Investigation of encapsulated water wire within self-assembled hydrophilic nanochannels, in a modified γ4-amino acid crystals: Tracking thermally induced changes of intermolecular interactions within a crystalline hydrate

Nanostructures formed by the self-assembly of modified/unmodified amino acids have the potential to be useful in several biological/nonbiological applications. In that regard, the greater conformational space provided by γ-amino acids, owing to their additional backbone torsional degrees of freedom and enhanced proteolytic stability, compared to their α-counterparts, should be explored. Though, modified single amino acid-based nanomaterials such as nanobelts or hydrogels are developed by utilizing the monosubstituted γ-amino acids derived from the backbone homologation of phenylalanine (Phe). Examples of a single γ-amino acid-based porous nanostructure capable of accommodating solvent molecules are not really known. The crystal structures of a modified γ4(R)Phe residue, Boc-γ4(R)Phe-OH, at different temperatures, showed that hydrogen-bonded water molecules are forming a wire inside hydrophilic nanochannels. The dynamics of intermolecular interactions between the water wire and the inner wall of the channel with relation to the temperature change was investigated by analyzing the natural bonding orbital (NBO) calculation results performed with the single crystal structures obtained at different temperature points. The NBO results showed that from 325 K onward, the strength of water-water interactions in the water wire are getting weaker, whereas, for the water-inner wall interactions, it getting stronger, suggesting a favorable change in the orientation of water molecules with temperatures, for the latter.

Design, synthesis, in vitro anticancer, molecular docking and SAR studies of new series of pyrrolo[2,3-d]pyrimidine derivatives

The current study involves the design and synthesis of a newly synthesized pyrrolo[2,3-d]pyrimidine derivatives to contain chlorine atoms in positions 4 and 6 and trichloromethyl group in position 2 using microwave technique as a new and robust approach for preparation of this type of pyrrolo[2,3-d]pyrimidine derivatives. The chemical structure of the synthesized pyrrolo[2,3-d]pyrimidine derivatives 3-19 was well-characterized using spectral and elemental analyses as well as single-crystal X-ray diffraction. All compounds were tested in vitro against seven selected human cancer cell lines, namely, MCF7, A549, HCT116, PC3, HePG2, PACA2 and BJ1 using MTT assay. It was found that compounds 14a, 16b and 18b were the most active toward MCF7 with IC50 (1.7, 5.7, and 3.4 μg/ml, respectively) relative to doxorubicin (Dox.) (26.1 μg/ml). Additionally, compound 17 exerted promising cytotoxic effects against HePG2 and PACA2 with IC50 (8.7 and 6.4 μg/ml, respectively) relative to Dox. (21.6 and 28.3 μg/ml, respectively). The molecular docking study confirmed our ELISA result which showed the promising binding affinities of compounds 14a and 17 against Bcl2 anti-apoptotic protein. At the gene expression level, P53, BAX, DR4 and DR5 were up-regulated, while Bcl2, Il-8, and CDK4 were down-regulated in 14a, 14b and 18b treated MCF7 cells. At the protein level, compound 14b increased the activity of Caspase 8 and BAX (18.263 and 14.25 pg/ml) relative to Dox. (3.99 and 4.92 pg/ml, respectively), while the activity of Bcl2 was greatly decreased in 14a treated MCF7 (2.4 pg/ml) compared with Dox. (14.37 pg/ml). Compounds 14a and 14b caused cell cycle arrest at the G1/S phase in MCF7. Compounds 16b and 18b induced the apoptotic death of MCF7 cells. In addition, the percentage of fragmented DNA was increased significantly in 14a treated MCF7 cells.

