1
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Almhjell PJ, Johnston KE, Porter NJ, Kennemur JL, Bhethanabotla VC, Ducharme J, Arnold FH. The β-subunit of tryptophan synthase is a latent tyrosine synthase. Nat Chem Biol 2024; 20:1086-1093. [PMID: 38744987 PMCID: PMC11288773 DOI: 10.1038/s41589-024-01619-z] [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: 11/21/2023] [Accepted: 04/04/2024] [Indexed: 05/16/2024]
Abstract
Aromatic amino acids and their derivatives are diverse primary and secondary metabolites with critical roles in protein synthesis, cell structure and integrity, defense and signaling. All de novo aromatic amino acid production relies on a set of ancient and highly conserved chemistries. Here we introduce a new enzymatic transformation for L-tyrosine synthesis by demonstrating that the β-subunit of tryptophan synthase-which natively couples indole and L-serine to form L-tryptophan-can act as a latent 'tyrosine synthase'. A single substitution of a near-universally conserved catalytic residue unlocks activity toward simple phenol analogs and yields exclusive para carbon-carbon bond formation to furnish L-tyrosines. Structural and mechanistic studies show how a new active-site water molecule orients phenols for a nonnative mechanism of alkylation, with additional directed evolution resulting in a net >30,000-fold rate enhancement. This new biocatalyst can be used to efficiently prepare valuable L-tyrosine analogs at gram scales and provides the missing chemistry for a conceptually different pathway to L-tyrosine.
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Affiliation(s)
- Patrick J Almhjell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Kadina E Johnston
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Merck & Co., Inc, South San Francisco, CA, USA
| | - Nicholas J Porter
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Codexis, Inc., Redwood City, CA, USA
| | - Jennifer L Kennemur
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Vignesh C Bhethanabotla
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Julie Ducharme
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
- Quebec Government Office, Los Angeles, CA, USA
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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2
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Wang L, Wu Y, Hu J, Yin D, Wei W, Wen J, Chen X, Gao C, Zhou Y, Liu J, Hu G, Li X, Wu J, Zhou Z, Liu L, Song W. Unlocking the function promiscuity of old yellow enzyme to catalyze asymmetric Morita-Baylis-Hillman reaction. Nat Commun 2024; 15:5737. [PMID: 38982157 PMCID: PMC11233575 DOI: 10.1038/s41467-024-50141-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024] Open
Abstract
Exploring the promiscuity of native enzymes presents a promising strategy for expanding their synthetic applications, particularly for catalyzing challenging reactions in non-native contexts. In this study, we explore the promiscuous potential of old yellow enzymes (OYEs) to facilitate the Morita-Baylis-Hillman reaction (MBH reaction), leveraging substrate similarities between MBH reaction and reduction reaction. Using mass spectrometry and spectroscopic techniques, we confirm promiscuity of GkOYE in both MBH and reduction reactions. By blocking H- and H+ transfer pathways, we engineer GkOYE.8, which loses its reduction ability but enhances its MBH activity. The structural basis of MBH reaction catalyzed by GkOYE.8 is obtained through mutation studies and kinetic simulations. Furthermore, enantiocomplementary mutants GkOYE.11 and GkOYE.13 are obtained by directed evolution, exhibiting the ability to accept various aromatic aldehydes and alkenes as substrates. This study demonstrates the potential of leveraging substrate similarities to unlock enzyme functionalities, enabling the catalysis of new-to-nature reactions.
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Affiliation(s)
- Lei Wang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yaoyun Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jun Hu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Dejing Yin
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Wanqing Wei
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jian Wen
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yiwen Zhou
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Jia Liu
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Guipeng Hu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Xiaomin Li
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Zhi Zhou
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China.
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3
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Wan C, Sun R, Xia W, Jiang H, Chen BX, Kuo PC, Zhang WR, Yang G, Li D, Chiang CW, Weng Y. Electrochemical Bioconjugation of Tryptophan Residues: A Strategy for Peptide Modification. Org Lett 2024; 26:5447-5452. [PMID: 38896796 DOI: 10.1021/acs.orglett.4c01662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Interest in electrocatalytic bioconjugation reactions has surged, particularly for modifying tryptophan and tyrosine residues in proteins. We used a cost-effective graphite felt electrode and low-current methodology to achieve selective bioconjugation of tryptophan with thiophenols, yielding up to 92%. This method exclusively labeled tryptophan residues and incorporated fluorinated tryptophan for NMR analysis. Eight polypeptides, including lanreotide and leuprorelin, were effectively coupled, demonstrating the method's versatility and potential for novel diagnostic and therapeutic agents.
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Affiliation(s)
- Chenggang Wan
- Hubei Key Laboratory of Precision Manufacturing for Small-molecular Active Pharmaceutical Ingredients, School of Chemistry and Chemical Engineering, Hubei University, Wuhan, P. R. China
| | - Rong Sun
- Hubei Key Laboratory of Precision Manufacturing for Small-molecular Active Pharmaceutical Ingredients, School of Chemistry and Chemical Engineering, Hubei University, Wuhan, P. R. China
| | - Wenjie Xia
- Hubei Key Laboratory of Precision Manufacturing for Small-molecular Active Pharmaceutical Ingredients, School of Chemistry and Chemical Engineering, Hubei University, Wuhan, P. R. China
| | - Haoyang Jiang
- Hubei Key Laboratory of Precision Manufacturing for Small-molecular Active Pharmaceutical Ingredients, School of Chemistry and Chemical Engineering, Hubei University, Wuhan, P. R. China
| | - Bo-Xun Chen
- Department of Chemistry, Soochow University, No. 70 Linhsi Road Shihlin District, Taipei 111002, Taiwan
| | - Pei-Chi Kuo
- Department of Chemistry, Soochow University, No. 70 Linhsi Road Shihlin District, Taipei 111002, Taiwan
| | - Wan-Rou Zhang
- Department of Chemistry, Soochow University, No. 70 Linhsi Road Shihlin District, Taipei 111002, Taiwan
| | - Guichun Yang
- Hubei Key Laboratory of Precision Manufacturing for Small-molecular Active Pharmaceutical Ingredients, School of Chemistry and Chemical Engineering, Hubei University, Wuhan, P. R. China
| | - Dingyu Li
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue Qiaokou District, Wuhan, P. R. China
| | - Chien-Wei Chiang
- Department of Chemistry, Soochow University, No. 70 Linhsi Road Shihlin District, Taipei 111002, Taiwan
| | - Yue Weng
- Hubei Key Laboratory of Precision Manufacturing for Small-molecular Active Pharmaceutical Ingredients, School of Chemistry and Chemical Engineering, Hubei University, Wuhan, P. R. China
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4
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Duran C, Casadevall G, Osuna S. Harnessing conformational dynamics in enzyme catalysis to achieve nature-like catalytic efficiencies: the shortest path map tool for computational enzyme redesign. Faraday Discuss 2024. [PMID: 38910409 DOI: 10.1039/d3fd00156c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Enzymes exhibit diverse conformations, as represented in the free energy landscape (FEL). Such conformational diversity provides enzymes with the ability to evolve towards novel functions. The challenge lies in identifying mutations that enhance specific conformational changes, especially if located in distal sites from the active site cavity. The shortest path map (SPM) method, which we developed to address this challenge, constructs a graph based on the distances and correlated motions of residues observed in nanosecond timescale molecular dynamics (MD) simulations. We recently introduced a template based AlphaFold2 (tAF2) approach coupled with 10 nanosecond MD simulations to quickly estimate the conformational landscape of enzymes and assess how the FEL is shifted after mutation. In this study, we evaluate the potential of SPM when coupled with tAF2-MD in estimating conformational heterogeneity and identifying key conformationally-relevant positions. The selected model system is the beta subunit of tryptophan synthase (TrpB). We compare how the SPM pathways differ when integrating tAF2 with different MD simulation lengths from as short as 10 ns until 50 ns and considering two distinct Amber forcefield and water models (ff14SB/TIP3P versus ff19SB/OPC). The new methodology can more effectively capture the distal mutations found in laboratory evolution, thus showcasing the efficacy of tAF2-MD-SPM in rapidly estimating enzyme dynamics and identifying the key conformationally relevant hotspots for computational enzyme engineering.
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Affiliation(s)
- Cristina Duran
- Departament de Química, Institut de Química Computacional i Catàlisi, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003, Girona, Spain.
| | - Guillem Casadevall
- Departament de Química, Institut de Química Computacional i Catàlisi, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003, Girona, Spain.
| | - Sílvia Osuna
- Departament de Química, Institut de Química Computacional i Catàlisi, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003, Girona, Spain.
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
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5
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Scheele R, Weber Y, Nintzel FEH, Herger M, Kaminski TS, Hollfelder F. Ultrahigh Throughput Evolution of Tryptophan Synthase in Droplets via an Aptamer Sensor. ACS Catal 2024; 14:6259-6271. [PMID: 38660603 PMCID: PMC11036396 DOI: 10.1021/acscatal.4c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/29/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
Tryptophan synthase catalyzes the synthesis of a wide array of noncanonical amino acids and is an attractive target for directed evolution. Droplet microfluidics offers an ultrahigh throughput approach to directed evolution (up to 107 experiments per day), enabling the search for biocatalysts in wider regions of sequence space with reagent consumption minimized to the picoliter volume (per library member). While the majority of screening campaigns in this format on record relied on an optically active reaction product, a new assay is needed for tryptophan synthase. Tryptophan is not fluorogenic in the visible light spectrum and thus falls outside the scope of conventional droplet microfluidic readouts, which are incompatible with UV light detection at high throughput. Here, we engineer a tryptophan DNA aptamer into a sensor to quantitatively report on tryptophan production in droplets. The utility of the sensor was validated by identifying five-fold improved tryptophan synthases from ∼100,000 protein variants. More generally, this work establishes the use of DNA-aptamer sensors with a fluorogenic read-out in widening the scope of droplet microfluidic evolution.
