NMR Data Research Articles

Two new quinoline alkaloid with neuroprotective activities from Xylaria longipes

Two new quinoline alkaloids with an α, β-unsaturated amide side chain, xylarinines A and B (1 and 2), were isolated from the ethyl acetate extracts of Xylaria longipes solid fermentation. The structures of these were primarily determined though NMR and HRESIMS data analysis. The absolute configuration of compound 1 was assigned using experimental and calculated ECD data. The neuroprotective effects of compounds 1 and 2 against glutamate-induced damage in PC12 cells were evaluated in vitro bioassay. The results demonstrated that both compounds significantly improved cell viability, inhibited apoptosis, decreased malondialdehyde (MDA) levels, increased superoxide dismutase (SOD) and glutathione (GSH) levels, and reduced intracellular reactive oxygen species (ROS) accumulation. These findings suggested that these mechanisms contribute to the neuroprotective effects of the compounds.

Sesquiterpene coumarins with anti-vitiligo and cytotoxic activities from Ferula samarkandica

Two undescribed sesquiterpene coumarins (1–2) and eight known analogues (3–10) were isolated from the roots of Ferula samarkandica Korovin, growing in Uzbekistan. Their structures were established by comprehensive spectroscopic analysis including NMR, HRESIMS, UV and IR data. The absolute configurations were determined based on ECD calculations and confirmed by single-crystal X-ray diffraction analysis. Six compounds carrying 7′-carbonyl, 3′-carbonyl and 3′-acetoxy (4, 5, 6, 7, 9, 10) demonstrated anti-vitiligo potentials, in addition to five (4, 7, 8, 9, 10) with cytotoxic effects. Evaluation of anti-vitiligo activity in B16 cells revealed that compounds 4–7 and 9 exhibited promotion effects on melanin synthesis in B16 cells more potent than the positive control 8-methoxypsoralen (8-MOP), while 5, 7, 9 and 10 could also stimulate the tyrosinase activity superior to 8-MOP. Besides, compounds 4 and 7–10 also presented certain cytotoxic activities against HeLa, HT-29 and A549 cell lines, wherein 8 displayed a significant cytotoxicity against HT-29 cells with an IC50 value of 8.33 ± 0.34 μM.

Albifimbrins A and B, a pair of epimeric tetrahydrofuran-containing linear polyketide derivatives from the marine-derived fungus Albifimbria verrucaria CD1-4

A pair of new epimeric polyketides, named albifimbrins A and B (1 and 2), were isolated from the cultures of the shellfish-derived fungus Albifimbria verrucaria CD1–4. Their structures were determined by extensive spectroscopic analysis including HR-MS, 1D and 2D NMR data, together with the CD exciton chirality method. Compounds 1 and 2 possess unusual tetrahydrofuran moiety in their linear molecule structures. The antimicroalgal assay indicated that compounds 1 and 2 shown moderate inhibitory activities against marine harmful microalgae, Prorocentrum donghaiense, Amphidinium carterae and Heterocapsa circulariaquama.

Synthesis and Biological Evaluation of 3-(2-Benzoyl-4-chlorophenyl)-4H-spiro [indole-3,2-[1,3]thiazolidine]-2,4(1H)- dione Derivatives for Anti-tubercular and Antimicrobial Activities

