title: Theoretical investigation on reaction of sulbactam with wild-type SHV-1 β-lactamase: acylation, tautomerization, and deacylation.
abstract: Molecular dynamics (MD) simulation and quantum mechanical (QM) calculations were used to investigate the reaction mechanism of sulbactam with class A wild-type SHV-1 β-lactamase including acylation, tautomerization, and deacylation. Five different sulbactam-enzyme configurations were investigated by MD simulations. In the acylation step, we found that Glu166 cannot activate Ser70 directly for attacking on the carbonyl carbon, and Lys73 would participate in the reaction acting as a relay. Additionally, we found that sulbactam carboxyl can also act as a general base. QM calculations were performed on the formation mechanism of linear intermediates. We suggest that both imine and trans-enamine intermediates can be obtained in the opening of a five-membered thiazolidine ring. By MD simulation, we found that imine intermediate can exist in two conformations, which can generate subsequent trans- and cis-enamine intermediates, respectively. The QM calculations revealed that trans-enamine intermediate is much more stable than other intermediates. The deacylation mechanism of three linear intermediates (imine, trans-enamine, cis-enamine) was investigated separately. It is remarkably noted that, in cis-enamine intermediate, Glu166 cannot activate water for attacking on the carbonyl carbon directly. This leads to a decreasing of the deacylation rate of cis-enamine. These findings will be potentially useful in the development of new inhibitors.
authors.affiliation: The Department of Chemistry, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan.
authors.forename: Rui
authors.initials: R
authors.lastname: Li
authors.forename: Jun-Min
authors.initials: JM
authors.lastname: Liao
authors.forename: Chi-Ruei
authors.initials: CR
authors.lastname: Gu
authors.forename: Yeng-Tseng
authors.initials: YT
authors.lastname: Wang
authors.forename: Cheng-Lung
authors.initials: CL
authors.lastname: Chen
mesh_terms: D000215:Acylation; D020134:Catalytic Domain; D055808:Drug Discovery; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011789:Quantum Theory; D013237:Stereoisomerism; D013407:Sulbactam / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D065093:beta-Lactamase Inhibitors; D001618:beta-Lactamases / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D004791:Enzyme Inhibitors; D065093:beta-Lactamase Inhibitors; C054882:beta-lactamase PIT-2; D001618:beta-Lactamases; D013407:Sulbactam