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Affiliation(s)
- Remkes
A. Scheele
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
| | - Yanik Weber
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
| | | | - Michael Herger
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
| | - Tomasz S. Kaminski
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
- Department
of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Florian Hollfelder
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
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6
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Weaver BR, Perkins LJ, Fernandez Candelaria FO, Burstyn JN, Buller AR. Molecular Determinants of Efficient Cobalt-Substituted Hemoprotein Production in E. coli. ACS Synth Biol 2023; 12:3669-3679. [PMID: 37963151 DOI: 10.1021/acssynbio.3c00481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Exchanging the native iron of heme for other metals yields artificial metalloproteins with new properties for spectroscopic studies and biocatalysis. Recently, we reported a method for the biosynthesis and incorporation of a non-natural metallocofactor, cobalt protoporphyrin IX (CoPPIX), into hemoproteins using the common laboratory strain Escherichia coli BL21(DE3). This discovery inspired us to explore the determinants of metal specificity for metallocofactor biosynthesis in E. coli. Herein, we report detailed kinetic analysis of the ferrochelatase responsible for metal insertion, EcHemH (E. coli ferrochelatase). This enzyme exhibits a small, less than 2-fold preference for Fe2+ over the non-native Co2+ substrate in vitro. To test how mutations impact EcHemH, we used a surrogate metal specificity screen to identify variants with altered metal insertion preferences. This engineering process led to a variant with an ∼30-fold shift in specificity toward Co2+. When assayed in vivo, however, the impact of this mutation is small compared to the effects of alteration of the external metal concentrations. These data suggest that incorporation of cobalt into PPIX is enabled by the native promiscuity of EcHemH coupled with BL21's impaired ability to maintain transition-metal homeostasis. With this knowledge, we generated a method for CoPPIX production in rich media, which yields cobalt-substituted hemoproteins with >95% cofactor purity and yields comparable to standard expression protocols for the analogous native hemoproteins.
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Affiliation(s)
- Brian R Weaver
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lydia J Perkins
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | | | - Judith N Burstyn
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Andrew R Buller
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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7
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Villalona J, Higgins PM, Buller AR. Engineered Biocatalytic Synthesis of β-N-Substituted-α-Amino Acids. Angew Chem Int Ed Engl 2023; 62:e202311189. [PMID: 37625129 PMCID: PMC10592029 DOI: 10.1002/anie.202311189] [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: 08/02/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 08/27/2023]
Abstract
Non-canonical amino acids (ncAAs) are useful synthons for the development of new medicines, materials, and probes for bioactivity. Recently, enzyme engineering has been leveraged to produce a suite of highly active enzymes for the synthesis of β-substituted amino acids. However, there are few examples of biocatalytic N-substitution reactions to make α,β-diamino acids. In this study, we used directed evolution to engineer the β-subunit of tryptophan synthase, TrpB, for improved activity with diverse amine nucleophiles. Mechanistic analysis shows that high yields are hindered by product re-entry into the catalytic cycle and subsequent decomposition. Additional equivalents of l-serine can inhibit product reentry through kinetic competition, facilitating preparative scale synthesis. We show β-substitution with a dozen aryl amine nucleophiles, including demonstration on a gram scale. These transformations yield an underexplored class of amino acids that can serve as unique building blocks for chemical biology and medicinal chemistry.
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Affiliation(s)
- Jairo Villalona
- Department of Chemistry, University of Wisconsin, Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Peyton M Higgins
- Department of Chemistry, University of Wisconsin, Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Andrew R Buller
- Department of Chemistry, University of Wisconsin, Madison, 1101 University Avenue, Madison, WI 53706, USA
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8
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Wohlgemuth R. Synthesis of Metabolites and Metabolite-like Compounds Using Biocatalytic Systems. Metabolites 2023; 13:1097. [PMID: 37887422 PMCID: PMC10608848 DOI: 10.3390/metabo13101097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 10/28/2023] Open
Abstract
Methodologies for the synthesis and purification of metabolites, which have been developed following their discovery, analysis, and structural identification, have been involved in numerous life science milestones. The renewed focus on the small molecule domain of biological cells has also created an increasing awareness of the rising gap between the metabolites identified and the metabolites which have been prepared as pure compounds. The design and engineering of resource-efficient and straightforward synthetic methodologies for the production of the diverse and numerous metabolites and metabolite-like compounds have attracted much interest. The variety of metabolic pathways in biological cells provides a wonderful blueprint for designing simplified and resource-efficient synthetic routes to desired metabolites. Therefore, biocatalytic systems have become key enabling tools for the synthesis of an increasing number of metabolites, which can then be utilized as standards, enzyme substrates, inhibitors, or other products, or for the discovery of novel biological functions.
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Affiliation(s)
- Roland Wohlgemuth
- MITR, Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego Street 116, 90-924 Lodz, Poland;
- Swiss Coordination Committee Biotechnology (SKB), 8021 Zurich, Switzerland
- European Society of Applied Biocatalysis (ESAB), 1000 Brussels, Belgium
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9
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Zmich A, Perkins LJ, Bingman C, Acheson JF, Buller AR. Multiplexed Assessment of Promiscuous Non-Canonical Amino Acid Synthase Activity in a Pyridoxal Phosphate-Dependent Protein Family. ACS Catal 2023; 13:11644-11655. [PMID: 37720819 PMCID: PMC10501158 DOI: 10.1021/acscatal.3c02498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Pyridoxal phosphate (PLP)-dependent enzymes afford access to a variety of non-canonical amino acids (ncAAs), which are premier buildings blocks for the construction of complex bioactive molecules. The vinylglycine ketimine (VGK) subfamily of PLP-dependent enzymes plays a critical role in sulfur metabolism and is home to a growing set of secondary metabolic enzymes that synthesize γ-substituted ncAAs. Identification of VGK enzymes for biocatalysis faces a distinct challenge because the subfamily contains both desirable synthases as well as lyases that break down ncAAs. Some enzymes have both activities, which may contribute to pervasive mis-annotation. To navigate this complex functional landscape, we used a substrate multiplexed screening approach to rapidly measure the substrate promiscuity of 40 homologs in the VGK subfamily. We found that enzymes involved in transsulfuration are less likely to have promiscuous activities and often possess undesirable lyase activity. Enzymes from direct sulfuration and secondary metabolism generally had a high degree of substrate promiscuity. From this cohort, we identified an exemplary γ-synthase from Caldicellulosiruptor hydrothermalis (CahyGS). This enzyme is thermostable and has high expression (~400 mg protein per L culture), enabling preparative scale synthesis of thioether containing ncAAs. When assayed with l-allylglycine, CahyGS catalyzes a stereoselective γ-addition reaction to afford access to a unique set of γ-methyl branched ncAAs. We determined high-resolution crystal structures of this enzyme that define an open-close transition associated with ligand binding and set the stage for future engineering within this enzyme subfamily.
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Affiliation(s)
- Anna Zmich
- Department of Biochemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lydia J. Perkins
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Craig Bingman
- Department of Biochemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Justin F Acheson
- Department of Biochemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Andrew R. Buller
- Department of Biochemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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10
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Cheng L, Li D, Mai BK, Bo Z, Cheng L, Liu P, Yang Y. Stereoselective amino acid synthesis by synergistic photoredox-pyridoxal radical biocatalysis. Science 2023; 381:444-451. [PMID: 37499030 PMCID: PMC10444520 DOI: 10.1126/science.adg2420] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 06/20/2023] [Indexed: 07/29/2023]
Abstract
Developing synthetically useful enzymatic reactions that are not known in biochemistry and organic chemistry is an important challenge in biocatalysis. Through the synergistic merger of photoredox catalysis and pyridoxal 5'-phosphate (PLP) biocatalysis, we developed a pyridoxal radical biocatalysis approach to prepare valuable noncanonical amino acids, including those bearing a stereochemical dyad or triad, without the need for protecting groups. Using engineered PLP enzymes, either enantiomeric product could be produced in a biocatalyst-controlled fashion. Synergistic photoredox-pyridoxal radical biocatalysis represents a powerful platform with which to discover previously unknown catalytic reactions and to tame radical intermediates for asymmetric catalysis.
