4-Benzylideneisoquinoline-1,3(2H, 4H)-diones as tyrosyl DNA phosphodiesterase 2 (TDP2) inhibitors

Abstract

Tyrosyl-DNA phosphodiesterase 2 (TDP2) repairs topoisomerase II (Top2) mediated DNA damages, including double-strand breaks (DSBs) that underpin the anticancer mechanism of clinical TOP2 poisons such as etoposide (ETP). Inhibition of TDP2 could sensitize cancer cells toward TOP2 poisons by increasing Top2 cleavage complex. We have previously identified isoquinoline-1,3-dione as a selective inhibitor type of TDP2. However, the reported structure-activity relationship (SAR) was limited to simple substitutions on the isoquinoline-1,3-dione core. Herein, we report the extended SAR consisting of the synthesis and testing of a total of 50 analogs featuring N-2 and C-4 modifications. Major SAR observations include the loss of potency upon N-2 substitution, the lack of inhibition with C-4 enamine analogs (subtype 11), or any other C-4 modifications (subtypes 13-15) except for the benzylidene substitution (subtype 12), where eight analogs showed low micromolar potency. The best analog, 12q, inhibited TDP2 with an IC50 of 4.8 μM. Molecular modeling was performed to help understand the observed SAR trends. Overall, these SAR observations which could significantly benefit future work on the design of improved TDP2 inhibitors.

Keywords: Anti-cancer; Tyrosyl-DNA phosphodiesterase 2 (TDP2); benzylideneisoquinoline-1,3(2H,4H)-dione.

Figure 1.

Structures of known TDP2 inhibitors

Figure 2.

Comparison of SAR investigated previously vs. this work

Figure 3.

Predicted optimal binding modes of (A) 1,3-dioxo-1,2,3,4-tetrahydroisoquinoline-7-carboxylic acid;[18] (B) overlay of compounds 8 and 10c; (C) overlay of compounds 11b and 12k;(D) 12q within active site of hTDP2 (numbering was based on hTDP2 sequence). The active site residues are shown as orange sticks and metal ions as red spheres. Important interactions are depicted as black dotted lines. Valency and hydrogen atoms are omitted for clarity. Homology model (hTDP2) was built using the crystal structure of mTDP2 (PDB code: 4GZ1).

Scheme 1.

Synthesis of different analogs investigated in this study ^a Reagents and conditions: (a) Conc. NH₄OH, 1,2-dichlorobenzene, 175 °C, MW,90%; (b) Triethyl orthoformate, Ac₂O, DMF, 120 °C, 72%; (c) H₂N-R, Et₃N, DMF, 115 °C, 50-88%; (d) aldehyde, piperidine, EtOH:C₆H₆ (3:2 v/v), 85 °C, 40-85%; (e) MeNH₂ (aq), 1,2-dichlorobenzene, reflux, 85%; (f) Benzyloxyamine, 1,2-dichlorobenzene, 175 °C, MW, 75%; (g) BBr₃, DCM, rt, 36%; (h) SOCl₂, MeOH, reflux, Quant.; (i) p-Anisaldehyde, NaOMe, MeOH then, SOCl₂, MeOH, 80%; (j) Pd/C, MeOH, H₂, Quant.; (k) 10% KOH, MeOH, reflux then Cone. NH₄OH, 1,2-dichlorobenzene, reflux, 35%; (I) BBr₃, DCM, rt, 60%; (m) Cs₂CO₃, air, MeCN, rt; (n) Bromobenzene, Pd(dba)₂, X-Phos, t-BuOK, toluene, 100 °C, 80%; (o) 4-Methoxybenzylamine, toluene, 180 °C, 75%; (p) NaN₃, m-HO₂CPhSO₂Cl, K₂CO₃, H₂O, rt, 80%; (q) Benzonitrile, Rh₂(OAc)₄, 120 °C, MW, 50%; (r) TFA, 41%; (s) Ethyl cyanoacetate, NaH, DMSO, 90 °C, 94%; (t) DMSO:H₂O (9:1), 120 °C, 55%; (u) ArB(OH)₂, Pd(PPh₃)₄, K₂CO₃, DME:H₂O (4:1), 110 °C, 87%; (v) cone HCl, 70 °C, 84%