Abstract
The nature of individual sensitivity to drugs associated with molecular polymorphism of human enzymes is discussed. The influence of molecular polymorphism on the activity of key human esterases, in particular, cholinesterases and carboxylesterase, responsible for hydrolytic metabolism of ester-containing drugs, is analyzed. A method was developed, which involves supercomputer-assisted modeling as a tool for assessment of molecular mechanism of the impact of point mutations on the catalytic activity of enzymes. This work is a part of a study aimed at elaboration of the concept and methods of personalized medicine.
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Molekulyarnyi polimorfizm cheloveka [Molecular Polymorphism in Humans], Ed. S. D. Varfolomeev, RUDN, Moscow, 2007, 810 pp. (in Russian).
Postgenomnye issledovaniya i tekhnologii [Postgenomic Research and Technologies], Ed. S. D. Varfolomeev, MSU, Moscow, 2011, 704 pp. (in Russian).
S. Lushchekina, A. Nemukhin, S. Varfolomeev, P. Masson, Chem.-Biol. Interact., 2016, 259, 223.
O. Lockridge, Pharmacol. Ther., 2015, 148, 34.
S. D. Varfolomeev, I. V. Uporov, E. V. Fedorov, Biochemistry (Moscow) (Engl. Transl.), 2002, 67, 1099 [Biochimiya, 2002, 67, 1328].
S. D. Varfolomeev, K. G. Gurevich, V. V. Poroikov, B. N. Sobolev, A. E. Fomenko, Dokl. Biochem. Biophys. (Engl. Transl.), 2001, 379, 252 [Dokl. AN, 2001, 379, 548].
S. D. Varfolomeev, K. G. Gurevich, Russ. Chem. Bull. (Int. Ed.), 2001, 50, 1709 [Izv. Akad. Nauk., Ser. Khim., 2001, 1629].
S. D. Varfolomeev, I. A. Gariev, I. V. Uporov, Russ. Chem. Rev., 2005, 74, 61 [Uspekhi Khimii, 2005, 74, 67].
V. S. Kurova, I. N. Kurochkin, G. R. Kalamkarov, A. E. Bugrova, K. Y. Fedortchenko, S. D. Varfolomeev, Biotechnology Adv., 2009, 27, 945.
V. V. Voevodin, S. A. Zhumatii, S. I. Sobolev, A. S. Antonov, P. A. Bryzgalov, D. A. Nikitenko, K. S. Stefanov, V. V. Voevodin, Open Systems J. (Engl. Transl.), 2012, 7 [Otkrytye Sistemy, 2012, 36].
V. Sadovnichy, A. Tikhonravov, V. Voevodin, V. Opanasenko, in: Contemporary High Performance Computing: From Petascale toward Exascale, Ed. J. S. Vetter, CRC Press, Boca Raton, USA, 2013, p. 283.
A. V. Nemukhin, B. L. Grigorenko, S. V. Lushchekina, S. D. Varfolomeev, Russ. Chem. Rev., 2012, 81, 1011 [Uspekhi Khimii, 2012, 81, 1011].
H. Delacour, S. Lushchekina, I. Mabboux, A. Bousquet, F. Ceppa, L. M. Schopfer, O. Lockridge, P. Masson, PLoS One, 2014, 9, e101552.
H. Delacour, S. Lushchekina, I. Mabboux, F. Ceppa, P. Masson, L. M. Schopfer, O. Lockridge, Biochem. Pharmacol., 2014, 92, 476.
Y. Nicolet, O. Lockridge, P. Masson, J. C. Fontecilla-Camps, F. Nachon, J. Biol. Chem., 2003, 278, 41141.
P. Masson, S. Lushchekina, L. M. Schopfer, O. Lockridge, Biochem. J., 2013, 454, 387.
S. V. Lushchekina, V. S. Polomskikh, S. D. Varfolomeev, P. Masson, Russ. Chem. Bull. (Int. Ed.), 2013, 62, 2527 [Izv. Akad. Nauk., Ser. Khim., 2013, 2527].
M. W. Schmidt, K. K. Baldridge, J. A. Boatz, S. T. Elbert, M. S. Gordon, J. H. Jensen, S. Koseki, N. Matsunaga, K. A. Nguyen, S. J. Su, T. L. Windus, M. Dupuis, J. A. Montgomery, J. Comput. Chem., 1993, 14, 1347.
