Zeta-Potential Read-Across Model Utilizing Nanodescriptors Extracted via the NanoXtract Image Analysis Tool Available on the Enalos Nanoinformatics Cloud Platform.

Zeta potential is one of the most critical properties of nanomaterials (NMs) which provides an estimation of the surface charge, and therefore electrostatic stability in medium and, in practical terms, influences the NM's tendency to form agglomerates and to interact with cellular membranes. This paper describes a robust and accurate read-across model to predict NM zeta potential utilizing as the input data a set of image descriptors derived from transmission electron microscopy (TEM) images of the NMs. The image descriptors are calculated using NanoXtract (http://enaloscloud.novamechanics.com/EnalosWebApps/NanoXtract/), a unique online tool that generates 18 image descriptors from the TEM images, which can then be explored by modeling to identify those most predictive of NM behavior and biological effects. NM TEM images are used to develop a model for prediction of zeta potential based on grouping of the NMs according to their nearest neighbors. The model provides interesting insights regarding the most important similarity features between NMs-in addition to core composition the main elongation emerged, which links to key drivers of NM toxicity such as aspect ratio. Both the NanoXtract image analysis tool and the validated model for zeta potential (http://enaloscloud.novamechanics.com/EnalosWebApps/ZetaPotential/) are freely available online through the Enalos Nanoinformatics platform.

Development of Deep Learning Models for Predicting the Effects of Exposure to Engineered Nanomaterials on Daphnia magna.

This study presents the results of applying deep learning methodologies within the ecotoxicology field, with the objective of training predictive models that can support hazard assessment and eventually the design of safer engineered nanomaterials (ENMs). A workflow applying two different deep learning architectures on microscopic images of Daphnia magna is proposed that can automatically detect possible malformations, such as effects on the length of the tail, and the overall size, and uncommon lipid concentrations and lipid deposit shapes, which are due to direct or parental exposure to ENMs. Next, classification models assign specific objects (heart, abdomen/claw) to classes that depend on lipid densities and compare the results with controls. The models are statistically validated in terms of their prediction accuracy on external D. magna images and illustrate that deep learning technologies can be useful in the nanoinformatics field, because they can automate time-consuming manual procedures, accelerate the investigation of adverse effects of ENMs, and facilitate the process of designing safer nanostructures. It may even be possible in the future to predict impacts on subsequent generations from images of parental exposure, reducing the time and cost involved in long-term reproductive toxicity assays over multiple generations.

MS-275 Chemical Analogues Promote Hemoglobin Production and Erythroid Differentiation of K562 Cells.

ß-Thalassemia (ß-thal) is a hemoglobinopathy characterized by reduced or absent ß-globin production. Pharmacological reactivation of the γ-globin gene for the production of fetal hemoglobin (Hb F) presents an attractive treatment strategy. In an effort to identify promising therapeutic agents, we evaluated 80 analogues of the histone deacetylase inhibitor MS-275, a known Hb F inducer. The chemical analogues were identified via molecular modeling and targeted chemical modifications. Nine novel agents exhibited significant hemoglobin (Hb)-inducing and erythroid differentiation activities in the human K562 erythroleukemia cell line. Five of them appeared to be stronger inducers than the lead compound, MS-275, demonstrating the effectiveness of our method.

NanoConstruct: A web application builder of ellipsoidal nanoparticles for the investigation of their crystal growth, stability, and the calculation of atomistic descriptors.

