R.B. Leveson-Gower

Nature, Published online: 01 June 2022; doi:10.1038/s41586-022-04456-z

Recent progress in computational enzyme design, active site engineering and directed evolution are reviewed, highlighting methodological innovations needed to deliver improved designer biocatalysts.

Nature, Published online: 01 June 2022; doi:10.1038/s41586-022-04773-3

Chimeric triterpene synthases are identified that catalyse non-squalene-dependent triterpene biosynthesis.

Bio-Chem collaboration: Escherichia coli fermentation and visible-light photocatalysis were combined in a complementary way for the first time, to realize the scaffold assembly in a “one-pot” fashion and the subsequent diversifications in a “one-step” manner, respectively, enabling the production of six sesquiterpenoids.

Abstract

The diversification of natural products to expand biologically relevant chemical space for drug discovery can be achieved by combining complementary bioprocessing and chemical transformations. Herein, genetically engineered Escherichia coli fermentation to produce amorphadiene and valencene was combined with metal-free photocatalysis transformations to further access nootkatone, cis-nootkatol and two hydration derivatives. In fermentation, using a closed, anaerobic condition avoided the use of organic overlay, increased the productivity, and simplified the work-up process. Metal-free photocatalysis hydration and allylic C−H oxidation were designed and implemented to make the whole process greener. It was shown that the anti-Markovnikov selectivity of photocatalyzed alkene hydration could be reversed by stereo-electronic and steric effects existing in complex natural products. The combination of bioprocessing and photocatalysis may provide an efficient and greener way to expand the chemical space for pharmaceutical, flavor and fragrance industry.

Styrene monooxygenase catalyzed enantioselective anti-Markovnikov hydration of aryl alkenes, rather than epoxidation, was made possible by simply removing oxygen from the reaction mixture. An acid–base mechanism with a carbanion-like intermediate enabled the reaction with excellent anti-Markovnikov regioselectivity.

Abstract

The addition of water to alkenes is an important method for the synthesis of alcohols, but the regioselectivity of acid-catalyzed hydration of terminal alkenes yields secondary alcohols according to Markovnikov's rule, making it difficult to obtain primary alcohols. Here we report a styrene monooxygenase that catalyzes the anti-Markovnikov hydration of the terminal aryl alkenes under anaerobic conditions. This hydration provides primary alcohols in good yields (up to 100 %), excellent anti-Markovnikov regioselectivity (>99 : 1), and good enantiomeric purity (60–83 % ee). Residues Asn46, Asp100, and Asn309 are essential for catalysis suggesting an acid–base mechanism with a carbanion-like intermediate that could account for the anti-Markovnikov regioselectivity. Our work reveals a new enzymatic tool with unusual regioselectivity based on the promiscuous catalytic activity of a monooxygenase.

Asymmetric catalysis has witnessed paramount lessons from terpene cyclase enzymology such as the ability to control dynamic carbocations or cationic cyclization cascades. In general, these cascades are stereodivergent and thus rely on the terpene’s double-bond geometry. In this work, we illuminate how the dynamic supramolecular framework of squalene-hopene cyclases (SHCs) can be tailored to break with this paradigm. Creating a locally electron-enriched confined active site, we enabled the stereoconvergent cationic cyclization of a cis/trans terpene mixture into one isomer. Our results suggest that a priorly unknown active site “memory” effect of the SHC aids this intricate transformation. Based on these findings, we employed synergistic active site and tunnel engineering to generate a most efficient (–)-ambroxide cyclase. Broad computational investigations evidently explain how the introduced mutations work in concert to improve substrate acquisition, flow and chaperoning. Nonetheless, kinetics disclosed a substrate-induced downregulation of the membrane-bound SHC as the major turnover limitation in vivo. Merging these new insights with the improved and stereoconvergent catalysis of the enzyme, we applied a feeding strategy to exceed 106 TTN with the SHC.

