Post-synthesis from Lewis acid–base interaction: an alternative way to generate light and harvest triplet excitons

• Hengjia Liu and
• Guohua Xie

Beilstein J. Org. Chem. 2022, 18, 825–836, doi:10.3762/bjoc.18.83

• determined from the optimized structures of compounds 21 and 22 (Figure 13a) by DFT suggest that pyridine is a better binding site than thiophene [43]. The effect of steric hindrance on the Lewis acid–base binding should not be ignored. If there is large steric hindrance of the Lewis basic molecules, it will

Structural basis for endoperoxide-forming oxygenases

• Takahiro Mori and
• Ikuro Abe

Beilstein J. Org. Chem. 2022, 18, 707–721, doi:10.3762/bjoc.18.71

• observed in typical Fe/2OG-dependent oxygenases (Figure 3A). The Fe(II) is coordinated by His129, Asp131, His205, and 2OG in the binary complex structure of FtmOx1 with 2OG. In this structure, Tyr224 is close to the putative oxygen binding site (Figure 3B). Furthermore, the variants in which Tyr224 is

Heteroleptic metallosupramolecular aggregates/complexation for supramolecular catalysis

• Prodip Howlader and
• Michael Schmittel

Beilstein J. Org. Chem. 2022, 18, 597–630, doi:10.3762/bjoc.18.62

• procedure developed by Sauvage on the basis of topological control [33] has found ample use in the preparation of rotaxane-based machines and devices [34]. A key element is a macrocyclic phenanthroline with an endotopic binding site as it precludes homoleptic complex formation. A further principle

(Phenylamino)pyrimidine-1,2,3-triazole derivatives as analogs of imatinib: searching for novel compounds against chronic myeloid leukemia

• Luiz Claudio Ferreira Pimentel,
• Lucas Villas Boas Hoelz,
• Henayle Fernandes Canzian,
• Frederico Silva Castelo Branco,
• Andressa Paula de Oliveira,
• Vinicius Rangel Campos,
• Floriano Paes Silva Júnior,
• Rafael Ferreira Dantas,
• Jackson Antônio Lamounier Camargos Resende,
• Anna Claudia Cunha,
• Nubia Boechat and
• Mônica Macedo Bastos

Beilstein J. Org. Chem. 2021, 17, 2260–2269, doi:10.3762/bjoc.17.144

• , with IC50 values between 1.0 and 7.3 μM, and were subjected to molecular docking studies. The results suggest that such compounds can interact at the same binding site as imatinib, probably sharing a competitive inhibition mechanism. One compound showed the greatest interaction affinity for BCR-Abl-1

• TKIs that are even more potent than IMT, such as nilotinib [6][7]. These drugs act as inhibitors at the ATP binding site in the inactive form of BCR-Abl-1, preventing the binding of the protein to ATP in a competitive manner and resulting in the interruption of the substrate phosphorylation process and

• interact with BCR-Abl-1 at the same binding site as IMT but show differences in the binding modes and with higher values of interaction energy. Compound 2c presented a MolDock value of −152.993 a.u. For compound 2d, the value was −152.127 a.u., and for compound 2g, it was −167.520 a.u. (Table 2

A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis

• Theodore Groth,
• Rudiyanto Gunawan and
• Sriram Neelamegham

Beilstein J. Org. Chem. 2021, 17, 1712–1724, doi:10.3762/bjoc.17.119

• relationships must be supported by ChIP-Seq evidence. Here, a nonlinear weighted sum called regulatory potential (RP) quantifies the strength of TF–gene interactions based on the proximity of TF binding site to the gene TSS and also the number of TF–gene binding interactions based experimentally detected ChIP

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

Synthetic strategies of phosphonodepsipeptides

• Jiaxi Xu

Beilstein J. Org. Chem. 2021, 17, 461–484, doi:10.3762/bjoc.17.41

• -aminophosphonodichloride 92 with phenol and methyl (S)-2-hydroxypentanoate (18). All synthetic phosphonodepsipeptides 99, 102, and 104 were considered as glutathione-analogue phosphonopeptides as mechanism-based inhibitors of γ-glutamyl transpeptidase for probing the cysteinyl-glycine binding site (Scheme 16) [31

¹⁹F NMR as a tool in chemical biology

• Diana Gimenez,
• Aoife Phelan,
• Cormac D. Murphy and
• Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

Multiswitchable photoacid–hydroxyflavylium–polyelectrolyte nano-assemblies

• Alexander Zika and
• Franziska Gröhn

Beilstein J. Org. Chem. 2021, 17, 166–185, doi:10.3762/bjoc.17.17

• transformation to the hydrolyzed form of the hydroxyflavylium molecule at state D leads to the removal of the positive charge and the addition of an extra binding site. Due to that, the ζ-potential increases while at the same time the effective surface charge density decreases followed by a destabilization of

• pH 7 (Figure 8), the data reveal that the first and third binding site are exothermic with ΔH1 = −4.3 kJ/mol and ΔH3 = −172.7 kJ/mol per polyelectrolyte binding site, respectively, which shows that strong ionic interactions and hydrogen bonding constitute these binding processes. Probably these

