1
|
Liu Y, Yang E, Zhang X, Liu X, Tang X, Wang Z, Wang H. Biosynthesis of Arabinoside from Sucrose and Nucleobase via a Novel Multi-Enzymatic Cascade. Biomolecules 2024; 14:1107. [PMID: 39334873 PMCID: PMC11430244 DOI: 10.3390/biom14091107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 08/26/2024] [Accepted: 09/02/2024] [Indexed: 09/30/2024] Open
Abstract
Arabinoside and derived nucleoside analogs, a family of nucleoside analogs, exhibit diverse typically biological activities and are widely used as antibacterial, antiviral, anti-inflammatory, antitumor, and other drugs in clinical and preclinical trials. Although with a long and rich history in the field of medicinal chemistry, the biosynthesis of arabinoside has only been sporadically designed and studied, and it remains a challenge. Here, we constructed an in vitro multi-enzymatic cascade for the biosynthesis of arabinosides. This artificial biosystem was systematically optimized, involving an exquisite pathway design, NADP+ regeneration, meticulous enzyme selection, optimization of the key enzyme dosage, and the concentration of inorganic phosphate. Under the optimized conditions, we achieved 0.37 mM of vidarabine from 5 mM of sucrose and 2 mM of adenine, representing 18.7% of the theoretical yield. Furthermore, this biosystem also has the capability to produce other arabinosides, such as spongouridine, arabinofuranosylguanine, hypoxanthine arabinofuranoside, fludarabine, and 2-methoxyadenine arabinofuranoside, from sucrose, and corresponding nucleobase by introducing different nucleoside phosphorylases. Overall, our biosynthesis approach provides a pathway for the biosynthesis of arabinose-derived nucleoside analogs, offering potential applications in the pharmaceutical industry.
Collapse
Affiliation(s)
| | | | | | | | | | - Zhenyu Wang
- Henan Engineering Research Center of Bioconversion Technology of Functional Microbes, College of Life Science, Henan Normal University, Xinxiang 453007, China; (Y.L.); (E.Y.); (X.Z.); (X.L.); (X.T.)
| | - Hailei Wang
- Henan Engineering Research Center of Bioconversion Technology of Functional Microbes, College of Life Science, Henan Normal University, Xinxiang 453007, China; (Y.L.); (E.Y.); (X.Z.); (X.L.); (X.T.)
| |
Collapse
|
2
|
Liu G, Wang J, Chu J, Jiang T, Qin S, Gao Z, He B. Engineering Substrate Promiscuity of Nucleoside Phosphorylase Via an Insertions-Deletions Strategy. JACS AU 2024; 4:454-464. [PMID: 38425912 PMCID: PMC10900210 DOI: 10.1021/jacsau.3c00581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 03/02/2024]
Abstract
Nucleoside phosphorylases (NPs) are the key enzymes in the nucleoside metabolism pathway and are widely employed for the synthesis of nucleoside analogs, which are difficult to access via conventional synthetic methods. NPs are generally classified as purine nucleoside phosphorylase (PNP) and pyrimidine or uridine nucleoside phosphorylase (PyNP/UP), based on their substrate preference. Here, based on the evolutionary information on the NP-I family, we adopted an insertions-deletions (InDels) strategy to engineer the substrate promiscuity of nucleoside phosphorylase AmPNPΔS2V102 K, which exhibits both PNP and UP activities from a trimeric PNP (AmPNP) of Aneurinibacillus migulanus. Furthermore, the AmPNPΔS2V102 K exerted phosphorylation activities toward arabinose nucleoside, fluorosyl nucleoside, and dideoxyribose, thereby broadening the unnatural-ribose nucleoside substrate spectrum of AmPNP. Finally, six purine nucleoside analogues were successfully synthesized, using the engineered AmPNPΔS2V102 K instead of the traditional "two-enzymes PNP/UP" approach. These results provide deep insights into the catalytic mechanisms of the PNP and demonstrate the benefits of using the InDels strategy to achieve substrate promiscuity in an enzyme, as well as broadening the substrate spectrum of the enzyme.
Collapse
Affiliation(s)
- Gaofei Liu
- College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Jialing Wang
- College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Jianlin Chu
- School
of Pharmaceutical Sciences, Nanjing Tech
University, Nanjing 211800, China
| | - Tianyue Jiang
- School
of Pharmaceutical Sciences, Nanjing Tech
University, Nanjing 211800, China
| | - Song Qin
- School
of Pharmaceutical Sciences, Nanjing Tech
University, Nanjing 211800, China
| | - Zhen Gao
- College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
| | - Bingfang He
- College
of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, China
- School
of Pharmaceutical Sciences, Nanjing Tech
University, Nanjing 211800, China
| |
Collapse
|
3
|
Hooe SL, Smith AD, Dean SN, Breger JC, Ellis GA, Medintz IL. Multienzymatic Cascades and Nanomaterial Scaffolding-A Potential Way Forward for the Efficient Biosynthesis of Novel Chemical Products. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2309963. [PMID: 37944537 DOI: 10.1002/adma.202309963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/25/2023] [Indexed: 11/12/2023]
Abstract
Synthetic biology is touted as the next industrial revolution as it promises access to greener biocatalytic syntheses to replace many industrial organic chemistries. Here, it is shown to what synthetic biology can offer in the form of multienzyme cascades for the synthesis of the most basic of new materials-chemicals, including especially designer chemical products and their analogs. Since achieving this is predicated on dramatically expanding the chemical space that enzymes access, such chemistry will probably be undertaken in cell-free or minimalist formats to overcome the inherent toxicity of non-natural substrates to living cells. Laying out relevant aspects that need to be considered in the design of multi-enzymatic cascades for these purposes is begun. Representative multienzymatic cascades are critically reviewed, which have been specifically developed for the synthesis of compounds that have either been made only by traditional organic synthesis along with those cascades utilized for novel compound syntheses. Lastly, an overview of strategies that look toward exploiting bio/nanomaterials for accessing channeling and other nanoscale materials phenomena in vitro to direct novel enzymatic biosynthesis and improve catalytic efficiency is provided. Finally, a perspective on what is needed for this field to develop in the short and long term is presented.
Collapse
Affiliation(s)
- Shelby L Hooe
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
- National Research Council, Washington, DC, 20001, USA
| | - Aaron D Smith
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Scott N Dean
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Joyce C Breger
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Gregory A Ellis
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| |
Collapse
|
4
|
Verma S, Paliwal S. Recent Developments and Applications of Biocatalytic and Chemoenzymatic Synthesis for the Generation of Diverse Classes of Drugs. Curr Pharm Biotechnol 2024; 25:448-467. [PMID: 37885105 DOI: 10.2174/0113892010238984231019085154] [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: 12/15/2022] [Revised: 08/26/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023]
Abstract
Biocatalytic and chemoenzymatic biosynthesis are powerful methods of organic chemistry that use enzymes to execute selective reactions and allow the efficient production of organic compounds. The advantages of these approaches include high selectivity, mild reaction conditions, and the ability to work with complex substrates. The utilization of chemoenzymatic techniques for the synthesis of complicated compounds has lately increased dramatically in the area of organic chemistry. Biocatalytic technologies and modern synthetic methods are utilized synergistically in a multi-step approach to a target molecule under this paradigm. Chemoenzymatic techniques are promising for simplifying access to essential bioactive compounds because of the remarkable regio- and stereoselectivity of enzymatic transformations and the reaction diversity of modern organic chemistry. Enzyme kits may include ready-to-use, reproducible biocatalysts. Its use opens up new avenues for the synthesis of active therapeutic compounds and aids in drug development by synthesizing active components to construct scaffolds in a targeted and preparative manner. This study summarizes current breakthroughs as well as notable instances of biocatalytic and chemoenzymatic synthesis. To assist organic chemists in the use of enzymes for synthetic applications, it also provides some basic guidelines for selecting the most appropriate enzyme for a targeted reaction while keeping aspects like cofactor requirement, solvent tolerance, use of whole cell or isolated enzymes, and commercial availability in mind.