G. M. Morris, R. Huey, W. Lindstrom, M. F. Sanner, R. K. Belew, D. S. Goodsell, A. J. Olson, J. Comput. Chem., 2009, 30, 2785.
N. P. Boltneva, G. F. Makhaeva, N. V. Kovaleva, S. V. Lushchekina, Ya. V. Burgart, E. V. Shchegol’kov, V. I. Saloutin, O. N. Chupakhin, Dokl. Biochem. Biophys. (Engl. Transl.), 2015, 465, 381 [Dokl. AN, 2015, 465, 367].
S. Bencharit, C. C. Edwards, C. L. Morton, E. L. HowardWilliams, P. Kuhn, P. M. Potter, M. R. Redinbo, J. Mol. Biol., 2006, 363, 201.
R. B. Best, X. Zhu, J. Shim, P. E. M. Lopes, J. Mittal, M. Feig, A. D. Mackerell, J. Chem. Theory Comput., 2012, 8, 3257.
K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov, A. D. Mackerell, J. Comput. Chem., 2010, 31, 671.
J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kalé, K. Schulten, J. Comput. Chem., 2005, 26, 1781.
W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graph., 1996, 14, 33.
S. V. Lushchekina, B. L. Grigorenko, A. V. Nemukhin, S. D. Varfolomeev, in Postgenomnye issledovaniya i tekhnologii [Postgenomic Research and Technologies], Ed. S. D. Varfolomeev, MSU, Moscow, 2011, 15 (in Russian).
A. V. Nemukhin, S. V. Lushchekina, A. V. Bochenkova, A. A. Golubeva, S. D. Varfolomeev, J. Mol. Modeling, 2008, 14, 409.
A. Shafferman, C. Kronman, Y. Flashner, M. Leitner, H. Grosfeld, A. Ordentlich, Y. Gozes, S. Cohen, N. Ariel, D. Barak, J. Biol. Chem., 1992, 267, 17640.
A. Shafferman, B. Velan, A. Ordentlich, C. Kronman, H. Grosfeld, M. Leitner, Y. Flashner, S. Cohen, D. Barak, N. Ariel, EMBO J., 1992, 11, 3561.
M. Harel, G. Kryger, T. L. Rosenberry, W. D. Mallender, T. Lewis, R. J. Fletcher, J. M. Guss, I. Silman, J. L. Sussman, Protein Sci., 2000, 9, 1063.
J. Wiesner, Z. Kriz, K. Kuca, D. Jun, J. Koca, J. Enzyme Inhib. Med. Chem., 2007, 22, 417.
J. Cheung, E. N. Gary, K. Shiomi, T. L. Rosenberry, ACS Med. Chem. Lett., 2013, 4, 1091.
A. D. Kharlamova, S. V. Lushchekina, K. A. Petrov, E. D. Kots, F. V. Nachon, M. Villard-Wandhammer, I. V. Zueva, E. Krejci, V. S. Reznik, V. V. Zobov, E. E. Nikolsky, P. Masson, Biochem. J., 2016, 473, 1225.
D. Kaplan, A. Ordentlich, D. Barak, N. Ariel, C. Kronman, B. Velan, A. Shafferman, Biochemistry, 2001, 40, 7433.
A. Ordentlich, C. Kronman, D. Barak, D. Stein, N. Ariel, D. Marcus, B. Velan, A. Shafferman, FEBS Lett., 1993, 334, 215.
Z. Kovarik, N. Macek Hrvat, M. Katalinic, R. K. Sit, A. Paradyse, S. Zunec, K. Musilek, V. V. Fokin, P. Taylor, Z. Radic, Chem. Res. Toxicol., 2015, 28, 1036.
P. Masson, S. V. Lushchekina, Arch. Biochem. Biophys., 2016, 593, 60.
M. R. Gätke, J. R. Bundgaard, J. Viby-Mogensen, Pharmacogenet. Genomics, 2007, 17, 995.
P. Masson, L. M. Schopfer, M. T. Froment, J. C. Debouzy, F. Nachon, E. Gillon, O. Lockridge, A. Hrabovska, B. N. Goldstein, Chem.-Biol. Interact., 2005, 157–158, 143.
