X-ray Crystallographic Studies Research Articles

Transition Metal Complexes with Appended Benzimidazole Groups for Sensing Dihydrogenphosphate.

Four new complexes [Ru(bpy)2(bbib)](PF6)2, [Ru(phen)2(bbib)](PF6)2, [Re(CO)3(bbib)(py)](PF6) and [Ir(ppy)2(bbib)](PF6) [where bbib = 4,4'-bis(benzimidazol-2-yl)-2,2'-bipyridine] have been prepared and their photophysical properties determined. Their behaviour has been studied with a variety of anions in acetonitrile, DMSO and 10% aquated DMSO. Acetate and dihydrogenphosphate demonstrate a redshift in the bbib ligand associated absorptions suggesting that the ligand is strongly interacting with these anions. The3MLCT emissive state is sensitive to the introduction of small quantities of anion (sub-stoichiometric quantities) and significant quenching is typically observed with acetate, although this is less pronounced in the presence of water. The emissivebehaviour with dihydrogenphosphate is variable, showing systematic changes as anion concentration increases with several distinct interactions evident .1H NMR and31P NMR titrations in a 10% D2O - D6-DMSO mixture suggest that with dihydrogenphosphate, the imidazole group able to act as both a proton acceptor and donor. It appears that all four complexes can form a {[complex]2-H2PO4} "dimer", a one-to-one species (which the X-ray crystallography study suggests is dimeric in the solid-state), and a complex with a combined bis(dihydrogenphosphate) complex anion. The speciation relies on complex equilibria dependent on several factors including the complex charge, the hydrophobicity of the associated ligands, and the solvent.

D4-Symmetric Dirhodium Tetrakis(binaphthylphosphate) Catalysts for Enantioselective Functionalization of Unactivated C-H Bonds.

Dirhodium tetrakis(2,2'-binaphthylphosphate) catalysts were successfully developed for asymmetric C-H functionalization with trichloroethyl aryldiazoacetates as the carbene precursors. The 2,2'-binaphthylphosphate (BNP) ligands were modified by introduction of aryl and/or chloro functionality at the 4,4',6,6' positions. As the BNP ligands are C2-symmetric, the resulting dirhodium tetrakis(2,2'-binaphthylphosphate) complexes were expected to be D4-symmetric, but X-ray crystallographic and computational studies revealed this is not always the case because of internal T-shaped CH-π and aryl-aryl interactions between the ligands. The optimum catalyst is Rh2(S-megaBNP)4, with 3,5-di(tert-butyl)phenyl substituents at the 4,4' positions and chloro substituents at the 6,6' positions. This catalyst adopts a D4-symmetric arrangement and is ideally suited for site-selective C-H functionalization at unactivated tertiary sites with high levels of enantioselectivity, outperforming the best dirhodium tetracarboxylate catalyst developed for this reaction. The standard reactions were conducted with a catalyst loading of 1 mol % but lower catalyst loadings can be used if desired, as illustrated in the C-H functionalization of cyclohexane in 91% ee with 0.0025 mol % catalyst loading (29,400 turnover numbers). These studies further illustrate the effectiveness of donor/acceptor carbenes in site-selective intermolecular C-H functionalization and expand the toolbox of catalysts available for catalyst-controlled C-H functionalization.

Intriguing steroid glycosides for cancer therapy by suppressing the DNA damage response and mTOR/S6K signaling pathways

Two rare 8-hydroxysteroid glycosides (6–7), and their downstream metabolites (1–5) with an unprecedented 6/6/5/5/5-pentacyclic scaffold, together with seven known analogues (8–14) were isolated from the twigs and leaves of Strophanthus divaricatus. Their structures were fully assigned by analysis of the spectroscopic and ECD data, NMR calculations, X-ray crystallographic study, and chemical methods. In addition, the inhibitory effects of 1–14 on liver and lung cancer cell lines were evaluated, and preliminary structure–activity relationship was discussed. Data-independent acquisition (DIA)-based quantitative proteomic analysis and biological verification of H1299 cells suggested that this family of compounds may play an anticancer role by suppressing both DNA damage response (DDR) and mTOR/S6K signaling pathways.

