Structural Basis for Inhibition of the Fat Mass and Obesity Associated Protein (FTO)

Aik, W.S.; Demetriades, Marina; Hamdan, Muhammad K. K.; Bagg, Eleanor A. L.; Yeoh, Kar Kheng; Lejeune, Clarisse; Zhang, Zhihong; McDonough, M.A.; Schofield, Christopher J.

doi:10.1021/jm400193d

Cited by 134 publications

(208 citation statements)

References 33 publications

(67 reference statements)

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“…The IC 50 of citrate for ALKBH5 was measured at 488 M, which is comparable to that for human FTO (300 M) under standard assay conditions (Fig. 4D) (35). Therefore, although citrate is observed to adopt different binding modes in the FTO and ALKBH5 crystal structures, it can act as an inhibitor for both human m 6 A demethylases.…”

Section: Resultssupporting

confidence: 52%

“…Recently, Aik et al (35) reported that citrate can act as a modest inhibitor of the human ALKBH enzyme FTO. In the FTO-citrate complex structure, the citrate molecule binds to FTO in a different manner, i.e.…”

Section: Resultsmentioning

confidence: 99%

“…Despite the important and diverse biological functions of the AlkB family, only a few human protein structures in the AlkB family have been characterized structurally, including ALKBH2 in complex with dsDNA (31), apo-ALKBH3 (32), ALKBH8 RRM-AlkB double domain (33), and FTO in complex with 3meT (34) and in complex with various inhibitors (35). As the first identified eukaryotic RNA demethylase, FTO catalyzes demethylation of 3meU in ssRNAs and 3meT in ssDNAs (9,29) and has been implicated in obesity (36,37).…”

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confidence: 99%

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Structures of Human ALKBH5 Demethylase Reveal a Unique Binding Mode for Specific Single-stranded N6-Methyladenosine RNA Demethylation

Liu

Tempel

et al. 2014

Journal of Biological Chemistry

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148

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Background: ALKBH5 catalyzes demethylation of m 6 A single-stranded RNA (ssRNA). Results: ALKBH5 structures reveal the structural basis of its substrate selectivity and inhibition by citrate. Conclusion: ALKBH5 specifically binds to and demethylates m 6 A ssDNA/ssRNA. Citrate is a modest inhibitor of ALKBH5. Significance: This study provides insights into the molecular mechanism of ALKBH5 as an m 6 A ssRNA demethylase and will facilitate the design of selective inhibitors.

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Section: Resultssupporting

confidence: 52%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

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Structures of Human ALKBH5 Demethylase Reveal a Unique Binding Mode for Specific Single-stranded N6-Methyladenosine RNA Demethylation

Liu

Tempel

et al. 2014

Journal of Biological Chemistry

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148

152

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“…BA is a moderate inhibitor of FTO (Fig. 1B) (31,49). AlkB repair remained intact, however, even in the presence of 100-fold excess BA (Fig.…”

Section: Resultsmentioning

confidence: 94%

“…5B). In contrast, rhein fully occupies the methylated DNA binding site in FTO (49). The structural superimposition of FTO and the complex of rhein bound to AlkB clearly shows that rhein would not bind to the 2OG pocket of FTO because of steric clashes to Tyr 295 and Met 297 (Fig.…”

Section: Resultsmentioning

confidence: 98%

Rhein Inhibits AlkB Repair Enzymes and Sensitizes Cells to Methylated DNA Damage

Huang

Liu

et al. 2016

Journal of Biological Chemistry

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The AlkB repair enzymes, including Escherichia coli AlkB and two human homologues, ALKBH2 and ALKBH3, are iron(II)-and 2-oxoglutarate-dependent dioxygenases that efficiently repair N 1 -methyladenine and N 3 -methylcytosine methylated DNA damages. The development of small molecule inhibitors of these enzymes has seen less success. Here we have characterized a previously discovered natural product rhein and tested its ability to inhibit AlkB repair enzymes in vitro and to sensitize cells to methyl methane sulfonate that mainly produces N 1 -methyladenine and N 3 -methylcytosine lesions. Our investigation of the mechanism of rhein inhibition reveals that rhein binds to AlkB repair enzymes in vitro and promotes thermal stability in vivo. In addition, we have determined a new structural complex of rhein bound to AlkB, which shows that rhein binds to a different part of the active site in AlkB than it binds to in fat mass and obesity-associated protein (FTO). With the support of these observations, we put forth the hypothesis that AlkB repair enzymes would be effective pharmacological targets for cancer treatment.The nucleic acids in living cells are subject to modification by both endogenous and environmental agents (1). Direct-acting chemicals constantly damage nucleic acids and generate various methyl lesions with mutagenic and/or cytotoxic consequences (2, 3). O 6 -Methylguanine (O 6 mG) 2 and N 3 -methyladenine lesions have the highest potential for methylating damage by an SN1 agent such as N-methyl-NЈ-nitro-N-nitrosoguanidine (MNNG), which block replication and are thought to be toxic (4, 5). For the most part, the SN2 agent such as methyl methane sulfonate (MMS) produces N 1 -methyladenine (m 1 A) and N 3 -methylcytosine (m 3 C) lesions in single-stranded DNA (ssDNA). Accumulation of these adducts can lead to cell death (6, 7). Organisms have evolved several mechanisms to efficiently remove various methyl lesions, including suicidal methyltransferases, DNA glycosylases, and the AlkB family dioxygenases (see Fig. 1A) (8, 9). To date, AlkB repair appears to be the major natural defense mechanism with the power to restore the canonical base structure in vivo. Escherichia coli AlkB and its human homologues, ALKBH2 and ALKBH3, utilize iron(II) and 2-oxoglutarate (2OG) to achieve oxidative demethylation of m 1 A and m 3 C (see Fig. 1B) (10 -12). The lack of AlkB repair results in increased sensitivity to MMS, elevated level of mutations, and reduced cell proliferation (13-16). Furthermore, the accumulation of m 1 A and m 3 C lesions could also occur on RNA. Research suggests that the oxidative demethylation in mRNA and tRNA acts as a part of AlkB or ALKBH3 repair to protect cells against MMS (17, 18). The scope of substrates for AlkB repair has been largely extended to all simple N-alkyl lesions at the WatsonCrick base-pairing interface on the four bases (19), thus indicating the importance of oxidative demethylation for cell survival. In addition, human enzymes have been broadly linked to cancer. The housekeeping ...

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Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active‐Site Residues

Zhu

2014

Angewandte Chemie

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The AlkB family demethylases AlkB, FTO, and ALKBH5 recognize differentially methylated RNA/DNA substrates, which results in their distinct biological roles. Here we identify key active‐site residues that contribute to their substrate specificity. Swapping such active‐site residues between the demethylases leads to partially switched demethylation activities. Combined evidence from X‐ray structures and enzyme kinetics suggests a role of the active‐site residues in substrate recognition. Such a divergent active‐site sequence may aid the design of selective inhibitors that can discriminate these homologue RNA/DNA demethylases.

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Structural Basis for Inhibition of the Fat Mass and Obesity Associated Protein (FTO)

Cited by 134 publications

References 33 publications

Structures of Human ALKBH5 Demethylase Reveal a Unique Binding Mode for Specific Single-stranded N6-Methyladenosine RNA Demethylation

Structures of Human ALKBH5 Demethylase Reveal a Unique Binding Mode for Specific Single-stranded N6-Methyladenosine RNA Demethylation

Rhein Inhibits AlkB Repair Enzymes and Sensitizes Cells to Methylated DNA Damage

Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active‐Site Residues

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