An asymmetric oxidative cross-coupling strategy that combines the non-natural catalytic activity of lipase with organic electrosynthesis was developed. This unprecedented protocol demonstrates that hydrolase catalysis is compatible with electrosynthesis.

Abstract

We describe the enantioselective oxidative cross-coupling of secondary amines with ketones by combining the non-natural catalytic activity of lipase with electrosynthesis. Various 2,2-disubstituted 3-carbonyl indoles with a stereogenic quaternary carbon center were synthesized from 2-substituted indoles in yields up to 78 % with good enantio- and diastereoselectivities (up to 96 : 4 e.r. and >20 : 1 d.r.). This unprecedented protocol demonstrated that hydrolase catalysis is compatible with electrosynthesis, and the reaction can be carried out in organic solvents with a broad substrate scope and good stereoselectivity. This work provides insights into enzymatic electrosynthesis.

ATP phosphoribosyltransferase catalyses the first step of histidine biosynthesis and is controlled via a complex allosteric mechanism where the regulatory protein HisZ enhances catalysis by the catalytic protein HisGS while mediating allosteric inhibition by histidine. Activation by HisZ was proposed to position HisGS Arg56 to stabilise departure of the pyrophosphate leaving group. Here we report active-site mutants of HisGS with impaired reaction chemistry which can be allosterically restored by HisZ despite the HisZ:HisGS interface lying ~20-Å away from the active site. MD simulations indicate HisZ binding constrains the dynamics of HisGS to favour a preorganised active site where both Arg56 and Arg32 are poised to stabilise leaving-group departure in WT-HisGS. In the Arg56Ala-HisGS mutant, HisZ modulates Arg32 dynamics so that it can partially compensate for the absence of Arg56. These results illustrate how remote protein:protein interactions translate into catalytic resilience by restoring damaged electrostatic preorganisation at the active site.

The power of carboxylates: Simple carboxylate salts can rival strong amidine bases, such as DBU, in their catalytic power to isomerize β,γ-unsaturated thioesters to corresponding conjugated α,β-unsaturated thioesters. The mechanism involves a rate-determining protonation step!

Abstract

We demonstrate herein the capacity of simple carboxylate salts – tetrametylammonium and tetramethylguanidinium pivalate – to act as catalysts in the isomerization of β,γ-unsaturated thioesters to α,β-unsaturated thioesters. The carboxylate catalysts gave reaction rates comparable to those obtained with DBU, but with fewer side reactions. The reaction exhibits a normal secondary kinetic isotope effect (k _1H/k _1D=1.065±0.026) with a β,γ-deuterated substrate. Computational analysis of the mechanism provides a similar value (k _1H/k _1D=1.05) with a mechanism where γ-reprotonation of the enolate intermediate is rate determining.

Metallotetraphenylporphyrins (metalloTPPs) are exceedingly hydrophobic, rendering them insoluble in aqueous solvents. Upon introduction of the bacterial haem-acquisition protein, HasA, which can incorporate bulky metalloTPPs in its haem-binding pocket, a stable, water-soluble HasA–TPP complex can be formed. This permits the utilisation of metalloTPPs, in the form of a HasA–TPP complex, with biological systems, as antimicrobial agents targeting the critical pathogen Pseudomonas aeruginosa or as biocatalysts. The picture was created by Yuma Shisaka and Mami Yoshimura. More information can be found in the Research Article by O. Shoji et al.

An enzymatic route to commercially important surfactants is presented. A truncated construct of carboxylic acid reductase (CARmm-A) catalyzes amide bond formation between fatty acids and amino alcohols with no esterification observed. The wide substrate scope of the enzyme, co-factor recycling, reaction engineering and up-scaling show the feasibility of this method for synthesis.

