Boron containing compounds (BCCs) aroused increasing interest in the scientific community due to their wide application as drugs in various fields. In order to design new compounds hopefully endowed with pharmacological activity and also investigate their conformational behavior, the support of computational studies is crucial. Nevertheless, the suitable molecular mechanics parameterization and the force fields needed to perform these simulations are not completely available for this class of molecules. In this paper, Amber force field parameters for phenyl-, benzyl-, benzylamino-, and methylamino-boronates, a group of boron-containing compounds involved in different branches of the medicinal chemistry, were created. The robustness of the obtained data was confirmed through molecular dynamics simulations on ligand/β-lactamases covalent complexes. The ligand torsional angles, populated over the trajectory frames, were confirmed by values found in the ligand geometries, located through optimizations at the DFT/B3LYP/6-31g(d) level, using water as a solvent. In summary, this study successfully provided a library of parameters, opening the possibility to perform molecular dynamics simulations of this class of boron-containing compounds.

Chiacchio, M., Legnani, L., Fassi, E., Roda, G., Grazioso, G. (2023). Development of AMBER parameters for molecular simulations 2 of selected boron-based covalent ligands. MOLECULES, 28(6) [10.3390/molecules28062866].

Development of AMBER parameters for molecular simulations 2 of selected boron-based covalent ligands

Legnani L.;
2023

Abstract

Boron containing compounds (BCCs) aroused increasing interest in the scientific community due to their wide application as drugs in various fields. In order to design new compounds hopefully endowed with pharmacological activity and also investigate their conformational behavior, the support of computational studies is crucial. Nevertheless, the suitable molecular mechanics parameterization and the force fields needed to perform these simulations are not completely available for this class of molecules. In this paper, Amber force field parameters for phenyl-, benzyl-, benzylamino-, and methylamino-boronates, a group of boron-containing compounds involved in different branches of the medicinal chemistry, were created. The robustness of the obtained data was confirmed through molecular dynamics simulations on ligand/β-lactamases covalent complexes. The ligand torsional angles, populated over the trajectory frames, were confirmed by values found in the ligand geometries, located through optimizations at the DFT/B3LYP/6-31g(d) level, using water as a solvent. In summary, this study successfully provided a library of parameters, opening the possibility to perform molecular dynamics simulations of this class of boron-containing compounds.
Articolo in rivista - Articolo scientifico
amber; boron; covalent ligand; force field; MD simulations; paramfit; β-lactamases;
English
22-mar-2023
2023
28
6
2866
none
Chiacchio, M., Legnani, L., Fassi, E., Roda, G., Grazioso, G. (2023). Development of AMBER parameters for molecular simulations 2 of selected boron-based covalent ligands. MOLECULES, 28(6) [10.3390/molecules28062866].
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/406295
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