Beyond symmetric self-assembly and effective molarity: unlocking functional enzyme mimics with robust organic cages

• Keith G. Andrews

Beilstein J. Org. Chem. 2025, 21, 421–443, doi:10.3762/bjoc.21.30

• catalysis has fared best using approaches such as destabilizing ground states by constrictive binding, guiding molecular collisions to reduce large entropic costs (e.g., pericyclic reactions), and broad, undirected coulombic stabilization of charged transition states [36], for example of cations by

• water (Figure 2A) [71][72][73], or by binding a hydrophobic substrate and holding it close to a functional(ized) rim (e.g., as in cyclodextrins) that performs a reaction (Figure 2B) [74][75][76][77][78][79]. These effects are driven mostly by effective concentration/molarity (i.e., proximity of reacting

• groups) with little [73], if any, transition-state binding [36][80][81]. Thus, these macrocycles depend on the catalytic concept of organization; polarization is a minor contributor. Size-exclusion and regioselective outcomes are possible [56][82][83][84][85], and symmetric arrays of chiral units (like

Synthesis, structure, ionochromic and cytotoxic properties of new 2-(indolin-2-yl)-1,3-tropolones

• Yurii A. Sayapin,
• Eugeny A. Gusakov,
• Inna O. Tupaeva,
• Alexander D. Dubonosov,
• Igor V. Dorogan,
• Valery V. Tkachev,
• Anna S. Goncharova,
• Gennady V. Shilov,
• Natalia S. Kuznetsova,
• Svetlana Y. Filippova,
• Tatyana A. Krasnikova,
• Yanis A. Boumber,
• Alexey Y. Maksimov,
• Sergey M. Aldoshin and
• Vladimir I. Minkin

Beilstein J. Org. Chem. 2025, 21, 358–368, doi:10.3762/bjoc.21.26

• h. *Significant difference compared to control samples, p < 0.05. Synthesis of 2-hetaryl-substituted 1,3-tropolones 1. Synthesis of 1,3-tropolones 7a,b and 8a,b. Reagents and conditions: method A: dioxane, reflux; method B: AcOH, 40–50 °C. Possible binding mode of 7 and 8 with CN− and F−. Total

Antibiofilm and cytotoxic metabolites from the entomopathogenic fungus Samsoniella aurantia

• Rita Toshe,
• Syeda J. Khalid,
• Blondelle Matio Kemkuignou,
• Esteban Charria-Girón,
• Paul Eckhardt,
• Birthe Sandargo,
• Kunlapat Nuchthien,
• J. Jennifer Luangsa-ard,
• Till Opatz,
• Hedda Schrey,
• Sherif S. Ebada and
• Marc Stadler

Beilstein J. Org. Chem. 2025, 21, 327–339, doi:10.3762/bjoc.21.23

• surfaces and the subsequent accumulation to form multilayered cell clusters [17]. To investigate the action of farinosones D (1) and A (2) on planktonic cells and their adherence to the substrate, growth curve and fibrinogen binding assay were conducted. The findings obtained from these assays demonstrated

• Information File 1). Additionally, in fibrinogen binding assay, both compounds reduced the initial attachment of planktonic cells by approximately 30% at a concentration of 62.5 µg/mL (Figure S1C, Supporting Information File 1). Based on the results of fibrinogen binding assay (Figure S1C, Supporting

• Information File 1), it is likely that the activity of farinosones D (1) and A (2) does not interfere with the factors essential for fibronectin binding, particularly the fibronectin-binding proteins such as fibronectin binding protein (FnBPA and B) [18]. FnBPs are adhesions and are known to play a key role

Quantifying the ability of the CF₂H group as a hydrogen bond donor

• Matthew E. Paolella,
• Daniel S. Honeycutt,
• Bradley M. Lipka,
• Jacob M. Goldberg and
• Fang Wang

Beilstein J. Org. Chem. 2025, 21, 189–199, doi:10.3762/bjoc.21.11

• . We expect this information to be useful for the rational application of the CF2H group in drug development and molecular design. Previous quantum mechanical calculations revealed that the CF2H···O binding energy (ΔE) ranges from 1.0 kcal/mol to 5.5 kcal/mol [14][15][18][21]. In addition, as measured

• inconsistent with the corresponding A values (Table 1), which typically provide reliable measurements of the HB donation ability of neutral compounds. We attribute the inconsistency to several factors. First, because the binding affinity is determined solely by the absorbance change of Reichardt's dye, the

• constructs. Although many of the CF2H HB donors studied here can promote relatively strong hydrogen bonding interactions with n-Bu3PO, even the strongest CF2H HB donor (3b) is still 30 times weaker than phenol (10), corresponding to about a 2 kcal/mol reduction in binding energy at 25 °C. These results

