Production of IFNa is one of the earliest host immune responses after viral infection. The fundamental importance of this Type I interferon, lies in its ability to induce downstream activation of both innate and adaptive immune cells via direct and indirect mechanisms. Because they promote potent anti-viral activity, Type I IFNs have been used as both a monotherapy and in combination with other small molecules for enhanced efficacy in the treatment of chronic viral infections, such as Hepatitis C. Despite the fact that only a portion of patients respond to treatment, and that adverse side-effects from long term dosing regimens are a significant barrier, IFNs remain the best standard of care. Thus, it is the overall goal of this project to develop, in parallel, two classes of IFNa enhancers, one protein and the other small molecule, that may be used alone or in combination with other therapeutics for the broad-spectrum treatment of viral infections. First, in an effort to improve functional responses to IFNs and reduce their toxicity, the Garcia group has developed an approach to re-engineer and expand the menu of existing IFNs with recombinant proteins that exhibit superior therapeutic properties. This method, known as in vitro evolution, has been previously and successfully employed by the Garcia group to engineer cytokines with unique structure-activity relationships and that have proven to be more efficacious than the natural cytokine. Second, the Khosia group will pursue chemical biological studies on a recently discovered polyketide natural product, A-74528, that has been found to enhance the antirviral effects of IFNa. The Khosia group will also engage in production and biochemical and structural analysis of A-74528 analogs.
In Aim 1 we will engineer and improve IFN antiviral activities using in vitro evolution to create IFNs with altered affinity or dimerization geometries with the receptor complex.
In Aim 2 we will conduct biophysical studies of candidate IFNs to determine their mechanisms of action, as monotherapies or in combination with other therapeutics.
In Aim 3 we will investigate the inhibitory mechanism and pharmacological properties of A- 74528 through kinetic and dose-response analyses.
In Aim 4 we will design and synthesize analogs of A- 74528 to define structure activity relationships. This unique interfacing of protein and small molecule medicinal chemistry will hopefully yield highly granular, predictive structure-activity metrics linking the molecular and mechanistic parameters of IFN action to antiviral function.

Public Health Relevance

Type I interferons (IFNs) are important for immunity to many types of viral pathogens. They bolster host immunity by helping to activate immune cells and promoting the production of other antiviral proteins to prevent replication and spread of the virus. IFNs have met with limited success as drugs for treating viral diseases, but still often are a patient's best option. Our goal is to engineer an expanded class of improved IFN drugs, and small molecule IFN-enhancers that will be used to treat a broad variety of viral infections.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Program--Cooperative Agreements (U19)
Project #
Application #
Study Section
Special Emphasis Panel (ZAI1-LR-M (J1))
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Stanford University
United States
Zip Code
Deans, Richard M; Morgens, David W; Ökesli, Ayşe et al. (2016) Parallel shRNA and CRISPR-Cas9 screens enable antiviral drug target identification. Nat Chem Biol 12:361-6
Haynes, Winston A; Vallania, Francesco; Liu, Charles et al. (2016) EMPOWERING MULTI-COHORT GENE EXPRESSION ANALYSIS TO INCREASE REPRODUCIBILITY. Pac Symp Biocomput 22:144-153
Cho, Nam-Joon; Pham, Edward A; Hagey, Rachel J et al. (2016) Reconstitution and Functional Analysis of a Full-Length Hepatitis C Virus NS5B Polymerase on a Supported Lipid Bilayer. ACS Cent Sci 2:456-66
Sweeney, Timothy E; Braviak, Lindsay; Tato, Cristina M et al. (2016) Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis. Lancet Respir Med 4:213-24
Ng, Cherie T; Mendoza, Juan L; Garcia, K Christopher et al. (2016) Alpha and Beta Type 1 Interferon Signaling: Passage for Diverse Biologic Outcomes. Cell 164:349-52
Kearnes, Steven; McCloskey, Kevin; Berndl, Marc et al. (2016) Molecular graph convolutions: moving beyond fingerprints. J Comput Aided Mol Des 30:595-608
Marceau, Caleb D; Puschnik, Andreas S; Majzoub, Karim et al. (2016) Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens. Nature 535:159-63
Pillay, S; Meyer, N L; Puschnik, A S et al. (2016) An essential receptor for adeno-associated virus infection. Nature 530:108-12
Cho, Nam-Joon; Lee, Choongho; Pang, Phillip S et al. (2015) Phosphatidylinositol 4,5-bisphosphate is an HCV NS5A ligand and mediates replication of the viral genome. Gastroenterology 148:616-25
Bekerman, Elena; Einav, Shirit (2015) Response—Applying antibiotics lessons to antivirals. Science 348:1437

Showing the most recent 10 out of 18 publications