R.B. Leveson-Gower

Nature Catalysis, Published online: 17 November 2022; doi:10.1038/s41929-022-00873-5

Artificial enzymes capable of catalysing significant transformations are highly desired but usually suffer from limitations in structural design and poor efficiency. Now, a monolayered metal–organic framework is reported as an editable biomimetic platform to achieve exceptional artificial photosynthesis performance.

Tertiary nitroalkanes and the corresponding α-tertiary amines represent important motifs in bioactive molecules and natural prod-ucts. The C-alkylation of secondary nitroalkanes with electrophiles is a straightforward strategy for constructing tertiary nitroal-kanes, however, controlling the stereoselectivity of this type of reaction remains challenging. Here we report a highly chemo- and stereoselective C-alkylation of nitroalkanes with alkyl halides catalyzed by an engineered flavin-dependent ‘ene’-reductase (ERED). Directed evolution of the old yellow enzyme from Geobacillus kaustophilus provided a triple mutant, GkOYE-G7, capable of synthesizing tertiary nitroalkanes with high yield and enantioselectivity. Mechanistic studies indicate that the excitation of an enzyme-templated charge-transfer complex formed between the substrates and cofactor is responsible for radical initiation. Moreover, a single-enzyme two-mechanism cascade reaction was developed to prepare tertiary nitroalkanes from simple nitroal-kenes, highlighting the potential to use one enzyme for two mechanistically distinct reactions.

Nature Chemistry, Published online: 14 November 2022; doi:10.1038/s41557-022-01083-z

Expanding the biocatalysis toolbox for C–N bond formation is of great value. Now, a biocatalytic amination strategy using a new-to-nature mechanism involving nitrogen-centred radicals has been developed. The transformations are enabled by synergistic photoenzymatic catalysis, providing intra- and intermolecular hydroamination products with high yields and levels of enantioselectivity.

The Prelog rule in l-threonine aldolase holds that when the C_α anion of PLP-Gly attacks the carbonyl carbon atom of the aldehyde from the re-face, the (2S,3S)-configured product is formed, whereas attack from the si-face forms the (2S,3R)-configured product. Guided by this rule, mutants of LTA with improved diastereoselectivity of 99.2 % _syn and 97.4 % _anti were obtained.

Abstract

l-threonine aldolase (LTA) catalyzes C−C bond synthesis with moderate diastereoselectivity. In this study, with LTA from Cellulosilyticum sp (CpLTA) as an object, a mutability landscape was first constructed by performing saturation mutagenesis at substrate access tunnel amino acids. The combinatorial active-site saturation test/iterative saturation mutation (CAST/ISM) strategy was then used to tune diastereoselectivity. As a result, the diastereoselectivity of mutant H305L/Y8H/V143R was improved from 37.2 % _syn to 99.4 % _syn . Furthermore, the diastereoselectivity of mutant H305Y/Y8I/W307E was inverted to 97.2 % _anti . Based on insight provided by molecular dynamics simulations and coevolution analysis, the Prelog rule was employed to illustrate the diastereoselectivity regulation mechanism of LTA, holding that the asymmetric formation of the C−C bond was caused by electrons attacking the carbonyl carbon atom of the substrate aldehyde from the re or si face. The study would be useful to expand LTA applications and guide engineering of other C−C bond-forming enzymes.

The chemical transformation of aromatic amino acids has emerged as an attractive alternative to non-selective lysine or cysteine labeling for the modification of biomolecules. However, this strategy has largely been limited by the scope of functional groups and biocompatible reaction conditions available. Herein, we report the implementation of near-infrared-activatable photocatalysts, TTMAPP and n-Pr-DMQA+, capable of generating fluoroalkyl radicals for selective tryptophan functionalization within simple and complex biological systems. At the peptide level, a diverse set of iodo-perfluoroalkyl reagents were used to install bioorthogonal handles for downstream applications or link inter- or intramolecular tryptophan residues for peptide stapling. We also found this photoredox transformation amenable to biotinylation of intracellular proteins in live cells for downstream confocal imaging and mass spectrometry-based analysis. Given the inherent tissue penetrant nature of near-infrared light we further demonstrated the utility of this technology to achieve photocatalytic protein fluoroalkylation in physiologically relevant tissue and tumor environments.

