1
|
Peng W, Shi M, Hu B, Jia J, Li X, Wang N, Man S, Ye S, Ma L. Nanotechnology-leveraged CRISPR/Cas systems: icebreaking in trace cancer-related nucleic acids biosensing. Mol Cancer 2025; 24:78. [PMID: 40087758 PMCID: PMC11908094 DOI: 10.1186/s12943-024-02222-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2024] [Accepted: 12/31/2024] [Indexed: 03/17/2025] Open
Abstract
As promising noninvasive biomarkers, nucleic acids provide great potential to innovate cancer early detection methods and promote subsequent diagnosis to improve the survival rates of patient. Accurate, straightforward and sensitive detection of such nucleic acid-based cancer biomarkers in complex biological samples holds significant clinical importance. However, the low abundance creates huge challenges for their routine detection. As the next-generation diagnostic tool, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas) with their high programmability, sensitivity, fidelity, single-base resolution, and precise nucleic acid positioning capabilities are extremely attractive for trace nucleic acid-based cancer biomarkers (NABCBs), permitting rapid, ultra-sensitive and specific detection. More importantly, by combing with nanotechnology, it can solve the long-lasting problems of poor sensitivity, accuracy and simplicity, as well as to achieve integrated miniaturization and portable point-of-care testing (POCT) detection. However, existing literature lacks specific emphasis on this topic. Thus, we intend to propose a timely one for the readers. This review will bridge this gap by providing insights for CRISPR/Cas-based nano-biosensing development and highlighting the current state-of-art, challenges, and prospects. We expect that it can provide better understanding and valuable insights for trace NABCBs detection, thereby facilitating advancements in early cancer screening/detection/diagnostics and win practical applications in the foreseeable future.
Collapse
Affiliation(s)
- Weipan Peng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Tianjin Key Laboratory of Industry Microbiology, International China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Ministry of Education, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Mengting Shi
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Tianjin Key Laboratory of Industry Microbiology, International China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Ministry of Education, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Bin Hu
- Department of Pharmacy, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471003, China
| | - Jingyu Jia
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Tianjin Key Laboratory of Industry Microbiology, International China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Ministry of Education, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Xinyue Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Tianjin Key Laboratory of Industry Microbiology, International China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Ministry of Education, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Nan Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Tianjin Key Laboratory of Industry Microbiology, International China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Ministry of Education, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Tianjin Key Laboratory of Industry Microbiology, International China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Ministry of Education, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science & Technology, Tianjin, 300457, China.
| | - Shengying Ye
- Pharmacy Department, The 983th Hospital of The Joint Logistics Support Force of The Chinese People's Liberation Army, Tianjin, China.
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Tianjin Key Laboratory of Industry Microbiology, International China International Science and Technology Cooperation Base of Food Nutrition/Safety and Medicinal Chemistry, College of Biotechnology, Ministry of Education, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science & Technology, Tianjin, 300457, China.
| |
Collapse
|
2
|
He H, Yan JX, Zhu JX, Liu SJ, Liu XQ, Chen P, Wang X, Jia ZJ. Enantioselective Trifluoromethylazidation of Styrenyl Olefins Catalyzed by an Engineered Nonheme Iron Enzyme. Angew Chem Int Ed Engl 2025; 64:e202423507. [PMID: 39853573 DOI: 10.1002/anie.202423507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Revised: 01/23/2025] [Accepted: 01/23/2025] [Indexed: 01/26/2025]
Abstract
Organofluorines, particularly those containing trifluoromethyl (CF3) groups, play a critical role in medicinal chemistry. While trifluoromethylation of alkenes provides a powerful synthetic route to construct CF3-containing compounds with broad structural and functional diversity, achieving enantioselective control in these reactions remains a formidable challenge. In this study, we engineered a nonheme iron enzyme, quercetin 2,3-dioxygenase from Bacillus subtilis (BsQueD), for the enantioselective trifluoromethylazidation of alkenes. Through directed evolution, the final variant BsQueD-CF3 exhibited excellent enantioselectivity, with an enantiomeric ratio (e.r.) of up to 98 : 2. Preliminary mechanistic studies suggest the involvement of radical intermediates. This work expands biocatalytic organofluorine chemistry by reprogramming metalloenzymes for innovative trifluoromethylation reactions.
