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Le HN, Kuchlyan J, Baladi T, Albinsson B, Dahlén A, Wilhelmsson LM. Synthesis and photophysical characterization of a pH-sensitive quadracyclic uridine (qU) analogue. Chemistry 2024:e202303539. [PMID: 38230625 DOI: 10.1002/chem.202303539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/18/2024]
Abstract
Fluorescent base analogues (FBAs) have become useful tools for applications in biophysical chemistry, chemical biology, live-cell imaging, and RNA therapeutics. Herein, two synthetic routes towards a novel FBA of uracil named qU (quadracyclic uracil/uridine) are described. The qU nucleobase bears a tetracyclic fused ring system and is designed to allow for specific Watson-Crick base pairing with adenine. We find that qU absorbs light in the visible region of the spectrum and emits brightly with a quantum yield of 27 % and a dual-band character in a wide pH range. With evidence, among other things, from fluorescence lifetime measurements we suggest that this dual emission feature results from an excited-state proton transfer (ESPT) process. Furthermore, we find that both absorption and emission of qU are highly sensitive to pH. The high brightness in combination with excitation in the visible and pH responsiveness makes qU an interesting native-like nucleic acid label in spectroscopy and microscopy applications in, for example, the field of mRNA and antisense oligonucleotide (ASO) therapeutics.
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Affiliation(s)
- Hoang-Ngoan Le
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
- Cell Gene and RNA Therapy, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 431 50, Gothenburg, Sweden
| | - Jagannath Kuchlyan
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
| | - Tom Baladi
- Cell Gene and RNA Therapy, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 431 50, Gothenburg, Sweden
| | - Bo Albinsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
| | - Anders Dahlén
- Cell Gene and RNA Therapy, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 431 50, Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
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Nilsson JR, Benitez-Martin C, Sansom HG, Pfeiffer P, Baladi T, Le HN, Dahlén A, Magennis SW, Wilhelmsson LM. Multiphoton characterization and live cell imaging using fluorescent adenine analogue 2CNqA. Phys Chem Chem Phys 2023. [PMID: 37475592 DOI: 10.1039/d3cp01147j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Fluorescent nucleobase analogues (FBAs) are established tools for studying oligonucleotide structure, dynamics and interactions, and have recently also emerged as an attractive option for labeling RNA-based therapeutics. A recognized drawback of FBAs, however, is that they typically require excitation in the UV region, which for imaging in biological samples may have disadvantages related to phototoxicity, tissue penetration, and out-of-focus photobleaching. Multiphoton excitation has the potential to alleviate these issues and therefore, in this work, we characterize the multiphoton absorption properties and detectability of the highly fluorescent quadracyclic adenine analogue 2CNqA as a ribonucleotide monomer as well as incorporated, at one or two positions, into a 16mer antisense oligonucleotide (ASO). We found that 2CNqA has a two-photon absorption cross section that, among FBAs, is exceptionally high, with values of σ2PA(700 nm) = 5.8 GM, 6.8 GM, and 13 GM for the monomer, single-, and double-labelled oligonucleotide, respectively. Using fluorescence correlation spectroscopy, we show that the 2CNqA has a high 2P brightness as the monomer and when incorporated into the ASO, comparing favorably to other FBAs. We furthermore demonstrate the usefulness of the 2P imaging mode for improving detectability of 2CNqA-labelled ASOs in live cells.
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Affiliation(s)
- Jesper R Nilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden.
| | - Carlos Benitez-Martin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden.
| | - Henry G Sansom
- School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Pauline Pfeiffer
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden.
| | - Tom Baladi
- Oligonucleotide Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Hoang-Ngoan Le
- Oligonucleotide Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Steven W Magennis
- School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden.
