Screening for low aquatic bioaccumulation. 1. Lipinski's 'Rule of 5' and molecular size

Optimized new Shengmai powder ameliorates myocardial fibrosis in rats with heart failure by inhibition of the MAPK signaling pathway

ETHNOPHARMACOLOGICAL RELEVANCE

Optimized New Shengmai Powder (ONSMP) is a traditional Chinese medicine (TCM) formula for heart failure treatment. MAPK signaling pathway is the key driver of myocardial fibrosis in heart failure. However, the mechanism of ONSMP on myocardial fibrosis and MAPK signaling pathway remains unclear.

AIM OF THE STUDY

To evaluate the effect of ONSMP against myocardial fibrosis in heart failure and the underlying mechanisms.

MATERIALS AND METHODS

Firstly, UHPLC-Q-Exactive-MS/MS was used to identify the active components in ONSMP. Secondly, a rat model of heart failure was established by ligating the left anterior descending branch of the coronary artery. After four weeks of intragastric administration of ONSMP, we used various classic tests, including echocardiography, exhaustive swimming, cardiopulmonary coefficient, heart failure markers, and cardiac pathological section, to assess the prescription's anti-myocardial fibrosis in heart failure properties. AGEs, Ang Ⅱ, VEGF, CTGF, and TGFβ levels in rat serum were quantified using ELISA. The positive expression of p-ERK1/2 and p-JNK1/2 of rat myocardium was determined immunohistochemical. The protein and mRNA levels of genes involved in the MAPK signaling pathway and myocardial fibrosis were measured using western blotting or real-time PCR.

RESULTS

The main components of ONSMP that regulate the MAPK signaling pathway are isorhamnetin, kaempferol, quercetin, and tanshinone ⅡA. ONSMP ameliorated cardiac function and exercise tolerance and reduced cardiopulmonary coefficient, heart failure marker levels, and myocardial fibrosis in the heart failure rats. In addition, ONSMP diminished the serum MAPK pathway activator levels, positive expression level of p-ERK1/2 and p-JNK1/2, protein and mRNA levels of components of the MAPK signaling pathway in the myocardial tissue of heart failure rat, indicating that it inhibits MAPK signaling pathway.

CONCLUSIONS

ONSMP delayed heart failure by inhibiting myocardial fibrosis via the MAPK signaling pathway.

Assessing the persistence, mobility and toxicity of emerging organic contaminants in Croatian karst springs used for drinking water supply

Emerging organic contaminants (EOCs) are a vast group of often (very)persistent, (very)mobile and toxic (PMT/vPvM) substances that are continuously released worldwide, posing environmental and human health risks. Research on occurrence and behavior of EOCs in karst is in its infancy, thus policy measures and legislative control of these compounds in groundwater are still lacking. The Dinaric karst aquifers are an essential source of drinking water for almost half of Croatia's territory. Intense karstification, complex heterogeneous characteristics, and high fracture-cavernous porosity result in rapid, far-reaching groundwater flow and large karst springs, but also high intrinsic vulnerability due to low contaminant attenuation. To prioritize future monitoring and establish appropriate thresholds for EOCs detected in Croatian karst drinking water resources, in silico tools based on quantitative structure-activity relationships were used in PBT (persistence, bioaccumulation, and toxicity) and PMT/vPvM analyzes, while toxicological assessment helped identify potential threats to human health. In 33 samples collected during two sampling campaigns in 2019 at 16 karst springs and one lake used for water supply, we detected 65 compounds (EOCs and some legacy chemicals), of which 7 were classified as potentially PBT or vPvB compounds (PFOS, PFHxS, PFHpA, PFOA, PFNA, boscalid, and azoxystrobin), while only 2 compounds were assessed as not PMT/vPvM. This finding underlines that most of detected EOCs potentially endanger karst (ground)water ecosystems and important drinking water sources in Croatia. Comparison of maximum concentrations with existing or derived drinking water guideline values revealed how 2 of 65 detected compounds represent a potential risk to human health at lifelong exposure (sulfadiazine and hydrochlorothiazide), while 5 chemicals warrant additional human health impacts studies and groundwater monitoring. Although most compounds do not individually pose a significant risk to human health at current environmental levels, their potential synergistic and long-term effects remain unknown.

