Theoretical and experimental studies of thermolysin inhibition

Abstract

Zinc-metalloproteinases play a key role in the biosythesis and metabolism of different bioactive peptides. As a member of zinc-metalloproteinases, thermolysin has served as a model system to study the inhibition mechanism of other metalloproteinases. Inhibitors of thermolysin have considerable potential as therapeutic agents. In the present master thesis, docking calculations were performed and reported for 25 potent non-peptidal thermolysin inhibitors retrieved from literatures. Docking software ICMTM was used. 8 out of 25 compounds were from X-ray crystal structure complexes with thermolysin. ICMTM reproduced 63% of the binding modes from 8 X-ray crystal complexes. Experimental assay were done with MS, R and M compounds. 2 out of 13 MS compounds were found to inhibit thermolysin (one was later found to be competitive inhibitor and the other one was found to be a non-competitive slow inhibitor). 12 out of 37 R compounds inhibited thermolysin with varying affinity and 2 out of 7 M compounds had thermolysin inhibition property. One of them was found to be very potent inhibitor, with IC50 value of 4,411x10-11 mM. Docking calculations were performed with all MS and active R compounds to predict the binding poses. However, the experimental verification showed that only two of the MS compounds are thermolysin binders. For R compounds, the correlation between binding energies and IC50 is not linear, which indicates that the docking poses were not yet ‘perfect’. The presence of metal ions as zinc is a problem for docking studies. Parameterization of zinc ion need to be taken directly into account by the docking program, and special treatment may be necessary.