Objectives: To synthesize a new scaff fold of 3'-(2-Benzoyl-4-chlorophenyl)-4'H-spiro [indole-3,2'-[1,3] thiazolidine]-2,4'(1H)-dione derivatives and to assess the compounds for anti-tubercular and antimicrobial activities. Methods : A new series of 3'-(2-Benzoyl-4-chlorophenyl)-4'H-spiro [indole-3,2'- [1,3] thiazolidine]-2,4'(1H)-dione derivatives were prepared by synthesizing schiff’s bases followed by condensing schiff base with 2-mercaptopropanoic acid in the presence of zinc chloride. Synthesized compounds were characterized by IR, NMR and Mass spectral data. Their antimicrobial, antitubercular and also docking simulations were evaluated. Findings : Compound 3c (floro substituent) showed potent activity against Mycobacterium tuberculosis H37Rv with MIC value of 3.125 µg/ml when compared with standard Isoniazid. Compound 3c, 3d and 3f displayed better antimicrobial activity against used bacterial and fungal species with MIC range of 3-20µg/ml comparable to standard drugs ciprofloxacin and ketoconazole respectively. In silico studies revealed that compound 3c, 3f and 3d had a better binding affinity with M. tuberculosis enoyl-CoA hydratase EchA6 with ΔG values of -9.6kcal/mol, -9.4kcal/mol, and -8.6kcal/mol respectively comparable to isoniazid of -5.4kcal/mol. Compound 3c, 3f and 3d also displayed good binding affinity with DNA gyrase and lanosterol methylase. Novelty : Introducing benzoyl moiety to the thiazolidine ring potentiates the antitubercular and antimicrobial activity of spiro indole derivatives. Keywords: AntiTB, Antimicrobial, Molecular Docking, Spiro indole, Thiazolidine

Diterpenoids from Acanthopanacis Cortex and their anti-inflammatory activity studies.

Acanthopanacis Cortex (A.-C) with a long history of more than1000years, has been used to treat rheumatism effectively. Nineteen diterpenoids have been isolated from A.-C, including six new compounds (1-6). Among them, compounds 7, 9-11, 13, and 17 were discovered from A.-C for the first time. The structures of 1-6 were determined by analyzing their NMR data and comparing their experimental and calculated electronic circular dichroism spectra. Moreover, the single-crystal X-ray diffraction data of 1, 2, 8, and 14 were provided. The anti-inflammatory activity of 1-5 and 7-18 on neutrophil elastase, cyclooxygenase-1 (COX-1), and cyclooxygenase-2 (COX-2) has been studied in vitro, and the results showed that 15 had almost no inhibitory effects on COX-1 at 200μM but a significant activity against COX-2 with an IC50 of 0.73±0.006 μΜ. It indicated that compound 15 can provide valuable information for the design of selective COX-2 inhibitors.

Helical twists and β-turns in structures at serine-proline sequences: Stabilization of cis-proline and type VI β-turns via C-H/O interactions.

Structures at serine-proline sites in proteins were analyzed using a combination of peptide synthesis with structural methods and bioinformatics analysis of the PDB. Dipeptides were synthesized with the proline derivative (2S,4S)-(4-iodophenyl)hydroxyproline [hyp(4-I-Ph)]. The crystal structure of Boc-Ser-hyp(4-I-Ph)-OMe had two molecules in the unit cell. One molecule exhibited cis-proline and a type VIa2 β-turn (BcisD). The cis-proline conformation was stabilized by a C-H/O interaction between Pro C-Hα and the Ser side-chain oxygen. NMR data were consistent with stabilization of cis-proline by a C-H/O interaction in solution. The other crystallographically observed molecule had trans-Pro and both residues in the PPII conformation. Two conformations were observed in the crystal structure of Ac-Ser-hyp(4-I-Ph)-OMe, with Ser adopting PPII in one and the β conformation in the other, each with Pro in the δ conformation and trans-Pro. Structures at Ser-Pro sequences were further examined via bioinformatics analysis of the PDB and via DFT calculations. Ser-Pro versus Ala-Pro sequences were compared to identify bases for Ser stabilization of local structures. C-H/O interactions between the Ser side-chain Oγ and Pro C-Hα were observed in 45% of structures with Ser-cis-Pro in the PDB, with nearly all Ser-cis-Pro structures adopting a type VI β-turn. 53% of Ser-trans-Pro sequences exhibited main-chain COi•••HNi+3 or COi•••HNi+4 hydrogen bonds, with Ser as the i residue and Pro as the i + 1 residue. These structures were overwhelmingly either type I β-turns or N-terminal capping motifs on α-helices or 310-helices. These results indicate that Ser-Pro sequences are particularly potent in favoring these structures. In each, Ser is in either the PPII or β conformation, with the Ser Oγ capable of engaging in a hydrogen bond with the amide N-H of the i + 2 (type I β-turn or 310-helix; Ser χ1 t) or i + 3 (α-helix; Ser χ1 g+) residue. Non-proline cis amide bonds can also be stabilized by C-H/O interactions.

