1
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Mori T, Sumida S, Sakata K, Shirakawa S. Efficient synthetic methods for α,β-dehydroamino acids as useful and environmentally benign building blocks in biological and materials science. Org Biomol Chem 2024; 22:4625-4636. [PMID: 38804977 DOI: 10.1039/d4ob00507d] [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: 05/29/2024]
Abstract
Both natural and unnatural amino acids, peptides, and proteins are widely recognized as green and sustainable organic chemicals, not only in the field of biological sciences but also in materials science. It has been discovered that artificially designed unnatural peptides and proteins exhibit advanced properties in medical and materials science. In this context, the development of precise chemical modification methods for amino acids and peptides is acknowledged as an important research project in the field of organic synthesis. While a wide variety of modification methods for amino acid residues have been developed to artificially modify peptides and proteins, the representative methods for modifying amino acid residues have traditionally relied on the nucleophilic properties of the functionalities on the residues. In this context, the development of different modification methods using an umpolung-like approach by utilizing the electrophilic nature of amino acid derivatives appears to be very attractive. One of the promising electrophilic amino acid compounds for realizing important modification methods of amino acid derivatives is α,β-dehydroamino acids, which possess an α,β-unsaturated carbonyl structure. This review article summarizes methods for the preparation of α,β-dehydroamino acids derived from natural and unnatural amino acid derivatives. The utilities of α,β-dehydroamino acid derivatives, including peptides and proteins containing dehydroalanine units, in bioconjugations are also discussed.
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Affiliation(s)
- Taiki Mori
- Institute of Integrated Science and Technology, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
| | - Sao Sumida
- Institute of Integrated Science and Technology, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
| | - Kazuki Sakata
- Spiber Inc., 234-1 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Seiji Shirakawa
- Institute of Integrated Science and Technology, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
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2
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Zhao B, Zhang Y, Zhang S, Hu T, Guo Y. Multifactorial interaction of selenium, iron, xylose, and glycine on cordycepin metabolism in Cordyceps militaris. Appl Microbiol Biotechnol 2023; 107:7403-7416. [PMID: 37773218 DOI: 10.1007/s00253-023-12792-x] [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: 07/19/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 10/01/2023]
Abstract
Cordycepin, a nucleoside analog, is the main antioxidative and antimicrobial substance in Cordyceps militaris. To improve the metabolism of cordycepin, carbon sources, nitrogen sources, trace elements, and precursors were studied by single factor, Plackett-Burman, and central composite designs in C. militaris mycelial fermentation. Under the regulation of the multifactorial interactions of selenite, ferrous chloride, xylose, and glycine, cordycepin production was increased by 5.2-fold compared with the control. The gene expression of hexokinase, ATP phosphoribosyltransferase, adenylosuccinate synthetase, and cns1-3 in the glycolysis, pentose phosphate, and adenosine synthesis pathways were increased by 3.2-7.5 times due to multifactorial interactions, while the gene expression of histidine biosynthesis trifunctional protein and histidinol-phosphate aminotransferase in histidine synthesis pathway were decreased by 23.4%-56.2%. Increasing with cordycepin production, glucose uptake was accelerated, mycelia growth was inhibited, and the cell wall was damaged. Selenomethionine (SeMet), selenocysteine (SeCys), and selenium nanoparticles (SeNPs) were the major Se species in C. militaris mycelia. This study provides a new insight for promoting cordycepin production by regulating glycolysis, pentose phosphate, and histidine metabolism. KEY POINTS: • Cordycepin production in the CCDmax group was 5.2-fold than that of the control. • Glucose uptake of the CCDmax group was accelerated and cell wall was damaged. • The metabolic flux was concentrated to the cordycepin synthesis pathway.
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Affiliation(s)
- Bingjie Zhao
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, China
| | - Yong Zhang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, China
| | - Sasa Zhang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, China
| | - Ting Hu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Yanbin Guo
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, China.
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3
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Abstract
The ability to manipulate the chemical composition of proteins and peptides has been central to the development of improved polypeptide-based therapeutics and has enabled researchers to address fundamental biological questions that would otherwise be out of reach. Protein ligation, in which two or more polypeptides are covalently linked, is a powerful strategy for generating semisynthetic products and for controlling polypeptide topology. However, specialized tools are required to efficiently forge a peptide bond in a chemoselective manner with fast kinetics and high yield. Fortunately, nature has addressed this challenge by evolving enzymatic mechanisms that can join polypeptides using a diverse set of chemical reactions. Here, we summarize how such nature-inspired protein ligation strategies have been repurposed as chemical biology tools that afford enhanced control over polypeptide composition.
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Affiliation(s)
- Rasmus Pihl
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA.
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, USA.
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
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4
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Fu XP, Yuan Y, Jha A, Levin N, Giltrap AM, Ren J, Mamalis D, Mohammed S, Davis BG. Stereoretentive Post-Translational Protein Editing. ACS CENTRAL SCIENCE 2023; 9:405-416. [PMID: 36968537 PMCID: PMC10037454 DOI: 10.1021/acscentsci.2c00991] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Indexed: 05/16/2023]
Abstract
Chemical post-translational methods allow convergent side-chain editing of proteins without needing to resort to genetic intervention. Current approaches that allow the creation of constitutionally native side chains via C-C bond formation, using off-protein carbon-centered C· radicals added to unnatural amino acid radical acceptor (SOMOphile, singly occupied molecular orbital (SOMO)) "tags" such as dehydroalanine, are benign and wide-ranging. However, they also typically create epimeric mixtures of d/l-residues. Here, we describe a light-mediated desulfurative method that, through the creation and reaction of stereoretained on-proteinl-alanyl Cβ· radicals, allows Cβ-Hγ, Cβ-Oγ, Cβ-Seγ, Cβ-Bγ, and Cβ-Cγ bond formation to flexibly generate site-selectively edited proteins with full retention of native stereochemistry under mild conditions from a natural amino acid precursor. This methodology shows great potential to explore protein side-chain diversity and function and in the construction of useful bioconjugates.
