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Zhang R, Yuan R, Tian B. PointGAT: A Quantum Chemical Property Prediction Model Integrating Graph Attention and 3D Geometry. J Chem Theory Comput 2024; 20:4115-4128. [PMID: 38727259 DOI: 10.1021/acs.jctc.3c01420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Predicting quantum chemical properties is a fundamental challenge for computational chemistry. While the development of graph neural networks has advanced molecular representation learning and property prediction, their performance could be further enhanced by incorporating three-dimensional (3D) structural geometry into two-dimensional (2D) molecular graph representation. In this study, we introduce the PointGAT model for quantum molecular property prediction, which integrates 3D molecular coordinates with graph-attention modeling. Comparison with other current models in molecular prediction tasks showed that PointGAT could provide higher predictive accuracy in various benchmark data sets from MoleculeNet, including ESOL, FreeSolv, Lipop, HIV, and 6 out of 12 tasks of the QM9 data set. To further examine PointGAT prediction of quantum mechanical (QM) energies, we constructed a C10 data set comprising 11,841 charged and chiral carbocation intermediates with QM energies calculated at the DM21/6-31G*//B3LYP/6-31G* levels. Notably, PointGAT achieved an R2 value of 0.950 and an MAE of 1.616 kcal/mol, outperforming even the best-performing graph neural network model with a reduction of 0.216 kcal/mol in MAE and an improvement of 0.050 in R2. Additional ablation studies indicated that incorporating molecular geometry into the model resulted in markedly higher predictive accuracy, reducing the MAE value from 1.802 to 1.616 kcal/mol. Moreover, visualization of PointGAT atomic attention weights suggested its predictions were interpretable. Findings in this study support the application of PointGAT as a powerful and versatile tool for quantum chemical property prediction that can facilitate high-accuracy modeling for fundamental exploration of chemical space as well as drug design and molecular engineering.
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Affiliation(s)
- Rong Zhang
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Rongqing Yuan
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Boxue Tian
- MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
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2
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Klucznik T, Syntrivanis LD, Baś S, Mikulak-Klucznik B, Moskal M, Szymkuć S, Mlynarski J, Gadina L, Beker W, Burke MD, Tiefenbacher K, Grzybowski BA. Computational prediction of complex cationic rearrangement outcomes. Nature 2024; 625:508-515. [PMID: 37967579 PMCID: PMC10864989 DOI: 10.1038/s41586-023-06854-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/08/2023] [Indexed: 11/17/2023]
Abstract
Recent years have seen revived interest in computer-assisted organic synthesis1,2. The use of reaction- and neural-network algorithms that can plan multistep synthetic pathways have revolutionized this field1,3-7, including examples leading to advanced natural products6,7. Such methods typically operate on full, literature-derived 'substrate(s)-to-product' reaction rules and cannot be easily extended to the analysis of reaction mechanisms. Here we show that computers equipped with a comprehensive knowledge-base of mechanistic steps augmented by physical-organic chemistry rules, as well as quantum mechanical and kinetic calculations, can use a reaction-network approach to analyse the mechanisms of some of the most complex organic transformations: namely, cationic rearrangements. Such rearrangements are a cornerstone of organic chemistry textbooks and entail notable changes in the molecule's carbon skeleton8-12. The algorithm we describe and deploy at https://HopCat.allchemy.net/ generates, within minutes, networks of possible mechanistic steps, traces plausible step sequences and calculates expected product distributions. We validate this algorithm by three sets of experiments whose analysis would probably prove challenging even to highly trained chemists: (1) predicting the outcomes of tail-to-head terpene (THT) cyclizations in which substantially different outcomes are encoded in modular precursors differing in minute structural details; (2) comparing the outcome of THT cyclizations in solution or in a supramolecular capsule; and (3) analysing complex reaction mixtures. Our results support a vision in which computers no longer just manipulate known reaction types1-7 but will help rationalize and discover new, mechanistically complex transformations.
