The goal of this R01 project is to identify allosteric inhibitors that trap inactive conformations of a family of proteolytic enzymes and have sufficient pharmacologic viability to serve as the starting point for lead optimization and animal studies. These studies seek to exploit dynamics associated with monomer-dimer equilibrium to offer a new approach for developing specificity against this class of protease targets that has so far been recalcitrant to selective inhibitors. Protein-protein interactions are ubiquitous in biology ad represent potential therapeutic targets for numerous diseases. The dimeric human herpes virus (HHV) proteases are one such example. HHVs make up one of the most prevalent viral families and are the etiological agents to a variety of devastating human illnesses for which there is lack of specific and effective treatments. As with all infectious diseases, resistance to therapy is constantly evolving and new therapies are needed for this virus family. There is significant interest in new viral protease inhibitors based on the recent success of antiproteolytic therapies. All HHVs express a dimeric serine protease that is essential to the viral life cycle. Genetic knockout of this protease in cell culture prevents viral replication, providing genetic validation f the target. We have identified a small molecule inhibitor of the protease of one member of this family, Kaposi's sarcoma-associated herpes virus (KSHV), by screening a biased helical mimetic library. By integrating multiple chemical-biology approaches we have determined a """"""""dimer disruption via monomer trap"""""""" mode of inhibition and mapped the binding site to a previously unreported allosteric pocket at the protease dimer interface. Recent chemistry efforts have improved potency and permeability while further informing mode of binding. Considering the structural and functional homology among HHV proteases, we propose to use diverse screening approaches and structure-based inhibitor design to develop allosteric inhibitor scaffolds that target protease dimerization or other allosteric sites in herpes virus proteases. These assays, including cell culture assays for viral infectivity, are currently in place for KSHV protease and CMV protease and will be established for other HHV proteases. We hypothesize that allosteric inhibitors of HHV proteases that trap inactive protease conformations can be identified and used to develop pharmacologically-viable compounds that prevent viral replication in cell-based assays.
Aim 1. Develop inhibitory scaffolds for HHV proteases using screening and structure-guided chemistry to achieve nanomolar inhibition and improved cell membrane permeability.
Aim 2. Characterize the specificity and binding mode of screening hits using NMR spectroscopy and crystallography and select allosteric inhibitors with a broad spectrum of activity towards KSHV, CMV, and HSV-2 proteases.
Aim 3. Determine the mechanism of action of selected inhibitors in herpes viral cell culture models.

Public Health Relevance

Our aim is to develop inhibitors by employing a novel strategy of targeting and stabilizing inactive forms of an enzyme so it cannot become active. These inhibitors will be for essential enzymes of the herpes virus family that ultimately could be developed as a drug for this class of virus that includes the diseases shingles, chickenpox, retinitis, genital herpes, mononucleosis, and Kaposi's sarcoma. There is a critical need for new and specific herpes virus therapies.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM104659-02
Application #
8698774
Study Section
Macromolecular Structure and Function E Study Section (MSFE)
Program Officer
Fabian, Miles
Project Start
2013-07-10
Project End
2017-03-31
Budget Start
2014-04-01
Budget End
2015-03-31
Support Year
2
Fiscal Year
2014
Total Cost
$305,247
Indirect Cost
$111,747
Name
University of California San Francisco
Department
Pharmacology
Type
Schools of Pharmacy
DUNS #
094878337
City
San Francisco
State
CA
Country
United States
Zip Code
94143
Debela, Mekdes; Magdolen, Viktor; Skala, Wolfgang et al. (2018) Structural determinants of specificity and regulation of activity in the allosteric loop network of human KLK8/neuropsin. Sci Rep 8:10705
Isaac, R Stefan; Sanulli, Serena; Tibble, Ryan et al. (2017) Biochemical Basis for Distinct Roles of the Heterochromatin Proteins Swi6 and Chp2. J Mol Biol 429:3666-3677
Guo, Chun-Jun; Chang, Fang-Yuan; Wyche, Thomas P et al. (2017) Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases. Cell 168:517-526.e18
Acker, Timothy M; Gable, Jonathan E; Bohn, Markus-Frederik et al. (2017) Allosteric Inhibitors, Crystallography, and Comparative Analysis Reveal Network of Coordinated Movement across Human Herpesvirus Proteases. J Am Chem Soc 139:11650-11653
Gable, Jonathan E; Lee, Gregory M; Acker, Timothy M et al. (2016) Fragment-Based Protein-Protein Interaction Antagonists of a Viral Dimeric Protease. ChemMedChem 11:862-9
Li, Hao; O'Donoghue, Anthony J; van der Linden, Wouter A et al. (2016) Structure- and function-based design of Plasmodium-selective proteasome inhibitors. Nature 530:233-6
Winter, Michael B; Salcedo, Eugenia C; Lohse, Matthew B et al. (2016) Global Identification of Biofilm-Specific Proteolysis in Candida albicans. MBio 7:
Gable, Jonathan E; Lee, Gregory M; Jaishankar, Priyadarshini et al. (2014) Broad-spectrum allosteric inhibition of herpesvirus proteases. Biochemistry 53:4648-60
Gable, Jonathan E; Acker, Timothy M; Craik, Charles S (2014) Current and potential treatments for ubiquitous but neglected herpesvirus infections. Chem Rev 114:11382-412
Lee, Gregory M; Balouch, Eaman; Goetz, David H et al. (2012) Mapping inhibitor binding modes on an active cysteine protease via nuclear magnetic resonance spectroscopy. Biochemistry 51:10087-98

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