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Nilsson JR, Baladi T, Gallud A, Baždarević D, Lemurell M, Esbjörner EK, Wilhelmsson LM, Dahlén A. Fluorescent base analogues in gapmers enable stealth labeling of antisense oligonucleotide therapeutics. Sci Rep 2021; 11:11365. [PMID: 34059711 PMCID: PMC8166847 DOI: 10.1038/s41598-021-90629-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/13/2021] [Indexed: 01/28/2023] Open
Abstract
To expand the antisense oligonucleotide (ASO) fluorescence labeling toolbox beyond covalent conjugation of external dyes (e.g. ATTO-, Alexa Fluor-, or cyanine dyes), we herein explore fluorescent base analogues (FBAs) as a novel approach to endow fluorescent properties to ASOs. Both cytosine and adenine analogues (tC, tCO, 2CNqA, and pA) were incorporated into a 16mer ASO sequence with a 3-10-3 cEt-DNA-cEt (cEt = constrained ethyl) gapmer design. In addition to a comprehensive photophysical characterization, we assess the label-induced effects on the gapmers' RNA affinities, RNA-hybridized secondary structures, and knockdown efficiencies. Importantly, we find practically no perturbing effects for gapmers with single FBA incorporations in the biologically critical gap region and, except for pA, the FBAs do not affect the knockdown efficiencies. Incorporating two cytosine FBAs in the gap is equally well tolerated, while two adenine analogues give rise to slightly reduced knockdown efficiencies and what could be perturbed secondary structures. We furthermore show that the FBAs can be used to visualize gapmers inside live cells using fluorescence microscopy and flow cytometry, enabling comparative assessment of their uptake. This altogether shows that FBAs are functional ASO probes that provide a minimally perturbing in-sequence labeling option for this highly relevant drug modality.
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Affiliation(s)
- Jesper R Nilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Tom Baladi
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.,Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.,Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Audrey Gallud
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden.,Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Dženita Baždarević
- Bioscience, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Malin Lemurell
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Elin K Esbjörner
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
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Baladi T, Nilsson JR, Gallud A, Celauro E, Gasse C, Levi-Acobas F, Sarac I, Hollenstein MR, Dahlén A, Esbjörner EK, Wilhelmsson LM. Stealth Fluorescence Labeling for Live Microscopy Imaging of mRNA Delivery. J Am Chem Soc 2021; 143:5413-5424. [PMID: 33797236 PMCID: PMC8154517 DOI: 10.1021/jacs.1c00014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
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Methods for tracking
RNA inside living cells without perturbing
their natural interactions and functions are critical within biology
and, in particular, to facilitate studies of therapeutic RNA delivery.
We present a stealth labeling approach that can efficiently, and with
high fidelity, generate RNA transcripts, through enzymatic incorporation
of the triphosphate of tCO, a fluorescent tricyclic cytosine
analogue. We demonstrate this by incorporation of tCO in
up to 100% of the natural cytosine positions of a 1.2 kb mRNA encoding
for the histone H2B fused to GFP (H2B:GFP). Spectroscopic characterization
of this mRNA shows that the incorporation rate of tCO is
similar to cytosine, which allows for efficient labeling and controlled
tuning of labeling ratios for different applications. Using live cell
confocal microscopy and flow cytometry, we show that the tCO-labeled mRNA is efficiently translated into H2B:GFP inside human
cells. Hence, we not only develop the use of fluorescent base analogue
labeling of nucleic acids in live-cell microscopy but also, importantly,
show that the resulting transcript is translated into the correct
protein. Moreover, the spectral properties of our transcripts and
their translation product allow for their straightforward, simultaneous
visualization in live cells. Finally, we find that chemically transfected
tCO-labeled RNA, unlike a state-of-the-art fluorescently
labeled RNA, gives rise to expression of a similar amount of protein
as its natural counterpart, hence representing a methodology for studying
natural, unperturbed processing of mRNA used in RNA therapeutics and
in vaccines, like the ones developed against SARS-CoV-2.
