Molecular engineering and activity improvement of acetylcholinesterase inhibitors: Insights from 3D-QSAR, docking, and molecular dynamics simulation studies

Noncovalent binding of carbofuran to acetylcholinesterase from Homo sapiens, Danio rerio, Apis mellifera and Caenorhabditis elegans: Homology modelling, molecular docking and dynamics, and quantum biochemistry description

Although various regulatory agencies have banned or severely restricted the use of carbofuran (CAR), recent reports indicate the presence of CAR residues in both cultivated and wild areas. This pesticide is a potent inhibitor of acetylcholinesterase (AChE), which acts by preventing the hydrolysis of acetylcholine (ACh). Given the critical role of AChE::ACh in the proper functioning of the nervous system, we thought it appropriate to investigate the binding of CAR to AChEs from Homo sapiens, Danio rerio, Apis mellifera, and Caenorhabditis elegans using homology modelling, molecular docking, molecular dynamics, and quantum biochemistry. Molecular docking and dynamics results indicated peculiar structural behavior in each AChE::CAR system. Quantum biochemistry results showed similar affinities for all complexes, confirming the description of carbofuran as a broad-spectrum pesticide, and have a limited correlation with IC50 values. We found the following decreasing affinity order of AChE species: H. sapiens > A. mellifera > C. elegans > D. rerio. The computational results suggest that CAR occupies different pockets in the AChEs studied. In addition, our results showed that CAR binds to hsAChE and ceAChE in a very similar manner: it has high affinities for the same subsites in both species and forms hydrogen bonds with residues (hsTYR124 and ceTRP107) occupying homologous positions in the peripheral site. This suggests that this nematode is a potential model to evaluate the toxicity of carbamates, even though the sequence identity between them is only 41 %. Interestingly, we also observed that the catalytic histidines of drAChE and amAChE exhibited favorable contacts with carbofuran, suggesting that the non-covalent binding of carbofuran to these proteins may promote faster carbamylation rates than the binding modes to human and worm acetylcholinesterases. Our computational results provide a better understanding of the binding mechanisms in these complexes, as well as new insights into the mechanism of carbamylation.

Insights into the quantitative structure-activity relationship for ionic liquids: a bibliometric mapping analysis

Environmental protection and sustainability is the development goal that countries all over the world are pursuing. Ionic liquids (ILs), as a new type of green material, have a great application prospect. And the quantitative structure-activity relationship (QSAR) is significant for the research of ILs. To better understand the role played by QSAR in the research of ILs, 4139 literatures published in the WOS database from 2002 to 2022 were used for bibliometric analysis, and different types of knowledge maps were mapped to obtain the current status and trends of IL research applied QSAR. The distribution pattern of the literature output chronology, country, institution, author cooperation, and major source journals can be obtained through the research of the distribution of literature. Through core literature, dual-map overlays, and evolutionary path analysis, the research knowledge base was obtained mainly including ionic liquid toxicological properties research, environmental protection and sustainability, ionic liquid design, and mild steel corrosion inhibition; through the co-occurrence and evolution of keywords, the current research hotspots are basic properties of ILs, corrosion inhibition of mild steel, the effect of toxicity on the environment, QSAR modeling methods, solvent application of ILs, and drug design.

QSAR study of tetrahydropteridin derivatives as polo-like kinase 1(PLK1) Inhibitors with molecular docking and dynamics study

PLK1 is the key target for dealing with different cancer because it plays an important role in cell proliferation. According to the regulation of OECD, a QSAR model was developed from a dataset of 68 tetrahydropteridin derivatives. Three descriptors (maxHaaCH, ATSC7i, AATS7m) were considered for the development of the QSAR model. The reliability and predictability of the developed QSAR model were evaluated by various statistical parameters (r² = 0.8213, r²_ext = 0.8771 and CCC_ext = 0.9364). The maxHaaCH descriptor is positively correlated to pIC₅₀ whereas, the ATSC7i and AATS7m are negatively correlated with pIC₅₀. The QSAR model explains all the structural features and shows a good correlation with the activity. Based on molecular modelling techniques, five compounds (D1-D5) were designed. Molecular docking and dynamics studies of the most active compound were performed with PDB ID: 2RKU. The results of the present investigation may be employed to identify and develop effective inhibitors for the treatment of PLK1-related pathophysiological disorders.