Catalytic reaction mechanism of homogentisate dioxygenase: a hybrid DFT study

Human homogentisate dioxygenase is an Fe(II)-dependent enzyme responsible for aromatic ring cleavage. The mechanism of its catalytic reaction has been investigated with the hybrid density functional method B3LYP. A relatively big model of the active site was first used to determine the substrate binding mode. It was found that binding of the substrate dianion with a vacant position trans to Glu341 is most favorable. The model was then truncated to include only the most relevant parts of the active-site residues involved in iron coordination and substrate binding. Thus, methylimidazole was used to model His292, His335, His365, and His371, while propionate modeled Glu341. The computational results suggest that the catalytic reaction of homogentisate dioxygenases involves three major chemical steps: formation of the peroxo intermediate, homolytic cleavage of the O-O bond leading to an arene oxide radical, and finally, cleavage of the six-membered ring. Calculated barriers for alternative reaction paths are markedly higher than for the proposed mechanism, and thus the computational results successfully explain the product specificity of the enzyme. Interestingly, the results indicate that the type of ring scission, intra or extra with respect to the substituents coordinating to iron, is controlled by the barrier heights for the decay of the arene oxide radical intermediate.     

Asymmetric sulfoxidation and amine binding by H64D/V68A and H64D/V68S Mb: mechanistic insight into the chiral discrimination step

The H64D/V68A and H64D/V68S mutants of Myoglobin are found to oxidize thioanisole with high enantioselectivity and reactivity. These mutants are also capable of enantioselective binding of alpha-methylbenzylamine, which mimics an expected sulfoxidation intermediate. The kinetic study of the amine binding shows that the Fe-O bond cleavage in the intermediate may be the chiral discrimination step of the sulfoxidation.     

Computational Study of Mechanism and Enantioselectivity of Imine Reductase from Amycolatopsis orientalis

Imine reductases (IREDs) are NADPH-dependent enzymes (NADPH=nicotinamide adenine dinucleotide phosphate) that catalyze the reduction of imines to amines. They exhibit high enantioselectivity for a broad range of substrates, making them of interest for biocatalytic applications. In this work, we have employed density functional theory (DFT) calculations to elucidate the reaction mechanism and the origins of enantioselectivity of IRED from Amycolatopsis orientalis. Two substrates are considered, namely 1-methyl-3,4-dihydroisoquinoline and 2-propyl-piperideine. A model of the active site is built on the basis of the available crystal structure. For both substrates, different binding modes are first evaluated, followed by calculation of the hydride transfer transition states from each complex. We have also investigated the effect of mutations of certain important active site residues (Tyr179Ala and Asn241Ala) on the enantioselectivity. The calculated energies are consistent with the experimental observations and the analysis of transition states geometries provides insights into the origins of enantioselectivity of this enzyme.     

Focusing mutations into the P. fluorescens esterase binding site increases enantioselectivity more effectively than distant mutations

Rational design of enzymes with improved properties, such as enantioselectivity, usually focuses mutations within the substrate binding site. On the other hand, directed evolution of enzymes usually targets the entire protein and discovers beneficial mutations far from the substrate binding site. In this paper, we propose an explanation for this discrepancy and show that a combined approach--random mutagenesis within the substrate binding site--is better. To increase the enantioselectivity (E) of a Pseudomonas fluorescens esterase (PFE) toward methyl 3-bromo-2-methylpropionate, we focused mutagenesis into the substrate binding site at Trp28, Val121, Phe198, and Val225. Five of the catalytically active mutants (13%) showed better enantioselectivity than wild-type PFE. The increases in enantioselectivity were higher (up to 5-fold, reaching E = 61) than with mutants identified by random mutagenesis of the entire enzyme.     

Transpeptidase-mediated incorporation of D-amino acids into bacterial peptidoglycan

The β-lactams are the most important class of antibiotics in clinical use. Their lethal targets are the transpeptidase domains of penicillin binding proteins (PBPs), which catalyze the cross-linking of bacterial peptidoglycan (PG) during cell wall synthesis. The transpeptidation reaction occurs in two steps, the first being formation of a covalent enzyme intermediate and the second involving attack of an amine on this intermediate. Here we use defined PG substrates to dissect the individual steps catalyzed by a purified E. coli transpeptidase. We demonstrate that this transpeptidase accepts a set of structurally diverse D-amino acid substrates and incorporates them into PG fragments. These results provide new information on donor and acceptor requirements as well as a mechanistic basis for previous observations that noncanonical D-amino acids can be introduced into the bacterial cell wall.     

