R.B. Leveson-Gower

Automation has fuelled dramatic advances in fields such as proteomics and genomics (e.g., in preparation of proteins and nucleic acids),1,2 enabling non-experts to prepare, test and analyse complex biological molecules. However, the field of automated organic synthesis lags far behind, partly because of the complexity and variety of organic molecules. As a result, only a handful of relatively simple organic molecules, requiring a small number of synthetic steps, have been made in an automated fashion. Herein, we report an automated assembly-line synthesis that allows iterative, stereocontrolled formation of C(sp3)–C(sp3) bonds with high stereochemical fidelity and reproducibility, enabling access to complex organic molecules even by non-synthesis experts. This was achieved on a commercially available robotic platform capable of handling air sensitive reactants and performing low temperature reactions, which enabled six sequenced one-carbon homologations of organoboron substrates to be performed iteratively without human intervention. Together with other automated functional group manipulations, this methodology has been exploited to rapidly build the core fragment of the natural product (+)-kalkitoxin, thus leading the way towards automated organic synthesis.

Though chiral pool synthesis is widely accepted as a powerful strategy in complex molecule synthesis, the effectiveness of the approach is intimately linked to the range of available chiral building blocks and the functional groups they possess. To date, there is still a pressing need for new remote functionalization methods that would allow the installation of useful chem-ical handles on these building blocks to enable a broader spectrum of synthetic manipulations. Herein, we report the engi-neering of a P450BM3 variant for the regioselective C–H oxidation of sclareol at C6. The synthetic utility of the resulting product was demonstrated in a formal synthesis of ansellone B and the first total synthesis of the 2,3-seco-labdane excolide B.

Organocatalysts meet proteins: Enzymatic activities by natural organocatalytic cofactors, non-natural derivatives of them and artificial cofactors are reviewed.

Abstract

Catalytically active non-metal cofactors in enzymes carry out a variety of different reactions. The efforts to develop derivatives of naturally occurring cofactors such as flavins or pyridoxal phosphate and the advances to design new, non-natural cofactors are reviewed here. We report the status quo for enzymes harboring organocatalysts as derivatives of natural cofactors or as artificial ones and their application in the asymmetric synthesis of various compounds.

A deaminative reductive coupling of amino acid pyridinium salts with aryl bromides has been developed to enable efficient synthesis of noncanonical amino acids and diversification of peptides. This method transforms natural, commercially available lysine, ornithine, diaminobutanoic acid (DAB), and diaminopropanoic acid (DAP) to aryl alanines and homologated derivatives with varying chain lengths. Attractive features include scalability, tolerance of pharma-relevant (hetero)aryls and functional groups, applicability to both monomeric amino acid and short peptide substrates, and compatibility with biorthogonal handles useful for chemical biology. Furthermore, these cross-couplings can be conducted in microscale and nanoscale and are amenable to solid-phase peptide synthesis platforms. The success of this work relied on an academic/industry collaboration and high-throughput experimentation to identify complementary conditions that proved critical for achieving broad scope of aryl bromides and pyridinium substrates.

Deuterated amino acids have been recognized for their utility in drug development, for facilitating NMR analysis, and as probes for enzyme mechanism. Small molecule-based methods for the site-selective synthesis of deuterated amino acids typically involve de novo synthesis of the compound from deuterated precursors. In comparison, enzymatic methods for introducing deuterium offer improved efficiency, operating directly on free amino acids to achieve hydrogendeuterium (H/D) exchange. However, site-selectivity remains a significant challenge for enzyme-mediated deuteration, limiting access to desirable deuteration motifs. Here we use enzyme-catalyzed deuteration, combined with steady-state kinetic analysis and UV-vis spectroscopy to probe the mechanism of a two-protein system responsible for the biosynthesis of L-alloIle. We show an aminotransferase (DsaD) can pair with a small partner protein (DsaE) to catalyze Cα and Cβ H/D exchange of amino acids, while reactions without DsaE lead exclusively to Cα-deuteration. With conditions for improved catalysis, we evaluate the substrate scope for Cα/Cβ-deuteration and demonstrate the utility of this system for preparative-scale, selective labeling of amino acids.

Nature, Published online: 09 March 2022; doi:10.1038/s41586-022-04499-2

Tryptophan depletion, which occurs in tumours, results in in-frame translation across tryptophan-encoding codons by phenylalanine substitution.

Biochemical characterization of HheG-682, a new homolog of halohydrin dehalogenase HheG sharing 46% sequence identity, is presented.

