Theoretical QSAR modelling and molecular docking studies of some 4-hydroxyphenylpyruvate dioxygenase (HPPD) enzyme inhibitors potentially used as herbicides

Uncovering the toxicity mechanisms of a series of carboxylic acids in liver cells through computational and experimental approaches

Hepatotoxicity poses a significant concern in drug design due to the potential liver damage that can be caused by new drugs. Among common manifestations of hepatotoxic damage is lipid accumulation in hepatic tissue, resulting in liver steatosis or phospholipidosis. Carboxylic derivatives are prone to interfere with fatty acid metabolism and cause lipid accumulation in hepatocytes. This study investigates the toxic behaviour of 24 structurally related carboxylic acids in hepatocytes, specifically their ability to cause accumulation of fatty acids and phospholipids. Using high-content screening (HCS) assays, we identified two distinct lipid accumulation patterns. Subsequently, we developed structure-activity relationship (SAR) and quantitative structure-activity relationship (QSAR) models to determine relevant molecular substructures and descriptors contributing to these adverse effects. Additionally, we calculated physicochemical properties associated with lipid accumulation in hepatocytes and examined their correlation with our chemical structure characteristics. To assess the applicability of our findings to a wide range of chemical compounds, we employed two external datasets to evaluate the distribution of our QSAR descriptors. Our study highlights the significance of subtle molecular structural variations in triggering hepatotoxicity, such as the presence of nitrogen or the specific arrangement of substitutions within the carbon chain. By employing our comprehensive approach, we pinpointed specific molecules and elucidated their mechanisms of toxicity, thus offering valuable insights to guide future toxicology investigations.

Design, synthesis and herbicidal activity of novel cyclohexanedione derivations containing pyrazole and pyridine groups as potential HPPD inhibitors

4-Hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27; HPPD) is one of the important target enzymes in the development of herbicides. To discover novel HPPD inhibitors with unique molecular, 39 cyclohexanedione derivations containing pyrazole and pyridine groups were designed and synthesized. The preliminary herbicidal activity test results showed that some compounds had obvious inhibitory effects on monocotyledon and dicotyledonous weeds. The herbicidal spectrums of the highly active compounds were further determined, and the compound G31 exhibited the best inhibitory rate over 90% against Plantago depressa Willd and Capsella bursa-pastoris at the dosages of 75.0 and 37.5 g ai/ha, which is comparable to the control herbicide mesotrione. Moreover, compound G31 showed excellent crop safety, with less than or equal to 10% injury rates to corn, sorghum, soybean and cotton at a dosage of 225 g ai/ha. Molecular docking and molecular dynamics simulation analysis revealed that the compound G31 could stably bind to Arabidopsis thaliana HPPD (AtHPPD). This study indicated that the compound G31 could be used as a lead molecular structure for the development of novel HPPD inhibitors, which provided an idea for the design of new herbicides with unique molecular scaffold.

Application of QSAR models for acute toxicity of tetrazole compounds administrated orally and intraperitoneally in rat and mouse

Tetrazoles and their derivatives possess various biological activities, such as antibacterial, anti-fungal, and other activities. However, these compounds may induce specific cumulative and toxic effects in living organisms. Therefore, quantitative structure-activity relationship (QSAR) models were constructed to study the acute oral toxicity of tetrazoles in rats and mice. The toxicity data of 111 tetrazole compounds were collected using the ChemIDplus, ChEMBL and ECHA databases as response variables, while the PaDEL-descriptor generated the 2D descriptors as independent variables. The models were developed and validated following the OECD guidelines by the DTC-QSAR tool. Three QSAR models were successfully established for the oral routes of rat and mouse and the intraperitoneal route of mouse, respectively. The scatter plots showed high consistency between the training and test data sets. All the models successfully met the external and internal validation criteria. Most of the descriptors kept in the final models exhibited positive correlations with toxicity, whereas only 6 descriptors exhibited negative associations. Several chemicals were identified as response or structural outliers, based on the standardized residuals and leverage values. In conclusion, the findings of this investigation demonstrate that the proposed QSAR models hold promise in forecasting the acute toxicity of recently developed or synthesized tetrazole compounds, thereby mitigating potential risks to human health and the environment.

Unsupervised machine learning, QSAR modelling and web tool development for streamlining the lead identification process of antimalarial flavonoids

Identification of lead compounds with the traditional laboratory approach is expensive and time-consuming. Nowadays, in silico techniques have emerged as a promising approach for lead identification. In this study, we aim to develop robust and predictive 2D-QSAR models to identify lead flavonoids by predicting the IC₅₀ against Plasmodium falciparum. We applied machine learning algorithms (Principal component analysis followed by K-means clustering) and Pearson correlation analysis to select 9 molecular descriptors (MDs) for model building. We selected and validated the three best QSAR models after execution of multiple linear regression (MLR) 100 times with different combinations of MDs. The developed models have fulfilled the five principles for QSAR models as specified by the Organization for Economic Co-operation and Development. The outcome of the study is a reliable and sustainable in silico method of IC₅₀ (Mean ± SD) prediction that will positively impact the antimalarial drug development process by reducing the money and time required to identify potential antimalarial lead compounds from the class of flavonoids. We also developed a web tool (JazQSAR, https://etflin.com/news/4) to offer an easily accessible platform for the developed QSAR models.

Based on the Virtual Screening of Multiple Pharmacophores, Docking and Molecular Dynamics Simulation Approaches toward the Discovery of Novel HPPD Inhibitors

4-Hydroxyphenylpyruvate dioxygenase (HPPD) is an iron-dependent non-heme oxygenase involved in the catabolic pathway of tyrosine, which is an important enzyme in the transformation of 4-hydroxyphenylpyruvic acid to homogentisic acid, and thus being considered as herbicide target. Within this study, a set of multiple structure-based pharmacophore models for HPPD inhibitors were developed. The ZINC and natural product database were virtually screened, and 29 compounds were obtained. The binding mode of HPPD and its inhibitors obtained through molecular docking study showed that the residues of Phe424, Phe381, His308, His226, Gln307 and Glu394 were crucial for activity. Molecular-mechanics-generalized born surface area (MM/GBSA) results showed that the coulomb force, lipophilic and van der Waals (vdW) interactions made major contributions to the binding affinity. These efforts will greatly contribute to design novel and effective HPPD inhibitory herbicides.