and can be used independently of the EEG signal.

Simultaneous real-time measurement of EEG/EMG and L-glutamate in mice: A biosensor study of neuronal activity during sleep

We report on electroencephalograph (EEG) and electromyograph (EMG) measurements concurrently with real-time changes in L-glutamate concentration. These data reveal a link between sleep state and extracellular neurotransmitter changes in a freely-moving (tethered) mouse. This study reveals, for the first time in mice, that the extracellular L-glutamate concentration in the pre-frontal cortex (PFC) increases during periods of extended wakefulness, decreases during extended sleep episodes and spikes during periods of REM sleep. Individual sleep epochs (10 s in duration) were scored as wake, slow-wave (SW) sleep or rapid eye movement (REM) sleep, and then correlated as a function of time with measured changes in L-glutamate concentrations. The observed L-glutamate levels show a statistically significant increase of 0.86 ± 0.26 μM (p < 0.05) over 37 wake episodes recorded from all mice (n = 6). Over the course of 49 measured sleep periods longer than 15 min, L-glutamate concentrations decline by a similar amount (0.88 ± 0.37 μM, p < 0.08). The analysis of 163 individual REM sleep episodes greater than one min in length across all mice (n = 6) demonstrates a significant rise in L-glutamate levels as compared to the 1 min preceding REM sleep onset (RM-ANOVA, DF = 20, F = 6.458, p < 0.001). The observed rapid changes in L-glutamate concentration during REM sleep last only between 1 and 3 min. The approach described can also be extended to other regions of the brain which are hypothesized to play a role in sleep. This study highlights the importance of obtaining simultaneous measurements of neurotransmitter levels in conjunction with sleep markers to help elucidate the underlying physiological and ultimately the genetic components of sleep.

The ABL switch control inhibitor DCC-2036 is active against the chronic myeloid leukemia mutant BCR-ABLT315I and exhibits a narrow resistance profile

Acquired point mutations within the BCR-ABL kinase domain represent a common mechanism of resistance to ABL inhibitor therapy in patients with chronic myeloid leukemia (CML). The BCR-ABL(T315I) mutant is highly resistant to imatinib, nilotinib, and dasatinib, and is frequently detected in relapsed patients. This critical gap in resistance coverage drove development of DCC-2036, an ABL inhibitor that binds the switch control pocket involved in conformational regulation of the kinase domain. We evaluated the efficacy of DCC-2036 against BCR-ABL(T315I) and other mutants in cellular and biochemical assays and conducted cell-based mutagenesis screens. DCC-2036 inhibited autophosphorylation of ABL and ABL(T315I) enzymes, and this activity was consistent with selective efficacy against Ba/F3 cells expressing BCR-ABL (IC(50): 19 nmol/L), BCR-ABL(T315I) (IC(50): 63 nmol/L), and most kinase domain mutants. Ex vivo exposure of CML cells from patients harboring BCR-ABL or BCR-ABL(T315I) to DCC-2036 revealed marked inhibition of colony formation and reduced phosphorylation of the direct BCR-ABL target CrkL. Cell-based mutagenesis screens identified a resistance profile for DCC-2036 centered around select P-loop mutations (G250E, Q252H, Y253H, E255K/V), although a concentration of 750 nmol/L DCC-2036 suppressed the emergence of all resistant clones. A decreased concentration of DCC-2036 (160 nmol/L) in dual combination with either nilotinib or dasatinib achieved the same zero outgrowth result. Further screens for resistance due to BCR-ABL compound mutations (two mutations in the same clone) identified BCR-ABL(E255V / T315I) as the most resistant mutant. Taken together, these findings support continued evaluation of DCC-2036 as an important new agent for treatment-refractory CML.

Conformational control inhibition of the BCR-ABL1 tyrosine kinase, including the gatekeeper T315I mutant, by the switch-control inhibitor DCC-2036

Acquired resistance to ABL1 tyrosine kinase inhibitors (TKIs) through ABL1 kinase domain mutations, particularly the gatekeeper mutant T315I, is a significant problem for patients with chronic myeloid leukemia (CML). Using structure-based drug design, we developed compounds that bind to residues (Arg386/Glu282) ABL1 uses to switch between inactive and active conformations. The lead "switch-control" inhibitor, DCC-2036, potently inhibits both unphosphorylated and phosphorylated ABL1 by inducing a type II inactive conformation, and retains efficacy against the majority of clinically relevant CML-resistance mutants, including T315I. DCC-2036 inhibits BCR-ABL1(T315I)-expressing cell lines, prolongs survival in mouse models of T315I mutant CML and B-lymphoblastic leukemia, and inhibits primary patient leukemia cells expressing T315I in vitro and in vivo, supporting its clinical development in TKI-resistant Ph(+) leukemia.