Intriguing steroid glycosides for cancer therapy by suppressing the DNA damage response and mTOR/S6K signaling pathways

Two rare 8-hydroxysteroid glycosides (6–7), and their downstream metabolites (1–5) with an unprecedented 6/6/5/5/5-pentacyclic scaffold, together with seven known analogues (8–14) were isolated from the twigs and leaves of Strophanthus divaricatus. Their structures were fully assigned by analysis of the spectroscopic and ECD data, NMR calculations, X-ray crystallographic study, and chemical methods. In addition, the inhibitory effects of 1–14 on liver and lung cancer cell lines were evaluated, and preliminary structure–activity relationship was discussed. Data-independent acquisition (DIA)-based quantitative proteomic analysis and biological verification of H1299 cells suggested that this family of compounds may play an anticancer role by suppressing both DNA damage response (DDR) and mTOR/S6K signaling pathways.

Designing Dual-State and Aggregation-Induced Emissive Luminogens from Lignocellulosic Biosourced Molecules.

Utilizing lignocellulosic biosourced platforms, we synthesized novel cyanostilbene (CS) derivatives featuring the 3,4-dimethoxyphenyl moiety. These derivatives were investigated for their emission properties in both solution and solid states. The two simple CS derivatives exhibit very weak luminescence in solution but significant luminescence in the solid state, indicating distinct Aggregation-Induced Emission (AIE) characteristic. Furthermore, combining these two CS units, without conjugation and with quasi perpendicular orientation, results in a Dual-State Emission (DSE) fluorophore showing luminescence both in solution and solid states. X-ray crystallography studies on the solid-state compounds reveal a structure-emission relationship, demonstrating that the colour emission correlates with the conformations adopted by the molecules in the solid state, which influence the type of stacking.

Palladium(II) complexes of amino acid derived ONO-tridentate enamine ligand for Suzuki-Miyaura cross-coupling reaction

Three palladium(II) complexes with an ONO-tridentate enamine ligand were synthesized by reacting the glycine derivative ligand with palladium(II) acetate in the presence of selected ancillary ligands. The structures of the Pd(II) complexes were determined through melting point, C, H, N elemental analysis, ATR-FTIR, and NMR. Additionally, the molecular structures of two complexes were confirmed using single-crystal X-ray crystallography studies, revealing that the ligand coordinates to palladium(II) via ONO-chelation, resulting in a square planar geometry around the metal center. Catalytic activities of these compounds were assessed in the Suzuki-Miyaura cross-coupling reaction of phenylboronic acid with the different aryl halides.

A highly neutralizing human monoclonal antibody targeting a novel linear epitope on staphylococcal enterotoxin B

ABSTRACT Staphylococcal Enterotoxin B (SEB), produced by Staphylococcus aureus (S. aureus), is a powerful superantigen that induces severe immune disruption and toxic shock syndrome (TSS) upon binding to MHC-II and TCR. Despite its significant impact on the pathogenesis of S. aureus, there are currently no specific therapeutic interventions available to counteract the mechanism of action exerted by this toxin. In this study, we have identified a human monoclonal antibody, named Hm0487, that specifically targets SEB by single-cell sequencing using PBMCs isolated from volunteers enrolled in a phase I clinical trial of the five-antigen S. aureus vaccine. X-ray crystallography studies revealed that Hm0487 exhibits high affinity for a linear B cell epitope in SEB (SEB138–147), which is located distantly from the site involved in the formation of the MHC-SEB-TCR ternary complex. Furthermore, in vitro studies demonstrated that Hm0487 significantly impacts the interaction of SEB with both receptors and the binding to immune cells, probably due to an allosteric effect on SEB rather than competing with receptors for binding sites. Moreover, both in vitro and in vivo studies validated that Hm0487 displayed efficient neutralizing efficacy in models of lethal shock and sepsis induced by either SEB or bacterial challenge. Our findings unveil an alternative mechanism for neutralizing the pathogenesis of SEB by Hm0487, and this antibody provides a novel strategy for mitigating both SEB-induced toxicity and S. aureus infection.

