ADMET-score - a comprehensive scoring function for evaluation of chemical drug-likeness.

Chemical absorption, distribution, metabolism, excretion, and toxicity (ADMET), play key roles in drug discovery and development. A high-quality drug candidate should not only have sufficient efficacy against the therapeutic target, but also show appropriate ADMET properties at a therapeutic dose. A lot of in silico models are hence developed for prediction of chemical ADMET properties. However, it is still not easy to evaluate the drug-likeness of compounds in terms of so many ADMET properties. In this study, we proposed a scoring function named the ADMET-score to evaluate drug-likeness of a compound. The scoring function was defined on the basis of 18 ADMET properties predicted via our web server admetSAR. The weight of each property in the ADMET-score was determined by three parameters: the accuracy rate of the model, the importance of the endpoint in the process of pharmacokinetics, and the usefulness index. The FDA-approved drugs from DrugBank, the small molecules from ChEMBL and the old drugs withdrawn from the market due to safety concerns were used to evaluate the performance of the ADMET-score. The indices of the arithmetic mean and p-value showed that the ADMET-score among the three data sets differed significantly. Furthermore, we learned that there was no obvious linear correlation between the ADMET-score and QED (quantitative estimate of drug-likeness). These results suggested that the ADMET-score would be a comprehensive index to evaluate chemical drug-likeness, and might be helpful for users to select appropriate drug candidates for further development.

[1]  Jie Shen,et al.  admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties , 2012, J. Chem. Inf. Model..

[2]  Asher Mullard 2017 FDA drug approvals , 2018, Nature Reviews Drug Discovery.

[3]  George Divine,et al.  Exemplary data set sample size calculation for Wilcoxon–Mann–Whitney tests , 2009, Statistics in medicine.

[4]  Matthew D Segall,et al.  Multi-parameter optimization: identifying high quality compounds with a balance of properties. , 2012, Current pharmaceutical design.

[5]  Robert Preissner,et al.  WITHDRAWN—a resource for withdrawn and discontinued drugs , 2015, Nucleic Acids Res..

[6]  Gunnar Rätsch,et al.  Classifying 'Drug-likeness' with Kernel-Based Learning Methods , 2005, J. Chem. Inf. Model..

[7]  George Papadatos,et al.  The ChEMBL database in 2017 , 2016, Nucleic Acids Res..

[8]  F. Cheng,et al.  Insights into Molecular Basis of Cytochrome P450 Inhibitory Promiscuity of Compounds , 2011, J. Chem. Inf. Model..

[9]  Matthew D Segall,et al.  Addressing toxicity risk when designing and selecting compounds in early drug discovery. , 2014, Drug discovery today.

[10]  Iskander Yusof,et al.  Considering the impact drug-like properties have on the chance of success. , 2013, Drug discovery today.

[11]  Tudor I. Oprea,et al.  Understanding drug‐likeness , 2011 .

[12]  Barry C. Jones,et al.  DRUG-DRUG INTERACTIONS FOR UDP-GLUCURONOSYLTRANSFERASE SUBSTRATES: A PHARMACOKINETIC EXPLANATION FOR TYPICALLY OBSERVED LOW EXPOSURE (AUCI/AUC) RATIOS , 2004, Drug Metabolism and Disposition.

[13]  Andreas Bender,et al.  A Large Descriptor Set and a Probabilistic Kernel-Based Classifier Significantly Improve Druglikeness Classification , 2007, J. Chem. Inf. Model..

[14]  Tingjun Hou,et al.  Drug-likeness analysis of traditional Chinese medicines: prediction of drug-likeness using machine learning approaches. , 2012, Molecular pharmaceutics.

[15]  Michael C Hutter,et al.  Selecting Relevant Descriptors for Classification by Bayesian Estimates: A Comparison with Decision Trees and Support Vector Machines Approaches for Disparate Data Sets , 2011, Molecular informatics.

[16]  David S. Wishart,et al.  DrugBank 5.0: a major update to the DrugBank database for 2018 , 2017, Nucleic Acids Res..

[17]  Youyong Li,et al.  ADMET evaluation in drug discovery. 12. Development of binary classification models for prediction of hERG potassium channel blockage. , 2012, Molecular pharmaceutics.

[18]  W. Patrick Walters,et al.  A guide to drug discovery: Designing screens: how to make your hits a hit , 2003, Nature Reviews Drug Discovery.

[19]  Ricardo Macarrón,et al.  Yin and Yang in medicinal chemistry: what does drug-likeness mean? , 2011, Future medicinal chemistry.

