1
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Cao L, Wang L. Biospecific Chemistry for Covalent Linking of Biomacromolecules. Chem Rev 2024; 124:8516-8549. [PMID: 38913432 PMCID: PMC11240265 DOI: 10.1021/acs.chemrev.4c00066] [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: 06/26/2024]
Abstract
Interactions among biomacromolecules, predominantly noncovalent, underpin biological processes. However, recent advancements in biospecific chemistry have enabled the creation of specific covalent bonds between biomolecules, both in vitro and in vivo. This Review traces the evolution of biospecific chemistry in proteins, emphasizing the role of genetically encoded latent bioreactive amino acids. These amino acids react selectively with adjacent natural groups through proximity-enabled bioreactivity, enabling targeted covalent linkages. We explore various latent bioreactive amino acids designed to target different protein residues, ribonucleic acids, and carbohydrates. We then discuss how these novel covalent linkages can drive challenging protein properties and capture transient protein-protein and protein-RNA interactions in vivo. Additionally, we examine the application of covalent peptides as potential therapeutic agents and site-specific conjugates for native antibodies, highlighting their capacity to form stable linkages with target molecules. A significant focus is placed on proximity-enabled reactive therapeutics (PERx), a pioneering technology in covalent protein therapeutics. We detail its wide-ranging applications in immunotherapy, viral neutralization, and targeted radionuclide therapy. Finally, we present a perspective on the existing challenges within biospecific chemistry and discuss the potential avenues for future exploration and advancement in this rapidly evolving field.
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Affiliation(s)
- Li Cao
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
| | - Lei Wang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
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2
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Cao L, Yu B, Li S, Zhang P, Li Q, Wang L. Genetically Enabling Phosphorus Fluoride Exchange Click Chemistry in Proteins. Chem 2024; 10:1868-1884. [PMID: 38975291 PMCID: PMC11225796 DOI: 10.1016/j.chempr.2024.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Phosphorus Fluoride Exchange (PFEx), recently debuted in small molecules, represents the forefront of click chemistry. To explore PFEx's potential in biological settings, we developed amino acids PFY and PFK featuring phosphoramidofluoridates and incorporated them into proteins through genetic code expansion. PFY/PFK selectively reacted with nearby His, Tyr, Lys, or Cys in proteins, both in vitro and in living cells, demonstrating that proximity enabled PFEx reactivity without external reagents. The reaction with His showed unique pH-dependent properties and created thermally sensitive linkages. Additionally, Na2SiO3 enhanced PFEx reactions with Tyr and Cys. PFEx, by generating defined covalent P-N/O linkages, extends the utility of phosphorus linkages in proteins, aligning with nature's use of phosphate connectors in other biomolecules. More versatile and durable than SuFEx, PFEx in proteins expands the latent bioreactive arsenal for covalent protein engineering and will facilitate the broad application of this potent click chemistry in biological and biomedical fields.
