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Liu R, Wang L, Meng Y, Tian Y, Li F, Lu H. Theoretical and Experimental Studies on Plant Light-Dependent Protochlorophyllide Oxidoreductase as a Novel Target for Searching Potential Herbicides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37467369 DOI: 10.1021/acs.jafc.3c01783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Herbicide resistance is a prevalent problem that has posed a foremost challenge to crop production worldwide. Light-dependent enzyme NADPH: protochlorophyllide oxidoreductase (LPOR) in plants is a metabolic target that could satisfy this unmet demand. Herein, for the first time, we embarked on proposing a new mode of action of herbicides by performing structure-based virtual screening targeting multiple LPOR binding sites, with the determination of further bioactivity on the lead series. The feasibility of exploiting high selectivity and safety herbicides targeting LPOR was discussed from the perspective of the origin and phylogeny. Besides, we revealed the structural rearrangement and the selection key for NADPH cofactor binding to LPOR. Based on these, multitarget virtual screening was performed and the result identified compounds 2 affording micromolar inhibition, in which the IC50 reached 4.74 μM. Transcriptome analysis revealed that compound 2 induced more genes related to chlorophyll synthesis in Arabidopsis thaliana, especially the LPOR genes. Additionally, we clarified that these compounds binding to the site enhanced the overall stability and local rigidity of the complex systems from molecular dynamics simulation. This study delivers a guideline on how to assess activity-determining features of inhibitors to LPOR and how to translate this knowledge into the design of novel and effective inhibitors against malignant weed that act by targeting LPOR.
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Affiliation(s)
- Ruiyuan Liu
- College of Science, China Agricultural University, Beijing 100193, China
| | - Leng Wang
- College of Science, China Agricultural University, Beijing 100193, China
| | - Yue Meng
- College of Science, China Agricultural University, Beijing 100193, China
| | - Yiyi Tian
- College of Science, China Agricultural University, Beijing 100193, China
| | - Fang Li
- College of Science, China Agricultural University, Beijing 100193, China
| | - Huizhe Lu
- College of Science, China Agricultural University, Beijing 100193, China
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2
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Chiral-phase HPLC separation of (divinyl-)protochlorophyllide-a enantiomers as key precursors in chlorophyll biosynthesis from their 13 2-stereoisomeric prime forms. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148960. [PMID: 36822491 DOI: 10.1016/j.bbabio.2023.148960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023]
Abstract
Protochlorophyllide(PChlide)-a and its 8-vinylated analog, divinyl(DV)-PChlide-a, are common and essential intermediates in the biosynthesis of all naturally occurring chlorophyll (Chl) pigments. These porphyrinoid-type pigments have a single optically active (asymmetric) carbon atom at the 132-position, so their stereoisomers are (132R)- and (132S)-enantiomers. The former and latter are called (DV-)PChlide-a and (DV-)PChlide-a', respectively. In this study, chiral-phase HPLC separation of enantiomeric (DV-)PChlides-a/a' was demonstrated. The (132R)-enantiomeric PChlide-a was eluted more slowly than the corresponding (132S)-enantiomeric PChlide-a' under the present HPLC conditions. On the other hand, the elution order of (132R)-DV-PChlide-a and (132S)-DV-PChlide-a' was reverse to that of PChlides-a/a'. After the separation of each enantiomer by the chiral-phase HPLC, the stereoisomeric configuration at the 132-position was characterized by means of circular dichroism spectroscopy. The present chiral-phase HPLC method enables us to evaluate optical purities of (DV-)PChlide-a species. For example, PChlide-a and/or DV-PChlide-a extracted from the spent medium and harvested cells of cultured purple photosynthetic bacterial mutants, the former of which has been often used as the source of (DV-)PChlide-a substrates for enzymatic reactions, were revealed to be mostly racemized, giving enantiomeric mixtures of (DV-)PChlides-a/a'.
