NMR-Based Investigation of Hydrogen Bonding in a Dihydroanthracen-1(4 H)one from Rubia philippinensis and Its Soluble Epoxide Hydrolase Inhibitory Potential

The Synergy between Nuclear Magnetic Resonance and Density Functional Theory Calculations

This paper deals with the synergy between Nuclear Magnetic Resonance (NMR) spectroscopic investigations and DFT calculations, mainly of NMR parameters. Both the liquid and the solid states are discussed here. This text is a mix of published results supplemented with new findings. This paper deals with examples in which useful results could not have been obtained without combining NMR measurements and DFT calculations. Examples of such cases are tautomeric systems in which NMR data are calculated for the tautomers; hydrogen-bonded systems in which better XH bond lengths can be determined; cage compounds for which assignment cannot be made based on NMR data alone; revison of already published structures; ionic compounds for which reference data are not available; assignment of solid-state spectra and crystal forms; and the creation of libraries for biological molecules. In addition to these literature cases, a revision of a cage structure and substituent effects on pyrroles is also discussed.

Chemical Investigation of Tetradium ruticarpum Fruits and Their Antibacterial Activity against Helicobacter pylori

The fruit of Tetradium ruticarpum, known as Evodiae Fructus, is a traditional herbal medicine used to treat gastric and duodenal ulcers, vomiting, and diarrhea. The traditional usage can be potentially associated with the antibacterial activity of T. ruticarpum fruits against Helicobacter pylori. However, so far, the antibacterial activity of T. ruticarpum fruits and antibacterial components against H. pylori has not been investigated despite the traditional folk use. The current study was conducted to investigate the bioactive chemical components of T. ruticarpum fruits and evaluate their antibacterial activity against H. pylori. Phytochemical investigation of the EtOH extract of T. ruticarpum fruits led to the isolation and identification of nine compounds (1-9), including phellolactone (1), the absolute configuration of which has not yet been determined. The chemical structures of the isolated compounds were elucidated by analyzing the spectroscopic data from one-dimensional (1D) and two-dimensional (2D) NMR and high-resolution electrospray ionization mass spectrometry (HR-ESIMS) experiments. Specifically, the absolute configuration of compound 1 was established by the application of computational methods, including electronic circular dichroism (ECD) calculation and the NOE/ROE-based interproton distance measurement technique via peak amplitude normalization for the improved cross-relaxation (PANIC) method. In the anti-H. pylori activity test, compound 3 showed the most potent antibacterial activity against H. pylori strain 51, with 94.4% inhibition (MIC₅₀ and MIC₉₀ values of 22 and 50 μM, respectively), comparable to that of metronidazole (97.0% inhibition, and MIC₅₀ and MIC₉₀ values of 17 and 46 μM, respectively). Moreover, compound 5 exhibited moderate antibacterial activity against H. pylori strain 51, with 58.6% inhibition (MIC₅₀ value of 99 μM), which was higher than that of quercetin (34.4% inhibition) as a positive control. Based on the bioactivity results, we also analyzed the structure-activity relationship of the anti-H. pylori activity. Conclusion: These findings demonstrated that T. ruticarpum fruits had antibacterial activity against H. pylori and could be used in the treatment of gastric and duodenal ulcers. Meanwhile, the active compound, 1-methyl-2-(8E)-8-tridecenyl-4(1H)-quinolinone (3), identified herein also indicated the potential application in the development of novel antibiotics against H. pylori.

Stereocalpin B, a New Cyclic Depsipeptide from the Antarctic Lichen Ramalina terebrata

Stereocalpin B, a new cyclic depsipeptide (1), and a new dibenzofuran derivative (3), were isolated from the Antarctic lichen, Ramalina terebrata (Ramalinaceae), along with a known cyclic depsipeptide (2). The structures of new compounds were characterized by comprehensive spectrometric analyses; high-resolution fast atom bombardment mass spectrometry (HR-FABMS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Stereocalpin B (1) existed in a rotameric equilibrium, which was confirmed using nuclear Overhauser effect spectroscopy (NOESY)/exchange spectroscopy (EXSY) spectrum. Absolute configurations of the amino acid units in 1 were assigned using the advanced Marfey’s method and subsequent NOESY analysis of the 5-hydroxy-2,4-dimethyl-3-oxo-decanoic acid residue confirmed the complete stereochemistry of 1. Compounds 1-3 exhibited moderate antimicrobial activities against E. coli, with the IC₅₀ values ranging from 18–30 μg/mL. Compound 2 exhibited cell growth inhibition against HCT116 cell lines, with the IC₅₀ value of 20 ± 1.20 μM, and compounds 1 and 2 also showed potent anti-inflammatory activities against lipopolysaccharide (LPS)-induced RAW264.7 macrophages with the IC₅₀ values ranging from 5–7 μM.

Structural Studies of β-Diketones and Their Implications on Biological Effects

The paper briefly summarizes methods to determine the structure of β-diketones with emphasis on NMR methods. Density functional calculations are also briefly treated. Emphasis is on the tautomeric equilibria of β-diketones in relation to biological effects. Relevant physical parameters such as acidity and solubility are treated. A series of biologically active molecules are treated with respect to structure (tautomerism). Characteristic molecules or groups of molecules are usnic acids, tetramic and tetronic acids, o-hydroxydibenzoylmethanes, curcumines, lupulones, and hyperforines.

