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

Ingebrigt Sylte,Rangita Dawadi,Jan-Olof Winberg,Ann Iren Solli,Olayiwola A Adekoya,Nabin Malla,Gunbjørg Svineng,Eli Berg,Tra-Mi Nguyen,Susannah Von Hofsten

doi:10.1371/journal.pone.0200237

Ingebrigt Sylte, Rangita Dawadi + Show 8 more

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https://doi.org/10.1371/journal.pone.0200237

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Journal: PloS one	Publication Date: Aug 3, 2018
Citations: 13	License type: CC BY 4.0

Affiliation: UiT The Arctic University of Norway

Abstract

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 Ki 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 Ki 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.

Highlights

Proteases are enzymes that cleave peptides and proteins at their N- or C-terminal ends or within the polypeptide chain
The pass through fraction from this column contained free proMMP-9, free TIMP-1, TIMP-1 linked to proMMP-9 and other proteins that was applied to a Gelatin-Sepharose column and eluted with 10% DMSO as described earlier [65]
TIMP-1 does not bind to the Gelatin-Sepharose column, but TIMP-1 binds through its C-terminal domain to the C-terminal hemopexin like domain (HPX)-domain of proMMP-9 [42, 63, 74, 75] and purified proMMP-9 from THP-1 cells will always contain some TIMP-1

Summary

Introduction

Proteases are enzymes that cleave peptides and proteins at their N- or C-terminal ends (exopeptidases) or within the polypeptide chain (endopeptidases) They are important for all organisms, and it is estimated that there are more than 66000 different proteases [1, 2]. Inhibition of human and bacterial metalloproteases microorganisms, proteases are important for generation of nutrition, invasion into host organisms as well as growth and survival [3,4,5,6,7,8,9]. Diseases are often associated with dysregulation of one or several proteases [10, 11, 15,16,17,18] and several proteases are important targets for therapeutic intervention [19,20,21,22]

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