Engineering and assaying of cytochrome P450 biocatalysts

Cytochrome P450s constitute a highly fascinating superfamily of enzymes which catalyze a broad range of reactions. They are essential for drug metabolism and promise industrial applications in biotechnology and biosensing. The constant search for cytochrome P450 enzymes with enhanced catalytic performances has generated a large body of research. This review will concentrate on two key aspects related to the identification and improvement of cytochrome P450 biocatalysts, namely the engineering and assaying of these enzymes. To this end, recent advances in cytochrome P450 development are reported and commonly used screening methods are surveyed.     

Directed evolution of enzymes: new biocatalysts for asymmetric synthesis

Directed evolution has been employed to generate new enzymes for the deracemisation of chiral amines.     

Oxygen evolution from BF3/MnO4-

MnO(4)(-) is activated by BF(3) to undergo intramolecular coupling of two oxo ligands to generate O(2). DFT calculations suggest that there should be a spin intercrossing between the singlet and triplet potential energy surfaces on going from the active intermediate [MnO(2)(OBF(3))(2)](-) to the O···O coupling transition state.     

Creation of biocatalysts with prescribed properties

Oxidoreductases are widely used in different branches of industry (particularly, in pharmaceutical) and analytical biotechnology. To optimize the use and to reduce production cost of a target product, the properties of a biocatalyst should be modified to meet requirements of a specific process or method of analysis. Problem of creation of biocatalysts with prescribed properties includes complex set of R&D such as an engineering of enzyme properties, construction of recombinant strains overproducing the target protein, development of a large-scale downstream process and preparation of a working form of a biocatalysts. In the present work, the basic features and practical examples of such an over-all approach are considered for formate dehydrogenase and D-amino acid oxidase. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1014–1022, May, 2008.     

Oxidation of nitrogen-containing heterocycles using biocatalysts

A method for stereospecific hydroxylation of 1,2-dihydro-3H-1,4-benzodiazepin-2-ones using free and immobilized cells of actinomycetes as biocatalysts was developed. The hydroxylation under the action of yeast results in the formation of racemates. Actinomyces do not hydroxylate quinazolinones, quinoxalinones, and tetrahydro-1,5-benzodiazepin-2-ones; derivatives of 1,2,3,4-tetrahydro-1,5-benzodiazocin-2-ones are transformed into 2-[N-(3-acetylaminopropionyl)amino]benzophenones. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1608–1613, August, 1998.     

Ligation independent cloning (LIC) as a rapid route to families of recombinant biocatalysts from sequenced prokaryotic genomes

A technique is presented for the high throughput generation of families of recombinant biocatalysts sourced from prokaryotic genomes, providing rapid access to the naturally evolved diversity of enzyme specificity for biocatalyst discovery. The method exploits a novel ligation independent cloning strategy, based on the locally engineered vector pET-YSBLIC and has been used for the rapid generation of a suite of expression plasmids containing genes encoding a family of six Baeyer-Villiger monooxygenases (BVMOs) from Mycobacterium tuberculosis H37Rv (MTb). The six resultant recombinant strains of E. coli B834 (DE3) expressing the genes were assayed for oxygenating activity in respect of the target reaction; the resolution of bicyclo[3.2.0]hept-2-en-6-one. The analysis of biotransformations catalysed by growing cells of E. coli was complicated by the production of indole in the reaction mixtures, possibly resulting from the in vivo activity of E. coli tryptophanase. Four of the recombinant strains expressing different BVMOs catalysed the oxidation of one or more of four screening substrates, well above controls that had been transformed with the re-ligated parent vector. One of the recombinant strains, E. coli B834 (DE3) pDB5, expressing the Rv3049c gene from MTb, was found to effectively resolve the target substrate, yielding a 19% yield of (1R, 5S)-(+)-bicyclo[3.2.0]hept-2-en-6-one with >95% enantiomeric excess in a 4 L fermentation reaction.     

New additions to the arsenal of biocatalysts for noncanonical amino acid synthesis

Noncanonical amino acids (ncAAs) merge the conformational behavior and native interactions of proteinogenic amino acids with nonnative chemical motifs and have proven invaluable in developing modern therapeutics. This blending of native and nonnative characteristics has resulted in essential drugs like nirmatrelvir, which comprises three ncAAs and is used to treat COVID-19. Enzymes are appearing prominently in recent syntheses of ncAAs, where they demonstrate impressive control over the stereocenters and functional groups found therein. Here we review recent efforts to expand the biocatalyst arsenal for synthesizing ncAAs with natural enzymes. We also discuss how new-to-nature enzymes can contribute to this effort by catalyzing reactions inspired by the vast repertoire of chemical catalysis and acting on substrates that would otherwise not be used in synthesizing ncAAs. Abiotic enzyme-catalyzed reactions exploit the selectivity afforded by a macromolecular catalyst to access molecules not available to natural enzymes and perhaps not even chemical catalysis.     