Synthesis, structure analysis, Hirshfeld surface studies, molecular docking studies against cyclin-dependent kinases (CDKs) of sulfonamide decorated N6-benzyl aminopurines for cancer treatment

Cyclin-dependent kinases (CDKs) are recognized as the primary regulators of the cell cycle. CDKs are over-expressed in various types of cancer. Inhibiting CDKs with small molecules can reduce tumor growth and benefit cancer patients. In the current study, sulfonamide-decorated N6-benzyl aminopurines such as ligand 1: (α- alpha (Purin-6-ylamino)-p-toluenesulfonamide) and ligand 2: (α-(2-Amino purin-6-ylamino)-p-toluenesulfonamide)) purine were synthesized and explored for their anticancer efficacy. Crystallographic analysis revealed that ligand 1 crystallizes in P-1 of the triclinic and ligand 2 molecule in C2/c or P21/c of the monoclinic systems. Hirshfeld surface and X-ray crystallographic studies discovered that ligand 2 possesses stronger noncovalent interaction ability than roscovitine. In silico analysis showed that ligand 2 had a higher binding affinity for ATP binding sites of CDK1, CDK2, and CDK4 receptors than roscovitine (a known CDK inhibitor). The enhanced binding affinity of ligand 2 with CDKs was found to be associated with strong noncovalent interactions between ligand 2 and specific amino acids in CDKs. Cytotoxicity studies were conducted on the glioblastoma cell line (U251) by incubating cells with ligands 0, 1, and 2, roscovitine, and the established anticancer drug Temozolomide (TMZ). Ligand 2 (66.12 ± 1.09 µM) demonstrated better cytotoxicity compared to ligand 1 (81.22 ± 0.30 µM), roscovitine (127.10 ± 0.47 µM), and TMZ (165.11 ± 1 µM). It was well known that CDK inhibition can lead to cell cycle arrest. Intriguingly, ligand 2 induced G2/M phase cell cycle arrest by increasing the percentage of the G2/M phase cell population from 21.08 % to 47.79 % in U251 cells. Based on these results, ligand 2 showed anticancer properties by binding to the ATP binding site of CDKs. Hence, ligand 2 can serve as a potential lead molecule in the development of effective anticancer agents.

2'-Fucosyllactose Inhibits Human Norovirus Replication in Human Intestinal Enteroids.

Human noroviruses (HuNoVs) are the leading cause of acute gastroenteritis worldwide. Currently, there are no targeted antivirals for the treatment of HuNoV infection. Histo-blood group antigens (HBGAs) on the intestinal epithelium are cellular attachment factors for HuNoVs; molecules that block the binding of HuNoVs to HBGAs thus have the potential to be developed as antivirals. Human milk oligosaccharides (HMOs) are glycans in human milk with structures analogous to HBGAs. HMOs have been shown to act as decoy receptors to prevent the attachment of multiple enteric pathogens to host cells. Previous X-ray crystallography studies have demonstrated the binding of HMO 2'-fucosyllactose (2'FL) in the same pocket as HBGAs for some HuNoV strains. We evaluated the effect of 2'FL on the replication of a globally dominant GII.4 Sydney [P16] HuNoV strain using human intestinal enteroids (HIEs) from adults and children. A significant reduction in GII.4 Sydney [P16] replication was seen in duodenal and jejunal HIEs from multiple adult donors, all segments of the small intestine from an adult organ donor and in two pediatric duodenal HIEs. However, 2'FL did not inhibit HuNoV replication in two infant jejunal HIEs that had significantly lower expression of α1-2-fucosylated glycans. 2'FL can be synthesized in large scale, and safety and tolerance have been assessed previously. Our data suggest that 2'FL has the potential to be developed as a therapeutic for HuNoV gastroenteritis.

Isomerization Pathways of a Mismatched Base Pair of A:8OG in Free Duplex DNA.

