A new mixed inhibitor of adenosine deaminase produced by endophytic Cochliobolus sp. from medicinal plant seeds.

Medicinal plants have been studied for potential endophytic interactions and numerous studies have provided evidence that seeds harbor diverse microbial communities, not only on their surfaces but also within the embryo. Adenosine deaminase (ADA) is known as a potential therapeutic target for the treatment of lymphoproliferative disorders and cancer. Therefore, in this study, 20 types of medicinal plant seeds were used to screen endophytic fungi with tissue homogenate and streak. In addition, 128 morphologically distinct endophyte strains were isolated and their ADA inhibitory activity determined by a spectrophotometric assay. The strain with the highest inhibitory activity was identified as Cochliobolus sp. Seven compounds were isolated from the strain using a chromatography method. Compound 3 showed the highest ADA inhibitory activity and was identified as 5-hydroxy-2-hydroxymethyl-4H-pyran-4-one, based on the results of 1H and 13C NMR spectroscopy. The results of molecular docking suggested that compound 3 binds to the active site and the nonspecific binding site of the ADA. Furthermore, we found that compound 3 is a mixed ADA inhibitor. These results indicate that endophytic strains are a promising source of ADA inhibitors and that compound 3 may be a superior source for use in the preparation of biologically active ADA inhibitor compounds used to treat cancer.

Reynoutria Japonica from Traditional Chinese Medicine: A Source of Competitive Adenosine Deaminase Inhibitors for Anticancer.

BACKGROUND: Adenosine deaminase (ADA) is an important enzyme in purine metabolism and is known as a potential therapeutic target for the treatment of lymphoproliferative disorders and cancer. Traditional Chinese Herbal Medicine (TCHM) is widely used alone or in combination with chemotherapy to treat cancer, due to its ability to deliver a broad variety of bioactive secondary metabolites as promising sources of novel organic natural agents. OBJECTIVE: In the present study, 29 varieties of medicinal plants were screened for the presence of ADA inhibitors. RESULTS: Extracts from Reynoutria japonica, Glycyrrhiza uralensis, Lithospermum erythrorhizon, Magnolia officinalis, Gardenia jasminoides, Stephania tetrandra, Commiphora myrrha, Raphanus sativus and Corydalis yanhusuo demonstrated strong ADA inhibition with rates greater than 50%. However, Reynoutria japonica possessed the highest ADA inhibitory activity at 95.26% and so was used in our study for isolating the ADA inhibitor to be further studied. Eight compounds were obtained and their structures were identified. The compound H1 had strong ADA inhibitory activity and was deduced to be emodin by 1H and 13C-NMR spectroscopic analysis with an IC50 of 0.629 mM. The molecular docking data showed that emodin could bind tightly to the active site of ADA. Our results demonstrated that emodin displayed a new biological activity which is ADA inhibitory activity with high cytotoxic activity against K562 leukemia cells. The bioactivity of cordycepin was significantly increased when used in combination with emodin. CONCLUSION: Emodin may represent a good candidate anti-cancer therapy and adenosine protective agent.

Does Local Structure Bias How a Crystal Nucleus Evolves?

The broad scientific and technological importance of crystallization has led to significant research probing and rationalizing crystal nucleation processes. Previous work has generally neglected the possibility of the molecular-level dynamics of individual crystal nuclei coupling to local structures. However, recent experimental work has conjectured that this can occur. Therefore, to address a deficiency in scientific understanding of crystallization, we have probed the nucleation of prototypical single and multicomponent crystals (specifically, ice and mixed gas hydrates). We establish that local structures can bias the evolution of nascent crystal phases on a nanosecond time scale by, for example, promoting the appearance or disappearance of specific crystal motifs and thus reveal a new facet of crystallization behavior. Moreover, we demonstrate structural biases are likely present during crystallization processes beyond ice and gas hydrate formation. Structurally biased dynamics are a lens for understanding existing computational and experimental results while pointing to future opportunities.

