Environmental contaminants modulate transport activity of zebrafish (Danio rerio) multidrug and toxin extrusion protein 3 (Mate3/Slc47a2.1).

Zebrafish Mate3 is one of six co-orthologs of human multidrug and toxin extrusion proteins. It is highly expressed in the kidneys, intestine, testes, and brain of males. Initial interaction studies showed its interaction with xenobiotic compounds, suggesting a role in the efflux of toxic compounds. In this study, we aimed to test various environmental contaminants for their interaction with zebrafish Mate3. We developed a stable zebrafish Mate3 cell line and optimized a high-throughput screening assay using DAPI and ASP+ as fluorescent model substrates. To gain insight into the structure and function of the Mate3 protein and relate these to the results of the DAPI and ASP+ transport measurements, we predicted its 3D structure using the AlphaFold2 algorithm. A 3D structure with high per residue confidence scores with 13 transmembrane segments (TMs) was obtained, with topology and mutual positioning characteristic of the Mate protein family in a shape open to the extracellular part. Molecular docking methods were used to identify DAPI and ASP+ binding sites on the surface and in the center of the protein cavity. Because our kinetics experiments combined with molecular docking indicated that there may be additional active sites in zebrafish Mate3, additional cytotoxicity experiments were performed and highly potent Mate3 interactors were identified from a set of 55 different environmental contaminants. Our results suggest that some of the identified interactors may be of environmental concern, as their interaction with Mate3 could lead to an impairment of its normal efflux function, making fish more sensitive to harmful substances commonly released into the aquatic environment. Finally, the quality of zebrafish Mate3 structures predicted by the AlphaFold2 algorithm opens up the possibility of successfully using this tool for in silico research on transport preferences of other Mate proteins.

Antioxidant Activity, Metabolism, and Bioavailability of Polyphenols in the Diet of Animals.

As the world's population grows, so does the need for more and more animal feed. In 2006, the EU banned the use of antibiotics and other chemicals in order to reduce chemical residues in food consumed by humans. It is well known that oxidative stress and inflammatory processes must be combated to achieve higher productivity. The adverse effects of the use of pharmaceuticals and other synthetic compounds on animal health and product quality and safety have increased interest in phytocompounds. With the use of plant polyphenols in animal nutrition, they are gaining more attention as a supplement to animal feed. Livestock feeding based on a sustainable, environmentally friendly approach (clean, safe, and green agriculture) would also be a win-win for farmers and society. There is an increasing interest in producing healthier products of animal origin with a higher ratio of polyunsaturated fatty acids (PUFAs) to saturated fatty acids by modulating animal nutrition. Secondary plant metabolites (polyphenols) are essential chemical compounds for plant physiology as they are involved in various functions such as growth, pigmentation, and resistance to pathogenic organisms. Polyphenols are exogenous antioxidants that act as one of the first lines of cell defense. Therefore, the discoveries on the intracellular antioxidant activity of polyphenols as a plant supplement have contributed significantly to the improvement of antioxidant activity, as polyphenols prevent oxidative stress damage and eliminate excessively produced free radicals. To achieve animal welfare, reduce stress and the need for medicines, and increase the quality of food of animal origin, the addition of polyphenols to research and breeding can be practised in part with a free-choice approach to animal nutrition.

In Silico Prediction of the Toxicity of Nitroaromatic Compounds: Application of Ensemble Learning QSAR Approach.

In this work, a dataset of more than 200 nitroaromatic compounds is used to develop Quantitative Structure-Activity Relationship (QSAR) models for the estimation of in vivo toxicity based on 50% lethal dose to rats (LD50). An initial set of 4885 molecular descriptors was generated and applied to build Support Vector Regression (SVR) models. The best two SVR models, SVR_A and SVR_B, were selected to build an Ensemble Model by means of Multiple Linear Regression (MLR). The obtained Ensemble Model showed improved performance over the base SVR models in the training set (R2 = 0.88), validation set (R2 = 0.95), and true external test set (R2 = 0.92). The models were also internally validated by 5-fold cross-validation and Y-scrambling experiments, showing that the models have high levels of goodness-of-fit, robustness and predictivity. The contribution of descriptors to the toxicity in the models was assessed using the Accumulated Local Effect (ALE) technique. The proposed approach provides an important tool to assess toxicity of nitroaromatic compounds, based on the ensemble QSAR model and the structural relationship to toxicity by analyzed contribution of the involved descriptors.

