1
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Hajili E, Sugawara A, Uyama H. Application of Hierarchically Porous Chitosan Monolith for Enzyme Immobilization. Biomacromolecules 2024; 25:3486-3498. [PMID: 38718188 DOI: 10.1021/acs.biomac.4c00109] [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: 06/11/2024]
Abstract
Enzyme immobilization is a crucial technique for improving the stability of enzymes. Compared with free enzymes, immobilized enzymes offer several advantages in industrial applications. Efficient enzyme immobilization requires a technique that integrates the advantages of physical absorption and covalent binding while addressing the limitations of conventional support materials. This study offers a practical approach for immobilizing α-amylase on a hierarchically porous chitosan (CS) monolith. An optimized CS monolith was fabricated using chemically modified chitin by thermally induced phase separation. By combining physical adsorption and covalent bonding, this technique leverages the amino and hydroxy groups present in CS to facilitate effective enzyme binding and stability. α-Amylase immobilized on the CS monolith demonstrated excellent stability, reusability, and increased activity compared to its soluble counterpart across various pH levels and temperatures. In addition, the CS monolith exhibited a significant potential to immobilize other enzymes, namely, lipase and catalase. Immobilized lipase and catalase exhibited higher loading capacities and enhanced activities than their soluble forms. This versatility highlights the broad applicability of CS monoliths as support materials for various enzymatic processes. This study provides guidelines for fabricating hierarchical porous monolith structures that can provide efficient enzyme utilization in flow systems and potentially enhance the cost-effectiveness of enzymes in industrial applications.
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Affiliation(s)
- Emil Hajili
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Akihide Sugawara
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Uyama
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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2
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Holtz M, Acevedo-Rocha CG, Jensen MK. Combining enzyme and metabolic engineering for microbial supply of therapeutic phytochemicals. Curr Opin Biotechnol 2024; 87:103110. [PMID: 38503222 DOI: 10.1016/j.copbio.2024.103110] [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: 01/09/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/21/2024]
Abstract
The history of pharmacology is deeply intertwined with plant-derived compounds, which continue to be crucial in drug development. However, their complex structures and limited availability in plants challenge drug discovery, optimization, development, and industrial production via chemical synthesis or natural extraction. This review delves into the integration of metabolic and enzyme engineering to leverage micro-organisms as platforms for the sustainable and reliable production of therapeutic phytochemicals. We argue that engineered microbes can serve a triple role in this paradigm: facilitating pathway discovery, acting as cell factories for scalable manufacturing, and functioning as platforms for chemical derivatization. Analyzing recent progress and outlining future directions, the review highlights microbial biotechnology's transformative potential in expanding plant-derived human therapeutics' discovery and supply chains.
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Affiliation(s)
- Maxence Holtz
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Carlos G Acevedo-Rocha
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
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3
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Zhang X, Liu J, Yang F, Zhang Q, Yang Z, Shah HA. Planning biosynthetic pathways of target molecules based on metabolic reaction prediction and AND-OR tree search. Comput Biol Chem 2024; 111:108106. [PMID: 38833912 DOI: 10.1016/j.compbiolchem.2024.108106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 06/06/2024]
Abstract
Bioretrosynthesis problem is to predict synthetic routes using substrates for given natural products (NPs). However, the huge number of metabolic reactions leads to a combinatorial explosion of searching space, which is high time-consuming and costly. Here, we propose a framework called BioRetro to predict bioretrosynthesis pathways using a one-step bioretrosynthesis network, termed HybridMLP combined with AND-OR tree heuristic search. The HybridMLP predicts precursors that will produce the target NPs, while the AND-OR tree generates the iterative multi-step biosynthetic pathways. The one-step bioretrosynthesis prediction experiments are conducted on MetaNetX dataset by using HybridMLP, which achieves 46.5%, 74.6%, 81.6% in terms of the top-1, top-5, top-10 accuracies. The great performance demonstrates the effectiveness of HybridMLP in one-step bioretrosynthesis. Besides, the evaluation of two benchmark datasets reveals that BioRetro can significantly improve the speed and success rate in predicting biosynthesis pathways. In addition, the BioRetro is further shown to find the synthetic pathway of compounds, such as ginsenoside F1 with the same substrates as reported but different enzymes, which may be the novel potential enzyme to have better catalytic performance.
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Affiliation(s)
- Xiaolei Zhang
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, 430072, China
| | - Juan Liu
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, 430072, China.
| | - Feng Yang
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, 430072, China
| | - Qiang Zhang
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, 430072, China
| | - Zhihui Yang
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, 430072, China
| | - Hayat Ali Shah
- Institute of Artificial Intelligence, School of Computer Science, Wuhan University, Wuhan, 430072, China
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4
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Hu H, Singh AN, Lehnherr D, Mdluli V, Chun SW, Makarewicz AM, Gouker JR, Ukaegbu O, Li S, Wen X, McLaren DG, Velasquez JE, Moore JC, Galanie S, Appiah-Amponsah E, Regalado EL. Accelerating Pharmaceutical Process Development with an Acoustic Droplet Ejection-Multiple Reaction Monitoring-Mass Spectrometry Workflow. Anal Chem 2024; 96:1138-1146. [PMID: 38165811 DOI: 10.1021/acs.analchem.3c04211] [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: 01/04/2024]
Abstract
Fast-paced pharmaceutical process developments (e.g., high-throughput experimentation, directed evolution, and machine learning) involve the introduction of fast, sensitive, and accurate analytical assays using limited sample volumes. In recent years, acoustic droplet ejection (ADE) coupled with an open port interface has been invented as a sampling technology for mass spectrometry, providing high-throughput nanoliter analytical measurements directly from the standard microplates. Herein, we introduce an ADE-multiple reaction monitoring-mass spectrometry (ADE-MRM-MS) workflow to accelerate pharmaceutical process research and development (PR&D). This systematic workflow outlines the selection of MRM transitions and optimization of assay parameters in a data-driven manner using rapid measurements (1 sample/s). The synergy between ADE sampling and MRM analysis enables analytical assays with excellent sensitivity, selectivity, and speed for PR&D reaction screenings. This workflow was utilized to develop new ADE-MRM-MS assays guiding a variety of industrial processes, including (1) screening of Ni-based catalysts for C-N cross-coupling reaction at 1 Hz and (2) high-throughput regioisomer analysis-enabled enzyme library screening for peptide ligation reaction. ADE-MRM-MS assays were demonstrated to deliver accurate results that are comparable to conventional liquid chromatography (LC) experiments while providing >100-fold throughput enhancement.
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Affiliation(s)
- Hang Hu
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Andrew N Singh
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Dan Lehnherr
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Velabo Mdluli
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Stephanie W Chun
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Amanda M Makarewicz
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Joseph R Gouker
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ophelia Ukaegbu
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Shasha Li
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Xiujuan Wen
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - David G McLaren
- Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Juan E Velasquez
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jeffrey C Moore
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Stephanie Galanie
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | | | - Erik L Regalado
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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5
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Chen Z, Wu T, Yu S, Li M, Fan X, Huo YX. Self-assembly systems to troubleshoot metabolic engineering challenges. Trends Biotechnol 2024; 42:43-60. [PMID: 37451946 DOI: 10.1016/j.tibtech.2023.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
Enzyme self-assembly is a technology in which enzyme units can aggregate into ordered macromolecules, assisted by scaffolds. In metabolic engineering, self-assembly strategies have been explored for aggregating multiple enzymes in the same pathway to improve sequential catalytic efficiency, which in turn enables high-level production. The performance of the scaffolds is critical to the formation of an efficient and stable assembly system. This review comprehensively analyzes these scaffolds by exploring how they assemble, and it illustrates how to apply self-assembly strategies for different modules in metabolic engineering. Functional modifications to scaffolds will further promote efficient strategies for production.
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Affiliation(s)
- Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Tong Wu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Min Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Xuanhe Fan
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China.
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6
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Liu N, Xiao H, Zang Y, Zhou L, Mencius J, Yang Z, Quan S, Chen X. Simultaneous Improvement in the Thermostability and Catalytic Activity of Epoxidase Lsd18 for the Synthesis of Lasalocid A. Int J Mol Sci 2023; 24:16795. [PMID: 38069118 PMCID: PMC10706071 DOI: 10.3390/ijms242316795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Enzymes used in the synthesis of natural products are potent catalysts, capable of efficient and stereoselective chemical transformations. Lsd18 catalyzes two sequential epoxidations during the biosynthesis of lasalocid A, a polyether polyketide natural product. We performed protein engineering on Lsd18 to improve its thermostability and catalytic activity. Utilizing structure-guided methods of FoldX and Rosetta-ddG, we designed 15 mutants of Lsd18. Screening of these mutants using thermal shift assay identified stabilized variants Lsd18-T189M, Lsd18-S195M, and the double mutant Lsd18-T189M-S195M. Trypsin digestion, molecular dynamic simulation, circular dichroism (CD) spectroscopy, and X-ray crystallography provided insights into the molecular basis for the improved enzyme properties. Notably, enhanced hydrophobic interaction within the enzyme core and interaction of the protein with the FAD cofactor appear to be responsible for its better thermostability.
