Enzymatic resolution of chiral phosphinate esters

The bacterial phosphotriesterase has been shown to catalyze the stereoselective hydrolysis of phosphinate esters. The wild-type enzyme preferentially hydrolyzes the SP-enantiomers of methyl phenyl p-X-phenylphosphinate esters by 3 orders of magnitude. The mutant enzyme, I106T/F132A/H254G/H257W, exhibits the opposite stereoselectivity and hydrolyzes the RP-enantiomer up to 30 times faster than the corresponding SP-enantiomer. The enantiomerically pure phosphinate esters, prepared from the kinetic resolution of racemic mixtures, can serve as the entry point for the chemoenzymatic preparation of P-chiral phosphines and phosphine oxides.     

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.     

The new way to synthesize ethyl 1-butyryloxy-1-phenylmethane(P-phenyl)phosphinate and whole-cell biocatalysis by Escherichia coli and Pseudomonas fluorescens

Abstract

A new compound, ethyl 1-carboxy-1-hydroxy-1-phenylmethane(P-phenyl)phosphinate, was synthesized and the configuration of its diastereoisomers was described using NMR spectroscopy. Acylation with butyryl chloride gave an unexpected product, ethyl butyryloxy(phenyl)methane(P-phenyl)phosphinate, which was then hydrolyzed using two bacterial species as biocatalysts. Good results were achieved for biocatalytic hydrolysis performed by Escherichia coli cells, giving optically active products with 84% enantiomeric excess, and enantioselectivity of 25.8 for one pair of enantiomers. Better results were obtained when the biocatalytic reaction was carrying out for a longer period and the conversion degree reached 71%, the enantiomeric excess of unreacted substrate was >99% and enantioselectivity increased to 32.1. In all cases, isomers bearing α–carbon atom of S configuration were hydrolyzed preferentially.     

Predicting substrates by docking high-energy intermediates to enzyme structures

With the emergence of sequences and even structures for proteins of unknown function, structure-based prediction of enzyme activity has become a pragmatic as well as an interesting question. Here we investigate a method to predict substrates for enzymes of known structure by docking high-energy intermediate forms of the potential substrates. A database of such high-energy transition-state analogues was created from the KEGG metabolites. To reduce the number of possible reactions to consider, we restricted ourselves to enzymes of the amidohydrolase superfamily. We docked each metabolite into seven different amidohydrolases in both the ground-state and the high-energy intermediate forms. Docking the high-energy intermediates improved the discrimination between decoys and substrates significantly over the corresponding standard ground-state database, both by enrichment of the true substrates and by geometric fidelity. To test this method prospectively, we attempted to predict the enantioselectivity of a set of chiral substrates for phosphotriesterase, for both wild-type and mutant forms of this enzyme. The stereoselectivity ratios of the six enzymes considered for those four substrate enantiomer pairs differed over a range of 10- to 10,000-fold and underwent 20 switches in stereoselectivities for favored enantiomers, compared to the wild type. The docking of the high-energy intermediates correctly predicted the stereoselectivities for 18 of the 20 substrate/enzyme combinations when compared to subsequent experimental synthesis and testing. The possible applications of this approach to other enzymes are considered.     

An approach to the synthesis and assignment of the absolute configuration of all enantiomers of ethyl hydroxy(phenyl)methane(P-phenyl)phosphinate

Ethyl butyryloxy(phenyl)methane(P-phenyl)phosphinate was hydrolyzed using four bacterial species as biocatalysts. In all cases the reaction was stereoselective and isomers bearing an α-carbon atom with an (S)-configuration were hydrolyzed preferentially. Also a lack of stereoselectivity toward the phosphorus atom was observed. Hydrolysis of one enantiomeric mixture, namely mixture of (S_P,R) and (R_P,S) configuration afforded enantiomerically pure ethyl (R_P,S)-hydroxy(phenyl)methane(P-phenyl)phosphinate, configuration of which was established by X-ray crystallography. The observed ¹H and ³¹P NMR chemical shifts of Mosher esters of ethyl hydroxy(phenyl)methane(P-phenyl)phosphinate were correlated with the configurations of both stereogenic centers of all four stereoisomers.     

