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11[beta]-hydroxysteroid dehydrogenase-type 2 evolved from an ancestral 17[beta]-hydroxysteroid dehydrogenase-type 2 Nature Precedings
Michael E. Baker.
11[beta]-hydroxysteroid dehydrogenase type-2 (11[beta]-HSD2) regulates the local concentration of cortisol that can activate the glucocorticoid receptor and mineralocorticoid receptor, as well as the concentration of 11-keto-testosterone, the active androgen in fish. Similarly, 17[beta]-HSD2 regulates the levels of testosterone and estradiol that activate the androgen receptor and estrogen receptor, respectively. Interestingly, although human 11[beta]-HSD2 and 17[beta]-HSD2 act at different positions on different steroids, these enzymes are paralogs. Despite the physiological importance of 11[beta]-HSD2 and 17[beta]-HSD2, details of their origins and divergence from a common ancestor are not known. An opportunity to understand their evolution is...
Tipo: Manuscript Palavras-chave: Cancer; Developmental Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4649/version/1
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3D models of lamprey corticoid receptor complexed with 11-deoxycortisol and deoxycorticosterone Nature Precedings
Michael E. Baker; Kayla Y. Uh; Paiyuam Asnaashari.
The serum of Atlantic sea lamprey, a basal vertebrate, contains two corticosteroids, 11-deoxycortisol and deoxycorticosterone. Only 11-deoxycortisol has high affinity [Kd~3 nM] for the corticoid receptor [CR] in lamprey gill cytosol. To investigate the binding of 11-deoxycortisol to the CR, we constructed 3D models of lamprey CR complexed with 11-deoxycortisol and deoxycorticosterone. These 3D models reveal that Leu-220 and Met-299 in lamprey CR have contacts with the 17[alpha]-hydroxyl on 11-deoxycortisol. Lamprey CR is the ancestor of the mineralocorticoid receptor [MR] and glucocorticoid receptor [GR]. Unlike human MR and human GR, the 3D model of lamprey CR finds a van der Waals contact between Cys-227 in helix 3 and Met-264 in helix 5. Mutant...
Tipo: Manuscript Palavras-chave: Cancer; Developmental Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6216/version/1
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A Critical Evaluation of Clinical Trials in Cancer and Pharmacogenomics Nature Precedings
I. C. Baianu.
A critical overview of recent clinical trials in cancer is presented focused on signaling pathways blockers or inhibitors with a view to developing successful clinical trials employing personalized cancer therapies. Rational, pharmacogenomic strategies in cancer trials should be adopted that include specific molecular targeting based on adequate data for, and detailed modeling of, cancer cell genomes, modifications of cancer signaling pathways and epigenetic mechanisms. Novel translational oncogenomics research is rapidly expanding through the application of highly sensitive and specific advanced technology, research findings and computational tools and complex models to both pharmaceutical and clinical problems. Multiple sample analyses from several...
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012 URL: http://precedings.nature.com/documents/7052/version/1
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A Drosophila systems model of withdrawal from chronic pentylenetetrazole relevant in post-epileptogenesis Nature Precedings
Priyanka Singh; Farhan Mohammad; Abhay Sharma.
Rodent kindling induced by pentylenetetrazole (PTZ) is an established model of epileptogenesis and antiepileptic drug (AED) testing. Recently, a Drosophila systems model has been described in which chronic PTZ causes a decreased climbing speed in adult males on 7th day. Some AEDs ameliorate development of this locomotor deficit. Time-series of microarray expression profiles of heads of flies treated with PTZ has been found to resemble transcriptomic alterations associated with epileptogenesis. In the fly model, withdrawal from seven day long PTZ treatment causes an increased climbing speed on 7th consequent day. Here, we present a systems model of the post-PTZ withdrawal regime. Unlike AED-untreated individuals, flies treated with any of the five AEDs...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3447/version/1
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A novel apparatus/protocol designed for optogenetic manipulation and recording of individual neurons during a motivation and working memory task in the rodent Nature Precedings
Samuel Dolzani; Donald C. Cooper.
