Search results

Search for "binding" in Full Text gives 977 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.

Using generative AI to transform peptide hits into small molecule leads

  • Joshua Mills and
  • Yu Heng Lau

Beilstein J. Org. Chem. 2026, 22, 672–679, doi:10.3762/bjoc.22.51

Graphical Abstract
  • drug targets, serving as rich inspiration for designing small molecule inhibitors which can recapitulate key binding interactions while improving pharmacokinetic properties. With the rapid advancement of artificial intelligence capabilities including powerful generative models, there is significant
  • , de novo peptide binder generation, diffusion models for generating novel small molecule scaffolds, and deep-learning predictors of binding affinity to rapidly triage candidates. Keywords: diffusion models; drug discovery; generative AI; peptides; small molecules; Introduction In drug discovery
  • , peptides serve as accessible starting points for designing molecules that bind and inhibit a chosen protein target. Many enzyme targets (e.g., proteases) natively process peptides as their substrates. Peptide domains are also common motifs in protein–protein interactions, mediating the binding between
PDF
Album
Perspective
Published 30 Apr 2026

Advantages of PROTACs in achieving selective degradation of homologous protein families

  • Luxi Yang,
  • Xinfei Mao,
  • Jingyi Zhang,
  • Jing Shu,
  • Wenhai Huang,
  • Xiaowu Dong,
  • Yinqiao Chen and
  • Mingfei Wu

Beilstein J. Org. Chem. 2026, 22, 628–661, doi:10.3762/bjoc.22.49

Graphical Abstract
  • targeting an E3 ubiquitin ligase and the other binding to a protein of interest (POI), covalently joined by a flexible linker [12]. Upon cellular entry, the PROTAC molecule facilitates the formation of a ternary complex by simultaneously recruiting the POI and the E3 ligase (Figure 1). This proximity
  • enables the proteasome to recognize the complex, subsequently degrading the target protein via the endogenous ubiquitin–proteasome system [13][14]. Notably, this mechanism does not necessitate prolonged occupancy of the POI binding site. Instead, the transient formation of the ternary complex is
  • inhibitors that rely on sustained occupancy of conserved ATP-binding pockets, PROTACs induce transient yet specific protein–protein interactions that dictate ubiquitination efficiency. By fine-tuning the length and composition of the linker, as well as the choice of E3 ligase and its attachment geometry
PDF
Album
Review
Published 27 Apr 2026

Towards the targeted protein degradation of CK2: design and synthesis of CAM4066-based PROTACs

  • Sophie Day-Riley,
  • Sona Krajcovicova,
  • Aryaman Raj Sokhal,
  • Jan L. Venne,
  • Paul Brear,
  • Marko Hyvönen,
  • Benjamin C. Whitehurst,
  • Jason S. Carroll and
  • David R. Spring

Beilstein J. Org. Chem. 2026, 22, 611–619, doi:10.3762/bjoc.22.47

Graphical Abstract
  • binding affinity comparable to CAM4066, confirming that linker installation is tolerated and preserves key interactions in the αD and ATP sites. Keywords: CAM4066; casein kinase 2 (CK2); PROTACs; targeted protein degradation; Introduction Protein kinases form a large family of more than 500 enzymes that
  • adjacent to the ATP-binding site of CK2α [5][6]. Fragment-based ligand discovery subsequently enabled the development of CAM4066, a selective inhibitor that simultaneously engages the αD and ATP sites. CAM4066 validated the αD region as a tractable and selective binding pocket for CK2 kinase inhibition
  • occupancy-driven pharmacology. Proteolysis-targeting chimeras (PROTACs) represent a rapidly advancing strategy for induced protein degradation. By transiently engaging both a target protein and an E3 ubiquitin ligase, PROTACs promote proteasomal elimination of the target rather than sustained binding [8
PDF
Album
Supp Info
Letter
Published 22 Apr 2026

Computational prediction of C–H hydricities and their use in predicting the regioselectivity of electron-rich C–H functionalisation reactions

