1
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Marin Ž, Lacombe C, Rostami S, Arasteh Kani A, Borgonovo A, Cserjan-Puschmann M, Mairhofer J, Striedner G, Wiltschi B. Residue-Specific Incorporation of Noncanonical Amino Acids in Auxotrophic Hosts: Quo Vadis?. Chem Rev 2025; 125:4840-4932. [PMID: 40378355 PMCID: PMC12123629 DOI: 10.1021/acs.chemrev.4c00280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 04/09/2025] [Accepted: 04/17/2025] [Indexed: 05/18/2025]
Abstract
The residue-specific incorporation of noncanonical amino acids in auxotrophic hosts allows the global exchange of a canonical amino acid with its noncanonical analog. Noncanonical amino acids are not encoded by the standard genetic code, but they carry unique side chain chemistries, e.g., to perform bioorthogonal conjugation reactions or to manipulate the physicochemical properties of a protein such as folding and stability. The method was introduced nearly 70 years ago and is still in widespread use because of its simplicity and robustness. In our study, we review the trends in the field during the last two decades. We give an overview of the application of the method for artificial post-translational protein modifications and the selective functionalization and directed immobilization of proteins. We highlight the trends in the use of noncanonical amino acids for the analysis of nascent proteomes and the engineering of enzymes and biomaterials, and the progress in the biosynthesis of amino acid analogs. We also discuss the challenges for the scale-up of the technique.
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Affiliation(s)
- Žana Marin
- Department
of Biotechnology and Food Sciences, Institute of Bioprocess Science
and Engineering, BOKU University, Muthgasse 18, 1190Vienna, Austria
- acib
- Austrian
Centre of Industrial Biotechnology, Muthgasse 18, 1190Vienna, Austria
| | - Claudia Lacombe
- Department
of Biotechnology and Food Sciences, Institute of Bioprocess Science
and Engineering, BOKU University, Muthgasse 18, 1190Vienna, Austria
| | - Simindokht Rostami
- Department
of Biotechnology and Food Sciences, Institute of Bioprocess Science
and Engineering, BOKU University, Muthgasse 18, 1190Vienna, Austria
| | - Arshia Arasteh Kani
- Department
of Biotechnology and Food Sciences, Institute of Bioprocess Science
and Engineering, BOKU University, Muthgasse 18, 1190Vienna, Austria
| | - Andrea Borgonovo
- Department
of Biotechnology and Food Sciences, Institute of Bioprocess Science
and Engineering, BOKU University, Muthgasse 18, 1190Vienna, Austria
- acib
- Austrian
Centre of Industrial Biotechnology, Muthgasse 18, 1190Vienna, Austria
| | - Monika Cserjan-Puschmann
- Department
of Biotechnology and Food Sciences, Institute of Bioprocess Science
and Engineering, BOKU University, Muthgasse 18, 1190Vienna, Austria
| | | | - Gerald Striedner
- Department
of Biotechnology and Food Sciences, Institute of Bioprocess Science
and Engineering, BOKU University, Muthgasse 18, 1190Vienna, Austria
| | - Birgit Wiltschi
- Department
of Biotechnology and Food Sciences, Institute of Bioprocess Science
and Engineering, BOKU University, Muthgasse 18, 1190Vienna, Austria
- acib
- Austrian
Centre of Industrial Biotechnology, Muthgasse 18, 1190Vienna, Austria
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2
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Zhu BF, Fatmi MQ, Pei XQ, Wu ZL, Liu Y. Continuous Engineering of Phenylalanine Ammonia Lyase from Lettuce ( Lactuca sativa L.) for Efficient Synthesis of 3,4-Substituted Phenylalanine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025; 73:10358-10368. [PMID: 40254840 DOI: 10.1021/acs.jafc.4c06986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/22/2025]
Abstract
Phenylalanine ammonia lyase (PAL) is a promising catalyst for synthesizing non-natural amino acids. LsPAL3 from lettuce is a potential candidate for protein engineering. Using alanine scanning and CASTing mutation strategies, we developed a highly effective triple mutant, L126C/F129I/L130C (named LsM3), which exhibited superior catalytic activity toward 3,4-dimethoxy-substituted substrates. Further enhancements of thermal stability resulted in a robust combined mutant, LsMC6 (which integrates LsM3 with additional mutations G62A/S516A/V705A). Its activity was 4.6 times that of LsM3 in the ammonia addition reaction of 3,4-dimethoxy-substituted cinnamic acid, and its half-life of thermal inactivation at 60 °C was 3.5 times that of LsM3. LsMC6 demonstrated significantly improved activity over previously described PALs in the ammonia addition reactions of seven 3,4-substituted cinnamic acid derivatives. Docking and molecular dynamics (MD) simulations revealed that L126C/F129I/L130C mutations reshaped the catalytic pocket, while the incorporation of G62A, S516A, and V705A mutations significantly reduced atomic displacements, thereby enhancing the activity and stability of LsMC6.
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Affiliation(s)
- Bo-Feng Zhu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Chengdu 610064, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - M Qaiser Fatmi
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- Department of Biosciences, COMSATS University Islamabad, Islamabad 45600, Pakistan
| | - Xiao-Qiong Pei
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Zhong-Liu Wu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Yan Liu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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3
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Iannuzzi M, Hohmann T, Dyrks M, Haoues K, Salamon-Krokosz K, Koksch B. Asymmetric synthesis of fluorinated derivatives of aromatic and γ-branched amino acids via a chiral Ni(II) complex. Beilstein J Org Chem 2025; 21:659-669. [PMID: 40130182 PMCID: PMC11931639 DOI: 10.3762/bjoc.21.52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2025] [Accepted: 02/18/2025] [Indexed: 03/26/2025] Open
Abstract
Fluorinated amino acids are essential building blocks in the spheres of protein engineering and medicinal chemistry. In the last decades, a large number of different synthetic strategies have been developed to produce a large variety of fluorinated amino acids. Still, obtaining fluorinated amino acids in great quantities can be challenging, or the corresponding pathways are heavily time-consuming and synthetically challenging. In this context, chiral Ni(II) complexes can be powerful tools to obtain tailor‑made non‑canonical amino acids. In this work, we wanted to take advantage of this strategy and extend the range of this method to include additional fluorinated amino acids. We synthesized two fluorinated analogs of phenylalanine, which are still unexplored in the context of peptide and protein chemistry. Furthermore, both diastereomers of trifluoroleucine were synthesized, demonstrating that the described strategy can also be applied to synthesize enantio‑ and diastereomerically pure γ‑branched fluorinated amino acids. This work further underlines the importance of chiral Ni(II) complexes in the synthesis of fluorinated amino acids.
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Affiliation(s)
- Maurizio Iannuzzi
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany
| | - Thomas Hohmann
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany
| | - Michael Dyrks
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany
| | - Kilian Haoues
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany
| | - Katarzyna Salamon-Krokosz
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany
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4
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Petchey MR, Schneider P, Harwood LA. Biocatalytic Amino Acid Functionalisation. ChemMedChem 2025; 20:e202400628. [PMID: 39540701 DOI: 10.1002/cmdc.202400628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 11/12/2024] [Accepted: 11/13/2024] [Indexed: 11/16/2024]
Abstract
The success of new therapeutic modalities relies on advancements in synthetic chemistry to produce compounds for evaluation throughout the drug discovery process. The use of non-canonical amino acids (ncAAs) allows the properties of peptide drugs to be modified and optimised beyond the defined characteristics of the 20 proteogenic amino acids. Synthesis of ncAAs can be either through a bespoke chemical synthesis, or directly from the parent compound - using either traditional chemical reagents or using enzymes - to achieve the desired modification. This review will highlight recent advancements in the enzymatic functionalisation of amino acids to produce a variety of ncAAs.
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Affiliation(s)
- Mark R Petchey
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pascal Schneider
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Lucy A Harwood
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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5
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Zhang Y, Huang Q, Lei F, Qian W, Zhang C, Wang Q, Liu C, Ji H, Wang F. Exploring New Bioorthogonal Catalysts: Scaffold Diversity in Catalysis for Chemical Biology. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2404431. [PMID: 39921286 PMCID: PMC11884534 DOI: 10.1002/advs.202404431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 01/11/2025] [Indexed: 02/10/2025]
Abstract
Bioorthogonal catalysis has revolutionized the field of chemical biology by enabling selective and controlled chemical transformations within living systems. Research has converged on the development of innovative catalyst scaffolds, seeking to broaden the scope of bioorthogonal reactions, boost their efficiency, and surpass the limitations of conventional catalysts. This review provides a comprehensive overview of the latest advancements in bioorthogonal catalyst research based on different scaffold materials. Through an in-depth analysis of fabrication strategies and applications of bioorthogonal catalysts, this review discusses the design principles, mechanisms of action, and applications of these novel catalysts in chemical biology. Current challenges and future directions in exploring the scaffold diversity are also highlighted. The integration of diverse catalyst scaffolds offers exciting prospects for precise manipulation of biomolecules and the development of innovative therapeutic strategies in chemical biology. In addition, the review fills in the gaps in previous reviews, such as in fully summarizing the presented scaffold materials applied in bioorthogonal catalysts, emphasizing the potential impact on advancing bioorthogonal chemistry, and offering prospects for future development in this field.
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Affiliation(s)
- Yan Zhang
- Institute of Special Environmental MedicineNantong UniversityNantong226019China
| | - Qizhen Huang
- School of Public HealthNantong UniversityNantong226019China
| | - Fang Lei
- School of Public HealthNantong UniversityNantong226019China
| | - Wanlong Qian
- Institute of Special Environmental MedicineNantong UniversityNantong226019China
| | - Chengfeng Zhang
- Institute of Special Environmental MedicineNantong UniversityNantong226019China
| | - Qi Wang
- School of Public HealthNantong UniversityNantong226019China
| | - Chaoqun Liu
- School of PharmacyHenan UniversityKaifeng475004China
| | - Haiwei Ji
- School of Public HealthNantong UniversityNantong226019China
| | - Faming Wang
- School of Public HealthNantong UniversityNantong226019China
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6
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Gare CL, White AM, Malins LR. From lead to market: chemical approaches to transform peptides into therapeutics. Trends Biochem Sci 2025:S0968-0004(25)00024-6. [PMID: 40011178 DOI: 10.1016/j.tibs.2025.01.009] [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: 11/11/2024] [Revised: 01/21/2025] [Accepted: 01/29/2025] [Indexed: 02/28/2025]
Abstract
Peptides are a powerful drug modality with potential to access difficult targets. This recognition underlies their growth in the global pharmaceutical market, with peptides representing ~8% of drugs approved by the FDA over the past decade. Currently, the peptide therapeutic landscape is evolving, with high-throughput display technologies driving the identification of peptide leads with enhanced diversity. Yet, chemical modifications remain essential for improving the 'drug-like' properties of peptides and ultimately translating leads to market. In this review, we explore two recent therapeutic candidates (semaglutide, a peptide hormone analogue, and MK-0616, an mRNA display-derived candidate) as case studies that highlight general approaches to improving pharmacokinetics (PK) and potency. We also emphasize the critical link between advances in medicinal chemistry and the optimisation of highly efficacious peptide therapeutics.
