639
Views
32
CrossRef citations to date
0
Altmetric
Research Article

Identification of selective MMP-9 inhibitors through multiple e-pharmacophore, ligand-based pharmacophore, molecular docking, and density functional theory approaches

ORCID Icon & ORCID Icon
Pages 944-965 | Received 30 Oct 2017, Accepted 15 Feb 2018, Published online: 09 Mar 2018

References

  • Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., … Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242.10.1093/nar/28.1.235
  • Castillo, J., & Rodríguez, I. (2003). Biochemical changes and inflammatory response as markers for brain ischaemia: Molecular markers of diagnostic utility and prognosis in human clinical practice. Cerebrovascular Diseases, 17(Suppl. 1), 7–18.
  • Chandler, S., Coates, R., Gearing, A., Lury, J., Wells, G., & Bone, E. (1995). Matrix metalloproteinases degrade myelin basic protein. Neuroscience Letters, 201(3), 223–226.10.1016/0304-3940(95)12173-0
  • Consonni, V., Ballabio, D., & Todeschini, R. (2009). Comments on the definition of the Q 2 parameter for QSAR validation. Journal of Chemical Information and Modeling, 49(7), 1669–1678.10.1021/ci900115y
  • Díaz, N., Suárez, D., & Sordo, T. L. (2006). Quantum chemical study on the coordination environment of the catalytic zinc ion in matrix metalloproteinases. The Journal of Physical Chemistry B, 110(47), 24222–24230.10.1021/jp0656882
  • Dixon, S. L., Smondyrev, A. M., Knoll, E. H., Rao, S. N., Shaw, D. E., & Friesner, R. A. (2006). PHASE: A new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. Journal of Computer-aided Molecular Design, 20(10–11), 647–671.10.1007/s10822-006-9087-6
  • Du, J., Sun, H., Xi, L., Li, J., Yang, Y., Liu, H., & Yao, X. (2011). Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and prime/MM–GBSA calculation. Journal of Computational Chemistry, 32(13), 2800–2809.10.1002/jcc.v32.13
  • Duffy, E. M., & Jorgensen, W. L. (2000). Prediction of properties from simulations: Free energies of solvation in hexadecane, octanol, and water. Journal of the American Chemical Society, 122(12), 2878–2888.10.1021/ja993663t
  • Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., ... Perry, J. K. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of medicinal chemistry, 47(7), 1739–1749.
  • Gill, P. M., Johnson, B. G., Pople, J. A., & Frisch, M. J. (1992). The performance of the Becke—Lee—Yang—Parr (B—LYP) density functional theory with various basis sets. Chemical Physics Letters, 197(4–5), 499–505.10.1016/0009-2614(92)85807-M
  • Halgren, T. A., Murphy, R. B., Friesner, R. A., Beard, H. S., Frye, L. L., Pollard, W. T., & Banks, J. L. (2004). Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. Journal of Medicinal Chemistry, 47(7), 1750–1759.10.1021/jm030644s
  • Hartung, H.-P., & Kieseier, B. C. (2000). The role of matrix metalloproteinases in autoimmune damage to the central and peripheral nervous system. Journal of Neuroimmunology, 107(2), 140–147. 10.1016/S0165-5728(00)00225-3
  • Huang, N., Kalyanaraman, C., Irwin, J. J., & Jacobson, M. P. (2006). Physics-based scoring of protein− ligand complexes: Enrichment of known inhibitors in large-scale virtual screening. Journal of Chemical Information and Modeling, 46(1), 243–253.10.1021/ci0502855
  • Itoh, T., Matsuda, H., Tanioka, M., Kuwabara, K., Itohara, S., & Suzuki, R. (2002). The role of matrix metalloproteinase-2 and matrix metalloproteinase-9 in antibody-induced arthritis. The Journal of Immunology, 169(5), 2643–2647.10.4049/jimmunol.169.5.2643