  • Rasmus M. Borup,
  • Nicolai Ree and
  • Jan H. Jensen

Beilstein J. Org. Chem. 2026, 22, 603–610, doi:10.3762/bjoc.22.46

Graphical Abstract
  • et al. [24][25], Ree et al. [10] and our previous work [3], we utilise the automated approach to compute CM5 atomic charges from semiempirical tight-binding (GFN1-xTB [32]) calculations. We modify the workflow to enhance the accuracy of the computed CM5 atomic charges. Instead of generating a single
  • photoredox activation, followed by anion-binding-catalysed functionalisation to form β-amino esters. Here, the reacting atom is the one with the lowest hydricity and BDE. Compounds 8–10 Schmidt et al. [44] reported the visible light-catalysed bromination of compound 8, Kamon et al. [45] reported the light
PDF
Album
Supp Info
Full Research Paper
Published 17 Apr 2026

Regioselective approach to 5-arylsulfonylisoxazoles and their antimicrobial activity

  • Artem S. Sazonov,
  • Dmitry A. Vasilenko,
  • Denis V. Porfiriev,
  • Yuri K. Grishin,
  • Rimma A. Gazzaeva,
  • Alisa P. Chernyshova,
  • Maxim A. Kryakvin,
  • Anna A. Baranova,
  • Vera A. Alferova and
  • Elena B. Averina

Beilstein J. Org. Chem. 2026, 22, 592–602, doi:10.3762/bjoc.22.45

Graphical Abstract
  • promising compounds with a wide spectrum of biological activity [1][2][3][4][5]. The attractiveness of isoxazole derivatives for medicinal chemistry is determined by high-affinity binding to many targets, low toxicity of isoxazole-containing compounds and the use of the isoxazole ring as a bioisoster of the
PDF
Album
Supp Info
Full Research Paper
Published 17 Apr 2026

Design and synthesis of an erdafitinib-based selective FGFR2 degrader

  • Yumeng Jin,
  • Shidong Wang,
  • Sihan Pan,
  • Shuqi Huang,
  • Weichen Zhou,
  • Xiaohao Huang,
  • Lei Zheng and
  • Lingfeng Chen

Beilstein J. Org. Chem. 2026, 22, 583–591, doi:10.3762/bjoc.22.44

Graphical Abstract
  • binding to ligands, which trigger intracellular signaling cascades to activate downstream substrates and pathways [4]. This process involves PLC γ-mediated PKC activation and pFRS2-induced activation of the PI3K/AKT and MAPK/ERK pathways, thereby regulating cell proliferation, differentiation, migration
  • proper ligand binding, thus promoting uncontrolled cell proliferation [11][14]. Mutations in FGFR2 may alter its structure, enabling it to bypass normal regulatory mechanisms and activate downstream oncogenic pathways independently of external stimuli, which also contributes to tumor development. Gene
PDF
Album
Supp Info
Full Research Paper
Published 15 Apr 2026

Continuous-flow carbonyl hydrogenation under subatmospheric to atmospheric hydrogen pressure enabled by robust heterogeneous Pt–Fe catalysts

  • Hiroyuki Miyamura,
  • Ryosuke Kajiyama,
  • Shun-ya Onozawa,
  • Yoshihiro Kon and
  • Shū Kobayashi

Beilstein J. Org. Chem. 2026, 22, 575–582, doi:10.3762/bjoc.22.43

Graphical Abstract
  • activity and selectivity. The binding energies of Pt 4d in Pt–Fe/DMPSi‒Al2O3 (332, 315 eV) are lower than those of Pt/DMPSi‒Al2O3 (333, 316 eV) and Pt–Ni/DMPSi‒Al2O3 (334, 317 eV) [30]. Thus, the Pt species in Pt–Fe/DMPSi‒Al2O3 is the most electronically negative among the catalysts, which leads to a
PDF
Album
Supp Info
Full Research Paper
Published 10 Apr 2026

Molecular tweezer–peptide conjugates disrupt the protein–protein interaction between survivin and histone H3 essential in mitosis

  • Catherine Gsell,
  • Philipp Rebmann,
  • Karina Opara,
  • Christine Beuck,
  • Peter Bayer,
  • David Bier,
  • Ingrid R. Vetter and
  • Thomas Schrader

