1
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Xiao Y, Zhou H, Shi P, Zhao X, Liu H, Li X. Clickable tryptophan modification for late-stage diversification of native peptides. SCIENCE ADVANCES 2024; 10:eadp9958. [PMID: 38985871 PMCID: PMC11235173 DOI: 10.1126/sciadv.adp9958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/10/2024] [Indexed: 07/12/2024]
Abstract
As the least abundant residue in proteins, tryptophan widely exists in peptide drugs and bioactive natural products and contributes to drug-target interactions in multiple ways. We report here a clickable tryptophan modification for late-stage diversification of native peptides, via catalyst-free C2-sulfenylation with 8-quinoline thiosulfonate reagents in trifluoroacetic acid (TFA). A wide range of groups including trifluoromethylthio (SCF3), difluoromethylthio (SCF2H), (ethoxycarbonyl)difluoromethylthio (SCF2CO2Et), alkylthio, and arylthio were readily incorporated. The rapid reaction kinetics of Trp modification and full tolerance with other 19 proteinogenic amino acids, as well as the super dissolving capability of TFA, render this method suitable for all kinds of Trp-containing peptides without limitations from sequences, hydrophobicity, and aggregation propensity. The late-stage modification of 15 therapeutic peptides (1.0 to 7.6 kilodaltons) and the improved bioactivity and serum stability of SCF3- and SCF2H-modified melittin analogs illustrated the effectiveness of this method and its potential in pharmacokinetic property improvement.
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Affiliation(s)
- Yisa Xiao
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| | - Haiyan Zhou
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
- Chemistry and Chemical Engineering Guangdong Laboratory, Shantou, Guangdong Province 515063, P. R. China
| | - Pengfei Shi
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| | - Xueqian Zhao
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, P. R. China
| | - Han Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
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2
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Ren JX, Zhou M, Feng XT, Zhao HY, Fu XP, Zhang X. Site-selective S-gem-difluoroallylation of unprotected peptides with 3,3-difluoroallyl sulfonium salts. Chem Sci 2024; 15:10002-10009. [PMID: 38966370 PMCID: PMC11220611 DOI: 10.1039/d4sc02681k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 05/20/2024] [Indexed: 07/06/2024] Open
Abstract
Bench-stable 3,3-difluoroallyl sulfonium salts (DFASs), featuring tunable activity and their editable C-β and gem-difluoroallyl group, proved to be versatile fluoroalkylating reagents for site-selective S-gem-difluoroallylation of cysteine residues in unprotected peptides. The reaction proceeds with high efficiency under mild conditions (ambient temperature and aqueous and weak basic conditions). Various protected/unprotected peptides, especially bioactive peptides, are site-selectively S-gem-difluoroallylated. The newly added gem-difluoroallyl group and other functional groups derived from C-β of DFASs are poised for ligation with bio-functional groups through click and radical chemistry. This stepwise "doubly orthogonal" modification of peptides enables the construction of bioconjugates with enhanced complexity and functionality. This proof of principle is successfully applied to construct a peptide-saccharide-biotin chimeric bioconjugate, indicating its great potential application in medicinal chemistry and chemical biology.
