FMO as a Tool for Structure-Based Drug Design

The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems

Volumn , Issue , 2009, Pages 217-244

  Ozawa, Tomonaga ^a   Okazaki, Kosuke ^a   Nishio, Motohiro ^b  

^a KISSEI PHARMACEUTICAL CO LTD   (Japan)

^b CHPI Institute   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85069154485     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/9781420078497-13     Document Type: Chapter

References (114)

1. Pimentel, G.C., McClellan, A.L. 1960. The Hydrogen Bond, W.H. Freeman, San Francisco, CA.
2. Desiraju, G.R., Steiner, T. 1999. The Weak Hydrogen Bond in Structural Chemistry and Biology, Oxford University Press, Oxford.
3. Nishio, M., Hirota, M., Umezawa, Y. 1998. The CH/π Interaction. Evidence, Nature, and Consequences, Wiley-VCH, New York.
4. Steiner, T. 2002. The hydrogen bond in the solid state. Angew. Chem. Int. Ed. 41: 48-76.
5. Nishio, M. 2008. Introduction to Weak Molecular Forces in Organic Chemistry and Life Science, Kodansha Scientific, Tokyo (in Japanese).
6. Stone, A.J. 1996. The Theory of Intermolecular Forces, Clarendon Press, Oxford;
7. Scheiner, S. 1997. Hydrogen Bonding, A Theoretical Perspective, Oxford University Press, Oxford.
8. Kitaura, K., Morokuma, K. 1976. A new energy decomposition scheme for molecular interactions within the Hartree-Fock approximation. Int. J. Comput. Chem. 10: 325.
9. Hayes, I.S., Stone, A. 1984. An intermolecular perturbation theory for the region of moderate overlap. J. Mol. Phys. 53: 83-105.
10. Popelier, P. 1998. Atoms in Molecule-An Introduction. Prentice-Hall.
11. Perutz, M.F. 1993. The role of aromatic rings as hydrogen-bond acceptors in molecular recognition. Phil. Trans. R. Soc. A 345: 105-112.
12. Rozas, I., Alkorta, I.E. 1997. Unusual hydrogen bonds: H•••πInteractions. J. Phys. Chem. A 101: 9457-9463;
13. Samanta, U., Chakrabarti, P., Chandrasekhar, J. 1998. Ab initio study of energetics of X-H•••π(X = N, O, and C) interactions involving a heteroaromatic ring. J. Phys. Chem. A 102: 8964-8969;
14. Tsuzuki, S., Honda, K., Uchimaru, T. et al. 2000. The magnitude of the CH/π interaction between benzene and some model hydrocarbons. J. Am. Chem. Soc. 122: 11450-11458;
15. Tarakeshwar, P., Kim, K.S. 2002. Comparison of the nature of π and conventional H-bonds: a theoretical investigation. J. Molec. Struct. 615: 227-238.
16. Steiner, T., Koellner, G. 2001. Hydrogen bonds with π-acceptors in proteins: frequencies and role in stabilizing local 3D structures. J. Mol. Biol. 305: 535-557.
17. Taylor, R., Kennard, O. 1982. Crystallographic evidence for the existence of CH/O, CH/N, and CH/Cl hydrogen bonds J. Am. Chem. Soc. 104: 5063-5070.
18. Desiraju, G.R. 1991. The CH/O Hydrogen Bond in Crystals: What is it? Acc. Chem. Res. 24: 290-296;
19. Steiner, T. 1996. Cryst. Rev. 6: 1-57;
20. Steiner, T. 1997. Unrolling the hydrogen bond properties of C-H•••O interactions. Chem. Commun. 727-734.
21. T. Steiner. 1998. Donor and acceptor strengths in C-H•••O hydrogen bonds quantified from crystallographic data of small solvent molecules. New J. Chem. 22: 1099-1103.
22. Houk, K.N., Menzer, S., Newton, S.P. et al. 1999. [C-H•••O] interactions as a control element in supramolecular complexes: experimental and theoretical evaluation of receptor affinities for the binding of bipyridinium-based guests by catenated hosts. J. Am. Chem. Soc. 121: 1479-1487.
