Analysis of the binding sites of vitamin D 1α-hydroxylase (CYP27B1) and vitamin D 24-hydroxylase (CYP24A1) for the design of selective CYP24A1 inhibitors: Homology modelling, molecular dynamics simulations and identification of key binding requirements

Bioorg Med Chem. 2017 Oct 15;25(20):5629-5636. doi: 10.1016/j.bmc.2017.08.036. Epub 2017 Aug 22.


A homology model of human CYP27B1 was built using MOE and was further optimised by molecular dynamics simulations of the hCYP27B1 homology model and a hCYP27B1-SDZ-88357 complex. Docking results from the hCYP27B1-SDZ-88357 complex showed amino acids Arg107, Asn387 and Asp320 have an important role in binding interaction, with Asp320 part of the important acid-alcohol pair situated in the I-helix with the conserved sequence (A/G) GX (E/D) (T/S), which assumes an essential role in the binding of an oxygen molecule for catalysis. Additional docking experiments with selective hCYP27B1 or hCYP24A1 inhibitors using both the hCYP27B1 model and a triple mutant hCYP24A1 model provided further support for the importance of H-bonding interactions with the three identified active site amino acids. To confirm the role of Arg107, Asn387 and Asp320 in the active site of hCYP27B1 compounds were designed that would form H-bonding interactions, as determined from docking experiments with the hCYP27B1 model. Subsequent synthesis and CYP24A1 and CYP27B1 enzyme assays of the designed compounds 1a and 1b showed a∼5-fold selectivity for CYP27B1 confirming the importance of Asp320 in particular and also Asn387 and Arg107 as important amino acids for CYP27B1 inhibitory activity.

Keywords: Drug synthesis; Enzyme assays; Molecular dynamics simulations; Molecular modelling; Vitamin D 1α-hydroxylase (CYP27B1); Vitamin D 24-hydroxylase (CYP24A1).

MeSH terms

  • 25-Hydroxyvitamin D3 1-alpha-Hydroxylase / chemistry*
  • 25-Hydroxyvitamin D3 1-alpha-Hydroxylase / metabolism*
  • Amino Acid Sequence
  • Binding Sites
  • Catalytic Domain
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / pharmacology
  • Humans
  • Ligands
  • Models, Chemical*
  • Molecular Dynamics Simulation*
  • Molecular Structure
  • Protein Binding / drug effects
  • Sequence Homology
  • Vitamin D3 24-Hydroxylase / chemistry*
  • Vitamin D3 24-Hydroxylase / metabolism*


  • Enzyme Inhibitors
  • Ligands
  • Vitamin D3 24-Hydroxylase
  • 25-Hydroxyvitamin D3 1-alpha-Hydroxylase