Experimental and computational approaches to reveal the potential of Ficus deltoidea leaves extract as α-amylase inhibitor

Ficus deltoidea leaves extract are known to have good therapeutic properties such as antioxidant, anti-inflammatory and anti-diabetic. We showed that 50% ethanol-water extract of F. deltoidea leaves and its pungent compounds vitexin and isovitexin exhibited significant (p < 0.05) α-amylase inhibition with IC₅₀ (vitexin: 4.6 μM [0.02 μg/mL]; isovitexin: 0.06 μg/mL [13.8 μM] and DPPH scavenging with IC₅₀ (vitexin: 92.5 μM [0.4 μg/mL]; isovitexin: 0.5 μg/mL [115.4 μM]). Additionally, molecular docking analysis confirmed that vitexin has a higher binding affinity (-7.54 kcal/mol) towards α-amylase compared to isovitexin (?5.61 kcal/mol). On the other hand, the molecular dynamics findings showed that vitexin-α-amylase complex is more stable during the simulation of 20 ns when compared to the isovitexin-α-amylase complex. Our results suggest that vitexin is more potent and stable against α-amylase enzyme, thus it could develop as a therapeutic drug for the treatment of diabetes.     

Study of 5-azidomethyl-8-hydroxyquinoline structure by X-ray diffraction and HF–DFT computational methods

5-Azidomethyl-8-hydroxyquinoline has been synthesized and characterized using IR, ¹H and ¹³C NMR spectroscopic methods. Thermal analysis revealed no solid-solid phase transitions. The crystal structure of this compound was refined by Rietveld method from powder X-ray diffraction data at 295 K. The single- crystal structure of the compound at 260 K was solved and refined using SHELX 97 program. According to the data obtained by both methods, the structure of the compound is monoclinic, space group P2₁/c, with Z = 4 and Z' = 1. For the single crystal at 260 K, a = 12.2879 (9) Å, b = 4.8782 (3) Å, c = 15.7423 (12) Å, β=100.807(14)°. Mechanisms of deformation resulting from intra- and intermolecular interactions, such as hydrogen bonding, induced slight torsions in the crystal structure. The optimized molecular geometry of 5-azidomethyl-8-hydroxyquinoline in the ground state is calculated using density functional theory (B3LYP) and Hartree-Fock (HF) methods with the 6-311G(d,p) basis set. The calculated results show good agreement with experimental values. Energy gap of the molecule was found using HOMO and LUMO calculation which reveals that charge transfer occurs within the molecule.

     

5-epi-Deoxyrhamnojirimycin is a potent inhibitor of an α-l-rhamnosidase: 5-epi-deoxymannojirimycin is not a potent inhibitor of an α-d-mannosidase

Whereas deoxyrhamnojirimycin (LRJ) 1 shows no significant inhibition of naringinase (an α-l-rhamnosidase), its C-5 epimer 2 is a potent and specific inhibitor of the enzyme and demonstrates the value of unambiguous chemical synthesis of such materials in the evaluation of their biological properties. In contrast, moderately weak inhibition towards an α-d-mannosidase is shown by both deoxymannojirimycin (DMJ) 5 and its C-5 epimer 6. Mimics of l-rhamnose which are recognised by enzymes that synthesise or process l-rhamnose may inhibit either the biosynthesis of the sugar or its incorporation into mycobacterial cell walls, providing new strategies for the treatment of diseases such as tuberculosis and leprosy. Molecular modelling studies provide a rationale for the surprisingly potent activity of the C-5 epimer 2 compared with LRJ 1 and support a general hypothesis that potent piperidine glycosidase inhibitors mimic the ⁴H₃ conformation of the relevant glycopyranosyl cation intermediate.     

The lithium–thiophene interaction: a critical study using highly correlated electronic structure approaches of quantum chemistry

The fundamental multicentric interaction of a lithium atom with a single thiophene ring is addressed. A systematic study of the interaction energy (IE) and geometry for the Li–T charge-transfer complex is done at the MP2 and CCSD(T) levels using increasingly large basis sets up to aug-cc-pVQZ (AVQZ). Basis set superposition errors (BSSE) are evaluated and shown to have a major impact on the value of the IE. The Fixed-Node Diffusion Monte Carlo (FN-DMC) method is used as an alternative basis-set-free approach to obtain what is likely to be the most accurate estimate of the IE obtained so far. While counterpoise-corrected MP2/AVQZ and CCSD(T)/AVTZ interaction energies are found to be ?3.8 and ?7.5 kcal/mol, the FN-DMC method yields +1.3 ± 1.7 kcal/mol. The slow convergence of the ab initio IE (and some key structural parameters) with respect to basis set quality and the discrepancy with the FN-DMC result is discussed. A visualization of the electron pairing using the electron pair localization function (EPLF) for the Li-doped versus undoped thiophene is also presented.     