Collapse
Affiliation(s)
- Hua He
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Children's Medicine Key Laboratory of Sichuan Province, Department of Pharmacy/Evidence-Based Pharmacy Center, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Jia-Xin Yan
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Children's Medicine Key Laboratory of Sichuan Province, Department of Pharmacy/Evidence-Based Pharmacy Center, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Jian-Xiang Zhu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Children's Medicine Key Laboratory of Sichuan Province, Department of Pharmacy/Evidence-Based Pharmacy Center, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Si-Jia Liu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Children's Medicine Key Laboratory of Sichuan Province, Department of Pharmacy/Evidence-Based Pharmacy Center, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiao-Qi Liu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Children's Medicine Key Laboratory of Sichuan Province, Department of Pharmacy/Evidence-Based Pharmacy Center, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Peng Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Children's Medicine Key Laboratory of Sichuan Province, Department of Pharmacy/Evidence-Based Pharmacy Center, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Xin Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Children's Medicine Key Laboratory of Sichuan Province, Department of Pharmacy/Evidence-Based Pharmacy Center, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhi-Jun Jia
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Children's Medicine Key Laboratory of Sichuan Province, Department of Pharmacy/Evidence-Based Pharmacy Center, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| |
Collapse
|
3
|
Yadav V, Wen L, Yadav S, Siegler MA, Goldberg DP. Nonheme Mononuclear and Dinuclear Iron(II) and Iron(III) Fluoride Complexes and Their Fluorine Radical Transfer Reactivity. Inorg Chem 2025; 64:682-691. [PMID: 39729544 DOI: 10.1021/acs.inorgchem.4c03335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2024]
Abstract
The nonheme iron(II) complexes containing a fluoride anion, FeII(BNPAPh2O)(F) (1) and [FeII(BNPAPh2OH)(F)(THF)](BF4) (2), were synthesized and structurally characterized. Addition of dioxygen to either 1 or 2 led to the formation of a fluoride-bridged, dinuclear iron(III) complex [Fe2III(BNPAPh2O)2(F)2(μ-F)]+ (4), which was characterized by single-crystal X-ray diffraction, 1H NMR, and elemental analysis. An iron(II)(iodide) complex, FeII(BNPAPh2O)(I) (3), was prepared and reacted with O2 to give the mononuclear complex cis-FeIII(BNPAPh2O)(OH)(I) (5). Addition of excess fluoride to 5 led to the formation of the oxo-bridged, dinuclear iron(III) complex [Fe2III(BNPAPh2O)2(F)2(μ-O)] (6), while the mononuclear iron(III)(fluoride) complex cis-FeIII(BNPAPh2O)(F)(Cl) (7) was prepared from the addition of excess F- to FeIII(BNPAPh2O)Cl2. The dinuclear complexes 4 and 6 were unreactive to fluorine radical transfer, but mononuclear 7 reacts with the radical substrate (p-MeO-C6H4)3C• to give the fluorine radical transfer products FeII(BNPAPh2O)(Cl) and (p-OMe-C6H4)3CF. These results show that a mononuclear FeIII(F) complex is capable of mediating fluorine radical transfer, even in the presence of second coordination sphere hydrogen bonds to the F- ligand. These findings are placed in context with what is known about the nonheme iron halogenases and related synthetic catalysts regarding their ability, or lack thereof, to mediate fluorine radical transfer reactions.
Collapse
Affiliation(s)
- Vishal Yadav
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Lyupeng Wen
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Sudha Yadav
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Maxime A Siegler
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| |
Collapse
|
4
|
Lowe PT, Lüddecke I, O'Hagan D. Exploring Fluorinase Substrate Tolerance at C-2 of SAM. Chembiochem 2025; 26:e202400861. [PMID: 39551710 DOI: 10.1002/cbic.202400861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Revised: 11/14/2024] [Accepted: 11/15/2024] [Indexed: 11/19/2024]
Abstract
The fluorinase enzyme (EC 2.5.1.63) utilises fluoride ion and S-adenosyl-L-methionine (SAM) as substrates for conversion to 5'-fluoro-5'-deoxy-adenosine (5'-FDA) and L-methionine (L-Met). The enzyme has a very strict substrate specificity, however it has been shown to tolerate acetylenes and NH2 replacements for H at C-2 of the adenine ring of SAM. This substrate tolerance is explored further here with -NHR, -N3, -OR and -SR substituents attached to C-2. New activities are demonstrated, for example with NH-methyl, NH-propyl,NH-butyl and O-butyl substrates at C-2, however azide and thioethers were not tolerated. Outcomes are supported by in silico analysis, revealing favourable H-bonding interactions involving NH and O substituents at the adenine C-2 position with N278 and the backbone amide of A279 at the active site respectively. The study informs on the selectivity of the fluorinase as a tool for radiolabelling candidate ligands with fluorine-18 for positron emission tomography programmes.
Collapse
Affiliation(s)
- Phillip T Lowe
- School of Chemistry and Biomedical Sciences Research Centre, University of St Andrews, North Haugh, KY16 9ST, St Andrews, UK
| | - Isabeau Lüddecke
- School of Chemistry and Biomedical Sciences Research Centre, University of St Andrews, North Haugh, KY16 9ST, St Andrews, UK
| | - David O'Hagan
- School of Chemistry and Biomedical Sciences Research Centre, University of St Andrews, North Haugh, KY16 9ST, St Andrews, UK
| |
Collapse
|
5
|
Dvorak KR, Tepe JJ. Advances in the total synthesis of bis- and tris-indole alkaloids containing N-heterocyclic linker moieties. Nat Prod Rep 2024; 41:1264-1293. [PMID: 38666377 PMCID: PMC11323739 DOI: 10.1039/d4np00012a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Indexed: 08/15/2024]
Abstract
The past several years have seen an increase in the discovery and isolation of natural products of the indole alkaloid class. Bis- and tris-indole alkaloids are classes of natural products that have been shown to display diverse, potent biological activities. Of particular interest are bis- and tris-indole alkaloids containing N-heterocyclic linker moieties. It has been reported that more than 85% of biologically active compounds contain one or more heterocyclic moieties; of these, N-heterocycles have been identified as the most prevalent. The goal of this review is to provide a detailed overview of the recent advances in isolation and total synthesis of bis- and tris-indole alkaloids that contain N-heterocyclic linker moieties. The known biological activities of these natural products will also be discussed.
