Energy Blocker Lonidamine Reverses Nimustine Resistance in Human Glioblastoma Cells through Energy Blockade, Redox Homeostasis Disruption, and O6-Methylguanine-DNA Methyltransferase Downregulation: In Vitro and In Vivo Validation.

Tumor resistance seriously hinders the clinical application of chloroethylnitrosoureas (CENUs), such as O6-methylguanine-DNA methylguanine (MGMT), which can repair O6-alkyl lesions, thereby inhibiting the formation of cytotoxic DNA interstrand cross-links (ICLs). Metabolic differences between tumor and normal cells provide a biochemical basis for novel therapeutic strategies aimed at selectively inhibiting tumor energy metabolism. In this study, the energy blocker lonidamine (LND) was selected as a chemo-sensitizer of nimustine (ACNU) to explore its potential effects and underlying mechanisms in human glioblastoma in vitro and in vivo. A series of cell-level studies showed that LND significantly increased the cytotoxic effects of ACNU on glioblastoma cells. Furthermore, LND plus ACNU enhanced the energy deficiency by inhibiting glycolysis and mitochondrial function. Notably, LND almost completely downregulated MGMT expression by inducing intracellular acidification. The number of lethal DNA ICLs produced by ACNU increased after the LND pretreatment. The combination of LND and ACNU aggravated cellular oxidative stress. In resistant SF763 mouse tumor xenografts, LND plus ACNU significantly inhibited tumor growth with fewer side effects than ACNU alone. Finally, we proposed a new "HMAGOMR" chemo-sensitizing mechanism through which LND may act as a potential chemo-sensitizer to reverse ACNU resistance in glioblastoma: moderate inhibition of hexokinase (HK) activity (H); mitochondrial dysfunction (M); suppressing adenosine triphosphate (ATP)-dependent drug efflux (A); changing redox homeostasis to inhibit GSH-mediated drug inactivation (G) and increasing intracellular oxidative stress (O); downregulating MGMT expression through intracellular acidification (M); and partial inhibition of energy-dependent DNA repair (R).

The rat acute oral toxicity of trifluoromethyl compounds (TFMs): a computational toxicology study combining the 2D-QSTR, read-across and consensus modeling methods.

All areas of the modern society are affected by fluorine chemistry. In particular, fluorine plays an important role in medical, pharmaceutical and agrochemical sciences. Amongst various fluoro-organic compounds, trifluoromethyl (CF3) group is valuable in applications such as pharmaceuticals, agrochemicals and industrial chemicals. In the present study, following the strict OECD modelling principles, a quantitative structure-toxicity relationship (QSTR) modelling for the rat acute oral toxicity of trifluoromethyl compounds (TFMs) was established by genetic algorithm-multiple linear regression (GA-MLR) approach. All developed models were evaluated by various state-of-the-art validation metrics and the OECD principles. The best QSTR model included nine easily interpretable 2D molecular descriptors with clear physical and chemical significance. The mechanistic interpretation showed that the atom-type electro-topological state indices, molecular connectivity, ionization potential, lipophilicity and some autocorrelation coefficients are the main factors contributing to the acute oral toxicity of TFMs against rats. To validate that the selected 2D descriptors can effectively characterize the toxicity, we performed the chemical read-across analysis. We also compared the best QSTR model with public OPERA tool to demonstrate the reliability of the predictions. To further improve the prediction range of the QSTR model, we performed the consensus modelling. Finally, the optimum QSTR model was utilized to predict a true external set containing many untested/unknown TFMs for the first time. Overall, the developed model contributes to a more comprehensive safety assessment approach for novel CF3-containing pharmaceuticals or chemicals, reducing unnecessary chemical synthesis whilst saving the development cost of new drugs.

Reaction sites of pyrimidine bases and nucleosides during chlorination: A computational study.

