Merging enzymes with chemocatalysis for amide bond synthesis

Switching Nitrilase With Enantioselective Hydration Activity for Efficient Synthesis of Chiral 2,2-Dimethylcyclopropanecarboxamide

Chiral 2,2-dimethylcyclopropanecarboxamides serve as important pharmaceutical intermediates. However, enantioselective synthesis of 2,2-dimethylcyclopropanecarboxamides is difficult due to the unique bond angle and rigid planar structure of the dimethylcyclopropane skeleton. Although nitrile hydratases are attractive for amide biosynthesis, their practical applications are restricted because of narrow substrate spectrum and poor enantioselectivity. The catalytic promiscuity of nitrilases has brought an opportunity to engineer them with specific hydration activity and strict enantioselectivity. Through regulation of the characteristic distances affecting reaction specificity, as well as the key interface structure regions, a nitrilase BaNIT was switched into a novel "nitrile hydratase-like" enzyme with enhanced hydration activity and enantioselectivity toward 2,2-dimethylcyclopropanecarbonitrile. It represented a paradigmatic example for chiral amide synthesis via nitrilase. Compared to the wild type, the proportion of amide synthesized by the mutant increased from 11.2% to 98.8% with enantiomeric ratio (E) value increased from 10.8 to 291. Moreover, in-depth structural-functional analyses provided valuable insights into the molecular mechanisms underlying the enhanced catalytic performance, laying a solid foundation for the rational design of nitrilases with tailored properties for their broader applications.

Enzymatic Cascades for Stereoselective and Regioselective Amide Bond Assembly

Amide bond formation is fundamental in nature and is widely used in the synthesis of pharmaceuticals and other valuable products. Current methods for amide synthesis are often step and atom inefficient, requiring the use of protecting groups, deleterious reagents and organic solvents that create significant waste. The development of cleaner and more efficient catalytic methods for amide synthesis remains an urgent unmet need. Herein, we present novel biocatalytic cascade reactions for synthesising various amides under mild aqueous conditions from readily available organic nitriles combining nitrile hydrolysing enzymes and amide bond synthetase enzymes. These cooperative biocatalytic cascades enable kinetic resolution of racemic nitriles and provide a highly enantioselective biocatalytic extension of the Strecker reaction. The regioselective non-directed C-H bond amidation of simple arenes was demonstrated through the incorporation of photoredox catalysis to the front end of the cascade. C-H bond amidation of simple aromatic precursors was also achieved via a CO2 fixation cascade combining enzymatic carboxylation and amide bond synthesis in one-pot.

β-Silyl alkynoates: Versatile reagents for biocompatible and selective amide bond formation

The study introduces a previously unidentified method for amide bond formation that addresses several limitations of conventional approaches. It uses the β-silyl alkynoate molecule, where the alkynyl group activates the ester for efficient amide formation, while the bulky TIPS (triisopropylsilane) group prevents unwanted 1,4-addition reactions. This approach exhibits high chemoselectivity for amines, making the method compatible with a wide range of substrates, including secondary amines, and targets the specific ε-amino group of lysine among the native amino ester's derivatives. It maintains stereochemistry during amide bond formation and TIPS group removal, allowing a versatile platform for postsynthesis modifications such as click reactions and peptide-drug conjugations. These advancements hold substantial promise for pharmaceutical development and peptide engineering, opening avenues for research applications.

Ferrocenyl conjugated oxazepines/quinolines: multiyne coupling and ring-expanding or rearrangement

Ferrocenyl conjugated oxazepine/quinoline derivatives were presented through the reaction of hexadehydro-Diels-Alder (HDDA) generated arynes with ferrocenyl oxazolines under mild conditions via ring-expanding or rearrangement processes. Water molecule participated in this unexpected rearrangement process to produce quinoline skeletons, and DFT calculations supported a ring-expanding and intramolecular hydrogen migration process for the formation of oxazepine derivatives. Two variants of this chemistry, expanded the reactivity between ferrocenyl conjugated substances and arynes, further providing an innovative approach for the synthesis of ferrocene derivatives.

