679
Views
16
CrossRef citations to date
0
Altmetric
Research Article

Novel tumor necrosis factor-α (TNF-α) inhibitors from small molecule library screening for their therapeutic activity profiles against rheumatoid arthritis using target-driven approaches and binary QSAR models

, ORCID Icon & ORCID Icon
Pages 2464-2476 | Received 18 Apr 2018, Accepted 28 May 2018, Published online: 23 Dec 2018

References

  • Abraham, M. J., & Gready, J. E. (2011). Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5. Journal of Computational Chemistry, 32(9), 2031–2040.
  • Banks, J. L., Beard, H. S., Cao, Y., Cho, A. E., Damm, W., Farid, R., … Levy, R. M. (2005). Integrated modeling program, applied chemical theory (IMPACT). Journal of Computational Chemistry, 26(16), 1752–1780.
  • Bas, D. C., Rogers, D. M., & Jensen, J. H. (2008). Very fast prediction and rationalization of pKa values for protein-ligand complexes. Proteins, 73(3), 765–783.
  • Bashford, D., & Case, D. A. (2000). Generalized born models of macromolecular solvation effects. Annual Review of Physical Chemistry, 51, 129–152.
  • Berendsen, H. J. C., Vanderspoel, D., & Vandrunen, R. (1995). Gromacs – A message-passing parallel molecular-dynamics implementation. Computer Physics Communications, 91(1–3), 43–56.
  • Berg, T. (2003). Modulation of protein-protein interactions with small organic molecules. Angewandte Chemie-International Edition, 42(22), 2462–2481.
  • Berg, T. (2006). Inhibition of TNF-alpha signaling: divide and conquer. ChemMedChem, 1(7), 687–688.
  • Best, R. B., Zhu, X., Shim, J., Lopes, P. E., Mittal, J., Feig, M., & Mackerell, A. D., Jr. (2012). Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone phi, psi and side-chain chi(1) and chi(2) dihedral angles. Journal of Chemical Theory Computation, 8(9), 3257–3273.
  • Black, R. A., Rauch, C. T., Kozlosky, C. J., Peschon, J. J., Slack, J. L., Wolfson, M. F., … Cerretti, D. P. (1997). A metalloproteinase disintegrin that releases tumour-necrosis factor-alpha from cells. Nature, 385(6618), 729–733.
  • Brenner, D., Blaser, H., & Mak, T. W. (2015). Regulation of tumour necrosis factor signalling: Live or let die. Nature Reviews Immunology, 15(6), 362–374.
  • Brzustewicz, E., & Bryl, E. (2015). The role of cytokines in the pathogenesis of rheumatoid arthritis – Practical and potential application of cytokines as biomarkers and targets of personalized therapy. Cytokine, 76(2), 527–536.
  • Buchwald, P. (2010). Small-molecule protein-protein interaction inhibitors: Therapeutic potential in light of molecular size, chemical space, and ligand binding efficiency considerations. Iubmb Life, 62(10), 724–731.
  • Case, D. A. (2002). Generalized born models of macromolecular solvation effects. Abstracts of Papers of the American Chemical Society, 223, C47–C47.
  • Chan, D. S., Lee, H. M., Yang, F., Che, C. M., Wong, C. C., Abagyan, R., … Ma, D. L. (2010). Structure-based discovery of natural-product-like TNF-α inhibitors. Angewandte Chemie International Edition English, 49(16), 2860–2864.
  • Chatzantoni, K., & Mouzaki, A. (2006). Anti-TNF-alpha antibody therapies in autoimmune diseases. Current Topics in Medicinal Chemistry, 6(16), 1707–1714.
  • Chen, S., Feng, Z., Wang, Y., Ma, S., Hu, Z., Yang, P., … Xie, X. (2017). Discovery of novel ligands for TNF-alpha and TNF receptor-1 through structure-based virtual screening and biological assay. Journal of Chemical Informative Model, 57(5), 1101–1111.
  • Clackson, T. (2006). Breaking and entering. Natural Chemistry Biology, 2(1), 14–15.
  • C.P., A., Subhramanian, S., Sizochenko, N., Melge, A.R., Leszczynski, J., & Mohan, C.G. (2018) Multiple e-Pharmacophore modeling to identify a single molecule that could target both streptomycin and paromomycin binding sites for 30S ribosomal subunit inhibition. Journal of Biomolecular Structure Dynamics, 7, 1–15. doi: 10.1080/07391102.2018.1462731
  • Darden, T., York, D., & Pedersen, L. (1993). Particle Mesh Ewald – An N.Log(N) method for Ewald sums in large systems. Journal of Chemical Physics, 98(12), 10089–10092.