Pericyclases, enzymes that catalyze pericyclic reactions, form an expanding family of enzymes that have biocatalytic utility. Despite the increasing number of pericyclases discovered, the Diels-Alder (DA) cyclization between a cyclopentadiene and an olefinic dienophile to form norbornene, which is among the best-studied cycloadditions in synthetic chemistry, has surprisingly no enzymatic counterpart to date. Here we report the discovery of a pathway featuring a norbornene synthase SdnG for the biosynthesis of sordaricin-the terpene precursor of antifungal natural product sordarin. Full reconstitution of sordaricin biosynthesis revealed a concise oxidative strategy used by Nature to transform an entirely hydrocarbon precursor into the highly functionalized substrate of SdnG for intramolecular Diels-Alder (IMDA) cycloaddition. SdnG generates the norbornene core of sordaricin and accelerates this reaction to suppress host-mediated redox modifications of the activated dienophile. Findings from this work expand the scopes of pericyclase-catalyzed reactions and P450-mediated terpene maturation.

TsrM is a B₁₂-dependent radical SAM enzyme catalyzing methylation reactions from carbon-atoms to nucleophilic atoms making it a unique and versatile alkylating agent. TsrM is able to directly transfer methyl groups on the less reactive carbon atom of the indole ring and to install several methyl groups on its substrate. TsrM has thus unique properties among radical SAM enzymes by notably catalyzing non-radical reactions. (SAM: S-adenosyl-L-methionine).

Abstract

B₁₂-dependent radical SAM enzymes are an emerging enzyme family with approximately 200,000 proteins. These enzymes have been shown to catalyze chemically challenging reactions such as methyl transfer to sp2- and sp3-hybridized carbon atoms. However, to date we have little information regarding their complex mechanisms and their biosynthetic potential. Here we show, using X-ray absorption spectroscopy, mutagenesis and synthetic probes that the vitamin B₁₂-dependent radical SAM enzyme TsrM catalyzes not only C- but also N-methyl transfer reactions further expanding its synthetic versatility. We also demonstrate that TsrM has the unique ability to directly transfer a methyl group to the benzyl core of tryptophan, including the least reactive position C4. Collectively, our study supports that TsrM catalyzes non-radical reactions and establishes the usefulness of radical SAM enzymes for novel biosynthetic schemes including serial alkylation reactions at particularly inert C−H bonds.

A one-pot, two-step enzymatic cascade reaction was developed for the synthesis of N-substituted chiral 1,2-amino alcohols from simple aldehydes and amines by coupling hydroxymethylation and reduction amination reactions. This methodology was then applied to rapidly access a key building block of various tetrahydroquinoline alkaloids of pharmaceutical importance.

Abstract

The chiral N-substituted 1,2-amino alcohol motif is found in many natural and synthetic bioactive compounds. In this study, enzymatic asymmetric reductive amination of α-hydroxymethyl ketones with enantiocomplementary imine reductases (IREDs) enabled the synthesis of chiral N-substituted 1,2-amino alcohols with excellent ee values (91–99 %) in moderate to high yields (41–84 %). Furthermore, a one-pot, two-step enzymatic process involving benzaldehyde lyase-catalyzed hydroxymethylation of aldehydes and subsequent asymmetric reductive amination was developed, offering an environmentally friendly and economical way to produce N-substituted 1,2-amino alcohols from readily available simple aldehydes and amines. This methodology was then applied to rapidly access a key synthetic intermediate of anti-malaria and cytotoxic tetrahydroquinoline alkaloids.

A tryptophan overproducing Corynebacterium glutamicum strain was metabolically engineered to produce 7-Br/Cl-indole and 7-Br/Cl-tryptamine. For this purpose, tryptophanases and aromatic l-amino acid decarboxylases from different origins were screened and utilized in combination with halogenase RebH. Fermentative production of 7-Br-tryptamine in a bioreactor resulted in a product titer of 0.36 g L⁻¹.

Abstract

The aromatic amino acid l-tryptophan serves as a precursor for many valuable compounds such as neuromodulators, indoleamines and indole alkaloids. In this work, tryptophan biosynthesis was extended by halogenation followed by decarboxylation to the respective tryptamines or cleavage to the respective indoles. Either the tryptophanase genes tnaAs from E. coli and Proteus vulgaris or the aromatic amino acid decarboxylase genes AADCs from Bacillus atrophaeus, Clostridium sporogenes, and Ruminococcus gnavus were expressed in Corynebacterium glutamicum strains producing (halogenated) tryptophan. Regarding indoles, final titers of 16 mg L⁻¹ 7-Cl-indole and 23 mg L⁻¹ 7-Br-indole were attained. Tryptamine production led to a much higher titer of 2.26 g L⁻¹ upon expression of AADC from B. atrophaeus. AADC enzymes were shown to be active with halogenated tryptophan in vitro and in vivo and supported production of 0.36 g L⁻¹ 7-Br-tryptamine with a volumetric productivity of 8.3 mg L⁻¹ h⁻¹ in a fed-batch fermentation.

