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The wide variation of nanomaterial (NM) characters (size, shape, and properties) and the related impacts on living organisms make it virtually impossible to assess their safety; the need for modeling has been urged for long. We here investigate the custom-designed 1-10% Fe-doped CuO NM library. Effects were assessed using the soil ecotoxicology model Enchytraeus crypticus (Oligochaeta) in the standard 21 days plus its extension (49 days). Results showed that 10%Fe-CuO was the most toxic (21 days reproduction EC50 = 650 mg NM/kg soil) and Fe3O4 NM was the least toxic (no effects up to 3200 mg NM/kg soil). All other NMs caused similar effects to E. crypticus (21 days reproduction EC50 ranging from 875 to 1923 mg NM/kg soil, with overlapping confidence intervals). Aiming to identify the key NM characteristics responsible for the toxicity, machine learning (ML) modeling was used to analyze the large data set [9 NMs, 68 descriptors, 6 concentrations, 2 exposure times (21 and 49 days), 2 endpoints (survival and reproduction)]. ML allowed us to separate experimental related parameters (e.g., zeta potential) from particle-specific descriptors (e.g., force vectors) for the best identification of important descriptors. We observed that concentration-dependent descriptors (environmental parameters, e.g., zeta potential) were the most important under standard test duration (21 day) but not for longer exposure (closer representation of real-world conditions). In the longer exposure (49 days), the particle-specific descriptors were more important than the concentration-dependent parameters. The longer-term exposure showed that the steepness of the concentration-response decreased with an increased Fe content in the NMs. Longer-term exposure should be a requirement in the hazard assessment of NMs in addition to the standard in OECD guidelines for chemicals. The progress toward ML analysis is desirable given its need for such large data sets and significant power to link NM descriptors to effects in animals. This is beyond the current univariate and concentration-response modeling analysis.

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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/).

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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.

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Natural and engineered nanoparticles (NPs) entering the environment are influenced by many physicochemical processes and show various behavior in different systems (e.g., natural waters showing different characteristics). Determining the physicochemical characteristics and predicting the behavior of nanoparticles ending up in the natural aquatic environment are key aspects of their risk assessment. Here, we show that the quantitative structure-property relationship modeling method used in nanoinformatics (nano-QSPR) can be successfully applied to predict environmental fate-relevant properties (electrophoretic mobility) of TiO2, ZnO, and CeO2 nanoparticles. However, in contrast to the previous works, we postulate to use, in parallel: (i) the nanoparticles' structure descriptors (S-descriptors) and (ii) the environment descriptors (E-descriptors) as the input variables. Thus, the method should be abbreviated more precisely as nano-QSEPR ("E" stands for the "environment"). As a proof-of-the-concept, we have developed a group of models (including MLR, GA-PLS, PCR, and Meta-Consensus models) with high predictive capabilities (QEXT2 = 0.931 for the GA-PLS model), where the S-descriptors are represented by the core-shell model descriptor and the E-descriptors - by different ambient water features (including ions concentration and the ionic strength). The newly proposed nano-QSEPR modeling scheme can be efficiently used to design safe and sustainable nanomaterials.

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When ROS production exceeds the cellular antioxidant capacity, the cell needs to eliminate the defective mitochondria responsible for excessive ROS production. It has been proposed that the removal of these defective mitochondria involves mitophagy, but the mechanism of this regulation remains unclear. Here, we demonstrate that moderate mitochondrial superoxide and hydrogen peroxide production oxidates KEAP1, thus breaking the interaction between this protein and PGAM5, leading to the inhibition of its proteasomal degradation. Accumulated PGAM5 interferes with the processing of the PINK1 in the mitochondria leading to the accumulation of PINK1 on the outer mitochondrial membrane. In turn, PINK1 promotes Parkin recruitment to mitochondria and sensitizes mitochondria for autophagic removal. We also demonstrate that inhibitors of the KEAP1-PGAM5 protein-protein interaction (including CPUY192018) mimic the effect of mitochondrial ROS and sensitize mitophagy machinery, suggesting that these inhibitors could be used as pharmacological regulators of mitophagy. Together, our results show that KEAP1/PGAM5 complex senses mitochondrially generated superoxide/hydrogen peroxide to induce mitophagy.

