Switchable molecular tweezers: design and applications

• Pablo Msellem,
• Maksym Dekthiarenko,
• Nihal Hadj Seyd and
• Guillaume Vives

Beilstein J. Org. Chem. 2024, 20, 504–539, doi:10.3762/bjoc.20.45

Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin

• Jon Lundstrøm,
• Emilie Gillon,
• Valérie Chazalet,
• Nicole Kerekes,
• Antonio Di Maio,
• Ten Feizi,
• Yan Liu,
• Annabelle Varrot and
• Daniel Bojar

Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31

• around W63 for the N-terminal domain and F273 for the C-terminal domain of CMA1. As binding specificities of melon lectins in general (beyond chitooligosaccharides), and CMA1 in particular, are still unknown, we set out to measure, quantify, and understand the glycan-binding properties of CMA1 in depth

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

• irradiation of the styrylpyridines and formation of the intercalator directly in the presence of DNA. In addition to the DNA-binding properties, the tested benzo[c]quinolizinium derivatives also operate as photosensitizers, which induce DNA damage at relative low concentrations and short irradiation times

• intercalators, and some currently applied anticancer drugs actually operate on the basis of intercalation [3]. Hence, several classes of compounds have been established, whose DNA-binding properties can be tailored and fine-tuned for that purpose, for example anthracyclines [5], indolocarbazoles [6], acridines

• [19]. As a result, several photoactive compounds have been developed, whose DNA-binding properties can be efficiently switched on and off by light [14][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34]. In addition to their DNA-binding properties some annelated quinolizinium derivatives have

Tying a knot between crown ethers and porphyrins

• Maksym Matviyishyn and
• Bartosz Szyszko

Beilstein J. Org. Chem. 2023, 19, 1630–1650, doi:10.3762/bjoc.19.120

• excellent metal-binding properties [67][122][123][124]. Accordion porphyrins and tripyrrane-crown ether hybrids The major contribution in the field of iminoporphyrinoids dates back to 1984 when Bowman-James and co-workers demonstrated a facile synthesis of the so-called accordion porphyrins (Scheme 4) [52

CuAAC-inspired synthesis of 1,2,3-triazole-bridged porphyrin conjugates: an overview

• Dileep Kumar Singh

Beilstein J. Org. Chem. 2023, 19, 349–379, doi:10.3762/bjoc.19.29

• % yield using Cu(MeCN)4PF6 and triethylamine in anhydrous DMF. This ‘capped’ porphyrin was designed so that the rigid triazole linkers prevent the capping group from collapsing onto the porphyrin. Gilday et al. [60] also synthesized porphyrin 142 and studied its anion-binding properties and found that it

Identification of the new prenyltransferase Ubi-297 from marine bacteria and elucidation of its substrate specificity

• Jamshid Amiri Moghaddam,
• Huijuan Guo,
• Karsten Willing,
• Thomas Wichard and
• Christine Beemelmanns

Beilstein J. Org. Chem. 2022, 18, 722–731, doi:10.3762/bjoc.18.72

• and A. machipongonensis sp. PR1 were synthesized. To gain more insights into the binding properties of UbiA-297 and the functional role of the conserved arginine moiety (R145), an additional point-mutated ubiA-297 (R145A) version was synthesized codon-optimized for expression in E. coli. Synthesized

Halides as versatile anions in asymmetric anion-binding organocatalysis

• Lukas Schifferer,
• Martin Stinglhamer,
• Kirandeep Kaur and
• Olga García Macheño

Beilstein J. Org. Chem. 2021, 17, 2270–2286, doi:10.3762/bjoc.17.145

• challenging to design small molecule catalysts that resemble anion-binding properties of enzymes. Hence, a major challenge of small organic receptors to mimic nature’s capability of binding to the targeted anions resides in the supramolecular properties of enzymes and co-factors to form exact matching binding

• excellent yields and enantioselectivities up to 95% and 98% ee, respectively. Cation–π interaction: expanding the functionality of hydrogen bond donor catalysts: The development of hydrogen bond donor anion-binding catalysts mainly focuses on the interaction and binding properties towards the anionic

