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Herein, a robust and reproducible eXplainable Artificial Intelligence (XAI) approach is presented, which allows prediction of developmental toxicity, a challenging human-health endpoint in toxicology. The application of XAI as an alternative method is of the utmost importance with developmental toxicity being one of the most animal-intensive areas of regulatory toxicology. In this work, the established CAESAR (Computer Assisted Evaluation of industrial chemical Substances According to Regulations) training set made of 234 chemicals for model learning is employed. Two test sets, including as a whole 585 chemicals, were instead used for validation and generalization purposes. The proposed framework favorably compares with the state-of-the-art approaches in terms of accuracy, sensitivity, and specificity, thus resulting in a reliable support system for developmental toxicity ensuring informativeness, uncertainty estimation, generalization, and transparency. Based on the eXtreme Gradient Boosting (XGB) algorithm, our predictive model provides easy interpretative keys based on specific molecular descriptors and structural alerts enabling one to distinguish toxic and nontoxic chemicals. Inspired by the Organisation for Economic Co-operation and Development (OECD) principles for the validation of Quantitative Structure-Activity Relationships (QSARs) for regulatory purposes, the results are summarized in a standard report in portable document format, enclosing also details concerned with a density-based model applicability domain and SHAP (SHapley Additive exPlanations) explainability, the latter particularly useful to better understand the effective roles played by molecular features. Notably, our model has been implemented in TIRESIA (Toxicology Intelligence and Regulatory Evaluations for Scientific and Industry Applications), a free of charge web platform available at http://tiresia.uniba.it.

Curcumin (Cur) is a hydrophobic polyphenol from the rhizome of Curcuma spp., while hydroxytyrosol (HT) is a water-soluble polyphenol from Olea europaea. Both show outstanding antioxidant properties but suffer from scarce bioavailability and low stability in biological fluids. In this work, the co-encapsulation of Cur and HT into liposomes was realized, and the liposomal formulation was improved using polymers to increase their survival in the gastrointestinal tract. Liposomes with different compositions were formulated: Type 1, composed of phospholipids and cholesterol; Type 2, also with a PEG coating; and Type 3 providing an additional shell of Eudragit® S100, a gastro-resistant polymer. Samples were characterized in terms of size, morphology, ζ-potential, encapsulation efficiency, and loading capacity. All samples were subjected to a simulated in vitro digestion and their stability was investigated. The Eudragit®S100 coating demonstrated prevention of early releases of HT in the mouth and gastric phases, while the PEG shell reduced bile salts and pancreatin effects during the intestinal digestion. In vitro antioxidant activity showed a cumulative effect for Cur and HT loaded in vesicles. Finally, liposomes with HT concentrations up to 40 μM and Cur up to 4.7 μM, alone or in combination, did not show cytotoxicity against Caco-2 cells.

A screening pool consisting of 617710 drug-like query molecules properly filtered from the ChEMBL database was employed for a ligand-based reverse screening toward the type 2 cannabinoid receptor (CB

Abstract: In the last decade, selective modulators of type-2 cannabinoid receptor (CB2) have become a major focus to target endocannabinoid signaling in humans. Indeed, heterogeneously expressed within our body, CB2 actively regulates several physio-pathological processes, thus representing a promising target for developing specific and safe therapeutic drugs. If CB2 modulation has been extensively studied since the very beginning for the treatment of pain and inflammation, the more recent involvement of this receptor in other pathological conditions has further strengthened the pursuit of novel CB2 agonists in the last five years. Against this background, here we discuss the most recent evidence of the protective effects of CB2 against pathological conditions, emphasizing central nervous system disorders, bone and synovial diseases, and cancer. We also summarize the most recent advances in the development of CB2 agonists, focusing on the correlation between different chemical classes and diverse therapeutic applications. Data mining includes a review of the CB2 ligands disclosed in patents also released in the last five years. Finally, we discuss how the recent elucidation of CB2 tertiary structure has provided new details for the rational design of novel and more selective CB2 agonists, thus supporting innovative strategies to develop effective therapeutics. Our overview of the current knowledge on CB2 agonists provides pivotal information on the structure and function of different classes of molecules and opens possible avenues for future research.

