Biocatalyzed C−C Bond Formation for the Production of Alkaloids

Recent advances in enzymatic carbon-carbon bond formation

Enzymatic carbon-carbon (C-C) bond formation reactions have become an effective and invaluable tool for designing new biological and medicinal molecules, often with asymmetric features. This review provides a systematic overview of key C-C bond formation reactions and enzymes, with the focus of reaction mechanisms and recent advances. These reactions include the aldol reaction, Henry reaction, Knoevenagel condensation, Michael addition, Friedel-Crafts alkylation and acylation, Mannich reaction, Morita-Baylis-Hillman (MBH) reaction, Diels-Alder reaction, acyloin condensations via Thiamine Diphosphate (ThDP)-dependent enzymes, oxidative and reductive C-C bond formation, C-C bond formation through C1 resource utilization, radical enzymes for C-C bond formation, and other C-C bond formation reactions.

Silylacetate-promoted addition reaction of isocyanides to nitrones: effective synthesis of C(1)-carboxamide derivatives

We report an efficient method for the synthesis of C(1)-carboxamide derivatives by adding isocyanides to 3,4-dihydroisoquinoline N-oxides and 3,4-dihydro-β-carboline 2-oxide in the presence of TMSOAc. 3,4-Dihydroisoquinoline-1-carboxylamide derivatives and 9-dihydro-3H-pyrido[3,4-b]indole-1-carboxamide derivatives were obtained in reasonable yields. The method could be used to synthesize alangiobussine, an alkaloid, in 61% yield.

Uncovering the Mechanism of Azepino-Indole Skeleton Formation via Pictet-Spengler Reaction by Strictosidine Synthase: A Quantum Chemical Investigation

Strictosidine synthase (STR) catalyzes the Pictet-Spengler (PS) reaction of tryptamine and secologanin to produce strictosidine. Recent studies demonstrated that the enzyme can also catalyze the reaction of non-natural substrates to form new alkaloid skeletons. For example, the PS condensation of 1H-indole-4-ethanamine with secologanin could be promoted by the STR from Rauvolfia serpentina (RsSTR) to generate a rare class of skeletons with a seven-membered ring, namely azepino-[3,4,5-cd]-indoles, which are precursors for the synthesis of new compounds displaying antimalarial activity. In the present study, the detailed reaction mechanism of RsSTR-catalyzed formation of the rare seven-membered azepino-indole skeleton through the PS reaction was revealed at the atomic level by quantum chemical calculations. The structures of the transition states and intermediates involved in the reaction pathway were optimized, and the energetics of the complete reaction were analyzed. Based on our calculation results, the most likely pathway of the enzyme-catalyzed reaction was determined, and the rate-determining step of the reaction was clarified. The mechanistic details obtained in the present study are important in understanding the promiscuous activity of RsSTR in the formation of the rare azepino-indole skeleton molecule and are also helpful in designing STR enzymes for the synthesis of other new alkaloid skeleton molecules.