Production of fumaric acid with immobilized biocatalysts

Immobilization ofRhizopus arrhizus mycelium improved fumaric acid production. The optimum conditions for fumaric acid production with immobilized cells were investigated using a statistical experimental design. Substrate concentration, carbon:nitrogen ratio, and residence time were chosen as independent variables. In the repeated batch shake flask fermentation, the fumaric acid yield from xylose was as much as 3.5 times higher with immobilized mycelium than with free mycelium. Polyurethane foam cubes, in this case, gave better results than nylon net cubes as a carrier.     

Catalytic antibodies as a new generation of biocatalysts

The present state and perspectives of the creation of a new generation of biocatalysts, catalytic antibodies (CA), and their application to organic synthesis are discussed. The problems to be solved for the development of the practical application of CA are especially noted. This paper was prepared in response to a request from the Editorial board in order to attract the attention of investigators to the creation of artificial enzymes, called catalytic antibodies, which is a new and important direction in science. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1568–1574, September, 1997     

Combinatorial libraries of biocatalysts: application and screening

Enzymes can perform intricate regioselective and/or enantioselective chemical transformations and can accelerate reaction rates by enormous factors all under mild conditions. However, enzymes almost always present problems for use on an industrial scale. Evolutionary design approaches can be applied to the generation of stable enzymes with improved or novel catalytic activities. Directed evolution can be considered as the biotechnological equivalent of combinatorial chemistry, where the expressed proteins are the combinatorial libraries of biocatalysts. This review will focus on the search of novel biocatalysts produced by genetic engineering with modified activity and stability in different environments, substrate specificity and enantioselectivity. Methods of screening and/or selection for the desired properties will also be described. Finally, the efforts in de novo enzyme design are mentioned.     

Creation of a pair of stereochemically complementary biocatalysts

N-Acetylneuraminic acid lyase (NAL) exhibits poor facial selectivity during carbon-carbon formation, and as such, its utility as a catalyst for use in synthetic chemistry is limited. For example, the NAL-catalyzed condensation between pyruvate and (2R,3S)-2,3-dihydroxy-4-oxo-N,N-dipropylbutyramide yields ca. 3:1 mixtures of diastereomeric products under either kinetic or thermodynamic control. Engineering the stereochemical course of NAL-catalyzed reactions could remove this limitation. We used directed evolution to create a pair of stereochemically complementary variant NALs for the synthesis of sialic acid mimetics. The E192N variant, a highly efficient catalyst for aldol reactions of (2R,3S)-2,3-dihydroxy-4-oxo-N,N-dialkylbutyramides, was chosen as a starting point. Initially, error-prone PCR identified residues in the active site of NAL that contributed to the stereochemical control of an aldolase-catalyzed reaction. Subsequently, an intense structure-guided program of saturation and site-directed mutagenesis was used to identify a complementary pair of variants, E192N/T167G and E192N/T167V/S208V, which were approximately 50-fold selective toward the cleavage of the alternative 4S- and 4R-configured condensation products, respectively. It was shown that wild-type NAL could not be used for the highly stereoselective synthesis of a 6-dipropylamide sialic acid mimetic because the 4S-configured product was only approximately 3-fold kinetically favored and only approximately 3-fold thermodynamically favored over the alternative 4R-configured product. However, the complementary 4R- and 4S-selective variants allowed the highly (>98:<2) diastereoselective synthesis of both 4S- and 4R-configured products under kinetic control from the same starting materials. Conversion of an essentially nonselective aldolase into a pair of complementary biocatalysts will be of enormous interest to synthetic chemists. Furthermore, since residues identified as critical for stereoselectivity are conserved among members of the NAL superfamily, the approach might be extended to the evolution of other useful biocatalysts for the stereoselective synthesis of biologically active molecules.     

The evolution of molecular dynamics from picoseconds to years

The dielectric relaxation of dipolar solutes in vitreous and viscous decalin is composed of at least two loss peaks. There is an universal γ process appearing at THz frequencies and equivalent to the Poley absorption in liquids, and a low frequency process sometimes resolved into α and β components. The complete spectrum covers twelve frequency decades or more.     