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Affiliation(s)
- Jin-Xiu Ren
- Key Laboratory of Fluorine and Nitrogen Chemistry and Advanced Materials, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Minqi Zhou
- Key Laboratory of Fluorine and Nitrogen Chemistry and Advanced Materials, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Xiao-Tian Feng
- Key Laboratory of Fluorine and Nitrogen Chemistry and Advanced Materials, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Hai-Yang Zhao
- Key Laboratory of Fluorine and Nitrogen Chemistry and Advanced Materials, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Xia-Ping Fu
- Key Laboratory of Fluorine and Nitrogen Chemistry and Advanced Materials, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Xingang Zhang
- Key Laboratory of Fluorine and Nitrogen Chemistry and Advanced Materials, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
- School of Chemistry and Material Sciences Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences Hangzhou 310024 China
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3
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Fernandes AJ, Giri R, Houk KN, Katayev D. Review and Theoretical Analysis of Fluorinated Radicals in Direct C Ar-H Functionalization of (Hetero)arenes. Angew Chem Int Ed Engl 2024; 63:e202318377. [PMID: 38282182 DOI: 10.1002/anie.202318377] [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: 11/30/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 01/30/2024]
Abstract
We highlight key contributions in the field of direct radical CAr- H (hetero)aromatic functionalization involving fluorinated radicals. A compilation of Functional Group Transfer Reagents and their diverse activation mechanisms leading to the release of radicals are discussed. The substrate scope for each radical is analyzed and classified into three categories according to the electronic properties of the substrates. Density functional theory computational analysis provides insights into the chemical reactivity of several fluorinated radicals through their electrophilicity and nucleophilicity parameters. Theoretical analysis of their reduction potentials also highlights the remarkable correlation between electrophilicity and oxidizing ability. It is also established that highly fluorinated radicals (e.g. ⋅OCF3) are capable of engaging in single-electron transfer (SET) processes rather than radical addition, which is in good agreement with experimental literature data. A reactivity scale, based on activation barrier of addition of these radicals to benzene is also elaborated using the high accuracy DLPNO-(U)CCSD(T) method.
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Affiliation(s)
- Anthony J Fernandes
- Department für Chemie und Biochemie, Universität Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Rahul Giri
- Department für Chemie und Biochemie, Universität Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Kendall N Houk
- Department of Chemistry and Biochemistry, University of California, 90095, Los Angeles, California, United States
| | - Dmitry Katayev
- Department für Chemie und Biochemie, Universität Bern, Freiestrasse 3, 3012, Bern, Switzerland
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4
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De Jesus IS, Vélez JAC, Pissinati EF, Correia JTM, Rivera DG, Paixao MW. Recent Advances in Photoinduced Modification of Amino Acids, Peptides, and Proteins. CHEM REC 2024; 24:e202300322. [PMID: 38279622 DOI: 10.1002/tcr.202300322] [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: 10/09/2023] [Revised: 12/01/2023] [Indexed: 01/28/2024]
Abstract
The chemical modification of biopolymers like peptides and proteins is a key technology to access vaccines and pharmaceuticals. Similarly, the tunable derivatization of individual amino acids is important as they are key building blocks of biomolecules, bioactive natural products, synthetic polymers, and innovative materials. The high diversity of functional groups present in amino acid-based molecules represents a significant challenge for their selective derivatization Recently, visible light-mediated transformations have emerged as a powerful strategy for achieving chemoselective biomolecule modification. This technique offers numerous advantages over other methods, including a higher selectivity, mild reaction conditions and high functional-group tolerance. This review provides an overview of the most recent methods covering the photoinduced modification for single amino acids and site-selective functionalization in peptides and proteins under mild and even biocompatible conditions. Future challenges and perspectives are discussed beyond the diverse types of photocatalytic transformations that are currently available.