One-pot chemo- and photo-enzymatic linear cascade processes

The combination of chemo- and photocatalyses with biocatalysis, which couples the flexible reactivity of the photo- and chemocatalysts with the highly selective and environmentally friendly nature of enzymes in one-pot linear cascades, represents a powerful tool in organic synthesis. However, the combination of photo-, chemo- and biocatalysts in one-pot is challenging because the optimal operating conditions of the involved catalyst types may be rather different, and the different stabilities of catalysts and their mutual deactivation are additional problems often encountered in one-pot cascade processes. This review explores a large number of transformations and approaches adopted for combining enzymes and chemo- and photocatalytic processes in a successful way to achieve valuable chemicals and valorisation of biomass. Moreover, the strategies for solving incompatibility issues in chemo-enzymatic reactions are analysed, introducing recent examples of the application of non-conventional solvents, enzyme-metal hybrid catalysts, and spatial compartmentalization strategies to implement chemo-enzymatic cascade processes.

A Catalytic Approach for the Synthesis of Peptide-Oligonucleotides Conjugates in Aqueous Solution or On-Column

Peptide-oligonucleotide conjugates (POCs) are covalent architectures composed of a DNA or RNA molecules linked to a peptide. These constructs have found widespread applications ranging from hybrid nanomaterials to gene-targeted therapies. Considering the important role of POCs, a new catalytic approach for their preparation is reported here, that could be applied either on solid support in anhydrous media, or post-synthetically in aqueous buffer. Single amino acids, peptides and cell penetrating peptides (CPPs) were conjugated to various oligo(ribo)nucleotides with high conversions and good isolated yields. The applicability of the method was demonstrated on more than 35 examples including an analogue of a commercial therapeutic oligonucleotide. Other conjugation partners, such as deoxycholic acid and biotin were also successfully conjugated to oligonucleotides. To highlight the potential of this catalytic approach, these conditions have been applied to iterative processes, which is of high interest for the development of DNA-Encoded Libraries.

Light Controlled Nanobiohybrids for Modulating Chiral Alcohol Synthesis

The modulation of whole-cell activity presents a considerable challenge in biocatalysis. Conventional approaches to whole-cell catalysis, while having their strengths, often rely on complex and deliberate enzyme designs, which could result in difficulties in activity modulation and prolonged response times. Additionally, the activity of intracellular enzymes in whole-cell catalysis is influenced by temperature. To address these limitations, we introduced a relationally designed nanobiohybrid system that utilized light to modulate whole-cell catalysis for chiral alcohol production. By incorporating platinum nanoparticles onto Rhodotorula sp. cell surfaces, the nanobiohybrid capitalized on the photothermal properties of the nanoparticles to regulate the overall cell activity. When exposed to light, the Pt nanoparticles generate heat through the photothermal effect, consequently leading to an increase in the catalytic activity of the whole cells. This innovative approach facilitates control over whole-cell production and provides an efficient method for regulating biocatalytic processes. The findings of this study demonstrate the significant potential of switchable control strategies in biomanufacturing across a wide range of industries.

Immobilization of Adenosine Derivatives onto Cellulose Nanocrystals via Click Chemistry for Biocatalysis Applications

Adenosine triphosphate (ATP) is a central molecule of organisms and is involved in many biological processes. It is also widely used in biocatalytic processes, especially as a substrate and precursor of many cofactors─such as nicotinamide adenine dinucleotide phosphate (NADP(H)), coenzyme A (CoA), and S-adenosylmethionine (SAM). Despite its great scientific interest and pivotal role, its use in industrial processes is impeded by its prohibitory cost. To overcome this limitation, we developed a greener synthesis of adenosine derivatives and efficiently selectively grafted them onto organic nanoparticles. In this study, cellulose nanocrystals were used as a model combined with click chemistry via a copper-catalyzed azide/alkyne cycloaddition reaction (CuAAC). The grafted adenosine triphosphate derivative fully retains its biocatalytic capability, enabling heterobiocatalysis for modern biochemical processes.

The low loading of metal in metal-organic framework-derived NiNx@NC promotes amide formation through C-N coupling

The pyrolysis of Ni-substituted zeolitic imidazolate framework-8 produces NiNx@NC with an ultra-low loading of Ni (7.4 × 10-6 mol%). The Ni-N coordination, subnanometer particle size, and uniform distribution of NiNx on the NC support lead to excellent catalytic activity (TON = 2702) and selectivity for the amination of aldehydes to produce amides.

