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Diet-induced metabolic changes of the human gut microbiome: importance of short-chain fatty acids, methylamines and indoles.
Abdul Rahim, MBH, Chilloux, J, Martinez-Gili, L, Neves, AL, Myridakis, A, Gooderham, N, Dumas, ME
Acta diabetologica. 2019;(5):493-500
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Abstract
The human gut is a home for more than 100 trillion bacteria, far more than all other microbial populations resident on the body's surface. The human gut microbiome is considered as a microbial organ symbiotically operating within the host. It is a collection of different cell lineages that are capable of communicating with each other and the host and has an ability to undergo self-replication for its repair and maintenance. As the gut microbiota is involved in many host processes including growth and development, an imbalance in its ecological composition may lead to disease and dysfunction in the human. Gut microbial degradation of nutrients produces bioactive metabolites that bind target receptors, activating signalling cascades, and modulating host metabolism. This review covers current findings on the nutritional and pharmacological roles of selective gut microbial metabolites, short-chain fatty acids, methylamines and indoles, as well as discussing nutritional interventions to modulate the microbiome.
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Chemical Aspects of Biological Activity of Isothiocyanates and Indoles, the Products of Glucosinolate Decomposition.
Kołodziejski, D, Koss-Mikołajczyk, I, Abdin, AY, Jacob, C, Bartoszek, A
Current pharmaceutical design. 2019;(15):1717-1728
Abstract
There is growing evidence that cancer chemoprevention employing natural, bioactive compounds may halt or at least slow down the different stages of carcinogenesis. A particularly advantageous effect is attributed to derivatives of sulfur-organic phytochemicals, such as glucosinolates (GLs) synthesized mainly in Brassicaceae plant family. GLs are hydrolysed enzymatically to bioactive isothiocyanates (ITC) and indoles, which exhibit strong anti-inflammatory and anti-carcinogenic activity. Highly bioavailable electrophilic ITC are of particular interest, as they can react with nucleophilic groups of important biomolecules to form dithiocarbamates, thiocarbamates and thioureas. These modifications seem responsible for the chemopreventive activity, but also for genotoxicity and mutagenicity. It was documented that ITC can permanently bind to important biomolecules such as glutathione, cytoskeleton proteins, transcription factors NF-κB and Nrf2, thiol-disulfide oxidoreductases, proteasome proteins or heat shock proteins. Furthermore, ITC may also affect epigenetic regulation of gene expression, e.g. by inhibition of histone deacetylases. Some other derivatives of glucosinolates, especially indoles, are able to form covalent bonds with nucleobases in DNA, which may result in genotoxicity and mutagenicity. This article summarizes the current state of knowledge about glucosinolates and their degradation products in terms of possible interactions with reactive groups of cellular molecules.
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3.
Dynamics of water and ions around DNA: What is so special about them?
Shweta, H, Sen, S
Journal of biosciences. 2018;(3):499-518
Abstract
Water around biomolecules is special for behaving strangely - both in terms of structure and dynamics, while ions are found to control various interactions in biomolecules such as DNA, proteins and lipids. The questions that how water and ions around these biomolecules behave in terms of their structure and dynamics, and how they affect the biomolecular functions have triggered tremendous research activities worldwide. Such activities not only unfolded important static and dynamic properties of water and ions around these biomolecules, but also provoked heated debate regarding their explanation and role in biological functions. DNA, being negatively charged, interacts strongly with the surrounding dipolar water and positively charged counterions, leading to complex electrostatic coupling of water and ions with the DNA. Recent timeresolved fluorescence Stokes shift experiments and related computer simulation studies from our and other laboratories have unfolded some unique dynamic characteristics of water and ions near different structures of DNA. These results are discussed here to showcase the specialty of water and ion dynamics around DNA.
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4.
Fluvastatin for lowering lipids.