The A:8OG base pair (bp) is the outcome of DNA replication of the mismatched C:8OG bp. A high A:8OG bp population increases the C/G to A/T transversion mutation, which is responsible for various diseases. MutY is an important enzyme in the error-proof cycle and reverts A:8OG to C:8OG bp by cleaving adenine from the A:8OG bp. Several X-ray crystallography studies have determined the structure of MutY during the lesion scanning and lesion recognition stages. Interestingly, glycosidic bond (χ) angles of A:8OG bp in those two lesion recognition structures were found to differ, which implies that χ-torsion isomerization should occur during the lesion recognition process. In this study, as a first step to understanding this isomerization process, we characterized the intrinsic dynamic features of A:8OG in free DNAs by a free energy landscape simulation at the all-atom level. In this study, four isomerization states were assigned in the order of abundance: Aanti:8OGsyn > Aanti:8OGanti > Asyn:8OGanti ≈ Asyn:8OGsyn. Of these bp states, only 8OG in Asyn:8OGanti was located in the extrahelical space, whereas the purine bases (A and 8OG) in the other bp states remained inside the DNA helix. Also, free energy landscapes showed that the isomerization processes connecting these four bp states proceeded mostly in the intrahelical space via successive single glycosidic bond rotations of either A or 8OG.

Preparation and crystal structure of D2d-C84(23)Cl24 chlorofullerene

Chlorofullerene D2d-C84(23)Cl24 was prepared by chlorination of D2d-C84(23) with VCl4 or SbCl5 at 320–350 °C. An X-ray crystallographic study with the use of synchrotron radiation revealed the addition pattern of 24 Cl atoms stabilized by the formation of isolated C=C bonds and benzenoid rings on the carbon cage.

Design, synthesis, and spectrofluorimetric analysis of a novel fluorene-based chemosensor for the selective detection of picric acid

Fluorene-based probes are efficient candidates for sensing nitroaromatics and toxins. A novel fluorophore based on fluorene and terephthalaldehyde 1,4-YBF (1,4-ylidene-bis-fluorene) has been designed and synthesized for the efficient sensing of 2,4,6-trinitrophenol (picric acid) in solution. X-ray crystallographic studies, NMR, and mass analyses revealed the molecular stacking and exact structure of 1,4-YBF, which was further structurally optimised using the DFT technique. The optical properties of the newly synthesized compound were studied using UV–Vis and spectrofluorimetric analyses. The fluorophore was subjected to detailed sensing studies of various nitroaromatics, among which it was identified that picric acid (PA) exhibited the maximum quenching efficiency. The excellent sensing ability of the fluorophore was probably attributed to the photoinduced electron transfer (PET) mechanism. Further, pH studies and interference studies, along with its high selectivity towards PA and an LOD of 0.314 µM, revealed 1,4-YBF to be efficient in the detection of picric acid at a micromolar level.

Synthesis and characterization of a unique fused spiro-dihydropyran based chemodosimeter for selective visual and fluorescent detection of Cu2+ ion in aqueous medium by “turn-on” mode

A realistically newly designed Cu2+ ion specific fluorescent chemodosimeter has been synthesized from α,α'-(E,E)-bis(benzylidene)cyclohexanone having a fused spiro-dihydropyran moiety characterized by 2D NMR and X-Ray Crystallographic study. It also demonstrates an irreversible, instant direct visualisation by unaided eye chemosensing property in aqueous buffer (pH 7.4) with a colour change from yellow to orange upto 0.3 × 10−6 M.

Reverse N-Substituted Hydroxamic Acid Derivatives of Fosmidomycin Target a Previously Unknown Subpocket of 1-Deoxy-d-xylulose 5-Phosphate Reductoisomerase (DXR).

Reverse analogs of the phosphonohydroxamic acid antibiotic fosmidomycin are potent inhibitors of the nonmevalonate isoprenoid biosynthesis enzyme 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR, IspC) of Plasmodium falciparum. Some novel analogs with large phenylalkyl substituents at the hydroxamic acid nitrogen exhibit nanomolar PfDXR inhibition and potent in vitro growth inhibition of P. falciparum parasites coupled with good parasite selectivity. X-ray crystallographic studies demonstrated that the N-phenylpropyl substituent of the newly developed lead compound 13e is accommodated in a subpocket within the DXR catalytic domain but does not reach the NADPH binding pocket of the N-terminal domain. As shown for reverse carba and thia analogs, PfDXR selectively binds the S-enantiomer of the new lead compound. In addition, some representatives of the novel inhibitor subclass are nanomolar Escherichia coli DXR inhibitors, whereas the inhibition of Mycobacterium tuberculosis DXR is considerably weaker.

Rim-Based Binding of Perfluorinated Acids to Pillararenes Purifies Water.