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Affiliation(s)
- Li Cao
- Department of Pharmaceutical Chemistry, the Cardiovascular Research Institute, and Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- These authors contributed equally
| | - Bingchen Yu
- Department of Pharmaceutical Chemistry, the Cardiovascular Research Institute, and Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- These authors contributed equally
| | - Shanshan Li
- Department of Pharmaceutical Chemistry, the Cardiovascular Research Institute, and Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Pan Zhang
- Department of Pharmaceutical Chemistry, the Cardiovascular Research Institute, and Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Qingke Li
- Department of Pharmaceutical Chemistry, the Cardiovascular Research Institute, and Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lei Wang
- Department of Pharmaceutical Chemistry, the Cardiovascular Research Institute, and Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Lead contact
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3
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Demir Ğ, Valjakka J, Turunen O, Aktaş F, Binay B. Cloning and expression heterologous alanine dehydrogenase genes: Investigation of reductive amination potential of L-alanine dehydrogenases for green synthesis of alanine derivatives. Heliyon 2024; 10:e26899. [PMID: 38463761 PMCID: PMC10923667 DOI: 10.1016/j.heliyon.2024.e26899] [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: 12/29/2023] [Revised: 02/09/2024] [Accepted: 02/21/2024] [Indexed: 03/12/2024] Open
Abstract
Unnatural amino acids (UAAs) offer significant promise in a wide range of applications, including drug discovery, the custom design of peptides and proteins, and their utility and use as markers for monitoring molecular interactions in biological research. The synthesis of UAAs presents a formidable challenge and can be classified into two primary categories: enzymatic and chemical synthesis. Notably, the enzymatic route, specifically asymmetric synthesis, emerges as a an attractive method for procuring enantiopure UAAs with high efficiency, owing to its streamlined and concise reaction mechanism. The current study investigated the reductive amination activity mechanisms of alanine dehydrogenase (L-AlaDH), sourced from a combination of newly and previously characterized microorganisms. Our principal aim was to evaluate the catalytic efficiency of these L-AlaDH enzymes concerning a range of specific ketoacids and pyruvate to ascertain their capability for facilitating the production of both natural and unnatural amino acids. After the characterization processes, mutation points for TtAlaDH were determined and as a result of the mutations, mutants that could use ketocaproate and ketovalerate more effectively than the wild type were obtained. Among the enzymes studied, MetAlaDH exhibited the highest specific activity against pyruvate, 173 U/mg, and a KM value of 1.3 mM. VlAlaDH displayed the most favourable catalytic efficiency with a rate constant of 170 s-1mM-1. On the other hand, AfAlaDH demonstrated the highest catalytic efficiency against α-ketobutyrate (34.0 s-1mM-1) and α-ketovalerate (2.7 s-1mM-1). Of the enzymes investigated in the study, TtAlaDH exhibited the highest effectiveness among bacterial enzymes in catalyzing ketocaproate with a measured catalytic efficiency of about 0.6 s-1mM-1 and a KM value of approximately 0.3 mM. These findings provide valuable insights into the substrate specificity and catalytic performance of L-AlaDHs, enhancing our understanding of their potential applications in various biocatalytic processes.
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Affiliation(s)
- Ğarip Demir
- Department of Molecular Biology and Genetics, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - Jarkko Valjakka
- Faculty of Medicine and Health Technology, Tampere University, FI-33100, Tampere, Finland
| | - Ossi Turunen
- School of Forest Sciences, University of Eastern Finland, FI-80101, Joensuu, Finland
| | - Fatih Aktaş
- Faculty of Engineering, Düzce University, 81600, Düzce, Turkey
| | - Barış Binay
- Department of Bioengineering, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
- BAUZYME Biotechnology Co., Gebze Technical University Technopark, 41400, Gebze, Kocaeli, Turkey
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4
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Yan X, Liu X, Zhao C, Chen GQ. Applications of synthetic biology in medical and pharmaceutical fields. Signal Transduct Target Ther 2023; 8:199. [PMID: 37169742 PMCID: PMC10173249 DOI: 10.1038/s41392-023-01440-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 05/13/2023] Open
Abstract
Synthetic biology aims to design or assemble existing bioparts or bio-components for useful bioproperties. During the past decades, progresses have been made to build delicate biocircuits, standardized biological building blocks and to develop various genomic/metabolic engineering tools and approaches. Medical and pharmaceutical demands have also pushed the development of synthetic biology, including integration of heterologous pathways into designer cells to efficiently produce medical agents, enhanced yields of natural products in cell growth media to equal or higher than that of the extracts from plants or fungi, constructions of novel genetic circuits for tumor targeting, controllable releases of therapeutic agents in response to specific biomarkers to fight diseases such as diabetes and cancers. Besides, new strategies are developed to treat complex immune diseases, infectious diseases and metabolic disorders that are hard to cure via traditional approaches. In general, synthetic biology brings new capabilities to medical and pharmaceutical researches. This review summarizes the timeline of synthetic biology developments, the past and present of synthetic biology for microbial productions of pharmaceutics, engineered cells equipped with synthetic DNA circuits for diagnosis and therapies, live and auto-assemblied biomaterials for medical treatments, cell-free synthetic biology in medical and pharmaceutical fields, and DNA engineering approaches with potentials for biomedical applications.
