Computational molecular biology approaches to ligand-target interactions

HFSP Journal

Volumn 3, Issue 4, 2009, Pages 228-239

  Lupieri, Paola ^a   Nguyen, Chuong Ha Hung ^a   Bafghi, Zhaleh Ghaemi ^a   Giorgetti, Alejandro ^b   Carloni, Paolo ^a,c  

^a SISSA   (Italy)

^b UNIVERSITY OF VERONA   (Italy)

^c ISTITUTO ITALIANO DI TECNOLOGIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 80051811105     PISSN: 19552068     EISSN: 1955205X     Source Type: Journal    
DOI: 10.2976/1.3092784     Document Type: Review

References (104)

1. Abdulaev, NG, Ngo, T, Ramon, E, Brabazon, DM, Marino, JP, and Ridge, KD (2006). "The receptor-bound 'empty pocket' state of the heterotrimeric G-protein alpha-subunit is conformationally dynamic." Biochemistry 45, 12986-12997.
2. Al-Madhoun, AS, Johnsamuel, J, Barth, RF, Tjarks, W, and Eriksson, S (2004). "Evaluation of human thymidine kinase 1 substrates as new candidates for boron neutron capture therapy." Cancer Res. 64, 6280-6286.
3. Alon, U (2006). An Introduction to Systems Biology: Design Principles of Biological Circuits, Chapman & Hall/CRC, Boca Raton, FL.
4. Altschul, SF, Gish, W, Miller, W, Myers, EW, and Lipman, DJ (1990). "Basic local alignment search tool." J. Mol. Biol. 215, 403-410.
5. Anselmi, C, Carloni, P, and Torre, V (2007). "Origin of functional diversity among tetrameric voltage-gated channels." Proteins 66, 136-146.
6. Ballesteros, JA, andWeinstein, H (1995). "Integrated methods for modeling G-protein coupled receptors." Methods Neurosci. 25, 366-428.
7. Bakalyar, HA, and Reed, RR (1990). "Identification of a specialized adenylyl cyclase that may mediate odorant detection." Science 250, 1403-1406.
8. Barth, RF, Yang, W, Al-Madhoun, AS, Johnsamuel, J, Byun, Y, Chandra, S, Smith, DR, Tjarks, W, and Eriksson, S (2004). "Boron-containing nucleosides as potential delivery agents for neutron capture therapy of brain tumors." Cancer Res. 64, 6287-6295.
9. Berendsen, HJC (2007). Simulating the PhysicalWorld: Hierarchical Modeling from Quantum Mechanics to Fluid Dynamics, Cambridge University Press, NY.
10. Berendsen, HJC, Postma, JPM, Di Nola, A, and Haak, JR (1984). "Molecular dynamics with coupling to an external bath." J. Phys. Chem. 81, 3684-3690.
11. Biel, M, and Michalakis, S (2007). "Function and dysfunction of CNG channels: insights from channelopathies and mouse models." Mol. Neurobiol. 35, 266-277.
12. Birringer, MS, Claus, MT, Folkers, G, Kloer, DP, Schulz, GE, and Scapozza, L (2005). "Structure of a type II thymidine kinase with bound dTTP." FEBS Lett. 579, 1376-1382.
13. Boccaccio, A, and Menini, A (2007). "Temporal development of cyclic nucleotide-gated and Ca2+-activated Cl& currents in isolated mouse olfactory sensory neurons." J. Neurophysiol. 98, 153-160.
14. Buck, L, and Axel, R (1991). "A novel multigene family may encode odorant receptors: a molecular basis for odor recognition." Cell 65, 175-187.
15. Byun, Y, Thirumamagal, BTS, Yang, W, Eriksson, S, Barth, RF, and Tjarks, W (2006). "Preparation and biological evaluation of 10B-enriched 3-[5-{2-(2,3-dihydroxypropyl)-o-carboranyl} pentanyl] thymidine (N5-2OH), a new boron delivery agent for boron neutron capture therapy of brain tumors." J. Med. Chem. 49, 5513-5523.
16. Byun, Y, Yan, J, Al-Madhoun, AS, Johnsamuel, J, Yang, W, Barth, RF, Eriksson, S, and Tjarks, W (2005). "Synthesis and biological evaluation of neutral and zwitterionic 3-carboranyl thymidine analogues for boron neutron capture therapy." J. Med. Chem. 48, 1188-1198.
17. Cavalli, A, Dezi, C, Folkers, G, Scapozza, L, and Recanatini, M (2001). "Three-dimensional model of the cyclin-dependent kinase 1 (CDK1): ab initio active site parameters for molecular dynamics studies of CDKS." Proteins 45, 478-485.