Polyphenols in Ruminant Nutrition and Their Effects on Reproduction.

The feeding of domestic animals with diets in which polyphenols are present is increasingly attracting the attention of nutritionists and scientists. This review summarizes the knowledge regarding polyphenols' possible positive and negative effects and their bioavailability. The bioavailability of substances is a prerequisite for any postabsorption effect in vivo. Positive and negative properties have been confirmed in previous studies on the diets of domestic animals rich in polyphenols, such as secondary metabolites of plants. Free radicals are formed in every organism, leading to oxidative stress. Free radicals are highly reactive molecules and can react in cells with macromolecules and can cause damage, including in reproductive cells. Some polyphenols at specific concentrations have antioxidant properties that positively affect animal reproduction by improving the quality of male and female gametes. The intake of phytoestrogens that mimic estrogen function can induce various pathological conditions in the female reproductive tract, including ovarian, fallopian, and uterine dysfunction. The metabolism of genistein and daidzein yields the metabolites equol and p-phenyl-phenol, leading to a decline in cow fertilization. The findings so far confirm that numerous questions still need to be answered. This review points out the importance of using polyphenols that have both benificial and some unfavorable properties in specific diets.

Predictive Capability of QSAR Models Based on the CompTox Zebrafish Embryo Assays: An Imbalanced Classification Problem.

The CompTox Chemistry Dashboard (ToxCast) contains one of the largest public databases on Zebrafish (Danio rerio) developmental toxicity. The data consists of 19 toxicological endpoints on unique 1018 compounds measured in relatively low concentration ranges. The endpoints are related to developmental effects occurring in dechorionated zebrafish embryos for 120 hours post fertilization and monitored via gross malformations and mortality. We report the predictive capability of 209 quantitative structure-activity relationship (QSAR) models developed by machine learning methods using penalization techniques and diverse model quality metrics to cope with the imbalanced endpoints. All these QSAR models were generated to test how the imbalanced classification (toxic or non-toxic) endpoints could be predicted regardless which of three algorithms is used: logistic regression, multi-layer perceptron, or random forests. Additionally, QSAR toxicity models are developed starting from sets of classical molecular descriptors, structural fingerprints and their combinations. Only 8 out of 209 models passed the 0.20 Matthew's correlation coefficient value defined a priori as a threshold for acceptable model quality on the test sets. The best models were obtained for endpoints mortality (MORT), ActivityScore and JAW (deformation). The low predictability of the QSAR model developed from the zebrafish embryotoxicity data in the database is mainly due to a higher sensitivity of 19 measurements of endpoints carried out on dechorionated embryos at low concentrations.

Effects of conjugation metabolism on radical scavenging and transport properties of quercetin - In silico study.

Quercetin (Q) is a natural polyphenol with high radical scavenging capacity, but low in vivo bioavailability. It is extensively transformed by host phase II metabolism and microbiota. Herein, effects of major in vitro and in vivo conjugation transformations of Q on its radical scavenging capacity and human serum albumin (HSA) binding were studied by using appropriate computational approaches, DFT (U)B3LYP/6-31 + G(d,p) and molecular docking, respectively. With regard to radical scavenging capacity of Q, conjugation transformations generally reduce its antioxidant capacity including regeneration efficiency through disproportionation of an intermediate radical species since these structural modifications occur mainly at its radical scavenging -OH groups. They were also found to alter dominant radical scavenging mechanism in a specific way dependent upon conjugation type and site. Concerning distribution by HSA, binding to this main plasma transporter protein may not be dominant transport mechanism for Q and its metabolites in vivo. Like Q aglycon, most of its metabolites are bound non-specifically at multiple binding sites of HSA, with relatively weak affinities. Only sulfo-conjugates including plasma abundant isomer Q-3'-O-SO3-, were predicted to bind specifically in warfarin-like manner, but also with relatively low binding affinity.

