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

Qi Li; Yue Huang; Xichun Liu; Jianhua Gan; Hao Chen; Cai-Guang Yang

doi:10.1074/jbc.M115.711895

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

J Biol Chem. 2016 May 20;291(21):11083-93. doi: 10.1074/jbc.M115.711895. Epub 2016 Mar 25.

Authors

Qi Li¹, Yue Huang¹, Xichun Liu², Jianhua Gan³, Hao Chen², Cai-Guang Yang⁴

Affiliations

¹ From the Laboratory of Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
² the Coordination Chemistry Institute and State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China, and.
³ the School of Life Sciences, Fudan University, Shanghai 200433, China.
⁴ From the Laboratory of Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China, [email protected].

Abstract

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.

Keywords: DNA repair; DNA-protein interaction; bacteria; cancer therapy; chemical biology; enzyme inhibitor; enzyme structure.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

AlkB Homolog 2, Alpha-Ketoglutarate-Dependent Dioxygenase / antagonists & inhibitors
AlkB Homolog 2, Alpha-Ketoglutarate-Dependent Dioxygenase / genetics
AlkB Homolog 2, Alpha-Ketoglutarate-Dependent Dioxygenase / metabolism
AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase / antagonists & inhibitors
AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase / genetics
AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase / metabolism
Anthraquinones / chemistry
Anthraquinones / pharmacology*
Catalytic Domain
Cell Line
Crystallography, X-Ray
DNA Damage
DNA Methylation
DNA Repair Enzymes / antagonists & inhibitors*
DNA Repair Enzymes / genetics
DNA Repair Enzymes / metabolism
Enzyme Inhibitors / chemistry
Enzyme Inhibitors / pharmacology*
Escherichia coli Proteins / antagonists & inhibitors*
Escherichia coli Proteins / genetics
Escherichia coli Proteins / metabolism
Humans
Methyl Methanesulfonate / pharmacology
Mixed Function Oxygenases / antagonists & inhibitors*
Mixed Function Oxygenases / genetics
Mixed Function Oxygenases / metabolism
Models, Molecular
RNA Interference
Recombinant Proteins / genetics
Recombinant Proteins / metabolism

Substances

Anthraquinones
Enzyme Inhibitors
Escherichia coli Proteins
Recombinant Proteins
Methyl Methanesulfonate
Mixed Function Oxygenases
ALKBH3 protein, human
AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase
AlkB protein, E coli
ALKBH2 protein, human
AlkB Homolog 2, Alpha-Ketoglutarate-Dependent Dioxygenase
DNA Repair Enzymes
rhein

Associated data

PDB/3I3Q
PDB/4IE7
PDB/4RFR