Collapse
Affiliation(s)
- Swati Verma
- Department of Pharmacy, ITS College of Pharmacy, Muradnagar, Ghaziabad, India
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, 304022, Rajasthan, India
| | - Sarvesh Paliwal
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, 304022, Rajasthan, India
| |
Collapse
|
5
|
Tan Z, Li J, Hou J, Gonzalez R. Designing artificial pathways for improving chemical production. Biotechnol Adv 2023; 64:108119. [PMID: 36764336 DOI: 10.1016/j.biotechadv.2023.108119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Metabolic engineering exploits manipulation of catalytic and regulatory elements to improve a specific function of the host cell, often the synthesis of interesting chemicals. Although naturally occurring pathways are significant resources for metabolic engineering, these pathways are frequently inefficient and suffer from a series of inherent drawbacks. Designing artificial pathways in a rational manner provides a promising alternative for chemicals production. However, the entry barrier of designing artificial pathway is relatively high, which requires researchers a comprehensive and deep understanding of physical, chemical and biological principles. On the other hand, the designed artificial pathways frequently suffer from low efficiencies, which impair their further applications in host cells. Here, we illustrate the concept and basic workflow of retrobiosynthesis in designing artificial pathways, as well as the most currently used methods including the knowledge- and computer-based approaches. Then, we discuss how to obtain desired enzymes for novel biochemistries, and how to trim the initially designed artificial pathways for further improving their functionalities. Finally, we summarize the current applications of artificial pathways from feedstocks utilization to various products synthesis, as well as our future perspectives on designing artificial pathways.
Collapse
Affiliation(s)
- Zaigao Tan
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Department of Bioengineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Jian Li
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Department of Bioengineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ramon Gonzalez
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA.
| |
Collapse
|
6
|
Van Giesen KJ, Thompson MJ, Meng Q, Lovelock SL. Biocatalytic Synthesis of Antiviral Nucleosides, Cyclic Dinucleotides, and Oligonucleotide Therapies. JACS AU 2023; 3:13-24. [PMID: 36711092 PMCID: PMC9875237 DOI: 10.1021/jacsau.2c00481] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/11/2022] [Accepted: 11/11/2022] [Indexed: 05/27/2023]
Abstract
Nucleosides, nucleotides, and oligonucleotides modulate diverse cellular processes ranging from protein production to cell signaling. It is therefore unsurprising that synthetic analogues of nucleosides and their derivatives have emerged as a versatile class of drug molecules for the treatment of a wide range of disease areas. Despite their great therapeutic potential, the dense arrangements of functional groups and stereogenic centers present in nucleic acid analogues pose a considerable synthetic challenge, especially in the context of large-scale manufacturing. Commonly employed synthetic methods rely on extensive protecting group manipulations, which compromise step-economy and result in high process mass intensities. Biocatalytic approaches have the potential to address these limitations, enabling the development of more streamlined, selective, and sustainable synthetic routes. Here we review recent achievements in the biocatalytic manufacturing of nucleosides and cyclic dinucleotides along with progress in developing enzymatic strategies to produce oligonucleotide therapies. We also highlight opportunities for innovations that are needed to facilitate widespread adoption of these biocatalytic methods across the pharmaceutical industry.
Collapse
Affiliation(s)
| | | | | | - Sarah L. Lovelock
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| |
Collapse
|
7
|
The Power of Biocatalysts for Highly Selective and Efficient Phosphorylation Reactions. Catalysts 2022. [DOI: 10.3390/catal12111436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Reactions involving the transfer of phosphorus-containing groups are of key importance for maintaining life, from biological cells, tissues and organs to plants, animals, humans, ecosystems and the whole planet earth. The sustainable utilization of the nonrenewable element phosphorus is of key importance for a balanced phosphorus cycle. Significant advances have been achieved in highly selective and efficient biocatalytic phosphorylation reactions, fundamental and applied aspects of phosphorylation biocatalysts, novel phosphorylation biocatalysts, discovery methodologies and tools, analytical and synthetic applications, useful phosphoryl donors and systems for their regeneration, reaction engineering, product recovery and purification. Biocatalytic phosphorylation reactions with complete conversion therefore provide an excellent reaction platform for valuable analytical and synthetic applications.
Collapse
|
8
|
Benítez-Mateos AI, Roura Padrosa D, Paradisi F. Multistep enzyme cascades as a route towards green and sustainable pharmaceutical syntheses. Nat Chem 2022; 14:489-499. [PMID: 35513571 DOI: 10.1038/s41557-022-00931-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 03/17/2022] [Indexed: 12/25/2022]
Abstract
Enzyme cascades are a powerful technology to develop environmentally friendly and cost-effective synthetic processes to manufacture drugs, as they couple different biotransformations in sequential reactions to synthesize the product. These biocatalytic tools can address two key parameters for the pharmaceutical industry: an improved selectivity of synthetic reactions and a reduction of potential hazards by using biocompatible catalysts, which can be produced from sustainable sources, which are biodegradable and, generally, non-toxic. Here we outline a broad variety of enzyme cascades used either in vivo (whole cells) or in vitro (purified enzymes) to specifically target pharmaceutically relevant molecules, from simple building blocks to complex drugs. We also discuss the advantages and requirements of multistep enzyme cascades and their combination with chemical catalysts through a series of reported examples. Finally, we examine the efficiency of enzyme cascades and how they can be further improved by enzyme engineering, process intensification in flow reactors and/or enzyme immobilization to meet all the industrial requirements.
Collapse
Affiliation(s)
- Ana I Benítez-Mateos
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - David Roura Padrosa
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Francesca Paradisi
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
| |
Collapse
|
9
|
Cosgrove SC, Miller GJ. Advances in biocatalytic and chemoenzymatic synthesis of nucleoside analogues. Expert Opin Drug Discov 2022; 17:355-364. [PMID: 35133222 DOI: 10.1080/17460441.2022.2039620] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Nucleoside analogues represent a cornerstone of achievement in drug discovery, rising to prominence particularly in the fields of antiviral and anticancer discovery over the last 60 years. Traditionally accessed using chemical synthesis, a paradigm shift to include the use of biocatalytic synthesis is now apparent. AREAS COVERED Herein, the authors discuss the recent advances using this technology to access nucleoside analogues. Two key aspects are covered, the first surrounding methodology concepts, effectively using enzymes to access diverse nucleoside analogue space and also for producing key building blocks. The second focuses on the use of biocatalytic cascades for de novo syntheses of nucleoside analogue drugs. Finally, recent advances in technologies for effecting enzymatic nucleoside synthesis are considered, chiefly immobilization and flow. EXPERT OPINION Enzymatic synthesis of nucleoside analogues is maturing but has yet to usurp chemical synthesis as a first-hand synthesis technology, with scalability and substrate modification primary issues. Moving forward, tandem approaches that harness expertise across molecular microbiology and chemical synthesis will be vital to unlocking the potential of next generation nucleoside analogue drug discovery.