We present a new quantitative ligand-based bioactivity prediction approach employing a multifingerprint similarity search algorithm, enabling the polypharmacological profiling of small molecules. Quantitative bioactivity predictions are made on the basis of the statistical distributions of multiple Tanimoto similarity θ values, calculated through 13 different molecular fingerprints, and of the variation of the measured biological activity, reported as ΔpIC50, for all of the ligands sharing a given protein drug target. The application data set comprises as much as 4241 protein drug targets as well as 418 485 ligands selected from ChEMBL (release 25) by employing a set of well-defined filtering rules. Several large internal and external validation studies were carried out to demonstrate the robustness and the predictive potential of the herein proposed method. Additional comparative studies, carried out on two freely available and well-known ligand-target prediction platforms, demonstrated the reliability of our proposed approach for accurate ligand-target matching. Moreover, two applicative cases were also discussed to practically describe how to use our predictive algorithm, which is freely available as a user-friendly web platform. The user can screen single or multiple queries at a time and retrieve the output as a terse html table or as a json file including all of the information concerning the explored similarities to obtain a deeper understanding of the results. High-throughput virtual reverse screening campaigns, allowing for a given query compound the quick detection of the potential drug target from a large collection of them, can be carried out in batch on demand.

Six halogenated trimethoxy chalcone derivatives (CH1–CH6) were synthesized and spectrally characterized. The compounds were further evaluated for their inhibitory potential against monoamine oxidases (MAOs) and β-secretase (BACE-1). Six compounds inhibited MAO-B more effectively than MAO-A, and the 2′,3′,4′-methoxy moiety in CH4–CH6 was more effective for MAO-B inhibition than the 2′,4′,6′-methoxy moiety in CH1–CH3. Compound CH5 most potently inhibited MAO-B, with an IC50 value of 0.46 µM, followed by CH4 (IC50 = 0.84 µM). In 2′,3′,4′-methoxy derivatives (CH4-CH6), the order of inhibition was –Br in CH5 &gt, Cl in CH4 &gt, F in CH6 at the para-position in ring B of chalcone. CH4 and CH5 were selective for MAO-B, with selectivity index (SI) values of 15.1 and 31.3, respectively, over MAO-A. CH4 and CH5 moderately inhibited BACE-1 with IC50 values of 13.6 and 19.8 µM, respectively. When CH4 and CH5 were assessed for their cell viability studies on the normal African Green Monkey kidney cell line (VERO) using MTT assays, it was noted that both compounds were found to be safe, and only a slightly toxic effect was observed in concentrations above 200 µg/mL. CH4 and CH5 decreased reactive oxygen species (ROS) levels of VERO cells treated with H2O2, indicating both compounds retained protective effects on the cells by antioxidant activities. All compounds showed high blood brain barrier permeabilities analyzed by a parallel artificial membrane permeability assay (PAMPA). Molecular docking and ADME prediction of the lead compounds provided more insights into the rationale behind the binding and the CNS drug likeness. From non-test mutagenicity and cardiotoxicity studies, CH4 and CH5 were non-mutagenic and non-/weak-cardiotoxic. These results suggest that CH4 and CH5 could be considered candidates for the cure of neurological dysfunctions.