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Affiliation(s)
- Tomasz Klucznik
- Allchemy, Highland, IN, USA
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Leonidas-Dimitrios Syntrivanis
- Roger Adams Laboratory, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Basel, Basel, Switzerland.
| | - Sebastian Baś
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Barbara Mikulak-Klucznik
- Allchemy, Highland, IN, USA
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | | | | | - Jacek Mlynarski
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Louis Gadina
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Wiktor Beker
- Allchemy, Highland, IN, USA.
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland.
| | - Martin D Burke
- Roger Adams Laboratory, School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Molecule Maker Laboratory Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Molecule Maker Laboratory at the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Konrad Tiefenbacher
- Department of Chemistry, University of Basel, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Bartosz A Grzybowski
- Allchemy, Highland, IN, USA.
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland.
- IBS Center for Algorithmic and Robotized Synthesis, CARS, Eonyang-eup, Ulju-gun, Ulsan, South Korea.
- Department of Chemistry, UNIST, Eonyang-eup, Ulju-gun, Ulsan, South Korea.
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3
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Jiang H, Wang X. Biosynthesis of monoterpenoid and sesquiterpenoid as natural flavors and fragrances. Biotechnol Adv 2023; 65:108151. [PMID: 37037288 DOI: 10.1016/j.biotechadv.2023.108151] [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: 11/03/2022] [Revised: 03/27/2023] [Accepted: 04/06/2023] [Indexed: 04/12/2023]
Abstract
Terpenoids are a large class of plant-derived compounds, that constitute the main components of essential oils and are widely used as natural flavors and fragrances. The biosynthesis approach presents a promising alternative route in terpenoid production compared to plant extraction or chemical synthesis. In the past decade, the production of terpenoids using biotechnology has attracted broad attention from both academia and the industry. With the growing market of flavor and fragrance, the production of terpenoids directed by synthetic biology shows great potential in promoting future market prospects. Here, we reviewed the latest advances in terpenoid biosynthesis. The engineering strategies for biosynthetic terpenoids were systematically summarized from the enzyme, metabolic, and cellular dimensions. Additionally, we analyzed the key challenges from laboratory production to scalable production, such as key enzyme improvement, terpenoid toxicity, and volatility loss. To provide comprehensive technical guidance, we collected milestone examples of biosynthetic mono- and sesquiterpenoids, compared the current application status of chemical synthesis and biosynthesis in terpenoid production, and discussed the cost drivers based on the data of techno-economic assessment. It is expected to provide critical insights into developing translational research of terpenoid biomanufacturing.
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Affiliation(s)
- Hui Jiang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, Zhejiang 311200, PR China
| | - Xi Wang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, Zhejiang 311200, PR China; College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, PR China.
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4
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Zeng T, Hess BA, Zhang F, Wu R. Bio-inspired chemical space exploration of terpenoids. Brief Bioinform 2022; 23:6586263. [PMID: 35576010 DOI: 10.1093/bib/bbac197] [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: 04/01/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 11/12/2022] Open
Abstract
Many computational methods are devoted to rapidly generating pseudo-natural products to expand the open-ended border of chemical spaces for natural products. However, the accessibility and chemical interpretation were often ignored or underestimated in conventional library/fragment-based or rule-based strategies, thus hampering experimental synthesis. Herein, a bio-inspired strategy (named TeroGen) is developed to mimic the two key biosynthetic stages (cyclization and decoration) of terpenoid natural products, by utilizing physically based simulations and deep learning models, respectively. The precision and efficiency are validated for different categories of terpenoids, and in practice, more than 30 000 sesterterpenoids (10 times as many as the known sesterterpenoids) are predicted to be linked in a reaction network, and their synthetic accessibility and chemical interpretation are estimated by thermodynamics and kinetics. Since it could not only greatly expand the chemical space of terpenoids but also numerate plausible biosynthetic routes, TeroGen is promising for accelerating heterologous biosynthesis, bio-mimic and chemical synthesis of complicated terpenoids and derivatives.
