R.B. Leveson-Gower

Nature Communications, Published online: 21 April 2022; doi:10.1038/s41467-022-29900-6

Single atom catalysts have been described for efficient and selective metal catalysis, while enzymes have been known for their recognition and binding. In this manuscript, the authors develop a photochemical method to combine the two platforms in one, and demonstrate it by anchoring Pd atoms on Candida Antarctic lipase B, for highly efficient alkyl-alkyl cross-coupling reactions.

The benefits of publishing research papers first in preprint form are substantial and long-lasting also in chemistry. Recounting the outcomes of our team’s nearly six-year journey through preprint publishing, we show evidence of how preprinting research findings and new ideas substantially benefits both early career and senior researchers in the chemical sciences.

The arylthiol 4-mercaptophenylacetic acid (MPAA) is a powerful catalyst of selenosulfide bond reduction by the triarylphosphine 3,3′,3′′-phosphanetriyltris(benzenesulfonic acid) trisodium salt (TPPTS). Both reagents are water-soluble at neutral pH and are particularly adapted for working with unprotected peptidic substrates. Contrary to trialkylphosphines such as tris(2-carboxyethyl)phosphine hydrochloride (TCEP), TPPTS has the advantage of not inducing deselenization reactions. We believe that the work reported here will be of value for those manipulating selenosulfide bonds in peptidic or protein molecules.

Nowadays, many chemical investigations can be supported theoretically by routine molecular structure calculations, conformer ensembles, reaction energies, barrier heights, and predicted spectroscopic properties. Such standard computational chemistry applications are most often conducted with density functional theory (DFT) and atom-centered atomic orbital basis sets implemented in many standard quantum chemistry software packages. This work aims to provide general guidance on the various technical and methodological aspects of DFT calculations for molecular systems, and how to achieve an optimal balance between accuracy, robustness, and computational efficiency through multi-level approaches. The main points discussed are the density functional, the atomic orbital basis sets, and the computational protocol to describe and predict experimental behavior properly. This is done in three main parts: Firstly, in the form of a step-by-step decision tree to guide the overall computational approach depending on the problem; secondly, using a recommendation matrix that addresses the most critical aspects regarding the functional and basis set depending on the computational task at hand (structure optimization, reaction energy calculations, etc.); and thirdly, by applying all steps to some representative examples to illustrate the recommended protocols and effect of methodological choices.

The conversion of carboxylic acids to thioesters is a key step in the biosynthesis of natural products, resulting in activation of the acyl groups for subsequent reactions, e.g. acylation of nucleophiles including carbon-carbon bond formation. For example, thioesters of Coenzyme A (CoA-SH; e.g. acetyl-S-CoA) are intermediates in many metabolic pathways, and are increasingly recognised as important cofactors for epigenetic post-translational modifications, such as N-, O- and S-acylations of proteins. However, the limited availability of a broad range of structurally diverse thioesters has limited their wider exploitation in biochemistry, cell biology and biotechnology. Furthermore, the high cost of CoA-SH impairs its use in stoichiometric quantities. To address these challenges we show that the adenylation (A-) domain of the carboxylic acid reductase (CAR) from Segniliparus rugosus (CARsr-A) can function as a broad spectrum acyl-S-CoA synthetase, to generate acyl-S-CoA intermediates from a wide range of carboxylic acids. In addition, CARsr-A was able to generate thioesters from structurally simpler thiols such as pantetheine. The resulting thioesters were then used as substrates for acyltransferases to synthesise a wide range of amides, including the more difficult to prepare, but pharmaceutically relevant aryl amides. Importantly, CoA-SH is recycled during the reaction and can be used in sub-stoichiometric quantities. This approach has also been applied to acylate a histone peptide H4-20 with a range of carboxylic acids, including non-natural chemical labels, by employing a lysine acetyltransferase (HATp300). Overall, this combination of a broad spectrum biocatalyst for thioester synthesis, together with in-situ CoA-SH recycling, provides a generic platform for thioester-dependent cell-free synthesis, with potential applications beyond amide bond formation.

