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Crystal structures of complexes of vitamin D receptor ligand-binding domain with lithocholic acid derivatives.

Masuno H, Ikura T, Morizono D, Orita I, Yamada S, Shimizu M, Ito N
J Lipid Res 54 2206-2213 (2013)
Related entries: 3w5p, 3w5q, 3w5t

Cited: 25 times
EuropePMC logo PMID: 23723390

Abstract

The secondary bile acid lithocholic acid (LCA) and its derivatives act as selective modulators of the vitamin D receptor (VDR), although their structures fundamentally differ from that of the natural hormone 1α,25-dihydroxyvitamin D3 [1,25(OH)2D3)]. Here, we have determined the crystal structures of the ligand-binding domain of rat VDR (VDR-LBD) in ternary complexes with a synthetic partial peptide of the coactivator MED1 (mediator of RNA polymerase II transcription subunit 1) and four ligands, LCA, 3-keto LCA, LCA acetate, and LCA propionate, with the goal of elucidating their agonistic mechanism. LCA and its derivatives bind to the same ligand-binding pocket (LBP) of VDR-LBD that 1,25(OH)2D3 binds to, but in the opposite orientation; their A-ring is positioned at the top of the LBP, whereas their acyclic tail is located at the bottom of the LBP. However, most of the hydrophobic and hydrophilic interactions observed in the complex with 1,25(OH)2D3 are reproduced in the complexes with LCA and its derivatives. Additional interactions between VDR-LBD and the C-3 substituents of the A-ring are also observed in the complexes with LCA and its derivatives. These may result in the observed difference in the potency among the LCA-type ligands.

Articles - 3w5r mentioned but not cited (2)

  1. Crystal structures of complexes of vitamin D receptor ligand-binding domain with lithocholic acid derivatives. Masuno H, Ikura T, Morizono D, Orita I, Yamada S, Shimizu M, Ito N. J Lipid Res 54 2206-2213 (2013)
  2. A multidisciplinary approach disclosing unexplored Aflatoxin B1 roles in severe impairment of vitamin D mechanisms of action. Persico M, Sessa R, Cesaro E, Dini I, Costanzo P, Ritieni A, Fattorusso C, Grosso M. Cell Biol Toxicol 39 1275-1295 (2023)


Reviews citing this publication (13)

  1. Endogenously produced nonclassical vitamin D hydroxy-metabolites act as "biased" agonists on VDR and inverse agonists on RORα and RORγ. Slominski AT, Kim TK, Hobrath JV, Oak ASW, Tang EKY, Tieu EW, Li W, Tuckey RC, Jetten AM. J Steroid Biochem Mol Biol 173 42-56 (2017)
  2. The Biosynthesis, Signaling, and Neurological Functions of Bile Acids. Kiriyama Y, Nochi H. Biomolecules 9 E232 (2019)
  3. Vitamin D and Its Synthetic Analogs. Maestro MA, Molnár F, Carlberg C. J Med Chem 62 6854-6875 (2019)
  4. Vitamin D receptor 2016: novel ligands and structural insights. Maestro MA, Molnár F, Mouriño A, Carlberg C. Expert Opin Ther Pat 26 1291-1306 (2016)
  5. Vitamin D receptor signaling and its therapeutic implications: Genome-wide and structural view. Carlberg C, Molnár F. Can J Physiol Pharmacol 93 311-318 (2015)
  6. Physiological Role of Bile Acids Modified by the Gut Microbiome. Kiriyama Y, Nochi H. Microorganisms 10 68 (2021)
  7. Structural considerations of vitamin D signaling. Molnár F. Front Physiol 5 191 (2014)
  8. Structure-activity relationship of nonsecosteroidal vitamin D receptor modulators. Yamada S, Makishima M. Trends Pharmacol Sci 35 324-337 (2014)
  9. Therapeutic application of vitamin D receptor ligands: an updated patent review. Takada I, Makishima M. Expert Opin Ther Pat 25 1373-1383 (2015)
  10. Relationship between Structure and Conformational Change of the Vitamin D Receptor Ligand Binding Domain in 1α,25-Dihydroxyvitamin D3 Signaling. Wan LY, Zhang YQ, Chen MD, Du YQ, Liu CB, Wu JF. Molecules 20 20473-20486 (2015)
  11. The bridge of the gut-joint axis: Gut microbial metabolites in rheumatoid arthritis. Xu X, Wang M, Wang Z, Chen Q, Chen X, Xu Y, Dai M, Wu B, Li Y. Front Immunol 13 1007610 (2022)
  12. The Role of CYP3A in Health and Disease. Klyushova LS, Perepechaeva ML, Grishanova AY. Biomedicines 10 2686 (2022)
  13. The Pathological Effects of Circulating Hydrophobic Bile Acids in Alzheimer's Disease. Ehtezazi T, Rahman K, Davies R, Leach AG. J Alzheimers Dis Rep 7 173-211 (2023)

