R.B. Leveson-Gower

The development of new methods for enantioselective reactions that generate stereogenic centres within molecules is a cornerstone of organic synthesis. In this minireview we highlight the recent advances in enantioselective main group catalysis of the p-block elements including boron, phosphorus, bismuth and aluminium.

Abstract

The development of new methods for enantioselective reactions that generate stereogenic centres within molecules are a cornerstone of organic synthesis. Typically, metal catalysts bearing chiral ligands as well as chiral organocatalysts have been employed for the enantioselective synthesis of organic compounds. In this review, we highlight the recent advances in main group catalysis for enantioselective reactions using the p-block elements (boron, aluminium, phosphorus, bismuth) as a complementary and sustainable approach to generate chiral molecules. Several of these catalysts benefit in terms of high abundance, low toxicity, high selectivity, and excellent reactivity. This minireview summarises the utilisation of chiral p-block element catalysts for asymmetric reactions to generate value-added compounds.

This guidebook aims to improve lab users’ everyday practices to become more sustainable. Specifically, this guidebook provides practical suggestions on how to effectively use lab instruments and resources and on how to acquire data. We provide advice to labs covering disciplines such as biology, chemistry, computational science, engineering, life sciences, materials sciences, medicine, pharmacy, and physics. As every lab is different, it may occur that alternative measures are required, advice may be outdated or not applicable, and sometimes laboratories may not be able to comply with measures of other laboratories.

Science, Volume 382, Issue 6674, Page 1056-1065, December 2023.

Science, Volume 382, Issue 6673, November 2023.

Performing transition metal-catalyzed reactions in cells and living systems has equipped scientists with a toolbox to study biological processes and release drugs on demand. Thus far, an impressive scope of reactions has been performed in these settings, but many are yet to be introduced. Nitrene transfer presents a rather unexplored new-to-nature reaction. The reaction products are frequently encountered motifs in pharmaceuticals, presenting opportunities for the controlled, intracellular synthesis of drugs. Hence, we explored the transition metal-catalyzed sulfimidation reaction in water for future in vivo application. Two Cu(I) complexes containing trispyrazolylborate ligands (Tpx) were selected, and the catalytic system was evaluated with the aid of three fitness factors. The excellent nitrene transfer reactivity and high chemoselectivity of the catalysts, coupled with good biomolecule compatibility, successfully enabled the sulfimidation of thioethers in aqueous media. We envision that this copper-catalyzed sulfimidation reaction could be an interesting starting point to unlock the potential of nitrene transfer catalysis in vivo.

Copying information is vital for life's propagation. Current life forms maintain a low error rate in replication using complex machinery to prevent and correct errors. However, primitive life had to deal with higher error rates, limiting its ability to evolve. Discovering mechanisms to reduce errors would alleviate this constraint. Here, we introduce a new mechanism that decreases error rates and corrects errors in synthetic self-replicating systems driven by self-assembly. Previous work showed that macrocycle replication occurs through the accumulation of precursor material on the sides of the fibrous replicator assemblies. Stochastic simulations now reveal that selective precursor binding to the fiber surface enhances replication fidelity and error correction. Centrifugation experiments show that replicator fibers can exhibit the necessary selectivity in precursor binding. Our results suggest that synthetic replicator systems are more evolvable than previously thought, encouraging further evolution-focused experiments.

The development of bimolecular homolytic substitution (SH2) catalysis has expanded cross-coupling logic by enabling the selective merger of any primary radical with any secondary or tertiary radical via a radical sorting mechanism. SH2 catalysis can be used to merge common feedstock chemicals—such as alcohols, acids, and halides—in any permutation for the construction of a single C(sp3)–C(sp3) bond. The ability to sort these two distinct radicals across commercially available alkenes in a three-component manner would enable the simultaneous construction of two C(sp3)–C(sp3) bonds, greatly accelerating access to drug-like chemical space. However, the simultaneous in situ formation of electrophilic and primary nucleophilic radicals in the presence of unactivated alkenes is problematic, typically leading to statistical radical recombination, hydrogen atom transfer, disproportionation, and other deleterious pathways. Herein, we report the use of bimolecular homolytic substitution catalysis to sort an electrophilic radical and a nucleophilic radical across an unactivated alkene. This reaction involves the in situ formation of three distinct radical species, which are then differentiated by size and electronics, allowing for regioselective formation of desired dialkylated products. This work accelerates access to pharmaceutically relevant C(sp3)-rich molecules and defines a novel mechanistic paradigm for alkene dialkylation.