Collapse
Affiliation(s)
- Sebastian C Cosgrove
- Lennard-Jones Laboratory, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire, UK.,Centre for Glycoscience Research, Keele University, Keele, Staffordshire, UK
| | - Gavin J Miller
- Lennard-Jones Laboratory, School of Chemical and Physical Sciences, Keele University, Keele, Staffordshire, UK.,Centre for Glycoscience Research, Keele University, Keele, Staffordshire, UK
| |
Collapse
|
10
|
Industrially Relevant Enzyme Cascades for Drug Synthesis and Their Ecological Assessment. Int J Mol Sci 2022; 23:ijms23073605. [PMID: 35408960 PMCID: PMC8998672 DOI: 10.3390/ijms23073605] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 02/05/2023] Open
Abstract
Environmentally friendly and sustainable processes for the production of active pharmaceutical ingredients (APIs) gain increasing attention. Biocatalytic synthesis routes with enzyme cascades support many stated green production principles, for example, the reduced need for solvents or the biodegradability of enzymes. Multi-enzyme reactions have even more advantages such as the shift of the equilibrium towards the product side, no intermediate isolation, and the synthesis of complex molecules in one reaction pot. Despite the intriguing benefits, only a few enzyme cascades have been applied in the pharmaceutical industry so far. However, several new enzyme cascades are currently being developed in research that could be of great importance to the pharmaceutical industry. Here, we present multi-enzymatic reactions for API synthesis that are close to an industrial application. Their performances are comparable or exceed their chemical counterparts. A few enzyme cascades that are still in development are also introduced in this review. Economic and ecological considerations are made for some example cascades to assess their environmental friendliness and applicability.
Collapse
|
11
|
Zarenezhad E, Marzi M. Review on molnupiravir as a promising oral drug for the treatment of COVID-19. Med Chem Res 2022; 31:232-243. [PMID: 35002192 PMCID: PMC8721938 DOI: 10.1007/s00044-021-02841-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/16/2021] [Indexed: 12/29/2022]
Abstract
During the COVID-19 pandemic, various drug candidates have been developed, molnupiravir (MK-4482 and EIDD-2801), which is a new orally anti-viral agent under development for the treatment of COVID-19, is under study in the final stage of the clinical trial. Molnupiravir enhances the replication of viral RNA mutations in animals and humans. Due to the high demand for the synthesis of this drug, it was essential to develop an efficient and suitable synthetic pathway from raw material. In this study, molecular docking analysis on molnupiravir is examined also, the mechanism of action (MOA) and the recent synthetic pathway is reported. This review will be helpful to different disciplines such as medicinal chemistry, organic chemistry, biochemistry, and pharmacology. ![]()
Collapse
Affiliation(s)
- Elham Zarenezhad
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Mahrokh Marzi
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| |
Collapse
|
12
|
Green biomanufacturing promoted by automatic retrobiosynthesis planning and computational enzyme design. Chin J Chem Eng 2022. [DOI: 10.1016/j.cjche.2021.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
13
|
McIntosh JA, Benkovics T, Silverman SM, Huffman MA, Kong J, Maligres PE, Itoh T, Yang H, Verma D, Pan W, Ho HI, Vroom J, Knight AM, Hurtak JA, Klapars A, Fryszkowska A, Morris WJ, Strotman NA, Murphy GS, Maloney KM, Fier PS. Engineered Ribosyl-1-Kinase Enables Concise Synthesis of Molnupiravir, an Antiviral for COVID-19. ACS CENTRAL SCIENCE 2021; 7:1980-1985. [PMID: 34963891 PMCID: PMC8704035 DOI: 10.1021/acscentsci.1c00608] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Indexed: 05/04/2023]
Abstract
Molnupiravir (MK-4482) is an investigational antiviral agent that is under development for the treatment of COVID-19. Given the potential high demand and urgency for this compound, it was critical to develop a short and sustainable synthesis from simple raw materials that would minimize the time needed to manufacture and supply molnupiravir. The route reported here is enabled through the invention of a novel biocatalytic cascade featuring an engineered ribosyl-1-kinase and uridine phosphorylase. These engineered enzymes were deployed with a pyruvate-oxidase-enabled phosphate recycling strategy. Compared to the initial route, this synthesis of molnupiravir is 70% shorter and approximately 7-fold higher yielding. Looking forward, the biocatalytic approach to molnupiravir outlined here is anticipated to have broad applications for streamlining the synthesis of nucleosides in general.
Collapse
Affiliation(s)
- John A. McIntosh
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Tamas Benkovics
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Steven M. Silverman
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Mark A. Huffman
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Jongrock Kong
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Peter E. Maligres
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Tetsuji Itoh
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Hao Yang
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Deeptak Verma
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Weilan Pan
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Hsing-I Ho
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Jonathan Vroom
- Codexis,
Inc., 200 Penobscot Drive, Redwood City, California 94063, United States
| | - Anders M. Knight
- Codexis,
Inc., 200 Penobscot Drive, Redwood City, California 94063, United States
| | - Jessica A. Hurtak
- Codexis,
Inc., 200 Penobscot Drive, Redwood City, California 94063, United States
| | - Artis Klapars
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Anna Fryszkowska
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - William J. Morris
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Neil A. Strotman
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Grant S. Murphy
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Kevin M. Maloney
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Patrick S. Fier
- Department
of Process Research and Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| |
Collapse
|
14
|
Getting the Most Out of Enzyme Cascades: Strategies to Optimize In Vitro Multi-Enzymatic Reactions. Catalysts 2021. [DOI: 10.3390/catal11101183] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In vitro enzyme cascades possess great benefits, such as their synthetic capabilities for complex molecules, no need for intermediate isolation, and the shift of unfavorable equilibria towards the products. Their performance, however, can be impaired by, for example, destabilizing or inhibitory interactions between the cascade components or incongruous reaction conditions. The optimization of such systems is therefore often inevitable but not an easy task. Many parameters such as the design of the synthesis route, the choice of enzymes, reaction conditions, or process design can alter the performance of an in vitro enzymatic cascade. Many strategies to tackle this complex task exist, ranging from experimental to in silico approaches and combinations of both. This review collates examples of various optimization strategies and their success. The feasibility of optimization goals, the influence of certain parameters and the usage of algorithm-based optimizations are discussed.
Collapse
|
15
|
Liu Z, Zhang X, Lei D, Qiao B, Zhao GR. Metabolic engineering of Escherichia coli for de novo production of 3-phenylpropanol via retrobiosynthesis approach. Microb Cell Fact 2021; 20:121. [PMID: 34176467 PMCID: PMC8237410 DOI: 10.1186/s12934-021-01615-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/18/2021] [Indexed: 02/07/2023] Open
Abstract
Background 3-Phenylpropanol with a pleasant odor is widely used in foods, beverages and cosmetics as a fragrance ingredient. It also acts as the precursor and reactant in pharmaceutical and chemical industries. Currently, petroleum-based manufacturing processes of 3-phenypropanol is environmentally unfriendly and unsustainable. In this study, we aim to engineer Escherichia coli as microbial cell factory for de novo production of 3-phenypropanol via retrobiosynthesis approach. Results Aided by in silico retrobiosynthesis analysis, we designed a novel 3-phenylpropanol biosynthetic pathway extending from l-phenylalanine and comprising the phenylalanine ammonia lyase (PAL), enoate reductase (ER), aryl carboxylic acid reductase (CAR) and phosphopantetheinyl transferase (PPTase). We screened the enzymes from plants and microorganisms and reconstructed the artificial pathway for conversion of 3-phenylpropanol from l-phenylalanine. Then we conducted chromosome engineering to increase the supply of precursor l-phenylalanine and combined the upstream l-phenylalanine pathway and downstream 3-phenylpropanol pathway. Finally, we regulated the metabolic pathway strength and optimized fermentation conditions. As a consequence, metabolically engineered E. coli strain produced 847.97 mg/L of 3-phenypropanol at 24 h using glucose-glycerol mixture as co-carbon source. Conclusions We successfully developed an artificial 3-phenylpropanol pathway based on retrobiosynthesis approach, and highest titer of 3-phenylpropanol was achieved in E. coli via systems metabolic engineering strategies including enzyme sources variety, chromosome engineering, metabolic strength balancing and fermentation optimization. This work provides an engineered strain with industrial potential for production of 3-phenylpropanol, and the strategies applied here could be practical for bioengineers to design and reconstruct the microbial cell factory for high valuable chemicals. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01615-1.
