Paper Citing NAMD - Abstract
Khrenova, Maria G.; Nemukhin, Alexander V.; Savitsky, Alexander P.
Computational Characterization of Ketone-Ketal Transformations at the Active Site of Matrix Metalloproteinases
JOURNAL OF PHYSICAL CHEMISTRY B, 118:4345-4350, APR 24 2014
We modeled the first steps of hydrolysis reactions of a natural oligopeptide substrate of matrix metalloproteinase MMP-2 as well as of a substrate analogue. In the latter, the scissile amide group is substituted by a ketomethylene group which can be transformed to the ketal group upon binding of this compound to the enzyme active site. According to our quantum mechanical molecular mechanical (QM/MM) calculations, the reaction of the ketone ketal transformation proceeds with a low energy barrier (3.4 kcal/mol) and a high equilibrium constant (10(4)). The reaction product with the ketal group formed directly at the active site of the enzyme works as an inhibitor that chelates the zinc ion. On the other hand, the oligopeptide mimetic retains molecular groups responsible for binding of this compound to the enzyme active site. This example illustrates a strategy to design MMP inhibitors in situ by using data on binding specificity of substrates to a particular type of MMP and details of the reaction mechanism.
