Braca

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.

Efficient drug discovery relies on accessing diverse small molecules expediently and reliably. Improvements to reliability through machine learning predictions are hampered by poor availability of high-quality reaction data. Here, we introduce an on-demand synthesis platform based on a three-component reaction that delivers drug-like molecules overnight. Miniaturization and automation enable the execution and analysis of 50,000 reactions on a 3 microliter scale with distinct substrates, producing the largest public reaction outcome dataset. With machine learning, we accurately predict the result of unknown reactions and analyze the impact of data set size on model training. This study advances the on-demand synthesis of drug-like molecules through concatenating chemoselective reactions and provides a sufficiently large data set to critically evaluate emerging machine learning approaches to predicting chemical reactivity.

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 Communications, Published online: 14 May 2024; doi:10.1038/s41467-024-48350-w

The direct alkenylation with simple alkenes stands out as the most ideal yet challenging strategy for obtaining high-valued desaturated alkanes. Herein, the authors present a direct asymmetric dehydrogenative α-C(sp3)-H alkenylation of carbonyls based on synergistic photoredox-cobalt-chiral primary amine catalysis under visible light.

Catalytic transformation of alkenes via the metal-hydride hydrogen atom transfer (MHAT) mechanism has notably advanced synthetic organic chemistry. This review focuses on MHAT/radical-polar crossover (MHAT/RPC) conditions, offering a novel perspective on generating electrophilic intermediates and facilitating various intramolecular reactions. Upon using cobalt hydrides, the MHAT mechanism displayed exceptional chemoselectivity and functional group tolerance, making it invaluable for the construction of complex biologically relevant molecules under mild conditions. Recent developments have enhanced regioselectivity and expanded the scope of MHAT-type reactions, enabling the formation of cyclic molecules via hydroalkoxylation, hydroacyloxylation, and hydroamination. Notably, the addition of an oxidant to traditional MHAT systems enables the synthesis of rare cationic alkylcobalt(IV) complexes, bridging radical mechanisms to ionic reaction systems. This review culminates with examples of natural product syntheses and exploration of asymmetric intramolecular hydroalkoxylation, highlighting the ongoing challenges and opportunities for future research to achieve higher enantioselectivity. This review revisits the historical evolution of the MHAT mechanism and provides the groundwork for further innovations in the synthesis of structurally diverse and complex natural products.

Indolines are ubiquitous structural motifs found in pharmaceuticals and natural products but modification of these scaffolds via selective C(sp3)–H functionalization represents a major challenge. Herein, we report the regio- and stereoselective C(sp3)–H functionalization of N-substituted indolines to produce both -and-functionalized indolines via carbene transfer chemistry with engineered iron-based CYP119 catalysts. These transformations are shown to proceed with high regio- (up to >99%) and enantioselectivity (up to 98% e.e.) as well as excellent catalytic efficiency (up to 99% yield and 8,900 TON), furnishing an efficient and regiodivergent route for diversification of this class of medicinally relevant molecules via direct C(sp3)–H functionalization. We further show that these catalysts can enable selective functionalization of exocyclic C(sp3)–H bond in N-methyl indolines and that enzyme-mediated a-and b-C(sp3)–H functionalization can be combined in a biocatalytic cascade to yield polycyclic indoline-containing scaffolds, which can be found in many drugs. Finally, computational and experimental mechanistic studies provide evidence for the occurrence of a radical-mediated C–H functionalization pathway, providing first insights into the mechanism of P450-catalyzed C(sp3)–H carbene insertion. Altogether, this work provides a direct and tunable strategy for the synthesis of functionalized indolines as key building blocks for medicinal chemistry and natural product synthesis and it sheds light into the mechanism of P450-catalyzed C(sp3)–H functionalization via carbene transfer.

Communications Chemistry, Published online: 09 May 2024; doi:10.1038/s42004-024-01188-1

Establishing biotechnological alternatives to chemical syntheses requires the rational design of biosynthetic pathways and degradation routes either as enzymatic cascades in vitro or as part of living organisms. Here, the authors use alanine dehydrogenase from Vibrio proteolyticus and the diaminopimelate dehydrogenase from Symbiobacterium thermophilum for the in vitro production of (R) and (S)-3-fluoroalanine, reaching >85% yield with complete enantiomeric excess.

