The Evolving Nature of Biocatalysis in Pharmaceutical Research and Development

JACS Au, Год журнала: 2023, Номер 3(3), С. 715 - 735

Опубликована: Фев. 27, 2023

Biocatalysis is a highly valued enabling technology for pharmaceutical research and development as it can unlock synthetic routes to complex chiral motifs with unparalleled selectivity efficiency. This perspective aims review recent advances in the implementation of biocatalysis across early late-stage focus on processes preparative-scale syntheses.

Язык: Английский

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Machine learning-guided co-optimization of fitness and diversity facilitates combinatorial library design in enzyme engineering

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Июль 29, 2024

Abstract The effective design of combinatorial libraries to balance fitness and diversity facilitates the engineering useful enzyme functions, particularly those that are poorly characterized or unknown in biology. We introduce MODIFY, a machine learning (ML) algorithm learns from natural protein sequences infer evolutionarily plausible mutations predict fitness. MODIFY co-optimizes predicted sequence starting libraries, prioritizing high-fitness variants while ensuring broad coverage. In silico evaluation shows outperforms state-of-the-art unsupervised methods zero-shot prediction enables ML-guided directed evolution with enhanced efficiency. Using we engineer generalist biocatalysts derived thermostable cytochrome c achieve enantioselective C-B C-Si bond formation via new-to-nature carbene transfer mechanism, leading six away previously developed enzymes exhibiting superior comparable activities. These results demonstrate MODIFY’s potential solving challenging problems beyond reach classic evolution.

Язык: Английский

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The Time and Place for Nature in Drug Discovery

JACS Au, Год журнала: 2022, Номер 2(11), С. 2400 - 2416

Опубликована: Окт. 14, 2022

The case for a renewed focus on Nature in drug discovery is reviewed; not terms of natural product screening, but how and why biomimetic molecules, especially those produced by processes, should deliver the age artificial intelligence screening vast collections both vitro silico. declining product-likeness licensed drugs consequent physicochemical implications this trend context current practices are noted. To arrest these trends, logic seeking new bioactive agents with enhanced mimicry considered; notably that molecules constructed proteins (enzymes) more likely to interact other (e.g., targets transporters), notion validated products. Nature's finite number building blocks their interactions necessarily reduce potential numbers structures, yet enable expansion chemical space inherent diversity physical characteristics, pertinent property-based design. feasible variations motifs considered expanded encompass pseudo-natural products, leading further logical step harnessing bioprocessing routes access them. Together, offer opportunities enhancing mimicry, thereby bringing innovation synthesis exploiting characteristics recognition processes. computational guidance help identifying binding commonalities route map opportunity design tailored "organic/biological" rather than purely "synthetic" structures. prototype structures pay dividends disposition efficacy while inherently enabling greener sustainable manufacturing techniques.

Язык: Английский

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Biocatalytic Enantioselective Synthesis of Atropisomers

Accounts of Chemical Research, Год журнала: 2022, Номер 55(23), С. 3362 - 3375

Опубликована: Ноя. 7, 2022

ConspectusAtropisomeric compounds are found extensively as natural products, ligands for asymmetric transition-metal catalysis, and increasingly bioactive pharmaceutically relevant targets. Their enantioselective synthesis is therefore an important ongoing research target. While a vast majority of known atropisomeric structures (hetero)biaryls, which display hindered rotation around C–C single bond, our group's long-standing interest in the control molecular conformation has led to identification stereoselective preparation variety other classes "nonbiaryl" displaying restricted C–C, C–N, C–O, C–S bonds.Biocatalytic transformations finding increasing application both academic industrial contexts result significant broadening range biocatalytic reactions sources enzymes available synthetic chemist. In this Account, we summarize main strategies currently biaryl, heterobiaryl, nonbiaryl atropisomers. As case with more traditional approaches these compounds, most methodologies construction enantioenriched atropisomers follow one two distinct strategies. The first direct bonds. Synthetically applicable type transformation limited, despite extensive into biosynthesis (hetero)biaryls by oxidative homocoupling or cross-coupling electron-rich arenes. second molecule bond that will form axis already exists, approach represents organic This strategy encompasses techniques including kinetic resolution (KR), desymmetrization, dynamic (DKR), (DYKAT).Nondynamic (KR) conformationally stable biaryl derivatives provided earliest numerous examples synthetically useful compounds. Lipases (i.e., mediate formation hydrolysis esters) particularly effective have attracted broad attention. success researchers broaden scope lipase-mediated desymmetrization reactions, addition limited number DKR DYKAT examples. By contrast, group used redox enzymes, engineered galactose oxidase (GOase) commercially ketoreductases (KREDs), desymmetrize prochiral diaryl ether derivatives. Building on experience conformational processes, later harnessed intramolecular noncovalent interactions facilitate at ambient temperatures, allowed development efficient heterobiaryl aldehydes using KREDs. With Account provide overview current prospective chemist molecules.

