Engineering Chemoselectivity in Hemoprotein-Catalyzed Indole Amidation

Expanding the structural diversity of terpenes by synthetic biology approaches

Terpenoids display chemical and structural diversities as well as important biological activities. Despite their extreme variability, the range of these structures is limited by the scope of natural products that canonically derive from interconvertible five-carbon (C5) isoprene units. New approaches have recently been developed to expand their structural diversity. This review systematically explores the combinatorial biosynthesis of noncanonical building blocks via the coexpression of the canonical mevalonate (MVA) pathway and C-methyltransferases (C-MTs), or by using the lepidopteran mevalonate (LMVA) pathway. Unnatural terpenoids can be created from farnesyl diphosphate (FPP) analogs by chemobiological synthesis and terpene cyclopropanation by artificial metalloenzymes (ArMs). Advanced technologies to accelerate terpene biosynthesis are discussed. This review provides a valuable reference for increasing the diversity of valuable terpenoids and their derivatives, as well as for expanding their potential applications.

Choose Your Own Adventure: A Comprehensive Database of Reactions Catalyzed by Cytochrome P450 BM3 Variants

Cytochrome P450 BM3 monooxygenase is the topic of extensive research as many researchers have evolved this enzyme to generate a variety of products. However, the abundance of information on increasingly diversified variants of P450 BM3 that catalyze a broad array of chemistry is not in a format that enables easy extraction and interpretation. We present a database that categorizes variants by their catalyzed reactions and includes details about substrates to provide reaction context. This database of >1500 P450 BM3 variants is downloadable and machine-readable and includes instructions to maximize ease of gathering information. The database allows rapid identification of commonly reported substitutions, aiding researchers who are unfamiliar with the enzyme in identifying starting points for enzyme engineering. For those actively engaged in engineering P450 BM3, the database, along with this review, provides a powerful and user-friendly platform to understand, predict, and identify the attributes of P450 BM3 variants, encouraging the further engineering of this enzyme.

Reagent Engineering for Group Transfer Biocatalysis

Biocatalysis has become a major driver in the innovation of preparative chemistry. Enzyme discovery, engineering and computational design have matured to reliable strategies in the development of biocatalytic processes. By comparison, substrate engineering has received much less attention. In this Minireview, we highlight the idea that the design of synthetic reagents may be an equally fruitful and complementary approach to develop novel enzyme-catalysed group transfer chemistry. This Minireview discusses key examples from the literature that illustrate how synthetic substrates can be devised to improve the efficiency, scalability and sustainability, as well as the scope of such reactions. We also provide an opinion as to how this concept might be further developed in the future, aspiring to replicate the evolutionary success story of natural group transfer reagents, such as adenosine triphosphate (ATP) and S-adenosyl methionine (SAM).

Computational Mechanistic Investigations of Biocatalytic Nitrenoid C-H Functionalizations via Engineered Heme Proteins

Engineered heme proteins were developed to possess numerous excellent biocatalytic nitrenoid C-H functionalizations. Computational approaches such as density functional theory (DFT), hybrid quantum mechanics/molecular mechanics (QM/MM), and molecular dynamics (MD) calculations were employed to help understand some important mechanistic aspects of these heme nitrene transfer reactions. This review summarizes advances of computational reaction pathway results of these biocatalytic intramolecular and intermolecular C-H aminations/amidations, focusing on mechanistic origins of reactivity, regioselectivity, enantioselectivity, diastereoselectivity as well as effects of substrate substituent, axial ligand, metal center, and protein environment. Some important common and distinctive mechanistic features of these reactions were also described with brief outlook of future development.

Highly Regioselective Cyclodehydrogenation of Diphenylporphyrin on Metal Surfaces

Exploring the effect of porphin tautomerism on the regioselectivity of its derivatives is a big challenge, which is significant for the development and application of porphyrin drugs. In this work, we demonstrate the regioselectivity of 2H-diphenylporphyrin (H2-DPP) in the planarization reaction on Au(111) and Ag(111) substrates. H2-DPP monomer forms two configurations (anti- and syn-) via a dehydrogenation coupling, between which the yield of the anti-configuration exceeds 90%. Using high-resolution scanning tunneling microscopy, we visualize the reaction processes from the H2-DPP monomer to the final two planar products. Combined with DFT calculations of the potential reaction pathway and comparative experiments on Au(111) and Ag(111) substrates. Using M-DPP (M = Cu and Fe), we confirm that the regioselectivity of H2-DPP is derived from the reaction energy barrier during the cyclodehydrogenation reaction of different tautomers. This work reveals the regioselectivity mechanism of H2-DPP on the atomic scale, which holds great significance for understanding the chemical conversion process of organic macrocyclic molecules.

