Homology modeling and atomic level binding study of Leishmania MAPK with inhibitors

The current therapy for leishmaniasis is not sufficient and it has two severe drawbacks, host-toxicity and drug resistance. The substantial knowledge of parasite biology is not yet translating into novel drugs for leishmaniasis. Based on this observation, a 3D structural model of Leishmania mitogen-activated protein kinase (MAPK) homologue has been developed, for the first time, by homology modeling and molecular dynamics simulation techniques. The model provided clear insight in its structure features, i.e. ATP binding pocket, phosphorylation lip, and common docking site. Sequence-structure homology recognition identified Leishmania CRK3 (LCRK3) as a distant member of the MAPK superfamily. Multiple sequence alignment and 3D structure model provided the putative ATP binding pocket of Leishmania with respect to human ERK2 and LCRK3. This analysis was helpful in identifying the binding sites and molecular function of the Leishmania specific MAPK homologue. Molecular docking study was performed on this 3D structural model, using different classes of competitive ATP inhibitors of LCRK3, to check whether they exhibit affinity and could be identified as Leishmania MAPK specific inhibitors. It is well known that MAP kinases are extracellular signal regulated kinases ERK1 and ERK2, which are components of the Ras-MAPK signal transduction pathway which is complexed with HDAC4 protein, and their inhibition is of significant therapeutic interest in cancer biology. In order to understand the mechanism of action, docking of indirubin class of molecules to the active site of histone deacetylase 4 (HDAC4) protein is performed, and the binding affinity of the protein-ligand interaction was computed. The new structural insights obtained from this study are all consistent with the available experimental data, suggesting that the homology model of the Leishmania MAPK and its ligand interaction modes are reasonable. Further the comparative molecular electrostatic potential and cavity depth analysis of Leishmania MAPK and human ERK2 suggested several important differences in its ATP binding pocket. Such differences could be exploited in the future for designing Leishmania specific MAPK inhibitors.     

Manganese and cobalt recovery by surface display of metal binding peptide on various loops of OmpC in <Emphasis Type="Italic">Escherichia coli</Emphasis>

In a cell-surface display (CSD) system, successful display of a protein or peptide is highly dependent on the anchoring motif and the position of the display in that anchoring motif. In this study, a recombinant bacterial CSD system for manganese (Mn) and cobalt (Co) recovery was developed by employing OmpC as an anchoring motif on three different external loops. A portion of Cap43 protein (TRSRSHTSEG)₃ was employed as a manganese and cobalt binding peptide (MCBP), which was fused with OmpC at three different external loops. The fusions were made at the loop 2 [fusion protein-2 (FP2)], loop 6 (FP6), and loop 8 (FP8) of OmpC, respectively. The efficacy of the three recombinant strains in the recovery of Mn and Co was evaluated by varying the concentration of the respective metal. Molecular modeling studies showed that the short trimeric repeats of peptide probably form a secondary structure with OmpC, thereby giving rise to a difference in metal recovery among the three recombinant strains. Among the three recombinant strains, FP6 showed increased metal recovery with both Mn and Co, at 1235.14 (1 mM) and 379.68 (0.2 mM) µmol/g dry cell weight (DCW), respectively.     

Synergy between the KEAP1/NRF2 and PI3K Pathways Drives Non-Small-Cell Lung Cancer with an Altered Immune Microenvironment

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Immunogenic gangliosides in human ovarian carcinoma

Ganglioside signatures of four poorly and three moderately differentiated ovarian epithelial cancer (OEC) cell lines reveal the presence of GM3, GM2, GD2, O-AcGD2, GD1a and GM1b. The expression of GM3, presence of GD1a and GM1b in the ascitic fluid and plasma, together with a positive correlation in the total-gangliosides levels between ascitic fluid and plasma of OEC patients support the earlier contention that the tumor-gangliosides may be released (or shed) into the tumor-microenvironment. The immunogenicity of OEC-gangliosides is determined by comparing anti-ganglioside-IgM titers in ascitic fluid (n = 14) and plasma (n = 23) of OEC-patients and age-matched healthy (n = 14). The titers were measured by ELISA. Strikingly, the level of anti-GD1a-IgM is significantly higher in ascitic fluid and plasma of patients than in the plasma of healthy volunteers. Paired sample analysis of ascitic fluid and plasma from the same patients confirmed the significant expression of anti-GD1a IgM in OEC patients, while no such difference was observed with other anti-ganglioside IgMs among different groups. The significance of the endogenous IgM response to GD1a may be to eliminate this immunosuppressive-ganglioside from the tumor-microenvironment.     

