Experimental and in silico characterization of a biologically active inosose
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- 作者：Venerando Pistarà (1)
Giuseppe M. Lombardo (1)
Antonio Rescifina (1)
Alessia Bacchi (2)
Felicia D’Andrea (3)
Francesco Punzo (1) - 关键词：Inososes ; Glycosidase inhibitors ; Docking ; Molecular dynamics simulation ; X ; ray structural analysis ; Atomic displacement parameters
- 刊名：Structural Chemistry
- 出版年：2013
- 出版时间：June 2013
- 年：2013
- 卷：24
- 期：3
- 页码：955-965
- 全文大小：722KB
- 参考文献：1. Berridge MJ, Irvine RF (1989) Inositol phosphates and cell signaling. Nature 341(6239):197-05. doi:10.1038/341197a0 CrossRef
2. Billington DC (1993) Inositol phosphates: chemical synthesis and biological significance. VCH Verlagsgeselschaft; VCH Publishers, Weinheim
3. Sasaki K, Taylor IEP (1986) / Myo-inositol synthesis from [1-H-3]glucose in / Phaseolus vulgaris L during early stages of germination. Plant Physiol 81(2):493-96. doi:10.1104/Pp.81.2.493 CrossRef
4. Schmalz H-G, Wirth T (2003) Organic synthesis highlights. Wiley, Weinheim (Great Britain) CrossRef
5. Larner J (2002) D- / chiro-inositol—its functional role in insulin action and its deficit in insulin resistance. Int J Exp Diabetes Res 3(1):47-0 CrossRef
6. Iuorno MJ, Jakubowicz DJ, Baillargeon JP, Dillon P, Gunn RD, Allan G, Nestler JE (2002) Effects of D- / chiro-inositol in lean women with the polycystic ovary syndrome. Endocr Pract 8(6):417-23 CrossRef
7. Sherman WR, Goodwin SL, Gunnell KD (1971) / Neo-Inositol in mammalian tissues. Identification, measurement, and enzymatic synthesis from mannose 6-phosphate. Biochemistry (Mosc) 10(19):3491-499 CrossRef
8. Martin JB, Laussmann T, Bakker-Grunwald T, Vogel G, Klein G (2000) / neo-Inositol polyphosphates in the amoeba / Entamoeba histolytica. J Biol Chem 275(14):10134-0140 CrossRef
9. Shapiro J, Belmaker RH, Biegon A, Seker A, Agam G (2000) / Scyllo-inositol in post-mortem brain of bipolar, unipolar and schizophrenic patients. J Neural Transm 107(5):603-07 CrossRef
10. Ichimura K, Kohata K, Yamaguchi Y, Douzono M, Ikeda H, Koketsu M (2000) Identification of l -inositol and scyllitol and their distribution in various organs in chrysanthemum. Biosci Biotechnol Biochem 64(4):865-68 CrossRef
11. Shaldubina A, Ju S, Vaden DL, Ding D, Belmaker RH, Greenberg ML (2002) / Epi-inositol regulates expression of the yeast INO1 gene encoding inositol-1-P synthase. Mol Psychiatry 7(2):174-80. doi:10.1038/sj.mp.4000965 CrossRef
12. Williams RS, Cheng L, Mudge AW, Harwood AJ (2002) A common mechanism of action for three mood-stabilizing drugs. Nature 417(6886):292-95. doi:10.1038/417292a CrossRef
13. Sherman WR, Stewart MA, Kurien MM, Goodwin SL (1968) The measurement of / myo-inositol, / myo-inosose-2 and / scyllo-inositol in mammalian tissues. Biochim Biophys Acta 158(2):197-05 CrossRef
14. Horner WH, Thaker IH (1968) The metabolism of / scyllo-inositol in / Streptomyces griseus. Biochim Biophys Acta 165(2):306-08 CrossRef
15. Kiely DE, Fletcher HG Jr (1969) Cyclization of d - / xylo-hexos-5-ulose, a chemical synthesis of / scyllo-and / myo-inositols from d -glucose. J Org Chem 34(5):1386-390 CrossRef
