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Articles by Binju Wang
Janus Reactivity of a Mononuclear Non-Heme Iron(III)-Peroxo Complex Toward Indole Oxidation
1 Introduction Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) are heme enzymes that catalyze the oxidative cleavage of the indole ring of L-tryptophan (L-Trp), thereby initiating the kynurenine pathway of tryptophan metabolism [1-12]. The active site of these enzymes features a heme iron center where molecular dioxygen (O2) is activated for substrate oxidations. In their reactions, TDO and IDO differ markedly in substrate tolerance.
Anchoring mechanism-inspired discovery of a bacterial P450 gene conferring resistance to auxin herbicides
Abstract Herbicides in combination with genetically modified herbicide-resistant crops have revolutionized modern weed management, increased crop yields, and facilitated farming practices. However, rapid evolution of herbicide-resistant weeds necessitates new resistance traits to sustain control efficacy.
Intracellular assembly of artificial enzymes for cytoplasmic enantioselective Mannich reactions
Abstract Artificial enzymes constructed by introducing abiological catalytic cofactors into protein scaffolds are emerging as promising biocatalysts for reactions that have no natural equivalents. However, the design of artificial enzymes for in cellulo stereoselective biosynthesis remains largely unexplored because of the numerous challenges posed by the complex cellular environment.
Enantioselective C( sp 3 )–C( sp 3 ) bond formation by synergistic thiamine-dependent radical biocatalysis and photoredox catalysis
Abstract Radical C(sp3)–C(sp3) bond formation has emerged as a promising strategy for constructing molecules rich in C(sp3)–stereocentres. However, achieving chemo- and enantioselective recombination of two prochiral alkyl radicals remains a substantial challenge. Here we synergistically repurpose a thiamine-dependent benzoylformate decarboxylase (PpBFD) with a photoinduced radical process, unlocking unnatural photobiocatalytic C(sp3)–C(sp3) bond formation.
A two-metalloenzyme cascade constructs the azetidine-containing pharmacophore - Nature Chemistry
Abstract Azetidine is a prominent pharmacophore present in dozens of drug-related molecules of both natural and synthetic origins. But how nature builds this moiety has long remained enigmatic. Here we address the full deciphering of a two-metalloenzyme cascade leading to polyoximic acid, an azetidine-containing moiety of the fungicide polyoxin. We demonstrate that the PolE enzyme functions as an Fe2+/pterin-dependent l-isoleucine desaturase.
Photobiocatalytic benzylic C–H acylation enabled by the synergy of a thiamine-dependent enzyme, an organophotocatalyst and hydrogen-atom transfer - Nature Synthesis
Abstract Direct functionalization of abundant C(sp3)–H bonds is highly attractive. Photobiocatalysis offers promise for expanding enzyme reactivity but has been limited to the use of preactivated radical precursors. Key challenges for C(sp3)–H bond activation include the lack of robust activation modes for the inert bonds under biocatalytic conditions and controlling the reactivity and stereochemistry of prochiral radicals.
An NAD⁺ analogue enables assembly of structurally diverse artificial photoenzymes for enantiodivergent [2 + 2] cycloadditions - Nature Catalysis
Abstract Although artificial enzymes have significantly expanded the scope of enzyme-catalysed transformations, their construction typically relies on the irreversible incorporation of non-natural active sites. Inspired by natural cofactors, here we show a reversible binding strategy for artificial enzyme design using benzophenone adenine dinucleotide (BpAD), a photoactive NAD⁺ analogue that can integrate seamlessly into a broad range of NAD⁺-dependent protein scaffolds.
Steering oxygen-centred radicals with ground-state ene-reductases for enantioselective intermolecular hydroalkoxylations - Nature Catalysis
Abstract Enzymes are emerging as promising catalysts for selective radical transformations. However, non-natural radical-type enzymatic catalysis is currently limited to utilizing C-, N- and S-centred radical species. Alkoxy radicals are recognized as versatile intermediates with high reactivity, typically engaging in reactivity modes such as hydrogen atom transfer, β-scission processes and intramolecular addition to alkenes.
Photoenzymatic enantioselective synthesis of fluorinated amides with remote stereocenter - Nature Communications
Abstract Fluorinated compounds are scarce in nature, albeit they are in high demand in pharmaceuticals, agrochemicals, and materials. Fluorinated amides serve as prevalent structural motifs in pharmaceuticals and bioactive molecules. However, enantioselective synthesis of fluorinated amides remains challenging. Herein, we develop a visible-light-driven ene-reductase system that effectively generates carbon-centered radicals from fluorine-containing brominated amides.
