Crystallographic investigation of the inhibition mode of a VIM-2 metallo-β-lactamase from Pseudomonas aeruginosa by a mercaptocarboxylate inhibitor

The VIM-2 metallo-beta-lactamase enzyme from Pseudomonas aeruginosa catalyzes the hydrolysis of most P-lactam antibiotics including carbapenems, and there are currently no potent inhibitors of such enzymes. We found rac-2-omega-phenylpropyl-3-mercaptopropionic acid, phenylC3SH, to be a potent inhibitor of VIM-2. The structure of the VIM-2-phenylC3SH complex was determined by X-ray crystallography to 2.3 angstrom. The structure revealed that the thiol group of phenylC3SH bridged to the two zinc(II) ions and the phenyl group interacted with Tyr67(47) on loop I near the active site, by pi-pi stacking interactions. The methylene group interacted with Phe61(42) located at the bottom of loop1 through CH-pi interactions. Dynamic movements were observed in Arg228(185) and Asn233(190) on loop2, compared with the native structure (PDB. code: 1KO3). These results suggest that the above-mentioned four residues play important roles in the binding and recognition of inhibitors or substrates and in stabilizing a loop in the VIM-2 enzyme.

铜绿假单胞菌的VIM - 2型金属β - 内酰胺酶可催化包括碳青霉烯类在内的大多数β - 内酰胺类抗生素的水解，目前尚无此类酶的有效抑制剂。我们发现外消旋 - 2 - ω - 苯丙基 - 3 - 巯基丙酸（phenylC3SH）是VIM - 2的一种有效抑制剂。通过X射线晶体学测定VIM - 2 - phenylC3SH复合物的结构，分辨率达到2.3埃。该结构显示，phenylC3SH的巯基与两个锌（II）离子桥连，苯环通过π - π堆积作用与活性位点附近环I上的Tyr67（47）相互作用。亚甲基通过C - H…π作用与位于环1底部的Phe61（42）相互作用。与天然结构（PDB代码：1KO3）相比，在环2上的Arg228（185）和Asn233（190）观察到动态运动。这些结果表明，上述四个残基在抑制剂或底物的结合与识别以及稳定VIM - 2酶中的一个环方面起着重要作用。