The Quantum Chemical Cluster Approach in Biocatalysis

ConspectusThe quantum chemical cluster approach has been used for modeling enzyme active sites and reaction mechanisms for more than two decades. In this methodology, a relatively small part of the enzyme around the active site is selected as a model, and quantum chemical methods, typically density functional theory, are used to calculate energies and other properties. The surrounding enzyme is modeled using implicit solvation and atom fixing techniques. Over the years, a large number of enzyme mechanisms have been solved using this method. The models have gradually become larger as a result of the faster computers, and new kinds of questions have been addressed. In this Account, we review how the cluster approach can be utilized in the field of biocatalysis. Examples from our recent work are chosen to illustrate various aspects of the methodology. The use of the cluster model to explore substrate binding is discussed first. It is emphasized that a comprehensive search is necessary in order to identify the lowest-energy binding mode(s). It is also argued that the best binding mode might not be the productive one, and the full reactions for a number of enzyme-substrate complexes have therefore to be considered to find the lowest-energy reaction pathway. Next, examples are given of how the cluster approach can help in the elucidation of detailed reaction mechanisms of biocatalytically interesting enzymes, and how this knowledge can be exploited to develop enzymes with new functions or to understand the reasons for lack of activity toward non-natural substrates. The enzymes discussed in this context are phenolic acid decarboxylase and metal-dependent decarboxylases from the amidohydrolase superfamily. Next, the application of the cluster approach in the investigation of enzymatic enantioselectivity is discussed. The reaction of strictosidine synthase is selected as a case study, where the cluster calculations could reproduce and rationalize the selectivities of both the natural and non-natural substrates. Finally, we discuss how the cluster approach can be used to guide the rational design of enzyme variants with improved activity and selectivity. Acyl transferase from Mycobacterium smegmatis serves as an instructive example here, for which the calculations could pinpoint the factors controlling the reaction specificity and enantioselectivity. The cases discussed in this Account highlight thus the value of the cluster approach as a tool in biocatalysis. It complements experiments and other computational techniques in this field and provides insights that can be used to understand existing enzymes and to develop new variants with tailored properties.

Asymmetric Synthesis of Fused-Ring Tetrahydroisoquinolines and Tetrahydro-β-carbolines from 2-Arylethylamines via a Chemoenzymatic Approach

While chiral fused-ring tetrahydroisoquinoline (THIQ) and tetrahydro-β-carboline (THβC) scaffolds have attracted considerable interest due to their wide spectrum of biological activities, the synthesis of optically pure chiral fused-ring THIQs and THβCs remains a challenging task. Herein, a group of active imine reductases were identified to convert the imine precursors into the corresponding enantiocomplementary fused-ring THIQs and THβCs with high enantioselectivity and conversion, establishing an efficient and green chemoenzymatic approach to fused-ring alkaloids from 2-arylethylamines.

Regioselective Biocatalytic C4-Prenylation of Unprotected Tryptophan Derivatives

Regioselective carbon-carbon bond formation belongs to the challenging tasks in organic synthesis. In this context, C-C bond formation catalyzed by 4-dimethylallyltryptophan synthases (4-DMATSs) represents a possible tool to regioselectively synthesize C4-prenylated indole derivatives without site-specific preactivation and circumventing the need of protection groups as used in chemical synthetic approaches. In this study, a toolbox of 4-DMATSs to produce a set of 4-dimethylallyl tryptophan and indole derivatives was identified. Using three wild-type enzymes as well as variants, various C5-substituted tryptophan derivatives as well as N-methyl tryptophan were successfully prenylated with conversions up to 90 %. Even truncated tryptophan derivatives like tryptamine and 3-indole propanoic acid were regioselectively prenylated in position C4. The acceptance of C5-substituted tryptophan derivatives was improved up to 5-fold by generating variants (e. g. T108S). The feasibility of semi-preparative prenylation of selected tryptophan derivatives was successfully demonstrated on 100 mg scale at 15 mM substrate concentration, allowing to reduce the previously published multistep chemical synthetic sequence to just a single step.

Biocatalysis making waves in organic chemistry

Biocatalysis has an enormous impact on chemical synthesis. The waves in which biocatalysis has developed, and in doing so changed our perception of what organic chemistry is, were reviewed 20 and 10 years ago. Here we review the consequences of these waves of development. Nowadays, hydrolases are widely used on an industrial scale for the benign synthesis of commodity and bulk chemicals and are fully developed. In addition, further enzyme classes are gaining ever increasing interest. Particularly, enzymes catalysing selective C-C-bond formation reactions and enzymes catalysing selective oxidation and reduction reactions are solving long-standing synthetic challenges in organic chemistry. Combined efforts from molecular biology, systems biology, organic chemistry and chemical engineering will establish a whole new toolbox for chemistry. Recent developments are critically reviewed.

