A USF Health-led team tests 40 million compounds and finds lead candidate that selectively relaxes airway smooth muscle cells with no detectable drug desensitization

TAMPA, Fla. (Dec. 2, 2021) – Beta-agonists (β-agonists) are the only drugs that directly open narrowed airways and make it easier to breathe for millions of people with asthma, a chronic respiratory disease. These inhaled medications activate the β₂-adrenergic receptors (β₂AR ) on airway smooth muscle cells and relax them, dilating airways and increasing air flow.

However, for a significant proportion of asthmatics, the effectiveness of existing β-agonists is insufficient to open tightly constricted airways and the clinical benefits realized appear to wane over time, leaving them constantly struggling with the disease.

“A lack of more effective therapies to treat or prevent shortness of breath is a major issue for patients with severe-to-moderate asthma,” said Stephen Liggett, MD, vice dean for research and a professor of medicine, molecular pharmacology and physiology, and biomedical engineering at the University of South Florida Health (USF Health) Morsani College of Medicine. “As regular use of β-agonists increases, the body becomes less sensitive to these bronchodilators.”

This process, known as tachyphylaxis or drug desensitization, contributes to insufficient asthma control, which leads to increased emergency department visits and hospitalizations — impacting the quality of life and extracting an economic toll in increased medical costs and missed days of work and school. Dr. Liggett’s laboratory works with collaborators across the country to understand the mechanisms of tachyphylaxis, with the aim of improving β-agonists.

Over the last three years, a multi-institutional research team led by USF Health studied 40 million compounds to identify those that activated β₂AR (β-agonists) without causing tachyphylaxis. The investigators found one such agonist, which was structurally distinct from all known traditional β-agonists. Their preclinical research suggests that a different class of β-agonists, known as biased agonists, offers promise for selectively treating asthma and other obstructive lung diseases. Such biased agonists offer a therapeutic option without causing the rapid turndown of these receptors (β₂AR) when the drug is used on an as-needed basis, or the even greater loss of effectiveness observed with chronic use.

The drug discovery study, published online recently in the Proceedings of the National Academy of Sciences of the United States (PNAS), was conducted by scientists with expertise in biochemistry, physiology, and computational biology. The team used molecular modeling driven by high speed, high-capacity supercomputers to define how this atypical agonist, named C1-S, works at the molecular level.

“This is the first β-agonist ever known to relax airway smooth muscle and treat asthma without any detectable tachyphylaxis and represents a significant breakthrough in asthma therapy,” said principal investigator Dr. Liggett, the PNAS paper’s senior author.

USF Health’s Stephen Liggett, MD, led a multi-institutional research team that studied 40 million compounds to identify those that activated β₂AR (beta-agonists) without causing tachyphylaxis (drug desensitization). — Photo by Allison Long, USF Health Communications and Marketing

β2-adrenergic receptors are G protein-coupled receptors (GPCR), present in airway smooth muscle cells to mediate various functions. The existing β-agonists used to treat asthma are all unbiased. That means the drug equally favors activating a G-protein signaling pathway that promotes airway smooth muscle cell relaxation (thus easier breathing) as well as engaging a beta arrestin (β-arrestin) signaling pathway that leads to the unwanted outcome of tachyphylaxis.

“Beta-arrestin is a protein that upon interaction with the G protein-coupled receptor begins to uncouple (inhibit) the receptor from stimulating the clinically important signaling pathway we want to preserve,” Dr. Liggett explained. “With unbiased beta agonists you have these dueling signaling processes essentially competing with each other.”

Research is underway to design biased agonists to help alleviate pain without addiction and to better treat certain cardiovascular conditions with minimal side effects; however, no GPCR-biased agonists are yet being developed for asthma.

The researchers approached this massive study with “no preconceived notions” about what compounds might work best, Dr. Liggett said. Among their key findings:

• Of the 40 million compounds screened, 12 agonists activated the target receptor (β₂AR), stimulating cyclic AMP production that causes airway smooth muscle relaxation. But only one of these 12 (C1-S) appeared to be strongly biased away from the b-arrestin signaling that limits airway smooth muscle response (and thus drug effectiveness) due to receptor desensitization.
• Through a series of biochemical experiments, the researchers verified for the first time that it was possible for an agonist to “split the signal” mediated by a G coupled-protein receptor (β₂AR). This split preferentially activates, or switches on, a signaling pathway beneficial for treating obstructive lung disease rather than a pathway believed to be physiologically harmful, Dr. Liggett said.
• In addition to measuring signaling at the cellular level, the researchers employed the magnetic twisting cytometry, a method pioneered by co-author Steven An, PhD, at Rutgers University that measures changes in human airway smooth muscle cell relaxation and contraction. All the biochemistry results correlated with the physiological response the researchers expected — relaxation of airway smooth muscle without desensitization.
• Computer modeling and docking was performed by investigators at Caltech (William Goddard III, PhD, and now graduate student Alina Tokmakova). These studies helped identify molecular contact points between the receptor and biased agonist C1-S; some of these binding sites were not seen with any other agonist before and thus point to the basis of the properties of this unique drug. The collection of 40 million compounds was assembled and maintained by Marc Giulianotti, PhD, of Florida International University.