An in vivo selection strategy is presented, in which bacteria addicted to non-canonical amino acids (ncAAs) are complemented by enzymes that can yield these building blocks from synthetic precursors. As growth rates under selective conditions correlate with enzyme activities, serial passaging elicited better biocatalysts from populations harboring enzyme libraries. The platform was used to improve the activity of carbamoylases for ncAA-precursors.

Abstract

In vivo selections are powerful tools for the directed evolution of enzymes. However, the need to link enzymatic activity to cellular survival makes selections for enzymes that do not fulfill a metabolic function challenging. Here, we present an in vivo selection strategy that leverages recoded organisms addicted to non-canonical amino acids (ncAAs) to evolve biocatalysts that can provide these building blocks from synthetic precursors. We exemplify our platform by engineering carbamoylases that display catalytic efficiencies more than five orders of magnitude higher than those observed for the wild-type enzyme for ncAA-precursors. As growth rates of bacteria under selective conditions correlate with enzymatic activities, we were able to elicit improved variants from populations by performing serial passaging. By requiring minimal human intervention and no specialized equipment, we surmise that our strategy will become a versatile tool for the in vivo directed evolution of diverse biocatalysts.

We report in vivo biocatalytic cascade reactions comprising a combination of canonical enzyme-catalysed reactions with an artificial-enzyme-catalysed new-to-nature reaction. The artificial enzyme contains a genetically encoded unnatural catalytic residue, which catalyses the formation of a hydrazone product from biosynthetically produced benzaldehydes in E. coli.

Abstract

Artificial enzymes utilizing the genetically encoded non-proteinogenic amino acid p-aminophenylalanine (pAF) as a catalytic residue are able to react with carbonyl compounds through an iminium ion mechanism to promote reactions that have no equivalent in nature. Herein, we report an in vivo biocatalytic cascade that is augmented with such an artificial enzyme-catalysed new-to-nature reaction. The artificial enzyme in this study is a pAF-containing evolved variant of the lactococcal multidrug-resistance regulator, designated LmrR_V15pAF_RMH, which efficiently converts benzaldehyde derivatives produced in vivo into the corresponding hydrazone products inside E. coli cells. These in vivo biocatalytic cascades comprising an artificial-enzyme-catalysed reaction are an important step towards achieving a hybrid metabolism.

Science Advances, Volume 8, Issue 44, November 2022.

The chiral building block 5-amino-2-hydroxymethyltetrahydropyran 1a has been previously synthesized through a cumbersome 9-step synthesis from tri-O-acetyl-D-glucal, which renders access to nemtabrutinib (2), a BTK inhibitor currently being evaluated for the treatment of various hematologic malignancies, inefficient and wasteful. Herein, we describe the development of a protecting group-free, 2-step synthesis of 1a from Cyrene, a biorenewable feedstock. The improved synthesis involves a biocatalytic transamination reaction of Cyrene to install the desired amine-stereocenter in a single step with high diastereoselectivity. The enzymatic reaction is followed by a stereo-retentive reductive acetal opening reaction of the chiral cyrene amine intermediate 3a to furnish 1a. A mechanistic investigation of the acetal opening reaction is also described which uncovered unprecedented reaction conditions for the in-situ generation of diborane mediated by the sulfolane co-solvent. The streamlined synthesis of 1a from Cyrene resulted in a > 27% yield improvement and a significant reduction in the environmental impact of the synthesis.

Halogenation of pyrrole requires strong electrophilic reagents and often leads to undesired polyhalogenated products. Biocatalytic halogenation is a highly attractive approach given its chemoselectivity and benign reaction conditions. Whilst there are several reports of enzymatic phenol and indole halogenation in organic synthesis, corresponding reports on enzymatic pyrrole halogenation has been lacking. Here we describe the first in vitro functional and structural characterization of PrnC, a flavin-dependent halogenase that can act on free-standing pyrroles. Computational modelling and site mutagenesis studies identified three key residues in the catalytic pocket. Moderate resolution map using single-particle cryogenic electron microscopy (CryoEM) reveals PrnC to be a dimer. This native PrnC can halogenate a library of structurally diverse pyrrolic heterocycles in a site-selective manner and was applied in the chemoenzymatic synthesis of a chlorinated analog of the agrochemical fungicide, Fludioxonil.

