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Li M, Shandilya SMD, Carpenter MA, Rathore A, Brown WL, Perkins AL, Harki DA, Solberg J, Hook DJ, Pandey KK, Parniak MA, Johnson JR, Krogan NJ, Somasundaran M, Ali A, Schiffer CA, Harris RS. First-in-class small molecule inhibitors of the single-strand DNA cytosine deaminase APOBEC3G. ACS Chem Biol 2012; 7:506-17. [PMID: 22181350 DOI: 10.1021/cb200440y] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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.
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Affiliation(s)
- Ming Li
- Department of Biochemistry, Molecular Biology & Biophysics, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, 321 Church Street S.E., Minneapolis, Minnesota 55455, United States
| | | | - Michael A. Carpenter
- Department of Biochemistry, Molecular Biology & Biophysics, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, 321 Church Street S.E., Minneapolis, Minnesota 55455, United States
| | - Anurag Rathore
- Department of Biochemistry, Molecular Biology & Biophysics, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, 321 Church Street S.E., Minneapolis, Minnesota 55455, United States
| | - William L. Brown
- Department of Biochemistry, Molecular Biology & Biophysics, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, 321 Church Street S.E., Minneapolis, Minnesota 55455, United States
| | | | | | | | | | - Krishan K. Pandey
- Institute for Molecular Virology, Saint Louis University Health Sciences Center, 1100
South Grand Boulevard, St. Louis, Missouri 63104, United States
| | - Michael A. Parniak
- Department of Microbiology and Molecular
Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, Pennsylvania 15219, United States
| | - Jeffrey R. Johnson
- Department of Cellular & Molecular Pharmacology, California Institute for Quantitative Biosciences, University of California−San Francisco, 600 16th Street, San Francisco, California 94107, United States
| | - Nevan J. Krogan
- Department of Cellular & Molecular Pharmacology, California Institute for Quantitative Biosciences, University of California−San Francisco, 600 16th Street, San Francisco, California 94107, United States
| | | | | | | | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology & Biophysics, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, 321 Church Street S.E., Minneapolis, Minnesota 55455, United States
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Bak A, Magdziarz T, Polanski J. Pharmacophore-based database mining for probing fragmental drug-likeness of diketo acid analogues. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2012; 23:185-204. [PMID: 22292781 DOI: 10.1080/1062936x.2011.645875] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A number of the structurally diverse chemical compounds with functional diketo acid (DKA) subunit(s) have been revealed by combined online and MoStBiodat 3D pharmacophore-guided ZINC and PubChem database screening. We used the structural data available from such screening to analyse the similarities of the compounds containing the DKA fragment. Generally, the analysis by principal component analysis and self-organizing neural network approaches reveals four families of compounds complying with the chemical constitution (aromatic, aliphatic) of the compounds. From a practical point of view, similar studies may reveal potential bioisosteres of known drugs, e.g. raltegravir/elvitegravir. In this context, it seems that mono-halogenated aryl substructures with para group show the closest similarity to these compounds, in contrast to structures where the aromatic ring is halogenated in both ortho- and para-locations.
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Affiliation(s)
- A Bak
- Department of Organic Chemistry , Institute of Chemistry, University of Silesia, Katowice, Poland.
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Serafin K, Mazur P, Bak A, Laine E, Tchertanov L, Mouscadet JF, Polanski J. Ethyl malonate amides: A diketo acid offspring fragment for HIV integrase inhibition. Bioorg Med Chem 2011; 19:5000-5. [DOI: 10.1016/j.bmc.2011.06.054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 06/16/2011] [Accepted: 06/18/2011] [Indexed: 12/24/2022]
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