Collapse
Affiliation(s)
- Zhenning Liu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Xue Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Dengwei Lei
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Bin Qiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Guang-Rong Zhao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China. .,Georgia Tech Shenzhen Institute, Tianjin University, Tangxing Road 133, Nanshan District, Shenzhen, 518071, China.
| |
Collapse
|
16
|
Del Arco J, Acosta J, Fernández-Lucas J. New trends in the biocatalytic production of nucleosidic active pharmaceutical ingredients using 2'-deoxyribosyltransferases. Biotechnol Adv 2021; 51:107701. [PMID: 33515673 DOI: 10.1016/j.biotechadv.2021.107701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/27/2020] [Accepted: 01/21/2021] [Indexed: 12/16/2022]
Abstract
Nowadays, pharmaceutical industry demands competitive and eco-friendly processes for active pharmaceutical ingredients (APIs) manufacturing. In this context, enzyme and whole-cell mediated processes offer an efficient, sustainable and cost-effective alternative to the traditional multi-step and environmentally-harmful chemical processes. Particularly, 2'-deoxyribosyltransferases (NDTs) have emerged as a novel synthetic alternative, not only to chemical but also to other enzyme-mediated synthetic processes. This review describes recent findings in the development and scaling up of NDTs as industrial biocatalysts, including the most relevant and recent examples of single enzymatic steps, multienzyme cascades, chemo-enzymatic approaches, and engineered biocatalysts. Finally, to reflect the inventive and innovative steps of NDT-mediated bioprocesses, a detailed analysis of recently granted patents, with specific focus on industrial synthesis of nucleoside-based APIs, is hereunder presented.
Collapse
Affiliation(s)
- Jon Del Arco
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, E-28670 Villaviciosa de Odón, Madrid, Spain
| | - Javier Acosta
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, E-28670 Villaviciosa de Odón, Madrid, Spain
| | - Jesús Fernández-Lucas
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, E-28670 Villaviciosa de Odón, Madrid, Spain; Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55 - 66, Barranquilla, Colombia.
| |
Collapse
|
17
|
Slagman S, Fessner WD. Biocatalytic routes to anti-viral agents and their synthetic intermediates. Chem Soc Rev 2021; 50:1968-2009. [DOI: 10.1039/d0cs00763c] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An assessment of biocatalytic strategies for the synthesis of anti-viral agents, offering guidelines for the development of sustainable production methods for a future COVID-19 remedy.
Collapse
Affiliation(s)
- Sjoerd Slagman
- Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- Germany
| | - Wolf-Dieter Fessner
- Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- Germany
| |
Collapse
|
18
|
Feng J, Li R, Zhang S, Bu Y, Chen Y, Cui Y, Lin B, Chen Y, Tao Y, Wu B. Bioretrosynthesis of Functionalized N-Heterocycles from Glucose via One-Pot Tandem Collaborations of Designed Microbes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001188. [PMID: 32995125 PMCID: PMC7507072 DOI: 10.1002/advs.202001188] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/29/2020] [Indexed: 05/10/2023]
Abstract
The design of multistrain systems has markedly expanded the prospects of using long biosynthetic pathways to produce natural compounds. However, the cooperative use of artificially engineered microbes to synthesize xenobiotic chemicals from renewable carbohydrates is still in its infancy. Here, a microbial system is developed for the production of high-added-value N-heterocycles directly from glucose. Based on a retrosynthetic analysis, eleven genes are selected, systematically modulated, and overexpressed in three Escherichia coli strains to construct an artificial pathway to produce 5-methyl-2-pyrazinecarboxylic acid, a key intermediate in the production of the important pharmaceuticals Glipizide and Acipimox. Via one-pot tandem collaborations, the designed microbes remarkably realize high-level production of 5-methyl-2-pyrazinecarboxylic acid (6.2 ± 0.1 g L-1) and its precursor 2,5-dimethylpyrazine (7.9 ± 0.7 g L-1). This study is the first application of cooperative microbes for the total biosynthesis of functionalized N-heterocycles and provides new insight into integrating bioretrosynthetic principles with synthetic biology to perform complex syntheses.
Collapse
Affiliation(s)
- Jing Feng
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
- University of Chinese Academy of SciencesBeijingChina
| | - Ruifeng Li
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
- University of Chinese Academy of SciencesBeijingChina
| | - Shasha Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
- University of Chinese Academy of SciencesBeijingChina
| | - Yifan Bu
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
- University of Chinese Academy of SciencesBeijingChina
| | - Yanchun Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
- University of Chinese Academy of SciencesBeijingChina
| | - Yinglu Cui
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
| | - Baixue Lin
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
| | - Yihua Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
| | - Bian Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijing100101P. R. China
| |
Collapse
|
19
|
Hwang S, Lee N, Cho S, Palsson B, Cho BK. Repurposing Modular Polyketide Synthases and Non-ribosomal Peptide Synthetases for Novel Chemical Biosynthesis. Front Mol Biosci 2020; 7:87. [PMID: 32500080 PMCID: PMC7242659 DOI: 10.3389/fmolb.2020.00087] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/16/2020] [Indexed: 12/16/2022] Open
Abstract
In nature, various enzymes govern diverse biochemical reactions through their specific three-dimensional structures, which have been harnessed to produce many useful bioactive compounds including clinical agents and commodity chemicals. Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are particularly unique multifunctional enzymes that display modular organization. Individual modules incorporate their own specific substrates and collaborate to assemble complex polyketides or non-ribosomal polypeptides in a linear fashion. Due to the modular properties of PKSs and NRPSs, they have been attractive rational engineering targets for novel chemical production through the predictable modification of each moiety of the complex chemical through engineering of the cognate module. Thus, individual reactions of each module could be separated as a retro-biosynthetic biopart and repurposed to new biosynthetic pathways for the production of biofuels or commodity chemicals. Despite these potentials, repurposing attempts have often failed owing to impaired catalytic activity or the production of unintended products due to incompatible protein–protein interactions between the modules and structural perturbation of the enzyme. Recent advances in the structural, computational, and synthetic tools provide more opportunities for successful repurposing. In this review, we focused on the representative strategies and examples for the repurposing of modular PKSs and NRPSs, along with their advantages and current limitations. Thereafter, synthetic biology tools and perspectives were suggested for potential further advancement, including the rational and large-scale high-throughput approaches. Ultimately, the potential diverse reactions from modular PKSs and NRPSs would be leveraged to expand the reservoir of useful chemicals.
Collapse
Affiliation(s)
- Soonkyu Hwang
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Namil Lee
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Suhyung Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Byung-Kwan Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Intelligent Synthetic Biology Center, Daejeon, South Korea
| |
Collapse
|
20
|
Huffman MA, Fryszkowska A, Alvizo O, Borra-Garske M, Campos KR, Canada KA, Devine PN, Duan D, Forstater JH, Grosser ST, Halsey HM, Hughes GJ, Jo J, Joyce LA, Kolev JN, Liang J, Maloney KM, Mann BF, Marshall NM, McLaughlin M, Moore JC, Murphy GS, Nawrat CC, Nazor J, Novick S, Patel NR, Rodriguez-Granillo A, Robaire SA, Sherer EC, Truppo MD, Whittaker AM, Verma D, Xiao L, Xu Y, Yang H. Design of an in vitro biocatalytic cascade for the manufacture of islatravir. Science 2019; 366:1255-1259. [DOI: 10.1126/science.aay8484] [Citation(s) in RCA: 238] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/24/2019] [Indexed: 12/14/2022]
Abstract
Enzyme-catalyzed reactions have begun to transform pharmaceutical manufacturing, offering levels of selectivity and tunability that can dramatically improve chemical synthesis. Combining enzymatic reactions into multistep biocatalytic cascades brings additional benefits. Cascades avoid the waste generated by purification of intermediates. They also allow reactions to be linked together to overcome an unfavorable equilibrium or avoid the accumulation of unstable or inhibitory intermediates. We report an in vitro biocatalytic cascade synthesis of the investigational HIV treatment islatravir. Five enzymes were engineered through directed evolution to act on non-natural substrates. These were combined with four auxiliary enzymes to construct islatravir from simple building blocks in a three-step biocatalytic cascade. The overall synthesis requires fewer than half the number of steps of the previously reported routes.