Innovative molecular tools allow neuroscientists to study neural circuitry associated with specific behaviors. Consequently, behavioral methods must be developed to interface with these new molecular tools in order for neuroscientists to identify the causal elements underlying behavior and decision-making processes. Here we present an apparatus and protocol for a novel Go/No-Go behavioral paradigm to study the brain attention and motivation/reward circuitry in awake, head-restrained rodents. This experimental setup allows: (1) Painless and stable restraint of the head and body; (2) Rapid acquisition to simple or complex operant tasks; (3) Repeated electrophysiological single and multiple unit recordings during ongoing behavior; (4) Pharmacological and...
Tipo: Manuscript Palavras-chave: Neuroscience; Pharmacology.
Ano: 2012 URL: http://precedings.nature.com/documents/7152/version/1
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A novel _Drosophila_ post-genomic CNS drug discovery model detects tetraethylammonium chloride with therapeutic potential Nature Precedings
Priyanka Singh; Farhan Mohammad*; Abhay Sharma.
A _Drosophila_ behavioral and transcriptomic model of locomotor plasticity induced by chronic pentylenetetrazole (PTZ) has recently been developed. In this model, two of the five antiepileptic drugs (AEDs) tested, sodium valproate (NaVP) and levetiracetam (LEV), not ethosuximide (ETH), gabapentin (GBP) and vigabatrin (VGB), ameliorate development of chronic PTZ induced locomotor alteration. Transcriptomic effect of the AEDs and PTZ in fly head has been described. Here, we analyze microarray expression profile of heads of flies treated with the convulsants tetraethylammonium chloride (TEA) and pilocarpine hydrochloride (PILO). Strikingly, microarray clustering placed TEA, not PILO, with LEV and NaVP in one group that was distinct from the other one...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3418/version/1
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A novel Drosophila transcriptomic and behavioral model detects potassium chloride with therapeutic potential Nature Precedings
Farhan Mohammad; Priyanka Singh; Abhay Sharma.
In a newly described _Drosophila_ model, two of the five antiepileptic drugs (AEDs) tested, sodium valproate (NaVP) and levetiracetam (LEV), not ethosuximide (ETH), gabapentin (GBP) and vigabatrin (VGB), ameliorate development of chronic pentylenetetrazole (PTZ) induced locomotor alteration. To further characterize the model, we analyze here the microarray expression profile of heads of flies treated with depolarizing compound potassium chloride (KCl). Surprisingly, microarray clustering showed unexpected similarity among KCl, LEV and NaVP. Further, like the two effective AEDs in the fly model, KCl regulated genes overrepresented ribosomal pathway. Interestingly, KCl also ameliorated development of locomotor deficit in the chronic PTZ model. Both...
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3429/version/1
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A novel strategy for the targeted analysis of protein and peptide metabolites Nature Precedings
Nicholas A. Williamson; Charles Reilly; Chor-Teck Tan; Sri-Harsha Ramarathinam; Alun Jones; Christie L. Hunter; Francis R. Rooney; Anthony W. Purcell.
The detection and quantitation of exogenously administered biological macromolecules (e.g. vaccines, peptide and protein therapeutics) and their metabolites is frequently complicated by the presence of a complex endogenous mixture of closely related compounds. We describe a method that incorporates stable isotope labeling of the compound of interest allowing the selective screening of the intact molecule and all metabolites using a modified precursor ion scan. This method involves monitoring the low molecular weight fragment ions produced during MS/MS that distinguish isotopically labelled material from related endogenous compounds. All isotopically labelled substances can be selected using this scanning technique for further analysis whilst other...
Tipo: Manuscript Palavras-chave: Biotechnology; Immunology; Pharmacology.
Ano: 2009 URL: http://precedings.nature.com/documents/3812/version/1
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A Novel Thermodynamic Method For Quantifying Ligand-Receptor Interactions: The IC (1/3) Standard Vs IC (50) Nature Precedings
Dr Sudarsan Prasad.