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Affiliation(s)
- Xia-Ping Fu
- Rosalind
Franklin Institute, Harwell, Oxfordshire OX11 0QX, United Kingdom
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, United Kingdom
| | - Yizhi Yuan
- Rosalind
Franklin Institute, Harwell, Oxfordshire OX11 0QX, United Kingdom
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, United Kingdom
| | - Ajay Jha
- Rosalind
Franklin Institute, Harwell, Oxfordshire OX11 0QX, United Kingdom
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, United Kingdom
| | - Nikita Levin
- Rosalind
Franklin Institute, Harwell, Oxfordshire OX11 0QX, United Kingdom
| | - Andrew M. Giltrap
- Rosalind
Franklin Institute, Harwell, Oxfordshire OX11 0QX, United Kingdom
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, United Kingdom
| | - Jack Ren
- Rosalind
Franklin Institute, Harwell, Oxfordshire OX11 0QX, United Kingdom
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Dimitrios Mamalis
- Rosalind
Franklin Institute, Harwell, Oxfordshire OX11 0QX, United Kingdom
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Shabaz Mohammed
- Rosalind
Franklin Institute, Harwell, Oxfordshire OX11 0QX, United Kingdom
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Benjamin G. Davis
- Rosalind
Franklin Institute, Harwell, Oxfordshire OX11 0QX, United Kingdom
- Department
of Pharmacology, University of Oxford, Oxford OX1 3QT, United Kingdom
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
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5
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Liu X, Henriques ST, Craik DJ, Chan LY. Unlocking the Potential of the Antimicrobial Peptide Gomesin: From Discovery and Structure-Activity Relationships to Therapeutic Applications. Int J Mol Sci 2023; 24:ijms24065893. [PMID: 36982972 PMCID: PMC10053013 DOI: 10.3390/ijms24065893] [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: 02/27/2023] [Revised: 03/17/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023] Open
Abstract
Gomesin is a cationic antimicrobial peptide which is isolated from the haemocytes of the Brazilian tarantula Acanthoscurria gomesiana and can be produced chemically by Fmoc solid-phase peptide synthesis. Gomesin exhibits a range of biological activities, as demonstrated by its toxicity against therapeutically relevant pathogens such as Gram-positive or Gram-negative bacteria, fungi, cancer cells, and parasites. In recent years, a cyclic version of gomesin has been used for drug design and development as it is more stable than native gomesin in human serum and can penetrate and enter cancer cells. It can therefore interact with intracellular targets and has the potential to be developed as a drug lead for to treat cancer, infectious diseases, and other human diseases. This review provides a perspective on the discovery, structure-activity relationships, mechanism of action, biological activity, and potential clinical applications of gomesin.
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Affiliation(s)
- Xiaorong Liu
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sónia T Henriques
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
- Translational Research Institute, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD 4102, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lai Yue Chan
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
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6
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Isenegger PG, Josephson B, Gaunt B, Davy MJ, Gouverneur V, Baldwin AJ, Davis BG. Posttranslational, site-directed photochemical fluorine editing of protein sidechains to probe residue oxidation state via 19F-nuclear magnetic resonance. Nat Protoc 2023; 18:1543-1562. [PMID: 36806799 DOI: 10.1038/s41596-022-00800-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 11/23/2022] [Indexed: 02/22/2023]
Abstract
The fluorination of amino acid residues represents a near-isosteric alteration with the potential to report on biological pathways, yet the site-directed editing of carbon-hydrogen (C-H) bonds in complex biomolecules to carbon-fluorine (C-F) bonds is challenging, resulting in its limited exploitation. Here, we describe a protocol for the posttranslational and site-directed alteration of native γCH2 to γCF2 in protein sidechains. This alteration allows the installation of difluorinated sidechain analogs of proteinogenic amino acids, in both native and modified states. This chemical editing is robust, mild, fast and highly efficient, exploiting photochemical- and radical-mediated C-C bonds grafted onto easy-to-access cysteine-derived dehydroalanine-containing proteins as starting materials. The heteroaryl-sulfonyl reagent required for generating the key carbon-centered C• radicals that install the sidechain can be synthesized in two to six steps from commercially available precursors. This workflow allows the nonexpert to create fluorinated proteins within 24 h, starting from a corresponding purified cysteine-containing protein precursor, without the need for bespoke biological systems. As an example, we readily introduce three γCF2-containing methionines in all three progressive oxidation states (sulfide, sulfoxide and sulfone) as D-/L- forms into histone eH3.1 at site 4 (a relevant lysine to methionine oncomutation site), and each can be detected by 19F-nuclear magnetic resonance of the γCF2 group, as well as the two diastereomers of the sulfoxide, even when found in a complex protein mixture of all three. The site-directed editing of C-H→C-F enables the use of γCF2 as a highly sensitive, 'zero-size-zero-background' label in protein sidechains, which may be used to probe biological phenomena, protein structures and/or protein-ligand interactions by 19F-based detection methods.
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Affiliation(s)
| | | | - Ben Gaunt
- The Rosalind Franklin Institute, Oxfordshire, UK
| | - Matthew J Davy
- The Rosalind Franklin Institute, Oxfordshire, UK.,Department of Pharmacology, University of Oxford, Oxford, UK
| | | | - Andrew J Baldwin
- Department of Chemistry, University of Oxford, Oxford, UK. .,The Rosalind Franklin Institute, Oxfordshire, UK. .,Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
| | - Benjamin G Davis
- Department of Chemistry, University of Oxford, Oxford, UK. .,The Rosalind Franklin Institute, Oxfordshire, UK. .,Department of Pharmacology, University of Oxford, Oxford, UK.
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7
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Liu H, Li G, Peng Z, Zhang S, Zhou X, Liu Q, Wang J, Liu Y, Jia T. Tagging Peptides with a Redox Responsive Fluorescent Probe Enabled by Photoredox Difunctionalization of Phenylacetylenes with Sulfinates and Disulfides. JACS AU 2022; 2:2821-2829. [PMID: 36590269 PMCID: PMC9795567 DOI: 10.1021/jacsau.2c00577] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/07/2022] [Indexed: 05/09/2023]
Abstract
Herein, we describe a photoredox three-component atom-transfer radical addition (ATRA) reaction of aryl alkynes directly with dialkyl disulfides and alkylsulfinates, circumventing the utilization of chemically unstable and synthetically challenging S-alkyl alkylthiosulfonates as viable addition partners. A vast array of (E)-β-alkylsulfonylvinyl alkylsulfides was prepared with great regio- and stereoselectivity. Moreover, this powerful tactic could be employed to tag cysteine residues of complex polypeptides in solution or on resin merging with solid phase peptide synthesis (SPPS) techniques. A sulfonyl-derived redox responsive fluorescent probe could be conveniently introduced on the peptide, which displays green fluorescence in cells while showing blue fluorescence in medium. The photophysical investigations reveal that the red shift of the emission fluorescence is attested to reduction of carbonyl group to the corresponding hydroxyl moiety. Interestingly, the fluorescence change of tagged peptide could be reverted in cells by treatment of H2O2, arising from the reoxidation of hydroxyl group back to ketone by the elevated level of reactive oxygen species (ROS).
