Key genes and regulatory networks involved in the initiation, progression and invasion of colorectal cancer.

AIM: Until now, identification of drug targets for treatment of patients with specific stages of colorectal cancer (CRC) has remained a challenging field of research. Herein, we aimed to identify the key genes and regulatory networks involved in each stage of CRC. RESULTS: The results of gene expression profiles were integrated with protein-protein interaction networks, and topologically analyzed. The most important regulatory genes (e.g., CDK1, UBC, ESR1 and ATXN1) and signaling pathways (e.g., Wnt, MAPK and JAK-STAT) in CRC initiation, progression and metastasis were identified. In vitro analysis confirmed some in silico findings. CONCLUSION: Our study introduces functional hub genes, subnetworks, prioritizes signaling pathways and novel biomarkers in CRC that may guide further development of targeted therapy programs.

Immunomodulatory effects of a rationally designed peptide mimetic of human IFNß in EAE model of multiple sclerosis.

The efficiency of interferon beta (IFNß)-based drugs is considerably limited due to their undesirable properties, especially high immunogenicity. In this study, for the first time we investigated the impact of a computationally designed peptide mimetic of IFNß, called MSPEP27, in the animal model of MS. A peptide library was constructed using the Rosetta program based on the predominant IFNAR1-binding site of IFNß. Molecular docking studies were carried out using ClusPro and HADDOCK tools. The GROMACS package was subsequently used for molecular dynamics (MD) simulations. Validation of peptide-receptor interaction was carried out using intrinsic fluorescence measurements. To explore in silico findings further, experimental autoimmune encephalomyelitis (EAE) was induced by subcutaneous immunization of myelin oligodendrocyte glycoprotein (MOG35-55). Mice were then separated into distinct groups and intravenously received 10 or 20mgkg-1 of MSPEP27 or IFNß. The inflammatory mediators were monitored by immunohistochemistry (IL17, CD11b, CD45), quantitative real-time PCR (MMP2, MMP9, TIMP-1) and enzyme-linked immunosorbent assay (IL1ß, TNFα) methods. Among the library of tolerated peptides, MSPEP27, a peptide with favorable physicochemical properties, was chosen for further experiments. This peptide was shown to significantly interact with IFNAR1 in a dose-dependent manner. Like IFNß, MSPEP27 could efficiently bind to IFNAR1 and form a stable peptide-receptor complex during 30ns MD simulations. In vivo analyses revealed that MSPEP27 could lessen inflammation by modulating the levels of inflammatory mediators. According to our results, MSPEP27 peptide could efficiently bind to IFNAR1 and suppress neuroinflammation in vivo. We conclude that MSPEP27 has protective effects against MOG-induced EAE via reduction of immune dysfunction and inflammation.

In silico enhancement of the stability and activity of keratinocyte growth factor.

Keratinocyte growth factor (KGF), a member of the fibroblast growth factor (FGF) family, has been implicated in some biological processes such as cell proliferation, development and differentiation. High mitogenic activity of this protein has made it very suitable for repairing radiation-and chemotherapy-induced damages. Palifermin, which has been developed from human KGF, is clinically applied to reduce the incidence and duration of cancer therapeutic agents. However, the activity of Palifermin is limited during treatment due to its poor stability. In this study, we have improved the stability and activity of recombinant human KGF (Palifermin) using a computational mutagenesis approach. According to the KGF multiple sequence alignment among different species as well as literature-based information, we have generated several mutations using PyMOL program and evaluated their effects on the stability and activity of KGF in silico. In order to preserve the KGF activity, we did not change the predicted functional residues. Prior to mutagenesis, the 3D structure of rhKGF was predicted by Modeller v9.15 program and quantitative evaluation of predicted models were carried out using VADAR and PROSESS servers. The stability and activity of rhKGF mutants were analyzed using GROMACS molecular dynamics (MD) simulations and docking tools, respectively. The results showed that N159S (N105S in rhKGF sequence) and I172V (I118V in rhKGF) substitutions caused an increased stability and affinity of the rhKGF to Fibroblast growth factor receptor 2 (FGFR2). We will evaluate the effects of favorable mutations on the rhKGF stability and activity in vitro.

Sequence characterized amplified region marker as a tool for selection of high-artemisinin containing species of Artemisia.

Malaria is currently one of the most important causes of mortality in developing countries. High resistance to available antimalarial drugs has been reported frequently, thus it is crucial to focus on the discovery of new antimalarial drugs. Artemisinin, an effective antimalarial medication, is isolated from various Artemisia species. To identify the Artemisia species producing high quantity of artemisinin, eight species of Artemisia were screened with the genetic sequence characterized amplified region (SCAR) marker for higher quantity of artemisinin. The DNA band corresponding to SCAR marker was cloned into pGEM®-T Easy vector and sequenced. The content of artemisinin in tested species was also measured using high-performance liquid chromatography (HPLC) assay. The primers designed for high-artemisinin SCAR marker could amplify a specific band of approximately 1000 bp which was present in two Artemisia annua and Artemisia absinthium species. These SCAR marker sequences for two selected species were submitted into the GenBank databases under KC337116 and KC465952 accession numbers. HPLC analysis indicated that two selected Artemisia species, genetically recognized as high-artemisinin yielding plants, had higher artemisinin content in comparison to other examined species. Therefore, in this study, we propose developed SCAR marker as a complementary tool for confidently detection of high-artemisinin content in Artemisia species.

Diurnal Variation of Essential of the Oil Components of Pycnocycla spinosa Decne. ex Boiss.

BACKGROUND: Pycnocycla spinosa Decne. ex Boiss is an aromatic plant which showed relaxant effects on isolated ileum contractions and antidiarrheal activity. Thirty four components have been extracted from P. spinosa essential oil, of which several major constituents were found to show seasonal variation. OBJECTIVES: The aim of this work is to evaluate the diurnal variation of its oil constituents during specific hours of the day. MATERIALS AND METHODS: The Pycnocycla spinosa samples were collected at different times of the day. The hydro-distilled aerial parts oils of collected P. spinosa were analyzed by GC and GC/MS. RESULTS: Fourteen monoterpenoid and nine sesquiterpenoid components were identified, of which the fluctuating constituents were p-cymene, trans-ß-ocimene, ß-citronellol, citronellyl pentanoate, geranyl isovalerate, α-humulene, caryophyllen oxide, α-cadinol, and α-eudesmol. The content of p-cymene in the essential oil in different daily times varied from 0.16 to 4.19%, and the geranyl isovalerate 7.75 -23.99%. CONCLUSIONS: Essential oils with different qualities can be obtained according to the harvest time of the plant in a day.