Per- and polyfluoroalkyl substances (PFAS) pose a rapidly increasing global problem as their widespread use and high stability lead worldwide to water contamination, with significant detrimental health effects.[1] Supramolecular chemistry has been invoked to develop materials geared towards the specific capture of PFAS from water,[2] to reduce the concentration below advisory safety limits (e.g., 70 ng/L for the sum of perfluorooctane sulfonic acid, PFOS and perfluorooctanoic acid, PFOA). Scale-up and use in natural waters with high PFAS concentrations has hitherto posed a problem. Here we report a new type of host-guest interaction between deca-ammonium-functionalized pillar[5]arenes (DAF-P5s) and perfluoroalkyl acids. DAF-P5 complexes show an unprecedented 1 : 10 stoichiometry, as confirmed by isothermal calorimetry and X-ray crystallographic studies, and high binding constants (up to 106 M-1) to various polyfluoroalkyl acids. In addition, non-fluorinated acids do not hamper this process significantly. Immobilization of DAF-P5s allows a simple single-time filtration of PFAS-contaminated water to reduce the PFOS/PFOA concentration 106 times to 15-50 ng/L level. The effective and fast (<5 min) orthogonal binding to organic molecules without involvement of fluorinated supramolecular hosts, high breakthrough capacity (90 mg/g), and robust performance (>10 regeneration cycles without decrease in performance) set a new benchmark in PFAS-absorbing materials.

Synthesis, biological activity, X-ray crystallographic, DFT calculations and molecular dynamics simulation studies of 2-phenylthiazole-1,3,5-triazine derivatives as potential cholinesterase inhibitors

Seven 2-phenylthiazole-1,3,5-triazine derivatives were synthesized and estimated for cholinesterase inhibitory activity. All target compounds were characterized by 1H NMR, 13C NMR, FT-IR, and HRMS, and their purity was tested by HPLC to be above 99%. The in vitro enzyme inhibitory activity assays determined that the majority of compounds exhibited moderate to good inhibitory effects on acetylcholinesterase or butyrylcholinesterase and compound 6g displayed the best acetylcholinesterase (IC50 = 0.26 μM) and butyrylcholinesterase inhibitory activity (IC50 = 0.78 μM). The structures of compounds 6a and 6g was further investigated by single-crystal X-ray diffraction, and the Hirshfeld surfaces, crystal voids, and molecular energy framework analysis were further discussed to study the molecular conformations, crystal packing modes, intermolecular interactions, and their energies. What's more, the density functional theory calculations including frontier molecular orbitals, global reactivity descriptors, and molecular electrostatic potential were carried out to reveal the chemical reactivity and stability of 6a and 6g molecules. Molecular docking study indicated that compound 6g could not only interact with acetylcholinesterase but also with butyrylcholinesterase. Molecular dynamics simulations study showed that compound 6g could bind to acetylcholinesterase stably. In addition, ADMET properties prediction implied the drug-like properties and safety of seven compounds. Considering these results, several of the target compounds could work as novel cholinesterase inhibitors, and compound 6g may possess the potential to become a lead compound to develop novel anti-Alzheimer drugs.

Phenolate-thiazole based reversible “turn-on” chemosensor for the selective detection of carbonate anion: X-ray crystallography, DFT/TDFT, and cell study

A new phenolate-thiazole derivative (L) has been synthesized and structurally characterized.The chemo-sensing activity of L is detected by the naked eye for the aqueous carbonate anion in the pH range of 4 to 8. The selective ‘turn-on’ fluorescence occurs through the formation of a stable intermediate L∙CO32–(1) following the PET mechanism. The limit of detection (LOD) is found 0.18 µM based on the absorbance-based assay.The quinonoid form of bromophenol unit binds strongly with CO32– through thiazole nitrogen and hydrazinic nitrogen. Further, the selective holding of CO32– anion over other planar tetranuclear anions (e.g., SO32–, NO3–) happens with several intra and intermolecular hydrogen bonds as envisaged by the DFT/TDFT study. The formation mechanism of L∙CO32– is proposed based on experimental and theoretical studies. The biological experiments (MTT and cell imaging)reveal the non-cytotoxicity nature of L and the biocompatible uptake of L mostly in the cytoplasm at physiological pH.

