BioStructNet: Structure-Based Network with Transfer Learning for Predicting Biocatalyst Functions.

Enzyme-substrate interactions are essential to both biological processes and industrial applications. Advanced machine learning techniques have significantly accelerated biocatalysis research, revolutionizing the prediction of biocatalytic activities and facilitating the discovery of novel biocatalysts. However, the limited availability of data for specific enzyme functions, such as conversion efficiency and stereoselectivity, presents challenges for prediction accuracy.

Structurally Diverse Nitrogen-Rich Scaffolds via Continuous Photo-Click Reactions.

Continuous flow technology was exploited for the effective generation of nitrile imines via photolysis of substituted aryl tetrazoles. The resulting photo-click process rapidly affords advanced nitrogen-rich scaffolds upon the subsequent trapping of the reactive dipole with alkenes, alkynes, and benzylic amines. Crucially, this approach uncovers the differential reactivity for ether vs amine tethers, thus providing facile and scalable access to underexplored medicinally relevant heterocyclic entities.

Continuous Flow Approach for Benzylic Photo-oxidations Using Compressed Air.

A continuous flow approach for the aerobic photo-oxidation of benzylic substrates to ketone and aldehyde products is presented. The resulting process exploits UV-A LEDs (375 nm) in combination with a Corning AFR reactor that ensures effective gas-liquid mixing and leads to short residence times of 1 min. A variety of benzylic substrates are converted to their corresponding carbonyl products, and scalability is demonstrated to produce multigram quantities of products within a few hours.

Expanding the toolbox of Baeyer-Villiger and flavin monooxygenase biocatalysts for the enantiodivergent green synthesis of sulfoxides.

Two new monooxygenase biocatalysts, the Baeyer-Villiger monooxygenase BVMO145 and the flavin monooxygenase FMO401 from Almac library, have been found to catalyse the enantiodivergent oxidation of sulfides bearing N-heterocyclic substituents into sulfoxides under mild and green conditions. The biocatalyst BVMO145 provides ()-sulfoxides while the flavin monooxygenase FMO401 affords ()-sulfoxides with good conversions and high ee.

Multiphase photochemistry in flow mode an integrated continuous stirred tank reactor (CSTR) approach.

A new photochemical CSTR system capable of handling solids in scaled continuous processes is presented. High-power UV-LEDs are integrated in these CSTRs containing an insoluble base that aids in generating pyrazolines cycloaddition between alkenes and generated diazo species. Contrary to reported batch methods product degradation ring contraction is suppressed whilst generating gram quantities of spirocyclic pyrazolines.

Application of rational enzyme engineering in a new route to etonogestrel and levonorgestrel: carbonyl reductase bioreduction of ethyl secodione.

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ALDELE: All-Purpose Deep Learning Toolkits for Predicting the Biocatalytic Activities of Enzymes.

Rapidly predicting enzyme properties for catalyzing specific substrates is essential for identifying potential enzymes for industrial transformations. The demand for sustainable production of valuable industry chemicals utilizing biological resources raised a pressing need to speed up biocatalyst screening using machine learning techniques. In this research, we developed an all-purpose deep-learning-based multiple-toolkit (ALDELE) workflow for screening enzyme catalysts.

Modular Synthesis of Benzoylpyridines Exploiting a Reductive Arylation Strategy.

Herein we disclose a telescoped flow strategy to access electronically differentiated bisaryl ketones as potentially new and tunable photosensitizers containing both electron-rich benzene systems and electron-deficient pyridyl moieties. Our approach merges a light-driven (365 nm) and catalyst-free reductive arylation between aromatic aldehydes and cyanopyridines with a subsequent oxidation process. The addition of electron-donating and withdrawing substituents on the scaffold allowed effective modification of the absorbance of these compounds in the UV-vis region, while the continuous flow process affords high yields, short residence time, and high throughput.

Origin of the enantioselectivity of alcohol dehydrogenase.

Alcohol dehydrogenases (ADH) are a family of enzymes that catalyse the interconversion between ketones/aldehydes and alcohols in the presence of NADPH cofactor. It is challenging to desymmetrise the substituted cyclopentane-1,3-dione by engineering an ADH, while the reaction mechanism of the metal independent ADH remains elusive. Here we measured the conversion of a model substrate 2-benzyl-2-methylcyclopentane-1,3-dione by ADH and found it predominately gave the (2,3) product.