Anionic complexes having vapochromic behavior are investigated: [K(H2O)][M(ppy)(CN)2], [K(H2O)][M(bzq)(CN)2], and [Li(H2O)n][Pt(bzq)(CN)2], where ppy = 2-phenylpyridinate, bzq = 7,8-benzoquinolate, and M = Pt(II) or Pd(II). These hydrated potassium/lithium salts exhibit a change in color upon being heated to 380 K, and they transform back into the original color upon absorption of water molecules from the environment. The challenging characterization of their structure in the vapochromic transition has been carried out by combining several experimental techniques, despite the availability of partially ordered and/or impure crystalline material. Room-temperature single-crystal and powder X-ray diffraction investigation revealed that [K(H2O)][Pt(ppy)(CN)2] crystallizes in the Pbca space group and is isostructural to [K(H2O)][Pd(ppy)(CN)2]. Variable-temperature powder X-ray diffraction allowed the color transition to be related to changes in the diffraction pattern and the decrease in sample crystallinity. Water loss, monitored by thermogravimetric analysis, occurs in two stages, well separated for potassium Pt compounds and strongly overlapped for potassium Pd compounds. The local structure of potassium compounds was monitored by in situ pair distribution function (PDF) measurements, which highlighted changes in the intermolecular distances due to a rearrangement of the crystal packing upon vapochromic transition. A reaction coordinate describing the structural changes was extracted for each compound by multivariate analysis applied to PDF data. It contributed to the study of the kinetics of the structural changes related to the vapochromic transition, revealing its dependence on the transition metal ion. Instead, the ligand influences the critical temperature, higher for ppy than for bzq, and the inclination of the molecular planes with respect to the unit cell planes, higher for bzq than for ppy. The first stage of water loss triggers a unit cell contraction, determined by the increase in the b axis length and the decrease in the a (for ppy) or c (for bzq) axis lengths. Consequent interplane distance variations and in-plane roto-translations weaken the π-stacking of the room-temperature structure and modify the distances and angles of Pt(II)/Pd(II) chains. The curve describing the intermolecular Pt(II)/Pd(II) distances as a function of temperature, validated by X-ray absorption spectroscopy, was found to reproduce the coordinate reaction determined by the model-free analysis., This research has been supported by the short-term mobility program of the National Research Council (CNR) of Italy and by the Spanish Ministerio de Economía y Competitividad (Ministerio de Ciencia Innovación y Universidades)/FEDER (Project PGC2018-094749-B-I00).

Aptamers are single-stranded oligonucleotides selected by SELEX (Systematic Evolution of Ligands by EXponential Enrichment) able to discriminate target molecules with high affinity and specificity, even in the case of very closely related structures. Aptamers have been produced for several targets including small molecules like mycotoxins, however, the high affinity for their respective target molecules is a critical requirement. In the last decade, the screening through computational methods of aptamers for their affinity against specific targets has greatly increased and is becoming a commonly used procedure due to its convenience and low costs. This paper describes an in-silico approach for rapid screening of ten ssDNA aptamer sequences against fumonisin B1 (FB1, n = 3), aflatoxin B1 (AFB1, n = 2) and ochratoxin A (OTA, n = 5). Theoretical results were compared with those obtained by testing the same aptamers by fluorescent microscale thermophoresis and by magnetic beads assay for their binding affinity (KD) revealing a good agreement.

In this work we report a new synthetic tactic for the straightforward preparation of hardly accessible sulfinamidines and sulfinamide esters, by using a simple metal-free protocol. The process is robust and uses readily available sulfenamides as the S-donor and sulfonyloxycarbamates as the N-source. The scope and mechanism have also been investigated.

This paper describes new features implemented in the EXPO2014 software and aimed at assisting crystallographers in the use of quantum-chemistry calculations in combination with experimental powder diffraction data. The implemented tools are useful in particular in two important steps of the process of crystal structure determination from powder diffraction data: (1) preparing accurate structural model suitable for crystal structure determination by real-space methods; (2) validating structure determination. The combination of experimental/quantum-chemical methods in EXPO2014 is now managed easily thanks to the following capabilities: (a) converting crystallographic data in input files and reading molecular geometry from output files of a wide variety of computational chemistry packages (GAMESS-US, NWChem, Gaussian, CRYSTAL, ABINIT, QUANTUM ESPRESSO); (b) optimizing the geometry of a molecule using Open Babel's force fields; (c) a graphical interface to run semi-empirical quantum calculation by MOPAC (Molecular Orbital PACkage); (d) producing input file for dispersion-corrected density functional theory.