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Affiliation(s)
- Lei Cheng
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Dian Li
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Zhiyu Bo
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Lida Cheng
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Yang Yang
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, USA
- Biomolecular Science and Engineering (BMSE) Program, University of California Santa Barbara, Santa Barbara, California 93106, USA
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11
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Cordoza J, Chen PYT, Blaustein LR, Lima ST, Fiore MF, Chekan JR, Moore BS, McKinnie SMK. Mechanistic and Structural Insights into a Divergent PLP-Dependent l-Enduracididine Cyclase from a Toxic Cyanobacterium. ACS Catal 2023; 13:9817-9828. [PMID: 37497377 PMCID: PMC10367076 DOI: 10.1021/acscatal.3c01294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/21/2023] [Indexed: 07/28/2023]
Abstract
Cyclic arginine noncanonical amino acids (ncAAs) are found in several actinobacterial peptide natural products with therapeutically useful antibacterial properties. The preparation of ncAAs like enduracididine and capreomycidine currently takes multiple biosynthetic or chemosynthetic steps, thus limiting the commercial availability and applicability of these cyclic guanidine-containing amino acids. We recently discovered and characterized the biosynthetic pathway of guanitoxin, a potent freshwater cyanobacterial neurotoxin, that contains an arginine-derived cyclic guanidine phosphate within its highly polar structure. The ncAA l-enduracididine is an early intermediate in guanitoxin biosynthesis and is produced by GntC, a unique pyridoxal-5'-phosphate (PLP)-dependent enzyme. GntC catalyzes a cyclodehydration from a stereoselectively γ-hydroxylated l-arginine precursor via a reaction that functionally and mechanistically diverges from previously established actinobacterial cyclic arginine ncAA pathways. Herein, we interrogate l-enduracididine biosynthesis from the cyanobacterium Sphaerospermopsis torques-reginae ITEP-024 using spectroscopy, stable isotope labeling techniques, and X-ray crystallography structure-guided site-directed mutagenesis. GntC initially facilitates the reversible deprotonations of the α- and β-positions of its substrate before catalyzing an irreversible diastereoselective dehydration and subsequent intramolecular cyclization. The comparison of holo- and substrate-bound GntC structures and activity assays on site-specific mutants further identified amino acid residues that contribute to the overall catalytic mechanism. These interdisciplinary efforts at structurally and functionally characterizing GntC enable an improved understanding of how nature divergently produces cyclic arginine ncAAs and generate additional tools for their biocatalytic production and downstream biological applications.
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Affiliation(s)
- Jennifer
L. Cordoza
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
| | - Percival Yang-Ting Chen
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, California 92093, United States
| | - Linnea R. Blaustein
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
| | - Stella T. Lima
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, California 92093, United States
- Center
for Nuclear Energy in Agriculture, University
of São Paulo, Piracicaba, São Paulo 13416-000, Brazil
| | - Marli F. Fiore
- Center
for Nuclear Energy in Agriculture, University
of São Paulo, Piracicaba, São Paulo 13416-000, Brazil
| | - Jonathan R. Chekan
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, California 92093, United States
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
| | - Bradley S. Moore
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92903, United States
| | - Shaun M. K. McKinnie
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
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12
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Cordoza JL, Chen PYT, Blaustein LR, Lima ST, Fiore MF, Chekan JR, Moore BS, McKinnie SMK. Mechanistic and structural insights into a divergent PLP-dependent L-enduracididine cyclase from a toxic cyanobacterium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.21.533663. [PMID: 36993528 PMCID: PMC10055224 DOI: 10.1101/2023.03.21.533663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Cyclic arginine noncanonical amino acids (ncAAs) are found in several actinobacterial peptide natural products with therapeutically useful antibacterial properties. The preparation of ncAAs like enduracididine and capreomycidine currently takes multiple biosynthetic or chemosynthetic steps, thus limiting the commercial availability and applicability of these cyclic guanidine-containing amino acids. We recently discovered and characterized the biosynthetic pathway of guanitoxin, a potent freshwater cya-nobacterial neurotoxin, that contains an arginine-derived cyclic guanidine phosphate within its highly polar structure. The ncAA L-enduracididine is an early intermediate in guanitoxin biosynthesis and is produced by GntC, a unique pyridoxal-5'-phosphate (PLP)-dependent enzyme. GntC catalyzes a cyclodehydration from a stereoselectively γ-hydroxylated L-arginine precursor via a reaction that functionally and mechanistically diverges from previously established actinobacterial cyclic arginine ncAA pathways. Herein, we interrogate L-enduracididine biosynthesis from the cyanobacterium Sphaerospermopsis torques-reginae ITEP-024 using spectroscopic, stable isotope labeling techniques, and X-ray crystal structure-guided site-directed mutagenesis. GntC initially facilitates the reversible deprotonations of the α- and β-positions of its substrate prior to catalyzing an irreversible diastereoselective dehydration and subsequent intramolecular cyclization. The comparison of holo- and substrate bound GntC structures and activity assays on sitespecific mutants further identified amino acid residues that contribute to the overall catalytic mechanism. These interdisciplinary efforts at structurally and functionally characterizing GntC enables an improved understanding of how Nature divergently produces cyclic arginine ncAAs and generates additional tools for their biocatalytic production and downstream biological applications.
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13
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Casadevall G, Duran C, Estévez‐Gay M, Osuna S. Estimating conformational heterogeneity of tryptophan synthase with a template‐based
Alphafold2
approach. Protein Sci 2022; 31:e4426. [PMID: 36173176 PMCID: PMC9601780 DOI: 10.1002/pro.4426] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/29/2022] [Accepted: 08/15/2022] [Indexed: 11/10/2022]
Abstract
The three‐dimensional structure of the enzymes provides very relevant information on the arrangement of the catalytic machinery and structural elements gating the active site pocket. The recent success of the neural network Alphafold2 in predicting the folded structure of proteins from the primary sequence with high levels of accuracy has revolutionized the protein design field. However, the application of Alphafold2 for understanding and engineering function directly from the obtained single static picture is not straightforward. Indeed, understanding enzymatic function requires the exploration of the ensemble of thermally accessible conformations that enzymes adopt in solution. In the present study, we evaluate the potential of Alphafold2 in assessing the effect of the mutations on the conformational landscape of the beta subunit of tryptophan synthase (TrpB). Specifically, we develop a template‐based Alphafold2 approach for estimating the conformational heterogeneity of several TrpB enzymes, which is needed for enhanced stand‐alone activity. Our results show the potential of Alphafold2, especially if combined with molecular dynamics simulations, for elucidating the changes induced by mutation in the conformational landscapes at a rather reduced computational cost, thus revealing its plausible application in computational enzyme design.
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Affiliation(s)
- Guillem Casadevall
- CompBioLab Group, Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona Girona Spain
| | - Cristina Duran
- CompBioLab Group, Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona Girona Spain
| | - Miquel Estévez‐Gay
- CompBioLab Group, Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona Girona Spain
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi and Departament de Química Universitat de Girona Girona Spain
- ICREA Barcelona Spain
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14
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Leveson‐Gower RB, Roelfes G. Biocatalytic Friedel-Crafts Reactions. ChemCatChem 2022; 14:e202200636. [PMID: 36606067 PMCID: PMC9804301 DOI: 10.1002/cctc.202200636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/10/2022] [Indexed: 01/07/2023]
Abstract
Friedel-Crafts alkylation and acylation reactions are important methodologies in synthetic and industrial chemistry for the construction of aryl-alkyl and aryl-acyl linkages that are ubiquitous in bioactive molecules. Nature also exploits these reactions in many biosynthetic processes. Much work has been done to expand the synthetic application of these enzymes to unnatural substrates through directed evolution. The promise of such biocatalysts is their potential to supersede inefficient and toxic chemical approaches to these reactions, with mild operating conditions - the hallmark of enzymes. Complementary work has created many bio-hybrid Friedel-Crafts catalysts consisting of chemical catalysts anchored into biomolecular scaffolds, which display many of the same desirable characteristics. In this Review, we summarise these efforts, focussing on both mechanistic aspects and synthetic considerations, concluding with an overview of the frontiers of this field and routes towards more efficient and benign Friedel-Crafts reactions for the future of humankind.
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Affiliation(s)
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of Groningen9747 AGGroningenThe Netherlands
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15
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Substrate multiplexed protein engineering facilitates promiscuous biocatalytic synthesis. Nat Commun 2022; 13:5242. [PMID: 36068220 PMCID: PMC9448781 DOI: 10.1038/s41467-022-32789-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/17/2022] [Indexed: 11/19/2022] Open
Abstract
Enzymes with high activity are readily produced through protein engineering, but intentionally and efficiently engineering enzymes for an expanded substrate scope is a contemporary challenge. One approach to address this challenge is Substrate Multiplexed Screening (SUMS), where enzyme activity is measured on competing substrates. SUMS has long been used to rigorously quantitate native enzyme specificity, primarily for in vivo settings. SUMS has more recently found sporadic use as a protein engineering approach but has not been widely adopted by the field, despite its potential utility. Here, we develop principles of how to design and interpret SUMS assays to guide protein engineering. This rich information enables improving activity with multiple substrates simultaneously, identifies enzyme variants with altered scope, and indicates potential mutational hot-spots as sites for further engineering. These advances leverage common laboratory equipment and represent a highly accessible and customizable method for enzyme engineering. Efficient engineering of enzymes for expanded substrate scope is currently challenging. Here, the authors develop simple principles of how to design and interpret Substrate Multiplexed Screening assays to guide protein engineering to enable activity improvements with simultaneously with multiple substrates.