Operational control of stereoselectivity during the enzymatic hydrolysis of racemic organophosphorus compounds

The wild-type bacterial phosphotriesterase catalyzes the stereoselective hydrolysis of racemic pairs of organophosphorus compounds. The enzymatic stereoselectivity can be substantially enhanced via systematic alteration of the pKa for the leaving group phenol in the target substrates. These changes alter the rate-limiting step for substrate turnover from a diffusional event to phosphorus-oxygen bond cleavage. Turnover ratios in excess of 5000:1 were achieved using phenols with pKa values greater than 8.5. This method has enabled the isolation of the RP-enantiomer of 4-acetylphenyl methyl phenylphosphonate with an enantiomeric excess of >99% via a kinetic resolution of the racemate.     

Optically pure (s)-3-phenylthio-1,2-propanediol: synthesis by the yeast reduction and use as a precursor of both enantiomers of secondary alcohols

Optically pure (S)-3-phenylthio-1,2-propanediol was obtained by the enantioselective reduction of 1-hydroxy-3-phenylthio-2-propanone with the Baker's yeast, and was found to be a convenient precursor for both enantiomers of secondary alcohols, which was demonstrated in the synthesis of both enantiomeric forms of 5-hexadecanolide via phenyl (S)-glycidyl sulfide as the key intermediate.     

Single-Point Mutant Inverts the Stereoselectivity of a Carbonyl Reductase toward β-Ketoesters with Enhanced Activity

Enzyme stereoselectivity control is still a major challenge. To gain insight into the molecular basis of enzyme stereo-recognition and expand the source of antiPrelog carbonyl reductase toward β-ketoesters, rational enzyme design aiming at stereoselectivity inversion was performed. The designed variant Q139G switched the enzyme stereoselectivity toward β-ketoesters from Prelog to antiPrelog, providing corresponding alcohols in high enantiomeric purity (89.1–99.1 % ee). More importantly, the well-known trade-off between stereoselectivity and activity was not found. Q139G exhibited higher catalytic activity than the wildtype enzyme, the enhancement of the catalytic efficiency (k_cat/K_m) varied from 1.1- to 27.1-fold. Interestingly, the mutant Q139G did not lead to reversed stereoselectivity toward aromatic ketones. Analysis of enzyme–substrate complexes showed that the structural flexibility of β-ketoesters and a newly formed cave together facilitated the formation of the antiPrelog-preferred conformation. In contrast, the relatively large and rigid structure of the aromatic ketones prevents them from forming the antiPrelog-preferred conformation.     

Simultaneous determination of phosphonate, phosphate, and diphosphate by capillary electrophoresis using in-capillary complexation with Mo(VI)

This study describes the simultaneous determination of phosphonate, phosphate, and diphosphate by CE with direct UV detection, based on in-capillary complexation with Mo(VI). When a mixture of phosphonate, phosphate, and diphosphate was injected into a capillary containing 3.0 mM Mo(VI), 0.05 M malonate buffer (pH 3.0) and 45% v/v CH3CN, three well-defined peaks, due to the migration of the corresponding polyoxomolybdate anions, were separated. The respective calibration graphs were linear in the concentration range of 2 x 10(-6)-2 x 10(-4) M for phosphonate, 1 x 10(-6)-5 x 10(-5) M for phosphate, and 1 x 10(-6)-2 x 10(-4) M for diphosphate; the correlation coefficients were better than 0.9990. The present CE method is successfully applied to the simultaneous determination of phosphonate, phosphate, and diphosphate in tap water.     

Unfavorable electrostatic and steric interactions in DNA polymerase β E295K mutant interfere with the enzyme's pathway

Mutations in DNA polymerase β (pol β) have been associated with approximately 30% of human tumors. The E295K mutation of pol β has been linked to gastric carcinoma via interference with base excision repair. To interpret the different behavior of E295K as compared to wild-type pol β in atomic and energetic detail, we resolve a binary crystal complex of E295K at 2.5 ? and apply transition path sampling (TPS) to delineate the closing pathway of the E295K pol β mutant. Conformational changes are important components in the enzymatic pathway that lead to and ready the enzyme for the chemical reaction. Our analyses show that the closing pathway of E295K mutant differs from the wild-type pol β in terms of the individual transition states along the pathway, associated energies, and the active site conformation in the final closed form of the mutant. In particular, the closed state of E295K has a more distorted active site than the active site in the wild-type pol β. In addition, the total energy barrier in the conformational closing pathway is 65 ± 11 kJ/mol, much higher than that estimated for both correct (e.g., G:C) and incorrect (e.g., G:A) wild-type pol β systems (42 ± 8 and 45 ± 7 kJ/mol, respectively). In particular, the rotation of Arg258 is the rate-limiting step in the conformational pathway of E295K due to unfavorable electrostatic and steric interactions. The distorted active site in the closed relative to open state and the high energy barrier in the conformational pathway may explain in part why the E295K mutant is observed to be inactive. Interestingly, however, following the closing of the thumb but prior to the rotation of Arg258, the E295K mutant complex has a similar energy level as compared to the wild-type pol β. This suggests that the E295K mutant may associate with DNA with similar affinity, but it may be hampered in continuing the process of chemistry. Supporting experimental data come from the observation that the catalytic activity of wild-type pol β is hampered when E295K is present: this may arise from the competition between E295K and wild-type enzyme for the DNA. These combined results suggest that the low insertion efficiency of E295K mutant as compared to wild-type pol β may be related to a closed form distorted by unfavorable electrostatic and steric interactions between Arg258 and other key residues. The active site is thus less competent for proceeding to the chemical reaction, which may also involve a higher reaction barrier than the wild-type or may not be possible in this mutant. Our analysis also suggests further experiments for other mutants to test the above hypothesis and dissect the roles of steric and electrostatic factors on enzyme behavior.     