Base-metal catalyzed nitrene transfer reactions in water are challenging, but have the potential to broaden the range of applications. Typically, these reactions suffer from the formation of oxygen containing side-products, of which the origin is not fully understood. Therefore, we set out to investigate aqueous styrene aziridination, using a water-soluble [Co^III(TAML^red)]– catalyst known to be active in radical-type nitrene transfer in organic solvents. The cobalt-catalyzed aziridination of styrene in water (pH = 7) yielded styrene oxide as the major product, next to minor amounts of aziridine. Based on 18O-labeling studies and catalysis experiments, we show that styrene oxide formation proceeds via hydrolysis of the nitrene-radical complex [Co^III(TAMLsq)(N•Ts)]–. Computational studies support that this process is facile and yields an oxyl-radical complex [Co^III(TAML^sq)(O•)]–, which is active in oxygen atom transfer to styrene. Based on these mechanistic insights, the pH was adjusted to afford selective aziridination in water.

Nature, Published online: 06 April 2022; doi:10.1038/s41586-022-04458-x

A biocatalytic enzyme originating from bacteria, EneIRED, facilitates amine-activated conjugate alkene reduction followed by reductive amination, efficiently preparing chiral amine diastereomers, which are commonly used in pharmaceuticals and agrochemicals.

Nature, Published online: 06 April 2022; doi:10.1038/d41586-022-00946-2

After controlling for importance, analysis finds that papers with funnier titles get more citations. But some researchers question these results.

Flavin-tag 2.0: The Flavin-tag method can be used for labelling of proteins with various chromo- and fluorophores and redox-active probes, including flavin (yellow), roseoflavin (red), 5-deazaflavin (fluorescent), and nicotinamide.

Abstract

Methods for facile site-selective modifications of proteins are in high demand. We have recently shown that a flavin transferase can be used for site-specific covalent attachment of a chromo- and fluorogenic flavin (FMN) to any targeted protein. Although this Flavin-tag method resulted in efficient labeling of proteins in vitro, labelling in E. coli cells resulted in partial flavin incorporation. It was also restricted in the type of installed label with only one type of flavin, FMN, being incorporated. Here, we report on an extension of the Flavin-tag method that addresses previous limitations. We demonstrate that co-expression of FAD synthetase improves the flavin incorporation efficiency, allowing complete flavin-labeling of a target protein in E. coli cells. Furthermore, we have found that various flavin derivatives and even a nicotinamide can be covalently attached to a target protein, rendering this method even more versatile and valuable.

Reviews are more important today than ever. With the glut of new publications, it has become increasing difficult to read all original papers in detail. So, scientists usually first get an overview from reviews. In the review on “Cyanine Dyes Containing Quinoline Moieties: History, Synthesis, Optical Properties and Applications” (Chem Eur. J. 2021, 27, 2430), some aspects were incorrectly described and discussed. This correspondence tries to clarify some basics that have been presented insufficiently in the review.

Abstract

In the review on “Cyanine Dyes Containing Quinoline Moieties: History, Synthesis, Optical Properties and Applications” (K. Ilina, M. Henary, Chem Eur. J. 2021, 27, 2430; https://doi.org/10.1002/chem.202003697), some essential aspects were incorrectly described and discussed. To avoid further confusion, this correspondence tries to clarify both the structures and the history of some cyanine and apocyanine dyes that were not presented sufficiently.

Nature Chemistry, Published online: 04 April 2022; doi:10.1038/s41557-022-00895-3

A straightforward method for synthesizing optically active α-amino acids from abundant carboxylic acids has been developed. Based on a nitrene-mediated stereocontrolled 1,3-nitrogen shift, this approach provides access to a large variety of unnatural α-amino acids with aryl, allyl, propargyl and alkyl side chains and enables late-stage amination of carboxylic-acid-containing drugs.

Nature Communications, Published online: 01 April 2022; doi:10.1038/s41467-022-29464-5

Photocatalytic radical cascade reactions enable the facile construction of diverse cyclic compounds, though they rely on templated precursors. In this paper, the authors report on stereoselective intermolecular radical cascade reaction between tryptophan or ɤ-alkenyl substituted amino acids and acrylamides to synthesise multi-substituted trans-fused hexahydrocarbazoles or 1,3,5-trisubstituted cyclohexanes.

An efficient protocol to produce Pretomanid is proposed and studied. The stereodetermining step of the proposed synthesis a ketone reduction by a ketoreductase. However, the unexpected stability of the ketal intermediate.

Using a phylogenetic tree-building approach, five novel tyrosine ammonia lyases (TALs) and three novel phenylalanine/tyrosine ammonia lyases (PTALs) were identified. The enzymes were biochemically characterized and the optimal conditions for a whole cell E. coli biotransformation were determined. Under these conditions p-coumaric acid (p-CA) yields of 2.03 g/L after 8 hours by TAL _clu and 2.35 g/L after 24 hours by TAL _rpc could be achieved.

