Use of van der Waals volume in structure-activity studies

Bidirectional selection of the functional properties and environmental friendliness of organophosphorus (OP) pesticide derivatives: Design, screening, and mechanism analysis

Organophosphorus pesticides (OPs) are widely used in agricultural production, but the resulting pollution and drug resistance have sparked widespread concern. Therefore, this paper built a model to design OP substitute molecules with high functionality and environmental friendliness, as well as conducted various human health and ecological environment evaluations, synthetic accessibility screening, and easy detection screening. The functionality of the two OP substitute molecules, DIM-100 and DIM-164, increased by 22.79 % and 22.18 %, respectively, and the environmental friendliness increased by 18.07 % and 24.02 %, respectively. The human health risk and ecological, environmental risks were significantly reduced. Both molecules are easy to synthesize, and their detection sensitivity is 9.85 % and 11.24 % higher than that of the target molecule, respectively. Furthermore, significant changes in the distribution of electrons and holes near the C8 and S1 atoms of the OP substitute molecule resulted in easier breakage of the C8-S1 bond, enhancing its photodegradation ability. The charge transfer ability between the atoms of the molecule (as increasing the electron-withdrawing group led to an increase in charge of the P atom) and the volume of the cholinesterase active pocket both affect the functionality of the DIM substitute molecule. That is, the volume of the cholinesterase active pocket of the bee is smaller than that of the brown planthopper and is more affected by the volume of the OP molecule. Furthermore, the mutual verification analysis of the bidirectional selectivity effect of OP substitute molecules between the BayesianRidge model and the 3D-QS(A² + ∀³)R model reveals that the overall charge transfer degree of DIM substitute molecules is the main reason for the increase in the bidirectional selectivity effect.

QSPR study on the polyacrylate-water partition coefficients of hydrophobic organic compounds

The partition coefficient is essential for the analysis of organic chemicals using solid-phase microextraction (SPME) techniques. In this study, a quantitative structure-property relationship (QSPR) model was developed with chemical descriptors for the prediction of the polyacrylate (PA)-water partition coefficient (K_PA-w). The major variables influencing K_PA-w in the QSPR model were CrippenlogP (crippen octanal-water partition coefficient), RNCG (relative negative charge-most negative charge/total negative charge), VE2_Dzv (average coefficient sum of the last eigenvector from the Barysz matrix/weighted by van der Waals volume), and ATSC4v (centred Broto-Moreau autocorrelation-lag 4/weighted by van der Waals volume). The relative determination coefficient (R²) and cross-validation coefficient (Q²) were 0.898 and 0.858, respectively, which implied that the model had excellent robustness. Mechanistic interpretation suggested that the factors affecting the partitioning process between PA and water are the hydrophobicity, relative negative charge, and van der Waals volume of a chemical. The results of this study provide a good tool for predicting the log K_PA-w values of diverse hydrophobic organic compounds (HOCs) within the applicability domain to reduce experimental costs and the time required for innovation.

Synthesis of novel substituted purine derivatives and identification of the cell death mechanism

Novel 9-(substituted amino/piperazinoethyl)adenines (4-12), 6-(substituted piperazino/amino)purines (15-27), 9-(p-toluenesulfonyl/cyclopentyl/ethoxycarbonylmethyl)-6-(substituted amino/piperazino)purines (28-34, 36, 37, 38-41) were synthesized and evaluated initially for their cytotoxic activities on liver Huh7, breast T47D and colon HCT116 carcinoma cells. N(6)-(4-Trifluoromethylphenyl)piperazine derivative (17) and its 9-(p-toluene-sulfonyl)/9-cyclopentyl analogues (28, 36) had promising cytotoxic activities. Compounds 17, 28 and 36 were further analysed for their cytotoxicity in a panel of a liver cancer cell lines. The compound 36 had better cytotoxic activities (IC50 ≤ 1 μM) than the nucleobase 5-FU and nucleosides fludarabine, cladribine, and pentostatine on Huh7 cells. Cytotoxicity induced by 36 was later identified as senescence associated cell death by SA-β-Gal assay.

Synthesis and antimicrobial evaluation of guanylsulfonamides

A series of guanylsulfonamides, 2-amino-9-[2-substituted-4-(4-substituted piperidin-1-sulfonyl)phenyl]-1,9-dihydropurin-6-ones, was synthesized by adopting reductive aminoformylation of 2-amino-5-nitro-6-[4-(piperidin-1-sulfonyl)phenylamino]-3H-pyrimidin- 4-one and subsequent intramolecular ring condensation as key steps. All the guanylsulfonamides were assayed for their in vitro antibacterial activities against Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, Staphylococcus aureus, and Streptococcus faecalis, and their antifungal activities against Aspergillus flavus, Aspergillus niger, and Candida albicans. Of the guanylsulfonamides, 13e and 13f displayed better antibacterial activities than that of Norfloxacin against the bacterial strains S. aureus and S. faecalis except 13f against S. faecalis, which exhibited the activity similar to that of Norfloxacin. Against the fungal strains A. flavus and A. niger, 13g and 13h showed similar activities to that of Griseoflavin-16 except 13h against A. niger, which displayed a profound drop in the activity compared to that of Griseoflavin-16. The remarkable inhibition of the growth of the bacterial and fungal strains makes these substances promising microbial agents.