An efficient new method of ytterbium(III) triflate catalysis approach to the synthesis of substituted pyrroles: DFT, ADMET, and molecular docking investigations

In this study, the one-pot synthetic methodology for the preparation of substituted pyrroles with diethyl acetylene-dicarboxylate is reported for the various pyrrole derivatives via the Trifimow synthesis process from oximes. This method also offers the literature as a cyclization pathway using a ytterbium triflate catalyst. Another importance of this study is the use of pyrrole derivatives in pharmaceuticals, biological processes, and agrochemicals. From this point of view, the development of a new catalyst in synthetic organic chemistry and the difference in the method is also important. The syntheses of the target substituted pyrroles are accomplished in high yields. Also, all synthesized structures were confirmed by 1H NMR, 13C NMR, and IR spectra. The DFT computations were leveraged for structural and spectroscopic validation of the compounds. Then, FMO and NBO analyses were subsequently employed to elucidate the reactivity characteristics and intramolecular interactions within these compounds. Also, ADMET indices were ascertained to assess potential pharmacokinetic properties, drug-like qualities, and possible adverse effects of these compounds. Last, optimized molecules were analyzed by molecular docking methods against crystal structures of Bovine Serum Albumin and Leukemia Inhibitory Factor, and their binding affinities, interaction details, and inhibition constants were determined.

Molecular recognition of bio-active triterpenoids from Swertia chirayita towards hepatitis Delta antigen: a mechanism through docking, dynamics simulation, Gibbs free energy landscape

Medicinal plants the underpinning of indigenous herbal serve, are the possible source of key compounds for the development of new drugs. Hepatitis D, one of the most widespread infectious diseases associated with global public health issues. Therefore, we aim to screen natural compounds to find out potent inhibitor towards hepatitis delta antigen. Through ADMET investigation, we have screened twenty phytochemicals for this study. Additionally, using molecular docking, these phytochemicals were docked with the HDV protease which signifies the phytochemicals beta-amyrin, chiratenol, episwertenol and swertanone have a significant capability to bind with hepatitis D virus protein. The docking study was further accompanied by analyzes RMSD, RMSF, Rg, SASA, Hbond number, and principal component analysis through 100 ns MD simulations. Based on our principal component analysis, beta-amyrin, chiratenol, episwertenol and swertanone phytochemicals can be a potential drug candidates for inhibition of hepatitis D. The above observation is also supported by our Gibbs free energy landscape study. The potential therapeutic characteristics of the phytochemicals against hepatitis D inhibition offer additional support for the in vitro and in vivo studies in future.

Synthesis, Characterization and Screening of Some Novel 2-Methyl-N'- [(Z)-Substituted-Phenyl ethylidene] Imidazo [1, 2-a] Pyridine-3-Carbohy drazide Derivatives as DPP-IV Inhibitors for the Treatment of Type 2 Diabetes Mellitus

Background:

One of the leading global metabolic diseases marked by insulin resistance and chronic hyperglycemia is type 2 diabetes mellitus (T2DM). Since the last decade, DPP-4 enzyme inhibition has proven to be a successful, safe, and well-established therapy for the treatment of T2DM.

Objective:

The present work reports the synthesis, characterization, and screening of some novel 2- methyl-N'-[(Z)-substituted-phenyl ethylidene] imidazo [1, 2-a] pyridine-3-carbohydrazide derivatives as DPP-IV inhibitors for the treatment of T2DM.

Methods:

The molecular docking was performed to study these derivatives' binding mode in the enzyme's allosteric site. All the synthesized compounds were subjected for DPP-IV enzyme assay and in vivo antihyperglycemic activity in STZ-induced diabetic rats.

Results:

The synthesized derivatives exhibited potent antidiabetic activity as compared to the standard drug Sitagliptin. Out of sixteen compounds, A1, A4, B4, C2, C3, and D4 have shown promising antidiabetic activity against the DPP-IV enzyme. The most promising compound, C2, showed a percentage inhibition of 72.02±0.27 at 50 μM concentration. On the 21st-day, compound C2 showed a significant reduction in serum blood glucose level, i.e., 156.16±4.87 mg/dL, then diabetic control, which was 280.00±13.29 mg/dL whereas, standard Sitagliptin showed 133.50±11.80 mg/dL. In the in vivo antihyperglycemic activity, the compounds have exhibited good hypoglycemic potential in fasting blood glucose in the T2DM animal model. All the docked molecules have exhibited perfect binding affinity towards the active pocket of the enzyme. The synthesized derivatives were screened through Lipinski's rule of five for better optimization, and fortunately, none of them violated the rule.

