A structure-based design approach for the identification of novel inhibitors: application to an alanine racemase

We report a new structure-based strategy for the identification of novel inhibitors. This approach has been applied to Bacillus stearothermophilus alanine racemase (AlaR), an enzyme implicated in the biosynthesis of the bacterial cell wall. The enzyme catalyzes the racemization of l- and d-alanine using pyridoxal 5-phosphate (PLP) as a cofactor. The restriction of AlaR to bacteria and some fungi and the absolute requirement for d-alanine in peptidoglycan biosynthesis make alanine racemase a suitable target for drug design. Unfortunately, known inhibitors of alanine racemase are not specific and inhibit the activity of other PLP-dependent enzymes, leading to neurological and other side effects.This article describes the development of a receptor-based pharmacophore model for AlaR, taking into account receptor flexibility (i.e. a `dynamic' pharmacophore model). In order to accomplish this, molecular dynamics (MD) simulations were performed on the full AlaR dimer from Bacillus stearothermophilus (PDB entry, 1sft) with a d-alanine molecule in one active site and the non-covalent inhibitor, propionate, in the second active site of this homodimer. The basic strategy followed in this study was to utilize conformations of the protein obtained during MD simulations to generate a dynamic pharmacophore model using the property mapping capability of the LigBuilder program. Compounds from the Available Chemicals Directory that fit the pharmacophore model were identified and have been submitted for experimental testing.The approach described here can be used as a valuable tool for the design of novel inhibitors of other biomolecular targets.     

Chiral liquid chromatography-mass spectrometry for high-throughput screening of enzymatic racemase activity

In finding suitable biocatalysts for processes in chemical industry, expression libraries are constructed containing typically >10,000 clones. Search for a desired activity is done by examination of all the clones in one or more libraries using a high-throughput screening assay. Here we describe a method for the screening of the enzymatic racemase activity of clones from an expression library on alpha-amino-epsilon-caprolactam (ACL) using a fast chiral LC separation and ionspray-MS as the detection technique. After substrate incubation with S-ACL, the 96-well microplates were centrifuged to remove cell material. The conversion of S-ACL to R-ACL was monitored by quantitation of the R-ACL enantiomer. Separation of the two ACL enantiomers was performed on a Crownpak CR+ column within 1 min. A Gilson 215 autosampler with a 889 multiple injection probe was used for injecting the samples into the LC system. The total analysis time for a 96-well microplate was 56 min. The MS was operated in the positive-ion mode using selected ion monitoring at m/z 129 [M+H]+ of ACL. Using this method over 12,000 samples were analyzed without loss in performance of the system. The LC column remained stable without loss of resolution and the MS system did not show loss in sensitivity throughout the screening. Inter-day reproducibility was within 15%.     

Complex formation reactions of palladium(II)-1,3-diaminopropane with various biologically relevant ligands. Kinetics of hydrolysis of glycine methyl ester through complex formation

The interaction of [Pd(DAP)(H₂O)₂]²⁺ (DAP = 1,3-diaminopropane) with some selected bio-relevant ligands, containing different functional groups, were investigated. The ligands used are dicarboxylic acids, amino acids, peptides and DNA constituents. Stoichiometry and stability constants of the complexes formed are reported at 25°C and 0.1 M ionic strength. The results show the formation of 1:1 complexes with amino acids and dicarboxylic acids. The effect of chelate ring size of the dicarboxylic acid complexes on their stability constants is examined. Peptides form both 1:1 complexes and the corresponding deprotonated amide species. DNA constituents form 1:1 and 1:2 complexes. The effect of dioxane on the acid dissociation constants of CBDCA and the formation constant of its complex with Pd(DAP)²⁺ was reported. The kinetics of hydrolysis of glycine methyl ester bound to [Pd(DAP)(H₂O)₂]²⁺ was studied at 25°C and 0.1M ionic strength.      