Abstract

N-alkanoyl-N-methylglucamides (MEGAs) are non-toxic surfactants widely used as commercial ingredients, but more sustainable syntheses towards these compounds are highly desirable. Here, we present a biocatalytic route towards MEGAs and analogues using a truncated carboxylic acid reductase construct tailored for amide bond formation (CARmm-A). CARmm-A is capable of selective amide bond formation without the competing esterification reaction observed in lipase catalysed reactions. A kinase was implemented to regenerate ATP from polyphosphate and by thorough reaction optimisation using design of experiments, the amine concentration needed for amidation was significantly reduced. The wide substrate scope of CARmm-A was exemplified by the synthesis of 24 commercially relevant amides, including selected examples on a preparative scale. This work establishes acyl-phosphate mediated chemistry as a highly selective strategy for biocatalytic amide bond formation in the presence of multiple competing alcohol functionalities.

Mononuclear non-heme Fe(II)- and -ketoglutarate dependent oxygenases (FeDOs) catalyze site-selective C-H hydroxylation. Variants of these enzymes in which a conserved Asp/Glu residue in the Fe(II)-binding facial triad is replaced by Ala/Gly can, in some cases, bind various anionic ligands and catalyze non-native chlorination and bromination reactions. In this study, we explore the binding of different anions to a FeDO facial triad variant, SadX, and the effects of that binding on HO• vs. X• rebound. We establish that chloride and bromide not only enable non-native halogenation reactions but that all anions investigated, including azide, cyanate, formate, and fluoride, significantly accelerate and influence the site selectivity of SadX hydroxylation catalysis. Azide and cyanate also lead to the formation of products resulting from N3•, NCO•, and OCN• rebound. While fluoride rebound is not observed, the rate acceleration provided by this ligand led us to calculate barriers for HO• and F• rebound from a putative Fe(III)(OH)(F) intermediate. These calculations suggest that the lack of fluorination is due to the relative barriers of the HO• and F• rebound transition states rather than an inaccessible barrier for F• rebound. Together, these results improve our understanding of FeDO facial triad variant tolerance of different anionic ligands, their ability to promote rebound involving those ligands, and inherent rebound preferences relative to HO• that will aid efforts to develop non-native catalysis using these enzymes.

Nature Communications, Published online: 20 May 2022; doi:10.1038/s41467-022-30354-z

Retraction Note: The Arabidopsis NOT4A E3 ligase promotes PGR3 expression and regulates chloroplast translation

The ability to programme new modes of catalysis into proteins would allow the development of enzyme families with functions beyond those found in nature. To this end, genetic code expansion methodology holds particular promise, as it allows the site-selective introduction of new functional elements into proteins as non-canonical amino acid side chains. Here, we exploit an expanded genetic code to develop a photoenzyme that operates via triplet energy transfer catalysis, a versatile mode of reactivity in organic synthesis that is currently not accessible to biocatalysis. Installation of a genetically encoded photosensitiser into the beta-propeller scaffold of DA_20_00 converts a de novo Diels-Alderase into a photoenzyme for [2+2]-cycloadditions (EnT1.0). Subsequent development and implementation of a platform for photoenzyme evolution afforded an efficient and enantioselective enzyme (EnT1.3, up to 99% e.e.) that can promote selective cycloadditions that have proven challenging to achieve with small molecule catalysts. EnT1.3 performs >300 turnovers and, in contrast to small molecule photocatalysts, can operate effectively under aerobic conditions. A 1.7 Å resolution X-ray crystal structure of an EnT1.3-product complex shows how multiple functional components work in synergy to promote efficient and selective photocatalysis. This study opens the door to a wealth of new excited-state chemistry in protein active sites and establishes the framework for developing a new generation of evolvable photocatalysts with efficiencies and specificities akin to natural enzymes.

Hybrid catalysts: Metal nanoparticles are deposited in a polymer-modified protein framework to obtain bifunctional hybrid catalysts that combine the transition metal activities with the host biocatalysts′ activation mode. A tailor-made lipase-silver nanobiohybrid is successfully exploited in a cascade design where a racemic allenic acetate is transformed to an enantioenriched dihydrofuran via a sequential hydrolytic kinetic resolution and a cycloisomerization.