Collapse
|
6
|
Zhao Q, Chen Z, Soler J, Chen X, Rui J, Ji NT, Yu QE, Yang Y, Garcia-Borràs M, Huang X. Engineering non-haem iron enzymes for enantioselective C(sp3)-F bond formation via radical fluorine transfer. NATURE SYNTHESIS 2024; 3:958-966. [PMID: 39364063 PMCID: PMC11446476 DOI: 10.1038/s44160-024-00507-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/21/2024] [Indexed: 10/05/2024]
Abstract
In recent years there has been a surge in the development of methods for the synthesis of organofluorine compounds. However, enzymatic methods for C-F bond formation have been limited to nucleophilic fluoride substitution. Here, we report the incorporation of iron-catalysed radical fluorine transfer, a reaction mechanism that is not used in naturally occurring enzymes, into enzymatic catalysis for the development of biocatalytic enantioselective C(sp 3)-F bond formation. Using this strategy, we repurposed (S)-2-hydroxypropylphosphonate epoxidase from Streptomyces viridochromogenes (SvHppE) to catalyse an N-fluoroamide directed C(sp 3)-H fluorination. Directed evolution has enabled SvHppE to be optimized, forming diverse chiral benzylic fluoride products with turnover numbers of up to 180 and with excellent enantiocontrol (up to 94% e.e.). Mechanistic investigations showed that the N-F bond activation is the rate-determining step, and the strong preference for fluorination in the presence of excess NaN3 can be attributed to the spatial proximity of the carbon-centered radical to the iron-bound fluoride.
Collapse
Affiliation(s)
- Qun Zhao
- School of Biotechnology, Jiangnan University, Wuxi 214122, P. R. China
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Zhenhong Chen
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jordi Soler
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, Girona E-17071, Catalonia, Spain
| | - Xiahe Chen
- State Key Laboratory Breeding Base of Green Chemistry-Synthesis Technology, Key Laboratory of Green Chemistry-Synthesis Technology of Zhejiang Province, College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Jinyan Rui
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Nathan Tianlin Ji
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| | | | - Yunfang Yang
- State Key Laboratory Breeding Base of Green Chemistry-Synthesis Technology, Key Laboratory of Green Chemistry-Synthesis Technology of Zhejiang Province, College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Marc Garcia-Borràs
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, Girona E-17071, Catalonia, Spain
| | - Xiongyi Huang
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
| |
Collapse
|
7
|
Li M, Yuan Y, Harrison W, Zhang Z, Zhao H. Asymmetric photoenzymatic incorporation of fluorinated motifs into olefins. Science 2024; 385:416-421. [PMID: 39052813 DOI: 10.1126/science.adk8464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 06/05/2024] [Indexed: 07/27/2024]
Abstract
Enzymes capable of assimilating fluorinated feedstocks are scarce. This situation poses a challenge for the biosynthesis of fluorinated compounds used in pharmaceuticals, agrochemicals, and materials. We developed a photoenzymatic hydrofluoroalkylation that integrates fluorinated motifs into olefins. The photoinduced promiscuity of flavin-dependent ene-reductases enables the generation of carbon-centered radicals from iodinated fluoroalkanes, which are directed by the photoenzyme to engage enantioselectively with olefins. This approach facilitates stereocontrol through interaction between a singular fluorinated unit and the enzyme, securing high enantioselectivity at β, γ, or δ positions of fluorinated groups through enzymatic hydrogen atom transfer-a process that is notably challenging with conventional chemocatalysis. This work advances enzymatic strategies for integrating fluorinated chemical feedstocks and opens avenues for asymmetric synthesis of fluorinated compounds.
Collapse
Affiliation(s)
- Maolin Li
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Yujie Yuan
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Wesley Harrison
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhengyi Zhang
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Huimin Zhao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- NSF Molecular Maker Lab Institute, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
8
|
Li SH, Zhang X, Mei ZL, Liu Y, Ma JA, Zhang FG. Chemoenzymatic Synthesis of Fluorinated Mycocyclosin Enabled by the Engineered Cytochrome P450-Catalyzed Biaryl Coupling Reaction. J Am Chem Soc 2024; 146:19962-19973. [PMID: 38985576 DOI: 10.1021/jacs.4c03499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Installing fluorine atoms onto natural products holds great promise for the generation of fluorinated molecules with improved or novel pharmacological properties. The enzymatic oxidative carbon-carbon coupling reaction represents a straightforward strategy for synthesizing biaryl architectures, but the exploration of this method for producing fluorine-substituted derivatives of natural products remains elusive. Here, in this study, we report the protein engineering of cytochrome P450 from Mycobacterium tuberculosis (MtCYP121) for the construction of a series of new-to-nature fluorine-substituted Mycocyclosin derivatives. This protocol takes advantage of a "hybrid" chemoenzymatic procedure consisting of tyrosine phenol lyase-catalyzed fluorotyrosine preparation from commercially available fluorophenols, intermolecular chemical condensation to give cyclodityrosines, and an engineered MtCYP121-catalyzed intramolecular biphenol coupling reaction to complete the strained macrocyclic structure. Computational mechanistic studies reveal that MtCYP121 employs Cpd I to abstract a hydrogen atom from the proximal phenolic hydroxyl group of the substrate to trigger the reaction. Then, conformational change makes the two phenolic hydroxyl groups close enough to undergo intramolecular hydrogen atom transfer with the assistance of a pocket water molecule. The final diradical coupling process completes the intramolecular C-C bond formation. The efficiency of the biaryl coupling reaction was found to be influenced by various fluorine substitutions, primarily due to the presence of distinct binding conformations.
