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When reporting the application or results obtained with CLARITY software, please cite it as this template sentence stands:

The [data/data analysis/prediction results] for this  [manuscript/report] [was/were] generated using CLARITYsoftware, Version 3.0 for [Unix]. Copyright © 2018 Chemotargets SL., Barcelona, Spain.
 

 

 

Last Update: 13th May 2019

Authorship
Application
CT Product
Article
Pharmacology, Metabolism
CT-link

Mechanistic investigations of the liver toxicity of the free fatty acid receptor 1 agonist fasiglifam (TAK875) and its primary metabolites. Ackerson T, Amberg A, Atzrodt J, Arabeyre C, Defossa E, Dorau M, Dudda A, Dwyer J, Holla W, Kissner T, Kohlmann M, Kürzel U, Pánczél J, Rajanna S, Riedel J, Schmidt F, Wäse K, Weitz D, Derdau V. J Biochem Mol Toxicol. 2019 May 8:e22345. doi: 10.1002/jbt.22345. 

Pharmacology
CLARITY

Assessing the Structural and Pharmacological Similarity of Newly Identified Drugs of Abuse to Controlled Substances Using Public Health Assessment via Structural Evaluation. Ellis CR, Racz R, Kruhlak NL, Kim MT, Hawkins EG, Strauss DG, Stavitskaya L. Clin Pharmacol Ther. 2019 Apr 8. doi: 10.1002/cpt.1418. [Epub ahead of print]

Pharmacology
CLARITY

Dual Inhibitors of PARPs and ROCKs. Antolín AA, Mestres J. ACS Omega. 2018 Oct 31;3(10):12707-12712    

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Safety

Legacy data sharing to improve drug safety assessment: the eTOX project. Sanz F, Pognan F, Steger-Hartmann T, Díaz C; eTOX, Cases M, Pastor M, Marc P, Wichard J, Briggs K, Watson DK, Kleinöder T, Yang C, Amberg A, Beaumont M, Brookes AJ, Brunak S, Cronin MTD, Ecker GF, Escher S, Greene N, Guzmán A, Hersey A, Jacques P, Lammens L, Mestres J, Muster W, Northeved H, Pinches M, Saiz J, Sajot N, Valencia A, van der Lei J, Vermeulen NPE, Vock E, Wolber G, Zamora I. Nat Rev Drug Discov.  2017 Dec;16(12):811-812

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CT-link

Biological substantiation of antipsychotic-associated pneumonia: Systematic literature review and computational analyses. Sultana J, Calabró M, Garcia-Serna R, Ferrajolo C, Crisafulli C, Mestres J, Trifirò' G. PLoS One. 2017 Oct 27;12(10):e0187034

Pharmacology
CT-link

Synthesis, pharmacological evaluation and molecular docking of pyranopyrazole-linked 1,4-dihydropyridines as potent positive inotropes. Kumar R, Yadav N, Lavilla R, Blasi D, Quintana J, Brea JM, Loza MI, Mestres J, Bhandari M, Arora R, Kakkar R, Prasad AK. Mol Divers. 2017 Aug;21(3):533-546.    

CT-link

Design, Synthesis and Biological Evaluation of Potent Antioxidant 1-(2,5-Dimethoxybenzyl)-4-arylpiperazines and N-Azolyl Substituted 2-(4-Arylpiperazin-1-yl). Saadeh HA, Khasawneh MA, Samadi A,  El-Haty IA, Satała G, Bojarski AJ, Ismaili L, Bautista-Aguilera ÓM, Yañez M, Mestres J.  ChemistrySelect 2017, 2, 3854– 3859    

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Target deconvolution

Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond. Van Voorhis WC, et al. PLoS Pathogens. 2016 Jul 28;12(7):e1005763

The In Vitro Pharmacological Profile of Drugs as a Proxy Indicator of Potential In Vivo Organ Toxicities. Remez N, Garcia-Serna R, Vidal D, Mestres J. Chem Res Toxicol. 2016 Apr 18;29(4):637-48.    

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Large-Scale Predictive Drug Safety: From Structural Alerts to Biological Mechanisms. Garcia-Serna R, Vidal D, Remez N, Mestres J.  Chem Res Toxicol. 2015 Oct 19;28(10):1875-87.    

Target identification
CT-link

Distant polypharmacology among MLP chemical probes. Antolín AA, Mestres J. ACS Chem Biol. 2015 Feb 20;10(2):395-400.    

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Target profiling
PredictFX

Computational prediction of off-target related safety liabilities of molecules: Cardiotoxicity, hepatotoxicity and reproductive toxicity. Schmidt F, Amberg A, Mulliner D, Stolte M, Matter H, Hessler G, Dietrich A, Remez N, Vidal D, Mestres J, Czich A. Toxicol Lett. 2014 Sept 10; 229:S164    

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Target deconvolution
PredictFX

Identification of host interactions for phenotypic antimalarial hits. Spitzmüller A, Mestres J. J Cheminform. 2014 Mar 11;6(Suppl 1):O12. eCollection 2014 Mar.    

