Download MendeleyA Small-Molecule Probe Induces a Conformation in HIV TAR RNA Capable of Binding Drug-Like Fragments.
Davidson, A., Begley, D.W., Lau, C., Varani, G.(2011) J Mol Biol 410: 984-996
- PubMed: 21763501
- DOI: https://doi.org/10.1016/j.jmb.2011.03.039
- Primary Citation of Related Structures:
2L8H - PubMed Abstract:
The HIV-1 transactivation response (TAR) element-Tat interaction is a potentially valuable target for treating HIV infection, but efforts to develop TAR-binding antiviral drugs have not yet yielded a successful candidate for clinical development. In this work, we describe a novel approach toward screening fragments against RNA that uses a chemical probe to target the Tat-binding region of TAR. This probe fulfills two critical roles in the screen: by locking the RNA into a conformation capable of binding other fragments, it simultaneously allows the identification of proximal binding fragments by ligand-based NMR. Using this approach, we have discovered six novel TAR-binding fragments, three of which were docked relative to the probe-RNA structure using experimental NMR restraints. The consistent orientations of functional groups in our data-driven docked structures and common electrostatic properties across all fragment leads reveal a surprising level of selectivity by our fragment-sized screening hits. These models further suggest linking strategies for the development of higher-affinity lead compounds for the inhibition of the TAR-Tat interaction.
Organizational Affiliation:
Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195, USA.