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Affiliation(s)
- Ning Liu
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, China; (N.L.); (H.X.)
| | - Hongli Xiao
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, China; (N.L.); (H.X.)
| | - Yongjian Zang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Y.Z.); (Z.Y.)
- Institute of Physics and Electronic Information, Yunnan Normal University, Kunming 650504, China
| | - Longji Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (L.Z.); (J.M.)
| | - Jun Mencius
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (L.Z.); (J.M.)
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Y.Z.); (Z.Y.)
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (L.Z.); (J.M.)
| | - Xi Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, China; (N.L.); (H.X.)
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7
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Zhang F, Zeng T, Wu R. QM/MM Modeling Aided Enzyme Engineering in Natural Products Biosynthesis. J Chem Inf Model 2023; 63:5018-5034. [PMID: 37556841 DOI: 10.1021/acs.jcim.3c00779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Natural products and their derivatives are widely used across various industries, particularly pharmaceuticals. Modern engineered biosynthesis provides an alternative way of producing and meeting the growing need for diverse natural products. Natural enzymes, on the other hand, often exhibit unsatisfactory catalytic characteristics and necessitate further enzyme engineering modifications. QM/MM, as a powerful and extensively used computational tool in the field of enzyme catalysis, has been increasingly applied in rational enzyme engineering over the past decade. In this review, we summarize recent advances in QM/MM computational investigation on enzyme catalysis and enzyme engineering for natural product biosynthesis. The challenges and perspectives for future QM/MM applications aided enzyme engineering in natural product biosynthesis will also be discussed.
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Affiliation(s)
- Fan Zhang
- Guangdong Provincial Key Laboratory of Translational Cancer Research of Chinese Medicines, Joint International Research Laboratory of Translational Cancer Research of Chinese Medicines, International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, P. R. China
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Tao Zeng
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, P. R. China
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8
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Xu L, Peng H, Huang Y, Huang C, Xie C, He G. Green extract rosemary acid as a viscosity-sensitive molecular sensor in liquid systems. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:1881-1887. [PMID: 36974992 DOI: 10.1039/d3ay00112a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The liquid micro-environment plays a momentous role in the regulation of various activities, and the abnormal changes are often closely related to the deterioration phenomena in multiple beverages. The local viscosity fluctuation has long been regarded as a key indicator to reflect the micro-environmental status changes. Herein, we proposed a versatile optical sensor, rosmarinic acid (RA), one kind of green natural product extracted from rosemary, for monitoring liquid micro-environmental viscosity alterations. RA displays a larger Stokes shift (123.8 nm) with narrow-band energy and exhibits wide adaptability, high selectivity, good sensitivity, and excellent photostability in various commercial liquids. When in high viscous media, a bright fluorescent signal of RA is specifically activated, and a high signal-to-noise ratio signal was released (58-fold). With the assistance of the fluorescence analytical technique, we have successfully achieved tracking the viscosity fluctuations during the deterioration stage of liquids via an in situ and visualization method. Our study will spur additional research on the molecular tools extracted from natural products for liquid safety inspection, and a convenient and sustainable application pathway has been established.
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Affiliation(s)
- Lingfeng Xu
- Key Laboratory of Biodiversity and Ecological Engineering of Jiangxi Province, Jinggangshan University, Ji'an, Jiangxi 343009, China.
- State Key Laboratory of Luminescent Materials & Devices, College of Materials Science & Engineering, South China University of Technology, Guangzhou 510640, China
| | - Hui Peng
- Key Laboratory of Biodiversity and Ecological Engineering of Jiangxi Province, Jinggangshan University, Ji'an, Jiangxi 343009, China.
| | - Yanrong Huang
- School of Modern Agriculture and Forestry Engineering, Ji'an Vocational and Technical College, Ji'an, Jiangxi 343009, China
| | - Chunfang Huang
- Key Laboratory of Biodiversity and Ecological Engineering of Jiangxi Province, Jinggangshan University, Ji'an, Jiangxi 343009, China.
| | - Chengning Xie
- College of Mechanical and Electrical Engineering, Jinggangshan University, Ji'an, Jiangxi 343009, China
| | - Genhe He
- Key Laboratory of Biodiversity and Ecological Engineering of Jiangxi Province, Jinggangshan University, Ji'an, Jiangxi 343009, China.
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9
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Xu L, Zou Y, Wu K, Han R, Huang Y, Yi X. Polydatin-based natural product as an activatable molecular sensor toward viscosity detection in liquid. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2023. [DOI: 10.1007/s11694-023-01920-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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10
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Wang Y, Yu L, Shao J, Zhu Z, Zhang L. Structure-driven protein engineering for production of valuable natural products. TRENDS IN PLANT SCIENCE 2023; 28:460-470. [PMID: 36473772 DOI: 10.1016/j.tplants.2022.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 09/25/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
Proteins are the most frequently used biocatalysts, and their structures determine their functions. Modifying the functions of proteins on the basis of their structures lies at the heart of protein engineering, opening a new horizon for metabolic engineering by efficiently generating stable enzymes. Many attempts at classical metabolic engineering have focused on improving specific metabolic fluxes and producing more valuable natural products by increasing gene expression levels and enzyme concentrations. However, most naturally occurring enzymes show limitations, and such limitations have hindered practical applications. Here we review recent advances in protein engineering in synthetic biology, chemoenzymatic synthesis, and plant metabolic engineering and describe opportunities for designing and constructing novel enzymes or proteins with desirable properties to obtain more active natural products.
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Affiliation(s)
- Yun Wang
- Institute of Interdisciplinary Integrative Medicine Research, Medical School of Nantong University, Nantong 226001, China; Biomedical Innovation R&D Centre, School of Medicine, Shanghai University, Shanghai 200444, China
| | - Luyao Yu
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Jie Shao
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Zhanpin Zhu
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Lei Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Medical School of Nantong University, Nantong 226001, China; Biomedical Innovation R&D Centre, School of Medicine, Shanghai University, Shanghai 200444, China; Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai 200433, China; Innovative Drug R&D Center, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
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11
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Mao C, Mao Y, Zhu X, Chen G, Feng C. Synthetic biology-based bioreactor and its application in biochemical analysis. Crit Rev Anal Chem 2023:1-18. [PMID: 36803337 DOI: 10.1080/10408347.2023.2180319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
In the past few years, synthetic biologists have established some biological elements and bioreactors composed of nucleotides under the guidance of engineering methods. Following the concept of engineering, the common bioreactor components in recent years are introduced and compared. At present, biosensors based on synthetic biology have been applied to water pollution monitoring, disease diagnosis, epidemiological monitoring, biochemical analysis and other detection fields. In this paper, the biosensor components based on synthetic bioreactors and reporters are reviewed. In addition, the applications of biosensors based on cell system and cell-free system in the detection of heavy metal ions, nucleic acid, antibiotics and other substances are presented. Finally, the bottlenecks faced by biosensors and the direction of optimization are also discussed.
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Affiliation(s)
- Changqing Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Yichun Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, P. R. China
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
- Shanghai Engineering Research Center of Organ Repair, Shanghai University, Shanghai, P. R. China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
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12
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Ouadhi S, López DMV, Mohideen FI, Kwan DH. Engineering the enzyme toolbox to tailor glycosylation in small molecule natural products and protein biologics. Protein Eng Des Sel 2023; 36:gzac010. [PMID: 36444941 DOI: 10.1093/protein/gzac010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/11/2022] [Accepted: 10/04/2022] [Indexed: 12/03/2022] Open
Abstract
Many glycosylated small molecule natural products and glycoprotein biologics are important in a broad range of therapeutic and industrial applications. The sugar moieties that decorate these compounds often show a profound impact on their biological functions, thus biocatalytic methods for controlling their glycosylation are valuable. Enzymes from nature are useful tools to tailor bioproduct glycosylation but these sometimes have limitations in their catalytic efficiency, substrate specificity, regiospecificity, stereospecificity, or stability. Enzyme engineering strategies such as directed evolution or semi-rational and rational design have addressed some of the challenges presented by these limitations. In this review, we highlight some of the recent research on engineering enzymes to tailor the glycosylation of small molecule natural products (including alkaloids, terpenoids, polyketides, and peptides), as well as the glycosylation of protein biologics (including hormones, enzyme-replacement therapies, enzyme inhibitors, vaccines, and antibodies).
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Affiliation(s)
- Sara Ouadhi
- Centre for Applied Synthetic Biology, Concordia University, Montreal, QC H4B 2A6, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
| | - Dulce María Valdez López
- Centre for Applied Synthetic Biology, Concordia University, Montreal, QC H4B 2A6, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
| | - F Ifthiha Mohideen
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - David H Kwan
- Centre for Applied Synthetic Biology, Concordia University, Montreal, QC H4B 2A6, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Quebec City, QC G1V 0A6, Canada
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13
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Khushboo, Singhvi N, Gupta V, Dhaka N, Dubey KK. Draft genome sequence of Streptomyces sp. KD18, isolated from industrial soil. 3 Biotech 2023; 13:34. [PMID: 36619820 PMCID: PMC9810780 DOI: 10.1007/s13205-022-03453-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/24/2022] [Indexed: 01/05/2023] Open
Abstract
The present study scrutinizes the presence of Streptomyces strains in the soil sample collected from industrial area of Bahadurgarh (Haryana) India. The morphological approach manifested the isolated strain belong to Streptomyces species and named as Streptomyces sp. KD18. Sequencing of Streptomyces sp. KD18 genome was performed by Illumina Nextseq500 platform. 65 contigs were generated via SPAdes v3.11.1 and harboured genome size of 7.2 Mb. AntiSMASH server revealed the presence of 25 biosynthetic gene clusters in KD18 genome where BGC of lipstatin was of more interest from industrial and pharmaceutical purpose. The draft genome sequence represented via ANI values claimed that the KD18 strain belongs to Streptomyces toxytricini and finally named as S. toxytricini KD18. The LC-MS analysis of the extracted metabolite confirmed the production of lipstatin. The genome sequence data have been deposited to NCBI under the accession number of GCA_014748315.1. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03453-3.