Chiral comprehensive two-dimensional gas chromatography with electron-capture detection applied to the analysis of chiral polychlorinated biphenyls in food samples

The feasibility of comprehensive two-dimensional gas chromatography with electron-capture detection (GC x GC-ECD) for the enantioseparation of chiral PCBs from other possible interfering compounds has been evaluated. Three commercially available enantioselective beta-cyclodextrin-based capillary columns (Chirasil-Dex, BGB-172 and BGB-176SE) have been tested as first-dimension columns. Three non-enantioselective stationary phases (HT-8, BPX-50 and Supelcowax-10) were combined with the enantioselective columns to allow the unambiguous determination of the enantiomers of the target chiral PCBs. Each enantioselective first-dimension column tested was able to separate into enantiomers different PCB congeners, but in all cases, the use of Supelcowax-10 as second-dimension column provided the most satisfactory results. The Chirasil-Dex x Supelcowax-10 column combination allowed the determination of the enantiomeric fraction (EF) of PCBs 84, 91, 95, 132, 136, 149, 174 and 176 in the working standard solution, while that of congener 135 was hindered. The BGB-172 x Supelcowax-10 column set allowed a proper EF determination of congeners 45, 84, 131, 132, 135, 171, 174 and 183, while that of PCB 91 was interfered with co-elutants. The column combination BGB-176SE x Supelcowax-10 allowed the determination of all congeners that this enantioselective stationary phase was able to separate into enantiomers, i.e. PCBs 45, 91, 95, 136, 149 and 176. These column combinations have also been evaluated for the simultaneous determination of the 12 congeners with a toxic equivalency factor assigned by the WHO (PCBs 77, 81, 105, 114, 118, 123, 126, 156, 157, 167, 169, 189) and the seven indicator congeners (PCBs 28, 52, 101, 118, 138, 153 and 180), and evaluated for the analysis of food samples.     

Mechanism of inhibition of the class C beta-lactamase of Enterobacter cloacae P99 by cyclic acyl phosph(on)ates: rescue by return.

As previously described (Pratt, R. F.; Hammar, N. J. J. Am. Chem. Soc. 1998, 120, 3004.), 1-hydroxy-4,5-benzo-2,6-dioxaphosphorinone(3)-1-oxide (salicyloyl cyclic phosphate) inactivates the class C beta-lactamase of Enterobacter cloacae P99 in a covalent fashion. The inactivated enzyme slowly reverts to the active form. This paper shows that reactivation involves a recyclization reaction that regenerates salicyloyl cyclic phosphate rather than hydrolysis of the covalent intermediate. The inactivation, therefore, is a slowly reversible covalent modification of the active site. The thermodynamic dissociation constant of the inhibitor from the inactivated enzyme is 0.16 microM. Treatment of the inactivated enzyme with alkali does not produce salicylic acid but does, after subsequent acid hydrolysis, yield one molar equivalent of lysinoalanine. This result proves that salicyloyl cyclic phosphate inactivates the enzyme by (slowly reversible) phosphorylation of the active site serine residue. This result contrasts sharply with the behavior of acyclic acyl phosphates which transiently inactivate the P99 beta-lactamase by acylation (Li, N.; Pratt, R. F. J. Am. Chem. Soc. 1998, 120, 4264.). This chemoselectivity difference is explored by means of molecular modeling. Rather counterintuitively, in view of the relative susceptibility of phosphates and phosphonates to nucleophilic attack at phosphorus, 1-hydroxy-4,5-benzo-2-oxaphosphorinanone(3)-1-oxide, the phosphonate analogue of salicyloyl cyclic phosphate, did not appear to inactivate the P99 beta-lactamase in a time-dependent fashion. It was found, however, to act as a fast reversible inhibitor (K(i) = 10 microM). A closer examination of the kinetics of inhibition revealed that both on and off rates (9.8 x 10(3) s(-1) x M(-1) and 0.098 s(-1), respectively) were much slower than expected for noncovalent binding. This result strongly indicates that the inhibition reaction of the phosphonate also involves phosphylation of the active site. Hence, unlike the situation with bacterial DD-peptidases covalently inactivated by beta-lactams, the P99 beta-lactamase inactivated by the above cyclic acyl phosph(on)ates can be rescued by return. Elimination of the recyclization reaction would lead to more effective inhibitors.     