Collapse
Affiliation(s)
- Mark A. Huffman
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Anna Fryszkowska
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Oscar Alvizo
- Codexis, Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | | | - Kevin R. Campos
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Keith A. Canada
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Paul N. Devine
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Da Duan
- Codexis, Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Jacob H. Forstater
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Shane T. Grosser
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Holst M. Halsey
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Gregory J. Hughes
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Junyong Jo
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Leo A. Joyce
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Joshua N. Kolev
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Jack Liang
- Codexis, Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Kevin M. Maloney
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Benjamin F. Mann
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Mark McLaughlin
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Jeffrey C. Moore
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Grant S. Murphy
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Jovana Nazor
- Codexis, Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Scott Novick
- Codexis, Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Niki R. Patel
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | - Sandra A. Robaire
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Edward C. Sherer
- Computational and Structural Chemistry, Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Matthew D. Truppo
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Aaron M. Whittaker
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Deeptak Verma
- Computational and Structural Chemistry, Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Li Xiao
- Computational and Structural Chemistry, Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Yingju Xu
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Hao Yang
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| |
Collapse
|
21
|
Zhang JJ, Tang X, Moore BS. Genetic platforms for heterologous expression of microbial natural products. Nat Prod Rep 2019; 36:1313-1332. [PMID: 31197291 PMCID: PMC6750982 DOI: 10.1039/c9np00025a] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Covering: 2005 up to 2019Natural products are of paramount importance in human medicine. Not only are most antibacterial and anticancer drugs derived directly from or inspired by natural products, many other branches of medicine, such as immunology, neurology, and cardiology, have similarly benefited from natural product-based drugs. Typically, the genetic material required to synthesize a microbial specialized product is arranged in a multigene biosynthetic gene cluster (BGC), which codes for proteins associated with molecule construction, regulation, and transport. The ability to connect natural product compounds to BGCs and vice versa, along with ever-increasing knowledge of biosynthetic machineries, has spawned the field of genomics-guided natural product genome mining for the rational discovery of new chemical entities. One significant challenge in the field of natural product genome mining is how to rapidly link orphan biosynthetic genes to their associated chemical products. This review highlights state-of-the-art genetic platforms to identify, interrogate, and engineer BGCs from diverse microbial sources, which can be broken into three stages: (1) cloning and isolation of genomic loci, (2) heterologous expression in a host organism, and (3) genetic manipulation of cloned pathways. In the future, we envision natural product genome mining will be rapidly accelerated by de novo DNA synthesis and refactoring of whole biosynthetic pathways in combination with systematic heterologous expression methodologies.
Collapse
Affiliation(s)
- Jia Jia Zhang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA.
| | - Xiaoyu Tang
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA.
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, USA. and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA
| |
Collapse
|
22
|
Pang B, Valencia LE, Wang J, Wan Y, Lal R, Zargar A, Keasling JD. Technical Advances to Accelerate Modular Type I Polyketide Synthase Engineering towards a Retro-biosynthetic Platform. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-019-0083-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
23
|
Stamm A, Biundo A, Schmidt B, Brücher J, Lundmark S, Olsén P, Fogelström L, Malmström E, Bornscheuer UT, Syrén P. A Retro-biosynthesis-Based Route to Generate Pinene-Derived Polyesters. Chembiochem 2019; 20:1664-1671. [PMID: 30793830 PMCID: PMC6618282 DOI: 10.1002/cbic.201900046] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Indexed: 12/21/2022]
Abstract
Significantly increased production of biobased polymers is a prerequisite to replace petroleum-based materials towards reaching a circular bioeconomy. However, many renewable building blocks from wood and other plant material are not directly amenable for polymerization, due to their inert backbones and/or lack of functional group compatibility with the desired polymerization type. Based on a retro-biosynthetic analysis of polyesters, a chemoenzymatic route from (-)-α-pinene towards a verbanone-based lactone, which is further used in ring-opening polymerization, is presented. Generated pinene-derived polyesters showed elevated degradation and glass transition temperatures, compared with poly(ϵ-decalactone), which lacks a ring structure in its backbone. Semirational enzyme engineering of the cyclohexanone monooxygenase from Acinetobacter calcoaceticus enabled the biosynthesis of the key lactone intermediate for the targeted polyester. As a proof of principle, one enzyme variant identified from screening in a microtiter plate was used in biocatalytic upscaling, which afforded the bicyclic lactone in 39 % conversion in shake flask scale reactions.
Collapse
Affiliation(s)
- Arne Stamm
- KTH Royal Institute of TechnologySchool of Engineering Sciences in ChemistryBiotechnology and Health, Department of Fibre and Polymer TechnologyTeknikringen 56–58100 44StockholmSweden
- KTH Royal Institute of TechnologyScience for Life LaboratorySchool of Engineering Sciences in ChemistryBiotechnology and HealthTomtebodavägen 23Box 1031171 21 SolnaStockholmSweden
| | - Antonino Biundo
- KTH Royal Institute of TechnologySchool of Engineering Sciences in ChemistryBiotechnology and Health, Department of Fibre and Polymer TechnologyTeknikringen 56–58100 44StockholmSweden
- KTH Royal Institute of TechnologyScience for Life LaboratorySchool of Engineering Sciences in ChemistryBiotechnology and HealthTomtebodavägen 23Box 1031171 21 SolnaStockholmSweden
| | - Björn Schmidt
- KTH Royal Institute of TechnologySchool of Engineering Sciences in ChemistryBiotechnology and Health, Department of Fibre and Polymer TechnologyTeknikringen 56–58100 44StockholmSweden
- KTH Royal Institute of TechnologyScience for Life LaboratorySchool of Engineering Sciences in ChemistryBiotechnology and HealthTomtebodavägen 23Box 1031171 21 SolnaStockholmSweden
| | | | - Stefan Lundmark
- Perstorp AB, InnovationPerstorp Industrial Park284 80PerstorpSweden
| | - Peter Olsén
- KTH Royal Institute of TechnologySchool of Engineering Sciences in ChemistryBiotechnology and Health, Department of Fibre and Polymer TechnologyTeknikringen 56–58100 44StockholmSweden
| | - Linda Fogelström
- KTH Royal Institute of TechnologySchool of Engineering Sciences in ChemistryBiotechnology and Health, Department of Fibre and Polymer TechnologyTeknikringen 56–58100 44StockholmSweden
- Wallenberg Wood Science CenterTeknikringen 56–58100 44StockholmSweden
| | - Eva Malmström
- KTH Royal Institute of TechnologySchool of Engineering Sciences in ChemistryBiotechnology and Health, Department of Fibre and Polymer TechnologyTeknikringen 56–58100 44StockholmSweden
- Wallenberg Wood Science CenterTeknikringen 56–58100 44StockholmSweden
| | - Uwe T. Bornscheuer
- Department of Biotechnology and Enzyme CatalysisInstitute of BiochemistryUniversität GreifswaldFelix-Hausdorff-Strasse 417487GreifswaldGermany
| | - Per‐Olof Syrén
- KTH Royal Institute of TechnologySchool of Engineering Sciences in ChemistryBiotechnology and Health, Department of Fibre and Polymer TechnologyTeknikringen 56–58100 44StockholmSweden
- KTH Royal Institute of TechnologyScience for Life LaboratorySchool of Engineering Sciences in ChemistryBiotechnology and HealthTomtebodavägen 23Box 1031171 21 SolnaStockholmSweden
- KTH Royal Institute of TechnologyScience for Life LaboratorySchool of Engineering Sciences in ChemistryBiotechnology and Health, Division of Protein TechnologyTomtebodavägen 23Box 1031171 21 SolnaStockholmSweden
- Wallenberg Wood Science CenterTeknikringen 56–58100 44StockholmSweden
| |
Collapse
|
24
|
Kershaw NM, Byrne DP, Parsons H, Berry NG, Fernig DG, Eyers PA, Cosstick R. Structure-based design of nucleoside-derived analogues as sulfotransferase inhibitors. RSC Adv 2019; 9:32165-32173. [PMID: 35530783 PMCID: PMC9072872 DOI: 10.1039/c9ra07567d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 10/03/2019] [Indexed: 12/12/2022] Open
Abstract
Regulated sulfation of biomolecules by sulfotransferases (STs) plays a role in many biological processes with implications for a number of disease areas. A structure-based approach and molecular docking were used to design a library of ST inhibitors.