Hydrogen-bonded macrocycle-mediated dimerization for orthogonal supramolecular polymerization

• Wentao Yu,
• Zhiyao Yang,
• Chengkan Yu,
• Xiaowei Li and
• Lihua Yuan

Beilstein J. Org. Chem. 2025, 21, 179–188, doi:10.3762/bjoc.21.10

• effectively applied to form orthogonal supramolecular polymers. The macrocycle-mediated connectivity was confirmed by single-crystal X-ray diffraction, which revealed a unique 2:2 binding motif between host and guest, bridged by two cationic pyridinium end groups through π-stacking interactions and other

• capable of dimerization by binding to a macrocycle in a 2:2 stoichiometry [22][23]. Such binding motifs are intriguing for macrocycle-mediated supramolecular dimerization since they may enable multiple modes of noncovalent connectivity through combination with other noninterfering interactions (e.g

• amide macrocycle with six aromatic residues (hereafter called cyclo[6]aramide for brevity, Scheme 1a) could mediate dimerization as a host. That is because such a 2D macrocycle has six carbonyl oxygen atoms pointing inwards as binding sites, demonstrating excellent affinity for cationic organic guests

Chemical glycobiology

• Elisa Fadda,
• Rachel Hevey,
• Benjamin Schumann and
• Ulrika Westerlind

Beilstein J. Org. Chem. 2025, 21, 8–9, doi:10.3762/bjoc.21.2

• . [12] in the context of photoswitchable ligands to the lectin LecA. Staying in the theme of lectin characterization, Lundstrøm et al. study the glycan binding profile of CMA1 originating from melon [13]. A time that sees great opportunities in computational biology also breeds innovative applications

Efficient synthesis of fluorinated triphenylenes with enhanced arene–perfluoroarene interactions in columnar mesophases

• Yang Chen,
• Jiao He,
• Hang Lin,
• Hai-Feng Wang,
• Ping Hu,
• Bi-Qin Wang,
• Ke-Qing Zhao and
• Bertrand Donnio

Beilstein J. Org. Chem. 2024, 20, 3263–3273, doi:10.3762/bjoc.20.270

• fluorine atoms, inserted in the aromatic rings, which considerably modifies the dipole moment of the corresponding fluorinated aromatic rings with respect to their hydrogenated homologs, thus influencing their behavior, binding affinities, and optoelectronic properties. These interactions already represent

Multicomponent reactions driving the discovery and optimization of agents targeting central nervous system pathologies

• Lucía Campos-Prieto,
• Aitor García-Rey,
• Eddy Sotelo and
• Ana Mallo-Abreu

Beilstein J. Org. Chem. 2024, 20, 3151–3173, doi:10.3762/bjoc.20.261

• (IC50 = 1.28 μM), and non-toxicity in liver HepG2 cells. Hantzsch-based strategies: As mentioned before, in response to the challenges posed by the multifactorial nature of AD, the MTDL approach has emerged as a promising strategy. This approach involves designing drugs capable of binding simultaneously

• heterocyclic core. The novel compounds were first evaluated using β-arrestin recruitment assays in CHO (chinese hamster ovary) cells overexpressing human GPR55. These new compounds have been evaluated in competitive binding assays for cannabinoid receptors, but all of them showed to be selective for GPR55 (>4

Advances in the use of metal-free tetrapyrrolic macrocycles as catalysts

• Mandeep K. Chahal

Beilstein J. Org. Chem. 2024, 20, 3085–3112, doi:10.3762/bjoc.20.257

• other binding sites required for substrate binding and/or promotion of the catalytic activity. Past studies have shown that modifying the porphyrin core with urea functionalities and amino acid substituents leads to the formation of ureaporphyrins, which significantly enhance sugar binding in non-polar

• solutions [18]. Similarly, Burns and co-workers reported di- and tetra-urea picket porphyrins highlighting, the impact of buried solvent molecules, such as DMSO, on the selectivity, affinity, and stoichiometry of anion binding [19]. Iron complexes of tetra-urea picket porphyrins further demonstrate how

• , and calixarenes has been extensively studied using both enzyme mimics and non-biomimetic systems, due to the presence of an internal cavity (binding sites) and nearby functional groups (catalytic sites) [27][28][29]. Tetrapyrrolic macrocycles contain an internal cavity with multiple inner –N/NH groups

Chemical structure metagenomics of microbial natural products: surveying nonribosomal peptides and beyond