Equilibrium studies of complex formation involving palladium(II)-(1,3-diaminopropane) and cyclobutane dicarboxylic acid,DNA units,amino acids or peptides

Complex formation equillibria of [Pd(DAP)(H₂O)₂]²⁺ (DAP = 1,3-diaminopropane) with Cl⁻, OH⁻, cyclobutane dicarboxylic acid (CBDCA), amino acids, peptides and DNA unit constituents have been investigated. Stoichiometries and stability constants of the complexes were determined at 37°C and 0.16 M NaNO₃ ionic strength. The results showed the formation of 1:1 complexes with amino acids and CBDCA. Peptides form both 1:1 complexes and the corresponding deprotonated amide species. DNA constituents form both 1:1 and 1:2 complexes. [Pd(DAP)(CBDCA)] was isolated and characterized. The concentration distribution of the complexes in solution was evaluated. This revised version was published online in June 2006 with corrections to the Cover Date.     

New dicholesteryl-based gelators: chirality and spacer length effect

Eight new diacid amides of dicholesteryl L(D)-alaninates were designed and prepared. The compounds with spacers containing three, four, five, or six carbon atoms and L-alanine residues are denoted as 1a, 2a, 3a, and 4a, respectively, and those containing D-alanine residues are denoted as 1b, 2b, 3b, and 4b, respectively. A gelation test revealed that a subtle change in the length of the spacer and an inverse in the chirality of the amino acid residue can produce a dramatic change in the gelation behavior of the compounds and the microstructures of the gels, as revealed by SEM, XRD, and CD measurements. Importantly, for the compounds 1 and 2, those containing d-alanine residues (1b, 2b) are more efficient gelators than their analogues with opposite chirality (1a, 2a). For the compounds of longer spacers (3, 4), however, those containing l-alanine residues (3a, 4a) are superior to the corresponding ones with d-alanine residues (3b, 4b). Very interestingly, of the 139 gel systems studied, at least 11 of them gel spontaneously at room temperature. Studies of the rheological properties of the example systems of these gels demonstrated that change in the spacer lengths of the gelators has a great effect upon the mechanical properties of the corresponding gels, and the studies also revealed the thixotropic properties of the gels. Furthermore, it was observed that 4a forms water-in-oil gel emulsions with some organic solvents by simple agitating the systems at room temperature.     

Conversion of a PLP-dependent racemase into an aldolase by a single active site mutation

Alanine racemase (Alr) [EC 5.1.1.1] from Geobacillus stearothermophilus is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes the first committed step in bacterial cell wall biosynthesis. It is converted to an aldolase upon replacement of Tyr265, which normally serves as a catalytic base in the racemase reaction, with alanine. The Y265A mutation increases catalytic efficiency for cleavage of beta-phenylserine to benzaldehyde and glycine by 2.3 x 105 fold as compared to the wild-type racemase, while racemase activity is greatly decreased. Additional mutagenesis suggests that His166 may act as the base that initiates the retroaldol reaction. The Y265A mutant is highly stereoselective for (2R,3S)-phenylserine, a d-amino acid, and does not process its enantiomer. This preference is consistent with the expected binding mode of substrate in the modified active site and supports the proposal that naturally occurring d-threonine aldolases and alanine racemases derive from a common ancestor.     

Attachment of tyrosinase on mixed self-assembled monolayers for the construction of electrochemical biosensor

<正>A mixed self-assembled monolayers(SAMs) of thioctic acid(T-COOH) and thioctic acid amide(T-NH_2) were used to immobilize tyrosinase for fabricating biosensor.The results showed that the mixed SAMs prepared from solution at the ratio of 1:4 provided an excellent microenvironment for enzymatic reaction between tyrosinase and substrate.The biosensor exhibited a fast response and high sensitivity for sensing substrate.     