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Affiliation(s)
- Hong Liu
- Research
Center for Chemical Biology and Omics Analysis, Department of Chemistry,
and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
| | - Guolin Li
- Research
Center for Chemical Biology and Omics Analysis, Department of Chemistry,
and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
- Department
of Pharmaceutical Engineering, College of Chemical Engineering, Northwest University, Taibai North Road 229, Xi’an, Shanxi 710069, P. R. China
| | - Zhiyuan Peng
- Research
Center for Chemical Biology and Omics Analysis, Department of Chemistry,
and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
| | - Shishuo Zhang
- Research
Center for Chemical Biology and Omics Analysis, Department of Chemistry,
and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
| | - Xin Zhou
- Research
Center for Chemical Biology and Omics Analysis, Department of Chemistry,
and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
- Department
of Pharmaceutical Engineering, College of Chemical Engineering, Northwest University, Taibai North Road 229, Xi’an, Shanxi 710069, P. R. China
| | - Qingchao Liu
- Department
of Pharmaceutical Engineering, College of Chemical Engineering, Northwest University, Taibai North Road 229, Xi’an, Shanxi 710069, P. R. China
| | - Junfeng Wang
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong
Key Laboratory of Marine Materia Medica/Innovation Academy of South
China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xinggang Road, Guangzhou 510301, P. R. China
| | - Yonghong Liu
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong
Key Laboratory of Marine Materia Medica/Innovation Academy of South
China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xinggang Road, Guangzhou 510301, P. R. China
- E-mail:
| | - Tiezheng Jia
- Research
Center for Chemical Biology and Omics Analysis, Department of Chemistry,
and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
- State
Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94
Weijin Road, Tianjin 300071, P. R. China
- E-mail:
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8
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Orr AA, Kuhlmann SK, Tamamis P. Computational design of a β-wrapin's N-terminal domain with canonical and non-canonical amino acid modifications mimicking curcumin's proposed inhibitory function. Biophys Chem 2022; 286:106805. [DOI: 10.1016/j.bpc.2022.106805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/14/2022] [Accepted: 03/18/2022] [Indexed: 12/14/2022]
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9
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Yang A, Tao H, Szymczak LC, Lin L, Song J, Wang Y, Bai S, Modica J, Huang SY, Mrksich M, Feng X. Efficient Enzymatic Incorporation of Dehydroalanine Based on SAMDI-Assisted Identification of Optimized Tags for OspF/SpvC. ACS Chem Biol 2022; 17:414-425. [PMID: 35129954 DOI: 10.1021/acschembio.1c00866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Site-specific modification of proteins has important applications in biological research and drug development. Reactive tags such as azide, alkyne, and tetrazine have been used extensively to achieve the abovementioned goal. However, bulky side-chain "ligation scars" are often left after the labeling and may hinder the biological application of such engineered protein products. Conjugation chemistry via dehydroalanine (Dha) may provide an opportunity for "traceless" ligation because the activated alkene moiety on Dha can then serve as an electrophile to react with radicalophile, thiol/amine nucleophile, and reactive phosphine probe to introduce a minimal linker in the protein post-translational modifications. In this report, we present a mild and highly efficient enzymatic approach to incorporate Dha with phosphothreonine/serine lyases, OspF and SpvC. These lyases originally catalyze an irreversible elimination reaction that converts a doubly phosphorylated substrate with phosphothreonine (pT) or phosphoserine (pS) to dehydrobutyrine (Dhb) or Dha. To generate a simple monophosphorylated tag for these lyases, we conducted a systematic approach to profile the substrate specificity of OspF and SpvC using peptide arrays and self-assembled monolayers for matrix-assisted laser desorption/ionization mass spectrometry. The optimized tag, [F/Y/W]-pT/pS-[F/Y/W] (where [F/Y/W] indicates an aromatic residue), results in a ∼10-fold enhancement of the overall peptide labeling efficiency via Dha chemistry and enables the first demonstration of protein labeling as well as live cell labeling with a minimal ligation linker via enzyme-mediated incorporation of Dha.
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Affiliation(s)
- Anming Yang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha 410082, China
| | - Huanyu Tao
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Lindsey C. Szymczak
- Departments of Chemistry and Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Liang Lin
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Junfeng Song
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha 410082, China
| | - Yi Wang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha 410082, China
| | - Silei Bai
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha 410082, China
| | - Justin Modica
- Departments of Chemistry and Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Milan Mrksich
- Departments of Chemistry and Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Xinxin Feng
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and Department of Chemistry, Hunan University, Changsha 410082, China
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10
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Cao Y, Bi X. Butelase-1 as the Prototypical Peptide Asparaginyl Ligase and Its Applications: A Review. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10320-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Chowdhury A, Chatterjee S, Pongen A, Sarania D, Tripathi NM, Bandyopadhyay A. nSite-Selective, Chemical Modification of Protein at Aromatic Side Chain and Their Emergent Applications. Protein Pept Lett 2021; 28:788-808. [PMID: 33511938 DOI: 10.2174/0929866528666210129152535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/11/2020] [Accepted: 12/20/2020] [Indexed: 11/22/2022]
Abstract
Site-selective chemical modification of protein side chain has probed enormous opportunities in the fundamental understanding of cellular biology and therapeutic applications. Primarily, in the field of biopharmaceutical where formulation of bioconjugates is found to be potential medicine than an individual constituent. In this regard, Lysine and Cysteine are the most widely used endogenous amino acid for these purposes. Recently, the aromatic side chain residues (Trp, Tyr, and His) that are low abundant in protein have gained more attention in therapeutic applications due to their advantages of chemical reactivity and specificity. This review discusses the site-selective bioconjugation methods for aromatic side chains (Trp, Tyr and His) and highlights the developed strategies in the last three years, along with their applications. Also, the review highlights the prevalent methods published earlier. We have examined that metal-catalyzed and photocatalytic reactions are gaining more attention for bioconjugation, though their practical operation is under development. The review has been summarized with the future perspective of protein and peptide conjugations contemplating therapeutic applications and challenges.
