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FAF-Drugs3: a web server for compound property calculation and chemical library design

David Lagorce, Olivier Sperandio, Jonathan B. Baell, Maria A. Miteva, Bruno O. Villoutreix
2015 Nucleic Acids Research  
Here, we present FAF-Drugs3, a web server that can be used for drug discovery and chemical biology projects to help in preparing compound libraries and to assist decision-making during the hit selection  ...  FAF-Drugs3 offers access to user-friendly html result pages and the possibility to download all computed data.  ...  ACKNOWLEDGEMENTS The authors thank INSERM and Paris Diderot University for supports. They are also grateful to Drs P. Tufféry, A. Saladin and J. Rey for helpful discussions on the Mobyle Portal.  ... 
doi:10.1093/nar/gkv353 pmid:25883137 pmcid:PMC4489254 fatcat:ehwxbuu36vh6bewmfkikoovbeu

MTiOpenScreen: a web server for structure-based virtual screening

Céline M. Labbé, Julien Rey, David Lagorce, Marek Vavruša, Jérome Becot, Olivier Sperandio, Bruno O. Villoutreix, Pierre Tufféry, Maria A. Miteva
2015 Nucleic Acids Research  
Open screening endeavors play and will play a key role to facilitate the identification of new bioactive compounds in order to foster innovation and to improve the effectiveness of chemical biology and  ...  MTiOpenScreen provides valuable starting collections for screening, two in-house prepared drug-like chemical libraries containing 150 000 PubChem compounds: the Diverse-lib containing diverse molecules  ...  Otherwise user has the freedom to upload his/her own chemical library containing up to 5000 molecules that can be prepared by using the freely accessible web servers FAF-Drugs3 (24) for ADME-Tox filtering  ... 
doi:10.1093/nar/gkv306 pmid:25855812 pmcid:PMC4489289 fatcat:rt6ebhk2gbfbbhnvmmalg4iybm

Open chemoinformatic resources to explore the structure, properties and chemical space of molecules

Mariana González-Medina, J. Jesús Naveja, Norberto Sánchez-Cruz, José L. Medina-Franco
2017 RSC Advances  
Open chemoinformatic servers facilitate analysis of chemical space and structure–activity relationships.  ...  MG-M thanks CONACyT-FUNED for the scholarship number 2017-000001-02EXTF-00177. JJN and NS-C are thankful to CONACyT for the granted scholarships number 622969 and 335997, respectively.  ...  Acknowledgements We thank funding from the 'Programa de Apoyo a la Investigación y el Posgrado' (PAIP) 50009163, Facultad de Química, UNAM.  ... 
doi:10.1039/c7ra11831g fatcat:jxncc4n6zzgltjzeus5cswh4sy

Computational analysis of calculated physicochemical and ADMET properties of protein-protein interaction inhibitors

David Lagorce, Dominique Douguet, Maria A. Miteva, Bruno O. Villoutreix
2017 Scientific Reports  
The present study highlights several trends and properties that could be considered to design future PPI inhibitors, either for drug discovery endeavors or for chemical biology projects.  ...  Several trends are reported that should assist the design and optimization of future PPI inhibitors, either for drug discovery endeavors or for chemical biology projects.  ...  Acknowledgements Supports from the Inserm Institute and University Paris Diderot are greatly appreciated. We thank the unknown reviewers for interesting suggestions.  ... 
doi:10.1038/srep46277 pmid:28397808 pmcid:PMC5387685 fatcat:iokufqkbtfd5rmwom5udc37dsm

Pyrazolyl-Tetrazoles and Imidazolyl-Pyrazoles as Potential Anticoagulants and their Integrated Multiplex Analysis Virtual Screening

André Lourenço, Percilene Vegi, Jéssica Faria, Gustavo Pinto, Maurício dos Santos, Plínio Sathler, Max Saito, Marcos Santana, Tatiana Dutra, Carlos Rodrigues, Robson Monteiro, Alice Bernardino (+1 others)
2018 Journal of the Brazilian Chemical Society  
After the virtual selection of potential anticoagulant hits, all molecules were synthesized and candidates were evaluated in vitro for their anticoagulant and hemolytic profile.  ...  All compounds were submitted to an in silico target-base pipeline named integrated multiplex analysis virtual screening (IMA-VS), which comprises the evaluation of their (i) fitting physicochemical properties  ...  We thank CAPES, CNPq, FAPERJ, and the Program for Technological Development in Tools for Health-RPT-Fiocruz for use of its facilities.  ... 
doi:10.21577/0103-5053.20180150 fatcat:f7sv7jullndfdnbxohwpy6qnqa

