Computational protocol: A smallest 6 kda metalloprotease, mini-matrilysin, in living world: a revolutionary conserved zinc-dependent proteolytic domain- helix-loop-helix catalytic zinc binding domain (ZBD)

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Protocol publication

[…] SC44463, BB94 and phosphoramidon docking and data analysis. BB94 is selected for positive binding and phosphoramidon for negative control on MMP7. The 3D structures of the human MMP7 protease [] (PDB code: 1MMR) and thermolysin [] (EC#: 3.4.24.11) ((PDB code: 1THL) were retrieved from the Protein Data Bank. PRODRG program (http://davapc1.bioch.dundee.ac.uk/ programs/prodrg/) were used to generate the coordinate and topology files of SC44463 [,], BB94 [-] and Phosphoramidon [,]. SC44463, BB94 and Phosphoramidon were computationally docked into the 3D structure of the human MMP7 protease and thermolysin using the docking program GOLD [] (version 2.1.2; Genetic Optimization for Ligand Docking, CCDC, Cambridge, UK) or PPDOCK program (http://140.112.135.49/ppdock/). GOLD operates with a genetic search algorithm and allows for complete ligand and partial-binding site flexibility []. Because SC44463, BB94 and Phosphoramidon may be the inhibitors of the catalytic centers which zinc-binding motif located in helix-2, we defined the binding site to the inhibitor as the putative znic catalytic pocket. The results were ranked by GOLD’s scoring function which is a molecular mechanics-like function with four terms based on protein–ligand hydrogen bond energy, protein–ligand van der Waals energy, ligand internal van der Waals energy, and ligand torsional strain. The 100 steps of energy minimization of the best docking structure were carried out using the CNS programs []. The interactions between SC44666 and the human MMP7 protease were analyzed and illustrated by Discovery Studio 3.0 (Accelrys Software Inc.) and Chimera (The University of California). […]

Pipeline specifications

Software tools PRODRG, CNS
Applications Drug design, Protein structure analysis
Organisms Escherichia coli, Homo sapiens
Chemicals Zinc