Collapse
Affiliation(s)
- Shuo-Han Li
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Xue Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Ze-Long Mei
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Jun-An Ma
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Fa-Guang Zhang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| |
Collapse
|
9
|
Gamba D, van Eijk N, Lányi K, Monostory K, Steinmetzer T, Marosi A, Rácz A, Bajusz D, Kruhl D, Böttcher-Friebertshäuser E, Pászti-Gere E. PK/PD investigation of antiviral host matriptase/TMPRSS2 inhibitors in cell models. Sci Rep 2024; 14:16621. [PMID: 39025978 PMCID: PMC11258351 DOI: 10.1038/s41598-024-67633-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024] Open
Abstract
Certain corona- and influenza viruses utilize type II transmembrane serine proteases for cell entry, making these enzymes potential drug targets for the treatment of viral respiratory infections. In this study, the cytotoxicity and inhibitory effects of seven matriptase/TMPRSS2 inhibitors (MI-21, MI-463, MI-472, MI-485, MI-1900, MI-1903, and MI-1904) on cytochrome P450 enzymes were evaluated using fluorometric assays. Additionally, their antiviral activity against influenza A virus subtypes H1N1 and H9N2 was assessed. The metabolic depletion rates of these inhibitors in human primary hepatocytes were determined over a 120-min period by LC-MS/MS, and PK parameters were calculated. The tested compounds, with the exception of MI-21, displayed potent inhibition of CYP3A4, while all compounds lacked inhibitory effects on CYP1A2, CYP2C9, CYP2C19, and CYP2D6. The differences between the CYP3A4 activity within the series were rationalized by ligand docking. Elucidation of PK parameters showed that inhibitors MI-463, MI-472, MI-485, MI-1900 and MI-1904 were more stable compounds than MI-21 and MI-1903. Anti-H1N1 properties of inhibitors MI-463 and MI-1900 and anti-H9N2 effects of MI-463 were shown at 20 and 50 µM after 24 h incubation with the inhibitors, suggesting that these inhibitors can be applied to block entry of these viruses by suppressing host matriptase/TMPRSS2-mediated cleavage.
Collapse
Affiliation(s)
- Dávid Gamba
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, István Utca 2, 1078, Budapest, Hungary
| | - Nicholas van Eijk
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, István Utca 2, 1078, Budapest, Hungary
| | - Katalin Lányi
- Department of Food Hygiene, University of Veterinary Medicine, István Utca 2, 1078, Budapest, Hungary
| | - Katalin Monostory
- Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok 2, 1117, Budapest, Hungary
| | - Torsten Steinmetzer
- Faculty of Pharmacy, Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - András Marosi
- Virology Research Group, Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Hungária krt 23, 1143, Budapest, Hungary
| | - Anita Rácz
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar Tudósok 2, 1117, Budapest, Hungary
| | - Dávid Bajusz
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar Tudósok 2, 1117, Budapest, Hungary
| | - Diana Kruhl
- Institute of Virology, Philipps-University Marburg, Hans-Meerwein-Str. 2, 35043, Marburg, Germany
| | | | - Erzsébet Pászti-Gere
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, István Utca 2, 1078, Budapest, Hungary.
| |
Collapse
|
10
|
Eletskaya BZ, Mironov AF, Fateev IV, Berzina MY, Antonov KV, Smirnova OS, Zatsepina AB, Arnautova AO, Abramchik YA, Paramonov AS, Kayushin AL, Khandazhinskaya AL, Matyugina ES, Kochetkov SN, Miroshnikov AI, Mikhailopulo IA, Esipov RS, Konstantinova ID. Enzymatic Transglycosylation Features in Synthesis of 8-Aza-7-Deazapurine Fleximer Nucleosides by Recombinant E. coli PNP: Synthesis and Structure Determination of Minor Products. Biomolecules 2024; 14:798. [PMID: 39062512 PMCID: PMC11275124 DOI: 10.3390/biom14070798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 07/28/2024] Open
Abstract
Enzymatic transglycosylation of the fleximer base 4-(4-aminopyridine-3-yl)-1H-pyrazole using recombinant E. coli purine nucleoside phosphorylase (PNP) resulted in the formation of "non-typical" minor products of the reaction. In addition to "typical" N1-pyrazole nucleosides, a 4-imino-pyridinium riboside and a N1-pyridinium-N1-pyrazole bis-ribose derivative were formed. N1-Pyrazole 2'-deoxyribonucleosides and a N1-pyridinium-N1-pyrazole bis-2'-deoxyriboside were formed. But 4-imino-pyridinium deoxyriboside was not formed in the reaction mixture. The role of thermodynamic parameters of key intermediates in the formation of reaction products was elucidated. To determine the mechanism of binding and activation of heterocyclic substrates in the E. coli PNP active site, molecular modeling of the fleximer base and reaction products in the enzyme active site was carried out. As for N1-pyridinium riboside, there are two possible locations for it in the PNP active site. The presence of a relatively large space in the area of amino acid residues Phe159, Val178, and Asp204 allows the ribose residue to fit into that space, and the heterocyclic base can occupy a position that is suitable for subsequent glycosylation. Perhaps it is this "upside down" arrangement that promotes secondary glycosylation and the formation of minor bis-riboside products.
