Past Projects

2021 Pilot Grants

Small molecule drugs for advanced cancer with ecDNA amplicons

Small molecule drugs for advanced cancer with ecDNA amplicons
Tae Yoo, Patrick Flynn, and Timothy Mitchison
Impact: There is a huge need for drugs to treat advanced and metastatic solid cancers. Cells in such cancers usually have aberrant genomes with highly amplified oncogenes. Drugs have been developed to target certain amplified oncogenes as proteins, but this has been difficult in many cases. Our idea is to target the amplified DNA itself by exploiting fundamental differences in its chromosomal organization compared to normal DNA. Recent analysis showed that 20-60% of common solid tumors contain amplified DNA in the form of small, circular chromosomes called extrachromosomal DNA (ecDNA). These autonomous genetic elements, previously called “double minutes”, are typically 0.2-2MB in length, present at 2-100copies per cancer cell and absent from normal cells. They lack centromeres and segregate inefficiently at mitosis, resulting in copy number fluctuations that allow rapid evolution of cancer genotype. ecDNA is a highly abnormal state of chromosome organization that is specific to cancer cells. We propose it constitutes a druggable vulnerability and have identified a candidate target based on its DepMap dependency scores and cell biology.
Research Objectives: Develop an enzyme assay suited for inhibitor screening on the candidate target and test inhibitor scaffolds from in silico prediction or/and HTS screens. In parallel, develop cell-based assays for genetic depletion of the candidate target and test if it is selectively required for mitosis in cancer cells with high ecDNA copy number.

Novel biologics for cancer therapy

Novel biologics for cancer therapy
Chun-Ting Wu, Raphael Ferreira, and George Church
Despite recent successful CAR-T outcomes in liquid tumors, its effect on solid tumors has not been achieved. This is mostly because the immunosuppressive tumor microenvironment inhibits the functions of T cells. Here, we have designed a novel biologic, which interacts with tumors in a different manner, that overcomes the CAR-T therapies’ limitations. This novel cancer-elimination mechanism is independent of inherent immune functions, such that it would not be inhibited by the tumor microenvironment. Our technology opens up brand new approaches for engineered cells to eliminate cancer.

Studies on Immunogenic Lipids from the Gut Microbiome

Studies on Immunogenic Lipids from the Gut Microbiome
Munhyung Bae, David Szamosvari, Sunghee Bang, and Jon Clardy
The gut microbiome’s composition influences human health both positively and negatively, and most of these influences involve regulating inflammatory immune responses. (1) For example, multiple studies, including in vivo human studies, have shown that Muciniphila akkermansia has positive effects on metabolism and response to cancer immunotherapy, but the underlying molecular mechanism for these responses remains unknown. Finding the answer to this and many similar questions is complicated because it requires deconvoluting the interaction of two complex systems: the gut microbiome and our immune systems. In collaboration with Ramnik Xavier’s laboratory (MGH, Broad, and Department of Genetics) we believe that we have found the answer: a small phospholipid making up part of the M. akkermansia’s cell membrane. Synthetic lipid recapitulates the effects of isolated lipid and of the intact bacteria. We plan to explore the structure-activity space to develop therapeutic agents that could be used as vaccine adjuvants, metabolic disease modifiers, and cancer chemotherapy enhancers.

2020 Pilot Grants

Target Identification for Alzheimer’s and Related Dementias

Target Identification of Neuroprotective Kinase Inhibitors for Alzheimer’s and Related Dementias

Mark Albers, Peter Sorger, Gary Bradshaw

Alzheimer’s dementia (AD) affects nearly 6 million US patients and costs > $250B/year. No therapies slow its devastating course. We have discovered a root cause of neuronal cell death in disease-relevant regions of autopsied AD brains: inflammation caused by cytoplasmic double stranded RNA (cdsRNA). cdsRNA triggers neurodegeneration in mouse models that can be recapitulated in cultured human neural cells. This proposal focuses on small molecule kinases inhibitors that we have shown to block cdsRNA-mediated neuronal death. The active molecules (some of which are approved therapeutics) are annotated as JAK kinase inhibitors but this class of compounds is known to have a complex poly-pharmacology. Moreover, not all JAK inhibitors on signal transduction in neurons rescue cell death. We have therefore conducted a genome-wide CRISPR/Cas9 screen and found than none of the three members of the JAK family rescue cdsRNA-mediated neuronal death when knocked down. Thus, JAK kinase inhibition does not appear to be sufficient (and perhaps not even necessary) to rescue neuronal death. We propose to identify “off-target” proteins – most likely kinases - that are preferentially bound by neuroprotective JAK inhibitors relative to inactive molecules. We will confirm the relevance of these targets by generating knockout human neural cells using CRISPR/Cas9 and then proceed to small molecule screening. This will allow us to leverage extensive experience in kinase inhibitors, particularly those exhibiting therapeutically relevant poly-pharmacology, to target AD and other neurodegenerative diseases.