Four undescribed ergostane-type steroids from Lasiodiplodia pseudotheobromae and their neuroprotective activity

Four undescribed ergostane-type steroids, (22E,24R)-4α,5α-epoxyergosta-9α,14β-dihydroxy-7,22-diene-3,6-dione, (22E,24R)-4α,5α-epoxyergosta-9α,14α-dihydroxy-7,22-diene-3,6-dione, 12α-hydroxyergosta-7,22,24(28)-triene-3-one, and 3β,12α-dihydroxyergosta-7,24(28)-diene, along with a known congener (22E,24R)-9α,14β-dihydroxyergosta-4,7,22-triene-3,6-dione, were isolated from the fungus Lasiodiplodia pseudotheobromae. Their structures were elucidated using NMR, HRESIMS, ECD calculation, and X-ray diffraction analyses. (22E,24R)-4α,5α-epoxyergosta-9α,14β-dihydroxy-7,22-diene-3,6-dione and (22E,24R)-4α,5α-epoxyergosta-9α,14α-dihydroxy-7,22-diene-3,6-dione are a pair of C-14 epimers possessing an unusual epoxy group between C-4 and C-5, which was demonstrated using single-crystal X-ray diffraction analyses. The absolute configurations of 12α-hydroxyergosta-7,22,24(28)-triene-3-one and 3β,12α-dihydroxyergosta-7,24(28)-diene were determined by ECD calculations. Moreover, 3β,12α-dihydroxyergosta-7,24(28)-diene exhibited neuroprotective activity in vitro in glutamate-treated SH-SY5Y cell lines.

Highly oxygenated isoryanodane diterpenoids from the leaves of Cinnamomum cassia and their immunomodulatory activities

A total of twelve highly oxygenated isoryanodane (also known as cinncassiol D-type) diterpenoids including nine undescribed ones, named cinnacassins A-I, were isolated from the leaves of Cinnamomum cassia. Their chemical structures were elucidated by extensive spectrometric and spectroscopic techniques including HRESIMS, 1D and 2D NMR, single-crystal X-ray diffraction analysis, calculated ¹³C-NMR DP4+ analysis, and chemical methods. The absolute configuration of cinnacassin A was unambiguously delineated by single-crystal X-ray diffraction analysis. Cinnacassin H represents the first example of 16-O-glucosylated isoryanodane diterpenoid, and cinnacassin I is the first isoryanod-13(18)-ene diterpenoid. The relationship of the configuration C-18 and the chemical shifts of H₂-19 and C-20 in the 19-hydroxy-isoryanodane diterpenoids was discussed, and the 18S-configuration of three known 19-hydroxy-isoryanodane diterpenoids, cinncassiol D₁, 19-O-β-D-glucopyranosyl-cinncassiol D₁, and cinncassiol D₃ was assigned. All the isolated isoryanodane diterpenoids were evaluated for their immunomodulatory effects in vitro, and cinnacassin A and cinncassiol D₁ enhanced the proliferation of Con A-induced murine T cells with enhancement rates ranging from 17.9% to 45.4%, which were more potent than the positive control, thymosin α1. In addition, cinncassiol D₁ significantly promoted the proliferation of LPS-induced murine B cells with an enhancement rate up to 116.1%, two-fold more potent than thymosin α1 at a concentration of 1.5625 μM.

Highly modified nor-clerodane diterpenoids from Croton yanhuii

Phytochemical investigation of the leaves and twigs of Croton yanhuii led to the isolation of seven highly modified nor-clerodane diterpenoids (1-7), including three new ones, croyanoids A-C (1-3), along with four known analogues (4-7). Compound 1 incorporates a 5,12-epoxy ring, forming a unique cage-like, 6/6/6/5-fused tetracyclic ring system. Their structures were established by extensive spectroscopic analysis, and the absolute configurations of 1-4 were determined by a combination of circular dichroism (CD) analysis and single-crystal X-ray diffraction. All compounds were tested in an array of bioassays, but were inactive. Crotoeurin A (7), a nor-clerodane dimer with a high yield of 0.2‰ isolated in current study, was considered as a chemotaxonomic marker for this species.