Bridging solution properties to gas hydrate nucleation through guest dynamics.

By investigating the aqueous solution properties of several hydrate guests with molecular simulations, we find that with increasing guest concentration, the guest's hydration shell becomes more ordered and the system entropy decreases. A common critical value of the self-diffusion coefficient of different guest molecules is identified, below which hydrates will nucleate very readily.

Effects of gas reservoir configuration and pore radius on shale gas nanoflow: A molecular dynamics study.

We calculated methane transport through cylindrical graphite nanopores in cyclical steady-state flows using non-equilibrium molecular dynamics simulations. First, two typical gas reservoir configurations were evaluated: open (OS) and closed (CS) systems in which pores connect to the gas reservoir without/with a graphite wall parallel to the gas flow. We found that the OS configuration, which is commonly used to study nanoflows, exhibited obvious size effects. Smaller gas reservoir cross-sectional areas were associated with faster gas flows. Because Knudsen diffusion and slip flow in pores are interrupted in a gas reservoir that does not have walls as constraints, OSs cannot be relied upon in cyclical nanoflow simulations. Although CSs eliminated size effects, they introduced surface roughness effects that stem from the junction surface between the gas reservoir and the pore. To obtain a convergent nanoflow, the length of a side of the gas reservoir cross-section should be at least 2 nm larger than the pore diameter. Second, we obtained methane flux data for various pore radii (0.5-2.5 nm) in CSs and found that they could be described accurately using the Javadpour formula. This is the first direct molecular simulation evidence to validate this formula. Finally, the radial density and flow-velocity distributions of methane in CS pores were analyzed in detail. We tested pores with a radius between 0.5 nm and 2.5 nm and determined that the maximum ratio (∼34%) of slip flow to overall flow occurred in the pore with a radius of 1.25 nm. This study will aid in the design of gas reservoir configurations for nanoflow simulations and is helpful in understanding shale gas nanoflows.

Identification of a New Uncompetitive Inhibitor of Adenosine Deaminase from Endophyte Aspergillus niger sp.

Adenosine deaminase (ADA) is an enzyme widely distributed from bacteria to humans. ADA is known as a potential therapeutic target for the treatment of lymphoproliferative disorders and cancer. Endophytes are endosymbionts, often bacteria or fungi, which live within plant tissues and internal organs or intercellular space. Endophytes have a broad variety of bioactive metabolites that are used for the identification of novel natural compounds. Here, 54 morphologically distinct endophyte strains were isolated from six plants such as Peganum harmala Linn., Rheum officinale Baill., Gentiana macrophylla Pall., Radix stephaniae tetrandrae, Myrrha, and Equisetum hyemale Linn. The isolated strains were used for the search of ADA inhibitors that resulted in the identification of the strain with the highest inhibition activity, Aspergillus niger sp. Four compounds were isolated from this strain using three-step chromatography procedure, and compound 2 was determined as the compound with the highest inhibition activity of ADA. Based on the results of 1H and 13C NMR spectroscopies, compound 2 was identified as 3-(4-nitrophenyl)-5-phenyl isoxazole. We showed that compound 2 was a new uncompetitive inhibitor of ADA with high cytotoxic effect on HepG2 and SMCC-7721 cells (the IC50 values were 0.347 and 0.380 mM, respectively). These results suggest that endophyte strains serve as promising sources for the identification of ADA inhibitors, and compound 2 could be an effective drug in the cancer treatment.

The effects of ice on methane hydrate nucleation: a microcanonical molecular dynamics study.