• Thomas Ma and
• John Chu

Beilstein J. Org. Chem. 2024, 20, 3050–3060, doi:10.3762/bjoc.20.253

• ][53][54][55][56][57]. The exception is the 10 residues that constitute the A domain active site, whose high variability creates binding pockets of varying shapes and sizes. These residues therefore dictate substrate BB specificity of an A domain and are referred to as the nonribosomal code (in analogy

• the glycopeptide antibiotic family [62][63]. Their aromatic rings undergo oxidative coupling to form biaryl moieties that restrict atropisomerism; the resulting rigid structure is key to their high affinity binding to peptidoglycan intermediates [64][65]. Glycopeptide antibiotics include vancomycin

• , the A domain (gray rectangles in a) is responsible for activating the substrate BB to be incorporated, and the substrate BB specificity is dictated by the nonribosomal code (the 10 residues that defines its binding pocket, small red circles). Algorithms for A domain substrate prediction were trained

Tailored charge-neutral self-assembled L₂Zn₂ container for taming oxalate

• David Ocklenburg and
• David Van Craen

Beilstein J. Org. Chem. 2024, 20, 3007–3015, doi:10.3762/bjoc.20.250

• can easily replace ligand strands leading to a partial or full receptor decomposition. Herein, we present a charge-neutral zinc(II)-based metallocontainer which was tuned to contest oxalate as most competitive dicarboxylate. The dianion is bound in a 1:1 fashion with a binding constant of log K = 4.39

• ][43][44]. Additionally, organic receptors featuring metal centers which are strongly bound in a multidentate fashion with the sole purpose of acting as binding sites are utilized beside the pure organic systems [26][45][46][47][48][49][50][51][52][53][54][55]. In the last decade, metallocages and

• inevitable presence of counteranions necessary to balance the positive charge increases the complexity of the underlying equilibria. Competition between the desired guest and the counteranions can lead to significantly weakened binding strength of the target analyte in the worst case. One option to mitigate

Recent advances in transition-metal-free arylation reactions involving hypervalent iodine salts

• Ritu Mamgain,
• Kokila Sakthivel and
• Fateh V. Singh

Beilstein J. Org. Chem. 2024, 20, 2891–2920, doi:10.3762/bjoc.20.243

• upon binding of the enolate molecule to iodine either through a carbon–iodine or an oxygen–iodine bond. Both intermediates, I and II, are in rapid equilibrium with each other and further undergo two different types of reactions: [1,2]-ligand coupling and [2,3]-rearrangement (Scheme 2). Either of these

Investigation of a bimetallic terbium(III)/copper(II) chemosensor for the detection of aqueous hydrogen sulfide

• Parvathy Mini,
• Michael R. Grace,
• Genevieve H. Dennison and
• Kellie L. Tuck

Beilstein J. Org. Chem. 2024, 20, 2818–2826, doi:10.3762/bjoc.20.237

• , highly sensitive chemosensors via a facile synthetic route/method, we have explored three chelates for lanthanide ions (DO3A, 2,6-pyridinedicarboxylic acid and DO2A), resulting in complexes with different overall charges. Additionally we have explored two copper(II) binding groups (di(2-picolyl)amine and

• program, was used to determine the binding constant of Cu2+ ions to Tb.1 in both Tris-HCl buffer and HEPES buffer. The host–guest binding modes (1:1, 1:2 or 2:1) were evaluated using the luminescent data (λex = 250 nm, λem = 450–650 nm) from the respective titration experiments. In both cases the 1:1 host

• –guest binding model gave an acceptable fit with low (co)variance of the fit (Table 1). Aqueous buffer HS− studies of [Tb.1·3Cu]3+ The response of [Tb.1·3Cu]3+ to Na2S (HS− in solution at pH 7.4) in both 10 mM HEPES and 10 mM Tris-HCl was investigated. The addition of HS−(aq) ions to a solution of [Tb.1

Synthesis and antimycotic activity of new derivatives of imidazo[1,2-a]pyrimidines

• Dmitriy Yu. Vandyshev,
• Daria A. Mangusheva,
• Khidmet S. Shikhaliev,
• Kirill A. Scherbakov,
• Oleg N. Burov,
• Alexander D. Zagrebaev,
• Tatiana N. Khmelevskaya,
• Alexey S. Trenin and
• Fedor I. Zubkov

Beilstein J. Org. Chem. 2024, 20, 2806–2817, doi:10.3762/bjoc.20.236

• this work was a preliminary evaluation of the potential bioactivity of the obtained compounds. In particular, a molecular docking experiment to investigate the binding mechanisms to the CYP51 enzyme and an evaluation of the antifungal activity of imidazo[1,2-a]pyrimidines against Candida albicans were

