Meclofenamic acid selectively inhibits FTO demethylation of m6A over ALKBH5

Nucleic Acids Res. 2015 Jan;43(1):373-84. doi: 10.1093/nar/gku1276. Epub 2014 Dec 1.

Abstract

Two human demethylases, the fat mass and obesity-associated (FTO) enzyme and ALKBH5, oxidatively demethylate abundant N(6)-methyladenosine (m(6)A) residues in mRNA. Achieving a method for selective inhibition of FTO over ALKBH5 remains a challenge, however. Here, we have identified meclofenamic acid (MA) as a highly selective inhibitor of FTO. MA is a non-steroidal, anti-inflammatory drug that mechanistic studies indicate competes with FTO binding for the m(6)A-containing nucleic acid. The structure of FTO/MA has revealed much about the inhibitory function of FTO. Our newfound understanding, revealed herein, of the part of the nucleotide recognition lid (NRL) in FTO, for example, has helped elucidate the principles behind the selectivity of FTO over ALKBH5. Treatment of HeLa cells with the ethyl ester form of MA (MA2) has led to elevated levels of m(6)A modification in mRNA. Our collective results highlight the development of functional probes of the FTO enzyme that will (i) enable future biological studies and (ii) pave the way for the rational design of potent and specific inhibitors of FTO for use in medicine.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine / analogs & derivatives*
  • Adenosine / metabolism
  • AlkB Homolog 5, RNA Demethylase
  • Alpha-Ketoglutarate-Dependent Dioxygenase FTO
  • Anti-Inflammatory Agents, Non-Steroidal / chemistry
  • Anti-Inflammatory Agents, Non-Steroidal / pharmacology*
  • Binding, Competitive
  • DNA, Single-Stranded / metabolism
  • Dioxygenases / antagonists & inhibitors
  • Dioxygenases / chemistry
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / pharmacology*
  • HeLa Cells
  • Humans
  • Meclofenamic Acid / chemistry
  • Meclofenamic Acid / pharmacology*
  • Membrane Proteins / antagonists & inhibitors
  • Membrane Proteins / chemistry
  • Proteins / antagonists & inhibitors*
  • Proteins / chemistry
  • Proteins / metabolism
  • RNA, Messenger / chemistry
  • RNA, Messenger / metabolism
  • Structure-Activity Relationship

Substances

  • Anti-Inflammatory Agents, Non-Steroidal
  • DNA, Single-Stranded
  • Enzyme Inhibitors
  • Membrane Proteins
  • Proteins
  • RNA, Messenger
  • N6-methyladenosine (m6A)
  • Meclofenamic Acid
  • Dioxygenases
  • ALKBH5 protein, human
  • AlkB Homolog 5, RNA Demethylase
  • Alpha-Ketoglutarate-Dependent Dioxygenase FTO
  • FTO protein, human
  • Adenosine