Abstract

Lipase/metal nanobiohybrids, generated by growth of silver or gold nanoparticles on protein matrixes are used as highly effective dual-activity heterogeneous catalysts for the production of enantiomerically enriched 2,5-dihydrofurans from allenic acetates in a one-pot cascade process combining a lipase-mediated hydrolytic kinetic resolution with a metal-catalyzed allene cycloisomerization. Incorporating a novel strategy based on enzyme-polymer bioconjugates in the nanobiohybrid preparation enables excellent conversions in the process. Candida antarctica lipase B (CALB) in combination with a dextran-based polymer modifier (DexAsp) proved to be most efficient when merged with silver nanoparticles. A range of hybrid materials were produced, combining Ag or Au metals with Thermomyces lanuginosus lipase (TLL) or CALB and its DexAsp or polyethyleneimine polymer bioconjugates. The wider applicability of the biohybrids is demonstrated by their use in allenic alcohol cyclizations, where a variety of dihydrofurans are obtained using a CALB/gold nanomaterial. These results underline the potential of the nanobiohybrid catalysis as promising approach to intricate one-pot synthetic strategies.

Directed evolution rendered P450_BSβ capable of β-hydroxylating unactivated C−H bonds in aliphatic carboxylic acids with broad substrate scope and excellent chemo-, regio-, and enantioselectivity. The crystal structure of the evolved variant rationalizes the improved reactivity and selectivity. This study demonstrates the potential of exploring biocatalysts to fulfill reactions that are otherwise elusive with chemical strategies.

Abstract

Catalytic selective hydroxylation of unactivated aliphatic (sp³) C−H bonds without a directing group represents a formidable task for synthetic chemists. Through directed evolution of P450_BSβ hydroxylase, we realize oxyfunctionalization of unactivated C−H bonds in a broad spectrum of aliphatic carboxylic acids with varied chain lengths, functional groups and (hetero-)aromatic moieties in a highly chemo-, regio- and enantioselective fashion (>30 examples, Cβ/Cα>20 : 1, >99 % ee). The X-ray structure of the evolved variant, P450_BSβ-L78I/Q85H/G290I, in complex with palmitic acid well rationalizes the experimentally observed regio- and enantioselectivity, and also reveals a reduced catalytic pocket volume that accounts for the increased reactivity with smaller substrates. This work showcases the potential of employing a biocatalyst to enable a chemical transformation that is particularly challenging by chemical methods.

This Minireview summarizes the different strategies used in the design and engineering of novel enzymes that accommodate iminium catalysis. The advantages and challenges of developing enzymes for this catalysis mode are discussed. Recent developments in iminium biocatalysis showcase the tremendous power of combining chemomimetic biocatalyst design and directed evolution to create useful biocatalysts for new-to-nature transformations.

Abstract

The application of biocatalysis in conquering challenging synthesis requires the constant input of new enzymes. Developing novel biocatalysts by absorbing catalysis modes from synthetic chemistry has yielded fruitful new-to-nature enzymes. Organocatalysis was originally bio-inspired and has become the third pillar of asymmetric catalysis. Transferring organocatalytic reactions back to enzyme platforms is a promising approach for biocatalyst creation. Herein, we summarize recent developments in the design of novel biocatalysts that adopt iminium catalysis, a fundamental branch in organocatalysis. By repurposing existing enzymes or constructing artificial enzymes, various biocatalysts for iminium catalysis have been created and optimized via protein engineering to promote valuable abiological transformations. Recent advances in iminium biocatalysis illustrate the power of combining chemomimetic biocatalyst design and directed evolution to generate useful new-to-nature enzymes.

Nature, Published online: 04 May 2022; doi:10.1038/s41586-022-04531-5

The development of confined organocatalysts for the enantioselective cyanosilylation of small, unbiased substrates, including 2-butanone, is shown to lead to catalysts that are as selective as enzymes, with excellent levels of control.