18. Ceruso, MA, Periole, X, and Weinstein, H (2004). "Molecular dynamics simulations of transducin: interdomain and front to back communication in activation and nucleotide exchange." J. Mol. Biol. 338, 469-481.
19. Cherezov, V et al. (2007). "High-resolution crystal structure of an engineered human beta2-adrenergic, G protein-coupled receptor." Science 318, 1258-1265.
20. Chothia, C, and Lesk, AM (1986). "The relation between the divergence of sequence and structure in proteins." EMBO J. 5, 823-826.
21. Costanzi, S (2008). "On the applicability of GPCR homology models to computer-aided drug discovery: a comparison between in silico and crystal structures of the beta2-adrenergic receptor." J. Med. Chem. 51, 2907-2914.
22. Dal Peraro, M, Ruggerone, P, Raugei, S, Gervasio, FL, and Carloni, P (2007). "Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations." Curr. Opin. Struct. Biol. 17, 149-156.
23. Ehrhardt, MR, Urbauer, JL, and Wand, AJ (1995). "The energetics and dynamics of molecular recognition by calmodulin." Biochemistry 34, 2731-2738.
24. Eldridge, MD, Murray, CW, Auton, TR, Paolini, GV, and Mee, RP (1997). "Empirical scoring functions. I: The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes." J. Comput.-Aided Mol. Des. 11, 424-445.
25. Ensing, B, De Vivo, M, Liu, Z, Moore, P, and Klein, ML (2006). "Metadynamics as a tool for exploring free energy landscapes of chemical reactions." Acc. Chem. Res. 39, 73-81.
26. See EPAPS Document No. E-HJFOA5-3-002905 for supplemental material. This document can be reached through a direct link in the online article's HTML reference section or via the EPAPS home page (http://www.aip.org/pubservs/epaps.html).
27. Eriksson, S, Munch-Petersen, B, Johansson, K, and Eklund, H (2002). "Structure and function of cellular deoxyribonucleoside kinases." Cell. Mol. Life Sci. 59, 1327-1346.
28. Filizola, M, and Weinstein, H (2005). "The structure and dynamics of GPCR oligomers: a new focus in models of cell-signaling mechanisms and drug design." Curr. Opin. Drug Discov. Devel. 8, 577-584.
29. Fiorin, G, Pastore, A, Carloni, P, and Parrinello, M (2006). "Using metadynamics to understand the mechanism of calmodulin/target recognition at atomic detail." Biophys. J. 91, 2768-2777.
30. Firestein, S (2001). "How the olfactory system makes sense of scents." Nature (London) 413, 211-218.
31. Floriano, WB, Vaidehi, N, and Goddard, WA, III (2004). "Making sense of olfaction through predictions of the 3D structure and function of olfactory receptors." Chem. Senses 29, 269-290.
32. Frenkel, D, and Smit, B (2002). Understanding Molecular Simulation: From Algorithms to Applications, 2nd Ed., Academic Press, San Diego, CA.
33. Frings, S, Hackos, DH, Dzeja, C, Ohyama, T, Hagen, V, Kaupp, UB, and Korenbrot, JI (2000). "Determination of fractional calcium ion current in cyclic nucleotide-gated channels." Methods Enzymol. 315, 797-817.
34. Galés, C, Van Durm, JJ, Schaak, S, Pontier, S, Percherancier, Y, Audet, M, Paris, H, and Bouvier, M (2006). "Probing the activation-promoted structural rearrangements in preassembled receptor-G protein complexes." Nat. Struct. Mol. Biol. 13, 778-786.
35. Gao, M, Sotomayor, M, Villa, E, Lee, EH, and Schulten, K (2006). "Molecular mechanisms of cellular mechanics." Phys. Chem. Chem. Phys. 8, 3692-3706.
36. George, SR, O'Dowd, BF, and Lee, SP (2002). "G-protein-coupled receptor oligomerization and its potential for drug discovery." Nat. Rev. Drug Discovery 1, 808-820.
37. Giorgetti, A, Nair, AV, Codega, P, Torre, V, and Carloni, P (2005). "Structural basis of gating of, CNG channels." FEBS Lett. 579, 1968-1972.
38. Goddard, WA, III, and Abrol, R (2007). "3-dimensional structures of G protein-coupled receptors and binding sites of agonists and antagonists." J. Nutr. 137, 1528S-1538S; discussion 1548S.
39. Hunter, PJ, Crampin, EJ, and Nielsen, PM F (2008). "Bioinformatics, multiscale modeling and the IUPS Physiome Project." Briefings Bioinf. 9, 333-343.