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16
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Sankaranarayanan K, Heid E, Coley CW, Verma D, Green WH, Jensen KF. Similarity based enzymatic retrosynthesis. Chem Sci 2022; 13:6039-6053. [PMID: 35685792 PMCID: PMC9132021 DOI: 10.1039/d2sc01588a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/26/2022] [Indexed: 11/29/2022] Open
Abstract
Enzymes synthesize complex natural products effortlessly by catalyzing chemo-, regio-, and enantio-selective transformations. Further, biocatalytic processes are increasingly replacing conventional organic synthesis steps because they use mild solvents, avoid the use of metals, and reduce overall non-biodegradable waste. Here, we present a single-step retrosynthesis search algorithm to facilitate enzymatic synthesis of natural product analogs. First, we develop a tool, RDEnzyme, capable of extracting and applying stereochemically consistent enzymatic reaction templates, i.e., subgraph patterns that describe the changes in connectivity between a product molecule and its corresponding reactant(s). Using RDEnzyme, we demonstrate that molecular similarity is an effective metric to propose retrosynthetic disconnections based on analogy to precedent enzymatic reactions in UniProt/RHEA. Using ∼5500 reactions from RHEA as a knowledge base, the recorded reactants to the product are among the top 10 proposed suggestions in 71% of ∼700 test reactions. Second, we trained a statistical model capable of discriminating between reaction pairs belonging to homologous enzymes and evolutionarily distant enzymes using ∼30 000 reaction pairs from SwissProt as a knowledge base. This model is capable of understanding patterns in enzyme promiscuity to evaluate the likelihood of experimental evolution success. By recursively applying the similarity-based single-step retrosynthesis and evolution prediction workflow, we successfully plan the enzymatic synthesis routes for both active pharmaceutical ingredients (e.g. Islatravir, Molnupiravir) and commodity chemicals (e.g. 1,4-butanediol, branched-chain higher alcohols/biofuels), in a retrospective fashion. Through the development and demonstration of the single-step enzymatic retrosynthesis strategy using natural transformations, our approach provides a first step towards solving the challenging problem of incorporating both enzyme- and organic-chemistry based transformations into a computer aided synthesis planning workflow. Using a large database of enzymatic transformations, similarity based enzymatic retrosynthesis search algorithm takes a holistic approach to enzymatic synthesis planning to yield a diverse set of single-step suggestions.![]()
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Affiliation(s)
- Karthik Sankaranarayanan
- Department of Chemical Engineering, Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge Massachusetts 02139 USA
| | - Esther Heid
- Department of Chemical Engineering, Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge Massachusetts 02139 USA .,Institute of Materials Chemistry, TU Wien 1060 Vienna Austria
| | - Connor W Coley
- Department of Chemical Engineering, Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge Massachusetts 02139 USA
| | - Deeptak Verma
- Computational and Structural Chemistry, Discovery Chemistry, Merck & Co., Inc. Kenilworth NJ 07033 USA
| | - William H Green
- Department of Chemical Engineering, Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge Massachusetts 02139 USA
| | - Klavs F Jensen
- Department of Chemical Engineering, Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge Massachusetts 02139 USA
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17
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Smith JL, Madrigal Harrison I, Bingman C, Buller AR. Investigation of β-substitution activity of O-acetylserine sulfhydrolase from Citrullus vulgaris. Chembiochem 2022; 23:e202200157. [PMID: 35476889 PMCID: PMC9401013 DOI: 10.1002/cbic.202200157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/24/2022] [Indexed: 11/17/2022]
Abstract
Pyridoxal‐5’‐phosphate (PLP)‐dependent enzymes have garnered interest for their ability to synthesize non‐standard amino acids (nsAAs). One such class of enzymes, O‐acetylserine sulfhydrylases (OASSs), catalyzes the final step in the biosynthesis of l‐cysteine. Here, we examine the β‐substitution capability of the OASS from Citrullus vulgaris (CvOASS), a putative l‐mimosine synthase. While the previously reported mimosine synthase activity was not reproducible in our hands, we successfully identified non‐native reactivity with a variety of O‐nucleophiles. Optimization of reaction conditions for carboxylate and phenolate substrates led to distinct conditions that were leveraged for the preparative‐scale synthesis of nsAAs. We further show this enzyme is capable of C−C bond formation through a β‐alkylation reaction with an activated nitroalkane. To facilitate understanding of this enzyme, we determined the crystal structure of the enzyme bound to PLP as the internal aldimine at 1.55 Å, revealing key features of the active site and providing information that may guide subsequent development of CvOASS as a practical biocatalyst.
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Affiliation(s)
| | | | - Craig Bingman
- University of Wisconsin-Madison, Biochemistry, UNITED STATES
| | - Andrew Richard Buller
- University of Wisconsin Madison, Chemistry, 1101 University Ave, 53706, Madison, UNITED STATES
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18
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Wang M, Liu X, Wang L, Lu H, Gao H. Cooperative Gold/Zinc‐Catalyzed Cascade Approach to Tryptophan Derivatives from N‐arylhydroxylamines and Alkynes. ASIAN J ORG CHEM 2022. [DOI: 10.1002/ajoc.202200054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Min Wang
- Shandong University School of Chemistry and Chemical Engineering 27 South Shanda Road 250100 Ji'nan CHINA
| | - Xiao Liu
- Shandong University School of Chemistry and Chemical Engineering 27 South Shanda Road 250100 Ji'nan CHINA
| | - Liying Wang
- Shandong University School of Chemistry and Chemical Engineering 27 South Shanda Road 250100 Ji'nan CHINA
| | - Haifeng Lu
- Shandong University School of chemistry and chemical engineering CHINA
| | - Hongyin Gao
- Shandong University School of Chemistry and Chemical Engineering 27 South Shanda Road 250100 Ji'nan CHINA
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19
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Ospina F, Schülke KH, Hammer SC. Biocatalytic Alkylation Chemistry: Building Molecular Complexity with High Selectivity. Chempluschem 2021; 87:e202100454. [PMID: 34821073 DOI: 10.1002/cplu.202100454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/05/2021] [Indexed: 12/28/2022]
Abstract
Biocatalysis has traditionally been viewed as a field that primarily enables access to chiral centers. This includes the synthesis of chiral alcohols, amines and carbonyl compounds, often through functional group interconversion via hydrolytic or oxidation-reduction reactions. This limitation is partly being overcome by the design and evolution of new enzymes. Here, we provide an overview of a recently thriving research field that we summarize as biocatalytic alkylation chemistry. In the past 3-4 years, numerous new enzymes have been developed that catalyze sp3 C-C/N/O/S bond formations. These enzymes utilize different mechanisms to generate molecular complexity by coupling simple fragments with high activity and selectivity. In many cases, the engineered enzymes perform reactions that are difficult or impossible to achieve with current small-molecule catalysts such as organocatalysts and transition-metal complexes. This review further highlights that the design of new enzyme function is particularly successful when off-the-shelf synthetic reagents are utilized to access non-natural reactive intermediates. This underscores how biocatalysis is gradually moving to a field that build molecules through selective bond forming reactions.
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Affiliation(s)
- Felipe Ospina
- Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Kai H Schülke
- Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Stephan C Hammer
- Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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20
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Maria-Solano MA, Kinateder T, Iglesias-Fernández J, Sterner R, Osuna S. In Silico Identification and Experimental Validation of Distal Activity-Enhancing Mutations in Tryptophan Synthase. ACS Catal 2021; 11:13733-13743. [PMID: 34777912 PMCID: PMC8576815 DOI: 10.1021/acscatal.1c03950] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/12/2021] [Indexed: 12/26/2022]
Abstract
Allostery is a central mechanism for the regulation of multi-enzyme complexes. The mechanistic basis that drives allosteric regulation is poorly understood but harbors key information for enzyme engineering. In the present study, we focus on the tryptophan synthase complex that is composed of TrpA and TrpB subunits, which allosterically activate each other. Specifically, we develop a rational approach for identifying key amino acid residues of TrpB distal from the active site. Those residues are predicted to be crucial for shifting the inefficient conformational ensemble of the isolated TrpB to a productive ensemble through intra-subunit allosteric effects. The experimental validation of the conformationally driven TrpB design demonstrates its superior stand-alone activity in the absence of TrpA, comparable to those enhancements obtained after multiple rounds of experimental laboratory evolution. Our work evidences that the current challenge of distal active site prediction for enhanced function in computational enzyme design has become within reach.