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Affiliation(s)
- Caitlin L Gare
- Research School of Chemistry, Australian National University, Canberra 2601, Australian Capital Territory, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra 2601, Australian Capital Territory, Australia
| | - Andrew M White
- Research School of Chemistry, Australian National University, Canberra 2601, Australian Capital Territory, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra 2601, Australian Capital Territory, Australia
| | - Lara R Malins
- Research School of Chemistry, Australian National University, Canberra 2601, Australian Capital Territory, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra 2601, Australian Capital Territory, Australia.
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7
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Chen B, Huang J, Liu Y, Yang L, Wang Q, Yu H. Computational Study on the Catalytic Mechanism of UstD Catalyzing the Synthesis of γ-Hydroxy-α-Amino Acids. J Chem Inf Model 2025; 65:2026-2037. [PMID: 39913657 DOI: 10.1021/acs.jcim.4c01998] [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: 02/25/2025]
Abstract
The catalytic mechanism of a pyridoxal 5'-phosphate (PLP)-dependent UstD was herein studied in atomic detail, employing the computational hybrid QM/MM methodology. UstD is a PLP-dependent enzyme that catalyzes the decarboxylative aldol reactions between l-aspartate and aldehyde or ketone derivatives to form γ-hydroxy-α-amino acids. In the reaction catalyzed by UstD, the loss of CO2 renders the C-C bond-forming reaction effectively irreversible, which makes UstD a special case among the enzymes catalyzing the C-C bond-forming reactions. This enzyme is currently seen as the optimal approach for the regioselective synthesis of γ-hydroxy-α-amino acids, which are very difficult to obtain by standard chemical methods. The results obtained herein showed that the catalytic mechanism of UstD might follow two paths to occur in three phases: (1) decarboxylation of substrate l-aspartate, (2) C-C bond formation by addition of aldehyde, and (3) the regeneration of catalytic sites. Although Path A and Path B showed a negligible difference in the energy barrier of the rate-determining step, Path A involves three additional steps in the overall pathway compared with Path B, which makes the reaction proceed more readily through Path B. According to the QM/MM energy profile of Path B, the rate-limiting step of the catalytic process is the decarboxylation of the side chain of l-aspartate, which has a calculated energy barrier of 19.19 kcal/mol. Two crucial residues, H263 and Y257, were identified to interact with the substrate aspartic acid. The knowledge about the transition states, intermediates, key residues, and protein conformational changes along the reaction path will be valuable for engineering UstD to improve the synthesis of γ-hydroxy-α-amino acids that serve as building blocks of various high-value chemicals such as antidiabetics and nutritional supplements.
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Affiliation(s)
- Binbin Chen
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China
| | - Jiahui Huang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Yingchun Liu
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China
| | - Qi Wang
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China
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8
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Cheng L, Bo Z, Krohn-Hansen B, Yang Y. Directed Evolution and Unusual Protonation Mechanism of Pyridoxal Radical C-C Coupling Enzymes for the Enantiodivergent Photobiocatalytic Synthesis of Noncanonical Amino Acids. J Am Chem Soc 2025; 147:4602-4612. [PMID: 39849356 DOI: 10.1021/jacs.4c16716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2025]
Abstract
Visible light-driven pyridoxal radical biocatalysis has emerged as a new strategy for the stereoselective synthesis of valuable noncanonical amino acids in a protecting-group-free fashion. In our previously developed dehydroxylative C-C coupling using engineered PLP-dependent tryptophan synthases, an enzyme-controlled unusual α-stereochemistry reversal and pH-controlled enantiopreference were observed. Herein, through high-throughput photobiocatalysis, we evolved a set of stereochemically complementary PLP radical enzymes, allowing the synthesis of both l- and d-amino acids with enhanced enantiocontrol across a broad pH window. These newly engineered l- and d-amino acid synthases permitted the use of a broad range of organoboron substrates, including boronates, trifluoroborates, and boronic acids, with excellent efficiency. Mechanistic studies unveiled unexpected PLP racemase activity with our earlier PLP enzyme variants. This promiscuous racemase activity was abolished in our evolved amino acid synthases, shedding light on the origin of enhanced enantiocontrol. Further mechanistic investigations suggest a switch of proton donor to account for the stereoinvertive formation of d-amino acids, highlighting an unusual stereoinversion mechanism that is rare in conventional two-electron PLP enzymology.
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Affiliation(s)
- Lei Cheng
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Zhiyu Bo
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Benjamin Krohn-Hansen
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Yang Yang
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
- Biomolecular Science and Engineering Program, University of California Santa Barbara, Santa Barbara, California 93106, United States
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9
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Okal EF, Romero PA, Heinzelman P. Droplet microfluidic screening to engineer angiotensin-converting enzyme 2 (ACE2) catalytic activity. J Biol Eng 2025; 19:12. [PMID: 39901286 PMCID: PMC11792573 DOI: 10.1186/s13036-025-00482-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Accepted: 01/23/2025] [Indexed: 02/05/2025] Open
Abstract
BACKGROUND Angiotensin-Converting Enzyme 2 (ACE2) is a crucial peptidase in human peptide hormone signaling, catalyzing the conversion of Angiotensin-II to Angiotensin-(1-7), which activates the Mas receptor and elicits vasodilation, increased blood flow, reduced inflammation, and decreased pathological tissue remodeling. This study leverages protein engineering to enhance ACE2's therapeutic potential for treating conditions such as respiratory viral infections, acute respiratory distress syndrome, and diabetes. Surrogate substrates used in traditional high-throughput screening methods for peptidases often fail to accurately mimic native substrates, leading to less effective enzyme variants. Here, we developed an ultra-high-throughput droplet microfluidic platform to screen peptidases on native peptide substrates. Our assay detects substrate cleavage via free amino acid release, providing a precise measurement of biologically relevant peptidase activity. RESULTS Using this new platform, we screened a large library of ACE2 variants, identifying position 187 as a hotspot for enhancing enzyme activity. Further focused screening revealed the K187T variant, which exhibited a fourfold increase in catalytic efficiency (kcat/KM) over wild-type ACE2. CONCLUSIONS This work demonstrates the potential of droplet microfluidics for therapeutic peptidase engineering, offering a robust and accessible method to optimize enzyme properties for clinical applications.
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Affiliation(s)
- Evelyn F Okal
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Philip A Romero
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
| | - Pete Heinzelman
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
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10
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Xu M, Zhang S, Liu J, Xin Y, Jiang Y, Zhang Y, Wang G, Zhang H. High selectivity electrocatalytic reductive amination of α-keto acids to alanine over cuprous oxide nanowires. Chem Commun (Camb) 2024; 61:306-309. [PMID: 39629723 DOI: 10.1039/d4cc05399k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2024]
Abstract
Herein, cuprous oxide (Cu2O) nanowires are synthesized by a simple process, realizing the high selectivity electrocatalytic reductive amination of biomass-derived pyruvate to alanine (organic product selectivity: ∼100%). Importantly, a total of 8 different amino acids can be efficiently synthesized using Cu2O nanowires, confirming the universality of Cu2O nanowires.
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Affiliation(s)
- Min Xu
- Key Laboratory of Materials Physics, Centre for Environmental and Energy Nanomaterials, Anhui Key Laboratory of Nanomaterials and Nanotechnology, CAS Center for Excellence in Nanoscience, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031, P. R. China.
- University of Science and Technology of China, Hefei 230026, P. R. China
| | - Shengbo Zhang
- Key Laboratory of Materials Physics, Centre for Environmental and Energy Nanomaterials, Anhui Key Laboratory of Nanomaterials and Nanotechnology, CAS Center for Excellence in Nanoscience, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031, P. R. China.
- University of Science and Technology of China, Hefei 230026, P. R. China
| | - Jiafang Liu
- Key Laboratory of Materials Physics, Centre for Environmental and Energy Nanomaterials, Anhui Key Laboratory of Nanomaterials and Nanotechnology, CAS Center for Excellence in Nanoscience, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031, P. R. China.
- University of Science and Technology of China, Hefei 230026, P. R. China
| | - Yaqian Xin
- Key Laboratory of Materials Physics, Centre for Environmental and Energy Nanomaterials, Anhui Key Laboratory of Nanomaterials and Nanotechnology, CAS Center for Excellence in Nanoscience, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031, P. R. China.
- University of Science and Technology of China, Hefei 230026, P. R. China
| | - Yong Jiang
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Yunxia Zhang
- Key Laboratory of Materials Physics, Centre for Environmental and Energy Nanomaterials, Anhui Key Laboratory of Nanomaterials and Nanotechnology, CAS Center for Excellence in Nanoscience, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031, P. R. China.
- University of Science and Technology of China, Hefei 230026, P. R. China
| | - Guozhong Wang
- Key Laboratory of Materials Physics, Centre for Environmental and Energy Nanomaterials, Anhui Key Laboratory of Nanomaterials and Nanotechnology, CAS Center for Excellence in Nanoscience, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031, P. R. China.
- University of Science and Technology of China, Hefei 230026, P. R. China
| | - Haimin Zhang
- Key Laboratory of Materials Physics, Centre for Environmental and Energy Nanomaterials, Anhui Key Laboratory of Nanomaterials and Nanotechnology, CAS Center for Excellence in Nanoscience, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031, P. R. China.