Novel therapeutic targets for treating pain/chronic itch

Identifying novel therapeutic targets for treating pain and chronic itch


David Ginty, Nikhil Sharma, Jing Peng


The perception of painful stimuli begins with detection of noxious stimuli by somatosensory neurons called nociceptors. Itch-inducing compounds, on the other hand, are detected by neurons called pruriceptors. We have recently identified the genes expressed in all somatosensory neuron subtypes, including nociceptors and pruriceptors, throughout development and into adulthood. This analysis revealed six transcriptionally distinct subtypes of nociceptors and two subtypes of pruriceptors, each with strikingly distinct gene expression profiles. Importantly, our findings reveal new candidate therapeutic targets to block nociceptors and pruriceptors. We found that select members of the GPCR superfamily, which account for nearly 1/3 of known drug targets, are expressed in nociceptors and pruriceptors, but not other sensory neuron subtypes. We will to leverage our knowledge of somatosensory neurons and the newly identified GPCRs they express to develop new drugs for treating pain and chronic itch while avoiding undesirable side effects. We will focus on drugs that activate Gi/o-coupled GPCRs expressed in nociceptors and pruriceptors because activation of these GPCR subtypes silence neuronal activity.

2019 Development Grants

Monoclonal antibody-based therapeutics for Argentine hemorrhagic

Monoclonal antibody-based therapeutics for Argentine hemorrhagic fever

Lars Clark, Brian Gowen (USU), and Jonathan Abraham

Viral hemorrhagic fevers (VHFs) pose continuing threats to public health. Most have limited treatment options or vaccines, which underscores a point of vulnerability in public health. Passive immunization is an attractive treatment strategy; for example, transfusion of the monoclonal antibody (mAb) cocktail ZMappTM was a lead approach during the 2014-2016 Ebola virus outbreak. Results of testing in humans with ZMappTM did not reach statistical significance, suggesting that further studies would be required to fine-tune the approach. A mAb derived from the blood of an Ebola survivor, mAb114, was also recently deployed for testing in humans in the ongoing Ebola virus outbreak in the Democratic Republic of Congo.

While these investigational therapies are promising, there remains a large, unmet need for therapies against all agents that cause VHFs. We chose to focus on Argentine hemorrhagic fever (AHF) caused by the arenavirus Junin because antibody transfusions have a well-established track record of successfully treating this infection. We will isolate mAbs from the blood of AHF survivors, characterize the molecular basis for their antiviral activity, and test these for therapeutic effect in small animal models. We will also determine if the antibodies we isolate cross-react with Machupo, Guanarito, Sabia, and Chapare viruses, which are related arenaviruses that cause VHFs in South America and lack effective therapies. Once completed, the work would position candidate mAbs for pre-clinical testing in non-human primates, thus facilitating their translation into human use.

Targeting apoptotic pathways for ALS, Alzheimer’s Disease and Pa

Targeting apoptotic pathways for ALS, Alzheimer’s Disease and Parkinson’s Disease

Sooyeon Jo, Laurel Heckman (BCH), Clifford Woolf (BCH), and Bruce Bean

The proposed work follows our recent discovery that targeting a class of voltage-dependent potassium channels inhibits death of motor neurons derived from induced pluripotent stem cells (iPSCs) from patients with ALS. These experiments were motivated by single cell RNA-expression data showing altered expression of a channel regulatory subunit in ALS motor neurons compared to their isogenic controls. This discovery serendipitously converged with an ongoing project developing small molecule modulators of these channels as investigational tools. We have now found that one of these compounds mitigates cell death of ALS patient iPSC-derived motor neurons. We therefore propose to test its ability to delay disease progression in a mouse model of ALS, to develop more potent inhibitors with drug-like properties, and to test the efficacy of these modulators in animal models of Parkinson’s disease and Alzheimer’s disease as a new treatment paradigm for preventing neurodegeneration by inhibiting apoptosis.