Beilstein J. Org. Chem. 2026, 22, 557–567, doi:10.3762/bjoc.22.41

Graphical Abstract
  • Pro26, corresponding to a previously unknown binding mode. Guided by the accessibility of survivin’s lysine residues in the CPC, a number of new promising peptide tweezers was synthesized, able to connect both binding sites on the protein. Keywords: click reaction; chromosomal passenger complex
  • . demonstrated that survivin contributes most of the binding energy to this critical complex with histone H3 [8]. In 2011, a crystal structure was solved depicting structural details of the H3 N-terminus (1–21) bound by survivin’s BIR domain (Figure 2). Only the first six residues (ARpTKQT) show electron density
  • and precisely the natural binding site in the wide 14-3-3-cleft [10]. These examples for designed protein–protein interaction (PPI) inhibitors demonstrated that short but highly flexible linkers are imperative to increase selectivity and minimize entropical penalty. The design was strongly supported
PDF
Album
Supp Info
Full Research Paper
Published 27 Mar 2026

Synthesis and uranyl(VI) extraction performance of a calix[4]pyrrole–tetrahydroxamic acid receptor

  • Sara Karnib,
  • Rana Baydoun,
  • Wissam Zaidan,
  • Nancy AlHaddad,
  • Omar El Samad,
  • Bilal Nsouli,
  • Francine Cazier-Dennin and
  • Pierre-Edouard Danjou

Beilstein J. Org. Chem. 2026, 22, 486–494, doi:10.3762/bjoc.22.36

Graphical Abstract
  • selective remediation strategies. Supramolecular materials, with their pre-organized structures, offer a promising route for uranium removal. Phenoxycalix[4]pyrroles (PCP) are well-known supramolecular scaffolds capable of selective metal binding, making them attractive candidates for designing uranium
  • receptors bearing both anion- and cation-binding sites, as well as systems capable of promoting ion-pair formation [23][24]. As effective chelating agents for a broad range of transition metals, hydroxamic acids constitute an important class of organic compounds that have attracted considerable attention
  • [4]resorcinarene hydroxamic acid has also shown a pronounced binding tendency and selectivity for uranyl and proved to be applicable for the determination of uranium in standard and environmental samples [34]. Importantly, more recent studies have demonstrated that pre-organized or cyclic hydroxamate
PDF
Album
Supp Info
Full Research Paper
Published 18 Mar 2026

Synthesis of a HDAC inhibitor–nanogold probe for cryo-EM visualization in class I HDAC co-repressor complexes

  • Wiktoria A. Pytel,
  • John W. R. Schwabe and
  • James T. Hodgkinson

Beilstein J. Org. Chem. 2026, 22, 480–485, doi:10.3762/bjoc.22.35

Graphical Abstract
  • , like other benzamide HDAC inhibitors, exhibits slow on/off binding kinetics, hence once bound to the HDAC within the complex it should not readily dissociate [16]. A crystal structure of HDAC2 bound to an analogue of CI-994 (PDB: 4LY1) revealed that the acetamide moiety is oriented outside the HDAC
  • active site [17]. Hence, we decided to functionalize this position with an alkyl linker consisting of 9 carbon atoms to mitigate any steric clashes between the HDAC inhibitor and the nanogold particle, which could be detrimental to the probe binding affinity (Figure 1). Further to this, we previously
  • complex on the EM grid, glutaraldehyde cross-linking was performed, with successful cross-linking confirmed by SDS-PAGE. The cross-linked ternary complex was incubated with the Au–(CI-994) probe for 2 hours in 2:1 molar ratio to minimize non-specific binding. Screening and data collection were carried out
PDF
Album
Supp Info
Full Research Paper
Published 17 Mar 2026

Synthesis and anti-cancer activity of naphthalimide–organylselanyl conjugates

  • Rajkumar Ravi and
  • Selvakumar Karuthapandi

Beilstein J. Org. Chem. 2026, 22, 416–435, doi:10.3762/bjoc.22.29

Graphical Abstract
  • 27.92 ± 3 µM and 23.06 ± 3 μM, respectively. Molecular docking simulations revealed that NAP-SePh and NAP-Se(n-Oct) show binding affinities of −10.39 and −8.53 kcal/mol for the (1M17) active, and −10.66 and −10.59 kcal/mol for the (4HJO) inactive conformation of the tyrosine kinase domain of the
  • binding components, including electron-deficient, electron-rich, and hydrophobic regions, which offer greater affinities towards biological targets. Structures of these compounds were confirmed through various spectroscopic analyses. The structure of compound 7 was confirmed using single-crystal XRD
  • cancer cell line. Molecular docking simulation revealed strong binding interaction and affinities towards the tyrosine kinase domain of epidermal growth factor receptor (EGFR), and the protein–ligand interaction resembles the interaction found in the co-crystallised protein–erlotinib complex. Result and
PDF
Album
Supp Info
Full Research Paper
Published 09 Mar 2026