QM/MM Unlocks the Catalytic mechanism of YtfE: The Structural Reorganization of the Active Site Enables Nitrite‐to‐NO Conversion
Supporting Information As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors.
Enhancing MM/P(G)BSA Methods: Integration of Formulaic Entropy for Improved Binding Free Energy Calculations
Conflicts of Interest The authors declare no conflicts of interest. Supporting Information Filename Description jcc70093-sup-0001-supinfo.docxWord 2007 document , 781.6 KB Data S1. Supporting Information. References 1, , , and , “Recent Developments in Free Energy Calculations for Drug Discovery,” Frontiers in Molecular Biosciences 8 (2021): 712085. 2 and , “Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods,” Chemical Reviews 116 (2016): 5520–5566.
An efficient catalytic route in haem peroxygenases mediated by O2/small-molecule reductant pairs for sustainable applications - Nature Catalysis
Abstract Haem peroxygenases are attractive biocatalysts for incorporating oxygen into organic molecules using H2O2. However, their practical applications are hindered by irreversible oxidative inactivation due to exogenous H2O2 usage. Here we present an alternative catalytic route in haem peroxygenases that uses O2 and small-molecule reductants such as ascorbic acid and dehydroascorbic acid (DHA) to drive reactions.
Synergistic photobiocatalysis for enantioselective triple radical sorting - Nature
Abstract Multicomponent reactions – those where three or more substrates combine into a product – have been highly useful in rapidly building chemical building blocks of increased complexity4, but achieving this enzymatically has remained rare.5 This limitation primarily arises because an enzyme’s active site is not typically set up to address multiple substrates, especially in cases involving multiple radical intermediates6.
A Human Feedback Strategy for Photoresponsive Molecules in Drug Delivery: Utilizing GPT-2 and Time-Dependent Density Functional Theory Calculations
All articles published by MDPI are made immediately available worldwide under an open access license. No special permission is required to reuse all or part of the article published by MDPI, including figures and tables. For articles published under an open access Creative Common CC BY license, any part of the article may be reused without permission provided that the original article is clearly cited. For more information, please refer to https://www.mdpi.com/openaccess.
Oligo-Adenine and Cyanuric Acid Supramolecular DNA-Based Hydrogels Exhibiting Acid-Resistance and Physiological pH-Responsiveness
RETURN TO ARTICLES ASAPPREVApplications of Poly...Applications of Polymer, Composite, and Coating MaterialsNEXT * Yuwei Hu Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore 138634, Republic of Singapore *Y.H.: email, ywhu@imre.a-star.edu.sg , Jia Liu State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry,...
Elucidating the Enzymatic Mechanism of Dihydrocoumarin Degradation: Insight into the Functional Evolution of Methyl-Parathion Hydrolase from QM/MM and MM MD Simulations
Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Phys. Chem. B 2024, XXXX, XXX Terms & Conditions Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses).
Elucidating the Enzymatic Mechanism of Dihydrocoumarin Degradation: Insight into the Functional Evolution of Methyl-Parathion Hydrolase from QM/MM and MM MD Simulations
RETURN TO ISSUEPREVB: Biophysical and B...B: Biophysical and Biochemical Systems and ProcessesNEXT Yuzhuang Fu State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China , Jun Yu State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry,...
Reshaping the QM Region On-the-Fly: Adaptive-Shape QM/MM Dynamic Simulations of a Hydrated Proton in Bulk Water
Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Chem. Theory Comput. 2024, XXXX, XXX Terms & Conditions Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses).
Flavin‐N5OOH Functions as both a Powerful Nucleophile and a Base in the Superfamily of Flavoenzymes
Conflict of interest The authors declare no conflict of interest. Supporting Information As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors.
Flavin‐N5OOH Functions as both a Powerful Nucleophile and a Base in the Superfamily of Flavoenzymes
Supporting Information As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors.
Rapidly determining the 3D structure of proteins by surface-enhanced Raman spectroscopy
Vertically stacked quantum well diodes for multifunctional applications
Dual-functioning multiple quantum well (MQW) diodes can simultaneously transmit and receive information through visible light. Here, we report vertically stacked red, green, and blue (RGB) MQW diodes for light detection and display applications. Both blue and green MQW diodes are monolithically integrated with distributed Bragg reflector (DBR) filters to realize the separation of light.