• desired pharmacological properties. Therefore, the design and synthesis of new compounds of this class with improved ADMET (absorption, distribution, metabolism, excretion, toxicity) pharmacological properties is an urgent task. Molecular docking was carried out to identify potential binding positions of

Computational design for enantioselective CO₂ capture: asymmetric frustrated Lewis pairs in epoxide transformations

• Maxime Ferrer,
• Iñigo Iribarren,
• Tim Renningholtz,
• Ibon Alkorta and
• Cristina Trujillo

Beilstein J. Org. Chem. 2024, 20, 2668–2681, doi:10.3762/bjoc.20.224

• catalysts located at the top. The top of the volcano plot corresponds to the scenario where the catalyst exhibits high catalytic activity, as it achieves an optimal balance in binding to the reactants, neither too strongly nor too weakly (Figure 1A, purple points). The catalysts with binding energies lower

• File 1). Notably, the CO2 capture exhibits a lower activation barrier compared to the capture of epoxide (+10.0 kcal·mol−1 vs +30.0 kcal·mol−1). Using transition state theory [40] as expressed in Equation 1, the rate constants were calculated for binding to either molecule at 273.0 K, resulting in k1

Deciphering the mechanism of γ-cyclodextrin’s hydrophobic cavity hydration: an integrated experimental and theoretical study

• Stiliyana Pereva,
• Stefan Dobrev,
• Tsveta Sarafska,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

Beilstein J. Org. Chem. 2024, 20, 2635–2643, doi:10.3762/bjoc.20.221

• substances. Host CDs are highly accommodative to water molecules as well and usually contain water in the native state. There is still an ongoing discussion on both the total number of water molecules and their preferred binding position inside the cavities of the CDs. To understand the hydration/dehydration

• (Figure 1B and C). Hydrated γ-CD Hydration and interaction with water (sequential binding of water molecules to the CD cavity) The γ-CD cavity was scanned for spots/sites with enhanced binding affinity for the incoming water molecules: γ-CD hydrates containing one to seven water molecules bound at various

•  3. The enthalpies estimated for the subsequent binding process of water molecules to γ-CD in both the gas phase (ΔH1) and aqueous medium (ΔH78) at both levels of theory are presented in Table 1. The two sets of calculations using different basis sets (M062X/6-31G(d,p) and M062X/6-311++G(d,p)//M062X

Synthesis and conformational analysis of pyran inter-halide analogues of ᴅ-talose

• Olivier Lessard,
• Mathilde Grosset-Magagne,
• Paul A. Johnson and
• Denis Giguère

Beilstein J. Org. Chem. 2024, 20, 2442–2454, doi:10.3762/bjoc.20.208

• ][3][4][5][6][7]. What about other halogens? Pyran inter-halide analogues of carbohydrates were rarely investigated as new tools in glycobiology [8]. This is surprising since the incorporation of halogens can improve cellular uptakes and enhance membrane binding and permeation [9][10][11]. In addition

Evaluating the halogen bonding strength of a iodoloisoxazolium(III) salt

• Dominik L. Reinhard,
• Anna Schmidt,
• Marc Sons,
• Julian Wolf,
• Elric Engelage and
• Stefan M. Huber

Beilstein J. Org. Chem. 2024, 20, 2401–2407, doi:10.3762/bjoc.20.204

• prototypic iodolium 1BArF with bromide (CCDC: 1145291) [5]. For the latter, such a dimeric binding motif was also found, with I–Br bond lengths of 3.1936(9) Å [83% of Σr] and 3.2299(9) Å [84% of Σr]. It can be concluded that stronger halogen bonding can be found in the crystal structure of iodoloisoxazolium

• 7Br, which hints that also in solution stronger binding to Lewis bases and therefore higher activity as catalyst may be expected (compared to prototypic iodolium 1Z). As a benchmark for the halogen-bonding strength in solution, the activation of (PPh3)AuCl was chosen. The activated gold(I) complex was

Asymmetric organocatalytic synthesis of chiral homoallylic amines

• Nikolay S. Kondratyev and
• Andrei V. Malkov

Beilstein J. Org. Chem. 2024, 20, 2349–2377, doi:10.3762/bjoc.20.201

• ; rearrangement; Introduction Nitrogen-containing organic compounds (sometimes referred to as alkaloids due to their basic properties) are of critical importance in medicinal chemistry because of their unique binding properties to biomolecules [1]. Out of 55 drug candidates, approved by the FDA in 2023, 28 (51

Improved deconvolution of natural products’ protein targets using diagnostic ions from chemical proteomics linkers