Switch control pocket inhibitors of p38-MAP kinase. Durable type II inhibitors that do not require binding into the canonical ATP hinge region

Switch control pocket inhibitors of p38-alpha kinase are described. Durable type II inhibitors were designed which bind to arginines (Arg67 or Arg70) that function as key residues for mediating phospho-threonine 180 dependant conformational fluxing of p38-alpha from an inactive type II state to an active type I state. Binding to Arg70 in particular led to potent inhibitors, exemplified by DP-802, which also exhibited high kinase selectivity. Binding to Arg70 obviated the requirement for binding into the ATP Hinge region. X-ray crystallography revealed that DP-802 and analogs induce an enhanced type II conformation upon binding to either the unphosphorylated or the doubly phosphorylated form of p38-alpha kinase.

Gram-scale syntheses of the (1→3)-linked and (1→4)-linked hyaluronan disaccharides

The first gram-scale syntheses of two hyaluronan disaccharides are described. Construction of the (1-->4)-linked disaccharide 12 was achieved in 12% overall yield using 2,3-bis-dimethyl acetal protection in combination with chlorosilane-induced carbamate cleavage methodologies. The uronic acid functionality was installed using TEMPO oxidation with NaOCl as the hypochlorite source. The (1-->3)-linked disaccharide 18 was achieved in 7% overall yield utilizing acetonide protection in addition to the chlorosilane-induced carbamate cleavage methodology and the TEMPO oxidation.

Ab initio calculation of inner-sphere reorganization energies of arenediazonium ion couples

The geometries of a series of substituted arenediazonium cations (p-NO2, p-CN, p-Cl, p-F, p-H, m-CH3, p-CH3, p-OH, p-OCH3, p-NH2) and the corresponding diazenyl radicals were optimized at the HF/6-31G, MP2/6-31G, B3LYP/6-31G, B3LYP/TZP, B3PW91/TZP, and CASSCF/6-31G levels of theory. Inner-sphere reorganization energies for the single electron-transfer reaction between the species were computed from the optimized geometries according to the NCG method and compared to experimental values determined by Doyle et al. All levels of theory predicted a CNN bond angle of 180 degrees in the cation. A bent neutral diazenyl radical was predicted at all levels of theory excepting B3LYP/TZP and B3PW91/TZP for the p-Cl-substituted compound. Inner-sphere reorganization energies determined at the HF, MP2, and CASSCF levels of theory correlated poorly with both experimental results and calculated geometries. Density functional methods correlated best with the experimental values, with B3LYP/6-31G yielding the most promising results, although the ROHF/6-31G survey also showed some promise. B3LYP/6-31G calculations correctly predicted the order of the inner-sphere reorganization energies for the series, excluding the halogen-substituted compounds, with values ranging from 42.8 kcal x mol(-1) for the p-NO2-substituted species to 55.1 kcal x mol(-1) for NH2. The magnitudes of these energies were lower than the experimental by a factor of 2. For the specific cases examined, the closed-shell cation geometries showed the expected geometry about the CNN bond, with variations in the CN and NN bond lengths correlating with the electron-donating/withdrawing capacity of the substituent. As predicted by Doyle et al., a large geometry change was observed upon reduction. The neutral diazenyl radicals showed a nominal CNN bond angle of 120 degrees and variations in the CN and NN bond lengths also correlated with the electron-donating/withdrawing capacity of the substituent. Changes in theta(CNN) and r(CN) both correlated well with calculated lambda(inner). The key parameters influencing inner-sphere reorganization energy were the CN and NN bond lengths and the CNN bond angle. This influence is explained qualitatively via resonance models produced from NRT analysis and is related to the amount of CN double bond character. Based on these observations, B3LYP/6-31G calculations are clearly the most amenable for calculating inner-sphere reorganization energies for the single electron-transfer reaction between cation/neutral arenediazonium ion couples.

The mild cleavage of 2-amino-2-deoxy-D-glucoside methoxycarbonyl derivatives

The conversion of methyl carbamate to the corresponding free amine is described for a series of 2-amino-2-deoxy-D-glucosamine derivatives. Cleavage of methoxycarbonyl moiety with MeSiCl(3) and triethylamine in dry THF at 60 degrees C and subsequent aqueous hydrolysis yields the free amine in 54 to 93% yields. The selective cleavage of methyl carbamates with MeSiCl(3) in the presence of a 2,2,2-trichloroethoxycarbonyl group or 2-azido glycosides affords selectively, orthogonal N-deprotected carbohydrates.

Synthesis of allophanate-derived branched glycoforms from alcohols and p-nitrophenyl carbamates

[reaction: see text] The formation of saccharide-derived carbamates and alkyl 2, 4-dialkylallophanates from alcohols and p-nitrophenyl carbamates is described. Optimization of allophanate formation has led to the synthesis of branched glycoforms with inter-saccharide allophanate linkages that are rigidified by intramolecular hydrogen bonds.

