Comparative molecular dynamics simulations of the potent synthetic classical cannabinoid ligand AMG3 in solution and at binding site of the CB1 and CB2 receptors

The C-1'-dithiolane Delta(8)-tetrahydrocannabinol (Delta(8)-THC) amphiphilic analogue (-)-2-(6a,7,10,10a-tetrahydro-6,6,9-trimethylhydroxy-6H-dibenzo[b,d]pyranyl)-2-hexyl-1,3-dithiolane (AMG3) is considered as one of the most potent synthetic analgesic cannabinoid (CB) ligands. Its structure is characterized by rigid tricyclic and flexible alkyl chain segments. Its conformational properties have not been fully explored. Structure-activity relationship (SAR) studies on classical CBs showed that the alkyl side chain is the most critical structural part for the receptor activation. However, reported low energy conformers of classical CB analogues vary mainly in the conformation of their alkyl side chain segment. Therefore, comparative molecular dynamics (MD) simulations of low energy conformers of AMG3 were performed in order to investigate its structural and dynamical properties in two different systems. System-I includes ligand and amphoteric solvent DMSO, simulating the biological environment and system-II includes ligand at active site of the homology models of CB1 and CB2 receptors in the solvent. The trajectory analysis results are compared for the systems I and II. In system-I, the dihedral angle defined between aromatic ring and dithiolane ring of AMG3 shows more resistance to be transformed into another torsional angle and the dihedral angle adjacent to dithiolane ring belonging in the alkyl chain has flexibility to adopt gauche+/- and trans dihedral angles. The rest of the dihedral angles within the alkyl chain are all trans. These results point out that wrapped conformations are dynamically less favored in solution than linear conformations. Two possible plane angles defined between the rigid and flexible segments are found to be the most favored and adopting values of approximately 90 degrees and approximately 140 degrees. In system-II, these values are approximately 90 degrees and approximately 120 degrees. Conformers of AMG3 at the CB1 receptor favor to establish a cis conformation defined between aromatic and dithiolane ring and a trans conformation in the CB2 receptor. These different orientations of ligand inside the binding pocket of CB1 and CB2 receptors may explain its different binding affinity in the two receptors. The results of this study can be applied to other synthetic classical CB ligands to produce low energy conformations and can be of general use for the molecules possessing flexible alkyl chain(s). In addition, this study can be useful when restraint of the alkyl chain is sought for optimizing drug design.     

A mechanical model representation of the in vivo creep behaviour of muscular bulk tissue

In vivo mechanical properties of bulk tissue have not yet been explored sufficiently. One of the major problems researchers face is the lack of agreement between the constitutive models and the standardised methodologies for experimental studies. The object of this study was to obtain bulk modulus of the upper arm under relaxed and controlled contraction that was 25% of the maximum voluntary contraction. A new testing machine was designed to generate constant load on the upper arm and measure the deformation over time. This device is effectively a cuff that applies controllable pressure on a 47-mm wide band of the upper arm. Six different loads (10, 20, 30, 40, 50 and 60 kgf) were applied over a time of up to a maximum of 120 s. The deflection-time curves obtained show strongly non-linear responses of the bulk tissue. The non-linearity manifested by these deflection-time curves is in terms of both time- and load-dependency. A specific mechanical model was developed to represent the creep behaviour of the bulk tissue. The creep behaviour of the upper arm can be simulated by using four Voigt viscoelastic models in series. The three obvious soft tissues of the upper arm, namely skin, fat and muscle, were modelled in series. The effects of blood vessels and connective tissue were also modelled in series with the previous ones. A mechanical model would provide a more controlled method of studying the mechanical properties of the bulk tissue. The purpose of the current research, therefore, was to develop a mechanical model, which would predict the non-linear, viscoelastic behaviour of the human muscular bulk tissue.     