Discrimination between enantioselective and non-selective binding sites on cellobiohydrolase-based stationary phases by site specific competing ligands.

A systematic study was performed to investigate the influence of cellobiose or lactose on the enantioselective retention behaviour of some beta-blockers in liquid chromatography using Cellobiohydrolase (CHB) I from Trichoderma reesei or Cellobiohydrolase 58 from Phanerochaete chrysosporium immobilized on silica as stationary phases. The results revealed that the retention could be described by the function [equation; see text] where the observed capacity factor corresponds to the sum of an enantioselective mode being influenced by a site specific competing ligand (competitor) and a non-selective mode unaffected by the competitor. A non-constrained non-linear least-square regression gave in all cases virtually identical nondisplacable capacity factors (k'ns) for both enantiomers of the same drug. The experimental capacity factors (k'(x,C)) of the enantiomers all show a close fit to the adapted function. The Kd values calculated for the competitor were also virtually identical for each pair of enantiomers and were in accordance with Ki data determined for the competitors in classical enzyme kinetics experiments, demonstrating that one unique site; namely, the catalytic site, was responsible for the enantioselective binding. Similar results were obtained with the resolution of rac-alprenolol and rac-metoprolol on CBH I phase.     

bis(L-amino acid amidato)copper(II) complexes as chiral eluents in the enantiomeric separation of D,L-dansylamino acids by reversed-phase high-performance liquid chromatography

Copper(II) complexes of L-amino acylamides (Phe, Val, Tyr, Ala) when added to the eluent (water-acetonitrile) in reversed-phase high-performance liquid chromatography (C18) are able to perform enantiomeric separation of dansylamino acids. The lipophilicity and bulk of the ligand greatly affect the stereoselectivity and the elution order of the enantiomers. The type and concentration of the copper complexes, pH and eluent polarity were examined in order to get some insights into the separation mechanism. This may be consistent with a ligand-exchange mechanism, probably occurring on the organic phase of the column, where the enantioselective complex is adsorbed. Mixtures of D,L-dansylamino acids were well separated by isocratic and gradient elution.     

羰基还原酶辅酶结合域位点突变对其不对称催化性能的影响

基于同源模型的比较和分析,发现羰基还原酶SCR1辅酶结合域P124和W125位点对辅酶NADPH的结合形成了一定的空间位阻效应.通过对该位点进行小侧基氨基酸的取代突变,该酶的底物专一性和立体选择性均发生了不同程度的改变,表明该位点是酶与辅酶有效结合的关键位点,而且它与辅酶结合的空间效应进一步影响了底物结合域活性中心对不同构型的底物及其对映体产物的亲和作用.在底物专一性方面,野生型酶对2-羟基苯乙酮和2-溴苯乙酮及其衍生物等底物表现出较高的催化活性,而突变株W125A,W125G,P124A/W125A和P124G/W125G对苯乙酮及其部分衍生物和2-辛酮等底物的催化活性均有所提高.对于酶的立体选择性,部分突变株发生了转化产物对映体构型反转的现象,突变株P124A/W125A和P124G/W125G催化还原2-羟基苯乙酮和4-氯乙酰乙酸乙酯均生成了(R)-型产物.     

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.     

Asymmetric oxidation catalyzed by myoglobin mutants

The sperm whale myoglobin active site mutants (L29H/H64L and F43H/H64L Mb) have been shown to catalyze the asymmetric oxidation of sulfides and olefins. Thioanisole, ethyl phenyl sulfide, and cis-β-methylstyrene are oxidized by L29H/H64L Mb with more than 95% enantiomeric excess (% ee). On the other hand, the F43H/H64L mutant transforms trans-β-methylstyrene into the trans-epoxide with 96% ee. The dominant sulfoxide product in the incubation of alkyl phenyl thioethers is the R isomer; however, the mutants afford dominantly the S isomer of aromatic bicyclic sulfoxides. The results help us to rationalize the difference in the preferred stereochemistry of the Mb mutant-catalyzed reactions. Furthermore, the Mb mutants exhibit an improvement in the oxidation rate up to 300-fold with respect to wild type.     