  • Jung, S., Moon, K.-S., Kim, S.-T., Ryu, H.-H., Lee, Y.-H., Jeong, Y.-I., … Kang, S.-S. (2007). Increased expression of intracystic matrix metalloproteinases in brain tumors: Relationship to the pathogenesis of brain tumor-associated cysts and peritumoral edema. Journal of Clinical Neuroscience, 14(12), 1192–1198.10.1016/j.jocn.2006.11.009
  • Kaminski, G. A., Friesner, R. A., Tirado-Rives, J., & Jorgensen, W. L. (2001). Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. The Journal of Physical Chemistry B, 105(28), 6474–6487.10.1021/jp003919d
  • Kurzepa, J., Szczepanska-Szerej, A., Stryjecka-Zimmer, M., Malecka-Massalska, T., & Stelmasiak, Z. (2006). Simvastatin could prevent increase of the serum MMP-9/TIMP-1 ratio in acute ischaemic stroke. Folia biologica, 52(6), 181–183.
  • Lewis, R. A. (2005). A general method for exploiting QSAR models in lead optimization. Journal of Medicinal Chemistry, 48(5), 1638–1648.10.1021/jm049228d
  • Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23(1–3), 3–25.10.1016/S0169-409X(96)00423-1
  • Loving, K., Salam, N. K., & Sherman, W. (2009). Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation. Journal of Computer-Aided Molecular Design, 23(8), 541–554.10.1007/s10822-009-9268-1
  • Lyne, P. D., Lamb, M. L., & Saeh, J. C. (2006). Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring. Journal of Medicinal Chemistry, 49(16), 4805–4808.10.1021/jm060522a
  • Matysiak, J. (2007). Evaluation of electronic, lipophilic and membrane affinity effects on antiproliferative activity of 5-substituted-2-(2, 4-dihydroxyphenyl)-1, 3, 4-thiadiazoles against various human cancer cells. European Journal of Medicinal Chemistry, 42(7), 940–947.10.1016/j.ejmech.2006.12.033
  • Morgunova, E., Tuuttila, A., Bergmann, U., Isupov, M., Lindqvist, Y., Schneider, G., & Tryggvason, K. (1999). Structure of human pro-matrix metalloproteinase-2: Activation mechanism revealed. Science, 284(5420), 1667–1670.10.1126/science.284.5420.1667
  • Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., & Olson, A. J. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19(14), 1639–1662.10.1002/(ISSN)1096-987X
  • Nash, A., Birch, H. L., & de Leeuw, N. H. (2017). Mapping intermolecular interactions and active site conformations: From human MMP-1 crystal structure to molecular dynamics free energy calculations. Journal of Biomolecular Structure and Dynamics, 35(3), 564–573.10.1080/07391102.2016.1153521
  • Ntie-Kang, F. (2013). An in silico evaluation of the ADMET profile of the StreptomeDB database. SpringerPlus, 2(1), 353–364.10.1186/2193-1801-2-353
  • Othman, H., Wieninger, S. A., ElAyeb, M., Nilges, M., & Srairi-Abid, N. (2017). In Silico prediction of the molecular basis of ClTx and AaCTx interaction with matrix metalloproteinase-2 (MMP-2) to inhibit glioma cell invasion. Journal of Biomolecular Structure and Dynamics, 35(13), 2815–2829.10.1080/07391102.2016.1231633
  • Petty, M., & Wettstein, J. (2001). Elements of cerebral microvascular ischaemia. Brain Research Reviews, 36(1), 23–34.10.1016/S0165-0173(01)00062-5
  • Planas, A. M., Solé, S., & Justicia, C. (2001). Expression and activation of matrix metalloproteinase-2 and-9 in rat brain after transient focal cerebral ischemia. Neurobiology of Disease, 8(5), 834–846.10.1006/nbdi.2001.0435
  • Pradiba, D., Aarthy, M., Shunmugapriya, V., Singh, S. K., & Vasanthi, M. (in press). Structural insights into the binding mode of flavonols with the active site of Matrix MetalloProteinase-9 through molecular docking and Molecular Dynamic Simulations studies. Journal of Biomolecular Structure & Dynamics. doi:10.1080/07391102.2017.1397058
