Mirror-image packing in enantiomer discrimination molecular basis for the enantioselectivity of B.cepacia lipase toward 2-methyl-3-phenyl-1-propanol

Synthetic chemists often exploit the high enantioselectivity of lipases to prepare pure enantiomers of primary alcohols, but the molecular basis for this enantioselectivity is unknown. The crystal structures of two phosphonate transition-state analogs bound to Burkholderia cepacia lipase reveal this molecular basis for a typical primary alcohol: 2-methyl-3-phenyl-1-propanol. The enantiomeric alcohol moieties adopt surprisingly similar orientations, with only subtle differences that make it difficult to predict how to alter enantioselectivity. These structures, along with a survey of previous structures of enzyme bound enantiomers, reveal that binding of enantiomers does not involve an exchange of two substituent positions as most researchers assumed. Instead, the enantiomers adopt mirror-image packing, where three of the four substituents at the stereocenter lie in similar positions. The fourth substituent, hydrogen, points in opposite directions.     

Hydrophobic surface induced activation of Pseudomonas cepacia lipase immobilized into mesoporous silica

Lipase from Pseudomonas cepacia (PCL) was successfully immobilized into siliceous mesocellular foams (MCFs) with various hydrophobic/hydrophilic surfaces. The catalytic performances of immobilized PCL were investigated using the transesterification reaction and hydrolytic reaction as model reactions. The specific activity of immobilized PCL greatly increased with enhanced surface hydrophobicity of MCFs, mainly because of lipase activation via hydrophobic interaction between alkyl groups in MCFs and the surface loop (so-called "lid") of PCL. Conformational changes of immobilized PCL were further investigated using time-resolved fluorescence spectroscopy with Trp as an intrinsic probe. When the immobilized PCL was suspended in phosphate buffer, short-lived τ(1) shortened and the fractional contribution of τ(1) significantly increased with the increasing level of surface hydrophobicity of MCFs. These results revealed that Trp(s) of the immobilized PCL were surrounded by a hydrophilic microenvironment because of the fact that the opened "lid" permitted the diffusion of water to the active site cleft. However, for the immobilized PCL suspended in n-hexane, long-lived τ(3) increased with the increase of surface hydrophobicity of MCFs. The reduced interaction between Trp(s) and the surrounding protein matrix was due to intercalation of n-hexane into the active site cleft when the lipase was in open conformation. The above results demonstrated that PCL immobilized into MCF with hydrophobic surfaces were in an activated open conformation.     

Directed evolution and axial chirality: optimization of the enantioselectivity of Pseudomonas aeruginosa lipase towards the kinetic resolution of a racemic allene

Directed evolution of Pseudomonas aeruginosa lipase by the use of combinatorial active site saturation test (CAST) criteria provided a highly enantioselective mutant (Leu162Phe) for kinetic resolution of an axially chiral allene, p-nitrophenyl 4-cyclohexyl-2-methylbuta-2,3-dienoate (E=111); the high enantioselectivity of the Leu162Phe mutant was rationalized by pi-pi stacking.     