Insight into functionalized-macrocycles-guided supramolecular photocatalysis

• Minzan Zuo,
• Krishnasamy Velmurugan,
• Kaiya Wang,
• Xueqi Tian and
• Xiao-Yu Hu

Beilstein J. Org. Chem. 2021, 17, 139–155, doi:10.3762/bjoc.17.15

• quantum yield of 3.8 × 10−2 and 0.4, respectively. In contrast, for flavins without the zinc(II)–cyclen unit, only small amounts of product were observed, and the quantum yield was 30 times lower compared to that of the assembly with the flavin chromophore possessing a binding site. The mechanism may be

Supramolecular polymerization of sulfated dendritic peptide amphiphiles into multivalent L-selectin binders

• David Straßburger,
• Svenja Herziger,
• Katharina Huth,
• Moritz Urschbach,
• Rainer Haag and
• Pol Besenius

Beilstein J. Org. Chem. 2021, 17, 97–104, doi:10.3762/bjoc.17.10

• of multivalent interactions is the extracellular adhesion protein L-selectin. L-Selectin plays a critical role in inflammation processes by supporting the migration of leukocytes to inflammatory sites via adhesion to endothelial cells [19][20][21]. On a molecular level, a cationic binding site [22

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• peptidic arms equipped with lysine and an artificial strong anion binding site, the guanidinocarbonylpyrrole (GCP) moiety (Figure 2A). These arms also contain tryptophan for dissimilar aromatic interactions with different nucleobases. The fluorescence intensity of probe 1 increases by more than 4-fold at

• -polyU) (log K = 3.8 and log K = 4.4 respectively for 4 and 5). Significant differential fluorescence responses of these probes with nucleic acids are due to the positioning of fluorophores within the polynucleotide binding site. Different studies explain their different mode of binding with dsDNA. Probe

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

• (GCPs). The use of UV laser excitation enables Raman binding studies of this class of supramolecular ligands at submillimolar concentrations in aqueous solution and provides a selective signal enhancement of the carboxylate binding site (CBS). A current limitation for the extension of this promising

• -covalent interactions namely hydrogen bonds, van der Waals, and/or hydrophobic interactions [1][2][3][4][5]. In this context, Schmuck and co-workers have introduced a class of synthetic receptors based on the guanidiniocarbonyl pyrrole (GCP) moiety (cf. Figure 1 top right) as a carboxylate binding site

Using multiple self-sorting for switching functions in discrete multicomponent systems

• Amit Ghosh and
• Michael Schmittel

Beilstein J. Org. Chem. 2020, 16, 2831–2853, doi:10.3762/bjoc.16.233

• binding site to nanoswitch [Cu(68)]+ preventing its action as an organocatalyst (OFF-1), while the copper catalyst [Cu(69)]+ was available to catalyze a click reaction between 4-nitrophenylacetylene (47) and benzyl azide (46) (ON-2). The addition of 1 equiv of phenanthroline 69 to the state SelfSORT-I

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

• ICD bands, which are mostly pronounced with a linker length of n = 4 (with a2) and n = 5 (with 22AG), thus indicating that each ligand–G4-DNA complex has a specific structure with respect to relative alignment and conformational flexibility of the ligand in the binding site. It was shown exemplarily

• , cyclodextrins or micelles [55][56][57][58]. Presumably the radiationless deactivation of the excited state by conformational changes, that leads to the low emission intensity in aqueous solution, is suppressed in the sterically restricted binding site. Therefore, it can be deduced that the increased emission of

• other parameters such as binding-site size, cooperativity between ligands, ionic strength, the enthalpy of the DNA denaturation, and on the binding constant and enthalpy of the ligand binding at the melting temperature. However, the binding constant is determined at temperatures below Tm and the

Vicinal difluorination as a C=C surrogate: an analog of piperine with enhanced solubility, photostability, and acetylcholinesterase inhibitory activity

• Yuvixza Lizarme-Salas,
• Alexandra Daryl Ariawan,
• Ranjala Ratnayake,
• Hendrik Luesch,
• Angela Finch and
• Luke Hunter

Beilstein J. Org. Chem. 2020, 16, 2663–2670, doi:10.3762/bjoc.16.216

• microenvironment of a protein binding site could also change the relative energies of the various F–C–C–F and F–C–C=O rotamers, offering the possibility that analog 2 might be an effective conformational mimic of 1 in some environments but not in others. Herein, we describe the optimisation of a synthetic route to

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

• -functionalized crown ether as for the TTF crown ethers, where the NDI unit is in a position more remote from the crown ether binding site. Yet, keeping the formal C2-symmetry of the macrocycle is important to avoid mixtures of isomers upon the threading of directional axles, such as A1·PF6 (Figure 1c) [40

• comparison of all absorption spectra clearly demonstrates that the rotaxane formation does not significantly influence the optoelectronic properties of the NDI unit. This can be explained by the position of the NDI moiety being rather remote from the binding site of the crown ether. Conclusion In conclusion

• binding and redox-switching properties can be fine-tuned for the construction of a desired crown ether-based switchable MIM: while bisTTFC8 shows interesting redox properties but very low binding constants and exTTFC8 displays a high binding constant, yet no strong interaction of the ammonium-binding site