Opportunities and Challenges of Metal-Organic Framework Micro/Nano Reactors for Cascade Reactions

Building bridges among different types of catalysts to construct cascades is a highly worthwhile pursuit, such as chemo-, bio-, and chemo-bio cascade reactions. Cascade reactions can improve the reaction efficiency and selectivity while reducing steps of separation and purification, thereby promoting the development of "green chemistry". However, compatibility issues in cascade reactions pose significant constraints on the development of this field, particularly concerning the compatibility of diverse catalyst types, reaction conditions, and reaction rates. Metal-organic framework micro/nano reactors (MOF-MNRs) are porous crystalline materials formed by the self-assembly coordination of metal sites and organic ligands, possessing a periodic network structure. Due to the uniform pore size with the capability of controlling selective transfer of substances as well as protecting active substances and the organic-inorganic parts providing reactive microenvironment, MOF-MNRs have attracted significant attention in cascade reactions in recent years. In this Perspective, we first discuss how to address compatibility issues in cascade reactions using MOF-MNRs, including structural design and synthetic strategies. Then we summarize the research progress on MOF-MNRs in various cascade reactions. Finally, we analyze the challenges facing MOF-MNRs and potential breakthrough directions and opportunities for the future.

Non-Native Site-Selective Enzyme Catalysis

The ability to site-selectively modify equivalent functional groups in a molecule has the potential to streamline syntheses and increase product yields by lowering step counts. Enzymes catalyze site-selective transformations throughout primary and secondary metabolism, but leveraging this capability for non-native substrates and reactions requires a detailed understanding of the potential and limitations of enzyme catalysis and how these bounds can be extended by protein engineering. In this review, we discuss representative examples of site-selective enzyme catalysis involving functional group manipulation and C-H bond functionalization. We include illustrative examples of native catalysis, but our focus is on cases involving non-native substrates and reactions often using engineered enzymes. We then discuss the use of these enzymes for chemoenzymatic transformations and target-oriented synthesis and conclude with a survey of tools and techniques that could expand the scope of non-native site-selective enzyme catalysis.

A Sustainable Green Enzymatic Method for Amide Bond Formation

A sustainable enzymatic strategy for the preparation of amides by using Candida antarctica lipase B as the biocatalyst and cyclopentyl methyl ether as a green and safe solvent was devised. The method is simple and efficient and it produces amides with excellent conversions and yields without the need for intensive purification steps. The scope of the reaction was extended to the preparation of 28 diverse amides using four different free carboxylic acids and seven primary and secondary amines, including cyclic amines. This enzymatic methodology has the potential to become a green and industrially reliable process for direct amide synthesis.

Development of fluorous boronic acid catalysts integrated with sulfur for enhanced amidation efficiency

A thermally stable, fluorous sulfur-containing boronic acid catalyst has been developed and was shown to efficiently promote dehydrative condensation between carboxylic acids and amines under environmentally friendly conditions. The methodology can be applied to aliphatic, aromatic and heteroaromatic acids as well as primary and secondary amines. N-Boc protected amino acids were also successfully coupled in good yields with very little racemization. The catalyst could be reused four times with no significant loss of activity.

Chemical Constituents of the Mushroom Dictyophora indusiata and Their Anti-Inflammatory Activities