磷酸缓冲盐和硫酸钠对洋葱假单胞菌脂肪酶的非水相激活

研究了kosmotropic型磷酸缓冲盐和硫酸钠对洋葱假单胞菌脂肪酶(Pseudomonas cepacia lipase, PCL)非水相催化性能的影响.以往磷酸缓冲盐被用来调控体系的pH值,其掺杂量对酶的催化活性无明显影响,而适量硫酸钠的掺杂则可有效提高酶在非水相的催化活性.本文研究发现,通过精确调控冻干过程,磷酸缓冲盐掺杂能够将PCL在有机相中的转酯化活性提高近10倍,达到其水相本征活性的50%,这一激活效果甚至高于硫酸钠掺杂.利用热重方法分析了盐掺杂PCL的含水量和蛋白结构,并将失重结果同其在有机相中的催化活性相关联,发现PCL在磷酸缓冲盐和硫酸钠掺杂下的催化构型与蛋白含水量及其周围盐环境具有不同的依赖关系.利用2-(4’-氨基-2’-羟基苯基)苯并恶唑作为荧光探针,研究了磷酸缓冲盐和硫酸钠掺杂的PCL悬浮于有机相时对荧光探针发射光谱的影响,发现盐掺杂酶制剂的存在能够大大增加荧光探针稳定于极性溶剂的构型含量,这可能与蛋白周围掺杂盐键和的水分子有关.如果用探针分子稳定于极性溶剂和非极性溶剂的构型比值间接表示悬浮酶制剂的极性结构,在正己烷体系中硫酸钠掺杂的PCL具有比磷酸缓冲盐掺杂的PCL大得多的极性,且酶制剂的极性大小与其非水相转酯化活性之间具有相似的变化趋势.上述研究结果表明,掺杂盐对粗PCL酶制剂的激活可能部分归因于掺杂盐键和的水分子在蛋白周围构筑的极性环境.     

Insights into the structure of the active site of the O2-tolerant membrane bound [NiFe] hydrogenase of R. eutropha H16 by molecular modelling

Structural models for the Ni-B state of the wild-type and C81S protein variant of the membrane-bound [NiFe] hydrogenase from Ralstonia eutropha H16 were derived by applying the homology model technique combined with molecular simulations and a hybrid quantum mechanical/molecular mechanical approach. The active site structure was assessed by comparing calculated and experimental IR spectra, confirming the view that the active site structure is very similar to those of anaerobic standard hydrogenases. In addition, the data suggest the presence of a water molecule in the second coordination sphere of the active centre.     

A molecular model for the active site of S-adenosyl-l-homocysteine hydrolase

Summary S-adenosyl-l-homocysteine hydrolase (AdoHcy hydrolase, EC 3.3.1.1.), a specific target for antiviral drug design, catalyzes the hydrolysis of AdoHcy to adenosine (Ado) and homocysteine (Hcy) as well as the synthesis of AdoHcy from Ado and Hcy. The enzyme isolated from different sources has been shown to contain tightly bound NAD⁺.Based on the 2.0 Å-resolution X-ray crystal structure of dogfish lactate dehydrogenase (LDH), which is functionally homologous to AdoHcy hydrolase, and the primary sequence of rat liver AdoHcy hydrolase, we have derived a molecular model of an extended active site for AdoHcy hydrolase. The computational mutation was performed using the software MUTAR (Yeh et al., University of Kansas, Lawrence), followed by molecular mechanics optimizations using the programs AMBER (Singh et al., University of California, San Francisco) and YETI (Vedani, University of Kansas). Solvation of the model structure was achieved by use of the program SOLVGEN (Jacober, University of Kansas); 56 water molecules were explicitly included in all refinements. Some of these may be involved in the catalytic reaction.We also studied a model of the complex of AdoHcy hydrolase with NAD⁺, as well as the ternary complexes of the redox reaction catalyzed by AdoHcy hydrolase and has been used to differentiate the relative binding strength of inhibitors.     

Gly311 residue triggers the enantioselectivity of Staphylococcus xylosus lipase: a monolayer study

Using emulsified triacylglycerols, we have shown recently [Mosbah et al., 2007, submitted for publication] that amino acid residue G311 of Staphylococcus xylosus lipase (SXL) is critically involved in substrate selectivity, pH and temperature dependency. Using the monomolecular film technique, we show in the present study that the four single mutants of this residue (G311L, G311W, G311D, and G311K), interact efficiently with egg-phosphatidyl choline (egg-PC) monomolecular films, comparably to the wild-type (G311). A critical surface pressure (pi(c)) of about 25 mN/m was obtained with the SXL wild-type (SXL-WT) and its mutants. These results support our conclusion that the G311 residue is not involved in the interfacial adsorption step of SXL. A kinetic study on the surface pressure dependency, stereoselectivity, and regioselectivity of SXL-WT and its G311 mutants was also performed using optically pure enantiomers of diacylglycerols (1,2-sn-dicaprin and 2,3-sn-dicaprin) and a prochiral isomer (1,3-sn-dicaprin) spread as monomolecular films at the air-water interface. Our results indicated that the mutation of one single residue at position 311 affects critically the catalytic activity, the stereo- and the regioselectivity of SXL. As previously observed with emulsified substrates [Mosbah et al., 2007, submitted for publication] we observed that an increase in the size of the 311 amino acid side chain residue was accompanied by a decrease of lipase activity measured on dicaprin monolayer. We also noticed that the substitution of G311 by a basic or acidic residue (G311K and G311D), induces a significant shift of the pH optimum from 8 to 9.5 or from 8 to 6.5, respectively.     