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Assessing the risks of nanomaterials/nanoparticles (NMs/NPs) under various environmental conditions requires a more systematic approach, including the comparison of effects across many NMs with identified different but related characters/descriptors. Hence, there is an urgent need to provide coherent (eco)toxicological datasets containing comprehensive toxicity information relating to a diverse spectra of NPs characters. These datasets are test benches for developing holistic methodologies with broader applicability. In the present study we assessed the effects of a custom design Fe-doped TiO2 NPs library, using the soil invertebrate Enchytraeus crypticus (Oligochaeta), via a 5-day pulse via aqueous exposure followed by a 21-days recovery period in soil (survival, reproduction assessment). Obviously, when testing TiO2, realistic conditions should include UV exposure. The 11 Fe-TiO2 library contains NPs of size range between 5-27 nm with varying %Fe (enabling the photoactivation of TiO2 at energy wavelengths in the visible-light range). The NPs were each described by 122 descriptors, being a mixture of measured and atomistic model descriptors. The data were explored using single and univariate statistical methods, combined with machine learning and multiscale modelling techniques. An iterative pruning process was adopted for identifying automatically the most significant descriptors. TiO2 NPs toxicity decreased when combined with UV. Notably, the short-term water exposure induced lasting biological responses even after longer-term recovery in clean exposure. The correspondence with Fe-content correlated with the band-gap hence the reduction of UV oxidative stress. The inclusion of both measured and modelled materials data benefitted the explanation of the results, when combined with machine learning.

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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.

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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).

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The inoculum biomass was collected from a pilot-scale (3 m3 process tank) nitritation-anaerobic ammonium oxidation (ANAMMOX) (deammonification moving bed biofilm (DeaMBBR)) reactor demonstrating the highest total nitrogen removal rate (TNRR) of 0.33 kg N m-3 day-1. This biomass was used for inoculating the anodic chamber of a microbial fuel cell (MFC) to investigate the capacity of DeaMBBR biomass to act as an exo-electrogenic consortia. Performance of MFCs inoculated with ANAMMOX-specific consortia collected from DeaMBBR (MFC-ANA) and another MFC-CON inoculated with a septic tank mixed anaerobic consortium as a control was investigated for electrochemical performance and wastewater treatment efficiency. These MFCs were operated for the total duration of 419 days during which regular feed was given and performance was monitored for first 30 cycles and last 30 cycles, with each cycle of 3 day duration. The MFC-ANA continuously generated bio-energy with higher volumetric power density (9.5 W m-3 and 6.0 W m-3) in comparison to MFC-CON (4.9 and 2.9 W m-3) during the first 30 and last 30 cycles of operational period, respectively. MFC-ANA also achieved 84 ± 2% and 80 ± 2% of COD removal efficiency and 89 ± 4% and 73 ± 2% of total nitrogen removal efficiency during first 30 and last 30 cycles of operational period, respectively. The improvement of nitrogen removal and power production in case of MFC-ANA over MFC-CON could be attributed to the ANAMMOX-denitrifiers populations and Trichococcus (14.92%) as denitrifying exo-electrogenic microbes (4.46%), respectively.

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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.

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In the search for novel tools to combat cancer, nanoparticles (NPs) have attracted a lot of attention. Recently, the controlled release of cancer-cell-killing metal ions from doped NPs has shown promise, but fine tuning of dissolution kinetics is required to ensure specificity and minimize undesirable toxic side-effects. Theoretical tools to help in reaching a proper understanding and finally be able to control the dissolution kinetics by NP design have not been available until now. Here, we present a novel set of true nanodescriptors to analyze the charge distribution, the effect of doping and surface coating of whole metal oxide NP structures. The polarizable model of oxygen atoms enables light to be shed on the charge distribution on the NP surface, allowing the in detail study of the factors influencing the release of metal ions from NPs. The descriptors and their capabilities are demonstrated on a Fe-doped ZnO nanoparticle system, a system with practical outlook and available experimental data.

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The development and implementation of safe-by-design strategies is key for the safe development of future generations of nanotechnology enabled products. The safety testing of the huge variety of nanomaterials that can be synthetized is unfeasible due to time and cost constraints. Computational modeling facilitates the implementation of alternative testing strategies in a time and cost effective way. The development of predictive nanotoxicology models requires the use of high quality experimental data on the structure, physicochemical properties and bioactivity of nanomaterials. The FP7 Project MODERN has developed and evaluated the main components of a computational framework for the evaluation of the environmental and health impacts of nanoparticles. This chapter describes each of the elements of the framework including aspects related to data generation, management and integration; development of nanodescriptors; establishment of nanostructure-activity relationships; identification of nanoparticle categories; hazard ranking and risk assessment.

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Human papillomaviruses (HPVs) are oncogenic viruses that cause numerous different cancers as well as benign lesions in the epithelia. To date, there is no effective cure for an ongoing HPV infection. Here, we describe the generation process of a platform for the development of anti-HPV drugs. This system consists of engineered full-length HPV genomes that express reporter genes for evaluation of the viral copy number in all three HPV replication stages. We demonstrate the usefulness of this system by conducting high-throughput screens to identify novel high-risk HPV-specific inhibitors. At least five of the inhibitors block the function of Tdp1 and PARP1, which have been identified as essential cellular proteins for HPV replication and promising candidates for the development of antivirals against HPV and possibly against HPV-related cancers.

