Rational Design of RNA Demethylase FTO Inhibitors with Enhanced Antileukemia Drug-Like Properties

Abstract

The fat mass and obesity-associated protein (FTO) is an RNA <i>N</i>⁶-methyladenosine (m⁶A) demethylase highly expressed in diverse cancers including acute myeloid leukemia (AML). To improve antileukemia drug-like properties, we have designed <b>44</b>/ZLD115, a flexible alkaline side-chain-substituted benzoic acid FTO inhibitor derived from FB23. A combination of structure-activity relationship analysis and lipophilic efficiency-guided optimization demonstrates that <b>44</b>/ZLD115 exhibits better drug-likeness than the previously reported FTO inhibitors, FB23 and <b>13a</b>/Dac85. Then, <b>44</b>/ZLD115 shows significant antiproliferative activity in leukemic NB4 and MOLM13 cell lines. Moreover, <b>44</b>/ZLD115 treatment noticeably increases m⁶A abundance on the AML cell RNA, upregulates <i>RARA</i> gene expression, and downregulates <i>MYC</i> gene expression in MOLM13 cells, which are consistent with <i>FTO</i> gene knockdown. Lastly, <b>44</b>/ZLD115 exhibits antileukemic activity in xenograft mice without substantial side effects. This FTO inhibitor demonstrates promising properties that can be further developed for antileukemia applications.