Understanding the conformational flexibility and electrostatic properties of curcumin in the active site of rhAChE via molecular docking,molecular dynamics,and charge density analysis

Acetylcholinesterase (AChE) is an important enzyme responsible for Alzheimer’s disease, as per report, keto-enol form of curcumin inhibits this enzyme. The present study aims to understand the binding mechanism of keto-enol curcumin with the recombinant human Acetylcholinesterase (rhAChE) from its conformational flexibility, intermolecular interactions, charge density distribution, and the electrostatic properties at the active site of rhAChE. To accomplish this, a molecular docking analysis of curcumin with the rhAChE was performed, which gives the structure and conformation of curcumin in the active site of rhAChE. Further, the charge density distribution and the electrostatic properties of curcumin molecule (lifted from the active site of rhAChE) were determined from the high level density functional theory (DFT) calculations coupled with the charge density analysis. On the other hand, the curcumin molecule was optimized (gas phase) using DFT method and further, the structure and charge density analysis were also carried out. On comparing the conformation, charge density distribution and the electrostatic potential of the active site form of curcumin with the corresponding gas phase form reveals that the above said properties are significantly altered when curcumin is present in the active site of rhAChE. The conformational stability and the interaction of curcumin in the active site are also studied using molecular dynamics simulation, which shows a large variation in the conformational geometry of curcumin as well as the intermolecular interactions.     

Dihedral angle preferences of amino acid residues forming various non-local interactions in proteins

In theory, a polypeptide chain can adopt a vast number of conformations, each corresponding to a set of backbone rotation angles. Many of these conformations are excluded due to steric overlaps. Ramachandran and coworkers were the first to look into this problem by plotting backbone dihedral angles in a two-dimensional plot. The conformational space in the Ramachandran map is further refined by considering the energetic contributions of various non-bonded interactions. Alternatively, the conformation adopted by a polypeptide chain may also be examined by investigating interactions between the residues. Since the Ramachandran map essentially focuses on local interactions (residues closer in sequence), out of interest, we have analyzed the dihedral angle preferences of residues that make non-local interactions (residues far away in sequence and closer in space) in the folded structures of proteins. The non-local interactions have been grouped into different types such as hydrogen bond, van der Waals interactions between hydrophobic groups, ion pairs (salt bridges), and ππ-stacking interactions. The results show the propensity of amino acid residues in proteins forming local and non-local interactions. Our results point to the vital role of different types of non-local interactions and their effect on dihedral angles in forming secondary and tertiary structural elements to adopt their native fold.     

Revealing Anisotropic Spinel Formation on Pristine Li‐ and Mn‐Rich Layered Oxide Surface and Its Impact on Cathode Performance

Surface properties of cathode particles play important roles in the transport of ions and electrons and they may ultimately dominate cathode's performance and stability in lithium‐ion batteries. Through the use of carefully prepared Li_1.2Ni_0.13Mn_0.54Co_0.13O₂ crystal samples with six distinct morphologies, surface transition‐metal redox activities and crystal structural transformation are investigated as a function of surface area and surface crystalline orientation. Complementary depth‐profiled core‐level spectroscopy, namely, X‐ray absorption spectroscopy, electron energy loss spectroscopy, and atomic‐resolution scanning transmission electron microscopy, are applied in the study, presenting a fine example of combining advanced diagnostic techniques with a well‐defined model system of battery materials. The present study reports the following findings: (1) a thin layer of defective spinel with reduced transition metals, similar to what is reported on cycled conventional secondary particles in the literature, is found on pristine oxide surface even before cycling, and (2) surface crystal structure and chemical composition of both pristine and cycled particles are facet dependent. Oxide structural and cycling stabilities improve with maximum expression of surface facets stable against transition‐metal reduction. The intricate relationships among morphology, surface reactivity and structural transformation, electrochemical performance, and stability of the cathode materials are revealed.     

<Emphasis Type="Italic">Hemidesmus indicus</Emphasis> Protects against ethanol-induced liver toxicity

Alcoholic liver disease (ALD) is one of the most common diseases in modern society. A large number of studies are in progress aiming to identify natural substances that would be effective in reducing the severity of ALD. Although there are currently a number of drugs on the market, their long-term use can have numerous side effects. Hemidesmus indicus is an indigenous Ayurvedic medicinal plant used in soft drinks in India. In this study, we examined the effects of its ethanolic root extract on experimental liver damage in order to evaluate its hepatoprotective effects against hepatotoxicity induced in rats by ethanol at a dosage of 5 g/kg body weight for 60 days. The H. indicus root extract was given at a dose of 500 mg/kg body weight for the last 30 days of the experiment. The animals were monitored for food intake and weight gain. The liver was analysed for the degree of lipid peroxidation using thiobarbituric acid reactive substances (TBARS) and antioxidant status using the activities of glutathione-depedendant enzymes. The degree of liver damage was analysed using serum marker enzyme activities, the total protein, albumin, globulin, ceruloplasmin and liver glycogen contents, and the A/G ratio. The Fourier transform infrared spectra (FT-IR) of the liver tissues were recorded in the region of 4000–400 cm⁻¹. The ethanol-fed rats showed significantly elevated liver marker enzyme activities, lipid peroxidation levels and reduced antioxidant levels as compared to the control rats. Oral administration of H. indicus for the latter 30 days resulted in an increased food intake and weight gain, decreased TBARS levels, near normal levels of glutathione-dependent enzymes, increased total protein, albumin, globulin and liver glycogen contents, an increased A/G ratio, and decreased liver marker enzyme activities and ceruloplasmin levels. The relative intensity of the liver FT-IR bands for the experimental groups were found to be altered significantly (p < 0.05) compared to the control samples. For the group that had H. indicus co-administered with ethanol, the intensity of the bands was near normal. Moreover, the results of the FT-IR study correlated with our biochemical results.