The molecular mechanism of P450-catalyzed amination of the pyrrolidine derivative of lidocaine: insights from multiscale simulations

• Published in: RSC advances 2021-08, Vol.11 (44), p.27674-2768
• Main Authors: Wang, Conger, Wu, Peng, Wang, Zhanfeng, Wang, Binju
• Format: Article
• Language: English
• Subjects: Chemical reactions; Chemical synthesis; Chemistry; Coupling (molecular); Cytochromes; Dehydration; Hydrogen bonds; Hydroxylation; Mathematical analysis; Molecular dynamics; Mutation; Nitrogen; Quantum mechanics; Simulation; Substrates; Transformations
• ISSN: 2046-2069; 2046-2069
• DOI: 10.1039/d1ra04564d

Nitrogen heterocycles are key and prevalent motifs in drugs. Evolved variants of cytochrome P450 BM3 (CYP102A1) from Bacillus megaterium employ high-valent oxo-iron( iv ) species to catalyze the synthesis of imidazolidine-4-ones via an intramolecular C-H amination. Herein, we use multi-scale simulations, including classical molecular dynamics (MD) simulations, quantum mechanical/molecular mechanical (QM/MM) calculations and QM calculations, to reveal the molecular mechanism of the intramolecular C-H amination of the pyrrolidine derivative of lidocaine bearing cyclic amino moieties catalyzed by the variant RP/FV/EV of P450 BM3 , which bears five mutations compared to wild type. Our calculations show that overall catalysis includes both the enzymatic transformation in P450 and non-enzymatic transformation in water solution. The enzymatic transformation involves the exclusive hydroxylation of the C-H bond of the pyrrolidine derivative of lidocaine, leading to the hydroxylated intermediate, during which the substrate radical would be bypassed. The following dehydration and C-N coupling reactions are found to be much favored in aqueous situation compared to that in the non-polar protein environment. The present findings expand our understanding of the P450-catalyzed C(sp 3 )-H amination reaction. Nitrogen heterocycles are key and prevalent motifs in drugs.