Polyhydroxylated Sirostanol Saponins from the Rhizomes of Paris dulongensis.

Three new polyhydroxylated spirostanol steroidal saponins, dulongenosides B-D (2-4), along with 14 known compounds, dulongenoside A (1), padelaoside B (5), parisyunnanoside G (6), polyphyllin D (7), ophiopogonin C' (8), formosanin C (9), dioscin (10), paris saponin VII (11), paris H (12), parisyunnanoside I (13), protodioscin (14), proprotogracillin (15), crustecdysone (16), and stigmasterol-3-O-β-d-glucopyranoside (17), were isolated from the rhizomes of Paris dulongensis (Melanthiaceae). Their chemical structures were elucidated based on extensive analyses of NMR and MS data and acidic hydrolyses. The isolates were evaluated for their cytotoxicity to five human cancer cell lines (HL-60, SW480, MDA-MB-231, A549, and A549/Taxol) and the normal human bronchial epithelial cell line BEAS-2B by the MTS test. Compounds 7-12 and 14 showed cytotoxic activity, with IC50 values ranging from 0.20 to 4.35 μM. Proprogracillin selectively inhibited A549(IC50 = 0.58 μM) and A549/Taxol (IC50 = 0.74 μM) cells, with no significant cytotoxic activity against HL-60, SW480, MDA-MB-231, or BEAS-2B cells, with IC50 values greater than 40 μM.

Flavonoids and triterpenoids isolated from the ethyl acetate extract of Maytenus quadrangulata leaves.

The new flavonoid 4'-O-methylepigallocatechin 5-O-β-D-glucopyranoside (1), along with four known triterpenes (2-4), a steroid (6), and a flavonoid (7) were isolated from the ethyl acetate extract of Maytenus quadrangulata leaves. The chemical structures of the isolated compounds were determined through analysis of 1D NMR (1H and 13C) spectroscopic data, in addition to 2D NMR and spectrometric (MS) data for compound 1. This is the first report of the isolation of compounds 3-O-β-D-glucosyl-β-sitosterol (6) and 4'-O-methylepigallocatechin (7) from this species. Compounds 1 and 7 were evaluated against the bacteria Staphylococcus aureus and Klebsiella pneumoniae, but neither exhibited activity even at the highest concentration tested.

Allosteric coupling asymmetry mediates paradoxical activation of BRAF by type II inhibitors.

The type II class of RAF inhibitors currently in clinical trials paradoxically activate BRAF at subsaturating concentrations. Activation is mediated by induction of BRAF dimers, but why activation rather than inhibition occurs remains unclear. Using biophysical methods tracking BRAF dimerization and conformation, we built an allosteric model of inhibitor-induced dimerization that resolves the allosteric contributions of inhibitor binding to the two active sites of the dimer, revealing key differences between type I and type II RAF inhibitors. For type II inhibitors the allosteric coupling between inhibitor binding and BRAF dimerization is distributed asymmetrically across the two dimer binding sites, with binding to the first site dominating the allostery. This asymmetry results in efficient and selective induction of dimers with one inhibited and one catalytically active subunit. Our allosteric models quantitatively account for paradoxical activation data measured for 11 RAF inhibitors. Unlike type II inhibitors, type I inhibitors lack allosteric asymmetry and do not activate BRAF homodimers. Finally, NMR data reveal that BRAF homodimers are dynamically asymmetric with only one of the subunits locked in the active αC-in state. This provides a structural mechanism for how binding of only a single αC-in inhibitor molecule can induce potent BRAF dimerization and activation.

Allosteric coupling asymmetry mediates paradoxical activation of BRAF by type II inhibitors

Allosteric coupling asymmetry mediates paradoxical activation of BRAF by type II inhibitors

Anti-inflammatory lindenane sesquiterpenoid dimers from the roots of Chloranthus holostegius var. trichoneurus.

