Fluorescent silicon nanoparticle-based quantitative hemin assay.

Hemin with functions such as oxygen carrying, oxygen storing, promoting redox, and performing electron transfer is important for the health of organisms. In this paper, green synthetic silicon nanoparticles (Si-NPs) were synthesized and used for free hemin detection in serum (a low limit of detection (LOD), 29.5 nM). The quenching mechanism was investigated by UV-vis absorption spectra, time-resolved luminescence decay curve, and circular dichroism (CD) spectra. It was confirmed that multiple redox centers of hemin led to intensified effective collision and increased the electron transfer rate, therefore enhancing the dynamic quenching, and it was undeniable that the inner filter effect (IFE) also played a role in the quenching.

Structural analysis of previously unknown natural products using computational methods.

Natural products exhibit structural diversity, and biologically active natural products with unprecedented molecular skeletons can potentially be isolated from natural resources in the future. Although it has often been difficult to determine the structures and configurations of new compounds that do not resemble known compounds, the determination of the chemical structures, including the absolute stereo configuration, is very important in drug discovery research. In our efforts to find new bioactive natural products, we have identified novel compounds such as the ubiquitin-proteasome system inhibitors and osteoclast differentiation inhibitors. Various natural products, mixtures of stereoisomers of natural products, and compounds with novel skeletal structures were studied. In cases where it was difficult to determine the structures by NMR spectroscopy, we could successfully determine the chemical structures by computational chemistry. This review presents the results of structural analysis obtained using computational methods for several natural products that we have recently isolated.

Inhibition of α-amylase Activity by Zn2+: Insights from Spectroscopy and Molecular Dynamics Simulations.

BACKGROUND: Inhibition of α-amylase activity is an important strategy in the treatment of diabetes mellitus. An important treatment for diabetes mellitus is to reduce the digestion of carbohydrates and blood glucose concentrations. Inhibiting the activity of carbohydrate-degrading enzymes such as α-amylase and glucosidase significantly decreases the blood glucose level. Most inhibitors of α-amylase have serious adverse effects, and the α-amylase inactivation mechanisms for the design of safer inhibitors are yet to be revealed. OBJECTIVE: In this study, we focused on the inhibitory effect of Zn2+ on the structure and dynamic characteristics of α-amylase from Anoxybacillus sp. GXS-BL (AGXA), which shares the same catalytic residues and similar structures as human pancreatic and salivary α-amylase (HPA and HSA, respectively). METHODS: Circular dichroism (CD) spectra of the protein (AGXA) in the absence and presence of Zn2+ were recorded on a Chirascan instrument. The content of different secondary structures of AGXA in the absence and presence of Zn2+ was analyzed using the online SELCON3 program. An AGXA amino acid sequence similarity search was performed on the BLAST online server to find the most similar protein sequence to use as a template for homology modeling. The pocket volume measurer (POVME) program 3.0 was applied to calculate the active site pocket shape and volume, and molecular dynamics simulations were performed with the Amber14 software package. RESULTS: According to circular dichroism experiments, upon Zn2+ binding, the protein secondary structure changed obviously, with the α-helix content decreasing and ß-sheet, ß-turn and randomcoil content increasing. The structural model of AGXA showed that His217 was near the active site pocket and that Phe178 was at the outer rim of the pocket. Based on the molecular dynamics trajectories, in the free AGXA model, the dihedral angle of C-CA-CB-CG displayed both acute and planar orientations, which corresponded to the open and closed states of the active site pocket, respectively. In the AGXA-Zn model, the dihedral angle of C-CA-CB-CG only showed the planar orientation. As Zn2+ was introduced, the metal center formed a coordination interaction with H217, a cation-π interaction with W244, a coordination interaction with E242 and a cation-π interaction with F178, which prevented F178 from easily rotating to the open state and inhibited the activity of the enzyme. CONCLUSION: This research may have uncovered a subtle mechanism for inhibiting the activity of α-amylase with transition metal ions, and this finding will help to design more potent and specific inhibitors of α-amylases.

Effects of dihydromyricetin on biological properties of Bloom syndrome helicase / 中国药理学通报

; Aim To explore the anti-tumor mechanism of dihydromyricetin (DMY), a kind of flavonoid compound with anti-inflammatory and anti-tumor effects, via studying the effect of DMY on biological activities of Bloom helicase. Methods The effect of DMY on the biological activities of BLM helicase was studied by ultraviolet spectrum (UV), circular dichroism (CD), fluorescence polarization and free phosphorus detection. Results The results of CD and UV showed that DMY could bind to a site of the BLM helicase. In the concentration of DMY in 0 ~ 25 μmol . L 1 range, DMY showed a positive correlation with the interference ability of BLM helicase secondary structure with the increase of concentration, while in the concentration of DMY in 25 ~ 75 μmol . L 1 range, DMY showed a negative correlation. Fluorescence polarization and free phosphorus detection experiments showed that DMY could bind to BLM helicase, thus inhibiting the helicase activity of BLM helicase. Conclusions DMY can competitively bind to the DNA binding site of BLM helicase and change the spatial structure of BLM helicase, inhibiting the binding of BLM helicase to DNA and the biological activity of BLM helicase accordingly.

