R.B. Leveson-Gower

G-type halohydrin dehalogenases convert 5- and 6-membered cyclic epoxides with a range of small anionic C-, N-, O- and S-nucleophiles.

Abstract

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 subfamily 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.

The cepafungins are a class of highly potent and selective eukaryotic proteasome inhibitor natural products with potential to treat refractory multiple myeloma and other cancers. The structure-activity relationship of the cepafungins is not fully understood. This account chronicles the development of a chemoenzymatic approach to cepafungin I. A failed initial route involving derivatization of pipecolic acid prompted us to examine the biosynthetic pathway for the production of 4-hydroxylysine, which culminated in the development of a 9-step synthesis of cepafungin I. An alkyne-tagged analog enabled chemoproteomic studies of cepafungin and comparison of its effects on global protein expression in human multiple myeloma cells to the clinical drug bortezomib. A preliminary series of analogs elucidated critical determinants of potency in proteasome inhibition. Herein we report the chemoenzymatic syntheses of 13 additional analogs of cepafungin I guided by a proteasome-bound crystal structure, 5 of which are more potent than the natural product. Enzymatic strategies enabled the facile synthesis of oxidized amino acids in the macrocycle warhead as well as the tail fragment. Additional analogs were prepared by chemical methods to further explore the SAR at other regions of the scaffold. These studies reveal the criticality of the macrocyclic L-lysine oxidation regio-/stereochemistry introduced in the natural product biosynthesis relative to other possible lysine oxidation patterns found in nature. The lead analog was found to have seven-fold greater proteasome b5 subunit inhibitory activity and has been evaluated against several multiple myeloma and mantle cell lymphoma cell lines in comparison to the clinical drug bortezomib.

The ubiquity of C–H bonds presents an attractive opportunity to elaborate and build complexity in organic molecules. Methods for selective functionalization, however, often must differentiate among multiple chemically similar and, in some cases indistinguishable, C–H bonds within the same molecule. An advantage of enzymes is that they can be finely tuned using directed evolution to achieve control over divergent C–H functionalization pathways. Here, we present engineered enzymes that effect a new-to-nature C–H alkylation (C–H carbene insertion) with unparalleled selectivity: two complementary carbene C–H transferases derived from a cytochrome P450 from Bacillus megaterium deliver an α-cyanocarbene into the α-amino C(sp3)–H bonds or the ortho-arene C(sp2)–H bonds of N-substituted arenes. These two transformations proceed via different mechanisms, yet only minimal changes to the protein scaffold (nine mutations, less than 2% of the sequence) were needed to adjust the enzyme’s control over the site-selectivity of cyanomethylation. The X-ray crystal structure of the selective C(sp3)–H alkylase, P411-PFA, reveals an unprecedented helical disruption which alters the shape and electrostatics in the enzyme active site. Overall, this work demonstrates the advantages of using enzymes as C–H functionalization catalysts for divergent molecular derivatization.

Benzoxazolinate is a rare bis-heterocyclic moiety that interacts with proteins and DNA. It was found that a putative acyl AMP-ligase mediates the last cyclization step to afford benzoxazolinate. The enzyme was then used as a probe for genome mining, which led to the discovery of a new class of benzoxazolinate-containing compounds in diverse bacteria.

Abstract

Benzoxazolinate is a rare bis-heterocyclic moiety that interacts with proteins and DNA and confers extraordinary bioactivities on natural products, such as C-1027. However, the biosynthetic gene responsible for the key cyclization step of benzoxazolinate remains unclear. Herein, we show a putative acyl AMP-ligase responsible for the last cyclization step. We used the enzyme as a probe for genome mining and discovered that the orphan benzobactin gene cluster in entomopathogenic bacteria prevails across Proteobacteria and Firmicutes. It turns out that Pseudomonas chlororaphis produces various benzobactins, whose biosynthesis is highlighted by a synergistic effect of two unclustered genes encoding enzymes on boosting benzobactin production; the formation of non-proteinogenic 2-hydroxymethylserine by a serine hydroxymethyltransferase; and the types I and II NRPS architecture for structural diversity. Our findings reveal the biosynthetic potential of a widespread benzobactin gene cluster.