As important components of soluble microbial products in water, nucleobases have attracted much attention due to the high toxicity of their direct aromatic halogenated disinfection by-products (AH-DBPs) during chlorination. However, multiple halogenation sites of AH-DBPs pose challenges to identify them. In this study, reaction sites of pyrimidine bases and nucleosides during chlorination were investigated by quantum chemical computational method. The results indicate that the anion salt forms play key roles in chlorination of uracil, thymine, and their nucleosides, while neutral forms make predominant contributions to cytosine and cytidine. In view of both kinetics and thermodynamics, C5 is the most reactive site for uracil and thymine, N3/C5 and N3 for respective uridine and thymidine, N1/C5/N4 and N4 for respective cytosine and cytidine, whose estimated apparent rate constants kobs-est of ∼103, 103/102, 106/102/104, and 103 M-1 s-1, respectively, in consistent with the known experimental results. C6 in all pyrimidine compounds is hardly attacked by Cl+ in HOCl ascribed to its positive charge, but readily attacked by OH‾ in hydrolysis and the N1=C6 bond was found to possess the highest reactivity in hydrolysis among all double bonds. In addition, the structure-kinetic reactivity relationship study reveals a relatively strong correlation between lgkobs-est and APT charge in all pyrimidine compounds rather than FED2 (HOMO). The results are helpful to further understand the reactivity of various reaction sites in aromatic compounds during chlorination.

Identification of reaction sites and chlorinated products of purine bases and nucleosides during chlorination: a computational study.

Hypochlorous acid (HOCl) released from activated leukocytes plays a significant role in the human immune system, but is also implicated in numerous diseases due to its inappropriate production. Chlorinated nucleobases induce genetic changes that potentially enable and stimulate carcinogenesis, and thus have attracted considerable attention. However, their multiple halogenation sites pose challenges to identify them. As a good complement to experiments, quantum chemical computation was used to uncover chlorination sites and chlorinated products in this study. The results indicate that anion salt forms of all purine compounds play significant roles in chlorination except for adenosine. The kinetic reactivity order of all reaction sites in terms of the estimated apparent rate constant kobs-est (in M-1 s-1) is heterocyclic NH/N (102-107) > exocyclic NH2 (10-2-10) > heterocyclic C8 (10-5-10-1), but the order is reversed for thermodynamics. Combining kinetics and thermodynamics, the numerical simulation results show that N9 is the most reactive site for purine bases to form the main initial chlorinated product, while for purine nucleosides N1 and exocyclic N2/N6 are the most reactive sites to produce the main products controlled by kinetics and thermodynamics, respectively, and C8 is a possible site to generate the minor product. The formation mechanisms of biomarker 8-Cl- and 8-oxo-purine derivatives were also investigated. Additionally, the structure-kinetic reactivity relationship study reveals a good correlation between lg kobs-est and APT charge in all purine compounds compared to FED2 (HOMO), which proves again that the electrostatic interaction plays a key role. The results are helpful to further understand the reactivity of various reaction sites in aromatic compounds during chlorination.

Mechanism of AGT-Mediated Repair of dG-dC Cross-Links in the Drug Resistance to Chloroethylnitrosoureas: Molecular Docking, MD Simulation, and ONIOM (QM/MM) Investigation.

Chloroethylnitrosoureas (CENUs) are important chemotherapies applied in the treatment of cancer. They exert anticancer activity by inducing DNA interstrand cross-links (ICLs) via the formation of two O6-alkylguanine intermediates, O6-chloroethylguanine (O6-ClEtG) and N1,O6-ethanoguanine (N1,O6-EtG). However, O6-alkylguanine-DNA alkyltransferase (AGT), a DNA-repair enzyme, can restore the O6-alkylguanine damages and thereby obstruct the formation of ICLs (dG-dC cross-link). In this study, the inhibitory mechanism of ICL formation was investigated to elucidate the drug resistance of CENUs mediated by AGT in detail. Based on the structures of the substrate-enzyme complexes obtained from docking and MD simulations, two ONIOM (QM/MM) models with different sizes of the QM region were constructed. The model with a larger QM region, which included the substrate (O6-ClEtG or N1,O6-EtG), a water molecule, and five residues (Tyr114, Cys145, His146, Lys165, and Glu172) in the active pocket of AGT, accurately described the repairing reaction and generated the results coinciding with the experimental outcomes. The repair process consists of two sequential steps: hydrogen transfer to form a thiolate anion on Cys145 and alkyl transfer from the O6 site of guanine (the rate-limiting step). The repair of N1,O6-EtG was more favorable than that of O6-ClEtG from both kinetics and thermodynamics aspects. Moreover, the comparison of the repairing process with the formation of dG-dC cross-link and the inhibition of AGT by O6-benzylguanine (O6-BG) showed that the presence of AGT could effectively interrupt the formation of ICLs leading to drug resistance, and the inhibition of AGT by O6-BG that was energetically more favorable than the repair of O6-ClEtG could not prevent the repair of N1,O6-EtG. Therefore, it is necessary to completely eliminate AGT activity before CENUs medication to enhance the chemotherapeutic effectiveness. This work provides reasonable explanations for the supposed mechanism of AGT-mediated drug resistance of CENUs and will assist in the development of novel CENU chemotherapies and their medication strategies.