Interface engineering has become one of the facile and effective approach to improve solar cells performance, its long-term stability and retard unwanted side reaction. We have developed three passivating agents which can functionalize the surface and induce hydrophobicity by employing substituted thiazolium iodide (TMI) for perovskite solar cells fabrication. The role of TMI interfacial layers on microstructure and electro-optical properties was assessed for structural as well as transient absorption (TA) measurements. TMI treatment resulted into VOC and FF enhancement by reducing possible recombination paths at perovskite/HTM interface and by reducing the shallow as well as deep traps. These in turn allowed to achieve higher performance as compared to the pristine surface. Additionally, TMI passivated perovskite layer reduces considerably CH3NH3+ thermal diffusion and degradation induced by humidity. The un-encapsulated perovskite solar cells employing TMI exhibited a remarkable stability under moisture levels (~50% RH) retaining ~95% of initial PCE after 800 h of fabrication, paving potential scalable endeavour.

The present study reports, for the first time, the synthesis and structural features of azetidine-borane complexes, as well as their reactivity in lithiation reactions. A temperature-dependent stereoselectivity has been disclosed in the reaction of borane with N-alkyl-2-arylazetidines, allowing for a stereoselective preparation of azetidine-borane complexes 2 and 3. A regioselective hydrogen/lithium permutation, at the benzylic position, was observed in lithiation reactions of complexes possessing a syn relationship, between the ring proton and the BH3 group. In contrast, scarce or no reactivity was noticed in complexes lacking such a stereochemical requirement. The configurational stability of the lithiated intermediates has also been investigated, in order to shed some light on the stereoselectivity of the lithiation/electrophile trapping sequence. Calculations helped in supporting experimental observations, concerning structure and reactivity of these azetidine-borane complexes. Data suggest that the BH3 group could promote the lithiation reaction likely by an electrostatic complex induced proximity effect. Interestingly, a new synthetic strategy for the synthesis of N-alkyl-2,2-disubstituted azetidines has been developed.

The photosynthetic reaction center (RC) is an integral membrane protein that, upon absorption of photons, generates a hole-electron couple with a yield close to one. This energetic state has numerous possible applications in several biotechnological fields given that its lifetime is long enough to allow non-metabolic ancillary redox chemistry to take place. Here we focus on RCs reconstituted in liposomes, formed with sole phospholipids or in blends with other lipids, and show that the electrical charge sitting on the polar head of such hydrophobic molecules does play an important role on the stability of the hole-electron couple. More specifically this study shows that the presence of negative charges in the surrounding of the protein stabilizes the charge-separated state while positive charges have a strong opposite effect.

The selection of high-affinity aptamers is of paramount interest for clinical and technological applications. A novel strategy is proposed to validate the reliability of the 3D structures of aptamers, produced in silico by using free software. The procedure consists of three steps: a. the production of a large set of conformations for each candidate aptamer, b. the rigid docking upon the receptor, c. the topological and electrical characterization of the products. Steps a. and b. allow a global binding score of the ligand-receptor complexes based on the distribution of the "effective affinity", i.e. the sum of the conformational and the docking energy. Step c. employs a complex network approach (Proteotronics) to characterize the electrical properties of the aptamers and the ligand-receptor complexes. The test-bed is represented by a group of anti- Angiopoietin-2 aptamers. In a previous literature these aptamers were processed both in vitro and in silico, by using an approach different from that here presented, and finally tested with a SPS experiment. Computational expectations and experimental outcomes did not agree, while our results show a good agreement with the known measurements. The devised procedure is not aptamer-specific and, integrating structure production with structure selection, candidates itself as a quite complete theoretical approach for aptamer selection., 17 pages, 9 figures

We present a program for the calculation of concentrations at chemical equilibrium in systems with one or more phases. We explain the main difficulties that such a program must surmount and the strategies that were devised for the present one, comparing them to others that can be found in the literature.