Preparation of core–shell composite polymer particles by a novel heterocoagulation based on hydrophobic interaction

Submicron-sized cationic polystyrene shell particles with active ester groups were effectively self-assembled on hydrophobic surfaces of cross-linked polystyrene (PST) particles, uncharged core particles with ca. 8.5-µm diameter in aqueous systems. The hydrophobic interactions between the shell particles and core particles play a key role in heterocoagulation. The resulting heterocoagulates were highly physically stable in water, and the morphology was controlled by several factors including the solid content of latex, self-assembling time, and electrolyte concentration. Composite polymer particles with a core–shell structure were successfully obtained from the heterocoagulates by heat treatment for 3 h at a temperature above the glass transition temperature (T_g) of the cationic polymer shell particles.     

Discovery of Elaphuri Davidiani Cornu–specific peptide biomarkers by peptidomics analysis–based method

Elaphuri Davidiani Cornu (EDC) is the antler of the male Père David's deer, which has been reported to have multiple biological activities, and its use as a traditional Chinese medicine (TCM) in China has been known for thousands of years. However, EDC is difficult to distinguish from other related species–derived antlers in powder or extract form in TCM clinic use, such as Cervus elaphus Cornu (CEC) and Cervus nippon Cornu (CNC), both derived from Cervidae and easily confused with EDC. In this study, a strategy using peptidomics combined with mathematics set analysis was used to identify EDC-specific peptide biomarkers, and four specific peptide biomarkers (Pep-E1–E4) were identified and validated. Pep-E1, Pep-E3, and Pep-E4 could be exclusively detected in EDC samples, with relative peak areas of 0.298 ± 0.060, 0.039 ± 0.015, and 0.037 ± 0.008, whereas Pep-E2 showed relative peak area of 0.516 ± 0.101 in EDC, 0.132 ± 0.026 in CEC, and 0.136 ± 0.047 in CNC samples, respectively. These four peptides are applicable to distinguish EDC from CEC and CNC, which is of great significance for the quality control of EDC.     

Mimicking anaesthetic-receptor interaction: a combined spectroscopic and computational study of propofol···phenol

Propofol is a general anaesthetic that exerts its action by interaction with the GABA(A) receptor. Crystallographic studies suggest that there is a direct interaction between propofol and the phenolic residue of a tyrosine in the channel. In this study we create propofol···phenol clusters by their co-expansion in jets. The complex is probed using a set of mass-resolved spectroscopic strategies: 2-color REMPI, UV/UV hole-burning, IR/UV double resonance and the novel technique IR/IR/UV triple resonance. The existence of at least six different isomers in the expansion is demonstrated. All the isomers are stabilized by interactions between their aromatic rings. Additionally, in some conformers the OH moieties form hydrogen bonds in some of the isomers, with propofol and phenol alternating their donor-acceptor roles, while in others the -OH···OH angle points to a dipole-dipole interaction. Interpretation of the data in the light of dispersion-corrected DFT calculations shows that shallow barriers separate all the isomers, both in the ground and excited electronic states. Comparison of the structures of the complex with the X-ray diffraction data is also offered.     

JR 400–NaAOT interaction: a detailed thermodynamic study of polymer–surfactant interaction bearing opposite charges

The present study entails interaction between the cationic polymer N,N-dimethylhydroxyethyl cellulose (JR 400) and the double-tailed anionic surfactant Na-bis-2-ethyhexylsulphosuccinate (NaAOT). This oppositely charged polymer and surfactant are expected to cause coacervation and precipitation; hence, we have observed formation of thick solution similar to diluted gel at [JR 400]?~?0.01 and 0.10 %?w/v in aqueous solution. Viscometry, conductometry, tensiometry, and microcalorimetry techniques are used to monitor the interaction process. The results are explained in the light of both intrachain and interchain linking by way of NaAOT reverse micelle formation. Adsorption of NaAOT monomers onto the charged side chains of the polymer shields interchain electrostatic repulsion, leading to the formation of hydrophobic microdomains and microscopic heterogeneity in the solution. The morphologies of the domains depend on the level of addition of NaAOT in the system. The different stages of physiochemical changes that arise in solution have been identified by the use of different techniques, and correlations of the results have been attempted in terms of pragmatic models.     