• , but also to cation–H or π–π interactions. Some of the advantages of multidentate, supramolecular anion-binding catalysis were recently exploited by the Feringa group, who designed an anion-binding catalyst 86 that fuses the known triazole binding properties with a light-switchable molecular motor. In

Sustainable manganese catalysis for late-stage C–H functionalization of bioactive structural motifs

• Jongwoo Son

Beilstein J. Org. Chem. 2021, 17, 1733–1751, doi:10.3762/bjoc.17.122

• protein–ligand binding properties as well as biological activities of small molecules, potentially leading to dramatic increases in potency, and thus has been widely explored in drug discovery [54][55][56]. Late-stage C–H methylation has recently been investigated using iron and cobalt catalysts as

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

• extensive studies reviewed below, PNA still needs innovative chemistry to break through in clinic and other in vivo applications. Review PNA binding modes to DNA and RNA PNA was originally designed with an expectation to improve the binding properties of negatively charged triplex-forming oligonucleotides

• –Crick base pairing at mixed sequences that do not have polypurine tracts is also possible, but requires chemical modifications to alter the binding properties of PNAs. These binding modes further illustrate the diversity of molecular recognition that can be achieved with PNAs. Taken together, the early

• discoveries that revealed the remarkable nucleic acid binding properties of PNA boosted enthusiasm about PNA’s potential as an antisense and antigene therapeutic agent [38]. Structures of PNA complexes Early NMR structural studies suggested that PNA formed heteroduplexes with DNA [39] and RNA [40] that

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

• functionality. Thus, this synthetic route represents the first successful Cu-mediated coupling reaction of berberine substrates. The DNA-binding properties of the 10-O-arylberberine derivatives with duplex and quadruplex DNA were studied by thermal DNA denaturation experiments, spectrometric titrations as well

• , it has been found that berberine (1a) exhibits a selective cytotoxicity against cancer cells [12][13], which is mainly based on its DNA-binding properties [14]. Since the complexation with DNA leads to significant changes of the fluorescent quantum yields of the bound berberine, it can also be used

• berberrubine. And herein, we report the application of this Cu-mediated coupling reaction for the synthesis of 10-O-arylated berberine derivatives as unexpected reaction product, along with first experiments that demonstrate the G4-DNA-binding properties of this class of berberine derivatives. Results and

Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

• Christopher Liczner,
• Kieran Duke,
• Gabrielle Juneau,
• Martin Egli and
• Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

• oligonucleotides challenging. Thio-LNA (Figure 7F), which has sulfur incorporated at the C2' position, has similar binding properties as amino-LNA and β-ᴅ-LNA, but with varying biodistribution patterns and a higher cellular uptake in mice [145]. Work looking at carba-LNA, which lacks the O2' functionality, has

• both the 3' and 5'-neighboring phosphate groups, allowing for a tailoring of the nuclease resistance [200]. In 2011, Rosenberg demonstrated the favorable binding properties of an oligothymidylate modified with 4'-methoxy or 4'-(2-methoxyethoxy) functionalities (Figure 9A,B) [201]. These modified

Au(III) complexes with tetradentate-cyclam-based ligands

• Ann Christin Reiersølmoen,
• Thomas N. Solvi and
• Anne Fiksdahl

Beilstein J. Org. Chem. 2021, 17, 186–192, doi:10.3762/bjoc.17.18

• binding properties [25] and reactions with bovine serum albumin [27]. Cyclam is known as a tetraamino-macrocyclic ligand, which binds strongly to give complexes with many transition metal cations. While catalytic applications of square planar cyclam complexes are reported for metals, such as Ni [30][31

Construction of pillar[4]arene[1]quinone–1,10-dibromodecane pseudorotaxanes in solution and in the solid state

• Xinru Sheng,
• Errui Li and
• Feihe Huang

Beilstein J. Org. Chem. 2020, 16, 2954–2959, doi:10.3762/bjoc.16.245

• the hydrogen atoms on the ethoxy groups. It is worth mentioning that we did not find any interaction of the benzoquinone subunit of the host with the guest molecule. Host–guest complexation in solution In order to further study the host–guest binding properties of H and G, we explored the complexation