Nature, Published online: 08 May 2024; doi:10.1038/s41586-024-07487-w

Accurate structure prediction of biomolecular interactions with AlphaFold 3

Metalloradical catalysis (MRC), predominantly exemplified by metalloporphyrin complexes, has emerged as a promising strategy for regulating radical reactions and broadening their synthetic applications. In this paper, we report that cobaloxime complexes, functioning as a surrogate for metalloporphyrin systems, can mediate radical cyclopropanation of olefins using donor/acceptor-type carbene precursor α-aryl diazoacetates through the MRC process. The reaction proceeds under mild conditions, yielding cyclopropane derivatives in good yields with high stereoselectivity. The reaction exhibits extensive substrate tolerance, encompassing gram-scale transformations and the synthesis of pharmaceutical compounds. Our discoveries underscore the potential of cobaloxime-catalyzed cyclopropanation as a valuable asset in organic syntheses and further expand the repertoire of metalloradical systems in catalysis.

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.

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.

Nature, Published online: 01 May 2024; doi:10.1038/s41586-024-07284-5

We report on the oxidative cross-coupling of organoboron reagents and amino acids via pyridoxal biocatalysis to produce non-canonical amino acids, uncovering stereoselective, intermolecular free-radical transformations.

Nature Synthesis, Published online: 26 April 2024; doi:10.1038/s44160-024-00536-2

Development of fluorine rebound processes at an enzymatic Fe(III) centre are a challenge. Now, a plant-derived non-haem iron enzyme, 1-aminocyclopropane-1-carboxylic acid oxidase, is repurposed and evolved to catalyse chemo- and enantioselective C(sp3)–H fluorination, forming a range of enantioenriched organofluorine products.

The assembly of artificial metalloenzymes provides a second coordination sphere around a metal catalyst. Such a well-defined microenvironment can lead to enhancing the activities and selectivity of the catalyst. Herein, we present the development of artificial hydroxylase (ArHase) by embedding a Fe-TAML (TAML = Tetra Amide Macrocyclic Ligand) catalyst into a human carbonic anhydrase II (hCAII). Incorporation of the Fe-TAML catalyst ([BS-Fe-bTAML]–) within hCAII enhanced the Total TurnOver Number (TTON) for the hydroxylation of benzylic C–H bonds. After engineering a thermostable variant of hCAII (hCAIITS), the resulting ArHase, [BS-Fe-bTAML]– · hCAIITS, was subjected to directed evolution using cell lysates in a 384-well format. After three rounds of laboratory evolution, the best-performing variants exhibited 36-fold enhancement in the initial rate (124.4 min-1) and 2.8-fold enhancement in the TTON (2629 TTON) for the hydroxylation of benzylic C–H bonds compared to the free cofactor. We surmise that an arginine residue introduced in the course of directed evolution engages in hydrogen bonding with [BS-Fe-bTAML]–. This study highlights the potential of relying on a thermostable host protein to improve the catalytic performance of the hCAII-based ArMs.

Publication date: 28 May 2024

Source: Cell Reports, Volume 43, Issue 5

Author(s): Guang Yang, Ognjen Pećanac, Hein J. Wijma, Henriëtte J. Rozeboom, Gonzalo de Gonzalo, Marco W. Fraaije, Maria Laura Mascotti

Laccase is an oxidase of great industrial interest due to its ability to catalyse oxidation processes of phenols and persistent organic pollutants. However, it is susceptible to denaturation at high temperatures, sensitive to pH and in the presence of high concentrations of solvents, which is a problem for industrial use. To solve this problem, this work develops the synthesis in aqueous medium of a new Mn metalloenzyme with laccase oxidase mimetic catalytic activity. To do this, Geobacillus thermocatenulatus lipase (GTL) is used as a "scaffold" enzyme, which is mixed with a manganese salt at 50ºC in an aqueous medium. This produces in situ formation of manganese (IV) oxide nanowires that interact with the enzyme, obtaining the GTL-Mn bionanohybrid. On the other hand, its oxidative activity was evaluated using the ABTS assay, obtaining a catalytic efficiency 300 times greater than the laccase from Trametes versicolor. These new Mn-metalloenzyme turned out to be 2 times more stable at 40 ºC, 3 times more stable in the presence of 10% acetonitrile and 10 times more stable at 20% acetonitrile than laccase Novozym 51003®. Furthermore, the site-selective immobilized GTL-Mn showed much higher stability then the soluble form. Oxidase-like activity of these Mn-metalloenzyme was successfully performed against other substrates such as L-DOPA or phloridzin in oligomerization reactions.

