1
|
Eichler C, Himmelstoß M, Plangger R, Weber LI, Hartl M, Kreutz C, Micura R. Advances in RNA Labeling with Trifluoromethyl Groups. Chemistry 2023; 29:e202302220. [PMID: 37534701 PMCID: PMC10947337 DOI: 10.1002/chem.202302220] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/04/2023]
Abstract
Fluorine labeling of ribonucleic acids (RNA) in conjunction with 19 F NMR spectroscopy has emerged as a powerful strategy for spectroscopic analysis of RNA structure and dynamics, and RNA-ligand interactions. This study presents the first syntheses of 2'-OCF3 guanosine and uridine phosphoramidites, their incorporation into oligoribonucleotides by solid-phase synthesis and a comprehensive study of their properties. NMR spectroscopic analysis showed that the 2'-OCF3 modification is associated with preferential C2'-endo conformation of the U and G ribose in single-stranded RNA. When paired to the complementary strand, slight destabilization of the duplex caused by the modification was revealed by UV melting curve analysis. Moreover, the power of the 2'-OCF3 label for NMR spectroscopy is demonstrated by dissecting RNA pseudoknot folding and its binding to a small molecule. Furthermore, the 2'-OCF3 modification has potential for applications in therapeutic oligonucleotides. To this end, three 2'-OCF3 modified siRNAs were tested in silencing of the BASP1 gene which indicated enhanced performance for one of them. Importantly, together with earlier work, the present study completes the set of 2'-OCF3 nucleoside phosphoramidites to all four standard nucleobases (A, U, C, G) and hence enables applications that utilize the favorable properties of the 2'-OCF3 group without any restrictions in placing the modification into the RNA target sequence.
Collapse
Affiliation(s)
- Clemens Eichler
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Maximilian Himmelstoß
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Raphael Plangger
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Leonie I. Weber
- Institute of BiochemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Markus Hartl
- Institute of BiochemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Christoph Kreutz
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Ronald Micura
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| |
Collapse
|
2
|
Fittolani G, Shanina E, Guberman M, Seeberger PH, Rademacher C, Delbianco M. Automated Glycan Assembly of 19 F-labeled Glycan Probes Enables High-Throughput NMR Studies of Protein-Glycan Interactions. Angew Chem Int Ed Engl 2021; 60:13302-13309. [PMID: 33784430 PMCID: PMC8252726 DOI: 10.1002/anie.202102690] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/19/2021] [Indexed: 12/23/2022]
Abstract
Protein–glycan interactions mediate important biological processes, including pathogen host invasion and cellular communication. Herein, we showcase an expedite approach that integrates automated glycan assembly (AGA) of 19F‐labeled probes and high‐throughput NMR methods, enabling the study of protein–glycan interactions. Synthetic Lewis type 2 antigens were screened against seven glycan binding proteins (GBPs), including DC‐SIGN and BambL, respectively involved in HIV‐1 and lung infections in immunocompromised patients, confirming the preference for fucosylated glycans (Lex, H type 2, Ley). Previously unknown glycan–lectin weak interactions were detected, and thermodynamic data were obtained. Enzymatic reactions were monitored in real‐time, delivering kinetic parameters. These results demonstrate the utility of AGA combined with 19F NMR for the discovery and characterization of glycan–protein interactions, opening up new perspectives for 19F‐labeled complex glycans.
Collapse
Affiliation(s)
- Giulio Fittolani
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Elena Shanina
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Mónica Guberman
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Current address: Medicinal Chemistry, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle Strasse 10, 13125, Berlin, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Christoph Rademacher
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany.,Current address: Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1080, Vienna, Austria.,Current address: Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Labs, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
| |
Collapse
|
3
|
Tähtinen V, Verhassel A, Tuomela J, Virta P. γ-(S)-Guanidinylmethyl-Modified Triplex-Forming Peptide Nucleic Acids Increase Hoogsteen-Face Affinity for a MicroRNA and Enhance Cellular Uptake. Chembiochem 2019; 20:3041-3051. [PMID: 31206960 DOI: 10.1002/cbic.201900393] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Indexed: 12/14/2022]
Abstract
γ-Modified (i.e., (S)-aminomethyl, (S)-acetamidomethyl, (R)-4-(hydroxymethyl)triazol-1-ylmethyl, and (S)-guanidinylmethyl) triplex-forming peptide nucleic acids (TFPNAs) were synthesized and the effect of the backbone modifications on the binding to a miR-215 model was studied. Among the modifications, an appropriate pattern of three γ-(S)-guanidinylmethyl modifications increased the affinity and Hoogsteen-face selectivity for the miR-215 model without ternary (PNA)2 /RNA complex formation. Moreover, the γ-(S)-guanidinylmethyl groups were observed to facilitate internalization of the TFPNAs into living PC-3 prostate cancer cells.