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Affiliation(s)
- Khushboo
- Department of Biotechnology, Central University of Haryana, Mahendergarh, 123031 India
| | - Nirjara Singhvi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, Uttarakhand 248007 India
| | - Vipin Gupta
- Ministry of Environment, Forest and Climate Change, Integrated Regional Office, Dehradun, Uttarakhand 248001 India
| | - Namrata Dhaka
- Department of Biotechnology, Central University of Haryana, Mahendergarh, 123031 India
| | - Kashyap Kumar Dubey
- Bioprocess Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
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14
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Alam K, Zhao Y, Lu X, Gong K, Zhong L, Hao J, Islam MM, Islam S, Li G, Zhang Y, Li R, Li A. Isolation, complete genome sequencing and in silico genome mining of Burkholderia for secondary metabolites. BMC Microbiol 2022; 22:323. [PMID: 36581815 PMCID: PMC9801586 DOI: 10.1186/s12866-022-02692-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 11/04/2022] [Indexed: 12/31/2022] Open
Abstract
Recent years, Burkholderia species have emerged as a new source of natural products (NPs) with increasing attractions. Genome mining suggests the Burkholderia genomes include many natural product biosynthetic gene clusters (BGCs) which are new targets for drug discovery. In order to collect more Burkholderia, here, a strain S-53 was isolated from the soil samples on a mountain area in Changde, P.R. China and verified by comparative genetic analysis to belong to Burkholderia. The complete genome of Burkholderia strain S-53 is 8.2 Mbps in size with an average G + C content of 66.35%. Its taxonomy was both characterized by 16S rRNA- and whole genome-based phylogenetic trees. Bioinformatic prediction in silico revealed it has a total of 15 NP BGCs, some of which may encode unknown products. It is expectable that availability of these BGCs will speed up the identification of new secondary metabolites from Burkholderia and help us understand how sophisticated BGC regulation works.
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Affiliation(s)
- Khorshed Alam
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Yiming Zhao
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Xuefei Lu
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Kai Gong
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Lin Zhong
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Jinfang Hao
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Md. Mahmudul Islam
- Department of Microbiology, Rajshahi Institute of Biosciences (RIB), Affi. University of Rajshahi, Rajshahi, 6212 Bangladesh
| | - Saiful Islam
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram Laboratories, Chattogram, 4220 Bangladesh
| | - Geng Li
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Ruijuan Li
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, 266237 People’s Republic of China
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, 266237 People’s Republic of China
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15
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Abstract
Natural enzymes catalyze biochemical transformations in superior catalytic efficiency and remarkable substrate specificity. The excellent catalytic repertoire of enzymes is attributed to the sophisticated chemical structures of their active sites, as a result of billions-of-years natural evolution. However, large-scale practical applications of natural enzymes are restricted due to their poor stability, difficulty in modification, and high costs of production. One viable solution is to fabricate supramolecular catalysts with enzyme-mimetic active sites. In this review, we introduce the principles and strategies of designing peptide-based artificial enzymes which display catalytic activities similar to those of natural enzymes, such as aldolases, laccases, peroxidases, and hydrolases (mainly the esterases and phosphatases). We also discuss some multifunctional enzyme-mimicking systems which are capable of catalyzing orthogonal or cascade reactions. We highlight the relationship between structures of enzyme-like active sites and the catalytic properties, as well as the significance of these studies from an evolutionary point of view.
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16
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Xu L, Kang M, Xiong F, Sui Y, Huang Y. Cinnamaldehyde‐based Natural Product as Viscosity‐Sensitive Sensor toward Liquid Safety Inspection. ChemistrySelect 2022. [DOI: 10.1002/slct.202203458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Lingfeng Xu
- Key Laboratory of Biodiversity and Ecological Engineering of Jiangxi Province Jinggangshan University Ji'an Jiangxi 343009 China
- State Key Laboratory of Luminescent Materials & Devices South China University of Technology Guangzhou Guangdong 510640 China
| | - Minqing Kang
- School of Chemistry and Chemical Engineering Jinggangshan University Ji'an Jiangxi 343009 China
| | - Fangzhi Xiong
- School of Chemistry and Chemical Engineering Jinggangshan University Ji'an Jiangxi 343009 China
| | - Yan Sui
- School of Chemistry and Chemical Engineering Jinggangshan University Ji'an Jiangxi 343009 China
| | - Yanrong Huang
- Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety South China University of Technology Guangzhou Guangdong 510640 China
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17
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Young RJ, Flitsch SL, Grigalunas M, Leeson PD, Quinn RJ, Turner NJ, Waldmann H. The Time and Place for Nature in Drug Discovery. JACS AU 2022; 2:2400-2416. [PMID: 36465532 PMCID: PMC9709949 DOI: 10.1021/jacsau.2c00415] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 05/31/2023]
Abstract
The case for a renewed focus on Nature in drug discovery is reviewed; not in terms of natural product screening, but how and why biomimetic molecules, especially those produced by natural processes, should deliver in the age of artificial intelligence and screening of vast collections both in vitro and in silico. The declining natural product-likeness of licensed drugs and the consequent physicochemical implications of this trend in the context of current practices are noted. To arrest these trends, the logic of seeking new bioactive agents with enhanced natural mimicry is considered; notably that molecules constructed by proteins (enzymes) are more likely to interact with other proteins (e.g., targets and transporters), a notion validated by natural products. Nature's finite number of building blocks and their interactions necessarily reduce potential numbers of structures, yet these enable expansion of chemical space with their inherent diversity of physical characteristics, pertinent to property-based design. The feasible variations on natural motifs are considered and expanded to encompass pseudo-natural products, leading to the further logical step of harnessing bioprocessing routes to access them. Together, these offer opportunities for enhancing natural mimicry, thereby bringing innovation to drug synthesis exploiting the characteristics of natural recognition processes. The potential for computational guidance to help identifying binding commonalities in the route map is a logical opportunity to enable the design of tailored molecules, with a focus on "organic/biological" rather than purely "synthetic" structures. The design and synthesis of prototype structures should pay dividends in the disposition and efficacy of the molecules, while inherently enabling greener and more sustainable manufacturing techniques.
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Affiliation(s)
| | - Sabine L. Flitsch
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Michael Grigalunas
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
| | - Paul D. Leeson
- Paul
Leeson Consulting Limited, The Malt House, Main Street, Congerstone, Nuneaton, Warwickshire CV13 6LZ, U.K.
| | - Ronald J. Quinn
- Griffith
Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Nicholas J. Turner
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Herbert Waldmann
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
- Faculty of
Chemistry and Chemical Biology, Technical
University of Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
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18
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Zhang N, Wu C. Tailoring Protein-Polymer Conjugates as Efficient Artificial Enzymes for Aqueous Asymmetric Aldol Reactions. ACS Synth Biol 2022; 11:3797-3804. [PMID: 36343337 DOI: 10.1021/acssynbio.2c00387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Artificial enzymes are becoming a powerful toolbox for selective organic syntheses. Herein, we first propose an advanced artificial enzyme by polymeric modularity as an efficient aldolase mimic for aqueous asymmetric aldol reactions. Based on an in-depth understanding of the aldolase reaction mechanism and our previous work, we demonstrate the modular design of protein-polymer conjugates by co-incorporating l-proline and styrene onto a noncatalytic protein scaffold with a high degree of controllability. The tailored conjugates exhibited remarkable catalytic performance toward the aqueous asymmetric aldol reaction of p-nitrobenzaldehyde and cyclohexanone, achieving 94% conversion and excellent selectivity (95/5 diastereoselectivity, 98% enantiomeric excess). In addition, this artificial enzyme showed high tolerance against extreme conditions (e.g., wide pH range, high temperature) and could be reused for more than four times without significant loss of reactivity. Experiments have shown that the artificial enzyme displayed broad specificity for various aldehydes.
