The goal of this SBIR project is to develop a general protocol for generating specific, high affinity, small molecule ligands for RNA drug targets. In Phase 1, we will create inhibitors to human telomerase, a validated anti-cancer target, using a novel site on the RNA moiety of the telomerase ribonucleoprotein. Despite two decades of development, molecular docking software cannot allow for induced fit of a drug molecule to its target RNA. MORDOR, a software program recently developed at the University of California San Francisco, permits both ligand and receptor flexibility, enabling induced fitting and making in silico ligand design for RNA targets practical for the first time. A wealth of data suggests that ligands for various conserved loci on human telomerase RNA (hTR) should lead to enzyme inhibition and ultimately tumor regression. The P2b domain represents one of these conserved hTR loci, as it is involved in a crucial molecular switch. We will test the hypothesis that induced-fit docking can be used to design hTR- P2b binders and consequently telomerase inhibitors and that through a tandem docking and experimental approach, we can successfully improve affinity and specificity of RNA ligands. We expect to achieve the following Phase 1 aims:
Aim 1 A. Select compounds from the NCI database of 130,000 drug-like compounds for use with MORDOR, and dock 35,000-50,000 of these structures to our hTR-P2b construct. Iteration of the approach followed similarity searching, docking, and NMR testing will enhance the pool of binders.
Aim 1 B. Use MORDOR to screen the 49,000- fragment subset of the ZINC database.
Aim 2. Use NMR to screen top computational """"""""hits"""""""" for binding, map the binding site on the target hTR, determine binding epitope for the ligand and measure KD values for the best hits using two control RNAs to determine selectivity.
Aim 3. Design new ligands with at least a five-fold increase in affinity over a starting structure obtained from Aim 1 compounds and that are selective for control RNAs.
Aim 4. Test the best compounds for activity using a gel-based P2b-P3 competition assay or a cell-based TRAP assay or both. At the end of Phase I of this project, we will have validated our ligand design protocol for flexible receptors and synthesized some early telomerase inhibitor leads for optimization. ? ?
Discovering drugs using computer models has been marginally successful, in part because the drug targets - proteins and RNA - change shape (usually modestly) when a drug is bound. We have developed software that takes the flexibility of the protein and RNA drug targets into account as well as the flexibility of the putative inhibitors. We propose to use this software to find inhibitors of telomerase, a complex ribonucleoprotein which is a known anti-cancer drug target. Specifically, we will use the initial binders to design and synthesize inhibitors of a crucial RNA component of telomerase. ? ? ?