NanoConstruct is a state-of-the-art computational tool that enables a) the digital construction of ellipsoidal neutral energy minimized nanoparticles (NPs) in vacuum through its graphical user-friendly interface, and b) the calculation of NPs atomistic descriptors. It allows the user to select NP's shape and size by inserting its ellipsoidal axes and rotation angle while the NP material is selected by uploading its Crystallography Information File (CIF). To investigate the stability of materials not yet synthesised, NanoConstruct allows the substitution of the chemical elements of an already synthesized material with chemical elements that belong into the same group and neighbouring rows of the periodic table. The process is divided into three stages: 1) digital construction of the unit cell, 2) digital construction of NP using geometry rules and keeping its stoichiometry and 3) energy minimization of the geometrically constructed NP and calculation of its atomistic descriptors. In this study, NanoConstruct was applied for the investigation of the crystal growth of Zirconia (ZrO2) NPs when in the rutile form. The most stable configuration and the crystal growth route were identified, showing a preferential direction for the crystal growth of ZrO2 in its rutile form. NanoConstruct is freely available through the Enalos Cloud Platform (https://enaloscloud.novamechanics.com/riskgone/nanoconstruct/).

ASCOT: A web tool for the digital construction of energy minimized Ag, CuO, TiO2 spherical nanoparticles and calculation of their atomistic descriptors.

ASCOT (an acronym derived from Ag-Silver, Copper Oxide, Titanium Oxide) is a user-friendly web tool for digital construction of electrically neutral, energy-minimized spherical nanoparticles (NPs) of Ag, CuO, and TiO2 (both Anatase and Rutile forms) in vacuum, integrated into the Enalos Cloud Platform (https://www.enaloscloud.novamechanics.com/sabydoma/ascot/). ASCOT calculates critical atomistic descriptors such as average potential energy per atom, average coordination number, common neighbour parameter (used for structural classification in simulations of crystalline phases), and hexatic order parameter (which measures how closely the local environment around a particle resembles perfect hexatic symmetry) for both core (over 4 Å from the surface) and shell (within 4 Å of the surface) regions of the NPs. These atomistic descriptors assist in predicting the most stable NP size based on lowest per atom energy and serve as inputs for developing machine learning models to predict the toxicity of these nanomaterials. ASCOT's automated backend requires minimal user input in order to construct the digital NPs: inputs needed are the material type (Ag, CuO, TiO2-Anatase, TiO2-Rutile), target diameter, a Force-Field from a pre-validated list, and the energy minimization parameters, with the tool providing a set of default values for novice users.

In silico assessment of nanoparticle toxicity powered by the Enalos Cloud Platform: Integrating automated machine learning and synthetic data for enhanced nanosafety evaluation.

The rapid advance of nanotechnology has led to the development and widespread application of nanomaterials, raising concerns regarding their potential adverse effects on human health and the environment. Traditional (experimental) methods for assessing the nanoparticles (NPs) safety are time-consuming, expensive, and resource-intensive, and raise ethical concerns due to their reliance on animals. To address these challenges, we propose an in silico workflow that serves as an alternative or complementary approach to conventional hazard and risk assessment strategies, which incorporates state-of-the-art computational methodologies. In this study we present an automated machine learning (autoML) scheme that employs dose-response toxicity data for silver (Ag), titanium dioxide (TiO2), and copper oxide (CuO) NPs. This model is further enriched with atomistic descriptors to capture the NPs' underlying structural properties. To overcome the issue of limited data availability, synthetic data generation techniques are used. These techniques help in broadening the dataset, thus improving the representation of different NP classes. A key aspect of this approach is a novel three-step applicability domain method (which includes the development of a local similarity approach) that enhances user confidence in the results by evaluating the prediction's reliability. We anticipate that this approach will significantly expedite the nanosafety assessment process enabling regulation to keep pace with innovation, and will provide valuable insights for the design and development of safe and sustainable NPs. The ML model developed in this study is made available to the scientific community as an easy-to-use web-service through the Enalos Cloud Platform (www.enaloscloud.novamechanics.com/sabydoma/safenanoscope/), facilitating broader access and collaborative advancements in nanosafety.

An In Vitro Dosimetry Tool for the Numerical Transport Modeling of Engineered Nanomaterials Powered by the Enalos RiskGONE Cloud Platform.

