A novel approach to predict aquatic toxicity from molecular structure.

The main aim of the study was to develop quantitative structure-activity relationship (QSAR) models for the prediction of aquatic toxicity using atom-based non-stochastic and stochastic linear indices. The used dataset consist of 392 benzene derivatives, separated into training and test sets, for which toxicity data to the ciliate Tetrahymena pyriformis were available. Using multiple linear regression, two statistically significant QSAR models were obtained with non-stochastic (R2=0.791 and s=0.344) and stochastic (R2=0.799 and s=0.343) linear indices. A leave-one-out (LOO) cross-validation procedure was carried out achieving values of q2=0.781 (scv=0.348) and q2=0.786 (scv=0.350), respectively. In addition, a validation through an external test set was performed, which yields significant values of Rpred2 of 0.762 and 0.797. A brief study of the influence of the statistical outliers in QSAR's model development was also carried out. Finally, our method was compared with other approaches implemented in the Dragon software achieving better results. The non-stochastic and stochastic linear indices appear to provide an interesting alternative to costly and time-consuming experiments for determining toxicity.

[1]  M. Diudea,et al.  QSTR Study on Aquatic Toxicity Against Poecilia reticulata and Tetrahymena pyriformis Using Topological Indices , 2006 .

[2]  Francisco Torrens,et al.  Estimation of ADME Properties in Drug Discovery: Predicting Caco-2 Cell Permeability Using Atom-Based Stochastic and Non-Stochastic Linear Indices , 2007 .

[3]  Chunsheng Yin,et al.  Holographic QSAR of selected esters. , 2004, Chemosphere.

[4]  Francisco Torrens,et al.  Atom, atom-type and total molecular linear indices as a promising approach for bioorganic and medicinal chemistry: theoretical and experimental assessment of a novel method for virtual screening and rational design of new lead anthelmintic. , 2005, Bioorganic & medicinal chemistry.

[5]  Yovani Marrero-Ponce,et al.  Ligand-Based Virtual Screening and in Silico Design of New Antimalarial Compounds Using Nonstochastic and Stochastic Total and Atom-Type Quadratic Maps , 2005, J. Chem. Inf. Model..

[6]  A. Hagler,et al.  Chemoinformatics and Drug Discovery , 2002, Molecules : A Journal of Synthetic Chemistry and Natural Product Chemistry.

[7]  Roberto Todeschini,et al.  Structure/Response Correlations and Similarity/Diversity Analysis by GETAWAY Descriptors, 1. Theory of the Novel 3D Molecular Descriptors , 2002, J. Chem. Inf. Comput. Sci..

[8]  Richard A. Johnson,et al.  Applied Multivariate Statistical Analysis , 1983 .

[9]  T. W. Schultz,et al.  TETRATOX: TETRAHYMENA PYRIFORMIS POPULATION GROWTH IMPAIRMENT ENDPOINTA SURROGATE FOR FISH LETHALITY , 1997 .

[10]  Yovani Marrero-Ponce,et al.  3D-chiral Atom, Atom-type, and Total Non-stochastic and Stochastic Molecular Linear Indices and their Applications to Central Chirality Codification , 2005, J. Comput. Aided Mol. Des..

[11]  Francisco Torrens,et al.  3D-chiral quadratic indices of the 'molecular pseudograph's atom adjacency matrix' and their application to central chirality codification: classification of ACE inhibitors and prediction of sigma-receptor antagonist activities. , 2004, Bioorganic & medicinal chemistry.

[12]  Francisco Torrens,et al.  Protein linear indices of the 'macromolecular pseudograph alpha-carbon atom adjacency matrix' in bioinformatics. Part 1: prediction of protein stability effects of a complete set of alanine substitutions in Arc repressor. , 2005, Bioorganic & medicinal chemistry.

[13]  Francisco Torrens,et al.  Atom, atom-type, and total linear indices of the "molecular pseudograph's atom adjacency matrix": application to QSPR/QSAR studies of organic compounds. , 2004, Molecules.