16. Nitz M, Fenili D, Darabie AA, Wu L, Cousins JE, McLaurin J (2008) Modulation of amyloid-β aggregation and toxicity by inosose stereoisomers. FEBS J 275(8):1663-674. doi:10.1111/j.1742-4658.2008.06321.x CrossRef
17. Barili PL, Berti G, Catelani G, Dandrea F (1992) New synthetic pathways to 5- / C-alkoxypyranosides and to hexos-5-ulose derivatives. Gazz Chim Ital 122(4):135-42
18. Catelani G, Corsaro A, D’Andrea F, Mariani M, Pistarà V, Vittorino E (2003) Convenient preparation of l - / arabino-hexos-5-ulose derivatives from lactose. Carbohydr Res 338(22):2349-358. doi:10.1016/j.carres.2003.08.001 CrossRef
19. Catelani G, D’Andrea F, Guazzelli L, Pistarà V (2009) Toward the synthesis of fine chemicals from lactose: preparation of d - / xylo and l - / lyxo-aldohexos-5-ulose derivatives. Carbohydr Res 344(6):717-24. doi:10.1016/j.carres.2009.01.014 CrossRef
20. Corsaro A, Catelani G, D’Andrea F, Fisichella S, Mariani M, Pistarà V (2003) A new route for the chemical valorisation of lactose. Environ Sci Pollut Res 10(5):325-28. doi:10.1065/espr2001.12.104.2 CrossRef
21. Pistarà V, Chiacchio MA, Corsaro A (2010) Towards the synthesis of new dideoxy δ-dicarbonyl heptoses. Carbohydr Res 345(10):1482-485. doi:10.1016/j.carres.2010.03.013 CrossRef
22. Corsaro A, Pistarà V, Catelani G, D’Andrea F, Adamo R, Chiacchio MA (2006) A new method for the synthesis of carba-sugar enones (gabosines) using a mercury(II)-mediated opening of 4, 5-cyclopropanated pyranosides as the key-step. Tetrahedron Lett 47(37):6591-594. doi:10.1016/j.tetlet.2006.07.023 CrossRef
23. Pistarà V, Barili PL, Catelani G, Corsaro A, D’Andrea F, Fisichella S (2000) A new highly diastereoselective synthesis of / epi-inositol from d -galactose. Tetrahedron Lett 41(17):3253-256. doi:10.1016/S0040-4039(00)00360-9 CrossRef
24. Catelani G, Corsaro A, D’Andrea F, Mariani M, Pistarà V (2002) Intramolecular aldol cyclization of l-lyxo-hexos-5-ulose derivatives: a new diastereoselective synthesis of d-chiro-inositol. Bioorg Med Chem Lett 12(22):3313-315. doi:10.1016/S0960-894x(02)00692-3 CrossRef
25. Pistarà V, Rescifina A, Punzo F, Greco G, Barbera V, Corsaro A (2011) Design, synthesis, molecular docking and crystal structure prediction of new azasugar analogues of α-glucosidase inhibitors. Eur J Org Chem 36:7278-287. doi:10.1002/ejoc.201100832 CrossRef
26. Alberti G, Lombardo GM, Pappalardo GC, Vivani R (2002) Modeling and analysis of the X-ray powder diffraction structure of gamma-zirconium phosphates pillared with butyl chains through molecular dynamics simulations. Chem Mater 14(1):295-03. doi:10.1021/Cm011156g CrossRef
27. Caminiti R, Gleria M, Lipkowitz KB, Lombardo GM, Pappalardo GC (1997) Molecular dynamics simulations combined with large angle X-ray scattering technique for the determination of the structure, conformation, and conformational dynamics of polyphosphazenes in amorphous phase: study of poly[di(4-methylphenoxy)phosphazene]. J Am Chem Soc 119(9):2196-204 CrossRef
28. Carriedo GA, Alonso FJG, Alvarez JLG, Lombardo GM, Pappalardo GC, Punzo F (2004) Molecular dynamics (MD) simulations and large-angle X-ray scattering (LAXS) studies of the solid-state structure and assembly of isotactic (R)-poly(2,2-dioxy-1,1-binaphthyl-)phosphazene in the bulk state and in the cast film. Chem Eur J 10(15):3775-782. doi:10.1002/chem.200400051 CrossRef