Configurational Assignment of a Flexible Benzo[g]isochromene Stereodiad from Rubia philippinensis and Inhibition of Soluble Epoxide Hydrolase Activity

A new benzo[g]isochromene possessing a conformationally mobile moiety was identified from Rubia philippinensis. The 2D structure was established utilizing spectrometric and spectroscopic techniques with variable temperatures. The configurational investigation of the flexible moiety was investigated utilizing contemporary NMR-combined computational tools such as DP4, direct J-DP4, and DP4 Plus. The probabilities computed from DP4 Plus analysis, featuring inclusion of an additional geometry optimization process, demonstrated more conclusive probability scores among the analyses used. The configurational assignment was also supported by compositional and molecular orbital analyses. Compound 1 inhibited soluble epoxide hydrolase (IC₅₀ = 0.6 ± 0.01 μM), an enzyme associated with cardiovascular disorders.

NMR of Natural Products as Potential Drugs

This review outlines methods to investigate the structure of natural products with emphasis on intramolecular hydrogen bonding, tautomerism and ionic structures using NMR techniques. The focus is on 1H chemical shifts, isotope effects on chemical shifts and diffusion ordered spectroscopy. In addition, density functional theory calculations are performed to support NMR results. The review demonstrates how hydrogen bonding may lead to specific structures and how chemical equilibria, as well as tautomeric equilibria and ionic structures, can be detected. All these features are important for biological activity and a prerequisite for correct docking experiments and future use as drugs.

Ergopyrone, a Styrylpyrone-Fused Steroid with a Hexacyclic 6/5/6/6/6/5 Skeleton from a Mushroom Gymnopilus orientispectabilis

A styrylpyrone-fused ergosterol derivative, ergopyrone (1), was isolated and structurally characterized from a mushroom, Gymnopilus orientispectabilis, along with five biosynthetically related metabolites (2-6). Compound 1 features an unprecedented hexacyclic 6/5/6/6/6/5 skeleton that would be formed from ergosterol and styrylpyrone precursors via [3 + 2] cycloaddition. The chemical structure of 1 was elucidated by conventional spectroscopic and spectrometric data analysis coupled with computational methods including DP4+ probability and ECD simulation and an NOE/ROE-based interproton distance measurement technique via peak amplitude normalization for the improved cross-relaxation (PANIC) method. Plausible biosynthetic pathways of 1-6 are proposed, and compound 6 significantly regulated lipid metabolism in adipocytes through the upregulation of the mRNA expression of Adipsin, Fabp4, SREBP1, and ATGL.

Paratrimerins J-Y, Dimeric Coumarins Isolated from the Stems of Paramignya trimera

Paratrimerins J-Y (1-13 and 16-18), new dimeric coumarins, were obtained from the EtOH(aq) extract of the stems of Paramignya trimera (Rutaceae) utilizing LC/MS guided isolation. The structures of the dimeric coumarins were elucidated based on 1D/2D NMR spectroscopic and HR-ESIMS data analyses. The absolute configurations of paratrimerins J-Y along with those of two known dimers paratrimerins A (14) and B (15) were established on the basis of the experimental and simulated ECD data. In addition, the absolute configurations of the sugar units of paratrimerins A, B, and J-V (1-15) were confirmed by LC/MS analysis on l-cysteine methyl ester and phenyl isothiocyanate derivatives. The variety of the absolute configurations of the dimeric diastereomers 1-15 highlighted a diversity in stereochemical outcomes following a Diels-Alder biosynthesis in P. trimera. With regard to P. trimera being a recently emerging medicinal resource for liver cancer, the dimers 1-18 were evaluated for cytotoxicity against a wide panel of human cancer cell lines. Paratrimerin W (16) was cytotoxic toward Huh7 hepatocellular carcinoma, HT1080 fibrosarcoma, and HT29 colorectal cancer cells with IC₅₀ values of 14.9, 18.4, and 22.5 μM, respectively.

Intercepted-Knoevenagel condensation for the synthesis of unsymmetrical fused-tricyclic 4H-pyrans

4H-Pyrans (4H-Pys) and 1,4-dihydropyridines (1,4-DHPs) are important classes of heterocyclic scaffolds in medicinal chemistry. Herein, an indium(III)-catalyzed one-pot domino reaction for the synthesis of highly functionalized 4H-Pys, and a model of 1,4-DHP is reported. This alternative approach to the challenging Hantzsch 4-component reaction enables the synthesis of fused-tricyclic heterocycles, and the mechanistic studies underline the importance of an intercepted-Knoevenagel adduct to achieve higher chemoselectivity towards these types of unsymmetrical heterocycles.

Accelerated degradation of cFLIPL and sensitization of the TRAIL DISC-mediated apoptotic cascade by pinoresinol, a lignan isolated from Rubia philippinensis

Plant-derived lignans have numerous biological effects including anti-tumor and anti-inflammatory activities. Screening of purified constituents of Rubia philippinensis from human glioblastoma cells resistant to TNF-related apoptosis-inducing ligand (TRAIL) has suggested that the lignan pinoresinol was a highly active TRAIL sensitizer. Here we show that treatment with nontoxic doses of pinoresinol in combination with TRAIL induced rapid apoptosis and caspase activation in many types of glioblastoma cells, but not in normal astrocytes. Analyses of apoptotic signaling events revealed that pinoresinol enhanced the formation of TRAIL-mediated death-inducing signaling complex (DISC) and complete processing of procaspase-8 within the DISC in glioblastoma cells, in which caspase-8 was inactivated. Mechanistically, pinoresinol downregulated the expression of cellular FLICE-inhibitory protein (cFLIP_L) and survivin through proteasome-mediated degradation, without affecting death receptors or downstream intracellular apoptosis-related proteins. Furthermore, the sensitization of TRAIL-mediated apoptosis by pinoresinol strictly depended on the expression level of cFLIP_L, which was regulated through de novo protein synthesis, rather than by NF-κB or p53 signaling. Taken together, our results indicate that pinoresinol facilitates DISC-mediated caspase-8 activation by targeting cFLIP_L in an early event in apoptotic signaling, which provides a potential therapeutic module for TRAIL-based chemotherapy.