Nitrilase mediated mild hydrolysis of a carbon-14 nitrile for the radiosynthesis of 4-(7-hydroxycarbamoyl-[1- C-heptanoyl]-oxy)-benzoic acid methyl ester, [ C]-SHP-141: A novel class I/II histone deacetylase (HDAC) inhibitor.

A strategy has been developed for the carbon-14 radiosynthesis of [ C]-SHP-141, a 4-(7-hydroxycarbamoyl-heptanoyloxy)-benzoic acid methyl ester derivative containing a terminal hydroxamic acid. The synthesis involved four radiochemical transformations. The key step in the radiosynthesis was the conversion of the 7-[ C]-cyano-heptanoic acid benzyloxyamide [ C]-4 directly into the carboxylic acid derivative, 7-benzyloxycarbamoyl-[ C]-heptanoic acid [ C]-8 using nitrilase-113 biocatalyst.

Discovery and Rational Mutagenesis of Methionine Sulfoxide Reductase Biocatalysts To Expand the Substrate Scope of the Kinetic Resolution of Chiral Sulfoxides.

Methionine sulfoxide reductase A (MsrA) enzymes have recently found applications as nonoxidative biocatalysts in the enantioselective kinetic resolution of racemic sulfoxides. This work describes the identification of selective and robust MsrA biocatalysts able to catalyze the enantioselective reduction of a variety of aromatic and aliphatic chiral sulfoxides at 8-64 mM concentration with high yields and excellent ees (up to 99%). Moreover, with the aim to expand the substrate scope of MsrA biocatalysts, a library of mutant enzymes has been designed via rational mutagenesis utilizing docking, molecular dynamics, and structural nuclear magnetic resonance (NMR) studies.

Convergent Biocatalytic Mediated Synthesis of siRNA.

New technologies are required to combat the challenges faced with manufacturing commercial quantities of oligonucleotide drug substances which are required for treating large patient populations. Herein we report a convergent biocatalytic synthesis strategy for an Alnylam model siRNA. The siRNA chemical structure includes several of the unnatural modifications and conjugations typical of siRNA drug substances.

Continuous Flow Epoxidation of Alkenes Using a Homogeneous Manganese Catalyst with Peracetic Acid.

Epoxidation of alkenes is a valuable transformation in the synthesis of fine chemicals. Described herein are the design and development of a continuous flow process for carrying out the epoxidation of alkenes with a homogeneous manganese catalyst at metal loadings as low as 0.05 mol%.

Discovery of New Carbonyl Reductases Using Functional Metagenomics and Applications in Biocatalysis.

Enzyme discovery for use in the manufacture of chemicals, requiring high stereoselectivities, continues to be an important avenue of research. Here, a sequence directed metagenomics approach is described to identify short chain carbonyl reductases. PCR from a metagenomic template generated 37 enzymes, with an average 25% sequence identity, twelve of which showed interesting activities in initial screens.

Interrupted Curtius Rearrangements of Quaternary Proline Derivatives: A Flow Route to Acyclic Ketones and Unsaturated Pyrrolidines.

Conversion of -Boc-protected quaternary proline derivatives under thermal Curtius rearrangement conditions was found to afford a series of ring-opened ketone and unsaturated pyrrolidine products instead of the expected carbamate species. The nature of the substituent on the quaternary carbon thereby governs the product outcome due to the stability of a postulated -acyliminium species. A continuous flow process with in-line scavenging was furthermore developed to streamline this transformation and safely create products on a gram scale.

Recent Trends in Enzyme Immobilization-Concepts for Expanding the Biocatalysis Toolbox.

Enzymes have been exploited by humans for thousands of years in brewing and baking, but it is only recently that biocatalysis has become a mainstream technology for synthesis. Today, enzymes are used extensively in the manufacturing of pharmaceuticals, food, fine chemicals, flavors, fragrances and other products. Enzyme immobilization technology has also developed in parallel as a means of increasing enzyme performance and reducing process costs.

Coupling biocatalysis with high-energy flow reactions for the synthesis of carbamates and β-amino acid derivatives.