29. Lombardo GM, Pappalardo GC (2008) Thermal effects on mixed metal (Zn/Al) layered double hydroxides: direct modeling of the X-ray powder diffraction line shape through molecular dynamics simulations. Chem Mater 20(17):5585-592. doi:10.1021/Cm801053d CrossRef
30. Lombardo GM, Pappalardo GC, Punzo F, Costantino F, Costantino U, Sisani M (2005) A novel integrated X-ray powder diffraction (XRPD) and molecular dynamics (MD) approach for modelling mixed-metal (Zn, Al) layered double hydroxides (LDHs). Eur J Inorg Chem 24:5026-034. doi:10.1002/ejic.200500666 CrossRef
31. Cremer D, Pople JA (1975) General definition of ring puckering coordinates. J Am Chem Soc 97:1354-358. doi:10.1021/ja00839a011 CrossRef
32. Alvarez JLG, Amato ME, Lombardo GM, Carriedo GA, Punzo F (2010) Self-organization by chiral recognition based on ad hoc chiral pockets in cyclotriphosphazenes with binaphthoxy and biphenoxy substituents: an X-ray, NMR and computational study. Eur J Inorg Chem 28:4483-491. doi:10.1002/ejic.201000586 CrossRef
33. Evans DG, Boeyens JCA (1989) Conformational-analysis of ring pucker. Acta Crystallogr B 45:581-90. doi:10.1107/S0108768189008190 CrossRef
34. Desiraju GR, Steiner T (1999) The weak hydrogen bond in structural chemistry and biology. international union of crystallography monographs on crystallography, vol 9. Oxford University Press, Oxford
35. Steiner T (1996) C–H···O hydrogen bonding in crystals. Crystallogr Rev 6:1-1. doi:10.1080/08893119608035394 CrossRef
36. Jeffrey GA, Maluszynska H, Mitra J (1985) Hydrogen-bonding in nucleosides and nucleotides. Int J Biol Macromol 7(6):336-48. doi:10.1016/0141-8130(85)90048-0 CrossRef
37. Dinadayalane TC, Leszczynski J (2009) Geometries and stabilities of various configurations of benzene dimer: details of novel V-shaped structure revealed. Struct Chem 20(1):11-0. doi:10.1007/s11224-009-9411-6 CrossRef
38. DiStasio RA, von Helden G, Steele RP, Head-Gordon M (2007) On the T-shaped structures of the benzene dimer. Chem Phys Lett 437(4-):277-83. doi:10.1016/j.cplett.2007.02.034 CrossRef
39. Fraga ARL, Destri GL, Forte G, Rescifina A, Punzo F (2010) Could / N-(diethylcarbamothioyl)benzamide be a good ionophore for sensor membranes? J Mol Struct 981(1-):86-2 CrossRef
40. Grimme S (2008) Do special noncovalent pi–pi stacking interactions really exist? Angew Chem Int Ed 47(18):3430-434. doi:10.1002/anie.200705157 CrossRef
41. Sato T, Tsuneda T, Hirao K (2005) A density-functional study on pi–aromatic interaction: benzene dimer and naphthalene dimer. J Chem Phys 123(10):104307. doi:10.1063/1.2011396 CrossRef
42. Kita?gorodski? AI (1973) Molecular crystals and molecules. Physical chemistry, a series of monographs, vol 29. Academic Press, New York
43. Burden CJ, Oakley AJ (2007) Anisotropic atomic motions in high-resolution protein crystallography molecular dynamics simulations. Phys Biol 4(2):79-0. doi:10.1088/1478-3975/4/2/002 CrossRef
44. Car R, Parrinello M (1985) Unified approach for molecular-dynamics and density-functional theory. Phys Rev Lett 55(22):2471-474 CrossRef
45. Hobza P, Sponer J (1999) Structure, energetics, and dynamics of the nucleic acid base pairs: nonempirical ab initio calculations. Chem Rev 99(11):3247-276 CrossRef