Novel method for preparation of poly(benzoxazinone‐imide)

A novel method was developed to prepare poly(benzoxazinone‐imide) by the dealcoholization of poly(amide‐imide), having pendent ethoxycarbonyl groups, which was prepared from poly(amide acid). The poly(amide acid) was prepared from the reaction of pyromellitic dianhydride and 4,4′‐diamino‐6‐ethoxycarbonyl benzanilide. The curing behavior of the poly(amide acid) was monitored by DSC, which indicated the presence of two broad endotherms, one with maximum at 153 °C due to imide‐ring formation and the other with maximum at 359 °C due to benzoxazinone‐ring formation. The poly(amide acid) was thermally treated at 300 °C/1 h to get poly(amide‐imide) with pendent ester groups, then at 350 °C/2 h to convert into poly(benzoxazinone‐imide) by dealcoholization. Viscoelastic measurements of the poly(amide‐imide) showed that the storage modulus dropped at about 280 °C with glass‐transition temperature (T_g ) at about 340 °C. The storage modulus of poly(benzoxazinone‐imide), however, was almost constant up to 400 °C and no T_g was detected below 400 °C. Also, the tensile modulus and tensile strength of the poly(benzoxazinone‐imide) was much higher than that of the poly(amide‐imide). The 5% decomposition of poly(benzoxazinone‐imide) film was at 535 °C, which reflects its excellent thermal stability. Also, poly(benzoxazinone‐imide) showed more hydrolytic stability against alkali in comparison to polyimides. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 1647–1655, 2000     

A simple route to tetrahydro-1,4-benzodiazepin-3-ones bearing diverse N1, N4, and C10 functionalization

We describe an efficient synthesis of enantiopure tetrahydro-1,4-benzodiazepine-3-ones derived from l-alanine. Diverse substitution at N1, N4, and C10 can be achieved by coupling various N-alkyl derivatives of l-alanine and N-allyl-(2-fluoro-5-nitro)benzylamine. Cyclization of this intermediate proceeds in high yield and without racemization, providing diversity at N1. The NO₂ group was easily transformed into other functional groups or removed, providing diversity at C10. Finally, oxidative deallylation allows diverse substitution to be installed at N4.     

Structural isotopic effects in the smallest chiral amino acid: observation of a structural phase transition in fully deuterated alanine

A first study of possible changes instigated by deuteration in amino acids was carried out using neutron diffraction, inelastic neutron scattering, and Raman scattering in l-alanine, C2H4(NH2)COOH. Careful analysis of the structural parameters shows that deuteration of l-alanine engenders significant geometric changes as a function of temperature, which can be directly related to the observation of new lattice vibration modes in the Raman spectra. The combination of the experimental data suggests that C2D4(ND2)COOD undergoes a structural phase transition (or a structural rearrangement) at about 170 K. Considering that this particular amino acid is a hydrogen-bonded system with short hydrogen bonds (O...H approximately 1.8 A), we evoke the Ubbelohde effect to conclude that substitution of hydrogen for deuterium gives rise to changes in the hydrogen-bonding interactions. The structural differences suggest distinct relative stabilities for the hydrogenous and deuterated l-alanine.     

Bound coefactor/dual enzyme electrode system for l-alanine

A dual enzyme-bound coenzyme electrode system for quantifying l-alanine is described. Commercially available dextran-bound NAD was incorporated into an l-alanine dehydrogenase (E.C. 1.4.1.1)/l-lactate dehydrogenase (E.C. 1.1.1.27) enzyme system and held at the surface of a potentiometric ammonia gas sensor. Using this system, l-alanine calibration curves with a slope of 45 mV/decade and 10^?5 M detection limit were obtained with a sensor lifetime of at least 10 days. This system is potentially useful for the clinical determination of l-alanine in serum.     

