Active Projects

Development of a new precision therapeutic for an important cancer target
Jonathan LaRochelle and Stephen Blacklow

The focus of this proposal is to develop a new class of potent and selective small molecule inhibitors of a genetically validated cancer target for further therapeutic development by enhancing the potency of our initial hit. Our inhibitors will occupy a unique niche in the landscape of small molecule precision therapeutics in cancer.

Targeting neuro-immune signaling to treat bacterial infections
Felipe Pinho-Ribeiro, Pankaj Baral, Kimbria Blake, and Isaac Chiu

Bacterial skin and soft tissue infections (SSTIs) are increasingly common due to the rise in prevalence of multi-drug resistant pathogens, necessitating novel non-antibiotic based treatments. While methicillin-resistantStaphylococcus aureus (MRSA) and Streptococcus pyogenesare the two leading causes of SSTIs, up to 20% of SSTIs are also caused by gram-negative bacteria. We have found that skin-innervating neurons play a key role in suppressing neutrophil function and the innate immune response against SSTIs. We have developed an approach to treat bacterial infections by targeting this neuro-immune axis using botulinumneurotoxins (BoNTs), thereby enhancing host immunity. In this project, we determine whether this therapeutic approach is broadly applicable by testing BoNTs against S. pyogenes, MRSA, K. pneumoniae and P. aeruginosa infections. We are in active discussions to partner with companies that produce both of these products. Utilizing BoNTs to enhance host immunity could be a transformative approach to treat challenging bacterial infections.

Development of New Antiviral Compounds
Jim Hogle, Hari Arthanari, David Scott, Han Chen, and Donald Coen

Herpesviruses cause severe diseases, particularly in immunocompromised and immune-naive individuals. Currently approved anti-herpesvirus drugs have important drawbacks, including limited efficacy, toxicities, and drug resistance, driving a need for new, improved agents. We have been exploring new targets for anti-herpesvirus drugs starting with a combination of structural, biochemical, and genetic studies. Using high throughput screening, we have identified compounds that selectively inhibit such targets in vitro, with some compounds selectively inhibiting viral replication in cell culture. We have evidence that at least one of these compounds “hits the target” in infected cells. We propose to optimize this compound into leads for further development towards anti-herpesvirus drugs.

Development of AAV-mediated Gene Therapy for Usher Syndrome Type 1F, a Combined Deafness and Blindness
Killian Hanlon, Olga Strelkova, Artur A. Indzhykulian, Casey A. Maguire, Marcos Sotomayor, David Corey

Usher syndrome is a devastating recessive hereditary syndrome of deafness and blindness, caused by mutations in any of 12 genes. One Usher gene, PCDH15 (encoding protocadherin-15) causes Usher syndrome type 1F, manifesting as profound congenital deafness and progressive blindness. There is no treatment.  Usher 1F occurs especially in the Ashkenazi Jewish population; there are ~1500 patients in the United States and ~5000 in the world.

Following the striking success of the Luxturna therapy for blindness by Spark Therapeutics, gene addition for Usher 1F is an attractive approach. Because the deafness phenotype is more severe than blindness in mouse models, we will assay successful rescue by testing cochlear function in vitro and hearing in vivo.  Because mechanical stress on PCDH15 is greater in the ear than in the eye, we believe that constructs that successfully rescue hearing will also rescue vision.  In future work, we will test these constructs to assess rescue of the blindness phenotype. 

Isoguvacine and benzodiazepine derivatives for the treatment of tactile hypersensitivity and anxiety in Autism Spectrum Disorders
Lauren Orefice and David Ginty