[14]  A. J. Hopfinger,et al.  Membrane-Interaction QSAR Analysis: Application to the Estimation of Eye Irritation by Organic Compounds , 1999, Pharmaceutical Research.

[15]  John D. Walker,et al.  Quantitative structure–activity relationships (QSARs) in toxicology: a historical perspective , 2003 .

[16]  Francisco Torrens,et al.  Nucleic acid quadratic indices of the "macromolecular graph's nucleotides adjacency matrix" , 2004 .

[17]  John D. Walker,et al.  Quantitative structure‐activity relationships for predicting potential ecological hazard of organic chemicals for use in regulatory risk assessments , 2003, Environmental toxicology and chemistry.

[18]  James W. McFarland,et al.  Cluster Significance Analysis: A New Qsar Tool for Asymmetric Data Sets , 1990 .

[19]  Gerald T Ankley,et al.  Overview of data and conceptual approaches for derivation of quantitative structure‐activity relationships for ecotoxicological effects of organic chemicals , 2003, Environmental toxicology and chemistry.

[20]  M. Cronin,et al.  Pitfalls in QSAR , 2003 .

[21]  Eduardo A. Castro,et al.  Tomocomd-Cardd, a novel approach for computer-aided ‘ rational’ drug design: I. Theoretical and experimental assessment of a promising method for computational screening and in silico design of new anthelmintic compounds , 2004, J. Comput. Aided Mol. Des..

[22]  J. Dearden,et al.  Assessment and modeling of the toxicity of organic chemicals to Chlorella vulgaris: development of a novel database. , 2004, Chemical research in toxicology.

[23]  T W Schultz,et al.  Structure-Toxicity Analyses of Tetrahymena Pyriformis Exposed to Pyridines - An Examination Into Extension of Surface-Response Domains , 2001, SAR and QSAR in environmental research.

[24]  Francisco Torrens,et al.  Atom-based stochastic and non-stochastic 3D-chiral bilinear indices and their applications to central chirality codification. , 2007, Journal of molecular graphics & modelling.

[25]  Francisco Torrens,et al.  Atom-based 3D-chiral quadratic indices. Part 2: prediction of the corticosteroid-binding globulinbinding affinity of the 31 benchmark steroids data set. , 2006, Bioorganic & medicinal chemistry.

[26]  J Devillers New trends in (Q)SAR modeling with topological indices. , 2000, Current opinion in drug discovery & development.

[27]  T W Schultz,et al.  Structure–activity relationships for aquatic toxicity to Tetrahymena: Halogen‐substituted aliphatic esters , 2001, Environmental toxicology.

[28]  Francisco Torrens,et al.  A new topological descriptors based model for predicting intestinal epithelial transport of drugs in Caco-2 cell culture. , 2004, Journal of pharmacy & pharmaceutical sciences : a publication of the Canadian Society for Pharmaceutical Sciences, Societe canadienne des sciences pharmaceutiques.

[29]  Han van de Waterbeemd,et al.  Chemometric Methods in Molecular Design: van de Waterbeemd/Chemometric , 1995 .

[30]  Johann Gasteiger,et al.  Use of Structure Descriptors To Discriminate between Modes of Toxic Action of Phenols , 2005, J. Chem. Inf. Model..

[31]  T W Schultz,et al.  Structure-toxicity relationships for benzenes evaluated with Tetrahymena pyriformis. , 1999, Chemical research in toxicology.

[32]  Maykel Pérez González,et al.  A novel approach to predict a toxicological property of aromatic compounds in the Tetrahymena pyriformis. , 2004, Bioorganic & medicinal chemistry.

[33]  A. Tropsha,et al.  Beware of q2! , 2002, Journal of molecular graphics & modelling.

[34]  Paola Gramatica,et al.  New 3D Molecular Descriptors: The WHIM theory and QSAR Applications , 2002 .