Molecular design of two sterol 14α-demethylase homology models and their interactions with the azole antifungals ketoconazole and bifonazole

Summary Sterol 14α-demethylase (CYP51) is one of the known major targets for azole antifungals. Therapeutic side effects of these antifungals are based on interactions of the azoles with the human analogue enzyme. This study describes for the first time a comparison of a human CYP51 (HU-CYP51) homology model with a homology model of the fungal CYP51 of Candida albicans (CA-CYP51). Both models are constructed by using the crystal structure of Mycobacterium tuberculosis MT-CYP51 (PDB code: 1EA1).The binding mode of the azole ketoconazole is investigated in molecular dynamics simulations with the GROMACS force field. The usage of special parameters for the iron azole complex binding is necessary to obtain the correct complex geometry in the active site of the enzyme models. Based on the dynamics simulations it is possible to explain the enantioselectivity of the human enzyme and also to predict the binding mode of the isomers of ketoconazole in the active site of the fungal model.     

Phase-transfer-catalyzed asymmetric acylimidazole alkylation

2-Acylimidazoles are alkylated under phase-transfer conditions with cinchonidinium catalysts at -40 degrees C with allyl and benzyl electrophiles in high yield with excellent enantioselectivity (79 to >99% ee). The acylimidazole substrates are made in three steps from bromoacetic acid via the N-acylmorpholine adduct. The catalyst is made in high purity allowing for S-product formation (6-20 h) under mild conditions, consistent with an ion-pair mechanism. The products are readily converted to useful ester products using methyltriflate and sodium methoxide, via a dimethylacylimidazolium intermediate without racemization. The process is efficient, direct, and amenable to other electrophiles and transformations that proceed through an enolate intermediate.     

Enantioselective transesterification catalysis by nanosized serine protease subtilisin Carlsberg particles in tetrahydrofuran

Enzyme catalysis in organic solvents is a powerful tool for stereo-selective synthesis but the enantioselectivity is still hard to predict. To overcome this obstacle, we employed a nanoparticulate formulation of subtilisin Carlsberg (SC) and designed a series of 14 structurally related racemic alcohols. They were employed in the model transesterification reaction with vinyl butyrate and the enantioselectivities were determined. In general, short alcohol side chains led to low enantioselectivties, while larger and bulky side chains caused better discrimination of the enantiomers by the enzyme. With several bulky substrates high enantioselectivities with E>100 were obtained. Computational modeling highlighted that key to high enantioselectivity is the discrimination of the R and S substrates by the sole hydrophobic binding pocket based on their size and bulkiness. While bulky S enantiomer side chains could be accommodated within the binding pocket, bulky R enantiomer side chains could not. However, when also the S enantiomer side chain becomes too large and does not fit into the binding pocket anymore, enantioselectivity accordingly drops.     

Short and efficient asymmetric synthesis of (-)-alpha-conhydrine

The short and efficient synthesis of (-)-alpha-conhydrine was accomplished with 41% overall yield in seven steps and high diastereo- and enantioselectivity. The anti-stereochemistry of the two stereogenic centers has been confirmed by the single-crystal X-ray analysis of an intermediate.     

Origins of Enantiopreference of Mycobacterium smegmatis Acyl Transferase: A Computational Analysis

Acyl transferase from Mycobacterium smegmatis (MsAcT) is a promising biocatalyst because it catalyzes an acyl transfer reaction in aqueous solution, thereby accepting many primary and secondary alcohols as substrates. MsAcT also exhibits high enantioselectivity for a selected number of secondary alcohols. To increase the applicability of this enzyme for the production of optically active compounds, a detailed understanding of the reaction mechanism and the factors that affect enantioselectivity is essential. Herein, quantum chemical calculations are employed to study the reactions of two secondary alcohols, 1-isopropyl propargyl alcohol and 2-hydroxy propanenitrile, for which the enzyme displays opposite enantiopreference, favoring the S enantiomer in the former case and R enantiomer in the latter. A model of the active site has been designed and for both substrates various binding modes are evaluated and the intermediates and transition states along the reaction path are then located. The calculated energy profiles agree with the experimental observations, and reproduce the selectivity outcome. Through a detailed analysis of the geometries of key transition states, insights into the origins of the enantiopreference are obtained.     