Abstract

p-Coumaric acid (p-CA) is a key precursor for the biosynthesis of flavonoids. Tyrosine ammonia lyases (TALs) specifically catalyze the synthesis of p-CA from l-tyrosine, which is a convenient enzymatic pathway. To explore novel and highly active TALs, a phylogenetic tree-building approach was conducted including 875 putative TALs and 46 putative phenylalanine/tyrosine ammonia lyases (PTALs). Among them, 5 TALs and 3 PTALs were successfully characterized and found to exhibit the proposed enzymatic activity. The TAL from Chryseobacterium luteum sp. nov (TAL _clu ) has the highest affinity (K _m =0.019 mm) and conversion efficiency (k _cat/K _m= 1631 s⁻¹ ⋅ mm ⁻¹) towards l-tyrosine. The reaction conditions for two purified enzymes and their E. coli recombinant cells were optimized and p-CA yields of 2.03 g/L after 8 hours by TAL _clu and 2.35 g/L after 24 h by TAL from Rivularia sp. PCC 7116 (TAL _rpc ) in whole cells were achieved. These TALs are thus candidates for the construction of whole-cell systems to produce the flavonoid precursor p-CA.

Catalytic regioselective C−H silylation of a variety of aromatic heterocycles such as thiophene, furan and indole derivatives with secondary hydrosilanes was achieved by using a calcium catalyst. This protocol provides an efficient route to the synthesis of silylated heteroaromatic compounds without the need for an H₂ acceptor and free of transition metal. Calcium thiophenyl complex (2), proposed as the catalytic reaction intermediate, was isolated and structurally characterized.

Abstract

Treatment of mononuclear calcium hydride complex [(Tp^Ad,iPr)Ca(H)(THP)] (1) (Tp^Ad,iPr=hydrotris(3-adamantyl-5-isopropyl-pyrazolyl)borate, THP=tetrahydropyran) with 2-methylthiophene, 2-methylfuran, and 1-methyl-1H-indole in THF/hexane solution led to the formation of calcium thiophenyl (2), furanyl (3), and indolyl (4) complexes, via sp² C−H bond activation. The reaction of complex 1 with 2-methylpyridine and quinoline afforded calcium benzyl pyridinyl (5) and 1,2-dihydroquinolide (6) complexes, through sp³ C−H bond activation and hydride insertion reaction, respectively. Under mild conditions, the catalytic regioselective sp² C−H silylation of a series of aromatic heterocycles with secondary hydrosilane was achieved by the use of complex 1. This protocol offers a straightforward method for the synthesis of silylated heteroaromatic compounds without a hydrogen acceptor and free of transition metal.

The intrinsic resilience of biofilms to environmental conditions makes them an attractive plat-form for biocatalysis, bioremediation, agriculture or consumer health. However, one of the main challenges in these areas is that beneficial bacteria are not necessarily good at biofilm formation. Currently, this problem is solved by genetic engineering or experimental evolution, techniques that can be costly and time consuming, require expertise in molecular biology and/or microbiolo-gy and, more importantly, are not suitable for all types of microorganisms or applications. Here we show that synthetic polymers can be used as an alternative, working as simple additives to nucleate the formation of biofilms. Using MC4100, a strain of Escherichia coli that forms bio-films poorly, we demonstrate that hydrophobic polymers induce clustering and promote biofilm formation in this bacterium, with increasingly hydrophobic polymers outperforming less hydro-phobic polymers. Moreover, we compare the effect of the polymers on MC4100 against PHL644, an E. coli strain that forms biofilms well due to a single point mutation which increases expres-sion of the adhesin curli. In the presence of selected polymers MC4100 can reach levels of bio-mass production and curli expression similar or higher than PHL644, demonstrating that syn-thetic polymers promote similar changes in microbial physiology than those introduced following genetic modification. Finally, we demonstrate that these polymers can be used to improve the performance of MC4100 biofilms in the biocatalytic transformation of 5-fluoroindole into 5-fluorotryptophan. Our results show that incubation with these synthetic polymers helps MC4100 match and even outperform PHL644 in this biotransformation, demonstrating that synthetic polymers can underpin the development of beneficial applications of biofilms.