Medium chain alcohol dehydrogenases usually perform a reversible 1,2-reduction of aldehydes to form the corresponding alcohols. Here we show how the active site of these dehydrogenases can be modified to perform 1,2-reduction of iminium moieties, as well 1,4-reduction of α,β-unsaturated iminium groups and 1,4-reduction of α,β-unsaturated aldehydes.

Abstract

Medium-chain alcohol dehydrogenases (ADHs) comprise a highly conserved enzyme family that catalyse the reversible reduction of aldehydes. However, recent discoveries in plant natural product biosynthesis suggest that the catalytic repertoire of ADHs has been expanded. Here we report the crystal structure of dihydroprecondylocarpine acetate synthase (DPAS), an ADH that catalyses the non-canonical 1,4-reduction of an α,β-unsaturated iminium moiety. Comparison with structures of plant-derived ADHs suggest the 1,4-iminium reduction does not require a proton relay or the presence of a catalytic zinc ion in contrast to canonical 1,2-aldehyde reducing ADHs that require the catalytic zinc and a proton relay. Furthermore, ADHs that catalysed 1,2-iminium reduction required the presence of the catalytic zinc and the loss of the proton relay. This suggests how the ADH active site can be modified to perform atypical carbonyl reductions, providing insight into how chemical reactions are diversified in plant metabolism.

Catalytic olefin metathesis can be performed in live microalgae, converting the fatty acids stored in lipid organelles to polymer building blocks and chemicals in vivo.

Abstract

Sustainable sources are key to future chemicals production. Microalgae are promising resources as they fixate carbon dioxide to organic molecules by photosynthesis. Thereby they produce unsaturated fatty acids as established raw materials for the industrial production of chemical building blocks. Although these renewable feedstocks are generated inside cells, their catalytic upgrading to useful products requires in vitro transformations. A synthetic catalysis inside photoautotrophic cells has remained elusive. Here we show that a catalytic conversion of renewable substrates can be realized directly inside living microalgae. Organometallic catalysts remain active inside the cells, enabling in vivo catalytic olefin metathesis as new-to-nature transformation. Stored lipids are converted to long-chain dicarboxylates as valuable building blocks for polymers. This is a key step towards the long-term goal of producing desired renewable chemicals in microalgae as living “cellular factories”.

N-Methylated and -alkylated unsaturated heterocycles are privileged scaffolds in pharmaceuticals that are often tedious to synthesize. Now, promiscuous and engineered enzymes can be used to access such molecules through alkylation with high regioselectivity, high yield and on a preparative scale using simple starting materials.

Abstract

Methods for regioselective N-methylation and -alkylation of unsaturated heterocycles with “off the shelf” reagents are highly sought-after. This reaction could drastically simplify synthesis of privileged bioactive molecules. Here we report engineered and natural methyltransferases for challenging N-(m)ethylation of heterocycles, including benzimidazoles, benzotriazoles, imidazoles and indazoles. The reactions are performed through a cyclic enzyme cascade that consists of two methyltransferases using only iodoalkanes or methyl tosylate as simple reagents. This method enables the selective synthesis of important molecules that are otherwise difficult to access, proceeds with high regioselectivity (r.r. up to >99 %), yield (up to 99 %), on a preparative scale, and with nearly equimolar concentrations of simple starting materials.

“My favorite way to spend a holiday is to do nothing … If I were not a scientist, I would be a school teacher …” Find out more about Apparao Draksharapu in his Introducing … Profile.

Despite the very low acidity of the inert α C−H bonds (pK _a≈42.6), direct asymmetric α-C(sp ³ )−H addition of N-unprotected propargylic amines to trifluoromethyl ketones has been achieved by using a chiral pyridoxal as the carbonyl catalyst, producing a broad variety of chiral alkynyl β-aminoalcohols in high yields with excellent stereoselectivities (up to 84 % yield, >20 : 1 dr, 99 % ee).

Abstract

Direct asymmetric functionalization of the inert α C−H bonds of N-unprotected propargylic amines is a big challenge in organic chemistry, due to the low acidity (pK _a≈42.6) of the α C−H bonds and interruption of the nucleophilic NH₂ group. By using a chiral pyridoxal as carbonyl catalyst, we have successfully realized direct asymmetric α-C−H addition of N-unprotected propargylic amines to trifluoromethyl ketones, producing a broad range of chiral alkynyl β-aminoalcohols in 54–84 % yields with excellent stereoselectivities (up to 20 : 1 dr and 99 % ee). The α C−H bonds of propargylic amines are greatly activated by the pyridoxal catalyst via the formation of an imine intermediate, resulting in the increase of acidity by up to 10²² times (from pK _a 42.6 to pK _a 20.1), which become acidic enough to be deprotonated under mild conditions for the asymmetric addition. This work presented an impressive example for asymmetric functionalization of inert C−H bonds enabled by an organocatalyst.

