A small molecule inhibitor of the UBE2F-CRL5 axis induces apoptosis and radiosensitization in lung cancer

Abstract

Protein neddylation is catalyzed by a neddylation activating enzyme (NAE, E1), an E2 conjugating enzyme, and an E3 ligase. In various types of human cancers, the neddylation pathway is abnormally activated. Our previous study validated that the neddylation E2 UBE2F is a promising therapeutic target in lung cancer. Although the NAE inhibitor MLN4924/pevonedistat is currently under clinical investigation as an anti-cancer agent, there are no small molecules available that selectively target UBE2F. Here, we report, for the first time, the discovery, via structure-based virtual screen and chemical optimization, of such a small molecule, designated as HA-9104. HA-9104 binds to UBE2F, reduces its protein levels, and consequently inhibits cullin-5 neddylation. Blockage of cullin-5 neddylation inactivates cullin-RING ligase-5 (CRL5) activity, leading to accumulation of the CRL5 substrate, NOXA, to induce apoptosis. Moreover, HA-9104 appears to form the DNA adduct via its 7-azaindole group to induce DNA damage and G2/M arrest. Biologically, HA-9104 effectively suppresses the growth and survival of lung cancer cells and confers radiosensitization in both in vitro cell culture and in vivo xenograft tumor models. In summary, we discovered a small molecule, designated HA-9104, that targets the UBE2F-CRL5 axis with anti-cancer activity alone or in combination with radiation.

NEDD8-conjugating enzyme E2s: critical targets for cancer therapy

“…HA-9104 interacts with UBE2F to reduce its protein levels (via a yet-to-defined mechanism), thereby inhibiting CUL5 neddylation. Blockage of CUL5 neddylation results in CRL5 inhibition and NOXA accumulation to trigger apoptosis [ 48 ]. Since UBE2F inhibition promotes apoptosis and suppresses cancer cell growth (Fig.…”

“…Nevertheless, the induction of drug-resistant mutations in UBA3 inhibits the formation of the MLN4924-NEDD8 adduct, necessitating the need to explore alternative targets against the neddylation pathway [ 45 , 46 ]. To address the limitations of MLN4924, specific inhibitors against neddylation E2s are being investigated [ 47 , 48 ]. This review summarizes the latest progress on validating the neddylation of these enzymes as promising anti-tumor targets.…”

Targeting cullin neddylation for cancer and fibrotic diseases

“…In 2022, Sun's research group, for the first time, reported an azaindole-based UBE2F inhibitor HA-9104, which was obtained through a structure-based virtual screen and multiple rounds of chemistry-based optimization 230 . HA-9104 could effectively bind to UBE2F protein and decrease its expression, resulting in the inhibition of cullin-5 neddylation.…”

Discovery of neddylation E2s inhibitors with therapeutic activity

“… [ 38 ] 2 HA-9104 IC 50 = 49 µM a UBE2F Inhibit CULLIN5 neddylation and accumulate CRL5 substrate NOXA [ 77 ] 3 Arctigenin IC 50 < 2.5 µM UBE2M Inhibit CULLIN 1-4 neddylation and accumulate tumor suppressor PDCD4 protein. [ 78 ] 4 NAcM-OPT IC 50 = 80 nM DCN1 Inhibit CULLIN1 and CULLIN3 neddylation in 10 µM in HCC95 cells. [ 79 ] 5 NAcM-COV IC 50 ≤ 40 nM DCN1 Inhibit CULLIN1 and cullin3 neddylation at 10 µM in HCC95 cells.…”

“…They demonstrated that HA-1141, a small molecule, can inhibit the collaboration between F56 and NAE [ 38 ]. Later, Tiantian Xu et al described HA-9104, another small molecule capable of inhibiting the interaction between UBE2F and NAE when targeted to the V30 pocket [ 78 ]. In addition, Yi-fan Chen et al conducted cell-based natural product inhibitor screening and observed UBE2M neddylation changes upon inhibitor application.…”