Crystalline sponge affinity screening: A fast tool for soaking condition optimization without the need of X-ray diffraction analysis

Structural elucidation of small molecules only available in low quantity (nanogram) is one of the big advantages of the crystalline sponge method. The optimization of various soaking parameters is crucial for effective analyte absorption and repetitive positioning in the pores of the crystal. Time-consuming X-ray diffraction measurements are necessary for data collection and confirmation of successful guest inclusion. In this work, we report a screening method to select optimal soaking conditions without the need of single-crystal X-ray diffraction analysis for individual compounds and mixtures. 14 substances were chosen as test compounds. Parallel guest soaking of individual compounds and mixtures was conducted using various soaking conditions. After evaporation of solvent, excessive material was removed, and guest molecules released through dissolution of the framework. Liquid chromatography-tandem mass spectrometry allowed the estimation of analyte trapped in the pores and the selection of optimal soaking condition dependent on the highest amount of analyte to crystal size (affinity factor). The tool allowed subsequent crystallographic analysis of ten compounds with minimal experiment time. Additionally, a study to examine the lower limit of detection of the crystalline sponge method was conducted. Determination of two target analytes was possible using only 5 ng of sample. Our study shows the potential of an affinity screening to prioritize soaking parameters by estimation of the guest concentration in a single crystal for one or multiple target compounds within a short period of time.

Structurally diverse triterpenoids with cytotoxicity from Euphorbia hypericifolia

Extensive phytochemical investigation on the whole herbs of Euphorbia hypericifolia led to the isolation of 18 structurally diverse tetracyclic and pentacyclic triterpenoids, including four 4α,14α-dimethyl-5α-ergostanes (1-4), two seco-adiananes (5 and 6), three dammaranes (7-9), four cycloartanes (10-13), one tirucallane (14), two fernanes (15 and 16), one ursane (17), and one oleanane (18). Among them, euphypenoids A (1) and B (5) were new triterpenoids. Their structures were elucidated on the basis of extensive spectroscopic analysis, single-crystal X-ray diffraction, and chemical transformation. All isolates were screened for their cytotoxic activities against the colorectal cancer cell line HCT-116, and compounds 1, 12, and 15 showed remarkable activities with IC50 values of 12.8 ± 1.6, 7.4 ± 0.2, and 10.6 ± 1.2 μM, respectively.

Synthesis and biological evaluation as well as in silico studies of arylpiperazine-1,2-benzothiazine derivatives as novel anti-inflammatory agents

Novel arylpiperazine-1,2-benzothiazine derivatives have been designed and synthesized as potential anti-inflammatory agents. Their structure and properties have been studied using spectroscopic techniques (¹H NMR, ¹³C NMR, FT-IR), MS, elemental analyses, and single-crystal X-ray diffraction (SCXRD, for compound 7b). This study aimed to evaluate the inhibitory activity of new derivatives against both cyclooxygenase isoforms COX-1 and COX-2 due to the similarity of new compounds to oxicams drugs from the NSAIDs group. All new compounds were divided into two series - A and B - with a different linker between thiazine and piperazines nitrogens. Series A included the three-carbon aliphatic linker and series B - two-carbon with a carbonyl group. According to in vitro and molecular docking studies all new compounds exhibited cyclooxygenase inhibitory activity. The series of A compounds included COX-1 inhibitors only. In contrast, the B series showed inhibition of both COX-1 and COX-2, which suggested the importance of the acetoxy linker for COX-2 inhibition. Moreover, the most selective compound 7b, towards COX-2, was non-toxic for the normal human cell line (in concentration of 10 µM) comparable to reference drug meloxicam. Additionally, investigation of influence on model membranes confirmed the ability of the compound 7b to penetrate lipid bilayers which seemed to be important to the influence with membrane protein-cyclooxygenase.

Grayanane diterpenoid glucosides as potent analgesics from Pieris japonica

A total of fifteen grayanane diterpenoid glucosides including eight undescribed ones, pierisjaponosides A-H, were isolated from the leaves of Pieris japonica (Thunb.) D. Don ex G. Don (Ericaceae). Their structures were established by extensive spectros copic techniques including HRESIMS and NMR, as well as chemical methods. The absolute configurations of pierisjaponosides A, B, and D were finally established by single-crystal X-ray diffraction with Cu Kα radiation. This is the first time to report the crystal structure of a 5,9-epoxygrayanane diterpenoid glucoside. Pierisjaponoside E represents the first example of a 9β-hydroxygrayan-1(10)-ene diterpenoid. All the isolated grayanane diterpenoid glucosides were evaluated for their analgesic activities in the acetic acid-induced writhing models in mice, and showed significant analgesic effects. Pierisjaponosides A and C-H, micranthanoside A, pieroside A, and craiobiosides A and B displayed significant analgesic effects with the writhe inhibition rates over 50% at a dose of 5.0 mg/kg. Pierisjaponoside E exhibited significant analgesic activities with the percentage inhibitions of 81.7%, 70.4%, and 52.1% at the doses of 5.0, 1.0, and 0.2 mg/kg, respectively. The preliminary structure-activity relationships of grayanane diterpenoid glucosides as potent analgesics were discussed, giving some clues to design novel analgesics.