‘Hidden’ catalysis plagues the development and understanding of all catalytic processes. Hidden acid catalysis and catalysis by trace metal contamination being two widely recognised examples. Since 2010, over 600 new catalysed hydroboration protocols have been reported despite the prevalence of hidden borane catalysis across hydroboration reactions using HBcat and HBpin. Nucleophilic species, present as either activators, additives or inherent to the catalyst structure, readily mediate the decomposition of HBpin and HBcat to boranes, including (ligated) BH3. These boranes are themselves catalysts for alkene and alkyne hydroboration, so often serve as the active, ‘hidden’, catalyst rather than the intended metal/metalloid species reported as a the ‘catalyst’. Following our introduction of the TMEDA test for hidden borane catalysis 2020, the proportion of catalysed hydroboration publications testing for hidden borane catalysis has increased from 5% to 23%, but this is still well short of routine. We now report, a simple, rapid and colourimetric method for the determination of hidden borane catalysis. This method uses nothing more than a colour change visible to the naked eye, akin to litmus paper acid/base indicators. The colourimetric test uses a bench-stable, widely commercially-available reagent, crystal violet, at low concentration to identify hidden borane catalysis in seconds. in situ BH3 formation from the decomposition of HBpin by species from across the periodic table has been positively identifed using this new test. The colourimetric indicator does inhibit the hydroboration reaction and shows no reactivity with substrates, HBpin, HBcat, nucleophilic species or any of the ‘catalysts’ tested. This test is easily applied to all past and future catalysed hydroboration reactions and represents the first example of a colour indicator for hidden catalysis.

Nature Chemical Biology, Published online: 20 November 2023; doi:10.1038/s41589-023-01484-2

Oxygen sensitivity hampers applications of metal-dependent CO2 reductases. Here, Oliveira et al. describe how an allosteric disulfide bond controls the activity of a CO2 reductase, preventing its physiological reduction during transient O2 exposure and allowing aerobic handling of the enzyme.

Short peptide-based amyloid nanotubes were able to demonstrate enantioselective covalent catalysis by exploiting chiral binding pockets with multiple solvent exposed residues. To achieve this, lysine was used for reversible imine formation, leucine for hydrophobic binding surface, and imidazole for the hydrolytic cleavage of the substrates.

Abstract

Extant enzymes with precisely arranged multiple residues in their three-dimensional binding pockets are capable of exhibiting remarkable stereoselectivity towards a racemic mixture of substrates. However, how early protein folds that possibly featured short peptide fragments facilitated enantioselective catalytic transformations important for the emergence of homochirality still remains an intriguing open question. Herein, enantioselective hydrolysis was shown by short peptide-based nanotubes that could exploit multiple solvent-exposed residues to create chiral binding grooves to covalently interact and subsequently hydrolyse one enantiomer preferentially from a racemic pool. Single or double-site chiral mutations led to opposite but diminished and even complete loss of enantioselectivities, suggesting the critical roles of the binding enthalpies from the precise localization of the active site residues, despite the short sequence lengths. This work underpins the enantioselective catalytic prowess of short peptide-based folds and argues their possible role in the emergence of homochiral chemical inventory.

Production of commodity chemicals from renewable resources is vital for a sustainable society. A non-natural three-enzyme cascade is reported for the one-pot conversion of biobased L-phenylalanine into ethylbenzene with up to 82 % conversion. The key enzyme, a photodecarboxylase, was semirationally engineered to boost productivity. The cascade was integrated with a fermentation process to yield ethylbenzene from biobased glycerol.

Abstract

Production of commodity chemicals, such as benzene, toluene, ethylbenzene, and xylenes (BTEX), from renewable resources is key for a sustainable society. Biocatalysis enables one-pot multistep transformation of bioresources under mild conditions, yet it is often limited to biochemicals. Herein, we developed a non-natural three-enzyme cascade for one-pot conversion of biobased l-phenylalanine into ethylbenzene. The key rate-limiting photodecarboxylase was subjected to structure-guided semirational engineering, and a triple mutant CvFAP(Y466T/P460A/G462I) was obtained with a 6.3-fold higher productivity. With this improved photodecarboxylase, an optimized two-cell sequential process was developed to convert l-phenylalanine into ethylbenzene with 82 % conversion. The cascade reaction was integrated with fermentation to achieve the one-pot bioproduction of ethylbenzene from biobased glycerol, demonstrating the potential of cascade biocatalysis plus enzyme engineering for the production of biobased commodity chemicals.