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Affiliation(s)
- Iva S De Jesus
- Laboratory for Sustainable Organic Synthesis and Catalysis, Department of Chemistry, Federal University of São Carlos - UFSCar, São Carlos, São Paulo, 13565-905, Brazil
| | - Jeimy A C Vélez
- Laboratory for Sustainable Organic Synthesis and Catalysis, Department of Chemistry, Federal University of São Carlos - UFSCar, São Carlos, São Paulo, 13565-905, Brazil
| | - Emanuele F Pissinati
- Laboratory for Sustainable Organic Synthesis and Catalysis, Department of Chemistry, Federal University of São Carlos - UFSCar, São Carlos, São Paulo, 13565-905, Brazil
| | - Jose Tiago M Correia
- Laboratory for Sustainable Organic Synthesis and Catalysis, Department of Chemistry, Federal University of São Carlos - UFSCar, São Carlos, São Paulo, 13565-905, Brazil
| | - Daniel G Rivera
- Laboratory of Synthetic and Biomolecular Chemistry, Faculty of Chemistry, University of Havana Zapata & G, Havana, 10400, Cuba
| | - Márcio W Paixao
- Laboratory for Sustainable Organic Synthesis and Catalysis, Department of Chemistry, Federal University of São Carlos - UFSCar, São Carlos, São Paulo, 13565-905, Brazil
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5
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Xuan W, Ma JA. Pinpointing Acidic Residues in Proteins. ChemMedChem 2024; 19:e202300623. [PMID: 38303683 DOI: 10.1002/cmdc.202300623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/18/2023] [Indexed: 02/03/2024]
Abstract
It is of great importance to pinpoint specific residues or sites of a protein in biological contexts to enable desired mechanism of action for small molecules or to precisely control protein function. In this regard, acidic residues including aspartic acid (Asp) and glutamic acid (Glu) hold great potential due to their great prevalence and unique function. To unlock the largely untapped potential, great efforts have been made recently by synthetic chemists, chemical biologists and pharmacologists. Herein, we would like to highlight the remarkable progress and particularly introduce the electrophiles that exhibit reactivity to carboxylic acids, the light-induced reactivities to carboxylic acids and the genetically encoded noncanonical amino acids that allow protein manipulations at acidic residues. We also comment on certain unresolved challenges, hoping to draw more attention to this rapidly developing area.
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Affiliation(s)
- Weimin Xuan
- Frontiers Science Center for Synthetic Biology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Jun-An Ma
- Department of Chemistry, Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, P. R. China
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6
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Xie X, Moon PJ, Crossley SWM, Bischoff AJ, He D, Li G, Dao N, Gonzalez-Valero A, Reeves AG, McKenna JM, Elledge SK, Wells JA, Toste FD, Chang CJ. Oxidative cyclization reagents reveal tryptophan cation-π interactions. Nature 2024; 627:680-687. [PMID: 38448587 PMCID: PMC11198740 DOI: 10.1038/s41586-024-07140-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 01/31/2024] [Indexed: 03/08/2024]
Abstract
Methods for selective covalent modification of amino acids on proteins can enable a diverse array of applications, spanning probes and modulators of protein function to proteomics1-3. Owing to their high nucleophilicity, cysteine and lysine residues are the most common points of attachment for protein bioconjugation chemistry through acid-base reactivity3,4. Here we report a redox-based strategy for bioconjugation of tryptophan, the rarest amino acid, using oxaziridine reagents that mimic oxidative cyclization reactions in indole-based alkaloid biosynthetic pathways to achieve highly efficient and specific tryptophan labelling. We establish the broad use of this method, termed tryptophan chemical ligation by cyclization (Trp-CLiC), for selectively appending payloads to tryptophan residues on peptides and proteins with reaction rates that rival traditional click reactions and enabling global profiling of hyper-reactive tryptophan sites across whole proteomes. Notably, these reagents reveal a systematic map of tryptophan residues that participate in cation-π interactions, including functional sites that can regulate protein-mediated phase-separation processes.
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Affiliation(s)
- Xiao Xie
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Patrick J Moon
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Steven W M Crossley
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Amanda J Bischoff
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Dan He
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gen Li
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Nam Dao
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Audrey G Reeves
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | | | - Susanna K Elledge
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - F Dean Toste
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
| | - Christopher J Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
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7
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Watanabe S, Wada Y, Kawano M, Higashibayashi S, Sugai T, Hanaya K. Selective modification of tryptophan in polypeptides via C-N coupling with azoles using in situ-generated iodine-based oxidants in aqueous media. Chem Commun (Camb) 2023; 59:13026-13029. [PMID: 37842839 DOI: 10.1039/d3cc03731b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
This study demonstrates the C-N coupling of tryptophan with azoles, promoted by an in situ-generated iodine-based oxidant. The protocol was successfully applied to the selective modification of tryptophan in nonprotected polypeptide bearing oxidatively sensitive residues in acidic aqueous media. The present method allows the attachment of reactive handles to polypeptides and the peptide stapling.