Natural Products as Chemopreventive Agents by Potential Inhibition of the Kinase Domain in ErbB Receptors

Maria Olivero-Acosta, Wilson Maldonado-Rojas, Jesus Olivero-Verbel
2017 Molecules  
In this work, we suggest the application of computational tools, including molecular docking methods, pharmacophores, and web server ADME/Tox property calculator for the identification of lead compounds  ...  In short, this methodology allowed the identification of several NPs as HER inhibitors, being useful in the discovery and design of more potent and selective anticancer drugs.  ...  Prediction of ADME-TOX Properties for Promisory Compounds Using FAF-Drugs3 Server During the developmental stages of more effective medication candidates, it is likely to have various unsuccessful attempts  ... 
doi:10.3390/molecules22020308 pmid:28218686 fatcat:23h6p6ztnvaw3n4ycfkd3glmnu

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  
Irwin J J and Shoichet B K 2005 ZINC-a free database of The Taverna workflow suite: Designing and executing commercially available compounds for virtual screening workflows of Web Services  ...  A structure-based chemical classification system of MPDS compound library. 3.2b Module 5: Descriptor calculation: In order to Storage and search  ... 
doi:10.1007/s12039-017-1268-4 fatcat:ph6apcd5xjhz3i2hsa2mqdodvy

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  
Thiazolidine-2,4-dione is a versatile scaffold in medicinal chemistry and a useful tool in the development of new antitumoral compounds.  ...  molecular docking on the oncoproteins K-Ras, N-Ras and B-Raf, and to investigate the cytotoxicity of the compounds, in order to select the best structural profile for potential anticancer agents.  ...  FAF-Drugs3: a web server for compound property calculation and chemical library design. Nucleic Acids Res. 2015, 43, W200–W207. [CrossRef] [PubMed] 37.  ... 
doi:10.3390/medicina55040085 fatcat:j3fsim4gozgdvampwrwsgnkehi

Imbalance in chemical space: How to facilitate the identification of protein-protein interaction inhibitors

Mélaine A. Kuenemann, Céline M. Labbé, Adrien H. Cerdan, Olivier Sperandio
2016 Scientific Reports  
, etc.), experimental screening procedures for PPI targets still suffer from the unavailability of suitable fragments and chemical libraries 2-4 .  ...  Such identified classes of targets could lead to the design of PPIclass-specific chemical libraries and therefore facilitate the development of iPPIs to the stage of drug candidates.  ...  Acknowledgements This work was financially supported by the French Ministry of Research and the French Institute for Health and Medical Research. Author Contributions  ... 
doi:10.1038/srep23815 pmid:27034268 pmcid:PMC4817116 fatcat:mpr66gkx5vc5nbo6nvaov2ddra

Design, Synthesis and Antifungal Activity Evaluation of New Thiazolin-4-ones as Potential Lanosterol 14α-Demethylase Inhibitors

Anca Stana, Dan Vodnar, Radu Tamaian, Adrian Pîrnău, Laurian Vlase, Ioana Ionuț, Ovidiu Oniga, Brînduşa Tiperciuc
2017 International Journal of Molecular Sciences  
Furthermore, the compounds' lipophilicity was assessed and the compounds were subjected to in silico screening for prediction of their ADME-Tox properties (absorbtion, distribution, metabolism, excretion  ...  The synthesized thiazolin-4-one derivatives were tested for antifungal properties against several strains of Candida and all compounds exhibited efficient anti-Candida activity, two of them (9b and 10)  ...  in quantitative elemental analysis, chemical synthesis and study design; and Brînduşa Tiperciuc participated in IR analysis, study design and article preparation.  ... 
doi:10.3390/ijms18010177 pmid:28106743 pmcid:PMC5297809 fatcat:iykfjim2vza2zhbfro3maixgvq