Язык: Английский

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Chemoenzymatic Cascades Combining Biocatalysis and Transition Metal Catalysis for Asymmetric Synthesis

Angewandte Chemie International Edition, Год журнала: 2023, Номер 62(18)

Опубликована: Фев. 6, 2023

Abstract The combination of catalytic methods provides multiple advantages in organic synthesis, allowing access to diverse molecules a straightforward manner. Merging metal and enzyme catalysis is currently receiving great attention due the possibility assemble C−C coupling, olefin metathesis, hydration other reactions with exquisite stereospecificity displayed by enzymes. Thus, this minireview organized based on action species (Pd, Ru, Au, Ir, Fe…) different Special will be paid design sequential processes concurrent cascades, presenting solutions such as use surfactants or compartmentalization strategies for those cases where incompatibilities could hamper overall process.

Язык: Английский

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Enzyme-controlled stereoselective radical cyclization to arenes enabled by metalloredox biocatalysis

Nature Catalysis, Год журнала: 2023, Номер 6(7), С. 628 - 636

Опубликована: Июль 20, 2023

Язык: Английский

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Iron Heme Enzyme-Catalyzed Cyclopropanations with Diazirines as Carbene Precursors: Computational Explorations of Diazirine Activation and Cyclopropanation Mechanism

Journal of the American Chemical Society, Год журнала: 2024, Номер 146(5), С. 2959 - 2966

Опубликована: Янв. 25, 2024

The mechanism of cyclopropanations with diazirines as air-stable and user-friendly alternatives to commonly employed diazo compounds within iron heme enzyme-catalyzed carbene transfer reactions has been studied by means density functional theory (DFT) calculations model systems, quantum mechanics/molecular mechanics (QM/MM) calculations, molecular dynamics (MD) simulations the cyclopropanation transition state in enzyme active site. reaction is initiated a direct diazirine-diazo isomerization occurring site enzyme. In contrast, an proceeding via formation free intermediate lieu direct, one-step process was observed for systems. Subsequent benzyl acrylate takes place through stepwise C–C bond diradical intermediate, delivering cyclopropane product. origin diastereo- enantioselectivity investigated MD simulations, which indicate preferred cis-cyclopropane steric control.

Язык: Английский

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Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products

Natural Product Reports, Год журнала: 2024, Номер 41(10), С. 1543 - 1578

Опубликована: Янв. 1, 2024

This review highlights methods for studying structure activity relationships of natural products and proposes that these are complementary could be used to build an iterative computational-experimental workflow.

Язык: Английский

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Engineered P450 Atom-Transfer Radical Cyclases are Bifunctional Biocatalysts: Reaction Mechanism and Origin of Enantioselectivity

Journal of the American Chemical Society, Год журнала: 2022, Номер 144(29), С. 13344 - 13355

Опубликована: Июль 13, 2022

New-to-nature radical biocatalysis has recently emerged as a powerful strategy to tame fleeting open-shell intermediates for stereoselective transformations. In 2021, we introduced novel metalloredox that leverages the innate redox properties of heme cofactor P450 enzymes, furnishing new-to-nature atom-transfer cyclases (ATRCases) with excellent activity and stereoselectivity. Herein, report combined computational experimental study shed light on mechanism origins enantioselectivity this system. Molecular dynamics quantum mechanics/molecular mechanics (QM/MM) calculations revealed an unexpected role key beneficial mutation I263Q. The glutamine residue serves essential hydrogen bond donor engages carbonyl moiety substrate promote bromine atom abstraction enhance cyclization. Therefore, evolved ATRCase is bifunctional biocatalyst, wherein enables biocatalysis, while further enhances enantioselectivity. Unlike many enzymatic stereocontrol rationales based rigid binding model, our computations demonstrate high degree rotational flexibility allyl in enzyme-substrate complex succeeding intermediates. controlled by cyclization transition states rather than orientation ground-state complexes preceding steps. During cyclization, anchoring effects Q263 steric interactions concurrently control π-facial selectivity, allowing highly enantioselective C-C formation. Our findings are corroborated experiments mutants generated from site-directed mutagenesis.

Язык: Английский

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Strategies for Transferring Photobiocatalysis to Continuous Flow Exemplified by Photodecarboxylation of Fatty Acids

ACS Catalysis, Год журнала: 2022, Номер 12(22), С. 14040 - 14049

Опубликована: Окт. 31, 2022

The challenges of light-dependent biocatalytic transformations lipophilic substrates in aqueous media are manifold. For instance, photolability the catalyst as well insufficient light penetration into reaction vessel may be further exacerbated by a heterogeneously dispersed substrate. Light addressed performing continuous flow, which allows two modes applying catalyst: (i) heterogeneously, immobilized on carrier, requires light-permeable supports, or (ii) homogeneously, dissolved mixture. Taking photodecarboxylation palmitic acid catalyzed fatty-acid photodecarboxylase from Chlorella variabilis (CvFAP) showcase, strategies for transfer photoenzyme-catalyzed flow were identified. A range different supports evaluated immobilization CvFAP, whereby Eupergit C250 L was carrier choice. As photostability limiting factor, homogeneous system preferred instead employing heterogenized enzyme. This implied that photolabile enzymes preferably applied solution if repair mechanisms cannot provided. Furthermore, when comparing wavelengths and intensities, extinction coefficients considered to ensure comparable absorption at each wavelength. Employing conditions CvFAP-catalyzed afforded space-time yield unsurpassed any reported batch process (5.7 g·L–1·h–1, 26.9 mmol·L–1·h–1) this reaction, demonstrating advantage attaining higher productivity photobiocatalytic processes.

Язык: Английский

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