P. Masson, Biochemistry (Moscow) (Engl. Transl.), 2012, 77, 1147 [Biochimiya, 2012, 77, 1383].
S. V. Lushchekina, A. V. Nemukhin, S. D. Varfolomeev, P. Masson, J. Mol. Neurosci., 2014, 52, 434.
A. V. Nemukhin, I. A. Gariev, A. V. Rogov, S. D. Varfolomeev, Mendeleev Commun., 2006, 16, 290.
C. B. Millard, O. Lockridge, C. A. Broomfield, Biochemistry, 1995, 34, 15925.
O. Lockridge, R. M. Blong, P. Masson, M. T. Froment, C. B. Millard, C. A. Broomfield, Biochemistry, 1997, 36, 786.
P. Masson, D. Roshu, Acta Naturae, 2009, 1, 68.
P. Masson, F. Nachon, C. A. Broomfield, D. E. Lenz, L. Verdier, L. M. Schopfer, O. Lockridge, Chem.-Biol. Interact., 2008, 175, 273.
P. Masson, S. V. Lushchekina, Chem.-Biol. Interact., 2016, 259, 319.
M. Amitay, A. Shurki, Proteins: Struct., Funct., Bioinf., 2011, 79, 352.
Y. Yao, J. Liu, C.-G. Zhan, Biochemistry, 2012, 51, 8980.
M. J. Field, T. W. Wymore, Phys. Scr., 2014, 89, 108004.
A. Kulakova, S. Lushchekina, B. Grigorenko, A. Nemukhin, J. Theor. Comput. Chem., 2015, 1550051.
A. V. Nemukhin, A. M. Kulakova, S. V. Lushchekina, A. Yu. Ermilov, S. D. Varfolomeev, Moscow Univ. Chem. Bull. Ser. Khim. (Engl. Transl.), 2015, 70, 274 [Vestn. MGU, Ser. 2. Khimiya, 2015, 56, 343].
W. Kalow, N. Staron, Biochem. Cell Biol., 1957, 35, 1305.
W. Kalow, R. O. Davies, Biochem. Pharmacol., 1958, 1, 183.
M. C. Mcguire, C. P. Nogueira, C. F. Bartels, H. Lightstone, A. Hajra, A. F. Van Der Spek, O. Lockridge, B. N. La Du, Proc. Natl. Acad. Sci. USA, 1989, 86, 953.
P. Masson, P. Legrand, C. F. Bartels, M.-T. Froment, L. M. Schopfer, O. Lockridge, Biochemistry, 1997, 36, 2266.
S. V. Lushchekina, B. L. Grigorenko, D. I. Morozov, I. V. Polyakov, A. V. Nemukhin, S. D. Varfolomeev, Russ. Chem. Bull. (Int. Ed.), 2010, 59, 55 [Izv. Akad. Nauk., Ser. Khim., 2010, 56].
V. Levitsky, W. Xie, M.-T. Froment, O. Lockridge, P. Masson, Biochim. Biophys. Acta, Protein Struct. Mol. Enzymol., 1999, 1429, 422.
P. Masson, C. Clery, P. Guerra, A. Redslob, C. Albaret, P. L. Fortier, Biochem. J., 1999, 343, 361.
P. Masson, W. Xie, M. T. Froment, V. Levitsky, P. L. Fortier, C. Albaret, O. Lockridge, Biochim. Biophys. Acta, 1999, 1433, 281.
P. Masson, W. Xie, M. T. Froment, O. Lockridge, Biochim. Biophys. Acta, 2001, 1544, 166.
I. A. Adzhubei, S. Schmidt, L. Peshkin, V. E. Ramensky, A. Gerasimova, P. Bork, A. S. Kondrashov, S. R. Sunyaev, Nat. Methods, 2010, 7, 248.
J. M. Schwarz, C. Rodelsperger, M. Schuelke, D. Seelow, Nat. Methods, 2010, 7, 575.
T. Satoh, M. Hosokawa, Toxicol. Lett., 1995, 82–83, 439.
T. Satoh, M. Hosokawa, Chem.-Biol. Interact., 2006, 162, 195.
M. J. Hatfield, R. A. Umans, J. L. Hyatt, C. C. Edwards, M. Wierdl, L. Tsurkan, M. R. Taylor, P. M. Potter, Chem. Biol. Interact., 2016.