Inverting the enantioselectivity of a carbonyl reductase via substrate-enzyme docking-guided point mutation

Substrate-enzyme docking-guided point mutation of a carbonyl reductase from Sporobolomyces salmonicolor led to mutant enzymes, which reversed the enantiopreference and enhanced the enantioselectivity toward the reduction of para-substituted acetophenones. Such a dramatic change in the enantioselectivity indicates that the 245 residue in the catalytic site plays a critical role in determining the enantioselectivity of these ketone reductions, providing valuable insight into our understanding of how residues involved in substrate binding affect the orientation of bound substrate and thus control the reduction stereoselectivity.     

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.     

Identification and molecular characterization of a novel DyP-type peroxidase from Pseudomonas aeruginosa PKE117

A new DyP-type peroxidase from Pseudomonas aeruginosa PKE117 was identified and characterized. The dypPa was first identified via sequence analysis and then cloned in Escherichia coli. Subsequently, the recombinant protein DyPPa was expressed and purified. Its DNA sequence analysis revealed an open reading frame of 897 bp, encoding a protein monomer of 299 amino acid residues with isoelectric point 4.62. According to SDS-PAGE analysis and FPLC result, DyPPa mainly existed as homodimer (64 kDa). DyPPa displayed typical heme absorbance of Soret band, with an Rz value of 1.18. Inductively coupled plasma-atomic absorption spectrum data also indicated DyPPa contained iron. Multiple amino acid sequence alignment of DyPPa with other members of the DyP-type peroxidases family showed the presence of conserved D139, H210, and R227 amino acids and GXXDG motifs, which were commonly shared by the DyP-type peroxidase family. Although the primary structure homology between DyPPa and other family members was very low, their secondary and tertiary structure displayed high homology, which explained the high decolorizing activity of DyPPa. Specifically, DyPPa displayed a good thermal stability and maximal activity on Reactive blue 5 under pH 3.5. Therefore, it was proposed that DyPPa, with a wide range of substrate specificity, was a novel member of the DyP-type peroxidases family.     

Towards an identification of the pyrethroid pharmacophore. A molecular modelling study of some pyrethroid esters

Summary A molecular modelling and computer graphics study of a series of pyrethroid insecticides has been carried out. The three-dimensional arrangement of the groups essential for the biological activity (pharmacophore) has been identified for the acid and the alcohol moieties, respectively. These pharmacophores are based on the relationship between molecular structure and biological activity for a number of pyrethroid esters. The pharmacophores, which describe the relative location in space of the unsaturated systems, the dimethyl groups and the ester moiety, may be useful in the design of novel compounds with pyrethroid activity.     

A study of the enantiopreference of lipase PS (Pseudomonas cepacia) towards diastereomeric dihydro-5-alkyl-4-hydroxymethyl-2(3H)-furanones

Lipase PS acetylation of diastereomeric dihydro-4-hydroxymethyl-2(3H)-furanones bearing a methyl or a pentyl group at C-5 have been studied. Higher enantioselectivities were found for the cis-isomers with respect to the trans-isomers. They were also higher for the systems bearing the longer alkyl chain. Lipase PS-catalyzed hydrolyses of racemic acetates were found to follow the same trend, although the efficiency of the enzyme was lower than in the acetylation reactions. These results were supported by molecular modelling studies that correctly predicted the maximum stereoselectivity for the cis-isomer of 5-pentyl substituted lactones both in acetylation and in hydrolysis reactions.     