Nature Chemistry, Published online: 17 April 2024; doi:10.1038/s41557-024-01494-0

Despite their intriguing photochemical activities, natural photoenzymes have not yet been repurposed for new-to-nature activities. Now, by leveraging the strongly oxidizing excited-state flavoquinone cofactor, fatty acid photodecarboxylases were engineered to catalyse unnatural decarboxylative radical cyclization with excellent chemo-, enantio- and diastereoselectivities.

An artificial metalloenzyme (ArM) based on biotin-streptavidin technology was repurposed for enantioselective nonannulative carboamination of alkenes. The combination of design of experiment (DoE) and genetic optimization led to a >630 % improvement in turnover number (TON).

Abstract

Relying on ubiquitous alkenes, carboamination reactions enable the difunctionalization of the double bond by the concurrent formation of a C−N and a C−C single bond. In the past years, several groups have reported on elegant strategies for the carboamination of alkenes relying on homogeneous catalysts or enzymes. Herein, we report on an artificial metalloenzyme for the enantioselective carboamination of dihydrofuran. Genetic optimization, combined with a Bayesian optimization of catalytic performance, afforded the disubstituted tetrahydrofuran product in up to 22 TON and 85 % ee. X-ray analysis of the evolved artificial carboaminase shed light on critical amino acid residues that affect catalytic performance.

Despite substantial progress made toward elucidating the elegant natural radical enzymology with thiamine pyrophosphate (TPP)-dependent pyruvate:ferredoxin oxidoreductases (PFORs) and pyruvate oxidases (POXs), repurposing naturally occurring two electron TPP-dependent enzymes to catalyze single-electron transformations with significant synthetic value remains a daunting task. Enabled by the synergistic use of visible-light photocatalyst fluorescein and a set of engineered TPP-dependent enzymes derived from benzoylformate decarboxylase (BFD) and benzaldehyde lyase (BAL), we developed an asymmetric photobiocatalytic decarboxylative alkylation of benzaldehydes and a-keto acids to produce highly enantioenriched a-branched ketones. Mechanistically, this dual catalytic radical alkylation involves single-electron oxidation of the enzyme-bound Breslow intermediate and subsequent interception of the photoredox-generated transient alkyl radical. In conjunction with visible light photoredox catalysis, thiamine radical biocatalysis represents a new platform to discover and optimize new asymmetric radical transformations which are unknown to biological systems and not amenable to small-molecule catalysis.

Benzimidazolium-based N-heterocyclic carbene (NHC)-boryl radical catalyzes cascade cyclization reactions to construct polycyclic compounds both intra- and intermolecularly. This catalytic cascade radical reaction allows rapid construction of complex molecular architectures through the formation of two or three bonds in a single operation, respectively.

Abstract

Cascade radical cyclization constitutes an atom- and step-economic route for rapid assembly of polycyclic molecular skeletons. Although an array of redox-active metal catalysts has recently shown robust applications in enabling various catalytic cascade radical processes, the use of free organic radical as the catalyst, which is capable of triggering strategically distinct cascades, has rarely been developed. Here, we disclosed that the benzimidazolium-based N-heterocyclic carbene (NHC)-boryl radical is capable of catalyzing cascade cyclization reactions in both intra- and intermolecular pathways, assembling [5,5] fused bicyclic and [6,6,6] fused tricyclic molecules, respectively. The catalytic reactions start with the chemo- and regioselective addition of the boryl radical catalyst to a tethered alkene or alkyne moiety, followed by either an intramolecular formal [3+2] or an intermolecular [2+2+2] cycloaddition process to construct bicyclo[3.3.0]octane or tetrahydrophenanthridine skeletons, respectively. Eventually, a β-elimination occurs to release the boryl radical catalyst, completing a catalytic cycle. High to excellent diastereoselectivity is achieved in both catalytic reactions under substrate control.