Copper-Mediated Decarboxylative Coupling between Arylacetic Acids and 1,3-Dicarbonyl Compounds

A copper-mediated decarboxylative coupling reaction between arylacetic acids and 1,3-dicarbonyl compounds was described. Significantly, methanocycloocta[b]indoles were also obtained by sequential intramolecular dehydrocyclization process in some cases. This protocol featured a broad substrate scope, simple operations, and good yields. Moreover, the products exhibited potent antiproliferative activity against the human cancer cell lines by a MTT assay.

Recent advances in biocatalysis of nitrogen-containing heterocycles

Nitrogen-containing heterocycles (N-heterocycles) are ubiquitous in both organisms and pharmaceutical products. Biocatalysts are providing green approaches for synthesizing various N-heterocycles under mild reaction conditions. This review summarizes the recent advances in the biocatalysis of N-heterocycles through the discovery and engineering of natural N-heterocycle synthetic pathway, and the design of artificial synthetic routes, with an emphasis on biocatalysts applied in retrosynthetic design for preparing complex N-heterocycles. Furthermore, this review discusses the future prospects and challenges of biocatalysts involved in the synthesis of N-heterocycles.

The role of biocatalysis in the asymmetric synthesis of alkaloids - an update

Alkaloids are a group of natural products with interesting pharmacological properties and a long history of medicinal application. Their complex molecular structures have fascinated chemists for decades, and their total synthesis still poses a considerable challenge. In a previous review, we have illustrated how biocatalysis can make valuable contributions to the asymmetric synthesis of alkaloids. The chemo-enzymatic strategies discussed therein have been further explored and improved in recent years, and advances in amine biocatalysis have vastly expanded the opportunities for incorporating enzymes into synthetic routes towards these important natural products. The present review summarises modern developments in chemo-enzymatic alkaloid synthesis since 2013, in which the biocatalytic transformations continue to take an increasingly 'central' role.

Recent trends in biocatalysis

Biocatalysis has undergone revolutionary progress in the past century. Benefited by the integration of multidisciplinary technologies, natural enzymatic reactions are constantly being explored. Protein engineering gives birth to robust biocatalysts that are widely used in industrial production. These research achievements have gradually constructed a network containing natural enzymatic synthesis pathways and artificially designed enzymatic cascades. Nowadays, the development of artificial intelligence, automation, and ultra-high-throughput technology provides infinite possibilities for the discovery of novel enzymes, enzymatic mechanisms and enzymatic cascades, and gradually complements the lack of remaining key steps in the pathway design of enzymatic total synthesis. Therefore, the research of biocatalysis is gradually moving towards the era of novel technology integration, intelligent manufacturing and enzymatic total synthesis.

Broadening the scope of biocatalytic C-C bond formation

The impeccable control over chemo-, site-, and stereoselectivity possible in enzymatic reactions has led to a surge in the development of new biocatalytic methods. Despite carbon-carbon (C-C) bonds providing the central framework for organic molecules, development of biocatalytic methods for their formation has been largely confined to the use of a select few lyases over the last several decades, limiting the types of C-C bond-forming transformations possible through biocatalytic methods. This Review provides an update on the suite of enzymes available for highly selective biocatalytic C-C bond formation. Examples will be discussed in reference to the (1) native activity of enzymes, (2) alteration of activity through protein or substrate engineering for broader applicability, and (3) utility of the biocatalyst for abiotic synthesis.

Coenzyme A thioester-mediated carbon chain elongation as a paintbrush to draw colorful chemical compounds

The biosynthesis of various useful chemicals from simple substrates using industrial microorganisms is becoming increasingly crucial to address the challenge of dwindling non-renewable resources. As the most common intermediate substrates in organisms, Coenzyme A (CoA) thioesters play a central role in the carbon chain elongation process of their products. As a result, numerous of chemicals can be synthesized by the iterative addition of various CoA thioester extender units at a given CoA thioester primer backbone. However, these elongation reactions and the product yields are still restricted due to the low enzymatic performance and supply of CoA thioesters. This review highlights the current protein and metabolic engineering strategies used to enhance the diversity and product yield by coupling different primers, extender units, enzymes, and termination pathways, in an attempt to provide a road map for producing a more diverse range of industrial chemicals.