Distinct Excitonic Circular Dichroism between Wurtzite and Zincblende CdSe Nanoplatelets.

Nanocrystals (NCs) with identical components and sizes but different crystal structures could not be distinguished by conventional absorption and emission spectra. Herein, we find that circular dichroism (CD) spectroscopy can easily distinguish the CdSe nanoplatelets (NPLs) with different crystal structures of wurtzite (WZ) and zincblende (ZB) with the help of chiral l- or d-cysteine ligands. In particular, the CD signs of the first excitonic transitions in WZ and ZB NPLs capped by the same chiral cysteine are opposite. Theoretic calculation supports the viewpoint of different crystal structures and surfaces arrangements between WZ and ZB NPLs contributing to this significant phenomenon. The CD peaks appearing at the first excitonic transition band of WZ or ZB CdSe NPLs are clearly assigned to the different transition polarizations along 4p( x,y,z),Se → 5sCd or 4p( x,y),Se → 5sCd. This work not only provides a deep insight into the origin of the optical activity inside chiral semiconductor nanomaterials but also proposes the design principle of chiral semiconductor nanocrystals with high optic activity.

MMP-7 cleaves amyloid ß fragment peptides and copper ion inhibits the degradation.

The extracellular deposition of amyloid ß (Aß) is known to be the fundamental cause of Alzheimer's disease (AD). Aß1-42, generated by ß-secretases from the amyloid precursor protein (APP), is the main component of neuritic plaque, and the aggregation of this protein is shown to be dependent to an extent on metal ions such as copper and zinc. However, the mechanism by which Cu2+ affects the physicochemical properties of Aß1-42 or the central nervous system is still under debate. A recent series of studies have demonstrated that both the soluble-type matrix metalloproteinases (MMP-2 and MMP-9) and the membrane-type matrix metalloproteinase (MT1-MMP) are capable of degrading Aß peptides. MMP-7, one of the soluble-type matrix metalloproteinases, is expressed in hippocampal tissue; however, less information is available concerning the pathophysiological roles of this enzyme in the process and/or progress of Alzheimer's disease. In this study, we examined the degradation activity of MMP-7 against various Aß1-42's fragment peptides and the effect of Cu2+. Although Aß22-40 was degraded by MMP-7 regardless of Cu2+, Cu2+ inhibited the degradation of Aß1-19, Aß11-20, and Aß11-29 by MMP-7. These results indicate that MMP-7 is capable of degrading Aß1-42, and that Aß1-42 acquired resistance against MMP-7 cleavage through Cu2+-binding and structure changes. Our results demonstrate that MMP-7 may play an important role in the defensive mechanism against the aggregation of Aß1-42, which gives rise to the pathology of AD.

Interaction between Pin1 and its natural product inhibitor epigallocatechin-3-gallate by spectroscopy and molecular dynamics simulations.

The binding of epigallocatechin-3-gallate (EGCG) to wild type Pin1 in solution was studied by spectroscopic methods and molecular dynamics simulations in this research to explore the binding mode and inhibition mechanism. The binding constants and number of binding sites per Pin1 for EGCG were calculated through the Stern-Volmer equation. The values of binding free energy and thermodynamic parameters were calculated and indicated that hydrogen bonds, electrostatic interaction and Van der Waals interaction played the major role in the binding process. The alterations of Pin1 secondary structure in the presence of EGCG were confirmed by far-UV circular dichroism spectra. The binding model at atomic-level revealed that EGCG was bound to the Glu12, Lys13, Arg14, Met15 and Arg17 in WW domain. Furthermore, EGCG could also interact with Arg69, Asp112, Cys113 and Ser114 in PPIase domain.

Two new cyclic bisbibenzyl derivatives from Hebertus dicranus.

