Isolation of four new pterocarpans from Zygophyllum eurypterum (Syn. Z. atriplicoides) with enzyme-inhibition properties

Four new pterocarpans, atricarpan A (=(-)-1,2-dihydroxy-4-(hydroxymethyl)-3,9-dimethoxypterocarpan; 1), atricarpan B (=(-)-2,3-ethylenedioxy)-1,4-dihydroxy-9-methoxypterocarpan; 2), atricarpan C (=(-)-1,9-dimethoxypterocarpan-3-carboxylic acid; 3), and atricarpan D (=(-)-2,9-dimethoxy-4-(5-oxohexyl)pterocarpan; 4) were isolated from the BuOH extract of the whole plant of Zygophyllum eurypterum. The structure elucidations of those compounds were based primarily on 1D- and 2D-NMR analysis, including COSY, HMBC, and HMQC correlations. Compounds 1-4 also inhibited butyrylcholinesterase (BChE; EC 3.1.1.8) enzyme in a concentration-dependent manner with IC(50) values between 12.5-65.0 microM. Similarly, compounds 1 and 4 inhibited lipoxygenase (LOX; EC 1.13.11.12) and acetylcholinesterase (AChE; EC 3.1.1.7) enzymes with IC50 values of 13.5 and 20.5 muM, respectively.     

Proteomics in clinical trials and practice: present uses and future promise

The study of clinical proteomics is a promising new field that has the potential to have many applications, including the identification of biomarkers and monitoring of disease, especially in the field of oncology. Expression proteomics evaluates the cellular production of proteins encoded by a particular gene and exploits the differential expression and post-translational modifications of proteins between healthy and diseased states. These biomarkers may be applied towards early diagnosis, prognosis, and prediction of response to therapy. Functional proteomics seeks to decipher protein-protein interactions and biochemical pathways involved in disease biology and targeted by newer molecular therapeutics. Advanced spectrometry technologies and new protein array formats have improved these analyses and are now being applied prospectively in clinical trials. Further advancement of proteomics technology could usher in an era of personalized molecular medicine, where diseases are diagnosed at earlier stages and where therapies are more effective because they are tailored to the protein expression of a patient's malignancy.     

Toxic and Antifeedant Effects of Different Pesticidal Plant Extracts against Beet Armyworm (<i>Spodoptera exigua</i>)

The beet armyworm (BAW), Spodoptera exigua (Lepidoptera: Noctuidae) is a highly destructive pest of vegetables and field crops. Management of beet armyworm primarily relies on synthetic pesticides, which is threatening the beneficial community and environment. Most importantly, the BAW developed resistance to synthetic pesticides with making it difficult to manage. Therefore, alternative and environment-friendly pest management tactics are urgently required. The use of pesticidal plant extracts provides an effective way for a sustainable pest management program. To evaluate the use of pesticidal plant extracts against BAW, we selected six plant species (Lantana camara, Aloe vera, Azadirachta indica, Cymbopogon citratus, Nicotianatabacum, and Ocimum basilicum) for initial screening experiment. Four out of six plant species such as A. indica, N. tabacum, C. citratus and O. basilicum showed promising mortality of more than 50%. Therefore, we selected these four plant extracts for the subsequent experiments. Through contact bioassay, A. indica showed high mortality 66.63%, followed by the N. tabacum 53.33%, at 10% w/v concentration. Similarly, N. tabacum showed the highest mortality rate, 66% at 10% w/v concentration, followed by the A. indica 46% through feeding bioassay. Furthermore, the feeding deterrence assay showed that C. citratus had a high antifeedant index (−50) followed by A. indica (−39), and N. tabacum (−28). In living plant assay, the N. tabacum extract showed a low mean damage score 3.6 on living cotton plant followed by C. citratus 4.5 and A. indica 5.5. Hence, extracts of three plant species provided promising results against the BAW, which can minimize the use of synthetic chemicals, particularly for small landholding farmers. Further studies are also required to evaluate the effects of these plant extract against BAW on cotton plants under field conditions to optimize the further use.     

Identification, sequence characterization, and analysis of expression profiles of three novel CC chemokines from domestic duck (Anas platyrhynchos)

Chemokines are low-molecular weight-chemotactic cytokines, which are involved in lymphocyte trafficking and migration of leucocytes to sites of injury, in immune surveillance and in healing process. They also play a role in pathogenesis of inflammatory diseases. Three novel CC chemokines were identified from domestic duck (Anas platyrhynchos) by screening of an enriched cDNA library constructed from mitogen-stimulated splenic mononuclear cells. Two of the clones (AB163 and AB330) had a very high nucleotide (both about 81%) and predicted amino acid level (71 and 76%, respectively) identity to the reported chicken macrophage inflammatory protein 1- (MIP-1; SCYA4) and regulated upon activation of normal T-cell expressed and secreted (RANTES; SCYA5) sequences. In phylogenetic analysis, these molecules clustered together with corresponding chemokines reported from other vertebrates. The third clone (AB187) had highest homology to chicken MIP-1 (36% amino acid identity) and showed closer relation to a number of chemokines belonging to monocyte chemoattractant proteins and MIP-1 chemokines. Expression of these molecules was upregulated upon mitogen stimulation of splenocytes as detected by semiquantitative RT-PCR. AB187 showed several fold increases (about 8.5 times) in the mRNA expression. Basal level expression of some of these chemokines was detected in both lymphoid and nonlymphoid tissues, including spleen, liver, lung, and bone marrow. Considering the importance of this animal species as a model for diseases such as chronic human hepatitis B, further studies will offer valuable insights into the role of these molecules in immunopathology of such diseases.The nucleotide sequences that are reported in this paper have been submitted to the NCBI Genbank database. Accession nos. AB163 (AY641435), AB187 (AY641436), and AB330 (AY641437).     

