In silico Study of the Interaction between the Modified B-ring Analogues of Colchicine with Tubulin Heterodimer
Abstract
Theoretical investigation of the interaction between the modifications at the C-5, C-6, and C-7 positions of the B-ring of colchicine and tubulin heterodimer has been investigated by using the molecular docking simulation. The docking results provide the energetic and structural information in terms of the binding energy, binding affinity, hydrogen bonding, and conformations of docked ligand poses with residues within colchicine binding site. Overall results show that the modified C-5 (in Model A) and C-7 (in Model C) of B-ring analogues give the highest binding affinities to tubulin, whereas all lowest-affinity isomers belong to the C-6 substituents (in Model B). As expected, the docked ligands of the C-5, C-6, and C-7 of B-ring analogues which are located at the a/b intradimer interface of tubulin were shifting toward the a-subunit binding space to form drug-tubulin complexes. Keywords : colchicine, B-ring analogues, tubulin, binding affinity, molecular dockingReferences
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Andrushko, V. (2013). Andrushko, V. & Andrushko, N., 2013. Stereoselective Synthesis of Drugs and Natural Products, Two Volume Set. New Jersey: John Wiley & Sons.
Bai, R., Covell, D.G., Pei, X.F., Ewelli, J.B., Nguyeni, N.Y., Brossi, A. & Hamel, E. (2000). Mapping the binding site of colchicinoids on -tubulin. J. Biol. Chem., 275, 40443-40452.
Bane, S., Puett, D., Macdonald, T.L. & Williams, Jr. R.C. (1984). Binding to tubulin of the colchicine analog
2-methyoxy-5-(2',3',4'-trimethoxyphenyl)tropone. J. Biol. Chem., 259, 7391-7398.
Banerjee, A., Engelborghs, Y., D’Hoore, A. & Fitzgerald, T.J. (1997). Interactions of a bicyclic analog of colchicine with -tubulin isoforms II, III and IV. Eur. J. Biochem., 246, 420-424.
Botta, M., Forli, S., Magnani, M. & Manetti, F. (2009). Molecular modeling approaches to study the binding mode on tubulin of microtubule destabilizing and stabilizing agents. Top. Curr. Chem., 286, 279-328.
Chakrabarti, G., Sengupta, S. & Bhattacharyya, B. (1996). Thermodynamics of colchicinoid-tubulin interactions: role of B-ring and C-7 substituents. J. Biol. Chem., 271, 2897-2901.
Chaudhuri, A.R., Seetharamalu, P., Schwarz, P.M., Hausheer, F.H. & Ludueña, R.F. (2000). The interaction of the B-ring of colchicine with -tubulin: a novel footprinting approach. J. Mol. Biol., 303, 679-692.
Choudhury, G.G., Banerjee, A., Bhattacharyya, B. & Biswas, B.B. (1983). Interaction of colchicine analogues with purified tubulin. FEBS LETTERS, 161, 55-59.
Choudhury, G.G., Maity, S., Bhattacharyya, B. & Biswas, B.B. (1986). B-ring of colchicine and its role in taxol-induced tubulin polymerization. FEBS LETTERS, 197, 31-34.
Cifuentes, M., Schilling B., Ravindra, R., Winter, J. & Janik M.E. (2006). Synthesis and biological evaluation of
B-ring modified colchicine and isocolchicine analogs, Bioorg. Med. Chem. Lett., 16, 2761-2764.
Dumortier, C., Gorbunoff, M.J., Andreu, J.M. & Engelborghs, Y. (1996). Alterations of rings B and C of colchicine are cumulative in overall binding to tubulin but modify each kinetic step. Biochem., 35, 15900-15906.
Dumortier, C., Yan Q., Bane, S. & Engelborghs, Y. (1997). Mechanism of tubulin-colchicine recognition: a kinetic study of the binding of the colchicine analogues colchicide and isocolchicine, Biochem. J., 327, 685-688.
Hahn, M. (1995). Receptor surface models: 1. Definition and construction, J. Med. Chem., 38, 2080-2090.
Hastie S.B., Williams, Jr. R.C., Puett, D. & Macdonald, T.L. (1989). The binding of isocolchicine to tubulin: mechanisms of ligand association with tubulin. J. Biol. Chem., 264, 6682-6688.
Koehn, F.E. (2014). Natural Products and Cancer Drug Discovery. Springer New York: Hamana Press.
Kozaka, T., Nakagawa-Goto, K., Shi, Q., Lai, C.Y., Hamel, E., Bastow, K.F., Brossi, A. & Lee, K.H. (2010). Antitumor agents 273. Design and synthesis of N-alkyl-thiocolchicinoids as potential antitumor agents, Bioorg. Med. Chem. Lett., 20, 4091-4094.