The Influence of In Vivo Metabolic Modifications on ADMET Properties of Green Tea Catechins-In Silico Analysis.

The health effects of green tea are associated with catechins: (-)-epigallocatechin-3-O-gallate (EGCG), (-)-epigallocatechin, (-)-epicatechin-3-O-gallate, and (-)-epicatechin. An understanding of compound absorption, distribution, metabolism, excretion, and toxicity characteristics is essential for explaining its biological activities. Herein, absorption, distribution, metabolism, excretion, and toxicity properties of in vivo detected metabolites of green tea catechins (GTCs) have been analyzed in silico. The influence of metabolic transformations on absorption, distribution, metabolism, and excretion profiles of GTCs corresponds to the effects of size, charge, and lipophilicity, as already observed for other small molecules. Mutagenic, carcinogenic, or liver toxic effects were predicted only for a few metabolites. Similar to galloylated GTCs EGCG and (--)-epicatechin-3-O-gallate, the sulfo-conjugates were predicted to bind at the warfarin binding site. The low free plasma concentration of these derivatives may be consequential to their serum albumin binding. The activity cliff detected for methylated conjugates of EGCG indicates that GTCs' pro-oxidative activity in bound state comes primarily from free hydroxyl groups of the pyrogallol ring B.

Free radical scavenging potency of quercetin catecholic colonic metabolites: Thermodynamics of 2H+/2e- processes.

Reaction energetics of the double (2H+/2e-), i.e., the first 1H+/1e- (catechol→ phenoxyl radical) and the second 1H+/1e- (phenoxyl radical→ quinone) free radical scavenging mechanisms of quercetin and its six colonic catecholic metabolites (caffeic acid, hydrocaffeic acid, homoprotocatechuic acid, protocatechuic acid, 4-methylcatechol, and catechol) were computationally studied using density functional theory, with the aim to estimate the antiradical potency of these molecules. We found that second hydrogen atom transfer (HAT) and second sequential proton loss electron transfer (SPLET) mechanisms are less energy demanding than the first ones indicating 2H+/2e- processes as inherent to catechol moiety. The Gibbs free energy change for reactions of inactivation of selected free radicals indicate that catecholic colonic metabolites constitute an efficient group of more potent scavengers than quercetin itself, able to deactivate various free radicals, under different biological conditions. They could be responsible for the health benefits associated with regular intake of flavonoid-rich diet.

Free radical scavenging and COX-2 inhibition by simple colon metabolites of polyphenols: A theoretical approach.

Free radical scavenging and inhibitory potency against cyclooxygenase-2 (COX-2) by two abundant colon metabolites of polyphenols, i.e., 3-hydroxyphenylacetic acid (3-HPAA) and 4-hydroxyphenylpropionic acid (4-HPPA) were theoretically studied. Different free radical scavenging mechanisms are investigated in water and pentyl ethanoate as a solvent. By considering electronic properties of scavenged free radicals, hydrogen atom transfer (HAT) and sequential proton loss electron transfer (SPLET) mechanisms are found to be thermodynamically probable and competitive processes in both media. The Gibbs free energy change for reaction of inactivation of free radicals indicates 3-HPAA and 4-HPPA as potent scavengers. Their reactivity toward free radicals was predicted to decrease as follows: hydroxyl>>alkoxyls>phenoxyl≈peroxyls>>superoxide. Shown free radical scavenging potency of 3-HPAA and 4-HPPA along with their high µM concentration produced by microbial colon degradation of polyphenols could enable at least in situ inactivation of free radicals. Docking analysis with structural forms of 3-HPAA and 4-HPPA indicates dianionic ligands as potent inhibitors of COX-2, an inducible enzyme involved in colon carcinogenesis. Obtained results suggest that suppressing levels of free radicals and COX-2 could be achieved by 3-HPAA and 4-HPPA indicating that these compounds may contribute to reduced risk of colon cancer development.