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Affiliation(s)
- Miguel A. Maria-Solano
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, Girona 17003, Spain
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Thomas Kinateder
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, Regensburg 93053, Germany
| | - Javier Iglesias-Fernández
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, Girona 17003, Spain
- Nostrum Biodiscovery, Carrer de Baldiri Reixac, 10-12, Barcelona 08028, Spain
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, Regensburg 93053, Germany
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany 69, Girona 17003, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
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21
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Yin XS, Qi WY, Shi BF. Synthesis of tryptophan-containing 2,5-diketopiperazines via sequential C-H activation: total syntheses of tryprostatin A, maremycins A and B. Chem Sci 2021; 12:13137-13143. [PMID: 34745544 PMCID: PMC8513992 DOI: 10.1039/d1sc02343h] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/06/2021] [Indexed: 01/23/2023] Open
Abstract
Indole 2,5-diketopiperazines (DKPs) are an important type of metabolic cyclic dipeptides containing a tryptophan (Trp) unit possessing a range of interesting biological activities. The intriguing structural features and divergent activities have stimulated tremendous efforts towards their efficient synthesis. Herein, we report the development of a unified strategy for the synthesis of three Trp-containing DKPs, namely tryprostatin A, and maremycins A and B, via a sequential C–H activation strategy. The key Trp skeletons were synthesized from the inexpensive, readily available alanine via a Pd(ii)-catalyzed β-methyl C(sp3)–H monoarylation. A subsequent C2-selective prenylation of the resulting 6-OMe-Trp by Pd/norbornene-promoted C–H activation led to the total synthesis of tryprostatin A in 12 linear steps from alanine with 25% overall yield. Meanwhile, total syntheses of maremycins A and B were successfully accomplished using a sequential Pd-catalyzed methylene C(sp3)–H methylation as the key step in 15 linear steps from alanine. Indole 2,5-diketopiperazines (DKPs) are an important type of metabolic cyclic dipeptides containing a tryptophan (Trp) unit possessing a range of interesting biological activities.![]()
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Affiliation(s)
- Xue-Song Yin
- Department of Chemistry, Zhejiang University Hangzhou 310027 China
| | - Wei-Yi Qi
- Department of Chemistry, Zhejiang University Hangzhou 310027 China
| | - Bing-Feng Shi
- Department of Chemistry, Zhejiang University Hangzhou 310027 China
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22
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Xu L, Li T, Huo Z, Chen Q, Xia Q, Jiang B. Directed Evolution Improves the Enzymatic Synthesis of L-5-Hydroxytryptophan by an Engineered Tryptophan Synthase. Appl Biochem Biotechnol 2021; 193:3407-3417. [PMID: 34097254 DOI: 10.1007/s12010-021-03589-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/28/2021] [Indexed: 12/01/2022]
Abstract
L-5-Hydroxytryptophan is an important amino acid that is widely used in food and medicine. In this study, L-5-hydroxytryptophan was synthesized by a modified tryptophan synthase. A direct evolution strategy was applied to engineer tryptophan synthase from Escherichia coli to improve the efficiency of L-5-hydroxytryptophan synthesis. Tryptophan synthase was modified by error-prone PCR. A high-activity mutant enzyme (V231A/K382G) was obtained by a high-throughput screening method. The activity of mutant enzyme (V231A/K382G) is 3.79 times higher than that of its parent, and kcat/Km of the mutant enzyme (V231A/K382G) is 4.36 mM-1∙s-1. The mutant enzyme (V231A/K382G) reaction conditions for the production of L-5-hydroxytryptophan were 100 mmol/L L-serine at pH 8.5 and 35°C for 15 h, reaching a yield of L-5-hydroxytryptophan of 86.7%. Directed evolution is an effective strategy to increase the activity of tryptophan synthase.
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Affiliation(s)
- Lisheng Xu
- School of Biological and Food Engineering, Suzhou University, Suzhou, 234000, China.
| | - Tingting Li
- School of Biological and Food Engineering, Suzhou University, Suzhou, 234000, China
| | - Ziyue Huo
- School of Biological and Food Engineering, Suzhou University, Suzhou, 234000, China
| | - Qiong Chen
- School of Biological and Food Engineering, Suzhou University, Suzhou, 234000, China
| | - Qiuxia Xia
- School of Biological and Food Engineering, Suzhou University, Suzhou, 234000, China
| | - Bianling Jiang
- School of Biological and Food Engineering, Suzhou University, Suzhou, 234000, China
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23
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Gao B, Yang B, Feng X, Li C. Recent advances in the biosynthesis strategies of nitrogen heterocyclic natural products. Nat Prod Rep 2021; 39:139-162. [PMID: 34374396 DOI: 10.1039/d1np00017a] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Covering: 2015 to 2020Nitrogen heterocyclic natural products (NHNPs) are primary or secondary metabolites containing nitrogen heterocyclic (N-heterocyclic) skeletons. Due to the existence of the N-heterocyclic structure, NHNPs exhibit various bioactivities such as anticancer and antibacterial, which makes them widely used in medicines, pesticides, and food additives. However, the low content of these NHNPs in native organisms severely restricts their commercial application. Although a variety of NHNPs have been produced through extraction or chemical synthesis strategies, these methods suffer from several problems. The development of biotechnology provides new options for the production of NHNPs. This review introduces the recent progress of two strategies for the biosynthesis of NHNPs: enzymatic biosynthesis and microbial cell factory. In the enzymatic biosynthesis part, the recent progress in the mining of enzymes that synthesize N-heterocyclic skeletons (e.g., pyrrole, piperidine, diketopiperazine, and isoquinoline), the engineering of tailoring enzymes, and enzyme cascades constructed to synthesize NHNPs are discussed. In the microbial cell factory part, with tropane alkaloids (TAs) and tetrahydroisoquinoline (THIQ) alkaloids as the representative compounds, the strategies of unraveling unknown natural biosynthesis pathways of NHNPs in plants are summarized, and various metabolic engineering strategies to enhance their production in microbes are introduced. Ultimately, future perspectives for accelerating the biosynthesis of NHNPs are discussed.
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Affiliation(s)
- Bo Gao
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China.
| | - Bo Yang
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xudong Feng
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China.
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China. and SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China and Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
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24
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Shenshin VA, Lescanne C, Gines G, Rondelez Y. A small-molecule chemical interface for molecular programs. Nucleic Acids Res 2021; 49:7765-7774. [PMID: 34223901 PMCID: PMC8287923 DOI: 10.1093/nar/gkab470] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/03/2021] [Accepted: 06/29/2021] [Indexed: 12/17/2022] Open
Abstract
In vitro molecular circuits, based on DNA-programmable chemistries, can perform an increasing range of high-level functions, such as molecular level computation, image or chemical pattern recognition and pattern generation. Most reported demonstrations, however, can only accept nucleic acids as input signals. Real-world applications of these programmable chemistries critically depend on strategies to interface them with a variety of non-DNA inputs, in particular small biologically relevant chemicals. We introduce here a general strategy to interface DNA-based circuits with non-DNA signals, based on input-translating modules. These translating modules contain a DNA response part and an allosteric protein sensing part, and use a simple design that renders them fully tunable and modular. They can be repurposed to either transmit or invert the response associated with the presence of a given input. By combining these translating-modules with robust and leak-free amplification motifs, we build sensing circuits that provide a fluorescent quantitative time-response to the concentration of their small-molecule input, with good specificity and sensitivity. The programmability of the DNA layer can be leveraged to perform DNA based signal processing operations, which we demonstrate here with logical inversion, signal modulation and a classification task on two inputs. The DNA circuits are also compatible with standard biochemical conditions, and we show the one-pot detection of an enzyme through its native metabolic activity. We anticipate that this sensitive small-molecule-to-DNA conversion strategy will play a critical role in the future applications of molecular-level circuitry.
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Affiliation(s)
- Vasily A Shenshin
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin 75005 Paris, France
| | - Camille Lescanne
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin 75005 Paris, France
| | - Guillaume Gines
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin 75005 Paris, France
| | - Yannick Rondelez
- Laboratoire Gulliver, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin 75005 Paris, France
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25
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Hoffarth ER, Kong S, He HY, Ryan KS. An engineered biosynthetic-synthetic platform for production of halogenated indolmycin antibiotics. Chem Sci 2021; 12:8817-8821. [PMID: 34257882 PMCID: PMC8246080 DOI: 10.1039/d0sc05843b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/15/2021] [Indexed: 11/21/2022] Open
Abstract
Indolmycin is an antibiotic from Streptomyces griseus ATCC 12648 with activity against Helicobacter pylori, Plasmodium falciparum, and methicillin-resistant Staphylococcus aureus. Here we describe the use of the indolmycin biosynthetic genes in E. coli to make indolmycenic acid, a chiral intermediate in indolmycin biosynthesis, which can then be converted to indolmycin through a three-step synthesis. To expand indolmycin structural diversity, we introduce a promiscuous tryptophanyl-tRNA synthetase gene (trpS) into our E. coli production system and feed halogenated indoles to generate the corresponding indolmycenic acids, ultimately allowing us to access indolmycin derivatives through synthesis. Bioactivity testing against methicillin-resistant Staphylococcus aureus showed modest antibiotic activity for 5-, 6-, and 7-fluoro-indolmycin.
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Affiliation(s)
- Elesha R Hoffarth
- Department of Chemistry, The University of British Columbia Vancouver Canada
| | - Sunnie Kong
- Department of Chemistry, The University of British Columbia Vancouver Canada
| | - Hai-Yan He
- Department of Chemistry, The University of British Columbia Vancouver Canada
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia Vancouver Canada
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26
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Computational investigations of allostery in aromatic amino acid biosynthetic enzymes. Biochem Soc Trans 2021; 49:415-429. [PMID: 33544132 DOI: 10.1042/bst20200741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/22/2022]
Abstract
Allostery, in which binding of ligands to remote sites causes a functional change in the active sites, is a fascinating phenomenon observed in enzymes. Allostery can occur either with or without significant conformational changes in the enzymes, and the molecular basis of its mechanism can be difficult to decipher using only experimental techniques. Computational tools for analyzing enzyme sequences, structures, and dynamics can provide insights into the allosteric mechanism at the atomic level. Combining computational and experimental methods offers a powerful strategy for the study of enzyme allostery. The aromatic amino acid biosynthesis pathway is essential in microorganisms and plants. Multiple enzymes involved in this pathway are sensitive to feedback regulation by pathway end products and are known to use allostery to control their activities. To date, four enzymes in the aromatic amino acid biosynthesis pathway have been computationally investigated for their allosteric mechanisms, including 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase, anthranilate synthase, chorismate mutase, and tryptophan synthase. Here we review the computational studies and findings on the allosteric mechanisms of these four enzymes. Results from these studies demonstrate the capability of computational tools and encourage future computational investigations of allostery in other enzymes of this pathway.