UV resonance Raman spectroscopy of the supramolecular ligand guanidiniocarbonyl indole (GCI) with 244 nm laser excitation

• Tim Holtum,
• Vikas Kumar,
• Daniel Sebena,
• Jens Voskuhl and
• Sebastian Schlücker

Beilstein J. Org. Chem. 2020, 16, 2911–2919, doi:10.3762/bjoc.16.240

• supramolecular ligands: guanidiniocarbonyl pyrrole (GCP) and guanidiniocarbonyl indole (GCI). The latter class of artificial carboxylate receptors is a potential next generation binder based on the GCI motif which maintains the good carboxylate binding properties of GCP. GCI comprises an indole ring instead of a

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

• several human cancer cells, but has only a relatively low cytotoxicity in healthy cells [31][32]. Berberine is also known as a G4-DNA ligand [33]. Especially berberine derivatives that carry additional substituents with varying alkyl chain lengths in the 9- and 13-position show enhanced binding properties

• ][41][42]. In the latter cases, the binding properties depend on the length of the alkyl chain. For example, the aminohexyl-substituted derivative 1b6 and the phenylpropyl-substituted compound 1d3 have the highest affinity to G-quadruplex DNA, whereas the derivatives with other alkyl chain lengths have

• may allow to deduce a relationship between the chain length and the binding properties. The adenine unit was supposed to establish binding interactions with the loop region of the quadruplex, namely through Watson–Crick base pairing with the complementary thymidine residues. Herein, we describe the

Easy access to a carbohydrate-based template for stimuli-responsive surfactants

• Thomas Holmstrøm,
• Daniel Raydan and
• Christian Marcus Pedersen

Beilstein J. Org. Chem. 2020, 16, 2788–2794, doi:10.3762/bjoc.16.229

• underlines that building block 5 is an ideal template for the synthesis of molecules with a 2,4- and 3,6-functional group pattern. However, after investigating the metal-binding properties of the synthesized diamines and the carboxylic acids, no conformational changes could be observed. Hence, the compounds

Selective recognition of ATP by multivalent nano-assemblies of bisimidazolium amphiphiles through “turn-on” fluorescence response

• Rakesh Biswas,
• Surya Ghosh,
• Shubhra Kanti Bhaumik and
• Supratim Banerjee

Beilstein J. Org. Chem. 2020, 16, 2728–2738, doi:10.3762/bjoc.16.223

• the synthesis, self-assembly and phosphate binding properties of four imidazolium-based receptors PBImN (N = 4, 10, 12, 14). The derivatives with N ≥ 10 chains were amphiphilic in nature and underwent self-assembly in aqueous buffer to produce nano-assemblies that displayed excimeric emission from the

Optical detection of di- and triphosphate anions with mixed monolayer-protected gold nanoparticles containing zinc(II)–dipicolylamine complexes

• Lena Reinke,
• Julia Bartl,
• Marcus Koch and
• Stefan Kubik

Beilstein J. Org. Chem. 2020, 16, 2687–2700, doi:10.3762/bjoc.16.219

• was clearly controlled by the nature and the binding properties of the immobilized receptors. The sensitivity of the detection increased with an increasing charge of the phosphates but did not depend on additional structural parameters as in many low-molecular-weight phosphate probes, in which the

Thermodynamic and electrochemical study of tailor-made crown ethers for redox-switchable (pseudo)rotaxanes

• Henrik Hupatz,
• Marius Gaedke,
• Hendrik V. Schröder,
• Julia Beerhues,
• Arto Valkonen,
• Fabian Klautzsch,
• Sebastian Müller,
• Felix Witte,
• Kari Rissanen,
• Biprajit Sarkar and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2020, 16, 2576–2588, doi:10.3762/bjoc.16.209

• ; redox chemistry; rotaxanes; supramolecular chemistry; Introduction Pedersen discovered crown ethers in 1967 while searching for multidentate ligands for the vanadyl group [1][2][3]. He was later awarded the Nobel Prize in Chemistry for his studies on the crown ether selective binding properties towards