A method based on the Concentration Derivative Product (CDP) is proposed to analyze the thermodynamics of Drug-Receptor interactions. CDP is defined as the product of the fractional inhibition f and it’s concentration derivative. Assuming Michaelis-Menten kinetics, it is shown that for a number of drug-receptor systems (HIV protease, ACE, HMG-CoA, Opioid receptor inhibitors, etc.) f max = 0.333, irrespective of the nature of bonding interactions and Ki. The CDP max = [4 / ( 27 Ki ) ], and gives a measure of the drug potency directly. CDP also gives thermodynamic information about the ratio of the gradients of the inhibitor chemical potential in the free and bound states.
Tipo: Manuscript Palavras-chave: Pharmacology.
Ano: 2011 URL: http://precedings.nature.com/documents/6006/version/1
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A Study of the Mechanism of Action of Zervamicin IIB Peptide Antibiotic by Molecular Dynamics Simulation Nature Precedings
Konstantin Shaitan; Olga V. Levtsova; Vladimir Makarov; Mikhail P. Kirpichnikov.
We model mechanism of action of a channel-forming peptide antibiotic, zervamicin IIB, by molecular dynamics (MD) simulation. Interaction of this peptide with neutral and negatively charged lipid bilayers is investigated. It is found that charge of membrane surface influences the orientation of zervamicin IIB molecule, that may in turn effect its permeation into the membrane. On this basis we propose modifications to ZrvIIB structure that may increase its affinity towards the prokaryotic cellular membrane. Zervamicin IIB transmembrane channels are modeled as bundles consisting of 4, 5 and 6 individual peptide monomers. Our results suggest that four monomers don’t form a stable water-filled ion channel. Thus the channel with the least number of...
Tipo: Manuscript Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3624/version/1
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A theory for the tissue specificity of BRCA1/2 related and other hereditary cancers Nature Precedings
Bernard Friedenson.
Women who inherit a defective BRCA1 or BRCA2 gene have risks for breast and ovarian cancer that are so high and seem so selective that many mutation carriers choose to have prophylactic surgery. There has been much conjecture to explain such apparently striking tissue specificity. All these suggestions share the assumption that some disabled function of normal tumor suppressor genes leads to a tissue specific cancer response. Here the idea is proposed and tested that major determinants of where BRCA1/2 hereditary cancers occur are related to tissue specificity of the cancer pathogen, the agent that causes chronic inflammation or the carcinogen. The target tissue may have receptors for the pathogen, become selectively exposed to an inflammatory process...
Tipo: Manuscript Palavras-chave: Cancer; Genetics & Genomics; Immunology; Pharmacology.
Ano: 2010 URL: http://precedings.nature.com/documents/4881/version/1
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ACBD: Database for Ascidian Chemical Genomics Nature Precedings
Yuichiro Hira; Jun Terai; Masaya Imoto; Etsu Tashiro; Kohji Hotta.
Chemical biology approach enables us to understand the complex biological systems, using small molecules such as a specific activator or inhibitor of protein, a hormone-like inducer, or a neurotransmitter. When such approach is performed genome-widely, that research is especially called "chemical genomics". We are planning to make a new start of chemical genomics using one of chordate model animal, ascidian. As a first step, we constructed a database called ACBD (Ascidians Chemical Biology Database). 

 First, we reviewed and annotated past articles which describe the uses of small chemicals in the field of ascidians biology. In ACBD, chemical information and effects on ascidian are manually extracted...
Tipo: Poster Palavras-chave: Developmental Biology; Pharmacology.
Ano: 2010 URL: http://precedings.nature.com/documents/5087/version/1
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ADME/Tox WEB in silico predictions of longer chain perfluoroalkyl carboxylic acid pKa values are more accurate than other computational methods Nature Precedings
Sierra Rayne; Kaya Forest.
Perfluoroalkyl carboxylates are contaminants whose environmental fate and toxicological effects are of broad interest within the academic, industrial, and governmental science and regulatory communities. In addition, coupled perfluoroalkyl and carboxylate moieties are often used in medicinal chemistry as part of the drug design process. However, to date there has been a notable absence of reliable acidity constant estimation programs for these compounds. Here we report that the ADME/Tox WEB method for in silico pKa value predictions is more accurate than the PM6, SPARC, and COSMOtherm methods for the longer chain perfluoroalkyl carboxylic acids, suggesting this may be a good general acidity constant estimation approach for these compounds.
