Computational study of the binding mechanism between farnesoid X receptor α and antagonist N-benzyl-N-(3-(tertbutyl)-4-hydroxyphenyl)-2,6-dichloro-4-(dimethylamino) benzamide

Abstract

Farnesoid X receptor α (FXRα) is a bile acid-activated transcription factor, which plays important roles in the regulation of multiple metabolic processes. Development of FXR antagonist has revealed great potential for the treatment of metabolic disorders. The compound N-Benzyl-N-(3-(tertbutyl)-4-hydroxyphenyl)-2,6-dichloro-4-(dimethylamino). Benzamide (NDB) was recently determined as a selective antagonist of FXRα, while the detailed interaction mechanism is not well understood. In this study, the combined computational methods including molecular dynamics simulations, binding free energy calculation, and principal component analysis were utilized to investigate the effect of NDB on the dynamics behaviors and dimerization of FXRα The binding free energy calculation indicated that the protein dimerization increases NDB affinity and the binding of NDB also stabilizes the interaction between two subunits of FXRα. Further decomposition of the overall binding free energies into individual residues identifies several residues significant for NDB binding, including Leu291, Met294, Ala295, His298, Met332, Ser336, Ala452, and Leu455. It also suggests that the interactions of L289(A)–W458(B), W458(A)–L289(B), R459(A)–N461(B), and N461(A)–R459(B) are important for the dimer stabilization. This study provides a molecular basis for the understanding of binding mechanism between antagonist NDB and FXRα and valuable information for the novel FXR modulators design for the treatment of metabolic syndrome.

Keywords:

• FXRα
• antagonist
• NDB
• molecular dynamics simulation
• binding free energy calculation

Abbreviations:

• FXRα: farnesoid X receptor α
• NDB: N-benzyl-N-(3-(tertbutyl)-4-hydroxyphenyl)-2,6-dichloro-4-(dimethylamino)
• benzamide
• MD: molecular dynamics
• RXRα: retinoid X receptor α
• AF1: activation function 1
• DBD: DNA-binding domain
• LBD: ligand-binding domain
• MM–GBSA: molecular mechanics–generalized born surface area
• GAFF: general amber force field
• RESP: restrained electrostatic potential
• MM: molecular mechanics
• RMSD: root-mean-square deviation
• RMSF: root-mean-square fluctuation
• PCA: principal component analysis
• 6ECDCA: 6α-ethyl-chenodeoxycholic acid