Enzymatic hydrolysis of alpha- and beta-oligo(L-aspartic acid)s by poly(aspartic acid) hydrolases-1 and 2 from Sphingomonas sp. KT-1

The enzymatic hydrolysis of alpha- and beta-oligo(L-aspartic acid)s by PAA hydrolase-1 and PAA hydrolase-2 (purified from Sphingomonas sp. KT-1) was performed to elucidate the mechanism of the microbial degradation by Sphingomonas sp. KT-1 of the thermally synthesized alpha,beta-poly(D,L-aspartic acid) (tPAA). GPC analysis of the hydrolyzed products of alpha- and beta-tetra(L-aspartic acid)s by PAA hydrolase-1 has showed that PAA hydrolase-1 is capable of hydrolyzing only the specific amide bonds between beta-aspartic acid units. The RP-HPLC analysis of the enzymatic hydrolysis of beta-oligo(L-aspartic acid)s (4 and 5 mers) by PAA hydrolase-1 has suggested that the enzymatic hydrolysis of beta-oligo(L-aspartic acid)s occurs via an endo-mode cleavage. In contrast, PAA hydrolase-2 hydrolyzed both alpha- and beta-oligo(L-aspartic acid)s via an exo-mode cleavage to yield L-aspartic acid as a final product. A kinetic study on the enzymatic hydrolysis of alpha-oligo(L-aspartic acid)s (3 to 7 mers) by PAA hydrolase-2 has indicated that Km values are almost independent of the number of monomer units in oligomers of 4 to 7 mers, while that Vmax values are markedly dependent on the chain length and show a maximum value at 5 mer.     

Simultaneous enzymatic synthesis of (S)-3-fluoroalanine and (R)-3-fluorolactic acid

A coupled enzymatic system for the simultaneous synthesis of (S)-3-fluoroalanine (1a) and (R)-3-fluorolactic acid (3) with l-alanine dehydrogenase (l-AlaDH) from Bacillus subtilis and rabbit muscle l-lactate dehydrogenase (l-LDH) using rac-1 and NAD⁺ is described. Analysis of isolated products of the laboratory preparative scale process revealed 1a in 60% yield and 88% ee and 3 in 80% yield and over 99% ee. The compounds 1a and 3 represent chiral building blocks for the synthesis of several products with pharmacological activity.     

Probing of lipase activity at air/water interface by sum-frequency generation spectroscopy

The infrared-visible sum-frequency generation (SFG) vibrational spectroscopy was used to probe enzymatic activity of Thermomyces lanuginosus lipase (TLL) at air/water interface. A monolayer of amphiphilic O-palmitoyl-2,3-dicyanohydroquinone (PDCHQ), containing target ester group and two CN groups serving as vibrational markers, was utilized as an enzyme substrate. SFG data revealed the detailed molecular scale structure and properties of the PDCHQ layer at the interface. In particular, we demonstrate that hydrophilic headgroup of PDCHQ is mainly in the form of an oxyanion, and the enzyme-induced cleavage of the ester bond could be spectroscopically monitored by the disappearance of the intense C tripple bond N resonance at 2224 cm(-1). The enzymatic nature of the ester bond cleavage was confirmed by the control experiments with deactivated S146A mutant variant of TLL. By comparing action of wild type (WT) TLL and its inactive S146A mutant, it was shown that two effects take place at the interface: disordering of the lipid monolayer due to the adsorption of enzyme and enzymatic cleavage of the ester bond. The concentration of enzyme as low as 10 nM could be easily sensed by the SFG spectroscopy. We present spectroscopic evidence that upon hydrolysis one of the products, 2,3-dicyanohydroquinone, leaves the surface, while the other, palmitic acid, remains at air/water interface in predominantly undissociated form with the mono-hydrogen-bonded carbonyl group. Strong amide I (1662 cm(-1)) and amide A (3320 cm(-1)) SFG signals from TLL suggest that enzyme molecules position themselves at air/water interface in an orderly fashion. Presented work demonstrates the potential of SFG spectroscopy for in situ real-time monitoring of enzymatic processes at air/water interface.     