A new chemoenzymatic Baylis-Hillman approach for the synthesis of enantiomerically enriched umbelactones

An efficient and convenient strategy for the enantioselective synthesis of enantiomerically enriched umbelactones is described utilizing a lipase-mediated resolution protocol, Baylis-Hillman reaction and ring closing metathesis as key steps. The lipase-resolution is carried out using several lipases from various sources in different solvents to afford the required intermediate 8 in good yield and high enantioselectivity.     

Biocatalytic asymmetric hydroxylation of hydrocarbons with the topsoil-microorganism Bacillus megaterium

A Bacillus megaterium strain was isolated from topsoil by a selective screening procedure with allylbenzene as a xenobiotic substrate. This strain performed the hydroxylation chemoselectively (no arene oxidation and overoxidized products) and enantioselectively (up to 99% ee) in the benzylic and nonbenzylic positions of a variety of unfunctionalized arylalkanes. Salycilate and phenobarbital, which are potent inducers of cytochrome P-450 activity, changed the regioselectivity of the microbial CH insertion, without an effect on the enantioselectivity. The biotransformation conditions were optimized in regard to product yield and enantioselectivity by variation of the oxygen-gas supply and the time of the substrate addition. The different product distributions (alpha- versus beta-hydroxylated product) that are obtained on induction of cytochrome P-450 enzyme activity demonstrate the involvement of two or more hydroxylating enzymes with distinct regioselectivities in this biotransformation. An oxygen-rebound mechanism is assumed for the cytochrome P-450-type monooxygenase activity, in which steric interactions between the substrate and the enzyme determine the preferred face of the hydroxy-group transfer to the radical intermediate.     

A catalytic, asymmetric formal synthesis of (+)-hamigeran B

A concise asymmetric, formal synthesis of (+)-hamigeran B is reported. A Pd-catalyzed, decarboxylative allylic alkylation, employing a trifluoromethylated derivative of t-BuPHOX, is utilized as the enantioselective step to form the critical quaternary carbon center in excellent yield and enantioselectivity. The product is converted in three steps to a late-stage intermediate previously used in the synthesis of hamigeran B.     

Theoretical investigation on mechanism of asymmetric Michael addition of trans-1-nitro-2-phenylethylene to 2-methylpropionaldehyde catalyzed by a Cinchona alkaloid-derived primary amine

Using cinchona alkaloid-derived primary amine as catalyst and benzoic acid as co-catalyst, Michael-type addition reactions between enolizable carbonyl compounds and nitroalkenes have been extensively studied; however, our understanding of the mechanism is far from complete. In this paper, a theoretical study is presented for the Michael addition reaction between trans-1-nitro-2-phenylethylene and 2-methylpropionaldehyde catalyzed by 9-epi-QDA and benzoic acid. By performing DFT and ab initio calculations, we have identified a detailed mechanism. The calculations indicated that four continuous steps are involved in the overall reaction: (1) the formation of an iminium intermediate, (2) an addition reaction between the iminium and trans-1-nitro-2-phenylethylene, (3) the proton transfer process, and (4) hydrolysis and regeneration of the catalyst. The rate-determining step is the second proton transfer from the amine group to β-carbon of trans-1-nitro-2-phenylethylene, and the enantioselectivity is also controlled by this step. The calculated results provide a general model that explains the mechanism and enantioselectivity of the title reaction.     

Directed evolution of an enantioselective lipase

BACKGROUND: The biocatalytic production of enantiopure compounds is of steadily increasing importance to the chemical and biotechnological industry. In most cases, however, it is impossible to identify an enzyme that possesses the desired enantioselectivity. Therefore, there is a strong need to create by molecular biological methods novel enzymes which display high enantioselectivity. RESULTS: A bacterial lipase from Pseudomonas aeruginosa (PAL) was evolved to catalyze with high enantioselectivity the hydrolysis of the chiral model substrate 2-methyldecanoic acid p-nitrophenyl ester. Successive rounds of random mutagenesis by ep-PCR and saturation mutagenesis resulted in an increase in enantioselectivity from E=1.1 for the wild-type enzyme to E=25.8 for the best variant which carried five amino acid substitutions. The recently solved three-dimensional structure of PAL allowed us to analyze the structural consequences of these substitutions. CONCLUSIONS: A highly enantioselective lipase was created by increasing the flexibility of distinct loops of the enzyme. Our results demonstrate that enantioselective enzymes can be created by directed evolution, thereby opening up a large area of novel applications in biotechnology.     

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.     