Conclusion:

The above results indicate that compound C2 is a relatively active and selective hit molecule that can be structurally modified to enhance the DPP-IV inhibitor's potency and overall pharmacological profile. From the present work, it has been concluded that substituted pyridine-3-carbohydrazide derivatives possess excellent DPP-IV inhibitory potential and can be better optimized further by generating more in vivo, in vitro models.

Novel pyrimidine-benzimidazole hybrids with antibacterial and antifungal properties and potential inhibition of SARS-CoV-2 main protease and spike glycoprotein

Objective

The study aimed to synthesize and characterize pyrimidine-linked benzimidazole hybrids, define their antimicrobial and antifungal activities in vitro, and determine their ability to inhibit the main protease and spike glycoprotein of SARS-CoV-2.

Methods

The ability of the synthesized compounds to inhibit the main protease and spike glycoprotein inhibitory of SARS-CoV-2 was investigated by assessing their mode of binding to the allosteric site of the enzyme using molecular docking. The structures of pyrimidine-linked benzimidazole derivatives synthesized with microwave assistance were confirmed by spectral analysis. Antibacterial and antifungal activities were determined by broth dilution.

Results

Gram-negative bateria (Escherichia coli and Pseudomonas aeruginosa) were more sensitive than gram-positive bateria (Staphylococcus aureus and Streptococcus pyogenes) to the derivatives. Candida albicans was sensitive to the derivatives at a minimal inhibitory concentration (MIC) of 250 μg/mL. The novel derivatives had better binding affinity (kcal/mol) than nelfinavir, lopinavir, ivermectin, remdesivir, and favipiravir, which are under investigation as treatment for SARS-CoV-2 infection. Compounds 2c, 2e, and 2g formed four hydrogen bonds with the active cavity of the main protease. Many derivatives had good binding affinity for the RBD of the of SARS-CoV-2 spike glycoprotein with the formation of up to four hydrogen bonds.

Conclusion

We synthesized novel pyrimidine-linked benzi-midazole derivatives that were potent antimicrobial agents with ability to inhibit the SARS-CoV-2 spike glycoprotein. Understanding the pharmacophore features of the main protease and spike glycoprotein offers much scope for the development of more potent agents. We plan to optimize the properties of the derivatives using models in vivo and in vitro so that they will serve as more effective therapeutic options against bacterial and SARS-CoV-2 infections.

Exploring the Antihyperglycemic Chemical Composition and Mechanisms of Tea Using Molecular Docking

Tea, a widely consumed beverage, has long been utilized for promoting human health with a close correlation to hyperglycemia. The Tea Metabolome Database (TMDB), the most complete and comprehensive curated collection of tea compounds data containing 1271 identified small molecule compounds from the tea plant (Camellia sinensis), was established previously by our research team. More recently, our studies have found that various tea types possess an antihyperglycemic effect in mice. However, the bioactive ingredients from tea have potential antihyperglycemic activity and their underlying molecular mechanisms remain unclear. In this study, we used a molecular docking approach to investigate the potential interactions between a selected 747 constituents contained in tea and 11 key protein targets of clinical antihyperglycemic drugs. According to our results, the main antihyperglycemic targets of tea composition were consistent with those of the drug rosiglitazone. The screening results showed that GCG, ECG3'Me, TMDB-01443, and CG had great target binding capacity. The results indicated that these chemicals of tea might affect hyperglycemia by acting on protein targets of rosiglitazone.

QSPR models for bioconcentration factor (BCF): are they able to predict data of industrial interest?

The bioconcentration factor (BCF), a key parameter required by the REACH regulation, estimates the tendency for a xenobiotic to concentrate inside living organisms. In silico methods can be valid alternatives to costly data measurements. However, in the industrial context, these theoretical approaches may fail to predict BCF with reasonable accuracy. We analyzed whether models built on public data only have adequate performances when challenged to predict industrial compounds. A new set of 1129 compounds has been collected by merging publicly available datasets. Generative Topographic Mapping was employed to compare this chemical space with a set of new compounds issued from the industry. Some new chemotypes absent in the training set (such as siloxanes) have been detected. A new BCF model has been built using ISIDA (In SIlico design and Data Analysis) fragment descriptors, support vector regression and random forest machine-learning methods. It has been externally validated on: (i) collected data from the literature and (ii) industrial data. The latter also served as benchmark for the freely available tools VEGA, EPISuite, TEST, OPERA. New model performs (RMSE of 0.58 log BCF units) comparably to existing ones but benefits of an extended applicability, covering the industrial set chemical space (78% data coverage).