Cone p-aminocalix[4]arenes enriched with ‘clickable’ alkyne or azide functionalities

  • Ilia Korniltsev,
  • Vasily Bazhenov,
  • Alexander Gorbunov,
  • Dmitry Cheshkov,
  • Stanislav Bezzubov,
  • Vladimir Kovalev and
  • Ivan Vatsouro

Beilstein J. Org. Chem. 2026, 22, 399–415, doi:10.3762/bjoc.22.28

Graphical Abstract
  • ]. (Multi)calix[4]arenes having (dialkyl)amino groups at the wide rims are soluble in aqueous media at physiological pHs and may be used in protein sensing [18], DNA binding/recognition [19][20][21][22][23], and cell transfection [24][25][26]. Their water-soluble guanidinium derivatives are also
  • affect the cycloaddition by, for instance, binding copper cations or counter anions, and thus their presence in the structures of calixarenes at the CuAAC step must be avoided. On the other hand, the unmodified amines may also contribute to undesired Cu(I) stabilization and complicate the CuAAC work up
  • calixarene 37, there were no problems encountered with the copper complex destruction and the yield of the isomeric calixarene 40 having four 2-(4-phenyltriazol-1-yl)ethyl moieties at the narrow rim was much higher, indicating a weaker binding in the 40/Cu+ system than in the 37/Cu+ one, due to the outer
PDF
Album
Supp Info
Full Research Paper
Published 09 Mar 2026

Design, synthesis and biological evaluation of 2,5-diaryloxazolo[4,5-d]pyrimidin-7-ylamines as selective cytotoxic agents against HeLa cells

  • Maryna V. Kachaeva,
  • Agnieszka B. Olejniczak,
  • Marta Denel-Bobrowska,
  • Victor V. Zhirnov,
  • Yevheniia S. Velihina,
  • Stepan G. Pilyo and
  • Volodymyr S. Brovarets

Beilstein J. Org. Chem. 2026, 22, 390–398, doi:10.3762/bjoc.22.27

Graphical Abstract
  • -mimicking scaffolds are a proven strategy in the design of anticancer drugs. Many cancer-related proteins (e.g., kinases, ATPases, DNA/RNA polymerases) have binding pockets designed for purine nucleotides (ATP, GTP). Oxazolopyrimidines can compete with purines or their analogues, inhibiting enzymatic
  • interference with the assay itself, but to binding to possible targets. Conclusion The results of anticancer screening and virtual analysis suggest that among the synthesized derivatives, compounds 1, 7, and 9 showed activity and high relevant selectivity against the HeLa cell line. While compound 1 exhibited
PDF
Album
Supp Info
Full Research Paper
Published 03 Mar 2026

Ring contraction and ring expansion reactions in terpenoid biosynthesis and their application to total synthesis

  • Nicolas Kratena,
  • Nicolas Heinzig and
  • Peter Gärtner

Beilstein J. Org. Chem. 2026, 22, 289–343, doi:10.3762/bjoc.22.21

Graphical Abstract
  • terpenoid modification in nature are depicted. Terpene synthase enzymes are centrally important for determining the carbon skeleton and thus family the terpenoid belongs to. These cyclisation enzymes are divided into Class I (active site cleft contains multiple Mg2+-binding motifs which are responsible for
PDF
Album
Review
Published 17 Feb 2026

Spirobarbiturates with a pyrrolizidine moiety: synthesis, structure and biological evaluation

  • Arthur A. Puzyrkov,
  • Andrew S. Drachuk,
  • Ekaterina A. Popova,
  • Alexander V. Stepakov and
  • Vitali M. Boitsov

