Molecular basis of two pyrimidine-sulfonylurea herbicides: from supramolecular arrangement to acetolactate synthase inhibition

• Published in: Journal of molecular modeling 2023-08, Vol.29 (8), p.241-241, Article 241
• Main Authors: Aguiar, Antônio S.N., Costa, Rogério F., Borges, Leonardo L., Dias, Lucas D., Camargo, Ademir J., Napolitano, Hamilton B.
• Format: Article
• Language: English
• Subjects: Acetolactate Synthase - chemistry; Acetolactate Synthase - metabolism; Atomic properties; Binding sites; Characterization and Evaluation of Materials; Chemistry; Chemistry and Materials Science; Computer Appl. in Life Sciences; Computer Applications in Chemistry; Density functional theory; Empirical analysis; Functional groups; Genetic algorithms; Herbicides; Herbicides - chemistry; Herbicides - pharmacology; IX Symposium on Electronic Structure and Molecular Dynamics – IX SeedMol; Models, Molecular; Molecular docking; Molecular Docking Simulation; Molecular Medicine; Molecular orbitals; Nitrogen dioxide; Original Paper; Pyrimidines; Sulfonylurea Compounds - chemistry; Sulfonylurea Compounds - pharmacology; Theoretical and Computational Chemistry
• ISSN: 1610-2940; 0948-5023
• DOI: 10.1007/s00894-023-05629-x

Context The design and synthesis of safe and highly active sulfonylurea herbicides is still a challenge. Therefore, following some principles of structure-activity relationship (SAR) of sulfonylurea herbicides, this work focuses on evaluating two sulfonylurea derivatives bearing electron-withdrawing substituents, namely, –(CO)OCH 3 and –NO 2 on the aryl group, on herbicidal activity. To understand the effects caused by the substituent groups, the molecular and electronic structures of the sulfonylureas were evaluated by density functional theory. Likewise, the crystalline supramolecular arrangements of both compounds were analyzed by Hirshfeld surface, QTAIM, and NBO, with the aim of verifying changes in intermolecular interactions caused by substituent groups. Finally, through a toxicophoric analysis, we were able to predict the interacting groups in their biological target, acetolactate synthase, and verify the interactions with the binding site. Methods All theoretical calculations were conducted using the highly parameterized empirical exchange-correlation functional M06-2X accompanied by the diffuse and polarized basis set 6-311++G(d,p). The atomic coordinates were obtained directly from the crystalline structures, and from the energies of the frontier molecular orbitals (HOMO and LUMO), chemical descriptors were obtained that indicated the influence of the functional groups in the sulfonylureas on the reactivity of the molecules. The intermolecular interactions in the crystals were analyzed using the Hirshfeld, QTAIM, and NBO surfaces. Toxicophoric modeling was performed by the PharmaGist webserver and molecular docking calculations were performed by the GOLD 2022.1.0 software package so that the ligand was fitted to the binding site in a 10 Å sphere. For this, genetic algorithm parameters were used using the ChemPLP scoring function for docking and ASP for redocking.