G. F. Makhaeva, S. V. Lushchekina, N. P. Boltneva, V. B. Sokolov, V. V. Grigoriev, O. G. Serebryakova, E. A. Vikhareva, A. Y. Aksinenko, G. E. Barreto, G. Aliev, S. O. Bachurin, Sci. Rep., 2015, 5, 13164.
M. Citron, Nat. Rev. Drug Discov., 2010, 9, 387.
V. E. Semenov, I. V. Zueva, M. A. Mukhamedyarov, S. V. Lushchekina, A. D. Kharlamova, E. O. Petukhova, A. S. Mikhailov, S. N. Podyachev, L. F. Saifina, K. A. Petrov, O. A. Minnekhanova, V. V. Zobov, E. E. Nikolsky, P. Masson, V. S. Reznik, Chem MedChem, 2015, 10, 1863.
G. F. Makhaeva, O. G. Serebryakova, N. P. Boltneva, T. G. Galenko, A. Y. Aksinenko, V. B. Sokolov, I. V. Martynov, Dokl. Biochem. Biophys. (Engl. Transl.), 2008, 423, 352 [Dokl. AN, 2008, 423, 826].
G. F. Makhaeva, N. P. Boltneva, S. V. Lushchekina, O. G. Serebryakova, T. S. Stupina, A. A. Terentiev, I. V. Serkov, A. N. Proshin, S. O. Bachurin, R. J. Richardson, Bioorg. Med. Chem., 2016, 24, 1050.
H. J. Zhu, K. S. Patrick, H. J. Yuan, J. S. Wang, J. L. Donovan, C. L. Devane, R. Malcolm, J. A. Johnson, G. L. Youngblood, D. H. Sweet, T. Y. Langaee, J. S. Markowitz, Am. J. Hum. Genet., 2008, 82, 1241.
H. J. Zhu, J. S. Markowitz, Drug Metab. Dispos., 2009, 37, 264.
H. J. Zhu, D. I. Appel, J. A. Johnson, K. D. Chavin, J. S. Markowitz, Biochem. Pharmacol., 2009, 77, 1266.
E. K. Tarkiainen, M. T. Holmberg, A. Tornio, M. Neuvonen, P. J. Neuvonen, J. T. Backman, M. Niemi, Clin. Pharmacol. Ther., 2015, 97, 650.
B. L. Hoh, Y. Gong, C. W. Mcdonough, M. F. Waters, A. J. Royster, T. O. Sheehan, B. Burkley, T. Y. Langaee, J. Mocco, S. L. Zuckerman, N. Mummareddy, M. L. Stephens, C. Ingram, C. M. Shaffer, J. C. Denny, M. H. Brilliant, T. E. Kitchner, J. G. Linneman, D. M. Roden, J. A. Johnson, J. Neurosurg., 2015, 1.
T. Jefferson, M. Jones, P. Doshi, E. A. Spencer, I. Onakpoya, C. J. Heneghan, BMJ, 2014, 348, g2545.
T. Jefferson, M. A. Jones, P. Doshi, C. B. Del Mar, R. Hama, M. J. Thompson, E. A. Spencer, I. Onakpoya, K. R. Mahtani, D. Nunan, J. Howick, C. J. Heneghan, The Cochrane Database of Systematic Reviews, 2014, 4, CD008965.
R. Thomsen, H. B. Rasmussen, K. Linnet, I. Consortium, J. Anal. Toxicol., 2012, 36, 560.
H. A. Spiller, H. L. Hays, A. Aleguas, CNS Drugs, 2013, 27, 531.
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Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1592—1607, June, 2016.
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Varfolomeev, S.D., Lushchekina, S.V., Nemukhin, A.V. et al. Molecular polymorphism of human enzymes as the basis of individual sensitivity to drugs. Supercomputer-assisted modeling as a tool for analysis of structural changes and enzymatic activity of proteins. Russ Chem Bull 65, 1592–1607 (2016). https://doi.org/10.1007/s11172-016-1487-8
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DOI: https://doi.org/10.1007/s11172-016-1487-8