Structure-activity relationships for non-congeneric structures. Application of substructural balance method for antiallergic activity

This paper presents a new research method of structure-activity relationships (SAR) based on the concept of substructural balance. By using antiallergic activity (PCA, rat, iv) of a non-congeneric set of 267 structures, the structural feature of active group is expressed in terms of substructural balance. Each structure was expressed with 100 new substructures and the number of each substructure in a molecule was counted. The substructural balance was expressed as their ratio. Structures were classified into three groups based on their potencies (ED50), active (44), median (33) and inactive (190) group. Using two substructural ratios, 80.53% of inactive and 57.58% of median structures were excluded from those that were active. Common features of active structures were shown as a zone indicating the optimal ranges of two substructural ratios. Two substructural ratios were determined out of 4950 substructural ratios, all possible combinations of 100 substructures (100C2), by selecting the greatest discriminatory power of inactive from active structures. The substructures used in this work include: the number of bonds comprising of the longest conjugate system, the number of skeletal atoms and the numbers of electron-donor pairs at certain distances in the molecule.

Difference of the liver and kidney in glycine conjugation of ortho-substituted benzoic acids

The relative importance of the liver and kidney for glycine conjugation of ortho-substituted benzoic acids was investigated. Glycine conjugation of ortho-substituted benzoic acids was investigated in mouse liver and kidney mitochondria. The extent of glycine conjugation of benzoic acids with the halogen group decreased in the order F > Cl > Br > I. The conjugation of salicylic acid with glycine took place in only the kidney. 2-Methoxybenzoic acid exhibited no activity in the liver and kidney. The difference in glycine conjugation of ortho-substituted benzoic acids was observed between liver and kidney. The kidney was more active in glycine conjugation of ortho-substituted acids than the liver. In addition, the relationship between glycine conjugation and the chemical structure of ortho-substituted acids was examined in the liver and kidney. The size of the substituent had a far greater influence over glycine conjugation in the liver and kidney. Glycine conjugation was also dependent on the substituent electronegativity. It may be important that the substrates undergoing glycine conjugation contain a flat region coplanar to the carboxylate group.

Prediction of the dermal penetration of polycyclic aromatic hydrocarbons (PAHs): a hierarchical QSAR approach

Attempts were made to develop hierarchical quantitative structure-activity relationship (QSAR) models for the dermal penetration of polycyclic aromatic hydrocarbons (PAHs) using four classes of theoretical structural parameters; viz., topostructural, topochemical, geometric, and quantum chemical descriptors; and physicochemical properties such as molecular weight (MW) and lipophilicity (log P--octanol/water). The results show that topostructural, topochemical, and geometric descriptors and molecular weight are equally effective in predicting the dermal penetration of PAHs. Quantum chemical parameters did not make any improvements in the predictive power of the QSAR models.

Predicting acute toxicity (LC50) of benzene derivatives using theoretical molecular descriptors: a hierarchical QSAR approach

Four classes of theoretical structural parameters, viz., topostructural, topochemical, geometrical and quantum chemical descriptors, have been used in the development of quantitative structure-activity relationship (QSAR) models for a set of sixty-nine benzene derivatives. None of the individual classes of parameters was very effective in predicting toxicity. A hierarchical approach was followed in using a combination of the four classes of indices in QSAR model development. The results show that the hierarchical QSAR approach using the algorithmically derived molecular descriptors can estimate the LC50 values of the benzene derivatives reasonably well.

Global structure-acute toxicity relationships for mice using structural parameter ratios: new approach to molecular design and screening

A method for a preliminary survey of the relationship between molecular structure and performance was described using 1506 random data of structure-acute toxicity for mice (intravenously dosed). The structural patterns of the weakest toxic structures (111) were extracted from the data and the patterns discriminated for 64.2% of the other structures (1395). As for the 826 structures of strongest toxicity, 78.3% were discriminated by these structural patterns. These results were obtained by using structural parameter ratios to describe the structural patterns and the exhaustive elimination process to select the best parameter ratio from many candidates. The results were summarized in the form of a chart which can be used for practical screening for the weakest toxic structures.

Pattern recognition study of QSAR substituent descriptors

Parameter values for 59 common substituents and 74 descriptors used in QSAR studies were compiled. This data matrix was analysed by a variety of multivariate techniques. Linear regression confirmed that lipophilicity can be factorized into two terms, one related to molecular bulk and the other to polarity. Principal component analysis (PCA) of parameters revealed 5 significant principal components and a grouping of lipophilic, steric and electronic parameters. The different loadings of parameters with 5 PCA were also explored. The classification of substituents by cluster analysis (CA) proved rather disappointing. In contrast, the SIMCA method classified substituents of increasing bulk into 5 groups of increasing polarity.