Although ice powders are widely used in gas hydrate formation experiments, the effects of ice on hydrate nucleation and what happens in the quasi-liquid layer of ice are still not well understood. Here, we used high-precision constant energy molecular dynamics simulations to study methane hydrate nucleation from vapor-liquid mixtures exposed to the basal, prismatic, and secondary prismatic planes of hexagonal ice (ice Ih). Although no significant difference is observed in hydrate nucleation processes for these different crystal planes, it is found, more interestingly, that methane hydrate can nucleate either on the ice surface heterogeneously or in the bulk solution phase homogeneously. Several factors are mentioned to be able to promote the heterogeneous nucleation of hydrates, including the adsorption of methane molecules at the solid-liquid interface, hydrogen bonding between hydrate cages and the ice structure, the stronger ability of ice to transfer heat than that of the aqueous solution, and the higher occurrence probability of hydrate cages in the vicinity of the ice surface than in the bulk solution. Meanwhile, however, the other factors including the hydrophilicity of ice and the ice lattice mismatch with clathrate hydrates can inhibit heterogeneous nucleation on the ice surface and virtually promote homogeneous nucleation in the bulk solution. Certainly, the efficiency of ice as a promoter and as an inhibitor for heterogeneous nucleation is different. We estimate that the former is larger than the latter under the working conditions. Additionally, utilizing the benefit of ice to absorb heat, the NVE simulation of hydrate formation with ice can mimic the phenomenon of ice shrinking during the heterogeneous nucleation of hydrates and lower the overly large temperature increase during homogeneous nucleation. These results are helpful in understanding the nucleation mechanism of methane hydrate in the presence of ice.

Antitumor activity of a Rhodococcus sp. Lut0910 isolated from polluted soil.

The actinomycetes strain, lut0910, was isolated from polluted soil and identified as the Rhodococcus species with 99% similarity based on the sequence analysis of 16S recombinant DNA. The extract of this strain demonstrated in vivo and in vitro antitumor activity. The treatment of two human cancer cell lines, hepatocellular carcinoma HepG2 and cervical carcinoma Hela cells, with the lut0910 extract caused the delay in cell propagation in a dose-dependent manner with an IC50 of 73.39 and 33.09 µg/mL, respectively. Also, the oral administration of lut0910 extract to the mice with a solid tumor resulted in the inhibition of tumor growth in comparison with a placebo group. The thymus and spleen indexes were significantly increased in mice groups treated with the lut0910 extract. The histopathological changes of the tumor tissues showed that there were massive necrotic areas in the tumor tissues after treatment with different doses of the lut0910 extract. Our result would provide a new way and potent source for development of new anticancer agent from the polluted environment.

Effects of ensembles on methane hydrate nucleation kinetics.

By performing molecular dynamics simulations to form a hydrate with a methane nano-bubble in liquid water at 250 K and 50 MPa, we report how different ensembles, such as the NPT, NVT, and NVE ensembles, affect the nucleation kinetics of the methane hydrate. The nucleation trajectories are monitored using the face-saturated incomplete cage analysis (FSICA) and the mutually coordinated guest (MCG) order parameter (OP). The nucleation rate and the critical nucleus are obtained using the mean first-passage time (MFPT) method based on the FS cages and the MCG-1 OPs, respectively. The fitting results of MFPT show that hydrate nucleation and growth are coupled together, consistent with the cage adsorption hypothesis which emphasizes that the cage adsorption of methane is a mechanism for both hydrate nucleation and growth. For the three different ensembles, the hydrate nucleation rate is quantitatively ordered as follows: NPT > NVT > NVE, while the sequence of hydrate crystallinity is exactly reversed. However, the largest size of the critical nucleus appears in the NVT ensemble, rather than in the NVE ensemble. These results are helpful for choosing a suitable ensemble when to study hydrate formation via computer simulations, and emphasize the importance of the order degree of the critical nucleus.

Genome-Wide Identification and Expression Analysis of WRKY Gene Family in Capsicum annuum L.