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Affiliation(s)
- Tao Zeng
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | | | - Fan Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
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5
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He W, Tashiro S, Shionoya M. Highly selective acid-catalyzed olefin isomerization of limonene to terpinolene by kinetic suppression of the overreactions in a confined space of porous metal-macrocycle framework. Chem Sci 2022; 13:8752-8758. [PMID: 35975147 PMCID: PMC9350587 DOI: 10.1039/d2sc01561g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/02/2022] [Indexed: 11/21/2022] Open
Abstract
Natural enzymes control the intrinsic reactivity of chemical reactions in the natural environment, giving only the necessary products. In recent years, challenging research on the reactivity control of terpenes with structural diversity using artificial host compounds that mimic such enzymatic reactions has been actively pursued. A typical example is the acid-catalyzed olefin isomerization of (+)-limonene, which generally gives a complex mixture due to over-isomerization to thermodynamically favored isomers. Herein we report a highly controlled conversion of (+)-limonene by kinetic suppression of over-isomerization in a confined space of a porous metal–macrocycle framework (MMF) equipped with a Brønsted acid catalyst. The terminal double bond of (+)-limonene migrated to one neighbor, preferentially producing terpinolene. This reaction selectivity was in stark contrast to the homogeneous acid-catalyzed reaction in bulk solution and to previously reported catalytic reactions. X-ray structural analysis and examination of the reaction with adsorption inhibitors suggest that the reactive substrates may bind non-covalently to specific positions in the confined space of the MMF, thereby inhibiting the over-isomerization reaction. The nanospaces of the MMF with substrate binding ability are expected to enable highly selective synthesis of a variety of terpene compounds. A porous metal–macrocycle framework (MMF) equipped with a Brønsted acid catalyst in nanochannels enables highly selective isomerization of limonene to terpinolene by kinetically suppressing over-isomerization at confined acid sites.![]()
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Affiliation(s)
- Wei He
- Department of Chemistry, Graduate School of Science, The University of Tokyo Tokyo 113-0033 Japan
| | - Shohei Tashiro
- Department of Chemistry, Graduate School of Science, The University of Tokyo Tokyo 113-0033 Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo Tokyo 113-0033 Japan
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6
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Hu T, Feng H, Zhao Y, Yang W, Liu R, Li G. Biochemical and functional characterization of two microbial type terpene synthases from moss Stereodon subimponens. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:750-760. [PMID: 34217131 DOI: 10.1016/j.plaphy.2021.06.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Terpenes constitute a large class of plant secondary metabolites. Usually, there is only one type of terpene synthase in seed plants, which is called typical plant terpene synthase. Currently, as a new family of plant terpene synthases, microbial terpene synthase-like (MTPSL) is identificated in nonseed plants. However, our knowledge about the biological function of most MTPSLs in nonseed plants is very limited. Here, we investigated the biochemical and functional characterization of the enzymes encoded by two MTPSLs from moss Stereodon subimponens, SsMTPSL1 and SsMTPSL2. A phylogenetic tree analysis showed that SsMTPSL1 and SsMTPSL2 are homologous to AaMTPSL1, AaMTPSL3, ApMTPSL1, and ApMTPSL3 from hornworts. The enzyme activity experiment demonstrated that SsMTPSL1 has monoterpene synthase and sesquiterpene synthase activity, and SsMTPSL2 has monoterpene synthase activity. Next, we selected SsMTPSL1 to study its biochemical functions. Anti-bacterial activity test in vitro showed that the products of SsMTPSL1 have an anti-bacterial effect on Escherichia coli, Pseudomonas syringae pv. Tomato DC3000 (Pst DC3000), and Staphylococcus aureus. To further understand the function of SsMTPSL1, the transgenic Arabidopsis thaliana plant of SsMTPSL1 is inoculated by Pst DC3000, and the result showed that SsMTPSL1 enhances the resistance of A. thaliana to Pst DC3000. All in all, this study provides new information about the functions of moss MTPSLs.
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Affiliation(s)
- Tian Hu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, The People's Republic of China
| | - Hao Feng
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, The People's Republic of China
| | - Yapei Zhao
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, The People's Republic of China
| | - Wei Yang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, The People's Republic of China
| | - Ruiqi Liu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, The People's Republic of China
| | - Guanglin Li
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, The People's Republic of China.