Overexpression of chaperones GroEL/ES from Escherichia coli enhances indigo biotransformation production of cytochrome P450 BM3 mutant

The self-sufficient cytochrome P450 BM3 mutant (A74G/F87V/D168H/L188Q) can serve as a biocatalyst for whole-cell catalysis process of indigo. Nevertheless, the bioconversion yield of indigo is generally low under normal cultivation conditions (37 °C, 250 rpm). In this study, a recombinant E. coli BL21(DE3) strain was constructed to co-express the P450 BM3 mutant gene and GroEL/ES genes to investigate whether GroEL/ES can promote the indigo bioconversion yield in E. coli. The results revealed that the GroEL/ES system could significantly increase the indigo bioconversion yield, and the indigo bioconversion yield of the strain co-expressing P450 BM3 mutant and GroEL/ES was about 21-fold that of the strain only expressing the P450 BM3 mutant. In addition, the P450 BM3 enzyme content and in vitro indigo bioconversion yield were determined to explore the underlying mechanism for the improvement of indigo bioconversion yield. The results revealed that GroEL/ES did not increase indigo bioconversion yield by increasing the content of P450 BM3 enzyme and its enzymatic transformation efficiency. Moreover, GroEL/ES could improve the intracellular nicotinamide adenine dinucleotide phosphate (NADPH)/NADP⁺ ratio. Given that NADPH is an important coenzyme in the catalytic process of indigo, the underlying mechanism for the improvement of indigo bioconversion yield is probably related to an increase in the intracellular NADPH/NADP⁺ ratio.

Use of engineered cytochromes P450 for accelerating drug discovery and development

Numerous steps in drug development, including the generation of authentic metabolites and late-stage functionalization of candidates, necessitate the modification of often complex molecules, such as natural products. While it can be challenging to make the required regio- and stereoselective alterations to a molecule using purely chemical catalysis, enzymes can introduce changes to complex molecules with a high degree of stereo- and regioselectivity. Cytochrome P450 enzymes are biocatalysts of unequalled versatility, capable of regio- and stereoselective functionalization of unactivated CH bonds by monooxygenation. Collectively they catalyze over 60 different biotransformations on structurally and functionally diverse organic molecules, including natural products, drugs, steroids, organic acids and other lipophilic molecules. This catalytic versatility and substrate range makes them likely candidates for application as potential biocatalysts for industrial chemistry. However, several aspects of the P450 catalytic cycle and other characteristics have limited their implementation to date in industry, including: their lability at elevated temperature, in the presence of solvents, and over lengthy incubation times; the typically low efficiency with which they metabolize non-natural substrates; and their lack of specificity for a single metabolic pathway. Protein engineering by rational design or directed evolution provides a way to engineer P450s for industrial use. Here we review the progress made to date toward engineering the properties of P450s, especially eukaryotic forms, for industrial application, and including the recent expansion of their catalytic repertoire to include non-natural reactions.

Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere

Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.

Nitrene transfers mediated by natural and artificial iron enzymes

Amines are ubiquitous in biology and pharmacy. As a consequence, introducing N functionalities in organic molecules is attracting strong continuous interest. The past decade has witnessed the emergence of very efficient and selective catalytic systems achieving this goal thanks to engineered hemoproteins. In this review, we examine how these enzymes have been engineered focusing rather on the rationale behind it than the methodology employed. These studies are put in perspective with respect to in vitro and in vivo nitrene transfer processes performed by cytochromes P450. An emphasis is put on mechanistic aspects which are confronted to current molecular knowledge of these reactions. Forthcoming developments are delineated.

Theoretical studies on iron-catalyzed azaindoline formation: mechanism and site-selectivity

The mechanism and site-selectivity for Fe-catalyzed azaindoline formation from 1,2,3,4-tetrazole were examined computationally. The H-atom abstraction/radical rebound stepwise mechanism is proposed. The aliphatic H-atom abstraction (HAA) vs. electrophilic aromatic substitution (EAS) steps are responsible for the sp³vs. sp² C-H amination site-selectivity and a larger steric congestion disfavors sp² EAS, thus resulting in Fe-catalyzed site-selectivity toward sp³ C-H amination.

Modification of pulse proteins for improved functionality and flavor profile: A comprehensive review

Consumers' preference to have a healthy eating pattern has led to an increasing demand for more nutrient-dense and healthier plant-based foods. Pulse proteins are exceptional quality ingredients with potential nutritional benefits, and might act as health-promoting agents for addressing the new-generation foods. However, the utilization of pulse protein in foods has been hampered by its relatively poor functionality and unpleasant flavor. Protein structure modification has been proved to be a useful means to improve the functionality and flavor profile of pulse protein. This paper begins with a brief introduction of hierarchical structure of pulse protein materials to better understand the structure characteristics. A comprehensive review is presented on the current techniques including chemical and enzymatic modifications and molecular breeding on pulse protein structure and functionality/flavor. The mechanism and the limitations and the toxicological concerns of these approaches are discussed. We conclude that understanding protein structure-functionality relationship is extremely valuable in tailoring proteins for specific functional outcomes and expanding the availability of pulse proteins. Furthermore, selective protein modification is a valuable in-depth toolkit for generating novel protein constructs with preferable functional attributes and flavor profiles. Innovative structure modification with special focus on the molecular basis for the exquisite protein designs is a pillar of pulse protein access to the desired functionality.