[20]  Tingjun Hou,et al.  ADME Evaluation in Drug Discovery, 6. Can Oral Bioavailability in Humans Be Effectively Predicted by Simple Molecular Property-Based Rules? , 2007, J. Chem. Inf. Model..

[21]  A. Ghose,et al.  A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases. , 1999, Journal of combinatorial chemistry.

[22]  T. Keller,et al.  A practical view of 'druggability'. , 2006, Current opinion in chemical biology.

[23]  I. Muegge,et al.  Simple selection criteria for drug-like chemical matter. , 2001, Journal of medicinal chemistry.

[24]  M. Bermejo,et al.  In Silico Prediction of Caco‐2 Cell Permeability by a Classification QSAR Approach , 2011, Molecular informatics.

[25]  Markus Wagener,et al.  Potential Drugs and Nondrugs: Prediction and Identification of Important Structural Features , 2000, J. Chem. Inf. Comput. Sci..

[26]  W Patrick Walters,et al.  Prediction of 'drug-likeness'. , 2002, Advanced drug delivery reviews.

[27]  Igor V. Pletnev,et al.  Drug Discovery Using Support Vector Machines. The Case Studies of Drug-likeness, Agrochemical-likeness, and Enzyme Inhibition Predictions , 2003, J. Chem. Inf. Comput. Sci..

[28]  Lei Yang,et al.  Classification of Cytochrome P450 Inhibitors and Noninhibitors Using Combined Classifiers , 2011, J. Chem. Inf. Model..

[29]  Jie Li,et al.  admetSAR 2.0: web‐service for prediction and optimization of chemical ADMET properties , 2018, Bioinform..

[30]  Jie Shen,et al.  Estimation of ADME Properties with Substructure Pattern Recognition , 2010, J. Chem. Inf. Model..

[31]  I. Kola,et al.  Can the pharmaceutical industry reduce attrition rates? , 2004, Nature Reviews Drug Discovery.

[32]  Miklos Feher,et al.  Property Distributions: Differences between Drugs, Natural Products, and Molecules from Combinatorial Chemistry , 2003, J. Chem. Inf. Comput. Sci..

[33]  Dan Li,et al.  The application of in silico drug-likeness predictions in pharmaceutical research. , 2015, Advanced drug delivery reviews.

[34]  H. Kubinyi,et al.  A scoring scheme for discriminating between drugs and nondrugs. , 1998, Journal of medicinal chemistry.

[35]  G. V. Paolini,et al.  Quantifying the chemical beauty of drugs. , 2012, Nature chemistry.

[36]  Andreas Bender,et al.  P-glycoprotein Substrate Models Using Support Vector Machines Based on a Comprehensive Data set , 2011, J. Chem. Inf. Model..

[37]  Tudor I. Oprea,et al.  Property distribution of drug-related chemical databases* , 2000, J. Comput. Aided Mol. Des..

[38]  Pär Matsson,et al.  Profiling of a prescription drug library for potential renal drug-drug interactions mediated by the organic cation transporter 2. , 2011, Journal of medicinal chemistry.

[39]  Tudor I. Oprea,et al.  A novel approach for predicting P-glycoprotein (ABCB1) inhibition using molecular interaction fields. , 2011, Journal of medicinal chemistry.

[40]  Klaus-Robert Müller,et al.  Benchmark Data Set for in Silico Prediction of Ames Mutagenicity , 2009, J. Chem. Inf. Model..

[41]  Xiao Li,et al.  In Silico Prediction of Chemical Acute Oral Toxicity Using Multi-Classification Methods , 2014, J. Chem. Inf. Model..

[42]  Ruili Huang,et al.  Comprehensive Characterization of Cytochrome P450 Isozyme Selectivity across Chemical Libraries , 2009, Nature Biotechnology.

[43]  Sanjivanjit K. Bhal,et al.  The Rule of Five revisited: applying log D in place of log P in drug-likeness filters. , 2007, Molecular pharmaceutics.

[44]  Gang Chen,et al.  A New Rapid and Effective Chemistry Space Filter in Recognizing a Druglike Database , 2005, J. Chem. Inf. Model..

[45]  Zengrui Wu,et al.  In Silico Estimation of Chemical Carcinogenicity with Binary and Ternary Classification Methods , 2015, Molecular informatics.

[46]  Jens Sadowski,et al.  Comparison of Support Vector Machine and Artificial Neural Network Systems for Drug/Nondrug Classification , 2003, J. Chem. Inf. Comput. Sci..