Integrating docking and molecular dynamics approaches for a series of proline-based 2,5-diketopiperazines as novel αβ-tubulin inhibitors

References

• Alan, D. B. (2012). 2,5-Diketopiperazines: Synthesis, reactions, medicinal chemistry, and bioactive natural products. Chemical Review , 112 , 3641–3716.
   PubMed Web of Science ®Google Scholar
• Alberto, M. , Antonio, C. , Romano, S. , Giovanni, S. , & Andrea, B. (2012). The tubulin colchicine domain: A molecular modeling perspective. ChemMedChem , 7 , 33–42.
   PubMed Web of Science ®Google Scholar
• Allen, J. D. , van Loevezijn, A. , Lakhai, J. M. , van der Valk, M. , van Tellingen, O. , Reid, G. , ... Schinkel, A. H. (2002). Potent and specific inhibition of the breast cancer resistance protein multidrug transporter in vitro and in mouse intestine by a novel analogue of fumitremorgin C. Cancer Therapy , 1 , 417–425.
   Google Scholar
• Amos, L. A. (2000). Focusing-in on microtubules. Current Opinion in Structural Biology , 10 , 236–241.10.1016/S0959-440X(00)00070-1
   PubMed Web of Science ®Google Scholar
• Arunrattiyakorn, P. , Ikeda, B. , Nitoda, T. , & Kanzaki, H. (2007). Enzymatic synthesis of dehydroderivatives from proline-containing cyclic dipeptides and their effects toward cell division. Bioscience, Biotechnology, and Biochemistry , 71 , 830–833.10.1271/bbb.60651
   PubMed Web of Science ®Google Scholar
• Baures, P. W. , Ojala, W. H. , Costain, W. J. , Ott, M. C. , Pradhan, A. , Gleason, W. B. , ... Johnson, R. L. (1997). Design, synthesis, and dopamine receptor modulating activity of diketopiperazine peptidomi metics of L-prolyl-L-leucylglycin amide. Journal of Medicinal Chemistry , 40 , 3594–3600.
   PubMed Web of Science ®Google Scholar
• Dennis, A. P. , & Lon, J. M. (2002). Five- and six-membered ring opening of pyroglutamic diketopiperazine. Journal of Organic Chemistry , 67 , 1820–1826.
   PubMed Web of Science ®Google Scholar
• Desai, A. , & Mitchison, T. J. (1997). Microtubule polymerization dynamics. Annual Review of Cell and Developmental Biology , 13 , 83–117.10.1146/annurev.cellbio.13.1.83
   PubMed Web of Science ®Google Scholar
• Essmann, U. , Perera, L. , Berkowitz, M. L. , Darden, T. , Lee, H. , & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics , 103 , 8577–8593.10.1063/1.470117
   Web of Science ®Google Scholar
• Fani, N. , Bordbar, A. K. , Ghayeb, Y. , & Sepehri, S. (In press). Computational design of Tryprostatin-A derivatives as novel αβ-tubulin inhibitors. Journal of Biomolecular Structure & Dynamics . doi:10.1080/07391102
   Web of Science ®Google Scholar
• Hess, B. , Bekker, H. , Berendsen, H. J. C. , & Fraaije, J. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry , 18 , 1463–1472.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• Howard, J. , & Hyman, A. A. (2003). Dynamics and mechanics of the microtubule plus end. Nature , 422 , 753–758.10.1038/nature01600
   PubMed Web of Science ®Google Scholar
• Irwin, J. J. , Sterling, T. , Mysinger, M. M. , Bolstad, E. S. , & Coleman, R. G. (2012). ZINC: A free tool to discover chemistry for biology. Journal of Chemical Information and Modeling , 52 , 1757–1768.10.1021/ci3001277
   PubMed Web of Science ®Google Scholar
• Jordan, M. A. , & Wilson, L. (2004). Microtubules as a target for anticancer drugs. Nature Reviews Cancer , 4 , 253–265.10.1038/nrc1317
   PubMed Web of Science ®Google Scholar