Towards an improved prediction of the free radical scavenging potency of flavonoids: the significance of double PCET mechanisms.

The 1H(+)/1e(-) and 2H(+)/2e(-) proton-coupled electron transfer (PCET) processes of free radical scavenging by flavonoids were theoretically studied for aqueous and lipid environments using the PM6 and PM7 methods. The results reported here indicate that the significant contribution of the second PCET mechanism, resulting in the formation of a quinone/quinone methide, effectively discriminates the active from inactive flavonoids. The predictive potency of descriptors related to the energetics of second PCET mechanisms (the second O-H bond dissociation enthalpy (BDE2) related to hydrogen atom transfer (HAT) mechanism, and the second electron transfer enthalpy (ETE2) related to sequential proton loss electron transfer (SPLET) mechanism) are superior to the currently used indices, which are related to the first 1H(+)/1e(-) processes, and could serve as primary descriptors in development of the QSAR (quantitative structure-activity relationships) of flavonoids.

Bond dissociation free energy as a general parameter for flavonoid radical scavenging activity.

Notwithstanding multiple mechanisms of radical scavenging (RS), measured RS activities (RSA) of flavonoids are usually related to O-H bond dissociation enthalpy (BDE) for hydrogen atom transfer (HAT). For 12 flavonoids the reaction free energies were calculated for: (1) HAT, (2) single electron transfer-proton transfer (SET-PT) and (3) sequential proton loss electron transfer (SPLET) in gas and aqueous phases. Aqueous free energies, like bond dissociation (BDFEaq), ionisation (IFEaq) and deprotonation (ΔGdeprot,aq) free energies were estimated using thermochemical cycles. While in gas HAT is a RS mechanism (BDFEg

The sum-connectivity index--an additive variant of the Randic connectivity index.

This review discusses structure-property modeling applications of a novel variant of the Randic connectivity index that is called the sum-connectivity index. We compare published one-descriptor quantitative structure-property relationship (QSPR) models obtained with the new sum-connectivity index and with the Randic connectivity index, called here the product-connectivity index. Additionally, the efficiency of both variants of connectivity indices in QSPR modeling is tested on five datasets of alkanes and two datasets of polycyclic hydrocarbons. Several physicochemical properties of alkanes (i.e. boiling and melting points, retention index, molar volume, molar refraction, heat of vaporization, standard Gibbs energy of formation, critical temperature, critical pressure, surface tension, density) and π- electronic energies of two sets of polycyclic hydrocarbons were correlated with the product- and sum-connectivity indices. A comparison of these QSPR models shows that both variants of connectivity indices are equivalent, and only slightly (but not significantly) better results are obtained with the sum-connectivity index. Inter-correlations between the product- and sum-connectivity indices are mostly linear with a slope very close to 1.0 for alkanes, and with a slope more different from 1.0 (0.88) for polycyclic compounds. The comparative analysis presented here supports the use of the sumconnectivity index in QSPR/QSAR studies together with the product-connectivity index. Further studies on larger and more heterogeneous datasets should test the sum-connectivity index in QSPR/QSAR models.

PM6 study of free radical scavenging mechanisms of flavonoids: why does O-H bond dissociation enthalpy effectively represent free radical scavenging activity?

It is well known that the bond dissociation enthalpy (BDE) of the O-H group is related to the hydrogen atom transfer (HAT) mechanism of free radical scavenging that is preferred in gas-phase and non-polar solvents. The present work shows that the BDE may also be related to radical scavenging processes taking place in polar solvents, i.e., single electron transfer followed by proton transfer (SET-PT) and sequential proton loss electron transfer (SPLET). This is so because the total energy requirements related to the SET-PT [sum of the ionization potential (IP) and proton dissociation enthalpy (PDE)] and the SPLET [sum of the proton affinity (PA) and electron transfer enthalpy (ETE)] are perfectly correlated with the BDE. This could explain why the published data for polyphenolic antioxidant activity measured by various assays are better correlated with the BDE than with other reaction enthalpies involved in radical scavenging mechanisms, i.e., the IP, PDE, PA and ETE. The BDE is fairly well able to rank flavonoids as antioxidants in any medium, but to conclude which radical scavenging mechanism represents the most probable reaction pathway from the thermodynamic point of view, the IP and PA (ETE) should also be considered. This is exemplified in the case of the radical scavenging activity of 25 flavonoids.

