Annual Report 2011 - Center for Advanced Biotechnology and ...

DNA-binding domain of AgrA, establishing a novel fold for the LytTR domain that
regulates virulence factor expression in many pathogenic bacteria. Recent studies
have focused on purification and characterization of full-length AgrA with an
emphasis on understanding the role of the extreme C terminus that is altered by a
phase-variation mechanism, inactivating AgrA at late stages of infection.
WATERGATE LOGSY NMR experiments were used to identify drug-like fragments
that bind to AgrA. All six ligands identified bind to the same site, overlapping the
surface required for binding. Three of the fragments have been shown to inhibit DNA
binding and are being pursued for inhibitor development. The Stock laboratory has
determined the structures of both inactive and activated full-length VraR, a
vancomycin-resistance-associated regulator that plays a central role in maintaining
the integrity of the cell wall peptidoglycan and in coordinating responses to cell wall
damage. These structures represent the first inactive and active pair of full-length
response regulator transcription factors. The structures establish the mechanism of
activation of VraR via dimerization and reveal an unusual deep binding pocket with
great potential for inhibitor development. Virtual docking analyses using the Zinc
database of available compounds have identified many compounds predicted to bind
to this pocket. In collaboration with Ed LaVoie (School of Pharmacy, Rutgers
University) and John Kerrigan (CINJ), these compounds have been ranked and several
have been selected as a starting point for inhibitor development.
Dimer interface of active VraR
receiver domain. The protruding
Methionine 13 from one monomer
fits into a deep binding cleft of the
other monomer, a site that is
being targeted for development of
inhibitors as leads for
development of novel antibiotics.
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