As regular use of β-agonists increases, the body becomes less sensitive to these inhaled bronchodilators, a process known as as tachyphylaxis (drug desensitization) that contributes to insufficient asthma control.

The researchers plan to evaluate the safety and efficacy of their lead drug candidate C1-S for potential use in humans, Dr. Liggett said.

“Every day we see breakthrough asthma symptoms in patients using albuterol, a beta-2 receptor agonist that is the cornerstone of treatment. When exacerbated, these symptoms sometimes require hospitalization, use of a ventilator, and occasionally even result in death,” said Kathryn S. Robinett, MD, assistant professor of medicine at the University of Maryland School of Medicine’s Division of Pulmonary and Critical Care Medicine, who was not involved in the research. “A new class of beta-agonists that do not cause tachyphylaxis, like the one characterized in this study, could provide rapid relief and add a powerful tool to our belt in the treatment of asthma.”

The study’s co-lead authors were Donghwa Kim, PhD, of the USF Health Morsani College of Medicine, and Alina Tokmakova, currently a graduate student at University of California San Francisco.

The work was supported by grants from the National Heart, Lung, and Blood Institute, part of the National Institutes of Health.

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Experts in airway bitter taste receptors and medicinal chemistry team up to advance a potential asthma and COPD treatment that works differently than existing bronchodilators

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TAMPA, Fla (Jan 4, 2021) — Despite the progress made in managing asthma and chronic obstructive pulmonary disease (COPD), poorly controlled symptoms for both respiratory diseases can lead to severe shortness of breath, hospitalizations or even death.

“Only about 50 percent of asthmatics, and an even lower percentage of people with COPD, achieve adequate control of lung inflammation and airway constriction with currently available medications,” said Stephen Liggett, MD, vice dean for research at the University of South Florida Morsani College of Medicine and a USF Health professor of medicine, molecular pharmacology and physiology, and biomedical engineering. “So, we’re clearly missing something from our drug armamentarium to help all these patients.”

Dr. Liggett’s laboratory has discovered several subtypes of bitter taste receptors (TAS2Rs) — G protein-coupled receptors expressed on human smooth airway muscle cells deep inside the lungs. In asthma and COPD, tightening of smooth muscles surrounding bronchial tubes narrows the airway and reduces air flow, and Dr Liggett’s lab found that these taste receptors open the airway when activated. They are now looking for new drugs to treat asthma and other obstructive lung diseases by targeting smooth muscle TAS2Rs to open constricted airways.

A promising bronchodilator agonist rises to the top

In a preclinical study published Nov. 5 in ACS Pharmacology and Translational Science, Dr. Liggett and colleagues identified and characterized 18 new compounds (agonists) that activate bitter taste receptor subtype TAS2R5 to promote relaxation (dilation) of human airway smooth muscle cells. The cross-disciplinary team found 1,10 phenanthroline-5,6-dione (T5-8 for short) to be the most promising of several lead compounds (drug candidates). T5-8 was 1,000 times more potent than some of the other compounds tested, and it demonstrated marked effectiveness in human airway smooth muscle cells grown in the laboratory.

For this drug discovery project, Dr. Liggett’s laboratory collaborated with Jim Leahy, PhD, professor and chair of chemistry at the USF College of Arts and Sciences, and Steven An, PhD, professor of pharmacology at the Rutgers Robert Wood Johnson Medical School.

In an extensive screening conducted previously, another research group identified only one compound that would bind to and specifically activate the TASR5 bitter taste receptor – although apparently with limited effectiveness. Using this particular agonist (called T5-1 in the paper) as a starting point, the team relied on their collective disciplines to devise new activators, aiming for a much better drug profile for administration to humans.

USF Health’s Stephen Liggett, MD

“The two key questions we asked were: ‘Is it possible to find a more potent agonist that activates this receptor?’ and ‘Is it feasible to deliver by inhalation given the potencies that we find?’” said Dr. Liggett, the paper’s senior author. “T5-8 was the bronchodilator agonist that worked best. There were a few others that were very good as well, so we now have multiple potential new drugs to carry out the next steps.”

The researchers developed screening techniques to determine just how potent and effective the 18 compounds were. A biochemical test assessed how well these new agonists activated TAS2R5 in airway smooth muscle cells isolated from non-asthmatic human donor lungs. Then, the researchers validated the effect on airway smooth muscle relaxation using a technique known as magnetic twisting cytometry, pioneered by Dr An.

“Team science” solves a structural problem

“The biggest challenge we faced was not having a 3-D crystal structure of TAS2R5, so we had no idea exactly how agonist T5-1 fit into this mysterious bitter taste receptor,” Dr. Liggett said. “By merging our strength in receptors, pharmacology, physiology, and drug development, our team was able to make the breakthrough.”

