Biopolym. Cell. 1991; 7(5):5-14.
http://dx.doi.org/10.7124/bc.0002EB
Reviews
A Monte Carlo simulation of purine series alkaloids' stacking
1Danilov V. I., 1Slyusarchuk O. N., 2Poltev V. I., 3Brickmann J. A. W., 4Alderfer J. L., 3Wollman R. M.
  1. Institute of Molecular Biology and Genetics, Academy of Sciences of the Ukrainian SSR
    Kiev, USSR
  2. Institute of Biological Physics, Academy of Sciences of the USSR
    Pushchino, Moscow Region, USSR
  3. Technische Hochschule zu Darmstadt
    Darmstadt, FRG
  4. Roswell Park Cancer Institute
    Elm and Carlton Str., Buffalo, New-York, USA, 14263

Abstract

Results on a Monte Carlo simulation of the hydration of monomer and possible stacked dimer forms of purine series alkaloids in the cluster of 200 molecules are presented. Investigation of different purine stacked dimers has shown that for caffeine there exists one, for theophylline two and for theobromine four dimers favourable energetically. It is found that the main factor stabilizing favourable stacks is the change in the interaction between water molecules connected with the change in water structure around monomers during their association. The analysis performed for the hydration energetic and structural characteristics has shown that the association process of the alkaloids' molecules in water is closely connected with the hydrophobic character of methyl groups. Change n the hydrated properties of purine series alkaloids upon transition from monomer forms to dimer ones may be decisive for interaction with biopolymers in the primary mechanisms of their pharmacological effect.
Full text: (PDF, in Russian)

References

[1] The year book of drug therapy . Ed. L. E. Hollister, D. L. Azarnoff, D. G. Shand. Chicago; London : Year Book Med. Publ., 1979. 468 p.
[2] Paoletti R, Cabtaluppi S. New trends in the pharmacology of caffeine. IX Colloq. Sci. Int. Cafe. Paris, 1981:41-53.
[3] Foote WE, Holmes P, Pritchard A. et al. New physiological and pharmacological studies of caffeine. Neuropharmacology. 1978; 17:7-12.
[4] Sernka TJ, Tseng CH. Effects of caffeine on transport, metabolism and ultrastructure of isolated rat colon. Gen Physiol Biophys. 1985;4(1):69-80.
[5] Trotta EE, Freire GL. Inhibition by caffeine of calcium uptake by brain microsomal vesicles. J Pharm Pharmacol. 1980;32(11):791-3.
[6] Lewis SE, Anderson P, Goldspink DF. The effects of calcium on protein turnover in skeletal muscles of the rat. Biochem J. 1982;204(1):257-64.
[7] Stone TW. Cell-membrane receptors for purines. Review. Biosci Rep. 1982;2(2):77-90.
[8] Henry JP, Stephens PM. Caffeine as an intensifier of stress-induced hormonal and pathophysiologic changes in mice. Pharmacol Biochem Behav. 1980;13(5):719-27.
[9] Ts'o POP. Bases, nucleosides and nucleotides. In: Basic principles in nucleic acid chemistry. Ed. P. O. P. Ts'o. New. York; London: Acad press, 1974; Vol. 1:453-584.
[10] Thakkar AL, Tensmeyer LG, Wilham WL. NMR evidence for self-association of theophylline in aqueous solution. J Pharm Sci. 1971;60(8):1267-9.
[11] Kirschbaum J. Self-association of theophylline in aqueous solution. J Pharm Sci. 1973;62(1):168-9.
[12] Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E. Equation of State Calculations by Fast Computing Machines. J Chem Phys. 1953;21(6):1087-92.
[13] Lee J, Barker JA, Abraham FF. Theory and Monte Carlo simulation of physical clusters in the imperfect vapor. J Chem Phys. 1973; 58(8):3166-80.
[14] Abraham F.F. Monte Carlo simulation of physical clusters of water molecules. J Chem Phys. 1974; 61(3):1221-5.
[15] Mruzik MR, Abraham FF, Schreiber DE, Pound GM. A Monte Carlo study of ion-water clusters. J Chem Phys. 1976; 64(2):481-91.
[16] Dyakonova LP, Malenkov GG. Modeling of the structure of liquid water by the Monte Carlo method. Zh strukt khim. 1979; 20(5):854-861.
[17] Zhurkin VB, Poltev VI, Florent'ev VL. Atom--atomic potential functions for conformational calculations of nucleic acids. Mol Biol (Mosk). 1980;14(5):1116-30.
[18] Poltev VI, Danilov VI, Sharafutdinov MR et al. Simulation of the interaction of nucleic acid fragments with solvent using atom-aiom Potential function. Stud biophys. 1982; 91(1):37-43.
[19] Cesaro A, Russo E, Crescenzi V. Thermodynamics of caffeine aqueous solutions. J Phys Chem. 1976;80(3):335–9.
[20] Bothe H, Cammenga HK. Phase transitions and thermodynamic properties of anhydrous caffeine. J Therm Anal. 1979;16(2):267–75.
[21] Danilov VI, Shestopalova AV. Hydrophobic effect in biological associates: A Monte Carlo simulation of caffeine molecules stacking. Int J Quantum Chem. 1989;35(1):103–12.
[22] Shestopalova AV, Danilov VI, Maleev VYa. Nature stackformation of caffeine molecules n water: Monte Carlo simulation. Dokl Akad Nauk SSSR. 1985; 282(4):1000-2.
[23] Danilov VI, Tolokh IS, Poltev VI. Nature of the stacking interactions of nucleotide bases in water: a Monte Carlo study of the hydration of thymine moleculeassociates. FEBS Lett. 1984; 171(2):325-328.
[24] Danilov VI, Tolokh IS. Nature of nucleotide base associations in water: the Monte Carlo simulation of the hydration of pyrimidine bases and their molecular associates. Biopolym Cell. 1985; 1(2):59-69.