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Wang S, Lei H, Ji Z. Exploring Oxidoreductases from Extremophiles for Biosynthesis in a Non-Aqueous System. Int J Mol Sci 2023; 24:ijms24076396. [PMID: 37047370 PMCID: PMC10094897 DOI: 10.3390/ijms24076396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 03/19/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
Organic solvent tolerant oxidoreductases are significant for both scientific research and biomanufacturing. However, it is really challenging to obtain oxidoreductases due to the shortages of natural resources and the difficulty to obtained it via protein modification. This review summarizes the recent advances in gene mining and structure-functional study of oxidoreductases from extremophiles for non-aqueous reaction systems. First, new strategies combining genome mining with bioinformatics provide new insights to the discovery and identification of novel extreme oxidoreductases. Second, analysis from the perspectives of amino acid interaction networks explain the organic solvent tolerant mechanism, which regulate the discrete structure-functional properties of extreme oxidoreductases. Third, further study by conservation and co-evolution analysis of extreme oxidoreductases provides new perspectives and strategies for designing robust enzymes for an organic media reaction system. Furthermore, the challenges and opportunities in designing biocatalysis non-aqueous systems are highlighted.
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Affiliation(s)
- Shizhen Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Xiamen Key Laboratory of Synthetic Biotechnology, Xiamen University, Xiamen 361005, China
| | - Hangbin Lei
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhehui Ji
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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Malihan‐Yap L, Grimm HC, Kourist R. Recent Advances in Cyanobacterial Biotransformations. CHEM-ING-TECH 2022. [DOI: 10.1002/cite.202200077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lenny Malihan‐Yap
- Graz University of Technology Institute of Molecular Biotechnology NAWI Graz 8010 Graz Austria
| | - Hanna C. Grimm
- Graz University of Technology Institute of Molecular Biotechnology NAWI Graz 8010 Graz Austria
| | - Robert Kourist
- Graz University of Technology Institute of Molecular Biotechnology NAWI Graz 8010 Graz Austria
- ACIB GmbH 8010 Graz Austria
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Bierbaumer S, Schmermund L, List A, Winkler CK, Glueck SM, Kroutil W. Synthesis of Enantiopure Sulfoxides by Concurrent Photocatalytic Oxidation and Biocatalytic Reduction. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202117103. [PMID: 38505243 PMCID: PMC10946591 DOI: 10.1002/ange.202117103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Indexed: 03/21/2024]
Abstract
The concurrent operation of chemical and biocatalytic reactions in one pot is still a challenging task, and, in particular for chemical photocatalysts, examples besides simple cofactor recycling systems are rare. However, especially due to the complementary chemistry that the two fields of catalysis promote, their combination in one pot has the potential to unlock intriguing, unprecedented overall reactivities. Herein we demonstrate a concurrent biocatalytic reduction and photocatalytic oxidation process. Specifically, the enantioselective biocatalytic sulfoxide reduction using (S)-selective methionine sulfoxide reductases was coupled to an unselective light-dependent sulfoxidation. Protochlorophyllide was established as a new green photocatalyst for the sulfoxidation. Overall, a cyclic deracemization process to produce nonracemic sulfoxides was achieved and the target compounds were obtained with excellent conversions (up to 91 %) and superb optical purity (>99 % ee).