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7
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Ronnebaum TA, Gardner SM, Christianson DW. An Aromatic Cluster in the Active Site of epi-Isozizaene Synthase Is an Electrostatic Toggle for Divergent Terpene Cyclization Pathways. Biochemistry 2020; 59:4744-4754. [PMID: 33270439 DOI: 10.1021/acs.biochem.0c00876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The sesquiterpene cyclase epi-isozizaene synthase (EIZS) catalyzes the cyclization of farnesyl diphosphate to form the tricyclic precursor of the antibiotic albaflavenone. The hydrophobic active site is largely defined by aromatic residues that direct a multistep reaction sequence through multiple carbocation intermediates. The previous substitution of polar residues for a key aromatic residue, F96, converts EIZS into a high-fidelity sesquisabinene synthase: the F96S, F96M, and F96Q variants generate 78%, 91%, and 97% sesquisabinene A, respectively. Here, we report high-resolution X-ray crystal structures of two of these reprogrammed cyclases. The structures of the F96M EIZS-Mg2+3-risedronate and F96M EIZS-Mg2+3-inorganic pyrophosphate-benzyltriethylammonium cation complexes reveal structural changes in the F96 aromatic cluster that redirect the cyclization pathway leading from the bisabolyl carbocation intermediate in catalysis. The structure of the F96S EIZS-Mg2+3-neridronate complex reveals a partially occupied inhibitor and an enzyme active site caught in transition between open and closed states. Finally, three structures of wild-type EIZS complexed with the bisphosphonate inhibitors neridronate, pamidronate, and risedronate provide a foundation for understanding binding differences between wild-type and variant enzymes. These structures provide new insight regarding active site flexibility, particularly with regard to the potential for subtle expansion and contraction to accommodate ligands of varying sizes as well as bound water molecules. Additionally, these structures highlight the importance of conformational changes in the F96 aromatic cluster that could influence cation-π interactions with carbocation intermediates in catalysis.
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Affiliation(s)
- Trey A Ronnebaum
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Sarah M Gardner
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
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8
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Exploring the catalytic cascade of cembranoid biosynthesis by combination of genetic engineering and molecular simulations. Comput Struct Biotechnol J 2020; 18:1819-1829. [PMID: 32695274 PMCID: PMC7365961 DOI: 10.1016/j.csbj.2020.06.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 12/04/2022] Open
Abstract
While chemical steps involved in bioactive cembranoid biosynthesis have been examined, the corresponding enzymatic mechanisms leading to their formation remain elusive. In the tobacco plant, Nicotiana tabacum, a putative cembratriene-ol synthase (CBTS) initiates the catalytic cascade that lead to the biosynthesis of cembratriene-4,6-diols, which displays antibacterial- and anti-proliferative activities. We report here on structural homology models, functional studies, and mechanistic explorations of this enzyme using a combination of biosynthetic and computational methods. This approach guided us to develop an efficient de novo production of five bioactive non- and monohydroxylated cembranoids. Our homology models in combination with quantum and classical simulations suggested putative principles of the CBTS catalytic cycle, and provided a possible rationale for the formation of premature olefinic side products. Moreover, the functional reconstruction of a N. tabacum-derived class II P450 with a cognate CPR, obtained by transcriptome mining provided for production of bioactive cembratriene-4,6-diols. Our combined findings provide mechanistic insights into cembranoid biosynthesis, and a basis for the sustainable industrial production of highly valuable bioactive cembranoids.
