A Chemical Probe for the ATAD2 Bromodomain

Abstract

ATAD2 is a cancer-associated protein whose bromodomain has been described as among the least druggable of that target class. Starting from a potent lead, permeability and selectivity were improved through a dual approach: 1) using CF2 as a sulfone bio-isostere to exploit the unique properties of fluorine, and 2) using 1,3-interactions to control the conformation of a piperidine ring. This resulted in the first reported low-nanomolar, selective and cell permeable chemical probe for ATAD2.

Keywords: bioisosteres; conformation analysis; epigenetics; fluorine; medicinal chemistry.

Figure 1

A) 2 views of the X-ray structure of 3 bound to ATAD2 (PDB 5a83). B) Superimposed X-ray structures of BRD4 BD1 bound to 1 (orange, PDB 5a5s) and 2 (cyan, PDB 5a85). C) Superimposed X-ray structures of BRD4 BD1 bound to 1 (orange, PDB 5a5s) and 4 (green, PDB 5lj2) showing the di-axial conformation of the piperidine ring. D) ATAD2 crystallographic binding modes of 16 (cyan, PDB 5lj0) and 3 (green, PDB 5a83). E) Binding modes in BRD4 BD1 of 16 (cyan, PDB 5lj1) and 4 (green, PDB 5lj2). For refinement statistics see Table S3; for density maps Figure S6, Supporting Information.

Figure 2

Unlike the impermeable sulfone analog 7 (grey circles), 16 (black diamonds) displaces the ATAD2 bromodomain construct in a cellular nanoBRET displacement assay. 16 does not displace full-length ATAD2 (crosses). (Error bars = SD).

Scheme 1

Conditions: a) m-CPBA, CH₂Cl₂, 0°C; b) NaH, MeI, DMF, 000B0;C, 83% (2 steps); c) LiClO₄, NaN₃, CH₃CN, 8000B0;C, 35%; d) tBuOK, THF, 0°C then RCH₂OTf, 70–72%; e) H₂, Pd/C, MeOH, room temperature, 90–91%; f) 14, tBuONa, BrettPhos, Pd(OAc)₂ or Pd(dba)₂, THF, 60°C, 37–43%; g) NBS, CH₂Cl₂, –10 °C, 94–97%; h) ArB(OH)₂, K₂CO₃, Pd(OAc)₂, cataCXium A, dioxane/H₂O, microwave, 100°C, 40–49 %; i) TFA, reflux, >93%.