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Affiliation(s)
- Ningning Zhang
- Institute of Microbiology, Technische Universität Dresden, Zellescher Weg 20b, 01217 Dresden, Germany
| | - Changzhu Wu
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.,Danish Institute for Advanced Study (DIAS), University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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19
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Alam K, Hao J, Zhong L, Fan G, Ouyang Q, Islam MM, Islam S, Sun H, Zhang Y, Li R, Li A. Complete genome sequencing and in silico genome mining reveal the promising metabolic potential in Streptomyces strain CS-7. Front Microbiol 2022; 13:939919. [PMID: 36274688 PMCID: PMC9581153 DOI: 10.3389/fmicb.2022.939919] [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: 05/09/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Gram-positive Streptomyces bacteria can produce valuable secondary metabolites. Streptomyces genomes include huge unknown silent natural product (NP) biosynthetic gene clusters (BGCs), making them a potential drug discovery repository. To collect antibiotic-producing bacteria from unexplored areas, we identified Streptomyces sp. CS-7 from mountain soil samples in Changsha, P.R. China, which showed strong antibacterial activity. Complete genome sequencing and prediction in silico revealed that its 8.4 Mbp genome contains a total of 36 BGCs for NPs. We purified two important antibiotics from this strain, which were structurally elucidated to be mayamycin and mayamycin B active against Staphylococcus aureus. We identified functionally a BGC for the biosynthesis of these two compounds by BGC direct cloning and heterologous expression in Streptomyces albus. The data here supported this Streptomyces species, especially from unexplored habitats, having a high potential for new NPs.
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Affiliation(s)
- Khorshed Alam
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jinfang Hao
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Lin Zhong
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Guoqing Fan
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qing Ouyang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Md. Mahmudul Islam
- Department of Microbiology, Rajshahi Institute of Biosciences (RIB), Affiliated University of Rajshahi, Rajshahi, Bangladesh
| | - Saiful Islam
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram Laboratories, Chattogram, Bangladesh
| | - Hongluan Sun
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Chinese Academy of Sciences, Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China
| | - Ruijuan Li
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Ruijuan Li,
| | - Aiying Li
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- *Correspondence: Aiying Li,
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20
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Molinaro C, Kawasaki Y, Wanyoike G, Nishioka T, Yamamoto T, Snedecor B, Robinson SJ, Gosselin F. Engineered Cytochrome P450-Catalyzed Oxidative Biaryl Coupling Reaction Provides a Scalable Entry into Arylomycin Antibiotics. J Am Chem Soc 2022; 144:14838-14845. [PMID: 35905381 DOI: 10.1021/jacs.2c06019] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report herein the first example of a cytochrome P450-catalyzed oxidative carbon-carbon coupling process for a scalable entry into arylomycin antibiotic cores. Starting from wild-type hydroxylating cytochrome P450 enzymes and engineered Escherichia coli, a combination of enzyme engineering, random mutagenesis, and optimization of reaction conditions generated a P450 variant that affords the desired arylomycin core 2d in 84% assay yield. Furthermore, this process was demonstrated as a viable route for the production of the arylomycin antibiotic core on the gram scale. Finally, this new entry affords a viable, scalable, and practical route for the synthesis of novel Gram-negative antibiotics.
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Affiliation(s)
- Carmela Molinaro
- Department of Small Molecule Process Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Yukie Kawasaki
- Applied Microbiotechnology Department, MicroBiopharm Japan Co. Ltd., 156 Nakagawara, Kiyosu, Aichi 452-0915, Japan
| | - George Wanyoike
- Production Technology Department, MicroBiopharm Japan Co. Ltd., 1808 Nakaizumi, Iwata, Shizuoka 438-0078, Japan
| | - Taiki Nishioka
- Applied Microbiotechnology Department, MicroBiopharm Japan Co. Ltd., 156 Nakagawara, Kiyosu, Aichi 452-0915, Japan
| | - Tsuyoshi Yamamoto
- Applied Microbiotechnology Department, MicroBiopharm Japan Co. Ltd., 156 Nakagawara, Kiyosu, Aichi 452-0915, Japan
| | - Brad Snedecor
- Department of Cell Culture and Bioprocess Operations, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sarah J Robinson
- Department of Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Francis Gosselin
- Department of Small Molecule Process Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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21
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Alcántara AR, Domínguez de María P, Littlechild JA, Schürmann M, Sheldon RA, Wohlgemuth R. Biocatalysis as Key to Sustainable Industrial Chemistry. CHEMSUSCHEM 2022; 15:e202102709. [PMID: 35238475 DOI: 10.1002/cssc.202102709] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/10/2022] [Indexed: 06/14/2023]
Abstract
The role and power of biocatalysis in sustainable chemistry has been continuously brought forward step by step to its present outstanding position. The problem-solving capabilities of biocatalysis have been realized by numerous substantial achievements in biology, chemistry and engineering. Advances and breakthroughs in the life sciences and interdisciplinary cooperation with chemistry have clearly accelerated the implementation of biocatalytic synthesis in modern chemistry. Resource-efficient biocatalytic manufacturing processes have already provided numerous benefits to sustainable chemistry as well as customer-centric value creation in the pharmaceutical, food, flavor, fragrance, vitamin, agrochemical, polymer, specialty, and fine chemical industries. Biocatalysis can make significant contributions not only to manufacturing processes, but also to the design of completely new value-creation chains. Biocatalysis can now be considered as a key enabling technology to implement sustainable chemistry.
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Affiliation(s)
- Andrés R Alcántara
- Department of Chemistry in Pharmaceutical Sciences (QUICIFARM), Complutense University of Madrid (UCM), 28040-, Madrid, Spain
| | - Pablo Domínguez de María
- Sustainable Momentum, SL, Av. Ansite 3, 4-6, 35011, Las Palmas de Gran Canaria, Canary Is., Spain
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | | | - Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Braamfontein, Johannesburg, South Africa
| | - Roland Wohlgemuth
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, 90-537, Lodz, Poland
- Swiss Coordination Committee for Biotechnology, 8021, Zurich, Switzerland
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22
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Liang Y, Luo J, Yang C, Guo S, Zhang B, Chen F, Su K, Zhang Y, Dong Y, Wang Z, Fu H, Sui G, Wang P. Directed evolution of the PobR allosteric transcription factor to generate a biosensor for 4-hydroxymandelic acid. World J Microbiol Biotechnol 2022; 38:104. [PMID: 35501522 DOI: 10.1007/s11274-022-03286-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 04/12/2022] [Indexed: 10/18/2022]
Abstract
Hydroxy-mandelic acid (HMA) is widely applied in pharmaceuticals, food and cosmetics. In this study, we aimed to develop an allosteric transcription factors (aTFs) based biosensor for HMA. PobR, an aTF for HMA analog 4-hydroxybenzoic acid, was used to alter its selectivity and create novel aTFs responsive to HMA by directed evolution. We established a PobR mutant library with a capacity of 550,000 mutants using error-prone PCR and Megawhop PCR. Through our screening, two mutants were obtained with responsiveness to HMA. Analysis of each missense mutation indicating residues 122-126 were involved in its PobR ligand specificity. These results showed the effectiveness of directed evolution in switching the ligand specificity of a biosensor and improving HMA production.
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Affiliation(s)
- YaoYao Liang
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, Heilongjiang, 150040, People's Republic of China
| | - Juan Luo
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Chenhao Yang
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Shuning Guo
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Bowen Zhang
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Fengqianrui Chen
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Kairui Su
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Yulong Zhang
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Yi Dong
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Zhihao Wang
- Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China.,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Hongda Fu
- NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China
| | - Guangchao Sui
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China. .,Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China. .,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China. .,Northeast Forestry University, No. 26 Hexing Road, Harbin, 150000, People's Republic of China.
| | - Pengchao Wang
- School of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China. .,Aulin College, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China. .,NEFU-China iGEM Team, Northeast Forestry University, Harbin, 150040, Heilongjiang, People's Republic of China. .,Key Laboratory for Enzymes and Enzyme-Like Material Engineering of Heilongjiang, Harbin, Heilongjiang, 150040, People's Republic of China. .,Northeast Forestry University, No. 26 Hexing Road, Harbin, 150000, People's Republic of China.
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23
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Cho YI, Armstrong CL, Sulpizio A, Acheampong KK, Banks KN, Bardhan O, Churchill SJ, Connolly-Sporing AE, Crawford CE, Cruz Parrilla PL, Curtis SM, De La Ossa LM, Epstein SC, Farrehi CJ, Hamrick GS, Hillegas WJ, Kang A, Laxton OC, Ling J, Matsumura SM, Merino VM, Mukhtar SH, Shah NJ, Londergan CH, Daly CA, Kokona B, Charkoudian LK. Engineered Chimeras Unveil Swappable Modular Features of Fatty Acid and Polyketide Synthase Acyl Carrier Proteins. Biochemistry 2022; 61:217-227. [PMID: 35073057 PMCID: PMC9357449 DOI: 10.1021/acs.biochem.1c00798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The strategic redesign of microbial biosynthetic pathways is a compelling route to access molecules of diverse structure and function in a potentially environmentally sustainable fashion. The promise of this approach hinges on an improved understanding of acyl carrier proteins (ACPs), which serve as central hubs in biosynthetic pathways. These small, flexible proteins mediate the transport of molecular building blocks and intermediates to enzymatic partners that extend and tailor the growing natural products. Past combinatorial biosynthesis efforts have failed due to incompatible ACP-enzyme pairings. Herein, we report the design of chimeric ACPs with features of the actinorhodin polyketide synthase ACP (ACT) and of the Escherichia coli fatty acid synthase (FAS) ACP (AcpP). We evaluate the ability of the chimeric ACPs to interact with the E. coli FAS ketosynthase FabF, which represents an interaction essential to building the carbon backbone of the synthase molecular output. Given that AcpP interacts with FabF but ACT does not, we sought to exchange modular features of ACT with AcpP to confer functionality with FabF. The interactions of chimeric ACPs with FabF were interrogated using sedimentation velocity experiments, surface plasmon resonance analyses, mechanism-based cross-linking assays, and molecular dynamics simulations. Results suggest that the residues guiding AcpP-FabF compatibility and ACT-FabF incompatibility may reside in the loop I, α-helix II region. These findings can inform the development of strategic secondary element swaps that expand the enzyme compatibility of ACPs across systems and therefore represent a critical step toward the strategic engineering of "un-natural" natural products.