The discovery of ligands for the “undruggable proteome” is likely to require the development of new chemical matter with a greater “molecular wingspan” than traditional Lipinski-compliant small molecules. A DNA-encoded library (DEL) of non-peptidic thioether macrocycles has been constructed and screened for high affinity protein ligands to a model protein, SA.

Abstract

There is considerable interest in the development of libraries of non-peptidic macrocycles as a source of ligands for difficult targets. We report here the solid-phase synthesis of a DNA-encoded library of several hundred thousand thioether-linked macrocycles. The library was designed to be highly diverse with respect to backbone scaffold diversity and to minimize the number of amide N−H bonds, which compromise cell permeability. The utility of the library as a source of protein ligands is demonstrated through the isolation of compounds that bind Streptavidin, a model target, with high affinity.

Nature Catalysis, Published online: 21 February 2022; doi:10.1038/s41929-022-00743-0

Enantioselective C–C bond-forming reactions are underdeveloped in the biocatalysis toolbox. Now, engineering an efficient and promiscuous decarboxylative aldolase enzyme provides a solution to facilitate the convenient synthesis of non-standard γ-hydroxy amino acids from simple building blocks.

Supported sub-nano clusters hold great promise as economical and highly active catalysts. However, they tend to deactivate rapidly by poisoning and sintering, impeding their widespread use. We find that self-limiting poisoning can stabilize and promote cluster catalysis, i.e., poisoning is not always detrimental, but can sometimes be exploited. Specifically, Pt-Ge alloy clusters supported on alumina undergo slow coking (carbon deposition) under conditions of thermal dehydrogenation, yet preserve strong binding sites. For the case of Pt4Ge/alumina, theory shows a number of thermally populated isomers, one of which catalyzes carbon deposition. Because the clusters are fluxional at high temperatures, this isomer acts as a gateway, slowly converting all the clusters to Pt4GeC2. The surprising result is that Pt4GeC2 is highly catalytically active and selective against further coking, i.e., coking produces functional, stable catalytic clusters. Ge and C2 have synergistic electronic effects, leading to efficient and highly selective catalytic dehydrogenation that stops at alkenes, and improving stability. Thus, under reaction conditions, the clusters develop into a robust catalyst, suggesting an approach to practicable cluster catalysis.

Adding function: A boronate-affinity ligand and an S-aryl thioester have been developed that are capable of labelling native Abs with a functional molecule. Additionally, a photoactivatable crosslinker allows purification of labelled Abs in a reagentless manner, thereby producing homogeneous Ab-drug conjugates.

Abstract

The excellent molecular recognition capabilities of monoclonal antibodies (mAbs) have opened up exciting opportunities for biotherapeutic discovery. Taking advantage of the full potential of this tool necessitates affinity ligands capable of conjugating directly with small molecules to a defined degree of biorthogonality, especially when modifying natural Abs. Herein, a bioorthogonal boronate-affinity-based Ab ligand featuring a 4-(dimethylamino)pyridine and an S-aryl thioester to label full-length Abs is reported. The photoactivatable linker in the acyl donor facilitated purification of azide-labelled Ab (N₃-Ab) was quantitatively cleaved upon brief exposure to UV light while retaining the original Ab activity. Click reactions enabled the precise addition of biotin, a fluorophore, and a pharmacological agent to the purified N₃-Abs. The resulting immunoconjugate showed selectivity against targeted cells. Bioorthogonal traceless design and reagentless purification allow this strategy to be a powerful tool to engineer native antibodies amenable to therapeutic intervention.

BioTrans2021: We created an artificial enzyme consisting of a non-enzymatic protein (LmrR) containing an unnatural catalytic residue with an aniline side chain (LmrR_pAF). Building on our previous work showing how LmrR_pAF can catalyse a Friedel-Crafts alkylation of indoles, here we show that when α-substituted acroleins are applied as substrates the protein scaffold enables enantioselective protonation with good selectivity.

Abstract

The incorporation of organocatalysts into protein scaffolds holds the promise of overcoming some of the limitations of this powerful catalytic approach. Previously, we showed that incorporation of the non-canonical amino acid para-aminophenylalanine into the non-enzymatic protein scaffold LmrR forms a proficient and enantioselective artificial enzyme (LmrR_pAF) for the Friedel-Crafts alkylation of indoles with enals. The unnatural aniline side-chain is directly involved in catalysis, operating via a well-known organocatalytic iminium-based mechanism. In this study, we show that LmrR_pAF can enantioselectively form tertiary carbon centres not only during C−C bond formation, but also by enantioselective protonation, delivering a proton to one face of a prochiral enamine intermediate. The importance of various side-chains in the pocket of LmrR is distinct from the Friedel-Crafts reaction without enantioselective protonation, and two particularly important residues were probed by exhaustive mutagenesis.