PBT assessment under REACH: Screening for low aquatic bioaccumulation with QSAR classifications based on physicochemical properties to replace BCF in vivo testing on fish

Aquatic bioconcentration factors (BCFs) are critical in PBT (persistent, bioaccumulative, toxic) and risk assessment of chemicals. High costs and use of more than 100 fish per standard BCF study (OECD 305) call for alternative methods to replace as much in vivo testing as possible. The BCF waiving scheme is a screening tool combining QSAR classifications based on physicochemical properties related to the distribution (hydrophobicity, ionisation), persistence (biodegradability, hydrolysis), solubility and volatility (Henry's law constant) of substances in water bodies and aquatic biota to predict substances with low aquatic bioaccumulation (nonB, BCF<2000). The BCF waiving scheme was developed with a dataset of reliable BCFs for 998 compounds and externally validated with another 181 substances. It performs with 100% sensitivity (no false negatives), >50% efficacy (waiving potential), and complies with the OECD principles for valid QSARs. The chemical applicability domain of the BCF waiving scheme is given by the structures of the training set, with some compound classes explicitly excluded like organometallics, poly- and perfluorinated compounds, aromatic triphenylphosphates, surfactants. The prediction confidence of the BCF waiving scheme is based on applicability domain compliance, consensus modelling, and the structural similarity with known nonB and B/vB substances. Compounds classified as nonB by the BCF waiving scheme are candidates for waiving of BCF in vivo testing on fish due to low concern with regard to the B criterion. The BCF waiving scheme supports the 3Rs with a possible reduction of >50% of BCF in vivo testing on fish. If the target chemical is outside the applicability domain of the BCF waiving scheme or not classified as nonB, further assessments with in silico, in vitro or in vivo methods are necessary to either confirm or reject bioaccumulative behaviour.

Can solid-phase microextraction replace solvent extraction for water analysis in fish bioconcentration studies with highly hydrophobic organic chemicals?

With the aim to refine water analysis in fish bioconcentration studies, automated solid-phase microextraction (SPME) was used as an alternative approach to conventional solvent extraction (liquid-liquid extraction [LLE]) for the extraction of 3 hydrophobic organic chemicals (HOCs; log K_OW 5.5-7.8) from flow-through studies with rainbow trout (Oncorhynchus mykiss). The results showed that total concentrations extracted by SPME combined with internal standards and LLE are equal. The results further verify the possibility of simultaneous extraction of total and freely dissolved HOC concentrations by SPME. Freely dissolved concentrations allow the assessment of sorption and bioavailability of HOCs in bioconcentration studies and their potential impact on resulting bioconcentration factors (BCFs). Reduction in freely dissolved water concentrations can result in an underestimation of BCFs if they are calculated based on total water concentrations. For polychlorinated biphenyl (PCB) 153, a significant increase in BCF value was observed when freely dissolved concentrations were taken into account. However, log BCF values calculated based on freely dissolved concentrations did not correlate linearly with log K_OW values above 5 to 6. This pointed to further influences besides a reduction in freely dissolved water concentrations by sorption to organic matter. The results can aid in assessment of the factors that influence bioconcentration systems and also give important information regarding the possible replacement of LLE by SPME for water analysis of highly HOCs in fish bioconcentration studies. Environ Toxicol Chem 2017;36:2887-2894. © 2017 The Authors. Environmental Toxicology and Chemistry Published by Wiley Periodicals, Inc. on behalf of SETAC.