Crotonyl-CoA carboxylase/reductase (Ccr) is one of the fastest CO2 fixing enzymes and has become part of efficient artificial CO2-fixation pathways in vitro, paving the way for future applications. The underlying mechanism of its efficiency, however, is not completely understood. X-ray structures of different intermediates in the catalytic cycle reveal tetramers in a dimer of dimers configuration with two open and two closed active sites. Upon binding a substrate, this active site changes its conformation from the open to the closed state. It is challenging to predict how these coupled conformational changes will alter the CO2 binding affinity to the reaction's active site. To determine whether the open or closed conformations of Ccr affect CO2 binding to the active site, we performed all-atom molecular simulations of the various conformations of Ccr. The open conformation without a substrate showed the highest binding affinity. The CO2 binding sites are located near the catalytic relevant Asn81 and His365 residues and in an optimal position for CO2 fixation. Furthermore, they are unaffected by substrate binding, and CO2 molecules stay in these binding sites for a longer time. Longer times in these reactive binding sites facilitate CO2 fixation through the nucleophilic attack of the reactive enolate in the closed conformation. We have previously demonstrated that the Asn81Leu variant cannot fix CO2. Simulations of the Asn81Leu variant explain the loss of activity through the removal of the Asn81 and His365 binding sites. Overall, our findings show that the conformational dynamics of the enzyme control CO2 binding. Conformational changes in Ccr increase CO2 in the open subunit before the substrate is bound, the active site closes, and the reaction starts. The full catalytic Ccr cycle alternates between CO2 addition, conformational change, and chemical reaction in the four subunits of the tetramer coordinated by communication between the two dimers.

Flavoenzymes can mediate a large variety of oxidation reactions via the activation of oxygen. As such, the chemistry of flavoenzymes is an important field that has not yet attained its full scope/recognition. Normally, the O2 activation occurs at the C4a site of the flavin cofactor, yielding the flavin C4a-(hydro)hydroperoxyl species in monooxygenases or oxidases. Using extensive MD simulations, QM/MM calculations and QM calculations, our studies reveal the formation of the common nucleophilic species, flavin-N5OOH, in two distinct flavoenzymes (RutA and EncM). Our studies show that flavin-N5OOH acts as a powerful nucleophile that promotes C–N cleavage of uracil in RutA, and a powerful base in the deprotonation of substrates in EncM. We reason that flavin-N5OOH can be a common reactive species in the superfamily of flavoenzymes, which accomplishes the generally selective general base catalysis, and the C–X (X= N, S, Cl, O) cleavage reactions that are otherwise challenging by solvated hydroxide ion base. These results expand our understanding of the chemistry and catalysis of flavoenzymes.

A catalyst possessing a broad substrate scope, in terms of both turnover and enantioselectivity, is sometimes called “general”. Despite their great utility in asymmetric synthesis, truly general catalysts are difficult or expensive to discover via traditional high-throughput screening and are, therefore, rare. Existing computational tools accelerate the evaluation of reaction conditions from a pre-defined set of experiments to identify the most general ones, but cannot generate entirely new catalysts with enhanced substrate breadth. For these reasons, we report an inverse design strategy based on the open-source genetic algorithm NaviCatGA and on the OSCAR database of organocatalysts to simultaneously probe the catalyst and substrate scope and optimize generality as primary target. We apply this strategy to the Pictet–Spengler condensation, for which we curate a database of 820 reactions, used to train statistical models of selectivity and activity. Starting from OSCAR, we define a combinatorial space of millions of catalyst possibilities, and perform evolutionary experiments on a diverse substrate scope that is representative of the whole chemical space of tetrahydro-β-carboline products. While privileged catalysts emerge, we show how genetic optimization can address the broader question of generality in asymmetric synthesis, extracting structure–performance relationships from the challenging areas of chemical space.

