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FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects

David Lagorce, Olivier Sperandio, Hervé Galons, Maria A Miteva, Bruno O Villoutreix
2008 BMC Bioinformatics  
Drug discovery and chemical biology are exceedingly complex and demanding enterprises.  ...  Results: This paper presents FAF-Drugs2, a free adaptable tool for ADMET filtering of electronic compound collections.  ...  Acknowledgements We would like to thank the Inserm institute, Paris Descartes University and Paris Diderot University for supports.  ... 
doi:10.1186/1471-2105-9-396 pmid:18816385 pmcid:PMC2561050 fatcat:csglhyqjqfcxnmgyo5rjfvktau

DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening

David Lagorce, Tania Pencheva, Bruno O Villoutreix, Maria A Miteva
2009 BMC Chemical Biology  
Abstract Background: Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor.  ...  DG-AMMOS: a new tool to generate 3d conformation of small molecules using distance geometry and automated molecular mechanics optimization for in silico screening..  ...  Acknowledgements We would like to thank the Inserm institute, Paris Descartes University and Paris Diderot University for supports.  ... 
doi:10.1186/1472-6769-9-6 pmid:19912625 pmcid:PMC2781789 fatcat:26k6tsknz5atlp55dan6zrpyhu

5-Arylidene(chromenyl-methylene)-thiazolidinediones: Potential New Agents against Mutant Oncoproteins K-Ras, N-Ras and B-Raf in Colorectal Cancer and Melanoma

Cristina Nastasă, Radu Tamaian, Ovidiu Oniga, Brîndușa Tiperciuc
2019 Medicina  
Materials and Methods: In our paper we studied the cytotoxicity of two series of thiazolidine-2,4-dione derivatives, their ADME-Tox properties and the molecular docking on a mutant protein of K-Ras, two  ...  The aim of our study was to predict the pharmacokinetic/pharmacodynamic properties, the drug-likeness and lead-likeness of two series of synthetic 5-arylidene(chromenyl-methylene)-thiazolidinediones, the  ...  FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects. BMC Bioinformatics 2008, 9, 396. [CrossRef] 70. Johnson, T.W.; Dress, K.R.; Edwards, M.  ... 
doi:10.3390/medicina55040085 fatcat:j3fsim4gozgdvampwrwsgnkehi

Drug-Like ProteinProtein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology

Bruno O. Villoutreix, Melaine A. Kuenemann, Jean-Luc Poyet, Heriberto Bruzzoni-Giovanelli, Céline Labbé, David Lagorce, Olivier Sperandio, Maria A. Miteva
2014 Molecular Informatics  
In this review article, written for the 2014 International Summer School in Chemoinformatics (Strasbourg, France), we discuss in silico tools (essentially post 2012) and databases that can assist the design  ...  about the modulation of PPIs with small drug-like molecules. In fact, several success stories were reported both, at the preclinical and clinical stages.  ...  Acknowledgements Supports from the Inserm Institute and the University Paris Diderot are greatly appreciated. We also would like to thank Prof. A. Varnek and Dr. D.  ... 
doi:10.1002/minf.201400040 pmid:25254076 pmcid:PMC4160817 fatcat:kryzjqycvrg5vd3surg4sdxrgy

Designing Focused Chemical Libraries Enriched in Protein-Protein Interaction Inhibitors using Machine-Learning Methods

Christelle Reynès, Hélène Host, Anne-Claude Camproux, Guillaume Laconde, Florence Leroux, Anne Mazars, Benoit Deprez, Robin Fahraeus, Bruno O. Villoutreix, Olivier Sperandio, Philip E. Bourne
2010 PLoS Computational Biology  
Here, we train machine-learning-based models, mainly decision trees, using a dataset of known PPI inhibitors and of regular drugs in order to determine a global physico-chemical profile for putative PPI  ...  We strongly believe that this new tool can be used as a global PPI inhibitor profiler prior to screening assays to reduce the size of the compound collections to be experimentally screened while keeping  ...  not only for drug discovery projects to avoid a fullscale screening but also for chemical biology projects.  ... 
doi:10.1371/journal.pcbi.1000695 pmid:20221258 pmcid:PMC2832677 fatcat:dwi7e2ndmfcublzqxiyfeogq6e