- University of Science and Technology of China, Hefei 230026, P. R. China
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11
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Zhao YX, Li HP, Cheng LH, Li CX, Pan J, Xu JH. A High-Throughput Visual Screen for the Directed Evolution of Cβ-stereoselectivity of L-threonine Aldolase. Chembiochem 2024; 25:e202400637. [PMID: 39292512 DOI: 10.1002/cbic.202400637] [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: 07/31/2024] [Revised: 09/18/2024] [Accepted: 09/18/2024] [Indexed: 09/20/2024]
Abstract
L-Threonine aldolase (L-TA) is a pyridoxal phosphate-dependent enzyme that catalyzes the reversible condensation of glycine and aldehydes to form β-hydroxy-α-amino acids. The combination of directed evolution and efficient high-throughput screening methods is an effective strategy for enhancing the enzyme's catalytic performance. However, few feasible high-throughput methods exist for engineering the Cβ-stereoselectivity of L-TAs. Here, we present a novel method of screening for variants with improved Cβ-stereoselectivity; this method couples an L-threo-phenylserine dehydrogenase, which catalyzes the specific oxidation of L-threo-4-methylsulfonylphenylserine (L-threo-MTPS), with the concurrent synthesis of NADPH, which is easily detectable via 340-nm UV absorption. This enables the visual detection of L-threo-MTPS produced by L-TA through the measurement of generated NADPH. Using this method, we discover an L-TA variant with significantly higher diastereoselectivity, increasing from 0.98 % de (for the wild-type) to 71.9 % de.
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Affiliation(s)
- You-Xue Zhao
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Hai-Peng Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Li-Hang Cheng
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Chun-Xiu Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Jiang Pan
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
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12
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Mashweu AR, Azov VA. Nanotechnology in Drug Delivery: Anatomy and Molecular Insight into the Self-Assembly of Peptide-Based Hydrogels. Molecules 2024; 29:5654. [PMID: 39683812 PMCID: PMC11643151 DOI: 10.3390/molecules29235654] [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: 10/24/2024] [Revised: 11/21/2024] [Accepted: 11/24/2024] [Indexed: 12/18/2024] Open
Abstract
The bioavailability, release, and stability of pharmaceuticals under physicochemical conditions is the major cause of drug candidates failing during their clinical trials. Therefore, extensive efforts have been invested in the development of novel drug delivery systems that are able to transport drugs to a desired site and improve bioavailability. Hydrogels, and peptide hydrogels in particular, have been extensively investigated due to their excellent biocompatibility and biodegradability properties. However, peptide hydrogels often have weak mechanical strength, which limits their therapeutic efficacy. Therefore, a number of methods for improving their rheological properties have been established. This review will cover the broad area of drug delivery, focusing on the recent developments in this research field. We will discuss the variety of different types of nanocarrier drug delivery systems and then, more specifically, the significance and perspectives of peptide-based hydrogels. In particular, the interplay of intermolecular forces that govern the self-assembly of peptide hydrogels, progress made in understanding the distinct morphologies of hydrogels, and applications of non-canonical amino acids in hydrogel design will be discussed in more detail.
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Affiliation(s)
- Adelaide R. Mashweu
- Department of Chemistry, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - Vladimir A. Azov
- Department of Chemistry, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
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13
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Cai S, Zhao Z, Yang G, Huang H. Dynamic amine sorting enables multiselective construction of unsymmetrical chiral diamines. Nat Chem 2024:10.1038/s41557-024-01673-z. [PMID: 39558140 DOI: 10.1038/s41557-024-01673-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 10/15/2024] [Indexed: 11/20/2024]
Abstract
Precisely differentiating chemicals featuring minor discrepancies is the prerequisite for achieving high selectivities in both chemical synthesis and biological activities. However, efficient strategies to differentiate and sort such congeneric compounds are lacking, posing daunting challenges for synthetic endeavours aimed at their orderly incorporation. Here we report a dynamic amine-sorting strategy that incorporates the chemoselective formation of the aminomethyl cyclopalladated complex to achieve the efficient differentiation of amine congeners. A series of amines sharing similar three-dimensional structures and properties, as well as possessing notoriously strong binding ability to metals, can be efficiently differentiated, enabling the highly chemo-, regio- and enantioselective multicomponent aminomethylamination of dienes to construct a variety of unsymmetrical chiral diamines. This dynamic amine-sorting strategy tackles the long-standing challenge of precise differentiation and orderly incorporation of aliphatic amines with subtle differences. From a broader perspective, the success demonstrates that meticulously designed metal complexes can provide flexible and general solutions for controlling delicate selectivities in sophisticated synthesis.
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Affiliation(s)
- Shoule Cai
- Key Laboratory of Precision and Intelligent Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, P. R. China
| | - Zeyu Zhao
- Key Laboratory of Precision and Intelligent Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, P. R. China
| | - Guoqing Yang
- Key Laboratory of Precision and Intelligent Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, P. R. China
| | - Hanmin Huang
- Key Laboratory of Precision and Intelligent Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, P. R. China.
- Key Laboratory of Green and Precise Synthetic Chemistry and Applications, Ministry of Education, Huaibei Normal University, Huaibei, P. R. China.
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14
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Costello A, Peterson AA, Chen PH, Bagirzadeh R, Lanster DL, Badran AH. Genetic Code Expansion History and Modern Innovations. Chem Rev 2024; 124:11962-12005. [PMID: 39466033 DOI: 10.1021/acs.chemrev.4c00275] [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: 10/29/2024]
Abstract
The genetic code is the foundation for all life. With few exceptions, the translation of nucleic acid messages into proteins follows conserved rules, which are defined by codons that specify each of the 20 proteinogenic amino acids. For decades, leading research groups have developed a catalogue of innovative approaches to extend nature's amino acid repertoire to include one or more noncanonical building blocks in a single protein. In this review, we summarize advances in the history of in vitro and in vivo genetic code expansion, and highlight recent innovations that increase the scope of biochemically accessible monomers and codons. We further summarize state-of-the-art knowledge in engineered cellular translation, as well as alterations to regulatory mechanisms that improve overall genetic code expansion. Finally, we distill existing limitations of these technologies into must-have improvements for the next generation of technologies, and speculate on future strategies that may be capable of overcoming current gaps in knowledge.
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Affiliation(s)
- Alan Costello
- Department of Chemistry The Scripps Research Institute; La Jolla, California 92037, United States
- Department of Integrative Structural and Computational Biology The Scripps Research Institute; La Jolla, California 92037, United States
| | - Alexander A Peterson
- Department of Chemistry The Scripps Research Institute; La Jolla, California 92037, United States
- Department of Integrative Structural and Computational Biology The Scripps Research Institute; La Jolla, California 92037, United States
| | - Pei-Hsin Chen
- Department of Chemistry The Scripps Research Institute; La Jolla, California 92037, United States
- Department of Integrative Structural and Computational Biology The Scripps Research Institute; La Jolla, California 92037, United States
- Doctoral Program in Chemical and Biological Sciences The Scripps Research Institute; La Jolla, California 92037, United States
| | - Rustam Bagirzadeh
- Department of Chemistry The Scripps Research Institute; La Jolla, California 92037, United States
- Department of Integrative Structural and Computational Biology The Scripps Research Institute; La Jolla, California 92037, United States
| | - David L Lanster
- Department of Chemistry The Scripps Research Institute; La Jolla, California 92037, United States
- Department of Integrative Structural and Computational Biology The Scripps Research Institute; La Jolla, California 92037, United States
- Doctoral Program in Chemical and Biological Sciences The Scripps Research Institute; La Jolla, California 92037, United States
| | - Ahmed H Badran
- Department of Chemistry The Scripps Research Institute; La Jolla, California 92037, United States
- Department of Integrative Structural and Computational Biology The Scripps Research Institute; La Jolla, California 92037, United States
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15
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Lino BR, Williams SJ, Castor ME, Van Deventer JA. Reaching New Heights in Genetic Code Manipulation with High Throughput Screening. Chem Rev 2024; 124:12145-12175. [PMID: 39418482 PMCID: PMC11879460 DOI: 10.1021/acs.chemrev.4c00329] [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] [Indexed: 10/19/2024]
Abstract
The chemical and physical properties of proteins are limited by the 20 canonical amino acids. Genetic code manipulation allows for the incorporation of noncanonical amino acids (ncAAs) that enhance or alter protein functionality. This review explores advances in the three main strategies for introducing ncAAs into biosynthesized proteins, focusing on the role of high throughput screening in these advancements. The first section discusses engineering aminoacyl-tRNA synthetases (aaRSs) and tRNAs, emphasizing how novel selection methods improve characteristics including ncAA incorporation efficiency and selectivity. The second section examines high-throughput techniques for improving protein translation machinery, enabling accommodation of alternative genetic codes. This includes opportunities to enhance ncAA incorporation through engineering cellular components unrelated to translation. The final section highlights various discovery platforms for high-throughput screening of ncAA-containing proteins, showcasing innovative binding ligands and enzymes that are challenging to create with only canonical amino acids. These advances have led to promising drug leads and biocatalysts. Overall, the ability to discover unexpected functionalities through high-throughput methods significantly influences ncAA incorporation and its applications. Future innovations in experimental techniques, along with advancements in computational protein design and machine learning, are poised to further elevate this field.
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Affiliation(s)
- Briana R. Lino
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Sean J. Williams
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Michelle E. Castor
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
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16
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Renno G, Chen D, Zhang QX, Gomila RM, Frontera A, Sakai N, Ward TR, Matile S. Pnictogen-Bonding Enzymes. Angew Chem Int Ed Engl 2024; 63:e202411347. [PMID: 38967094 DOI: 10.1002/anie.202411347] [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: 06/17/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/06/2024]
Abstract
The objective of this study was to create artificial enzymes that capitalize on pnictogen bonding, a σ-hole interaction that is essentially absent in biocatalysis. For this purpose, stibine catalysts were equipped with a biotin derivative and combined with streptavidin mutants to identify an efficient transfer hydrogenation catalyst for the reduction of a fluorogenic quinoline substrate. Increased catalytic activity from wild-type streptavidin to the best mutants coincides with the depth of the σ hole on the Sb(V) center, and the emergence of saturation kinetic behavior. Michaelis-Menten analysis reveals transition-state recognition in the low micromolar range, more than three orders of magnitude stronger than the millimolar substrate recognition. Carboxylates preferred by the best mutants contribute to transition-state recognition by hydrogen-bonded ion pairing and anion-π interactions with the emerging pyridinium product. The emergence of challenging stereoselectivity in aqueous systems further emphasizes compatibility of pnictogen bonding with higher order systems catalysis.