  • Pratim Roy, P., Paul, S., Mitra, I., & Roy, K. (2009). On two novel parameters for validation of predictive QSAR models. Molecules, 14(5), 1660–1701.10.3390/molecules14051660
  • Salam, N. K., Nuti, R., & Sherman, W. (2009). Novel method for generating structure-based pharmacophores using energetic analysis. Journal of Chemical Information and Modeling, 49(10), 2356–2368.10.1021/ci900212v
  • Shigemori, Y., Katayama, Y., Mori, T., Maeda, T., & Kawamata, T. (2006). Matrix metalloproteinase-9 is associated with blood-brain barrier opening and brain edema formation after cortical contusion in rats. In: J. T. Hoff, R. F. Keep., G. Xi, & Y. Hua (Eds.), Brain Edema XIII. Acta Neurochirurgica Supplementum, vol 96. Vienna: Springer. 10.1007/3-211-30714-1
  • Stephens, P., Devlin, F., Chabalowski, C., & Frisch, M. J. (1994). Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields. The Journal of Physical Chemistry, 98(45), 11623–11627.10.1021/j100096a001
  • Terp, G. E., Cruciani, G., Christensen, I. T., & Jørgensen, F. S. (2002). Structural differences of matrix metalloproteinases with potential implications for inhibitor selectivity examined by the GRID/CPCA approach. Journal of Medicinal Chemistry, 45(13), 2675–2684.10.1021/jm0109053
  • Truchon, J.-F., & Bayly, C. I. (2007). Evaluating virtual screening methods: Good and bad metrics for the “early recognition” problem. Journal of Chemical Information and Modeling, 47(2), 488–508.10.1021/ci600426e
  • Uhm, J., Dooley, N., Villemure, J.-G., & Yong, V. (1997). Mechanisms of glioma invasion: Role of matrix-metalloproteinases. Canadian Journal of Neurological Sciences, 24(1), 3–15.10.1017/S0317167100021028
  • Vandenbroucke, R. E., & Libert, C. (2014). Is there new hope for therapeutic matrix metalloproteinase inhibition? Nature Reviews Drug Discovery, 13(12), 904–927.10.1038/nrd4390
  • Wang, H., Aslanian, R., & Madison, V. S. (2008). Induced-fit docking of mometasone furoate and further evidence for glucocorticoid receptor 17α pocket flexibility. Journal of Molecular Graphics and Modelling, 27(4), 512–521.
  • Wang, Y., Yang, L., Hou, J., Zou, Q., Gao, Q., Yao, W., … Zhang, J. (in press). Hierarchical virtual screening of the dual MMP-2/HDAC-6 inhibitors from natural products based on pharmacophore models and molecular docking. Journal of Biomolecular Structure & Dynamics. doi:10.1080/07391102.2018.1434833
  • Wei, T., Zhang, H., Cetin, N., Miller, E., Moak, T., Suen, J. Y., & Richter, G. T. (2016). Elevated expression of matrix metalloproteinase-9 not matrix metalloproteinase-2 contributes to progression of extracranial arteriovenous malformation. Scientific reports, 6, 24378. doi:10.1038/srep24378
  • Yu, Z., Jacobson, M. P., & Friesner, R. A. (2006). What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules. Journal of Computational Chemistry, 27(1), 72–89.10.1002/(ISSN)1096-987X
  • Zhan, C.-G., Nichols, J. A., & Dixon, D. A. (2003). Ionization potential, electron affinity, electronegativity, hardness, and electron excitation energy: Molecular properties from density functional theory orbital energies. The Journal of Physical Chemistry A, 107(20), 4184–4195.10.1021/jp0225774
  • Zheng, Y., Zheng, M., Ling, X., Liu, Y., Xue, Y., An, L., … Jin, M. (2013). Design, synthesis, quantum chemical studies and biological activity evaluation of pyrazole–benzimidazole derivatives as potent Aurora A/B kinase inhibitors. Bioorganic & Medicinal Chemistry Letters, 23(12), 3523–3530.10.1016/j.bmcl.2013.04.039

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.