R.B. Leveson-Gower

This investigation demonstrates that the appropriate positioning of a customized boronic acid probe into a sialic acid binding epitope leverages a selective and potent binder of sialyl-glycan. Such synergistic peptide probe is promising in clinical oncology for diagnosis.

Abstract

Boronic acid-containing molecules are substantially popularized in chemical biology and medicinal chemistry due to the broad spectrum of covalent conjugations as well as interaction modules offered by the versatile boron atom. Apparently, the WGA peptide (wheat germ agglutinin, 62–73), which shows a considerably low binding affinity to sialic acid, turned into a selective and >5 folds potent binder with the aid of a suitable boronic acid probe installed chemoselectively. In silico studies prompted us to install BA probes on the cysteine residue, supposedly located in close proximity to the bound sialic acid. In vitro studies revealed that the tailored boronopeptides show enhanced binding ability due to the synergistic recognition governed by selective non-covalent interactions and cis-diol boronic acid conjugation. The intense binding is observed even in 10 % serum, thus enabling profiling of sialyl-glycan on cancer cells, as compared with the widely used lectin, Sambucus nigra. The synergistic binding mode between the best boronopeptide (P3) binder and sialic acid was analyzed via ¹H and ¹¹B NMR.

An M9 minimum media based on ¹³C-depleted glucose and ¹⁵N-depleted salt dissolved in D,¹⁸O-depleted water (Depleted media) was formulated. E. coli bacteria grow faster in Depleted media compared with isotopically natural media (Normal media). In addition, four different enzymes recombinantly produced in Depleted media showed faster kinetics compared with the enzymes produced in Normal media.

Abstract

Inorganic materials depleted of heavy stable isotopes are known to deviate strongly in some physicochemical properties from their isotopically natural counterparts. Here we explored for the first time the effect of simultaneous depletion of the heavy carbon, hydrogen, oxygen and nitrogen isotopes on the bacterium E. coli and the enzymes expressed in it. Bacteria showed faster growth, with most proteins exhibiting higher thermal stability, while for recombinant enzymes expressed in depleted media, faster kinetics was discovered. At room temperature, luciferase, thioredoxin and dihydrofolate reductase and Pfu DNA polymerase showed up to a 250 % increase in activity compared to the native counterparts, with an additional ∼50 % increase at 10 °C. Diminished conformational and vibrational entropy is hypothesized to be the cause of the accelerated kinetics. Ultralight enzymes may find an application where extreme reaction rates are required.

Nature Chemical Biology, Published online: 07 December 2023; doi:10.1038/s41589-023-01495-z

Macrocyclic peptides are promising scaffolds for chemical tools and potential therapeutics, but their synthesis is currently difficult. Here, the authors report the characterization of Ulm16, a peptide cyclase of the penicillin-binding protein (PBP)-type class of thioesterases, that catalyzes head-to-tail macrolactamization of nonribosmal peptides of 4–6 amino acids in length.

Nature Catalysis, Published online: 06 December 2023; doi:10.1038/s41929-023-01068-2

Chiral lactams are important pharmacophores and strategies for their synthesis through direct C–H functionalization are highly sought after. Now, intramolecular C–H amidation of dioxazolones via biocatalytic nitrene transfer enables the synthesis of enantioenriched lactams with various ring sizes.

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.

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 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.