title: First-in-class small molecule inhibitors of the single-strand DNA cytosine deaminase APOBEC3G.
abstract: APOBEC3G is a single-stranded DNA cytosine deaminase that comprises part of the innate immune response to viruses and transposons. Although APOBEC3G is the prototype for understanding the larger mammalian polynucleotide deaminase family, no specific chemical inhibitors exist to modulate its activity. High-throughput screening identified 34 compounds that inhibit APOBEC3G catalytic activity. Twenty of 34 small molecules contained catechol moieties, which are known to be sulfhydryl reactive following oxidation to the orthoquinone. Located proximal to the active site, C321 was identified as the binding site for the inhibitors by a combination of mutational screening, structural analysis, and mass spectrometry. Bulkier substitutions C321-to-L, F, Y, or W mimicked chemical inhibition. A strong specificity for APOBEC3G was evident, as most compounds failed to inhibit the related APOBEC3A enzyme or the unrelated enzymes E. coli uracil DNA glycosylase, HIV-1 RNase H, or HIV-1 integrase. Partial, but not complete, sensitivity could be conferred to APOBEC3A by introducing the entire C321 loop from APOBEC3G. Thus, a structural model is presented in which the mechanism of inhibition is both specific and competitive, by binding a pocket adjacent to the APOBEC3G active site, reacting with C321, and blocking access to substrate DNA cytosines.
authors.affiliation: Department of Biochemistry, Molecular Biology & Biophysics, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States.
authors.forename: Ming
authors.initials: M
authors.lastname: Li
authors.forename: Shivender M D
authors.initials: SM
authors.lastname: Shandilya
authors.forename: Michael A
authors.initials: MA
authors.lastname: Carpenter
authors.forename: Anurag
authors.initials: A
authors.lastname: Rathore
authors.forename: William L
authors.initials: WL
authors.lastname: Brown
authors.forename: Angela L
authors.initials: AL
authors.lastname: Perkins
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Harki
authors.forename: Jonathan
authors.initials: J
authors.lastname: Solberg
authors.forename: Derek J
authors.initials: DJ
authors.lastname: Hook
authors.forename: Krishan K
authors.initials: KK
authors.lastname: Pandey
authors.forename: Michael A
authors.initials: MA
authors.lastname: Parniak
authors.forename: Jeffrey R
authors.initials: JR
authors.lastname: Johnson
authors.forename: Nevan J
authors.initials: NJ
authors.lastname: Krogan
authors.forename: Mohan
authors.initials: M
authors.lastname: Somasundaran
authors.forename: Akbar
authors.initials: A
authors.lastname: Ali
authors.forename: Celia A
authors.initials: CA
authors.lastname: Schiffer
authors.forename: Reuben S
authors.initials: RS
authors.lastname: Harris
mesh_terms: D000071480:APOBEC-3G Deaminase; D002478:Cells, Cultured; D018360:Crystallography, X-Ray; D003564:Cytidine Deaminase / Q000037:antagonists & inhibitors* / Q000302:isolation & purification / Q000378:metabolism; D004305:Dose-Response Relationship, Drug; D004789:Enzyme Activation / Q000187:drug effects; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D057809:HEK293 Cells; D019427:HIV Integrase / Q000378:metabolism; D006801:Humans; D008958:Models, Molecular; D015394:Molecular Structure; D016914:Ribonuclease H / Q000037:antagonists & inhibitors / Q000378:metabolism; D054852:Small Molecule Libraries / Q000737:chemistry / Q000494:pharmacology*; D013329:Structure-Activity Relationship
chemical_list: D004791:Enzyme Inhibitors; D054852:Small Molecule Libraries; D019427:HIV Integrase; D016914:Ribonuclease H; D000071480:APOBEC-3G Deaminase; C464924:APOBEC3G protein, human; D003564:Cytidine Deaminase; C514801:p31 integrase protein, Human immunodeficiency virus 1