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Affiliation(s)
- Xu Yan
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Xu Liu
- PhaBuilder Biotech Co. Ltd., Shunyi District, Zhaoquan Ying, 101309, Beijing, China
| | - Cuihuan Zhao
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, 100084, Beijing, China.
- Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China.
- MOE Key Lab for Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, 100084, Beijing, China.
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5
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Ma B, Niu W, Guo J. Proximity-enhanced protein crosslinking through an alkene-tetrazine reaction. Bioorg Chem 2023; 132:106359. [PMID: 36642019 PMCID: PMC9957846 DOI: 10.1016/j.bioorg.2023.106359] [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: 10/20/2022] [Revised: 11/21/2022] [Accepted: 12/01/2022] [Indexed: 01/13/2023]
Abstract
The inverse electron demand Diels-Alder (iEDDA) reaction between a tetrazine and a strained alkene has been widely explored as useful bioorthogonal chemistry for selective labeling of biomolecules. In this work, we exploit the slow reaction between a non-conjugated terminal alkene and a tetrazine, and apply this reaction to achieving a proximity-enhanced protein crosslinking. In one protein subunit, a terminal alkene-containing amino acid was site-specifically incorporated in response to an amber nonsense codon. In another protein subunit, a tetrazine moiety was introduced through the attachment to a cysteine residue. Fast protein crosslinking was achieved due to a large increase in effective molarity of the two reactants that were brought to close proximity by the two interacting protein subunits. Such a proximity-enhanced protein crosslinking is useful for the study of protein-protein interactions.
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Affiliation(s)
- Bin Ma
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, United States
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, United States
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, United States; The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE 68588, United States.
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6
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Ji Y, Sun L, Chen Y, Qin H, Xuan W. Sirtuin‐Derived Covalent Binder for the Selective Recognition of Protein Crotonylation. Angew Chem Int Ed Engl 2022; 61:e202205522. [DOI: 10.1002/anie.202205522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Yanli Ji
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Lin Sun
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Yao Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences (CAS) Dalian 116023 China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences (CAS) Dalian 116023 China
| | - Weimin Xuan
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
- School of Life Sciences Tianjin University Tianjin 300072 China
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7
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Sirtuin‐Derived Covalent Binder for the Selective Recognition of Protein Crotonylation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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8
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Cao L, Wang L. New covalent bonding ability for proteins. Protein Sci 2022; 31:312-322. [PMID: 34761448 PMCID: PMC8819847 DOI: 10.1002/pro.4228] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 02/03/2023]
Abstract
To expand protein's covalent bonding ability, latent bioreactive unnatural amino acids have been designed and genetically encoded into proteins, which react with specific natural amino acid residues through proximity-enabled bioreactivity. The resultant new covalent bonds can be selectively created within and between proteins in vitro, in cells, and in vivo. Offering diverse properties previously unattainable, these covalent linkages have been harnessed to enhance protein properties, to modulate protein function, to probe ligand-receptor binding, to identify elusive protein interactions, and to develop covalent protein drugs. Selective introduction of covalent bonds into proteins is affording novel avenues for biological studies, synthetic biology, and biotherapeutics.
