ABSTRACT
Class A carbapenemases are a major threat to the potency of carbapenem antibiotics. A widespread carbapenemase, KPC-2, is not easily inhibited by β-lactamase inhibitors (i.e., clavulanic acid, sulbactam, and tazobactam). To explore different mechanisms of inhibition of KPC-2, we determined the crystal structures of KPC-2 with two β-lactamase inhibitors that follow different inactivation pathways and kinetics. The first complex is that of a small boronic acid compound, 3-nitrophenyl boronic acid (3-NPBA), bound to KPC-2 with 1.62-Å resolution. 3-NPBA demonstrated a
K
m
value of 1.0 ± 0.1 μM (mean ± standard error) for KPC-2 and blocks the active site by making a reversible covalent interaction with the catalytic S70 residue. The two boron hydroxyl atoms of 3-NPBA are positioned in the oxyanion hole and the deacylation water pocket, respectively. In addition, the aromatic ring of 3-NPBA provides an edge-to-face interaction with W105 in the active site. The structure of KPC-2 with the penam sulfone PSR-3-226 was determined at 1.26-Å resolution. PSR-3-226 displayed a
K
m
value of 3.8 ± 0.4 μM for KPC-2, and the inactivation rate constant (
k
inact
) was 0.034 ± 0.003 s
−1
. When covalently bound to S70, PSR-3-226 forms a
trans
-enamine intermediate in the KPC-2 active site. The predominant active site interactions are generated via the carbonyl oxygen, which resides in the oxyanion hole, and the carboxyl moiety of PSR-3-226, which interacts with N132, N170, and E166. 3-NPBA and PSR-3-226 are the first β-lactamase inhibitors to be trapped as an acyl-enzyme complex with KPC-2. The structural and inhibitory insights gained here could aid in the design of potent KPC-2 inhibitors.
摘要
A 类碳青霉烯酶是碳青霉烯类抗生素效力的主要威胁。一种广泛存在的碳青霉烯酶 KPC-2 不易被β-内酰胺酶抑制剂(即克拉维酸、舒巴坦和他唑巴坦)抑制。为了探索 KPC-2 的不同抑制机制,我们测定了 KPC-2 与两种β-内酰胺酶抑制剂的晶体结构,这两种抑制剂遵循不同的失活途径和动力学。第一个复合物是一种小型硼酸化合物--3-硝基苯硼酸(3-NPBA)与 KPC-2 结合的复合物,分辨率为 1.62 Å。3-NPBA 与 KPC-2
K
m
对 KPC-2 的 K m 值为 1.0 ± 0.1 μM(平均值 ± 标准误差),并通过与催化 S70 残基的可逆共价作用阻断活性位点。3-NPBA 的两个硼羟基原子分别位于氧阴离子孔和脱酰化水袋中。此外,3-NPBA 的芳香环还与活性位点中的 W105 形成了边对边的相互作用。以 1.26 埃的分辨率测定了 KPC-2 与五价砜 PSR-3-226 的结构。PSR-3-226 显示了
K
m
值为 3.8 ± 0.4 μM,而 KPC-2 的失活速率常数 (
k
inact
)为 0.034 ± 0.003 s
-1
.当与 S70 共价结合时,PSR-3-226 会形成一个
反式
-烯胺中间体。主要的活性位点相互作用是通过羰基氧(位于氧阴离子孔中)和 PSR-3-226 的羧基(与 N132、N170 和 E166 相互作用)产生的。3-NPBA 和 PSR-3-226 是第一种与 KPC-2 形成酰酶复合物的β-内酰胺酶抑制剂。本研究在结构和抑制方面获得的启示有助于设计强效的 KPC-2 抑制剂。