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PredictFX

Effects of BDE-209 contaminated sediments on zebrafish development and potential implications to human health. Garcia-Reyero N, Escalon BL, Prats E, Stanley JK, Thienpont B, Melby NL, Barón E, Eljarrat E, Barceló D. Mestres J, Babin PJ, Perkins EJ, Raldúa D.   Environ Int. 2014 Feb;63:216-23  

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Target deconvulation
PredictFX

Prediction of the P. falciparum Target Space Relevant to Malaria Drug Discovery. Spitzmüller A, Mestres J. PLoS Comput Biol. 2013;9(10):e1003257.    

Target identification
PredictFX

Identification of Pim Kinases as Novel Targets for PJ34 with Confounding Effects in PARP Biology. Antolín AA, Jalencas X, Yélamos J, Mestres J. ACS Chem Biol. 2012 Dec 21;7(12):1962-7

Target deconvulation
SHED profiling

Identification of Small Molecule Inhibitors of Amyloid β‐Induced Neuronal Apoptosis Acting through the Imidazoline I2 Receptor. Montolio M1, Gregori-Puigjané E, Pineda D, Mestres J, Navarro P. J Med Chem. 2012 Nov 26;55(22):9838-46

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PredictFX

New chromene scaffolds for adenosine A2A receptors: Synthesis, pharmacology and structureeactivity relationships. Areias F, Costa M, Castro M, Brea J, Gregori-Puigjané E, Proença MF, Mestres J, Loza MI. Eur J Med Chem. 2012 Aug;54:303-10    

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Pharmacology
PHRAG, FPD and SHED profiling

Combination of biological screening in a cellular model of viral latency and virtual screening identifies novel compounds that reactivate HIV-1. Gallastegui E, Marshall B, Vidal D, Sanchez-Duffhues G, Collado JA, Alvarez-Fernández C, Luque N, Terme JM, Gatell JM, Sánchez-Palomino S, Muñoz E, Mestres J, Verdin E, Jordan A. J Virol. 2012 Apr;86(7):3795-808    

Target deconvulation
PHRAG, FPD and SHED profiling

A Chemocentric Approach to the Identification of Cancer Targets. Flachner B, Lörincz Z, Carotti A, Nicolotti O, Kuchipudi P, Remez N, Sanz F, Tóvári J, Szabó MJ, Bertók B, Cseh S, Mestres J, Dormán G. PLoS One. 2012;7(4):e35582.    

Pharmacology

Ligand-based approaches to in silico pharmacology. Vidal D, Garcia-Serna R, Mestres J. Methods Mol Biol. 2011; 672: 489-502    

Target profiling

Cross-pharmacology analysis of G protein-coupled receptors. Briansó F1, Carrascosa MC, Oprea TI, Mestres J. Curr Top Med Chem. 2011;11(15):1956-63.    

Pharmacology & Safety

Linking Pharmacology to Clinical Reports: Cyclobenzaprine and Its Possible Association With Serotonin Syndrome. Mestres J, Seifert SA, Oprea TI. Clin Pharmacol Ther. 2011 Nov;90(5):662-5

Safety

Shaping the Future of Safer Innovative Drugs in Europe. Mestres J, Bryant SD, Zamora I, Gasteiger J. Nat Biotechnol. 2011; 29: 789-790    

Target profiling
PHRAG, FPD and SHED profiling

Multi-targeted activity of maslinic acid as an antimalarial natural compound. Moneriz C, Mestres J, Bautista JM, Diez A, Puyet A. FEBS J. 2011 Aug;278(16):2951-61    

Target profiling
SHED profiling

In Silico Target Profiling of One Billion Molecules. Nonell-Canals A, Mestres J. Mol Inform. 2011 May 16;30(5):405-9.    

Pharmacology & Safety

Anticipating drug side effects by comparative pharmacology. Garcia-Serna R, Mestres J. Expert Opin Drug Metab Toxicol. 2010; 6: 1253-1263

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Target profiling
PHRAG, FPD and SHED profiling

In Silico Receptorome Screening of Antipsychotic Drugs. Vidal D, Mestres J. Mol Inform. 2010 Jul 12;29(6-7):543-51    

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Target profiling
SHED profiling

In silico directed chemical probing of the adenosine receptor family. Areias FM, Brea J, Gregori-Puigjané E, Zaki ME, Carvalho MA, Domínguez E, Gutiérrez-de-Terán H, Proença MF, Loza MI, Mestres J. Bioorg Med Chem. 2010 May 1;18(9):3043-52

Coverage and bias in chemical library design. Gregori-Puigjané E, Mestres J. Curr Opin Chem Biol. 2008; 12: 359-365

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Target profiling
SHED profiling

A Ligand-Based Approach to Mining the Chemogenomic Space of Drugs. Gregori-Puigjané E, Mestres J. Comb Chem High Throughput Screen. 2008 Sep;11(8):669-76.

Methodology
Drug-Target networks

Data completeness--the Achilles heel of drug-target networks. Mestres J, Gregori-Puigjané E, Valverde S, Solé RV.  Nat Biotechnol. 2008 Sep;26(9):983-4.

Target profiling
SHED profiling

Ligand-Based Approach to In Silico Pharmacology: Nuclear Receptor Profiling. Mestres J, Martín-Couce L, Gregori-Puigjané E, Cases M, Boyer S. J Chem Inf Model. 2006 Nov-Dec;46(6):2725-36.

Methodology
SHED profiling

SHED: Shannon Entropy Descriptors from Topological Feature Distributions. Gregori-Puigjané E, Mestres J. J Chem Inf Model. 2006 Jul-Aug;46(4):1615-22.