R.B. Leveson-Gower

Nature Chemical Biology, Published online: 11 July 2022; doi:10.1038/s41589-022-01070-y

A combination of engineering a fluorine-selective trans-acyltransferase and manipulation of the fluorinated extender unit pool in Escherichia coli enables the production of site-selectively fluorinated erythromycin precursors in vitro in vitroin vitro and in vivo.

Nature, Published online: 11 July 2022; doi:10.1038/d41586-022-01894-7

The UK government must stop picking fights with universities and reset the country’s relationship with the European Union.

Stapling of peptides renders them ideal drug candidates. The individual characteristics of synthetic staple moities impact directly on the peptide’s final properties. We report a bioinspired ketenamine-based peptide staple resembling the natural metabolite lanthionine ketenamine. The strategy is orthogonal to most canonical amino acids, proceeds in water and allows for tailored linkers.

Nature, Published online: 07 July 2022; doi:10.1038/d41586-022-01878-7

Maya Gosztyla decided to rethink her approach to research papers after she had trouble keeping track of the published literature.

Directed evolution is an enzyme engineering approach based on the generation and screening of large mutagenesis libraries, with a view to discovering enzymes with improved properties such as activity, specificity or stability. Recently, droplet-based microfluidics has emerged as a powerful technology enabling ultra-high throughput screening of enzyme libraries and the effective identification and isolation of novel, improved enzyme variants, outperforming conventional enzyme screening platforms by several orders of magnitude in terms of speed and chemical consumption. When using droplet-based platforms fluorescence remains the predominant choice for detection of enzymatic activity due to its high sensitivity and low limits of detection. However, this approach often requires the use of labeled, non-natural substrates, which are typically not commercially available. In addition, fluorescence detection is only suitable for a few enzyme classes such as hydrolases or oxidases, whose reactions can often lead to a fluorescent signal. Herein, we describe an assay that enables fluorescence detection of enzymatic activity through a reaction cascade for the industrially important enzyme subclass of dehydrogenases. By applying a hydrogen peroxide-forming NADH oxidase coupled with peroxidase-catalyzed fluorescence generation, quantification of NADH and dehydrogenase activity becomes possible. We explored the utility of this assay in the evolution of a low performing alcohol dehydrogenase from Sphingomonas species A1 (SpsADH). A fluorescence-activated droplet sorting (FADS) platform was utilized for the screening of a 50,000 variant SpsADH library towards the non-native substrate L-guluronate, a primary component of macroalgae, with the potential to serve as raw material for the bio-based production of chemicals. Significantly, we found an enzyme variant with a 2.6-fold improvement in catalytic efficiency kcat/Km towards the non-native substrate, with only a single round of mutagenesis. The screening of SpsADH libraries confirms the ability of the developed method to enrich active enzyme variants.

Halohydrin dehalogenases are promiscuous biocatalysts, which enable asymmetric ring opening reactions of epoxides with various anionic nucleophiles. However, despite the increasing interest in such asymmetric transformations, the substrate scope of G-type halohydrin dehalogenases toward cyclic epoxides has remained largely unexplored, even though this family is the only one known to display activity with these sterically demanding substrates. Herein, we report on the exploration of the substrate scope of the two G-type halohydrin dehalogenases HheG and HheG2 and a newly identified, more thermostable member of the family, HheG3, with a variety of sterically demanding cyclic epoxides and anionic nucleophiles. This work shows that, in addition to azide and cyanide, these enzymes facilitate ring-opening reactions with cyanate, thiocyanate, formate, and nitrite, significantly expanding the known repertoire of accessible transformations.

Computational approaches to organocatalysis: This review is focused on the different computational approaches that have been applied within the organocatalysis field. A huge effort from the theoretical chemistry field has been made in order to prove that de novo design of effective catalysts for different types of reactions is a long-term target, yet a palpable phenomenon.

Abstract

It is clear that the field of organocatalysis is continuously expanding during the last decades. With increasing computational capacity and new techniques, computational methods have provided a more economic approach to explore different chemical systems. This review offers a broad yet concise overview of current state-of-the-art studies that have employed novel strategies for catalyst design. The evolution of the all different theoretical approaches most commonly used within organocatalysis is discussed, from the traditional approach, manual-driven, to the most recent one, machine-driven.