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Affiliation(s)
- Sarah Bierbaumer
- Institute of Chemistry, Department of Organic and Bioorganic ChemistryUniversity of GrazNAWI GrazBioTechMed GrazField of Excellence BioHealthHeinrichstraße 288010GrazAustria
| | - Luca Schmermund
- Institute of Chemistry, Department of Organic and Bioorganic ChemistryUniversity of GrazNAWI GrazBioTechMed GrazField of Excellence BioHealthHeinrichstraße 288010GrazAustria
| | - Alexander List
- Institute of Chemistry, Department of Organic and Bioorganic ChemistryUniversity of GrazNAWI GrazBioTechMed GrazField of Excellence BioHealthHeinrichstraße 288010GrazAustria
| | - Christoph K. Winkler
- Institute of Chemistry, Department of Organic and Bioorganic ChemistryUniversity of GrazNAWI GrazBioTechMed GrazField of Excellence BioHealthHeinrichstraße 288010GrazAustria
| | - Silvia M. Glueck
- Institute of Chemistry, Department of Organic and Bioorganic ChemistryUniversity of GrazNAWI GrazBioTechMed GrazField of Excellence BioHealthHeinrichstraße 288010GrazAustria
| | - Wolfgang Kroutil
- Institute of Chemistry, Department of Organic and Bioorganic ChemistryUniversity of GrazNAWI GrazBioTechMed GrazField of Excellence BioHealthHeinrichstraße 288010GrazAustria
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Bierbaumer S, Schmermund L, List A, Winkler CK, Glueck SM, Kroutil W. Synthesis of Enantiopure Sulfoxides by Concurrent Photocatalytic Oxidation and Biocatalytic Reduction. Angew Chem Int Ed Engl 2022; 61:e202117103. [PMID: 35188997 PMCID: PMC9310851 DOI: 10.1002/anie.202117103] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Indexed: 11/18/2022]
Abstract
The concurrent operation of chemical and biocatalytic reactions in one pot is still a challenging task, and, in particular for chemical photocatalysts, examples besides simple cofactor recycling systems are rare. However, especially due to the complementary chemistry that the two fields of catalysis promote, their combination in one pot has the potential to unlock intriguing, unprecedented overall reactivities. Herein we demonstrate a concurrent biocatalytic reduction and photocatalytic oxidation process. Specifically, the enantioselective biocatalytic sulfoxide reduction using (S)‐selective methionine sulfoxide reductases was coupled to an unselective light‐dependent sulfoxidation. Protochlorophyllide was established as a new green photocatalyst for the sulfoxidation. Overall, a cyclic deracemization process to produce nonracemic sulfoxides was achieved and the target compounds were obtained with excellent conversions (up to 91 %) and superb optical purity (>99 % ee).
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Affiliation(s)
- Sarah Bierbaumer
- Institute of Chemistry, Department of Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Field of Excellence BioHealth, Heinrichstraße 28, 8010, Graz, Austria
| | - Luca Schmermund
- Institute of Chemistry, Department of Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Field of Excellence BioHealth, Heinrichstraße 28, 8010, Graz, Austria
| | - Alexander List
- Institute of Chemistry, Department of Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Field of Excellence BioHealth, Heinrichstraße 28, 8010, Graz, Austria
| | - Christoph K Winkler
- Institute of Chemistry, Department of Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Field of Excellence BioHealth, Heinrichstraße 28, 8010, Graz, Austria
| | - Silvia M Glueck
- Institute of Chemistry, Department of Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Field of Excellence BioHealth, Heinrichstraße 28, 8010, Graz, Austria
| | - Wolfgang Kroutil
- Institute of Chemistry, Department of Organic and Bioorganic Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, Field of Excellence BioHealth, Heinrichstraße 28, 8010, Graz, Austria
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7
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Winkler CK, Simić S, Jurkaš V, Bierbaumer S, Schmermund L, Poschenrieder S, Berger SA, Kulterer E, Kourist R, Kroutil W. Accelerated Reaction Engineering of Photo(bio)catalytic Reactions through Parallelization with an Open‐Source Photoreactor. CHEMPHOTOCHEM 2021. [DOI: 10.1002/cptc.202100109] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Christoph K. Winkler
- Institute of Chemistry NAWI Graz University of Graz Heinrichstraße 28 8010 Graz Austria
| | - Stefan Simić
- Institute of Chemistry NAWI Graz University of Graz Heinrichstraße 28 8010 Graz Austria
| | - Valentina Jurkaš
- Institute of Chemistry NAWI Graz University of Graz Heinrichstraße 28 8010 Graz Austria
| | - Sarah Bierbaumer
- Institute of Chemistry NAWI Graz University of Graz Heinrichstraße 28 8010 Graz Austria
| | - Luca Schmermund
- Institute of Chemistry NAWI Graz University of Graz Heinrichstraße 28 8010 Graz Austria
| | - Silvan Poschenrieder