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Affiliation(s)
- Tom Baladi
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jesper R Nilsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Audrey Gallud
- Department of Biology and Biological Engineering, Chemical Biology, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Emanuele Celauro
- Department of Biology and Biological Engineering, Chemical Biology, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Cécile Gasse
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Fabienne Levi-Acobas
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, Institut Pasteur, 28, Rue du Docteur Roux, 75724 Paris CEDEX 15, France
| | - Ivo Sarac
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, Institut Pasteur, 28, Rue du Docteur Roux, 75724 Paris CEDEX 15, France
| | - Marcel R Hollenstein
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, Institut Pasteur, 28, Rue du Docteur Roux, 75724 Paris CEDEX 15, France
| | - Anders Dahlén
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Elin K Esbjörner
- Department of Biology and Biological Engineering, Chemical Biology, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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Baladi T, Hamouda-Tekaya N, Gonçalves LCP, Rocchi S, Ronco C, Benhida R. Sulfonylguanidine Derivatives as Potential Antimelanoma Agents. ChemMedChem 2020; 15:1113-1117. [PMID: 32347004 DOI: 10.1002/cmdc.202000218] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 04/07/2020] [Revised: 04/26/2020] [Indexed: 12/11/2022]
Abstract
Sulfonylguanidines are interesting bioactive compounds with a broad range of applications in the treatment of different pathologies. 2-Aminobenzazole-based structures are well employed in the development of new anticancer drugs. Two series of novel N-benzazol-2-yl-N'-sulfonyl guanidine derivatives were synthesized with the sulfonylguanidine in either an extra- or intracyclic frame. They were evaluated for their antiproliferative activity against malignant melanoma tumor cells, thus allowing structure-activity relationships to be defined. Additionally, NCI-60 screening was performed for the best analogue to study its efficiency against a panel of other cancer cell lines. The stability profile of this promising compound was then validated. During the synthetic process, an unexpected new deamidination of the sulfonylguanidine towards sulfonamide function was also identified.
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Affiliation(s)
- Tom Baladi
- Institut de Chimie de Nice CRNS UMR7272, Université Côte d'Azur, 28 Avenue Valrose, 06108, Nice, France
| | - Nedra Hamouda-Tekaya
- Centre Méditerranéen de Médecine Moléculaire (C3M) - INSERM, U1065, Université Côte d'Azur, 151 Route de Saint-Antoine, 06200, Nice, France
| | | | - Stéphane Rocchi
- Centre Méditerranéen de Médecine Moléculaire (C3M) - INSERM, U1065, Université Côte d'Azur, 151 Route de Saint-Antoine, 06200, Nice, France
| | - Cyril Ronco
- Institut de Chimie de Nice CRNS UMR7272, Université Côte d'Azur, 28 Avenue Valrose, 06108, Nice, France
| | - Rachid Benhida
- Institut de Chimie de Nice CRNS UMR7272, Université Côte d'Azur, 28 Avenue Valrose, 06108, Nice, France.,Mohamed VI Polytechnic University, UM6P, 43150, Ben Guerir, Morocco
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6
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Affiliation(s)
- Jessy Aziz
- Institut
Curie, PSL Research University, CNRS, INSERM, UMR9187-U1196, F-91405, Orsay, France
| | - Tom Baladi
- Institut
Curie, PSL Research University, CNRS, INSERM, UMR9187-U1196, F-91405, Orsay, France
| | - Sandrine Piguel
- Institut
Curie, Université Paris Sud, Université Paris-Saclay, F-91405, Orsay, France
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Baladi T, Granzhan A, Piguel S. Microwave-Assisted C-2 Direct Alkenylation of Imidazo[4,5-b]pyridines: Access to Fluorescent Purine Isosteres with Remarkably Large Stokes Shifts. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600166] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Baladi T, Abet V, Piguel S. State-of-the-art of small molecule inhibitors of the TAM family: the point of view of the chemist. Eur J Med Chem 2015; 105:220-37. [PMID: 26498569 DOI: 10.1016/j.ejmech.2015.10.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 10/01/2015] [Accepted: 10/03/2015] [Indexed: 01/04/2023]
Abstract
The TAM family of tyrosine kinases receptors (Tyro3, Axl and Mer) is implicated in cancer development, autoimmune reactions and viral infection and is therefore emerging as an effective and attractive therapeutic target. To date, only a few small molecules have been intentionally designed to block the TAM kinases, while most of the inhibitors were developed for blocking different protein kinases and then identified through selectivity profile studies. This minireview will examine in terms of chemical structure the different compounds able to act on either one, two or three TAM kinases with details about structure-activity relationships, drug-metabolism and pharmacokinetics properties where they exist.
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Affiliation(s)
- Tom Baladi
- Institut Curie/UMR9187-U1196, 91405 Orsay cedex, France; Univ Paris Sud, 91405 Orsay cedex, France
| | | | - Sandrine Piguel
- Institut Curie/UMR9187-U1196, 91405 Orsay cedex, France; Univ Paris Sud, 91405 Orsay cedex, France.
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