Autism spectrum disorders (ASD) are neurodevelopmental disorders characterized by impairments in social communication and interactions, and restricted and repetitive behaviors. ASD is well-established to be associated with aberrant reactivity in multiple sensory domains, including touch, and indeed aberrant sensory reactivity is now considered a key diagnostic feature of ASD. We have used a range of mouse genetic models of ASD combined with behavioral testing, synaptic analyses, and electrophysiology to define both the etiology of aberrant tactile sensitivity in ASD and the contribution of somatosensory dysfunction to the expression of ASD-like traits (Orefice et al., Cell, 2016; Orefice et al., unpublished; Tasnim et al., unpublished). We found that mutations in genes associated with both syndromic and non-syndromic forms of ASD cause tactile dysfunction, and that the RTT- and autism-associated genes Mecp2, Shank3, and Gabrb3 function cell autonomously in peripheral somatosensory neurons for normal tactile behaviors. Remarkably, these somatosensory deficits during development contribute to aberrant social behaviors, including anxiety-like behaviors and social interactions, in adulthood. Our findings raise the exciting possibility that GABAA receptor agonists, which attenuate the activity of peripheral mechanosensory neurons, may be useful for treating tactile hypersensitivity and thus anxiety and social impairments in ASD patients. A key consideration for our work is that physicians are reluctant to prescribe GABAA receptor agonists and positive allosteric modulators because of undesirable side effects, including sedation, and serious complications associated with interference of brain development. Therefore, we aim to use peripherally-restricted GABAA receptor agonists and modulators, compounds that do not cross the blood-brain barrier, to treat tactile dysfunction and core ASD behaviors. Importantly, peripherally-restricted GABAA receptor drugs should not promote undesirable side effects observed with all currently used, FDA-approved GABAA receptor agonists that act in the brain. Thus, for this Q-FASTR application, we propose to determine the efficacy of isoguvacine, a known peripherally-restricted GABAA receptor agonist, as well as novel isoguvacine and nonbenzodiazepine derivatives designed to be peripherally-restricted, for treating tactile hypersensitivity and core ASD behaviors in animal models of ASD.

Computationally designed therapy targeting inflammation in neurodegenerative diseases
Jinkuk Kim, Timothy Yu, and Peter Park

By 2020, more than twenty million people will suffer from neurodegenerative diseases, including Alzheimer and Parkinson's diseases. One of the major hallmarks of neurodegeneration is spurious activation of neuronal inflammation, called microgliosis. Recent studies showed that normalization of the disrupted expression of a key immunoregulatory factor in the central nervous system can reverse the pathology. Through the integrative computational analysis of a massive body of genomic datasets, we found a key mechanism regulating the expression of the factor. We have designed a set of molecules that are predicted to correct the expression based on our algorithm. A screening experiment to identify a lead molecule is underway.

Small molecule modulators of gut bacterial bile acid metabolism to treat metabolic syndrome and associated non-alcoholic fatty liver disease (NAFLD)
Arijit Adhikari and A. Sloan Devlin

Obesity is a growing worldwide health epidemic that is placing ever-growing medical and economic burdens on society. The prevalence of the associated condition non-alcoholic fatty liver disease (NAFLD) is also rising, and this condition is now the leading cause of chronic liver disease in the West. As a result of the multifaceted nature of these diseases and the lack of mechanistic understanding of their molecular underpinnings, doctors must resort to “trial and error” to identify effective treatments. The goal of this research is to develop small molecules that modulate gut bacterial metabolism of bile acids, compounds that play crucial roles in human metabolism, as new potential treatments for metabolic syndrome and NAFLD. These first-in-class molecules that target the microbiota will also allow us to better understand how the human microbiome contributes to obesity on a molecular level, knowledge that will pave the way for the development of future microbiome-based therapies.

A novel system for rational discovery of Polycystic Kidney Disease therapeutics
Cherry Liu and Adrian Salic

Polycystic kidney disease (PKD) is the most frequent life-threatening genetic disease, affecting almost 1 million people in the US alone. It is characterized by growth of numerous cysts that progressively replace normal kidney tissue, which eventually leads to kidney failure, requiring chronic dialysis or transplantation. Currently without treatment, PKD constitutes a very large unmet medical need. PKD is caused by inhibitory mutations in PKD1 or PKD2, two interacting membrane proteins that activate a poorly understood signal transduction pathway (hereby, the PKD pathway) that is normally required for suppressing cyst formation. An attractive therapeutic strategy would be to rescue signaling activity downstream of defective PKD1 and PKD2. A major barrier has been the lack of a tractable system for dissecting the PKD pathway. We have recently developed a robust cell-based system that recapitulates PKD signaling, which allows, for the first time, rapid and quantitative measurements of PKD signaling, in a manner not possible in more complicated animal or tissue models. Currently, we are using this powerful system to comprehensively identify and dissect PKD pathway components. Here, we propose to use this novel system to discover small molecules capable of correcting defective signaling in PKD.