A comparison of density functionals was carried out for systems consisting of a methanethiyl radical adsorbed on gold in different configurations. PW91, PBE, B3LYP and BLYP were tested in a periodic slab approach. Cluster calculations were carried out so as to compare the above mentioned functionals and many others with CR-CCSD (T) and MRMP2 as references. PW91 and PBE provide close results. Energy surfaces calculated by means of PW91, PBE, M06 and TPSSh are in good agreement with the references. M11 performs dissimilarly from M06, in particular it predicts slightly shorter bond lenghts. BLYP gives rather poor results. The semiempirical scheme of Grimme as parameterized in B97-d and the local response dispersion as parameterized in long range corrected BOP-LRD provide very different estimates of the dispersion energy. Unexpectedly rPBE, B3LYP and CAM-B3LYP perform alike and do not match well with the references, though application of a dispersion energy correction in the Grimme scheme, brings them in a much more favorable position.

Liposomes represent a versatile biomimetic environment for studying the interaction between integral membrane proteins and hydrophobic ligands. In this paper, the quinone binding to the QB-site of the photosynthetic reaction centers (RC) from Rhodobacter sphaeroides has been investigated in liposomes prepared with either the zwitterionic phosphatidylcholine (PC) or the negatively charged phosphatidylglycerol (PG) to highlight the role of the different phospholipid polar heads. Quinone binding (K Q) and interquinone electron transfer (L AB) equilibrium constants in the two type of liposomes were obtained by charge recombination reaction of QB-depleted RC in the presence of increasing amounts of ubiquinone-10 over the temperature interval 6-35 °C. The kinetic of the charge recombination reactions has been fitted by numerically solving the ordinary differential equations set associated with a detailed kinetic scheme involving electron transfer reactions coupled with quinone release and uptake. The entire set of traces at each temperature was accurately fitted using the sole quinone release constants (both in a neutral and a charge separated state) as adjustable parameters. The temperature dependence of the quinone exchange rate at the QB-site was, hence, obtained. It was found that the quinone exchange regime was always fast for PC while it switched from slow to fast in PG as the temperature rose above 20 °C. A new method was introduced in this paper for the evaluation of constant K Q using the area underneath the charge recombination traces as the indicator of the amount of quinone bound to the QB-site.

In an explorative study of the opportunities for synthesis provided by oxidation of natural aminoacidic compound with methyl-(trifluoromethyl)dioxirane, we noticed that oxidation of the cyclic compound, when successful, leads to the ?-hydroxy compound, notwithstanding the presence of the isopropyl groups that are usually easy targets for this reaction, as verified with the homologous acyclic compound. We therefore initiated an ab-initio study of the reactions aimed at determining the role of the ring and explaining the reactivity differences of the cis and trans configurations. Consistently with recent literature, we confirm the fundamental role of an adduct configuration in which the dioxirane O-O bond is largely divaricated and electron pairing is broken, often denoted in the literature as diradicaloid.

We present a method that adapts the parameters describing the surface dynamics of an epitaxial system to a set of experimental intensities of He scattering at thermal energies. The method is applied to the problem of Ag growth on a Pt(111) surface at temperatures between 250 and 600 K.

The sudden approximation can be the foundation of a code for performing inexpensive calculations on light particle scattering from huge surface systems. The paper describes the mathematical framework and a sample code which can be used to perform sudden calculations either in the semiclassical approximation or in an exact numerical approach. Also a straightforward extension to the treatment of inelastic collisions in a discrete set of excited states is derived and implemented.

The interaction among Ag adatoms on a Pt(1 1 1) surface was modelled and the resultant thermodynamics simulated on the basis of a Monte Carlo approach. The parameters of the interaction were adjusted so as to yield a reasonable comparison between calculated He diffraction intensity from the obtained samples and experimental data.