Development of a sleeve gastrectomy-induced metabolite as therapy for T2D and obesity

Development of synthetic analogs of a sleeve gastrectomy-induced metabolite as a novel therapy for type 2 diabetes and obesity

Sloan Devlin, Snehal N. Chaudhari, and Eric Sheu (BWH)

New therapies are needed to address the related worldwide epidemics of obesity and type 2 diabetes (T2D). Bariatric surgery is currently the most effective and sustainable treatment for obesity. While weight loss occurs 6 months-1 year following surgery, patients see immediate resolution of their diabetic phenotypes within hours of surgery. This remarkable remission of T2D is maintained for over 7 years, suggesting that the change is durable. We have identified a metabolite whose levels are significantly increased in both mice and humans following surgery and that ameliorates diabetic phenotypes in vivo in an acute mouse model. The goal of this research is to develop analogs of this metabolite as a potential therapy for T2D and obesity.

Next-generation AAV therapies for chronic pain

Next-generation AAV therapies for management of intractable chronic pain

Aurel Nagy, Sinisa Hrvatin, Spencer Price, and Michael Greenberg

Chronic pain represents an enormous unmet need (~$635 billion in the US in 2011). The primary treatment for severe chronic pain, opioid administration, causes unacceptable side effects including addiction and fatal respiratory depression while failing to provide therapeutic relief in patients seeking care.1 Without effective alternatives, opioid prescription

numbers continue to climb: there were 70,237 prescription-opioid-overdose-related deaths in 2017.2,3 The opioid epidemic highlights the urgent need for new therapeutics to manage chronic pain. Gene therapy, the delivery of genetic material to permanently change gene expression in target cells, could provide long-term pain management with a single dose and is

therefore, worthy of investigation. Recombinant adeno-associated virus (rAAV)-delivered gene therapies in particular have shown striking clinical success recently, suggesting a prime opportunity to develop rAAV-based therapeutics for treating chronic pain.

We propose to generate a rAAV that specifically targets nociceptors, the neurons that transduce pain, to deliver ligand-gated silencing ion channels that will allow patients to control pain without opioids. Current rAAV engineering approaches lack the cell-type-specificity required to selectively infect nociceptors while sparing non-nociceptor neuronal

subtypes however, and off-target silencing of these cells could cause unacceptable toxicity and anesthesia. We developed PESCA, the Paralleled Enhancer Single-Cell Assay, to overcome this limitation and engineer rAAVs that drive unprecedentedly cell-type-specific payload expression. Through PESCA, we aim to create a next-generation therapy that will provide lasting and patient-controlled relief upon administration of a single dose, revolutionizing treatment for the most debilitating and common chronic health condition in the world.

Engineered proteins for treatment of pancreatitis

Engineered proteins for treatment of pancreatitis

Katherine Redfield, Daniel Heid, Dominik Niopek, Jeffrey Way, Jungmin Lee, and Pamela Silver

We are developing a treatment for pancreatitis based on a protease inhibitor with enhanced pharmacokinetics and tissue distribution. Initial experiments indicate that an engineered protein lead compound can be inexpensively produced at high levels, is active in vitro, and is active in initial animal tests.

2019 Pilot Grants

Evaluating splicing modulators for therapeutic impact

Evaluating splicing modulators for therapeutic impact in cohesin-mutant AML and MDS cells

Benjamin Martin, Zuzana Tothova (DFCI), and Karen Adelman

Cohesin is a multi-subunit protein complex that forms a ring-like structure around DNA. Cohesin is essential for sister chromatid cohesion, chromosome organization into looped domains, DNA damage repair and transcription regulation. Germline loss-of-function mutations in cohesin subunits cause a family of developmental disorders termed cohesinopathies. In addition, cohesin is one of the most frequently mutated protein complexes in cancer, including myeloid malignancies, with recurrent somatic loss-of-function mutations in core components of the cohesin ring and its modulators. Importantly, cancer-associated mutations in cohesin rarely affect chromosome integrity, but instead selectively impair gene-regulatory functions. However, how cohesin affects gene activity remains enigmatic, offering no clues towards intervention. Consequently, there are no targeted therapeutic approaches available to treat disease involving cohesin mutations. Recently, we discovered that cohesin mutations common in myeloid malignancies such as myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) disrupt RNA splicing. We propose to define the aberrant RNA species generated in cohesin-mutant AML cells, using state-of-the-art molecular and computational approaches to capture nascent transcripts and characterize RNA processing. Through detailed investigation of gene activity and splicing profiles in cohesin-mutant AML cells, we hope to discover genes with alternative splicing events that may present opportunities for therapeutic targeting. Our goal is to leverage this knowledge to develop targeted approaches that will selectively kill cohesin-mediated disease. The findings from these studies have the potential to lead directly to one or more clinical trials within the next several years.