Bioactive A-ring rearranged limonoids from the root barks of Walsura robusta

Screening active natural products, rapid identification, and accurate isolation are of great important for modern natural lead compounds discovery1. We hereby reported the isolation of seven new neotecleanin-type limonoids (1-7), seven new limonoids with 5-oxatricyclo[5.4.0.11., 4.]hendecane ring system (8-14), and two new precursors (15-16) together with four known limonoids (17-20) from the root barks of Walsura robusta. Their structures, including their absolute configurations, were elucidated based on analyses of HR-ESI-MS, 1D/2D NMR, ECD spectrum calculations and single-crystal X-ray diffraction techniques. Compounds 2, 8, 9, 11, 13, 14, 18 showed significant anti-inflammatory activities in LPS-induced RAW 264.7 cell line, BV2 microglial cells, and Propionibacterium acnes-stimulated THP-1 human monocytic cells. Walrobsin M (11) exhibited anti-inflammatory activity with IC50 value of 7.96±0.36 μmol/L, and down-regulated phosphorylation levels of ERK and p38 in a dose-dependent manner.

Monitoring a simple hydrolysis process in an organic solid by observing methyl group rotation

We report a variety of experiments and calculations and their interpretations regarding methyl group (CH₃) rotation in samples of pure 3-methylglutaric anhydride (1), pure 3-methylglutaric acid (2), and samples where the anhydride is slowly absorbing water from the air and converting to the acid [C₆H₈O₃(1) + H₂O → C₆H₁₀O₄(2)]. The techniques are solid state ¹H nuclear magnetic resonance (NMR) spin-lattice relaxation, single-crystal X-ray diffraction, electronic structure calculations in both isolated molecules and in clusters of molecules that mimic the crystal structure, field emission scanning electron microscopy, differential scanning calorimetry, and high resolution ¹H NMR spectroscopy. The solid state ¹H spin-lattice relaxation experiments allow us to observe the temperature dependence of the parameters that characterize methyl group rotation in both compounds and in mixtures of the two compounds. In the mixtures, both types of methyl groups (that is, molecules of 1 and 2) can be observed independently and simultaneously at low temperatures because the solid state ¹H spin-lattice relaxation is appropriately described by a double exponential. We have followed the conversion 1 → 2 over periods of two years. The solid state ¹H spin-lattice relaxation experiments in pure samples of 1 and 2 indicate that there is a distribution of NMR activation energies for methyl group rotation in 1 but not in 2 and we are able to explain this in terms of the particle sizes seen in the field emission scanning electron microscopy images.

Gliclazide

Gliclazide is a second-generation oral hypoglycemic drug used for the treatment of noninsulin-dependent diabetes mellitus. It belongs to the sulfonylurea class that stimulates insulin secretion from pancreatic β-cells by inhibiting ATP-dependent potassium channels. Gliclazide also possesses unique antioxidant properties and other beneficial hemobiological effects. This profile represents a comprehensive description of the physical properties, chemical synthesis, spectroscopic characterization (FTIR, ¹H NMR, ¹³C NMR, UV, and single-crystal X-ray), methods of analysis, pharmacological actions, and pharmacokinetic and pharmacodynamic properties of the title drug.

