Structure-guided discovery of potent acly inhibitors with therapeutic potential in ALK+ anaplastic large cell lymphoma and other hematologic malignancies Free

Background: ATP-citrate lyase (ACLY) is a central metabolic enzyme that produces cytosolic acetyl-CoA, a key metabolite linking cellular metabolism to lipid biosynthesis and epigenetic regulation. ACLY is overexpressed and hyperactivated in multiple hematologic malignancies—including ALK+ anaplastic large cell lymphoma (ALCL), mantle cell lymphoma (MCL), acute myeloid leukemia (AML), diffuse large B-cell lymphoma (DLBCL), and T-cell acute lymphoblastic leukemia (T-ALL) where it promotes oncogenic signaling, metabolic reprogramming, and therapy resistance. The recent FDA approval of Bempedoic Acid (ETC-1002) for hypercholesterolemia clinically validates ACLY as a druggable target. However, Bempedoic Acid and other ACLY inhibitors such as EVT0185 are liver-specific prodrugs, activated by hepatocyte-restricted enzymes (e.g., ACSVL1, FATP2), limiting their systemic utility in cancer. Moreover, currently available ACLY inhibitors exhibit poor potency and limited cellular activity, and no direct, systemically active ACLY inhibitors have been identified for therapeutic use in malignancies.

Methods: We employed structure-based virtual screening targeting the ATP-binding site of human ACLY (PDB ID: 3PFF) to identify novel inhibitors with improved potency and cell permeability. Over 300,000 compounds from the NCI database were screened, focusing on interactions with the ATP-grasp domain. Top hits were evaluated in ALK+ ALCL cell lines for ACLY enzymatic inhibition and antiproliferative effects.

Results: Initial virtual screening identified 11 candidate compounds, which were evaluated for ACLY enzymatic inhibition in ALK+ ALCL cell lines. Among them, compound-7 reduced ACLY activity by 50% at 10 µM. Building on this hit, a second-round screen of over 16,000 analogs led to the selection of 100 high-ranking compounds. Follow-up testing identified compound-1 and compound-2 as potent ACLY inhibitors. In ALK+ ALCL cells, both compound-1 and compound-7 demonstrated ACLY inhibition with IC₅₀ values of approximately 5 µM, whereas known inhibitors such as BMS-303141 failed to exhibit cellular activity in the same context. In biochemical assays using recombinant ACLY, compound-1 (IC₅₀ = 0.9 µM), compound-2 (IC₅₀ = 0.46 µM), and compound-7 (IC₅₀ = 1.19 µM) effectively inhibited enzyme activity, with BMS-303141 showing the strongest inhibition (IC₅₀ = 0.24 µM). Despite its potency in vitro, BMS-303141 lacked efficacy in cellular assays. Both compound-1 and compound-7 showed superior antiproliferative activity compared to BMS-303141 in ALK+ ALCL and MCL cell lines. Notably, ACLY expression was elevated in ALK inhibitor (ALKi)-resistant ALCL cells compared to sensitive lines. In ALKi-sensitive and -resistant ALCL cells, compound-1 exhibited IC₅₀ values of 0.38 µM and 1.9 µM, respectively; compound-7 showed IC₅₀ values of 1.5 µM and 3.8 µM. In contrast, BMS-303141 showed minimal activity, with IC₅₀ values exceeding 20 µM and 70 µM in sensitive and resistant cells, respectively.

Conclusions: Our structure-guided virtual screening approach led to the discovery of novel, cell-permeable ACLY inhibitors with potent enzymatic and cellular activity in ALK+ ALCL and other hematologic malignancies. These compounds overcome limitations of existing ACLY inhibitors and hold promise as a new class of metabolic therapeutics targeting ACLY systemically in blood cancers. Further preclinical development is warranted.

Disclosures: NP and JB are listed as inventors on a provisional patent application filed by Fox Chase Cancer Center for discovering ACLY lead compounds, Comp-1, Comp-2, and Comp-7, which are novel ACLY inhibitors. This patent application relates to the content discussed or presented in this work.