Polyethylene terephthalate (PET) is the most common polyester plastic in the packaging industry, and a major source of environmental pollution due to its single use. Several enzymes, termed PET hydrolases (PETases), have been found to hydrolyze this polymer at different temperatures, with the enzyme from I. sakaiensis (IsPETase) having optimal catalytic activity at 40ºC. Crystal structures of IsPETase have revealed that the side chain of a conserved tryptophan residue within an active site loop (W185) shifts between 3 conformations to enable substrate binding and product release. This is facilitated by two residues unique to IsPETase, S214 and I218 (S/I). When these residues are inserted into other PETases in place of the otherwise strictly conserved His/Phe (H/F) residues found at their respective positions, they enhance activity and decrease Topt. Herein, we combine conventional molecular dynamics and well-tempered metadynamics simulations to investigate dynamic changes of the S/I and H/F variants of IsPETase, as well as three other mesophilic and thermophilic PETases, at their respective temperature and pH optima. Our simulations show that the S/I insertion both increases the flexibility of active site loop regions harboring key catalytic residues and the conserved Trp, as well as expanding the conformational plasticity of this Trp side chain, allowing the conformational transitions that allow for substrate binding and product release in IsPETase. The observed catalytic enhancement caused by this substitution in other PETases appears to be due to conformational selection, by capturing the conformational ensemble observed in IsPETase.

Described are ligand-directed catalysts for live-cell, photocatalytic activation of bioorthogonal chemistry. Catalytic groups are localized via a tethered ligand either to DNA or to tubulin, and red-light (660 nm) photocatalysis is used to initiate a cascade of DHTz-oxidation, intramolecular Diels-Alder reaction, and elimination to release phenolic compounds. Silarhodamine (SiR) dyes, more conventionally used as biological fluorophores, serve as photocatalysts that have high cytocompatibility and produce minimal singlet oxygen. Commercially-available conjugates of Hoechst dye (SiR-H) and Taxol (SiR-T) are used to localize SiR to the nucleus and tubulin, respectively. Computation was used to assist the design of a new class of redox-activated photocage to release either phenol or n-CA4, a microtubule-destabilizing agent. In model studies, uncaging is complete within 5 min using only 2 µM of SiR and 40 µM of the photocage. In situ spectroscopic studies support a mechanism involving rapid intramolecular Diels-Alder reaction and a rate determining elimination step. In cellular studies, this uncaging process is successful at low concentration of both the photocage (25 nM) and the SiR-H dye (500 nM). Uncaging n-CA4 causes microtubule depolymerization and an accompanying reduction in cell area. Control studies demonstrate that SiR-H catalyzes uncaging inside the cell, and not in the extracellular environment. With SiR-T, the same dye serves as photocatalyst and the fluorescent reporter for tubulin depolymerization, and with confocal microscopy it was possible to visualize tubulin depolymerization in real time as the result of photocatalytic uncaging in live cells.

Dinitroalkanes are powerful synthetic building blocks because of the versatility of the 1,3-dinitro motif. Here, we show that dinitroalkanes can be synthesized from alcohol substrates using a combination of biocatalysis and organocatalysis in a single-flask process. Alcohol oxidase oxidizes alcohol substrates to an intermediate aldehyde, which is sequentially converted to a nitroalcohol, then a nitroalkene, and finally, to a 1,3-dinitroalkane with a combination of phosphate buffer and lysine catalysis. Simultaneous addition of all reagents gives a maximal yield of 52%, whereas staggering the introduction of the amino acid catalyst and nitromethane substrate boosts the yield to 71% with near-quantitative conversion. Taken together, this work shows that biocatalysed oxidation can be coupled to multi-step catalytic cascades to expand the types of products available from bioprocesses.