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Affiliation(s)
- Yae In Cho
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | - Ariana Sulpizio
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | | | - Oishi Bardhan
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | | | | | | | - Sarah M. Curtis
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | | | | | | | | | - Austin Kang
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | - Joie Ling
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | | | | | - Neel J. Shah
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | | | - Clyde A. Daly
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | - Bashkim Kokona
- Department of Chemistry, Haverford College, Haverford, PA 19041
- Spark Therapeutics, Philadelphia PA 19041
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24
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Wurlitzer JM, Stanišić A, Ziethe S, Jordan PM, Günther K, Werz O, Kries H, Gressler M. Macrophage-targeting oligopeptides from Mortierella alpina. Chem Sci 2022; 13:9091-9101. [PMID: 36091214 PMCID: PMC9365243 DOI: 10.1039/d2sc00860b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/15/2022] [Indexed: 12/27/2022] Open
Abstract
The realm of natural products of early diverging fungi such as Mortierella species is largely unexplored. Herein, the nonribosomal peptide synthetase (NRPS) MalA catalysing the biosynthesis of the surface-active biosurfactants, malpinins, has been identified and biochemically characterised. The investigation of the substrate specificity of respective adenylation (A) domains indicated a substrate-tolerant enzyme with an unusual, inactive C-terminal NRPS module. Specificity-based precursor-directed biosynthesis yielded 20 new congeners produced by a single enzyme. Moreover, MalA incorporates artificial, click-functionalised amino acids which allowed postbiosynthetic coupling to a fluorophore. The fluorescent malpinin conjugate penetrates mammalian cell membranes via an phagocytosis-mediated mechanism, suggesting Mortierella oligopeptides as carrier peptides for directed cell targeting. The current study demonstrates substrate-specificity testing as a powerful tool to identify flexible NRPS modules and highlights basal fungi as reservoir for chemically tractable compounds in pharmaceutical applications. Specificity profiling of a nonribosomal peptide synthetase of an early diverging fungus revealed high substrate flexibility. Feeding studies with click-functionalised amino acids enabled the production of fluorescent peptides targeting macrophages.![]()
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Affiliation(s)
- Jacob M. Wurlitzer
- Department Pharmaceutical Microbiology at the Leibniz Institute for Natural Product Research and Infection Biology (Hans-Knöll-Institute), Friedrich-Schiller-University, Winzerlaer Strasse 2, Jena 07745, Germany
| | - Aleksa Stanišić
- Junior Group Biosynthetic Design of Natural Products at the Leibniz Institute for Natural Product Research and Infection Biology (Hans-Knöll-Institute), Beutenbergstrasse 11a, Jena 07745, Germany
| | - Sebastian Ziethe
- Department Pharmaceutical Microbiology at the Leibniz Institute for Natural Product Research and Infection Biology (Hans-Knöll-Institute), Friedrich-Schiller-University, Winzerlaer Strasse 2, Jena 07745, Germany
| | - Paul M. Jordan
- Department Pharmaceutical/Medicinal Chemistry at the Friedrich-Schiller-University, Philosophenweg 14, Jena 07743, Germany
| | - Kerstin Günther
- Department Pharmaceutical/Medicinal Chemistry at the Friedrich-Schiller-University, Philosophenweg 14, Jena 07743, Germany
| | - Oliver Werz
- Department Pharmaceutical/Medicinal Chemistry at the Friedrich-Schiller-University, Philosophenweg 14, Jena 07743, Germany
| | - Hajo Kries
- Junior Group Biosynthetic Design of Natural Products at the Leibniz Institute for Natural Product Research and Infection Biology (Hans-Knöll-Institute), Beutenbergstrasse 11a, Jena 07745, Germany
| | - Markus Gressler
- Department Pharmaceutical Microbiology at the Leibniz Institute for Natural Product Research and Infection Biology (Hans-Knöll-Institute), Friedrich-Schiller-University, Winzerlaer Strasse 2, Jena 07745, Germany
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25
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Breger JC, Ellis GA, Walper SA, Susumu K, Medintz IL. Implementing Multi-Enzyme Biocatalytic Systems Using Nanoparticle Scaffolds. Methods Mol Biol 2022; 2487:227-262. [PMID: 35687240 DOI: 10.1007/978-1-0716-2269-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Interest in multi-enzyme synthesis outside of cells (in vitro) is becoming far more prevalent as the field of cell-free synthetic biology grows exponentially. Such synthesis would allow for complex chemical transformations based on the exquisite specificity of enzymes in a "greener" manner as compared to organic chemical transformations. Here, we describe how nanoparticles, and in this specific case-semiconductor quantum dots, can be used to both stabilize enzymes and further allow them to self-assemble into nanocomplexes that facilitate high-efficiency channeling phenomena. Pertinent protocol information is provided on enzyme expression, choice of nanoparticulate material, confirmation of enzyme attachment to nanoparticles, assay format and tracking, data analysis, and optimization of assay formats to draw the best analytical information from the underlying processes.
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Affiliation(s)
- Joyce C Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, Washington, DC, USA
| | - Gregory A Ellis
- Center for Bio/Molecular Science and Engineering, Code 6900, Washington, DC, USA
| | - Scott A Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, Washington, DC, USA
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC, USA
- Jacobs Corporation, Hanover, MD, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, Washington, DC, USA.
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26
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Meyer J, Meyer L, Kara S. Enzyme immobilization in hydrogels: A perfect liaison for efficient and sustainable biocatalysis. Eng Life Sci 2021; 22:165-177. [PMID: 35382546 PMCID: PMC8961036 DOI: 10.1002/elsc.202100087] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 12/11/2022] Open
Abstract
Biocatalysis is an established chemical synthesis technology that has by no means been restricted to research laboratories. The use of enzymes for organic synthesis has evolved greatly from early development to proof‐of‐concept – from small batch production to industrial scale. Different enzyme immobilization strategies contributed to this success story. Recently, the use of hydrogel materials for the immobilization of enzymes has been attracting great interest. Within this review, we pay special attention to recent developments in this key emerging field of research. Firstly, we will briefly introduce the concepts of both biocatalysis and hydrogel worlds. Then, we list recent interesting publications that link both concepts. Finally, we provide an outlook and comment on future perspectives of further exploration of enzyme immobilization strategies in hydrogels.
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Affiliation(s)
- Johanna Meyer
- Institute of Technical Chemistry Leibniz University Hannover Hannover Germany
| | - Lars‐Erik Meyer
- Biocatalysis and Bioprocessing Group Department of Biological and Chemical Engineering Aarhus University Aarhus Denmark
| | - Selin Kara
- Institute of Technical Chemistry Leibniz University Hannover Hannover Germany
- Biocatalysis and Bioprocessing Group Department of Biological and Chemical Engineering Aarhus University Aarhus Denmark
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27
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Perez Ortiz G, Sidda JD, de Los Santos ELC, Hubert CB, Barry SM. In vitro elucidation of the crucial but complex oxidative tailoring steps in rufomycin biosynthesis enables one pot conversion of rufomycin B to rufomycin C. Chem Commun (Camb) 2021; 57:11795-11798. [PMID: 34676855 PMCID: PMC8577248 DOI: 10.1039/d1cc04794a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The antimycobacterial peptides, rufomycins, have their antibiotic activity conferred by oxidative tailoring of the cyclic peptide. Here we elucidate the roles of cytochrome P450s RufS and RufM in regioselective epoxidation and alkyl oxidation respectively and demonstrate how RufM and RufS create a complex product profile dependent on redox partner availability. Finally, we report the in vitro one pot conversion of rufomycin B to rufomycin C.
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Affiliation(s)
- Gustavo Perez Ortiz
- Department of Chemistry, Faculty of Natural, Mathematical & Engineering Sciences, Britannia House, 7 Trinity St, London, SE1 1DB, UK.
| | - John D Sidda
- Department of Chemistry, Faculty of Natural, Mathematical & Engineering Sciences, Britannia House, 7 Trinity St, London, SE1 1DB, UK.
| | | | - Catherine B Hubert
- Department of Chemistry, Faculty of Natural, Mathematical & Engineering Sciences, Britannia House, 7 Trinity St, London, SE1 1DB, UK.
| | - Sarah M Barry
- Department of Chemistry, Faculty of Natural, Mathematical & Engineering Sciences, Britannia House, 7 Trinity St, London, SE1 1DB, UK.