Two new lindenane-type sesquiterpenoid dimers, chlotrichenes C and D (1 and 2) together with five known lindenane-type sesquiterpenoid dimers (3-7) were isolated from the roots of Chloranthus holostegius var. trichoneurus, a famous natural medicine named as "Sikuaiwa" for subduing swellings and relieving pain. The structures including absolute configuration were elucidated by their 1D and 2D NMR, HRESIMS, and ECD data. Compounds 1 and 2 were classical [4 + 2] lindenane-type sesquiterpenoid dimers that differed from known analogs in oxidation profile, side chain profile, and double bond position. The new isolates and compound 3 exhibited significant inhibitory activity on IL-1β production (IC50: 1-15μM) in LPS-induced THP-1 cells and other compounds exhibited inhibitory activity on NO production in LPS-induced RAW 264.7 cells (IC50: 24-33μM).

Adamantylated Calix[4]arenes Bearing CuAAC-Ready 2-Azidoethyl or Propargyl Functionalities

1,3-Alternate calix[4]arenes were prepared, having bulky adamantyl groups in the p-positions of all four aromatic units of the macrocycles and pairs of propargyl or 2-azidoethyl groups alternating with n-propyl groups at the phenol oxygen atoms. The step-wise syntheses were carried out through a selective distal alkylation of the parent p-adamantylcalix[4]arene with propargyl bromide or 1,2-dibromoethane, resulting in calix[4]arenes bearing pairs of propargyl or 2-bromoethyl groups at their narrow rims. The bromine atoms were replaced by azide groups, and then both calix[4]arene diethers were exhaustively alkylated at the remaining OH-groups with 1-iodopropane under stereoselective conditions to fix the macrocycles in an 1,3-alternate shape. The structures of the prepared p-adamantylcalix[4]arenes were confirmed by NMR and HRMS data, and, for the 1,3-alternate dipropargyl ether, the X-ray diffraction data were also collected. Preliminary data on the reactivity of the prepared calixarenes under the CuAAC conditions suggested a strong steric hampering created by the adamantane units nearby the reacting alkyne or azide groups that affected the outcome of the two-fold cycloaddition involving the calixarene bis(azides) or bis(alkynes) as complementary partners.

Retrobisabolane A, a Novel Bisabolane-Derived Sesquiterpenoid Isolated from Deep-Sea-Derived Fungus Retroconis fusiformis MCCC 3A00792.

One novel bisabolane-derived sesquiterpenoid retrobisabolane A (1), featuring a methyl group location at the C-4 position instead of C-3 in the bisabolanes, and a known ester-substituted eremophilane-type sesquiterpenoid cryptosphaerolide (2), along with three known indole alkaloids (3-5) were discovered from the fermented cultures of a deep-sea-derived fungus Retroconis fusiformis MCCC 3A00792. The planar structure of new compound 1 was determined by extensive analysis of the NMR and HRESIMS spectra. The relative and absolute configurations of 1 were resolved by the coupling constant (J), calculation of ECD and NMR spectra, and the DP4+ probability analysis of the 1H and 13CNMR data. Interestingly, retrobisabolane A was the new subclass of bisabolanes bearing a methyl group linkage at C-4 instead of C-3 position. Three human cancer cell lines (Hela, AGS, and BIU-87) were subjected to evaluate the cytotoxic activities of compounds 1-5. As a result, compound 2 exhibited significant inhibitory activities against three cell lines with IC50 values ranging from 9.95 to 18.77 μM.

New alkaloids from Stemona tuberosa and structural revision of tuberostemonols P and R

Three Stemona alkaloids named stemotuberines A–C (1–3) with unique C17N frameworks, presumably formed by elimination of the C-11–C-15 lactone ring of the stichoneurine skeleton, were isolated from the roots of Stemona tuberosa. Their structures were elucidated by spectroscopic analysis, X-ray diffraction, and computational methods. Compounds 2 and 3 showed inhibition (IC50 values of 37.1 and 23.2 μM, respectively) against LPS-induced nitric oxide production in RAW 264.7 cells. In addition, concern was expressed about the reported plant origin (S. sessilifolia) of the recently described alkaloids tuberostemonols O–R (4–7), which should be S. tuberosa. NMR calculations indicated structural misassignment of these compounds except for 6. Isolation of tuberostemonol P (5) from our material of S. tuberosa allowed for a close examination of the spectroscopic data leading to the revised structure 5a. Tuberostemonol R (7) was found to have identical 1H and 13C NMR data to the well-known alkaloid croomine, and therefore its structure including relative stereochemistry must be revised as 7a.

