Using molecular simulations to probe pharmaceutical materials

Journal of Pharmaceutical Sciences

Volumn 100, Issue 6, 2011, Pages 2000-2019

  Cui, Yong ^a  

^a GENENTECH INC   (United States)

Author keywords

Force field; Materials science; Molecular dynamics; Molecular modeling; Monte Carlo; Stochasticity; Thermodynamics statistical mechanics

Indexed keywords

ANALYTIC METHOD; MOLECULAR DYNAMICS; MOLECULAR MODEL; MONTE CARLO METHOD; REVIEW; STATISTICS; STOCHASTIC MODEL; THERMODYNAMICS;

EID: 79954452616     PISSN: 00223549     EISSN: 15206017     Source Type: Journal    
DOI: 10.1002/jps.22392     Document Type: Review

References (53)

1. Metropolis N, Ulam S. 1949. The Monte Carlo method. J Am Stat Assoc 44:335-341.
2. Beichl I, Sullivan F. 2000. The Metropolis algorithm. Comput Sci Eng 2:65-69.
3. Gavezzotti A. 1999. A molecular dynamics view of some kinetic and structural aspects of melting in the acetic acid crystal. J Mol Struct (L.S.Bartell Special Issue) 486:485-499.
4. Svishchev IM, Kusalik PG. 1995. Crystallization of molecular liquids in computer simulations: Carbon dioxide. Phys Rev Lett 75:3289-3292.
5. Laasonen K, Wonczak S, Strey R. 2000. Molecular dynamics simulations of gas-liquid nucleation of Lennard-Joses fluid. J Chem Phys 113:9741-9747.
6. Ferrari ES, Burton C, Davey RJ, Gavezzotti A. 2006. Simulation of phase separation in alcohol/water mixture using two-body force field and standard molecular dynamics. J Comput Chem 27:1211-1219.
7. Yoneya M, Nishikawa E. 2004. Sponteneous three-dimensional nanostructure formation of perfluoroalkyl terminated liquid crystal: A molecular dynamics simulation study. J Chem Phys 121:7520-7525.
8. Sellner B, Zifferer G, Kornherr A, Krois D, Brinker UH. 2008. Molecular dynamics simulations of β-cyclodextrin-aziadamantane complexes in water. J Phys Chem B 112:710-714.
9. Gavezzotti A. 2007. Molecular aggregation. New York: Oxford University Press Inc. Chapt. 4. pp87-113.
10. Silbey RJ, Alberty RA, Bawendi MG. 2005. Physical chemistry. 4th ed. Hoboken, New Jersey: John Wiley & Sons, Inc. p 77.
11. Chandler D. 1987. Introduction to modern statistical mechanics. New York: Oxford University Press. Chapt. 3.
12. Agarwal BK, Eisner M. 1998. Statistical mechanics. 2nd ed. New Delhi, India: New Age International Ltd. p 12.
13. Uffink J. 2004. Boltzmann's work in statistical physics. In The Stanford encyclopedia of philosophy (Winter 2004 Edition); Edward N. Zalta, Ed. The Metaphysics Research Lab, Stanford University, Stanford, CA. last accessed 03-Nov-2010.
14. Dill KA, Bromberg S. 2003. Molecular driving forces: Statistical thermodynamics in chemistry and biology. New York: Garland Science. p175.
15. Grinstead CM, Snell JL. Introduction to probability. 2nd ed. Providence, Rhode Island. American Mathemetical Sociaty. Chapt. 9. pp 325-355.
16. Jaynes ET. 2003. In Probability theory: The logic of science; Bretthorst GL, ed. Cambridge, UK: Cambridge University Press, Chapt. 3.
17. Sinha SK. 2005. Introduction to statistical mechanics. Oxford, U.K. Alpha Science International Ltd. pp 372-373.
18. Carter AH. 2001. Classical and statistical thermodynamics. New Jersey: Prentice-Hall, Inc. Chapt. 13. pp 233-238.
19. Bernal JD. 1964. The Bakerian lecture, 1962. The structure of liquids. Proc R Soc 280:299-322.
20. Haile JM. 1997. Molecular dynamics simulation. New York: John Wiley & Sons, Inc. pp 117-127.
21. Rapaport DC. 1995. The art of molecular dynamics simulation. Cambridge, UK: Cambridge University Press. Chapts. 2 and 3.
22. Frenkel D, Smit B. 2002. Understanding molecular simulation: From algorithms to applications. San Diego, California: Academic Press. Chapt. 3.
23. MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field ML, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnik S, Ngo T, Nguyen DT, Prodhom B, Reiher WE III, Roux B, Schlenkrich B, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586-3616.
24. Weiner SJ, Kollman PA, Nguyen TA, Case DA. 1986. An all atom force field for simulations for proteins and nuclei acids. J Comput Chem 7:230-252.
25. Wallace DC. 2002. Statistical physics of crystals and liquids. Singapore: World Scientific Publishing Co. Pte. Ltd. Chapt. 2.
26. Sun H. 1998. COMPASS: An ab initio force-field optimized for condensed-phase: Applications overview with details on alkane and benzene compounds. J Phys Chem B 102:7338.
27. Mooij WTM, van Duijneveldt FB, van Duijneveldt-van de Rijdt JGCM, van Eijck BP. 1999. Transferable ab initio intermolecular potentials. 1. Derivation from methanol dimmer and trimer calculations. J Phys Chem A 103:9872-9882.