46. Lombardo GM, Portalone G, Chiacchio U, Rescifina A, Punzo F (2012) Potassium caffeate/caffeic acid co-crystal: the rat race between the catecholic and carboxylic moieties in an atypical co-crystal. Dalton Trans 41(47):14337-4344. doi:10.1039/c2dt31092a CrossRef
47. Lombardo GM, Portalone G, Colapietro M, Rescifina A, Punzo F (2011) From the X-rays to a reliable “low cost-computational structure of caffeic acid: dFT, MP2, HF and integrated molecular dynamics-X-ray diffraction approach to condensed phases. J Mol Struct 994(1-):87-6. doi:10.1016/j.molstruc.2011.03.001 CrossRef
48. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules. J Am Chem Soc 117(19):5179-197 CrossRef
49. Reilly AM, Habershon S, Morrison CA, Rankin DW (2010) Simulating thermal motion in crystalline phase-I ammonia. J Chem Phys 132(13):134511. doi:10.1063/1.3387952 CrossRef
50. Reilly AM, Wann DA, Morrison CA, Rankin DWH (2007) Experimental equilibrium crystal structures: molecular dynamics as a probe for atomic probability density functions. Chem Phys Lett 448(1-):61-4. doi:10.1016/j.cplett.2007.09.073 CrossRef
51. Falshaw A, Hart JB, Tyler PC (2000) New syntheses of 1D-and 1L-, 2-anhydro-myo-inositol and assessment of their glycosidase inhibitory activities. Carbohydr Res 329(2):301-08. doi:10.1016/S0008-6215(00)00192-0 CrossRef
52. Freeman S, Hudlicky T (2004) New oligomers of conduritol-F and muco-inositol, synthesis and biological evaluation as glycosidase inhibitors. Bioorg Med Chem Lett 14(5):1209-212. doi:10.1016/j.bmcl.2003.12.050 CrossRef
53. Painter GF, Eldridge PJ, Falshaw A (2004) Syntheses of tetrahydroxyazepanes from chiro-inositols and their evaluation as glycosidase inhibitors. Bioorg Med Chem 12(1):225-32. doi:10.1016/j.bmc.2003.10.003 CrossRef
54. Paul BJ, Willis J, Martinot TA, Ghiviriga I, Abboud KA, Hudlicky T (2002) Synthesis, structure, and biological evaluation of novel N- and O-linked diinositols. J Am Chem Soc 124(35):10416-0426. doi:10.1021/Ja0205378 CrossRef
55. Sun M, Wang T, Shu X (2009) The use of inositol derivative or salts thereof in the manufacture of medicaments as glycosidase inhibitors or medicaments for treating diabetes. WO2009155753(A1), 30 Dec 2009
56. Sureshan KM, Ikeda K, Asano N, Watanabe Y (2008) Efficient syntheses of optically pure chiro- and allo-inositol derivatives, azidocyclitols and aminocyclitols from myo-inositol. Tetrahedron 64(18):4072-080. doi:10.1016/j.tet.2008.02.032 CrossRef
57. Sim L, Jayakanthan K, Mohan S, Nasi R, Johnston BD, Pinto BM, Rose DR (2010) New Glucosidase inhibitors from an ayurvedic herbal treatment for type 2 diabetes: structures and inhibition of human intestinal maltase-glucoamylase with compounds from / Salacia reticulata. Biochemistry (Mosc) 49(3):443-51. doi:10.1021/Bi9016457 CrossRef
58. http://www.rcsb.org/PDBcode 3L4W
59. Mazue F, Colin D, Gobbo J, Wegner M, Rescifina A, Spatafora C, Fasseur D, Delmas D, Meunier P, Tringali C, Latruffe N (2010) Structural determinants of resveratrol for cell proliferation inhibition potency: experimental and docking studies of new analogs. Eur J Med Chem 45(7):2972-980. doi:10.1016/j.ejmech.2010.03.024 CrossRef
60. de Melo EB, Gomes AD, Carvalho I (2006) Alpha- and beta-glucosidase inhibitors: chemical structure and biological activity. Tetrahedron 62(44):10277-0302. doi:10.1016/j.tet.2006.08.055 CrossRef
