Chemically Triggered Crosslinking with Bioorthogonal Cyclopropenones

Overview

Journal Chem Commun (Camb)

Publisher Royal Society of Chemistry

Specialty Chemistry

Date 2020 Aug 19

PMID 32808608

Citations 9

Authors

R David Row

Sean S Nguyen

Andrew J Ferreira

Jennifer A Prescher

Affiliations

Soon will be listed here.

Abstract

We report a proximity-driven crosslinking strategy featuring bioorthogonal cyclopropenones. These motifs react with phosphines to form electrophilic ketene-ylides. Such intermediates can be trapped by neighboring proteins to form covalent adducts. Successful crosslinking was achieved using a model split reporter, and the rate of crosslinking could be tuned using different phosphine triggers. We further demonstrated that the reaction can be performed in cell lysate. Based on these features, we anticipate that cyclopropenones will enable unique studies of protein-protein and other biomolecule interactions.

Citing Articles

Bioorthogonal Cyclopropenones for Investigating RNA Structure.

Chen S, Sibley C, Latifi B, Balaratnam S, Dorn R, Luptak A ACS Chem Biol. 2024; 19(12):2406-2411.

PMID: 39641920 PMC: 11667673. DOI: 10.1021/acschembio.4c00633.

Mutually Orthogonal Bioorthogonal Reactions: Selective Chemistries for Labeling Multiple Biomolecules Simultaneously.

Venrooij K, de Bondt L, Bonger K Top Curr Chem (Cham). 2024; 382(3):24.

PMID: 38971884 PMC: 11227474. DOI: 10.1007/s41061-024-00467-8.

Bioorthogonally activated reactive species for target identification.

Siriwongsup S, Schmoker A, Ficarro S, Marto J, Kim J Chem. 2024; 10(4):1306-1315.

PMID: 38617077 PMC: 11008434. DOI: 10.1016/j.chempr.2024.03.002.

Recent Advances in Bioorthogonal Ligation and Bioconjugation.

Zielke F, Rutjes F Top Curr Chem (Cham). 2023; 381(6):35.

PMID: 37991570 PMC: 10665463. DOI: 10.1007/s41061-023-00445-6.

Platform for Orthogonal -Cysteine-Specific Protein Modification Enabled by Cyclopropenone Reagents.

Istrate A, Geeson M, Navo C, Sousa B, Marques M, Taylor R J Am Chem Soc. 2022; 144(23):10396-10406.

PMID: 35658467 PMC: 9490850. DOI: 10.1021/jacs.2c02185.

References

Coin I, Katritch V, Sun T, Xiang Z, Siu F, Beyermann M . Genetically encoded chemical probes in cells reveal the binding path of urocortin-I to CRF class B GPCR. Cell. 2013; 155(6):1258-69. PMC: 3916339. DOI: 10.1016/j.cell.2013.11.008. View

Cigler M, Muller T, Horn-Ghetko D, von Wrisberg M, Fottner M, Goody R . Proximity-Triggered Covalent Stabilization of Low-Affinity Protein Complexes In Vitro and In Vivo. Angew Chem Int Ed Engl. 2017; 56(49):15737-15741. DOI: 10.1002/anie.201706927. View

Nguyen T, Cigler M, Lang K . Expanding the Genetic Code to Study Protein-Protein Interactions. Angew Chem Int Ed Engl. 2018; 57(44):14350-14361. DOI: 10.1002/anie.201805869. View

Joiner C, Breen M, Clayton J, Mapp A . A Bifunctional Amino Acid Enables Both Covalent Chemical Capture and Isolation of in Vivo Protein-Protein Interactions. Chembiochem. 2016; 18(2):181-184. DOI: 10.1002/cbic.201600578. View

Lin S, He D, Long T, Zhang S, Meng R, Chen P . Genetically encoded cleavable protein photo-cross-linker. J Am Chem Soc. 2014; 136(34):11860-3. DOI: 10.1021/ja504371w. View

Niessen S, Dix M, Barbas S, Potter Z, Lu S, Brodsky O . Proteome-wide Map of Targets of T790M-EGFR-Directed Covalent Inhibitors. Cell Chem Biol. 2017; 24(11):1388-1400.e7. PMC: 5693604. DOI: 10.1016/j.chembiol.2017.08.017. View

