The overall project goal is to develop new approaches for discovering "drug-like" small molecule inhibitors against challenging protein-protein interaction (PPI) interfaces. It tests the hypothesis that appropriately designed synthetic macrocycles can inhibit PPI targets while maintaining good drug-like properties. The test system is the intracellular PPI target NF-?B essential modulator (NEMO), a component of the inhibitor of ?B kinase (IKK) complex. Chronic hyperactivity of the NF-?B pathway is found in human inflammatory diseases and cancers. Inhibiting the interaction of NEMO with IKK, as a more targeted alternative to completely ablating all IKK kinase activity, represents a promising new approach for attenuating inflammation. The three Specific Aims are: 1. Perform a virtual fragment screen of the IKK binding domain of NEMO. A novel algorithm (FTMAP) will be used against the PPI target sites. The results will inform the design of novel synthetic acyclic and macrocyclic libraries for synthesis and testing as NEMO inhibitors. 2. Synthesize macrocycles and acyclic inhibitors (from Aim 1), and test them for inhibition of NEMO/IKK binding in a fluorescence polarization assay. Hits will be characterized biochemically and structurally and further optimized through medicinal chemistry. All the compounds will be assessed in assays that measure ADME properties (e.g., solubility, cell permeability and liver microsome stability). The consequences of different macrocyclic designs for these key pharmaceutical properties will thus be determined independently of their activity against NEMO. 3. Characterize promising hits and leads (from Aim 2) using biochemical, biophysical, structural and biological approaches, to elucidate the nature of their interactions with NEMO, determine the origins of the binding energy they generate with the target, and assess their utility as biological probes and/or drug leads. The project team encompasses strong expertise and highly relevant experience across every aspect of the project, including computational chemistry, macrocycle synthesis, X-ray crystallography, drug discovery, and NF-?B pathway biology. The project will provide theoretical and methodological advances in drug discovery against PPI targets. It will elucidate the physicochemical and structural origins and hallmarks of druggability at a PPI interface, and will establish the utility of novel in silico fragment-based approaches and synthetic macrocycles as sources for drug-like inhibitors against such targets.

Public Health Relevance

The goal of this project is to target a particularly challenging class of drug targets, - protein-protein interactions - with small molecule (i.e., synthetic organic) drugs.
It aims to inhibit NF-?B Essential Modulator (NEMO), a component of the NF-?B signaling pathway, which is misregulated in human pathologies such as inflammatory disease and cancer. Inhibiting this pathway represents a promising new approach for the development of effective drugs and, consequently, is highly relevant to public health.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM094551-04
Application #
8520334
Study Section
Synthetic and Biological Chemistry B Study Section (SBCB)
Program Officer
Fabian, Miles
Project Start
2010-09-01
Project End
2014-07-31
Budget Start
2013-08-01
Budget End
2014-07-31
Support Year
4
Fiscal Year
2013
Total Cost
$369,959
Indirect Cost
$143,961
Name
Boston University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
049435266
City
Boston
State
MA
Country
United States
Zip Code
02215
Villar, Elizabeth A; Beglov, Dmitri; Chennamadhavuni, Spandan et al. (2014) How proteins bind macrocycles. Nat Chem Biol 10:723-31
Day, Eric S; Capili, Allan D; Borysenko, Christopher W et al. (2013) Determining the affinity and stoichiometry of interactions between unmodified proteins in solution using Biacore. Anal Biochem 440:96-107
Golden, Mary S; Cote, Shaun M; Sayeg, Marianna et al. (2013) Comprehensive experimental and computational analysis of binding energy hot spots at the NF-ýýB essential modulator/IKKýý protein-protein interface. J Am Chem Soc 135:6242-56
Silvian, Laura F; Friedman, Jessica E; Strauch, Kathy et al. (2011) Small molecule inhibition of the TNF family cytokine CD40 ligand through a subunit fracture mechanism. ACS Chem Biol 6:636-47
Whitty, Adrian (2011) Growing PAINS in academic drug discovery. Future Med Chem 3:797-801
Kozakov, Dima; Hall, David R; Chuang, Gwo-Yu et al. (2011) Structural conservation of druggable hot spots in protein-protein interfaces. Proc Natl Acad Sci U S A 108:13528-33