23. Derewenda, Z.S., Lee, L., Derewenda, U. 1995. The occurence of C-H • • • O hydrogen bonds in proteins. J. Mol. Biol. 252: 248-262;
24. Chakrabarti, P., Chakrabarti, S. 1998. C-H• • •O hydrogen bond involving proline residues in α-helices. J. Mol. Biol. 284: 867-873;
25. Fabiola, G.F., Krishnaswamy, S., Nagarajan, V. 1997. Acta Cryst., Sect. A. 53: 316-320.
26. Gu, Y., Kar, T., Scheiner, S. 1999. Fundamental properties of the CH•••O interaction: is it a true hydrogen bond? J. Am. Chem. Soc. 121: 9411-9422.
27. Hartmann, M., Wetmore, S.D., Radom, L. 2001. C-H•••X hydrogen bonds of acetylene, ethylene, and ethane with first-and second-row hydrides. J. Phys. Chem. A. 105: 4470-4479.
28. Steiner, T. 1998. Donor and acceptor strengths in C-H•••O hydrogen bonds quantified from crystallographic data of small solvent molecules. New J. Chem. 22: 1099-1103.
29. Madhavi, N.N.L., Katz, A.M., Carrell, H.L. et al. 1997. Evidence for the characterisation of the C-H•••πinteraction as a weak hydrogen bond: toluene and chlorobenzene solvates of 2, 3, 7, 8-tetraphenyl-1, 9, 10-anthyridine Chem. Commun. 1953-1954.
30. Suezawa, H., Hashimoto, T., Tsuchinaga, K. et al. 2000. Electronic substituent effect on intramolecular CH/π interaction as evidenced by NOE experiments. J. Chem. Soc., Perkin Trans. 2. 1243-1249.
31. Sundararajan, K., Sankaran, K.S., Viswanathan, K.S. et al. 2002. H-π complexes of acetylene-ethylene: a matrix isolation and computational study. J. Phys. Chem. A 106: 1504-1510;
32. Fujii, A., Morita, S., Miyazaki, M. et al. 2004. A molecular cluster study on activated CH/π interactions: infrared spectroscopy of aromatic molecule-acetylene clusters. J. Phys. Chem. A 108: 2652-2658.
33. Umezawa, Y., Tsuboyama, S., Honda, K. et al. 1998. CH/π interaction in the crystal structure of organic compounds. A database study. Bull. Chem. Soc. Jpn. 71: 1207-1213;
34. Suezawa, H., Yoshida, T., Hirota, M. et al. 2001. The CH/π interaction as an important factor in the crystal packing and in determining the structure of clathrates. J. Chem. Soc., Perkin Trans. 2. 2053-2058.
35. Suezawa, H., Yoshida, T., Umezawa, Y. et al. 2002. CH/π interactions implicated in the crystal structure of transition metal compounds. A database study. Eur. J. Inorg. Chem. 3148-3155.
36. Sakaki, S., Kato, K., Miyazaki, T. et al. 1993. Structures and binding energies of benzene-methane and benzene-benzene complexes. J. Chem. Soc., Faraday Trans. 2. 89; 659-664.
37. Novoa, J.J., Mota, F. 2000. The CH/π bonds: strength, identification, and hydrogenbonded nature: a theoretical study. Chem. Phys. Lett. 318: 345-354;
38. Tsuzuki, S., Honda, K., Uchimaru, T. 2000. The magnitude of the CH/π interaction between benzene and some model hydrocarbons. J. Am. Chem. Soc. 122: 3746-3753;
39. Scheiner, S., Grabowski, S.J. 2002. Acetylene as potential hydrogen-bond proton acceptor. J. Molec. Struct. 615: 209-218;
40. Bagno, A., Saielli, G., Scorrano, G. 2002. Through-space spin-spin coupling in van der Waals dimers and CH/π interacting systems. An ab initio and DFT study. Chem., Eur. J. 8: 2047-2056;
41. Ugozzoli, F., Arduini, A., Massera, C. et al. 2002. CH/π interaction between benzene and model neutral organic molecules bearing acid CH groups. New J. Chem. 26: 1718-1723;
42. Kobayashi, Y., Saigo. K. 2005. Periodic ab initio approach for the cooperative effect of CH/π interaction in crystals: relative energy of CH/π and hydrogen-bonding interactions. J. Am. Chem. Soc. 127: 15054-15060;
43. Ran, J., Wong, M.W. 2006. Saturated hydrocarbon-benzene complexes: theoretical study of cooperative CH/π interactions. J. Phys. Chem. A 110: 9702-9729.