Collapse
Affiliation(s)
- Barbara Z. Eletskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Anton F. Mironov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
- Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia Named after Patrice Lumumba, Miklukho-Maklaya St. 6, Moscow 117198, Russia
| | - Ilya V. Fateev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Maria Ya. Berzina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Konstantin V. Antonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Olga S. Smirnova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Alexandra B. Zatsepina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Alexandra O. Arnautova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Yulia A. Abramchik
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Alexander S. Paramonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Alexey L. Kayushin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Anastasia L. Khandazhinskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia; (A.L.K.); (E.S.M.); (S.N.K.)
| | - Elena S. Matyugina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia; (A.L.K.); (E.S.M.); (S.N.K.)
| | - Sergey N. Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia; (A.L.K.); (E.S.M.); (S.N.K.)
| | - Anatoly I. Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Igor A. Mikhailopulo
- Institute of Bioorganic Chemistry, National Academy of Sciences, Acad. Kuprevicha 5/2, 220141 Minsk, Belarus;
| | - Roman S. Esipov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Irina D. Konstantinova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| |
Collapse
|
11
|
Mkrtchyan S, Shalimov O, Garcia MG, Zapletal J, Iaroshenko VO. Mechanochemical synthesis of aromatic ketones: pyrylium tetrafluoroborate mediated deaminative arylation of amides. Chem Sci 2024; 15:9155-9163. [PMID: 38903233 PMCID: PMC11186303 DOI: 10.1039/d4sc00904e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/30/2024] [Indexed: 06/22/2024] Open
Abstract
A new method has been introduced that is able to tackle the complexities of N-C(O) activation in amide moieties through utilization of pyrylium tetrafluoroborate in a mechanochemical setting, where amide bonds undergo activation and subsequent conversion to biaryl ketones. Due to the employment of a mechanochemical setting, the reaction conforms to green chemistry principles, offering an environmentally friendly approach to traditional amide derivatization techniques that rely on transition metals to achieve further functionalization.
Collapse
Affiliation(s)
- Satenik Mkrtchyan
- Department of Chemistry, Faculty of Natural Sciences, Matej Bel University Tajovského 40 97401 Banska Bystrica Slovakia
| | - Oleksandr Shalimov
- Department of Heteroatom Chemistry, Institute of Organic Chemistry, National Academy of Sciences of Ukraine 5 Murmans'ka 02660 Kyiv Ukraine
| | - Michael G Garcia
- Department of Biology/Chemistry, Center for Cellular Nanoanalytics (CellNanOs), Universität Osnabrück Barbarastr. 7 D-49076 Osnabrück Germany
| | - Jiří Zapletal
- Department of Chemistry, Faculty of Natural Sciences, Matej Bel University Tajovského 40 97401 Banska Bystrica Slovakia
| | - Viktor O Iaroshenko
- Department of Chemistry, Faculty of Natural Sciences, Matej Bel University Tajovského 40 97401 Banska Bystrica Slovakia
- Division of Wood Chemistry and Pulp Technology, Department of Fiber and Polymer Technology, School of Chemistry, Biotechnology and Health, KTH Royal Institute of Technology Teknikringen 56-58 SE-100 44 Stockholm Sweden
- Functional Materials Group, Gulf University for Science and Technology Mubarak Al-Abdullah 32093 Kuwait
- Centre of Research Impact and Outcome, Chitkara University Institute of Engineering and Technology, Chitkara University Rajpura 140401 Punjab India
| |
Collapse
|
12
|
Vennelakanti V, Li GL, Kulik HJ. Why Nonheme Iron Halogenases Do Not Fluorinate C-H Bonds: A Computational Investigation. Inorg Chem 2023; 62:19758-19770. [PMID: 37972340 DOI: 10.1021/acs.inorgchem.3c03215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Selective halogenation is necessary for a range of fine chemical applications, including the development of therapeutic drugs. While synthetic processes to achieve C-H halogenation require harsh conditions, enzymes such as nonheme iron halogenases carry out some types of C-H halogenation, i.e., chlorination or bromination, with ease, while others, i.e., fluorination, have never been observed in natural or engineered nonheme iron enzymes. Using density functional theory and correlated wave function theory, we investigate the differences in structural and energetic preferences of the smaller fluoride and the larger chloride or bromide intermediates throughout the catalytic cycle. Although we find that the energetics of rate-limiting hydrogen atom transfer are not strongly impacted by fluoride substitution, the higher barriers observed during the radical rebound reaction for fluoride relative to chloride and bromide contribute to the difficulty of C-H fluorination. We also investigate the possibility of isomerization playing a role in differences in reaction selectivity, and our calculations reveal crucial differences in terms of isomer energetics of the key ferryl intermediate between fluoride and chloride/bromide intermediates. While formation of monodentate isomers believed to be involved in selective catalysis is shown for chloride and bromide intermediates, we find that formation of the fluoride monodentate intermediate is not possible in our calculations, which lack additional stabilizing interactions with the greater protein environment. Furthermore, the shorter Fe-F bonds are found to increase isomerization reaction barriers, suggesting that incorporation of residues that form a halogen bond with F and elongate Fe-F bonds could make selective C-H fluorination possible in nonheme iron halogenases. Our work highlights the differences between the fluoride and chloride/bromide intermediates and suggests potential steps toward engineering nonheme iron halogenases to enable selective C-H fluorination.