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Affiliation(s)
- Giacomo Renno
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, BPR 1095, Basel, Switzerland
| | - Dongping Chen
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, BPR 1095, Basel, Switzerland
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Qing-Xia Zhang
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, BPR 1095, Basel, Switzerland
| | - Rosa M Gomila
- Departament de Química, Universitat de les Illes Balears, 07122, Palma de Mallorca, Spain
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, 07122, Palma de Mallorca, Spain
| | - Naomi Sakai
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, BPR 1095, Basel, Switzerland
| | - Thomas R Ward
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, BPR 1095, Basel, Switzerland
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
- National Centre of Competence in Research (NCCR) Molecular Systems Engineering, BPR 1095, Basel, Switzerland
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17
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Brouwer B, Della-Felice F, Illies JH, Iglesias-Moncayo E, Roelfes G, Drienovská I. Noncanonical Amino Acids: Bringing New-to-Nature Functionalities to Biocatalysis. Chem Rev 2024; 124:10877-10923. [PMID: 39329413 PMCID: PMC11467907 DOI: 10.1021/acs.chemrev.4c00136] [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: 02/14/2024] [Revised: 08/21/2024] [Accepted: 08/26/2024] [Indexed: 09/28/2024]
Abstract
Biocatalysis has become an important component of modern organic chemistry, presenting an efficient and environmentally friendly approach to synthetic transformations. Advances in molecular biology, computational modeling, and protein engineering have unlocked the full potential of enzymes in various industrial applications. However, the inherent limitations of the natural building blocks have sparked a revolutionary shift. In vivo genetic incorporation of noncanonical amino acids exceeds the conventional 20 amino acids, opening new avenues for innovation. This review provides a comprehensive overview of applications of noncanonical amino acids in biocatalysis. We aim to examine the field from multiple perspectives, ranging from their impact on enzymatic reactions to the creation of novel active sites, and subsequent catalysis of new-to-nature reactions. Finally, we discuss the challenges, limitations, and promising opportunities within this dynamic research domain.
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Affiliation(s)
- Bart Brouwer
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Franco Della-Felice
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Jan Hendrik Illies
- Department
of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
| | - Emilia Iglesias-Moncayo
- Department
of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
| | - Gerard Roelfes
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Ivana Drienovská
- Department
of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
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18
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Gu X, Zhang YA, Zhang S, Wang L, Ye X, Occhialini G, Barbour J, Pentelute BL, Wendlandt AE. Synthesis of non-canonical amino acids through dehydrogenative tailoring. Nature 2024; 634:352-358. [PMID: 39208846 PMCID: PMC11904927 DOI: 10.1038/s41586-024-07988-8] [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: 11/22/2023] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Amino acids are essential building blocks in biology and chemistry. Whereas nature relies on a small number of amino acid structures, chemists desire access to a vast range of structurally diverse analogues1-3. The selective modification of amino acid side-chain residues represents an efficient strategy to access non-canonical derivatives of value in chemistry and biology. While semisynthetic methods leveraging the functional groups found in polar and aromatic amino acids have been extensively explored, highly selective and general approaches to transform unactivated C-H bonds in aliphatic amino acids remain less developed4,5. Here we disclose a stepwise dehydrogenative method to convert aliphatic amino acids into structurally diverse analogues. The key to the success of this approach lies in the development of a selective catalytic acceptorless dehydrogenation method driven by photochemical irradiation, which provides access to terminal alkene intermediates for downstream functionalization. Overall, this strategy enables the rapid synthesis of new amino acid building blocks and suggests possibilities for the late-stage modification of more complex oligopeptides.
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Affiliation(s)
- Xin Gu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yu-An Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shuo Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Leon Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xiyun Ye
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gino Occhialini
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonah Barbour
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alison E Wendlandt
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
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19
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Sun C, Lu G, Chen B, Li G, Wu Y, Brack Y, Yi D, Ao YF, Wu S, Wei R, Sun Y, Zhai G, Bornscheuer UT. Direct asymmetric synthesis of β-branched aromatic α-amino acids using engineered phenylalanine ammonia lyases. Nat Commun 2024; 15:8264. [PMID: 39327443 PMCID: PMC11427684 DOI: 10.1038/s41467-024-52613-x] [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: 03/14/2024] [Accepted: 09/16/2024] [Indexed: 09/28/2024] Open
Abstract
β-Branched aromatic α-amino acids are valuable building blocks in natural products and pharmaceutically active compounds. However, their chemical or enzymatic synthesis is challenging due to the presence of two stereocenters. We design phenylalanine ammonia lyases (PAL) variants for the direct asymmetric synthesis of β-branched aromatic α-amino acids. Based on extensive computational analyses, we unravel the enigma behind PAL's inability to accept β-methyl cinnamic acid (β-MeCA) as substrate and achieve the synthesis of the corresponding amino acids of β-MeCA and analogs using a double (PcPAL-L256V-I460V) and a triple mutant (PcPAL-F137V-L256V-I460V). The reactions are scaled-up using an optimized E. coli based whole-cell biotransformation system to produce ten β-branched phenylalanine analogs with high diastereoselectivity (dr > 20:1) and enantioselectivity (ee > 99.5%) in yields ranging from 41-71%. Moreover, we decipher the mechanism of PcPAL-L256V-I460V for the acceptance of β-MeCA and converting it with excellent stereoselectivity by computational simulations. Thus, this study offers an efficient method for synthesizing β-branched aromatic α-amino acids.
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Affiliation(s)
- Chenghai Sun
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany.
| | - Gen Lu
- School of Pharmacy, Tongji Medical College of Huazhong University of Science and Technology, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Wuhan, China
| | - Baoming Chen
- School of Pharmacy, Tongji Medical College of Huazhong University of Science and Technology, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Wuhan, China
| | - Guangjun Li
- School of Pharmacy, Tongji Medical College of Huazhong University of Science and Technology, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Wuhan, China
| | - Ya Wu
- School of Pharmacy, Tongji Medical College of Huazhong University of Science and Technology, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Wuhan, China
| | - Yannik Brack
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Dong Yi
- Research Center for Systems Biosynthesis, China State Institute of Pharmaceutical Industry, National Key Laboratory of Lead Druggability Research, Shanghai, China
| | - Yu-Fei Ao
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Shuke Wu
- College of Life Science and Technology, Huazhong Agriculture University, Wuhan, China
| | - Ren Wei
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Yuhui Sun
- School of Pharmacy, Tongji Medical College of Huazhong University of Science and Technology, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Wuhan, China
| | - Guifa Zhai
- School of Pharmacy, Tongji Medical College of Huazhong University of Science and Technology, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Wuhan, China.
| | - Uwe T Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany.
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20
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Yu K, Ward TR. C-H functionalization reactions catalyzed by artificial metalloenzymes. J Inorg Biochem 2024; 258:112621. [PMID: 38852295 DOI: 10.1016/j.jinorgbio.2024.112621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/23/2024] [Accepted: 05/25/2024] [Indexed: 06/11/2024]
Abstract
CH functionalization, a promising frontier in modern organic chemistry, facilitates the direct conversion of inert CH bonds into many valuable functional groups. Despite its merits, traditional homogeneous catalysis, often faces challenges in efficiency, selectivity, and sustainability towards this transformation. In this context, artificial metalloenzymes (ArMs), resulting from the incorporation of a catalytically-competent metal cofactor within an evolvable protein scaffold, bridges the gap between the efficiency of enzymatic transformations and the versatility of transition metal catalysis. Accordingly, ArMs have emerged as attractive tools for various challenging catalytic transformations. Additionally, the coming of age of directed evolution has unlocked unprecedented avenues for optimizing enzymatic catalysis. Taking advantage of their genetically-encoded protein scaffold, ArMs have been evolved to catalyze various CH functionalization reactions. This review delves into the recent developments of ArM-catalyzed CH functionalization reactions, highlighting the benefits of engineering the second coordination sphere around a metal cofactor within a host protein.
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Affiliation(s)
- Kun Yu
- Department of Chemistry, University of Basel, Mattenstrasse 22, Basel CH-4058, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, Mattenstrasse 22, Basel CH-4058, Switzerland.
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21
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Wang TC, Zhang Z, Rao G, Li J, Shirah J, Britt RD, Zhu Q, Yang Y. Threonine Aldolase-Catalyzed Enantioselective α-Alkylation of Amino Acids through Unconventional Photoinduced Radical Initiation. J Am Chem Soc 2024; 146:22476-22484. [PMID: 38961805 PMCID: PMC11376206 DOI: 10.1021/jacs.4c05949] [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] [Indexed: 07/05/2024]
Abstract
Visible light-driven pyridoxal radical biocatalysis has emerged as a promising strategy for the stereoselective synthesis of valuable noncanonical amino acids (ncAAs). Previously, the use of well-tailored photoredox catalysts represented the key to enable efficient pyridoxal phosphate (PLP) enzyme-catalyzed radical reactions. Here, we report a PLP-dependent threonine aldolase-catalyzed asymmetric α-C-H alkylation of abundant amino acids using Katritzky pyridinium salts as alkylating agents. The use of engineered threonine aldolases allowed for this redox-neutral radical alkylation to proceed efficiently, giving rise to challenging α-trisubstituted and -tetrasubstituted ncAA products in a protecting-group-free fashion with excellent enantiocontrol. Mechanistically, this enantioselective α-alkylation capitalizes on the unique reactivity of the persistent enzymatic quinonoid intermediate derived from the PLP cofactor and the amino acid substrate to allow for novel radical C-C coupling. Surprisingly, this photobiocatalytic process does not require the use of well-established photoredox catalysts and operates through an unconventional photoinduced radical generation involving a PLP-derived aldimine. The ability to develop photobiocatalytic reactions without relying on classic photocatalysts or photoenzymes opens up new avenues for advancing stereoselective intermolecular radical reactions that are not known in either organic chemistry or enzymology.
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Affiliation(s)
- Tian-Ci Wang
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Zheng Zhang
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Guodong Rao
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Jiedong Li
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Josephine Shirah
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - R David Britt
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Qilei Zhu
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Yang Yang
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
- Biomolecular Science and Engineering Program, University of California Santa Barbara, Santa Barbara, California 93106, United States
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22
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Liu XY, Mykhailenko O, Faraone A, Waser J. Hypervalent Iodine Amino Acid Building Blocks for Bioorthogonal Peptide Macrocyclization. Angew Chem Int Ed Engl 2024; 63:e202404747. [PMID: 38807563 DOI: 10.1002/anie.202404747] [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: 03/08/2024] [Revised: 05/02/2024] [Accepted: 05/27/2024] [Indexed: 05/30/2024]
Abstract
Ethynylbenziodoxol(on)es (EB(X)xs) reagents have emerged as useful reagents for peptide/protein modification due to their versatile reactivity and high selectivity. Herein, we report the successful introduction of ethynylbenziodoxoles (EBxs) on different amino acid building blocks (Lys/Orn/Dap), and show their compatibility with both solid phase peptide synthesis (SPPS) and solution phase peptide synthesis (SPS). The selective incorporation of the EBx core into peptide sequences enable efficient macrocyclizations under mild conditions for the synthesis of topologically unique cyclic and bicyclic peptides.