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9
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Reddy GK, Leferink NGH, Umemura M, Ahmed ST, Breitling R, Scrutton NS, Takano E. Exploring novel bacterial terpene synthases. PLoS One 2020; 15:e0232220. [PMID: 32353014 PMCID: PMC7192455 DOI: 10.1371/journal.pone.0232220] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/09/2020] [Indexed: 01/15/2023] Open
Abstract
Terpenes are the largest class of natural products with extensive structural diversity and are widely used as pharmaceuticals, herbicides, flavourings, fragrances, and biofuels. While they have mostly been isolated from plants and fungi, the availability and analysis of bacterial genome sequence data indicates that bacteria also possess many putative terpene synthase genes. In this study, we further explore this potential for terpene synthase activity in bacteria. Twenty two potential class I terpene synthase genes (TSs) were selected to represent the full sequence diversity of bacterial synthase candidates and recombinantly expressed in E. coli. Terpene synthase activity was detected for 15 of these enzymes, and included mono-, sesqui- and diterpene synthase activities. A number of confirmed sesquiterpene synthases also exhibited promiscuous monoterpene synthase activity, suggesting that bacteria are potentially a richer source of monoterpene synthase activity then previously assumed. Several terpenoid products not previously detected in bacteria were identified, including aromandendrene, acora-3,7(14)-diene and longiborneol. Overall, we have identified promiscuous terpene synthases in bacteria and demonstrated that terpene synthases with substrate promiscuity are widely distributed in nature, forming a rich resource for engineering terpene biosynthetic pathways for biotechnology.
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Affiliation(s)
- Gajendar Komati Reddy
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, England, United Kingdom
| | - Nicole G. H. Leferink
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, England, United Kingdom
- Future Biomanfacturing Research Hub (FBRH), Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, England, United Kingdom
| | - Maiko Umemura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Tsukuba, Ibaraki, Japan
| | - Syed T. Ahmed
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, England, United Kingdom
| | - Rainer Breitling
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, England, United Kingdom
| | - Nigel S. Scrutton
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, England, United Kingdom
- Future Biomanfacturing Research Hub (FBRH), Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, England, United Kingdom
| | - Eriko Takano
- Manchester Synthetic Biology Research Centre SYNBIOCHEM, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, England, United Kingdom
- Future Biomanfacturing Research Hub (FBRH), Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, England, United Kingdom
- * E-mail:
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10
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Zhang Q, Catti L, Syntrivanis LD, Tiefenbacher K. En route to terpene natural products utilizing supramolecular cyclase mimetics. Nat Prod Rep 2019; 36:1619-1627. [PMID: 31021352 DOI: 10.1039/c9np00003h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: literature up to 2018 Terpenes are a class of natural products characterized by remarkable structural diversity. Much of this diversity arises biosynthetically from a handful of linear precursors through the so-called tail-to-head terpene cyclization reaction. This reaction is one of the most complex observed in nature, and historically attempts to replicate it with non-enzymatic means have met with little success. In recent years, however, the development of manmade binding pockets that allow such reactions to take place has been reported. This Highlight provides an overview of this nascent field, and outlines the challenges that need to be overcome moving forward.
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Affiliation(s)
- Qi Zhang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, China
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11
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Zeng T, Liu Z, Liu H, He W, Tang X, Xie L, Wu R. Exploring Chemical and Biological Space of Terpenoids. J Chem Inf Model 2019; 59:3667-3678. [DOI: 10.1021/acs.jcim.9b00443] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Tao Zeng
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Zhihong Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, P.R. China
| | - Huawei Liu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Wengan He
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Xiaowen Tang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Liwei Xie
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, P.R. China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P.R. China
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12
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Pahima E, Zhang Q, Tiefenbacher K, Major DT. Discovering Monoterpene Catalysis Inside Nanocapsules with Multiscale Modeling and Experiments. J Am Chem Soc 2019; 141:6234-6246. [PMID: 30907083 DOI: 10.1021/jacs.8b13411] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Large-scale production of natural products, such as terpenes, presents a significant scientific and technological challenge. One promising approach to tackle this problem is chemical synthesis inside nanocapsules, although enzyme-like control of such chemistry has not yet been achieved. In order to better understand the complex chemistry inside nanocapsules, we design a multiscale nanoreactor simulation approach. The nanoreactor simulation protocol consists of hybrid quantum mechanics-molecular mechanics-based high temperature Langevin molecular dynamics simulations. Using this approach we model the tail-to-head formation of monoterpenes inside a resorcin[4]arene-based capsule (capsule I). We provide a rationale for the experimentally observed kinetics of monoterpene product formation and product distribution using capsule I, and we explain why additional stable monoterpenes, like camphene, are not observed. On the basis of the in-capsule I simulations, and mechanistic insights, we propose that feeding the capsule with pinene can yield camphene, and this proposal is verified experimentally. This suggests that the capsule may direct the dynamic reaction cascades by virtue of π-cation interactions.
