Modeling the Dispersibility of Single Walled Carbon Nanotubes in Organic Solvents by Quantitative Structure-Activity Relationship Approach

Predicting Antitumor Activity of Anthrapyrazole Derivatives using Advanced Machine Learning Techniques

BACKGROUND

Anthrapyrazoles are a new class of antitumor agents and successors to anthracyclines possessing a broad range of antitumor activity in various model tumors.

OBJECTIVES

The present study introduces novel QSAR models for the prediction of antitumor activity of anthrapyrazole analogues.

METHODS

The predictive performance of four machine learning algorithms, namely artificial neural networks, boosted trees, multivariate adaptive regression splines, and random forest, was studied in terms of variation of the observed and predicted data, internal validation, predictability, precision, and accuracy.

RESULTS

ANN and boosted trees algorithms met the validation criteria. It means that these procedures may be able to forecast the anticancer effects of the anthrapyrazoles studied. Evaluation of validation metrics, calculated for each approach, indicated the artificial neural network (ANN) procedure as the algorithm of choice, especially with regard to the obtained predictability as well as the lowest value of mean absolute error. The designed multilayer perceptron (MLP)-15-7-1 network displayed a high correlation between the predicted and the experimental pIC50 value for the training, test, and validation set. A conducted sensitivity analysis enabled an indication of the most important structural features of the studied activity.

CONCLUSION

The ANN strategy combines topographical and topological information and can be used for the design and development of novel anthrapyrazole analogues as anticancer molecules.

Practices and Trends of Machine Learning Application in Nanotoxicology

Machine Learning (ML) techniques have been applied in the field of nanotoxicology with very encouraging results. Adverse effects of nanoforms are affected by multiple features described by theoretical descriptors, nano-specific measured properties, and experimental conditions. ML has been proven very helpful in this field in order to gain an insight into features effecting toxicity, predicting possible adverse effects as part of proactive risk analysis, and informing safe design. At this juncture, it is important to document and categorize the work that has been carried out. This study investigates and bookmarks ML methodologies used to predict nano (eco)-toxicological outcomes in nanotoxicology during the last decade. It provides a review of the sequenced steps involved in implementing an ML model, from data pre-processing, to model implementation, model validation, and applicability domain. The review gathers and presents the step-wise information on techniques and procedures of existing models that can be used readily to assemble new nanotoxicological in silico studies and accelerates the regulation of in silico tools in nanotoxicology. ML applications in nanotoxicology comprise an active and diverse collection of ongoing efforts, although it is still in their early steps toward a scientific accord, subsequent guidelines, and regulation adoption. This study is an important bookend to a decade of ML applications to nanotoxicology and serves as a useful guide to further in silico applications.

Computational models for the assessment of manufactured nanomaterials: Development of model reporting standards and mapping of the model landscape

Different types of computational models have been developed for predicting the biokinetics, environmental fate, exposure levels and toxicological effects of chemicals and manufactured nanomaterials (MNs). However, these models are not described in a consistent manner in the scientific literature, which is one of the barriers to their broader use and acceptance, especially for regulatory purposes. Quantitative structure-activity relationships (QSARs) are in silico models based on the assumption that the activity of a substance is related to its chemical structure. These models can be used to provide information on (eco)toxicological effects in hazard assessment. In an environmental risk assessment, environmental exposure models can be used to estimate the predicted environmental concentration (PEC). In addition, physiologically based kinetic (PBK) models can be used in various ways to support a human health risk assessment. In this paper, we first propose model reporting templates for systematically and transparently describing models that could potentially be used to support regulatory risk assessments of MNs, for example under the REACH regulation. The model reporting templates include (a) the adaptation of the QSAR Model Reporting Format (QMRF) to report models for MNs, and (b) the development of a model reporting template for PBK and environmental exposure models applicable to MNs. Second, we show the usefulness of these templates to report different models, resulting in an overview of the landscape of available computational models for MNs.

Concentration dependent adsorption of aromatic organic compounds by SWCNTs: Quantum-mechanical descriptors for nano-toxicological studies of biomolecules and agrochemicals

For evaluating the environmental risk associated using carbon nanotubes (CNTs), a successful prediction is desired for the adsorption of organic compounds (OCs) by CNTs at different adsorbate concentrations. This is most often achieved through poly-parameter linear solvation energy relationships (LSERs) based on solvatochromic descriptors. This study examines the real predictivity of the existing LSERs for predicting the adsorption of OCs by single-walled CNTs (SWCNTs) while comparing it with that of the models developed in the present work using quantum-mechanical descriptors. The real predictivity of the quantum-mechanical models and existing LSERs is compared using state-of-the-art statistical procedures employing an external prediction set of compounds not used in the model development. The quantum-mechanically computed mean polarizability, but originating from the interactions between electrons of parallel spin, is found to play an essential role in the adsorption of OCs by SWCNTs. Besides the solvatochromic descriptors (McGowan volume and molar excess refractivity), the instantaneous inter-electronic interactions, captured through electron-correlation based quantum-mechanical descriptors, are found to significantly affect the adsorption at varying adsorbate concentration. The models developed using a combination of quantum-mechanical and solvatochromic descriptors are found to be quite reliable. The models proposed were further employed to predict the adsorption of agrochemicals such as insecticides, pesticides, herbicides, as well as adsorption of endocrine disruptors and biomolecules such as nucleobases and steroid hormones. These are predicted to be strongly adsorbed by SWCNTs with Progesterone and Guanine exhibiting maximal interaction with the SWCNTs among biomolecules. The quantum-mechanical descriptors proposed in this work can be used for the risk assessment of SWCNTs in systems where adsorption is the primary process.

Automatic Echographic Detection of Halloysite Clay Nanotubes in a Low Concentration Range

Aim of this work was to investigate the automatic echographic detection of an experimental drug delivery agent, halloysite clay nanotubes (HNTs), by employing an innovative method based on advanced spectral analysis of the corresponding "raw" radiofrequency backscatter signals. Different HNT concentrations in a low range (5.5-66 × 1010 part/mL, equivalent to 0.25-3.00 mg/mL) were dispersed in custom-designed tissue-mimicking phantoms and imaged through a clinically-available echographic device at a conventional ultrasound diagnostic frequency (10 MHz). The most effective response (sensitivity = 60%, specificity = 95%), was found at a concentration of 33 × 1010 part/mL (1.5 mg/mL), representing a kind of best compromise between the need of enough particles to introduce detectable spectral modifications in the backscattered signal and the necessity to avoid the losses of spectral peculiarity associated to higher HNT concentrations. Based on theoretical considerations and quantitative comparisons with literature-available results, this concentration could also represent an optimal concentration level for the automatic echographic detection of different solid nanoparticles when employing a similar ultrasound frequency. Future dedicated studies will assess the actual clinical usefulness of the proposed approach and the potential of HNTs for effective theranostic applications.

The dispersion, solubilization and stabilization in “solution” of single-walled carbon nanotubes

Methods for the solubilization and dispersion of single-walled carbon nanotubes in water and organic solvents by physical and chemical methods have been reviewed.