Assessment of the free binding energy of 1,25-dihydroxyvitamin D3 and its analogs with the human VDR receptor model

Acta Biochimica Polonica

Volumn 59, Issue 4, 2012, Pages 653-660

  Kamel, Karol ^a   Kolinski, Andrzej ^a  

^a UNIVERSITY OF WARSAW   (Poland)

Author keywords

Docking; Drug design; EB 1089; KH 1060; RO 25 9022; Vitamin D

Indexed keywords

EID: 84873717393     PISSN: 0001527X     EISSN: 1734154X     Source Type: Journal    
DOI: 10.18388/abp.2012_2106     Document Type: Article

References (46)

1. Barthel TK, Mathern DR, Whitfield GK, Haussler CA, Andrew Hopper IV H, Hsieh J-C, Slater SA, Hsieh G, Kaczmarska M, Jurutka PW, Kolek OI, Ghishan FK, Haussler MR. (2007) 1,25-dihydroxyvitamin D3/VDR-mediated induction of FGF23 as well as transcriptional control of other bone anabolic and catabolic genes that orchestrate the regulation of phosphate and calcium mineral metabolism. J Steroid Biochem 103: 381-388.
2. Van den Bemd GJCM, Chang GTG. (2002) Vitamin D and Vitamin D Analogs in Cancer Treatment. Curr Drug Targets 3: 85-94.
3. Boyle BJ, Zhao XY, Cohen P, Feldman D (2001) Insulin-like growth factor binding protein-3 mediates 1 alpha,25-dihydroxyvitamin D3 growth inhibition in the LNCaP prostate cancer cell line through p21/WAF1. J Urol 165: 1319-1324.
4. Brown AJ, Slatopolsky E (2008) Vitamin D analogs: Therapeutic applications and mechanisms for selectivity. Mol Aspects Med 29: 433-452.
5. Cantorna MT, Hayes CE, DeLuca HF (1996) 1,25-Dihydroxyvitamin D3 reversibly blocks the progression of relapsing encephalomyelitis, a model of multiple sclerosis. Proc Natl Acad Sci USA 93: 7861-7864.
6. Cantorna MT, Mahon BD (2004) Mounting Evidence for Vitamin D as an Environmental Factor Affecting Autoimmune Disease Prevalence. Exp Biol Med 229: 1136-1142.
7. Chiang K-C, Chen TC (2009) Vitamin D for the prevention and treatment of pancreatic cancer. World J Gastroenterol 15: 3349-3354.
8. nd generation force field for the simulation of proteins, nucleic acids and organic molecules. J Am Chem Soc 117: 5179-5197.
9. Evans SR, Soldatenkov V, Shchepotin EB, Bogrash E, Shchepotin IB (1999) Novel 19-nor-hexafluoride vitamin D3 analog (Ro 25-6760) inhibits human colon cancer in vitro via apoptosis. Int J Oncol 14: 979-985.
10. Fanfrlík J, Bronowska AK, Rezac J, Prenosil O, Konvalinka J, Hobza P (2010) A reliable docking/scoring scheme based on the semiempirical quantum mechanical PM6-DH2 method accurately covering dispersion and H-bonding: HIV-1 protease with 22 ligands. J Phys Chem B 114: 12666-12678.
11. Fretz JA, Zella LA, Kim S, Shevde KN, Pike JW (2006) 1,25-Dihydroxyvitamin D3 regulates the expression of low-density lipoprotein receptor-related protein 5 via deoxyribonucleic acid sequence elements located downstream of the start site of transcription. Mol Endocrinol 20: 2215-2230.
12. Gaschott T, Wachtershauser A, Steinhilber D, Stein J (2001) 1,25-Dihydroxycholecalciferol enhances butyrate-induced p21(Waf1/Cip1) expression. Biochem Biophys Res Commun 283: 80-85.
13. Guyton KZ, Kensler TW, Posner GH (2003) Vitamin D and vitamin D analogs as cancer chemopreventive agents. Nutr Rev 61: 227-238.