Recent advances in chemometric modelling of inhibitors against SARS-CoV-2.

The outbreak of the novel coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused great harm to all countries worldwide. This disease can be prevented by vaccination and managed using various treatment methods, including injections, oral medications, or aerosol therapies. However, the selection of suitable compounds for the research and development of anti-SARS-CoV-2 drugs is a daunting task because of the vast databases of available compounds. The traditional process of drug research and development is time-consuming, labour-intensive, and costly. The application of chemometrics can significantly expedite drug R&D. This is particularly necessary and important for drug development against pandemic public emergency diseases, such as COVID-19. Through various chemometric techniques, such as quantitative structure-activity relationship (QSAR) modelling, molecular docking, and molecular dynamics (MD) simulations, compounds with inhibitory activity against SARS-CoV-2 can be quickly screened, allowing researchers to focus on the few prioritised candidates. In addition, the ADMET properties of the screened candidate compounds should be further explored to promote the successful discovery of anti-SARS-CoV-2 drugs. In this case, considerable time and economic costs can be saved while minimising the need for extensive animal experiments, in line with the 3R principles. This paper focuses on recent advances in chemometric modelling studies of COVID-19-related inhibitors, highlights current limitations, and outlines potential future directions for development.

Prioritization of the ecotoxicological hazard of PAHs towards aquatic species spanning three trophic levels using 2D-QSTR, read-across and machine learning-driven modelling approaches.

Polycyclic aromatic hydrocarbons (PAHs) represent a common group of environmental pollutants that endanger various aquatic organisms via various pathways. To better prioritize the ecotoxicological hazard of PAHs to aquatic environment, we used 2D descriptors-based quantitative structure-toxicity relationship (QSTR) to assess the toxicity of PAHs toward six aquatic model organisms spanning three trophic levels. According to strict OECD guideline, six easily interpretable, transferable and reproducible 2D-QSTR models were constructed with high robustness and reliability. A mechanistic interpretation unveiled the key structural factors primarily responsible for controlling the aquatic ecotoxicity of PAHs. Furthermore, quantitative read-across and different machine learning approaches were employed to validate and optimize the modelling approach. Importantly, the optimum QSTR models were further applied for predicting the ecotoxicity of hundreds of untested/unknown PAHs gathered from Pesticide Properties Database (PPDB). Especially, we provided a priority list in terms of the toxicity of unknown PAHs to six aquatic species, along with the corresponding mechanistic interpretation. In summary, the models can serve as valuable tools for aquatic risk assessment and prioritization of untested or completely new PAHs chemicals, providing essential guidance for formulating regulatory policies.

Development and in vitro evaluation of carmustine delivery platform: A hypoxia-sensitive anti-drug resistant nanomicelle with BBB penetrating ability.

Glioma is extremely difficult to be completely excised by surgery due to its invasive nature. Thus, chemotherapy still is the mainstay in the treatment of glioma after surgery. However, the natural blood-brain barrier (BBB) greatly restricts the penetration of chemotherapeutic agents into the central nervous system. As a front-line anti-glioma agent in clinical, carmustine (BCNU) exerts antitumor effect by inducing DNA damage at the O6 position of guanine. However, the therapeutic effect of BCNU was largely decreased because of the drug resistance mediated by O6-alkylguanine-DNA alkyltransferase (AGT) and insufficient local drug concentrations. To overcome these obstacles, we synthesized a BCNU-loaded hypoxia-responsive nano-micelle with BBB penetrating capacity and AGT inhibitory activity, named as T80-HA-AZO-BG/BCNU NPs. In this nano-system, Tween 80 (T80) serves as a functional coating on the surface of the micelle, promoting transportation across the BBB. Hyaluronic acid (HA) with active tumor-targeting capability was linked with the hydrophobic O6-benzylguanine (BG) analog via a hypoxia-sensitive azo bond. Under hypoxic tumor microenvironment, the azo bond selectively breaks to release O6-BG as AGT inhibitor and BCNU as DNA alkylating agent. The synthesized T80-HA-AZO-BG/BCNU NPs showed good stability, favorable biocompatibility and hypoxia-responsive drug-releasing ability. T80 modification improved the transportation of the micelle across an in vitro BBB model. Moreover, T80-HA-AZO-BG/BCNU NPs exhibited significantly enhanced cytotoxicity against glioma cell lines with high AGT expression compared with traditional combined medication of BCNU plus O6-BG. We expect that the tumor-targeting nano-micelle designed for chloroethylnitrosourea will provide new tools for the development of effective glioma therapy.

