spacer Human MMP12 in complex with a PEG-linked bifunctional L-glutamate motif inhibitor
Primary citation
Title Crystallization of bi-functional ligand protein complexes.
Authors Antoni,; Vera,; Devel,; Catalani,; Czarny,; Cassar-Lajeunesse,; Nuti,; Rossello,; Dive,; Stura,
Journal vol:182, pag:246-254 (2013), Identifiers: PubMed ID (23567804)search DOI (10.1016/j.jsb.2013.03.015)
Abstract Homodimerization is important in signal transduction and can play a crucial role in many other biological systems. To obtaining structural information for the design of molecules able to control the signalization pathways, the proteins involved will have to be crystallized in complex with ligands that induce dimerization. Bi-functional drugs have been generated by linking two ligands together chemically and the relative crystallizability of complexes with mono-functional and bi-functional ligands has been evaluated. There are problems associated with crystallization with such ligands, but overall, the advantages appear to be greater than the drawbacks. The study involves two matrix metalloproteinases, MMP-12 and MMP-9. Using flexible and rigid linkers we show that it is possible to control the crystal packing and that by changing the ligand-enzyme stoichiometric ratio, one can toggle between having one bi-functional ligand binding to two enzymes and having the same ligand bound to each enzyme. The nature of linker and its point of attachment on the ligand can be varied to aid crystallization, and such variations can also provide valuable structural information about the interactions made by the linker with the protein. We report here the crystallization and structure determination of seven ligand-dimerized complexes. These results suggest that the use of bi-functional drugs can be extended beyond the realm of protein dimerization to include all drug design projects.
MeSH terms
Secondary citations
Title A new development of matrix metalloproteinase inhibitors: twin hydroxamic acids as potent inhibitors of MMPs.
Authors Rossello,; Nuti,; Catalani,; Carelli,; Orlandini,; Rapposelli,; Tuccinardi,; Atkinson,; Murphy,; Balsamo,
Journal vol:15, pag:2311-2314 (2005), Identifiers: PubMed ID (15837315)search DOI (10.1016/j.bmcl.2005.03.002)
Abstract Starting from the observation that the CbzNH(CH2)2 side chain of the potent MMP-2/MMP-14 inhibitor, benzyl-(3R)-4-(hydroxyamino)-3-[isopropoxy(1,1'-biphenyl-4-yl-sulfonyl)amino]-4-oxobutylcarbamate, (R)-1 lies in a hydrophobic region (S1) exposed to the solvent of the protease active site, we hypothesized that an aminoethylcarboxamido chain structurally related to that of (R)-1 might be an useful tool to bind another linker stretching out from the protein. This would be able to interact either with a enzyme region adjacent to the active site, or with other molecules of matrix metalloproteinases (MMPs), or other proteins of the extracellular matrix (ECM) that may be involved in the enzyme activation. On these basis we describe new dimeric compounds of type 2, twin hydroxamic acids, obtained by the joint of two drug entities of (R)-1 linked in P1 by extendable semirigid linkers. Type 2 compounds are potentially able to undergo more complex inhibitor-enzyme interactions than those occurring with monomeric compounds of type 1, thus influencing positively the potency, selectivity and/or cytotoxicity of the new compounds.
MeSH terms Binding Sitessearch, Enzyme Inhibitorssearch, Hydroxamic Acidssearch, Indicators and Reagentssearch, Matrix Metalloproteinase 2search, Matrix Metalloproteinase Inhibitorssearch, Matrix Metalloproteinasessearch, Modelssearch, Molecularsearch, Molecular Conformationsearch, Protein Conformationsearch, Structure-Activity Relationshipsearch