Free radical scavenging activity of morin 2'-O(-) phenoxide anion.

Due to intramolecular H-atom transfer, deprotonation of the most acidic 3-OH group of morin yields 2'-O(-) phenoxide anion. The reaction enthalpies related to mechanisms of free radical scavenging activity of this dominant species at a physiological pH of 7.4 were calculated by PM6 and DFT methods in gas-phase, water, benzene and DMSO. Results indicate the 4'-OH group of 2'-O(-) phenoxide anion is the active site for radical inactivation. The thermodynamically favoured mechanism depends on the polarity of the reaction media: in polar solvents (water and DMSO), the sequential proton loss electron transfer (SPLET) mechanism is preferred while in non-polar benzene (and in gas-phase), the hydrogen atom transfer (HAT) mechanism is responsible for the free radical scavenging activity of the morin phenoxide anion. Results show that the fast, semiempirical PM6 method fairly mimics more accurate, though time-consuming DFT methodologies.

PM6 and DFT study of free radical scavenging activity of morin.

Flavonoids have long been recognised for their general health-promoting properties, of which their antioxidant activity may play an important role. In this work, we have studied the properties of flavonoid morin using semiempirical and density functional theory (DFT) methods in order to validate the application of the recently developed parametric method 6 (PM6). Reaction enthalpies related to mechanisms of free radical scavenging by flavonoid morin were calculated by DFT and PM6 methods in gas-phase, water, DMSO and benzene. It has been shown that fast semiempirical PM6 method can mimic results obtained by means of more accurate time consuming DFT calculations. Thermodynamically favoured mechanism depends on reaction medium: SPLET (sequential proton loss electron transfer) is preferred in water and DMSO, and HAT (hydrogen atom transfer) is predominant in gas-phase. In benzene these two mechanisms are competitive.

Knowledge-based computational methods for identifying or designing novel, non-homologous antimicrobial peptides.

We describe computational approaches for identifying promising lead candidates for the development of peptide antibiotics, in the context of quantitative structure-activity relationships (QSAR) studies for this type of molecule. A first approach deals with predicting the selectivity properties of generated antimicrobial peptide sequences in terms of measured therapeutic indices (TI) for known antimicrobial peptides (AMPs). Based on a training set of anuran AMPs, the concept of sequence moments was used to construct algorithms that could predict TIs for a second test set of natural AMPs and could also predict the effect of point mutations on TI values. This approach was then used to design peptide antibiotics (adepantins) not homologous to known natural or synthetic AMPs. In a second approach, many novel putative AMPs were identified from DNA sequences in EST databases, using the observation that, as a rule, specific subclasses of highly conserved signal peptides are associated exclusively with AMPs. Both anuran and teleost sequences were used to elucidate this observation and its implications. The predicted therapeutic indices of identified sequences could then be used to identify new types of selective putative AMPs for future experimental verification.

Master connectivity index and master connectivity polynomial.

We give the standard expressions of the Zagreb indices, Randic indices and their variants. Then we present the master connectivity index and show how this index can generate all connectivity indices of both varieties. We also present the master connectivity polynomial and show the relationship between this polynomial and the master connectivity index. Because of this relationship, the master connectivity polynomial can also be used to generate connectivity indices.

Prediction of carcinogenicity for diverse chemicals based on substructure grouping and SVM modeling.

