Discovery of a novel allosteric inhibitor scaffold for polyadenosine-diphosphate-ribose polymerase 14 (PARP14) macrodomain 2

Abstract

The polyadenosine-diphosphate-ribose polymerase 14 (PARP14) has been implicated in DNA damage response pathways for homologous recombination. PARP14 contains three (ADP ribose binding) macrodomains (MD) whose exact contribution to overall PARP14 function in pathology remains unclear. A medium throughput screen led to the identification of N-(2(-9H-carbazol-1-yl)phenyl)acetamide (GeA-69, 1) as a novel allosteric PARP14 MD2 (second MD of PARP14) inhibitor. We herein report medicinal chemistry around this novel chemotype to afford a sub-micromolar PARP14 MD2 inhibitor. This chemical series provides a novel starting point for further development of PARP14 chemical probes.

Keywords: Inhibitor Design; Macrodomain; PARP; Poly-ADP ribsose.

Graphical abstract

Figure 1

Initial hit PARP14 MD2 inhibitor GeA-69 (1) and sulfonamide analogue 2.

Figure 2

(A) Overlay of bound ADPR (Green sticks) (PDB ID 3Q71) superimposed with PARP14 MD2 (cyan sheets and helices, grey loops): compound 2 (yellow sticks) structure (PDB ID 5O2D). (B) H-Bonding displayed in co-crystal structure of PARP14 MD2 (cyan sticks): compound 2 (yellow sticks) structure (PDB ID 5O2D).

Figure 3

SAR studies of carbazoles GeA-69 (1) and 2.

Scheme 1

Suzuki-Miyaura coupling of 1-bromo-9(H)-carbazole with arylboronic acids or pinacol esters.

Figure 4

1-Aryl- and 1-heteroarylcarbazoles 3–14 from the initial compound library. PARP14 MD2 IC₅₀ > 50 µM for all compounds.

Figure 5

Aza analogues of screening hit GeA-69 (1): compounds 15–18 and analogues bearing tetracyclic core structures canthin-4-one 19, desazacanthin-4-one 20.

Figure 6

Analogues of GeA-69 (1) with the acetylaminophenyl residue shifted to other positions.

Figure 7

Analogues of GeA-69 (1) bearing substituents an N-9, as well as dibenzofuran (26), dibenzothiophene (27), fluorenone (28), and fluorenol (29) analogues.

Scheme 2

Synthesis of seco analogue 31 and acridone analogue 33.

Scheme 3

Synthesis of analogues of of GeA-69 (1) bearing additional substituents at ring A.

Scheme 4

Synthesis of an 8-aza analogue 43 of GeA-69 (1).

Scheme 5

Analogues of GeA-69 (1) with partially hydrogenated or truncated ring A.

Scheme 6

Variations of the acetamide group (thioamide 52, reduced N-ethylamine 53, N-ethyl analogue 54, urea analogue 49). Synthesis of the proposed amide bioisoster 51 from aniline 48.

Scheme 7

Synthesis of amide and sulfonamide derivatives of aniline 48.

Figure 8

Flexible side-chain docking studies of carbazole108 with PARP14 MD2 (from PDB ID 5O2D) reveal new potential hydrophobic interactions with M1108, L1137 and F1144 after rotation of F1144 (black arrow, conformation in PDB ID 5O2D shown in green sticks) to accommodate the 3-cyanophenyl group.