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Affiliation(s)
- Xing-Yu Liu
- Laboratory of Catalysis and Organic Synthesis (LCSO), Ecole Polytechnique Fédérale de Lausanne, EPFL, 1015, Lausanne, Switzerland
| | - Olha Mykhailenko
- Laboratory of Catalysis and Organic Synthesis (LCSO), Ecole Polytechnique Fédérale de Lausanne, EPFL, 1015, Lausanne, Switzerland
| | - Adriana Faraone
- Laboratory of Catalysis and Organic Synthesis (LCSO), Ecole Polytechnique Fédérale de Lausanne, EPFL, 1015, Lausanne, Switzerland
| | - Jerome Waser
- Laboratory of Catalysis and Organic Synthesis (LCSO), Ecole Polytechnique Fédérale de Lausanne, EPFL, 1015, Lausanne, Switzerland
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23
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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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24
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Buslov I, Desmons S, Duhoo Y, Hu X. Engineered Phenylalanine Ammonia-Lyases for the Enantioselective Synthesis of Aspartic Acid Derivatives. Angew Chem Int Ed Engl 2024; 63:e202406008. [PMID: 38713131 DOI: 10.1002/anie.202406008] [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: 03/28/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/08/2024]
Abstract
Biocatalytic hydroamination of alkenes is an efficient and selective method to synthesize natural and unnatural amino acids. Phenylalanine ammonia-lyases (PALs) have been previously engineered to access a range of substituted phenylalanines and heteroarylalanines, but their substrate scope remains limited, typically including only arylacrylic acids. Moreover, the enantioselectivity in the hydroamination of electron-deficient substrates is often poor. Here, we report the structure-based engineering of PAL from Planctomyces brasiliensis (PbPAL), enabling preparative-scale enantioselective hydroaminations of previously inaccessible yet synthetically useful substrates, such as amide- and ester-containing fumaric acid derivatives. Through the elucidation of cryo-electron microscopy (cryo-EM) PbPAL structure and screening of the structure-based mutagenesis library, we identified the key active site residue L205 as pivotal for dramatically enhancing the enantioselectivity of hydroamination reactions involving electron-deficient substrates. Our engineered PALs demonstrated exclusive α-regioselectivity, high enantioselectivity, and broad substrate scope. The potential utility of the developed biocatalysts was further demonstrated by a preparative-scale hydroamination yielding tert-butyl protected l-aspartic acid, widely used as intermediate in peptide solid-phase synthesis.
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Affiliation(s)
- Ivan Buslov
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne ISIC-LSCI, BCH 3305, 1015, Lausanne, Switzerland
| | - Sarah Desmons
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne ISIC-LSCI, BCH 3305, 1015, Lausanne, Switzerland
| | - Yoan Duhoo
- Protein Production and Structure Core Facility (PTPSP), School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Xile Hu
- Laboratory of Inorganic Synthesis and Catalysis, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne ISIC-LSCI, BCH 3305, 1015, Lausanne, Switzerland
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25
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Jo WS, Curtis BJ, Rehan M, Adrover-Castellano ML, Sherman DH, Healy AR. N-to- S Acyl Transfer as an Enabling Strategy in Asymmetric and Chemoenzymatic Synthesis. JACS AU 2024; 4:2058-2066. [PMID: 38818054 PMCID: PMC11134368 DOI: 10.1021/jacsau.4c00257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024]
Abstract
The observation of thioester-mediated acyl transfer processes in nature has inspired the development of novel protein synthesis and functionalization methodologies. The chemoselective transfer of an acyl group from S-to-N is the basis of several powerful ligation strategies. In this work, we sought to apply the reverse process, the transfer of an acyl group from N-to-S, as a method to convert stable chiral amides into more reactive thioesters. To this end, we developed a novel cysteine-derived oxazolidinone that serves as both a chiral imide auxiliary and an acyl transfer agent. This auxiliary combines the desirable features of rigid chiral imides as templates for asymmetric transformations with the synthetic applicability of thioesters. We demonstrate that the auxiliary can be applied in a range of highly selective asymmetric transformations. Subsequent intramolecular N-to-S acyl transfer of the chiral product and in situ trapping of the resulting thioester provides access to diverse carboxylic acid derivatives under mild conditions. The oxazolidinone thioester products can also be isolated and used in Pd-mediated transformations to furnish highly valuable chiral scaffolds, such as noncanonical amino acids, cyclic ketones, tetrahydropyrones, and dihydroquinolinones. Finally, we demonstrate that the oxazolidinone thioesters can also serve as a surrogate for SNAC-thioesters, enabling their seamless use as non-native substrates in biocatalytic transformations.
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Affiliation(s)
- Woonkee S Jo
- Chemistry Program, New York University Abu Dhabi (NYUAD), Saadiyat Island, Abu Dhabi 129188, United Arab Emirates (UAE)
| | - Brian J Curtis
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Mohammad Rehan
- Chemistry Program, New York University Abu Dhabi (NYUAD), Saadiyat Island, Abu Dhabi 129188, United Arab Emirates (UAE)
| | | | - David H Sherman
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA
- Departments of Medicinal Chemistry, Chemistry, and Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109USA
| | - Alan R Healy
- Chemistry Program, New York University Abu Dhabi (NYUAD), Saadiyat Island, Abu Dhabi 129188, United Arab Emirates (UAE)
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26
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Ouyang Y, Page CG, Bilodeau C, Hyster TK. Synergistic Photoenzymatic Catalysis Enables Synthesis of a-Tertiary Amino Acids Using Threonine Aldolases. J Am Chem Soc 2024; 146:13754-13759. [PMID: 38739748 PMCID: PMC11694721 DOI: 10.1021/jacs.4c04661] [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] [Indexed: 05/16/2024]
Abstract
a-Tertiary amino acids are essential components of drugs and agrochemicals, yet traditional syntheses are step-intensive and provide access to a limited range of structures with varying levels of enantioselectivity. Here, we report the α-alkylation of unprotected alanine and glycine by pyridinium salts using pyridoxal (PLP)-dependent threonine aldolases with a Rose Bengal photoredox catalyst. The strategy efficiently prepares various a-tertiary amino acids in a single chemical step as a single enantiomer. UV-vis spectroscopy studies reveal a ternary interaction between the pyridinium salt, protein, and photocatalyst, which we hypothesize is responsible for localizing radical formation to the active site. This method highlights the opportunity for combining photoredox catalysts with enzymes to reveal new catalytic functions for known enzymes.
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Affiliation(s)
- Yao Ouyang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Claire G. Page
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Catherine Bilodeau
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Todd K. Hyster
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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27
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Wang TC, Mai BK, Zhang Z, Bo Z, Li J, Liu P, Yang Y. Stereoselective amino acid synthesis by photobiocatalytic oxidative coupling. Nature 2024; 629:98-104. [PMID: 38693411 PMCID: PMC11299865 DOI: 10.1038/s41586-024-07284-5] [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: 12/08/2023] [Accepted: 03/07/2024] [Indexed: 05/03/2024]
Abstract
Photobiocatalysis-where light is used to expand the reactivity of an enzyme-has recently emerged as a powerful strategy to develop chemistries that are new to nature. These systems have shown potential in asymmetric radical reactions that have long eluded small-molecule catalysts1. So far, unnatural photobiocatalytic reactions are limited to overall reductive and redox-neutral processes2-9. Here we report photobiocatalytic asymmetric sp3-sp3 oxidative cross-coupling between organoboron reagents and amino acids. This reaction requires the cooperative use of engineered pyridoxal biocatalysts, photoredox catalysts and an oxidizing agent. We repurpose a family of pyridoxal-5'-phosphate-dependent enzymes, threonine aldolases10-12, for the α-C-H functionalization of glycine and α-branched amino acid substrates by a radical mechanism, giving rise to a range of α-tri- and tetrasubstituted non-canonical amino acids 13-15 possessing up to two contiguous stereocentres. Directed evolution of pyridoxal radical enzymes allowed primary and secondary radical precursors, including benzyl, allyl and alkylboron reagents, to be coupled in an enantio- and diastereocontrolled fashion. Cooperative photoredox-pyridoxal biocatalysis provides a platform for sp3-sp3 oxidative coupling16, permitting the stereoselective, intermolecular free-radical transformations that are unknown to chemistry or biology.
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Affiliation(s)
- Tian-Ci Wang
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zheng Zhang
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Zhiyu Bo
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Jiedong Li
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Yang Yang
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA.
- Biomolecular Science and Engineering (BMSE) Program, University of California Santa Barbara, Santa Barbara, CA, USA.
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28
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Pecchini P, Fochi M, Bartoccini F, Piersanti G, Bernardi L. Enantioselective organocatalytic strategies to access noncanonical α-amino acids. Chem Sci 2024; 15:5832-5868. [PMID: 38665517 PMCID: PMC11041364 DOI: 10.1039/d4sc01081g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
Organocatalytic asymmetric synthesis has evolved over the years and continues to attract the interest of many researchers worldwide. Enantiopure noncanonical amino acids (ncAAs) are valuable building blocks in organic synthesis, medicinal chemistry, and chemical biology. They are employed in the elaboration of peptides and proteins with enhanced activities and/or improved properties compared to their natural counterparts, as chiral catalysts, in chiral ligand design, and as chiral building blocks for asymmetric syntheses of complex molecules, including natural products. The linkage of ncAA synthesis and enantioselective organocatalysis, the subject of this perspective, tries to imitate the natural biosynthetic process. Herein, we present contemporary and earlier developments in the field of organocatalytic activation of simple feedstock materials, providing potential ncAAs with diverse side chains, unique three-dimensional structures, and a high degree of functionality. These asymmetric organocatalytic strategies, useful for forging a wide range of C-C, C-H, and C-N bonds and/or combinations thereof, vary from classical name reactions, such as Ugi, Strecker, and Mannich reactions, to the most advanced concepts such as deracemisation, transamination, and carbene N-H insertion. Concurrently, we present some interesting mechanistic studies/models, providing information on the chirality transfer process. Finally, this perspective highlights, through the diversity of the amino acids (AAs) not selected by nature for protein incorporation, the most generic modes of activation, induction, and reactivity commonly used, such as chiral enamine, hydrogen bonding, Brønsted acids/bases, and phase-transfer organocatalysis, reflecting their increasingly important role in organic and applied chemistry.