Synthesis of carbamate-containing cyclodextrin analogues

[formula: see text] The one-pot cyclooligomerization of a saccharide-derived p-nitrophenyl carbamate monomer was developed to generate a series of novel carbamate-containing cyclodextrin analogues. The "transcarbamoylation" occurs by initial base-induced activation to the isocyanate, followed by polycondensation/cyclization of the isocyanato alcohol. In the presence of NaH, only cyclized oligomers were observed, suggesting the importance of Na+ in promoting the efficiency of the cyclization process. The facile deprotection of the oligomers was achieved.

Towards a molecular understanding of arthritis

Several different agents including free radicals, oxidizing compounds and proteases are believed to play a role in the onset of arthritis. The evidence and underlying chemistry presently available for each destructive agent are presented.

Synthesis of Lipophilic Paramagnetic Contrast Agents

The facile, high-yielding synthesis of a series of macrocycles 7a-k in 75-100% yield is reported. The transformation of these compounds to their carboxymethylated analogues 8a-k in 75-90% yield and subsequent gadolinium complexes 9a-k provides a series of homologous neutral paramagnetic contrast agents (PCAs) with tunable lipophilicity. Alkylated cationic intermediates 6a-k are prepared in yields of 72-94% from glyoxal adduct of cyclen (5) and slight excesses of alkyl iodides. The methodology is selective for monoalkylation and amenable to large-scale synthesis.

Construction and characterization of a manganese-binding site in cytochrome c peroxidase: towards a novel manganese peroxidase

BACKGROUND

Manganese-binding sites are found in several heme peroxidases, namely manganese peroxidase (MnP), chloroperoxidase, and the cationic isozyme of peanut peroxidase. The Mn-binding site in MnP is of particular interest. Oxidation of Mn(II) to Mn(III) is a key step in the biodegradation of lignin, a complex phenylpropanoid polymer, as well as many aromatic pollutants. Cytochrome c peroxidase (CcP), which is structurally homologous to MnP despite a poor sequence homology, does not bind manganese. Thus, engineering a Mn-binding site into CcP will allow us to elucidate principles behind designing metal-binding sites in proteins, to understand the structure and function of this class of Mn-binding centers, and to prepare novel enzymes that can degrade both lignin and other xenobiotic compounds.

RESULTS

Based on a comparison of the crystal structures of CcP and MnP, a site-directed triple mutant (Gly41-->Glu, Val45-->Glu, His181-->Asp) of residues near the putative Mn-binding site in CcP was prepared and purified to homogeneity. Titrating MnSO4 into freshly prepared mutant CcP resulted in electronic absorption spectral changes similar to those observed in MnP. The calculated apparent dissociation constant and the stoichiometry of Mn-binding of CCP were also similar to MnP. Titration with MnSO4 resulted in the disappearance of specific paramagnetically shifted nuclear magnetic resonance spectroscopy signals assigned to residues close to the putative Mn-binding site in the mutant CcP. None of the spectral features were observed in wild-type CcP. In addition, the triple mutant was capable of oxidizing Mn(II) at least five times more efficiently than the native CcP.

CONCLUSIONS

A Mn-binding site has been created in CcP and based on our spectroscopic studies the designed Mn-binding site is similar to the Mn-binding site in MnP. The results provide a basis for understanding the structure and function of the Mn-binding site and its role in different heme peroxidases.

The solution conformation of hyaluronan: a combined NMR and molecular dynamics study

Hyaluronan (HA) is a negatively charged glycosaminoglycan that exhibits a wide variety of biological effects mediated by binding to cell-surface and extracellular matrix proteins (hyaladherins). Short HA oligosaccharides have been shown to retain the specific interactions and biological effects of high molecular weight HA. Although it has a simple disaccharide repeating unit, the aqueous solution conformation of HA has been very difficult to determine because of strong coupling and overlapping resonances. In this study, we propose aqueous solution conformations for an octasaccharide of HA, derived from proton-proton NOE data and restrained molecular dynamics. To overcome spectral overlap and strong coupling, alternate methods for extracting distance restraints were employed. Restrained molecular dynamics calculations yielded one set of interglycosidic angle values for the beta (1,3) linkage (phi 13 = 46 degrees, psi 13 = 24 degrees). In contrast, two sets of values for the beta (1,4) linkage were consistent with the NOE restraints (phi 14 = 24 degrees, psi 14 = -53 degrees or phi 14 = 48 degrees, psi 14 = 8 degrees). The potential difference in flexibility for the two linkages is consistent with unrestrained as well as the restrained molecular dynamics trajectories described here. The conformational parameters obtained from restrained molecular dynamics are used to predict helical parameters of high molecular weight HA and will provide a basis for studies of HA binding to proteins.