A freely available "in vitro dosimetry" web application is presented enabling users to predict the concentration of nanomaterials reaching the cell surface, and therefore available for attachment and internalization, from initial dispersion concentrations. The web application is based on the distorted grid (DG) model for the dispersion of engineered nanoparticles (NPs) in culture medium used for in vitro cellular experiments, in accordance with previously published protocols for cellular dosimetry determination. A series of in vitro experiments for six different NPs, with Ag and Au cores, are performed to demonstrate the convenience of the web application for calculation of exposure concentrations of NPs. Our results show that the exposure concentrations at the cell surface can be more than 30 times higher compared to the nominal or dispersed concentrations, depending on the NPs' properties and their behavior in the cell culture medium. Therefore, the importance of calculating the exposure concentration at the bottom of the cell culture wells used for in vitro arrays, i.e., the particle concentration at the cell surface, is clearly presented, and the tool introduced here allows users easy access to such calculations. Widespread application of this web tool will increase the reliability of subsequent toxicity data, allowing improved correlation of the real exposure concentration with the observed toxicity, enabling the hazard potentials of different NPs to be compared on a more robust basis.

Computational enrichment of physicochemical data for the development of a ζ-potential read-across predictive model with Isalos Analytics Platform.

The physicochemical characterisation data from a library of 69 engineered nanomaterials (ENMs) has been exploited in silico following enrichment with a set of molecular descriptors that can be easily acquired or calculated using atomic periodicity and other fundamental atomic parameters. Based on the extended set of twenty descriptors, a robust and validated nanoinformatics model has been proposed to predict the ENM ζ-potential. The five critical parameters selected as the most significant for the model development included the ENM size and coating as well as three molecular descriptors, metal ionic radius (rion), the sum of metal electronegativity divided by the number of oxygen atoms present in a particular metal oxide (Σχ/nO) and the absolute electronegativity (χabs), each of which is thoroughly discussed to interpret their influence on ζ-potential values. The model was developed using the Isalos Analytics Platform and is available to the community as a web service through the Horizon 2020 (H2020) NanoCommons Transnational Access services and the H2020 NanoSoveIT Integrated Approach to Testing and Assessment (IATA).

Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials.

Toxicogenomics (TGx) approaches are increasingly applied to gain insight into the possible toxicity mechanisms of engineered nanomaterials (ENMs). Omics data can be valuable to elucidate the mechanism of action of chemicals and to develop predictive models in toxicology. While vast amounts of transcriptomics data from ENM exposures have already been accumulated, a unified, easily accessible and reusable collection of transcriptomics data for ENMs is currently lacking. In an attempt to improve the FAIRness of already existing transcriptomics data for ENMs, we curated a collection of homogenized transcriptomics data from human, mouse and rat ENM exposures in vitro and in vivo including the physicochemical characteristics of the ENMs used in each study.

Enalos Suite of Tools: Enhancing Cheminformatics and Nanoinfor - matics through KNIME.

Drug discovery as well as (nano)material design projects demand the in silico analysis of large datasets of compounds with their corresponding properties/activities, as well as the retrieval and virtual screening of more structures in an effort to identify new potent hits. This is a demanding procedure for which various tools must be combined with different input and output formats. To automate the data analysis required we have developed the necessary tools to facilitate a variety of important tasks to construct workflows that will simplify the handling, processing and modeling of cheminformatics data and will provide time and cost efficient solutions, reproducible and easier to maintain. We therefore develop and present a toolbox of >25 processing modules, Enalos+ nodes, that provide very useful operations within KNIME platform for users interested in the nanoinformatics and cheminformatics analysis of chemical and biological data. With a user-friendly interface, Enalos+ Nodes provide a broad range of important functionalities including data mining and retrieval from large available databases and tools for robust and predictive model development and validation. Enalos+ Nodes are available through KNIME as add-ins and offer valuable tools for extracting useful information and analyzing experimental and virtual screening results in a chem- or nano- informatics framework. On top of that, in an effort to: (i) allow big data analysis through Enalos+ KNIME nodes, (ii) accelerate time demanding computations performed within Enalos+ KNIME nodes and (iii) propose new time and cost efficient nodes integrated within Enalos+ toolbox we have investigated and verified the advantage of GPU calculations within the Enalos+ nodes. Demonstration data sets, tutorial and educational videos allow the user to easily apprehend the functions of the nodes that can be applied for in silico analysis of data.