Characterization and structure-based protein engineering of a regiospecific saponin acetyltransferase from Astragalus membranaceus - Nature Communications
Abstract Acetylation contributes to the bioactivity of numerous medicinally important natural products. However, little is known about the acetylation on sugar moieties. Here we report a saponin acetyltransferase from Astragalus membranaceus. AmAT7-3 is discovered through a stepwise gene mining approach and characterized as the xylose C3′/C4′-O-acetyltransferse of astragaloside IV (1).
Direct visible-light-excited flavoproteins for redox-neutral asymmetric radical hydroarylation - Nature Catalysis
Abstract State-of-the-art non-natural photoenzymatic catalysis typically relies on either ultraviolet light activation or the formation of electron donor–acceptor complexes. Inspired by nature, herein we develop a biocatalytic scheme based on direct visible-light excitation of flavoprotein to achieve stereocontrolled intermolecular radical hydroarylation of alkenes with electron-rich arenes.
Reply to Correspondence on “Structural Insight into the Catalytic Mechanism of the Endoperoxide Synthase FtmOx1′′
Graphical Abstract The 2-oxoglutarate (2OG)-dependent non-heme enzyme FtmOx1 can catalyze the endoperoxidation of fumitremorgin B, producing verruculogen. The side product of deisoprenylation becomes the major product when the analogue 13-oxo-fumitremorgin B is used as the substrate. Fumitremorgin B and 13-oxo-fumitremorgin B show similar substrate-binding patterns with FtmOx1 but different enzymatic conversions.
Reply to Correspondence on “Structural Insight into the Catalytic Mechanism of the Endoperoxide Synthase FtmOx1′′
Abstract The high-resolution X-ray crystal structure of the ternary complex FtmOx1 ⋅ 2OG ⋅ fumitremorgin B and the catalytic mechanism were recently reported by us (DOI 10.1002/anie.202112063). In their Correspondence, Zhang, Costello, Liu et al. criticize our work in several aspects. Herein, we address these questions one by one. These structural clarifications and new computational results further support the CarC-like mechanistic model.
Miniature GaN optoelectronic temperature sensor
Abstract The combination of plastic optical fiber (POF) with monolithically integrated transmitter and receiver is becoming increasingly attractive for the development of miniature optoelectronic sensing systems. Here, we propose a temperature sensing system by integrating a GaN optoelectronic chip with a POF and aluminum (Al) reflector.
Photoenzymatic enantioselective intermolecular radical hydroamination - Nature Catalysis
Author notes These authors contributed equally: Zhengyi Zhang, Jianqiang Feng.
Preorganized Internal Electric Field Promotes a Double-Displacement Mechanism for the Adenine Excision Reaction by Adenine DNA Glycosylase
Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Phys. Chem. B 2023, 127, 40 Terms & Conditions Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses).
Palladium-Catalyzed Multicomponent Assembly of (Z)-Alkenylborons via Carbopalladation/Boronation/Retro-Diels-Alder Cascade Reaction
A palladium-catalyzed multicomponent cascade reaction of aryl iodides, oxanorbornadiene, and diborns to access (Z)-alkenylborons is reported. This transformation proceeds through the sequential carbopalladation/boronation/retro-Diels–Alder domino reaction. The oxanorbornadiene used in this reaction serves as an acetylene surrogate, which is generated via a retro-Diels–Alder reaction.
Catalytic cycle of formate dehydrogenase captured by single-molecule conductance - Nature Catalysis
Author notes These authors contributed equally: Aihui Zhang, Xiaoyan Zhuang, Jia Liu, Jiacheng Huang. Authors and Affiliations State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, P. R.
Structural Insight into the Catalytic Mechanism of the Endoperoxide Synthase FtmOx1
Research Article Lian Wu, Lian Wu orcid.org/0000-0003-3110-7380 The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine (IRI), Shanghai University of Traditional Chinese Medicine, Shanghai, 201203 China Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, University of Chinese Academy of Sciences, Shanghai, 200032 China These authors contributed equally to this work.
Brønsted Acid Catalyzed Dearomatization by Intramolecular Hydroalkoxylation/Claisen Rearrangement: Diastereo‐ and Enantioselective Synthesis of Spirolactams
Research Article Peng-Fei Chen, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China These authors contributed equally to this work.
Spin‐Regulated Electron Transfer and Exchange‐Enhanced Reactivity in Fe4S4‐Mediated Redox Reaction of the Dph2 Enzyme During the Biosynthesis of Diphthamide
Research Article Dr. Jianqiang Feng, State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China Search for more papers by this author Prof. Sason Shaik, Corresponding Author sason@yfaat.ch.huji.ac.il Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401 Israel Search for more papers by this author Prof.