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27
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Simeth NA, Kinateder T, Rajendran C, Nazet J, Merkl R, Sterner R, König B, Kneuttinger AC. Towards Photochromic Azobenzene-Based Inhibitors for Tryptophan Synthase. Chemistry 2021; 27:2439-2451. [PMID: 33078454 PMCID: PMC7898615 DOI: 10.1002/chem.202004061] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/16/2020] [Indexed: 01/25/2023]
Abstract
Light regulation of drug molecules has gained growing interest in biochemical and pharmacological research in recent years. In addition, a serious need for novel molecular targets of antibiotics has emerged presently. Herein, the development of a photocontrollable, azobenzene-based antibiotic precursor towards tryptophan synthase (TS), an essential metabolic multienzyme complex in bacteria, is presented. The compound exhibited moderately strong inhibition of TS in its E configuration and five times lower inhibition strength in its Z configuration. A combination of biochemical, crystallographic, and computational analyses was used to characterize the inhibition mode of this compound. Remarkably, binding of the inhibitor to a hitherto-unconsidered cavity results in an unproductive conformation of TS leading to noncompetitive inhibition of tryptophan production. In conclusion, we created a promising lead compound for combatting bacterial diseases, which targets an essential metabolic enzyme, and whose inhibition strength can be controlled with light.
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Affiliation(s)
- Nadja A. Simeth
- Institute for Organic ChemistryDepartment of Chemistry and PharmacyUniversity of RegensburgUniversitätsstrasse 3193040RegensburgGermany
- Stratingh Institute for ChemistryFaculty of Science and EngineeringUniversity of GroningenNijenborgh 49747AGGroningenThe Netherlands
| | - Thomas Kinateder
- Institute for Biophysics and Physical BiochemistryRegensburg Center for BiochemistryUniversity of RegensburgUniversitätsstrasse 3193040RegensburgGermany
| | - Chitra Rajendran
- Institute for Biophysics and Physical BiochemistryRegensburg Center for BiochemistryUniversity of RegensburgUniversitätsstrasse 3193040RegensburgGermany
| | - Julian Nazet
- Institute for Biophysics and Physical BiochemistryRegensburg Center for BiochemistryUniversity of RegensburgUniversitätsstrasse 3193040RegensburgGermany
| | - Rainer Merkl
- Institute for Biophysics and Physical BiochemistryRegensburg Center for BiochemistryUniversity of RegensburgUniversitätsstrasse 3193040RegensburgGermany
| | - Reinhard Sterner
- Institute for Biophysics and Physical BiochemistryRegensburg Center for BiochemistryUniversity of RegensburgUniversitätsstrasse 3193040RegensburgGermany
| | - Burkhard König
- Institute for Organic ChemistryDepartment of Chemistry and PharmacyUniversity of RegensburgUniversitätsstrasse 3193040RegensburgGermany
| | - Andrea C. Kneuttinger
- Institute for Biophysics and Physical BiochemistryRegensburg Center for BiochemistryUniversity of RegensburgUniversitätsstrasse 3193040RegensburgGermany
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28
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Ferreira M, Sharma SK, Paudyal S, Leblanc RM. Interfacial behavior of Lactate Oxidase at Air-Subphase interface. J Colloid Interface Sci 2021; 589:173-178. [PMID: 33460849 DOI: 10.1016/j.jcis.2020.12.120] [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: 11/23/2020] [Revised: 12/27/2020] [Accepted: 12/30/2020] [Indexed: 11/25/2022]
Abstract
This article investigates the main aspects of the surface chemistry properties of the lactate oxidase (LacOx) enzyme monolayer at the air-subphase interface. Surface chemistry study determined the important properties like the surface packing and stability of the formed layer, whereas the spectroscopic experiments provided information regarding its secondary structure conformation of the enzyme. We have demonstrated that the LacOx in the monolayer form remained active for extended time period. In accordance to the data obtained from the isotherm it was also found that LacOx forms a stable monolayer that does not aggregate at the air-subphase interface. The stability of the monolayer at the air-subphase interface was studied by using compression-decompression cycles which revealed the stability with no significant evidence of aggregates or irreversible domains. This was further confirmed by UV-vis absorption and fluorescence measurements. Spectra from circular dichroism (CD) showed that the LB film retains the characteristic of an α-helix conformation.
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Affiliation(s)
- Marystela Ferreira
- Department of Mathematic, Physical, Chemistry, Federal University of São Paulo, Sorocaba, São Paulo, 18052-720, Brazil
| | - Shiv K Sharma
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, United States
| | - Suraj Paudyal
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, United States
| | - Roger M Leblanc
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, United States.
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29
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Watkins-Dulaney E, Straathof S, Arnold F. Tryptophan Synthase: Biocatalyst Extraordinaire. Chembiochem 2021; 22:5-16. [PMID: 32677310 PMCID: PMC7935429 DOI: 10.1002/cbic.202000379] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/15/2020] [Indexed: 12/23/2022]
Abstract
Tryptophan synthase (TrpS) has emerged as a paragon of noncanonical amino acid (ncAA) synthesis and is an ideal biocatalyst for synthetic and biological applications. TrpS catalyzes an irreversible, C-C bond-forming reaction between indole and serine to make l-tryptophan; native TrpS complexes possess fairly broad specificity for indole analogues, but are difficult to engineer to extend substrate scope or to confer other useful properties due to allosteric constraints and their heterodimeric structure. Directed evolution freed the catalytically relevant TrpS β-subunit (TrpB) from allosteric regulation by its TrpA partner and has enabled dramatic expansion of the enzyme's substrate scope. This review examines the long and storied career of TrpS from the perspective of its application in ncAA synthesis and biocatalytic cascades.
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Affiliation(s)
- Ella Watkins-Dulaney
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Sabine Straathof
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Frances Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA 91125, USA
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30
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Wu S, Snajdrova R, Moore JC, Baldenius K, Bornscheuer UT. Biocatalysis: Enzymatic Synthesis for Industrial Applications. Angew Chem Int Ed Engl 2021; 60:88-119. [PMID: 32558088 PMCID: PMC7818486 DOI: 10.1002/anie.202006648] [Citation(s) in RCA: 522] [Impact Index Per Article: 174.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Indexed: 12/12/2022]
Abstract
Biocatalysis has found numerous applications in various fields as an alternative to chemical catalysis. The use of enzymes in organic synthesis, especially to make chiral compounds for pharmaceuticals as well for the flavors and fragrance industry, are the most prominent examples. In addition, biocatalysts are used on a large scale to make specialty and even bulk chemicals. This review intends to give illustrative examples in this field with a special focus on scalable chemical production using enzymes. It also discusses the opportunities and limitations of enzymatic syntheses using distinct examples and provides an outlook on emerging enzyme classes.
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Affiliation(s)
- Shuke Wu
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
| | - Radka Snajdrova
- Novartis Institutes for BioMedical ResearchGlobal Discovery Chemistry4056BaselSwitzerland
| | - Jeffrey C. Moore
- Process Research and DevelopmentMerck & Co., Inc.126 E. Lincoln AveRahwayNJ07065USA
| | - Kai Baldenius
- Baldenius Biotech ConsultingHafenstr. 3168159MannheimGermany
| | - Uwe T. Bornscheuer
- Institute of BiochemistryDept. of Biotechnology & Enzyme CatalysisGreifswald UniversityFelix-Hausdorff-Strasse 417487GreifswaldGermany
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31
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Zhang R, Tan J, Luo Z, Dong H, Ma N, Liao C. Stereo-selective synthesis of non-canonical γ-hydroxy-α-amino acids by enzymatic carbon–carbon bond formation. Catal Sci Technol 2021. [DOI: 10.1039/d1cy00955a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A feasible and sustainable approach for stereo-selective synthesis of non-canonical γ-hydroxy-α-amino acids from l-aspartic acid and different aldehydes has been developed.
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Affiliation(s)
- Rui Zhang
- Chemical Biology Research Center, Shanghai Institute of Material Medica, Chinese Academy of Science, Shanghai 201203, China
| | - Jiamu Tan
- Chemical Biology Research Center, Shanghai Institute of Material Medica, Chinese Academy of Science, Shanghai 201203, China
- University of the Chinese Academy of Sciences, Shijingshan District, Beijing 100049, China
| | - Zhenzhen Luo
- Nanjing University of Chinese Medicine School of Pharmacy, Qixia District, Nanjing 210023, China
| | - Haihong Dong
- Chemical Biology Research Center, Shanghai Institute of Material Medica, Chinese Academy of Science, Shanghai 201203, China
| | - Ningshan Ma
- Chemical Biology Research Center, Shanghai Institute of Material Medica, Chinese Academy of Science, Shanghai 201203, China
| | - Cangsong Liao
- Chemical Biology Research Center, Shanghai Institute of Material Medica, Chinese Academy of Science, Shanghai 201203, China
- University of the Chinese Academy of Sciences, Shijingshan District, Beijing 100049, China
- Nanjing University of Chinese Medicine School of Pharmacy, Qixia District, Nanjing 210023, China
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32
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Wang L, Wang M, Fu Y, Huang P, Kong D, Niu G. Engineered biosynthesis of thaxtomin phytotoxins. Crit Rev Biotechnol 2020; 40:1163-1171. [PMID: 32819175 DOI: 10.1080/07388551.2020.1807461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Herbicide-resistant weeds are a growing problem worldwide. Thaxtomin phytotoxins are a group of nitrated diketopiperazines produced by the potato common scab-causing pathogen Streptomyces scabies and other actinobacterial plant pathogens. They represent a unique class of microbial natural products with distinctive structural features and promising herbicidal activity. The biosynthesis of thaxtomins proceeds through multiple steps of unusual enzymatic reactions. Advances in understanding of thaxtomins biosynthetic machinery have provided the basis for precursor-directed biosynthesis, pathway refactoring, and one-pot biocombinatorial synthesis to generate thaxtomin analogues. We herein summarize recent findings on the biosynthesis of thaxtomins and highlight recent advances in the rational generation of novel thaxtomins for the development of potent herbicidal agents.