Production of 12-hydroxy dodecanoic acid methyl ester using a signal peptide sequence-optimized transporter AlkL and a novel monooxygenase

In this study, a signal peptide of AlkL was replaced with other signal peptides to improve the soluble expression and thereby facilitate the transport of dodecanoic acid methyl ester (DAME) substrate into the E. coli. Consequently, AlkL with signal peptide FadL (AlkL_f) showed higher transport activity toward DAME. Furthermore, the promoter optimization for the efficient heterologous expression of the transporter AlkL_f and alkane monooxygenase (AlkBGT) system was conducted and resulted in increased ω-oxygenation activity of AlkBGT system. Moreover, bioinformatic studies led to the identification of novel monooxygenase from Pseudomonas pelagia (Pel), which exhibited 20% higher activity towards DAME as substrate compared to AlkB. Finally, the construction of a chimeric transporter and the expression of newly identified monooxygenase enabled the production of 44.8 ± 7.5 mM of 12-hydroxy dodecanoic acid methyl ester (HADME) and 31.8 ± 1.7 mM of dodecanedioic acid monomethyl ester (DDAME) in a two-phase reaction system.

Kinetic Resolution of Racemic Amines to Enantiopure (S)-amines by a Biocatalytic Cascade Employing Amine Dehydrogenase and Alanine Dehydrogenase

Amine dehydrogenases (AmDHs) efficiently catalyze the NAD(P)H-dependent asymmetric reductive amination of prochiral carbonyl substrates with high enantioselectivity. AmDH-catalyzed oxidative deamination can also be used for the kinetic resolution of racemic amines to obtain enantiopure amines. In the present study, kinetic resolution was carried out using a coupled-enzyme cascade consisting of AmDH and alanine dehydrogenase (AlaDH). AlaDH efficiently catalyzed the conversion of pyruvate to alanine, thus recycling the nicotinamide cofactors and driving the reaction forward. The ee values obtained for the kinetic resolution of 25 and 50 mM rac-α-methylbenzylamine using the purified enzymatic systems were only 54 and 43%, respectively. The use of whole-cells apparently reduced the substrate/product inhibition, and the use of only 30 and 40 mgDCW/mL of whole-cells co-expressing AmDH and AlaDH efficiently resolved 100 mM of rac-2-aminoheptane and rac-α-methylbenzylamine into the corresponding enantiopure (S)-amines. Furthermore, the applicability of the reaction protocol demonstrated herein was also successfully tested for the efficient kinetic resolution of wide range of racemic amines.

Biosynthesis of Nylon 12 Monomer, ω-Aminododecanoic Acid Using Artificial Self-Sufficient P450, AlkJ and ω-TA

ω-Aminododecanoic acid is considered as one of the potential monomers of Nylon 12, a high-performance member of the bioplastic family. The biosynthesis of ω-aminododecanoic acid from renewable sources is an attractive process in the polymer industry. Here, we constructed three artificial self-sufficient P450s (ArtssP450s) using CYP153A13 from Alcanivorax borkumensis and cytochrome P450 reductase (CPR) domains of natural self-sufficient P450s (CYP102A1, CYP102A5, and 102D1). Among them, artificial self-sufficient P450 (CYP153A13BM3CPR) with CYP102A1 CPR showed the highest catalytically activity for dodecanoic acid (DDA) substrate. This form of ArtssP450 was further co-expressed with ω-TA from Silicobacter pomeroyi and AlkJ from Pseudomonas putida GPo1. This single-cell system was used for the biotransformation of dodecanoic acid (DDA) to ω-aminododecanoic acid (ω-AmDDA), wherein we could successfully biosynthesize 1.48 mM ω-AmDDA from 10 mM DDA substrate in a one-pot reaction. The productivity achieved in the present study was five times higher than that achieved in our previously reported multistep biosynthesis method (0.3 mM).