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Affiliation(s)
- Li Cao
- Department of Pharmaceutical Chemistry and the Cardiovascular Research InstituteUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Lei Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research InstituteUniversity of California San FranciscoSan FranciscoCaliforniaUSA
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9
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Lateef OM, Akintubosun MO, Olaoba OT, Samson SO, Adamczyk M. Making Sense of "Nonsense" and More: Challenges and Opportunities in the Genetic Code Expansion, in the World of tRNA Modifications. Int J Mol Sci 2022; 23:938. [PMID: 35055121 PMCID: PMC8779196 DOI: 10.3390/ijms23020938] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 01/09/2023] Open
Abstract
The evolutional development of the RNA translation process that leads to protein synthesis based on naturally occurring amino acids has its continuation via synthetic biology, the so-called rational bioengineering. Genetic code expansion (GCE) explores beyond the natural translational processes to further enhance the structural properties and augment the functionality of a wide range of proteins. Prokaryotic and eukaryotic ribosomal machinery have been proven to accept engineered tRNAs from orthogonal organisms to efficiently incorporate noncanonical amino acids (ncAAs) with rationally designed side chains. These side chains can be reactive or functional groups, which can be extensively utilized in biochemical, biophysical, and cellular studies. Genetic code extension offers the contingency of introducing more than one ncAA into protein through frameshift suppression, multi-site-specific incorporation of ncAAs, thereby increasing the vast number of possible applications. However, different mediating factors reduce the yield and efficiency of ncAA incorporation into synthetic proteins. In this review, we comment on the recent advancements in genetic code expansion to signify the relevance of systems biology in improving ncAA incorporation efficiency. We discuss the emerging impact of tRNA modifications and metabolism in protein design. We also provide examples of the latest successful accomplishments in synthetic protein therapeutics and show how codon expansion has been employed in various scientific and biotechnological applications.
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Affiliation(s)
- Olubodun Michael Lateef
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
| | | | - Olamide Tosin Olaoba
- Laboratory of Functional and Structural Biochemistry, Federal University of Sao Carlos, Sao Carlos 13565-905, SP, Brazil;
| | - Sunday Ocholi Samson
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
| | - Malgorzata Adamczyk
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
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10
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Wang XS, Chen PC, Hampton JT, Tharp JM, Reed CA, Das SK, Wang D, Hayatshahi HS, Shen Y, Liu J, Liu WR. A Genetically Encoded, Phage‐Displayed Cyclic‐Peptide Library. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | - J. Trae Hampton
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
| | - Jeffery M. Tharp
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
| | - Catrina A. Reed
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
| | - Sukant K. Das
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
| | - Duen‐Shian Wang
- Department of Pharmaceutical Sciences UNT Health Science Center Fort Worth TX 76107 USA
| | - Hamed S. Hayatshahi
- Department of Pharmaceutical Sciences UNT Health Science Center Fort Worth TX 76107 USA
| | - Yang Shen
- Department of Electrical and Computer Engineering Texas A&M University College Station TX 77843-3218 USA
| | - Jin Liu
- Department of Pharmaceutical Sciences UNT Health Science Center Fort Worth TX 76107 USA
| | - Wenshe Ray Liu
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
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11
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Wang XS, Chen PHC, Hampton JT, Tharp JM, Reed CA, Das SK, Wang DS, Hayatshahi HS, Shen Y, Liu J, Liu WR. A Genetically Encoded, Phage-Displayed Cyclic-Peptide Library. Angew Chem Int Ed Engl 2019; 58:15904-15909. [PMID: 31398275 PMCID: PMC6803038 DOI: 10.1002/anie.201908713] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Indexed: 11/10/2022]
Abstract
Superior to linear peptides in biological activities, cyclic peptides are considered to have great potential as therapeutic agents. To identify cyclic-peptide ligands for therapeutic targets, phage-displayed peptide libraries in which cyclization is achieved by the covalent conjugation of cysteines have been widely used. To resolve drawbacks related to cysteine conjugation, we have invented a phage-display technique in which its displayed peptides are cyclized through a proximity-driven Michael addition reaction between a cysteine and an amber-codon-encoded Nϵ -acryloyl-lysine (AcrK). Using a randomized 6-mer library in which peptides were cyclized at two ends through a cysteine-AcrK linker, we demonstrated the successful selection of potent ligands for TEV protease and HDAC8. All selected cyclic peptide ligands showed 4- to 6-fold stronger affinity to their protein targets than their linear counterparts. We believe this approach will find broad applications in drug discovery.