New 19(10 → 9)abeo-euphane-type triterpenoids from Trichilia dregeana leaves and NO production inhibitory activities

Phytochemical investigation of the EtOAc soluble fraction from leaves of Trichilia dregeana Sond. (Meliaceae) afforded naturally rare four new pentacyclic triterpenoids (1–4), together with five known pentacyclic analogs (5–8, and 11) and two steroids (9 and 10). Their structures were elucidated by extensive spectroscopic techniques such as 1D and 2D NMR and HRESIMS data analyses. The absolute configuration of 1 was determined by using the single-crystal X-ray diffraction analysis. The nitric oxide (NO) production inhibitory assay indicated that the EtOAc fraction as well as 4 and 7 inhibited the NO production in lipopolysaccharide (LPS)-stimulated RAW264.7 macrophage cells with the IC50 values of 83.53 μg/mL and 81.31 and 85.71 μM, respectively. Compounds 1–4 are rare 19(10 → 9)abeo-euphane-type triterpenoids bearing a 3,10-ether bridge. To the best of our knowledge, this study is the first isolation of triterpenoids with the 3,10-ether bridge in their skeleton from the genus Trichilia, providing new insights into the chemodiversity of the terpenoids in T. dregeana.

Invisible photochromism and on-off switch based on thiophene-imidazole fused derivatives: Synthesis, properties and applications

Three novel diarylethene fluorescent molecules based on a thiophene-imidazole core have been successfully synthesized. Their photophysical properties, including photocyclization and ions response characteristics, as well as quantum chemical calculations were systematically investigated. All compounds exhibited significant invisible photochromism upon photocyclization, resulting in remarkable fluorescence “turn-off” properties. This phenomenon can be attributed to photoisomerization, specifically the transition from the open-ring isomer to the closed-ring isomer during this process, which was confirmed by 1H NMR data analysis. Moreover, AT-DPIo demonstrated high selectivity toward I− with pronounced changes in absorption from colorless to yellow and fluorescence from bright yellow to dark, enabling a limit of detection for I− at 9.75 × 10−7 mol L−1. These exceptional sensing properties make it suitable for rapid “naked-eye” detection of I− using test strips.

Synthesis and in silico inhibitory action studies of azo-anchored imidazo[4,5-b]indole scaffolds against the COVID-19 main protease (Mpro)

The present work elicits a novel approach to combating COVID-19 by synthesizing a series of azo-anchored 3,4-dihydroimidazo[4,5-b]indole derivatives. The envisaged methodology involves the l-proline-catalyzed condensation of para-amino-functionalized azo benzene, indoline-2,3-dione, and ammonium acetate precursors with pertinent aryl aldehyde derivatives under ultrasonic conditions. The structures of synthesized compounds were corroborated through FT-IR, 1H NMR, 13C NMR, and mass analysis data. Molecular docking studies assessed the inhibitory potential of these compounds against the main protease (Mpro) of SARS-CoV-2. Remarkably, in silico investigations revealed significant inhibitory action surpassing standard drugs such as Remdesivir, Paxlovid, Molnupiravir, Chloroquine, Hydroxychloroquine (HCQ), and (N3), an irreversible Michael acceptor inhibitor. Furthermore, the highly active compound was also screened for cytotoxicity activity against HEK-293 cells and exhibited minimal toxicity across a range of concentrations, affirming its favorable safety profile and potential suitability. The pharmacokinetic properties (ADME) of the synthesized compounds have also been deliberated. This study paves the way for in vitro and in vivo testing of these scaffolds in the ongoing battle against SARS-CoV-2.