Expression of Estrogen-Related Gene Markers in Breast Cancer Tissue Predicts Aromatase Inhibitor Responsiveness

Aromatase inhibitors (AIs) are the most effective class of drugs in the endocrine treatment of breast cancer, with an approximate 50% treatment response rate. Our objective was to determine whether intratumoral expression levels of estrogen-related genes are predictive of AI responsiveness in postmenopausal women with breast cancer. Primary breast carcinomas were obtained from 112 women who received AI therapy after failing adjuvant tamoxifen therapy and developing recurrent breast cancer. Tumor ERα and PR protein expression were analyzed by immunohistochemistry (IHC). Messenger RNA (mRNA) levels of 5 estrogen-related genes–AKR1C3, aromatase, ERα, and 2 estradiol/ERα target genes, BRCA1 and PR–were measured by real-time PCR. Tumor protein and mRNA levels were compared with breast cancer progression rates to determine predictive accuracy. Responsiveness to AI therapy–defined as the combined complete response, partial response, and stable disease rates for at least 6 months–was 51%; rates were 56% in ERα-IHC-positive and 14% in ERα-IHC-negative tumors. Levels of ERα, PR, or BRCA1 mRNA were independently predictive for responsiveness to AI. In cross-validated analyses, a combined measurement of tumor ERα and PR mRNA levels yielded a more superior specificity (36%) and identical sensitivity (96%) to the current clinical practice (ERα/PR-IHC). In patients with ERα/PR-IHC-negative tumors, analysis of mRNA expression revealed either non-significant trends or statistically significant positive predictive values for AI responsiveness. In conclusion, expression levels of estrogen-related mRNAs are predictive for AI responsiveness in postmenopausal women with breast cancer, and mRNA expression analysis may improve patient selection.     

Simultaneous determination of urinary 1- and 2-naphthols, 3- and 9-phenanthrols,and 1-pyrenol in coke oven workers

A method was developed for simultaneous quantification of urinary 1- and 2-naphthols, 3- and 9-phenanthrols and 1-pyrenol using gas chromatography with mass spectrometry (GC-MS). This method was applied to urine samples from coke oven workers (n =28) and controls (n =22) from Northern China. Geometric mean levels of urinary 1-naphthol (58.8 μg l^?1), 2-naphthol (34.1 μg l^?1), 3-phenanthrol (7.35 μg l^?1), 9-phenanthrol (1.28 μg l^?1) and 1-pyrenol (25.4 μg l^?1) were significantly higher among coke oven workers than controls. All the substances tested were highest among top-of-oven workers, who had 15-fold higher 1-naphthol, eight-fold higher 2-naphthol and 20-fold higher 1-pyrenol levels compared with controls. Using multiple linear regression models, 72.5% of the variation in 1- and 2-naphthol and 82.8% of the variation in 1-pyrenol were explained by the concentration of naphthalene or pyrene in the urine, the work category and the smoking intensity. Cigarette consumption significantly contributed to levels of urinary 1-pyrenol and naphthols, particularly 2-naphthol. A negative relationship between work category and the ratio of naphthols/1-pyrenol was observed among smokers. Our results suggest that urinary naphthols and phenanthrols reflect polycyclic aromatic hydrocarbon (PAH) exposure as well as the widely used 1-pyrenol, and that interactions between cigarette smoking and PAH exposure result in different patterns of metabolism for individual PAHs.     

Accurate determination of the binding free energy for KcsA-charybdotoxin complex from the potential of mean force calculations with restraints

Free energy calculations for protein-ligand dissociation have been tested and validated for small ligands (50 atoms or less), but there has been a paucity of studies for larger, peptide-size ligands due to computational limitations. Previously we have studied the energetics of dissociation in a potassium channel-charybdotoxin complex by using umbrella sampling molecular-dynamics simulations, and established the need for carefully chosen coordinates and restraints to maintain the physiological ligand conformation. Here we address the ligand integrity problem further by constructing additional potential of mean forces for dissociation of charybdotoxin using restraints. We show that the large discrepancies in binding free energy arising from simulation artifacts can be avoided by using appropriate restraints on the ligand, which enables determination of the binding free energy within the chemical accuracy. We make several suggestions for optimal choices of harmonic potential parameters and restraints to be used in binding studies of large ligands.     