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Affiliation(s)
- Arnab Chowdhury
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Birla Farms, Punjab-781039. India
| | - Saurav Chatterjee
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Birla Farms, Punjab-781039. India
| | - Akumlong Pongen
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Birla Farms, Punjab-781039. India
| | - Dhanjit Sarania
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Birla Farms, Punjab-781039. India
| | - Nitesh Mani Tripathi
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Birla Farms, Punjab-781039. India
| | - Anupam Bandyopadhyay
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Birla Farms, Punjab-781039. India
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12
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Jones LH. Dehydroamino acid chemical biology: an example of functional group interconversion on proteins. RSC Chem Biol 2020; 1:298-304. [PMID: 34458767 PMCID: PMC8341704 DOI: 10.1039/d0cb00174k] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022] Open
Abstract
In nature, dehydroalanine (Dha) and dehydrobutyrine (Dhb) residues are byproducts of protein aging, intermediates in the biosynthesis of lanthipeptides and products of bacterial phospholyases that inactivate host kinase immune responses. Recent chemical biology studies have demonstrated the possibility of mapping dehydroamino acids in complex proteomes in an unbiased manner that could further our understanding of the role of Dha and Dhb in biology and disease more broadly. From a synthetic perspective, chemical mutagenesis through site-selective formation of the unsaturated residue and subsequent addition chemistry has yielded homogeneous proteins bearing a variety of post-translational modifications (PTMs) which have assisted fundamental biological research. This Opinion discusses these recent advances and presents new opportunities for protein engineering and drug discovery. The chemical biology of dehydroalanine and dehydrobutyrine in proteins is summarized and new concepts are presented.![]()
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Affiliation(s)
- Lyn H Jones
- Center for Protein Degradation, Dana-Farber Cancer Institute 360 Longwood Avenue Boston MA 02215 USA
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13
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Josephson B, Fehl C, Isenegger PG, Nadal S, Wright TH, Poh AWJ, Bower BJ, Giltrap AM, Chen L, Batchelor-McAuley C, Roper G, Arisa O, Sap JBI, Kawamura A, Baldwin AJ, Mohammed S, Compton RG, Gouverneur V, Davis BG. Light-driven post-translational installation of reactive protein side chains. Nature 2020; 585:530-537. [PMID: 32968259 DOI: 10.1038/s41586-020-2733-7] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 07/15/2020] [Indexed: 02/07/2023]
Abstract
Post-translational modifications (PTMs) greatly expand the structures and functions of proteins in nature1,2. Although synthetic protein functionalization strategies allow mimicry of PTMs3,4, as well as formation of unnatural protein variants with diverse potential functions, including drug carrying5, tracking, imaging6 and partner crosslinking7, the range of functional groups that can be introduced remains limited. Here we describe the visible-light-driven installation of side chains at dehydroalanine residues in proteins through the formation of carbon-centred radicals that allow C-C bond formation in water. Control of the reaction redox allows site-selective modification with good conversions and reduced protein damage. In situ generation of boronic acid catechol ester derivatives generates RH2C• radicals that form the native (β-CH2-γ-CH2) linkage of natural residues and PTMs, whereas in situ potentiation of pyridylsulfonyl derivatives by Fe(II) generates RF2C• radicals that form equivalent β-CH2-γ-CF2 linkages bearing difluoromethylene labels. These reactions are chemically tolerant and incorporate a wide range of functionalities (more than 50 unique residues/side chains) into diverse protein scaffolds and sites. Initiation can be applied chemoselectively in the presence of sensitive groups in the radical precursors, enabling installation of previously incompatible side chains. The resulting protein function and reactivity are used to install radical precursors for homolytic on-protein radical generation; to study enzyme function with natural, unnatural and CF2-labelled post-translationally modified protein substrates via simultaneous sensing of both chemo- and stereoselectivity; and to create generalized 'alkylator proteins' with a spectrum of heterolytic covalent-bond-forming activity (that is, reacting diversely with small molecules at one extreme or selectively with protein targets through good mimicry at the other). Post-translational access to such reactions and chemical groups on proteins could be useful in both revealing and creating protein function.
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Affiliation(s)
- Brian Josephson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Charlie Fehl
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | - Patrick G Isenegger
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Simon Nadal
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Tom H Wright
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Adeline W J Poh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Ben J Bower
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Andrew M Giltrap
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- The Rosalind Franklin Institute, Harwell, UK
| | - Lifu Chen
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | | | - Grace Roper
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Oluwatobi Arisa
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Jeroen B I Sap
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Andrew J Baldwin
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Shabaz Mohammed
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
- The Rosalind Franklin Institute, Harwell, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Richard G Compton
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Veronique Gouverneur
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
| | - Benjamin G Davis
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
- The Rosalind Franklin Institute, Harwell, UK.
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14
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Ganguly HK, Basu G. Conformational landscape of substituted prolines. Biophys Rev 2020; 12:25-39. [PMID: 31953795 PMCID: PMC7040156 DOI: 10.1007/s12551-020-00621-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/09/2020] [Indexed: 12/16/2022] Open
Abstract
The cyclic side chain of the amino acid proline confers unique conformational restraints on its backbone and side chain dihedral angles. This affects two equilibria-one at the backbone (cis/trans) and the other at the side chain (endo/exo). Substitutions on the proline ring impose additional steric and stereoelectronic effects that can further modulate both these equilibria, which in turn can also affect the backbone dihedral angle (ϕ, ψ) preferences. In this review, we have explored the conformational landscape of several termini capped mono-(2-, 3-, 4-, and 5-) substituted proline derivatives in the Cambridge Structural Database, correlating observed conformations with the nature of substituents and deciphering the underlying interactions for the observed structural biases. The impact of incorporating these derivatives within model peptides and proteins are also discussed for selected cases. Several of these substituents have been used to introduce bioorthogonal functionality and modulate structure-specific ligand recognition or used as spectroscopic probes. The incorporation of these diversely applicable functional groups, coupled with their ability to define an amino acid conformation via stereoelectronic effects, have a broad appeal among chemical biologists, molecular biophysicists, and medicinal chemists.
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Affiliation(s)
- Himal Kanti Ganguly
- Department of Biophysics, Bose Institute, P-1/12 CIT scheme VII M, Kolkata, 700054, India.
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT scheme VII M, Kolkata, 700054, India.
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15
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Nadal S, Raj R, Mohammed S, Davis BG. Synthetic post-translational modification of histones. Curr Opin Chem Biol 2018; 45:35-47. [DOI: 10.1016/j.cbpa.2018.02.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/17/2018] [Accepted: 02/10/2018] [Indexed: 12/14/2022]
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16
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de Bruijn AD, Roelfes G. Catalytic Modification of Dehydroalanine in Peptides and Proteins by Palladium-Mediated Cross-Coupling. Chemistry 2018; 24:12728-12733. [PMID: 29923249 PMCID: PMC6146911 DOI: 10.1002/chem.201802846] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 06/18/2018] [Indexed: 11/16/2022]
Abstract
Dehydroalanine (Dha) is a remarkably versatile non‐canonical amino acid often found in antimicrobial peptides. Herein, we present the catalytic modification of Dha by a palladium‐mediated cross‐coupling reaction. By using Pd(EDTA)(OAc)2 as water‐soluble catalyst, a variety of arylboronic acids was coupled to the dehydrated residues in proteins and peptides, such as Nisin. The cross‐coupling reaction gave both the Heck product, in which the sp2‐hybridisation of the α‐carbon is retained, as well as the conjugated addition product. The reaction can be performed under mild aqueous conditions, which makes this method an attractive addition to the palette of bio‐orthogonal catalytic methods.
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Affiliation(s)
- A Dowine de Bruijn
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
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17
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Dadová J, Galan SR, Davis BG. Synthesis of modified proteins via functionalization of dehydroalanine. Curr Opin Chem Biol 2018; 46:71-81. [PMID: 29913421 DOI: 10.1016/j.cbpa.2018.05.022] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/02/2018] [Accepted: 05/29/2018] [Indexed: 12/17/2022]
Abstract
Dehydroalanine has emerged in recent years as a non-proteinogenic residue with strong chemical utility in proteins for the study of biology. In this review we cover the several methods now available for its flexible and site-selective incorporation via a variety of complementary chemical and biological techniques and examine its reactivity, allowing both creation of modified protein side-chains through a variety of bond-forming methods (C-S, C-N, C-Se, C-C) and as an activity-based probe in its own right. We illustrate its utility with selected examples of biological and technological discovery and application.
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Affiliation(s)
- Jitka Dadová
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sébastien Rg Galan
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Benjamin G Davis
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom.