Computational design of a thermostable mutant of cocaine esterase via molecular dynamics simulations

Cocaine esterase (CocE) has been known as the most efficient native enzyme for metabolizing naturally occurring cocaine. A major obstacle to the clinical application of CocE is the thermoinstability of native CocE with a half-life of only ～11 min at physiological temperature (37 °C). It is highly desirable to develop a thermostable mutant of CocE for therapeutic treatment of cocaine overdose and addiction. To establish a structure-thermostability relationship, we carried out molecular dynamics (MD) simulations at 400 K on wild-type CocE and previously known thermostable mutants, demonstrating that the thermostability of the active form of the enzyme correlates with the fluctuation (characterized as the root-mean square deviation and root-mean square fluctuation of atomic positions) of the catalytic residues (Y44, S117, Y118, H287, and D259) in the simulated enzyme. In light of the structure-thermostability correlation, further computational modelling including MD simulations at 400 K predicted that the active site structure of the L169K mutant should be more thermostable. The prediction has been confirmed by wet experimental tests showing that the active form of the L169K mutant had a half-life of 570 min at 37 °C, which is significantly longer than those of the wild-type and previously known thermostable mutants. The encouraging outcome suggests that the high-temperature MD simulations and the structure-thermostability relationship may be considered as a valuable tool for the computational design of thermostable mutants of an enzyme.     

Structure-based redesign of GST A2-2 for enhanced catalytic efficiency with azathioprine

Glutathione transferase (GST) A2-2 is the most efficient human enzyme in the biotransformation of the prodrug azathioprine (Aza). The activation of Aza has therapeutic potential for possible use of GSTs in targeted enzyme-prodrug treatment of diseases. Based on the assumed catalytic mechanism and computational docking of Aza to the active site of the enzyme, active-site residues were selected for construction of focused mutant libraries, which were thereafter screened for Aza activity. Mutants with elevated Aza activity were identified, DNA sequenced, and the proteins purified. The two most active mutants showed up to 70-fold higher catalytic efficiency than the parental GST A2-2. The structure of the most active triple mutant (L107G/L108D/F222H) enzyme was determined by X-ray crystallography demonstrating significant changes in the topography of the active site facilitating productive binding of Aza as a substrate.     

Free energy perturbation (FEP) simulation on the transition states of cocaine hydrolysis catalyzed by human butyrylcholinesterase and its mutants

A novel computational protocol based on free energy perturbation (FEP) simulations on both the free enzyme and transition state structures has been developed and tested to predict the mutation-caused shift of the free energy change from the free enzyme to the rate-determining transition state for human butyrylcholinesterase (BChE)-catalyzed hydrolysis of (-)-cocaine. The calculated shift, denoted by DeltaDeltaG(1 --> 2), of such kind of free energy change determines the catalytic efficiency (kcat/KM) change caused by the simulated mutation transforming enzyme 1 to enzyme 2. By using the FEP-based computational protocol, the DeltaDeltaG(1 --> 2) values for the mutations A328W/Y332A --> A328W/Y332G and A328W/Y332G --> A328W/Y332G/A199S were calculated to be -0.22 and -1.94 kcal/mol, respectively. The calculated DeltaDeltaG(1 --> 2) values predict that the change from the A328W/Y332A mutant to the A328W/Y332G mutant should slightly improve the catalytic efficiency and that the change from the A328W/Y332G mutant to the A328W/Y332G/A199S mutant should significantly improve the catalytic efficiency of the enzyme for the (-)-cocaine hydrolysis. The predicted catalytic efficiency increases are supported by the experimental data showing that kcat/KM = 8.5 x 10(6), 1.4 x 10(7), and 7.2 x 10(7) min(-1) M(-1) for the A328W/Y332A, A328W/Y332G, and A328W/Y332G/A199S mutants, respectively. The qualitative agreement between the computational and experimental data suggests that the FEP simulations may provide a promising protocol for rational design of high-activity mutants of an enzyme. The general computational strategy of the FEP simulation on a transition state can be used to study the effects of a mutation on the activation free energy for any enzymatic reaction.