61. Wallace AC, Laskowski RA, Thornton JM (1995) Ligplot: a program to generate schematic diagrams of protein ligand interactions. Protein Eng 8(2):127-34. doi:10.1093/protein/8.2.127 CrossRef
62. Perrin DD, Armarego WLF, Perrin DR (1980) Purification of laboratory chemicals, 2nd edn. Pergamon Press, Oxford
63. Hirshfeld FL (1976) Can X-ray data distinguish bonding effects from vibrational smearing? Acta Crystallogr a 2:239-44. doi:10.1107/s0567739476000533 CrossRef
64. Vandersluis P, Spek AL (1990) Bypass: an effective method for the refinement of crystal-structures containing disordered solvent regions. Acta Crystallogr A 46:194-01. doi:10.1107/S0108767389011189 CrossRef
65. Bruker (2007) SAINT-Plus. Bruker AXS Inc, Madison
66. Bruker (2001) SADABS. Bruker AXS Inc, Madison
67. Macrae CF, Edgington PR, McCabe P, Pidcock E, Shields GP, Taylor R, Towler M, van De Streek J (2006) Mercury: visualization and analysis of crystal structures. J Appl Crystallogr 39:453-57. doi:10.1107/S002188980600731x CrossRef
68. Rappe AK, Goddard WA (1991) Charge equilibration for molecular-dynamics simulations. J Phys Chem 95(8):3358-363. doi:10.1021/J100161a070 CrossRef
69. Parrinello M, Rahman A (1982) Strain fluctuations and elastic constants. J Chem Phys 76:2662-666 CrossRef
70. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684-690 CrossRef
71. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19(14):1639-662. doi:10.1002/(Sici)1096-987x(19981115)19:14<1639:Aid-Jcc10>3.0.Co;2-B CrossRef
72. Sanner MF (1999) Python: a programming language for software integration and development. J Mol Graph Model 17(1):57-1 - 作者单位：Venerando Pistarà (1)
Giuseppe M. Lombardo (1)
Antonio Rescifina (1)
Alessia Bacchi (2)
Felicia D’Andrea (3)
Francesco Punzo (1)
1. Divisione Chimica, Dipartimento di Scienze del Farmaco, Università degli Studi di Catania, Viale Andrea Doria 6, 95125, Catania, Italy
2. Dipartimento di Chimica Generale ed Inorganica, Chimica Analitica, Chimica Fisica, Università degli Studi di Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy
3. Dipartimento di Scienze Farmaceutiche, Università degli Studi di Pisa, Via Bonanno 33, 56126, Pisa, Italy - ISSN：1572-9001
文摘
Inositols have been recently reported to show a biological activity as inhibitors of both glycosidase and amyloid-β protein. After having harvested good crystals suitable for single crystal X-ray diffraction, we performed a comparison with the data inferred by means of a molecular dynamics simulation, based on the use of an appropriate Force Field coupled to the most performing charging scheme. This approach allowed a detailed analysis extended to ultra-fine details, such as atomic displacement parameters. It confirmed the good validity of a robust approach already tested by us in previous studies. A NMR analysis of the molecule in solution was also carried out, to compare the structural findings suggested by the X-ray analysis with the ones in solution and avoid confining them to the solid-state. In this framework, we investigated the above-mentioned inhibiting activity of a class of inososes, by means of a molecular docking investigation, which proved the suggested validity of the studied compound as inhibitor of the α-glucosidase.