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Affiliation(s)
- Xiaoshan Shayna Wang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Peng-Hsun Chase Chen
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - J Trae Hampton
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Jeffery M Tharp
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Catrina A Reed
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Sukant K Das
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Duen-Shian Wang
- Department of Pharmaceutical Sciences, UNT Health Science Center, Fort Worth, TX, 76107, USA
| | - Hamed S Hayatshahi
- Department of Pharmaceutical Sciences, UNT Health Science Center, Fort Worth, TX, 76107, USA
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843-3218, USA
| | - Jin Liu
- Department of Pharmaceutical Sciences, UNT Health Science Center, Fort Worth, TX, 76107, USA
| | - Wenshe Ray Liu
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
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12
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Nguyen TA, Cigler M, Lang K. Expanding the Genetic Code to Study Protein-Protein Interactions. Angew Chem Int Ed Engl 2018; 57:14350-14361. [PMID: 30144241 DOI: 10.1002/anie.201805869] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/20/2018] [Indexed: 12/19/2022]
Abstract
Protein-protein interactions are central to many biological processes. A considerable challenge consists however in understanding and deciphering when and how proteins interact, and this can be particularly difficult when interactions are weak and transient. The site-specific incorporation of unnatural amino acids (UAAs) that crosslink with nearby molecules in response to light provides a powerful tool for mapping transient protein-protein interactions and for defining the structure and topology of protein complexes both in vitro and in vivo. Complementary strategies consist in site-specific incorporation of UAAs bearing electrophilic moieties that react with natural nucleophilic amino acids in a proximity-dependent manner, thereby chemically stabilizing low-affinity interactions and providing additional constraints on distances and geometries in protein complexes. Herein, we review how UAAs bearing fine-tuned chemical moieties that react with proteins in their vicinity can be utilized to map, study, and characterize weak and transient protein-protein interactions in living systems.
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Affiliation(s)
- Tuan-Anh Nguyen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Marko Cigler
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
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13
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Nguyen TA, Cigler M, Lang K. Expanding the Genetic Code to Study Protein-Protein Interactions. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805869] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Tuan-Anh Nguyen
- Center for Integrated Protein Science Munich (CIPSM); Department of Chemistry; Group of Synthetic Biochemistry; Technical University of Munich; Institute for Advanced Study; Lichtenbergstr. 4 85748 Garching Germany
| | - Marko Cigler
- Center for Integrated Protein Science Munich (CIPSM); Department of Chemistry; Group of Synthetic Biochemistry; Technical University of Munich; Institute for Advanced Study; Lichtenbergstr. 4 85748 Garching Germany
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM); Department of Chemistry; Group of Synthetic Biochemistry; Technical University of Munich; Institute for Advanced Study; Lichtenbergstr. 4 85748 Garching Germany
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14
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Shang X, Chen Y, Wang N, Niu W, Guo J. Oxidation-induced generation of a mild electrophile for proximity-enhanced protein-protein crosslinking. Chem Commun (Camb) 2018; 54:4172-4175. [PMID: 29629441 PMCID: PMC5908726 DOI: 10.1039/c8cc01639a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a strategy to introduce a reactive electrophile into proteins through the conversion of a chemically inert group into a bioreactive group in response to an inducer molecule. This strategy was demonstrated by oxidation-induced and proximity-enhanced protein-protein crosslinking in the presence of a large excess of free nucleophile.
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Affiliation(s)
- X Shang
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA.
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15
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Cigler M, Müller TG, Horn-Ghetko D, von Wrisberg MK, Fottner M, Goody RS, Itzen A, Müller MP, Lang K. Proximity-Triggered Covalent Stabilization of Low-Affinity Protein Complexes In Vitro and In Vivo. Angew Chem Int Ed Engl 2017; 56:15737-15741. [PMID: 28960788 DOI: 10.1002/anie.201706927] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/13/2017] [Indexed: 12/31/2022]
Abstract
The characterization of low-affinity protein complexes is challenging due to their dynamic nature. Here, we present a method to stabilize transient protein complexes in vivo by generating a covalent and conformationally flexible bridge between the interaction partners. A highly active pyrrolysyl tRNA synthetase mutant directs the incorporation of unnatural amino acids bearing bromoalkyl moieties (BrCnK) into proteins. We demonstrate for the first time that low-affinity protein complexes between BrCnK-containing proteins and their binding partners can be stabilized in vivo in bacterial and mammalian cells. Using this approach, we determined the crystal structure of a transient GDP-bound complex between a small G-protein and its nucleotide exchange factor. We envision that this approach will prove valuable as a general tool for validating and characterizing protein-protein interactions in vitro and in vivo.