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28
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Cervinka R, Becker D, Lüdeke S, Albers S, Netscher T, Müller M. Enzymatic Asymmetric Reduction of Unfunctionalized C=C Bonds with Archaeal Geranylgeranyl Reductases. Chembiochem 2021; 22:2693-2696. [PMID: 34296507 PMCID: PMC8457153 DOI: 10.1002/cbic.202100290] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Indexed: 11/07/2022]
Abstract
The asymmetric reduction of activated C=C bonds such as enones is well established for non-enzymatic methods as well as in biocatalysis. However, the asymmetric reduction of unfunctionalized C=C bonds is mainly performed with transition metal catalysts whereas biocatalytic approaches are lacking. We have tested two FAD-dependent archaeal geranylgeranyl reductases (GGR) for the asymmetric reduction of isolated C=C bonds. The reduction of up to four double bonds in terpene chains with different chain lengths and head groups was confirmed. Methyl-branched E-alkenes were chemoselectively reduced in the presence of cyclic, terminal or activated alkenes. Using a removable succinate "spacer", farnesol and geraniol could be quantitatively reduced (>99 %). The reduction is strictly (R)-selective (enantiomeric excess >99 %). Hence, GGRs are promising biocatalysts for the asymmetric reduction of unactivated isolated C=C bonds, opening new opportunities for the synthesis of enantiopure branched alkyl chains.
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Affiliation(s)
- Richard Cervinka
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Daniel Becker
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
- Institut für Pharmazeutische und Medizinische ChemieHeinrich-Heine-Universität Düsseldorf40225DüsseldorfGermany
| | - Steffen Lüdeke
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Sonja‐Verena Albers
- Institute for Biology IIMolecular Biology of ArchaeaFaculty of BiologyAlbert-Ludwigs-Universität Freiburg79104FreiburgGermany
| | - Thomas Netscher
- Research and DevelopmentDSM Nutritional Products Ltd.P.O. Box 26764002BaselSwitzerland
| | - Michael Müller
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
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29
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Cigan E, Eggbauer B, Schrittwieser JH, Kroutil W. The role of biocatalysis in the asymmetric synthesis of alkaloids - an update. RSC Adv 2021; 11:28223-28270. [PMID: 35480754 PMCID: PMC9038100 DOI: 10.1039/d1ra04181a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/30/2021] [Indexed: 12/19/2022] Open
Abstract
Alkaloids are a group of natural products with interesting pharmacological properties and a long history of medicinal application. Their complex molecular structures have fascinated chemists for decades, and their total synthesis still poses a considerable challenge. In a previous review, we have illustrated how biocatalysis can make valuable contributions to the asymmetric synthesis of alkaloids. The chemo-enzymatic strategies discussed therein have been further explored and improved in recent years, and advances in amine biocatalysis have vastly expanded the opportunities for incorporating enzymes into synthetic routes towards these important natural products. The present review summarises modern developments in chemo-enzymatic alkaloid synthesis since 2013, in which the biocatalytic transformations continue to take an increasingly 'central' role.
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Affiliation(s)
- Emmanuel Cigan
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth Heinrichstrasse 28/II 8010 Graz Austria
| | - Bettina Eggbauer
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth Heinrichstrasse 28/II 8010 Graz Austria
| | - Joerg H Schrittwieser
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth Heinrichstrasse 28/II 8010 Graz Austria
| | - Wolfgang Kroutil
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth Heinrichstrasse 28/II 8010 Graz Austria
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30
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Pickl M. Recent trends in the stereoselective synthesis of (poly)-substituted 2-oxo acids by biocatalyzed aldol reaction. CURRENT OPINION IN GREEN AND SUSTAINABLE CHEMISTRY 2021; 30:100476. [PMID: 34141957 PMCID: PMC7610986 DOI: 10.1016/j.cogsc.2021.100476] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Recently, an increased interest toward enzymatic carboligation was observed, as biocatalytic carbon-carbon bond formation is a common obstacle in retrosynthetic planning. The construction of extended 2-oxoacid frameworks by 2-oxoacid aldolases and enzymes acting as aldolases is a potent tool for synthetic chemists since a broad spectrum of downstream reactions through functional group interconversions gives access to a plethora of compound classes. In the search for selective biocatalysts, successful protein engineering efforts and high throughput screenings from biodiversity expand the structural diversity of nucleophile and electrophile substrates. Several successful examples with an emphasis on reactions catalyzed by class II aldolases and enzymes acting as class II aldolases are highlighted, including reactions in which both enantiomeric products and in selected cases even diastereomeric products are accessed.
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Affiliation(s)
- Mathias Pickl
- Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
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31
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32
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Renata H. Synthetic utility of oxygenases in site-selective terpenoid functionalization. J Ind Microbiol Biotechnol 2021; 48:6119916. [PMID: 33928356 PMCID: PMC8180501 DOI: 10.1093/jimb/kuab002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 11/19/2020] [Indexed: 12/24/2022]
Abstract
Terpenoids are one of the largest classes of natural products whose members possess a wide variety of biological activities. With several exceptions, scalable production of complex terpenoids with either purely biological or chemical methods still remains a major challenge. However, recent efforts to combine the two approaches in chemoenzymatic synthesis hold tremendous promise to address this challenge. Central to this paradigm is the development of useful biocatalytic methods, such as regioselective C–H oxidation, for terpene modifications. This review highlights recent applications of biocatalytic hydroxylation for site-selective modification of terpenoids.
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Affiliation(s)
- Hans Renata
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
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33
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Daley SK, Cordell GA. Alkaloids in Contemporary Drug Discovery to Meet Global Disease Needs. Molecules 2021; 26:molecules26133800. [PMID: 34206470 PMCID: PMC8270272 DOI: 10.3390/molecules26133800] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/05/2021] [Accepted: 06/14/2021] [Indexed: 12/15/2022] Open
Abstract
An overview is presented of the well-established role of alkaloids in drug discovery, the application of more sustainable chemicals, and biological approaches, and the implementation of information systems to address the current challenges faced in meeting global disease needs. The necessity for a new international paradigm for natural product discovery and development for the treatment of multidrug resistant organisms, and rare and neglected tropical diseases in the era of the Fourth Industrial Revolution and the Quintuple Helix is discussed.
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Affiliation(s)
| | - Geoffrey A. Cordell
- Natural Products Inc., Evanston, IL 60202, USA;
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
- Correspondence:
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34
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Liu D, Rubin GM, Dhakal D, Chen M, Ding Y. Biocatalytic synthesis of peptidic natural products and related analogues. iScience 2021; 24:102512. [PMID: 34041453 PMCID: PMC8141463 DOI: 10.1016/j.isci.2021.102512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Peptidic natural products (PNPs) represent a rich source of lead compounds for the discovery and development of therapeutic agents for the treatment of a variety of diseases. However, the chemical synthesis of PNPs with diverse modifications for drug research is often faced with significant challenges, including the unavailability of constituent nonproteinogenic amino acids, inefficient cyclization protocols, and poor compatibility with other functional groups. Advances in the understanding of PNP biosynthesis and biocatalysis provide a promising, sustainable alternative for the synthesis of these compounds and their analogues. Here we discuss current progress in using native and engineered biosynthetic enzymes for the production of both ribosomally and nonribosomally synthesized peptides. In addition, we highlight new in vitro and in vivo approaches for the generation and screening of PNP libraries.
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Affiliation(s)
- Dake Liu
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Garret M. Rubin
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Manyun Chen
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
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35
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Revolutionizing enzyme engineering through artificial intelligence and machine learning. Emerg Top Life Sci 2021; 5:113-125. [PMID: 33835131 DOI: 10.1042/etls20200257] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 12/20/2022]
Abstract
The combinatorial space of an enzyme sequence has astronomical possibilities and exploring it with contemporary experimental techniques is arduous and often ineffective. Multi-target objectives such as concomitantly achieving improved selectivity, solubility and activity of an enzyme have narrow plausibility under approaches of restricted mutagenesis and combinatorial search. Traditional enzyme engineering approaches have a limited scope for complex optimization due to the requirement of a priori knowledge or experimental burden of screening huge protein libraries. The recent surge in high-throughput experimental methods including Next Generation Sequencing and automated screening has flooded the field of molecular biology with big-data, which requires us to re-think our concurrent approaches towards enzyme engineering. Artificial Intelligence (AI) and Machine Learning (ML) have great potential to revolutionize smart enzyme engineering without the explicit need for a complete understanding of the underlying molecular system. Here, we portray the role and position of AI techniques in the field of enzyme engineering along with their scope and limitations. In addition, we explain how the traditional approaches of directed evolution and rational design can be extended through AI tools. Recent successful examples of AI-assisted enzyme engineering projects and their deviation from traditional approaches are highlighted. A comprehensive picture of current challenges and future avenues for AI in enzyme engineering are also discussed.