Collapse
Affiliation(s)
- Neil M. Kershaw
- Department of Chemistry
- University of Liverpool
- Liverpool L69 7ZD
- UK
| | - Dominic P. Byrne
- Department of Biochemistry
- Institute of Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
- UK
| | - Hollie Parsons
- Department of Chemistry
- University of Liverpool
- Liverpool L69 7ZD
- UK
| | - Neil G. Berry
- Department of Chemistry
- University of Liverpool
- Liverpool L69 7ZD
- UK
| | - David G. Fernig
- Department of Biochemistry
- Institute of Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
- UK
| | - Patrick A. Eyers
- Department of Biochemistry
- Institute of Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
- UK
| | - Richard Cosstick
- Department of Chemistry
- University of Liverpool
- Liverpool L69 7ZD
- UK
| |
Collapse
|
25
|
Ren J, Zhou L, Wang C, Lin C, Li Z, Zeng AP. An Unnatural Pathway for Efficient 5-Aminolevulinic Acid Biosynthesis with Glycine from Glyoxylate Based on Retrobiosynthetic Design. ACS Synth Biol 2018; 7:2750-2757. [PMID: 30476433 DOI: 10.1021/acssynbio.8b00354] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The design of novel metabolic pathways for efficient biosynthesis of natural products has received much interest, but often lacks systematic approach and chemistry-based guideline. Here we propose carbon skeleton reconstruction based on retrobiosynthetic design as a new approach and chemistry-guideline to solve the problem of properly matching precursors, one of the key issues for efficient biosynthesis. It is demonstrated for the development of an unnatural pathway for efficient biosynthesis of 5-aminolevulinic acid. The new pathway has several advantages compared to the existing natural ones such as high carbon utilization efficiency and orthogonality. It is particularly useful for overcoming the problem of glycine supply. The unnatural pathway is verified in vitro in an enzymatic cascade and in vivo in recombinant E. coli with an exogenous glyoxylate transaminase as a key enzyme.
Collapse
Affiliation(s)
- Jie Ren
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, 100029, Beijing, China
| | - Libang Zhou
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, 100029, Beijing, China
| | - Chuang Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, 100029, Beijing, China
| | - Chen Lin
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestrasse 15, D-21073 Hamburg, Germany
| | - Zhidong Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, 100029, Beijing, China
| | - An-Ping Zeng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, 100029, Beijing, China
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestrasse 15, D-21073 Hamburg, Germany
| |
Collapse
|
26
|
Del Arco J, Fernández-Lucas J. Purine and pyrimidine salvage pathway in thermophiles: a valuable source of biocatalysts for the industrial production of nucleic acid derivatives. Appl Microbiol Biotechnol 2018; 102:7805-7820. [PMID: 30027492 DOI: 10.1007/s00253-018-9242-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/11/2018] [Accepted: 07/11/2018] [Indexed: 12/25/2022]
Abstract
Due to their similarity to natural counterparts, nucleic acid derivatives (nucleobases, nucleosides, and nucleotides, among others) are interesting molecules for pharmaceutical, biomedical, or food industries. For this reason, there is increasing worldwide demand for the development of efficient synthetic processes for these compounds. Chemical synthetic methodologies require numerous protection-deprotection steps and often lead to the presence of undesirable by-products or enantiomeric mixtures. These methods also require harsh operating conditions, such as the use of organic solvents and hazard reagents. Conversely, enzymatic production by whole cells or enzymes improves regio-, stereo-, and enantioselectivity and provides an eco-friendly alternative. Because of their essential role in purine and pyrimidine scavenging, enzymes from purine and pyrimidine salvage pathways are valuable candidates for the synthesis of many different nucleic acid components. In recent years, many different enzymes from these routes, such as nucleoside phosphorylases, nucleoside kinases, 2'-deoxyribosyltransferases, phosphoribosyl transferases, or deaminases, have been successfully employed as biocatalysts in the production of nucleobase, nucleoside, or nucleotide analogs. Due to their great activity and stability at extremely high temperatures, the use of enzymes from thermophiles in industrial biocatalysis is gaining momentum. Thermophilic enzymes not only display unique characteristics such as temperature, chemical, and pH stability but also provide many different advantages from an industrial perspective. This mini-review aims to cover the most representative enzymatic approaches for the synthesis of nucleic acid derivatives. In this regard, we provide detailed comments about enzymes involved in crucial steps of purine and pyrimidine salvage pathways in thermophiles, as well as their biological role, biochemical characterization, active site mechanism, and substrate specificity. In addition, the most interesting synthetic examples reported in the literature are also included.
Collapse
Affiliation(s)
- Jon Del Arco
- Applied Biotechnology Group, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Urbanización El Bosque, c/ Tajo, s/n, E-28670, Villaviciosa de Odón, Madrid, Spain
| | - Jesús Fernández-Lucas
- Applied Biotechnology Group, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Urbanización El Bosque, c/ Tajo, s/n, E-28670, Villaviciosa de Odón, Madrid, Spain. .,Grupo de Investigación en Desarrollo Agroindustrial Sostenible, Universidad de la Costa, CUC, Calle 58 #55-66, Barranquilla, Colombia.
| |
Collapse
|
27
|
Noda-Garcia L, Liebermeister W, Tawfik DS. Metabolite–Enzyme Coevolution: From Single Enzymes to Metabolic Pathways and Networks. Annu Rev Biochem 2018; 87:187-216. [DOI: 10.1146/annurev-biochem-062917-012023] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
How individual enzymes evolved is relatively well understood. However, individual enzymes rarely confer a physiological advantage on their own. Judging by its current state, the emergence of metabolism seemingly demanded the simultaneous emergence of many enzymes. Indeed, how multicomponent interlocked systems, like metabolic pathways, evolved is largely an open question. This complexity can be unlocked if we assume that survival of the fittest applies not only to genes and enzymes but also to the metabolites they produce. This review develops our current knowledge of enzyme evolution into a wider hypothesis of pathway and network evolution. We describe the current models for pathway evolution and offer an integrative metabolite–enzyme coevolution hypothesis. Our hypothesis addresses the origins of new metabolites and of new enzymes and the order of their recruitment. We aim to not only survey established knowledge but also present open questions and potential ways of addressing them.