Mutational spectrum of BRAF gene in colorectal cancer patients in Saudi Arabia

Colorectal cancer (CRC) is one of the topmost causes of death in males in Saudi Arabia. In females, it was also within the top five cancer types. CRC is heterogeneous in terms of pathogenicity and molecular genetic pathways. It is very important to determine the genetic causes of CRC in the Saudi population. BRAF is one of the major genes involved in cancers, it participates in transmitting chemical signals from outside the cells into the nucleus of the cells and it is also shown to participate in cell growth. In this study, we mapped the spectrum of BRAF mutations in 100 Saudi patients with CRC. We collected tissue samples from colorectal cancer patients, sequenced the BRAF gene to identify gene alterations, and analyzed the data using different bioinformatics tools. We designed a three-dimensional (3D) homology model of the BRAF protein using the Swiss Model automated homology modeling platform to study the structural impact of these mutations using the Missense3D algorithm. We found six mutations in 14 patients with CRC. Four of these mutations are being reported for the first time. The novel frameshift mutations observed in CRC patients, such as c.1758delA (E586E), c.1826insT (Q609L), c.1860insA and c.1860insA/C (M620I), led to truncated proteins of 589, 610, and 629 amino acids, respectively, and potentially affected the structure and the normal functions of BRAF. These findings provide insights into the molecular etiology of CRC in general and to the Saudi population. BRAF genetic testing may also guide treatment modalities, and the treatment may be optimized based on personalized gene variations.     

Disease associated cellular machinery in anaphylaxis – And the de novo paradigm shift

Anaphylaxis is a sudden immune reaction against an allergen that can potentially lead to Anaphylactic Shock (AS). This immune reaction is characterized by an increase in Immunoglobulin-E (IgE) type of antibodies that bind with FcεRI receptors on mast cells to release inflammatory mediators. Various intracellular signaling molecules downstream of IgE/ FcεRI axis play a potential role in cytokine, chemokine and eicosanoid secretion as well as degranulation of immune cells causing vasodilation, vascular permeability, and reduction of intravascular volume leading to cardiovascular collapse. Here, we discuss the cellular machinery of anaphylaxis and the de novo paradigm shift in the cellular aspects of AS.     

A Ubl/ubiquitin switch in the activation of Parkin

Mutations in Parkin and PINK1 cause an inherited early‐onset form of Parkinson's disease. The two proteins function together in a mitochondrial quality control pathway whereby PINK1 accumulates on damaged mitochondria and activates Parkin to induce mitophagy. How PINK1 kinase activity releases the auto‐inhibited ubiquitin ligase activity of Parkin remains unclear. Here, we identify a binding switch between phospho‐ubiquitin (pUb) and the ubiquitin‐like domain (Ubl) of Parkin as a key element. By mutagenesis and SAXS, we show that pUb binds to RING1 of Parkin at a site formed by His302 and Arg305. pUb binding promotes disengagement of the Ubl from RING1 and subsequent Parkin phosphorylation. A crystal structure of Parkin Δ86–130 at 2.54 Å resolution allowed the design of mutations that specifically release the Ubl domain from RING1. These mutations mimic pUb binding and promote Parkin phosphorylation. Measurements of the E2 ubiquitin‐conjugating enzyme UbcH7 binding to Parkin and Parkin E3 ligase activity suggest that Parkin phosphorylation regulates E3 ligase activity downstream of pUb binding.     

Comparative proteomics analysis of sarcosine insoluble outer membrane proteins from clarithromycin resistant and sensitive strains of Helicobacter pylori

Helicobacter pylori causes disease manifestations in humans including chronic gastric and peptic ulcers, gastric cancer, and lymphoid tissue lymphoma. Increasing rates of H. pylori clarithromycin resistance has led to higher rates of disease development. Because antibiotic resistance involves modifications of outer membrane proteins (OMP) in other Gram-negative bacteria, this study focuses on identification of H. pylori OMP’s using comparative proteomic analyses of clarithromycin-susceptible and -resistant H. pylori strains. Comparative proteomics analyses of isolated sarcosine-insoluble OMP fractions from clarithromycin-susceptible and -resistant H. pylori strains were performed by 1) one dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis protein separation and 2) in-gel digestion of the isolated proteins and mass spectrometry analysis by Matrix Assisted Laser Desorption Ionization-tandem mass spectrometry. Iron-regulated membrane protein, UreaseB, EF-Tu, and putative OMP were down-regulated; HopT (BabB) transmembrane protein, HofC, and OMP31 were up-regulated in clarithromycin-resistant H. pylori. Western blotting and real time PCR, respectively, validated UreaseB subunit and EF-Tu changes at the protein level, and mRNA expression of HofC and HopT. This limited proteomic study provides evidence that alteration of the outer membrane proteins’ profile may be a novel mechanism involved in clarithromycin resistance in H. pylori.     

iDRP-PseAAC: Identification of DNA Replication Proteins Using General PseAAC and Position Dependent Features

International Journal of Peptide Research and Therapeutics - DNA replication is one of the specific processes to be considered in all the living organisms, specifically eukaryotes. The prevalence...