Ionic liquids for regulating biocatalytic process: Achievements and perspectives

Biocatalysis has found enormous applications in sorts of fields as an alternative to chemical catalysis. In the pursue of green and sustainable chemistry, ionic liquids (ILs) have been considered as promising reaction media for biocatalysis, owing to their unique characteristics, such as nonvolatility, inflammability and tunable properties as regards polarity and water miscibility behavior, compared to organic solvents. In recent years, great developments have been achieved in respects to biocatalysis in ILs, especially for preparing various chemicals. This review tends to give illustrative examples with a focus on representative chemicals production by biocatalyst in ILs and elucidate the possible mechanism in such systems. It also discusses how to regulate the catalytic efficiency from several aspects and finally provides an outlook on the opportunities to broaden biocatalysis in ILs.

Molecular evolution of a cytochrome P450 for the synthesis of potential antidepressant (2R,6R)-hydroxynorketamine

Saturation mutagenesis at seven first-sphere residues of the cytochrome P450 monooxygenase 154E1 (CYP154E1) from Thermobifida fusca YX was applied to construct a variant with only three substitutions that enabled the effective two-step synthesis of the potential antidepressant (2R,6R)-hydroxynorketamine. A recombinant E. coli whole-cell system was essential for GC/MS based medium-throughput screening and at the same time facilitated the oxidation of the substrate (R)-ketamine at a higher scale for product isolation and subsequent NMR analysis.

Unravelling nitrene chemistry from acyclic precursors: recent advances and challenges

Recent advances in nitrene chemistry from acyclic precursors are reviewed in this paper.

Mechanistic and chemoselective insights on sp3- and sp2-C–H bond aminations: Fe- vs. Ir-based catalysis

The mechanisms of Fe- and Ir-catalyzed sp³- and sp²-C–H bond aminations of a styryl substrate have been studied using the BPW91 method, with an emphasis on the origin of sp³-to-sp²-C–H amination chemoselectivity.

Direct intramolecular C(sp3)–H bond sulfonamidation to synthesize benzosultam derivatives under metal-free conditions

An efficient intramolecular C(sp3)–H bond amination under metal-free conditions has been developed to provide a straightforward method for the synthesis of 5-membered cyclic sulfonamides (benzosultams).

Organic synthesis with the most abundant transition metal–iron: from rust to multitasking catalysts

The promising aspects of iron in synthetic chemistry are being explored for three-four decades as a green and eco-friendly alternative to late transition metals. This present review unveils these rich iron-chemistry towards different transformations.

Enzymatic Bioreactors: An Electrochemical Perspective

Biocatalysts provide a number of advantages such as high selectivity, the ability to operate under mild reaction conditions and availability from renewable resources that are of interest in the development of bioreactors for applications in the pharmaceutical and other sectors. The use of oxidoreductases in biocatalytic reactors is primarily focused on the use of NAD(P)-dependent enzymes, with the recycling of the cofactor occurring via an additional enzymatic system. The use of electrochemically based systems has been limited. This review focuses on the development of electrochemically based biocatalytic reactors. The mechanisms of mediated and direct electron transfer together with methods of immobilising enzymes are briefly reviewed. The use of electrochemically based batch and flow reactors is reviewed in detail with a focus on recent developments in the use of high surface area electrodes, enzyme engineering and enzyme cascades. A future perspective on electrochemically based bioreactors is presented.

Expanding the applicability of cytochrome P450s and other haemoproteins

Cytochrome P450BM3 has long been regarded as a promising candidate for use as a biocatalyst, owing to its excellent efficiency for the hydroxylation of unactivated C-H bonds. However, because of its high substrate specificity, its possible applications have been severely limited. Consequently, various approaches have been proposed to overcome the enzyme's natural limitations, thereby expanding its substrate scope to encompass non-native substrates, evoking chemoselectivity, regioselectivity and stereoselectivity and enabling previously inaccessible chemical conversions. Herein, these approaches will be classified into three categories: (1) mutagenesis including directed evolution, (2) haem substitution with artificial cofactors and (3) use of substrate mimics, 'decoy molecules'. Herein, we highlight the representative work that has been conducted in above three categories for discussion of the future outlook of P450BM3 in green chemistry.