Tipo: Manuscript Palavras-chave: Chemistry; Pharmacology; Earth & Environment.
Ano: 2009 URL: http://precedings.nature.com/documents/2936/version/1
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Adopting Nrf2 and NF-κB from cancer: Is there any role of the duo in diabetes? Nature Precedings
Geeta Negi; Ashutosh Kumar; Shyam S. Sharma.
Oxidative stress and inflammation are two well-recognized events occurring in normal cells during cancer chemotherapy. Several antioxidant and anti-inflammatory agents have therefore been tried as rational and effective strategies for chemoprotection. Elaborate studies on antioxidants and anti-inflammatory agents in various experimental models of cancer revealed that these agents act by modulating the expression and/or activity of the transcription factors nuclear factor erythroid 2-related factor 2 (Nrf2) and nuclear factor-kappa B (NF-κB). Nrf2 is considered the main sentinel of antioxidant defense as it induces many antioxidant and phase 2 enzymes in response to stressful conditions. Likewise, NF-κB is considered as a denominator of...
Tipo: Manuscript Palavras-chave: Cancer; Pharmacology.
Ano: 2011 URL: http://precedings.nature.com/documents/6581/version/1
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Aging-associated Alteration in the Cardiac MIF-AMPK Cascade in Response to Ischemic Stress Nature Precedings
Heng Ma; Jingying Wang; Erin Lane; Lin Leng; Wenkui Wang; Jun Ren; Richard Bucala; Ji Li.
An important role for a macrophage migration inhibitory factor (MIF)-AMP-activated protein kinase (AMPK) signaling pathway in ameliorating myocardial damage following ischemia/reperfusion has been described. An aging-associated reduction in AMPK activity may be associated with a decline in the ability of cardiac cells to activate the MIF-AMPK cascade, thereby resulting in reduced tolerance to ischemic insults. To test this hypothesis, _in vivo_ regional ischemia was induced by occlusion of the left anterior descending (LAD) coronary artery in young (4-6 months) and aged (24-26 months) mice. The ischemic AMPK activation response was impaired in aged hearts compared to young ones (p<0.01). Notably, cardiac MIF expression in aged hearts was lower...
Tipo: Manuscript Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2008 URL: http://precedings.nature.com/documents/2466/version/1
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Ajuvant effect of a Synthetic Aluminium - Magnesium Silicate on chloroquine phosphate, against Plasmodium berghei. Nature Precedings
madike ezeibe; obianuju obianuju Okoroafor; nnenna elendu-eleke; Augustine Ngene.
Abstract effect of a synthetic Aluminium - Magnesium Silicate (AMS) on antiplasmodial activity of chloroquine was tested. Plasmodium berghei-infected mice were treated with 7 mg/kg, 5 mg/kg and 3 mg/kg chloroquine, respectively. The two subgroups in each experiment were treated with chloroquine alone and with chloroquine in AMS respectively. Parasitaemia (%) of the group treated with 7 mg/kg was higher than that of the control. At 5 mg/kg, chloroquine treatment significantly reduced parasitaemia from 3.60 to 2.46 (P =0.01). Incorporating chloroquine in AMS significantly improved its ability to reduce P. berghei parasitaemia at 5 mgkg and at 3 mg/kg, from 2.46 0.21 to 1.57 0.25 (P = 0.01) and from 3.82 0.06 to 2.12 0.08 (P =0.01 ). It also increased...
Tipo: Manuscript Palavras-chave: Pharmacology.
Ano: 2012 URL: http://precedings.nature.com/documents/6749/version/1
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Allosteric modulation of beta1 integrin function induces lung repair in animal model of emphysema. Nature Precedings
Rehab J. Al-Jamal; Linda Wilson; Chris J. Armit; Susan McIntyre; Mark Marsden; Steven D. Shapiro; David J. Harrison.
