Molecular Docking on Recomposed versus Crystallographic Structures of Zn-Dependent Enzymes and their Natural Inhibitors

Authors: Tudor Petreuş, Andrei Neamţu, Cristina Dascălu, Paul Dan Sîrbu, Carmen E. Cotrutz

Abstract:

Matrix metalloproteinases (MMP) are a class of structural and functional related enzymes involved in altering the natural elements of the extracellular matrix. Most of the MMP structures are cristalographycally determined and published in WorldWide ProteinDataBank, isolated, in full structure or bound to natural or synthetic inhibitors. This study proposes an algorithm to replace missing crystallographic structures in PDB database. We have compared the results of a chosen docking algorithm with a known crystallographic structure in order to validate enzyme sites reconstruction there where crystallographic data are missing.

Keywords: matrix metalloproteinases, molecular docking, structure superposition, surface complementarity.

Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1076446

References:

[1] S.D. Shapiro A concise yet informative stroll through matrix metalloproteinases and TIMPs, J Cell Sci., 2000, 113:19,3355-3356.
[2] J.F. Woessner Jr., Matrix metalloproteinase inhibition. From the Jurassic to the third millennium, 1999, Ann N Y Acad Sci., 30, 878, pp.388-403, June 1999.
[3] K. Brew, D. Dinakarpandian, H. Nagase, Tissue inhibitors of metalloproteinases: evolution, structure and function, Biochim Biophys Acta, 2000, 1477, 1-2.
[4] L. Fang, F. Huber-Abel, M. Teuchert, C. Hendrich, J. Dorst, D. Schattauer, H. Zettlmeissel, M. Wlaschek, K. Scharffetter-Kochanek, H. Tumani, A.C. Ludolph, J. Brettschneider, Linking neuron and skin: Matrix metalloproteinases in amyotrophic lateral sclerosis (ALS), J Neurol Sci. 2009, e-pub.
[5] B.F. Ribeiro, D.P. Iglesias, G.J. Nascimento, H.C. Galvão, A.M. Medeiros, R.A. Freitas, Immunoexpression of MMPs-1, -2, and -9 in ameloblastoma and odontogenic adenomatoid tumor, Oral Dis., 2009, epub.
[6] E. Korpos, C. Wu, L. Sorokin, Multiple roles of the extracellular matrix in inflammation, Curr Pharm Des., 2009, 15:12, 1349-57.
[7] A. Ando, Y. Hagiwara, M. Tsuchiya, Y. Onoda, H. Suda, E. Chimoto, E. Itoi, Increased expression of metalloproteinase-8 and -13 on articular cartilage in a rat immobilized knee model, Tohoku J Exp Med., 2009, 217:4, 27127-8.
[8] B. Gentner, A. Wein, R.S. Croner, I. Zeittraeger, R.M. Wirtz, F. Roedel, A. Dimmler, L. Dorlaque, W. Hohenberger, E. G. Hahn, W.M. Brueckl, Differences in the gene expression profile of matrix metalloproteinases (MMPs) and their inhibitors (TIMPs) in primary colorectal tumors and their synchronous liver metastases, Anticancer Res., 2009, 29:1, 67-74.
[9] V.P. Rajeshwar, H. Corwin, Matrix metalloproteinases (MMPs) Chemical-biological functions and (Q)SARs, Bioorganic & Medicinal Chemistry, 2007, 15:6, 2223-2268.
[10] B. Lovejoy, A. Cleasby, A.M. Hassell, K. Longley, M.A. Luther, D. Weigl, G. McGeehan, A.B. McElroy, D. Drewry, M.H. Lambert, S.R. Jorden, Structural Analysis of the Catalytic Domain of Human Fibroblast Collagenase, Science, 1994, 263, 375.
[11] E. Morgunova, A. Tuuttila, U. Bergmann, K. Tryggvason, Structural insight into the complex formation of latent matrix metalloproteinase 2 with tissue inhibitor of metalloproteinase 2. Proc Natl Acad Sci U S A. 2002, 28;99(11):7414-9.
[12] H.M. Berman, K. Henrick, H. Nakamura, Announcing the worldwide Protein Data Bank Nature Structural Biology, 2003, 10 (12): 98
[13] W. Humphrey, A. Dalke, . K. Schulten, VMD - Visual Molecular Dynamics, J. Molec. Graphics, 1996, 14: 33-38