The Carcinogenicity Reliability Database (CRDB) was constructed by collecting experimental carcinogenicity data on about 1,500 chemicals from six sources, including IARC, and NTP databases, and then by ranking their reliabilities into six unified categories. A wide variety of 911 organic chemicals were selected from the database for QSAR modeling, and 1,504 kinds of different molecular descriptors were calculated, based on their 3D molecular structures as modeled by the Dragon software. Positive (carcinogenic) and negative (non-carcinogenic) chemicals containing various substructures were counted using atom and functional group count descriptors, and the statistical significance of ratios of positives to negatives was tested for those substructures. Very few were judged to be strongly related to carcinogenicity, among substructures known to be responsible for carcinogens as revealed from biomedical studies. In order to develop QSAR models for the prediction of the carcinogenicities of a wide variety of chemicals with a satisfactory performance level, the relationship between the carcinogenicity data with improved reliability and a subset of significant descriptors selected from 1,504 Dragon descriptors was analyzed with a support vector machine (SVM) method: the classification function (SVC) for weighted data in LIBSVM program was used to classify chemicals into two carcinogenic categories (positive or negative), where weights were set depending on the reliabilities of the carcinogenicity data. The quality and stability of the models presented were tested by performing a dual cross-validation procedure. A single SVM model as the first step was developed for all the 911 chemicals using 250 selected descriptors, achieving an overall accuracy level, i.e., positive and negative correct estimate, of about 70%. In order to improve the accuracy of the final model, the 911 chemicals were classified into 20 mutually overlapping subgroups according to contained substructures, a specific SVM model was optimized for each subgroup, and the predicted carcinogenicities of the 911 chemicals were determined by the majorities of the outputs of the corresponding SVM models. The model developed on the basis of grouping of chemicals into 20 substructures predicts the carcinogenicities of a wide variety of chemicals with a satisfactory overall accuracy of approximately 80%.

Reliability of bond dissociation enthalpy calculated by the PM6 method and experimental TEAC values in antiradical QSAR of flavonoids.

The applicability of the newly developed RM1 and PM6 methods implemented in the semiempirical quantum chemistry mopac2009 software package in modeling free radical scavenging activity of flavonoids was examined. Bond dissociation enthalpy (BDE) of OH groups could be calculated much faster than with DFT method but with similar quality. Despite the known shortcomings of the Trolox equivalent antioxidant capacity (TEAC) assay, we show that taking into account the hydrogen atom transfer (HAT) mechanism of free radical scavenging of flavonoids encoded by minimal BDE values (BDE(min)) and the number of OH groups (nOH), as well as experimental data, reasonable QSAR models could be developed. For TEAC values of 38 flavonoids measured by the ABTS free radical, a model based on BDE(min) and nOH was developed, having very good statistical parameters (r=0.983, r(cv)=0.976). The applicability of this model to three different data sets of flavonoids and reliability of TEAC values measured in distinct laboratories were discussed. Finally, a reasonably good model of experimental vitamin C equivalent antioxidant capacity (VCEAC) of 36 flavonoids was obtained (r=0.954, r(cv)=0.947), involving BDE(min) and nOH as descriptors. Additionally, all presented models have comparable fit and cross-validated statistical parameters, as well as significant regression coefficients.

Bond dissociation enthalpies calculated by the PM3 method confirm activity cliffs in radical scavenging of flavonoids.

Radical scavenging potency of flavonoids is associated with activity cliffs, i.e., small chemical modifications on flavonoid core can have a significant effect on activity. The presence or absence of the 3',4'-diOH and/or 3-OH group may serve as an activity switch for radical scavenging. The physicochemical background of such an indicator variable, defined previously (Amic et al. (2003) Croat Chem Acta 76:55-61), is confirmed by computation of bond dissociation enthalpies and selecting the minimal of all values relating to flavonoid OH groups. Bond dissociation enthalpies for hydrogen abstraction from OH groups for 29 flavonoids were calculated by the PM3 method. Minimal bond dissociation enthalpy values were obtained for OH groups attached to C-3, C-3' and C-4' positions, and they correspond to the previously introduced indicator variable. Taking into account some driving forces of the radical scavenging mechanism, it is possible to relate structural characteristics of flavonoids to their radical scavenging potency as well as to develop reliable structure-activity models.