R.B. Leveson-Gower

Nature Communications, Published online: 09 July 2024; doi:10.1038/s41467-024-50141-2

Exploring the promiscuity of native enzymes is a promising strategy for expanding their synthetic applications. Here, the authors show that old yellow enzymes (OYEs) can facilitate the Morita-Baylis-Hillman reaction (MBH reaction), leveraging substrate similarities between MBH reaction and reduction, and engineer GkOYE.8 with no reduction activity, but enhanced MBH activity.

Nature Chemistry, Published online: 19 July 2024; doi:10.1038/s41557-024-01562-5

Although natural terpenoid cyclases generate polycyclic structures through cationic intermediates, alternative radical cyclization pathways are underexplored. Now an artificial radical cyclase has been prepared by anchoring a biotinylated cobalt Schiff-base complex within a chimeric streptavidin scaffold. Chemogenetic optimization of the catalytic performance affords enantioenriched terpenoids via a metal-catalysed H-atom transfer mechanism.

The catalytic repertoire of nature has been expanded over the past decades by the introduction of artificial metalloenzymes. These are enzymes containing a synthetic metal complex or a non-native metal ion. However, combining noble metal catalysis and enzymes remains challenging due to the lack of suitable ligands to bind these complexes. So far, noble metal artificial metalloenzyme design mostly involves in vitro approaches of ligand anchoring, like covalent modification of a cysteine residue or via supramolecular assembly. Here, we show a facile strategy to anchor a variety of 4d and 5d-transition metal complexes via genetic incorporation of a thiophenolic metal-binding ligand. We created a methodology to efficiently incorporate 4-mercaptophenylalanine in a protein scaffold using the stop codon suppression technology. The incorporated non-canonical amino acid was capable of binding a variety of noble metal complexes. To showcase the catalytic applications of this methodology, we developed an artificial hydroaminase by binding gold ions to the thiophenol-containing protein. The benefit of in vivo incorporation of the ligand is demonstrated by the susceptibility of catalytic activity to the microenvironment around the metal site, which can be modulated by changing the position of the ligand within the protein or by mutation of residues in its proximity.

Artificial enzymes that operate with pnictogen bonds or σ-hole interactions in general are introduced: Transfer hydrogenation of quinolines accelerates with biotinylated pnictogen-bonding cofactors and their interfacing with streptavidin and mutants, shows saturation behavior with transition-state recognition three orders of magnitude beyond substrate recognition, and the emergence of stereoselectivity.

Abstract

The objective of this study was to create artificial enzymes that capitalize on pnictogen bonding, a σ-hole interaction that is essentially absent in biocatalysis. For this purpose, stibine catalysts were equipped with a biotin derivative and combined with streptavidin mutants to identify an efficient transfer hydrogenation catalyst for the reduction of a fluorogenic quinoline substrate. Increased catalytic activity from wild-type streptavidin to the best mutants coincides with the depth of the σ hole on the Sb(V) center, and the emergence of saturation kinetic behavior. Michaelis–Menten analysis reveals transition-state recognition in the low micromolar range, more than three orders of magnitude stronger than the millimolar substrate recognition. Carboxylates preferred by the best mutants contribute to transition-state recognition by hydrogen-bonded ion pairing and anion-π interactions with the emerging pyridinium product. The emergence of challenging stereoselectivity in aqueous systems further emphasizes compatibility of pnictogen bonding with higher order systems catalysis.

“If I could be granted a superpower, it would be the ability to fluently speak and understand every language (especially German) in the world because it would allow me to connect with people from all cultures and backgrounds … My group has fun by challenging each other in basketball matches, fostering friendly competition and team spirit both in and out of the lab …” Find out more about Babis Pappas in his Introducing… Profile.

Medicinal chemists in the modern era are targeting molecules with greater complexity to address increasingly challenging biological targets, a drive to enhance on-target specificity as well as physiochemical properties. As such, structures with greater fraction sp3 (Fsp3) character, reminiscent to those found in nature, are being synthesized. Many decades of synthetic methodology development have democratized access to flat, high sp2 (for example biaryl linkages) which has led to the commercialization of innumerable medicines. Those approaches rely heavily on electrophilic aromatic substitution (such as halogenation) followed by Pd-based cross coupling. In contrast, methods and strategies that allow for similarly modular and rapid construction of three-dimensional saturated molecules are less well developed. Here we exemplify a new approach for the rapid, modular, enantioselective construction of piperidine frameworks (the saturated analog of pyridine) that combines robust, tunable, and scalable biocatalytic methods with the logic of radical cross coupling. Thus, a set of reliable enzymatic systems (analogous to site-selective aromatic functionalization) provides scalable access to enantiopure hydroxyacid- containing piperidine derivatives that can be utilized to dramatically simplify routes to medicinally important molecules and natural products by employing recently developed electrocatalytic couplings (analogous to Pd-based cross couplings in aromatic systems). This study points to a different approach to rapidly access complex architectures that may appeal to both medicinal and process chemists alike.

Nature, Published online: 26 June 2024; doi:10.1038/d41586-024-02105-1

Prioritizing family life has earned me respect in my field — and my research has improved, too, says Dritjon Gruda.

Nature, Published online: 19 June 2024; doi:10.1038/s41586-024-07601-y

A deep learning approach enables accurate computational design of soluble and functional analogues of membrane proteins, expanding the soluble protein fold space and facilitating new approaches to drug screening and design.