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Affiliation(s)
- Pietro Pecchini
- Department of Industrial Chemistry "Toso Montanari", Center for Chemical Catalysis C3 & INSTM RU Bologna V. Gobetti 85 40129 Bologna Italy
| | - Mariafrancesca Fochi
- Department of Industrial Chemistry "Toso Montanari", Center for Chemical Catalysis C3 & INSTM RU Bologna V. Gobetti 85 40129 Bologna Italy
| | - Francesca Bartoccini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo Piazza Rinascimento 6 61029 Urbino PU Italy
| | - Giovanni Piersanti
- Department of Biomolecular Sciences, University of Urbino Carlo Bo Piazza Rinascimento 6 61029 Urbino PU Italy
| | - Luca Bernardi
- Department of Industrial Chemistry "Toso Montanari", Center for Chemical Catalysis C3 & INSTM RU Bologna V. Gobetti 85 40129 Bologna Italy
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29
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Liu S, Yeh C, Reavill C, Jones B, Zou Y, Hai Y. Molecular and Structural Basis for Cγ-C Bond Formation by PLP-Dependent Enzyme Fub7. Angew Chem Int Ed Engl 2024; 63:e202317161. [PMID: 38308582 PMCID: PMC10947850 DOI: 10.1002/anie.202317161] [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: 11/12/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/05/2024]
Abstract
Pyridoxal 5'-phosphate (PLP)-dependent enzymes that catalyze γ-replacement reactions are prevalent, yet their utilization of carbon nucleophile substrates is rare. The recent discovery of two PLP-dependent enzymes, CndF and Fub7, has unveiled unique C-C bond forming capabilities, enabling the biocatalytic synthesis of alkyl- substituted pipecolic acids from O-acetyl-L-homoserine and β-keto acid or aldehyde derived enolates. This breakthrough presents fresh avenues for the biosynthesis of pipecolic acid derivatives. However, the catalytic mechanisms of these enzymes remain elusive, and a dearth of structural information hampers their extensive application. Here, we have broadened the catalytic scope of Fub7 by employing ketone-derived enolates as carbon nucleophiles, revealing Fub7's capacity for substrate-dependent regioselective α-alkylation of unsymmetrical ketones. Through an integrated approach combining X-ray crystallography, spectroscopy, mutagenesis, and computational docking studies, we offer a detailed mechanistic insight into Fub7 catalysis. Our findings elucidate the structural basis for its substrate specificity, stereoselectivity, and regioselectivity. Our work sets the stage ready for subsequent protein engineering effort aimed at expanding the synthetic utility of Fub7, potentially unlocking novel methods to access a broader array of noncanonical amino acids.
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Affiliation(s)
- Shaonan Liu
- Department of Chemistry and Biochemistry, University of California Santa Barbara, 93110, Santa Barbara, CA, USA
| | - Christopher Yeh
- Department of Chemistry and Biochemistry, University of California Santa Barbara, 93110, Santa Barbara, CA, USA
| | - Chloe Reavill
- Department of Chemistry and Biochemistry, University of California Santa Barbara, 93110, Santa Barbara, CA, USA
| | - Benjamin Jones
- Department of Chemistry and Biochemistry, University of California Santa Barbara, 93110, Santa Barbara, CA, USA
| | - Yike Zou
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 94550, Livermore, CA, USA
| | - Yang Hai
- Department of Chemistry and Biochemistry, University of California Santa Barbara, 93110, Santa Barbara, CA, USA
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30
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Bell EL, Hutton AE, Burke AJ, O'Connell A, Barry A, O'Reilly E, Green AP. Strategies for designing biocatalysts with new functions. Chem Soc Rev 2024; 53:2851-2862. [PMID: 38353665 PMCID: PMC10946311 DOI: 10.1039/d3cs00972f] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Indexed: 03/19/2024]
Abstract
The engineering of natural enzymes has led to the availability of a broad range of biocatalysts that can be used for the sustainable manufacturing of a variety of chemicals and pharmaceuticals. However, for many important chemical transformations there are no known enzymes that can serve as starting templates for biocatalyst development. These limitations have fuelled efforts to build entirely new catalytic sites into proteins in order to generate enzymes with functions beyond those found in Nature. This bottom-up approach to enzyme development can also reveal new fundamental insights into the molecular origins of efficient protein catalysis. In this tutorial review, we will survey the different strategies that have been explored for designing new protein catalysts. These methods will be illustrated through key selected examples, which demonstrate how highly proficient and selective biocatalysts can be developed through experimental protein engineering and/or computational design. Given the rapid pace of development in the field, we are optimistic that designer enzymes will begin to play an increasingly prominent role as industrial biocatalysts in the coming years.
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Affiliation(s)
- Elizabeth L Bell
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Amy E Hutton
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Ashleigh J Burke
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA
| | - Adam O'Connell
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Amber Barry
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Elaine O'Reilly
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Anthony P Green
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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31
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Zhang R, Zhang C, Tan J, He Y, Zhuo D, Zhang J, Luo Z, Li Q, Yao J, Ke C, Tang C, Ye Y, He S, Sheng X, Liao C. Enzymatic Synthesis of Noncanonical α-Amino Acids Containing γ-Tertiary Alcohols. Angew Chem Int Ed Engl 2024; 63:e202318550. [PMID: 38155101 DOI: 10.1002/anie.202318550] [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: 12/04/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 12/30/2023]
Abstract
Noncanonical amino acids (ncAAs) containing tertiary alcohols are valuable as precursors of natural products and active pharmaceutical ingredients. However, the assembly of such ncAA scaffolds from simple material by C-C bond formation remains a challenging task due to the presence of multiple stereocenters and large steric hindrance. In this study, we present a novel solution to this problem through highly selective enzymatic decarboxylative aldol addition. This method allows for the streamlined assembly of multifunctionalized ncAAs with γ-tertiary alcohols from readily available materials, such as L -aspartatic acid and isatins, vicinal diones and keto esters. The modularity of electrophiles furnished four classes of ncAAs with decent efficiency as well as excellent site and stereocontrol. Computational modeling was employed to gain detailed insight into the catalytic mechanism and to provide a rationale for the observed selectivities. The method offers a single-step approach to producing multifunctionalized ncAAs, which can be directly utilized in peptide synthesis and bioactivity assessment.
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Affiliation(s)
- Rui Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Chenghua Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- School of Pharmacy, North Sichuan Medical College, Nanchong, 637100, P. R. China
| | - Jiamu Tan
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yifan He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dan Zhuo
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jingxuan Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenzhen Luo
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qiaoqiao Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jiaying Yao
- Graduate School, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Changqiang Ke
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Chunping Tang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yang Ye
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Shijun He
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiang Sheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, National Engineering Research Center of Industrial Enzymes and Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin, 300308, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cangsong Liao
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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32
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Hooe SL, Smith AD, Dean SN, Breger JC, Ellis GA, Medintz IL. Multienzymatic Cascades and Nanomaterial Scaffolding-A Potential Way Forward for the Efficient Biosynthesis of Novel Chemical Products. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2309963. [PMID: 37944537 DOI: 10.1002/adma.202309963] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/25/2023] [Indexed: 11/12/2023]
Abstract
Synthetic biology is touted as the next industrial revolution as it promises access to greener biocatalytic syntheses to replace many industrial organic chemistries. Here, it is shown to what synthetic biology can offer in the form of multienzyme cascades for the synthesis of the most basic of new materials-chemicals, including especially designer chemical products and their analogs. Since achieving this is predicated on dramatically expanding the chemical space that enzymes access, such chemistry will probably be undertaken in cell-free or minimalist formats to overcome the inherent toxicity of non-natural substrates to living cells. Laying out relevant aspects that need to be considered in the design of multi-enzymatic cascades for these purposes is begun. Representative multienzymatic cascades are critically reviewed, which have been specifically developed for the synthesis of compounds that have either been made only by traditional organic synthesis along with those cascades utilized for novel compound syntheses. Lastly, an overview of strategies that look toward exploiting bio/nanomaterials for accessing channeling and other nanoscale materials phenomena in vitro to direct novel enzymatic biosynthesis and improve catalytic efficiency is provided. Finally, a perspective on what is needed for this field to develop in the short and long term is presented.
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Affiliation(s)
- Shelby L Hooe
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
- National Research Council, Washington, DC, 20001, USA
| | - Aaron D Smith
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Scott N Dean
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Joyce C Breger
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Gregory A Ellis
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
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33
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Chen Z, Wu T, Yu S, Li M, Fan X, Huo YX. Self-assembly systems to troubleshoot metabolic engineering challenges. Trends Biotechnol 2024; 42:43-60. [PMID: 37451946 DOI: 10.1016/j.tibtech.2023.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
Enzyme self-assembly is a technology in which enzyme units can aggregate into ordered macromolecules, assisted by scaffolds. In metabolic engineering, self-assembly strategies have been explored for aggregating multiple enzymes in the same pathway to improve sequential catalytic efficiency, which in turn enables high-level production. The performance of the scaffolds is critical to the formation of an efficient and stable assembly system. This review comprehensively analyzes these scaffolds by exploring how they assemble, and it illustrates how to apply self-assembly strategies for different modules in metabolic engineering. Functional modifications to scaffolds will further promote efficient strategies for production.
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Affiliation(s)
- Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Tong Wu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Min Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Xuanhe Fan
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China.
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34
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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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35
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Liu M, Ohashi M, Zhou Q, Sanders JN, McCauley EP, Crews P, Houk KN, Tang Y. Enzymatic Benzofuranoindoline Formation in the Biosynthesis of the Strained Bridgehead Bicyclic Dipeptide (+)-Azonazine A. Angew Chem Int Ed Engl 2023; 62:e202311266. [PMID: 37589717 PMCID: PMC10868402 DOI: 10.1002/anie.202311266] [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: 08/03/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023]
Abstract
We uncovered and reconstituted a concise biosynthetic pathway of the strained dipeptide (+)-azonazine A from marine-derived Aspergillus insulicola. Formation of the hexacyclic benzofuranoindoline ring system from cyclo-(l-Trp-N-methyl-l-Tyr) is catalyzed by a P450 enzyme through an oxidative cyclization. Supplementing the producing strain with various indole-substituted tryptophan derivatives resulted in the generation of a series of azonazine A analogs.