As an edible and medicinal fungus, Dictyophora indusiata is well-known for its morphological elegance, distinctive taste, high nutritional value, and therapeutic properties. In this study, eighteen compounds (1-18) were isolated and identified from the ethanolic extract of D. indusiata; four (1-4) were previously undescribed. Their molecular structures and absolute configurations were determined via a comprehensive analysis of spectroscopic data (1D/2D NMR, HRESIMS, ECD, and XRD). Seven isolated compounds were examined for their anti-inflammatory activities using an in vitro model of lipopolysaccharide (LPS)-simulated BV-2 microglial cells. Compound 3 displayed the strongest inhibitory effect on tumor necrosis factor-α (TNF-α) expression, with an IC₅₀ value of 11.9 μM. Compound 16 exhibited the highest inhibitory activity on interleukin-6 (IL-6) production, with an IC₅₀ value of 13.53 μM. Compound 17 showed the most potent anti-inflammatory capacity by inhibiting the LPS-induced generation of nitric oxide (NO) (IC₅₀: 10.86 μM) and interleukin-1β (IL-1β) (IC₅₀: 23.9 μM) and by significantly suppressing induced nitric oxide synthase (iNOS) and phosphorylated nuclear factor-kappa B inhibitor-α (p-IκB-α) expression at concentrations of 5 μM and 20 μM, respectively (p < 0.01). The modes of interactions between the isolated compounds and the target inflammation-related proteins were investigated in a preliminary molecular docking study. These results provided insight into the chemodiversity and potential anti-inflammatory activities of metabolites with small molecular weights in the mushroom D. indusiata.

Comprehensive Theoretical Study of Cp*IrIII-Catalyzed Intermolecular Enantioselective Allylic C-H Amidation: Reaction Mechanism, Electronic Processes, and Regioselectivity

Density functional theory was used to elucidate the reaction mechanism of Cp*Ir^III-catalyzed intermolecular regioselective C(sp³)-H amidation of alkenes with methyl dioxazolones. All substrates, intermediates, and transition states were fully optimized at the ωB97XD/6-31G(d,p) level (LANL2DZ(f) for Ir). The computational results revealed that this amidation occurred through the Ir^III/Ir^V catalytic cycle, involving four important elementary steps: C-H bond activation, oxidative addition of methyl dioxazolone, reductive elimination, and proto-demetalation, and the first was the rate-determining step. The C-H bond activation showed good α- and branch-regioselectivity, decided by the distortion energy of 2-pentene and the interaction energy of the transition state, respectively. The oxidative addition of dioxazolone occurred in one elementary step with CO₂ disassociation. The reductive elimination showed good branch-regioselectivity determined by the distorted energy of the allyl group. In the proto-demetalation, hydrogen directly transferred from the oxygen atom to the nitrogen atom. Moreover, to clarify the effect of the substituted groups, selected 12 substrates were also discussed in this text.

Effective Production of Selected Dioxolanes by Sequential Bio- and Chemocatalysis Enabled by Adapted Solvent Switching

Most combinations of chemo- and biocatalysis take place in aqueous media or require a solvent change with complex intermediate processing. Using enzymes in the same organic solvent as the chemocatalyst eliminates this need. Here, it was shown that a complete chemoenzymatic cascade to form dioxolanes could be carried out in a purely organic environment. The result, including downstream processing, was compared with a classical mode, shifting solvent. First, a two-step enzyme cascade starting from aliphatic aldehydes to chiral diols (3,4-hexanediol and 4,5-octanediol) was run either in an aqueous buffer or in the potentially biobased solvent cyclopentyl methyl ether. Subsequently, a ruthenium molecular catalyst enabled the conversion to dioxolanes [e. g., (4S,5S)-dipropyl-1,3-dioxolane]. Importantly, the total synthesis of this product was not only highly stereoselective but also based on the combination of biomass, CO₂ , and hydrogen, thus providing an important example of a bio-hybrid chemical.

Expanding the Synthetic Toolbox through Metal-Enzyme Cascade Reactions

The combination of metal-, photo-, enzyme-, and/or organocatalysis provides multiple synthetic solutions, especially when the creation of chiral centers is involved. Historically, enzymes and transition metal species have been exploited simultaneously through dynamic kinetic resolutions of racemates. However, more recently, linear cascades have appeared as elegant solutions for the preparation of valuable organic molecules combining multiple bioprocesses and metal-catalyzed transformations. Many advantages are derived from this symbiosis, although there are still bottlenecks to be addressed including the successful coexistence of both catalyst types, the need for compatible reaction media and mild conditions, or the minimization of cross-reactivities. Therefore, solutions are here also provided by means of catalyst coimmobilization, compartmentalization strategies, flow chemistry, etc. A comprehensive review is presented focusing on the period 2015 to early 2022, which has been divided into two main sections that comprise first the use of metals and enzymes as independent catalysts but working in an orchestral or sequential manner, and later their application as bionanohybrid materials through their coimmobilization in adequate supports. Each part has been classified into different subheadings, the first part based on the reaction catalyzed by the metal catalyst, while the development of nonasymmetric or stereoselective processes was considered for the bionanohybrid section.

