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Article ; Online: Synthesis and Photophysical Characterization of a pH-Sensitive Quadracyclic Uridine (qU) Analogue.

Le, Hoang-Ngoan / Kuchlyan, Jagannath / Baladi, Tom / Albinsson, Bo / Dahlén, Anders / Wilhelmsson, L Marcus

Chemistry (Weinheim an der Bergstrasse, Germany)

2024 Volume 30, Issue 18, Page(s) e202303539

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/ ... ...

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.
MeSH term(s)	Uridine/chemistry ; Fluorescent Dyes/chemistry ; Nucleic Acids ; Hydrogen-Ion Concentration ; Uracil
Chemical Substances	Uridine (WHI7HQ7H85) ; Fluorescent Dyes ; Nucleic Acids ; Uracil (56HH86ZVCT)
Language	English
Publishing date	2024-02-09
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1478547-X
ISSN	1521-3765 ; 0947-6539
ISSN (online)	1521-3765
ISSN	0947-6539
DOI	10.1002/chem.202303539
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Multiphoton characterization and live cell imaging using fluorescent adenine analogue 2CNqA.

Nilsson, Jesper R / Benitez-Martin, Carlos / Sansom, Henry G / Pfeiffer, Pauline / Baladi, Tom / Le, Hoang-Ngoan / Dahlén, Anders / Magennis, Steven W / Wilhelmsson, L Marcus

Physical chemistry chemical physics : PCCP

2023 Volume 25, Issue 30, Page(s) 20218–20224

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, ... ...

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
MeSH term(s)	Fluorescent Dyes/chemistry ; Oligonucleotides ; Spectrometry, Fluorescence/methods ; Purine Nucleosides ; Adenine/chemistry
Chemical Substances	Fluorescent Dyes ; Oligonucleotides ; Purine Nucleosides ; Adenine (JAC85A2161)
Language	English
Publishing date	2023-08-02
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d3cp01147j
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Article ; Online: Sulfonylguanidine Derivatives as Potential Antimelanoma Agents.

Baladi, Tom / Hamouda-Tekaya, Nedra / Gonçalves, Leticia Christina Pires / Rocchi, Stéphane / Ronco, Cyril / Benhida, Rachid

ChemMedChem

2020 Volume 15, Issue 13, Page(s) 1113–1117

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- ... ...

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.
MeSH term(s)	Antineoplastic Agents/chemical synthesis ; Antineoplastic Agents/chemistry ; Antineoplastic Agents/pharmacology ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Cell Survival/drug effects ; Dose-Response Relationship, Drug ; Drug Screening Assays, Antitumor ; Guanidine/analogs & derivatives ; Guanidine/chemical synthesis ; Guanidine/chemistry ; Guanidine/pharmacology ; Humans ; Hydrogen-Ion Concentration ; Melanoma/drug therapy ; Melanoma/pathology ; Molecular Docking Simulation ; Molecular Structure ; Skin Neoplasms/drug therapy ; Skin Neoplasms/pathology ; Structure-Activity Relationship
Chemical Substances	Antineoplastic Agents ; sulfonylguanidine ; Guanidine (JU58VJ6Y3B)
Language	English
Publishing date	2020-05-12
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2218496-X
ISSN	1860-7187 ; 1860-7179
ISSN (online)	1860-7187
ISSN	1860-7179
DOI	10.1002/cmdc.202000218
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Article ; Online: Fluorescent base analogues in gapmers enable stealth labeling of antisense oligonucleotide therapeutics.

Nilsson, Jesper R / Baladi, Tom / Gallud, Audrey / Baždarević, Dženita / Lemurell, Malin / Esbjörner, Elin K / Wilhelmsson, L Marcus / Dahlén, Anders

Scientific reports

2021 Volume 11, Issue 1, Page(s) 11365

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 ... ...

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, tC
MeSH term(s)	Cell Survival/drug effects ; Flow Cytometry ; Fluorescent Dyes/chemistry ; HEK293 Cells ; Humans ; Microscopy, Fluorescence ; Nucleic Acid Conformation ; Oligonucleotides, Antisense/chemistry ; Oligonucleotides, Antisense/pharmacology ; Real-Time Polymerase Chain Reaction ; Reverse Transcription ; Spectrophotometry, Ultraviolet
Chemical Substances	Fluorescent Dyes ; Oligonucleotides, Antisense
Language	English
Publishing date	2021-05-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-90629-1
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Article ; Online: Direct Alkynylation of 3H-Imidazo[4,5-b]pyridines Using gem-Dibromoalkenes as Alkynes Source.

