Last Update: February 13, 2024
Authorship
Application
CT Product
Article
Target Profiling
CLARITY
Evaluation of QSAR models for predicting mutagenicity: outcome of the Second Ames/QSAR international challenge project. Furuhama A, Kitazawa A, Yao J, Matos Dos Santos CE, Rathman J, Yang C, Ribeiro JV, Cross K, Myatt G, Raitano G, Benfenati E, Jeliazkova N, Saiakhov R, Chakravarti S, Foster RS, Bossa C, Battistelli CL, Benigni R, Sawada T, Wasada H, Hashimoto T, Wu M, Barzilay R, Daga PR, Clark RD, Mestres J, Montero A, Gregori-Puigjané E, Petkov P, Ivanova H, Mekenyan O, Matthews S, Guan D, Spicer J, Lui R, Uesawa Y, Kurosaki K, Matsuzaka Y, Sasaki S, Cronin MTD, Belfield SJ, Firman JW, Spînu N, Qiu M, Keca JM, Gini G, Li T, Tong W, Hong H, Liu Z, Igarashi Y, Yamada H, Sugiyama KI, Honma M. SAR QSAR Environ Res. 2023; 34(12):983-1001. doi: 10.1080/1062936X.2023.2284902. Epub 2023 Dec 4.
Toxicology
CLARITYPV
In silico approaches in carcinogenicity hazard assessment: case study of pregabalin, a nongenotoxic mouse carcinogen. Keller DA, Bassan A, Amberg A, Burns Naas LA, Chambers J, Cross K, Hall F, Jahnke GD, Luniwal A, Manganelli S, Mestres J, Mihalchik-Burhans AL, Wooley D, Tice RR. Front Toxicol 2023; 5:1234498. doi: 10.3389/ftox.2023.1234498.
Pharmacovigilance
CLARITY VISTA
Impact of the COVID-19 pandemic on the spontaneous reporting and signal detection of adverse drug events. Montes-Grajales D, Garcia-Serna R, Mestres J. Sci Rep. 2023; 13:18817. https://doi.org/10.1038/s41598-023-46275-w.
Pharmacology, Target Profiling
Artificial Intelligence/Machine Learning-Driven Small Molecule Repurposing via Off-Target Prediction and Transcriptomics. Rao M, McDuffie E, Sachs C. Toxics. 2023; 11, 875. https://doi.org/10.3390/toxics11100875.
Pharmacology
A multiscale orchestrated computational framework to reveal emergent phenomena in neuroblastoma. Borau C, Wertheim KY, Hervas-Raluy S, Sainz-DeMena D, Walker D, Chisholm R, Richmond P, Varella V, Viceconti M, Montero A, Gregori-Puigjané E, Mestres J, Kasztelnik M, García-Aznar JM. Comput Methods Programs Biomed. 2023; (241)107742. doi:10.1016/j.cmpb.2023.107742.
Target Profiling, Pharmacology, Safety
CLARITY
AI/ML Models to Predict the Severity of Drug-Induced Liver Injury for Small Molecules. Rao M, Nassiri V, Alhambra C, Snoeys J, Van Goethem F, Irrechukwu O, Aleo MD, Geys H, Mitra K, Will Y. Chem Res Toxicol. 2023; 36(7):1129-1139. doi: 10.1021/acs.chemrestox.3c00098. Epub 2023 Jun 9.
Target Profiling, Pharmacology, Safety
CLARITY
Predicting binding between 55 cannabinoids and 4799 biological targets by in silico methods. Santillo MF, Sprando RL. J Appl Toxicol. 2023; 43(10):1476-1487. doi: 10.1002/jat.4478. Epub 2023 May 10.
Target Profiling, Pharmacology
Illuminating the Chemical Space of Untargeted Proteins. Falaguera MJ, Mestres J. J. Chem. Inf. Model. 2023; 63(9):2603-2894. doi: 10.1021/acs.jcim.2c01364.
Target Profiling, Pharmacology
CLARITY
Picamilon, a γ-aminobutyric acid (GABA) analogue and marketed nootropic, is inactive against 50 biological targets. Santillo MF, Sprandro RL. Basic Clin Pharmacol Toxicol. 2023; 132(4):355-358. doi: 10.1111/bcpt.13836.
Drug Discovery, Virtual Screening
ProSurfScan
Fragment-based virtual screening identifies a first-in-class preclinical drug candidate for Huntington’s disease. Galyan SM, Ewald CY, Jalencas X, Masrani S, Meral S, Mestres J. Sci Rep. 2022; 12(1):19642. doi: 10.1038/s41598-022-21900-2.
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; 14(1):51. doi: 10.1186/s13321-022-00628-1.
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 Med. 2022; (1):e003391. 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; 62(3):718-729. 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; 13(2):261-267. doi: 10.1002/dta.2992.
Toxicology
ELIXIR and Toxicology: a community in development. Martens M, Stierum R, Schymanski EL et al. [version 2; peer review: 1 approved, 1 approved with reservations]. 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; 28(10):1433-1445.e3. doi:10.1016/j.chembiol.2021.05.004. (previous at bioRxiv).
Safety
Skin sensitization in Silico protocol. Johnson C, Ahlberg E, Anger LT, et al. Regul Toxicol Pharmacol. 2020; 116:104688. doi: 10.1016/j.yrtph.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. doi: 10.1371/journal.pone.0229646.
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. doi: 10.1021/acs.chemrestox.9b00227.