Effect of gel formation on the dissolution behavior of clarithromycin tablets

Clarithromycin (CAM) is a macrolide antibiotic that is widely used at clinical sites. We found that release of CAM is suppressed when tablets of CAM were exposed to an external solvent containing carboxylate buffers such as citrate. The suppressed release of CAM can be attributed to the formation of gels on the tablet surfaces, which inhibits penetration of the solvent into the tablet and thus disintegration of the tablets. Delayed disintegration of the tablets was also observed for commercial tablets. This suggests that taking CAM and carboxylates at the same time might be avoided. The crystal structure of CAM citrate reveals that molecular chains of CAM are cross-linked by hydrogen bond between citrate groups in the crystal. The crystal structure indicates that cross-linked CAM chains of the three-dimensional mesh structure might also be formed in high concentration CAM solutions in the presence of carboxylates, resulting in gel formation.

Triterpenoids from the branch and leaf of Abies fargesii

Eighteen triterpenoids, abifarines A-R, including fourteen previously unknown and four artifacts, together with six known ones, were isolated from the branch and leaf of Abies fargesii. Their structures were elucidated by spectroscopic data analysis. The relative configurations of abifarines A and F were further confirmed by single-crystal X-ray diffraction analysis with Mo Kα irradiation. All compounds were evaluated for their in vitro cytotoxicity against the mouse cancer B16 cell line, and human cancer HepG2 and MCF7 cell lines. (24R)-cycloartane-3β,24,25-triol and (24R)-cycloartane-3β,24,25,28-tetrol showed moderate anti-proliferative effect for B16 and HepG2 cell lines with IC50 values of 32.9, 19.5 μM and 26.4, 21.5 μM, respectively.

Regioselectivity of the alkylation of S-substituted 1,2,4-triazoles with dihaloalkanes

Background

1,2,4-Triazole3-thiones are good scaffolds for preparation of new lead compounds. Their derivatives attracted the attention of chemists due to their wide spectrum of biological activities. Alkylsulfanyl-1,2,4-triazoles have three nucleophilic sites (nitrogens) ready for reaction with electrophiles. Herein, new regioselective isomers were synthesized by the reaction of benzylsulfanyl-1,2,4-triazole with various dihaloalkanes. Regioselectivity was determined by X-ray crystallography and NMR.

Results

Coupling of 3-benzylsufanyl-5-(1H-indolyl)-1,2,4-triazole with dibromomethane, 1,2-dichloroethane, 1,3-dibromopropane and di(bromomethyl)quinoxaline was investigated in the presence of potassium carbonate in acetone. In the case of dibromomethane three different bis(triazolyl)methane isomers (–N¹–CH₂–N¹-4, –N¹–CH₂–N²-5, –N²–CH₂–N²-6) were formed in which the two bromide atoms were replaced by two triazole moieties. Among these isomers the reaction was regioselective towards the –N¹–CH₂–N²-5 isomer due to the steric effect. In the case of 1,3-dibromopropane two compounds were obtained due to the alkylation at N(2) to give 2-(3-bromopropyl)-triazole 8 and alkylation at N(1) was followed by cyclization at the indole nitrogen to form a condensed indolo-triazolo-diazepine 10. Upon alkylation of 3-benzylsufanyl-5-(1H-indolyl)-1,2,4-triazole with di(bromomethyl)quinoxaline, two bis(triazolyl-methyl)quinoxaline isomers were separated and characterized as (–N¹–CH₂–N¹–) 11 and (–N²–CH₂–N²–) 12. Single-crystal X-ray diffraction assisted the elucidation and confirmation of the structures of the isomers. An AM1 theoretical study explained the regioselectivity of the alkylation.

Conclusions

On reacting S-protected 1,2,4-triazoles with various alkylating agents, only N(1) and N(2) attack the electrophilic carbons. N(2) alkylated isomers are preferentially formed.

Electronic supplementary material

The online version of this article (doi:10.1186/s13065-016-0165-0) contains supplementary material, which is available to authorized users.

