Statistical learning approaches for predicting pharmacological properties of pharmaceutical agents

Ph.DDOCTOR OF PHILOSOPH

Machine learning approach in pharmacokinetics and toxicity prediction

Ph.DDOCTOR OF PHILOSOPH

Review of QSAR Models and Software Tools for predicting Biokinetic Properties

In the assessment of industrial chemicals, cosmetic ingredients, and active substances in pesticides and biocides, metabolites and degradates are rarely tested for their toxicologcal effects in mammals. In the interests of animal welfare and cost-effectiveness, alternatives to animal testing are needed in the evaluation of these types of chemicals. In this report we review the current status of various types of in silico estimation methods for Absorption, Distribution, Metabolism and Excretion (ADME) properties, which are often important in discriminating between the toxicological profiles of parent compounds and their metabolites/degradation products. The review was performed in a broad sense, with emphasis on QSARs and rule-based approaches and their applicability to estimation of oral bioavailability, human intestinal absorption, blood-brain barrier penetration, plasma protein binding, metabolism and. This revealed a vast and rapidly growing literature and a range of software tools. While it is difficult to give firm conclusions on the applicability of such tools, it is clear that many have been developed with pharmaceutical applications in mind, and as such may not be applicable to other types of chemicals (this would require further research investigation). On the other hand, a range of predictive methodologies have been explored and found promising, so there is merit in pursuing their applicability in the assessment of other types of chemicals and products. Many of the software tools are not transparent in terms of their predictive algorithms or underlying datasets. However, the literature identifies a set of commonly used descriptors that have been found useful in ADME prediction, so further research and model development activities could be based on such studies.JRC.DG.I.6-Systems toxicolog

Prediction of Human Intestinal Absorption by GA Feature Selection and Support Vector Machine Regression

QSAR (Quantitative Structure Activity Relationships) models for the prediction of human intestinal absorption (HIA) were built with molecular descriptors calculated by ADRIANA.Code, Cerius2 and a combination of them. A dataset of 552 compounds covering a wide range of current drugs with experimental HIA values was investigated. A Genetic Algorithm feature selection method was applied to select proper descriptors. A Kohonen's self-organizing Neural Network (KohNN) map was used to split the whole dataset into a training set including 380 compounds and a test set consisting of 172 compounds. First, the six selected descriptors from ADRIANA.Code and the six selected descriptors from Cerius2 were used as the input descriptors for building quantitative models using Partial Least Square (PLS) analysis and Support Vector Machine (SVM) Regression. Then, another two models were built based on nine descriptors selected by a combination of ADRIANA.Code and Cerius2 descriptors using PLS and SVM, respectively. For the three SVM models, correlation coefficients (r) of 0.87, 0.89 and 0.88 were achieved; and standard deviations (s) of 10.98, 9.72 and 9.14 were obtained for the test set

Asymmetric bagging and feature selection for activities prediction of drug molecules

<p>Abstract</p> <p>Background</p> <p>Activities of drug molecules can be predicted by QSAR (quantitative structure activity relationship) models, which overcomes the disadvantages of high cost and long cycle by employing the traditional experimental method. With the fact that the number of drug molecules with positive activity is rather fewer than that of negatives, it is important to predict molecular activities considering such an unbalanced situation.</p> <p>Results</p> <p>Here, asymmetric bagging and feature selection are introduced into the problem and asymmetric bagging of support vector machines (asBagging) is proposed on predicting drug activities to treat the unbalanced problem. At the same time, the features extracted from the structures of drug molecules affect prediction accuracy of QSAR models. Therefore, a novel algorithm named PRIFEAB is proposed, which applies an embedded feature selection method to remove redundant and irrelevant features for asBagging. Numerical experimental results on a data set of molecular activities show that asBagging improve the AUC and sensitivity values of molecular activities and PRIFEAB with feature selection further helps to improve the prediction ability.</p> <p>Conclusion</p> <p>Asymmetric bagging can help to improve prediction accuracy of activities of drug molecules, which can be furthermore improved by performing feature selection to select relevant features from the drug molecules data sets.</p

PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence

Sequence-derived structural and physicochemical features have frequently been used in the development of statistical learning models for predicting proteins and peptides of different structural, functional and interaction profiles. PROFEAT (Protein Features) is a web server for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. It computes six feature groups composed of ten features that include 51 descriptors and 1447 descriptor values. The computed features include amino acid composition, dipeptide composition, normalized Moreau–Broto autocorrelation, Moran autocorrelation, Geary autocorrelation, sequence-order-coupling number, quasi-sequence-order descriptors and the composition, transition and distribution of various structural and physicochemical properties. In addition, it can also compute previous autocorrelations descriptors based on user-defined properties. Our computational algorithms were extensively tested and the computed protein features have been used in a number of published works for predicting proteins of functional classes, protein–protein interactions and MHC-binding peptides. PROFEAT is accessible a

Applicability domains of neural networks for toxicity prediction

In this paper, the term "applicability domain" refers to the range of chemical compounds for which the statistical quantitative structure-activity relationship (QSAR) model can accurately predict their toxicity. This is a crucial concept in the development and practical use of these models. First, a multidisciplinary review is provided regarding the theory and practice of applicability domains in the context of toxicity problems using the classical QSAR model. Then, the advantages and improved performance of neural networks (NNs), which are the most promising machine learning algorithms, are reviewed. Within the domain of medicinal chemistry, nine different methods using NNs for toxicity prediction were compared utilizing 29 alternative artificial intelligence (AI) techniques. Similarly, seven NN-based toxicity prediction methodologies were compared to six other AI techniques within the realm of food safety, 11 NN-based methodologies were compared to 16 different AI approaches in the environmental sciences category and four specific NN-based toxicity prediction methodologies were compared to nine alternative AI techniques in the field of industrial hygiene. Within the reviewed approaches, given known toxic compound descriptors and behaviors, we observed a difficulty in being able to extrapolate and predict the effects with untested chemical compounds. Different methods can be used for unsupervised clustering, such as distance-based approaches and consensus-based decision methods. Additionally, the importance of model validation has been highlighted within a regulatory context according to the Organization for Economic Co-operation and Development (OECD) principles, to predict the toxicity of potential new drugs in medicinal chemistry, to determine the limits of detection for harmful substances in food to predict the toxicity limits of chemicals in the environment, and to predict the exposure limits to harmful substances in the workplace. Despite its importance, a thorough application of toxicity models is still restricted in the field of medicinal chemistry and is virtually overlooked in other scientific domains. Consequently, only a small proportion of the toxicity studies conducted in medicinal chemistry consider the applicability domain in their mathematical models, thereby limiting their predictive power to untested drugs. Conversely, the applicability of these models is crucial; however, this has not been sufficiently assessed in toxicity prediction or in other related areas such as food science, environmental science, and industrial hygiene. Thus, this review sheds light on the prevalent use of Neural Networks in toxicity prediction, thereby serving as a valuable resource for researchers and practitioners across these multifaceted domains that could be extended to other fields in future research

Efficacy of different protein descriptors in predicting protein functional families

10.1186/1471-2105-8-300BMC Bioinformatics8-BBMI

A Knowledge Based Approach of Toxicity Prediction for Drug Formulation. Modelling Drug Vehicle Relationships Using Soft Computing Techniques

This multidisciplinary thesis is concerned with the prediction of drug formulations for the reduction of drug toxicity. Both scientific and computational approaches are utilised to make original contributions to the field of predictive toxicology. The first part of this thesis provides a detailed scientific discussion on all aspects of drug formulation and toxicity. Discussions are focused around the principal mechanisms of drug toxicity and how drug toxicity is studied and reported in the literature. Furthermore, a review of the current technologies available for formulating drugs for toxicity reduction is provided. Examples of studies reported in the literature that have used these technologies to reduce drug toxicity are also reported. The thesis also provides an overview of the computational approaches currently employed in the field of in silico predictive toxicology. This overview focuses on the machine learning approaches used to build predictive QSAR classification models, with examples discovered from the literature provided. Two methodologies have been developed as part of the main work of this thesis. The first is focused on use of directed bipartite graphs and Venn diagrams for the visualisation and extraction of drug-vehicle relationships from large un-curated datasets which show changes in the patterns of toxicity. These relationships can be rapidly extracted and visualised using the methodology proposed in chapter 4. The second methodology proposed, involves mining large datasets for the extraction of drug-vehicle toxicity data. The methodology uses an area-under-the-curve principle to make pairwise comparisons of vehicles which are classified according to the toxicity protection they offer, from which predictive classification models based on random forests and decisions trees are built. The results of this methodology are reported in chapter 6