Pharmacokinetic studies of a novel tubulin inhibitor SK1326 in rat plasma by UPLC–MS/MS

A sensitive method for quantitation of SK1326 in rat plasma has been established using ultra-performance liquid chromatography–electrospray ionization tandem mass spectrometry (UPLC–ESI/MS/MS). SK1326 and the internal standard (tramadol) in plasma sample were extracted using acetonitrile. A centrifuged upper layer was then evaporated and reconstituted with a mobile phase of 0.5% formic acid–acetonitrile (35:65, v/v). The reconstituted samples were injected into a C₁₈ reversed-phase column. Using MS/MS in the multiple reaction monitoring mode, SK1326 and tramadol were detected without severe interference from the rat plasma matrix. SK1326 produced a protonated precursor ion ([M + H]⁺) at m/z 432.3 and a corresponding product ion at m/z 114.4. The internal standard produced a protonated precursor ion ([M + H]⁺) at m/z 264.4 and a corresponding product ion at m/z 58.1. Detection of SK1326 in rat plasma by the UPLC–ESI/MS/MS method was accurate and precise with a quantitation limit of 1.0 ng/mL. The validation, reproducibility, stability and recovery of the method were evaluated. The method has been successfully applied to pharmacokinetic studies of SK1326 in rat plasma. The pharmacokinetic parameters of SK1326 were evaluated after intravenous (at a dose of 10 mg/kg) and oral (at a dose of 20 mg/kg) administration of SK1326 in rats. After oral administration (20 mg/kg) of SK1326, the F (fraction absorbed) value was ~77.1%.     

Analysis of amprolium by hydrophilic interaction liquid chromatography–tandem mass spectrometry

We present a fast liquid chromatography–tandem mass spectrometry (LC–MS/MS) method for the analysis of the coccidiostat amprolium in food samples. Tandem mass spectrometry in a triple quadrupole was used for quantitative purposes, and the information from multiple-stage mass spectrometry in an ion-trap mass analyzer contributed to fragmentation studies. Hydrophilic interaction liquid chromatography (HILIC) in a Fused-Core™ column using isocratic elution (acetonitrile:formic acid/ammonium formate buffer pH 4, 50 mM (60:40)) successfully analyzed this compound in less than 3 min. The HILIC system was coupled to heated electrospray-MS/MS using highly selective-selected reaction monitoring (H-SRM) to improve sensitivity and selectivity for the analysis of amprolium, after a simple sample treatment based on an “extract and shoot” strategy. Accurate mass measurements were performed to identify the interfering compound responsible for causing matrix ion enhancement in the signal of amprolium. The addition of l-carnitine (the interfering compound) (1 μg L⁻¹) to standards and sample extracts allowed the use of the external calibration method for quantitative purposes. The LC–MS/MS (H-SRM) method showed good precision (relative standard deviation, RSD, lower than 13%), accuracy and linearity and allowed the determination of amprolium down to the ppb level (LODs between 0.1 and 0.6 μg kg⁻¹).     

Discovery of a potent and highly β1 specific proteasome inhibitor from a focused library of urea-containing peptide vinyl sulfones and peptide epoxyketones

Syringolins, a class of natural products, potently and selectively inhibit the proteasome and show promising antitumour activity. To gain insight in the mode of action of syringolins, the ureido structural element present in syringolins is incorporated in oligopeptide vinyl sulfones and peptide epoxyketones yielding a focused library of potent new proteasome inhibitors. The distance of the ureido linkage with respect to the electrophilic trap strongly influences subunit selectivity within the proteasome. Compounds 13 and 15 are β5 selective and their potency exceeds that of syringolin A. In contrast, 5 may well be the most potent β1 selective compound active in living cells reported to date.     

Study of tungstate–protein interaction in human serum by LC–ICP-MS and MALDI-TOF

Oral administration of sodium tungstate is an effective treatment for type 1 and 2 diabetes in animal models; it does not incur significant side effects, and it may constitute an alternative to insulin. However, the mechanism by which tungstate exerts its observed metabolic effects in vivo is still not completely understood. In this work, serum-containing proteins which bind tungstate have been characterized. Size exclusion chromatography (SEC) coupled to inductively coupled plasma mass spectrometry (ICP-MS) with a Phenomenex Bio-Sep-S 2000 column and 20 mM HEPES and 150 mM NaCl at pH 7.4 as the mobile phase was chosen as the most appropriate methodology to screen for tungsten–protein complexes. When human serum was incubated with tungstate, three analytical peaks were observed, one related to tungstate–albumin binding, one to free tungstate, and one to an unknown protein binding (MW higher than 300 kDa). Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometric analysis of the tungsten-containing fractions collected from SEC–ICP-MS chromatograms, after desalting and preconcentration processes, confirmed the association of tungstate with albumin and the other unknown protein. Figure SEC-ICP-MS // MALDI-TOF     