Dorman G, Nakamura H, Pulsipher A, Prestwich G . The Life of Pi Star: Exploring the Exciting and Forbidden Worlds of the Benzophenone Photophore. Chem Rev. 2016; 116(24):15284-15398. DOI: 10.1021/acs.chemrev.6b00342. View

Parker C, Galmozzi A, Wang Y, Correia B, Sasaki K, Joslyn C . Ligand and Target Discovery by Fragment-Based Screening in Human Cells. Cell. 2017; 168(3):527-541.e29. PMC: 5632530. DOI: 10.1016/j.cell.2016.12.029. View

Aguilar X, Weise C, Sparrman T, Wolf-Watz M, Wittung-Stafshede P . Macromolecular crowding extended to a heptameric system: the Co-chaperonin protein 10. Biochemistry. 2011; 50(14):3034-44. DOI: 10.1021/bi2002086. View

10.

Martin-Gago P, Olsen C . Arylfluorosulfate-Based Electrophiles for Covalent Protein Labeling: A New Addition to the Arsenal. Angew Chem Int Ed Engl. 2018; 58(4):957-966. PMC: 6518939. DOI: 10.1002/anie.201806037. View

11.

Chin J, Santoro S, Martin A, King D, Wang L, Schultz P . Addition of p-azido-L-phenylalanine to the genetic code of Escherichia coli. J Am Chem Soc. 2002; 124(31):9026-7. DOI: 10.1021/ja027007w. View

12.

Preston G, Wilson A . Photo-induced covalent cross-linking for the analysis of biomolecular interactions. Chem Soc Rev. 2013; 42(8):3289-301. DOI: 10.1039/c3cs35459h. View

13.

Kleiner P, Heydenreuter W, Stahl M, Korotkov V, Sieber S . A Whole Proteome Inventory of Background Photocrosslinker Binding. Angew Chem Int Ed Engl. 2016; 56(5):1396-1401. DOI: 10.1002/anie.201605993. View

14.

Qiu Z, Lu L, Jian X, He C . A diazirine-based nucleoside analogue for efficient DNA interstrand photocross-linking. J Am Chem Soc. 2008; 130(44):14398-9. PMC: 2945524. DOI: 10.1021/ja805445j. View

15.

Tomabechi Y, Hosoya T, Ehara H, Sekine S, Shirouzu M, Inouye S . Crystal structure of nanoKAZ: The mutated 19 kDa component of Oplophorus luciferase catalyzing the bioluminescent reaction with coelenterazine. Biochem Biophys Res Commun. 2016; 470(1):88-93. DOI: 10.1016/j.bbrc.2015.12.123. View

16.

Ni H, Chan W, Lu Y . Phosphine-Catalyzed Asymmetric Organic Reactions. Chem Rev. 2018; 118(18):9344-9411. DOI: 10.1021/acs.chemrev.8b00261. View

17.

Shindo N, Fuchida H, Sato M, Watari K, Shibata T, Kuwata K . Selective and reversible modification of kinase cysteines with chlorofluoroacetamides. Nat Chem Biol. 2019; 15(3):250-258. DOI: 10.1038/s41589-018-0204-3. View

18.

Niphakis M, Lum K, Cognetta 3rd A, Correia B, Ichu T, Olucha J . A Global Map of Lipid-Binding Proteins and Their Ligandability in Cells. Cell. 2015; 161(7):1668-80. PMC: 4615699. DOI: 10.1016/j.cell.2015.05.045. View

19.

Row R, Shih H, Alexander A, Mehl R, Prescher J . Cyclopropenones for Metabolic Targeting and Sequential Bioorthogonal Labeling. J Am Chem Soc. 2017; 139(21):7370-7375. DOI: 10.1021/jacs.7b03010. View

20.

Shih H, Prescher J . A Bioorthogonal Ligation of Cyclopropenones Mediated by Triarylphosphines. J Am Chem Soc. 2015; 137(32):10036-9. DOI: 10.1021/jacs.5b06969. View