QSAR and Chemical Read-Across Analysis of 370 Potential MGMT Inactivators to Identify the Structural Features Influencing Inactivation Potency.

O6-methylguanine-DNA methyltransferase (MGMT) constitutes an important cellular mechanism for repairing potentially cytotoxic DNA damage induced by guanine O6-alkylating agents and can render cells highly resistant to certain cancer chemotherapeutic drugs. A wide variety of potential MGMT inactivators have been designed and synthesized for the purpose of overcoming MGMT-mediated tumor resistance. We determined the inactivation potency of these compounds against human recombinant MGMT using [3H]-methylated-DNA-based MGMT inactivation assays and calculated the IC50 values. Using the results of 370 compounds, we performed quantitative structure-activity relationship (QSAR) modeling to identify the correlation between the chemical structure and MGMT-inactivating ability. Modeling was based on subdividing the sorted pIC50 values or on chemical structures or was random. A total of nine molecular descriptors were presented in the model equation, in which the mechanistic interpretation indicated that the status of nitrogen atoms, aliphatic primary amino groups, the presence of O-S at topological distance 3, the presence of Al-O-Ar/Ar-O-Ar/R..O..R/R-O-C=X, the ionization potential and hydrogen bond donors are the main factors responsible for inactivation ability. The final model was of high internal robustness, goodness of fit and prediction ability (R2pr = 0.7474, Q2Fn = 0.7375-0.7437, CCCpr = 0.8530). After the best splitting model was decided, we established the full model based on the entire set of compounds using the same descriptor combination. We also used a similarity-based read-across technique to further improve the external predictive ability of the model (R2pr = 0.7528, Q2Fn = 0.7387-0.7449, CCCpr = 0.8560). The prediction quality of 66 true external compounds was checked using the "Prediction Reliability Indicator" tool. In summary, we defined key structural features associated with MGMT inactivation, thus allowing for the design of MGMT inactivators that might improve clinical outcomes in cancer treatment.

A multi-functional hypoxia/esterase dual stimulus responsive and hyaluronic acid-based nanomicelle for targeting delivery of chloroethylnitrosouea.

Carmustine (BCNU), a vital type of chloroethylnitrosourea (CENU), inhibits tumor cells growth by inducing DNA damage at O6 position of guanine and eventually forming dG-dC interstrand cross-links (ICLs). However, the clinical application of BCNU is hindered to some extent by the absence of tumor selectivity, poor stability and O6-alkylguanine-DNA alkyltransferase (AGT) mediated drug resistance. In recent years, tumor microenvironment has been widely utilized for advanced drug delivery. In the light of the features of tumor microenvironment, we constructed a multifunctional hypoxia/esterase-degradable nanomicelle with AGT inhibitory activity named HACB NPs for tumor-targeting BCNU delivery and tumor sensitization. HACB NPs was self-assembled from hyaluronic acid azobenzene AGT inhibitor conjugates, in which O6-BG analog acted as an AGT inhibitor, azobenzene acted as a hypoxia-responsive linker and carboxylate ester bond acted as both an esterase-sensitive switch and a connector with hyaluronic acid (HA). The obtained HACB NPs possessed good stability, favorable biosafety and hypoxia/esterase-responsive drug-releasing ability. BCNU-loaded HACB/BCNU NPs exhibited superior cytotoxicity and apoptosis-inducing ability toward the human uterine cervix carcinoma HeLa cells compared with traditional combined medication of BCNU plus O6-BG. In vivo studies further demonstrated that after a selective accumulation in the tumor site, the micelles could respond to hypoxic tumor tissue for rapid drug release to an effective therapeutic dosage. Thus, this multifunctional stimulus-responsive nanocarrier could be a new promising strategy to enhance the anticancer efficacy and reduce the side effects of BCNU and other CENUs.