Collapse
Affiliation(s)
- Vyshnavi Vennelakanti
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Grace L Li
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
13
|
Feng X, Zhang Q, Clarke DJ, Deng H, O’Hagan D. 3'- O-β-Glucosyl-4',5'-didehydro-5'-deoxyadenosine Is a Natural Product of the Nucleocidin Producers Streptomyces virens and Streptomyces calvus. JOURNAL OF NATURAL PRODUCTS 2023; 86:2326-2332. [PMID: 37748016 PMCID: PMC10616807 DOI: 10.1021/acs.jnatprod.3c00521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Indexed: 09/27/2023]
Abstract
3'-O-β-Glucosyl-4',5'-didehydro-5'-deoxyadenosine 13 is identified as a natural product of Streptomyces calvus and Streptomyces virens. It is also generated in vitro by direct β-glucosylation of 4',5'-didehydro-5'-deoxyadenosine 12 with the enzyme NucGT. The intact incorporation of oxygen-18 and deuterium isotopes from (±)[1-18O,1-2H2]-glycerol 14 into C-5' of nucleocidin 1 and its related metabolites precludes 3'-O-β-glucosyl-4',5'-didehydro-5'-deoxyadenosine 13 as a biosynthetic precursor to nucleocidin 1.
Collapse
Affiliation(s)
- Xuan Feng
- School
of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, U.K.
| | - Qingzhi Zhang
- School
of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, U.K.
| | - David J. Clarke
- EaStChem
School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh, EH9 3FJ, U.K.
| | - Hai Deng
- Department
of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, U.K.
| | - David O’Hagan
- School
of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, U.K.
| |
Collapse
|
14
|
Wang P, Cheng T, Pan J. Nucleoside Analogs: A Review of Its Source and Separation Processes. Molecules 2023; 28:7043. [PMID: 37894522 PMCID: PMC10608831 DOI: 10.3390/molecules28207043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Nucleoside analogs play a crucial role in the production of high-value antitumor and antimicrobial drugs. Currently, nucleoside analogs are mainly obtained through nucleic acid degradation, chemical synthesis, and biotransformation. However, these methods face several challenges, such as low concentration of the main product, the presence of complex matrices, and the generation of numerous by-products that significantly limit the development of new drugs and their pharmacological studies. Therefore, this work aims to summarize the universal separation methods of nucleoside analogs, including crystallization, high-performance liquid chromatography (HPLC), column chromatography, solvent extraction, and adsorption. The review also explores the application of molecular imprinting techniques (MITs) in enhancing the identification of the separation process. It compares existing studies reported on adsorbents of molecularly imprinted polymers (MIPs) for the separation of nucleoside analogs. The development of new methods for selective separation and purification of nucleosides is vital to improving the efficiency and quality of nucleoside production. It enables us to obtain nucleoside products that are essential for the development of antitumor and antiviral drugs. Additionally, these methods possess immense potential in the prevention and control of serious diseases, offering significant economic, social, and scientific benefits to the fields of environment, biomedical research, and clinical therapeutics.
Collapse
Affiliation(s)
| | | | - Jianming Pan
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, China; (P.W.); (T.C.)
| |
Collapse
|
15
|
Wojnowska M, Feng X, Chen Y, Deng H, O'Hagan D. Identification of Genes Essential for Fluorination and Sulfamylation within the Nucleocidin Gene Clusters of Streptomyces calvus and Streptomyces virens. Chembiochem 2023; 24:e202200684. [PMID: 36548247 PMCID: PMC10946740 DOI: 10.1002/cbic.202200684] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 12/24/2022]
Abstract
The gene cluster in Streptomyces calvus associated with the biosynthesis of the fluoro- and sulfamyl-metabolite nucleocidin was interrogated by systematic gene knockouts. Out of the 26 gene deletions, most did not affect fluorometabolite production, nine abolished sulfamylation but not fluorination, and three precluded fluorination, but had no effect on sulfamylation. In addition to nucI, nucG, nucJ, nucK, nucL, nucN, nucO, nucQ and nucP, we identified two genes (nucW, nucA), belonging to a phosphoadenosine phosphosulfate (PAPS) gene cluster, as required for sulfamyl assembly. Three genes (orf(-3), orf2 and orf3) were found to be essential for fluorination, although the activities of their protein products are unknown. These genes as well as nucK, nucN, nucO and nucPNP, whose knockouts produced results differing from those described in a recent report, were also deleted in Streptomyces virens - with confirmatory outcomes. This genetic profile should inform biochemistry aimed at uncovering the enzymology behind nucleocidin biosynthesis.