In vitro antiplasmodial activity, pharmacokinetic profiles and interference in isoprenoid pathway of 2-aniline-3-hydroxy-1.4-naphthoquinone derivatives

Valeska S. de Sena Pereira, Flávio da Silva Emery, Lis Lobo, Fátima Nogueira, Jonas I. N. Oliveira, Umberto L. Fulco, Eudenilson L. Albuquerque, Alejandro M. Katzin, Valter F. de Andrade-Neto
2018 Malaria Journal  
The cell viability in vitro against RAW Cell Line displayed IC 50 = 483.5 and 714.9 μM, whereas, in primary culture tests using murine macrophages, IC 50 were 315.8 and 532.6 μM for the two selected compounds  ...  Conclusions: These derivatives have a high potential for the development of new anti-malarial drugs since they showed low toxicity associated to a satisfactory antiplasmodial activity and possible inhibition  ...  To do that, we applied the Lipinski's rule of five (R05), Lead-like soft, Drug-like soft, REOS and ZINC rules in compounds 4a and 4c using FAF-Drugs3 web-server [24] .  ... 
doi:10.1186/s12936-018-2615-8 fatcat:tibdm7u4qjdwtljuhgomdna6pa

Molecular modeling of natural and synthesized inhibitors against SARS-CoV-2 spike glycoprotein

Masume Jomhori, Hamid Mosaddeghi
2021 Research on Biomedical Engineering  
Thus, this receptor is a significant target for antiviral drug design.  ...  The FAF-Drugs3, Pan-Assay Interference Compounds (PAINS), ADME (absorption, distribution, metabolism, excretion) databases along with Lipinski's rules were used to evaluate the drug-like properties of  ...  Acknowledgements The authors are thankful for helpful feedback and observations to the reviewers and editors, which helped enhance the paper quality.  ... 
doi:10.1007/s42600-020-00122-3 fatcat:xivilbyxvvfzlpx3xwmnk7n7ye

Computational evaluation of natural compounds as potential inhibitors of human PEPCK-M: an alternative for lung cancer therapy

Baptista LPR, Sinatti VVC, Da Silva JHM, Dardenne LE, Guimarães AC
2019 Advances and Applications in Bioinformatics and Chemistry  
The selected compounds were evaluated according to its chemical diversity and clustered based on chemical similarity.Results: The pharmacophore hypotheses, generated based on known PEPCK inhibitors, were  ...  the human PEPCK-M (HsPEPCK-M) based on a computer-aided approach.Methods: Comparative modeling was used to generate 3D models for HsPEPCK-M.  ...  FAF-drugs3: a web server for compound property calculation and chemical library design. Nucleic Acids Res . 2015;43(W1):W200–W207. doi:10.1093/nar/gkv353 43.  ... 
doaj:4a14ef6d04cb452ebe249082ca5e3a18 fatcat:3aiwa4l4fff4vpepnmuopfjtiq

High Impact: The Role of Promiscuous Binding Sites in Polypharmacology

Cerisier, Petitjean, Regad, Bayard, Réau, Badel, Camproux
2019 Molecules  
The selective sites that interacted with one ligand type presented less favorable pocket properties for establishing ligand contacts.  ...  The literature focuses on drug promiscuity, which is a drug's ability to bind to several targets, because it plays an essential role in polypharmacology.  ...  Acknowledgments: We would like to thank Colette Geneix for her technical help, Laurence Le Gall for her administrative support and Alexandre Borrel for helpful discussion.  ... 
doi:10.3390/molecules24142529 pmid:31295958 pmcid:PMC6680532 fatcat:mxb5zhkfercdveabqbs3aut2ym

Designing and Virtual Screening of Potential Inhibitors of PFHGPRT against Malaria

Preeti Verma, Bukhsh Dev, Singh, Ajay Gupta
2016 Journal of Chemical and Pharmaceutical Research   unpublished
ZINC Pharmer and FAF-Drugs3 were used for pharmacophore and ADMET studies respectively.  ...  ; there is a constant need for the discovery of novel antimalarials and drug targets.  ...  In addition to filtered collections, FAF-Drugs3 can provide, via Gnuplot, several distribution diagrams of major physicochemical properties of the screened compound libraries [14] .FAF-Drugs3, a web server  ... 
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