Aziz, Jessy / Baladi, Tom / Piguel, Sandrine

The Journal of organic chemistry

2016 Volume 81, Issue 10, Page(s) 4122–4133

Abstract: C2 direct alkynylation of 3H-imidazo[4,5-b]pyridine derivatives is explored for the first time. Stable and readily available 1,1-dibromo-1-alkenes, electrophilic alkyne precursors, are used as coupling partners. The simple reaction conditions include an ... ...

Abstract	C2 direct alkynylation of 3H-imidazo[4,5-b]pyridine derivatives is explored for the first time. Stable and readily available 1,1-dibromo-1-alkenes, electrophilic alkyne precursors, are used as coupling partners. The simple reaction conditions include an inexpensive copper catalyst (CuBr·SMe2 or Cu(OAc)2), a phosphine ligand (DPEphos) and a base (LiOtBu) in 1,4-dioxane at 120 °C. This C-H alkynylation method revealed to be compatible with a variety of substitutions on both coupling partners: heteroarenes and gem-dibromoalkenes. This protocol allows the straightforward synthesis of various 2-alkynyl-3H-imidazo[4,5-b]pyridines, a valuable scaffold in drug design.
Language	English
Publishing date	2016-05-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	123490-0
ISSN	1520-6904 ; 0022-3263
ISSN (online)	1520-6904
ISSN	0022-3263
DOI	10.1021/acs.joc.6b00406
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Article ; Online: State-of-the-art of small molecule inhibitors of the TAM family: the point of view of the chemist.

Baladi, Tom / Abet, Valentina / Piguel, Sandrine

European journal of medicinal chemistry

2015 Volume 105, Page(s) 220–237

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 ... ...

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.
MeSH term(s)	Animals ; Dose-Response Relationship, Drug ; Humans ; Models, Molecular ; Molecular Structure ; Protein Kinase Inhibitors/chemical synthesis ; Protein Kinase Inhibitors/chemistry ; Protein Kinase Inhibitors/pharmacology ; Receptor Protein-Tyrosine Kinases/antagonists & inhibitors ; Receptor Protein-Tyrosine Kinases/metabolism ; Small Molecule Libraries/chemical synthesis ; Small Molecule Libraries/chemistry ; Small Molecule Libraries/pharmacology ; Structure-Activity Relationship
Chemical Substances	Protein Kinase Inhibitors ; Small Molecule Libraries ; Receptor Protein-Tyrosine Kinases (EC 2.7.10.1)
Language	English
Publishing date	2015-11-13
Publishing country	France
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	188597-2
ISSN	1768-3254 ; 0009-4374 ; 0223-5234
ISSN (online)	1768-3254
ISSN	0009-4374 ; 0223-5234
DOI	10.1016/j.ejmech.2015.10.003
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Article ; Online: Fluorescent base analogues in gapmers enable stealth labeling of antisense oligonucleotide therapeutics

Jesper R. Nilsson / Tom Baladi / Audrey Gallud / Dženita Baždarević / Malin Lemurell / Elin K. Esbjörner / L. Marcus Wilhelmsson / Anders Dahlén

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 13

Abstract: 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 ... ...

Abstract	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.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Stealth Fluorescence Labeling for Live Microscopy Imaging of mRNA Delivery.

Baladi, Tom / Nilsson, Jesper R / Gallud, Audrey / Celauro, Emanuele / Gasse, Cécile / Levi-Acobas, Fabienne / Sarac, Ivo / Hollenstein, Marcel R / Dahlén, Anders / Esbjörner, Elin K / Wilhelmsson, L Marcus

Journal of the American Chemical Society

2021 Volume 143, Issue 14, Page(s) 5413–5424

Abstract: 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 ... ...

Abstract	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 tC
MeSH term(s)	COVID-19/drug therapy ; Cell Line, Tumor ; Cytosine/analogs & derivatives ; Cytosine/analysis ; Cytosine/chemical synthesis ; Cytosine/chemistry ; Fluorescence ; Fluorescent Dyes/analysis ; Fluorescent Dyes/chemical synthesis ; Fluorescent Dyes/chemistry ; Green Fluorescent Proteins/metabolism ; Histones/metabolism ; Humans ; Molecular Imaging ; Molecular Structure ; RNA, Messenger/analysis ; RNA, Messenger/chemistry ; RNA, Messenger/metabolism ; RNA, Messenger/therapeutic use ; Spectrometry, Fluorescence
Chemical Substances	Fluorescent Dyes ; Histones ; RNA, Messenger ; Green Fluorescent Proteins (147336-22-9) ; Cytosine (8J337D1HZY)
Language	English
Publishing date	2021-04-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.1c00014
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Article: Direct Alkynylation of 3H-Imidazo[4,5-b]pyridines Using gem-Dibromoalkenes as Alkynes Source

