Coralyne Targets the Catalytic Domain of MMP9: An In Silico and In Vitro Investigation

Coralyne (COR) is a protoberberine-like isoquinoline alkaloid, and it is known for double-stranded (ds) DNA intercalation and topoisomerase inhibition. It can also sensitize cancer cells through various mechanisms. COR reduces the proliferation and migration of breast cancer cells by inhibiting the expression and activity of matrix metalloproteinase 9 (MMP9). However, the mechanism involved in the inhibitory activity of COR on MMP9 is not known. In the present study, in silico docking studies showed that COR binds to the active site of MMP9 catalytic domain (MMP9-CD) with considerable affinity. The binding affinity of COR to the MMP9-CD, estimated by three different web servers: CB Dock, Seam Dock, and PyRx, was found to be either -7.4 or -7.5 kcal/mol. Another web server that is routinely used for docking studies, Docking Server, has predicted a binding affinity of -5.9 kcal/mol. All four docking servers predicted the same binding site for COR within the MMP9-CD. Corroborating our docking results, molecular dynamic simulation studies have also shown that COR interacts with the same key active site amino acid residues of the MMP9-CD that are essential for its proteolytic function. Molecular mechanics with generalized born and surface area (MMGBSA) calculations using Schrodinger's prime module have shown that the binding free energy with which COR binds to MMP9 is -50 kcal/mol. It inhibited activity of recombinant human MMP9 activity and induced significant cytotoxicity and reduced the proliferation of MDA-MB 468 cells. Overall, our in silico and in vitro experiments show that COR potentially inhibits the activity of MMP9 by directly binding to the active site of its catalytic domain and possibly inhibits proliferation of MDA-MB 468 cells.