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Affiliation(s)
- Shunsuke Watanabe
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan.
| | - Yuki Wada
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Masaki Kawano
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Shuhei Higashibayashi
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan.
| | - Takeshi Sugai
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan.
| | - Kengo Hanaya
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan.
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8
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Kuehl NJ, Taylor MT. Rapid Biomolecular Trifluoromethylation Using Cationic Aromatic Sulfonate Esters as Visible-Light-Triggered Radical Photocages. J Am Chem Soc 2023; 145:22878-22884. [PMID: 37819426 PMCID: PMC11076010 DOI: 10.1021/jacs.3c08098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Described here is a photodecaging approach to radical trifluoromethylation of biomolecules. This was accomplished by designing a quinolinium sulfonate ester that, upon absorption of visible light, achieves decaging via photolysis of the sulfonate ester to ultimately liberate free trifluoromethyl radicals that are trapped by π-nucleophiles in biomolecules. This photodecaging process enables protein and protein-interaction mapping experiments using trifluoromethyl radicals that require only 1 s reaction times and low photocage concentrations. In these experiments, aromatic side chains are labeled in an environmentally dependent fashion, with selectivity observed for tryptophan (Trp), followed by histidine (His) and tyrosine (Tyr). Scalable peptide trifluoromethylation through photodecaging is also demonstrated, where bespoke peptides harboring trifluoromethyl groups at tryptophan residues can be synthesized with 5-7 min reaction times and good yields.
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Affiliation(s)
- Nicholas J. Kuehl
- Department of Chemistry, University of Wyoming, Laramie, WY 82071, United States
| | - Michael T. Taylor
- Department of Chemistry & Biochemistry, University of Arizona, Tucson, AZ 85721, United States
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9
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Chen X, Josephson B, Davis BG. Carbon-Centered Radicals in Protein Manipulation. ACS CENTRAL SCIENCE 2023; 9:614-638. [PMID: 37122447 PMCID: PMC10141601 DOI: 10.1021/acscentsci.3c00051] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Indexed: 05/03/2023]
Abstract
Methods to directly post-translationally modify proteins are perhaps the most straightforward and operationally simple ways to create and study protein post-translational modifications (PTMs). However, precisely altering or constructing the C-C scaffolds pervasive throughout biology is difficult with common two-electron chemical approaches. Recently, there has been a surge of new methods that have utilized single electron/radical chemistry applied to site-specifically "edit" proteins that have started to create this potential-one that in principle could be near free-ranging. This review provides an overview of current methods that install such "edits", including those that generate function and/or PTMs, through radical C-C bond formation (as well as C-X bond formation via C• where illustrative). These exploit selectivity for either native residues, or preinstalled noncanonical protein side-chains with superior radical generating or accepting abilities. Particular focus will be on the radical generation approach (on-protein or off-protein, use of light and photocatalysts), judging the compatibility of conditions with proteins and cells, and novel chemical biology applications afforded by these methods. While there are still many technical hurdles, radical C-C bond formation on proteins is a promising and rapidly growing area in chemical biology with long-term potential for biological editing.
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Affiliation(s)
- Xuanxiao Chen
- Department
of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K.
- The
Rosalind Franklin Institute, Oxfordshire, OX11 OFA, U.K.
| | - Brian Josephson
- Department
of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K.
| | - Benjamin G. Davis
- Department
of Chemistry, University of Oxford, Oxford, OX1 3TA, U.K.
- The
Rosalind Franklin Institute, Oxfordshire, OX11 OFA, U.K.
- Department
of Pharmacology, University of Oxford, Oxford, OX1 3QT, U.K.