Adams, SP, Sekhon, SS, Tsang, M, Wright, JM
The Cochrane database of systematic reviews. 2018;(3):CD012282
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Abstract
BACKGROUND Fluvastatin is thought to be the least potent statin on the market, however, the dose-related magnitude of effect of fluvastatin on blood lipids is not known. OBJECTIVES Primary objectiveTo quantify the effects of various doses of fluvastatin on blood total cholesterol, low-density lipoprotein (LDL cholesterol), high-density lipoprotein (HDL cholesterol), and triglycerides in participants with and without evidence of cardiovascular disease.Secondary objectivesTo quantify the variability of the effect of various doses of fluvastatin.To quantify withdrawals due to adverse effects (WDAEs) in randomised placebo-controlled trials. SEARCH METHODS The Cochrane Hypertension Information Specialist searched the following databases for randomised controlled trials up to February 2017: the Cochrane Central Register of Controlled Trials (CENTRAL) (2017, Issue 1), MEDLINE (1946 to February Week 2 2017), MEDLINE In-Process, MEDLINE Epub Ahead of Print, Embase (1974 to February Week 2 2017), the World Health Organization International Clinical Trials Registry Platform, CDSR, DARE, Epistemonikos and ClinicalTrials.gov. We also contacted authors of relevant papers regarding further published and unpublished work. No language restrictions were applied. SELECTION CRITERIA Randomised placebo-controlled and uncontrolled before and after trials evaluating the dose response of different fixed doses of fluvastatin on blood lipids over a duration of three to 12 weeks in participants of any age with and without evidence of cardiovascular disease. DATA COLLECTION AND ANALYSIS Two review authors independently assessed eligibility criteria for studies to be included, and extracted data. We entered data from placebo-controlled and uncontrolled before and after trials into Review Manager 5 as continuous and generic inverse variance data, respectively. WDAEs information was collected from the placebo-controlled trials. We assessed all trials using the 'Risk of bias' tool under the categories of sequence generation, allocation concealment, blinding, incomplete outcome data, selective reporting, and other potential biases. MAIN RESULTS One-hundred and forty-five trials (36 placebo controlled and 109 before and after) evaluated the dose-related efficacy of fluvastatin in 18,846 participants. The participants were of any age with and without evidence of cardiovascular disease, and fluvastatin effects were studied within a treatment period of three to 12 weeks. Log dose-response data over doses of 2.5 mg to 80 mg revealed strong linear dose-related effects on blood total cholesterol and LDL cholesterol and a weak linear dose-related effect on blood triglycerides. There was no dose-related effect of fluvastatin on blood HDL cholesterol. Fluvastatin 10 mg/day to 80 mg/day reduced LDL cholesterol by 15% to 33%, total cholesterol by 11% to 25% and triglycerides by 3% to 17.5%. For every two-fold dose increase there was a 6.0% (95% CI 5.4 to 6.6) decrease in blood LDL cholesterol, a 4.2% (95% CI 3.7 to 4.8) decrease in blood total cholesterol and a 4.2% (95% CI 2.0 to 6.3) decrease in blood triglycerides. The quality of evidence for these effects was judged to be high. When compared to atorvastatin and rosuvastatin, fluvastatin was about 12-fold less potent than atorvastatin and 46-fold less potent than rosuvastatin at reducing LDL cholesterol. Very low quality of evidence showed no difference in WDAEs between fluvastatin and placebo in 16 of 36 of these short-term trials (risk ratio 1.52 (95% CI 0.94 to 2.45). AUTHORS' CONCLUSIONS Fluvastatin lowers blood total cholesterol, LDL cholesterol and triglyceride in a dose-dependent linear fashion. Based on the effect on LDL cholesterol, fluvastatin is 12-fold less potent than atorvastatin and 46-fold less potent than rosuvastatin. This review did not provide a good estimate of the incidence of harms associated with fluvastatin because of the short duration of the trials and the lack of reporting of adverse effects in 56% of the placebo-controlled trials.
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Clinical pharmacokinetics of panobinostat, a novel histone deacetylase (HDAC) inhibitor: review and perspectives.