Nature, Published online: 01 November 2023; doi:10.1038/s41586-023-06613-4

A new type of transformation converting a heteroaromatic carbon atom into a nitrogen atom, turning quinolines into quinazolines to enable manipulation of molecular properties, is reported.

Nature Chemistry, Published online: 16 November 2023; doi:10.1038/s41557-023-01368-x

The inherent rigidity of the azaarene ring structure has made it challenging to achieve remote stereocontrol through asymmetric catalysis on these substrates. Now, through a photoenzymatic process, an ene-reductase system facilitates the production of diverse azaarenes with distant γ-stereocentres, highlighting the potential of biocatalysts for stereoselectivity at remote sites.

Nature, Published online: 15 November 2023; doi:10.1038/s41586-023-06728-8

Evolution has produced a range of diverse proteins, and now a generative model called Chroma can expand that set by allowing the user to design new proteins and protein complexes with desired properties and functions.

Atroposelective metathesis catalyzed by artificial enzymes in aqueous solution would provide an attractive and sustainable route to drug molecules and other compounds of interest. We demonstrate that this is possible using artificial metalloenzymes harboring a ruthenium cofactor.

Abstract

Atropisomers – separable conformers that arise from restricted single-bond rotation – are frequently encountered in medicinal chemistry. However, preparing such compounds with the desired configuration can be challenging. Herein, we present a biocatalytic strategy for achieving atroposelective synthesis relying on artificial metalloenzymes (ArMs). Based on the biotin-streptavidin technology, we constructed ruthenium-bearing ArMs capable of producing atropisomeric binaphthalene compounds through ring-closing metathesis in aqueous media. Further, we show that atroposelectivity can be fine-tuned by engineering two close-lying amino acid residues within the streptavidin host protein. The resulting ArMs promote product formation with enantiomeric ratios of up to 81 : 19, while small-molecule catalysts for atroposelective metathesis under aqueous reaction conditions are yet unknown. This study represents the first demonstration that stereoselective metathesis can be achieved by an artificial metalloenzyme.

Aldolases are prodigious C-C bond forming enzymes, but their reactivity has only been extended past activated carbonyl electrophiles in special cases. We have used a pair of pyridoxal-phosphate-dependent aldolases to probe the mechanistic origins of this limitation. Our results reveal how aldolases are limited by thermodynamically favorable proton transfer with solvent, which undermines aldol addition into ketones. However, we show how a transaldolase can circumvent this limitation by protecting the enzyme-bound enolate from solvent protons and thereby enabling efficient addition into unactivated ketones. The resulting products are non-canonical amino acids with side chains that contain chiral tertiary alcohols. This study reveals the principles for extending aldolase catalysis beyond its previous limits and enables convergent, enantioselective C-C bond formation from simple starting materials.

Dinuclear monooxygenases mediate challenging C-H bond oxidation reactions throughout Nature. Many of these enzymes are presumed to exclusively utilize diiron cofactors. Herein, we report the bioinformatic discovery of an orphan dinuclear monooxygenase that preferentially utilizes a heterobimetallic manganese-iron (Mn/Fe) cofactor to mediate an O2 dependent C-H bond hydroxylation reaction. Unlike the structurally similar Mn/Fe-dependent monooxygenase AibH2, the diiron form of this enzyme (SfbO) exhibits nascent enzymatic activity. This behavior raises the possibility that many other dinuclear monooxygenases may be endowed with the capacity to harness cofactors with variable metal content.

Nucleosides functionalized at the 2′-position play a crucial role in therapeutics, serving as both small molecule drugs and modifications in therapeutic oligonucleotides. However, the synthesis of these molecules often presents significant synthetic challenges. In this study, we present an approach to the synthesis of 2′-functionalized nucleosides based on enzymes from the purine nucleoside salvage pathway. Initially active-site variants of DERA aldolase were generated for the highly stereoselective synthesis of D-ribose-5-phosphate analogs with a broad range of functional groups at the 2-position. Thereafter these 2-modified pentose phosphates were converted into 2′-modified purine analogs by construction of one-pot multi-enzyme cascade reactions, leading to the synthesis of guanosine (2′-OH) and adenosine (2′-OH, 2′-Me, 2′-F) analogues. Our findings demonstrate the capability of these biocatalytic cascades to efficiently generate 2′ functionalized nucleosides, starting from simple starting materials.