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18
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Bertoldo JB, Rodrigues T, Dunsmore L, Aprile FA, Marques MC, Rosado LA, Boutureira O, Steinbrecher TB, Sherman W, Corzana F, Terenzi H, Bernardes GJL. A Water-Bridged Cysteine-Cysteine Redox Regulation Mechanism in Bacterial Protein Tyrosine Phosphatases. Chem 2017; 3:665-677. [PMID: 29094109 PMCID: PMC5656095 DOI: 10.1016/j.chempr.2017.07.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 06/01/2017] [Accepted: 07/07/2017] [Indexed: 11/25/2022]
Abstract
The emergence of multidrug-resistant Mycobacterium tuberculosis (Mtb) strains highlights the need to develop more efficacious and potent drugs. However, this goal is dependent on a comprehensive understanding of Mtb virulence protein effectors at the molecular level. Here, we used a post-expression cysteine (Cys)-to-dehydrolanine (Dha) chemical editing strategy to identify a water-mediated motif that modulates accessibility of the protein tyrosine phosphatase A (PtpA) catalytic pocket. Importantly, this water-mediated Cys-Cys non-covalent motif is also present in the phosphatase SptpA from Staphylococcus aureus, which suggests a potentially preserved structural feature among bacterial tyrosine phosphatases. The identification of this structural water provides insight into the known resistance of Mtb PtpA to the oxidative conditions that prevail within an infected host macrophage. This strategy could be applied to extend the understanding of the dynamics and function(s) of proteins in their native state and ultimately aid in the design of small-molecule modulators.
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Affiliation(s)
- Jean B Bertoldo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.,Centro de Biologia Molecular Estrutural, Departamento de Bioquímica, Universidade Federal de Santa Catarina, 88040-970 Florianópolis-SC, Brazil
| | - Tiago Rodrigues
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisbon, Portugal
| | - Lavinia Dunsmore
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Francesco A Aprile
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Marta C Marques
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisbon, Portugal
| | - Leonardo A Rosado
- Centro de Biologia Molecular Estrutural, Departamento de Bioquímica, Universidade Federal de Santa Catarina, 88040-970 Florianópolis-SC, Brazil
| | - Omar Boutureira
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | | | - Woody Sherman
- Schrödinger, 120 West 45th Street, New York, NY 10036, USA
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006 Logroño, Spain
| | - Hernán Terenzi
- Centro de Biologia Molecular Estrutural, Departamento de Bioquímica, Universidade Federal de Santa Catarina, 88040-970 Florianópolis-SC, Brazil
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.,Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisbon, Portugal
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19
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Fadeyi OO, Hoth LR, Choi C, Feng X, Gopalsamy A, Hett EC, Kyne RE, Robinson RP, Jones LH. Covalent Enzyme Inhibition through Fluorosulfate Modification of a Noncatalytic Serine Residue. ACS Chem Biol 2017; 12:2015-2020. [PMID: 28718624 DOI: 10.1021/acschembio.7b00403] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Irreversible enzyme inhibitors and covalent chemical biology probes often utilize the reaction of a protein cysteine residue with an appropriately positioned electrophile (e.g., acrylamide) on the ligand template. However, cysteine residues are not always available for site-specific protein labeling, and therefore new approaches are needed to expand the toolkit of appropriate electrophiles ("warheads") that target alternative amino acids. We previously described the rational targeting of tyrosine residues in the active site of a protein (the mRNA decapping scavenger enzyme, DcpS) using inhibitors armed with a sulfonyl fluoride electrophile. These inhibitors subsequently enabled the development of clickable probe technology to measure drug-target occupancy in live cells. Here we describe a fluorosulfate-containing inhibitor (aryl fluorosulfate probe (FS-p1)) with excellent chemical and metabolic stability that reacts selectively with a noncatalytic serine residue in the same active site of DcpS as confirmed by peptide mapping experiments. Our results suggest that noncatalytic serine targeting using fluorosulfate electrophilic warheads could be a suitable strategy for the development of covalent inhibitor drugs and chemical probes.
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Affiliation(s)
- Olugbeminiyi O. Fadeyi
- Medicine
Design, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Lise R. Hoth
- Medicine
Design, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Chulho Choi
- Medicine
Design, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Xidong Feng
- Medicine
Design, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ariamala Gopalsamy
- Medicine
Design, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Erik C. Hett
- Medicine
Design, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Robert E. Kyne
- Medicine
Design, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ralph P. Robinson
- Medicine
Design, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Lyn H. Jones
- Medicine
Design, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
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20
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He D, Luo W, Wang Z, Lv P, Yuan Z, Huang S, Xv J. Establishment and application of a modified membrane-blot assay for Rhizomucor miehei lipases aimed at improving their methanol tolerance and thermostability. Enzyme Microb Technol 2017; 102:35-40. [DOI: 10.1016/j.enzmictec.2017.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 10/19/2022]
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21
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Guha TK, Wai A, Hausner G. Programmable Genome Editing Tools and their Regulation for Efficient Genome Engineering. Comput Struct Biotechnol J 2017; 15:146-160. [PMID: 28179977 PMCID: PMC5279741 DOI: 10.1016/j.csbj.2016.12.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/24/2016] [Accepted: 12/27/2016] [Indexed: 12/26/2022] Open
Abstract
Targeted genome editing has become a powerful genetic tool for studying gene function or for modifying genomes by correcting defective genes or introducing genes. A variety of reagents have been developed in recent years that can generate targeted double-stranded DNA cuts which can be repaired by the error-prone, non-homologous end joining repair system or via the homologous recombination-based double-strand break repair pathway provided a suitable template is available. These genome editing reagents require components for recognizing a specific DNA target site and for DNA-cleavage that generates the double-stranded break. In order to reduce potential toxic effects of genome editing reagents, it might be desirable to control the in vitro or in vivo activity of these reagents by incorporating regulatory switches that can reduce off-target activities and/or allow for these reagents to be turned on or off. This review will outline the various genome editing tools that are currently available and describe the strategies that have so far been employed for regulating these editing reagents. In addition, this review will examine potential regulatory switches/strategies that can be employed in the future in order to provide temporal control for these reagents.