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  1. Nuclear Receptors in Drug Metabolism, Drug Response and Drug Interactions. Prakash C, Zuniga B, Song CS, Jiang S, Cropper J, Park S, Chatterjee B. Nucl Receptor Res 2 101178 (2015)
  2. Resveratrol potentiates vitamin D and nuclear receptor signaling. Dampf Stone A, Batie SF, Sabir MS, Jacobs ET, Lee JH, Whitfield GK, Haussler MR, Jurutka PW. J Cell Biochem 116 1130-1143 (2015)
  3. Functional diversification of vitamin D receptor paralogs in teleost fish after a whole genome duplication event. Kollitz EM, Hawkins MB, Whitfield GK, Kullman SW. Endocrinology 155 4641-4654 (2014)
  4. Evolutionary and Functional Diversification of the Vitamin D Receptor-Lithocholic Acid Partnership. Kollitz EM, Zhang G, Hawkins MB, Whitfield GK, Reif DM, Kullman SW. PLoS One 11 e0168278 (2016)
  5. Synthesis and evaluation of vitamin D receptor-mediated activities of cholesterol and vitamin D metabolites. Teske KA, Bogart JW, Sanchez LM, Yu OB, Preston JV, Cook JM, Silvaggi NR, Bikle DD, Arnold LA. Eur J Med Chem 109 238-246 (2016)
  6. Cell-based and in silico evidence against quercetin and structurally-related flavonols as activators of vitamin D receptor. Lau AJ, Politi R, Yang G, Chang TK. J Steroid Biochem Mol Biol 163 59-67 (2016)
  7. Lithocholic Acid Amides as Potent Vitamin D Receptor Agonists. Yoshihara A, Kawasaki H, Masuno H, Takada K, Numoto N, Ito N, Hirata N, Kanda Y, Ishizawa M, Makishima M, Kagechika H, Tanatani A. Biomolecules 12 130 (2022)
  8. Parallel Chemistry Approach to Identify Novel Nuclear Receptor Ligands Based on the GW0742 Scaffold. Teske KA, Rai G, Nandhikonda P, Sidhu PS, Feleke B, Simeonov A, Yasgar A, Jadhav A, Maloney DJ, Arnold LA. ACS Comb Sci 19 646-656 (2017)
  9. Oligoarginine-Conjugated Peptide Foldamers Inhibiting Vitamin D Receptor-Mediated Transcription. Takyo M, Sato Y, Hirata N, Tsuchiya K, Ishida H, Kurohara T, Yanase Y, Ito T, Kanda Y, Yamamoto K, Misawa T, Demizu Y. ACS Omega 7 46573-46582 (2022)
  10. Synthesis and biological evaluation of steroidal derivatives bearing a small ring as vitamin D receptor agonists. Arichi N, Fujiwara S, Ishizawa M, Makishima M, Hua DH, Yamada KI, Yamaoka Y, Takasu K. Bioorg Med Chem Lett 27 3408-3411 (2017)


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