Simulated specular scattering intensity of He particles from Xe and CO adsorbed on Pt surfaces shows distinctive features of the surface order parameters which are, however, not observed in experiments. Inferences may be drawn about the influence of long-range order on the scattering properties.

The computational platform ENVIRONMENT, developed to simulate stochastically reaction systems in varying compartmentalized conditions [Mavelli and Ruiz-Mirazo: Philos Trans R Soc Lond B Biol Sci 362:1789-1802, 2007; Physical Biology 7(3): 036002, 2010], is here applied to study the dynamic properties and stability of model protocells that start producing their own lipid molecules (e.g., phospholipids), which get inserted in previously self-assembled vesicles, made of precursor amphiphiles (e.g., fatty acids). Attention is mainly focused on the changes that this may provoke in the permeability of the compartment, as well as in its eventual osmotic robustness.

The computational platform ENVIRONMENT, developed to simulate stochastically reaction systems in varying compartmentalized conditions [Mavelli and Ruiz-Mirazo: Philos Trans R Soc Lond B Biol Sci 362:1789–1802, 2007; Physical Biology 7(3): 036002, 2010], is here applied to study the dynamic properties and stability of model protocells that start producing their own lipid molecules (e.g., phospholipids), which get inserted in previously self-assembled vesicles, made of precursor amphiphiles (e.g., fatty acids). Attention is mainly focused on the changes that this may provoke in the permeability of the compartment, as well as in its eventual osmotic robustness.

The electronic structure of tin oxide was studied with ab initio methods with an emphasis on changes induced by adsorption of CO molecules at different surface sites. Purpose of this investigation was to gain a better understanding of the processes underlying the dependence of the conductivity of SnOx based materials on the composition of atmosphere, which is the basis for their usage in gas sensing devices. It was inferred that two different mechanisms could be operating: a mechanism by which CO adsorption modifies the band structure and the order of the electronic levels and another mechanism involving the redox equilibrium between SnOx and CO/CO2 species and the dependence of SnOx conductivity on oxygen saturation. The present results favour the first mechanism.

This paper shows that the He diffraction specular intensity does not depend in a simple, predictable way on single statistical parameters describing the surface defect lateral distribution. In particular it shows the lack of correlation between specular intensity and the geometrical overlap of single defect cross sections, a parameter widely used in the literature for a qualitative interpretation of He atom diffraction data. An approach to the problem of surface structure determination is attempted on the basis of a cluster expansion of the scattering matrix at reflection angle.

The theoretical interpretation of experimental results on He scattering from metal adatoms epitaxially grown on metal substrates makes use, in general, of an interaction potential that, as far as the He-adatom interaction is concerned, is a pairwise sum of Lennard-Jones ( V LJ ) terms. This approach results in more corrugated metal surfaces than expected on the basis of both experimental data and qualitative considerations on the contribution of the electron densities of the metal adatoms to the repulsive part of the interaction potential. The present work suggests a very simple way to significantly reduce or eliminate the surface corrugation by averaging the He-adsorbate potential over a unit cell of the substrate lattice. The so obtained potential ( V AV ) was compared with V LJ for the HeAg/Pt(111) colliding system on the basis of turning point surfaces, specular and diffractive intensities vs. surface coverage and angular intensity distribution of scattered atoms, calculated under the sudden approximation. These data show that V AV , although too simple to correctly reproduce all the features of the He-adatom interaction, could represent a useful tool in the study of the growth of metal adlayers.

Since the specular intensity and scattering matrix are related by a quadratical relation, a term is present in the intensity which scales as the square of the defect surface coverage. One can directly account for the term in every calculation which provides the scattering matrix. The explicit formulas under the sudden approximation are reported and their implications discussed. Any relation between cross-section and specular intensity which does not take it into account is demonstrated to be inadequate even at very low coverage values. Consequently cross-sections calculated on phenomenological grounds cannot give correct information on surface structure.