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Affiliation(s)
- Efrat Pahima
- Department of Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
| | - Qi Zhang
- Department of Chemistry , University of Basel , Mattenstrasse 24a , 4058 Basel , Switzerland
| | - Konrad Tiefenbacher
- Department of Chemistry , University of Basel , Mattenstrasse 24a , 4058 Basel , Switzerland.,Department of Biosystems Science and Engineering , ETH Zurich , Mattenstrasse 24 , 4058 Basel , Switzerland
| | - Dan T Major
- Department of Chemistry , Bar-Ilan University , Ramat-Gan 52900 , Israel
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13
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Durairaj J, Di Girolamo A, Bouwmeester HJ, de Ridder D, Beekwilder J, van Dijk AD. An analysis of characterized plant sesquiterpene synthases. PHYTOCHEMISTRY 2019; 158:157-165. [PMID: 30446165 DOI: 10.1016/j.phytochem.2018.10.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 05/04/2023]
Abstract
Plants exhibit a vast array of sesquiterpenes, C15 hydrocarbons which often function as herbivore-repellents or pollinator-attractants. These in turn are produced by a diverse range of sesquiterpene synthases. A comprehensive analysis of these enzymes in terms of product specificity has been hampered by the lack of a centralized resource of sufficient functionally annotated sequence data. To address this, we have gathered 262 plant sesquiterpene synthase sequences with experimentally characterized products. The annotated enzyme sequences allowed for an analysis of terpene synthase motifs, leading to the extension of one motif and recognition of a variant of another. In addition, putative terpene synthase sequences were obtained from various resources and compared with the annotated sesquiterpene synthases. This analysis indicated regions of terpene synthase sequence space which so far are unexplored experimentally. Finally, we present a case describing mutational studies on residues altering product specificity, for which we analyzed conservation in our database. This demonstrates an application of our database in choosing likely-functional residues for mutagenesis studies aimed at understanding or changing sesquiterpene synthase product specificity.
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Affiliation(s)
- Janani Durairaj
- Bioinformatics Group, Department of Plant Sciences, Wageningen University, Netherlands.
| | - Alice Di Girolamo
- Laboratory of Plant Physiology, Department of Plant Sciences, Wageningen University, Netherlands.
| | - Harro J Bouwmeester
- Swammerdam Institute for Life Sciences, University of Amsterdam, Netherlands.
| | - Dick de Ridder
- Bioinformatics Group, Department of Plant Sciences, Wageningen University, Netherlands.
| | - Jules Beekwilder
- Laboratory of Plant Physiology, Department of Plant Sciences, Wageningen University, Netherlands; Bioscience, Wageningen Plant Research, Wageningen University, Netherlands.
| | - Aalt Dj van Dijk
- Bioinformatics Group, Department of Plant Sciences, Wageningen University, Netherlands; Biometris, Department of Plant Sciences, Wageningen University, Netherlands.