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10
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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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11
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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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12
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Fischer NH, Oliveira MT, Diness F. Chemical modification of proteins - challenges and trends at the start of the 2020s. Biomater Sci 2023; 11:719-748. [PMID: 36519403 DOI: 10.1039/d2bm01237e] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribosomally expressed proteins perform multiple, versatile, and specialized tasks throughout Nature. In modern times, chemically modified proteins, including improved hormones, enzymes, and antibody-drug-conjugates have become available and have found advanced industrial and pharmaceutical applications. Chemical modification of proteins is used to introduce new functionalities, improve stability or drugability. Undertaking chemical reactions with proteins without compromising their native function is still a core challenge as proteins are large conformation dependent multifunctional molecules. Methods for functionalization ideally should be chemo-selective, site-selective, and undertaken under biocompatible conditions in aqueous buffer to prevent denaturation of the protein. Here the present challenges in the field are discussed and methods for modification of the 20 encoded amino acids as well as the N-/C-termini and protein backbone are presented. For each amino acid, common and traditional modification methods are presented first, followed by more recent ones.
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Affiliation(s)
- Niklas Henrik Fischer
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark. .,Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Maria Teresa Oliveira
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Frederik Diness
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark. .,Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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13
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Lin D, Krishnamurti V, Prakash S. Visible Light Mediated Metal‐free Chlorodifluoromethylation of Arenes and Heteroarenes via a Hypervalent Iodine EDA Complex. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Daniel Lin
- University of Southern California Department of Chemistry and Loker Hydrocarbon Research Institute UNITED STATES
| | - Vinayak Krishnamurti
- University of Southern California Department of Chemistry and Loker Hydrocarbon Research Institute UNITED STATES
| | - Surya Prakash
- University of Southern California Loker Hydrocarbon Research Institute 837 Bloom WalkUniversity Park 90089-1661 Los Angeles UNITED STATES
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14
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Hoopes CR, Garcia FJ, Sarkar AM, Kuehl NJ, Barkan DT, Collins NL, Meister GE, Bramhall TR, Hsu CH, Jones MD, Schirle M, Taylor MT. Donor-Acceptor Pyridinium Salts for Photo-Induced Electron-Transfer-Driven Modification of Tryptophan in Peptides, Proteins, and Proteomes Using Visible Light. J Am Chem Soc 2022; 144:6227-6236. [PMID: 35364811 PMCID: PMC10124759 DOI: 10.1021/jacs.1c10536] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tryptophan (Trp) plays a variety of critical functional roles in protein biochemistry; however, owing to its low natural frequency and poor nucleophilicity, the design of effective methods for both single protein bioconjugation at Trp as well as for in situ chemoproteomic profiling remains a challenge. Here, we report a method for covalent Trp modification that is suitable for both scenarios by invoking photo-induced electron transfer (PET) as a means of driving efficient reactivity. We have engineered biaryl N-carbamoyl pyridinium salts that possess a donor-acceptor relationship that enables optical triggering with visible light whilst simultaneously attenuating the probe's photo-oxidation potential in order to prevent photodegradation. This probe was assayed against a small bank of eight peptides and proteins, where it was found that micromolar concentrations of the probe and short irradiation times (10-60 min) with violet light enabled efficient reactivity toward surface exposed Trp residues. The carbamate transferring group can be used to transfer useful functional groups to proteins including affinity tags and click handles. DFT calculations and other mechanistic analyses reveal correlations between excited state lifetimes, relative fluorescence quantum yields, and chemical reactivity. Biotinylated and azide-functionalized pyridinium salts were used for Trp profiling in HEK293T lysates and in situ in HEK293T cells using 440 nm LED irradiation. Peptide-level enrichment from live cell labeling experiments identified 290 Trp modifications, with 82% selectivity for Trp modification over other π-amino acids, demonstrating the ability of this method to identify and quantify reactive Trp residues from live cells.