The WRKY family of transcription factors is one of the most important families of plant transcriptional regulators with members regulating multiple biological processes, especially in regulating defense against biotic and abiotic stresses. However, little information is available about WRKYs in pepper (Capsicum annuum L.). The recent release of completely assembled genome sequences of pepper allowed us to perform a genome-wide investigation for pepper WRKY proteins. In the present study, a total of 71 WRKY genes were identified in the pepper genome. According to structural features of their encoded proteins, the pepper WRKY genes (CaWRKY) were classified into three main groups, with the second group further divided into five subgroups. Genome mapping analysis revealed that CaWRKY were enriched on four chromosomes, especially on chromosome 1, and 15.5% of the family members were tandemly duplicated genes. A phylogenetic tree was constructed depending on WRKY domain' sequences derived from pepper and Arabidopsis. The expression of 21 selected CaWRKY genes in response to seven different biotic and abiotic stresses (salt, heat shock, drought, Phytophtora capsici, SA, MeJA, and ABA) was evaluated by quantitative RT-PCR; Some CaWRKYs were highly expressed and up-regulated by stress treatment. Our results will provide a platform for functional identification and molecular breeding studies of WRKY genes in pepper.

Microcanonical molecular simulations of methane hydrate nucleation and growth: evidence that direct nucleation to sI hydrate is among the multiple nucleation pathways.

The results of six high-precision constant energy molecular dynamics (MD) simulations initiated from methane-water systems equilibrated at 80 MPa and 250 K indicate that methane hydrates can nucleate via multiple pathways. Five trajectories nucleate to an amorphous solid. One trajectory nucleates to a structure-I hydrate template with long-range order which spans the simulation box across periodic boundaries despite the presence of several defects. While experimental and simulation data for hydrate nucleation with different time- and length-scales suggest that there may exist multiple pathways for nucleation, including metastable intermediates and the direct formation of the globally-stable phase, this work provides the most compelling evidence that direct formation to the globally stable crystalline phase is one of the multiple pathways available for hydrate nucleation.

Solubility of aqueous methane under metastable conditions: implications for gas hydrate nucleation.

To understand the prenucleation stage of methane hydrate formation, we measured methane solubility under metastable conditions using molecular dynamics simulations. Three factors that influence solubility are considered: temperature, pressure, and the strength of the modeled van der Waals attraction between methane and water. Moreover, the naturally formed water cages and methane clusters in the methane solutions are analyzed. We find that both lowering the temperature and increasing the pressure increase methane solubility, but lowering the temperature is more effective than increasing the pressure in promoting hydrate nucleation because the former induces more water cages to form while the latter makes them less prevalent. With an increase in methane solubility, the chance of forming large methane clusters increases, with the distribution of cluster sizes being exponential. The critical solubility, beyond which the metastable solutions spontaneously form hydrate, is estimated to be ~0.05 mole fraction in this work, corresponding to the concentration of 1.7 methane molecules/nm(3). This value agrees well with the cage adsorption hypothesis of hydrate nucleation.

Using the face-saturated incomplete cage analysis to quantify the cage compositions and cage linking structures of amorphous phase hydrates.

Recent advances in the molecular dynamics simulations of spontaneous nucleation and growth of methane hydrate show that an amorphous phase of the hydrate is first reached. However, the amorphous hydrate has not been well described, due to the insufficient identification of cage structures. Here, we develop a method, called "face-saturated incomplete cage analysis", which can identify all face-saturated cages in a given system. As a result, it is found that thousands of cage types and abundant occupancy states are present in the amorphous hydrate. Moreover, the crystallinity of amorphous hydrate is evaluated according to the quantitative calculation of cage linking structures, and the critical nucleus of hydrate is also estimated on the basis of clustering analysis for all face-saturated cages.

Why can water cages adsorb aqueous methane? A potential of mean force calculation on hydrate nucleation mechanisms.

