Rational Drug Design

Volume 928 of the series Methods in Molecular Biology pp 119-131


A Screening Strategy for Trapping the Inactive Conformer of a Dimeric Enzyme with a Small Molecule Inhibitor

  • Charles S. CraikAffiliated withDepartment of Pharmaceutical Chemistry, University of California, San Francisco
  • , Tina ShahianAffiliated withGraduate Group in Biochemistry and Molecular Biology, University of California, San Francisco Email author 

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Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi’s sarcoma (KS), the most common cancer in AIDS patients. All herpesviruses express a conserved dimeric serine protease that is required for generating infectious virions and is therefore of pharmaceutical interest. Given the past challenges of developing drug-like active-site inhibitors to this class of proteases, small-molecules targeting allosteric sites are of great value. In light of evidence supporting a strong structural linkage between the dimer interface and the protease active site, we have focused our efforts on the dimer interface for identifying dimer disrupting inhibitors. Here, we describe a high throughput screening approach for identifying small molecule dimerization inhibitors of KSHV protease. The helical mimetic, small molecule library used, as well as general strategies for selecting compound libraries for this application will also be discussed. This methodology can be applicable to other systems where an alpha helical moiety plays a dominant role at the interaction site of interest, and in vitro assays to monitor function are in place.

Key words

Human herpesvirus protease Kaposi’s sarcoma-associated herpesvirus (KSHV) Dimer disruptor Allosteric inhibitor Fluorogenic enzyme assay Alpha helical mimetic molecules High throughput screening