[35]  T. Wayne Schultz,et al.  Population growth impairment of aliphatic alcohols to Tetrahymena , 2004, Environmental toxicology.

[36]  Ovidiu Ivanciuc,et al.  Applications of Support Vector Machines in Chemistry , 2007 .

[37]  I. W Nowell,et al.  Molecular Connectivity in Structure-Activity Analysis , 1986 .

[38]  Francisco Torrens,et al.  Protein quadratic indices of the "macromolecular pseudograph's alpha-carbon atom adjacency matrix". 1. Prediction of Arc repressor alanine-mutant's stability. , 2004, Molecules.

[39]  S. Morgan,et al.  Outlier detection in multivariate analytical chemical data. , 1998, Analytical chemistry.

[40]  Yovani Marrero-Ponce,et al.  Linear Indices of the "Molecular Pseudograph's Atom Adjacency Matrix": Definition, Significance-Interpretation, and Application to QSAR Analysis of Flavone Derivatives as HIV-1 Integrase Inhibitors , 2004, J. Chem. Inf. Model..

[41]  D. Roberts,et al.  Chemistry-toxicity relationships for the effects of di- and trihydroxybenzenes to Tetrahymena pyriformis. , 2005, Chemical research in toxicology.

[42]  S. Bradbury,et al.  Quantitative structure-activity relationships and ecological risk assessment: an overview of predictive aquatic toxicology research. , 1995, Toxicology letters.

[43]  J. Vervoort,et al.  Quantum chemistry based quantitative structure‐activity relationships for modeling the (sub)acute toxicity of substituted mononitrobenzenes in aquatic systems , 2006, Environmental toxicology and chemistry.

[44]  J V Nabholz,et al.  Mode of action and the assessment of chemical hazards in the presence of limited data: use of structure-activity relationships (SAR) under TSCA, Section 5. , 1990, Environmental health perspectives.

[46]  M. C. Newman,et al.  The practice of structure activity relationships (SAR) in toxicology. , 2000, Toxicological sciences : an official journal of the Society of Toxicology.

[47]  Yovani Marrero-Ponce,et al.  Non-stochastic and stochastic linear indices of the 'molecular pseudograph's atom adjacency matrix': application to 'in silico' studies for the rational discovery of new antimalarial compounds. , 2005, Bioorganic & medicinal chemistry.

[48]  Yovani Marrero Ponce Total and Local Quadratic Indices of the Molecular Pseudograph’s Atom Adjacency Matrix: Applications to the Prediction of Physical Properties of Organic Compounds , 2003, Molecules : A Journal of Synthetic Chemistry and Natural Product Chemistry.

[49]  Tatiana I. Netzeva,et al.  Development and Evaluation of QSARs for Ecotoxic Endpoints: The Benzene Response- Surface Model for Toxicity , 2004 .

[50]  Haralambos Sarimveis,et al.  Prediction of toxicity using a novel RBF neural network training methodology , 2006, Journal of molecular modeling.

[51]  Francisco Torrens,et al.  Atom, atom-type, and total nonstochastic and stochastic quadratic fingerprints: a promising approach for modeling of antibacterial activity. , 2005, Bioorganic & medicinal chemistry.

[52]  Yovani Marrero Ponce Total and local (atom and atom type) molecular quadratic indices: significance interpretation, comparison to other molecular descriptors, and QSPR/QSAR applications. , 2004, Bioorganic & medicinal chemistry.

[53]  Tatiana I Netzeva,et al.  QSARs for the aquatic toxicity of aromatic aldehydes from Tetrahymena data. , 2005, Chemosphere.

[54]  F. Torrens,et al.  Prediction of Intestinal Epithelial Transport of Drug in ( Caco – 2 ) Cell Culture from Molecular Structure using in silico Approaches During Early Drug Discovery , 2005 .

[55]  David W Roberts,et al.  Mechanistic applicability domains for nonanimal-based prediction of toxicological end points: general principles and application to reactive toxicity. , 2006, Chemical research in toxicology.