  • Davis, J. M., & Colangelo, J. (2013). Small-molecule inhibitors of the interaction between TNF and TNFR. Future Medicinal Chemistry, 5(1), 69–79.
  • Deepu, K. P., Thomas, B., & Harindran, J. (2016) Design, synthesis and evaluation of specific TNF-α inhibitory novel dithioic acid derivative from natural acids as anti-inflammatory agents. International Journal of Pharmateutical Chemistry, 6, 42–44
  • 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 Computational Aided Molecular Design, 20(10–11), 647–671.
  • Douni, E., & Kollias, G. (1998). A critical role of the p75 tumor necrosis factor receptor (p75TNF-R) in organ inflammation independent of TNF, lymphotoxin alpha, or the p55TNF-R. Journal of Experimental Medicine, 188(7), 1343–1352.
  • Ekhteiari Salmas, R., Unlu, A., Bektaş, M., Yurtsever, M., Mestanoglu, M., & Durdagi, S. (2017) Virtual screening of small molecules databases for discovery of novel PARP-1 inhibitors: Combination of in silico and in vitro studies. Journal of Biomolecular Structure & Dynamics, 35(9), 1899–1915.
  • Elliott, M. J., Maini, R. N., Feldmann, M., Longfox, A., Charles, P., Katsikis, P., … Woody, J. N. (1993). Treatment of rheumatoid-arthritis with chimeric monoclonal-antibodies to tumor-necrosis-factor-alpha. Arthritis and Rheumatism, 36(12), 1681–1690.
  • Ertl, P., Roggo, S., & Schuffenhauer, A. (2008). Natural product-likeness score and its application for prioritization of compound libraries. Journal of Chemical Informative Model, 48(1), 68–74.
  • Evans, D. J., & Holian, B. L. (1985). The Nose-Hoover thermostat. Journal of Chemical Physics, 83(8), 4069–4074.
  • Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., … Shenkin, P. S. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medical Chemistry, 47(7), 1739–1749.
  • Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., … Mainz, D. T. (2006). Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. Journal of Medical Chemistry, 49(21), 6177–6196.
  • Grell, M., Douni, E., Wajant, H., Lohden, M., Clauss, M., Maxeiner, B., … Scheurich, P. (1995). The transmembrane form of tumor-necrosis-factor is the prime activating ligand of the 80 Kda tumor-necrosis-factor receptor. Cell, 83(5), 793–802.
  • 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 Medical Chemistry, 47(7), 1750–1759.
  • Haraguchi, S., Day, N. K., Kamchaisatian, W., Beigier-Pompadre, M., Stenger, S., Tangsinmankong, N., … Cianciolo, G. J. (2006). LMP-420, a small-molecule inhibitor of TNF-alpha, reduces replication of HIV-1 and Mycobacterium tuberculosis in human cells. AIDS Research Therapy, 3, 8.
  • He, M. M., Smith, A. S., Oslob, J. D., Flanagan, W. M., Braisted, A. C., Whitty, A., … Cunningham, B. C. (2005). Small-molecule inhibition of TNF-alpha. Science, 310(5750), 1022–1025.
  • Horiuchi, T., Mitoma, H., Harashima, S., Tsukamoto, H., & Shimoda, T. (2010). Transmembrane TNF-alpha: Structure, function and interaction with anti-TNF agents. Rheumatology (Oxford) , 49(7), 1215–1228.
  • Huang, J., & MacKerell, A. D., Jr. (2013). CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data. Journal of Computational Chemistry, 34(25), 2135–2145.
  • Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphical Model, 14(1), 33–38.
  • Jana, S., & Singh, S. K. (in press). Identification of selective MMP-9 inhibitors through multiple e-pharmacophore, ligand-based pharmacophore, molecular docking, and density functional theory approaches. Journal of Biomolecular Structure &Dynamics, doi: 10.1080/07391102.2018.1444510
  • Keffer, J., Probert, L., Cazlaris, H., Georgopoulos, S., Kaslaris, E., Kioussis, D., & Kollias, G. (1991). Transgenic mice expressing human tumor-necrosis-factor – A predictive genetic model of arthritis. EMBO Journal, 10(13), 4025–4031.
  • Kollias, G., & Kontoyiannis, D. (2002). Role of TNF/TNFR in autoimmunity: Specific TNF receptor blockade may be advantageous to anti-TNF treatments. Cytokine & Growth Factor Reviews, 13(4–5), 315–321.