Where Chemocatalysis Meets Biocatalysis: In Water

Chemoenzymatic catalysis, by definition, involves the merging of sequential reactions using both chemocatalysis and biocatalysis, typically in a single reaction vessel. A major challenge, the solution to which, however, is associated with numerous advantages, is to run such one-pot processes in water: the majority of enzyme-catalyzed processes take place in water as Nature's reaction medium, thus enabling a broad synthetic diversity when using water due to the option to use virtually all types of enzymes. Furthermore, water is cheap, abundantly available, and environmentally friendly, thus making it, in principle, an ideal reaction medium. On the other hand, most chemocatalysis is routinely performed today in organic solvents (which might deactivate enzymes), thus appearing to make it difficult to combine such reactions with biocatalysis toward one-pot cascades in water. Several creative approaches and solutions that enable such combinations of chemo- and biocatalysis in water to be realized and applied to synthetic problems are presented herein, reflecting the state-of-the-art in this blossoming field. Coverage has been sectioned into three parts, after introductory remarks: (1) Chapter 2 focuses on historical developments that initiated this area of research; (2) Chapter 3 describes key developments post-initial discoveries that have advanced this field; and (3) Chapter 4 highlights the latest achievements that provide attractive solutions to the main question of compatibility between biocatalysis (used predominantly in aqueous media) and chemocatalysis (that remains predominantly performed in organic solvents), both Chapters covering mainly literature from ca. 2018 to the present. Chapters 5 and 6 provide a brief overview as to where the field stands, the challenges that lie ahead, and ultimately, the prognosis looking toward the future of chemoenzymatic catalysis in organic synthesis.

Fast quinazolinone synthesis by combining enzymatic catalysis and photocatalysis

A fast and highly efficient method for the synthesis of functionalized quinazolinones by combining enzymatic catalysis and photocatalysis is reported. The α-Chymotrypsin catalyzed the cyclization of aldehyde and 2-aminobenzamide, which was subsequently followed by White LED-induced oxidation of 2-phenyl-2, 3-dihydroquinazolin-4(1H)-one to obtain quinazolinone. The reaction process was highly efficient with a reaction yield of 99% in just 2 h, and a wide range of quinazolinones could be synthesized. Furthermore, the plausible mechanism was investigated by control experiments and DFT calculations. This protocol provides an alternative synthetic route for the preparation of quinazolinone derivatives.

Combined chemoenzymatic strategy for sustainable continuous synthesis of the natural product hordenine

To improve sustainability, safety and cost-efficiency of synthetic methodologies, biocatalysis can be a helpful ally. In this work, a novel chemoenzymatic stategy ensures the rapid synthesis of hordenine, a valuable phenolic phytochemical under mild working conditions. In a two-step cascade, the immobilized tyrosine decarboxylase from Lactobacillus brevis (LbTDC) is here coupled with the chemical reductive amination of tyramine. Starting from the abundant and cost-effective amino acid l-tyrosine, the complete conversion to hordenine is achieved in less than 5 minutes residence time in a fully-automated continuous flow system. Compared to the metal-catalyzed N,N-dimethylation of tyramine, this biocatalytic approach reduces the process environmental impact and improves its STY to 2.68 g L^-1 h^-1.

A Boron-Nitrogen Double Transborylation Strategy for Borane-Catalyzed Hydroboration of Nitriles

Organoborane-catalyzed hydroboration of nitriles provides N,N-diborylamines, which act as efficient synthons for the synthesis of primary amines and secondary amides. Known nitrile hydroboration methods are dominated by metal catalysis. Simple and metal-free hydroboration of nitriles using diborane [H-B-9-BBN]₂ as a catalyst and pinacolborane as a turnover reagent is reported. The reaction of monomeric H-B-9-BBN with nitriles leads to the hydrido-bridged diborylimine intermediate; a subsequent sequential double hydroboration-transborylation pathway involving B-N/B-H σ bond metathesis is proposed.