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Affiliation(s)
- Marko Cigler
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Thorsten G Müller
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Daniel Horn-Ghetko
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Marie-Kristin von Wrisberg
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Maximilian Fottner
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Roger S Goody
- Department of Structural Biochemistry, MPI of Molecular Physiology, Otto-Hahn Srasse 11, 442277, Dortmund, Germany
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Protein Biochemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Matthias P Müller
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn Str. 4a, 44227, Dortmund, Germany
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
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Cigler M, Müller TG, Horn-Ghetko D, von Wrisberg MK, Fottner M, Goody RS, Itzen A, Müller MP, Lang K. Proximitäts-vermittelte kovalente Stabilisierung niedrig-affiner Proteinkomplexe in vitro und in vivo. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706927] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Marko Cigler
- Center for Integrated Protein Science Munich, CIPSM, Department Chemie, Professur für Synthetische Biochemie; Technische Universität München; Institute for Advanced Study; Lichtenbergstraße 4 85748 Garching Deutschland
| | - Thorsten G. Müller
- Center for Integrated Protein Science Munich, CIPSM, Department Chemie, Professur für Synthetische Biochemie; Technische Universität München; Institute for Advanced Study; Lichtenbergstraße 4 85748 Garching Deutschland
| | - Daniel Horn-Ghetko
- Center for Integrated Protein Science Munich, CIPSM, Department Chemie, Professur für Synthetische Biochemie; Technische Universität München; Institute for Advanced Study; Lichtenbergstraße 4 85748 Garching Deutschland
| | - Marie-Kristin von Wrisberg
- Center for Integrated Protein Science Munich, CIPSM, Department Chemie, Professur für Synthetische Biochemie; Technische Universität München; Institute for Advanced Study; Lichtenbergstraße 4 85748 Garching Deutschland
| | - Maximilian Fottner
- Center for Integrated Protein Science Munich, CIPSM, Department Chemie, Professur für Synthetische Biochemie; Technische Universität München; Institute for Advanced Study; Lichtenbergstraße 4 85748 Garching Deutschland
| | - Roger S. Goody
- Abteilung Strukturbiochemie; Max-Planck-Institut für molekulare Physiologie; Otto-Hahn Straße 11 442277 Dortmund Deutschland
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich (CIPSM); Department Chemie, Professur für Proteinchemie; Technische Universität München; Lichtenbergstraße 4 85748 Garching Deutschland
| | - Matthias P. Müller
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn Straße 4a 44227 Dortmund Deutschland
| | - Kathrin Lang
- Center for Integrated Protein Science Munich, CIPSM, Department Chemie, Professur für Synthetische Biochemie; Technische Universität München; Institute for Advanced Study; Lichtenbergstraße 4 85748 Garching Deutschland
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Boutureira O, Martínez‐Sáez N, Brindle KM, Neves AA, Corzana F, Bernardes GJL. Site-Selective Modification of Proteins with Oxetanes. Chemistry 2017; 23:6483-6489. [PMID: 28261889 PMCID: PMC5434895 DOI: 10.1002/chem.201700745] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Indexed: 12/14/2022]
Abstract
Oxetanes are four-membered ring oxygen heterocycles that are advantageously used in medicinal chemistry as modulators of physicochemical properties of small molecules. Herein, we present a simple method for the incorporation of oxetanes into proteins through chemoselective alkylation of cysteine. We demonstrate a broad substrate scope by reacting proteins used as apoptotic markers and in drug formulation, and a therapeutic antibody with a series of 3-oxetane bromides, enabling the identification of novel handles (S-to-S/N rigid, non-aromatic, and soluble linker) and reactivity modes (temporary cysteine protecting group), while maintaining their intrinsic activity. The possibility to conjugate oxetane motifs into full-length proteins has potential to identify novel drug candidates as the next-generation of peptide/protein therapeutics with improved physicochemical and biological properties.