Assessing therapeutic potential of molecules: molecular property diagnostic suite for tuberculosis $$(\mathbf{MPDS}^{\mathbf{TB}})$$ ( MPDS TB )

Anamika Singh Gaur, Anshu Bhardwaj, Arun Sharma, Lijo John, M Ram Vivek, Neha Tripathi, Prasad V Bharatam, Rakesh Kumar, Sridhara Janardhan, Abhaysinh Mori, Anirban Banerji, Andrew M Lynn (+38 others)
2017 Proceedings of the Indian Academy of sciences. Chemical sciences  
Winter M J, Owen S F, Murray-Smith R, Panter G H, and Optimisation Workbench; FAF-Drugs3: Free Hetheridge M J and Kinter L B 2010 Using data from ADME-Tox Filtering Tool; FDA: Food  ...  Drug Discovery Chemical cell wall of Mycobacterium tuberculosis: an analogue Biology S L Schreiber, T M Kapoor and G Wess based approach Mol.  ... 
doi:10.1007/s12039-017-1268-4 fatcat:ph6apcd5xjhz3i2hsa2mqdodvy

Exploring G Protein-Coupled Receptors (GPCRs) Ligand Space via Cheminformatics Approaches: Impact on Rational Drug Design

Shaherin Basith, Minghua Cui, Stephani J. Y. Macalino, Jongmi Park, Nina A. B. Clavio, Soosung Kang, Sun Choi
2018 Frontiers in Pharmacology  
A., and Villoutreix, B. O. (2008). FAF-Drugs2: free ADME/tox filtering tool to assist drug discovery and chemical biology projects.  ...  S., and Coleman, R. G. (2012). ZINC: a free tool to discover chemistry for biology. J. Chem. Inf.  ... 
doi:10.3389/fphar.2018.00128 pmid:29593527 pmcid:PMC5854945 fatcat:drx2x7lo7jcehcto2ntknqsawe

Molecular Informatics Studies of the Iron-Dependent Regulator (ideR) Reveal Potential Novel Anti-Mycobacterium ulcerans Natural Product-Derived Compounds

Samuel K. Kwofie, Kweku S. Enninful, Jaleel A. Yussif, Lina A. Asante, Mavis Adjei, Kwabena Kan-Dapaah, Elvis K. Tiburu, Wilhelmina A. Mensah, Whelton A. Miller, Lydia Mosi, Michael D. Wilson
2019 Molecules  
Induced Fit Docking (IFD) was also performed to account for the protein's flexibility upon ligand binding and to estimate the best plausible conformation of the complexes.  ...  Also, ZINC000005357841 was predicted to possess anti-inflammatory and anti-oxidative activities, which are relevant in Buruli ulcer and iron acquisition mechanisms, respectively.  ...  FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects. BMC Bioinform. 2008, 9, 396. [CrossRef] 42. Sliwoski, G.; Kothiwale, S.; Meiler, J.; Lowe, E.W.  ... 
doi:10.3390/molecules24122299 fatcat:vky6pnlwpbecjeycchv7wox5s4

Pocket-Based Drug Design: Exploring Pocket Space

Xiliang Zheng, LinFeng Gan, Erkang Wang, Jin Wang
2012 AAPS Journal  
Also, the pockets at the proteinprotein interfaces (PPI) have been considered to further explore the pocket space for drug discovery.  ...  In one of two cases, we also included some applications of pockets located at the dimer interfaces to emphasize the role of PPI in drug discovery.  ...  The ADME/Tox Filtering was carried out via the online FAF-Drugs2 tool (85) . Finally, we have obtained 90 chemical entities for the subsequent screenings.  ... 
doi:10.1208/s12248-012-9426-6 pmid:23180158 pmcid:PMC3535113 fatcat:7y65lisiyjbklnbbajbl6xzy7q