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Cancer cells have unique but widely varying characteristics that have proven them difficult to be treated by classical therapeutics and calls for novel and selective treatment options. Nanomaterials (NMs) have been shown to display biological effects as a function of their chemical composition, and the extent and exact nature of these effects can vary between different biological environments. Here, ZnO NMs are doped with increasing levels of Fe, which allows to finely tune their dissolution rate resulting in significant differences in their biological behavior on cancer or normal cells. Based on in silico analysis, 2% Fe-doped ZnO NMs are found to be optimal to cause selective cancer cell death, which is confirmed in both cultured cells and syngeneic tumor models, where they also reduce metastasis formation. These results show that upon tuning NM chemical composition, NMs can be designed as a targeted selective anticancer therapy.

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BACKGROUND: Human immunodeficiency virus type 1 (HIV-1) is the causative agent of AIDS occurs across mucosal surfaces or by direct inoculation. OBJECTIVE: The objective of this study was to consider chemically diverse scaffold sets of HIV-1 Reverse Transcriptase Inhibitors (HIV-1 RTI) subjected to ideal oriented QSAR with large descriptor space. METHOD: We generated a four-parameter QSAR model based on 111 data points, which provided an optimum prediction of HIV-1 RTI for overall 367 experimentally measured compounds. RESULTS: The robustness of the model is demonstrated by its statistical validation (Ntraining = 111, R2 = 0.85, Q2lmo = 0.84) and by the prediction of HIV-1 inhibition activity for experimentally measured compounds. CONCLUSION: Finally, 5 novel hit compounds were designed in silico by using a virtual screening approach. The new hits met all the pharmacophore constraints and predicted pIC50 values within the binding ability of HIV-1 RT protein targets.

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Novel, cyclic peptidomimetics were synthesized by facile acylation reactions using benzotriazole chemistry. Microbiological testing of the synthesized compounds revealed an exceptionally high activity against Candida albicans with a minimum inhibitory concentration (MIC) two orders of magnitude lower than the MIC of the antifungal reference drug amphotericin B. A strikingly high activity was also observed against three Gram-negative bacterial strains (Pseudomonas aeruginosa, Klebsiella pneumoniae and Proteus vulgaris), two of which are known human pathogens. Thus the discovered chemotype is a potential polypharmacological agent. The toxicity against mammalian tumor cells was found to be low, as demonstrated in five different human cell lines (HeLa, cervical; PC-3, prostate; MCF-7, breast; HepG2, liver; and HCT-116, colon). The internal consistency of the experimental data was studied using 3D-pharmacophore and 2D-QSAR.

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Structure-activity relationships in a data set of HPV6-E1 helicase ATPase inhibitors were investigated based on two different sets of descriptors. Statistically significant four parameter Quantitative Structure-Activity Relationships (QSAR) models were constructed and validated in both cases (R(2)=0.849; R(2) cv=0.811; F=52.20; s(2)=0.25; N=42). A Fragment based QSAR (FQSAR) approach was applied for developing a fragment-QSAR equation, which enabled the construction of virtual structures for novel ATPase inhibitors with desired or pre-defined activity.

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The article deals with a challenging attempt to model and predict "difficult" properties as long-term subchronic oral and inhalation toxicities (90 days) using nonlinear QSAR approach. This investigation is one of the first to tackle such multicomplex properties where we have employed nonlinear models based on artificial neural network for the prediction of NOAEL (no observable adverse effect level). Despite the complex nature of the NOAEL property based on in vivo rat experiments, the successful models can be used as alternative tools to non-animal tests for the initial assessment of these chronic toxicities. The model for oral subchronic toxicity is able to describe 88 %, and the inhalation model 87 % of the statistical variance. For the sake of future predictions, we have also defined in a quantitative way the applicability domain of all neural network models.

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A novel computational technology based on fragmentation of the chemical compounds has been used for the fast and efficient prediction of activities of prospective protease inhibitors of the hepatitis C virus. This study spans over a discovery cycle from the theoretical prediction of new HCV NS3 protease inhibitors to the first cytotoxicity experimental tests of the best candidates. The measured cytotoxicity of the compounds indicated that at least two candidates would be suitable further development of drugs.

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CODESSA Pro derivative descriptors were calculated for a data set of 426 azeotropic mixtures by the centroid approximation and the weighted-contribution-factor approximation. The two approximations produced almost identical four-descriptor QSPR models relating the structural characteristic of the individual components of azeotropes to the azeotropic boiling points. These models were supported by internal and external validations. The descriptors contributing to the QSPR models are directly related to the three components of the enthalpy (heat) of vaporization.

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