Efficient synthesis and resolution of novel 2-(hydroxymethyl)-7,8-dihydro-1H-indeno[5,4-b] furan-6(2H)-one by lipase Pseudomonas cepacia

Lipase Pseudomonas cepacia catalyzed acylation of (±)-2-(hydroxymethyl)-7,8-dihydro-1H-indeno[5,4-b] furan-6(2H)-one using vinyl acetate as the acyl donor in acetone gave (−)-(R)-2-acetoxy-2-(methyl)-7,8-dihydro-1H-indeno[5,4-b] furan-6(2H)-one and (+)-(S)-2-(hydroxymethyl)-7,8-dihydro-1H-indeno[5,4-b] furan-6(2H)-one with high enantiomeric excess. Enantiomerically pure 2-(hydroxymethyl)-7,8-dihydro-1H-indeno[5,4-b] furan-6(2H)-one are useful intermediates for the preparation of Ramelteon, an FDA approved drug for the treatment of insomnia.     

Stereoselective total syntheses of the racemic form and the natural enantiomer of the marine alkaloid lepadiformine via a novel N-acyliminium ion/allylsilane spirocyclization strategy

Stereoselective total syntheses of the racemic form and the natural enantiomer of the tricyclic marine alkaloid lepadiformine (6) have been accomplished using a novel intramolecular spirocyclization of an N-acyliminium ion with an allylsilane to form the A/C rings as the key step. Introduction of the hydroxymethyl group at C-13 of the racemic spirocycle 11 was achieved using our methodology for oxidative radical-based remote functionalization of o-aminobenzamides, followed by copper-catalyzed addition of Grignard reagent 16 to the N-acyliminium ion intermediate derived from 15. Subsequent Tamao oxidation of silane 17 then afforded the requisite hydroxymethyl compound 19, which was converted to the dimethyl acetal 25 via hydroformylation followed by aldehyde protection. Hydrolysis of the benzamide moiety of 25 and subsequent protection of the primary alcohol gave amino acetal 27. The synthesis was concluded from 27 by a four-step procedure: acid-catalyzed ring closure, amino nitrile formation, introduction of the hexyl chain by a Grignard reaction to an iminium salt, and removal of the O-benzyl protecting group to give (+/-)-lepadiformine (6). The enantioselective total synthesis of 6 started from known optically pure bromide 37, derived from (S)-pyroglutamic acid, and followed a similar sequence involving the key spirocyclization of N-acyliminium ion 42. This synthesis has established the absolute configuration of naturally occurring lepadiformine to be 2(R),5(S),10(S),13(S).     

Enhanced degradation of chemical warfare agents through molecular engineering of the phosphotriesterase active site

The bacterial phosphotriesterase has been utilized as a template for the evolution of improved enzymes for the catalytic decomposition of organophosphate nerve agents. A combinatorial library of active site mutants was constructed by randomizing residues His-254, His-257, and Leu-303. The collection of mutant proteins was screened for the ability to hydrolyze a chromogenic analogue of the most toxic stereoisomer of the chemical warfare agent, soman. The mutant H254G/H257W/L303T catalyzed the hydrolysis of the target substrate nearly 3 orders of magnitude faster than the wild-type enzyme. The X-ray crystal structure was solved in the presence and absence of diisopropyl methyl phosphonate. The mutant enzyme was ligated to an additional divalent cation at the active site that was displaced upon the binding of the substrate analogue inhibitor. These studies demonstrate that substantial changes in substrate specificity can be achieved by relatively minor changes to the primary amino acid sequence.     

Preparation of a novel diphosphine-palladium macrocyclic complex possessing a molecular recognition site. Oxidative addition studies

A disphosphine-palladium(0) complex capable of recognising barbiturates has been prepared. Oxidative addition studies with a barbitiurate:aryl iodide conjugate provided new Pd(ii) complexes where the positioning of the Pd-bound aryl group is controlled by the molecular recognition event.