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Affiliation(s)
- Linqi Wang
- Biotechnology Research Center, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Meiyan Wang
- Biotechnology Research Center, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yudie Fu
- Biotechnology Research Center, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Pengju Huang
- Biotechnology Research Center, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Dekun Kong
- Biotechnology Research Center, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Guoqing Niu
- Biotechnology Research Center, Southwest University, Chongqing, China.,State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China.,Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Southwest University, Chongqing, China
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33
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Wu S, Snajdrova R, Moore JC, Baldenius K, Bornscheuer UT. Biokatalyse: Enzymatische Synthese für industrielle Anwendungen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006648] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shuke Wu
- Institut für Biochemie Abt. Biotechnologie & Enzymkatalyse Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
| | - Radka Snajdrova
- Novartis Institutes for BioMedical Research Global Discovery Chemistry 4056 Basel Schweiz
| | - Jeffrey C. Moore
- Process Research and Development Merck & Co., Inc. 126 E. Lincoln Ave Rahway NJ 07065 USA
| | - Kai Baldenius
- Baldenius Biotech Consulting Hafenstraße 31 68159 Mannheim Deutschland
| | - Uwe T. Bornscheuer
- Institut für Biochemie Abt. Biotechnologie & Enzymkatalyse Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Deutschland
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34
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Martínez-Rodríguez S, Torres JM, Sánchez P, Ortega E. Overview on Multienzymatic Cascades for the Production of Non-canonical α-Amino Acids. Front Bioeng Biotechnol 2020; 8:887. [PMID: 32850740 PMCID: PMC7431475 DOI: 10.3389/fbioe.2020.00887] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022] Open
Abstract
The 22 genetically encoded amino acids (AAs) present in proteins (the 20 standard AAs together with selenocysteine and pyrrolysine), are commonly referred as proteinogenic AAs in the literature due to their appearance in ribosome-synthetized polypeptides. Beyond the borders of this key set of compounds, the rest of AAs are generally named imprecisely as non-proteinogenic AAs, even when they can also appear in polypeptide chains as a result of post-transductional machinery. Besides their importance as metabolites in life, many of D-α- and L-α-"non-canonical" amino acids (NcAAs) are of interest in the biotechnological and biomedical fields. They have found numerous applications in the discovery of new medicines and antibiotics, drug synthesis, cosmetic, and nutritional compounds, or in the improvement of protein and peptide pharmaceuticals. In addition to the numerous studies dealing with the asymmetric synthesis of NcAAs, many different enzymatic pathways have been reported in the literature allowing for the biosynthesis of NcAAs. Due to the huge heterogeneity of this group of molecules, this review is devoted to provide an overview on different established multienzymatic cascades for the production of non-canonical D-α- and L-α-AAs, supplying neophyte and experienced professionals in this field with different illustrative examples in the literature. Whereas the discovery of new or newly designed enzymes is of great interest, dusting off previous enzymatic methodologies by a "back and to the future" strategy might accelerate the implementation of new or improved multienzymatic cascades.
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35
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Thompson CM, McDonald AD, Yang H, Cavagnero S, Buller AR. Modular control of l-tryptophan isotopic substitution via an efficient biosynthetic cascade. Org Biomol Chem 2020; 18:4189-4192. [PMID: 32452506 DOI: 10.1039/d0ob00868k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Isotopologs are powerful tools for investigating biological systems. We report a biosynthetic-cascade synthesis of Trp isotopologs starting from indole, glycine, and formaldehyde using the enzymes l-threonine aldolase and an engineered β-subunit of tryptophan synthase. This modular route to Trp isotopologs is simple and inexpensive, enabling facile access to these compounds.
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Affiliation(s)
- Clayton M Thompson
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, WI. 53706, USA.
| | - Allwin D McDonald
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, WI. 53706, USA.
| | - Hanming Yang
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, WI. 53706, USA.
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, WI. 53706, USA.
| | - Andrew R Buller
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, WI. 53706, USA.
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36
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Song W, Chen X, Wu J, Xu J, Zhang W, Liu J, Chen J, Liu L. Biocatalytic derivatization of proteinogenic amino acids for fine chemicals. Biotechnol Adv 2020; 40:107496. [DOI: 10.1016/j.biotechadv.2019.107496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/13/2019] [Accepted: 11/18/2019] [Indexed: 01/09/2023]
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37
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Liao C, Seebeck FP. Asymmetric β‐Methylation of
l
‐ and
d
‐α‐Amino Acids by a Self‐Contained Enzyme Cascade. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916025] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Cangsong Liao
- Department for ChemistryUniversity of Basel Mattenstrasse 24a, BPR 1002 4056 Basel Switzerland
| | - Florian P. Seebeck
- Department for ChemistryUniversity of Basel Mattenstrasse 24a, BPR 1002 4056 Basel Switzerland
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38
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Liao C, Seebeck FP. Asymmetric β‐Methylation of
l
‐ and
d
‐α‐Amino Acids by a Self‐Contained Enzyme Cascade. Angew Chem Int Ed Engl 2020; 59:7184-7187. [DOI: 10.1002/anie.201916025] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Indexed: 01/14/2023]
Affiliation(s)
- Cangsong Liao
- Department for Chemistry University of Basel Mattenstrasse 24a, BPR 1002 4056 Basel Switzerland
| | - Florian P. Seebeck
- Department for Chemistry University of Basel Mattenstrasse 24a, BPR 1002 4056 Basel Switzerland
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39
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Qian Y, Lu C, Liu J, Song W, Chen X, Luo Q, Liu L, Wu J. Engineering protonation conformation of
l
‐aspartate‐α‐decarboxylase to relieve mechanism‐based inactivation. Biotechnol Bioeng 2020; 117:1607-1614. [DOI: 10.1002/bit.27316] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/22/2020] [Accepted: 02/22/2020] [Indexed: 01/01/2023]
Affiliation(s)
- Yuanyuan Qian
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
| | - Cui Lu
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
- School of Pharmaceutical ScienceJiangnan University Wuxi China
| | - Jia Liu
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
| | - Wei Song
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
- School of Pharmaceutical ScienceJiangnan University Wuxi China
| | - Xiulai Chen
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
| | - Qiuling Luo
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
| | - Liming Liu
- State Key Laboratory of Food Science and TechnologyJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University Wuxi China
| | - Jing Wu
- School of Pharmaceutical ScienceJiangnan University Wuxi China
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40
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41
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Abstract
Natural nonproteinogenic amino acids vastly outnumber the well-known 22 proteinogenic amino acids. Such amino acids are generated in specialized metabolic pathways. In these pathways, diverse biosynthetic transformations, ranging from isomerizations to the stereospecific functionalization of C-H bonds, are employed to generate structural diversity. The resulting nonproteinogenic amino acids can be integrated into more complex natural products. Here we review recently discovered biosynthetic routes to freestanding nonproteinogenic α-amino acids, with an emphasis on work reported between 2013 and mid-2019.
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Affiliation(s)
- Jason B Hedges
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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42
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Dick M, Sarai NS, Martynowycz MW, Gonen T, Arnold FH. Tailoring Tryptophan Synthase TrpB for Selective Quaternary Carbon Bond Formation. J Am Chem Soc 2019; 141:19817-19822. [PMID: 31747522 PMCID: PMC6939453 DOI: 10.1021/jacs.9b09864] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We previously engineered the β-subunit of tryptophan synthase (TrpB), which catalyzes the condensation of l-serine and indole to l-tryptophan, to synthesize a range of noncanonical amino acids from l-serine and indole derivatives or other nucleophiles. Here we employ directed evolution to engineer TrpB to accept 3-substituted oxindoles and form C-C bonds leading to new quaternary stereocenters. Initially, the variants that could use 3-substituted oxindoles preferentially formed N-C bonds on N1 of the substrate. Protecting N1 encouraged evolution toward C-alkylation, which persisted when protection was removed. Six generations of directed evolution resulted in TrpB Pfquat with a 400-fold improvement in activity for alkylation of 3-substituted oxindoles and the ability to selectively form a new, all-carbon quaternary stereocenter at the γ-position of the amino acid products. The enzyme can also alkylate and form all-carbon quaternary stereocenters on structurally similar lactones and ketones, where it exhibits excellent regioselectivity for the tertiary carbon. The configurations of the γ-stereocenters of two of the products were determined via microcrystal electron diffraction (MicroED), and we report the MicroED structure of a small molecule obtained using the Falcon III direct electron detector. Highly thermostable and expressed at >500 mg/L E. coli culture, TrpB Pfquat offers an efficient, sustainable, and selective platform for the construction of diverse noncanonical amino acids bearing all-carbon quaternary stereocenters.