Collapse
Affiliation(s)
- Lianet Noda-Garcia
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel;,
| | - Wolfram Liebermeister
- INRA, Unité MaIAGE, 78352 Jouy en Josas, France
- Institute of Biochemistry, Charité Universitätsmedizin, Berlin, 10117 Berlin, Germany
| | - Dan S. Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel;,
| |
Collapse
|
28
|
Wohlgemuth R. Horizons of Systems Biocatalysis and Renaissance of Metabolite Synthesis. Biotechnol J 2018; 13:e1700620. [DOI: 10.1002/biot.201700620] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/26/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Roland Wohlgemuth
- European Federation of Biotechnology; Section on Applied Biocatalysis (ESAB); Theodor-Heuss-Allee 25,Frankfurt am Main 60486 Germany
- Sigma-Aldrich; Member of Merck Group; Industriestrasse 25,Buchs 9470 Switzerland
| |
Collapse
|
29
|
Wang Y, Ren H, Zhao H. Expanding the boundary of biocatalysis: design and optimization of in vitro tandem catalytic reactions for biochemical production. Crit Rev Biochem Mol Biol 2018; 53:115-129. [PMID: 29411648 PMCID: PMC6112242 DOI: 10.1080/10409238.2018.1431201] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/17/2018] [Accepted: 01/18/2018] [Indexed: 10/18/2022]
Abstract
Biocatalysts have been increasingly used in the synthesis of fine chemicals and medicinal compounds due to significant advances in enzyme discovery and engineering. To mimic the synergistic effects of cascade reactions catalyzed by multiple enzymes in nature, researchers have been developing artificial tandem enzymatic reactions in vivo by harnessing synthetic biology and metabolic engineering tools. There is also growing interest in the development of one-pot tandem enzymatic or chemo-enzymatic processes in vitro due to their neat and concise catalytic systems and product purification procedures. In this review, we will briefly summarize the strategies of designing and optimizing in vitro tandem catalytic reactions, highlight a few representative examples, and discuss the future trend in this field.
Collapse
Affiliation(s)
- Yajie Wang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 6180
| | - Hengqian Ren
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 6180
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 6180
- Departments of Chemistry, Biochemistry, and Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| |
Collapse
|
30
|
Mori Y, Shirai T. Designing artificial metabolic pathways, construction of target enzymes, and analysis of their function. Curr Opin Biotechnol 2018; 54:41-44. [PMID: 29452926 DOI: 10.1016/j.copbio.2018.01.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 12/26/2017] [Accepted: 01/22/2018] [Indexed: 11/24/2022]
Abstract
Artificial design of metabolic pathways is essential for the production of useful compounds using microbes. Based on this design, heterogeneous genes are introduced into the host, and then various analysis and evaluation methods are conducted to ensure that the target enzyme reactions are functionalized within the cell. In this chapter, we list successful examples of useful compounds produced by designing artificial metabolic pathways, and describe the methods involved in analyzing, evaluating, and optimizing the target enzyme reaction.
Collapse
Affiliation(s)
- Yutaro Mori
- Biomass Engineering Research Division, Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tomokazu Shirai
- Biomass Engineering Research Division, Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| |
Collapse
|
31
|
Synthetic metabolism: metabolic engineering meets enzyme design. Curr Opin Chem Biol 2017; 37:56-62. [PMID: 28152442 DOI: 10.1016/j.cbpa.2016.12.023] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/15/2016] [Accepted: 12/16/2016] [Indexed: 01/29/2023]
Abstract
Metabolic engineering aims at modifying the endogenous metabolic network of an organism to harness it for a useful biotechnological task, for example, production of a value-added compound. Several levels of metabolic engineering can be defined and are the topic of this review. Basic 'copy, paste and fine-tuning' approaches are limited to the structure of naturally existing pathways. 'Mix and match' approaches freely recombine the repertoire of existing enzymes to create synthetic metabolic networks that are able to outcompete naturally evolved pathways or redirect flux toward non-natural products. The space of possible metabolic solution can be further increased through approaches including 'new enzyme reactions', which are engineered on the basis of known enzyme mechanisms. Finally, by considering completely 'novel enzyme chemistries' with de novo enzyme design, the limits of nature can be breached to derive the most advanced form of synthetic pathways. We discuss the challenges and promises associated with these different metabolic engineering approaches and illuminate how enzyme engineering is expected to take a prime role in synthetic metabolic engineering for biotechnology, chemical industry and agriculture of the future.
Collapse
|
32
|
Richardson-Sanchez T, Tieu W, Codd R. Reverse Biosynthesis: Generating Combinatorial Pools of Drug Leads from Enzyme-Mediated Fragmentation of Natural Products. Chembiochem 2017; 18:368-373. [DOI: 10.1002/cbic.201600636] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Tomas Richardson-Sanchez
- School of Medical Sciences (Pharmacology); The University of Sydney; Camperdown NSW 2006 Australia
| | - William Tieu
- School of Medical Sciences (Pharmacology); The University of Sydney; Camperdown NSW 2006 Australia
| | - Rachel Codd
- School of Medical Sciences (Pharmacology); The University of Sydney; Camperdown NSW 2006 Australia
| |
Collapse
|
33
|
Kuenzl T, Sroka M, Srivastava P, Herdewijn P, Marlière P, Panke S. Overcoming the membrane barrier: Recruitment of γ-glutamyl transferase for intracellular release of metabolic cargo from peptide vectors. Metab Eng 2017; 39:60-70. [DOI: 10.1016/j.ymben.2016.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/21/2016] [Accepted: 10/25/2016] [Indexed: 11/25/2022]
|
34
|
Chen Z, Zeng AP. Protein engineering approaches to chemical biotechnology. Curr Opin Biotechnol 2016; 42:198-205. [DOI: 10.1016/j.copbio.2016.07.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 06/10/2016] [Accepted: 07/30/2016] [Indexed: 01/09/2023]
|
35
|
Lapponi MJ, Rivero CW, Zinni MA, Britos CN, Trelles JA. New developments in nucleoside analogues biosynthesis: A review. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.08.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
36
|
Applied evolutionary theories for engineering of secondary metabolic pathways. Curr Opin Chem Biol 2016; 35:133-141. [PMID: 27736648 DOI: 10.1016/j.cbpa.2016.09.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/18/2016] [Accepted: 09/19/2016] [Indexed: 11/20/2022]
Abstract
An expanded definition of 'secondary metabolism' is emerging. Once the exclusive provenance of naturally occurring organisms, evolved over geological time scales, secondary metabolism increasingly encompasses molecules generated via human engineered biocatalysts and biosynthetic pathways. Many of the tools and strategies for enzyme and pathway engineering can find origins in evolutionary theories. This perspective presents an overview of selected proposed evolutionary strategies in the context of engineering secondary metabolism. In addition to the wealth of biocatalysts provided via secondary metabolic pathways, improving the understanding of biosynthetic pathway evolution will provide rich resources for methods to adapt to applied laboratory evolution.
Collapse
|
37
|
Moustafa HM, Zaghloul TI, Zhang YHP. A simple assay for determining activities of phosphopentomutase from a hyperthermophilic bacterium Thermotoga maritima. Anal Biochem 2016; 501:75-81. [DOI: 10.1016/j.ab.2016.02.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 10/22/2022]
|
38
|
van der Lee TAJ, Medema MH. Computational strategies for genome-based natural product discovery and engineering in fungi. Fungal Genet Biol 2016; 89:29-36. [PMID: 26775250 DOI: 10.1016/j.fgb.2016.01.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 01/08/2016] [Accepted: 01/11/2016] [Indexed: 12/20/2022]
Abstract
Fungal natural products possess biological activities that are of great value to medicine, agriculture and manufacturing. Recent metagenomic studies accentuate the vastness of fungal taxonomic diversity, and the accompanying specialized metabolic diversity offers a great and still largely untapped resource for natural product discovery. Although fungal natural products show an impressive variation in chemical structures and biological activities, their biosynthetic pathways share a number of key characteristics. First, genes encoding successive steps of a biosynthetic pathway tend to be located adjacently on the chromosome in biosynthetic gene clusters (BGCs). Second, these BGCs are often are located on specific regions of the genome and show a discontinuous distribution among evolutionarily related species and isolates. Third, the same enzyme (super)families are often involved in the production of widely different compounds. Fourth, genes that function in the same pathway are often co-regulated, and therefore co-expressed across various growth conditions. In this mini-review, we describe how these partly interlinked characteristics can be exploited to computationally identify BGCs in fungal genomes and to connect them to their products. Particular attention will be given to novel algorithms to identify unusual classes of BGCs, as well as integrative pan-genomic approaches that use a combination of genomic and metabolomic data for parallelized natural product discovery across multiple strains. Such novel technologies will not only expedite the natural product discovery process, but will also allow the assembly of a high-quality toolbox for the re-design or even de novo design of biosynthetic pathways using synthetic biology approaches.
