Photoinduced in situ generation of DNA-targeting ligands: DNA-binding and DNA-photodamaging properties of benzo[c]quinolizinium ions

• Julika Schlosser,
• Olga Fedorova,
• Yuri Fedorov and
• Heiko Ihmels

Beilstein J. Org. Chem. 2024, 20, 101–117, doi:10.3762/bjoc.20.11

• delivered without effect to the binding site, where the DNA-binding benzoquinolizinium ligand can then be generated as needed upon irradiation. Notably, the use of light for the activation of photo-controllable DNA ligands offers several advantages because it is easy to apply, traceless, and non-invasive

• determine the binding constants, Kb, of the DNA ligands. Thus, the derivatives 3c, 3e, and 3g bind to ct DNA with Kb values of 6.0 × 104 M−1, 5.9 × 104 M–1, and 6.4 × 104 M−1, respectively, whereas the affinity of ligand 3f is slightly higher with Kb = 1.1 × 105 M−1, which is in the same range as the

Synthesis of 10-O-aryl-substituted berberine derivatives by Chan–Evans–Lam coupling and investigation of their DNA-binding properties

• Peter Jonas Wickhorst,
• Mathilda Blachnik,
• Denisa Lagumdzija and
• Heiko Ihmels

Beilstein J. Org. Chem. 2021, 17, 991–1000, doi:10.3762/bjoc.17.81

• , specifically 13- and 9-substituted berberine derivatives have gained much interest as selective DNA ligands that specifically target quadruplex DNA (G4-DNA) [23][24][25][26][27][28][29], i.e., non-canonical, biologically relevant DNA structures that are formed by the association of four guanine-rich DNA

• F21T are comparable to the one of the parent berberine (1a) under similar conditions (∆Tm = 3.1 °C) [27]. As compared to other known G4-DNA ligands [23][27][28][29], these shifts of the melting temperature in the presence of 5b–e are rather small and indicate a relatively weak stabilizing effect on the

Synthesis and investigation of quadruplex-DNA-binding, 9-O-substituted berberine derivatives

• Jonas Becher,
• Daria V. Berdnikova,
• Heiko Ihmels and
• Christopher Stremmel

Beilstein J. Org. Chem. 2020, 16, 2795–2806, doi:10.3762/bjoc.16.230

• not provide evidence for a significant effect of the adenine unit on the binding affinity of the ligands, for example, by additional association with the loops, presumably because the adenine residue is sterically shielded by the neighboring triazole unit. Keywords: berberine alkaloids; DNA ligands

• successfully developed as G4-DNA ligands [17], the natural product berberine (1a) has attracted special attention. Berberine (1a) is an isoquinoline alkaloid with an exceptionally wide range of biological activities [23][24]. It has been shown that berberine (1a) and its derivatives act, for example, as anti

• a lower affinity [38]. Along the same line, the influence of the length and substituents of the side chains at the G4-DNA ligands have been assessed for quinolinium [43], indoloquinoline [44][45], phenanthroline [46], phenothiazine [47], and thiazole orange [48] derivatives. In these studies, the

Cation-induced ring-opening and oxidation reaction of photoreluctant spirooxazine–quinolizinium conjugates

• Phil M. Pithan,
• Sören Steup and
• Heiko Ihmels

Beilstein J. Org. Chem. 2020, 16, 904–916, doi:10.3762/bjoc.16.82

• -binding properties to be used as DNA-sensitive fluorescent probes in cell imaging [60][61][62] or as photoswitchable DNA ligands [63]. Therefore, we were interested in a combination of the photochromic properties of the spirooxazine moiety with the advantageous photophysical and biological properties of

Reversible photoswitching of the DNA-binding properties of styrylquinolizinium derivatives through photochromic [2 + 2] cycloaddition and cycloreversion

• Sarah Kölsch,
• Heiko Ihmels,
• Jochen Mattay,
• Norbert Sewald and
• Brian O. Patrick

Beilstein J. Org. Chem. 2020, 16, 111–124, doi:10.3762/bjoc.16.13

• -33501 Bielefeld, Germany Department of Chemistry, Structural Chemistry Facility, The University of British Columbia, 2036 Main Mall, V6T 1Z1, Vancouver, BC, Canada 10.3762/bjoc.16.13 Abstract It was demonstrated that styrylquinolizinium derivatives may be applied as photoswitchable DNA ligands. At

• the intercalating monomers upon irradiation at 315 nm in the presence of DNA. As a result, it is possible to switch between these two ligands and likewise between two different binding modes by irradiation with different excitation wavelengths. Keywords: azoniahetarenes; DNA ligands

• release the DNA-binding ligand have not been reported so far. Herein, we report on the photochemical and DNA-binding properties of the selected styrylquinolizinium derivatives 3a–d and demonstrate their ability to operate as photoswitchable DNA ligands. Results and Discussion Synthesis 2