Computer simulations of enantioselective ester hydrolyses catalyzed by Pseudomonas cepacia lipase

On the basis of the X-ray crystal structure of the lipase from Pseudomonas cepacia (PcL)-an enzyme representative for a whole family of Pseudomonas lipases (lipase PS, SAM-2, AK 10, and others with a high degree of homology with PcL)-a computational study was performed to rationalize both the enantioselectivity and substrate specificity (tolerance) displayed by this lipase in the enantioselective hydrolysis of racemic esters 1a-12a from various secondary aromatic alcohols. The major goal of this project was the development of a binding model for PcL which is able to rationalize the experimental findings to predict "a priori the enantioselective behavior of PcL toward a wider range of substrates. A two-step modeling procedure, namely, docking experiments followed by construction of tetrahedral intermediates, was used for the simulation of the involved enzyme-substrate recognition/hydrolysis processes. The study of the recognition process (docking experiments) led to unambiguous identification of the binding geometry for the two enantiomeric series of substrates, but did not suggest a definitive interpretation of the behavior of PcL. Taking into consideration the stereoelectronic requirements of the enzymatic hydrolysis reaction, both the enantioselectivity and tolerance of the enzyme were then explained through the study of the tetrahedral intermediates, in turn constructed from the calculated docking geometries of 1a-12a.     

Cu-catalyzed asymmetric allylic alkylations of aromatic and aliphatic phosphates with alkylzinc reagents. An effective method for enantioselective synthesis of tertiary and quaternary carbons

Efficient enantioselective Cu-catalyzed allylic alkylations of aromatic and aliphatic allylic phosphates bearing di- and trisubstituted olefins are disclosed. Enantioselective C-C bond forming reactions are promoted in the presence of 10 mol % readily available chiral amino acid-based ligand (5 steps, 40% overall yield synthesis) and 5 mol % (CuOTf)2 x C6H6. Reactions deliver tertiary and quaternary stereogenic carbon centers regioselectively and in 78-96% ee. Data regarding the effect of variations in ligand structure on the efficiency and enantioselectivity of the alkylation process, as well as a mechanistic working model, are presented. The suggested model involves a dual role for the chiral Cu complex: association of the Cu(I) center to the olefin is facilitated by a two-point binding between the carbonyl of the ligand's amide terminus and the P=O of the substrate.     

Hydrogen‐Bond‐Induced Chiral Axis Construction: Theoretical Study of Cinchonine–Thiourea‐Catalyzed Enantioselective Intramolecular Cycloaddition

Theoretical calculations were performed to investigate the mechanism and enantioselectivity of cinchonine–thiourea‐catalyzed intramolecular hetero‐Diels–Alder cycloaddition of ethynylphenol derivatives to afford axial chirality naphthalenylpyran products via a vinylidene ortho‐quinone methide (VQM) intermediate. The results show that this transformation occurs through a reaction pathway involving the deprotonation of the naphthol moiety by the quinuclidine base, intramolecular proton transfer in ammonium naphthalenolate, and [4+2] cycloaddition. It is found that the axial chirality of the VQM intermediate is generated by the protonation step, which affects the enantioselectivity of the reaction. The enantioselectivity for the generation of the VQM intermediate is controlled by steric repulsion with the cinchonine framework, which provides an R‐axial chirality VQM as the major intermediate. Moreover, the enantioselectivity for the axial chirality of the naphthopyran product is controlled by the cycloaddition step, in which an extra hydrogen bond between the naphthalenol and cinchonine moieties leads to a favorable configuration for the generation of the S‐axial chirality naphthopyran product. The calculated enantioselectivity and enantiomeric excesses coincide with experimental observations.     

Connecting simulated,bioanalytical, and molecular docking data on the stereoselective binding of (±)-catechin to human serum albumin

The stereoselective binding of the frequently ingested nutraceutical (±)-catechin, with demonstrated differential biological activity between enantiomers, to human serum albumin (HSA), with the largest complexation and enantioselectivity potential among the plasmatic proteins, is studied by combining simulations to optimize the experimental design, robust in vitro electrokinetic chromatographic data, and molecular docking–chiral recognition estimates. Methodological and mathematical drawbacks in previous reports on (±)-catechin–HSA are detected and eliminated. Recent and novel direct equations extracted from the classical interaction model allows advantageous univariate mathematical data treatment, providing the first evidence of quantitative (±)-catechin–HSA enantioselectivity. Also, the binding site in HSA of the enantiomers is approached, and both the experimental enantioselectivity and the main binding site information are contrasted with a molecular docking approach.