Development of an inexpensive at-home influenza kit and detection technology
Jason Qian, Zhixiang Lu, Victoria Jones, Sarah Boswell, Michael Baym, and Michael Springer

Influenza is a major drain on the US economy. Antiviral drugs are most effective against influenza when taken early, often before patients seek medical help. Tests exist for influenza but are only effective when influenza titer is high and/or require sophisticated medical equipment. Here we will build off of methods we are combining and developing for the specific detection of barcoded microorganisms (a DARPA funded project) to develop and optimize a quantitative, cheap, rapid, sensitive, selective, and field-deployable method for detecting influenza. We aim to develop this influenza detection system into an affordable ‘at-home’ system allowing individuals to detect influenza early, thereby increasing the efficacy of antiviral drugs and eliminating unnecessary trips to the ER.

 

Developing therapeutics for treating Rett Syndrome by correcting neuronal long-gene misregulation – Lead compound optimization and in vivo validation
Rock Liao and Michael Greenberg

Disruption of X-linked methyl CpG-binding protein 2 (MECP2) causes Rett syndrome (RTT) - a devastating neurodevelopmental disorder leading to nonsyndromic mental retardation, learning disability, and autism. Currently there is no cure. We recently identified a molecular defect that is a likely cause of RTT – the mis-regulation of long highly methylated genes through MECP2 dysfunction. Notably, many of the mis-regulated highly methylated long genes are required for proper neuronal functions including synapses that underlie learning and memory. We hypothesize that restoring the expression of mis-regulated long genes and synaptic development may be key to treating RTT. A score of hits were identified and the majority were successfully validated by a series of in vitro experiments. Moreover, structural, pharmacokinetic (PK) and blood-brain-barrier (BBB) permeability analyses suggest favorable chemistry for therapeutics. In the next phase of study, we plan to further the drug development by focusing on behavioral testing while starting to investigate potential drug targets and mechanism of action (MOA).

Identification of dengue virus inhibitors
Jared Pitts, Lorilee Tallorin, Marc-Philipp Pfeil, Chih-Yun (Angela) Hsia, and Priscilla L. Yang

1. Zika, and other members of the Flavivirus genus are major human pathogens for which we lack effective countermeasures. Development of safe and effective vaccines against dengue virus (DENV) has been complicated by the propensity of non-neutralizing antibodies to worsen disease through antibody-dependent enhancement of infection. Antibody responses to the four DENV serotypes and Zika virus (ZIKV) cross-react to a significant extent but do not cross-neutralize. Antibody responses elicited by a vaccine can thus worsen disease upon subsequent infection. Antivirals provide an alternative approach to reduce disease and transmission of DENV and ZIKV. Persistence of ZIKV in immune-privileged sites, as evidenced by detection of ZIKV in semen and saliva for months, represents an additional opportunity for antiviral intervention. We are developing novel assays to identify flavivirus antivirals that act by both established and new mechanisms.

Development of small molecule modulators of autophagy and ER stress as novel therapeutics for AD
Jiefei Geng, Mingzhi Jin, Slawomir Dziedzic, Albert D. Yu, Hong Zhu, Amanda Tomie Ouchida, Jiachen Chu and Junying Yuan

The goal of this project is to isolate inhibitors of apoptosis that can activate autophagy. Apoptosis has been implicated in a wide array of human inflammatory and degenerative diseases. However, after more than 30 years of research, the field failed to deliver a target that can be pharmacologically manipulated to inhibit apoptosis, as direct inhibition of caspases leads to necroptosis. Activating autophagy will support cell survival under stress condition.

Developing CRISPR-Cas9 Reagents for Editing Lytic and Latent Herpes Simplex Virus Genomes
Hyungsuk Oh and David Knipe

Herpes simplex virus (HSV) 1 and 2 cause significant morbidity and mortality, and HSV-2 infection increases the risk of HIV infection. Furthermore, HSV-1 infection is associated with increased risk of Alzheimer’s disease. HSV undergoes an acute lytic infection at the mucosal epithelium and spreads to establish a latent infection in sensory and central nervous system neurons for the life of the individual. Reactivation from latent infection is a major cause of herpetic disease. Drugs that target lytic infection are available, but drugs that target latent infection are not available. Thus, a therapeutic targeting HSV latent infection could reduce HSV latent infection and reactivation and the associated herpetic disease, Alzheimer’s disease, and AIDS.

We have identified a highly active CRISPR-Cas9 reagent that effectively edits lytic and latent HSV-1 genomes in cell culture. Therefore, we propose experiments to further refine the use of this approach for prophylactic and therapeutic treatment of acute and latent HSV infection in animal models. Commercial entities have expressed interest in latent HSV targets, and there is obviously a large market and demand for a “cure” for herpes as well as preventatives for AIDS and Alzheimer’s disease.