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36
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Xue F, Li C, Xu Q. Biocatalytic approaches for the synthesis of optically pure vic-halohydrins. Appl Microbiol Biotechnol 2021; 105:3411-3421. [PMID: 33851239 DOI: 10.1007/s00253-021-11266-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/28/2021] [Accepted: 04/04/2021] [Indexed: 11/30/2022]
Abstract
Enantiopure vicinal halohydrins (vic-halohydrins) are highly valuable building blocks for the synthesis of many different natural products and pharmaceuticals, and biocatalytic methods for their synthesis have received considerable interest. This review emphasizes the application of biocatalytic approaches as an efficient alternative or complement to conventional chemical reactions, with a special focus on the asymmetric reductions catalyzed by ketoreductases, kinetic resolution catalyzed using lipases or esterases, stereoselective biotransformation catalyzed by halohydrin dehalogenases, asymmetric hydroxylation catalyzed by cytochrome P450 monooxygenases, asymmetric dehalogenation catalyzed by haloalkane dehalogenases, and aldehyde condensation catalyzed by aldolases. Although many chiral vic-halohydrins have been successfully synthesized using wild-type biocatalysts, their enantioselectivity is often too low for enantiopure synthesis. To overcome these limitations, catalytic properties of wild-type enzymes have been improved by rational and semi-rational protein design or directed evolution. This review briefly introduces the research status in this field, highlighting aspects of basic academic research in the biocatalytic synthesis of optically active vic-halohydrins by employing such unconventional approaches. KEY POINTS: • Outlines the enzymatic strategies for the production of enantiopure vic-halohydrins • Highlights recent advances in biocatalytic production of enantiopure vic-halohydrins • Provide guidance for efficient preparation of enantiopure vic-halohydrins.
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Affiliation(s)
- Feng Xue
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, NO 1, Wenyuan Road, Nanjing, 210023, People's Republic of China
| | - Changfan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, NO 1, Wenyuan Road, Nanjing, 210023, People's Republic of China
| | - Qing Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, NO 1, Wenyuan Road, Nanjing, 210023, People's Republic of China.
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37
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Phung Hai TA, Tessman M, Neelakantan N, Samoylov AA, Ito Y, Rajput BS, Pourahmady N, Burkart MD. Renewable Polyurethanes from Sustainable Biological Precursors. Biomacromolecules 2021; 22:1770-1794. [PMID: 33822601 DOI: 10.1021/acs.biomac.0c01610] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Due to the depletion of fossil fuels, higher oil prices, and greenhouse gas emissions, the scientific community has been conducting an ongoing search for viable renewable alternatives to petroleum-based products, with the anticipation of increased adaptation in the coming years. New academic and industrial developments have encouraged the utilization of renewable resources for the development of ecofriendly and sustainable materials, and here, we focus on those advances that impact polyurethane (PU) materials. Vegetable oils, algae oils, and polysaccharides are included among the major renewable resources that have supported the development of sustainable PU precursors to date. Renewable feedstocks such as algae have the benefit of requiring only sunshine, carbon dioxide, and trace minerals to generate a sustainable biomass source, offering an improved carbon footprint to lessen environmental impacts. Incorporation of renewable content into commercially viable polymer materials, particularly PUs, has increasing and realistic potential. Biobased polyols can currently be purchased, and the potential to expand into new monomers offers exciting possibilities for new product development. This Review highlights the latest developments in PU chemistry from renewable raw materials, as well as the various biological precursors being employed in the synthesis of thermoset and thermoplastic PUs. We also provide an overview of literature reports that focus on biobased polyols and isocyanates, the two major precursors to PUs.
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Affiliation(s)
- Thien An Phung Hai
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Marissa Tessman
- Algenesis Materials Inc., 1238 Sea Village Drive, Cardiff, California 92007, United States
| | - Nitin Neelakantan
- Algenesis Materials Inc., 1238 Sea Village Drive, Cardiff, California 92007, United States
| | - Anton A Samoylov
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Yuri Ito
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Bhausaheb S Rajput
- Food and Fuel for the 21st Century, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0435, United States
| | - Naser Pourahmady
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States.,Algenesis Materials Inc., 1238 Sea Village Drive, Cardiff, California 92007, United States.,Food and Fuel for the 21st Century, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0435, United States
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38
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Abedini E, Khodadadi E, Zeinalzadeh E, Moaddab SR, Asgharzadeh M, Mehramouz B, Dao S, Samadi Kafil H. A Comprehensive Study on the Antimicrobial Properties of Resveratrol as an Alternative Therapy. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2021; 2021:8866311. [PMID: 33815561 PMCID: PMC7987421 DOI: 10.1155/2021/8866311] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 02/16/2021] [Accepted: 03/10/2021] [Indexed: 12/15/2022]
Abstract
Resveratrol is a polyphenolic antioxidant whose possible health benefits include anticarcinogenic, antiaging, and antimicrobial properties that have gained significant attention. The compound is well accepted by individuals and has been commonly used as a nutraceutical in recent decades. Its widespread usage makes it essential to study as a single agent as well as in combination with traditional prescription antibiotics as regards to antimicrobial properties. Resveratrol demonstrates the action of antimicrobials against a remarkable bacterial diversity, viruses, and fungus. This report explains resveratrol as an all-natural antimicrobial representative. It may modify the bacterial virulence qualities resulting in decreased toxic substance production, biofilm inhibition, motility reduction, and quorum sensing disturbance. Moreover, in conjunction with standard antibiotics, resveratrol improves aminoglycoside efficacy versus Staphylococcus aureus, while it antagonizes the deadly function of fluoroquinolones against S. aureus and also Escherichia coli. The present study aimed to thoroughly review and study the antimicrobial potency of resveratrol, expected to help researchers pave the way for solving antimicrobial resistance.
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Affiliation(s)
- Ehsan Abedini
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ehsaneh Khodadadi
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elham Zeinalzadeh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyyed Reza Moaddab
- Pharmaceutical Nanotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahareh Mehramouz
- Connective Tissue Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sounkalo Dao
- Faculté de Médecine, de Pharmacie et d'Odonto-Stomatologie (FMPOS), University of Bamako, Bamako, Mali
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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39
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Majer HM, Ehrlich RL, Ahmed A, Earl JP, Ehrlich GD, Beld J. Whole genome sequencing of Streptomyces actuosus ISP-5337, Streptomyces sioyaensis B-5408, and Actinospica acidiphila B-2296 reveals secondary metabolomes with antibiotic potential. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 29:e00596. [PMID: 33643857 PMCID: PMC7893419 DOI: 10.1016/j.btre.2021.e00596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/20/2021] [Accepted: 02/01/2021] [Indexed: 12/31/2022]
Abstract
Whole genome sequencing of Actinomycetes reveals metabolic potential. High quality genomes are necessary for mining of biosynthetic gene clusters. Characterization of thiopeptides by high resolution mass spectrometry. Thiopeptides are potent antibacterials against Staphylococcus aureus.
Streptomycetes are bacteria of biotechnological importance since they are avid producers of secondary metabolites, including antibiotics. Progress in genome mining has recently shown that Streptomyces species encode for many biosynthetic gene clusters which are mostly unexplored. Here, we selected three Actinomycetes species for whole genome sequencing that are known to produce potent thiopeptide antibiotics. Streptomyces actuosus biosynthesizes nosiheptide, Streptomyces sioyaensis produces siomycin, and Actinospica acidiphila is a member of the Actinomycete subfamily. Bioinformatic analyses demonstrated diverse secondary metabolomes with multiple antibiotic-encoding gene clusters. Detailed mass spectrometry analysis of metabolite extracts verified the active expression of nosiheptide and siomycin from S. actuosus and S. sioyaensis while fractionation of the bacterial extracts and subsequent challenge against Staphylococcus aureus demonstrated potent antibiotic activity of fractions containing these compounds. Whole genome sequencing of these species facilitates future bioengineering efforts for thiopeptides and characterization of relevant secondary metabolites.
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Affiliation(s)
- Haley M Majer
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15 St, Philadelphia, PA 19102, USA
| | - Rachel L Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15 St, Philadelphia, PA 19102, USA
| | - Azad Ahmed
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15 St, Philadelphia, PA 19102, USA
| | - Joshua P Earl
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15 St, Philadelphia, PA 19102, USA
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15 St, Philadelphia, PA 19102, USA
| | - Joris Beld
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15 St, Philadelphia, PA 19102, USA
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40
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Li W, Sun W, Li C. Engineered microorganisms and enzymes for efficiently synthesizing plant natural products. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.12.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Nazor J, Liu J, Huisman G. Enzyme evolution for industrial biocatalytic cascades. Curr Opin Biotechnol 2021; 69:182-190. [PMID: 33517157 DOI: 10.1016/j.copbio.2020.12.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/04/2020] [Accepted: 12/15/2020] [Indexed: 12/13/2022]
Abstract
Multi-step, biocatalytic cascades are poised to lead to further adoption of enzymes by the chemical industry. Over the past twenty years, the promise of in vitro enzyme evolution for the sustainable biocatalytic synthesis of complex chemicals at large scale has materialized. Recently, the field of biocatalysis is seeing further expansion, with biocatalytic processes becoming more complex and involving multiple consecutive enzymatic conversions. These biocatalytic cascades are assembled in single reaction vessels to accomplish difficult chemistry under mild reaction conditions, with minimal waste generation and attractive economics. Advances in enzyme engineering have enabled the increasingly efficient optimization of enzymes in the context of such cascades, where each enzyme operates in the presence of others, under continuously changing conditions as substrate, reaction intermediates, and product concentrations fluctuate over the course of the reaction. Enzyme evolution has provided biocatalysts with greatly improved traits, including activity, selectivity, and stability. This review focuses on recently developed, industrially relevant enzyme cascades.
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Affiliation(s)
- Jovana Nazor
- Codexis Inc, 200 Penobscot Drive, Redwood City, CA 94063, United States
| | - Joyce Liu
- Codexis Inc, 200 Penobscot Drive, Redwood City, CA 94063, United States
| | - Gjalt Huisman
- Codexis Inc, 200 Penobscot Drive, Redwood City, CA 94063, United States.