Hypoxia and CD44 receptors dual-targeted nano-micelles with AGT-inhibitory activity for the targeting delivery of carmustine.

Carmustine (BCNU) is a typical chemotherapy used for treatment of cerebroma and other solid tumors, which exerts antitumor effect by inducing DNA damage at O6 position of guanine. However, the clinical application of BCNU was extremely limited due to the drug resistance mainly mediated by O6-alkylguanine-DNA alkyltransferase (AGT) and absence of tumor-targeting ability. To overcome these limitations, we developed a hypoxia-responsive nanomicelle with AGT inhibitory activity, which was successfully loaded with BCNU. In this nano-system, hyaluronic acid (HA) acts as an active tumor-targeting ligand to bind the overexpressing CD44 receptors on the surface of tumor cells. An azo bond selectively breaks in hypoxic tumor microenvironment to release O6-benzylguanine (BG) as AGT inhibitor and BCNU as DNA alkylating agent. The obtained HA-AZO-BG NPs with shell core structure had an average particle size of 176.98 ± 11.19 nm and exhibited good stability. Meanwhile, HA-AZO-BG NPs possessed a hypoxia-responsive drug release profile. After immobilizing BCNU into HA-AZO-BG NPs, the obtained HA-AZO-BG/BCNU NPs exhibited obvious hypoxia-selectivity and superior cytotoxicity in T98G, A549, MCF-7 and SMMC-7721 cells with IC50 at 189.0, 183.2, 90.1 and 100.1 µm, respectively, under hypoxic condition. Near-infrared imaging in HeLa tumor xenograft models showed that HA-AZO-BG/DiR NPs could effectively accumulate in tumor site at 4 h of post-injection, suggesting its good tumor-targetability. In addition, in vivo anti-tumor efficacy and toxicity evaluation indicated that HA-AZO-BG/BCNU NPs was more effective and less harmful compared to the other groups. After treatment, the tumor weight of HA-AZO-BG/BCNU NPs group was 58.46 % and 63.33 % of the control group and BCNU group, respectively. Overall, HA-AZO-BG/BCNU NPs was expected to be a promising candidate for targeted delivery of BCNU and elimination of chemoresistance.

Modulating MGMT expression through interfering with cell signaling pathways.

Guanine O6-alkylating agents are widely used as first-line chemotherapeutic drugs due to their ability to induce cytotoxic DNA damage. However, a major hurdle in their effectiveness is the emergence of chemoresistance, largely attributed to the DNA repair pathway mediated by O6-methylguanine-DNA methyltransferase (MGMT). MGMT plays an important role in removing the alkyl groups from lethal O6-alkylguanine (O6-AlkylG) adducts formed by chemotherapeutic alkylating agents. By doing so, MGMT enables tumor cells to evade apoptosis and develop drug resistance toward DNA alkylating agents. Although covalent inhibitors of MGMT, such as O6-benzylguanine (O6-BG) and O6-(4-bromothenyl)guanine (O6-4-BTG or lomeguatrib), have been explored in clinical settings, their utility is limited due to severe delayed hematological toxicity observed in most patients when combined with alkylating agents. Therefore, there is an urgent need to identify new targets and unravel the underlying molecular mechanisms and to develop alternative therapeutic strategies that can overcome MGMT-mediated tumor resistance. In this context, the regulation of MGMT expression via interfering the specific cell signaling pathways (e.g., Wnt/ß-catenin, NF-κB, Hedgehog, PI3K/AKT/mTOR, JAK/STAT) emerges as a promising strategy for overcoming tumor resistance, and ultimately enhancing the efficacy of DNA alkylating agents in chemotherapy.

Computational Investigations of Reaction Mechanisms and Transformation Products of Olefins with Hypochlorous Acid.