Facile reductions of carboxylic acids to aldehydes or alcohols can be effected under mild conditions upon initial conversion to their corresponding S-2-pyridyl thioesters. Upon treatment with a commercially available and air-stable nickel pre-catalyst and silane as a stoichiometric reductant, aldehydes are formed in moderate to good yields. Alternatively, the 1-pot conversion of acids to their thioester derivatives can be followed by reduction to the alcohol upon treatment with sodium borohydride. A variety of starting materials ranging from highly functionalized acids to educts from the Merck Informer Library can be transformed using these green reaction media.

Radical addition to the dehydroalanine (Dha) residue of a peptide could diversify the peptide sequence with noncanonical residues, but this strategy is currently limited by the lack of control over the stereochemistry. This work addresses this important challenge by applying chiral nickel catalysts to control the stereoselective radical addition to Dha on oligopeptides.

Abstract

Radical addition to dehydroalanine (Dha) represents an appealing, modular strategy to access non-canonical peptide analogues for drug discovery. Prior studies on radical addition to the Dha residue of peptides and proteins have demonstrated outstanding functional group compatibility, but the lack of stereoselectivity has limited the synthetic utility of this approach. Herein, we address this challenge by employing chiral nickel catalysts to control the stereoselectivity of radical addition to Dha on oligopeptides. The conditions accommodate a variety of primary and secondary electrophiles to introduce polyethylene glycol, biotin, halo-tag, and hydrophobic and hydrophilic side chains to the peptide. The reaction features catalyst control to largely override substrate-based control of stereochemical outcome for modification of short peptides. We anticipate that the discovery of chiral nickel complexes that confer catalyst control will allow rapid, late-stage modification of peptides featuring nonnatural sidechains.

Predicting the reaction kinetics, that is, how fast a reaction can happen in a solution, is essential information for many processes, such as industrial chemical manufacturing, refining, synthesis and separation of petroleum products, environmental processes in air and water, biological reactions in cells, biosensing, and drug delivery. Collision theory was originally developed to explain the reaction kinetics of gas reactions with no dilution. For a reaction in a diluted inert gas solution or a diluted liquid solution, diffusion often dominates the collision process. Thus, it is necessary to include diffusion in such a calculation. Traditionally the classical Smoluchowski rate is used as a starting point to predict the collision frequency of two molecules in a diluted solution. In this report, a different collision model is derived from the adsorption of molecules on a flat surface. A surprising result is obtained showing that the reaction order for biomolecular reaction should be 2 and 1/3 instead of 2, following a fractal reaction kinetics.

Late-stage halogenation of peptides has become feasible using a highly flexible halogenase that catalyses bromination of a wide range of amides and peptides. Upon optimization studies, even longer peptides carrying a terminal tryptophan residue were reasonably accepted leading to high conversions and remarkable selectivity. This novel bioorthogonal approach was exemplified by halogenating an RGD peptide derivative in the final step.

Abstract

The late-stage site-selective derivatisation of peptides has many potential applications in structure-activity relationship studies and postsynthetic modification or conjugation of bioactive compounds. The development of orthogonal methods for C−H functionalisation is crucial for such peptide derivatisation. Among them, biocatalytic methods are increasingly attracting attention. Tryptophan halogenases emerged as valuable catalysts to functionalise tryptophan (Trp), while direct enzyme-catalysed halogenation of synthetic peptides is yet unprecedented. Here, it is reported that the Trp 6-halogenase Thal accepts a wide range of amides and peptides containing a Trp moiety. Increasing the sequence length and reaction optimisation made bromination of pentapeptides feasible with good turnovers and a broad sequence scope, while regioselectivity turned out to be sequence dependent. Comparison of X-ray single crystal structures of Thal in complex with d-Trp and a dipeptide revealed a significantly altered binding mode for the peptide. The viability of this bioorthogonal approach was exemplified by halogenation of a cyclic RGD peptide.

Science Advances, Volume 8, Issue 41, October 2022.