Predicting Cytotoxicity of Metal Oxide Nanoparticles using Isalos Analytics Platform.

A literature curated dataset containing 24 distinct metal oxide (MexOy) nanoparticles (NPs), including 15 physicochemical, structural and assay-related descriptors, was enriched with 62 atomistic computational descriptors and exploited to produce a robust and validated in silico model for prediction of NP cytotoxicity. The model can be used to predict the cytotoxicity (cell viability) of MexOy NPs based on the colorimetric lactate dehydrogenase (LDH) assay and the luminometric adenosine triphosphate (ATP) assay, both of which quantify irreversible cell membrane damage. Out of the 77 total descriptors used, 7 were identified as being significant for induction of cytotoxicity by MexOy NPs. These were NP core size, hydrodynamic size, assay type, exposure dose, the energy of the MexOy conduction band (EC), the coordination number of the metal atoms on the NP surface (Avg. C.N. Me atoms surface) and the average force vector surface normal component of all metal atoms (v⟂ Me atoms surface). The significance and effect of these descriptors is discussed to demonstrate their direct correlation with cytotoxicity. The produced model has been made publicly available by the Horizon 2020 (H2020) NanoSolveIT project and will be added to the project's Integrated Approach to Testing and Assessment (IATA).

Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies?

Chemoinformatics has developed efficient ways of representing chemical structures for small molecules as simple text strings, simplified molecular-input line-entry system (SMILES) and the IUPAC International Chemical Identifier (InChI), which are machine-readable. In particular, InChIs have been extended to encode formalized representations of mixtures and reactions, and work is ongoing to represent polymers and other macromolecules in this way. The next frontier is encoding the multi-component structures of nanomaterials (NMs) in a machine-readable format to enable linking of datasets for nanoinformatics and regulatory applications. A workshop organized by the H2020 research infrastructure NanoCommons and the nanoinformatics project NanoSolveIT analyzed issues involved in developing an InChI for NMs (NInChI). The layers needed to capture NM structures include but are not limited to: core composition (possibly multi-layered); surface topography; surface coatings or functionalization; doping with other chemicals; and representation of impurities. NM distributions (size, shape, composition, surface properties, etc.), types of chemical linkages connecting surface functionalization and coating molecules to the core, and various crystallographic forms exhibited by NMs also need to be considered. Six case studies were conducted to elucidate requirements for unambiguous description of NMs. The suggested NInChI layers are intended to stimulate further analysis that will lead to the first version of a "nano" extension to the InChI standard.

NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment.

Nanotechnology has enabled the discovery of a multitude of novel materials exhibiting unique physicochemical (PChem) properties compared to their bulk analogues. These properties have led to a rapidly increasing range of commercial applications; this, however, may come at a cost, if an association to long-term health and environmental risks is discovered or even just perceived. Many nanomaterials (NMs) have not yet had their potential adverse biological effects fully assessed, due to costs and time constraints associated with the experimental assessment, frequently involving animals. Here, the available NM libraries are analyzed for their suitability for integration with novel nanoinformatics approaches and for the development of NM specific Integrated Approaches to Testing and Assessment (IATA) for human and environmental risk assessment, all within the NanoSolveIT cloud-platform. These established and well-characterized NM libraries (e.g. NanoMILE, NanoSolutions, NANoREG, NanoFASE, caLIBRAte, NanoTEST and the Nanomaterial Registry (>2000 NMs)) contain physicochemical characterization data as well as data for several relevant biological endpoints, assessed in part using harmonized Organisation for Economic Co-operation and Development (OECD) methods and test guidelines. Integration of such extensive NM information sources with the latest nanoinformatics methods will allow NanoSolveIT to model the relationships between NM structure (morphology), properties and their adverse effects and to predict the effects of other NMs for which less data is available. The project specifically addresses the needs of regulatory agencies and industry to effectively and rapidly evaluate the exposure, NM hazard and risk from nanomaterials and nano-enabled products, enabling implementation of computational 'safe-by-design' approaches to facilitate NM commercialization.