Hypochlorous acid (HOCl) as the main component in chlorination and also as the innate immune factor relevant to immune defense has attracted considerable attention. Electrophilic addition reaction of olefins with HOCl, one of the most important prototype of chemical reactions, has been intensively studied for a long time; however, it has not been fully understood yet. In this study, addition reaction mechanisms and transformation products of model olefins with HOCl were systematically investigated by the density functional theory method. The results indicate that the traditionally believed stepwise mechanism with a chloronium-ion intermediate is only suitable for olefins substituted with electron-donating groups (EDGs) and weak electron-withdrawing groups (EWGs) but it is a carbon-cation intermediate that is favorable for EDGs featuring p-π or π-π conjugation with the C═C moiety. Moreover, olefins substituted with moderate or/and strong EWGs prefer the concerted and nucleophilic addition mechanisms, respectively. Epoxide and truncated aldehyde as the main transformation products can be generated from chlorohydrin through a series of reactions involving hypochlorite; however, their generation is kinetically not as feasible as the formation of chlorohydrin. The reactivity of three chlorinating agents (HOCl, Cl2O, and Cl2) and the case study of chlorination and degradation of cinnamic acid were also explored. Additionally, APT charge on the double-bond moiety in olefin and energy gap (ΔE) between the highest occupied molecular orbital (HOMO) energy of olefin and the lowest unoccupied molecular orbital (LUMO) energy of HOCl were found to be good parameters to distinguish the regioselectivity of chlorohydrin and reactivity of olefin, respectively. The findings of this work are helpful in further understanding the chlorination reactions of unsaturated compounds and identifying complicated transformation products.

Insights into C-C Bond Cleavage Mechanisms in Dichloroacetonitrile Formation during Chlorination of Long-Chain Primary Amines, Amino Acids, and Dipeptides.

Dichloroacetonitrile (DCAN) as one of the potentially prioritized regulated DBPs has drawn great attention; however, understanding its formation, especially the C-C bond cleavage mechanisms, is limited. In this study, DCAN formation mechanisms from long-chain primary amines, amino acids, and dipeptides during chlorination were investigated by a combined computational and experimental approach. The results indicate that nitriles initially generate for all of the above precursors, then they undergo ß-C-hydroxylation or/and α-C-chlorination processes, and finally, DCAN is produced through the Cα-Cß bond cleavage. For the first time, the underlying mechanism of the C-C bond cleavage was unraveled to be electron transfer from the O- anion into its attached C atom in the chlorinated nitriles, leading to the strongly polarized Cα-Cß bond heterocleavage and DCAN- formation. Moreover, DCAN molar yields of precursors studied in the present work were found to be determined by their groups at the γ-site of the amino group, where the carbonyl group including -CO2-, -COR, and -CONHR, the aromatic group, and the -OH group can all dramatically facilitate DCAN formation by skipping over or promoting the time-consuming ß-C-hydroxylation process and featuring relatively lower activation free energies in the C-C bond cleavage. Importantly, 4-amino-2-hydroxybutyric acid was revealed to possess the highest DCAN yield among all the known aliphatic long-chain precursors to date during chlorination. Additionally, enonitriles, (chloro-)isocyanates, and nitriles can be generated during DCAN formation and should be of concern due to their high toxicities.

Ecotoxicological QSAR study of fused/non-fused polycyclic aromatic hydrocarbons (FNFPAHs): Assessment and priority ranking of the acute toxicity to Pimephales promelas by QSAR and consensus modeling methods.

Fused/non-fused polycyclic aromatic hydrocarbons (FNFPAHs) have a variety of toxic effects on ecosystems and human body, but the acquisition of their toxicity data is greatly limited by the limited resources available. Here, we followed the EU REACH regulation and used Pimephales promelas as a model organism to investigate the quantitative structure-activity relationship (QSAR) between the FNFPAHs and their toxicity for the aquatic environment for the first time. We developed a single QSAR model (SM1) containing five simple and interpretable 2D molecular descriptors, which met the validation of OECD QSAR-related principles, and analyzed their mechanistic relationships with toxicity in detail. The model had good degree of fitting and robustness, and had better external prediction performance (MAEtest = 0.4219) than ECOSAR model (MAEtest = 0.5614). To further enhance its prediction accuracy, the three qualified single models (SMs) were used for constructing consensus models (CMs), the best one CM2 (MAEtest = 0.3954) had a significantly higher prediction accuracy for test compounds than SM1, and also outperformed the T.E.S.T. consensus model (MAEtest = 0.4233). Subsequently, the toxicity of 252 true external FNFPAHs from Pesticide Properties Database (PPDB) was predicted by SM1, the prediction results showed that 94.84 % compounds were reliably predicted within the model's application domain (AD). We also applied the best CM2 to predict the untested 252 FNFPAHs. Furthermore, we provided a mechanistic analysis and explanation for pesticides ranked as top 10 most toxic FNFPAHs. In summary, all developed QSAR and consensus models can be used as efficient tools for predicting the acute toxicity of unknown FNFPAHs to Pimephales promelas, thus being important for the risk assessment and regulation of FNFPAHs contamination in aquatic environment.