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Ionic liquids for regulating biocatalytic process: Achievements and perspectives. Biotechnol Adv 2021; 51:107702. [PMID: 33515671 DOI: 10.1016/j.biotechadv.2021.107702] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/26/2020] [Accepted: 01/15/2021] [Indexed: 12/26/2022]
Abstract
Biocatalysis has found enormous applications in sorts of fields as an alternative to chemical catalysis. In the pursue of green and sustainable chemistry, ionic liquids (ILs) have been considered as promising reaction media for biocatalysis, owing to their unique characteristics, such as nonvolatility, inflammability and tunable properties as regards polarity and water miscibility behavior, compared to organic solvents. In recent years, great developments have been achieved in respects to biocatalysis in ILs, especially for preparing various chemicals. This review tends to give illustrative examples with a focus on representative chemicals production by biocatalyst in ILs and elucidate the possible mechanism in such systems. It also discusses how to regulate the catalytic efficiency from several aspects and finally provides an outlook on the opportunities to broaden biocatalysis in ILs.
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43
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Transcription factor-based biosensors: a molecular-guided approach for natural product engineering. Curr Opin Biotechnol 2021; 69:172-181. [PMID: 33493842 DOI: 10.1016/j.copbio.2021.01.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/21/2020] [Accepted: 01/10/2021] [Indexed: 12/13/2022]
Abstract
Natural products and their derivatives offer a rich source of chemical and biological diversity; however, traditional engineering of their biosynthetic pathways to improve yields and access to unnatural derivatives requires a precise understanding of their enzymatic processes. High-throughput screening platforms based on allosteric transcription-factor based biosensors can be leveraged to overcome the screening bottleneck to enable searching through large libraries of pathway/strain variants. Herein, the development and application of engineered allosteric transcription factor-based biosensors is described that enable optimization of precursor availability, product titers, and downstream product tailoring for advancing the natural product bioeconomy. We discuss recent successes for tailoring biosensor design, including computationally-based approaches, and present our future outlook with the integration of cell-free technologies and de novo protein design for rapidly generating biosensor tools.
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44
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Tang H, Ju X, Zhao J, Li L. Engineering ribose-5-phosphate isomerase B from a central carbon metabolic enzyme to a promising sugar biocatalyst. Appl Microbiol Biotechnol 2021; 105:509-523. [PMID: 33394147 DOI: 10.1007/s00253-020-11075-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/12/2020] [Accepted: 12/23/2020] [Indexed: 10/22/2022]
Abstract
Ribose-5-phosphate isomerase B (RpiB) was first identified in the pentose phosphate pathway responsible for the inter-conversion of ribose-5-phosphate and ribulose-5-phosphate. Though there are seldom key enzymes in central carbon metabolic system developed as useful biocatalysts, RpiB with the advantages of wide substrate scope and high stereoselectivity has become a potential biotechnological tool to fulfill the demand of rare sugars currently. In this review, the pivotal roles of RpiB in carbon metabolism are summarized, and their sequence identity and structural similarity are discussed. Substrate binding and catalytic mechanisms are illustrated to provide solid foundations for enzyme engineering. Interesting differences in origin, physiological function, structure, and catalytic mechanism between RpiB and ribose-5-phosphate isomerase A are introduced. Moreover, enzyme engineering efforts for rare sugar production are stressed, and prospects of future development are concluded briefly in the viewpoint of biocatalysis. Aided by the progresses of structural and computational biology, the application of RpiB will be promoted greatly in the preparation of valuable molecules. KEY POINTS: • Detailed illustration of RpiB's vital function in central carbon metabolism. • Potential of RpiB in sequence, substrate scope, and mechanism for application. • Enzyme engineering efforts to promote RpiB in the preparation of rare sugars.
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Affiliation(s)
- Hengtao Tang
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, No.99 Xuefu Rd., Huqiu district, Suzhou, 215009, Jiangsu Province, People's Republic of China
| | - Xin Ju
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, No.99 Xuefu Rd., Huqiu district, Suzhou, 215009, Jiangsu Province, People's Republic of China
| | - Jing Zhao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, People's Republic of China
| | - Liangzhi Li
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, No.99 Xuefu Rd., Huqiu district, Suzhou, 215009, Jiangsu Province, People's Republic of China.
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Wu S, Snajdrova R, Moore JC, Baldenius K, Bornscheuer UT. Biocatalysis: Enzymatic Synthesis for Industrial Applications. Angew Chem Int Ed Engl 2021; 60:88-119. [PMID: 32558088 PMCID: PMC7818486 DOI: 10.1002/anie.202006648] [Citation(s) in RCA: 498] [Impact Index Per Article: 166.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Indexed: 12/12/2022]
Abstract
Biocatalysis has found numerous applications in various fields as an alternative to chemical catalysis. The use of enzymes in organic synthesis, especially to make chiral compounds for pharmaceuticals as well for the flavors and fragrance industry, are the most prominent examples. In addition, biocatalysts are used on a large scale to make specialty and even bulk chemicals. This review intends to give illustrative examples in this field with a special focus on scalable chemical production using enzymes. It also discusses the opportunities and limitations of enzymatic syntheses using distinct examples and provides an outlook on emerging enzyme classes.
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Affiliation(s)
- Shuke Wu
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
| | - Radka Snajdrova
- Novartis Institutes for BioMedical ResearchGlobal Discovery Chemistry4056BaselSwitzerland
| | - Jeffrey C. Moore
- Process Research and DevelopmentMerck & Co., Inc.126 E. Lincoln AveRahwayNJ07065USA
| | - Kai Baldenius
- Baldenius Biotech ConsultingHafenstr. 3168159MannheimGermany
| | - Uwe T. Bornscheuer
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
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Hansen ASL, Dunham MJ, Arsovska D, Zhang J, Keasling JD, Herrgard MJ, Jensen MK. Dietary Change Enables Robust Growth-Coupling of Heterologous Methyltransferase Activity in Yeast. ACS Synth Biol 2020; 9:3408-3415. [PMID: 33179905 DOI: 10.1021/acssynbio.0c00348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Genetic modifications of living organisms and proteins are made possible by a catalogue of molecular and synthetic biology tools, yet proper screening assays for genetic variants of interest continue to lag behind. Synthetic growth-coupling (GC) of enzyme activities offers a simple, inexpensive way to track such improvements. In this follow-up study we present the optimization of a recently established GC design for screening of heterologous methyltransferases (MTases) and related pathways in the yeast Saccharomyces cerevisiae. Specifically, upon testing different media compositions and genetic backgrounds, improved GC of different heterologous MTase activities is obtained. Furthermore, we demonstrate the strength of the system by screening a library of catechol O-MTase variants converting protocatechuic acid into vanillic acid. We demonstrated high correlation (R2 = 0.775) between vanillic acid and cell density as a proxy for MTase activity. We envision that the improved MTase GC can aid evolution-guided optimization of biobased production processes for methylated compounds with yeast in the future.
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Affiliation(s)
- Anne Sofie Lærke Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Maitreya J. Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Dushica Arsovska
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jie Zhang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jay D. Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, California 94720, United States
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen 518055, China
| | - Markus J. Herrgard
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- BioInnovation Institute, 2200 Copenhagen, Denmark
| | - Michael K. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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Abstract
Cascade reactions have been described as efficient and universal tools, and are of substantial interest in synthetic organic chemistry. This review article provides an overview of the novel and recent achievements in enzyme cascade processes catalyzed by multi-enzymatic or chemoenzymatic systems. The examples here selected collect the advances related to the application of the sequential use of enzymes in natural or genetically modified combination; second, the important combination of enzymes and metal complex systems, and finally we described the application of biocatalytic biohybrid systems on in situ catalytic solid-phase as a novel strategy. Examples of efficient and interesting enzymatic catalytic cascade processes in organic chemistry, in the production of important industrial products, such as the designing of novel biosensors or bio-chemocatalytic systems for medicinal chemistry application, are discussed
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48
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Zhang X, King-Smith E, Dong LB, Yang LC, Rudolf JD, Shen B, Renata H. Divergent synthesis of complex diterpenes through a hybrid oxidative approach. Science 2020; 369:799-806. [PMID: 32792393 DOI: 10.1126/science.abb8271] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/19/2020] [Indexed: 12/11/2022]
Abstract
Polycyclic diterpenes exhibit many important biological activities, but de novo synthetic access to these molecules is highly challenging because of their structural complexity. Semisynthetic access has also been limited by the lack of chemical tools for scaffold modifications. We report a chemoenzymatic platform to access highly oxidized diterpenes by a hybrid oxidative approach that strategically combines chemical and enzymatic oxidation methods. This approach allows for selective oxidations of previously inaccessible sites on the parent carbocycles and enables abiotic skeletal rearrangements to additional underlying architectures. We synthesized a total of nine complex natural products with rich oxygenation patterns and skeletal diversity in 10 steps or less from ent-steviol.
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Affiliation(s)
- Xiao Zhang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Emma King-Smith
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Liao-Bin Dong
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Li-Cheng Yang
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Ben Shen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA.,Department of Molecular Medicine, Natural Products Discovery Center at Scripps Research, Jupiter, FL 33458, USA
| | - Hans Renata
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA.
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