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Affiliation(s)
- Caleb R Hoopes
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Francisco J Garcia
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Akash M Sarkar
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Nicholas J Kuehl
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
| | - David T Barkan
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Nicole L Collins
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Glenna E Meister
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Taylor R Bramhall
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Chien-Hsiang Hsu
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Michael D Jones
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Markus Schirle
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Michael T Taylor
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
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15
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Wang S, Zhou Q, Zhang X, Wang P. Site‐Selective Itaconation of Complex Peptides by Photoredox Catalysis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Siyao Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Shanghai Jiao Tong University No. 800, Dongchuan Rd Shanghai 200240 China
| | - QingQing Zhou
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Shanghai Jiao Tong University No. 800, Dongchuan Rd Shanghai 200240 China
| | - Xiaheng Zhang
- School of Chemistry and Materials Science Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences 1 Sub-lane Xiangshan Hangzhou 310024 China
| | - Ping Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Shanghai Jiao Tong University No. 800, Dongchuan Rd Shanghai 200240 China
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16
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Wang S, Zhou Q, Zhang X, Wang P. Site-Selective Itaconation of Complex Peptides by Photoredox Catalysis. Angew Chem Int Ed Engl 2022; 61:e202111388. [PMID: 34845804 DOI: 10.1002/anie.202111388] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Indexed: 12/20/2022]
Abstract
Site-selective peptide functionalization provides a straightforward and cost-effective access to diversify peptides for biological studies. Among many existing non-invasive peptide conjugations methodologies, photoredox catalysis has emerged as one of the powerful approaches for site-specific manipulation on native peptides. Herein, we report a highly N-termini-specific method to rapidly access itaconated peptides and their derivatives through a combination of transamination and photoredox conditions. This strategy exploits the facile reactivity of peptidyl-dihydropyridine in the complex peptide settings, complementing existing approaches for bioconjugations with excellent selectivity under mild conditions. Distinct from conventional methods, this method utilizes the highly reactive carbamoyl radical derived from a peptidyl-dihydropyridine. In addition, this itaconated peptide can be further functionalized as a Michael acceptor to access the corresponding peptide-protein conjugate.
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Affiliation(s)
- Siyao Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, No. 800, Dongchuan Rd, Shanghai, 200240, China
| | - QingQing Zhou
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, No. 800, Dongchuan Rd, Shanghai, 200240, China
| | - Xiaheng Zhang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, China
| | - Ping Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, No. 800, Dongchuan Rd, Shanghai, 200240, China
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17
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Sap JBI, Meyer CF, Straathof NJW, Iwumene N, am Ende CW, Trabanco AA, Gouverneur V. Late-stage difluoromethylation: concepts, developments and perspective. Chem Soc Rev 2021; 50:8214-8247. [DOI: 10.1039/d1cs00360g] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review describes the conceptual advances that have led to the multiple difluoromethylation processes making use of well-defined CF2H sources.
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Affiliation(s)
- Jeroen B. I. Sap
- Chemistry Research Laboratory
- Department of Chemistry
- Oxford University
- OX1 3TA Oxford
- UK
| | - Claudio F. Meyer
- Chemistry Research Laboratory
- Department of Chemistry
- Oxford University
- OX1 3TA Oxford
- UK
| | - Natan J. W. Straathof
- Chemistry Research Laboratory
- Department of Chemistry
- Oxford University
- OX1 3TA Oxford
- UK
| | - Ndidi Iwumene
- Chemistry Research Laboratory
- Department of Chemistry
- Oxford University
- OX1 3TA Oxford
- UK
| | - Christopher W. am Ende
- Pfizer Inc
- Medicine Design, Eastern Point Road, Groton, Connecticut 06340, and 1 Portland Street
- Cambridge
- USA
| | | | - Véronique Gouverneur
- Chemistry Research Laboratory
- Department of Chemistry
- Oxford University
- OX1 3TA Oxford
- UK
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