A continuous flow process is presented that couples a Curtius rearrangement step with a biocatalytic impurity tagging strategy to produce a series of valuable Cbz-carbamate products. Immobilized CALB was exploited as a robust hydrolase to transform residual benzyl alcohol into easily separable benzyl butyrate. The resulting telescoped flow process was effectively applied across a series of acid substrates rendering the desired carbamate structures in high yield and purity.

A mild and chemoselective CALB biocatalysed synthesis of sulfoxides exploiting the dual role of AcOEt as solvent and reagent.

A mild, chemoselective and sustainable biocatalysed synthesis of sulfoxides has been developed exploiting CALB and using AcOEt with a dual role of more environmentally friendly reaction solvent and enzyme substrate. A series of sulfoxides, including the drug omeprazole, have been synthesised in high yields and with excellent E-factors.

Regio- and stereoselectivity in the CYP450-catalyzed hydroxylation of complex terpenoids: a QM/MM study.

The site-selective C-H oxidation of terpenoids by P450 attracts great attention because of their wide range of biological activities. However, the binding and catalytic mechanism of P450 for the hydroxylation of complex terpenoid substrates remains elusive, which has limited the rational engineering of P450 as a biocatalyst for terpenoid biosynthesis. Here, we studied the origin of the selectivity and reactivity of P450BM3 in the hydroxylation of terpenoids by combining molecular dynamics simulations and QM/MM calculations, using artemisinin as a model compound.

Unconventional Biocatalytic Approaches to the Synthesis of Chiral Sulfoxides.

Sulfoxides are a class of organic compounds that find wide application in medicinal and organic chemistry. Several biocatalytic approaches have been developed to synthesise enantioenriched sulfoxides, mainly by exploiting oxidative enzymes. Recently, the use of reductive enzymes such as Msr and Dms has emerged as a new, alternative method to obtain enantiopure sulfoxides from racemic mixtures.

Biocatalysis in seawater: Investigating a halotolerant ω-transaminase capable of converting furfural in a seawater reaction medium.

The increasing demand for freshwater and the continued depletion of available resources has led to a deepening global water crisis. Significant water consumption required by many biotechnological processes contributes to both the environmental and economic cost of this problem. Relatively few biocatalytic processes have been developed to utilize the more abundant supply of seawater, with seawater composition and salinity limiting its use with many mesophilic enzymes.

Fluorescent molecular logic gates based on photoinduced electron transfer (PET) driven by a combination of atomic and biomolecular inputs.

Molecular AND logic gates 1, 3, 5 and 7, which are designed according to principles of photoinduced electron transfer (PET) switching, respond to co-existing Candida antarctica lipase B and H+ (and Na+).

Transaminases for industrial biocatalysis: novel enzyme discovery.

Transaminases (TAms) are important enzymes for the production of chiral amines for the pharmaceutical and fine chemical industries. Novel TAms for use in these industries have been discovered using a range of approaches, including activity-guided methods and homologous sequence searches from cultured microorganisms to searches using key motifs and metagenomic mining of environmental DNA libraries. This mini-review focuses on the methods used for TAm discovery over the past two decades, analyzing the changing trends in the field and highlighting the advantages and drawbacks of the respective approaches used.

Sequential Palladium-Catalyzed Allylic Alkylation/retro-Dieckmann Fragmentation Strategy for the Synthesis of α-Substituted Acrylonitriles.

A straightforward synthesis of α-substituted acrylonitriles is described using 4-cyano-3-oxotetrahydro-thiophene (c-THT) as an acrylonitrile surrogate. This unprecedented two-step sequence featuring a palladium-catalyzed allylic alkylation (Pd-AA) and a retro-Dieckmann fragmentation provides a general entry into diversely substituted 1,4-dienes.

Metagenomic ene-reductases for the bioreduction of sterically challenging enones.

Ene-reductases (ERs) of the Old Yellow Enzyme family catalyse asymmetric reduction of activated alkenes providing chiral products. They have become an important method in the synthetic chemists' toolbox offering a sustainable alternative to metal-catalysed asymmetric reduction. Development of new biocatalytic alkene reduction routes, however needs easy access to novel biocatalysts.