Chemoenzymatic synthesis of natural products using plant biocatalysts

Many small-molecule chemicals from plants display extraordinarily complex structures and potent bioactivities with significant pharmacological and industrial implications. While the medicinal and economic relevance of plants' bioactive compounds is widely recognized, their industrial-scale chemical synthesis for distribution and development of new derivatives is hampered by challenges associated with their structural complexity. Extraction from the native plants is usually not viable due to the chemicals' low natural abundance, and the plants’ sub-optimal growing conditions due to climate change and the destruction of natural habitats. All of these challenges ultimately highlight the need to expand the (bio)chemical toolbox with strategies that support continuous discovery and sustainable production of relevant chemicals. This article highlights some of the most recent discoveries of plant-derived biocatalysts and how they pave the way for more sustainable and greener approaches to produce chemicals with unmatched complexity and applications.     

Free energy of solvation from molecular dynamics simulation applying Voronoi-Delaunay triangulation to the cavity creation

The free energy of solvation for a large number of representative solutes in various solvents has been calculated from the polarizable continuum model coupled to molecular dynamics computer simulation. A new algorithm based on the Voronoi-Delaunay triangulation of atom-atom contact points between the solute and the solvent molecules is presented for the estimation of the solvent-accessible surface surrounding the solute. The volume of the inscribed cavity is used to rescale the cavitational contribution to the solvation free energy for each atom of the solute atom within scaled particle theory. The computation of the electrostatic free energy of solvation is performed using the Voronoi-Delaunay surface around the solute as the boundary for the polarizable continuum model. Additional short-range contributions to the solvation free energy are included directly from the solute-solvent force field for the van der Waals-type interactions. Calculated solvation free energies for neutral molecules dissolved in benzene, water, CCl4, and octanol are compared with experimental data. We found an excellent correlation between the experimental and computed free energies of solvation for all the solvents. In addition, the employed algorithm for the cavity creation by Voronoi-Delaunay triangulation is compared with the GEPOL algorithm and is shown to predict more accurate free energies of solvation, especially in solvents composed by molecules with nonspherical molecular shapes.     

A generic platform for the immobilisation of engineered biocatalysts

The application of biocatalysis in the pharmaceutical industry is rapidly growing as a result of increased access to enzymes that meet the demands of industrial processes. This expansion of activity has led to a corresponding increase in the demand for immobilised enzymes. EziG? (EnginZyme AB, Sweden) is marketed as a general matrix for enzyme immobilisation on controlled porosity glass. In this work we identified criteria for a “general” enzyme immobilisation technology in the context of the requirements of the pharmaceutical industry. We subsequently evaluated EziG? for generality in a series of case studies for the application of immobilised biocatalysts. In this study we have focussed on the challenges facing both academic and industrial applications such as enzyme stability, multistep reactions and reactions in continuous flow.     

Spin-locking of half-integer quadrupolar nuclei in nuclear magnetic resonance of solids: creation and evolution of coherences

Spin-locking of half-integer quadrupolar nuclei, such as 23Na (I=3/2) and 27Al (I=5/2), is of renewed interest owing to the development of variants of the multiple-quantum and satellite-transition magic angle spinning (MAS) nuclear magnetic resonance experiments that either utilize spin-locking directly or offer the possibility that spin-locked states may arise. However, the large magnitude and, under MAS, the time dependence of the quadrupolar interaction often result in complex spin-locking phenomena that are not widely understood. Here we show that, following the application of a spin-locking pulse, a variety of coherence transfer processes occur on a time scale of approximately 1/omegaQ before the spin system settles down into a spin-locked state which may itself be time dependent if MAS is performed. We show theoretically for both spin I=3/2 and 5/2 nuclei that the spin-locked state created by this initial rapid dephasing typically consists of a variety of single- and multiple-quantum coherences and nonequilibrium population states and we discuss the subsequent evolution of these under MAS. In contrast to previous work, we consider spin-locking using a wide range of radio frequency field strengths, i.e., a range that covers both the "strong-field" (omega1 > omegaQPAS and "weak-field" (omega1 < omegaQPAS limits. Single- and multiple-quantum filtered spin-locking experiments on NaNO2, NaNO3, and Al(acac)3, under both static and MAS conditions, are used to illustrate and confirm the results of the theoretical discussion.