A safe-by-design tool for functionalised nanomaterials through the Enalos Nanoinformatics Cloud platform.

Multi-walled carbon nanotubes are currently used in numerous industrial applications and products, therefore fast and accurate evaluation of their biological and toxicological effects is of utmost importance. Computational methods and techniques, previously applied in the area of cheminformatics for the prediction of adverse effects of chemicals, can also be applied in the case of nanomaterials (NMs), in an effort to reduce expensive and time consuming experimental procedures. In this context, a validated and predictive nanoinformatics model has been developed for the accurate prediction of the biological and toxicological profile of decorated multi-walled carbon nanotubes. The nanoinformatics workflow was fully validated according to the OECD principles before it was released online via the Enalos Cloud platform. The web-service is a ready-to-use, user-friendly application whose purpose is to facilitate decision making, as part of a safe-by-design framework for novel carbon nanotubes.

Enalos+ KNIME Nodes: New Cheminformatics Tools for Drug Discovery.

In this chapter we present and discuss Enalos+ nodes designed and developed by NovaMechanics Ltd. for the open-source KNIME platform, as a useful aid when dealing with cheminformatics and nanoinformatics problems or medicinal applications. Enalos+ nodes facilitate tasks performed in molecular modeling and allow access, data mining, and manipulation for multiple chemical databases through the KNIME interface. Enalos+ nodes automate common procedures that greatly facilitate the rapid workflow prototyping within KNIME. Μethods and techniques that are included in Enalos+ nodes are presented in order to offer a deeper understanding of the theoretical background of the incorporated functionalities. An emphasis is given to demonstrate the usefulness of Enalos+ nodes in different cheminformatics applications by presenting four indicative case studies. Specifically, we present case studies that underline the value and the effectiveness of the nodes for molecular descriptors calculation and QSAR predictive model development. In addition, case studies are also presented demonstrating the benefits of the use of Enalos+ nodes for database exploitation within a drug discovery project.

Enalos Suite: New Cheminformatics Platform for Drug Discovery and Computational Toxicology.

In this chapter we present and discuss, with the aid of several representative case studies from drug discovery and computational toxicology, a new cheminformatics platform, Enalos Suite, that was developed with open source and freely available software. Enalos Suite ( http://enalossuite.novamechanics.com/ ) was designed and developed as a useful tool to address a variety of cheminformatics problems, given that it expedites tasks performed in predictive modeling and allows access, data mining and manipulation for multiple chemical databases (PubChem, UniChem, etc.). Enalos Suite was carefully designed to permit its extension and adjustment to the special field of interest of each user, including, for instance, nanoinformatics, biomedical, and other applications. To demonstrate the functionalities of Enalos Suite that are useful in different cheminformatics applications, we present indicative case studies that include the exploitation of chemical databases within a drug discovery project, the calculation of molecular descriptors, and finally the development of a predictive QSAR model validated according to OECD principles. We aspire that at the end of this chapter, the reader will capture the effectiveness of different functionalities included in the Enalos Suite that could be of significant value in a multitude of cheminformatics applications.

A nanoinformatics decision support tool for the virtual screening of gold nanoparticle cellular association using protein corona fingerprints.