Srinivas, NR
Xenobiotica; the fate of foreign compounds in biological systems. 2017;(4):354-368
Abstract
1. Panobinostat is a recently approved histone deacetylase (HDAC) inhibitor. 2. The pharmacokinetic data of panobinostat in patients with hematologic malignancies and advanced solid tumors have been collated and reviewed from the various published clinical studies for over a decade. Further perspectives and anticipated challenges in the clinical therapy with panobinostat are discussed in the review. 3. Regardless of intravenous or oral dosing, panobinostat showed a high degree of inter-patient variability in the pharmacokinetics. After oral administration, most of the administered dose is extensively metabolized and the metabolites are either fecally or renally excreted with trace amount of intact panobinostat. Both cytochrome p450 (CYP) 3A4 and non-CYP mechanisms govern the clearance of panobinostat. CYP3A4-related drug-drug interactions with panobinostat have been documented with ketoconazole (inhibitor) and dexamethasone (inducer). 4. In summary, the clinical pharmacokinetic data of panobinostat, a promising HDAC inhibitor, obtained from various clinical studies do not appear to limit the utility of panobinostat in the clinic.
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Efficacy of sequential therapies with sorafenib-sunitinib versus sunitinib-sorafenib in metastatic renal cell carcinoma: A systematic review and meta-analysis.
Wen, T, Xiao, H, Luo, C, Huang, L, Xiong, M
Oncotarget. 2017;(12):20441-20451
Abstract
The most efficient sequence of targeted agents for metastatic renal cell carcinoma patients has yet to be identified. Whether the sequence of sorafenib and sunitinib really matters is controversial and not answered clearly until now. This meta-analysis aims to estimate the efficacy of receptor tyrosine kinase inhibitors sorafenib-sunitinib and sunitinib-sorafenib for metastatic renal cell carcinoma, on the outcome of first-line progression-free survival, second-line progression-free survival, total progression-free survival and overall survival.We searched PubMed, Embase, Cochrane Library and ClinicalTrails.gov for eligible studies. Data were analyzed using random or fixed effects model depending on the heterogeneity of the eligible studies. Heterogeneity across studies were analyzed using Q and I2 statistics.Of 902 identified studies, ten were qualified in our analysis (N = 1732 patients). Sorafenib-sunitinib yielded no statistically significant benefit in first-line progression-free survival (fixed effects; HR = 0.95; 95%CI 0.75-1.21; p = 0.702), total progression-free survival (random effects; HR = 0.92; 95%CI 0.71-1.19; p = 0.531) and overall survival (fixed effects; HR = 0.89; 95%CI 0.72-1.09; p = 0.257), compared with sunitinib-sorafenib. Second-line progression-free survival was longer for sorafenib-sunitinib than sunitinib-sorafenib (fixed effects; HR = 0.55; 95%CI 0.44-0.68; p = 0.000).Sequential therapies with sorafenib and sunitinib is well tolerated and efficient in mRCC. However, there are no evidence supported that sorafenib-sunitinib has the superiority to sunitinib-sorafenib in sequence. The ideal sequence of targeted agents requires further elucidation.
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A cautionary (spectral) tail: red-shifted fluorescence by DAPI-DAPI interactions.
Omelon, S, Georgiou, J, Habraken, W
Biochemical Society transactions. 2016;(1):46-9
Abstract
The fluorescent dye DAPI is useful for its association with and consequent amplification of an ∼460 nm emission maximum upon binding to dsDNA. Labelling with higher DAPI concentrations is a technique used to reveal Pi polymers [polyphosphate (polyP)], with a red-shift to ∼520-550 nm fluorescence emission. DAPI-polyP emissions of ∼580 nm are also generated upon 415 nm excitation. Red-shifted DAPI emission has been associated with polyP and RNA and has more recently been reported with polyadenylic acid (polyA), specific inositol phosphates (IPs) and heparin. We find that amorphous calcium phosphate (ACP) also demonstrates red-shifted DAPI emission at high DAPI concentrations. This DAPI spectral shift has been attributed to DAPI-DAPI electrostatic interactions enabled by molecules with high negative charge density that increase the local DAPI concentration and favour DAPI molecular proximity, as observed by increasing the dye/phosphate ratio. Excitation of dry DAPI (∼360 nm) confirmed a red-shifted DAPI emission. Whereas enzymatic approaches to modify substrates can help define the nature of DAPI fluorescence signals, multiple approaches beyond red-shifted DAPI excitation/emission are advised before conclusions are drawn about DAPI substrate identification.
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Evolutionary formation of gene clusters by reorganization: the meleagrin/roquefortine paradigm in different fungi.