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Affiliation(s)
- Omar Boutureira
- Department of ChemistryUniversity of CambridgeLensfield RoadCB2 1EWCambridgeUK
- Current address: Departament de Química Analítica i Química OrgànicaFacultat de QuímicaUniversitat Rovira i VirgiliC/ Marcel⋅lí Domingo 143007TarragonaSpain
| | - Nuria Martínez‐Sáez
- Department of ChemistryUniversity of CambridgeLensfield RoadCB2 1EWCambridgeUK
| | - Kevin M. Brindle
- Li Ka Shing CentreCancer Research (UK) Cambridge InstituteRobinson WayCB2 0RECambridgeUK
- Department of BiochemistryUniversity of CambridgeTennis Court RoadCB2 1GACambridgeUK
| | - André A. Neves
- Li Ka Shing CentreCancer Research (UK) Cambridge InstituteRobinson WayCB2 0RECambridgeUK
| | - Francisco Corzana
- Department of ChemistryUniversity of CambridgeLensfield RoadCB2 1EWCambridgeUK
- Departamento de QuímicaCentro de Investigación en Síntesis QuímicaUniversidad de La Rioja26006LogroñoSpain
| | - Gonçalo J. L. Bernardes
- Department of ChemistryUniversity of CambridgeLensfield RoadCB2 1EWCambridgeUK
- Instituto de Medicina MolecularFaculdade de MedicinaUniversidade de LisboaAvenida Professor Egas Moniz1649-028LisboaPortugal
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18
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Xuan W, Shao S, Schultz PG. Protein Crosslinking by Genetically Encoded Noncanonical Amino Acids with Reactive Aryl Carbamate Side Chains. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611841] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Weimin Xuan
- Department of Chemistry; the Scripps Research Institute; 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Sida Shao
- Department of Chemistry; the Scripps Research Institute; 10550 N. Torrey Pines Road La Jolla CA 92037 USA
| | - Peter G. Schultz
- Department of Chemistry; the Scripps Research Institute; 10550 N. Torrey Pines Road La Jolla CA 92037 USA
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Xuan W, Shao S, Schultz PG. Protein Crosslinking by Genetically Encoded Noncanonical Amino Acids with Reactive Aryl Carbamate Side Chains. Angew Chem Int Ed Engl 2017; 56:5096-5100. [PMID: 28371162 DOI: 10.1002/anie.201611841] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/06/2017] [Indexed: 01/08/2023]
Abstract
The use of genetically encoded noncanonical amino acids (ncAAs) to construct crosslinks within or between proteins has emerged as a useful method to enhance protein stability, investigate protein-protein interactions, and improve the pharmacological properties of proteins. We report ncAAs with aryl carbamate side chains (PheK and FPheK) that can react with proximal nucleophilic residues to form intra- or intermolecular protein crosslinks. We evolved a pyrrolysyl-tRNA synthetase that incorporates site-specifically PheK and FPheK into proteins in both E. coli and mammalian cells. PheK and FPheK when incorporated into proteins showed good stability during protein expression and purification. FPheK reacted with adjacent Lys, Cys, and Tyr residues in thioredoxin in high yields. In addition, crosslinks could be formed between FPheK and Lys residue of two interacting proteins, including the heavy chain and light chain of an antibody Fab.
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Affiliation(s)
- Weimin Xuan
- Department of Chemistry, the Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Sida Shao
- Department of Chemistry, the Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Peter G Schultz
- Department of Chemistry, the Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
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Malcolm McIntosh Prize: R. J. Payne / Heinrich Wieland Prize: P. G. Schultz / FCI Dozentenpreis: T. Magauer / Bohlmann Lectureship: F. H. Arnold. Angew Chem Int Ed Engl 2016; 55:15469. [DOI: 10.1002/anie.201610316] [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]
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21
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Malcolm-McIntosh-Preis: R. J. Payne / Heinrich-Wieland-Preis: P. G. Schultz / FCI-Dozentenpreis: T. Magauer / Bohlmann-Vorlesung: F. H. Arnold. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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