Molecular dynamics simulation of matrix metalloproteinases S′₁ binding pocket

To study the dynamic behavior of matrix metalloproteinases(MMPs)S′₁ binding pocket, and the structural properties relevant for the design of specific inhibitors at the molecular level, long-time molecular dynamics simulation of apo proteases of MMP-7, MMP-2 and MMP-3 were performed. It was found that the S′₁ binding pocket of MMP-7 and MMP-2 was closed, while S′₁ binding pocket of MMP-3 was semi-closed. Thus, the flexibility of S′₁ binding pocket loop region may play an important role in binding inhibitors.