14. Haussler MR, Haussler CA, Whitfield GK, Hsieh J-C, Thompson PD, Barthel TK, Bartik L, Egan JB, Wu Y, Kubicek JL, Lowmiller CL, Moffet EW, Forster RE, Jurutka PW (2010) The nuclear vitamin D receptor controls the expression of genes encoding factors which feed the "Fountain of Youth" to mediate healthful aging. J Steroid Biochem Mol Biol 121: 88-97.
15. Haussler MR, Jurutka PW, Mizwicki M, Norman AW (2011) Vitamin D receptor (VDR)-mediated actions of 1α,25(OH)2vitamin D3: Genomic and non-genomic mechanisms. Best Pract Res Cl En 25: 543-559.
16. Holick MT (2008) Vitamin D: a D-lightful health perspective. Nutr Rev 66: S182-S194.
17. James SY, Mackay AG, Colston KW (1996) Effects of 1,25 dihydroxyvitamin D3 and its analogues on induction of apoptosis in breast cancer cells. J Steroid Biochem Mol Biol 58: 395-401.
18. Kamel K, Kolinski A (2011) Computational study of binding of epothilone A to β-tubulin. Acta Biochim Pol 58: 255-260.
19. Kawa S, Nikaido T, Aoki Y, Zhai Y, Kumagai T, Furihata K, Fujii S, Kiyosawa K (1997) Vitamin D analogues up-regulate p21 and p27 during growth inhibition of pancreatic cancer cell lines. Br J Cancer 76: 884-889.
20. Klamt A, Schuurmann G (1993) COSMO - a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J Chem Soc, Perkin Trans 2: 799-805.
21. Korth M, Pitonak M, Rezac J, Hobza P (2010) A transferable H-bonding correction for semiempirical quantum-chemical methods. J Chem Theory Comput 6: 344-352.
22. Li P, Li C, Zhao X, Zhang X, Nicosia SV, Bai W (2004) p27(Kip1) stabilization and G(1) arrest by 1,25-dihydroxyvitamin D(3) in ovarian cancer cells mediated through down-regulation of cyclin E/cyclin-dependent kinase 2 and Skp1-Cullin-F-box protein/Skp2 ubiquitin ligase. J Biol Chem 279: 25260-25267.
23. Malinen M, Saramaki A, Ropponen A, Degenhardt T, Vaisanen S, Carlberg C (2008) Distinct HDACs regulate the transcriptional response of human cyclin-dependent kinase inhibitor genes to Trichostatin A and 1alpha,25-dihydroxyvitamin D3. Nucleic Acids Res 36: 121-132.
24. Meyer MB, Watanuki M, Kim S, Shevde NK, Pike JW (2006) The human transient receptor potential vanilloid type 6 distal promoter contains multiple vitamin D receptor binding sites that mediate activation by 1,25-dihydroxyvitamin D3 in intestinal cells. Mol Endocrinol 20: 1447-1461.
25. Milat F, Ng KW (2009) Is Wnt signalling the final common pathway leading to bone formation? Mol Cell Endocrinol 310: 52-62.
26. Moffatt KA, Johannes WU, Hedlund TE (2001) Growth inhibitory effects of 1a, 25-dihydroxyvitamin D3 Are Mediated by Increased Levels of p21 in the Prostatic Carcinoma Cell Line ALVA-31. Cancer Res 61: 7122-7129.
27. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart J, Belew RK, Olson AJ (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19: 1639-1662.
28. Narvaez CJ, Welsh J (1997) Differential effects of 1,25-dihydroxyvitamin D3 and tetradecanoylphorbol acetate on cell cycle and apoptosis of MCF-7 cells and a vitamin D3-resistant variant. Endocrinology 138: 4690-4698.
29. Nickeleit I, Zender S, Kossatz U, Malek NP (2007) p27kip1: a target for tumor therapies? Cell Div 2: 13. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera - a visualization system for exploratory research and analysis. J Comput Chem 25: 1605-1612.