Highly efficient H2S scavengers via thiolysis of positively-charged NBD amines

H2S is a well-known toxic gas and also a gaseous signaling molecule involved in many biological processes. Advanced chemical tools that can regulate H2S levels in vivo are useful for understanding H2S biology as well as its potential therapeutic effects. To this end, we have developed a series of 7-nitro-1,2,3-benzoxadiazole (NBD) amines as potential H2S scavengers. The kinetic studies of thiolysis reactions revealed that incorporation of positively-charged groups onto the NBD amines greatly increased the rate of the H2S-specific thiolysis reaction. We demonstrate that these reactions proceed effectively, with second order rate constants (k 2) of >116 M-1 s-1 at 37 °C for NBD-S8. Additionally, we demonstrate that NBD-S8 can effectively scavenge enzymatically-produced and endogenous H2S in live cells. Furthering the biological significance, we demonstrate NBD-S8 mediates scavenging of H2S in mice.

Mechanism-Guided Design and Discovery of Efficient Cytochrome P450-Derived C-H Amination Biocatalysts

Cytochromes P450 have been recently identified as a promising class of biocatalysts for mediating C-H aminations via nitrene transfer, a valuable transformation for forging new C-N bonds. The catalytic efficiency of P450s in these non-native transformations is however significantly inferior to that exhibited by these enzymes in their native monooxygenase function. Using a mechanism-guided strategy, we report here the rational design of a series of P450_BM3-based variants with dramatically enhanced C-H amination activity acquired through disruption of the native proton relay network and other highly conserved structural elements within this class of enzymes. This approach further guided the identification of XplA and BezE, two "atypical" natural P450s implicated in the degradation of a man-made explosive and in benzastatins biosynthesis, respectively, as very efficient C-H aminases. Both XplA and BezE could be engineered to further improve their C-H amination reactivity, which demonstrates their evolvability for abiological reactions. These engineered and natural P450 catalysts can promote the intramolecular C-H amination of arylsulfonyl azides with over 10 000-14 000 catalytic turnovers, ranking among the most efficient nitrene transfer biocatalysts reported to date. Mechanistic and structure-reactivity studies provide insights into the origin of the C-H amination reactivity enhancement and highlight the divergent structural requirements inherent to supporting C-H amination versus C-H monooxygenation reactivity within this class of enzymes. Overall, this work provides new promising scaffolds for the development of nitrene transferases and demonstrates the value of mechanism-driven rational design as a strategy for improving the catalytic efficiency of metalloenzymes in the context of abiological transformations.

The Hitchhiker's guide to biocatalysis: recent advances in the use of enzymes in organic synthesis

Enzymes are excellent catalysts that are increasingly being used in industry and academia. This perspective is primarily aimed at synthetic organic chemists with limited experience using enzymes and provides a general and practical guide to enzymes and their synthetic potential, with particular focus on recent applications.

Recent advances in the field of artificial hemoproteins: New efficient eco-compatible biocatalysts for nitrene-, oxene- and carbene-transfer reactions

In the last few years, the field of artificial hemoproteins has been expanding through two main strategies involving either the incorporation of synthetic metalloporphyrin derivatives into the chiral cavity of a protein or the directed evolution of natural hemoproteins such as myoglobin and cytochromes P450. First, various synthetic water-soluble porphyrins including ions of transition metals such as iron and manganese have been inserted covalently or by supramolecular anchoring into non-specifically designed native proteins or into proteins modified by a minimum number of mutations. The obtained artificial hemoproteins were able to catalyze oxene transfer reactions such as epoxidation of alkenes or sulfoxidation of sulfides and cyclopropanation reactions with good activities and moderate enantioselectivities. Recently, a second approach, based on the design of the active site of already existing native hemoproteins such as myoglobin and cytochromes P450 by directed evolution, has led to new artificial hemoproteins that are able to catalyze oxene transfer reactions with improved activities as well as with abiological reactions. This approach thus provided promising tools for the catalysis of reactions such as intramolecular or intermolecular carbene and nitrene transfer reactions with high efficiencies. In addition, in all cases, after a few rounds of mutagenesis, mutants that were able to catalyze those reactions with a high enantioselectivity could be obtained. Finally, several groups showed that these new artificial metalloenzymes could also be used for the preparative scale-production of compounds with an excellent enantioselectivity, opening new pathways for the industrial synthesis of compounds of pharmaceutical interest.

Copper-catalyzed nitrene transfer/cyclization cascade to synthesize 3a-nitrogenous furoindolines and pyrroloindolines

Copper-catalyzed nitrene transfer for amination/cyclization of tryptophols and tryptamines to generate the corresponding indole alkaloids in good to excellent yields was successfully developed.

Hot off the Press

A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as burlemarxione A from Clusia burle-marxii.