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Affiliation(s)
- Mengting Liu
- Department of Chemical and Biomolecular Engineering; Department of Chemistry and Biochemistry University of California, Los Angeles, California 90095, USA
| | - Masao Ohashi
- Department of Chemical and Biomolecular Engineering; Department of Chemistry and Biochemistry University of California, Los Angeles, California 90095, USA
| | - Qingyang Zhou
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Jacob N. Sanders
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Erin P. McCauley
- Department of Chemistry and Biochemistry, California State University–Dominguez Hills, Carson, California 90747, USA
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering; Department of Chemistry and Biochemistry University of California, Los Angeles, California 90095, USA; Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
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36
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Liu XY, Yang YL, Dang Y, Marek I, Zhang FG, Ma JA. Tetrazole Diversification of Amino Acids and Peptides via Silver-Catalyzed Intermolecular Cycloaddition with Aryldiazonium Salts. Angew Chem Int Ed Engl 2023; 62:e202304740. [PMID: 37212541 DOI: 10.1002/anie.202304740] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 05/23/2023]
Abstract
Selective structural modification of amino acids and peptides is a central strategy in organic chemistry, chemical biology but also in pharmacology and material science. In this context, the formation of tetrazole rings, known to possess significant therapeutic properties, would expand the chemical space of unnatural amino acids but has received less attention. In this study, we demonstrated that the classic unimolecular Wolff rearrangement of α-amino acid-derived diazoketones could be replaced by a faster intermolecular cycloaddition reaction with aryldiazonium salts under identical practical conditions. This strategy provides an efficient synthetic platform that could transform proteinogenic α-amino acids into a plethora of unprecedented tetrazole-decorated amino acid derivatives with preservation of the stereocenters. Density functional theory studies shed some light on the reaction mechanism and provided information regarding the origins of the chemo- and regioselectivity. Furthermore, this diazo-cycloaddition protocol was applied to construct tetrazole-modified peptidomimetics and drug-like amino acid derivatives.
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Affiliation(s)
- Xuan-Yu Liu
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
| | - Yi-Lin Yang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
| | - Yanfeng Dang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
| | - Ilan Marek
- Schulich Faculty of Chemistry and the Resnick Sustainability Center for Catalysis, Technion-Israel Institute of Technology, Haifa, 3200009, Israel
| | - Fa-Guang Zhang
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
| | - Jun-An Ma
- Department of Chemistry, Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
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37
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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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38
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Yang H, Yu H, Stolarzewicz IA, Tang W. Enantioselective Transformations in the Synthesis of Therapeutic Agents. Chem Rev 2023; 123:9397-9446. [PMID: 37417731 DOI: 10.1021/acs.chemrev.3c00010] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
The proportion of approved chiral drugs and drug candidates under medical studies has surged dramatically over the past two decades. As a consequence, the efficient synthesis of enantiopure pharmaceuticals or their synthetic intermediates poses a profound challenge to medicinal and process chemists. The significant advancement in asymmetric catalysis has provided an effective and reliable solution to this challenge. The successful application of transition metal catalysis, organocatalysis, and biocatalysis to the medicinal and pharmaceutical industries has promoted drug discovery by efficient and precise preparation of enantio-enriched therapeutic agents, and facilitated the industrial production of active pharmaceutical ingredient in an economic and environmentally friendly fashion. The present review summarizes the most recent applications (2008-2022) of asymmetric catalysis in the pharmaceutical industry ranging from process scales to pilot and industrial levels. It also showcases the latest achievements and trends in the asymmetric synthesis of therapeutic agents with state of the art technologies of asymmetric catalysis.
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Affiliation(s)
- He Yang
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Hanxiao Yu
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Izabela A Stolarzewicz
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Wenjun Tang
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
- School of Chemistry and Material Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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39
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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: 52] [Impact Index Per Article: 26.0] [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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40
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Stockhammer L, Craik R, Monkowius U, Cordes DB, Smith AD, Waser M. Isothiourea-Catalyzed Enantioselective Functionalisation of Glycine Schiff Base Aryl Esters via 1,6- and 1,4-Additions. CHEMISTRYEUROPE 2023; 1:e202300015. [PMID: 38882579 PMCID: PMC7616101 DOI: 10.1002/ceur.202300015] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Indexed: 06/18/2024]
Abstract
The enantioselective α-functionalisation of glycine Schiff base aryl esters through isothiourea catalysis is successfully demonstrated for 1,6-additions to para-quinone methides (21 examples, up to 95:5 dr and 96:4 er) and 1,4-additions to methylene substituted dicarbonyl or disulfonyl Michael acceptors (17 examples, up to 98:2 er). This nucleophilic organocatalysis approach gives access to a range of α-functionalised α-amino acid derivatives and further transformations of the activated aryl ester group provide a straightforward entry to advanced amino acid-based esters, amides or thioesters.
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Affiliation(s)
- Lotte Stockhammer
- Institute of Organic Chemistry, Johannes Kepler University Linz, Altenbergerstrasse 69, 4040 Linz (Austria)
| | - Rebecca Craik
- EaStCHEM, School of Chemistry, University of St Andrews, KY16 9ST St Andrews, Fife, (UK)
| | - Uwe Monkowius
- School of Education, Chemistry, Johannes Kepler University Linz, Altenbergerstrasse 69, 4040 Linz (Austria)
| | - David B. Cordes
- EaStCHEM, School of Chemistry, University of St Andrews, KY16 9ST St Andrews, Fife, (UK)
| | - Andrew D. Smith
- EaStCHEM, School of Chemistry, University of St Andrews, KY16 9ST St Andrews, Fife, (UK)
| | - Mario Waser
- Institute of Organic Chemistry, Johannes Kepler University Linz, Altenbergerstrasse 69, 4040 Linz (Austria)
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41
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Kim M, Jo H, Jung GY, Oh SS. Molecular Complementarity of Proteomimetic Materials for Target-Specific Recognition and Recognition-Mediated Complex Functions. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2208309. [PMID: 36525617 DOI: 10.1002/adma.202208309] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/29/2022] [Indexed: 06/02/2023]
Abstract
As biomolecules essential for sustaining life, proteins are generated from long chains of 20 different α-amino acids that are folded into unique 3D structures. In particular, many proteins have molecular recognition functions owing to their binding pockets, which have complementary shapes, charges, and polarities for specific targets, making these biopolymers unique and highly valuable for biomedical and biocatalytic applications. Based on the understanding of protein structures and microenvironments, molecular complementarity can be exhibited by synthesizable and modifiable materials. This has prompted researchers to explore the proteomimetic potentials of a diverse range of materials, including biologically available peptides and oligonucleotides, synthetic supramolecules, inorganic molecules, and related coordination networks. To fully resemble a protein, proteomimetic materials perform the molecular recognition to mediate complex molecular functions, such as allosteric regulation, signal transduction, enzymatic reactions, and stimuli-responsive motions; this can also expand the landscape of their potential bio-applications. This review focuses on the recognitive aspects of proteomimetic designs derived for individual materials and their conformations. Recent progress provides insights to help guide the development of advanced protein mimicry with material heterogeneity, design modularity, and tailored functionality. The perspectives and challenges of current proteomimetic designs and tools are also discussed in relation to future applications.
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Affiliation(s)
- Minsun Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Hyesung Jo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Seung Soo Oh
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
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42
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Alfonzo E, Das A, Arnold FH. New Additions to the Arsenal of Biocatalysts for Noncanonical Amino Acid Synthesis. CURRENT OPINION IN GREEN AND SUSTAINABLE CHEMISTRY 2022; 38:100701. [PMID: 36561208 PMCID: PMC9770695 DOI: 10.1016/j.cogsc.2022.100701] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Noncanonical amino acids (ncAAs) merge the conformational behavior and native interactions of proteinogenic amino acids with nonnative chemical motifs and have proven invaluable in developing modern therapeutics. This blending of native and nonnative characteristics has resulted in essential drugs like nirmatrelvir, which comprises three ncAAs and is used to treat COVID-19. Enzymes are appearing prominently in recent syntheses of ncAAs, where they demonstrate impressive control over the stereocenters and functional groups found therein. Here we review recent efforts to expand the biocatalyst arsenal for synthesizing ncAAs with natural enzymes. We also discuss how new-to-nature enzymes can contribute to this effort by catalyzing reactions inspired by the vast repertoire of chemical catalysis and acting on substrates that would otherwise not be used in synthesizing ncAAs. Abiotic enzyme-catalyzed reactions exploit the selectivity afforded by a macromolecular catalyst to access molecules not available to natural enzymes and perhaps not even chemical catalysis.
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Affiliation(s)
- Edwin Alfonzo
- Division of Chemistry and Chemical Engineering, 210-41, California Institute of Technology, 1200 East California Blvd, Pasadena, CA 91125, USA
| | - Anuvab Das
- Division of Chemistry and Chemical Engineering, 210-41, California Institute of Technology, 1200 East California Blvd, Pasadena, CA 91125, USA
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, 210-41, California Institute of Technology, 1200 East California Blvd, Pasadena, CA 91125, USA
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43
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Zackin MT, Stieglitz JT, Van Deventer JA. Genome-Wide Screen for Enhanced Noncanonical Amino Acid Incorporation in Yeast. ACS Synth Biol 2022; 11:3669-3680. [PMID: 36346914 PMCID: PMC10065164 DOI: 10.1021/acssynbio.2c00267] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Numerous applications of noncanonical amino acids (ncAAs) in basic biology and therapeutic development require efficient protein biosynthesis using an expanded genetic code. However, achieving such incorporation at repurposed stop codons in cells is generally inefficient and limited by complex cellular processes that preserve the fidelity of protein synthesis. A more comprehensive understanding of the processes that contribute to ncAA incorporation would aid in the development of genomic engineering strategies for augmenting genetic code manipulation. In this work, we used a series of fluorescent reporters to screen a pooled Saccharomyces cerevisiae molecular barcoded yeast knockout (YKO) collection. Fluorescence-activated cell sorting enabled isolation of strains encoding single-gene deletions exhibiting improved ncAA incorporation efficiency in response to the amber (TAG) stop codon; 55 unique candidate deletions were identified. The deleted genes encoded for proteins that participate in diverse cellular processes, including many genes that have no known connection with protein translation. We then verified that two knockouts, yil014c-aΔ and alo1Δ, exhibited improved ncAA incorporation efficiency starting from independently acquired strains possessing the knockouts. Using additional orthogonal translation systems and ncAAs, we determined that yil014c-aΔ and alo1Δ enhance ncAA incorporation efficiency without loss of fidelity over a wide range of conditions. Our findings highlight opportunities for further modulating gene expression with genetic, genomic, and synthetic biology approaches to improve ncAA incorporation efficiency. In addition, these discoveries have the potential to enhance our fundamental understanding of protein translation. Ultimately, cells that efficiently biosynthesize ncAA-containing proteins will streamline the realization of applications utilizing expanded genetic codes ranging from basic biology to drug discovery.