The molecular mechanism of P450-catalyzed amination of the pyrrolidine derivative of lidocaine: insights from multiscale simulations
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Efficient Catalysts for the Green Synthesis of Adipic Acid from Biomass
Research Article Dr. Weiping Deng State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, National Engineering Laboratory for Green Chemical Productions of Alcohols, Ethers and Esters, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China These authors contributed equally to this work.
How Oxygen Binding Enhances Long‐Range Electron Transfer: Lessons From Reduction of Lytic Polysaccharide Monooxygenases by Cellobiose Dehydrogenase
Research Article Dr. Zhanfeng Wang State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China Search for more papers by this author Dr. Shishi Feng State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical...
Photoenzymatic enantioselective intermolecular radical hydroalkylation
This is an unedited manuscript that has been accepted for publication. Nature Research are providing this early version of the manuscript as a service to our authors and readers. The manuscript will undergo copyediting, typesetting and a proof review before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers apply.
Quantum-Mechanical/Molecular-Mechanical Studies of CYP11A1-Catalyzed Biosynthesis of Pregnenolone from Cholesterol Reveal a C-C Bond Cleavage Reaction That Occurs by a Compound I-Mediated Electron Transfer | Journal of the American Chemical Society
We explore here a long-standing mechanistic question by using quantum-mechanical/molecular-mechanical (QM/MM) methodology. The question concerns the mechanism of steroid hormone biosynthesis, whereby the P450 enzyme, CYP11A1, catalyzes the C20–C22 bond-cleavage in the 20,22-hydroxylated cholesterol, 20R,22R-DiOHCH, leading to pregnenolone, which is critical for the subsequent production of all steroid hormones.
Zirconia-supported rhenium oxide as an efficient catalyst for the synthesis of biomass-based adipic acid ester
Zirconia-supported rhenium oxide as an efficient catalyst for the synthesis of biomass-based adipic acid ester Synthesis of adipic acid, a key monomer of nylon-66 and polyurethane, from biomass is highly attractive for establishing green and sustainable chemical processes.
Fenton-Derived OH Radicals Enable the MPnS Enzyme to Convert 2-Hydroxyethylphosphonate to Methylphosphonate: Insights from Ab Initio QM/MM MD Simulations
The mechanism for dioxygen activation represents one of the core issues in metalloenzymes. In most cases, the activation of the O2 molecule requires additional electrons from an external reducant. However, nonheme hydroxyethylphosphonate dioxygenase (HEPD) and methylphosphonate synthase (MPnS) are exceptional C–H oxygenases.
Chemo‐ and Regioselective Dihydroxylation of Benzene to Hydroquinone Enabled by Engineered Cytochrome P450 Monooxygenase
Corresponding Author E-mail address: reetz@mpi-muelheim.mpg.de http://orcid.org/0000-0001-6246-647X Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, , Tianjin, 300308 China Max-Planck-Institut für Kohlenforschung, , 45470 Muelheim, Germany Department of Chemistry, Philipps-University, , 35032 Marburg, Germany Search for more papers by this author
Chemo‐ and Regioselective Dihydroxylation of Benzene to Hydroquinone Enabled by Engineered Cytochrome P450 Monooxygenase
Hydroquinone (HQ) is produced commercially from benzene by multi‐step Hock‐type processes with equivalent amounts of acetone as side‐product. We describe an efficient biocatalytic alternative using the cytochrome P450‐BM3 monooxygenase. Since the wildtype enzyme does not accept benzene, a semi‐rational protein engineering strategy was developed.
Transformation of cellulose and related carbohydrates into lactic acid with bifunctional Al(III)–Sn(II) catalysts
Catalytic transformation of cellulose into valuable chemicals such as lactic acid under mild conditions represents a promising route for efficient utilization of renewable biomass. Here, we report that the combination of Al(III) and Sn(II) cations can efficiently catalyse the conversion of cellulose and related carbohydrates into lactic acid in water. The Al(III)?Sn(II) is the most efficient combination for lactic acid formation among many dual cations investigated.
Computation Sheds Insight into Iron Porphyrin Carbenes’ Electronic Structure, Formation, and N-H Insertion Reactivity
Iron porphyrin carbenes constitute a new frontier of species with considerable synthetic potential. Exquisitely engineered myoglobin and cytochrome P450 enzymes can generate these complexes and facilitate the transformations they mediate.
How do Enzymes Utilize Reactive OH Radicals? Lessons from Nonheme HppE and Fenton Systems
The iron(IV)–oxo (ferryl) intermediate has been amply established as the principal oxidant in nonheme enzymes and the key player in C–H bond activations and functionalizations.
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