44. Tsuzuki, S., Honda, K., Uchimaru, T. 2002. The interaction of benzene with chloroand fluoromethanes: effects of halogenation on CH/π Interaction. J. Phys. Chem. A 106: 4423-4428.
45. Hunter, C.A. 1994. Meldola Lecture. The role of aromatic interactions in molecular recognition. Chem. Soc. Rev. 101-109.
46. Carver, F.J., Hunter, C.A., Seward, E.M. 1998. Structure-activity relationship for quantifying aromatic interactions. Chem. Commun. 775-776.
47. Burley, S.K., Petsko, G.A. 1988. Weakly polar interactions in proteins. Adv. Protein Chem. 39: 125-189.
48. Hildebrand, J.H. 1979. Is there a “hydrophobic effect?" Proc. Natl. Acad. Sci. USA 76: 194.
49. Cantrill, S.J., Preece, J.A., Stoddart, J.F. et al. 2000. The idiosyncrasies of tetrabenzo[24]crown-8 in the solid state. Tetrahedron 56: 6675-6681.
50. O’Leary, B.M., Grotzfeld, R.M., Rebek, J. 1997. Ring inversion dynamics of encapsulated cyclohexane. J. Am. Chem. Soc. 119: 11701-11702;
51. Chapman, R.G., Olovsson, G., Trotter, J. et al. 1998. Crystal structure and thermodynamics of reversible molecular capsules. J. Am. Chem. Soc. 120: 6252-6260;
52. Biradha, K., Dennis, D., MacKinnonn, V.A. 1998. Supramolecular synthesis of organic laminates with affinity for aromatic guests: a new class of clay mimics. J. Am. Chem. Soc. 120: 11894-11903;
53. Arduini, A., Nachtigall, F., Pochini, A. 2000. Supramol. Chem. 12: 273-291;
54. Takahashi, H., Tsuboyama, S., Umezawa, Y. et al. 2000. CH/π interactions as demonstrated in the crystal structure of host/guest compounds. A database study. Tetrahedron 56: 6185-6191.
55. Umezawa, K., Kawakami, M., Watanabe, T. 2003. Molecular design and biological activities of protein-tyrosine phosphatase inhibitors. Pharmacology and Therapeutics 99: 15-24.
56. Kinbara, K., Oishi, K., Harada, Y. et al. 2000. Effect of a substituent on an aromatic group in diastereomeric resolution. Tetrahedron 56: 6651-6655;
57. Fujii, I., Hirayama, N. 2002. Chiral space formed by (+)-(1S)-1, 1′-binaphthalene-2, 2′-diyl phosphate: recognition of aliphatic L-α-amino acids. Helv. Chim. Acta 85: 2946-2960;
58. H. Suezawa et al. 2004. Aromatic CH/π hydrogen bond as an important factor deciding the relative stability of diastereomeric salts relevant to enantiomeric resolution. A crystallographic database study. Eur. J. Org. Chem. 23: 4816-4822.
59. Hashihayata, T., Punniyamurthy, T., Irie, R. et al. 1999. Conformational analysis of cationic (R, S)-and (R, R)-(salen)manganese complexes possessing axial chirality as a chiral element based on x-ray crystallography: an explanation of the effect of apical ligand on enantioselection by (salen)manganese catalyst. Tetrahedron 55: 14599-14610;
60. Yamakawa, M., Yamada, I., and Noyori, R. 2001. CH/π attraction: the origin of enantioselectivity in transfer hydrogenation of aromatic carbonyl compounds catalyzed by chiral 6-arene-ruthenium(II) complexes. Angew. Chem. Int. Ed. 40: 2818-2821.