Beilstein J. Org. Chem. 2026, 22, 274–288, doi:10.3762/bjoc.22.20

Graphical Abstract
  • absorption (HIA), in vitro permeability to Caco-2 cells (Caco2), in vitro binding to plasma proteins (PPB), solubility, and inhibition of CYP2D6. The following were selected as descriptors of toxicity: carcinogenicity for rats and mice, mutagenicity according to the Ames test, and cardiotoxicity by
  • inhibition of hERG in vitro. The results are shown in Supporting Information File 1, Table S5. As can be seen from the table, the obtained results suggest that the compounds have a good intestinal absorption and medium permeability. However they are expected to have low plasma protein binding and permeation
  • . Taking into account that the conformation of the actin monomer in the described structures is basically the same, the structure of non-muscle β-actin (8DNH, 2.99 Å) obtained by cryo-electron microscopy was used for this study. Docking was performed to both known clefts (hydrophobic or target-binding one
PDF
Album
Supp Info
Full Research Paper
Published 17 Feb 2026

Arene activation via π-bond localization: concepts and opportunities

  • Paul Meiners,
  • Julian J. Melder and
  • Tobias Morack

Beilstein J. Org. Chem. 2026, 22, 257–273, doi:10.3762/bjoc.22.19

Graphical Abstract
  • configuration promotes strong binding to π-acidic ligands, effectively compensating for the loss of aromaticity upon η2-coordination to arenes, while disfavoring oxidative addition due to geometric constraints of the octahedral complex. The resulting η2-arene complexes, encompassing both arenes and heteroarenes
  • (Figure 6C), so suitable aromatic ligands are limited to those lacking strongly π-acidic functional groups, e.g., alkenes, alkynes, aldehydes, certain ketones, and nitriles. Lewis-basic heteroarenes, such as pyridines or imidazoles, tend to coordinate via nitrogen instead, disfavoring η2-binding (Figure
  • aromatic complexes is their fluxionality [47]. Despite clear thermodynamic preferences for specific binding sites, the metal can migrate across the π-system without detaching from the aromatic ring (Figure 7A). This flexibility allows for the generation of multiple organic functionalities from a single
PDF
Album
Review
Published 09 Feb 2026

A mild and atom-efficient four-component cascade strategy for the construction of biologically relevant 4-hydroxyquinolin-2(1H)-one derivatives

  • Dmitrii A. Grishin,
  • Kseniia I. Sharkovskaia,
  • Ilya G. Kolmakov,
  • Daria A. Ipatova,
  • Rostislav A. Petrov,
  • Nikolai D. Dagaev,
  • Dmitry A. Skvortsov,
  • Maria G. Khrenova,
  • Valeriy V. Andreychev,
  • Sergei A. Evteev,
  • Yan A. Ivanenkov,
  • Roman L. Antipin,
  • Olga А. Dontsova and
  • Elena K. Beloglazkina

Beilstein J. Org. Chem. 2026, 22, 244–256, doi:10.3762/bjoc.22.18

Graphical Abstract
  • activity [33]. Halogen substituents in this position have been shown to modulate antibacterial, antiviral, and antiproliferative activities, likely through electronic effects and improved target binding. The C3 position was functionalized with a propanoic acid moiety, explored in both its open-chain (acid
PDF
Album
Supp Info
Full Research Paper
Published 09 Feb 2026

Conformational analysis of difluoromethylornithine: factors influencing its gas-phase and bioactive conformations

  • Matheus P. Freitas

Beilstein J. Org. Chem. 2026, 22, 237–243, doi:10.3762/bjoc.22.17

Graphical Abstract
  • decarboxylase from Leishmania infantum complexed with PLP and DFMO, the bound ligand corresponds instead to human arginase I (PDB code 3GN0). While binding to arginase I is not related to DFMO’s pharmacological activity, both enzymes recognize ornithine-related substrates, allowing DFMO to occupy the arginase
  • amino acid residues and water molecules, while the ligand is delineated by a contour line to distinguish it from the binding cavity. Lowest-energy type-I, type-II, and type-III conformers of the zwitterionic form of (S)-DFMO. Color labels: H = blue, C = pink, N = orange, O = red, F = yellow. DFT
PDF
Album
Supp Info
Full Research Paper
Published 05 Feb 2026

Silica gel with covalently attached bambusuril macrocycle for dicyanoaurate sorption from water