Pollen morphology and anatomical features of Lilium (Liliaceae) taxa from Turkey

In this study, pollen grains and anatomical features of Turkish lilies were investigated under the electron (SEM) and light (LM) microscope. LM and SEM observations showed that the pollen grains are monosulcate, heteropolar, elliptical in polar view and oblate. Numerical results based on combined palynological and anatomical characters were discussed and compared with traditional taxonomic treatments. It was found that the midrib shape, mesophyll type, P/E (polar/equatorial), sulcus length, and lumina width are the most valuable traits in separating the examined taxa. The numerical analysis showed that Lilium candidum L. differs from the rest Turkish Lilium and also confirmed a close relationship between L. szovitsianum Fisch. & Avé-Lall. and L. armenum Miscz. ex Grossh. Also this study is the first report dealing with anatomical and palynological features of all Turkish lilies.     

Evaluation of Factor V G1691A,prothrombin G20210A,Factor XIII V34L,MTHFR A1298C,MTHFR C677T and PAI-1 4G/5G genotype frequencies of patients subjected to cardiovascular disease (CVD) panel in south-east region of Turkey

Cardiovascular disease (CVD) risk factors, such as arterial hypertension, obesity, dyslipidemia or diabetes mellitus, as well as CVDs, including myocardial infarction, coronary artery disease or stroke, are the most prevalent diseases and account for the major causes of death worldwide. In the present study, 4,709 unrelated patients subjected to CVD panel in south-east part of Turkey between the years 2010 and 2013 were enrolled and DNA was isolated from the blood samples of these patients. Mutation analyses were conducted using the real-time polymerase chain reaction method to screen six common mutations (Factor V G1691A, PT G20210A, Factor XIII V34L, MTHFR A1298C and C677T and PAI-1 ?675 4G/5G) found in CVD panel. The prevalence of these mutations were 0.57, 0.25, 2.61, 13.78, 9.34 and 24.27 % in homozygous form, respectively. Similarly, the mutation percent of them in heterozygous form were 7.43, 3.44, 24.91, 44.94, 41.09 and 45.66 %, respectively. No mutation was detected in 92 (1.95 %) patients in total. Because of the fact that this is the first study to screen six common mutations in CVD panel in south-east region of Turkey, it has a considerable value on the diagnosis and treatment of these diseases. Upon the results of the present and previous studied a careful examination for these genetic variants should be carried out in thrombophilia screening programs, particularly in Turkish population.     

Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network

Background

Mycobacterium tuberculosis is characterized by a low mutation rate and a lack of genetic recombination. Yet, the rise of extensively resistant strains paints a picture of a microbe with an impressive adaptive potential. Here we describe the first documented case of extensively drug-resistant tuberculosis evolved from a susceptible ancestor within a single patient.

Results

Genome sequences of nine serial M. tuberculosis isolates from the same patient uncovered a dramatic turnover of competing lineages driven by the emergence, and subsequent fixation or loss of single nucleotide polymorphisms. For most drugs, resistance arose through independent emergence of mutations in more than one clone, of which only one ultimately prevailed as the clone carrying it expanded, displacing the other clones in the process. The vast majority of mutations identified over 3.5 years were either involved in drug resistance or hitchhiking in the genetic background of these. Additionally, RNA-sequencing of isolates grown in the absence of drug challenge revealed that the efflux-associated iniBAC operon was up-regulated over time, whereas down-regulated genes include those involved in mycolic acid synthesis.

Conclusions

We observed both rapid acquisitions of resistance to antimicrobial compounds mediated by individual mutations as well as a gradual increase in fitness in the presence of antibiotics, likely driven by stable gene expression reprogramming. The rapid turnover of resistance mutations and hitchhiking neutral mutations has major implications for inferring tuberculosis transmission events in situations where drug resistance evolves within transmission chains.     

Presentation of a new mutation in FMF and evaluating the frequency of distribution of the MEFV gene mutation in our region with clinical findings

Molecular Biology Reports - Familial Mediterranean Fever (FMF), which is an autosomal recessive disease characterized by recurrent self-limiting fever, peritonitis, pleuritis, arthritis and...