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Affiliation(s)
| | | | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba R3T2N2, Canada
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22
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Wright TH, Bower BJ, Chalker JM, Bernardes GJL, Wiewiora R, Ng WL, Raj R, Faulkner S, Vallée MRJ, Phanumartwiwath A, Coleman OD, Thézénas ML, Khan M, Galan SRG, Lercher L, Schombs MW, Gerstberger S, Palm-Espling ME, Baldwin AJ, Kessler BM, Claridge TDW, Mohammed S, Davis BG. Posttranslational mutagenesis: A chemical strategy for exploring protein side-chain diversity. Science 2016; 354:science.aag1465. [PMID: 27708059 DOI: 10.1126/science.aag1465] [Citation(s) in RCA: 220] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/12/2016] [Indexed: 12/26/2022]
Abstract
Posttranslational modification of proteins expands their structural and functional capabilities beyond those directly specified by the genetic code. However, the vast diversity of chemically plausible (including unnatural but functionally relevant) side chains is not readily accessible. We describe C (sp3)-C (sp3) bond-forming reactions on proteins under biocompatible conditions, which exploit unusual carbon free-radical chemistry, and use them to form Cβ-Cγ bonds with altered side chains. We demonstrate how these transformations enable a wide diversity of natural, unnatural, posttranslationally modified (methylated, glycosylated, phosphorylated, hydroxylated), and labeled (fluorinated, isotopically labeled) side chains to be added to a common, readily accessible dehydroalanine precursor in a range of representative protein types and scaffolds. This approach, outside of the rigid constraints of the ribosome and enzymatic processing, may be modified more generally for access to diverse proteins.
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Affiliation(s)
- Tom H Wright
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Ben J Bower
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Justin M Chalker
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | | | - Rafal Wiewiora
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Wai-Lung Ng
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Ritu Raj
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Sarah Faulkner
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | | | | | - Oliver D Coleman
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Marie-Laëtitia Thézénas
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Headington, Oxford OX3 7FZ, UK
| | - Maola Khan
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | | | - Lukas Lercher
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | | | | | | | - Andrew J Baldwin
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Headington, Oxford OX3 7FZ, UK
| | | | - Shabaz Mohammed
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Benjamin G Davis
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.
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23
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Gunnoo SB, Madder A. Chemical Protein Modification through Cysteine. Chembiochem 2016; 17:529-53. [DOI: 10.1002/cbic.201500667] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Smita B. Gunnoo
- Organic & Biomimetic Chemistry Research Group; Department of Organic and Macromolecular Chemistry; Ghent University; Krijgslaan 281 9000 Gent Belgium
| | - Annemieke Madder
- Organic & Biomimetic Chemistry Research Group; Department of Organic and Macromolecular Chemistry; Ghent University; Krijgslaan 281 9000 Gent Belgium
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24
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Forbes CR, Pandey AK, Ganguly HK, Yap GPA, Zondlo NJ. 4R- and 4S-iodophenyl hydroxyproline, 4R-pentynoyl hydroxyproline, and S-propargyl-4-thiolphenylalanine: conformationally biased and tunable amino acids for bioorthogonal reactions. Org Biomol Chem 2016; 14:2327-46. [PMID: 26806113 PMCID: PMC5824642 DOI: 10.1039/c5ob02473k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bioorthogonal reactions allow the introduction of new functionalities into peptides, proteins, and other biological molecules. The most readily accessible amino acids for bioorthogonal reactions have modest conformational preferences or bases for molecular interactions. Herein we describe the synthesis of 4 novel amino acids containing functional groups for bioorthogonal reactions. (2S,4R)- and (2S,4S)-iodophenyl ethers of hydroxyproline are capable of modification via rapid, specific Suzuki and Sonogashira reactions in water. The synthesis of these amino acids, as Boc-, Fmoc- and free amino acids, was achieved through succinct sequences. These amino acids exhibit well-defined conformational preferences, with the 4S-iodophenyl hydroxyproline crystallographically exhibiting β-turn (ϕ, ψ∼-80°, 0°) or relatively extended (ϕ, ψ∼-80°, +170°) conformations, while the 4R-diastereomer prefers a more compact conformation (ϕ∼-60°). The aryloxyproline diastereomers present the aryl groups in a highly divergent manner, suggesting their stereospecific use in molecular design, medicinal chemistry, and catalysis. Thus, the 4R- and 4S-iodophenyl hydroxyprolines can be differentially applied in distinct structural contexts. The pentynoate ester of 4R-hydroxyproline introduces an alkyne functional group within an amino acid that prefers compact conformations. The propargyl thioether of 4-thiolphenylalanine was synthesized via copper-mediated cross-coupling reaction of thioacetic acid with protected 4-iodophenylalanine, followed by thiolysis and alkylation. This amino acid combines an alkyne functional group with an aromatic amino acid and the ability to tune aromatic and side chain properties via sulfur oxidation. These amino acids provide novel loci for peptide functionalization, with greater control of conformation possible than with other amino acids containing these functional groups.
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Affiliation(s)
- Christina R. Forbes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Anil K. Pandey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Himal K. Ganguly
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Glenn P. A. Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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25
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Nguyen GKT, Cao Y, Wang W, Liu CF, Tam JP. Site‐Specific N‐Terminal Labeling of Peptides and Proteins using Butelase 1 and Thiodepsipeptide. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506810] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Giang K. T. Nguyen
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore)
| | - Yuan Cao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore)
| | - Wei Wang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore)
| | - Chuan Fa Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore)
| | - James P. Tam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore)
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26
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Nguyen GKT, Cao Y, Wang W, Liu CF, Tam JP. Site-Specific N-Terminal Labeling of Peptides and Proteins using Butelase 1 and Thiodepsipeptide. Angew Chem Int Ed Engl 2015; 54:15694-8. [PMID: 26563575 DOI: 10.1002/anie.201506810] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 10/21/2015] [Indexed: 12/15/2022]
Abstract
An efficient ligase with exquisite site-specificity is highly desirable for protein modification. Recently, we discovered the fastest known ligase called butelase 1 from Clitoria ternatea for intramolecular cyclization. For intermolecular ligation, butelase 1 requires an excess amount of a substrate to suppress the reverse reaction, a feature similar to other ligases. Herein, we describe the use of thiodepsipeptide substrates with a thiol as a leaving group and an unacceptable nucleophile to render the butelase-mediated ligation reactions irreversible and in high yields. Butelase 1 also accepted depsipeptides as substrates, but unlike a thiodesipeptide, the desipeptide ligation was partially reversible as butelase 1 can tolerate an alcohol group as a poor nucleophile. The thiodesipeptide method was successfully applied in N-terminal labeling of ubiquitin and green fluorescent protein using substrates with or without a biotin group in high yields.
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Affiliation(s)
- Giang K T Nguyen
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore)
| | - Yuan Cao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore)
| | - Wei Wang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore)
| | - Chuan Fa Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore)
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore).
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Narayanan A, Jones LH. Sulfonyl fluorides as privileged warheads in chemical biology. Chem Sci 2015; 6:2650-2659. [PMID: 28706662 PMCID: PMC5489032 DOI: 10.1039/c5sc00408j] [Citation(s) in RCA: 343] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 03/16/2015] [Indexed: 01/10/2023] Open
Abstract
The use of sulfonyl fluoride probes in chemical biology is reviewed.
Sulfonyl fluoride electrophiles have found significant utility as reactive probes in chemical biology and molecular pharmacology. As warheads they possess the right balance of biocompatibility (including aqueous stability) and protein reactivity. Their functionality is privileged in this regard as they are known to modify not only reactive serines (resulting in their common use as protease inhibitors), but also context-specific threonine, lysine, tyrosine, cysteine and histidine residues. This review describes the application of sulfonyl fluoride probes across various areas of research and explores new approaches that could further enhance the chemical biology toolkit. We believe that sulfonyl fluoride probes will find greater utility in areas such as covalent enzyme inhibition, target identification and validation, and the mapping of enzyme binding sites, substrates and protein–protein interactions.