Collapse
Affiliation(s)
- Marta Wojnowska
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
| | - Xuan Feng
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
| | - Yawen Chen
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
| | - Hai Deng
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
| | - David O'Hagan
- School of ChemistryUniversity of St AndrewsSt AndrewsFifeKY16 9STUK
| |
Collapse
|
16
|
Haas R, Nikel PI. Challenges and opportunities in bringing nonbiological atoms to life with synthetic metabolism. Trends Biotechnol 2023; 41:27-45. [PMID: 35786519 DOI: 10.1016/j.tibtech.2022.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 06/05/2022] [Accepted: 06/09/2022] [Indexed: 02/06/2023]
Abstract
The relatively narrow spectrum of chemical elements within the microbial 'biochemical palate' limits the reach of biotechnology, because several added-value compounds can only be produced with traditional organic chemistry. Synthetic biology offers enabling tools to tackle this issue by facilitating 'biologization' of non-canonical chemical atoms. The interplay between xenobiology and synthetic metabolism multiplies routes for incorporating nonbiological atoms into engineered microbes. In this review, we survey natural assimilation routes for elements beyond the essential biology atoms [i.e., carbon (C), hydrogen (H), nitrogen (N), oxygen (O), phosphorus (P), and sulfur (S)], discussing how these mechanisms could be repurposed for biotechnology. Furthermore, we propose a computational framework to identify chemical elements amenable to biologization, ranking reactions suitable to build synthetic metabolism. When combined and deployed in robust microbial hosts, these approaches will offer sustainable alternatives for smart chemical production.
Collapse
Affiliation(s)
- Robert Haas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| |
Collapse
|
17
|
Calero P, Gurdo N, Nikel PI. Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride. Environ Microbiol 2022; 24:5082-5104. [PMID: 35726888 PMCID: PMC9796867 DOI: 10.1111/1462-2920.16110] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/16/2022] [Accepted: 06/19/2022] [Indexed: 01/07/2023]
Abstract
The presence of mineral fluoride (F- ) in the environment has both a geogenic and anthropogenic origin, and the halide has been described to be toxic in virtually all living organisms. While the evidence gathered in different microbial species supports this notion, a systematic exploration of the effects of F- salts on the metabolism and physiology of environmental bacteria remained underexplored thus far. In this work, we studied and characterized tolerance mechanisms deployed by the model soil bacterium Pseudomonas putida KT2440 against NaF. By adopting systems-level omic approaches, including functional genomics and metabolomics, we gauged the impact of this anion at different regulatory levels under conditions that impair bacterial growth. Several genes involved in halide tolerance were isolated in a genome-wide Tn-Seq screening-among which crcB, encoding an F- -specific exporter, was shown to play the predominant role in detoxification. High-resolution metabolomics, combined with the assessment of intracellular and extracellular pH values and quantitative physiology experiments, underscored the key nodes in central carbon metabolism affected by the presence of F- . Taken together, our results indicate that P. putida undergoes a general, multi-level stress response when challenged with NaF that significantly differs from that caused by other saline stressors. While microbial stress responses to saline and oxidative challenges have been extensively studied and described in the literature, very little is known about the impact of fluoride (F- ) on bacterial physiology and metabolism. This state of affairs contrasts with the fact that F- is more abundant than other halides in the Earth crust (e.g. in some soils, the F- concentration can reach up to 1 mg gsoil -1 ). Understanding the global effects of NaF treatment on bacterial physiology is not only relevant to unveil distinct mechanisms of detoxification but it could also guide microbial engineering approaches for the target incorporation of fluorine into value-added organofluorine molecules. In this regard, the soil bacterium P. putida constitutes an ideal model to explore such scenarios, since this species is particularly known for its high level of stress resistance against a variety of physicochemical perturbations.
Collapse
Affiliation(s)
- Patricia Calero
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| | - Nicolás Gurdo
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| |
Collapse
|
18
|
Leong BJ, Folz JS, Bathe U, Clark DG, Fiehn O, Hanson AD. Fluoroacetate distribution, response to fluoridation, and synthesis in juvenile Gastrolobium bilobum plants. PHYTOCHEMISTRY 2022; 202:113356. [PMID: 35934105 DOI: 10.1016/j.phytochem.2022.113356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/23/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Like angiosperms from several other families, the leguminous shrub Gastrolobium bilobum R.Br. produces and accumulates fluoroacetate, indicating that it performs the difficult chemistry needed to make a C-F bond. Bioinformatic analyses indicate that plants lack homologs of the only enzymes known to make a C-F bond, i.e., the Actinomycete flurorinases that form 5'-fluoro-5'-deoxyadenosine from S-adenosylmethionine and fluoride ion. To probe the origin of fluoroacetate in G. bilobum we first showed that fluoroacetate accumulates to millimolar levels in young leaves but not older leaves, stems or roots, that leaf fluoroacetate levels vary >20-fold between individual plants and are not markedly raised by sodium fluoride treatment. Young leaves were fed adenosine-13C-ribose, 13C-serine, or 13C-acetate to test plausible biosynthetic routes to fluoroacetate from S-adenosylmethionine, a C3-pyridoxal phosphate complex, or acetyl-CoA, respectively. Incorporation of 13C into expected metabolites confirmed that all three precursors were taken up and metabolized. Consistent with the bioinformatic evidence against an Actinomycete-type pathway, no adenosine-13C-ribose was converted to 13C-fluoroacetate; nor was the characteristic 4-fluorothreonine product of the Actinomycete pathway detected. Similarly, no 13C from acetate or serine was incorporated into fluoroacetate. While not fully excluding the hypothetical pathways that were tested, these negative labeling data imply that G. bilobum creates the C-F bond by an unprecedented biochemical reaction. Enzyme(s) that mediate such a reaction could be of great value in pharmaceutical and agrochemical manufacturing.