In the present study, two new cyclic bisbibenzyls (1, 2) co-occuring with a known compound, isoplagiochins C (3) were isolated from Hebertus dicranus. The structures were determined mainly by extensive 1D and 2D NMR experiments, and the absolute configurations of 1 and 2 were established by the circular dichroism spectrum. Furthermore, all these three rare compounds were tested in vitro for inhibitory activity against the growth of human cancer cell lines (A549, HCT116, MDA-MB-231, and BEL7404) by the MTT assay, and compound 2 exhibited moderately inhibitory activity with IC50 values ranging from 13.89 to 31.62 µmol·L(-1). In conclusion, our results provided a basis for future development and modification of these compounds for cancer therapy.

Two new cyclic bisbibenzyl derivatives from Hebertus dicranus / 中国天然药物

In the present study, two new cyclic bisbibenzyls (1, 2) co-occuring with a known compound, isoplagiochins C (3) were isolated from Hebertus dicranus. The structures were determined mainly by extensive 1D and 2D NMR experiments, and the absolute configurations of 1 and 2 were established by the circular dichroism spectrum. Furthermore, all these three rare compounds were tested in vitro for inhibitory activity against the growth of human cancer cell lines (A549, HCT116, MDA-MB-231, and BEL7404) by the MTT assay, and compound 2 exhibited moderately inhibitory activity with IC50 values ranging from 13.89 to 31.62 μmol·L(-1). In conclusion, our results provided a basis for future development and modification of these compounds for cancer therapy.

Study on the interaction between Besifloxacin and bovine serum albumin by spectroscopic techniques.

The interaction between Besifloxacin (BFLX) and bovine serum albumin (BSA) was investigated by spectroscopic (fluorescence, UV-Vis absorption and circular dichroism) techniques under imitated physiological conditions. The experiments were conducted at different temperatures (298, 304 and 310 K) and the results showed that the BFLX caused the fluorescence quenching of BSA through a static quenching procedure. The binding constant (Ka), binding sites (n) were obtained. The corresponding thermodynamic parameters (ΔH, ΔS and ΔG) of the interaction system were calculated at different temperatures. The results revealed that the binding process was spontaneous and the acting force between BFLX and BSA were mainly electrostatic forces. According to Förster non-radiation energy transfer theory, the binding distance between BFLX and BSA was calculated to be 4.96 nm. What is more, both synchronous fluorescence and circular dichroism spectra confirmed conformational changes of BSA.

Thermal- and urea-induced unfolding processes of glutathione S-transferase by molecular dynamics simulation.

The Schistosoma juponicum 26 kDa glutathione S-transferase (sj26GST) consists of the N-terminal domain (N-domain), containing three alpha-helices (named H1-H3) and four anti-parallel beta-strands (S1-S4), and the C-terminal domain (C-domain), comprising five alpha-helices (named H4-H8). In present work, molecular dynamics simulations and fluorescence spectroscopic were used to gain insights into the unfolding process of sj26GST. The molecular dynamics simulations on sj26GST subunit both in water and in 8 M urea were carried out at 300 K, 400 K and 500 K, respectively. Spectroscopic measurements were employed to monitor structural changes. Molecular dynamics simulations of sj26GST subunit induced by urea and temperature showed that the initial unfolding step of sj26GST both in water and urea occurred on N-domain, involving the disruption of helices H2, H3 and strands S3 and S4, whereas H6 was the last region exposed to solution and was the last helix to unfold. Moreover, simulations analyses combining with fluorescence and circular dichroism spectra indicated that N-domain could not fold independent, suggesting that correct folding of N-domain depended on its interactions with C-domain. We further proposed that the folding of GSTs could begin with the hydrophobic collapse of C-domain whose H4, H5, H6 and H7 could move close to each other and form a hydrophobic core, especially H6 wrapped in the hydrophobic center and beginning spontaneous formation of the helix. S3, S4, H3, and H2 could form in the wake of the interaction between C-domain and N-domain. The paper can offer insights into the molecular mechanism of GSTs unfolding.

Absolute determination of stereochemical configuration of some marine natural products / 国际药学研究杂志

The determination of stereochemical absolute structure is an important issue in structural elucidation of natural products. The absolute configuration of natural compounds with a chiral α, β -unsaturated ketone chromorphore can be determined by the Cotton effect in 320-350 nm (n→π,* transition) and 220-260 nm (π→π,* transition) regions of the circular dichroism (CD) spectrum. This paper reviews the absolute stereochemical asignment of some α, β-unsaturated ketone compounds as well as some of the longer fatty chain derived compounds.

The CHARMM-TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties.

