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Inhibitors targeting bacterial enzymes should not interfere with enzymes of the host, and knowledge about structural determinants for selectivity is important for designing inhibitors with a therapeutic potential. We have determined the binding strengths of two hydroxamate compounds, galardin and compound  1b  for the bacterial zinc metalloproteases, thermolysin, pseudolysin and auerolysin, known to be bacterial virulence factors, and the two human zinc metalloproteases MMP-9 and MMP-14. The active sites of the bacterial and human enzymes have huge similarities. In addition, we also studied the enzyme-inhibitor interactions by molecular modelling. The obtained  K  i  values of galardin for MMP-9 and MMP-14 and compound  1b  for MMP-9 are approximately ten times lower than previously reported. Compound  1b  binds stronger than galardin to both MMP-9 and MMP-14, and docking studies indicated that the diphenyl ether moiety of compound  1b  obtains more favourable interactions within the S´ 1 -subpocket than the 4-methylpentanoyl moiety of galardin. Both compounds bind stronger to MMP-9 than to MMP-14, which appears to be due to a larger S´ 1 -subpocket in the former enzyme. Galardin, but not  1b , inhibits the bacterial enzymes, but the galardin  K  i  values were much larger than for the MMPs. The docking indicates that the S´ 1 -subpockets of the bacterial proteases are too small to accommodate the diphenyl ether moiety of  1b , while the 4-methylpentanoyl moiety of galardin enters the pocket. The present study indicates that the size and shape of the ligand structural moiety entering the S´ 1 -subpocket is an important determinant for selectivity between the studied MMPs and bacterial MPs.

The selectivity of galardin and an azasugar-based hydroxamate compound for human matrix metalloproteases and bacterial metalloproteases