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14
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Karunanithi PS, Zerbe P. Terpene Synthases as Metabolic Gatekeepers in the Evolution of Plant Terpenoid Chemical Diversity. FRONTIERS IN PLANT SCIENCE 2019; 10:1166. [PMID: 31632418 PMCID: PMC6779861 DOI: 10.3389/fpls.2019.01166] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/26/2019] [Indexed: 05/18/2023]
Abstract
Terpenoids comprise tens of thousands of small molecule natural products that are widely distributed across all domains of life. Plants produce by far the largest array of terpenoids with various roles in development and chemical ecology. Driven by selective pressure to adapt to their specific ecological niche, individual species form only a fraction of the myriad plant terpenoids, typically representing unique metabolite blends. Terpene synthase (TPS) enzymes are the gatekeepers in generating terpenoid diversity by catalyzing complex carbocation-driven cyclization, rearrangement, and elimination reactions that enable the transformation of a few acyclic prenyl diphosphate substrates into a vast chemical library of hydrocarbon and, for a few enzymes, oxygenated terpene scaffolds. The seven currently defined clades (a-h) forming the plant TPS family evolved from ancestral triterpene synthase- and prenyl transferase-type enzymes through repeated events of gene duplication and subsequent loss, gain, or fusion of protein domains and further functional diversification. Lineage-specific expansion of these TPS clades led to variable family sizes that may range from a single TPS gene to families of more than 100 members that may further function as part of modular metabolic networks to maximize the number of possible products. Accompanying gene family expansion, the TPS family shows a profound functional plasticity, where minor active site alterations can dramatically impact product outcome, thus enabling the emergence of new functions with minimal investment in evolving new enzymes. This article reviews current knowledge on the functional diversity and molecular evolution of the plant TPS family that underlies the chemical diversity of bioactive terpenoids across the plant kingdom.
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Affiliation(s)
- Prema S Karunanithi
- Department of Plant Biology, University of California Davis, Davis, CA, United States
| | - Philipp Zerbe
- Department of Plant Biology, University of California Davis, Davis, CA, United States
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15
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Affiliation(s)
- Jacquelyn S. Fetrow
- Office of the President, Albright College, Reading, Pennsylvania, United States of America
- * E-mail:
| | - Patricia C. Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
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16
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Abstract
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The
year 2017 marks the twentieth anniversary of terpenoid cyclase
structural biology: a trio of terpenoid cyclase structures reported
together in 1997 were the first to set the foundation for understanding
the enzymes largely responsible for the exquisite chemodiversity of
more than 80000 terpenoid natural products. Terpenoid cyclases catalyze
the most complex chemical reactions in biology, in that more than
half of the substrate carbon atoms undergo changes in bonding and
hybridization during a single enzyme-catalyzed cyclization reaction.
The past two decades have witnessed structural, functional, and computational
studies illuminating the modes of substrate activation that initiate
the cyclization cascade, the management and manipulation of high-energy
carbocation intermediates that propagate the cyclization cascade,
and the chemical strategies that terminate the cyclization cascade.
The role of the terpenoid cyclase as a template for catalysis is paramount
to its function, and protein engineering can be used to reprogram
the cyclization cascade to generate alternative and commercially important
products. Here, I review key advances in terpenoid cyclase structural
and chemical biology, focusing mainly on terpenoid cyclases and related
prenyltransferases for which X-ray crystal structures have informed
and advanced our understanding of enzyme structure and function.
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Affiliation(s)
- David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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17
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Bian G, Han Y, Hou A, Yuan Y, Liu X, Deng Z, Liu T. Releasing the potential power of terpene synthases by a robust precursor supply platform. Metab Eng 2017; 42:1-8. [PMID: 28438645 DOI: 10.1016/j.ymben.2017.04.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 03/27/2017] [Accepted: 04/19/2017] [Indexed: 12/15/2022]
Abstract
Terpenoids represent the largest family of natural products. Their structural diversity is largely due to variable skeletons generated by terpene synthases. However, terpene skeletons found in nature are much more than those generated from known terpene synthases. Most promiscuous terpene synthases (i.e. those that can generate more than one product) have not been comprehensively characterised. Here, we first demonstrated that the promiscuous terpene synthases can produce more variable terpenoids in vivo by converting precursor polyisoprenoid diphosphates of different lengths (C10, C15, C20, C25). To release the synthetic potential of these enzymes, we integrated the engineered MVA pathway, combinatorial biosynthesis, and point mutagenesis to depict the comprehensive product profiles. In total, eight new terpenoids were characterised by NMR and three new skeletons were revealed. This work highlights the key role of metabolic engineering for natural product discovery.
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Affiliation(s)
- Guangkai Bian
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, PR China
| | - Yichao Han
- J1 Biotech Co., Ltd., Wuhan 430075, PR China
| | - Anwei Hou
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, PR China
| | - Yujie Yuan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, PR China
| | - Xinhua Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, PR China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, PR China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, PR China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, PR China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, PR China.
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