Comparison of nitrate formation mechanisms from free amino acids and amines during ozonation: a computational study.

Nitrate as a potential surrogate parameter for abatement of micropollutants, oxidant exposure, and characterizing oxidant-reactive DON during ozonation has attracted extensive attention, however, understanding of its formation mechanisms is still limited. In this study, nitrate formation mechanisms from amino acids (AAs) and amines during ozonation were investigated by the DFT method. The results indicate that N-ozonation initially occurs to produce competitive nitroso- and N,N-dihydroxy intermediates, and the former is preferred for both AAs and primary amines. Then, oxime and nitroalkane are generated during further ozonation, which are the important last intermediate products for nitrate formation from the respective AAs and amines. Moreover, the ozonation of the above important intermediates is the nitrate yield-controlling step, where the relatively higher reactivity of the CN moiety in the oxime compared to the general Cα atom in the nitroalkane explains why the nitrate yields of most AAs are higher than those from general amines, and it is the larger number of released Cα- anions, which are the real reaction sites attacked by ozone, that leads to the higher nitrate yield for nitroalkane with an electron-withdrawing group bound to the Cα atom. The good relationship between nitrate yields and activation free energies of the rate-limiting step (ΔG≠rls) and nitrate yield-controlling step (ΔG≠nycs) for the respective AAs and amines verifies the reliability of the proposed mechanisms. Additionally, the bond dissociation energy of Cα-H in the nitroalkanes formed from amines was found to be a good parameter to evaluate the reactivity of the amines. The findings here are helpful for further understanding nitrate formation mechanisms and predicting nitrate precursors during ozonation.

Ecotoxicological QSAR modelling of the acute toxicity of fused and non-fused polycyclic aromatic hydrocarbons (FNFPAHs) against two aquatic organisms: Consensus modelling and comparison with ECOSAR.

Fused and non-fused polycyclic aromatic hydrocarbons (FNFPAHs) are a type of organic compounds widely occurring in the environment that pose a potential hazard to ecosystem and public health, and thus receive extensive attention from various regulatory agencies. Here, quantitative structure-activity relationship (QSAR) models were constructed to model the ecotoxicity of FNFPAHs against two aquatic species, Daphnia magna and Oncorhynchus mykiss. According to the stringent OECD guidelines, we used genetic algorithm (GA) plus multiple linear regression (MLR) approach to establish QSAR models of the two aquatic toxicity endpoints: D. magna (48 h LC50) and O. mykiss (96 h LC50). The models were established using simple 2D descriptors with explicit physicochemical significance and evaluated using various internal/external validation metrics. The results clearly show that both models are statistically robust (QLOO2 = 0.7834 for D. magna and QLOO2 = 0.8162 for O. mykiss), have good internal fitness (R2 = 0.8159 for D. magna and R2 = 0.8626 for O. mykiss and external predictive ability (D. magna: Rtest2 = 0.8259, QFn2 = 0.7640∼0.8140, CCCtest = 0.8972; O. mykiss:Rtest2 = 0.8077, QFn2 = 0.7615∼0.7722, CCCtest = 0.8910). To prove the predictive performance of the developed models, an additional comparison with the standard ECOSAR tool obviously shows that our models have lower RMSE values. Subsequently, we utilized the best models to predict the true external set compounds collected from the PPDB database to further fill the toxicity data gap. In addition, consensus models (CMs) that integrate all validated individual models (IMs) were more externally predictive than IMs, of which CM2 has the best prediction performance towards the two aquatic species. Overall, the models presented here could be used to evaluate unknown FNFPAHs inside the domain of applicability (AD), thus being very important for environmental risk assessment under current regulatory frameworks.