• Andreas Wiest and
• Pavel Kielkowski

Beilstein J. Org. Chem. 2024, 20, 2323–2341, doi:10.3762/bjoc.20.199

• –azide (DTB–azide) linker still possesses strong binding to streptavidin (Kd ≈ 1 × 10−11 M), but it can be released by mild washing conditions with organic solvent and low pH (Figure 8C) [105][106]. Similarly, desthiobiotin releases upon HCD fragmentation a set of characteristic diagnostic ions including

• acid, base, or redox-labile parts of the linker [52]. Most recently, Wozniak et al. mapped the binding sites of a large small molecules library, which were equipped with a photo-crosslinker [110]. The study used the acid-cleavable dialkoxydiphenylsilane (DADPS) linker to release the probe–peptide

Hydrogen-bond activation enables aziridination of unactivated olefins with simple iminoiodinanes

• Phong Thai,
• Lauv Patel,
• Diyasha Manna and
• David C. Powers

Beilstein J. Org. Chem. 2024, 20, 2305–2312, doi:10.3762/bjoc.20.197

• , signaling the binding of HFIP to 2c enhanced the electron transfer kinetics between the hypervalent iodine reagent and the electrode [45]. Further additions of HFIP further increased the current response and shifted the peak potential, with 10 µL and 15 µL of HFIP showing responses with Epr at −1.55 V and

Novel truxene-based dipyrromethanes (DPMs): synthesis, spectroscopic characterization and photophysical properties

• Shakeel Alvi and
• Rashid Ali

Beilstein J. Org. Chem. 2024, 20, 2163–2170, doi:10.3762/bjoc.20.186

• the importance of DPMs in mind due to their utmost significance as a building block in the construction of porphyrinogens, related polypyrrolic macrocycles, and pigments [39][40][41]. As shown in Figure 1, these DPMs and many more have fruitfully been used by several research groups in sensing/binding

• outstanding optical properties [43]. Herein, we present for the first time three new mono-, di-, tri-dipyrromethane appended truxene derivatives with the intention to explore them for future sensing and/or binding properties. Results and Discussion To achieve our goal towards the construction of truxene

• prepared compounds. The anion sensing/binding studies of these DPMs in addition to their formylated derivatives is under progress in our laboratory and will be published in due course. As mention above truxene and its congeners have shown a plethora of uses in diverse fields. To our best knowledge, their

Factors influencing the performance of organocatalysts immobilised on solid supports: A review

• Zsuzsanna Fehér,
• Dóra Richter,
• Gyula Dargó and
• József Kupai

Beilstein J. Org. Chem. 2024, 20, 2129–2142, doi:10.3762/bjoc.20.183

• ]. An advantage of dendrimer-supported organocatalysts are their enzyme-like properties [111][112]. Selective binding and cooperative catalysis can give the catalyst high selectivity and activity. Interactions between the support and other components The interaction between the solid support and the

• binding with an electron-withdrawing group. This acidity can result in stronger hydrogen bonds between the substrate and the catalyst C30, which contains a bis(trifluoromethyl)phenyl-modified squaramide moiety. This stronger interaction potentially enhances the catalyst–substrate interaction, allowing for

Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

• –ligand complexes, and analyse MD outcomes. Moreover, selected case studies have been reported to highlight the importance of computational tools in studying protein–glycan systems, revealing the capability of these tools to provide valuable insights into the binding kinetics, energetics, and structural

• a wide array of glycan-binding proteins (GBP) [17], which have a unique capability to specifically interact with endogenous and/or exogenous glycans [18][19]. Thus, disclosing the molecular basis of protein–glycan interactions has a unique potential to help modulate a myriad of complex biological

• events affecting the health and well-being of living organisms and the natural environment. Being key participants in the molecular dialogue, glycan binding proteins emerge as fascinating and critical components of molecular events that regulate life at its core. Their functions span from the catalysis

Regioselective alkylation of a versatile indazole: Electrophile scope and mechanistic insights from density functional theory calculations

• Pengcheng Lu,
• Luis Juarez,
• Paul A. Wiget,
• Weihe Zhang,
• Krishnan Raman and
• Pravin L. Kotian

Beilstein J. Org. Chem. 2024, 20, 1940–1954, doi:10.3762/bjoc.20.170

• the treatment of paroxysmal nocturnal hemoglobinuria, and CPI-637 (2), an inhibitor of both cyclic-AMP response element binding protein (CBP) and adenoviral E1A binding protein [14][15][16]. The N2-substituted indazole analogs pazopanib (3), an FDA-approved tyrosine kinase inhibitor used for the