Collapse
Affiliation(s)
- Ville Tähtinen
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland
| | - Alejandra Verhassel
- FICAN West Cancer Research Laboratory, University of Turku and Turku University Hospital, Institution of Biomedicine, Medisiina D, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Johanna Tuomela
- FICAN West Cancer Research Laboratory, University of Turku and Turku University Hospital, Institution of Biomedicine, Medisiina D, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Pasi Virta
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland
| |
Collapse
|
4
|
Li W, Zou J, Zhu S, Mao X, Tian H, Wang X. Fluorodibenzocyclooctynes: A Trackable Click Reagent with Enhanced Reactivity. Chemistry 2019; 25:10328-10332. [PMID: 31243812 DOI: 10.1002/chem.201902834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Indexed: 12/16/2022]
Abstract
Bioorthogonal reactions have widespread applications in biological systems, and development of new bioorthogonal reactions has been of great interest over the past two decades. In this work, the design and synthesis of a family of fluorinated dibenzocyclooctynes (FDIBOs) are reported. The electron-deficient nature of fluorine atoms significantly accelerated the reaction of cyclooctynes in 1,3-dipolar cycloadditions, with either benzyl azide or ethyl diazoacetate, compared to conventional dibenzocyclooctyne (DIBO). In addition, FDIBOs showed unique trackable properties owing to the high NMR sensitivity of the naturally abundant 19 F isotope. Biological molecules, including a monosaccharide, a peptide, and a protein, were tested with FDIBOs, and these reactions could be easily monitored by 19 F NMR spectroscopy to evaluate the progress of the conjugation reactions. In addition, labeling of live cells was also demonstrated with metabolically modified bacteria to expand the possible applications of FDIBOs.
Collapse
Affiliation(s)
- Wei Li
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, P. R. China
| | - Juan Zou
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, P. R. China
| | - Shiyu Zhu
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, P. R. China
| | - Xianxian Mao
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, P. R. China
| | - Hongyan Tian
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, P. R. China
| | - Xiaojian Wang
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, P. R. China
| |
Collapse
|
5
|
Glas A, Wamhoff EC, Krüger DM, Rademacher C, Grossmann TN. Increased Conformational Flexibility of a Macrocycle-Receptor Complex Contributes to Reduced Dissociation Rates. Chemistry 2017; 23:16157-16161. [PMID: 28777495 PMCID: PMC5724689 DOI: 10.1002/chem.201702776] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Indexed: 11/06/2022]
Abstract
Constraining a peptide in its bioactive conformation by macrocyclization represents a powerful strategy to design modulators of challenging biomolecular targets. This holds particularly true for the development of inhibitors of protein‐protein interactions which often involve interfaces lacking defined binding pockets. Such flat surfaces are demanding targets for traditional small molecules rendering macrocyclic peptides promising scaffolds for novel therapeutics. However, the contribution of peptide dynamics to binding kinetics is barely understood which impedes the design process. Herein, we report unexpected trends in the binding kinetics of two closely related macrocyclic peptides that bind their receptor protein with high affinity. Isothermal titration calorimetry, 19F NMR experiments and molecular dynamics simulations reveal that increased conformational flexibility of the macrocycle–receptor complex reduces dissociation rates and contributes to complex stability. This observation has impact on macrocycle design strategies that have so far mainly focused on the stabilization of bioactive ligand conformations.