40. Jaakola, V, Griffith, MT, Hanson, MA, Cherezov, V, Chien, EYT, Lane, JR, Ijzerman, AP, and Stevens, RC (2008). "The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist." Science 322, 1211-1217.
41. Jentsch, TJ, Stein, V, Weinreich, F, and Zdebik, AA (2002). "Molecular structure and physiological function of chloride channels." Physiol. Rev. 82, 503-568.
42. Johnston, CA, and Siderovski, DP (2007). "Receptor-mediated activation of heterotrimeric G-proteins: current structural insights." Mol. Pharmacol. 72, 219-230.
43. Jørgensen, AM, Tagmose, L, Jørgensen, AMM, Topiol, S, Sabio, M, Gundertofte, K, Bøgesø, KP, and Peters, GH (2007). "Homology modeling of the serotonin transporter: insights into the primary escitalopram-binding site." Chem Med Chem 2, 815-826.
44. Katada, S, Hirokawa, T, Oka, Y, Suwa, M, and Touhara, K (2005). "Structural basis for a broad but selective ligand spectrum of a mouse olfactory receptor: mapping the odorant-binding site." J. Neurosci. 25, 1806-1815.
45. Kaupp, UB, and Seifert, R (2002). "Cyclic nucleotide-gated ion channels." Physiol. Rev. 82, 769-824.
46. Khafizov, K, Anselmi, C, Menini, A, and Carloni, P (2007). "Ligand specificity of odorant receptors." J. Mol. Model. 13, 401-409.
47. Kitchen, DB, Decornez, H, Furr, JR, and Bajorath, J (2004). "Docking and scoring in virtual screening for drug discovery: methods and applications." Nat. Rev. Drug Discovery 3, 935-949.
48. Kleene, SJ (1993). "The cyclic nucleotide-activated conductance in olfactory cilia: effects of cytoplasmic Mg2+ and Ca2+." J. Membr. Biol. 131, 237-243.
49. Kolakowski, LFJ (1994). "GCRDb: a G-protein-coupled receptor database." Recept. Channels 2, 1-7.
50. Kristiansen, K (2004). "Molecular mechanisms of ligand binding, signaling, and regulation within the superfamily of G-protein-coupled receptors: molecular modeling and mutagenesis approaches to receptor structure and function." Pharmacol. Ther. 103, 21-80.
51. Kroeze, WK, Sheffler, DJ, and Roth, BL (2003). "G-protein-coupled receptors at a glance." J. Cell. Sci. 116, 4867-4869.
52. Krogh, A, Brown, M, Main, IS, Sjolander, K, and Haussler, D (1994). "Hidden Markov models in computational biology: applications to protein modeling." J. Mol. Biol. 235, 1501-1531.
53. Laio, A, and Parrinello, M (2002). "Escaping free energy minima." Proc. Natl. Acad. Sci. U.S.A. 99, 12562-12566.
54. Landry, Y, and Gies, J (2008). "Drugs and their molecular targets: an updated overview." Fundam. Clin. Pharmacol. 22, 1-18.
55. Leach, AR (2001). Molecular Modelling: Principles and Applications AddisonWesley Longman, Essex, UK.
56. Lee, E, Taussig, R, and Gilman, AG (1992). "The G226A mutant of Gs alpha highlights the requirement for dissociation of G protein subunits." J. Biol. Chem. 267, 1212-1218.
57. Lensink, MF, Méndez, R, and Wodak, SJ (2007). "Docking and scoring protein complexes: CAPRI 3rd edition." Proteins 69, 704-718.
58. Lipman, DJ, and Pearson, WR (1985). "Rapid and sensitive protein similarity searches." Science 22, 1435-1441.
59. Loewen, ME, and Forsyth, GW (2005). "Structure and function of CLCA proteins." Physiol. Rev. 85, 1061-1092.
60. Lowe, G, and Gold, GH (1993). "Nonlinear amplification by calciumdependent chloride channels in olfactory receptor cells." Nature (London) 366, 283-286.
61. Magistrato, A, Ruggerone, P, Spiegel, K, Carloni, P, and Reedijk, J (2006). "Binding of novel azole-bridged dinuclear platinum(II), anticancer drugs to DNA: insights from hybrid QM/MM molecular dynamics simulations." J. Phys. Chem. B 110, 3604-3613.
62. Malnic, B, Hirono, J, Sato, T, and Buck, LB (1999). "Combinatorial receptor codes for odors." Cell 96, 713-723.
63. Markwick, PR, Malliavin, T, and Nilges, M (2008). "Structural biology by NMR: structure, dynamics, and interactions." PLOS Comput. Biol. 4, 1-7.