The dual role of DNA repair protein MGMT in cancer prevention and treatment.

Alkylating agents are genotoxic chemicals that can induce and treat various types of cancer. This occurs through covalent bonding with cellular macromolecules, in particular DNA, leading to the loss of functional integrity under the persistence of modifications upon replication. O6-alkylguanine (O6-AlkylG) adducts are proposed to be the most potent DNA lesions induced by alkylating agents. If not repaired correctly, these adducts can result, at the molecular level, in DNA point mutations, chromosome aberrations, recombination, crosslinking, and single- and double-strand breaks (SSB/DSBs). At the cellular level, these lesions can result in malignant transformation, senescence, or cell death. O6-methylguanine-DNA methyltransferase (MGMT) is a DNA repair protein capable of removing the alkyl groups from O6-AlkylG adducts in a damage reversal process that can prevent the adverse biological effects of DNA damage caused by guanine O6-alkylation. MGMT can thereby defend normal cells against tumor initiation, however it can also protect tumor cells against the beneficial effects of chemotherapy. Hence, MGMT can play an important role in both the prevention and treatment of cancer; thus, it can be considered as a double-edged sword. From a clinical perspective, MGMT is a therapeutic target, and it is important to explore the rational development of its clinical exploitation.

Environmental toxicity risk evaluation of nitroaromatic compounds: Machine learning driven binary/multiple classification and design of safe alternatives.

Nitroaromatic compounds (NACs) represent a significant source of organic pollutants in the environment. In this study, a well-rounded dataset containing 371 NACs with rat oral median lethal doses (LD50s) was developed. Based on the dataset, binary and multiple classification models were established. Seven machine learning algorithms were used to establish the prediction models in combination with six fingerprints. In the binary classification models, the overall predictive accuracy of 10-fold cross-validation for training set in the top ten models ranged from 0.823 to 0.874. In the multiple classification models, the combination of graph fingerprint and random forest (Graph-RF) yielded the best predictive effects with AUC values of 0.929 and 0.956 for the training set and the test set, respectively. Model prediction performance was further evaluated using the true external set comprising 1366 NACs, including 96.6% belonging to the applicability domain. Further, we determined the structural features influencing the acute oral toxicity based on information gain and substructure frequency analysis. Finally, we identified highly toxic compounds based on the structural alerts and successfully transformed a representative highly toxic compound into low-toxic alternatives via structural modification. Overall, the models constructed facilitate environmental risk assessment and the design of green and safe chemicals.

Identification of chlorinated products from tyrosine and tyrosyl dipeptides during chlorination: a computational study.

Chlorinated amino acids and peptides, as the model modified protein structures relevant to pathogen inactivation and an emerging class of disinfection byproducts (DBPs) with potential health risks to humans, have attracted much attention. However, due to a large variety of peptides (over 600) identified in source water and most of them featuring multiple reaction sites, it is a huge challenge to identify all the chlorinated amino acids and peptides. As a good complement to the experiment, quantum chemical computation can be used to uncover the chlorination sites and chlorinated products. In this study, frequently detected tyrosine (Tyr) and tyrosine-amide (Tyr-Am) as well as N-acetyl-tyrosine (NacTyr) were chosen as the model amino acid and model dipeptides, respectively. The results indicate that the kinetic reactivity order of reactive sites with estimated apparent rate constants (kobs-est, in M-1 s-1) is amino N (107-8) ≫ mono-chlorinated amino N (101-3) >/≈ phenol ortho-C (100-3) ≫ meta-C (10-3), and phenol ortho-C5 (102-3) > ortho-C3 (100-2) for dipeptides, while in thermodynamics, phenol C sites are more favorable than amino N sites. Moreover, due to the smaller differences of kobs-est values between the mono-chlorinated amino N and the phenol ortho-C sites in tyrosyl dipeptides compared to free Tyr, more kinds of C-chloro-tyrosyl dipeptides are likely to be generated. Additionally, a structure-kinetic reactivity relationship study reveals good correlations between lg kobs-est and NPA charges and BDEs of protons released from amino/hydroxyl groups in tyrosyl compounds rather than FED2 (HOMO). The results are helpful to further understand the reactivity of various reaction sites in peptides and identify chlorinated products from tyrosyl peptides during chlorination.