Kumbhar, B.V., Borogaon, A., Panda, D. & Kunwar, A. (2016). Exploring the origin of differential binding affinities of human tubulin isotypes II, III and IV for DAMA-colchicine using homology modeling, molecular docking and molecular mechanics simulations. PLOS ONE 11(5): e0156048. DOI:10.1371/ journal.pone.0156048.
Leung, Y.Y. (2015). Colchicine-Update on mechanisms of action and therapeutic uses. Semin. Arthritis. Rheum., 45, 341-350.
Lu, Y., Chen, J., Xiao, M., Li, W. & Miller, D.D. (2012). An overview of tubulin inhibitors that interact with colchicine binding site, Pharm. Res., 29, 2943-2971.
Maity, S.N. & Bhattacharyya, B. (1987). Properties of B-ring analogues of colchicine. FEBS LETTERS, 218, 102-106.
Morris, G.M., Huey, R., Lindstrom, W., Sanner, M.F., Belew, R.K., Goodsell, D.S. & Olson, A.J. (2009). AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility. J. Comput. Chem., 30, 2785-2791.
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. J. Comput. Chem., 19, 1639-1662.
Niel, E. & Scherrmann, J.-M. (2006). Colchicine today, Joint Bone Spine, 73, 672-678.
Nguyen, T.L., McGrath, C., Hermone, A.R., Burnett, J.C., Zaharevitz, D.W., Day, B.W., Wipf, P., Hamel, E. & Gussio, R. (2005). A common pharmacophore for a diverse set of colchicine site inhibitors using a structure-based approach. J. Med. Chem., 50, 6107-6116.
Ravelli R.B., Gigant, B., Curmi, P.A., Jourdain, I., Lachkar, S., Sobel, A. & Knossow, M. (2004). Insight into tubulin regulation from a complex with colchicine and a stathmin-like domain. Nature, 428, 198-202.
Ray, K., Bhattacharyya, B. & Biswas, B.B. (1981). Role of B-ring of colchicine in its binding to tubulin. J. Biol. Chem., 256, 6241-6244.
Terkeltaub, R.A. (2009). Colchicine Update: 2008. Semin. Arthritis. Rheum., 38, 411-419.
Trott, O. & Olson, A.J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, J. Comput. Chem., 31, 455-461.
Wolff, J. & Knipling, L. (1995). Colchicine binding by the “isolated” -monomer of tubulin. J. Biol. Chem., 270, 16809-16812.
Zefirova, O.N., Diikov, A.G., Zyk, N.V. & Zefirov, N.S. (2007). Ligands of the colchicine site of tubulin: a common pharmacophore and new structural classes. Russ. Chem. Bull., Int. Ed., 56, 680-688.
Andrushko, V. (2013). Andrushko, V. & Andrushko, N., 2013. Stereoselective Synthesis of Drugs and Natural Products, Two Volume Set. New Jersey: John Wiley & Sons.
Bai, R., Covell, D.G., Pei, X.F., Ewelli, J.B., Nguyeni, N.Y., Brossi, A. & Hamel, E. (2000). Mapping the binding site of colchicinoids on -tubulin. J. Biol. Chem., 275, 40443-40452.
Bane, S., Puett, D., Macdonald, T.L. & Williams, Jr. R.C. (1984). Binding to tubulin of the colchicine analog
2-methyoxy-5-(2',3',4'-trimethoxyphenyl)tropone. J. Biol. Chem., 259, 7391-7398.
Banerjee, A., Engelborghs, Y., D’Hoore, A. & Fitzgerald, T.J. (1997). Interactions of a bicyclic analog of colchicine with -tubulin isoforms II, III and IV. Eur. J. Biochem., 246, 420-424.
Botta, M., Forli, S., Magnani, M. & Manetti, F. (2009). Molecular modeling approaches to study the binding mode on tubulin of microtubule destabilizing and stabilizing agents. Top. Curr. Chem., 286, 279-328.
Chakrabarti, G., Sengupta, S. & Bhattacharyya, B. (1996). Thermodynamics of colchicinoid-tubulin interactions: role of B-ring and C-7 substituents. J. Biol. Chem., 271, 2897-2901.
Chaudhuri, A.R., Seetharamalu, P., Schwarz, P.M., Hausheer, F.H. & Ludueña, R.F. (2000). The interaction of the B-ring of colchicine with -tubulin: a novel footprinting approach. J. Mol. Biol., 303, 679-692.
Choudhury, G.G., Banerjee, A., Bhattacharyya, B. & Biswas, B.B. (1983). Interaction of colchicine analogues with purified tubulin. FEBS LETTERS, 161, 55-59.
