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A Competitive Nucleotide Binding Inhibitor: In Vitro Characterization of Rab7 GTPase Inhibition

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    A Competitive Nucleotide Binding Inhibitor: In Vitro Characterization of Rab7 GTPase Inhibition
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    † ∥ †Department of Pathology, ‡Center for Molecular Discovery, §Biocomputing Division, Department of Biochemistry and Molecular Biology, and ∥Cancer Center, University of New Mexico School of Medicine, Albuquerque, New Mexico 87131, United States
    ⊥ University of Kansas Specialized Chemistry Center, Lawrence, Kansas 66047, United States
    # Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
    *E-mail: [email protected]
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    ACS Chemical Biology

    Cite this: ACS Chem. Biol. 2012, 7, 6, 1095–1108
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    https://doi.org/10.1021/cb3001099
    Published April 9, 2012
    Copyright © 2012 American Chemical Society
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    Mapping the functionality of GTPases through small molecule inhibitors represents an underexplored area in large part due to the lack of suitable compounds. Here we report on the small chemical molecule 2-(benzoylcarbamothioylamino)-5,5-dimethyl-4,7-dihydrothieno[2,3-c]pyran-3-carboxylic acid (PubChem CID 1067700) as an inhibitor of nucleotide binding by Ras-related GTPases. The mechanism of action of this pan-GTPase inhibitor was characterized in the context of the Rab7 GTPase as there are no known inhibitors of Rab GTPases. Bead-based flow cytometry established that CID 1067700 has significant inhibitory potency on Rab7 nucleotide binding with nanomolar inhibitor (Ki) values and an inhibitory response of ≥97% for BODIPY-GTP and BODIPY-GDP binding. Other tested GTPases exhibited significantly lower responses. The compound behaves as a competitive inhibitor of Rab7 nucleotide binding based on both equilibrium binding and dissociation assays. Molecular docking analyses are compatible with CID 1067700 fitting into the nucleotide binding pocket of the GTP-conformer of Rab7. On the GDP-conformer, the molecule has greater solvent exposure and significantly less protein interaction relative to GDP, offering a molecular rationale for the experimental results. Structural features pertinent to CID 1067700 inhibitory activity have been identified through initial structure–activity analyses and identified a molecular scaffold that may serve in the generation of more selective probes for Rab7 and other GTPases. Taken together, our study has identified the first competitive GTPase inhibitor and demonstrated the potential utility of the compound for dissecting the enzymology of the Rab7 GTPase, as well as serving as a model for other small molecular weight GTPase inhibitors.

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    Cite this: ACS Chem. Biol. 2012, 7, 6, 1095–1108
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    https://doi.org/10.1021/cb3001099
    Published April 9, 2012
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