Collapse
Affiliation(s)
- Bryan J Leong
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - Jacob S Folz
- West Coast Metabolomics Center, University of California Davis, Davis, CA, USA
| | - Ulschan Bathe
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - David G Clark
- Department of Environmental Horticulture, University of Florida, Gainesville, FL, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California Davis, Davis, CA, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA.
| |
Collapse
|
19
|
Liu W, Yuan S, Jin M, Xian M. Biocatalytic synthesis of 2-fluoro-3-hydroxypropionic acid. Front Bioeng Biotechnol 2022; 10:969012. [PMID: 36061447 PMCID: PMC9428585 DOI: 10.3389/fbioe.2022.969012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Fluorine has become an important element for the design of synthetic molecules for use in medicine, agriculture, and materials. The introduction of fluorine atoms into organic compound molecules can often give these compounds new functions and make them have better performance. Despite the many advantages provided by fluorine for tuning key molecular properties, it is rarely found in natural metabolism. We seek to expand the molecular space available for discovery through the development of new biosynthetic strategies that cross synthetic with natural compounds. Towards this goal, 2-fluoro-3-hydroxypropionic acid (2-F-3-HP) was first synthesized using E. coli coexpressing methylmalonyl CoA synthase (MatBrp), methylmalonyl CoA reductase (MCR) and malonate transmembrane protein (MadLM). The concentration of 2-F-3-HP reached 50.0 mg/L by whole-cell transformation after 24 h. 2-F-3-HP can be used as the substrate to synthesize other fluorides, such as poly (2-fluoro-3-hydroxypropionic acid) (FP3HP). Being entirely biocatalytic, our procedure provides considerable advantages in terms of environmental and safety impacts over reported chemical methods.
Collapse
Affiliation(s)
- Wei Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Shandong, China
- *Correspondence: Mo Xian, ; Wei Liu,
| | - Shan Yuan
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Miaomiao Jin
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Shandong, China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Shandong, China
- *Correspondence: Mo Xian, ; Wei Liu,
| |
Collapse
|
20
|
Kittilä T, Calero P, Fredslund F, Lowe PT, Tezé D, Nieto-Domínguez M, O'Hagan D, Nikel PI, Welner DH. Oligomerization engineering of the fluorinase enzyme leads to an active trimer that supports synthesis of fluorometabolites in vitro. Microb Biotechnol 2022; 15:1622-1632. [PMID: 35084776 PMCID: PMC9049626 DOI: 10.1111/1751-7915.14009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 12/15/2022] Open
Abstract
The fluorinase enzyme represents the only biological mechanism capable of forming stable C–F bonds characterized in nature thus far, offering a biotechnological route to the biosynthesis of value‐added organofluorines. The fluorinase is known to operate in a hexameric form, but the consequence(s) of the oligomerization status on the enzyme activity and its catalytic properties remain largely unknown. In this work, this aspect was explored by rationally engineering trimeric fluorinase variants that retained the same catalytic rate as the wild‐type enzyme. These results ruled out hexamerization as a requisite for the fluorination activity. The Michaelis constant (KM) for S‐adenosyl‐l‐methionine, one of the substrates of the fluorinase, increased by two orders of magnitude upon hexamer disruption. Such a shift in S‐adenosyl‐l‐methionine affinity points to a long‐range effect of hexamerization on substrate binding – likely decreasing substrate dissociation and release from the active site. A practical application of trimeric fluorinase is illustrated by establishing in vitro fluorometabolite synthesis in a bacterial cell‐free system.
Collapse
Affiliation(s)
- Tiia Kittilä
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Patricia Calero
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Folmer Fredslund
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Phillip T Lowe
- School of Chemistry, University of St. Andrews, St. Andrews, KY16 9ST, UK
| | - David Tezé
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - David O'Hagan
- School of Chemistry, University of St. Andrews, St. Andrews, KY16 9ST, UK
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Ditte H Welner
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| |
Collapse
|
21
|
Cros A, Alfaro-Espinoza G, De Maria A, Wirth NT, Nikel PI. Synthetic metabolism for biohalogenation. Curr Opin Biotechnol 2021; 74:180-193. [PMID: 34954625 DOI: 10.1016/j.copbio.2021.11.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 12/19/2022]
Abstract
The pressing need for novel bioproduction approaches faces a limitation in the number and type of molecules accessed through synthetic biology. Halogenation is widely used for tuning physicochemical properties of molecules and polymers, but traditional halogenation chemistry often lacks specificity and generates harmful by-products. Here, we pose that deploying synthetic metabolism tailored for biohalogenation represents an unique opportunity towards economically attractive and environmentally friendly organohalide production. On this background, we discuss growth-coupled selection of functional metabolic modules that harness the rich repertoire of biosynthetic and biodegradation capabilities of environmental bacteria for in vivo biohalogenation. By rationally combining these approaches, the chemical landscape of living cells can accommodate bioproduction of added-value organohalides which, as of today, are obtained by traditional chemistry.
Collapse
Affiliation(s)
- Antonin Cros
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Gabriela Alfaro-Espinoza
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; Division Biodeterioration and Reference Organisms, Federal Institute for Materials Research and Testing (BAM), 12205 Berlin, Germany
| | - Alberto De Maria
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| |
Collapse
|