Emphysema is a progressive lung disease characterised by loss of lung parenchyma with associated functional changes including decreased tissue elastance. Here we report beta1 integrin is a novel target for tissue repair and regeneration in emphysema. We show a single dose of a monoclonal antibody against beta1 integrin induced both functional and structural reversal of elastase-induced lung injury in vivo, and we found that similar matrix remodelling changes occurred in human lung tissue. We also identified a potential mechanism of action as this allosteric modulation of beta1 integrin inhibited elastase-induced caspase activation, F-actin aggregate formation and changes in cellular ATP levels. This was accompanied by maintenance of beta1?integrin levels...
Tipo: Manuscript Palavras-chave: Pharmacology.
Ano: 2007 URL: http://precedings.nature.com/documents/437/version/1
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Aluminium - Magnesium Silicate enhances antibacterial activity of Ampicillin trihydrate, against Salmonella gallinarum Nature Precedings
Madike Ezeibe; George Anosa; Okechi Okorie; Nnenna Elendu-Eleke; Obianuju Okoroafor; Augustine Ngene; Ogechukwu Chikelu.
Solutions of different concentrations, of Ampicillin trihydrate (AT) and of a formulation of AT in Aluminium Magnesium Silicate (AMS), were used for sensitivity test on Salmonella gallinarum cultures. Also, S. gallinarum-infected chicks were treated with; 10 mg / Kg (AT), 10 mg / Kg (AT in AMS), 7.5 mg / Kg ( AT), 7.5 mg /Kg (AT in AMS). Mean inhibition area, 28.39 mm produced by AT did not vary significantly (P ) from 26.36 mm produced by AT in AMS. However, 17.5 105 Salmonella gallinarum culture forming units per ml of bile of the untreated chicks and 3.4 105 (80.58 % reduction), 2.5 105 (85.7 % reduction) , 5.4 105 (69.2 % reduction ) and 0.38 105 (97.8 % reduction ) of the respective treated groups, showed AMS significantly (P 0.01) improved AT`s...
Tipo: Manuscript Palavras-chave: Pharmacology.
Ano: 2012 URL: http://precedings.nature.com/documents/6814/version/1
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An emerging protagonist: Sodium Glucose Co-transporters (SGLTs) as a burgeoning target for the treatment of diabetes mellitus Nature Precedings
Danish Ahmed; Manju Sharma; Vikas Kumar; Pankaj S Yadav.
Contemporary therapies to rationalize the hyperglycaemia in type 2 diabetes mellitus (T2DM) generally involve insulin-dependent mechanisms and lose their effectiveness as pancreatic b-cell function decreases to a greater extent. The kidney emerges out as a novel and potential target to trim down the T2DM. The filtered glucose is reabsorbed principally through the sodium glucose co-transporter-2 (SGLT2), a low affinity transport system, which is present at the luminal surface cells that cover the first segment of proximal tubules. Competitive inhibition of SGLT2 therefore represents an innovative therapeutic strategy for the treatment of hyperglycaemia and/or obesity in patients with type 1 or type 2 diabetes by enhancing glucose and energy loss through the...
Tipo: Manuscript Palavras-chave: Pharmacology.
Ano: 2012 URL: http://precedings.nature.com/documents/7057/version/1
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Analysis of circadian pattern reveals tissue-specific alternative transcription in leptin signaling pathway Nature Precedings
Andrey Ptitsyn; Jeffrey Gimble.
*Background*
It has been previously reported that most mammalian genes display a circadian oscillation in their baseline expression. Consequently, the phase and amplitude of each component of a signal transduction cascade has downstream consequences. 

*Results*
We report our analysis of alternative transcripts in the leptin signaling pathway which is responsible for the systemic regulation of macronutrient storage and energy balance. We focused on the circadian expression pattern of a critical component of the leptin signaling system, suppressor of cytokine signaling 3 (SOCS3). On an Affymetrix GeneChip 430A2 microarray, this gene is represented by three probe sets targeting different...
Tipo: Manuscript Palavras-chave: Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007 URL: http://precedings.nature.com/documents/858/version/1
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