30. Raha K, Merz KM Jr. (2005) Large-scale validation of a quantum mechanics based scoring function: predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes. J Med Chem 48: 4558-4575.
31. Rochel N, Wurtz JM, Mitschler A, Klaholz B, Moras D (2000) The crystal structure of the nuclear receptor for vitamin D bound to its natural ligand. Mol Cell 5: 173-179.
32. Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su SJ, Windus TL, Dupuis M, Montgomery JA (1993) General atomic and molecular electronic structure system. J Comput Chem 14: 1347-1363.
33. Schutz CN, Warshel A (2001) What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins 44: 400-417.
34. Schwartz GG, Eads D, Naczki C, Northrup S, Chen T, Koumenis C (2008) 19-Nor-1 alpha,25-dihydroxyvitamin D2 (paricalcitol) inhibits the proliferation of human pancreatic cancer cells in vitro and in vivo. Cancer Biol Ther 7: 430-436.
35. Singarapu KK, Zhu J, Tonelli M, Rao H, Assadi-Porter FM, Westler WM, Deluca HF, Markley JL (2011) Ligand-specific structural changes in the vitamin D receptor in solution. Biochemistry 50: 11025-11033.
36. Stewart JJP (2007) Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements. J Mol Model 13: 1173-1213.
37. Stewart JJP (2008) Stewart Computational Chemistry, Colorado Springs, CO, MOPAC2009; http://OpenMOPAC.net.
38. Stewart JJP (2009) Application of the PM6 method to modeling proteins. J Mol Model 15: 765-805.
39. Swain CG, Unger SH, Rosenquist NR, Swain MS (1983) Substituent effects on chemical reactivity. improved evaluation of field and resonance components. J Am Chem Soc 105: 492-502.
40. Tocchini-Valentini G, Rochel N, Wurtz JM, Mitschler A, Moras D (2001) Crystal structures of the vitamin D receptor complexed to superagonist 20-epi ligands. P Natl Acad Sci USA 98: 5491-5496.
41. Tocchini-Valentini G, Rochel N, Wurtz JM, Moras D (2004) Crystal Structures of the Vitamin D Nuclear Receptor Liganded with the Vitamin D Side Chain Analogues Calcipotriol and Seocalcitol, Receptor Agonists of Clinical Importance. Insights into a Structural Basis for the Switching of Calcipotriol to a Receptor Antagonist by Further Side Chain Modification. J Med Chem 47: 1956-1961.
42. Uskokovic MR, Norman AW, Manchand PS, Studzinski GP, Campbell MJ, Koeffler HP, Takeuchi A, Siu-Caldera M-L, Rao DS, Reddy GS (2001) Highly active analogs of 1a,25-dihydroxyvitamin D3 that resist metabolism through C-24 oxidation and C-3 epimerization pathways. Steroids 66: 463-471.
43. Vaisanen S, Ryhanen S, Saarela JTA, Perakyla M, Andersin T, Maenpaa PH (2002) Structurally and functionally important amino acids of the agonistic conformation of the human Vitamin D receptor. Mol Pharmacol 62: 788-794.
44. Wu G, Fan RS, Li W, Ko TC, Brattain MG (1997) Modulation of cell cycle control by vitamin D3 and its analogue, EB1089, in human breast cancer cells. Oncogene 15: 1555-1563.
45. Zella JB, DeLuca HF (2003) Vitamin D and autoimmune diabetes. J Cell Biochem 88: 216-222.
46. Zhuang S-H, Burnstein KR (1998) Antiproliferative effect of 1α,25-dihydroxyvitamin D3 in human prostate cancer cell line LNCaP involves reduction of cyclin-dependent kinase 2 activity and persistent G1 accumulation. Endocrinology 139: 1197-1207.