  • Michaela Šusterová and
  • Vladimír Šindelář

Beilstein J. Org. Chem. 2025, 21, 2604–2611, doi:10.3762/bjoc.21.201

Graphical Abstract
  • competing dicyanoargentate(I) anions. We also examine the recyclability of the material and assess its stability in organic solvents, comparing its performance with that of a previously developed material containing noncovalently bound bambusuril. Keywords: anion binding; anion extraction; anion receptor
  • -sized” molecular box has been used to extract various anions from water [12]. Another family of macrocyclic compounds suitable for anion recognition and binding are bambusurils (BUs). BUs act as very potent anion receptors in both organic solvents and water. Furthermore, their portals can be variously
  • , exhibiting near-quantitative binding at millimolar concentrations [17]. The lower binding efficiency of BUs attached to the material compared to the free macrocycle in solution can likely be attributed to the heterogeneous nature of the solid-phase system. Moreover, the anion binding ability of BU1 may be
PDF
Album
Supp Info
Full Research Paper
Published 24 Nov 2025

Total syntheses of highly oxidative Ryania diterpenoids facilitated by innovations in synthetic strategies

  • Zhi-Qi Cao,
  • Jin-Bao Qiao and
  • Yu-Ming Zhao

Beilstein J. Org. Chem. 2025, 21, 2553–2570, doi:10.3762/bjoc.21.198

Graphical Abstract
  • core, successfully completing the first asymmetric total synthesis of ryanodol (4) in 41 steps. To elucidate the role of the C15 hemiacetal hydroxy group in ryanodine (1)-type diterpenoid natural products in binding to ryanodine receptors, the authors initially proposed reducing the lactone moiety in
  • , epoxidation of the C1–C2 double bond, and Li/NH3-promoted reductive cyclization to construct the core E ring, completing the asymmetric total synthesis of (+)-ryanodol (4). The 800-fold greater binding affinity of (+)-ryanodine (1) for cardiac ryanodine receptors (RyRs) compared to its hydrolysis product
  • , (+)-ryanodol (4), indicates that the pyrrole-2-carboxylate unit at the C3 position is critical for receptor binding, as established by structure–activity relationship (SAR) studies [28]. However, the direct and selective modification of the highly sterically hindered C3 hydroxy group within this
PDF
Album
Review
Published 19 Nov 2025

Synthesis and characterization of a isothiouronium-calix[4]arene derivative: self-assembly and anticancer activity

  • Giuseppe Granata,
  • Loredana Ferreri,
  • Claudia Giovanna Leotta,
  • Giovanni Mario Pitari and
  • Grazia Maria Letizia Consoli

Beilstein J. Org. Chem. 2025, 21, 2535–2541, doi:10.3762/bjoc.21.195

Graphical Abstract
  • . Multiple ligand–receptor interactions can significantly enhance receptor binding affinity and cellular uptake, as well as more effectively modulate signal transduction pathways, for instance when receptor clustering is necessary on the cell membrane [3]. Designing multivalent bioactive compounds thus
PDF
Album
Full Research Paper
Published 14 Nov 2025

Isoorotamide-based peptide nucleic acid nucleobases with extended linkers aimed at distal base recognition of adenosine in double helical RNA

  • Grant D. Walby,
  • Brandon R. Tessier,
  • Tristan L. Mabee,
  • Jennah M. Hoke,
  • Hallie M. Bleam,
  • Angelina Giglio-Tos,
  • Emily E. Harding,
  • Vladislavs Baskevics,
  • Martins Katkevics,
  • Eriks Rozners and
  • James A. MacKay

Beilstein J. Org. Chem. 2025, 21, 2513–2523, doi:10.3762/bjoc.21.193

Graphical Abstract
  • regions of RNA. We herein report the synthesis and binding studies of new isoorotamide-based PNA monomers that target uridine–adenosine base pairs via a distal base recognition strategy. Monomers were designed with an arylisoorotamide core attached to a linker aimed at bypassing the uridine in a U–A pair
  • distal binding monomers (Db) demonstrated slightly higher affinity for A–U base pairs while one demonstrated slightly higher affinity for the G–C base pair. These results provide insight into the nature of PNA monomer design particularly around linker design and rigidity. Keywords: Hoogsteen hydrogen
  • possible base pairs (G–C, A–U, C–G, and U–A). Notably, each synthetic nucleobase takes advantage of favorable hydrogen bonding interactions to the proximal nucleobase in the Watson–Crick base pair. Strong binding has been reported for purine recognition given the propensity for two Hoogsteen hydrogen bonds
PDF
Album
Supp Info
Full Research Paper
Published 12 Nov 2025