  • Kontermann, R. E., Scheurich, P., & Pfizenmaier, M. (2009). Antagonists of TNF action: Clinical experience and new developments. Expert Opinion on Drug Discovery, 4(3), 279–292.
  • Lee, J., Cheng, X., Swails, J. M., Yeom, M. S., Eastman, P. K., Lemkul, J. A., … Im, W. (2016). CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. Journal of Chemical Theory Computation, 12(1), 405–413.
  • Lee, M. R., & Dominguez, C. (2005). MAP kinase p38 inhibitors: Clinical results and an intimate look at their interactions with p38alpha protein. Current Medical Chemistry, 12(25), 2979–2994.
  • Li, H., Robertson, A. D., & Jensen, J. H. (2005). Very fast empirical prediction and rationalization of protein pKa values. Proteins, 61(4), 704–721.
  • Li, J., Abel, R., Zhu, K., Cao, Y., Zhao, S., & Friesner, R. A. (2011). The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling. Proteins, 79(10), 2794–2812.
  • Mateen, S., Zafar, A., Moin, S., Khan, A. Q., & Zubair, S. (2016). Understanding the role of cytokines in the pathogenesis of rheumatoid arthritis. Clinical Chimica Acta, 455, 161–171.
  • McInnes, I. B., & Schett, G. (2011). Mechanisms of disease the pathogenesis of rheumatoid arthritis. New England Journal of Medicine, 365(23), 2205–2219.
  • Melagraki, G., Ntougkos, E., Rinotas, V., Papaneophytou, C., Leonis, G., Mavromoustakos, T., … Kollias, G. (2017). Cheminformatics-aided discovery of small-molecule protein-protein interaction (PPI) dual inhibitors of tumor necrosis factor (TNF) and receptor activator of NF-kappaB Ligand (RANKL). PLoS Computational Biology, 13(4), e1005372.
  • MetaCoreTM, MetaCore/MetaDrug version 6.31, Clarivate Analytics (2018)
  • Newman, D. J., & Cragg, G. M. (2007). Natural products as sources of new drugs over the last 25 years. Journal of Natural Products, 70(3), 461–477.
  • Palladino, M. A., Bahjat, F. R., Theodorakis, E. A., & Moldawer, L. L. (2003). Anti-TNF-alpha therapies: The next generation. Nature Reviews Drug Discovery, 2(9), 736–746.
  • Rasmussen, H. S., & McCann, P. P. (1997). Matrix metalloproteinase inhibition as a novel anticancer strategy: A review with special focus on batimastat and marimastat. Pharmacological Therapy, 75(1), 69–75.
  • Sansom, M. S. P., Tieleman, D. P., Forrest, L. R., & Berendsen, H. J. C. (1998). Molecular dynamics simulations of membranes with embedded proteins and peptides: Porin, alamethicin and influenza virus M2. Biochemical Society Transactions, 26(3), 438–443.
  • Sastry, G. M., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. Journal of Computational Aided Molecular Design, 27(3), 221–234.
  • Schrodinger LLC (2014), Maestro Molecular Modeling Package, New York.
  • Schrodinger LLC (2014), Maestro Molecular Modeling Package, Prime Module, New York.
  • Sfikakis, P. P. (2010). The first decade of biologic TNF antagonists in clinical practice: Lessons learned, unresolved issues and future directions. Currents Directions in Autoimmunity, 11, 180–210.
  • Shelley, J. C., Cholleti, A., Frye, L. L., Greenwood, J. R., Timlin, M. R., & Uchimaya, M. (2007). Epik: A software program for pK(a) prediction and protonation state generation for drug-like molecules. Journal of Computational Aided Molecular Design, 21(12), 681–691.
  • Siu, S. W., Pluhackova, K., & Bockmann, R. A. (2012). Optimization of the OPLS-AA force field for long hydrocarbons. Journal of Chemical Theory Computation, 8(4), 1459–1470.
  • Verdonk, M. L., Cole, J. C., Hartshorn, M. J., Murray, C. W., & Taylor, R. D. (2003). Improved protein-ligand docking using GOLD. Proteins, 52(4), 609–623.
  • Wajant, H., Pfizenmaier, K., & Scheurich, P. (2003). Tumor necrosis factor signaling. Cell Death Differ, 10, 45–65.
  • Zaka, M., Sehgal, S. A., Shafique, S., & Abbasi, B. H. (2017). Comparative in silico analyses of Cannabis sativa, Prunella vulgaris and Withania somnifera compounds elucidating the medicinal properties against rheumatoid arthritis. Journal of Molecular Graphical Model, 74, 296–304.

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.