Variable‐Temperature Powder X‐ray Diffraction of Aromatic Carboxylic Acid and Carboxamide Cocrystals

The effect of temperature on the cocrystallization of benzoic acid (BA), pentafluorobenzoic acid (FBA), benzamide (BAm), and pentafluorobenzamide (FBAm) is examined in the solid state. BA and FBA formed a 1:1 complex 1 at ambient temperature by grinding with a mortar and pestle. Grinding FBA and BAm together resulted in partial conversion into the 1:1 adduct 2 at 28 °C and complete transformation into the product cocrystal at 78 °C. Further heating (80–100 °C) and then cooling to room temperature gave a different powder pattern from that of 2 . BAm and FBAm hardly reacted at ambient temperature, but they afforded the 1:1 cocrystal 3 by melt cocrystallization at 110–115 °C. Both BA+FBAm ( 4 ) and BA+BAm ( 5 ) reacted to give new crystalline phases upon heating, but the structures of these products could not be determined owing to a lack of diffraction‐quality single crystals. The stronger COOH and CONH₂ hydrogen‐bonding groups of FBA and FBAm yielded the equimolar cocrystal 6 at room temperature, and heating of these solids to 90–100 °C gave a new crystalline phase. The X‐ray crystal structures of 1 , 2 , 3 , and 6 are sustained by the acid–acid/amide–amide homosynthons or acid–amide heterosynthon, with additional stabilization from phenyl–perfluorophenyl stacking in 1 and 3 . The temperature required for complete transformation into the cocrystal was monitored by in situ variable‐temperature powder X‐ray diffraction (VT‐PXRD), and formation of the cocrystal was confirmed by matching the experimental peak profile with the simulated diffraction pattern. The reactivity of H‐bonding groups and the temperature for cocrystallization are in good agreement with the donor and acceptor strengths of the COOH and CONH₂ groups. It was necessary to determine the exact temperature range for quantitative cocrystallization in each case because excessive heating caused undesirable phase transitions.     

Comparative effects of different triazole compounds on antioxidant metabolism of Solenostemon rotundifolius

The effect of different triazole compounds, viz., triadimefon (TDM) and hexaconazole (HEX) treatments on the antioxidant metabolism of Solenostemon rotundifolius Poir., Morton plants was investigated in the present study under pot culture. Plants were treated with TDM at 15 mg l⁻¹ and HEX at 10 mg l⁻¹ separately by soil drenching on 80, 110 and 140 days after planting (DAP). The plants were harvested randomly on 90, 120 and 150 DAP for determining the effect of both the triazoles on non-enzymatic antioxidant contents like ascorbic acid (AA), reduced glutathione (GSH) and -tocopherol (-toc), activities of antioxidant enzymes like superoxide dismutase (SOD) and ascorbate peroxidase (APX). All the analyses were made in leaf, stem and tubers of both control and treated plants. It was found that both these triazole compounds have profound effects on the antioxidant metabolism and caused an enhancement in both non-enzymatic and enzymatic antioxidant potentials under treatments. These results suggest that, the application of triazoles may be a useful tool to increase the antioxidant production in S. rotundifolius and thereby make it an economical food crop.     

Efficient Production of γ-GABA Using Recombinant <Emphasis Type="Italic">E. coli</Emphasis> Expressing Glutamate Decarboxylase (GAD) Derived from Eukaryote <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>

A cellulase-producing bacterium, designated as strain AK9, was isolated from a hot spring of Tatta Pani, Azad Kashmir, Pakistan. The bacterium was identified as Bacillus amyloliquefaciens through 16S rRNA sequencing. Cellulase from strain AK9 was able to liberate glucose from soluble cellulose and carboxymethyl cellulose (CMC). Enzyme was purified through size exclusion chromatography and a single band of ～47 kDa was observed on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The enzyme was purified with recovery of 35.5%, 3.6-fold purity with specific activity of 31 U mg^?1. The purified cellulase retained its activity over a wide range of temperature (50–70 °C) and pH (3–7) with maximum stability at 60 °C and pH 5.0. The activity inhibited by ethylenediaminetetraacetic acid (EDTA), suggested that it was metalloenzyme. Diethyl pyrocarbonate (DEPC) and β-mercaptoethanol significantly inhibited cellulase activity that revealed the essentiality of histidine residues and disulfide bonds for its catalytic function. It was stable in non-ionic surfactants, in the presence of various metal ions, and in water-insoluble organic solvents. Approximately 9.1% of reducing sugar was released after enzymatic saccharification of DAP-pretreated agro-residue, compared to a very low percentage by autohydrolysis treatment. Hence, it is concluded that cellulase from B. amyloliquefaciens AK9 can potentially be used in bioconversion of lignocellulosic biomass to fermentable sugars.     