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Affiliation(s)
- Arjun Narayanan
- Chemical Biology Group , BioTherapeutics Chemistry , WorldWide Medicinal Chemistry , Pfizer , 610 Main Street , Cambridge , MA 02139 , USA .
| | - Lyn H Jones
- Chemical Biology Group , BioTherapeutics Chemistry , WorldWide Medicinal Chemistry , Pfizer , 610 Main Street , Cambridge , MA 02139 , USA .
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Khoury GA, Smadbeck J, Tamamis P, Vandris AC, Kieslich CA, Floudas CA. Forcefield_NCAA: ab initio charge parameters to aid in the discovery and design of therapeutic proteins and peptides with unnatural amino acids and their application to complement inhibitors of the compstatin family. ACS Synth Biol 2014; 3:855-69. [PMID: 24932669 PMCID: PMC4277759 DOI: 10.1021/sb400168u] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We describe the development and testing of ab initio derived, AMBER ff03 compatible charge parameters for a large library of 147 noncanonical amino acids including β- and N-methylated amino acids for use in applications such as protein structure prediction and de novo protein design. The charge parameter derivation was performed using the RESP fitting approach. Studies were performed assessing the suitability of the derived charge parameters in discriminating the activity/inactivity between 63 analogs of the complement inhibitor Compstatin on the basis of previously published experimental IC50 data and a screening procedure involving short simulations and binding free energy calculations. We found that both the approximate binding affinity (K*) and the binding free energy calculated through MM-GBSA are capable of discriminating between active and inactive Compstatin analogs, with MM-GBSA performing significantly better. Key interactions between the most potent Compstatin analog that contains a noncanonical amino acid are presented and compared to the most potent analog containing only natural amino acids and native Compstatin. We make the derived parameters and an associated web interface that is capable of performing modifications on proteins using Forcefield_NCAA and outputting AMBER-ready topology and parameter files freely available for academic use at http://selene.princeton.edu/FFNCAA . The forcefield allows one to incorporate these customized amino acids into design applications with control over size, van der Waals, and electrostatic interactions.
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Affiliation(s)
- George A. Khoury
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - James Smadbeck
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Phanourios Tamamis
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Andrew C. Vandris
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Chris A. Kieslich
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Christodoulos A. Floudas
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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29
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Khoury GA, Bhatia N, Floudas CA. Hydration free energies calculated using the AMBER ff03 charge model for natural and unnatural amino acids and multiple water models. Comput Chem Eng 2014. [DOI: 10.1016/j.compchemeng.2014.07.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Spicer CD, Davis BG. Selective chemical protein modification. Nat Commun 2014; 5:4740. [PMID: 25190082 DOI: 10.1038/ncomms5740] [Citation(s) in RCA: 716] [Impact Index Per Article: 71.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 07/21/2014] [Indexed: 02/06/2023] Open
Abstract
Chemical modification of proteins is an important tool for probing natural systems, creating therapeutic conjugates and generating novel protein constructs. Site-selective reactions require exquisite control over both chemo- and regioselectivity, under ambient, aqueous conditions. There are now various methods for achieving selective modification of both natural and unnatural amino acids--each with merits and limitations--providing a 'toolkit' that until 20 years ago was largely limited to reactions at nucleophilic cysteine and lysine residues. If applied in a biologically benign manner, this chemistry could form the basis of true Synthetic Biology.
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Affiliation(s)
- Christopher D Spicer
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Benjamin G Davis
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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31
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Ma J, Zeng J, Wan Q. Postligation-Desulfurization: A General Approach for Chemical Protein Synthesis. Top Curr Chem (Cham) 2014; 363:57-101. [DOI: 10.1007/128_2014_594] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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32
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Hemphill J, Chou C, Chin JW, Deiters A. Genetically encoded light-activated transcription for spatiotemporal control of gene expression and gene silencing in mammalian cells. J Am Chem Soc 2013; 135:13433-9. [PMID: 23931657 DOI: 10.1021/ja4051026] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photocaging provides a method to spatially and temporally control biological function and gene expression with high resolution. Proteins can be photochemically controlled through the site-specific installation of caging groups on amino acid side chains that are essential for protein function. The photocaging of a synthetic gene network using unnatural amino acid mutagenesis in mammalian cells was demonstrated with an engineered bacteriophage RNA polymerase. A caged T7 RNA polymerase was expressed in cells with an expanded genetic code and used in the photochemical activation of genes under control of an orthogonal T7 promoter, demonstrating tight spatial and temporal control. The synthetic gene expression system was validated with two reporter genes (luciferase and EGFP) and applied to the light-triggered transcription of short hairpin RNA constructs for the induction of RNA interference.
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Affiliation(s)
- James Hemphill
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
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33
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Steiner M, Hartmann I, Perrino E, Casi G, Brighton S, Jelesarov I, Bernardes GJL, Neri D. Spacer length shapes drug release and therapeutic efficacy of traceless disulfide-linked ADCs targeting the tumor neovasculature. Chem Sci 2013. [DOI: 10.1039/c2sc21107f] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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34
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Chalker JM. Prospects in the Total Synthesis of Protein Therapeutics. Chem Biol Drug Des 2012; 81:122-35. [DOI: 10.1111/cbdd.12007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Williamson DJ, Fascione MA, Webb ME, Turnbull WB. Efficient N-Terminal Labeling of Proteins by Use of Sortase. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204538] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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36
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Williamson DJ, Fascione MA, Webb ME, Turnbull WB. Efficient N-terminal labeling of proteins by use of sortase. Angew Chem Int Ed Engl 2012; 51:9377-80. [PMID: 22890696 DOI: 10.1002/anie.201204538] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Indexed: 01/30/2023]
Affiliation(s)
- Daniel J Williamson
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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37
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Peer CJ, Younis IR, Leonard SS, Gannett PM, Minarchick VC, Kenyon AJ, Rojanasakul Y, Callery PS. Glutathione conjugation of busulfan produces a hydroxyl radical-trapping dehydroalanine metabolite. Xenobiotica 2012; 42:1170-7. [DOI: 10.3109/00498254.2012.696740] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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38
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Pavic K, Köhn M. Chemical Biology Techniques Unlock the Secrets of Casein Kinase 2 Regulation by Phosphorylation and Glycosylation. Chembiochem 2012; 13:1253-5. [DOI: 10.1002/cbic.201200235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Indexed: 01/17/2023]
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39
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Arunachalam TS, Wichert C, Appel B, Müller S. Mixed oligonucleotides for random mutagenesis: best way of making them. Org Biomol Chem 2012; 10:4641-50. [PMID: 22552713 DOI: 10.1039/c2ob25328c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The generation of proteins, especially enzymes, with pre-deliberated, novel properties is a big challenge in the field of protein engineering. This aim, over the years was critically facilitated by newly emerging methods of combinatorial and evolutionary techniques, such as combinatorial gene synthesis followed by functional screening of many structural variants generated in parallel (library). Libraries can be generated by a large number of available methods. Therein the use of mixtures of pre-formed trinucleotide blocks representing codons for the 20 canonical amino acids for oligonucleotide synthesis stands out as allowing fully controlled partial (or total) randomization individually at any number of arbitrarily chosen codon positions of a given gene. This has created substantial demand of fully protected trinucleotide synthons of good reactivity in standard oligonucleotide synthesis. We here review methods for the preparation of oligonucleotide mixtures with a strong focus on codon-specific trinucleotide blocks.
