X-ray Crystallographic Studies Research Articles

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.

New diarylcyclopentenone enantiomers and biphenyl derivatives from the fungus Talaromyces adpressus

Ten new compounds, including three pairs of diarylcyclopentenone enantiomers (±) talaromycesins A−C (1–3) and four biphenyl derivatives talaromycesins D−G (4–7), along with four known compounds (8–11), were isolated from the fungus Talaromyces adpressus. Their structures were determined by analyses of extensive NMR spectroscopic and HRESIMS data, and their absolute configurations were elucidated by the dimolybdenum tetraacetate [Mo2(AcO)4]-induced ECD spectra, X-ray crystallographic studies, and ECD calculations. These new compounds were evaluated for their immunosuppressive activities for the first time, and compound 7 probably exerted liver-protective and anti-inflammatory effects on Con A-induced AIH by decreasing the levels of inflammatory cytokines, modulating immune homeostasis, and decreasing hepatocyte apoptosis, which may become a potential drug for the treatment of autoimmune diseases.

Asperustins A-J: Austocystins with Immunosuppressive and Cytotoxic Activities from Aspergillus ustus NRRL 5856.

Ten new (1-10) and nine known (11-19) austocystins, along with four known anthraquinones (20-23), were isolated from the culture of Aspergillus ustus NRRL 5856 by bioactivity-guided fractionation. The structures of the new compounds were elucidated by spectroscopic data analysis, X-ray crystallographic study, the modified Mosher's method, [Rh2(OCOCF3)4]-induced ECD spectral analysis, and comparison of the experimental ECD spectra with those of the similar analogues. Compounds 1-8 represent the first examples of austocystins with a C-4' oxygenated substitution. The absolute configuration of 1″-hydroxy austocystin D (11) was determined by single-crystal X-ray diffraction and consideration of its biosynthetic origin. Compounds 5, 9, and 11 exhibited significant inhibitory effects against the proliferation of ConA-induced T cells with IC50 values of 1.1, 1.0, and 0.93 μM, respectively. Furthermore, these compounds suppressed the expression of IL-6 in a dose-dependent manner. Compounds 10-12 and 14 showed pronounced cytotoxicities against MCF-7 with IC50 values of 3.9, 1.3, 0.46, and 2.3 μM, respectively.

A Comparative Study of New Fluorescent Anthraquinone and Benzanthrone α-Aminophosphonates: Synthesis, Spectroscopy, Toxicology, X-ray Crystallography, and Microscopy of Opisthorchis felineus.

In this research, we explore the synthesis of and characterize α-aminophosphonates derived from anthraquinone and benzanthrone, focusing on their fluorescence properties and potential applications in confocal laser scanning microscopy (CLSM). The synthesized compounds exhibit notable solvatochromic behavior, emitting fluorescence from green to red across various solvents. Spectroscopic analysis, including 1H-, 13C-, and 31P-NMR, FTIR, and mass spectrometry, confirms the chemical structures. The compounds' toxicity is evaluated using etiolated wheat sprouts, revealing varying degrees of impact on growth and oxidative damage. Furthermore, the study introduces these α-aminophosphonates for CLSM imaging of the parasitic flatworm Opisthorchis felineus, demonstrating their potential in visualizing biological specimens. Additionally, an X-ray crystallographic study of an anthraquinone α-aminophosphonate provides valuable structural insights.

Structural and Spectroscopic Characterization of Co(II) Bis(Benzenedichlorodithiolate): An Intermediate in Hydrogen Evolution Catalysis

Co bis(benzenedithiolate) type complexes have captivated chemists for decades for their interesting geometric and electronic structures and more recently, for their impressive ability to mediate the hydrogen evolution reaction (HER) both photo- and electrocatalytically. However, these complexes have nearly exclusively been characterized in their air-stable Co(III) oxidation states. In this work, Co(II) bis(benzenedichlorodithiolate) was prepared by chemical and electrochemical one-electron reduction. This reduced Co(II) complex was characterized by X-ray crystallography and in-depth spectroscopic studies—including UV-Vis, magnetic circular dichroism, and electron paramagnetic resonance spectroscopy. [Co(II)(Cl2bdt)2]2− is thereby shown to be a square planar complex, with a primarily metal-centered reduction, and an St = 1/2 spin state. This study informs our understanding of the first step in the HER catalytic cycle of Co bis(benzenedithiolate) type complexes and paves the way for future mechanistic studies on this catalyst family.

Styryl-extended Azopyrroles and their boron difluoride complexes: Synthesises, structures, spectra, and DFT calculation

Three styryl-extended azopyrrole compounds (2–4) with different substituents (-H, -NO2, and -N(CH3)2) have been synthesized by Knoevenagel condensation reaction between azopyrrole and substituted benzaldehyde. Their BF2 complexes (5–7) were also synthesized. The planar structure of compound 3 was characterized by X-ray crystallographic study. Hirshfeld surface analysis reveals that van der Waals interactions and hydrogen-bonding are the dominant interactions in the crystal packing. All compounds have λmax absorption greatly red-shift even to deep-red light region (646 nm) due to the extended π-conjugation by styryl group and the introduction of BF2 group. The structures, frontier molecular orbitals (FMOs), energy gaps (ΔE) and UV–Vis spectra of these compounds were evaluated by DFT calculations. The results reveal that the styryl, electron donating and withdrawing groups, and BF2 group all can reduce the energy gap (ΔE) of the compounds, and finally cause their long-wavelength absorption.