Metabolite profiling of arginase inhibitor activity guided fraction of Ficus religiosa leaves by LC–HRMS

Cardiovascular disease is one of the major causes of deaths worldwide. Increased arginase activity is associated with cardiovascular disease. The literature shows that plants are a good source of arginase inhibitors. Hence in the present work arginase inhibitor activity is studied from Ficus religiosa leaves. A fine powder of F. religiosa leaves was serially extracted in various solvents, viz. hexane, chloroform, ethyl acetate and methanol. Out of those four solvent extracts, the one showing highest arginase inhibitor activity was loaded onto the column for further fractionation. Among the collected fractions, the one showing the highest activity was subjected to identification of metabolites by using LC–HRMS. Total compounds including acipimox, edoxudine, levulinic acid, hydroxyhydroquinone, ramiprilglucuronide, berberine, antimycin A, swietenine and some short peptides were identified from the fraction showing the highest arginase inhibitory activity. Identification of these metabolites from F. religiosa and their biological importance may help to promote its use as medicinal plant. Further purification and characterization of therapeutically novel molecules will be the subject of future work.     

The intricacies of the stacking interaction in a pyrrole–pyrrole system

Extensive calculations of potential energy surfaces for parallel-displaced configurations of pyrrole–pyrrole systems have been carried out by the use of a dispersion-corrected density functional. System geometries associated with the energy minima have been found. The minimum interaction energy has been calculated as ?5.38 kcal/mol. However, bonding boundaries appeared to be relatively broad, and stacking interactions can be binding even for ring centroid distances larger than 6 Å. Though the contribution of the correlation energy to intermolecular interaction in pyrrole dimers appeared to be relatively small (around 1.6 smaller than it is in a benzene–benzene system), this system’s minimum interaction energy is lower than those calculated for benzene–benzene, benzene–pyridine and even pyridine–pyridine configurations. The calculation of the charges and energy decomposition analysis revealed that the specific charge distribution in a pyrrole molecule and its relatively high polarization are the significant source of the intermolecular interaction in pyrrole dimer systems.     

Discovery of Hexagonal Structured Pd–B Nanocrystals

We report on hexagonal close-packed (hcp) palladium (Pd)–boron (B) nanocrystals (NCs) by heavy B doping into face-centered cubic (fcc) Pd NCs. Scanning transmission electron microscopy–electron energy loss spectroscopy and synchrotron powder X-ray diffraction measurements demonstrated that the B atoms are homogeneously distributed inside the hcp Pd lattice. The large paramagnetic susceptibility of Pd is significantly suppressed in Pd–B NCs in good agreement with the reduction of density of states at Fermi energy suggested by X-ray absorption near-edge structure and theoretical calculations.     

Discovery of new inhibitor for the protein arginine deiminase type 4 (PAD4) by rational design of α-enolase-derived peptides

Rheumatoid arthritis (RA) is an inflammatory autoimmune disease affecting about 0.24 % of the world population. Protein arginine deiminase type 4 (PAD4) is believed to be responsible for the occurrence of RA by catalyzing citrullination of proteins. The citrullinated proteins act as autoantigens by stimulating an immune response. Citrullinated α-enolase has been identified as one of the autoantigens for RA. Hence, α-enolase serves as a suitable template for design of potential peptide inhibitors against PAD4. The binding affinity of α-enolase-derived peptides and PAD4 was virtually determined using PatchDock and HADDOCK docking programs. Synthesis of the designed peptides was performed using a solid phase peptide synthesis method. The inhibitory potential of each peptide was determined experimentally by PAD4 inhibition assay and IC₅₀ measurement. PAD4 assay data show that the N-P2 peptide is the most favourable substrate among all peptides. Further modification of N-P2 by changing the Arg residue to canavanine [P2 (Cav)] rendered it an inhibitor against PAD4 by reducing the PAD4 activity to 35 % with IC₅₀ 1.39 mM. We conclude that P2 (Cav) is a potential inhibitor against PAD4 and can serve as a starting point for the development of even more potent inhibitors.