Choudhury, G.G., Maity, S., Bhattacharyya, B. & Biswas, B.B. (1986). B-ring of colchicine and its role in taxol-induced tubulin polymerization. FEBS LETTERS, 197, 31-34.
Cifuentes, M., Schilling B., Ravindra, R., Winter, J. & Janik M.E. (2006). Synthesis and biological evaluation of
B-ring modified colchicine and isocolchicine analogs, Bioorg. Med. Chem. Lett., 16, 2761-2764.
Dumortier, C., Gorbunoff, M.J., Andreu, J.M. & Engelborghs, Y. (1996). Alterations of rings B and C of colchicine are cumulative in overall binding to tubulin but modify each kinetic step. Biochem., 35, 15900-15906.
Dumortier, C., Yan Q., Bane, S. & Engelborghs, Y. (1997). Mechanism of tubulin-colchicine recognition: a kinetic study of the binding of the colchicine analogues colchicide and isocolchicine, Biochem. J., 327, 685-688.
Hahn, M. (1995). Receptor surface models: 1. Definition and construction, J. Med. Chem., 38, 2080-2090.
Hastie S.B., Williams, Jr. R.C., Puett, D. & Macdonald, T.L. (1989). The binding of isocolchicine to tubulin: mechanisms of ligand association with tubulin. J. Biol. Chem., 264, 6682-6688.
Koehn, F.E. (2014). Natural Products and Cancer Drug Discovery. Springer New York: Hamana Press.
Kozaka, T., Nakagawa-Goto, K., Shi, Q., Lai, C.Y., Hamel, E., Bastow, K.F., Brossi, A. & Lee, K.H. (2010). Antitumor agents 273. Design and synthesis of N-alkyl-thiocolchicinoids as potential antitumor agents, Bioorg. Med. Chem. Lett., 20, 4091-4094.
Kumbhar, B.V., Borogaon, A., Panda, D. & Kunwar, A. (2016). Exploring the origin of differential binding affinities of human tubulin isotypes II, III and IV for DAMA-colchicine using homology modeling, molecular docking and molecular mechanics simulations. PLOS ONE 11(5): e0156048. DOI:10.1371/ journal.pone.0156048.
Leung, Y.Y. (2015). Colchicine-Update on mechanisms of action and therapeutic uses. Semin. Arthritis. Rheum., 45, 341-350.
Lu, Y., Chen, J., Xiao, M., Li, W. & Miller, D.D. (2012). An overview of tubulin inhibitors that interact with colchicine binding site, Pharm. Res., 29, 2943-2971.
Maity, S.N. & Bhattacharyya, B. (1987). Properties of B-ring analogues of colchicine. FEBS LETTERS, 218, 102-106.
Morris, G.M., Huey, R., Lindstrom, W., Sanner, M.F., Belew, R.K., Goodsell, D.S. & Olson, A.J. (2009). AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility. J. Comput. Chem., 30, 2785-2791.
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. J. Comput. Chem., 19, 1639-1662.
Niel, E. & Scherrmann, J.-M. (2006). Colchicine today, Joint Bone Spine, 73, 672-678.
Nguyen, T.L., McGrath, C., Hermone, A.R., Burnett, J.C., Zaharevitz, D.W., Day, B.W., Wipf, P., Hamel, E. & Gussio, R. (2005). A common pharmacophore for a diverse set of colchicine site inhibitors using a structure-based approach. J. Med. Chem., 50, 6107-6116.
Ravelli R.B., Gigant, B., Curmi, P.A., Jourdain, I., Lachkar, S., Sobel, A. & Knossow, M. (2004). Insight into tubulin regulation from a complex with colchicine and a stathmin-like domain. Nature, 428, 198-202.
Ray, K., Bhattacharyya, B. & Biswas, B.B. (1981). Role of B-ring of colchicine in its binding to tubulin. J. Biol. Chem., 256, 6241-6244.
Terkeltaub, R.A. (2009). Colchicine Update: 2008. Semin. Arthritis. Rheum., 38, 411-419.
Trott, O. & Olson, A.J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, J. Comput. Chem., 31, 455-461.
Wolff, J. & Knipling, L. (1995). Colchicine binding by the “isolated” -monomer of tubulin. J. Biol. Chem., 270, 16809-16812.
Zefirova, O.N., Diikov, A.G., Zyk, N.V. & Zefirov, N.S. (2007). Ligands of the colchicine site of tubulin: a common pharmacophore and new structural classes. Russ. Chem. Bull., Int. Ed., 56, 680-688.
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2018-01-05
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