A de novo molecular design workflow can be used together with technologies such as reinforcement learning to navigate the chemical space. A bottleneck in the workflow that remains to be solved is how to integrate human feedback in the exploration of the chemical space to optimize molecules. A human drug designer still needs to design the goal, expressed as a scoring function for the molecules that captures the designer’s implicit knowledge about the optimization task. Little support for this task exists and, consequently, a chemist usually resorts to iteratively building the objective function of multi-parameter optimization (MPO) in de novo design. We propose a principled approach to use human-in-the-loop machine learning to help the chemist to adapt the MPO scoring function to better match their goal. An advantage is that the method can learn the scoring function directly from the user’s feedback while they browse the output of the molecule generator, instead of the current manual tuning of the scoring function with trial and error. The proposed method uses a probabilistic model that captures the user’s idea and uncertainty about the scoring function, and it uses active learning to interact with the user. We present two case studies for this: In the first use-case, the parameters of an MPO are learned, and in the second use-case a non-parametric component of the scoring function to capture human domain knowledge is developed. The results show the effectiveness of the methods in two simulated example cases with an oracle, achieving significant improvement in less than 200 feedback queries, for the goals of a high QED score and identifying potent molecules for the DRD2 receptor, respectively. We further demonstrate the performance gains with a medicinal chemist interacting with the system.

Nature, Published online: 30 June 2022; doi:10.1038/d41586-022-01764-2

Two viruses that cause tropical diseases manipulate their hosts into emitting more of a mosquito-attracting molecule.

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.

Nature, Published online: 29 June 2022; doi:10.1038/d41586-022-01792-y

Scientists in Thailand have established that a tabby passed SARS-CoV-2 to a veterinary surgeon — although such cases of cat-to-human transmission are probably rare.

During efforts to explore the range of reactions catalyzed by the previously-engineered B12-dependent enzyme CarH*, we found that this enzyme catalyzes N-alkylation of aniline using ethyl diazoacetate but that B12 itself provides only trace conversion for this reaction. This observation suggested that the unique primary and second coordination sphere provided by CarH* accelerates non-native N-alkylation catalysis and that other B12-dependent proteins could provide further improvements in activity. We used a structural homology search to identify the corrinoid protein MtaC, which was reconstituted with B12 to generate a catalyst with significantly-improved aniline N-alkylation activity on a range of substrates. MtaC also displays remarkable thermal stability and organic solvent tolerance, remaining folded even in pure methanol. These results highlight how protein scaffolds can be used to impart new activity and other beneficial properties to metal catalysts and suggest that MtaC could serve as a useful platform for non-native B12 catalysis.

A route involving both enzymatic and spontaneous chemical reactions was designed for the synthesis of L-homophenylalanine from inexpensive building blocks. One enzyme in the cascade, EcQOR, was identified as the first ene reductase to catalyze the reduction of an unsaturated aromatic keto acid. This study shows the potential of introducing spontaneous chemical reactions into enzymatic cascades for the synthesis of valuable chemicals.

Abstract

L-Homophenylalanine (L-HPA) is a vital building block for the synthesis of numerous chiral drugs. However, the high cost of starting materials limits the industrial production of L-HPA. In this study, an enzymatic-spontaneous chemical cascade route for L-HPA production was designed based on retrosynthetic analysis. This route, using simple benzaldehyde and pyruvate as starting materials, is extremely cost-effective. The enzymes were screened and further assembled in E. coli, and TipheDH was identified as the rate-limiting enzyme. Therefore, TipheDH was engineered to improve its specific activity (by 82 %) and expression level (by 254 %), thus generating the best strain (W14). W14 exhibited the optimum enzyme activity ratio (1.7 : 1.1 : 1 : 1.8) and demonstrated production of 100.9 g L⁻¹ of L-HPA (with 94 % conversion, >99 % ee) in a 5-L reactor. This route effectively exploits the power of cascades and offers insight into avenues for synthesizing other valuable chemicals from inexpensive building blocks.