A tiered assessment strategy for more effective evaluation of bioaccumulation of chemicals in fish

There is currently limited guidance available for regulators and risk assessors on how to use data from non-guideline methods when assessing the bioaccumulation potential of a chemical. Furthermore, bioaccumulation assessments can be more subjective than they need to be due to the lack of a guidance framework on how to use/include the range of information that may be available for a substance. Under some circumstances, in silico, in vitro and/or in vivo non-test guideline data may be sufficient to classify whether a substance is bioaccumulative without the need for further animal testing. Classifying the bioaccumulative potential of a substance is especially difficult when the bioconcentration factor (BCF) is close to the threshold for defining it as bioaccumulative/very bioaccumulative (B/vB), and a more structured process is required to reduce uncertainty in the BCF estimates. In these situations, in silico and in vitro data can, and should, be used to provide greater confidence in classifying these substances. To aid future evaluations of bioaccumulation data, a proposed tiered assessment strategy is presented incorporating all available data on the bioaccumulative properties of a substance. In addition, a revised scheme is recommended for improving the classification of the bioaccumulative potential of a substance.

Classifying bio-concentration factor with random forest algorithm, influence of the bio-accumulative vs. non-bio-accumulative compound ratio to modelling result, and applicability domain for random forest model

In environmental risk assessment, the bio-concentration factor (BCF) is a widely used parameter in the estimation of the bio-accumulation potential of chemicals. BCF data often have an uneven distribution of classes (bio-accumulative vs. non-bio-accumulative), which could severely bias the classification results towards the prevailing class. The present study focuses on the influence of uneven distribution of the classes in training phase of Random Forest (RF) classification models. Three different training set designs were used and descriptors selected to the models based on the occurrence frequency in RF trees and considering the mechanistic aspects they reflect. Models were compared and their classification performance was analysed, indicating good predictive characteristics (sensitivity = 0.90 and specificity = 0.83) for the balanced set; also imbalanced sets have their strengths in certain application scenarios. The confidence of classifications was assessed with a new schema for the applicability domain that makes use of the RF proximity matrix by analysing the similarity between the predicted compound and the training set of the model. All developed models were made available in the transparent, accessible and reproducible way in QsarDB repository (http://dx.doi.org/10.15152/QDB.116).

Screening for PBT chemicals among the "existing" and "new" chemicals of the EU

Under the European chemicals legislation, REACH, industrial chemicals that are imported or manufactured at more than 10 t/yr need to be evaluated with respect to their persistence (P), bioaccumulation potential (B), and toxicity (T). This assessment has to be conducted for several 10,000 of chemicals but, at the same time, empirical data on degradability, bioaccumulation potential and toxicity of industrial chemicals are still scarce. Therefore, the identification of PBT chemicals among all chemicals on the market remains a challenge. We present a PBT screening of approximately 95,000 chemicals based on a comparison of estimated P, B, and T properties of each chemical with the P, B, and T thresholds defined under REACH. We also apply this screening procedure to a set of 2576 high production volume chemicals and a set of 2781 chemicals from the EU's former list of "new chemicals" (ELINCS). In the set of 95,000 chemicals, the fraction of potential PBT chemicals is around 3%, but in the ELINCS chemicals it reaches 5%. We identify the most common structural elements among the potential PBT chemicals. Analysis of the P, B, and T data for all chemicals considered here shows that the uncertainty in persistence data contributes most to the uncertainty in the number of potential PBT chemicals.

Screening for low aquatic bioaccumulation (2): physico-chemical constraints

Physico-chemical properties related to the bioavailability of xenobiotics in aquatic environments have been tested for their ability to identify chemicals with low bioconcentration potential. Cut-offs in lipophilicity (log K(OW) < 3 or > 10), solubility and volatility (log Henry constant <-11 [atm (mol L(-1))(-1)]), degradability (ready biodegradability, hydrolysis) and ionisation (>5% ionisation at pH 7) have been adopted and combined into a decision tree based on 382 industrial chemicals. The five-parameter classification scheme was externally validated with 49 pesticides and successfully confirmed with 83 bioaccumulative compounds. The applicability domain of the model has been described in terms of chemical classes (excluding polybrominated compounds (>4 Br), organometallics, compounds with perfluorinated fragments, substances with an acyclic alkyl moiety (chain length > C7) and thiols) and ranges of physico-chemical properties. The present tool allows to securely de-prioritize more than 50% chemicals of low concern with regard to the B criterion (BCF < 2000). Bioassays with compounds with these physico-chemical constraints may be waived because testing may be technically not possible and does not appear scientifically necessary in persistent, bioaccumulative, toxic (PBT) substances and risk assessments.