By performing constrained molecular dynamics simulations in the methane-water system, we successfully calculated the potential of mean force (PMF) between a dodecahedral water cage (DWC) and dissolved methane for the first time. As a function of the distance between DWC and methane, this is characterized by a deep well at approximately 6.2 A and a shallow well at approximately 10.2 A, separated by a potential barrier at approximately 8.8 A. We investigated how the guest molecule, cage rigidity and the cage orientation affected the PMF. The most important finding is that the DWC itself strongly adsorbs methane and the adsorption interaction is independent of the guests. Moreover, the activation energy of the DWC adsorbing methane is comparable to that of hydrogen bonds, despite differing by a factor of approximately 10% when considering different water-methane interaction potentials. We explain that the cage-methane adsorption interaction is a special case of the hydrophobic interaction between methane molecules. The strong net attraction in the DWC shell with radii between 6.2 and 8.8 A may act as the inherent driving force that controls hydrate formation. A cage adsorption hypothesis for hydrate nucleation is thus proposed and discussed.

Can the dodecahedral water cluster naturally form in methane aqueous solutions? A molecular dynamics study on the hydrate nucleation mechanisms.

By performing a large scale of molecular dynamics simulations, we analyze 60 x 10(6) hydration shells of methane to examine whether the dodecahedral water cluster (DWC) can naturally form in methane aqueous solutions--a fundamental question relevant to the nucleation mechanisms of methane hydrate. The analyzing method is based on identifying the incomplete cages (ICs) from the hydration shells and quantifying their cagelike degrees (zetaC=0-1). Here, the zetaC is calculated according to the H-bond topological network of IC and reflects how the IC resembles the complete polyhedral cage. In this study, we obtain the zetaC distributions of ICs in methane solutions and find the occurrence probabilities of ICs reduce with zetaC very rapidly. The ICs with zetaC>or=0.65 are studied, which can be regarded as the acceptable cagelike structures in appearance. Both increasing the methane concentration and lowering the temperature can increase their occurrence probabilities through slowing down the water molecules. Their shapes, cage-maker numbers, and average radii are also discussed. About 13-14 of these ICs are face saturated, meaning that every edges are shared by two faces. The face-saturated ICs have the potential to act as precursors of hydrate nucleus because they can prevent the encaged methane from directly contacting other dissolved methane when an event of methane aggregation occurs. The complete cages, i.e., the ICs with zetaC=1, form only in the solutions with high methane concentration, and their occurrence probabilities are about 10(-6). Most of their shapes are different from the known hydrate cages, but we indeed observe a standard 5(12)6(2) hydrate cage. We do not find the expected DWC, and its occurrence probability is estimated to be far less than 10(-7). Additionally, the IC analysis proposed in this work is also very useful in other studies not only on the formation, dissociation, and structural transition of hydrates but also on the hydrophobic hydration of apolar solutes.

Lifetimes of cagelike water clusters immersed in bulk liquid water: a molecular dynamics study on gas hydrate nucleation mechanisms.

Molecular dynamics simulations were performed to observe the evolution of cagelike water clusters immersed in bulk liquid water at 250 and 230 K. Totally, we considered four types of clusters--dodecahedral (5(12)) and tetrakaidecahedral (5(12)6(2)) cagelike water clusters filled with or without a methane molecule, respectively. The lifetimes of these clusters were calculated according to their Lindemann index (delta) using the criterion of delta> or =0.07. The lifetimes of the clusters at 230 K are longer than that at 250 K, and their ratios are the same as the ratio of structure relaxation times of bulk water at these temperatures. For both the filled and empty clusters, the lifetimes of 5(12)6(2) cagelike clusters are similar to that of 5(12) cagelike clusters. Although the methane molecules indeed make the filled cagelike water clusters live longer than the empty ones, the empty cagelike water clusters still have the chance of being long lived. These observations support the cluster nucleation hypothesis for the formation mechanisms of gas hydrates.

Comment on "Computation of the viscosity of a liquid from time averages of stress fluctuations".

In a recent paper, Hess and Evans [Phys. Rev. E 64, 011207 (2001)] propose a method different from the conventional Green-Kubo and Einstein methods to calculate viscosity in equilibrium molecular dynamics simulations. For a comparison, we calculate the shear viscosity of SPC/E water at 303 K using these three different methods. We find that the Hess-Evans method is not as good as the other two in practical application, especially for the fluids with high viscosity and complicated relaxation.