64. Mello, LV, van Aalten, DM, and Findlay, JB (1998). "Dynamic properties of the guanine nucleotide binding protein alpha subunit and comparison of its guanosine triphosphate hydrolase domain with that of ras p21." Biochemistry 37, 3137-3142.
65. Menini, A (1999). "Calcium signalling and regulation in olfactory neurons." Curr. Opin. Neurobiol. 9, 419-426.
66. Miani, A, Raugei, S, Carloni, P, and Helfand, MS (2007). "Structure and Raman spectrum of clavulanic acid in aqueous solution." J. Phys. Chem. B 111, 2621-2630.
67. Miller, RT, Masters, SB, Sullivan, KA, Beiderman, B, and Bourne, HR (1988). "A mutation that prevents GTP-dependent activation of the alpha chain of Gs." Nature (London) 334, 712-715.
68. Moitessier, N, Englebienne, P, Lee, D, Lawandi, J, and Corbeil, CR (2008). "Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go." Br. J. Pharmacol. 153, S7-S26.
69. Nair, AV, Mazzolini, M, Codega, P, Giorgetti, A, and Torre, V (2006). "Locking CNGA1 channels in the open and closed state." Biophys. J. 90, 3599-3607.
70. Narayanasamy, S et al. (2006). "Hydrophilically enhanced 3-carboranyl thymidine analogues (3CTAs), for boron neutron capture therapy (BNCT), of cancer." Bioorg. Med. Chem. 14, 6886-6899.
71. Neylon, C (2008). "Small angle neutron and X-ray scattering in structural biology: recent examples from the literature." Eur. Biophys. J. 37, 531-541.
72. Oldham, WM, and Hamm, HE (2006). "Structural basis of function in heterotrimeric G proteins." Q. Rev. Biophys. 39, 117-166.
73. Oldham, WM, Van Eps, N, Preininger, AM, Hubbell, WL, and Hamm, HE (2006). "Mechanism of the receptor-catalyzed activation of heterotrimeric G proteins." Nat. Struct. Mol. Biol. 13, 772-777.
74. Piana, S, Sebastiani, D, Carloni, P, and Parrinello, M (2001). "Ab initio molecular dynamics-based assignment of the protonation state of pepstatin A/HIV-1 protease cleavage site." J. Am. Chem. Soc. 36, 8730-8737.
75. Pifferi, S, Boccaccio, A, and Menini, A (2006a). "Cyclic nucleotide-gated ion channels in sensory transduction." FEBS Lett. 580, 2853-2859.
76. Pifferi, S, Pascarella, G, Boccaccio, A, Mazzatenta, A, Gustincich, S, Menini, A, and Zucchelli, S (2006b). "Bestrophin-2 is a candidate calcium-activated chloride channel involved in olfactory transduction." Proc. Natl. Acad. Sci. U.S.A. 103, 12929-12934.
77. Pin, J, Neubig, R, Bouvier, M, Devi, L, Filizola, M, Javitch, JA, Lohse, MJ, Milligan, G, Palczewski, K, Parmentier, M, and Spedding, M (2007). "International Union of Basic and Clinical Pharmacology. LXVII. Recommendations for the recognition and nomenclature of G protein-coupled receptor heteromultimers." Pharmacol. Rev. 59, 5-13.
78. Quigley, D, and Probert, MIJ (2004). "Langevin dynamics in constant pressure extended systems." J. Chem. Phys. 120, 11432-11441.
79. Reggio, PH (2006). "Computational methods in drug design: modeling G protein-coupled receptor monomers, dimers, and oligomers." AAPS J. 8, E322-E336.
80. Riekel, C, Burghammer, M, and Schertler, G (2005). "Protein crystallography microdiffraction." Curr. Opin. Struct. Biol. 15, 556-562.
81. Rothlisberger, U, and Carloni, P (2007). "Drug-target binding investigated by quantum mechanical/molecular mechanical (QM/MM) methods." In Computer Simulations in Condensed Matter: From Materials to Chemical Biology, Ferrario, M, Ciccotti, G, and Binder, K, eds., Vol. 2, pp 449-479, Springer, Heidelberg, Germany.
82. Sakmar, TP (2002). "Structure of rhodopsin and the superfamily of sevenhelical receptors: the same and not the same." Curr. Opin. Cell Biol. 14, 189-195.
83. Scheerer, P, Park, JH, Hildebrand, PW, Kim, YJ, Krauss, N, Choe, H, Hofmann, KP, and Ernst, OP (2008). "Crystal structure of opsin in its G-protein-interacting conformation." Nature (London) 455, 497-502.