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Affiliation(s)
- Matthew T. Zackin
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
| | - Jessica T. Stieglitz
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, USA
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44
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Ji P, Chen J, Meng X, Gao F, Dong Y, Xu H, Wang W. Design of Photoredox-Catalyzed Giese-Type Reaction for the Synthesis of Chiral Quaternary α-Aryl Amino Acid Derivatives via Clayden Rearrangement. J Org Chem 2022; 87:14706-14714. [PMID: 36264622 DOI: 10.1021/acs.joc.2c02029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Chiral quaternary α-aryl amino acids are biologically valued but synthetically challenging building blocks. Herein, we report a strategy for the synthesis of molecular architectures by unifying a photoredox catalytic asymmetric Giese-type reaction and Clayden rearrangement. A new class of chiral Karady-Beckwith dehydroalanines is designed and serves as a versatile handle for the photoredox-mediated highly stereoselective Giese-type reaction with feedstock carboxylic acids and tertiary amines. Subsequent Clayden rearrangement delivers chiral quaternary α-aryl amino acid derivatives with high stereoselectivity. The versatile approach offers a reliable source for the assembly of highly demanding chiral building blocks.
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Affiliation(s)
- Peng Ji
- Departments of Pharmacology and Toxicology and Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0207, United States
| | - Jing Chen
- Departments of Pharmacology and Toxicology and Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0207, United States
| | - Xiang Meng
- Departments of Pharmacology and Toxicology and Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0207, United States
| | - Feng Gao
- Departments of Pharmacology and Toxicology and Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0207, United States
| | - Yue Dong
- Departments of Pharmacology and Toxicology and Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0207, United States
| | - Hang Xu
- Departments of Pharmacology and Toxicology and Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0207, United States
| | - Wei Wang
- Departments of Pharmacology and Toxicology and Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0207, United States
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45
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Jeon H, Pagar AD, Kang H, Giri P, Nadarajan SP, Sarak S, Khobragade TP, Lim S, Patil MD, Lee SG, Yun H. Creation of a ( R)-β-Transaminase by Directed Evolution of d-Amino Acid Aminotransferase. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hyunwoo Jeon
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Amol D. Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Hyeona Kang
- Department of Chemical and Biomolecular Engineering, Pusan National University, 63 Busan Daehak-ro, Beon-gil, Busan 46241, Korea
| | - Pritam Giri
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Saravanan P. Nadarajan
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Sharad Sarak
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Taresh P. Khobragade
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Seonga Lim
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D. Patil
- Department of Nanomaterials and Application Technology, Center of Innovative and Applied Bioprocessing (CIAB), Sector-81, PO Manauli, S.A.S. Nagar, Mohali, Punjab 140306, India
| | - Sun-Gu Lee
- Department of Chemical and Biomolecular Engineering, Pusan National University, 63 Busan Daehak-ro, Beon-gil, Busan 46241, Korea
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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46
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Zhu F, Miller E, Powell WC, Johnson K, Beggs A, Evenson GE, Walczak MA. Umpolung Ala
B
Reagents for the Synthesis of Non‐Proteogenic Amino Acids, Peptides and Proteins**. Angew Chem Int Ed Engl 2022; 61:e202207153. [PMID: 35653581 PMCID: PMC9329247 DOI: 10.1002/anie.202207153] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Indexed: 11/07/2022]
Abstract
Non-proteogenic amino acids and functionalized peptides are important motifs in modern drug discovery. Here we report that AlaB can serve as universal building blocks in the synthesis of a diverse collection of modified amino acids, peptides, and proteins. First, we develop the synthesis of AlaB from redox-active esters of aspartic acid resulting in a series of β-boronoalanine derivatives. Next, we show that AlaB can be integrated into automated oligopeptide solid-phase synthesis. AlaB is compatible with common transformations used in preparative peptide chemistry such as native chemical ligation and radical desulfurization as showcased by total synthesis of AlaB -containing ubiquitin. Furthermore, AlaB reagents participate in Pd-catalyzed reactions, including C-C cross-couplings and macrocyclizations. Taken together, AlaB synthons are practical reagents to access modified peptides, proteins, and in the synthesis of cyclic/stapled peptides.
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Affiliation(s)
- Feng Zhu
- Frontiers Science Center for Transformative Molecules Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs School of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Eric Miller
- Department of Chemistry University of Colorado Boulder CO 80309 USA
| | - Wyatt C. Powell
- Department of Chemistry University of Colorado Boulder CO 80309 USA
| | - Kelly Johnson
- Department of Chemistry University of Colorado Boulder CO 80309 USA
| | - Alexander Beggs
- Department of Chemistry University of Colorado Boulder CO 80309 USA
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47
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Smith JL, Harrison IM, Bingman CA, 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] [MESH Headings] [Grants] [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)
- Jamorious L. Smith
- Department of ChemistryUniversity of Wisconsin-Madison1101 University AvenueMadisonWisconsin53706USA
| | - Isa Madrigal Harrison
- Department of ChemistryUniversity of Wisconsin-Madison1101 University AvenueMadisonWisconsin53706USA
| | - Craig A. Bingman
- Department of BiochemistryUniversity of Wisconsin-Madison433 Babcock DriveMadisonWisconsin53706USA
| | - Andrew R. Buller
- Department of ChemistryUniversity of Wisconsin-Madison1101 University AvenueMadisonWisconsin53706USA
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48
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Zhu F, Miller E, Powell W, Johnson K, Beggs A, Evenson G, Walczak MA. Umpolung AlaB Reagents for the Synthesis of Non‐Proteogenic Amino Acids, Peptides and Proteins. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Feng Zhu
- Shanghai Jiao Tong University Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs CHINA
| | - Eric Miller
- University of Colorado Boulder Department of Chemistry UNITED STATES
| | - Wyatt Powell
- University of Colorado Boulder Department of Chemistry UNITED STATES
| | - Kelly Johnson
- University of Colorado Boulder Department of Chemistry UNITED STATES
| | - Alexander Beggs
- University of Colorado Boulder Department of Chemistry UNITED STATES
| | - Garrett Evenson
- University of Colorado Boulder Department of Chemistry UNITED STATES
| | - Maciej A. Walczak
- University of Colorado Boulder Department of Chemistry and Biochemistry 215 UCB 80309 Boulder UNITED STATES
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49
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Xie VC, Styles MJ, Dickinson BC. Methods for the directed evolution of biomolecular interactions. Trends Biochem Sci 2022; 47:403-416. [PMID: 35427479 PMCID: PMC9022280 DOI: 10.1016/j.tibs.2022.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/27/2021] [Accepted: 01/13/2022] [Indexed: 02/06/2023]
Abstract
Noncovalent interactions between biomolecules such as proteins and nucleic acids coordinate all cellular processes through changes in proximity. Tools that perturb these interactions are and will continue to be highly valuable for basic and translational scientific endeavors. By taking cues from natural systems, such as the adaptive immune system, we can design directed evolution platforms that can generate proteins that bind to biomolecules of interest. In recent years, the platforms used to direct the evolution of biomolecular binders have greatly expanded the range of types of interactions one can evolve. Herein, we review recent advances in methods to evolve protein-protein, protein-RNA, and protein-DNA interactions.
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Affiliation(s)
| | - Matthew J Styles
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA.
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50
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Choi W, Heo D, Kim T, Jung S, Choi M, Heo J, Kwon J, Kim B, Lee W, Koh W, Cho JH, Lee S, Hong J. Stress Dissipation Encoded Silk Fibroin Electrode for the Athlete-Beneficial Silk Bioelectronics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105420. [PMID: 35001517 PMCID: PMC8922117 DOI: 10.1002/advs.202105420] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Indexed: 06/14/2023]
Abstract
The kinetic body motions have guided the core-shell fabrics of wearable bioelectronics to be elastoplastic. However, the polymeric electrodes follow the trade-off relationship between toughness and stretchability. To this end, the stress dissipation encoded silk fibroin electrode is proposed as the core electrode of wearable bioelectronics. Significantly, the high degree of intrinsic stress dissipation is realized via an amino acid crosslink. The canonical phenolic amino acid (i.e., tyrosine) of silk fibroin is engineered to bridge the secondary structures. A sufficient crosslink network is constructed when tyrosine is exposed near the amorphous strand. The stress dissipative tyrosine crosslink affords 12.5-fold increments of toughness (4.72 to 58.9 MJ m-3 ) and implements the elastoplastic silk fibroin. The harmony of elastoplastic core electrodes with shell fabrics enables the wearable bioelectronics to employ mechanical performance (elastoplasticity of 750 MJ m-3 ) and stable electrical response. The proposed wearable is capable of assisting the effective workouts via triboelectricity. In principle, active mobility with suggested wearables potentially relieves muscular fatigues and severe injuries during daily fitness.
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Affiliation(s)
- Woojin Choi
- Department of Chemical and Biomolecular Engineering, College of EngineeringYonsei UniversitySeoul03722Republic of Korea
| | - Deokjae Heo
- School of Mechanical EngineeringChung‐ang University84, Heukseok‐ro, Dongjak‐guSeoul06974Republic of Korea
| | - Taeho Kim
- Department of Chemical and Biomolecular Engineering, College of EngineeringYonsei UniversitySeoul03722Republic of Korea
| | - Sungwon Jung
- Department of Chemical and Biomolecular Engineering, College of EngineeringYonsei UniversitySeoul03722Republic of Korea
| | - Moonhyun Choi
- Department of Chemical and Biomolecular Engineering, College of EngineeringYonsei UniversitySeoul03722Republic of Korea
| | - Jiwoong Heo
- Department of Chemical and Biomolecular Engineering, College of EngineeringYonsei UniversitySeoul03722Republic of Korea
| | - Jae‐Sung Kwon
- Department and Research Institute of Dental Biomaterials and Bioengineering and BK21 FOUR ProjectYonsei University College of DentistrySeoul03722Republic of Korea
| | - Byeong‐Su Kim
- Department of ChemistryYonsei UniversitySeoul03722Republic of Korea
| | - Wonhwa Lee
- Department of ChemistrySungkyunkwan UniversitySuwon16419Republic of Korea
| | - Won‐Gun Koh
- Department of Chemical and Biomolecular Engineering, College of EngineeringYonsei UniversitySeoul03722Republic of Korea
| | - Jeong Ho Cho
- Department of Chemical and Biomolecular Engineering, College of EngineeringYonsei UniversitySeoul03722Republic of Korea
| | - Sangmin Lee
- School of Mechanical EngineeringChung‐ang University84, Heukseok‐ro, Dongjak‐guSeoul06974Republic of Korea
| | - Jinkee Hong
- Department of Chemical and Biomolecular Engineering, College of EngineeringYonsei UniversitySeoul03722Republic of Korea
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