Biocatalytic cascades can be used for the efficient, asymmetric synthesis of bioactive compounds. A substrate multiplexed screening (SUMS) based directed evolution approach was implemented to improve the substrate scope overlap between a transaldolase and a decarboxylase. The matched substrate scope of the enzymes was leveraged to produce a variety of enantiomerically pure 1,2-amino alcohols in a one-pot cascade from aldehydes or styrene oxides.

Abstract

Biocatalytic cascades are uniquely powerful for the efficient, asymmetric synthesis of bioactive compounds. However, high substrate specificity can hinder the scope of biocatalytic cascades because the constituent enzymes may have non-complementary activity. In this study, we implemented a substrate multiplexed screening (SUMS) based directed evolution approach to improve the substrate scope overlap between a transaldolase (ObiH) and a decarboxylase for the production of chiral 1,2-amino alcohols. To generate a promiscuous cascade, we engineered a tryptophan decarboxylase to act efficiently on β-OH amino acids while avoiding activity on l-threonine, which is needed for ObiH activity. We leveraged this exquisite selectivity with matched substrate scope to produce a variety of enantiopure 1,2-amino alcohols in a one-pot cascade from aldehydes or styrene oxides. This demonstration shows how SUMS can be used to guide the development of promiscuous, C−C bond forming cascades.

An artificial metalloenzyme was screened in vivo using a high-throughput microfluidics-based assay. Single E. coli cells expressing streptavidin were encapsulated in double emulsion droplets together with a fluorogenic substrate and a cofactor catalyzing the reaction to yield a fluorescent product. Using this method, a 400-member library was screened, and the same hits found previously in a 96-well plate assay were identified.

Abstract

The potential for ultrahigh-throughput compartmentalization renders droplet microfluidics an attractive tool for the directed evolution of enzymes. Importantly, it ensures maintenance of the phenotype-genotype linkage, enabling reliable identification of improved mutants. Herein, we report an approach for ultrahigh-throughput screening of an artificial metalloenzyme in double emulsion droplets (DEs) using commercially available fluorescence-activated cell sorters (FACS). This protocol was validated by screening a 400 double-mutant streptavidin library for ruthenium-catalyzed deallylation of an alloc-protected aminocoumarin. The most active variants, identified by next-generation sequencing, were in good agreement with hits obtained using a 96-well plate procedure. These findings pave the way for the systematic implementation of FACS for the directed evolution of (artificial) enzymes and will significantly expand the accessibility of ultrahigh-throughput DE screening protocols.

In this study, we describe the creation of an artificial protein cage housing a dual metal-tagged guest protein that catalyzes a linear, two-step sequential cascade reaction. The guest protein consists of a fusion protein of HaloTag and monomeric rhizavidin. Inside the protein capsid, we establish a ruthenium-catalyzed alloc-deprotection followed by a gold-catalyzed ring-closing hydroamination reaction that leads to indoles and phenanthridines with an overall yield of up to 67% in aqueous solutions. Furthermore, we show that the encapsulation stabilizes the metal catalysts against deactivation by air, proteins and cell lysate.

Nature, Published online: 21 September 2022; doi:10.1038/s41586-022-05342-4

Enantioselective [2+2]-cycloadditions with triplet photoenzymes

Nature, Published online: 21 September 2022; doi:10.1038/s41586-022-05335-3

A Designed Photoenzyme for Enantioselective [2+2]-Cycloadditions

Nature Catalysis, Published online: 20 September 2022; doi:10.1038/s41929-022-00836-w

Metabolic engineering of microbes constitutes a promising strategy to make the industrial production of chemicals more sustainable. This Review discusses recent advances of targeted high-throughput genome editing to construct next-generation cell factories for bioproduction.

Nature Chemical Biology, Published online: 15 September 2022; doi:10.1038/s41589-022-01127-y

Polyketides are assembled by modular polyketide synthases and undergo chemical tailoring reactions. A dehydratase domain variant catalyzes two sequential elimination reactions from thioester intermediates to produce conjugated diene modifications.

Biocatalytic Synthesis: This study focuses on the reversal of cofactor preference for short-chain dehydrogenases/reductases and the excellent NADH-dependent recombinant LfSDR1-V186A/G92V/E141L/G38D/T15A variant (Mu2) was obtained. Meanwhile, a co-expressed E. coli whole-cell biocatalyst containing the genes of Mu2 and PpFDH was developed to reduce ketone 1. Finally, ketone 1 was almost completely converted into the product (R)-2 with a space-time yield of 115.7 g⋅L⁻¹⋅d⁻¹ and a 98.8 % ee value.