Multiplex editing the human genome

Multiplex editing the human genome


Eriona Hysolli, Yuting Chen, and George Church


We aim to make cells virus-resistant by recoding human cells. This universal ultrasafe and virus-resistant cell line will be utilized for safe manufacturing of therapeutics and avoid bioreactor contamination like the Genzyme incident of 2009.

Non-invasive intracellular delivery of molecules for therapeutic applications

A high-throughput platform for the non-invasive intracellular delivery of molecules for therapeutic applications

Martina Righi and Johan Paulsson

Existing methods for intracellular delivery of drugs, proteins or nucleic acids have either been system specific and inefficient, or based on methods like electroporation or chemical treatment that can greatly perturb cells. A recent method, now in co-development by a biotech startup and a pharma giant as a novel cell therapy platform, improved this process by squeezing cells through narrow constrictions, which slightly and temporarily deforms cells and porates the membrane. This allows for efficient uptake of many types of components while reducing the stress on cells. We developed, and Harvard patented, an alternative methodthat could more gently squeeze cells of varying sizes.

Target validation and testing of a broad-spectrum antiviral

Target validation and in vivo testing of a broad-spectrum antiviral

Melissanne de Wispelaere and Priscilla Yang

Dengue virus (DENV) and other flaviviruses are human pathogens that cause significant disease. About 40% of the world lives in areas with substantial risk of DENV transmission. Up to 100 million people are infected annually with an estimated 500,000 hospitalizations and 20,000 deaths due to dengue hemorrhagic fever and dengue shock syndrome2. DENV presents a long-standing challenge for vaccine development due to antigenic diversity of the four DENV serotypes and the propensity of non-protective antibodies to enhance infection and disease severity4. There are no specific antivirals to counteract DENV.

We discovered QL47 and related tricyclic quinolones as potent covalent, host-targeted antivirals with broadspectrum activity against DENV and other RNA viruses of biomedical significance. Due to their broad-spectrum activity against the Flaviviridae and other viruses and their high natural barrier to resistance these compounds are of interest as antivirals. We have performed medicinal chemistry optimization to generate YKL-04-085, a candidate suitable for testing antiviral efficacy in vivo and have also performed chemoproteomic experiments to

identify the cellular targets responsible for antiviral activity. We propose to validate the antiviral target(s) of QL47/YKL-04-085 and to evaluate the antiviral activity of YKL-04-085 in a murine model of viral infection.

2018 Development Grants

2018 Development Grants 1

Development of a new precision therapeutic for an important cancer target
Vidyasiri Vemulapalli, 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

Targeting neuro-immune signaling to treat bacterial infections
Felipe Pinho-Ribeiro, Pankaj Baral, Kimbria Blake, Samantha Choi, Liwen Deng, 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 botulinum neurotoxins (BoNTs) serotype A and serotype E, thereby blocking neuro-immune signaling and enhancing host immunity. In this project, we determine whether this therapeutic approach is broadly applicable by testing BoNTs against S. pyogenes, MRSA, 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

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 Mini-Gene Therapy for Usher Syndrome Type 1F, a Combined Deafness and Blindness

Development of AAV-mediated Mini-Gene Therapy for Usher Syndrome Type 1F, a Combined Deafness and Blindness
Maryna Ivanchenko, Olga Strelkova, Pedro De La Torre, Daniel Hathaway, Marcos Sotomayor, Artur A. Indzhykulian, and David Corey.
Deafness and blindness are two of the most common and most devastating neurological disorders.  Seldom fatal, they separate patients from the world they live in and the people they love, for a lifetime.  In many cases, combined deafness and blindness result from a single gene defect, usually with a mutant gene copy inherited from both parents.  Usher syndrome is a hereditary deafness and blindness caused by mutation of any of nine genes. One gene, PCDH15, 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 ~3000 patients in the United States.
Following the striking success of Luxturna therapy for RPE65 blindness, gene addition for Usher 1F is an attractive approach. However the PCDH15 coding sequence, at 5.8 kb, is too large for AAV.  PCDH15 is a chain-like protein of 11 links, with binding domains at N- and C-termini.  We developed a number of mini-PCDH15 constructs that retain the binding domains but lack 3-8 links, and that consequently fit in AAV vectors.  Many mini-PCDH15 variants show normal binding in vitro. Since the deafness phenotype is more severe than blindness in mouse models, we assay function by testing cochlear receptor cells in vitro and hearing in vivo. AAVs encoding mini-PCDH15s have been assayed for their ability to preserve hearing in a Pcdh15-deficient mouse model that normally becomes completely deaf.   Some (but not all) of the minis, when injected into the cochleas of neonatal Pcdh15-deficient mice, produce substantial rescue of hearing. 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 in the eye to assess rescue of the blindness phenotype.