The remarkable efficiency with which enzymes catalyze small molecule reactions has driven their widespread application in organic chemistry. Here, we employ automated fast-flow solid-phase synthesis to access full-length enzymes without restrictions on the number and structure of non-canonical amino acids incorporated. We demonstrate the total syntheses of Fe-dependent Bacillus subtilis myoglobin (BsMb) and sperm whale myoglobin (SwMb), which displayed excellent enantioselectivity and yield in carbene transfer reactions. Absolute control over enantioselectivity in styrene cyclopropanation was achieved using L- and D-BsMb mutants which delivered each enantiomer of cyclopropane product in identical and opposite enantiomeric enrichment. BsMb mutants outfitted with non-canonical amino acids were used to facilitate detailed structure-activity relationship studies, revealing a previously unrecognized hydrogen-bonding interaction as the primary driver of enantioselectivity in styrene cyclopropanation.

The discovery of small-molecule agents for chemical biology and therapeutic applications depends upon the ability to access and explore new biologically relevant regions of chemical space, a goal often pursued through diversity-oriented synthesis (DOS). In this report, we describe the design and implementation of P450-mediated chemoenzymatic diversity-oriented synthesis (CeDOS), a strategy that leverages chemo- and regiodivergent P450-catalyzed oxyfunctionalizations as key steps for enabling the synthesis of complex molecules that resemble natural products, a major source of bioactive molecules and drugs. Using this strategy, a library of over 50 novel and structurally diverse natural product-like compounds was generated through skeletal rearrangement and diversification of a plant-derived terpene via divergent chemoenzymatic routes enabled by selective C–H hydroxylation and epoxidation reactions catalyzed by engineered P450s. This CeDOS library encompass many unique and unprecedented organic scaffolds, many of which were determined to exhibit notable cytotoxicity against human cancer cells as well as diversified anticancer activity profiles. This work demonstrates the power of the present chemoenzymatic diversity-oriented synthesis strategy for directing the construction and discovery of novel bioactive molecules and it offers a blueprint for the broader application of this approach toward the creation and exploration of natural product-like chemical libraries.

Nature Catalysis, Published online: 29 May 2024; doi:10.1038/s41929-024-01176-7

A boronic enzyme

Nature Catalysis, Published online: 29 May 2024; doi:10.1038/s41929-024-01163-y

The understanding of protein evolution is a central challenge in biology. Now, the evolution of a β-lactamase in vitro reveals that the total effect of mutations can change the rate-limiting step of the catalytic mechanism.

Highly stereoselective Michael addition of cyclic ketones to nitroolefins was promoted by a designer artificial enzyme harboring a catalytic pyrrolidine residue through enamine catalysis. Diverse chiral γ-nitroketones were prepared by this efficient biocatalytic strategy for ketone functionalization in a study highlighting the utility of artificial enzymes for new-to-nature reactions.

Abstract

Consistent introduction of novel enzymes is required for developing efficient biocatalysts for challenging biotransformations. Absorbing catalytic modes from organocatalysis may be fruitful for designing new-to-nature enzymes with novel functions. Herein we report a newly designed artificial enzyme harboring a catalytic pyrrolidine residue that catalyzes the asymmetric Michael addition of cyclic ketones to nitroolefins through enamine activation with high efficiency. Diverse chiral γ-nitro cyclic ketones with two stereocenters were efficiently prepared with excellent stereoselectivity (up to 97 % e.e., >20 : 1 d.r.) and good yield (up to 86 %). This work provides an efficient biocatalytic strategy for cyclic ketone functionalization, and highlights the usefulness of artificial enzymes for extending biocatalysis to further non-natural reactions.

Science, Volume 384, Issue 6698, Page 858-859, May 2024.

Nature Chemical Biology, Published online: 14 May 2024; doi:10.1038/s41589-024-01619-z

Biochemical pathways for aromatic amino acid synthesis are ancient and highly conserved. Directed evolution of the β-subunit of tryptophan synthase (TrpB)—a proficient biocatalyst that converts indole to l-tryptophan—enabled this enzyme to make l-tyrosines from phenols, a pathway not (yet) known in nature.

Nature, Published online: 08 May 2024; doi:10.1038/s41586-024-07391-3

A completely genetically encoded boronic-acid-containing designer enzyme was created and characterized using X-ray crystallography, high-resolution mass spectrometry and 11B NMR spectroscopy, allowing chemistry that is unknown in nature and currently not possible with small-molecule catalysts.

Nature, Published online: 02 May 2024; doi:10.1038/s41586-024-07474-1

A deconstruction-reconstruction strategy for pyrimidine diversification

a-Tertiary amino acids are essential components of drugs and agrochemicals, yet traditional syntheses are step-intensive and provide access to a limited range of structures with vary-ing levels of enantioselectivity. Here, we report the α-alkylation of unprotected alanine and glycine by pyridinium salts using pyridoxal (PLP)-dependent threonine aldolases with a Rose Bengal photoredox catalyst. The strategy efficient-ly prepares various a-tertiary amino acids in a single chemical step as a single enantiomer. UV-vis spectroscopy studies re-veal a ternary interaction between the pyridinium salt, pro-tein, and photocatalyst, which we hypothesize is responsible for localizing radical formation to the protein active site. This method highlights the opportunity for combining photoredox catalysts with enzymes to reveal new catalytic functions for known enzymes.

Science, Volume 384, Issue 6695, Page 496-497, May 2024.

Nature Catalysis, Published online: 03 May 2024; doi:10.1038/s41929-024-01149-w

Direct stereoselective amination of tertiary C–H bonds without the assistance of directing groups is a challenging task in synthetic organic chemistry. Now a nitrene transferase is engineered to aminate tertiary C–H bonds with high enantioselectivity, providing direct access to valuable chiral α-tertiary primary amines.