Molecular interactions between a diphenyl scaffold and PED/PEA15: Implications for type II diabetes therapeutics targeting PED/PEA15 – Phospholipase D1 interaction

In a recent study, we have identified BPH03 as a promising scaffold for the development of compounds aimed at modulating the interaction between PED/PEA15 (Phosphoprotein Enriched in Diabetes/Phosphoprotein Enriched in Astrocytes 15) and PLD1 (phospholipase D1), with potential applications in type II diabetes therapy. PED/PEA15 is known to be overexpressed in certain forms of diabetes, where it binds to PLD1, thereby reducing insulin-stimulated glucose transport. The inhibition of this interaction reestablishes basal glucose transport, indicating PED as a potential target of ligands capable to recover glucose tolerance and insulin sensitivity. In this study, we employ computational methods to provide a detailed description of BPH03 interaction with PED, evidencing the presence of a hidden druggable pocket within its PLD1 binding surface. We also elucidate the conformational changes that occur during PED interaction with BPH03. Moreover, we report new NMR data supporting the in-silico findings and indicating that BPH03 disrupts the PED/PLD1 interface displacing PLD1 from its interaction with PED. Our study represents a significant advancement toward the development of potential therapeutics for the treatment of type II diabetes.

One Pot Synthesis and Biological Activity Studies of New Spirooxindoles.

This article reports one-pot synthesis of ten novel spirooxindoles using 5-methyl-2-thiohydantoin, isatin derivatives, and malononitrile in good to high yields (65-90 %). The structures of the synthesized compounds were deduced by 1H-NMR, 13C NMR, FT-IR, and Mass spectral data. The antibacterial activity of the compounds was evaluated against two Gram-positive bacteria (Staphylococcus aureus and Bacillus subtilis) and two Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa) based on the Kirby-Bauer method. According to the obtained data, the synthesized compounds show more activity against Gram-positive bacteria than Gram-negative bacteria. Also, the antioxidant activity of these compounds was measured using the DPPH radical scavenging test method, which showed good to excellent activity (59.65-94.03 %). Among them, the chlorinated derivatives (4 f-j) exhibited more antioxidant activity (84.85-94.03 %) than the other compounds (4 a-e) (56.65-74.4 %) and even ascorbic acid as a standard antioxidant compound (82.3 %).

Phosphorus–nitrogen compounds: part 75—design, synthesis, stereogenic and conformational properties of chiral dispiro(N/N)cyclotriphosphazenes: structural analysis and photophysical and bioactivity studies

AbstractMultiheterocyclic inorganic–organic hybrid phosphazenes have robust inorganic ring systems with the stabilities of the phosphorus nitrogen skeleton and many different substituents bonded to the P atoms. In present study, unsymmetrical dispirocyclotriphosphazenes were prepared due to their potential to depict steric hindrance and electronic rearrangement in creating permanent chirality for certain conformational and configurational isomers. These isomers may have an effect on DNA bindings and activitiy against selected fungi and bacteria, remarkably. Herein, tetrachlorocyclotriphosphazenes (1 and 2) were reacted with 9-ethyl-N-methyl-3-carbazolyl-1,2-diaminoethane (3), 9-ethyl-N-ethyl-3-carbazolyl-1,2-diaminoethane (4) and 9-ethyl-N-methyl-3-carbazolyl-1,3-diaminopropane (5) to give the new unsymmetrical cis/trans-dispirocyclotriphosphazenes, [(ClBz/BzSpiro-6)R1(N3P3)(CzSpiro-n)R2]Cl2 (Cz: Carbazolyl; R1:Me R2:Me or Et; n = 5 or 6; trans 6a–11a and cis 6b–11b). Characterizations, chiralities, and photophysical and biological properties of the new compounds were examined. The molecular and crystal structures of cis-6b, cis-7b, trans-9a, cis-9b, trans-10a and cis-10b were determined by single crystal X-ray crystallography. The chiralities of these compounds with unsymmetrical spiro-architectures were confirmed by X-ray crystallography. These results were further proven by 31P NMR data recorded with the addition of a chiral solvent (CSA). Additionally, circular dichroism (CD) spectra also supported the results. Photophysical measurements indicate that these compounds show emission with lifetimes of approximately 5.6–5.9 ns. In addition, the bioactivities of some isomers were found to be different and quite high against some bacterial and yeast strains. Trans-8a was very active against B. cereus (MBC = 78.1 µM), while cis-6b, trans-9a and cis-9b were very active against the pathogenic yeast C. albicans (MFC = 156.3 µM). Graphical abstract