Abstract

Switching cofactor preference of oxidoreductases from NADPH to NADH by rational engineering, replacing the expensive cofactor NADP⁺ with the cheap cofactor NAD⁺, is a focus of attention in the industrial application of oxidoreductases. This study focuses on the reversal of cofactor preference for short-chain dehydrogenases/reductases (SDRs). Combined with bioinformatics analyses and in silico analyses, a small and smart mutant library (Mu1-Mu3) of LfSDR1 was rationally designed and constructed. Thus, the excellent NADH-dependent recombinant LfSDR1-V186A/G92V/E141L/G38D/T15A variant (Mu2) was obtained. Meanwhile, novel enzymatic processes for synthesis of the key intermediates [(R)-2 and (S)-4] of telotristat ethyl and crizotinib were successfully created, which mainly relied on Mu2 coupled with an FDH-catalyzed cofactor regeneration system. A co-expressed E. coli whole-cell biocatalyst containing the genes of Mu2 and PpFDH was developed to reduce ketones 1 and 3. Finally, ketone 1 was almost completely converted into the product (R)-2 with a space-time yield of 115.7 g⋅L⁻¹⋅d⁻¹ and a 98.8 % ee value.

Mechanisms: A comprehensive review of the catalytic mechanisms of imine reductase (IRED)-catalyzed imine reduction (IR), reductive amination (RA), recently reported conjugate reduction (CR), and stepwise CR-RA. Mechanistic insights from protein engineering were also included.

Abstract

The synthesis of chiral amines is significant in the pharmaceutical industry. Imine reductase (IRED), a promising biocatalyst that was previously known to only catalyze asymmetric imine reduction (IR), was revealed to achieve direct asymmetric reductive amination (RA) of ketones with excess amines, producing secondary and tertiary amines. Moreover, conjugate reduction (CR) and RA activity by a single IRED has been reported for the preparation of valuable amine diastereomers. IREDs catalyzing these different reactions share the same standard quaternary structure, but possess varying active sites, indicating correlations and differences between their catalytic mechanisms. In this review, we trace the catalytic mechanisms reported for IRED-catalyzed IR, RA, and CR-RA. Insights obtained from structural and protein engineering in understanding the IRED-catalyzed asymmetric synthesis are also included. This review will help readers acquire comprehensive insights into the catalytic mechanism of IREDs and ultimately inspire the engineering of IREDs for industrial applications.

Nature Communications, Published online: 14 September 2022; doi:10.1038/s41467-022-33131-0

The biosynthesis of xanthones has not been well documented. Here, the authors report that monooxygenase FlsO1 catalyzes three successive oxidations – hydroxylation, epoxidation and Baeyer–Villiger oxidation—to form the xanthone scaffold in actinomycetes.

Selective functionalization of aliphatic C–H bonds, ubiquitous in molecular structures, could allow ready access to diverse chemical products. While enzymatic oxygenation of C–H bonds is well established, the analogous enzymatic nitrogen functionalization is still unknown; nature is reliant on pre-oxidized compounds for nitrogen incorporation. Likewise, synthetic methods for selective nitrogen derivatization of unbiased C–H bonds remain elusive. In this work, new-to-nature heme-containing nitrene transferases were used as starting points for the directed evolution of enzymes to selectively aminate and amidate unactivated C(sp3)–H sites. The desymmetrization of methyl- and ethylcyclohexane with divergent site selectivity is offered as demonstration. The evolved enzymes in these lineages are highly promiscuous and show activity towards a wide array of substrates, providing a foundation for further evolution of nitrene transferase function. Computational studies and kinetic isotope effects (KIEs) are consistent with a stepwise radical pathway involving an irreversible, enantiodetermining hydrogen atom transfer (HAT), followed by a lower-barrier diastereoselectivity determining radical rebound step. In-enzyme molecular dynamics (MD) simulations reveal a predominantly hydrophobic pocket with favorable dispersion interactions with the substrate. By offering a direct path from saturated precursors, these enzymes present a new biochemical logic for accessing nitrogen-containing compounds.