Isoguvacine and benzodiazepine derivatives for the treatment of tactile hypersensitivity & anxiety

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 proposed 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. Indeed, we were able to show that isoguvacine reduces tactile sensitivity in mice. Also, chronic isoguvacine treatment improves a subset of ASD-related phenotypes in mice such as overall body condition, body weight, and anxiety-like behaviors. This project, which was co-funded by BBA, has moved into Lab1636, a major strategic R&D alliance between Harvard and the healthcare investment firm Deerfield, where these results will be validated and advanced to late-stage preclinical development.

Computationally designed therapy targeting inflammation in neurodegenerative diseases

Computationally designed therapy targeting lysosomal function and inflammation in neurodegenerative diseases
Jinkuk Kim, Yu-Han Huang, Timothy Yu, and Peter Park

Progranulin is a GRN-encoded protein that plays critical lysosomal and anti-neuroinflammatory functions. A therapy that boosts GRN expression would address the root genetic cause (GRN haploinsufficiency) of GRN-subtype frontotemporal dementia (GRN-FTD), a fatal and orphan neurodegenerative disease that affects 3,000-6,000 patients in the US alone. The therapy would also be effective for other neurodegenerative diseases including Alzheimer’s and Parkinson’s diseases. However, no such therapy is available currently. The recent remarkable success of Spinraza/nusinersen for spinal muscular atrophy has clearly demonstrated that antisense oligonucleotide (ASO)-based therapies can be highly effective for neuronal diseases. We have developed three ASOs that can increase the progranulin protein level in a human neuroblastoma cell line by multiple folds. These ASOs have the potential to become effective treatments for GRN-FTD and other neurodegenerative diseases.

2018 Pilot Grants

Small molecule modulators of gut bacterial bile acid metabolism to treat metabolic syndrome and associated NAFLD

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

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

Development of an inexpensive at-home influenza kit and detection technology
Sarah Boswell, Jason Qian, Zhixiang Lu, Mary Pettit, 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.


2017 Development Grants

Developing therapeutics for treating Rett Syndrome by correcting neuronal long-gene misregulation

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

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

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.

2017 Pilot Grants

Developing CRISPR-Cas9 Reagents for Editing Lytic and Latent Herpes Simplex Virus Genomes

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.

2016 Development Grants

Developing a ubiquitin-dependent proteasome activity reporter

Developing a ubiquitin-dependent proteasome activity reporter to screen for activators and inhibitors
Ying Lu and Marc Kirschner

The 26S proteasome mediates both ubiquitin-dependent and ubiquitin-independent protein degradation and plays critical roles in the immune response, stress response and gene regulation. Current proteasome inhibitors, targeting only the rather nonspecific core particle, have nevertheless shown efficacy in cancer but they indiscriminately affect most functions of the proteasomes. With the help of Q-FASTR grant, we have successfully invented a novel and powerful screening platform for testing inhibitors that distinguish between ubiquitin-dependent and independent activities. We have performed initial screening and identified novel inhibitors with such specificity. By precisely modulating selected activities of the proteasome, these new classes of inhibitors could advance the treatment of cancer, inflammation and neurodegenerative disease. Currently, we are looking for partners to bring the project to the next phase.

Restoring Cortical Function and Plasticity Treatment of AD

Restoring Cortical Function and Plasticity for the Treatment of Alzheimer’s Disease
Brian Chow, Adam Granger, Sarah Melzer, and Bernardo Sabatini

Alzheimer’s disease (AD)is characterized by degeneration and dysfunction of the brain. In particular, a large folded expanse of the brain known as cortex is severely affected. Treatments for AD can aim at either stopping the degeneration or at maximizing the function of the remaining cortex. Here we proposed a new approach for the latter. We proposed to manipulate a specific cell type in cortex, known as VIP cells, which have the ability to regulate cortical function, plasticity, and blood flow. We have identified a molecular regulator that is uniquely expressed in VIP cells that provides a means to control these cells, and thereby cortex. We have been working to characterize the regulation of cortex by this pathway and establish it as a preclinical model for the enhancement of cortical function. If our hypotheses are correct, we will have identified a druggable pathway to enhance cognitive function in disease states