Collapse
Affiliation(s)
- Adrian Glas
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227, Dortmund, Germany
| | - Eike-Christian Wamhoff
- Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, Am Mühlenberg 1, 14424, Potsdam, Germany.,Freie Universität Berlin, Department of Biology, Chemistry and Pharmacy, Takustr. 3, 14195, Berlin, Germany
| | - Dennis M Krüger
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227, Dortmund, Germany.,Present address: Uppsala University, Department of Cell and Molecular Biology, BMC Box 596, 75124, Uppsala, Sweden
| | - Christoph Rademacher
- Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, Am Mühlenberg 1, 14424, Potsdam, Germany.,Freie Universität Berlin, Department of Biology, Chemistry and Pharmacy, Takustr. 3, 14195, Berlin, Germany
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227, Dortmund, Germany.,VU University Amsterdam, Department of Chemistry and Pharmaceutical Sciences, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| |
Collapse
|
6
|
Jin Y, Richards NG, Waltho JP, Blackburn GM. Metal Fluorides as Analogues for Studies on Phosphoryl Transfer Enzymes. Angew Chem Int Ed Engl 2017; 56:4110-4128. [PMID: 27862756 DOI: 10.1002/anie.201606474] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Indexed: 12/27/2022]
Abstract
The 1994 structure of a transition-state analogue with AlF4- and GDP complexed to G1α, a small G protein, heralded a new field of research into the structure and mechanism of enzymes that manipulate the transfer of phosphoryl (PO3- ) groups. The number of enzyme structures in the PDB containing metal fluorides (MFx ) as ligands that imitate either a phosphoryl or a phosphate group was 357 at the end of 2016. They fall into three distinct geometrical classes: 1) Tetrahedral complexes based on BeF3- that mimic ground-state phosphates; 2) octahedral complexes, primarily based on AlF4- , which mimic "in-line" anionic transition states for phosphoryl transfer; and 3) trigonal bipyramidal complexes, represented by MgF3- and putative AlF30 moieties, which mimic the geometry of the transition state. The interpretation of these structures provides a deeper mechanistic understanding into the behavior and manipulation of phosphate monoesters in molecular biology. This Review provides a comprehensive overview of these structures, their uses, and their computational development.
Collapse
Affiliation(s)
- Yi Jin
- Department of Chemistry, University of York, York, YO10 5DD, UK
| | | | | | - G Michael Blackburn
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| |
Collapse
|
7
|
Abstract
2'-O-[(4-Trifluoromethyl-triazol-1-yl)methyl] reporter groups have been incorporated into guanosine-rich RNA models (including a known bistable Qd/Hp RNA and two G-rich regions of mRNA of human prion protein, PrP) and applied for the 19 F NMR spectroscopic characterization of plausible G-quadruplex/hairpin (Qd/Hp) transitions in these RNA structures. For the synthesis of the CF3 -labeled RNAs, phosphoramidite building blocks of 2'-O-[(4-CF3 -triazol-1-yl)methyl] nucleosides (cytidine, adenosine, and guanosine) were prepared and used as an integral part of the standard solid-phase RNA synthesis. The obtained 19 F NMR spectra supported the usual characterization data (obtained by UV- and CD-melting profiles and by 1 H NMR spectra of the imino regions) and additionally gave more detailed information on the Qd/Hp transitions. The molar fractions of the secondary structural species (Qd, Hp) upon thermal denaturation and under varying ionic conditions could be determined from the intensities and shifts of the 19 F NMR signals. For a well-behaved Qd/Hp transition, thermodynamic parameters could be extracted.
Collapse
Affiliation(s)
- Lotta Granqvist
- Department of Chemistry, University of Turku, Turku, 20014, Finland.
| | - Pasi Virta
- Department of Chemistry, University of Turku, Turku, 20014, Finland.
| |
Collapse
|
8
|
Horst R, Liu JJ, Stevens RC, Wüthrich K. β₂-adrenergic receptor activation by agonists studied with ¹⁹F NMR spectroscopy. Angew Chem Int Ed Engl 2013; 52:10762-5. [PMID: 23956158 DOI: 10.1002/anie.201305286] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Reto Horst
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA); Present address: Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340 (USA)
| | | | | | | |
Collapse
|