• Kim, H. O. , Nakanishi, H. , Lee, M. S. , & Kahn, M. (2000). Design and synthesis of novel conformationally restricted peptide secondary structure mimetics. Organic Letters , 2 , 301–302.10.1021/ol990355r
   PubMed Web of Science ®Google Scholar
• Li, W. , & Peng, S. (1998). Rational design and synthesis of unsaturated 2,5-dioxopiperazine derivatives as potential protein tyrosine kinase inhibitors. Tetrahedron Letters , 39 , 7373–7376.10.1016/S0040-4039(98)01599-8
   Web of Science ®Google Scholar
• Maiato, H. , Sampaio, P. , & Sunkel, C. E. (2004). Microtubule-associated proteins and their essential roles during mitosis. International Review of Cytology , 241 , 53–153.10.1016/S0074-7696(04)41002-X
   PubMed Web of Science ®Google Scholar
• Margolis, R. L. , & Wilson, L. (1978). Opposite end assembly and disassembly of microtubules at steady state in vitro. Cell , 13 , 1–8.10.1016/0092-8674(78)90132-0
   PubMed Web of Science ®Google Scholar
• Mitchison, T. J. , & Kirschner, M. (1984). Dynamic instability of microtubule growth. Nature , 312 , 237–242.10.1038/312237a0
   PubMed Web of Science ®Google Scholar
• 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 , 1639–1662.10.1002/(ISSN)1096-987X
   Web of Science ®Google Scholar
• O’Neill, J. C. , & Blackwell, H. E. (2007). Solid-phase and microwave-assisted syntheses of 2,5-diketopiperazines: Small molecules with great potential. Journal of Combinatorial Chemistry , 10 , 857.
   Web of Science ®Google Scholar
• Panda, D. , Samuel, J. C. , Massie, M. , Feinstein, S. C. , & Wilson, L. (2003). Differential regulation of microtubule dynamics by three- and four-repeat tau: Implications for the onset of neurodegenerative disease. Proceedings of the National Academy of Sciences , 100 , 9548–9553.10.1073/pnas.1633508100
   PubMed Web of Science ®Google Scholar
• Parrinello, M. , & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics , 52 , 7182–7190.10.1063/1.328693
   Web of Science ®Google Scholar
• Rivail, L. , Chipot, C. , Maigret, B. , Bestel, I. , Sicsic, S. , & Tarek, M. (2007). Large-scale molecular dynamics of a G protein-coupled receptor, the human 5-HT4 serotonin receptor, in a lipid bilayer. Journal of Molecular Structure: THEOCHEM , 817 , 19–26.10.1016/j.theochem.2007.04.012
   Web of Science ®Google Scholar
• Steven, L. S. (2005). Short and novel stereospecific synthesis of trisubstituted 2,5-diketopiperazines. Journal of Organic Chemistry , 70 , 4735–4740.
   PubMed Web of Science ®Google Scholar
• Van Aalten, D. M. F. , Bywater, R. , Findlay, J. B. C. , Hendlich, M. , Hooft, R. W. W. , & Vriend, G. (1996). PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. Journal of Computer-Aided Molecular Design , 10 , 255–262.10.1007/BF00355047
   PubMed Web of Science ®Google Scholar
• Van Der Spoel, D. , Lindahl, E. , Hess, B. , Groenhof, G. , Mark, A. E. , & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry , 26 , 1701–1718.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Wang, H. , Usui, T. , Osada, H. , & Ganesan, A. (2000). Synthesis and evaluation of tryprostatin B and demethoxy fumitremorgin C analogues. Journal of Medicinal Chemistry , 43 , 1577–1585.10.1021/jm9905662
   PubMed Web of Science ®Google Scholar
• Zhao, S. , Smith, K. S. , Deveau, A. M. , Dieckhaus, C. M. , Johnson, M. A. , Macdonald, T. L. , & Cook, J. M. (2002). Biological activity of the tryprostatins and their diastereomers on human carcinoma cell lines. Journal of Medicinal Chemistry , 45 , 1559–1562.
   PubMed Web of Science ®Google Scholar