The increasing use of nanoparticles (NPs) in a wide range of consumer and industrial applications has necessitated significant effort to address the challenge of characterizing and quantifying the underlying nanostructure - biological response relationships to ensure that these novel materials can be exploited responsibly and safely. Such efforts demand reliable experimental data not only in terms of the biological dose-response, but also regarding the physicochemical properties of the NPs and their interaction with the biological environment. The latter has not been extensively studied, as a large surface to bind biological macromolecules is a unique feature of NPs that is not relevant for chemicals or pharmaceuticals, and thus only limited data have been reported in the literature quantifying the protein corona formed when NPs interact with a biological medium and linking this with NP cellular association/uptake. In this work we report the development of a predictive model for the assessment of the biological response (cellular association, which can include both internalized NPs and those attached to the cell surface) of surface-modified gold NPs, based on their physicochemical properties and protein corona fingerprints, utilizing a dataset of 105 unique NPs. Cellular association was chosen as the end-point for the original experimental study due to its relevance to inflammatory responses, biodistribution, and toxicity in vivo. The validated predictive model is freely available online through the Enalos Cloud Platform ( http://enalos.insilicotox.com/NanoProteinCorona/ ) to be used as part of a regulatory or NP safe-by-design decision support system. This online tool will allow the virtual screening of NPs, based on a list of the significant NP descriptors, identifying those NPs that would warrant further toxicity testing on the basis of predicted NP cellular association.

Increased levels of 3-hydroxykynurenine parallel disease severity in human acute pancreatitis.

Inhibition of kynurenine 3-monooxygenase (KMO) protects against multiple organ dysfunction (MODS) in experimental acute pancreatitis (AP). We aimed to precisely define the kynurenine pathway activation in relation to AP and AP-MODS in humans, by carrying out a prospective observational study of all persons presenting with a potential diagnosis of AP for 90 days. We sampled peripheral venous blood at 0, 3, 6, 12, 24, 48, 72 and 168 hours post-recruitment. We measured tryptophan metabolite concentrations and analysed these in the context of clinical data and disease severity indices, cytokine profiles and C-reactive protein (CRP) concentrations. 79 individuals were recruited (median age: 59.6 years; 47 males, 59.5%). 57 met the revised Atlanta definition of AP: 25 had mild, 23 moderate, and 9 severe AP. Plasma 3-hydroxykynurenine concentrations correlated with contemporaneous APACHE II scores (R2 = 0.273; Spearman rho = 0.581; P < 0.001) and CRP (R2 = 0.132; Spearman rho = 0.455, P < 0.001). Temporal profiling showed early tryptophan depletion and contemporaneous 3-hydroxykynurenine elevation. Furthermore, plasma concentrations of 3-hydroxykynurenine paralleled systemic inflammation and AP severity. These findings support the rationale for investigating early intervention with a KMO inhibitor, with the aim of reducing the incidence and severity of AP-associated organ dysfunction.

PFAS-Biomolecule Interactions: Case Study Using Asclepios Nodes and Automated Workflows in KNIME for Drug Discovery and Toxicology.

The Asclepios suite of KNIME nodes represents an innovative solution for conducting cheminformatics and computational chemistry tasks, specifically tailored for applications in drug discovery and computational toxicology. This suite has been developed using open-source and publicly accessible software. In this chapter, we introduce and explore the Asclepios suite through the lens of a case study. This case study revolves around investigating the interactions between per- and polyfluorinated alkyl substances (PFAS) and biomolecules, such as nuclear receptors. The objective is to characterize the potential toxicity of PFAS and gain insights into their chemical mode of action at the molecular level. The Asclepios KNIME nodes have been designed as versatile tools capable of addressing a wide range of computational toxicology challenges. Furthermore, they can be adapted and customized to accomodate the specific needs of individual users, spanning various domains such as nanoinformatics, biomedical research, and other related applications. This chapter provides an in-depth examination of the technical underpinnings and foundations of these tools. It is accompanied by a practical case study that demonstrates the utilization of Asclepios nodes in a computational toxicology investigation. This showcases the extendable functionalities that can be applied in diverse computational chemistry contexts. By the end of this chapter, we aim for readers to have a comprehensive understanding of the effectiveness of the Asclepios node functions. These functions hold significant potential for enhancing a wide spectrum of cheminformatics applications.