Calculations suggest that a coordination switch of the sulfoxide intermediate is involved in the catalysis of ergothioneine synthase (EgtB). This coordination switch from S to O is driven by the S/π nonbonding electrostatic interactions, which efficiently promotes the observed stereoselective C−S bond formation while bypassing cysteine dioxygenation.

Abstract

The non-heme iron ergothioneine synthase (EgtB) is a sulfoxide synthase that catalyzes oxidative C−S bond formation in the synthesis of ergothioneine, which plays roles against oxidative stress in cells. Despite extensive experimental and computational studies of the catalytic mechanisms of EgtB, the root causes for the selective C−S bond formation remain elusive. Using quantum mechanics/molecular mechanics (QM/MM) calculations, we show herein that a coordination switch of the sulfoxide intermediate is involved in the catalysis of the non-heme iron EgtB. This coordination switch from the S to the O atom is driven by the S/π electrostatic interactions, which efficiently promotes the observed stereoselective C−S bond formation while bypassing cysteine dioxygenation. The present mechanism is in agreement with all available experimental data, including regioselectivity, stereoselectivity and KIE results. This match underscores the critical role of coordination switching in the catalysis of non-heme enzymes.

Cyclic amines are ubiquitous structural motifs found in pharmaceuticals and biologically active natural products, making methods for their elaboration via direct C–H functionalization of considerable synthetic value. Herein, we report the development of an iron-based biocatalytic strategy for enantioselective a-C–H functionalization of pyrrolidines via a carbene transfer reaction with diazoacetone. Currently unreported for organometallic catalysts, this transformation can be accomplished in high yields, high catalytic activity and high stereoselectivity (up to 99:1 e.r. and 20,350 TON) using engineered variants of cytochrome P450 CYP119 from Sulfolobus solfataricus. This methodology was further extended to enable enantioselective a-C–H functionalization in the presence of ethyl diazoacetate as carbene donor (up to 89:11 e.r. and 8,920 TON), and the two strategies were combined to achieve a one-pot as well as a tandem dual C–H functionalization of the cyclic amine substrate with enzyme-controlled diastereo- and enantiodivergent selectivity. This biocatalytic approach is amenable to gram-scale synthesis and can be applied to drug scaffolds for late-stage C–H functionalization. This work provides an efficient and tunable method for direct asymmetric a-C–H functionalization of saturated N-heterocycles which should offer new opportunities for the synthesis, discovery, and optimization of bioactive molecules.

The combination of photochemistry with enzyme catalysis offers exciting opportunities to induce new reactivities and to create novel enzymes for reactions other than their native ones. Recently, Hyster and co-workers demonstrated this for a photoenzymatic asymmetric Csp ³−Csp ³ cross-electrophile coupling, a reactivity previously unknown to enzymes.

Abstract

Enzymes have several advantages over conventional catalysts for organic synthesis. Over the last two decades, much effort has been made to further extend the scope of biocatalytic reactions available to synthetic chemists, particularly by expanding the repertoire of enzymes for abiological transformations. In this regard, exciting new developments in the area of photobiocatalysis enable now the introduction of non-natural reactivity in enzymes to solve long-standing synthetic challenges. A recently described example from the Hyster group demonstrates in an unprecedented way how the combination of photochemistry with enzyme catalysis empowers the catalytic asymmetric construction of Csp ³−Csp ³ bonds with high chemo- and enantioselectivity.

Of the different classes of halogenases characterized to date, flavin dependent halogenases (FDHs) are most commonly associated with site-selective halogenation of electron rich arenes and enol(ate) moieties in the biosynthesis of halogenated natural products. This capability has made them attractive biocatalysts, and extensive efforts have been devoted to both discovering and engineering these enzymes for different applications. We have established that engineered FDHs can catalyze different enantioselective halogenation processes, including halolactonization of simple alkenes with a tethered carboxylate nucleophile. In this study, we expand the scope of this reaction to include alcohol nucleophiles and a greater diversity of alkene substitution patterns to access a variety of chiral tetrahydrofurans. We also demonstrate that FDHs can be interfaced with ketoreductases to enable halocyclization using ketone substrates in one-pot cascade reactions and that the halocyclization products can undergo subsequent rearrangements to form novel hydroxylated and halogenated products. Together, these advances expand the utility of FDHs for enantio- and diastereoselective olefin functionalization.