Collapse
Affiliation(s)
- Theo A J van der Lee
- Biointeractions & Plant Health, Plant Research International, Wageningen UR, Wageningen, The Netherlands.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
| |
Collapse
|
39
|
Morgado G, Gerngross D, Roberts TM, Panke S. Synthetic Biology for Cell-Free Biosynthesis: Fundamentals of Designing Novel In Vitro Multi-Enzyme Reaction Networks. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 162:117-146. [PMID: 27757475 DOI: 10.1007/10_2016_13] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cell-free biosynthesis in the form of in vitro multi-enzyme reaction networks or enzyme cascade reactions emerges as a promising tool to carry out complex catalysis in one-step, one-vessel settings. It combines the advantages of well-established in vitro biocatalysis with the power of multi-step in vivo pathways. Such cascades have been successfully applied to the synthesis of fine and bulk chemicals, monomers and complex polymers of chemical importance, and energy molecules from renewable resources as well as electricity. The scale of these initial attempts remains small, suggesting that more robust control of such systems and more efficient optimization are currently major bottlenecks. To this end, the very nature of enzyme cascade reactions as multi-membered systems requires novel approaches for implementation and optimization, some of which can be obtained from in vivo disciplines (such as pathway refactoring and DNA assembly), and some of which can be built on the unique, cell-free properties of cascade reactions (such as easy analytical access to all system intermediates to facilitate modeling).
Collapse
Affiliation(s)
- Gaspar Morgado
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Daniel Gerngross
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Tania M Roberts
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Sven Panke
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.
| |
Collapse
|
40
|
Reinvigorating natural product combinatorial biosynthesis with synthetic biology. Nat Chem Biol 2015; 11:649-59. [PMID: 26284672 DOI: 10.1038/nchembio.1893] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/22/2015] [Indexed: 12/24/2022]
Abstract
Natural products continue to play a pivotal role in drug-discovery efforts and in the understanding if human health. The ability to extend nature's chemistry through combinatorial biosynthesis--altering functional groups, regiochemistry and scaffold backbones through the manipulation of biosynthetic enzymes--offers unique opportunities to create natural product analogs. Incorporating emerging synthetic biology techniques has the potential to further accelerate the refinement of combinatorial biosynthesis as a robust platform for the diversification of natural chemical drug leads. Two decades after the field originated, we discuss the current limitations, the realities and the state of the art of combinatorial biosynthesis, including the engineering of substrate specificity of biosynthetic enzymes and the development of heterologous expression systems for biosynthetic pathways. We also propose a new perspective for the combinatorial biosynthesis of natural products that could reinvigorate drug discovery by using synthetic biology in combination with synthetic chemistry.
Collapse
|
41
|
Fernández-Lucas J. Multienzymatic synthesis of nucleic acid derivatives: a general perspective. Appl Microbiol Biotechnol 2015; 99:4615-27. [PMID: 25952113 DOI: 10.1007/s00253-015-6642-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 04/22/2015] [Accepted: 04/24/2015] [Indexed: 11/28/2022]
Abstract
Living cells are most perfect synthetic factory. The surprising synthetic efficiency of biological systems is allowed by the combination of multiple processes catalyzed by enzymes working sequentially. In this sense, biocatalysis tries to reproduce nature's synthetic strategies to perform the synthesis of different organic compounds using natural catalysts such as cells or enzymes. Nowadays, the use of multienzymatic systems in biocatalysis is becoming a habitual strategy for the synthesis of organic compounds that leads to the realization of complex synthetic schemes. By combining several steps in one pot, a significant step economy can be realized and the potential for environmentally benign synthesis is improved. Using this sustainable synthetic system, several work-up steps can be avoided and pure products are ideally isolated after a series of reactions in one single vessel after just one straightforward purification step. In recent years, enzymatic methodology for the preparation of nucleic acid derivatives (NADs) has become a standard technique for the synthesis of a wide variety of natural NADs. Enzymatic methods have been shown to be an efficient alternative for the synthesis of nucleoside and nucleotide analogs to the traditional multistep chemical methods, since chemical glycosylation reactions include several protection-deprotection steps and the use of chemical reagents and organic solvents that are expensive and environmentally harmful. In this minireview, we want to illustrate what we consider the most current relevant examples of in vivo and in vitro multienzymatic systems used for the synthesis of nucleic acid derivatives showing advantages and disadvantages of each methodology. Finally, a detailed perspective about the impact of -omics in multienzymatic systems has been described.
Collapse
Affiliation(s)
- Jesús Fernández-Lucas
- Applied Biotechnology Group, Department of Pharmacy and Biotechnology, Faculty of Biomedical Sciences, European University of Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670, Villaviciosa de Odón, Madrid, Spain,
| |
Collapse
|
42
|
Sprague D, Nugent BM, Yoder RA, Vara BA, Johnston JN. Adaptation of a small-molecule hydrogen-bond donor catalyst to an enantioselective hetero-Diels-Alder reaction hypothesized for brevianamide biosynthesis. Org Lett 2015; 17:880-3. [PMID: 25697748 PMCID: PMC4339957 DOI: 10.1021/ol503626w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Indexed: 12/22/2022]
Abstract
Chiral diamine-derived hydrogen-bond donors were evaluated for their ability to effect stereocontrol in an intramolecular hetero-Diels-Alder (HDA) reaction hypothesized in the biosynthesis of brevianamides A and B. Collectively, these results provide proof of principle that small-molecule hydrogen-bond catalysis, if even based on a hypothetical biosynthesis construct, holds significant potential within enantioselective natural product synthesis.
Collapse
Affiliation(s)
- Daniel
J. Sprague
- Department of Chemistry and
Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Benjamin M. Nugent
- Department of Chemistry and
Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ryan A. Yoder
- Department of Chemistry and
Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Brandon A. Vara
- Department of Chemistry and
Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey N. Johnston
- Department of Chemistry and
Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| |
Collapse
|
43
|
Köhler V, Turner NJ. Artificial concurrent catalytic processes involving enzymes. Chem Commun (Camb) 2014; 51:450-64. [PMID: 25350691 DOI: 10.1039/c4cc07277d] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The concurrent operation of multiple catalysts can lead to enhanced reaction features including (i) simultaneous linear multi-step transformations in a single reaction flask (ii) the control of intermediate equilibria (iii) stereoconvergent transformations (iv) rapid processing of labile reaction products. Enzymes occupy a prominent position for the development of such processes, due to their high potential compatibility with other biocatalysts. Genes for different enzymes can be co-expressed to reconstruct natural or construct artificial pathways and applied in the form of engineered whole cell biocatalysts to carry out complex transformations or, alternatively, the enzymes can be combined in vitro after isolation. Moreover, enzyme variants provide a wider substrate scope for a given reaction and often display altered selectivities and specificities. Man-made transition metal catalysts and engineered or artificial metalloenzymes also widen the range of reactivities and catalysed reactions that are potentially employable. Cascades for simultaneous cofactor or co-substrate regeneration or co-product removal are now firmly established. Many applications of more ambitious concurrent cascade catalysis are only just beginning to appear in the literature. The current review presents some of the most recent examples, with an emphasis on the combination of transition metal with enzymatic catalysis and aims to encourage researchers to contribute to this emerging field.
Collapse
Affiliation(s)
- Valentin Köhler
- Department of Chemistry, University of Basel, Spitalststrasse 51, CH-4056 Basel, Switzerland.
| | | |
Collapse
|