Invention of MK-7845, a SARS-CoV-2 3CL Protease Inhibitor Employing a Novel Difluorinated Glutamine Mimic.

As SARS-CoV-2 continues to circulate, antiviral treatments are needed to complement vaccines. The virus's main protease, 3CLPro, is an attractive drug target in part because it recognizes a unique cleavage site, which features a glutamine residue at the P1 position and is not utilized by human proteases. Herein, we report the invention of MK-7845, a novel reversible covalent 3CLPro inhibitor. While most covalent inhibitors of SARS-CoV-2 3CLPro reported to date contain an amide as a Gln mimic at P1, MK-7845 bears a difluorobutyl substituent at this position. SAR analysis and X-ray crystallographic studies indicate that this group interacts with His163, the same residue that forms a hydrogen bond with the amide substituents typically found at P1. In addition to promising in vivo efficacy and an acceptable projected human dose with unboosted pharmacokinetics, MK-7845 exhibits favorable properties for both solubility and absorption that may be attributable to the unusual difluorobutyl substituent.

Identification of small-molecule binding sites of a ubiquitin-conjugating enzyme-UBE2T through fragment-based screening.

UBE2T is an attractive target for drug development due to its linkage with several types of cancers. However, the druggability of ubiquitin-conjugating E2 (UBE2T) is low because of the lack of a deep and hydrophobic pocket capable of forming strong binding interactions with drug-like small molecules. Here, we performed fragment screening using 19 F-nuclear magnetic resonance (NMR) and validated the hits with 1 H-15 N-heteronuclear single quantum coherence (HSQC) experiment and X-ray crystallographic studies. The cocrystal structures obtained revealed the binding modes of the hit fragments and allowed for the characterization of the fragment-binding sites. Further screening of structural analogues resulted in the identification of a compound series with inhibitory effect on UBE2T activity. Our current study has identified two new binding pockets in UBE2T, which will be useful for the development of small molecules to regulate the function of this protein. In addition, the compounds identified in this study can serve as chemical starting points for the development of UBE2T modulators.

Helical BODIPY Dyes as Heavy-Atom-Free Triplet Photosensitizers for Photodynamic Therapy of Cancer.

Despite of having many advantages over the popular cancer therapies, photodynamic therapy still is not widely acceptable for clinical applications. Scarcity of efficient triplet photosensitizers (PSs) is one of the main bottlenecks for this. Although numerous heavy atom attached PSs are developed as PDT agents, but these are not suitable for clinical applications due to several reasons. Thus, development of heavy-atom-free organic PSs is urgently required. In this context, development of new type of helical BODIPYs as PSs for PDT is discussed. BODIPYs have rich photophysical properties and structural helicity further enhances their triplet conversion rates. This new concept of structural helicity to enhance the triplet conversion of BODIPYs is discussed with reported helical BODIPYs. Helical geometries of these dyes are checked by X-ray crystallography studies and their high triplet conversions as compared to planar BODIPYs are also confirmed. Importantly, these dyes have high triplet lifetimes and are capable of generating high singlet oxygens even in hypoxia condition as compared to conventional heavy atom attached BODIPYs. All these make the helical BODIPYs excellent candidates as PDT agents. Finally, their successful applications as PDT agents in killing of various types of cancer cells are also discussed. The results are encouraging which indicate that helical BODIPYs could be next generation heavy-atom-free PSs for PDT applications.

Reaction hijacking inhibition of Plasmodium falciparum asparagine tRNA synthetase

Malaria poses an enormous threat to human health. With ever increasing resistance to currently deployed drugs, breakthrough compounds with novel mechanisms of action are urgently needed. Here, we explore pyrimidine-based sulfonamides as a new low molecular weight inhibitor class with drug-like physical parameters and a synthetically accessible scaffold. We show that the exemplar, OSM-S-106, has potent activity against parasite cultures, low mammalian cell toxicity and low propensity for resistance development. In vitro evolution of resistance using a slow ramp-up approach pointed to the Plasmodium falciparum cytoplasmic asparaginyl-tRNA synthetase (PfAsnRS) as the target, consistent with our finding that OSM-S-106 inhibits protein translation and activates the amino acid starvation response. Targeted mass spectrometry confirms that OSM-S-106 is a pro-inhibitor and that inhibition of PfAsnRS occurs via enzyme-mediated production of an Asn-OSM-S-106 adduct. Human AsnRS is much less susceptible to this reaction hijacking mechanism. X-ray crystallographic studies of human AsnRS in complex with inhibitor adducts and docking of pro-inhibitors into a model of Asn-tRNA-bound PfAsnRS provide insights into the structure-activity relationship and the selectivity mechanism.