New organosoluble and thermally stable poly(amide‐imide)s with benzoxazole or benzothiazole pendent groups: synthesis and characterization

Two new benzoxazole or benzothiazole‐containing diimide‐dicarboxylic acid monomers, such as 2‐[3,5‐bis(N‐trimellitimidoyl)phenyl]benzoxazole ( 2 _o ) or 2‐[3,5‐bis(N‐trimellitimidoyl)phenyl]benzothiazole ( 2 _s ) were synthesized from the condensation reaction between 3,5‐diaminobenzoic acid and 2‐aminophenol or 2‐aminothiophenol in polyphosphoric acid (PPA) with subsequent reaction of trimellitic anhydride in the presence of glacial acetic acid, respectively, and two new series of modified aromatic poly(amide‐imide)s were prepared. This preparation was done with pendent benzoxazole or benzothiazole units from the newly synthesized diimide‐dicarboxylic acid and various aromatic diamines by triphenyl phosphite‐activated polycondensation. In addition, the corresponding unsubstituted poly(amide‐imide)s were prepared under identical experimental conditions for comparative purposes. Characterization of polymers was accomplished by inherent viscosity measurements, FT‐IR, UV–visible, ¹H‐NMR spectroscopy and thermogravimetry. The polymers were obtained in quantitative yields with inherent viscosities between 0.39 and 0.81 dl g^?1. The solubilities of modified poly(amide‐imide)s in common organic solvents as well as their thermal stability were enhanced compared to those of the corresponding unmodified poly(amide‐imide)s. The glass transition temperature, 10% weight loss temperature, and char yields at 800°C were, respectively, 7–26°C, 17–46°C and 2–5% higher than those of the unmodified polymers. Copyright © 2010 John Wiley & Sons, Ltd.     

14N Nuclear quadrupole interaction in Cu(II) doped l-alanine

The ¹⁴N nuclear quadrupole interaction tensor P_N measured by ENDOR in Cu(II) doped l-alanine is analyzed in terms of the Townes and Dailey theory assuming a tetrahedrally bonded N atom. The results of this analysis are compared with those for the ¹⁴N in pure l-alanine and it is found that the principal directions of the P_N tensor are drastically changed upon metal complexation as a consequence of the higher electron affinity of Cu(II) with respect to C and H. Comparison of the corresponding bond populations in pure and Cu(II) doped l-alanine indicates that the Cu draws 0.11 more electron from the N than the substituted H atom.     

New synthetic approach to paullones and characterization of their SIRT1 inhibitory activity

A series of 7,12-dihydroindolo[3,2-d][1]benzazepine-6(5H)-ones (paullones) substituted at C9/C10 (Br) and C2 (Me, CF(3), CO(2)Me) have been synthesized by a one-pot Suzuki-Miyaura cross-coupling of an o-aminoarylboronic acid and methyl 2-iodoindoleacetate followed by intramolecular amide formation. Other approaches to the paullone scaffold based on Pd-catalyzed C-H activation were unsuccessful. In vitro enzymatic assay with recombinant human SIRT-1 indicated a strong inhibitory profile for the series, in particular the analogue with a methoxycarbonyl group at C2 and a bromine at C9. These compounds are, in general, inducers of granulocyte differentiation of the U937 acute leukemia cell line and cause a marked increase in pre-G1 of the cell cycle.