- Institute of Chemistry NAWI Graz University of Graz Heinrichstraße 28 8010 Graz Austria
| | - Sarah A. Berger
- Institute of Chemistry NAWI Graz University of Graz Heinrichstraße 28 8010 Graz Austria
| | - Elisa Kulterer
- Institute of Chemistry NAWI Graz University of Graz Heinrichstraße 28 8010 Graz Austria
| | - Robert Kourist
- Institute of Molecular Biotechnology NAWI Graz Graz University of Technology Petersgasse 14 8010 Graz Austria
| | - Wolfgang Kroutil
- Institute of Chemistry NAWI Graz University of Graz Heinrichstraße 28 8010 Graz Austria
- BioTechMed Graz 8010 Graz Austria
- Field of Excellence BioHealth University of Graz 8010 Graz Austria
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Özgen FF, Runda ME, Schmidt S. Photo-biocatalytic Cascades: Combining Chemical and Enzymatic Transformations Fueled by Light. Chembiochem 2021; 22:790-806. [PMID: 32961020 PMCID: PMC7983893 DOI: 10.1002/cbic.202000587] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/22/2020] [Indexed: 12/13/2022]
Abstract
In the field of green chemistry, light - an attractive natural agent - has received particular attention for driving biocatalytic reactions. Moreover, the implementation of light to drive (chemo)enzymatic cascade reactions opens up a golden window of opportunities. However, there are limitations to many current examples, mostly associated with incompatibility between the enzyme and the photocatalyst. Additionally, the formation of reactive radicals upon illumination and the loss of catalytic activities in the presence of required additives are common observations. As outlined in this review, the main question is how to overcome current challenges to the exploitation of light to drive (chemo)enzymatic transformations. First, we highlight general concepts in photo-biocatalysis, then give various examples of photo-chemoenzymatic (PCE) cascades, further summarize current synthetic examples of PCE cascades and discuss strategies to address the limitations.
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Affiliation(s)
- Fatma Feyza Özgen
- Groningen Research Institute of PharmacyDepartment of Chemical and Pharmaceutical BiologyAntonius Deusinglaan 19713 AVGroningen (TheNetherlands
| | - Michael E. Runda
- Groningen Research Institute of PharmacyDepartment of Chemical and Pharmaceutical BiologyAntonius Deusinglaan 19713 AVGroningen (TheNetherlands
| | - Sandy Schmidt
- Groningen Research Institute of PharmacyDepartment of Chemical and Pharmaceutical BiologyAntonius Deusinglaan 19713 AVGroningen (TheNetherlands
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Heyes DJ, Zhang S, Taylor A, Johannissen LO, Hardman SJO, Hay S, Scrutton NS. Photocatalysis as the 'master switch' of photomorphogenesis in early plant development. NATURE PLANTS 2021; 7:268-276. [PMID: 33686224 DOI: 10.1038/s41477-021-00866-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
Enzymatic photocatalysis is seldom used in biology. Photocatalysis by light-dependent protochlorophyllide oxidoreductase (LPOR)-one of only a few natural light-dependent enzymes-is an exception, and is responsible for the conversion of protochlorophyllide to chlorophyllide in chlorophyll biosynthesis. Photocatalysis by LPOR not only regulates the biosynthesis of the most abundant pigment on Earth but it is also a 'master switch' in photomorphogenesis in early plant development. Following illumination, LPOR promotes chlorophyll production, plastid membranes are transformed and the photosynthetic apparatus is established. Given these remarkable, light-induced pigment and morphological changes, the LPOR-catalysed reaction has been extensively studied from catalytic, physiological and plant development perspectives, highlighting vital, and multiple, cellular roles of this intriguing enzyme. Here, we offer a perspective in which the link between LPOR photocatalysis and plant photomorphogenesis is explored. Notable breakthroughs in LPOR structural biology have uncovered the structural-mechanistic basis of photocatalysis. These studies have clarified how photon absorption by the pigment protochlorophyllide-bound in a ternary LPOR-protochlorophyllide-NADPH complex-triggers photocatalysis and a cascade of complex molecular and cellular events that lead to plant morphological changes. Photocatalysis is therefore the master switch responsible for early-stage plant development and ultimately life on Earth.
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Affiliation(s)
- Derren J Heyes
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK.
| | - Shaowei Zhang
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK
| | - Aoife Taylor
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK
| | - Linus O Johannissen
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK
| | - Samantha J O Hardman
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK.
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