61. M. Soduple et al. 1997. J. Am. Chem. Soc. 119: 4332-4238;
62. Ujaque, G., Lee, P.S., Houk, K.N. et al. 2002. The origin of endo stereoselectivity in the hetero-Diels-Alder reactions of aldehydes with ortho-xylylenes: CH-π, π-π, and steric effects on stereoselectivity. Chem. Eur. J. 8: 3423-3430.
63. Obata, T., Shimo., T., Yasutake, M. et al. 2001. Remarkable interaction effects of molecular packing on site-and stereoselectivity in photocycloaddition of 2-pyrones with maleimide in the solid state. Tetrahedron 57: 1531-1541;
64. Nagahama, S., Inoue, K., Sada, K. et al. 2003. Two-dimensional hydrogen bond networks supported by CH/π interaction leading to a molecular packing appropriate for topochemical polymerization of 1, 3-diene monomers. Crystal Growth and Design 3: 247-256.
65. Umezawa, Y., Nishio, M. 1998. CH/π interactions in the crystal structure of guaninenucleotide binding proteins, Src Homology-2 Domains and human growth hormone in complex with their specific ligands. Bioorg. Med. Chem. 6: 493-504.
66. Umezawa, Y., Nishio, M. 1998. CH/π interactions in the crystal structure of class I MHC antigens and their complexes with peptides. Bioorg. Med. Chem. 6: 2507-2515.
67. Umezawa, Y., Nishio, M. 2000. CH/π interactions in the crystal structure of TATAbox binding protein/DNA complexes. Bioorg. Med. Chem. 8: 2643-2650.
68. Muraki, M. 2002. The importance of CH/π in interactions to the function of carbohydrate binding proteins. Protein and Peptide Lett. 9: 195-209.
69. Y. Umezawa, M. Nishio. 2005. CH/π hydrogen bonds as evidenced in the substrate specificity of acetylcholine esterase. Biopolymers 79: 248-258.
70. Spiwok, V., Lipovova, P., Skalova, T. et al. 2004. Role of CH/π interactions in substrate binding by Escherichia coli beta-galactosidase. Carbohydr. Res. 339: 2275-2280.;
71. ++** Study on galactose-and glucose-aromatic residue analogue complexes. Biochemistry. 44: 8554-8562.
72. Sujatha, M.S., Sasidhar, Y.M., Balaji, P.V. 2007. MP2/6-311++G(d, p) study on galactose-aromatic residue analog complexes in different position-orientations of the saccharide relative to aromatic residue. J. Mol. Struct (THEOCHEM) 814: 11-24.
73. Harigai, M., Kataoka, M., Imamoto, Y. 2006. A single CH/π weak hydrogen bond governs stability and the photocycle of the photoactive yellow protein. J. Am. Chem. Soc. 128: 10646-10647.
74. Fantini, J., Garmy, N., Yahi, N. 2006. Prediction of glycolipid-binding domains from the amino acid sequence of lipid raft-associated proteins: application to HpaA, a protein involved in the adhesion of Helicobacter pylori to gastrointestinal cells. Biochemistry 45: 10957-10962.
75. Chakrabarti, P., Samanta, U. 1995. CH/π interaction in the packing of the adenine ring in protein structures. J. Mol. Biol. 251: 9-14.
76. Brandi, M., Weiss, M.S., Jabs, A. et al. 2001. CH/π-interactions in proteins. J. Mol. Biol. 307: 357-377.
77. Nishio, M., Umezawa, Y., Hirota, M. et al. 1995. The CH/π interaction: significance in molecular recognition. Tetrahedron 51: 8665-8701.
78. Nishinaka, T., Ito, Y., Yokoyama, S. et al. 1997. An extended DNA structure through deoxyribose-base stacking induced by RecA protein. Proc. Natl. Acad. Sci. U.S.A. 94: 6623-6628.;
79. Chou, S.H, and Tseng, Y.Y. 1999. Cross-strandpurine-pyrimidine stack and sheared purine•pyrimidine pairing in the human HIV-1 reverse transcriptase inhibitors. J. Mol. Biol. 285: 41-48;
80. Umezawa, Y., Nishio, M. 2002. Thymine-methyl/pi interaction implicated in the sequence-dependent deformability of DNA. Nucleic Acids Res. 30: 2183-2192.