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Affiliation(s)
- Markus Dick
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Nicholas S. Sarai
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Michael W. Martynowycz
- Howard Hughes Medical Institute, David Geffen School of Medicine, Departments of Biological Chemistry and Physiology, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Tamir Gonen
- Howard Hughes Medical Institute, David Geffen School of Medicine, Departments of Biological Chemistry and Physiology, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
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43
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Yu J, Li J, Gao X, Zeng S, Zhang H, Liu J, Jiao Q. Dynamic Kinetic Resolution for Asymmetric Synthesis of L-Noncanonical Amino Acids from D-Ser Using Tryptophan Synthase and Alanine Racemase. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jinhai Yu
- State Key Laboratory of Pharmaceutical Biotechnology; School of Life Science; Nanjing University; 210093 Nanjing P. R. China
| | - Jing Li
- State Key Laboratory of Pharmaceutical Biotechnology; School of Life Science; Nanjing University; 210093 Nanjing P. R. China
| | - Xia Gao
- State Key Laboratory of Pharmaceutical Biotechnology; School of Life Science; Nanjing University; 210093 Nanjing P. R. China
| | - Shuiyun Zeng
- State Key Laboratory of Pharmaceutical Biotechnology; School of Life Science; Nanjing University; 210093 Nanjing P. R. China
| | - Hongjuan Zhang
- School of Pharmacy; Nanjing Medical University; 211166 Nanjing China
| | - Junzhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology; School of Life Science; Nanjing University; 210093 Nanjing P. R. China
| | - Qingcai Jiao
- State Key Laboratory of Pharmaceutical Biotechnology; School of Life Science; Nanjing University; 210093 Nanjing P. R. China
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44
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Romney DK, Sarai NS, Arnold FH. Nitroalkanes as Versatile Nucleophiles for Enzymatic Synthesis of Noncanonical Amino Acids. ACS Catal 2019; 9:8726-8730. [PMID: 33274115 DOI: 10.1021/acscatal.9b02089] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
C-C bond-forming reactions often require nucleophilic carbon species rarely compatible with aqueous reaction media, thus restricting their appearance in biocatalysis. Here we report the use of nitroalkanes as a structurally versatile class of nucleophilic substrates for C-C bond formation catalyzed by variants of the β-subunit of tryptophan synthase (TrpB). The enzymes accept a wide range of nitroalkanes to form noncanonical amino acids, here the nitro group can serve as a handle for further modification. Using nitroalkane nucleophiles greatly expands the scope of compounds made by TrpB variants and establishes nitroalkanes as a valuable substrate class for biocatalytic C-C bond formation.
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Affiliation(s)
- David K. Romney
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Nicholas S. Sarai
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
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Pubill‐Ulldemolins C, Sharma SV, Cartmell C, Zhao J, Cárdenas P, Goss RJM. Heck Diversification of Indole-Based Substrates under Aqueous Conditions: From Indoles to Unprotected Halo-tryptophans and Halo-tryptophans in Natural Product Derivatives. Chemistry 2019; 25:10866-10875. [PMID: 31125453 PMCID: PMC6772188 DOI: 10.1002/chem.201901327] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/21/2019] [Indexed: 12/17/2022]
Abstract
The blending of synthetic chemistry with biosynthetic processes provides a powerful approach to synthesis. Biosynthetic halogenation and synthetic cross-coupling have great potential to be used together, for small molecule generation, access to natural product analogues and as a tool for chemical biology. However, to enable enhanced generality of this approach, further synthetic tools are needed. Though considerable research has been invested in the diversification of phenylalanine and tyrosine, functionalisation of tryptophans thorough cross-coupling has been largely neglected. Tryptophan is a key residue in many biologically active natural products and peptides; in proteins it is key to fluorescence and dominates protein folding. To this end, we have explored the Heck cross-coupling of halo-indoles and halo-tryptophans in water, showing broad reaction scope. We have demonstrated the ability to use this methodology in the functionalisation of a brominated antibiotic (bromo-pacidamycin), as well as a marine sponge metabolite, barettin.
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Affiliation(s)
- Cristina Pubill‐Ulldemolins
- Department of Chemistry and BSRCUniversity of St AndrewsSt AndrewsKY16 9STUK
- Present address: Department of ChemistrySchool of Life SciencesUniversity of SussexBrightonBN19QJUK
| | - Sunil V. Sharma
- Department of Chemistry and BSRCUniversity of St AndrewsSt AndrewsKY16 9STUK
| | | | - Jinlian Zhao
- Department of Chemistry and BSRCUniversity of St AndrewsSt AndrewsKY16 9STUK
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal ChemistryUppsala UniversityUppsala75123Sweden
| | - Rebecca J. M. Goss
- Department of Chemistry and BSRCUniversity of St AndrewsSt AndrewsKY16 9STUK
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McDonald AD, Perkins LJ, Buller AR. Facile in Vitro Biocatalytic Production of Diverse Tryptamines. Chembiochem 2019; 20:1939-1944. [PMID: 30864270 PMCID: PMC6800669 DOI: 10.1002/cbic.201900069] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/08/2019] [Indexed: 01/01/2023]
Abstract
Tryptamines are a medicinally important class of small molecules that serve as precursors to more complex, clinically used indole alkaloid natural products. Typically, tryptamine analogues are prepared from indoles through multistep synthetic routes. In the natural world, the desirable tryptamine synthon is produced in a single step by l-tryptophan decarboxylases (TDCs). However, no TDCs are known to combine high activity and substrate promiscuity, which might enable a practical biocatalytic route to tryptamine analogues. We have now identified the TDC from Ruminococcus gnavus as the first highly active and promiscuous member of this enzyme family. RgnTDC performs up to 96 000 turnovers and readily accommodates tryptophan analogues with substituents at the 4, 5, 6, and 7 positions, as well as alternative heterocycles, thus enabling the facile biocatalytic synthesis of >20 tryptamine analogues. We demonstrate the utility of this enzyme in a two-step biocatalytic sequence with an engineered tryptophan synthase to afford an efficient, cost-effective route to tryptamines from commercially available indole starting materials.
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Affiliation(s)
- Allwin D McDonald
- Department of Chemistry, University of Wisconsin, Madison, Madison, WI, 53705, USA
| | - Lydia J Perkins
- Department of Chemistry, University of Wisconsin, Madison, Madison, WI, 53705, USA
| | - Andrew R Buller
- Department of Chemistry, University of Wisconsin, Madison, Madison, WI, 53705, USA
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47
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Maria-Solano MA, Iglesias-Fernández J, Osuna S. Deciphering the Allosterically Driven Conformational Ensemble in Tryptophan Synthase Evolution. J Am Chem Soc 2019; 141:13049-13056. [DOI: 10.1021/jacs.9b03646] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Miguel A. Maria-Solano
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Girona 17003, Spain
| | - Javier Iglesias-Fernández
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Girona 17003, Spain
| | - Sílvia Osuna
- CompBioLab group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Girona 17003, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
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48
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Chang Z. The 2018 Nobel Prize in Chemistry: Engineering proteins (enzymes/peptide/antibodies) towards desired properties via the construction of random libraries. SCIENCE CHINA-LIFE SCIENCES 2019; 62:713-724. [PMID: 30931497 DOI: 10.1007/s11427-019-9498-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/01/2019] [Indexed: 10/27/2022]
Affiliation(s)
- Zengyi Chang
- School of Life Sciences, State Key Laboratory of Protein and Plant Engineering Research, Center for Protein Science, Center of History and Philosophy of Science, Peking University, Beijing, 100871, China.
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49
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Parmeggiani F, Rué Casamajo A, Walton CJW, Galman JL, Turner NJ, Chica RA. One-Pot Biocatalytic Synthesis of Substituted d-Tryptophans from Indoles Enabled by an Engineered Aminotransferase. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00739] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Fabio Parmeggiani
- Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Arnau Rué Casamajo
- Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Curtis J. W. Walton
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, K1N 6N5, Ottawa, Ontario, Canada
- Centre for Catalysis Research and Innovation, University of Ottawa, 30 Marie-Curie, K1N 6N5, Ottawa, Ontario, Canada
| | - James L. Galman
- Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Turner
- Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Roberto A. Chica
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, K1N 6N5, Ottawa, Ontario, Canada
- Centre for Catalysis Research and Innovation, University of Ottawa, 30 Marie-Curie, K1N 6N5, Ottawa, Ontario, Canada
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50
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Ali R, Ahamad MZ, Singh S, Haq W. Regioselective Synthesis of Symmetrical and Unsymmetrical Bis(heteroaryl)methane (BHM)-Containing Amino Acids. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Rafat Ali
- Medicinal and Process Chemistry Division; CSIR-Central Drug Research Institute; -226031 Lucknow India
| | - Mohd. Zisan Ahamad
- Medicinal and Process Chemistry Division; CSIR-Central Drug Research Institute; -226031 Lucknow India
| | - Shalini Singh
- Medicinal and Process Chemistry Division; CSIR-Central Drug Research Institute; -226031 Lucknow India
| | - Wahajul Haq
- Medicinal and Process Chemistry Division; CSIR-Central Drug Research Institute; -226031 Lucknow India
- Academy of Scientific and Innovative Research; -11000 New Delhi India
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