Conformational effects on iodide binding: a comparative study of flexible and rigid carbazole macrocyclic analogs

  • Guang-Wei Zhang,
  • Yong Zhang,
  • Le Shi,
  • Chuang Gao,
  • Hong-Yu Li and
  • Lei Xue

Beilstein J. Org. Chem. 2025, 21, 2369–2375, doi:10.3762/bjoc.21.181

Graphical Abstract
  • work represents one of the earliest comparative studies on the anion-binding behaviors of carbazole-based structural analogs, demonstrating that a flexible macrocycle markedly improves iodide binding affinity via an induced-fit mechanism. The flexible analog PBG exhibits a 22.78-fold higher
  • fluorescence quenching efficiency upon iodide binding compared to the rigid WDG (KPBG/KWDG = 22.78), demonstrating its potential as a highly sensitive optical probe and offering a novel strategy for engineering dynamic supramolecular receptors. Two carbazole-based macrocyclic probes, PBG (flexible benzene ring
  • demonstrated that flexible PBG achieves superior I− binding (KPBG = 1.387 × 105 M−1) through induced-fit conformational adjustments, whereas rigid WDG (KWDG = 6.089 × 103 M−1) is constrained by preorganized cavity geometry, adhering to a conformational selection mechanism. This work elucidates the synergistic
PDF
Album
Supp Info
Full Research Paper
Published 03 Nov 2025

Rotaxanes with integrated photoswitches: design principles, functional behavior, and emerging applications

  • Jullyane Emi Matsushima,
  • Khushbu,
  • Zuliah Abdulsalam,
  • Udyogi Navodya Kulathilaka Conthagamage and
  • Víctor García-López

Beilstein J. Org. Chem. 2025, 21, 2345–2366, doi:10.3762/bjoc.21.179

Graphical Abstract
  • reported in 2014 the first examples of rotaxanes with a dithienylethene switch on the axle [57]. They synthesized [3]- and [5]rotaxanes with a symmetric axle containing a dithienylethene in the center and alkylammonium binding sites on each side, which interact with N-hetero crown ether macrocycles
  • fluorescence quenching phenomena with aggregate-induced emission (AIE) in aqueous media. They synthesized a [2]rotaxane with one dithienylethene unit as a stopper, and one BAA and one urea binding site, as well as one DB24C8 macrocycle with a tetraphenylethene (TPE) fluorophore [16] (Figure 7). Addition of
  • incorporation of functional hydrazone photoswitches into rotaxanes began more recently with Leigh. Thus, these photoswitches are underexplored in MIMs. Specifically, Leigh and co-workers synthesized [2]rotaxanes in which a pyridyl-acyl hydrazone moiety functioned as both photo- and thermal-switchable binding
PDF
Album
Review
Published 31 Oct 2025

Insoluble methylene-bridged glycoluril dimers as sequestrants for dyes

  • Suvenika Perera,
  • Peter Y. Zavalij and
  • Lyle Isaacs

Beilstein J. Org. Chem. 2025, 21, 2302–2314, doi:10.3762/bjoc.21.176

Graphical Abstract
  • cucurbit[n]uril (CB[n]) molecular containers [21][22]. Macrocyclic CB[n] display ultratight binding toward hydrophobic cations in water which renders them an attractive new class of sequestrants [23][24][25][26]. For example, Buschmann and Jekel demonstrated the use of CB[6] (Figure 1) for the removal of
  • have studied water-soluble acyclic CB[n] based on methylene-bridged glycoluril monomer–tetramer and found that glycoluril tetramer-derived hosts displayed the highest binding affinity toward hydrophobic alicyclic dications due to enhanced ion–dipole interactions [40][41]. Separately, we studied
PDF
Album
Supp Info
Full Research Paper
Published 29 Oct 2025
Other Beilstein-Institut Open Science Activities