Anomeric sugar boronic acid analogues as potential agents for boron neutron capture therapy

• Daniela Imperio,
• Erika Del Grosso,
• Silvia Fallarini,
• Grazia Lombardi and
• Luigi Panza

Beilstein J. Org. Chem. 2019, 15, 1355–1359, doi:10.3762/bjoc.15.135

• or DNA ligands [4][5]. In the frame of a more general research program, we have recently published the synthesis of boronic acids derivatives of monosaccharides in which one of the sugar hydroxy groups is substituted by a boronic acid moiety [6]. A related approach has been described [7] recently

Synthesis of 9-arylalkynyl- and 9-aryl-substituted benzo[b]quinolizinium derivatives by Palladium-mediated cross-coupling reactions

• Siva Sankar Murthy Bandaru,
• Darinka Dzubiel,
• Heiko Ihmels,
• Mohebodin Karbasiyoun,
• Mohamed M. A. Mahmoud and
• Carola Schulzke

Beilstein J. Org. Chem. 2018, 14, 1871–1884, doi:10.3762/bjoc.14.161

• topoisomerase inhibitors [5]. More recently, much interest in this research area is focused on the non-canonical quadruplex DNA (G4-DNA) [6][7][8]. Mostly based on the principles and requirements of ligands that bind to duplex DNA, numerous G4-DNA ligands have been developed to study their selectivity and

• ]quinolizinium derivatives with a large extension of the π-system, which should provide promising properties as G4-DNA ligands, we also focused our attention on the Sonogashira reaction as synthetic route to arylalkynyl-substituted derivatives. In this case, we aimed at donor-substituted derivatives such as 2b–d

• pH-sensitive light-up probe. Photometric and fluorimetric titrations of duplex and quadruplex DNA to 9-(arylethynyl)benzo[b]quinolizinium derivatives revealed a significant binding affinity of these compounds towards both DNA forms with binding constants of Kb = 0.2–2.2 × 105 M−1. Keywords: DNA

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• , which is ideal for the selective study of DNA ligands that strongly change fluorescence upon binding [3]. In a sense complementary to FDCD, also circularly polarized luminescence (CPL) is a chiroptical emission technique which has been employed in the same context for the first time recently [12]. The

A journey in bioinspired supramolecular chemistry: from molecular tweezers to small molecules that target myotonic dystrophy

• Steven C. Zimmerman

Beilstein J. Org. Chem. 2016, 12, 125–138, doi:10.3762/bjoc.12.14

• coworkers reported that a cyclic bisnaphthalenediimide formed a complex with d(CGGTACCG)2 that provided a well-resolved NMR and clear NOE signals between the linking chains and both the major and minor grooves [50]. Additional studies on this class of DNA ligands as part of an excellent review of other

Synthesis of bi- and bis-1,2,3-triazoles by copper-catalyzed Huisgen cycloaddition: A family of valuable products by click chemistry

• Zhan-Jiang Zheng,
• Ding Wang,
• Zheng Xu and
• Li-Wen Xu

Beilstein J. Org. Chem. 2015, 11, 2557–2576, doi:10.3762/bjoc.11.276

• corresponding primary guanidine or diisopropylguanidine analogs (60 and 61, Scheme 20) [40], which could be used as potential G4 DNA ligands with high selectivity over duplexed DNA. Similar to the above strategies or methods, a number of researchers have developed various dialkyne substrates with varied spacers

Beyond catalyst deactivation: cross-metathesis involving olefins containing N-heteroaromatics

• Kevin Lafaye,
• Cyril Bosset,
• Lionel Nicolas,
• Amandine Guérinot and
• Janine Cossy

Beilstein J. Org. Chem. 2015, 11, 2223–2241, doi:10.3762/bjoc.11.241

• partner such as cis-1,4-diacetoxy-2-butene may statistically prevent the formation of 80 thus allowing the CM to occur. In 2010, Harding et al. attempted to use reversible aqueous metathesis for the construction of a dynamic combinatorial library aimed at identifying DNA ligands [76]. Toward that goal

A comparative study of the interactions of cationic hetarenes with quadruplex-DNA forming oligonucleotide sequences of the insulin-linked polymorphic region (ILPR)

• Darinka Dzubiel,
• Heiko Ihmels,
• Mohamed M. A. Mahmoud and
• Laura Thomas

Beilstein J. Org. Chem. 2014, 10, 2963–2974, doi:10.3762/bjoc.10.314

• ligand-ILPR complexes are different from the ones observed with other native quadruplex-forming DNA sequences. Keywords: DNA ligands; fluorescent probes; ILPR; nucleic acids; quadruplex DNA; Introduction The “insulin-linked polymorphic region” (ILPR) is a physiologically relevant G-rich DNA sequence