• alkali metal ions [2]. Crown ethers and their binding properties nowadays find frequent application, e.g., as cation sensors [4][5][6][7], as phase-transfer catalysts [8][9][10], or as drug delivery systems [11][12][13]. Already at the early stages of crown ether research, considerable effort has been

• /ammonium (pseudo)rotaxanes. One reason is that functionalized crown ethers can cause major obstacles in the synthesis of (pseudo)rotaxanes, as their functionalization can strongly interfere with the binding properties of the crown ether [24][25]. Recently, we have investigated examples for redox-switchable

Design, synthesis and application of carbazole macrocycles in anion sensors

• Alo Rüütel,
• Ville Yrjänä,
• Sandip A. Kadam,
• Indrek Saar,
• Mihkel Ilisson,
• Astrid Darnell,
• Kristjan Haav,
• Tõiv Haljasorg,
• Lauri Toom,
• Johan Bobacka and
• Ivo Leito

Beilstein J. Org. Chem. 2020, 16, 1901–1914, doi:10.3762/bjoc.16.157

• residues (from glutaric to thapsic acid) with different chain lengths, allowing manipulation of the ring size. Similar strategies for closing macrocycles have previously been published [26][27][28]. To predict possible binding properties, all methylene-bridged macrocycles and their binding to several

• coupling of the corresponding amino derivatives according to Scheme 1. The synthesis of CZ016 is also described in Scheme 1. Details of all synthetic procedures can be found in Supporting Information File 1. Binding measurements The binding properties of the macrocycles are expressed by the logarithms of

Synthesis, antiinflammatory activity, and molecular docking studies of bisphosphonic esters as potential MMP-8 and MMP-9 inhibitors

• Abimelek Cortes-Pacheco,
• María Adelina Jiménez-Arellanes,
• Francisco José Palacios-Can,
• José Antonio Valcarcel-Gamiño,
• Rodrigo Said Razo-Hernández,
• María del Carmen Juárez-Vázquez,
• Adolfo López-Torres and
• Oscar Abelardo Ramírez-Marroquín

Beilstein J. Org. Chem. 2020, 16, 1277–1287, doi:10.3762/bjoc.16.108

• the binding properties of a molecule. Besides the dipole moment, 3 and 4 have the greatest chemical hardness of the bisphosphonates. This descriptor is related to the chemical susceptibility to an external potential. Therefore, the antiinflammatory activity of these compounds can be related to 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

• structural changes of the nucleic acid. In turn, both of these processes interfere with biologically relevant recognition processes between DNA and enzymes, e.g., topoisomerase [10]. Therefore, many potential lead structures of chemotherapeutic anticancer drugs exhibit DNA-binding properties [1][2][3][4][5

• switching of binding properties [36]. Apparently, styryl-substituted aromatic derivatives could fill this gap because the [2 + 2] photocyclization reaction of stilbenes and derivatives thereof is a well-established reversible photoreaction [37][38][39][40][41][42][43][44][45][46], and styryl dyes, in

• 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

Photocontrolled DNA minor groove interactions of imidazole/pyrrole polyamides

• Sabrina Müller,
• Jannik Paulus,
• Jochen Mattay,
• Heiko Ihmels,
• Veronica I. Dodero and
• Norbert Sewald

Beilstein J. Org. Chem. 2020, 16, 60–70, doi:10.3762/bjoc.16.8

• contacts to the bottom of the cognate minor groove. However, previous studies on distamycin A-like derivatives containing only pyrrole moieties and 4,4'-substituted azobenzene as a photoswitchable linker showed that the binding properties of the Z- and E-isomers were quite similar. Hence, there was no

Design, synthesis and investigation of water-soluble hemi-indigo photoswitches for bioapplications

• Daria V. Berdnikova

Beilstein J. Org. Chem. 2019, 15, 2822–2829, doi:10.3762/bjoc.15.275

• solubility in aqueous medium and potential RNA-binding properties, the dimethylaminopropyl substituent [19] was introduced to hemi-indigo Z-1c. Two synthetically straightforward approaches of the alkylamino group introduction were considered: (i) N-alkylation of the indoxyl core and (ii) O-alkylation of the