Science

Last Update: 4th August 2022

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Target Profiling, Pharmacology

CLARITY

Paths to Cheminformatics: Q&A with Norberto Sánchez-Cruz and Emma Schymanski. Sánchez-Cruz, N., Schymanski, E.L.  J Cheminform. 2022. 1451.

Target Profiling

CLARITY

Rare Variation in Drug Metabolism and Long QT Genes and the Genetic Susceptibility to Acquired Long QT Syndrome. Gray B, Baruteau AE, Antolin AA, Pittman A, Sarganas G, Molokhia M, Blom MT, Bastiaenen R, Bardai A, Priori SG, Napolitano C, Weeke PE, Shakir SA, Haverkamp W, Mestres J, Winkel B, Witney AA, Chis-Ster I, Sangaralingam A, Camm AJ, Tfelt-Hansen J, Roden DM, Tan HL, Garbe E, Sturkenboom M, Behr ER. Circ Genom Precis Med2022. doi: 10.1161/CIRCGEN.121.003391.

Pharmacology

CLARITY

A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. Zahoránszky-Kőhalmi G, Siramshetty VB, Kumar P, Gurumurthy M, Grillo B, Mathew B, Metaxatos D, Backus M, Mierzwa T, Simon R, Grishagin I, Brovold L, Mathé EA, Hall MD, Michael SG, Godfrey AG, Mestres J, Jensen LJ, Oprea TI. J Chem Inf Model. 2022. doi: 10.1021/acs.jcim.1c00431.

Pharmacology

CLARITY

β2-Adrenoceptor agonist activity of higenamine. Thomas J Hudzik, Metul Patel, Andrew Brown. Drug Test Anal. 2021 Feb;13(2):261-267. doi: 10.1002/dta.2992.

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Toxicology

ELIXIR and Toxicology: a community in development. Martens M, Stierum R, Schymanski EL et al. [version 1; peer review: awaiting peer review]. F1000Research. 2021, 10(ELIXIR):1129. doi:10.12688/f1000research.74502.1.

Pharmacology

CLARITY

Evolution of kinase polypharmacology across HSP90 drug discovery. Antolin AA, Clarke PA, Collins I, Workman P, Al-Lazikani B. Cell Chem Biol. 2021. doi:10.1016/j.chembiol.2021.05.004. (previous at bioRxiv).

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Safety

Skin Sensitization in Silico Protocol. Johnson C, Ahlberg E, Anger LT, et al. Regul Toxicol Pharmacol. 2020;104688.

Pharmacology

CLARITY

The target landscape of N4-hydroxycytidine based on its chemical neighborhood. Mestres J. bioRxiv. 2020. doi:10.1101/2020.03.30.016485.

Pharmacology

CLARITY

Evaluating kratom alkaloids using PHASE. Ellis CR, Racz R, Kruhlak NL, et al. PLoS One. 2020,15(3):e0229646. Published 2020 Mar 3.


Methodology

An Overview of Machine Learning and Big Data for Drug Toxicity Evaluation. Vo AH, Van Vleet TR, Gupta RR, Liguori M, Rao MS. Chem Res Toxicol. 2020, 33(1), 20-37.


Metabolism

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Closing the Gap Between Therapeutic Use and Mode of Action in Remedial Herbs. Olivés J, Mestres J. Front Pharmacol. 2019, 10, 1132.


Pharmacology & Metabolism

CLARITY

Novel Computational Approach to Predict Off-Target Interactions for Small Molecules. Rao M, Gupta R, Liguori MJ, Hu M, Huang X, Mantena SR, Mittelstadt SW, Blomme EAG, Van Vleet TR. Front Big Data. 2019 Jul; 2: Article 25.

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Pharmacology & Safety

CLARITY

Comparison of zebrafish larvae and hiPSC cardiomyocytes for predicting drug induced cardiotoxicity in humans. Dyballa S, Miñana R, Rubio-Brotons M, Cornet C, Pederzani T, Escaramis G, Garcia-Serna R, Mestres J, Terriente J. Toxicol Sci. 2019, 171(2), 283–295.

Pharmacology & Metabolism

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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.

Pharmacology

CLARITY

Pharmacology

CLARITY

Rationalizing Secondary Pharmacology Screening Using Human Genetic and Pharmacological Evidence. Deaton AM, Fan F, Zhang W, Nguyen PA, Ward LD, Nioi P. Toxicol Sci. 2019 Feb 1;167(2):593-603.

Target deconvolution, Target profiling

CLARITY

Screening Strategies and Methods for Better Off-Target Liability Prediction and Identification of Small-Molecule Pharmaceuticals. Van Vleet TR, Liguori MJ, Lynch JJ, Rao M, Warder S. SLAS Discov. 2019 Jan;24(1):1-24.

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

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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.

Pharmacology

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

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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 deconvolution

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.

Target deconvulation

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.

Pharmacology

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.