Recent Advances in QSAR Studies

Since the inception of this volume, the world s nancial climate has radically changed. Theemphasishasshiftedfromboomingeconomiesandeconomicgrowth totherealityofrecessionanddiminishingoutlook. Witheconomicdownturncomes opportunity, inallareasofchemistryfromresearchanddevelopmentthroughto productregistrationandriskassessment, replacementsarebeingsoughtforcostly time-consumingprocesses. Leadingamongstthereplacementsaremodelswithtrue predictivecapability. Ofthesecomputationalmodelsarepreferred. This volume addresses a broad need within various areas of the chemical industries, from pharmaceuticals and pesticides to personal products to provide computationalmethodstopredicttheeffects, activitiesandpropertiesofmolecules. Itaddressestheuseofmodelstodesignnewmoleculesandassesstheirfateand effectsbothtotheenvironmentandtohumanhealth. Thereisanemphasisrunning throughoutthisvolumetoproducerobustmodelssuitableforpurpose. Thevolume aimstoallowthereaderto nddataanddescriptorsanddevelop, discoverandutilise validmodels. Gdansk, Poland TomaszPuzyn Jackson, MS, USA JerzyLeszczynski Liverpool, UK MarkT. D. Cronin May2009 CONTENTS Part I Theory of QSAR 1 QuantitativeStructure ActivityRelationships(QSARs) ApplicationsandMethodology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Mark T. D. Cronin 1. 1. Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 1. 2. PurposeofQSAR. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 1. 3. ApplicationsofQSAR. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 1. 4. Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1. 5. TheCornerstonesofSuccessfulPredictiveModels . . . . . . . . . . . . 7 1. 6. AValidated(Q)SARoraValidPrediction? . . . . . . . . . . . . . . . . . . 9 1. 7. UsinginSilicoTechniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 1. 8. NewAreasforinSilicoModels. . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 1. 9. Conclusions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 2 TheUseofQuantumMechanicsDerivedDescriptorsin ComputationalToxicology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 Steven J. Enoch 2. 1. Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 2. 2. TheSchrodingerEquation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 2. 3. Hartree FockTheory. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 2. 4. Semi-EmpiricalMethods: AM1andRM1. . . . . . . . . . . . . . . . . . . . 18 2. 5. ABInitio: DensityFunctionalTheory. . . . . . . . . . . . . . . . . . . . . . . 19 2. 6. QSARforNon-ReactiveMechanismsofAcute(Aquatic) Toxicity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 2. 7. QSARsforReactiveToxicityMechanisms. . . . . . . . . . . . . . . . . . . 21 2. 7. 1. AquaticToxicityandSkinSensitisation. . . . . . . . . . . . . 21 2. 7. 2. QSARsforMutagenicity . . . . . . . . . . . . . . . . . . . . . . . . . 24 2. 8. FutureDirectionsandOutlook. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 2. 9. Conclusions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 vii viii Contents 3 MolecularDescriptors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 Viviana Consonni and Roberto Todeschini 3. 1. Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 3. 1. 1. De nitions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 3. 1. 2. History. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 3. 1. 3. Theoreticalvs. ExperimentalDescriptors. . . . . . . . . . . . 33 3. 2. MolecularRepresentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 3. 3. TopologicalIndexes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 3. 3. 1. MolecularGraphs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 3. 3. 2. De nitionandCalculationofTopologicalIndexes(TIs) 39 3. 3. 3. Graph-TheoreticalMatrixes. . . . . . . . . . . . . . . . . . . . . . . 42 3. 3. 4. ConnectivityIndexes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 3. 3. 5. CharacteristicPolynomial . . . . . . . . . . . . . . . . . . . . . . . . 50 3. 3. 6. SpectralIndexes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 3. 4. AutocorrelationDescriptors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ."

Recent Advances in QSAR Studies: Methods and Applications presents an interdisciplinary overview on the most recent advances in QSAR studies. The first part of this volume is handbook-esque and consists of a comprehensive review of QSAR methodology written by outstanding scientists and highly experienced lecturers. It focuses on methodology and new ideas, providing readers with an idea of recent trends and developments in each part of QSAR strategy (descriptors, methods of modelling, validation). The second part of this volume highlights the interdisciplinary aspects and new areas of QSAR modelling. It outlines the theoretical framework together with practical applications. The most optimal solutions (descriptors, mathematical/statistical methods, validation) in the individual areas of interest (environmental risk assessment, drug design, etc.) are also discussed in more detail.

Recent Advances in QSAR Studies: Methods and Applications is targeted at scientists who are focussed on developing new methodologies as well as researchers who are engaged in trying to solve specific problems via QSAR. Additionally, this volume should serve as an essential reference to promote interactions between members of the academic community and industry.