28. Xiang TX, Anderson BD. 2003. A molecular dynamics simulation of reactant mobility in an amorphous formulation of a peptide in poly(vinylpyrrolidone). J Pharm Sci 93:855-876.
29. Xiang TX, Anderson BD. 2005. Distribution and effect of water content on molecular mobility in poly(vinylpyrrolidone) glasses: A molecular dynamics simulation. Pharm Res 22:1205-1214.
30. Xiang TX, Anderson BD. 2005. Conformational structure, dynamics, and salvation energies of small alanine peptide in water and carbon tetrachloride. J Pharm Sci 95:1269-1287.
31. Conrad PB, de Pablo JJ. 1999. Computer simulation of the cryoprotectant disaccharide α, α-trehalose in aqueous solution. J Phys Chem A 103:4049-4055.
32. Jain N, Yalkowsky S. 2001. Estimation of the aqueous solubility I: Application to organic nonelectrolytes J Pharm Sci 90:234-252.
33. Westergren J, Lindfors L, Hoglund T, Luder K, Nordholm S, Kjellander R. 2007. In solico prediction of drug solubility: 1. Free energy of hydration. J Phys Chem B 111:1872-1882.
34. Luder K, Lindfors L, Westergren J, Nordholm S, Kjellander R. 2007. In solico prediction of drug solubility: 2. Free energy of salvation in pure melts. J Phys Chem B 111:1883-1892.
35. Luder K, Lindfors L, Westergren J, Nordholm S, Kjellander R. 2007. In solico prediction of drug solubility: 3. Free energy of salvation in pure amorphous matter. J Phys Chem B 111:1872-1882.
36. Huynh L, Grant J, Leroux JC, Delmas P, Allen C. 2008. Predicting the solubility of the anti-cancer agent docetaxel in small molecule excipients using computational methods. Pharm Res 25:147-157.
37. Rane SS, Anderson BD. 2008. Molecular dynamics simulations of functional group effects on salvation thermodynamics of model solutes in decane and tricaprylin. Mol Pharm 5:1023-1036.
38. Zhang HY, Feng W, Li C, Tan TW. 2010. Investigation of the inclusions of puerarin and daidzin with β-cyclodextrin by molecular dynamics simulation. J Phys Chem B 114:4876-4883.
39. Figueiras A, Sarraguca JMG, Pais ACC, Carvalho RA, Veiga JF. 2010. The role of L-arginine in the inclusion complexes of omeprazole with cyclodextrin. AAPS PharmSciTech 11:233-240.
40. Yong CW, Washington C, Smith W. 2008. Structural behavior of 2-hydroxypropyl-β-cyclodextrin in water: molecular dynamics simulation studies. Pharm Res 25:1092-1099.
41. Shire SJ, Shahrokh Z, Liu J. 2004. Challenges in the development of high protein concentration formulations. J Pharm Sci 93:1390-1402.
42. Vagenende V, Yap MGS, Trout BL. 2009. Mechanisms of protein stabilization and prevention of protein aggregation by glycerol. Biochemistry 48:11084-11096.
43. Shukla D, Schneider CP, Trout BL. 2010. Mechanism by which arginine inhibits protein aggregation. Abstracts of Papers, 239th ACS National Meeting, San Francisco, California, March 21-25.
44. Chennamsetty N, Voynov V, Kayser V, Helk B, Trout BL. 2009. Design of therapeutic proteins with enhanced stability. Proc Nat Acad Sci 106:11937-11942.
45. Boylan J. 1986. Liquids In The theory and practice of industrial pharmacy; Lachman L, Lieberman HA, Kanig, JL Eds. 3rd ed. Philadelphia, Pennsylvania: Lea and Febiger, pp 246.
46. Cui Y, Xing C, Ran Y. 2010. Molecular dynamics simulations of hydrotropic solubilization and self-aggregation of nicotinamide. J Pharm Sci 99:3048-3059.
47. Mukerjee P. 1974. Micellar properties of drugs: Micellar and nonmicellar patterns of self-association of hydrophobic solutes of different molecular structures - monomer fraction, availability, and misuses of micellar hypothesis. J Pharm Sci 63:972-981.
48. Ni N, Sanghavi T, Yalkowsky SH. 2002. Solubilization and preformulation of carbendazim. Int J Pharm 244:99-104.
49. Kenley RA, Jackson SE, Winderle JS, Shunko Y, Visor GC. 1986. Water soluble complexes of the antiviral drugs, 9-[(1, 3-dihydroxy-2-propoxy)methyl]guanine and acyclovir: The role of hydrophobicity in complex formation. J Pharm Sci 75:648-653.
50. Rasool AA, Hussain AA, Dittert LW. 1991. Solubility enhancement of some water-insoluble drugs by nicotinamide and related compounds. J Pharm Sci 80:387-393.
51. Baranovskii SF, Bolotin PA. 2007. Association of riboflavin, caffeine, and sodium slicylate in aqueous solution. J Appl Spectrosc 74:211-218.
52. Cui Y. 2010. Parallel stacking of caffeine with riboflavin in aqueous solutions: The potential mechanism for hydrotropic solubilization of riboflavin. Int J Pharm 397:36-43.
53. 1H NMR study of the association of caffeine with flavine mononucleotide in aqueous solutions. Russ J Phys Chem 79:573-578.