Journal
CHEMMEDCHEM
Volume 11, Issue 8, Pages 862-869Publisher
WILEY-V C H VERLAG GMBH
DOI: 10.1002/cmdc.201500526
Keywords
dimer disruption; fragment-based screening; human herpesviruses; NMR spectroscopy; proteases
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Funding
- US National Institutes of Health (NIH) [R01-AI090592, 1F32M111012-01]
- NIH Structural Biology Training Grant [GM008284]
- National Science Foundation [1144247]
- National Center for Research Resources
- National Center for Advancing Translational Sciences (NIH), through the UCSF Clinical and Translational Science Institute (CTSI) [UL1 TR000004, UL1 RR024131]
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Fragment-based drug discovery has shown promise as an approach for challenging targets such as protein-protein interfaces. We developed and applied an activity-based fragment screen against dimeric Kaposi's sarcoma-associated herpesvirus protease (KSHV Pr) using an optimized fluorogenic substrate. Dose-response determination was performed as a confirmation screen, and NMR spectroscopy was used to map fragment inhibitor binding to KSHV Pr. Kinetic assays demonstrated that several initial hits also inhibit human cytomegalovirus protease (HCMV Pr). Binding of these hits to HCMV Pr was also confirmed by NMR spectroscopy. Despite the use of a target-agnostic fragment library, more than 80% of confirmed hits disrupted dimerization and bound to a previously reported pocket at the dimer interface of KSHV Pr, not to the active site. One class of fragments, an aminothiazole scaffold, was further explored using commercially available analogues. These compounds demonstrated greater than 100-fold improvement of inhibition. This study illustrates the power of fragment-based screening for these challenging enzymatic targets and provides an example of the potential druggability of pockets at protein-protein interfaces.
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