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Affiliation(s)
- Tamil Selvi Arunachalam
- Institut für Biochemie, Ernst Moritz Arndt Universität, Felix Hausdorff Strasse 4, Greifswald, D-17487, Germany
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40
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Chalker JM, Bernardes GJL, Davis BG. A "tag-and-modify" approach to site-selective protein modification. Acc Chem Res 2011; 44:730-41. [PMID: 21563755 DOI: 10.1021/ar200056q] [Citation(s) in RCA: 295] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Covalent modification can expand a protein's functional capacity. Fluorescent or radioactive labeling, for instance, allows imaging of a protein in real time. Labeling with an affinity probe enables isolation of target proteins and other interacting molecules. At the other end of this functional spectrum, protein structures can be naturally altered by enzymatic action. Protein-protein interactions, genetic regulation, and a range of cellular processes are under the purview of these post-translational modifications. The ability of protein chemists to install these covalent additions selectively has been critical for elucidating their roles in biology. Frequently the transformations must be applied in a site-specific manner, which demands the most selective chemistry. In this Account, we discuss the development and application of such chemistry in our laboratory. A centerpiece of our strategy is a "tag-and-modify" approach, which entails sequential installation of a uniquely reactive chemical group into the protein (the "tag") and the selective or specific modification of this group. The chemical tag can be a natural or unnatural amino acid residue. Of the natural residues, cysteine is the most widely used as a tag. Early work in our program focused on selective disulfide formation in the synthesis of glycoproteins. For certain applications, the susceptibility of disulfides to reduction was a limitation and prompted the development of several methods for the synthesis of more stable thioether modifications. The desulfurization of disulfides and conjugate addition to dehydroalanine are two routes to these modifications. The dehydroalanine tag has since proven useful as a general precursor to many modifications after conjugate addition of various nucleophiles; phosphorylated, glycosylated, peptidylated, prenylated, and even mimics of methylated and acetylated lysine-containing proteins are all accessible from dehydroalanine. While cysteine is a useful tag for selective modification, unnatural residues present the opportunity for bio-orthogonal chemistry. Azide-, arylhalide-, alkyne-, and alkene-containing amino acids can be incorporated into proteins genetically and can be specifically modified through various transformations. These transformations often rely on metal catalysis. The Cu-catalyzed azide-alkyne addition, Ru-catalyzed olefin metathesis, and Pd-catalyzed cross-coupling are examples of such transformations. In the course of adapting these reactions to protein modification, we learned much about the behavior of these reactions in water, and in some cases entirely new catalysts were developed. Through a combination of these bio-orthogonal transformations from the panel of tag-and-modify reactions, multiple and distinct modifications can be installed on protein surfaces. Multiple modifications are common in natural systems, and synthetic access to these proteins has enabled study of their biological role. Throughout these investigations, much has been learned in chemistry and biology. The demands of selective protein modification have revealed many aspects of reaction mechanisms, which in turn have guided the design of reagents and catalysts that allow their successful deployment in water and in biological milieu. With this ability to modify proteins, it is now possible to interrogate biological systems with precision that was not previously possible.
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Affiliation(s)
- Justin M. Chalker
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Gonçalo J. L. Bernardes
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Benjamin G. Davis
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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41
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Dettin M, Muncan N, Bugatti A, Grezzo F, Danesin R, Rusnati M. Chemoselective surface immobilization of proteins through a cleavable peptide. Bioconjug Chem 2011; 22:1753-7. [PMID: 21819154 DOI: 10.1021/bc200254u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Surface immobilization of biomolecules is a fundamental step in several experimental techniques such as surface plasmon resonance analysis and microarrays. Oxime ligation allows reaching chemoselective protein immobilization with the retention of native-like conformation by proteins. Beside the need for chemoselective ligation of molecules to surface/particle, equally important is the controlled release of the immobilized molecules, even after a specific binding event. For this purpose, we have designed and assessed in an SPR experiment a peptide linker able to (i) anchor a given protein (enzymes, receptors, or antibodies) to a surface in a precise orientation and (ii) release the immobilized protein after selective enzymatic cleavage. These results open up the possibility to anchor to a surface a protein probe leaving bioactive sites free for interaction with substrates, ligands, antigens, or drugs and successively remove the probe-ligand complex by enzymatic cleavage. This peptide linker can be considered both an improvement of SPR analysis for macromolecular interaction and a novel strategy for drug delivery and biomaterial developments.
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Affiliation(s)
- Monica Dettin
- Department of Chemical Process Engineering, University of Padova, Via Marzolo 9, Padua, Italy.
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42
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Friedman M, Levin CE. Nutritional and medicinal aspects of D-amino acids. Amino Acids 2011; 42:1553-82. [PMID: 21519915 DOI: 10.1007/s00726-011-0915-1] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 04/06/2011] [Indexed: 02/07/2023]
Abstract
This paper reviews and interprets a method for determining the nutritional value of D-amino acids, D-peptides, and amino acid derivatives using a growth assay in mice fed a synthetic all-amino acid diet. A large number of experiments were carried out in which a molar equivalent of the test compound replaced a nutritionally essential amino acid such as L-lysine (L-Lys), L-methionine (L-Met), L-phenylalanine (L-Phe), and L-tryptophan (L-Trp) as well as the semi-essential amino acids L-cysteine (L-Cys) and L-tyrosine (L-Tyr). The results show wide-ranging variations in the biological utilization of test substances. The method is generally applicable to the determination of the biological utilization and safety of any amino acid derivative as a potential nutritional source of the corresponding L-amino acid. Because the organism is forced to use the D-amino acid or amino acid derivative as the sole source of the essential or semi-essential amino acid being replaced, and because a free amino acid diet allows better control of composition, the use of all-amino-acid diets for such determinations may be preferable to protein-based diets. Also covered are brief summaries of the widely scattered literature on dietary and pharmacological aspects of 27 individual D-amino acids, D-peptides, and isomeric amino acid derivatives and suggested research needs in each of these areas. The described results provide a valuable record and resource for further progress on the multifaceted aspects of D-amino acids in food and biological samples.
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Affiliation(s)
- Mendel Friedman
- Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Albany, CA 94710, USA.
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