81. Ozawa, T., Tsuji, E., Ozawa, M. et al. 2008. The importance of CH/π hydrogen bonds in rational drug design: an ab initio fragment molecular orbital study to leukocytespecific protein tyrosine (LCK) kinase. Bioorg. Med. Chem. 16: 10311-10318.
82. Susva, M., Missbach, M., Green, J. 2000. Src inhibitors: drugs for the treatment of osteoporosis, cancer or both? Trends in Pharmacological Sciences 21: 489-495.
83. Marth, J.D., Lewis, D.B., Cooke, M.P. et al. 1989. Lymphocyte activation provokes modification of a lymphocyte-specific protein tyrosine kinase (p56lck). J. Immunol. 142: 2430-2437.
84. Palacios, E.H., Weiss, A. 2004. Function of the Src-family kinases, Lck and Fyn, in T-cell development and activation. Oncogene. 23: 7990-8000.
85. Hanke, J.H., Gardner, J.P., Dow, R.L. et al. 1996. Discovery of a novel, potent, and Src family-selective tyrosine kinase inhibitor. J. Biol. Chem. 271: 695-701.
86. Trevillyan1, J.M., Chiou, G. Gr., Ballaron. S. et al. 1999. Inhibition of p56lck tyrosine kinase by isothiazolones. Arch. Biochem. Biophys. 364: 19-29.
87. Snow, R.J., Cardozo, M.G., Morwick. et al. 2002. Discovery of 2-phenylaminoimidazo[4, 5-h]isoquinolin-9-ones: a new class of inhibitors of lck kinase. J. Med. Chem. 45: 3394-3405.
88. Goldberg, D.R., Butz, T., Cardozo, M.G. et al. 2003. Optimization of 2-phenylaminoimidazo[4, 5-h]isoquinolin-9-ones: orally active inhibitors of lck kinase. J. Med. Chem. 46: 1337-1349.
89. Chen, P., Norris, D., Iwanowicz, E.J. et al. 2002. Discovery and initial SAR of imidazoquinoxalines as inhibitors of the Src-family kinase p56Lck. Bioorg. Med. Chem. Lett. 12: 1361-1364.
90. Chen, P., Iwanowicz, E.J., Norris, D. et al. 2002. Synthesis and SAR of novel imidazoquinoxaline-based Lck inhibitors: improvement of cell potency. Bioorg. Med. Chem. Lett. 12: 3153-3156.
91. Das, J., Lin, J., Moquin, R.V. et al. 2003. Discovery of 2-amino-heteroarylbenzothiazole-6-anilides as potent p56lck inhibitors. Bioorg. Med. Chem. Lett. 13: 2145-2149.
92. Chen, P., Norris, D., Das, J. et al. 2004. Discovery of novel 2-(aminoheteroaryl)-thiazole-5-carboxamides as potent and orally active Src-family kinase p56lck inhibitors. Bioorg. Med. Chem. Lett. 14: 6061-6066.
93. Chen, P., Doweyko, A.M., Norris, D. et al. 2004. Imidazoquinoxaline Src-family kinase p56Lck inhibitors: SAR, QSAR, and the Discovery of (S)-N-(2-Chloro-6-methylphenyl)-2-(3-methyl-1-piperazinyl)imidazo-[1, 5-a]pyrido[3, 2-e]pyrazin-6-amine (BMS-279700) as a potent and orally active inhibitor with excellent in vivo antiinflammatory activity. J. Med. Chem. 47: 4517-4529.
94. Arnold, L.D., Calderwood, D.J., Dixon, R.W. et al. 2000. Pyrrolo[2, 3-d]pyrimidines containing an extended 5-substituent as potent and selective inhibitors of lck II. Bioorg. Med. Chem. Lett. 10: 2167-2170.
95. Burchat, A.F., Calderwood, D.J., Friedman, M.M. et al. 2002. Pyrazolo[3, 4-d]pyrimidines containing an extended 3-substituent as potent inhibitors of Lck-a selectivity insight. Bioorg. Med. Chem. Lett. 12: 1687-1690.
96. Borhani, D.W., Calderwood, D.J., Friedman, M.M. et al. 2004. A-420983: a potent, orally active inhibitor of lck with efficacy in a model of transplant rejection. Bioorg Med. Chem. Lett. 14: 2613-2616.