84. Schmidt, CJ, Thomas, TC, Levine, MA, and Neer, EJ (1992). "Specificity of G protein beta and gamma subunit interactions." J. Biol. Chem. 267, 13807-13810.
85. Schneider, T, and Stoll, E (1978). "Molecular-dynamics study of a threedimensional one-component model for distortive phase transitions." Phys. Rev. B 17, 1302-1322.
86. Schwede, T, and Peitsch, MC (2008). Computational Structural Biology: Methods and Applications,World Scientific, Hackensack, NJ.
87. Segrè, D., Vitkup, D, and Church, GM (2002). "Analysis of optimality in natural and perturbed metabolic networks." Proc. Natl. Acad. Sci. U.S.A. 99, 15112-15117.
88. Segura-Peña, D., Lutz, S, Monnerjahn, C, Konrad, M, and Lavie, A (2007). "Binding of ATP to TK1-like enzymes is associated with a conformational change in the quaternary structure." J. Mol. Biol. 369, 129-141.
89. Senn, HM, and Thiel, W (2008). "QM/MM methods for biomolecular systems." Angew. Chem., Int. Ed. 48, 1198-1229.
90. Sherwood, P, Brooks, BR, and Sansom, MS (2008). "Multiscale methods for macromolecular simulations." Curr. Opin. Struct. Biol. 18, 630-640.
91. Singer, MS (2000). "Analysis of the molecular basis for octanal interactions in the expressed rat 17 olfactory receptor." Chem. Senses 25, 155-165.
92. Soloway, AH, Tjarks, W, Barnum, BA, Rong, F, Barth, RF, Codogni, IM, and Wilson, JG (1998). "The chemistry of neutron capture therapy." Chem. Rev. (Washington, D.C.) 98, 1515-1562.
93. Spiegel, K, Rothlisberger, U, and Carloni, P (2006). "Duocarmycins binding to DNA investigated by molecular simulation." J. Phys. Chem. B 110, 3647-3660.
94. Strader, CD, Fong, TM, Tota, MR, Underwood, D, and Dixon, RA (1994). "Structure and function of G protein-coupled receptors." Annu. Rev. Biochem. 63, 101-132.
95. Takeda, S, Kadowaki, S, Haga, T, Takaesu, H, and Mitaku, S (2002). "Identification of G protein-coupled receptor genes from the human genome sequence." FEBS Lett. 520, 97-101.
96. Tesmer, JJ, Sunahara, RK, Gilman, AG, and Sprang, SR (1997). "Crystal structure of the catalytic domains of adenylyl cyclase in a complex with Gs_ ·GTP_S." Science 278, 1907-1916.
97. Tramontano, A (2006). Protein Structure Prediction: Concepts and Applications, JohnWiley & Sons, Ltd,Weinheim, Germany.
98. van Rompay, AR, Johansson, M, and Karlsson, A (2003). "Substrate specificity and phosphorylation of antiviral and anticancer nucleoside analogues by human deoxyribonucleoside kinases and ribonucleoside kinases." Pharmacol. Ther. 100, 119-139.
99. Wall, MA, Posner, BA, and Sprang, SR (1998). "Structural basis of activity and subunit recognition in G protein heterotrimers." Structure (London) 6, 1169-1183.
100. Warne, T, Serrano-Vega, MJ, Baker, JG, Moukhametzianov, R, Edwards, PC, Henderson, R, Leslie, AG W, Tate, CG, and Schertler, GF X (2008). "Structure of a beta1-adrenergic G-protein-coupled receptor." Nature (London) 454, 486-491.
101. Warshel, A, and Levitt, M (1976). "Theoretical studies of enzymic reactions-dielectric, electrostatic and steric stabilization of carbonium-ion in reaction of lysozyme." J. Mol. Biol. 103, 227-249.
102. Welin, M, Kosinska, U, Mikkelsen, N, Carnrot, C, Zhu, C, Wang, L, Eriksson, S, Munch-Petersen, B, and Eklund, H (2004). "Structures of thymidine kinase 1 of human and mycoplasmic origin." Proc. Natl. Acad. Sci. U.S.A. 101, 17970-17975.
103. Whitesides, GM, Snyder, PW, Moustakas, DT, and Mirica, KA (2008). "Designing ligands to bind tightly to proteins." In Physical Biology: From Atoms to Medicine, Zewail, AH, ed., pp 189-216, Imperial College Press, London, UK.
104. Xiao, Q, Prussia, A, Yu, K, Cui, Y, and Hartzell, HC (2008). "Regulation of bestrophin Cl channels by calcium: role of the C terminus." J. Gen. Physiol. 132, 681-692.