Aziz, Jessy / Baladi Tom / Piguel Sandrine

Journal of organic chemistry. 2016 May 20, v. 81, no. 10

2016

Abstract	C2 direct alkynylation of 3H-imidazo[4,5-b]pyridine derivatives is explored for the first time. Stable and readily available 1,1-dibromo-1-alkenes, electrophilic alkyne precursors, are used as coupling partners. The simple reaction conditions include an inexpensive copper catalyst (CuBrÂ·SMeâ or Cu(OAc)â), a phosphine ligand (DPEphos) and a base (LiOtBu) in 1,4-dioxane at 120 Â°C. This CâH alkynylation method revealed to be compatible with a variety of substitutions on both coupling partners: heteroarenes and gem-dibromoalkenes. This protocol allows the straightforward synthesis of various 2-alkynyl-3H-imidazo[4,5-b]pyridines, a valuable scaffold in drug design.
Keywords	acetates ; alkynes ; catalysts ; chemical reactions ; chemical structure ; copper ; drugs ; Lewis acids ; ligands ; organic chemistry ; phosphine ; pyridines
Language	English
Dates of publication	2016-0520
Size	p. 4122-4133.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	123490-0
ISSN	1520-6904 ; 0022-3263
ISSN (online)	1520-6904
ISSN	0022-3263
DOI	10.1021%2Facs.joc.6b00406
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Design, synthesis, biological evaluation and cellular imaging of imidazo[4,5-b]pyridine derivatives as potent and selective TAM inhibitors.

Baladi, Tom / Aziz, Jessy / Dufour, Florent / Abet, Valentina / Stoven, Véronique / Radvanyi, François / Poyer, Florent / Wu, Ting-Di / Guerquin-Kern, Jean-Luc / Bernard-Pierrot, Isabelle / Garrido, Sergio Marco / Piguel, Sandrine

Bioorganic & medicinal chemistry

2018 Volume 26, Issue 20, Page(s) 5510–5530

Abstract: The TAM kinase family arises as a new effective and attractive therapeutic target for cancer therapy, autoimmune and viral diseases. A series of 2,6-disubstituted imidazo[4,5-b]pyridines were designed, synthesized and identified as highly potent TAM ... ...

Abstract	The TAM kinase family arises as a new effective and attractive therapeutic target for cancer therapy, autoimmune and viral diseases. A series of 2,6-disubstituted imidazo[4,5-b]pyridines were designed, synthesized and identified as highly potent TAM inhibitors. Despite remarkable structural similarities within the TAM family, compounds 28 and 25 demonstrated high activity and selectivity in vitro against AXL and MER, with IC
MeSH term(s)	A549 Cells ; Drug Design ; Humans ; Imidazoles/chemical synthesis ; Imidazoles/chemistry ; Imidazoles/pharmacokinetics ; Imidazoles/pharmacology ; Models, Molecular ; Protein Kinase Inhibitors/chemical synthesis ; Protein Kinase Inhibitors/chemistry ; Protein Kinase Inhibitors/pharmacokinetics ; Protein Kinase Inhibitors/pharmacology ; Proto-Oncogene Proteins/antagonists & inhibitors ; Proto-Oncogene Proteins/metabolism ; Pyridines/chemical synthesis ; Pyridines/chemistry ; Pyridines/pharmacokinetics ; Pyridines/pharmacology ; Receptor Protein-Tyrosine Kinases/antagonists & inhibitors ; Receptor Protein-Tyrosine Kinases/metabolism ; Structure-Activity Relationship ; c-Mer Tyrosine Kinase/antagonists & inhibitors ; c-Mer Tyrosine Kinase/metabolism
Chemical Substances	Imidazoles ; Protein Kinase Inhibitors ; Proto-Oncogene Proteins ; Pyridines ; imidazopyridine ; MERTK protein, human (EC 2.7.10.1) ; Receptor Protein-Tyrosine Kinases (EC 2.7.10.1) ; TYRO3 protein, human (EC 2.7.10.1) ; axl receptor tyrosine kinase (EC 2.7.10.1) ; c-Mer Tyrosine Kinase (EC 2.7.10.1)
Language	English
Publishing date	2018-09-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1161284-8
ISSN	1464-3391 ; 0968-0896
ISSN (online)	1464-3391
ISSN	0968-0896
DOI	10.1016/j.bmc.2018.09.031
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