Grayanane and leucothane diterpenoids from the leaves of Rhododendron micranthum

Eleven grayanane diterpenoids, 1-epi-grayanotoxin IV, 1-epi-grayanotoxin II, 6-deoxy-1-epi-grayanotoxin XVII, 6-deoxygrayanotoxin XVII, 16-acetylgrayanotoxin II, 3-oxograyanotoxin IX, 14-deoxygrayanotoxin VIII, 14-acetylisograyanotoxin II, rhodomicranols C-E, and a leucothane diterpenoid, rhodomicranol F, together with eleven known diterpenoids were isolated from leaves of Rhododendron micranthum. Their structures were elucidated by spectroscopic analyses, with the absolute configurations of 1-epi-grayanotoxin IV and rhodomicranol C determined by single-crystal X-ray diffraction with Cu Kα radiation, and the structures of 14-acetylisograyanotoxin II and known grayanotoxins IX and X confirmed by single-crystal X-ray diffraction. All twenty-three diterpenoids were evaluated for their in vitro immunomodulatory activities, and none showed significant immunomodulatory activities in a dose-dependent manner. In addition, they are non-toxic to the murine lymphocytes in the general cytotoxicity assay.

Synthesis and structural study of precursors of novel methylsilanediols by IR and Raman spectroscopies, single-crystal X-ray diffraction and DFT calculations

On the way towards the development of a synthetic route aimed at obtaining new methylsilanediol derivatives with an aminocarbonyl group in β to silicon (which may have a potential biological interest), we have synthesized, isolated and purified five diphenylic possible precursors, namely chloromethyl(methyl)diphenylsilane, 2-{[methyl(diphenyl)silyl]methyl}-1H-isoindole-1,3(2H)-dione, N-[(methyl(diphenyl) silanyl)-methyl]-benzamide, N-[(methyl(diphenyl)silyl)-methyl]-acetamide and N-[(methyl(diphenyl)silyl)-methyl]-formamide. The conformational landscape of the five species in this study are explored by means of DFT calculations at the B3LYP/6-311++G(∗∗) level. The theoretical molecular structures predicted are confirmed by the reproduction of their respective IR and Raman spectral profiles, that are completely assigned. Some evidence in the vibrational spectra points to the occurrence of conformational mixtures in the samples. Further, single-crystal X-ray diffraction has allowed the elucidation of the crystalline structure of 2-{[methyl(diphenyl)silyl]methyl}-1H-isoindole-1,3(2H)-dione.

Identification of mixed bromidochloridotellurate anions in disordered crystal structures of (bdmim)2[TeX2Y4] (X, Y=Br, Cl; bdmim=1-butyl-2,3-dimethylimidazolium) by combined application of Raman spectroscopy and solid-state DFT calculations

The discrete mixed [TeBrxCl6-x](2-) anions in their disordered crystal structures have been identified by using the phases prepared by the reaction of 1-butyl-2,3-dimethylimidazolium halogenides (bdmim)X with tellurium tetrahalogenides TeX4 (X=Cl, Br) as examples. Homoleptic (bdmim)2[TeX6] [X=Cl (1), Br (2)] and mixed (bdmim)2[TeBr2Cl4] (3), and (bdmim)2[TeBr4Cl2] (4) are formed depending on the choice of the reagents, and their crystal structures have been determined by single-crystal X-ray diffraction. The coordination environments of tellurium in all hexahalogenidotellurates are almost octahedral. Because of the crystallographic disorder, the mixed [TeBr2Cl4](2-) and [TeBr4Cl2](2-) anions in 3 and 4 cannot be identified in their crystal structures. Pawley refinement of the X-ray powder diffraction patterns of 1-4 indicates the presence of single phases in all four products. The solid state Raman spectra of 1-4 were assigned with help of DFT calculations that were performed both for the discrete anions in vacuum and for the complete crystal structures employing periodic boundary conditions. The fundamental vibrations of the homoleptic [TeX6](2-) (X=Cl, Br) anions could be well reproduced by the solid-state DFT computations and enabled a complete assignment of the Raman spectra. While the presence of cis-isomers in both [TeBr2Cl4](2-) and [TeBr4Cl2](2-) could be inferred by the computed fundamental vibrations, that of trans-isomers among the reaction products is, however, also possible. The pathway of the formation of [TeX4Y2](2-) isomers from TeX4 and Y(-) (X, Y=Cl, Br) was also explored by DFT calculations both in vacuum and in solution and indicated that both reactions afforded 80 mol% of cis-isomers and 20 mol% of trans-isomers.