1H, 13C, and 15N resonance assignments and solution structure of the N-terminal divergent calponin homology (NN-CH) domain of human intraflagellar transport protein 54.

The intraflagellar transport (IFT) machinery plays a crucial role in the bidirectional trafficking of components necessary for ciliary signaling, such as the Hedgehog, Wnt/PCR, and cAMP/PKA systems. Defects in some components of the IFT machinery cause dysfunction, leading to a wide range of human diseases and developmental disorders termed ciliopathies, such as nephronophthisis. The IFT machinery comprises three sub-complexes: BBsome, IFT-A, and IFT-B. The IFT protein 54 (IFT54) is an important component of the IFT-B sub-complex. In anterograde movement, IFT54 binds to active kinesin-II, walking along the cilia microtubule axoneme and carrying the dynein-2 complex in an inactive state, which works for retrograde movement. Several mutations in IFT54 are known to cause Senior-Loken syndrome, a ciliopathy. IFT54 possesses a divergent Calponin Homology (CH) domain termed as NN-CH domain at its N-terminus. However, several aspects of the function of the NN-CH domain of IFT54 are still obscure. Here, we report the 1H, 15N, and 13C resonance assignments of the NN-CH domain of human IFT54 and its solution structure. The NN-CH domain of human IFT54 adopts essentially the α1-α2-α3-α4-α5 topology as that of mouse IFT54, whose structure was determined by X-ray crystallographic study. The structural information and assignments obtained in this study shed light on the molecular function of the NN-CH domain in IFT54.

A trapped covalent intermediate as a key catalytic element in the hydrolysis of a GH3 β-glucosidase: An X-ray crystallographic and biochemical study

Glycoside hydrolases (GHs) are industrially important enzymes that hydrolyze glycosidic bonds in glycoconjugates. In this study, we found a GH3 β-glucosidase (CcBgl3B) from Cellulosimicrobium cellulans sp. 21 was able to selectively hydrolyze the β-1,6-glucosidic bond linked glucose of ginsenosides. X-ray crystallographic studies of the ligand complex ginsenoside-specific β-glucosidase provided a novel finding that support the catalytic mechanism of GH3. The substrate was clearly identified within the catalytic center of wild-type CcBgl3B, revealing that the C1 atom of the glucose was covalently bound to the Oδ1 group of the conserved catalytic nucleophile Asp264 as an enzyme–glycosyl intermediate. The glycosylated Asp264 could be identified by mass spectrometry. Through site-directed mutagenesis studies with Asp264, it was found that the covalent intermediate state formed by Asp264 and the substrate was critical for catalysis. In addition, Glu525 variants (E525A, E525Q and E525D) showed no or marginal activity against pNPβGlc; thus, this residue could supply a proton for the reaction. Overall, our study provides an insight into the catalytic mechanism of the GH3 enzyme CcBgl3B.

Sulfonamide-incorporated bis(α-aminophosphonates) as promising carbonic anhydrase inhibitors: Design, synthesis, biological evaluation, and X-ray crystallographic studies.

A novel series of sulfonamide-incorporated bis(α-aminophosphonates) acting as effective carbonic anhydrase (CA, EC 4.2.1.1) inhibitors is reported. The synthesized bivalent ligands were tested against five human (h) isoforms, hCA I, hCA II, hCA VII, hCA IX, and hCA XIII. Such derivatives showed high activity and selectivity against the cancer-related, membrane-bound isoform hCA IX, and among them, compound 5h, tetraisopropyl (1,3-phenylenebis{[(4-sulfamoylphenyl)amino]methylene})bis(phosphonate)showed a KI of 15.1 nM, being highly selective against this isoform over all other investigated ones (hCA I/IX = 42; hCA II/IX = 6, hCA VII/IX = 3, hCA XIII/IX = 5). Therefore, compound 5h could be a potential lead for the development of selective anticancer agents. The newly developed sulfonamides were also found effective inhibitors against the cytosolic hCA XIII isoform. Compound 5i displayed the best inhibition against this isoform with a KI of 17.2 nM, equal to that of the well-known inhibitor acetazolamide (AAZ), but significantly more selective over all other tested isoforms (hCA I/XIII = 239; hCA II/XIII = 23, hCA VII/XIII = 2, hCA IX/XIII = 3) compared to AAZ.