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• binding site. Here we discuss protein-based solution NMR techniques including classic 1H,15N-HSQC spectra, TROSY variants for large proteins, fast acquisition techniques and specific isotope labeling strategies, as well as the use of 13C-edited spectra and side chain specific spectra for lysine and

• the ligand needs to dissociate again from the protein in order to be detected. Therefore, strong (nM or better) binders are not suitable for these experiments. No information about the binding site(s) on the protein is obtained. Magnetization transfer via NOE depends on a molecule’s correlation

• and this residue must also be in close enough proximity to the ligand binding site. In cases where supramolecular ligands contain peptidic scaffolds with methyl-bearing residues (like alanine, valine, leucine or isoleucine) whose NMR signals overlap with the protein methyl signals, finding a protein

Recent developments in enantioselective photocatalysis

• Callum Prentice,
• James Morrisson,
• Andrew D. Smith and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2020, 16, 2363–2441, doi:10.3762/bjoc.16.197

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• CD experiment (Figure 3b) does not contribute significantly to the binding enthalpy. The analysis of the binding parameters collected in Table 3 at excess of DNA/RNA over compound 4 (n < 0.3, binding to primary binding site) revealed a large negative reaction enthalpy change and a large positive

• reaction entropy change, indicating favourable enthalpic (exothermic) and entropic contribution to the reaction Gibbs free energy change. This means that the reaction is both enthalpically and entropically driven. However, secondary binding site (n > 0.4; excess of 4 over DNA primarily binding site) is

Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA

• Annike Weißenstein,
• Myroslav O. Vysotsky,
• Ivo Piantanida and
• Frank Würthner

Beilstein J. Org. Chem. 2020, 16, 2032–2045, doi:10.3762/bjoc.16.170

• )-polynucleotides. The DNA/RNA binding-induced circular dichroism (ICD) response of NDI at 450–550 nm strongly depended on the length and rigidity of the linker to the amino acid unit, which controls the orientation of the NDI unit inside within the intercalative binding site. The ICD selectivity also depends on

• both, the minor and major groove of the polynucleotide. Such bulky groups positioning requires the DNA double helix to shortly open at a binding site and close upon threading intercalator insertion. Also, the chosen NDI chromophore is characterised by easily tuneable emission wavelengths [23], and

• –polynucleotide systems, thereby providing insight into the aromatic core position within the intercalative binding site. Conclusion The new amino acid conjugates 3a, 3b, and reference compound 5 bearing the fluorescent NDI tag molecules showed moderate absorbance in the mid-visible range (λabs 520–540 nm) and

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

• , starting with formate. MC008 was able to fit acetate and lactate. Thus, an additional binding site was available for lactate. In the complexes of lactate with MC006–MC009, a hydrogen bond was present between the oxygen of the hydroxy group of lactate and the NH group of the macrocyclic amide. See Figure 5

A dynamic combinatorial library for biomimetic recognition of dipeptides in water

• Florian Klepel and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2020, 16, 1588–1595, doi:10.3762/bjoc.16.131

• motifs were developed and if arranged correctly can be used to synthesize artificial receptors with high affinity [2][3]. Schmuck et al. have been hugely successful in designing artificial peptide receptors [4][5]. For example, they combined a carboxylate binding site with an aromatic bowl-shaped cavity

A smart deoxyribozyme-based fluorescent sensor for in vitro detection of androgen receptor mRNA

• Ekaterina A. Bryushkova,
• Erik R. Gandalipov and
• Julia V. Nuzhina

Beilstein J. Org. Chem. 2020, 16, 1135–1141, doi:10.3762/bjoc.16.100

• technique is more frequently used in diagnostic laboratories than the direct sequencing method [6]. A serious problem for the detection of full-sized nucleic acids is the secondary structure, which interrupts the access of sensors to the binding site. For single-stranded RNA this problem may be partially

Synthesis and herbicidal activities of aryloxyacetic acid derivatives as HPPD inhibitors

• Man-Man Wang,
• Hao Huang,
• Lei Shu,
• Jian-Min Liu,
• Jian-Qiu Zhang,
• Yi-Le Yan and
• Da-Yong Zhang

Beilstein J. Org. Chem. 2020, 16, 233–247, doi:10.3762/bjoc.16.25

• revealed the bioactive binding site positions of potential inhibitors within the targets active site. We modeled the interactions of I12 and II4 (C) with AtHPPD (PDB ID: 1TFZ). The structure of AtHPPD was taken from the PDB data bank. All molecular modeling studies were carried out as previously reported

• process, all water molecules were removed. The ligand and protein were prepared with the Dock Ligands tool before docking. By using Define and Edit Binding Site tool to identify the active site. Then the center of the native ligand was deleted. Utilizing the CDOCKER, the prepared ligand was docked into

• the protein receptor binding site. After the docking calculations were performed, the best binding modes were determined by docking scores and also compared with the simulated binding mode of mesotrione with AtHPPD. Enzyme inhibition study AtHPPD was prepared and purified according to the reported