Meshkat S.,Ansaris |
Klon A.E.,Ansaris |
Zou J.,Ansaris |
Wiseman J.S.,Ansaris |
And 2 more authors.
Journal of Chemical Information and Modeling | Year: 2011
We introduce TICRA (transplant-insert-constrain-relax-assemble), a method for modeling the structure of unknown protein-ligand complexes using the X-ray crystal structures of homologous proteins and ligands with known activity. We present results from modeling the structures of protein kinase-inhibitor complexes using p38 and Lck as examples. These examples show that the TICRA method may be used prospectively to create and refine models for protein kinase-inhibitor complexes with an overall backbone rmsd of less than 0.75 Å for the kinase domain, when compared to published X-ray crystal structures. Further refinement of the models of the kinase domains of p38 and Lck in complex with their cognate ligands from the published crystal structures was able to improve the rmsd's of the model complexes to below 0.5 Å. Our results show that TICRA is a useful approach to the problem of structure-based drug design in cases where little structural information is available for the target proteins and the binding mode of active compounds is unknown. © 2011 American Chemical Society.
Mast N.,Case Western Reserve University |
Li Y.,Case Western Reserve University |
Linger M.,Case Western Reserve University |
Clark M.,Pharmatrope Ltd |
And 4 more authors.
Journal of Biological Chemistry | Year: 2014
Background: Elevation of cerebral cholesterol turnover in mice due to increased CYP46A1 expression has palliative effects on hallmarks of Alzheimer disease. Results: CYP46A1 could also be activated post-translationally by drugs in vitro and in vivo. Conclusion: CYP46A1 is a viable therapeutic target. Significance: Pharmacologic stimulation of CYP46A1 and cerebral cholesterol turnover may lead to new therapeutic strategies for the treatment of brain disorders. Cytochrome P450 46A1 (CYP46A1) is a brain-specific cholesterol 24-hydroxylase responsible for the majority of cholesterol elimination from the brain. Genetically increased CYP46A1 expression in mice leads to improved cognition and decreases manifestations of Alzheimer disease. We found that four pharmaceuticals (efavirenz (EFV), acetaminophen, mirtazapine, and galantamine) prescribed for indications unrelated to cholesterol maintenance increased CYP46A1 activity in vitro. We then evaluated the anti-HIV medication EFV for the mode of interaction with CYP46A1 and the effect on mice. We propose a model for CYP46A1 activation by EFV and show that EFV enhanced CYP46A1 activity and cerebral cholesterol turnover in animals with no effect on the levels of brain cholesterol. The doses of EFV administered to mice and required for the stimulation of their cerebral cholesterol turnover are a hundred times lower than those prescribed to HIV patients. At such small doses, EFV may be devoid of adverse effects elicited by high drug concentrations. CYP46A1 could be a novel therapeutic target and a tool to further investigate the physiological and medical significance of cerebral cholesterol turnover.© 2014 by The American Society for Biochemistry and Molecular Biology, Inc.
Jennings P.,Innsbruck Medical University |
Schwarz M.,University of Tubingen |
Landesmann B.,EU Joint Research Centre |
Maggioni S.,Istituto di Ricerche Farmacologiche Mario Negri |
And 4 more authors.
Archives of Toxicology | Year: 2014
There is an urgent need for the development of alternative methods to replace animal testing for the prediction of repeat dose chemical toxicity. To address this need, the European Commission and Cosmetics Europe have jointly funded a research program for ‘Safety Evaluation Ultimately Replacing Animal Testing.’ The goal of this program was the development of in vitro cellular systems and associated computational capabilities for the prediction of hepatic, cardiac, renal, neuronal, muscle, and skin toxicities. An essential component of this effort is the choice of appropriate reference compounds that can be used in the development and validation of assays. In this review, we focus on the selection of reference compounds for liver pathologies in the broad categories of cytotoxicity and lipid disorders. Mitochondrial impairment, oxidative stress, and apoptosis are considered under the category of cytotoxicity, while steatosis, cholestasis, and phospholipidosis are considered under the category of lipid dysregulation. We focused on four compound classes capable of initiating such events, i.e., chemically reactive compounds, compounds with specific cellular targets, compounds that modulate lipid regulatory networks, and compounds that disrupt the plasma membrane. We describe the molecular mechanisms of these compounds and the cellular response networks which they elicit. This information will be helpful to both improve our understanding of mode of action and help in the selection of appropriate mechanistic biomarkers, allowing us to progress the development of animal-free models with improved predictivity to the human situation. © 2014, Springer-Verlag Berlin Heidelberg.