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理解碳青霉烯酶 KPC-2 中底物和抑制剂特异性的分子决定因素:探讨 Arg220 和 Glu276 的作用。

Understanding the molecular determinants of substrate and inhibitor specificities in the Carbapenemase KPC-2: exploring the roles of Arg220 and Glu276.

机构信息

Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA.

出版信息

Antimicrob Agents Chemother. 2012 Aug;56(8):4428-38. doi: 10.1128/AAC.05769-11. Epub 2012 Jun 11.

Abstract

β-Lactamases are important antibiotic resistance determinants expressed by bacteria. By studying the mechanistic properties of β-lactamases, we can identify opportunities to circumvent resistance through the design of novel inhibitors. Comparative amino acid sequence analysis of class A β-lactamases reveals that many enzymes possess a localized positively charged residue (e.g., R220, R244, or R276) that is critical for interactions with β-lactams and β-lactamase inhibitors. To better understand the contribution of these residues to the catalytic process, we explored the roles of R220 and E276 in KPC-2, a class A β-lactamase that inactivates carbapenems and β-lactamase inhibitors. Our study reveals that substitutions at R220 of KPC-2 selectively impact catalytic activity toward substrates (50% or greater reduction in k(cat)/K(m)). In addition, we find that residue 220 is central to the mechanism of β-lactamase inhibition/inactivation. Among the variants tested at Ambler position 220, the R220K enzyme is relatively "inhibitor susceptible" (K(i) of 14 ± 1 μM for clavulanic acid versus K(i) of 25 ± 2 μM for KPC-2). Specifically, the R220K enzyme is impaired in its ability to hydrolyze clavulanic acid compared to KPC-2. In contrast, the R220M substitution enzyme demonstrates increased K(m) values for β-lactamase inhibitors (>100 μM for clavulanic acid versus 25 ± 3 μM for the wild type [WT]), which results in inhibitor resistance. Unlike other class A β-lactamases (i.e., SHV-1 and TEM-1), the amino acid present at residue 276 plays a structural rather than kinetic role with substrates or inhibitors. To rationalize these findings, we constructed molecular models of clavulanic acid docked into the active sites of KPC-2 and the "relatively" clavulanic acid-susceptible R220K variant. These models suggest that a major 3.5-Å shift occurs of residue E276 in the R220K variant toward the active S70 site. We anticipate that this shift alters the shape of the active site and the positions of two key water molecules. Modeling also suggests that residue 276 may assist with the positioning of the substrate and inhibitor in the active site. These biochemical and molecular modeling insights bring us one step closer to understanding important structure-activity relationships that define the catalytic and inhibitor-resistant profile of KPC-2 and can assist the design of novel compounds.

摘要

β-内酰胺酶是细菌表达的重要抗生素耐药决定簇。通过研究β-内酰胺酶的机制特性,我们可以通过设计新型抑制剂来寻找克服耐药性的机会。对 A 类β-内酰胺酶的氨基酸序列进行比较分析表明,许多酶具有局部带正电荷的残基(例如 R220、R244 或 R276),这些残基对于与β-内酰胺和β-内酰胺酶抑制剂的相互作用至关重要。为了更好地理解这些残基对催化过程的贡献,我们研究了 R220 和 E276 在 KPC-2 中的作用,KPC-2 是一种 A 类β-内酰胺酶,可使碳青霉烯类和β-内酰胺酶抑制剂失活。我们的研究表明,KPC-2 中 R220 的取代会选择性地影响对底物的催化活性(kcat/Km 降低 50%或更多)。此外,我们发现残基 220 是β-内酰胺酶抑制/失活机制的核心。在测试的安布勒位置 220 中的变体中,R220K 酶相对“抑制剂敏感”(克拉维酸的 K(i)为 14±1 μM,而 KPC-2 的 K(i)为 25±2 μM)。具体而言,与 KPC-2 相比,R220K 酶水解克拉维酸的能力受损。相比之下,R220M 取代酶对β-内酰胺酶抑制剂的 K(m)值升高(克拉维酸的 K(m)值>100 μM,而野生型 [WT]的 K(m)值为 25±3 μM),导致抑制剂耐药性。与其他 A 类β-内酰胺酶(即 SHV-1 和 TEM-1)不同,残基 276 上存在的氨基酸在与底物或抑制剂相互作用时起着结构而不是动力学的作用。为了合理化这些发现,我们构建了克拉维酸与 KPC-2 的活性位点以及“相对”克拉维酸敏感的 R220K 变体对接的分子模型。这些模型表明,E276 残基在 R220K 变体中发生了主要为 3.5 Å 的位移,朝向活性 S70 位点。我们预计这种位移会改变活性位点的形状和两个关键水分子的位置。建模还表明,残基 276 可能有助于将底物和抑制剂定位在活性位点中。这些生化和分子建模的见解使我们更接近于理解定义 KPC-2 的催化和抑制剂抗性特征的重要结构-活性关系,并有助于设计新型化合物。

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