The quantum mechanical (QM)/molecular mechanical (MM) interface between Chemistry at HARvard Molecular Mechanics (CHARMM) and TURBOMOLE is described. CHARMM provides an extensive set of simulation algorithms, like molecular dynamics (MD) and free energy perturbation, and support for mature nonpolarizable and Drude polarizable force fields. TURBOMOLE provides fast QM calculations using density functional theory or wave function methods and excited state properties. CHARMM-TURBOMOLE is well-suited for extended QM/MM MD simulations using first principles methods with large (triple-ζ) basis sets. We demonstrate these capabilities with a QM/MM simulation of Mg(2+) (aq), where the MM outer sphere water molecules are represented using the SWM4-NDP Drude polarizable force field and the ion and inner coordination sphere are represented using QM PBE, PBE0, and MP2 methods. The relative solvation free energies of Mg(2+) and Zn(2+) were calculated using thermodynamic integration. We also demonstrate the features for excited state properties. We calculate the time-averaged solution absorption spectrum of indole, the emission spectrum of the indole 1La excited state, and the electronic circular dichroism spectrum of an oxacepham.

Spectroscopic studies on the interaction of Phacolysin and bovine serum albumin.

The interaction between Phacolysin (PCL) and bovine serum albumin (BSA) under imitated physiological conditions was investigated by spectroscopic (fluorescence, UV-Vis absorption and Circular dichroism) techniques. The experiments were conducted at different temperatures (294K, 302K, 306K and 310K) and the results showed that the PCL caused the fluorescence quenching of BSA through a static quenching procedure. The binding constant (Ka), binding sites (n) were obtained. The corresponding thermodynamic parameters (ΔH, ΔS and ΔG) of the interaction system were calculated at different temperatures. The results revealed that the binding process was spontaneous and the acting force between PCL and BSA were mainly hydrogen bonding and van der Waals forces. According to Förster non-radiation energy transfer theory, the binding distance between PCL and BSA was calculated to be 2.41nm. What is more, both synchronous fluorescence and Circular dichroism spectra confirmed the interaction, which indicated the conformational changes of BSA.

Enantioseparation of racemic trans-δ-viniferin using high speed counter-current chromatography based on induced circular dichroism technology.

A preparative chiral high speed counter-current chromatography (HSCCC) method based on induced circular dichroism (ICD) spectrum was developed to separate trans-δ-viniferin (TVN) enantiomers successfully. The important parameters for the chiral HSCCC separation process, including the type of chiral selector (CS), the concentration of chiral selector and the equilibrium temperature, were optimized using induced circular dichroism spectrum. The final separation procedure was established with a biphasic solvent system composed of n-hexane-ethyl acetate-25 mmol L(-1) hydroxypropyl-ß-cyclodextrin aqueous solution (5:5:10, v/v/v) in the head-to-tail elution mode at 5 °C. Under optimum chiral HSCCC separation conditions, 8.2mg of (7S, 8S)-TVN (1) and 9.4 mg of (7R, 8R)-TVN (2) were successfully separated from 20mg TVN enantiomers with the purity of 99.51% and 99.36%, respectively.

Arsenite binding-induced zinc loss from PARP-1 is equivalent to zinc deficiency in reducing PARP-1 activity, leading to inhibition of DNA repair.

Inhibition of DNA repair is a recognized mechanism for arsenic enhancement of ultraviolet radiation-induced DNA damage and carcinogenesis. Poly(ADP-ribose) polymerase-1 (PARP-1), a zinc finger DNA repair protein, has been identified as a sensitive molecular target for arsenic. The zinc finger domains of PARP-1 protein function as a critical structure in DNA recognition and binding. Since cellular poly(ADP-ribosyl)ation capacity has been positively correlated with zinc status in cells, we hypothesize that arsenite binding-induced zinc loss from PARP-1 is equivalent to zinc deficiency in reducing PARP-1 activity, leading to inhibition of DNA repair. To test this hypothesis, we compared the effects of arsenite exposure with zinc deficiency, created by using the membrane-permeable zinc chelator TPEN, on 8-OHdG formation, PARP-1 activity and zinc binding to PARP-1 in HaCat cells. Our results show that arsenite exposure and zinc deficiency had similar effects on PARP-1 protein, whereas supplemental zinc reversed these effects. To investigate the molecular mechanism of zinc loss induced by arsenite, ICP-AES, near UV spectroscopy, fluorescence, and circular dichroism spectroscopy were utilized to examine arsenite binding and occupation of a peptide representing the first zinc finger of PARP-1. We found that arsenite binding as well as zinc loss altered the conformation of zinc finger structure which functionally leads to PARP-1 inhibition. These findings suggest that arsenite binding to PARP-1 protein created similar adverse biological effects as zinc deficiency, which establishes the molecular mechanism for zinc supplementation as a potentially effective treatment to reverse the detrimental outcomes of arsenic exposure.