Nature Chemical Biology, Published online: 27 June 2022; doi:10.1038/s41589-022-01068-6

Several venomous predators and pathogens use insulins to capture prey and to manipulate host physiology. This Review provides an overview of the discovery and potential biomedical application of these and other weaponized hormones found in nature.

Nature Chemical Biology, Published online: 27 June 2022; doi:10.1038/s41589-022-01054-y

Sea stars and sea cucumbers biosynthesize protective glycosylated steroids and triterpenes via divergent oxidosqualene cyclases (OSCs) that produce these distinct saponins in different species as well as in different tissues of a single species.

Nature Catalysis, Published online: 24 June 2022; doi:10.1038/s41929-022-00799-y

Although pyrene-containing molecules have been studied for their optical properties, the outcome of their incorporation into mechanically interlocked structures remains underexplored. Here, the authors install pyrene units into homo[2]catenanes and investigate the formation of long-lived triplet states, which can be exploited for photocatalysis.

Come together: Asymmetric aminocatalysis plays a pivotal role on the development in stereoselective transformations, synergistically combined with organo-, metal, photoredox and electrocatalysis. In this scenario, the HOMO-raising and LUMO-lowering activation of carbonyl compounds open new gateways to complex architectures and new sustainable reactivities. Last but not least, this research area will keep driving the development of the whole organocatalysis, toward its synergistic combination with other activation strategies.

Abstract

Synergistic catalysis offers the unique possibility of simultaneous activation of both the nucleophile and the electrophile in a reaction. A requirement for this strategy is the stability of the active species towards the reaction conditions and the two concerted catalytic cycles. Since the beginning of the century, aminocatalysis has been established as a platform for the stereoselective activation of carbonyl compounds through HOMO-raising or LUMO-lowering. The burgeoning era of aminocatalysis has been driven by a deep understanding of these activation and stereoinduction modes, thanks to the introduction of versatile and privileged chiral amines. The aim of this review is to cover recent developments in synergistic strategies involving aminocatalysis in combination with organo-, metal-, photo-, and electro-catalysis, focusing on the evolution of privileged aminocatalysts architectures.

Ecotoxicity: Organocatalysis is a widely used method of green and sustainable chemistry. The toxicity of a library of selected organocatalysts is determined, and it is found that aminocatalysts are of low ecotoxicity, but thioureas and squaramides prove about 10-fold more toxic. Thus, the latter compounds may be harmful to the environment and need more thorough (eco)toxicological evaluation.

Abstract

The importance of asymmetric organocatalysis in contemporary organic synthesis is widely acknowledged. However, there are practically no data on the environmental safety of organocatalysts, although this aspect is crucial for the sustainability of all new materials, chemicals, and technologies. To start to fill this data-gap, a library of 26 organocatalysts containing hydrogen-bonding catalysts [(thio)ureas and squaramides] and aminocatalysts (primary or secondary amines) was evaluated for their toxicity using the naturally luminescent Vibrio fischeri bacteria (ISO assay; one of the most widely used ecotoxicity tests). Thioureas and squaramides were shown to be relatively toxic: none of them was ranked as “not harmful” (i. e., half maximal effective concentration EC₅₀>100 mg L⁻¹), whereas the presence of the trifluoromethyl moiety increased their toxic effect. Importantly, the aminocatalysts, whose EC₅₀ values ranged from 25 to >300 mg L⁻¹, could be considered remarkably more environmentally safe or green alternatives.

The combination of small molecule catalysis and enzyme catalysis represents an underexploited area of research with huge potential in asymmetric synthetic chemistry due to both compatibility in reaction conditions and complementary reactivity. In this manuscript, we describe the telescopic synthesis of chiral nitro alcohols starting from commercially available benzaldehyde derivatives via the one-pot three-step chemoenzymatic cascade combination of a Wittig reaction, chiral thiourea-catalysed asymmetric conjugate addition, and a ketoreductase-mediated reduction to access the corresponding target compounds in moderate to excellent overall isolated yields (36-80%) and high diastereomeric and enantiomeric ratios (up to >97:3). This represents the first example of the combination of an organocatalysed asymmetric conjugate addition via iminium ion activation and a bioreduction step catalysed by ketoreductases.