97. Zhu, X., Kim, J.L., Newcomb, J.R. et al. 1999. Structural analysis of the lymphocytespecific kinase Lck in complex with non-selective and Src family selective kinase inhibitors. Structure 7: 651-661.
98. Chery, M., Williams, D.H. 2004. Recent kinase and kinase inhibitor X-ray structures: mechanisms of inhibition and selectivity insights. Current Med. Chem. 11: 663-673.
99. Mukaiyama, H., Nishimura, T., Kobayashi, S. et al. 2007. Synthesis and c-Src inhibitory activity of imidazo[1, 5-a]pyrazine derivatives as an agent for treatment of acute ischemic stroke. Bioorg Med Chem. 15: 868-885.
100. ABINIT-MP. Available at www.ciss.iis.u-tokyo.ac.jp/rss21/result/download/index. php#download_2.
101. Lipinski, C.A., Lombardo, F., Dominy, B.W. 2001. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev. 46: 3-26.
102. Congreve, M., Carr, R., Murray, C. 2003. A “Rule of Three” for fragment-based lead discovery? Drug Discov. Today 8: 876-877.
103. Sarkhel, S., Desiraju, G.R. 2004. NH/O, OH/O, and CH/O hydrogen bonds in proteinligand complexes: strong and weak interactions in molecular recognition. PROTEINS: Structure, Function, and Bioinformatics 54: 247-259.
104. Pierce, A.C., Sandretto, K.L., Bemis, G.W. 2002. Kinase inhibitors and the case for CH/O hydrogen bonds in protein-ligand binding. PROTEINS: Structure, Function, and Bioinformatics 49: 567-576.
105. Pierce, A.C., Haar, E., Binch, H.M. 2005. CH•••O and CH•••N hydrogen bonds in ligand design: a novel quinazolin-4-ylthiazol-2-ylamine protein kinase inhibitor. J. Med. Chem. 48: 1278-1281.
106. Ehama, R., Tsushima, M., Yuzuri, T. et al. 1993. Substituent effect on the enthalpies of formation of CH/π complexes of aromatic π-bases. Bull. Chem. Soc. Jpn. 66: 814-818.
107. Suezawa, H., Mori, A., Sato, M. et al. 1993. Evidence for the presence of the CH/π interacted ap-conformers of benzyl formats. J. Phys. Org. Chem. 6: 399-406.
108. Chowdhury, S.K., Joshi, V.S., Samuel, A.G. 1994. Conformational preferences in molybdenum(II) π-allyl complexes: role of CH/π interaction. Organometallics 13: 4092-4096.
109. Lee, E.C., Hong, B.H., Lee, J.Y. 2005. Substituent effects on the edge-to-face aromatic interactions. J. Am. Chem. Soc., 127: 4530-4537.
110. Coffey, A.J., Brooksbank, R.A., Brandau, O. et al. 1998. Host response to EBV infection in X-linked lymphoproliferative disease results from mutations in an SH2-domain encoding gene. Nat. Genet. 20: 129-135.
111. Sayos, J., Wu, C., Morra, M. et al. 1998. The X-linked lymphoproliferative-disease gene product SAP regulates signals induced through the co-receptor SLAM. Nature 395: 462-469.
112. Roussel, R.R., Brodeur, S.R., Shalloway, D. et al. 1991. Selective binding of activated pp60c-src by an immobilized synthetic phosphopeptide modeled on the carboxyl terminus of pp60c-src. Proc. Natl. Acad. Sci. U.S.A. 88: 10696-10700.
113. Poy, F., Yaffe, M.B., Sayos, J. et al. 1999. Crystal structures of the XLP protein SAP reveal a class of SH2 domains with extended, phosphotyrosine-independent sequence recognition. Mol. Cell 4: 555-561.
114. Ozawa, T. Okazaki, K. 2008. CH/π hydrogen bonds determine the selectivity of the Src homology 2 (SH2) domain to tyrosine phosphotyrosyl peptides: an ab initio fragment molecular orbital (FMO) study. J. Comput. Chem. 29: 2656-2666.