Metabolism
CT-link
Closing the gap between therapeutic use and mode of action in remedial herbs. Olivés J, Mestres J. Front Pharmacol. 2019; 10:1132. doi: 10.3389/fphar.2019.01132.
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; 2:25. doi: 10.3389/fdata.2019.00025.
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):283–95. doi: 10.1093/toxsci/kfz165.
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; 33(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; 106(1):116-122. doi: 10.1002/cpt.1418.
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; 167(2):593-603. doi: 10.1093/toxsci/kfy265.
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; 24(1):1-24. doi: 10.1177/2472555218799713.
Pharmacology
CLARITY
Dual inhibitors of PARPs and ROCKs. Antolín AA, Mestres J. ACS Omega. 2018; 3(10):12707-12712. doi: 10.1021/acsomega.8b02337.
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; 16(12):811-812. doi: 10.1038/nrd.2017.177.
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; 12(10):e0187034. doi: 10.1371/journal.pone.0187034.
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; 21(3):533-546. doi: 10.1007/s11030-017-9738-7.
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. doi:10.1002/slct.201700397.
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; 12(7):e1005763. doi: 10.1371/journal.ppat.1005763.
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; 29(4):637-48. doi: 10.1021/acs.chemrestox.5b00470.
Large-scale predictive drug safety: from structural alerts to biological mechanisms. Garcia-Serna R, Vidal D, Remez N, Mestres J. Chem Res Toxicol. 2015; 28(10):1875-87. doi: 10.1021/acs.chemrestox.5b00260.
Target identification
CT-link
Distant polypharmacology among MLP chemical probes. Antolín AA, Mestres J. ACS Chem Biol. 2015; 10(2):395-400. doi: 10.1021/cb500393m.
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; 229:S164.
Target deconvolution
PredictFX
Identification of host interactions for phenotypic antimalarial hits. Spitzmüller A, Mestres J. J Cheminform. 2014; 6(Suppl 1):O12. doi: 10.1186/1758-2946-6-S1-O12.
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; 63:216-23. doi: 10.1016/j.envint.2013.11.012.
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. doi: 10.1371/journal.pcbi.1003257.
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; 7(12):1962-7. doi: 10.1021/cb300317y.
Target deconvolution
SHED profiling
Identification of small molecule inhibitors of Amyloid β-induced neuronal apoptosis acting through the Imidazoline I(2) receptor. Montolio M1, Gregori-Puigjané E, Pineda D, Mestres J, Navarro P. J Med Chem. 2012; 55(22):9838-46. doi: 10.1021/jm301055g.
PredictFX
New chromene scaffolds for adenosine A2A receptors: synthesis, pharmacology and structure-activity relationships. Areias F, Costa M, Castro M, Brea J, Gregori-Puigjané E, Proença MF, Mestres J, Loza MI. Eur J Med Chem. 2012; 54:303-10. doi: 10.1016/j.ejmech.2012.05.009.
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; 86(7):3795-808. doi: 10.1128/JVI.05972-11.
Target deconvolution
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. doi: 10.1371/journal.pone.0035582.
Target deconvolution
Ligand-based approaches to in Silico pharmacology. Vidal D, Garcia-Serna R, Mestres J. Methods Mol Biol. 2011; 672:489-502. doi: 10.1007/978-1-60761-839-3_19.
Target profiling
Cross-pharmacology analysis of G protein-coupled receptors. Briansó F, Carrascosa MC, Oprea TI, Mestres J. Curr Top Med Chem. 2011; 11(15):1956-63. doi: 10.2174/156802611796391285.
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; 90(5):662-5. doi: 10.1038/clpt.2011.177.
Safety
Shaping the future of safer innovative drugs in Europe. Mestres J, Bryant SD, Zamora I, Gasteiger J. Nat Biotechnol. 2011; 29:789-790. doi: 10.1038/nbt.1973.
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; 278(16):2951-61. doi: 10.1111/j.1742-4658.2011.08220.x.
Target profiling
SHED profiling
In Silico target profiling of one billion molecules. Nonell-Canals A, Mestres J. Mol Inform. 2011; 30(5):405-9. doi: 10.1002/minf.201100018.
Pharmacology & Safety
Anticipating drug side effects by comparative pharmacology. Garcia-Serna R, Mestres J. Expert Opin Drug Metab Toxicol. 2010; 6:1253-1263. doi: 10.1517/17425255.2010.509343.
Target profiling
PHRAG, FPD and SHED profiling
In Silico receptorome screening of antipsychotic drugs. Vidal D, Mestres J. Mol Inform. 2010; 29(6-7):543-51. doi: 10.1002/minf.201000055.
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; 18(9):3043-52. doi: 10.1016/j.bmc.2010.03.048.
Pharmacology
Coverage and bias in chemical library design. Gregori-Puigjané E, Mestres J. Curr Opin Chem Biol. 2008; 12:359-365. doi: 10.1016/j.cbpa.2008.03.015.
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; 11(8):669-76. doi: 10.2174/138620708785739952.
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; 26(9):983-4. doi: 10.1038/nbt0908-983.
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; 46(6):2725-36. doi: 10.1021/ci600300k.
Methodology
SHED profiling
SHED: Shannon entropy descriptors from topological feature distributions. Gregori-Puigjané E, Mestres J. J Chem Inf Model. 2006; 46(4):1615-22. doi: 10.1021/ci0600509.