Targeted protein degradation as a strategy for potent antivirals

Assessment of targeted protein degradation as a strategy for potent antivirals with high barriers to resistance
Mélissanne de Wispelaere, Deirdre Costello, Tinghu Zhang, Guangyan Du, Nathaniel J. Henning, Supanee Potisopon, Eric S. Fischer, Radoslaw Nowak, Matthew Ponthier, Bethany Berry, Nathanael S. Gray, and Priscilla L. Yang

There is a major need for antivirals to combat the diverse viral pathogens causing human disease. Drugs that potently inhibit one or more related viruses with high natural barriers to resistance remain a much-desired but elusive goal. “Degronimids” represent a new class of inhibitors that induce degradation of their targets through recruitment of the E3 ubiquitin ligase cereblon. This inhibitory strategy can alleviate the need for stoichiometric target engagement and also suppress drug resistance. Recent examples in cancer biology demonstrate that degronimids against kinases and transcriptional enzymes deplete their requisite targets and have superior efficacy and resistance profiles relative to the parental compounds. Here, we propose to develop and evaluate degronimids that inhibit hepatitis C virus and dengue virus through inhibition and targeted degradation of specific viral targets. The goal of this work is to provide proof of concept that degronimid antivirals have superior antiviral potency and resistance profile when compared to the parental compounds. Viral targets and parent inhibitors have been judiciously selected to allow synthesis and characterization of antiviral degronimids on a relatively short time scale by leveraging our virological tools and expertise as well as by taking advantage of resistance mutations that have already been well-documented in the literature

2016 Pilot Grants

Building Better Screens and Identifying Ligands for Human MS4A

Building Better Screens and Identifying Ligands for Human MS4A proteins
Maria Lissitsinya Bloom, Talya Kassessian, and Sandeep Robert Datta

In the nose, a family of proteins called the MS4As act as small molecule detectors. These receptors detect ethologically relevant molecules from the environment, including nitrogenous heterocyclics and long chain fatty acids. The MS4As have been strongly implicated by human genetic studies in the development of Alzheimer’s Disease, although the mechanism through which the MS4As are linked to disease are completely unknown. The MS4As are expressed within microglia, a chemosensory cell type within the brain that have been associated with AD progression. We hypothesize that the ability of the MS4As to detect endogenous ligands found in the brain might mediate neuroinflammation associated with AD; if true, this suggests that the MS4As might define a completely new molecular mechanism underlying the AD progression. However, a major challenge in de-orphanizing the MS4As and in identifying chemical activators and inhibitors is the poor behavior of these receptors when expressed on their own in typical reconstitution systems like HEK cells. With support from Q-FASTR, we screened through a variety of cell lines and tested several chaperone candidates, in an attempt to convert our single cell screen for MS4A-dependent responses into a platform useful for high-throughput screening. This work continues, in the hope that identified ligands will be important starting templates for the development of molecules that manipulate MS4A activity, which may have significant therapeutic potential for treating AD.

Microtubule stabilizing drugs-neurodegenerative disease and SCI

Microtubule stabilizing drugs for neurodegenerative disease and spinal cord injury
Yuyu Song and Timothy Mitchison

Our 3-5 year goal is to develop small molecules drugs for neurodegenerative diseases and/or spinal cord injury that bind directly to microtubules and stabilize them in CNS neurons and glia. This well-defined pharmacological mechanism protects neurons from degenerative pathologies, and promotes axon growth in damaged spinal cord. It showed considerable promise in rodent models of neurodegeneration, spinal cord injury and schizophrenia using epothilone-D and -B as CNS-penetrating tool compounds. The potential efficacy of epothilones in man is limited by high peripheral toxicity. They kill dividing cells by stabilizing mitotic spindle microtubules and were originally developed as cytotoxic cancer drugs, making them a poor starting point for neurology drugs, despite their promising mechanism. To develop fundamentally less toxic microtubule stabilizing drugs that retain neuro-protective and neuro–regenerative activities we will adopt approaches from GPCR pharmacology that have never been applied to microtubule drugs. We will use ligand displacement assays as our primary screen, and then evaluate neuroprotective, cytotoxic and microtubule stabilizing activities in follow-up assays. In a 1-year pilot we propose to test the concept that we can obtain scaffolds which bind to the epothilone site and exhibit superior neuroprotective to cytotoxic ratios compared to current tool compounds. If we validate this concept, we will pursue a drug development project based using the assays and concepts we develop during the pilot phase.