Martín, JF, Liras, P
Applied microbiology and biotechnology. 2016;(4):1579-1587
Abstract
The biosynthesis of secondary metabolites in fungi is catalyzed by enzymes encoded by genes linked in clusters that are frequently co-regulated at the transcriptional level. Formation of gene clusters may take place by de novo assembly of genes recruited from other cellular functions, but also novel gene clusters are formed by reorganization of progenitor clusters and are distributed by horizontal gene transfer. This article reviews (i) the published information on the roquefortine/meleagrin/neoxaline gene clusters of Penicillium chrysogenum (Penicillium rubens) and the short roquefortine cluster of Penicillium roqueforti, and (ii) the correlation of the genes present in those clusters with the enzymes and metabolites derived from these pathways. The P. chrysogenum roq/mel cluster consists of seven genes and includes a gene (roqT) encoding a 12-TMS transporter protein of the MFS family. Interestingly, the orthologous P. roquefortine gene cluster has only four genes and the roqT gene is present as a residual pseudogene that encodes only small peptides. Two of the genes present in the central region of the P. chrysogenum roq/mel cluster have been lost during the evolutionary formation of the short cluster and the order of the structural genes in the cluster has been rearranged. The two lost genes encode a N1 atom hydroxylase (nox) and a roquefortine scaffold-reorganizing oxygenase (sro). As a consequence P. roqueforti has lost the ability to convert the roquefortine-type carbon skeleton to the glandicoline/meleagrin-type scaffold and is unable to produce glandicoline B, meleagrin and neoxaline. The loss of this genetic information is not recent and occurred probably millions of years ago when a progenitor Penicillium strain got adapted to life in a few rich habitats such as cheese, fermented cereal grains or silage. P. roqueforti may be considered as a "domesticated" variant of a progenitor common to contemporary P. chrysogenum and related Penicillia.
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New treatments in idiopathic pulmonary fibrosis.
Strâmbu, I
Pneumologia (Bucharest, Romania). 2016;(3):127-32
Abstract
Idiopathic pulmonary fibrosis is a chronic fibrotic pulmonary disease of unknown origin, with an unfavourable prognosis, leading to death by respiratory failure in most patients within 3-5 years ofdiagnosis. Several drugs were studied for the treatment of this disease, and most of them were not able to stop the relentless evolution of the disease (warfarin, corticosteroids in combination with azathioprine, N-acetylcysteine, ambrisentan, bosentan, sildenafil, antiacids). Two novel drugs, pirfenidone and nintedanib, proved effective in reducing lung function decline, improving the patient’s quality of life, and increasing the patient’s probability of survival. These drugs were approved by international health authorities for use in the treatment of IPF patients. The paper refers also to the status of IPF patients in Romania, where epidemiological data are not known, and where the disease is most likely severely underdiagnosed. Patients are typically diagnosed late, and are therefore in advanced stages of the disease. A proactive attitude, in favour of identification and early diagnosis of IPF patients is highly needed in order to offer to these patients the opportunity of treatment, improved survival, and a better quality of life.
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A decade of pharmacogenomics research on tyrosine kinase inhibitors in metastatic renal cell cancer: a systematic review.
Diekstra, MH, Swen, JJ, Gelderblom, H, Guchelaar, HJ
Expert review of molecular diagnostics. 2016;(5):605-18
Abstract
OBJECTIVE The individual response to targeted tyrosine kinase inhibitors (TKIs) in the treatment of metastatic renal cell cancer (mRCC) is highly variable. Outlined in this article are findings on potential biomarkers for TKI treatment outcome in mRCC and an evaluation of the status of clinical implementation. METHODS Articles were selected by two independent reviewers using a systematic search in five medical databases on renal cell carcinoma, TKIs, and pharmacogenetics. RESULTS Many researchers have focused on predictive biomarkers for treatment outcome of targeted therapies in mRCC patients. Attempts to explain differences in efficacy and toxicity of TKIs by use of genetic variants in genes related to the pharmacokinetics and pharmacodynamics of the drug have been successful. CONCLUSION Most findings on potential biomarkers have not been validated and therefore biomarker testing to guide choice of therapy and dose in mRCC is not yet feasible.