T5-8 was superior to all the other bronchodilator agonists screened, exhibiting a maximum relaxation response (50%) substantially greater than that of albuterol (27%). Albuterol belongs to the only class of direct bronchodilators (beta-2 agonists) available to treat wheezing and shortness of breath caused by asthma and COPD. However, this drug or its derivatives, often prescribed as a rescue inhaler, does not work for all patients and overuse has been linked to increased hospitalizations, Dr. Liggett said. “Having two distinct classes of drugs that work in different ways to open the airways would be an important step to help patients optimally control their symptoms.”

The ACS Pharmacology paper highlights the importance of translational research in bridging the gap between laboratory discoveries and new therapies to improve human health, he added. “This study yielded a drug discovery that successfully meets most of the criteria needed to advance the compound toward its first trial as a potential first-in-class bronchodilator targeting airway receptor TAS2R5.”

The study was supported by a grant from the NIH’s National Heart, Lung, and Blood Institute.

A University of Arizona-University of South Florida team  identified and analyzed four promising antiviral drug candidates in the preclinical study

TAMPA, Fla. (July 6, 2020) — As the death toll from the COVID-19 pandemic mounts, scientists worldwide continue their push to develop effective treatments and a vaccine for the highly contagious respiratory virus.

University of South Florida Health (USF Health) Morsani College of Medicine scientists recently worked with colleagues at the University of Arizona College of Pharmacy to identify several existing compounds that block replication of the COVID-19 virus (SARS-CoV-2) within human cells grown in the laboratory. The inhibitors all demonstrated potent chemical and structural interactions with a viral protein critical to the virus’s ability to proliferate.

Yu Chen, PhD, an associate professor of molecular medicine with expertise in structure-based drug design, has turned toward looking for new or existing drugs to stop SARS-CoV-2.

The research team’s drug discovery study appeared June 15 in Cell Research, a high-impact Nature journal.

The most promising drug candidates – including the FDA-approved hepatitis C medication boceprevir and an investigational veterinary antiviral drug known as GC-376 – target the SARS-CoV-2 main protease (M^pro), an enzyme that cuts out proteins from a long strand that the virus produces when it invades a human cell. Without M^pro, the virus cannot replicate and infect new cells. This enzyme had already been validated as an antiviral drug target for the original SARS and MERS, both genetically similar to SARS-CoV-2.

“With a rapidly emerging infectious disease like COVID-19, we don’t have time to develop new antiviral drugs from scratch,” said Yu Chen, PhD, USF Health associate professor of molecular medicine and a coauthor of the Cell Research paper. “A lot of good drug candidates are already out there as a starting point. But, with new information from studies like ours and current technology, we can help design even better (repurposed) drugs much faster.”

Before the pandemic, Dr. Chen applied his expertise in structure-based drug design to help develop inhibitors (drug compounds) that target bacterial enzymes causing resistance to certain commonly prescribed antibiotics such as penicillin. Now his laboratory focuses its advanced techniques, including X-ray crystallography and molecular docking, on looking for ways to stop SARS-CoV-2.

Using 3D computer modeling, Michael Sacco (left), a doctoral student in the Department of Molecular Medicine, worked with Dr. Chen to determine the interactions between antiviral drug candidate GC-376 and COVID-19’s main protease.

M^pro represents an attractive target for drug development against COVID-19 because of the enzyme’s essential role in the life cycle of the coronavirus and the absence of a similar protease in humans, Dr. Chen said. Since people do not have the enzyme, drugs targeting this protein are less likely to cause side effects, he explained.

The four leading drug candidates identified by the University of Arizona-USF Health team as the best (most potent and specific) for fighting COVID-19 are described below. These inhibitors rose to the top after screening more than 50 existing protease compounds for potential repurposing:

• Boceprevir, a drug to treat Hepatitis C, is the only one of the four compounds already approved by the FDA. Its effective dose, safety profile, formulation and how the body processes the drug (pharmacokinetics) are already known, which would greatly speed up the steps needed to get boceprevir to clinical trials for COVID-19, Dr. Chen said.
• GC-376, an investigational veterinary drug for a deadly strain of coronavirus in cats, which causes feline infectious peritonitis. This agent was the most potent inhibitor of the M^pro enzyme in biochemical tests, Dr. Chen said, but before human trials could begin it would need to be tested in animal models of SARS-CoV-2. Dr. Chen and his doctoral student Michael Sacco determined the X-ray crystal structure of GC-376 bound by M^pro, and characterized molecular interactions between the compound and viral enzyme using 3D computer modeling. 

• Calpain inhibitors II and XII, cysteine inhibitors investigated in the past for cancer, neurodegenerative diseases and other conditions, also showed strong antiviral activity. Their ability to dually inhibit both M^pro and calpain/cathepsin protease suggests these compounds may include the added benefit of suppressing drug resistance, the researchers report.

All four compounds were superior to other M^pro inhibitors previously identified as suitable to clinically evaluate for treating SARS-CoV-2, Dr. Chen said.

Michael Sacco looks at COVID-19 viral protein crystals under a microscope.

A promising drug candidate – one that kills or impairs the virus without destroying healthy cells — fits snugly, into the unique shape of viral protein receptor’s “binding pocket.” GC-376 worked particularly well at conforming to (complementing) the shape of targeted M^pro enzyme binding sites, Dr. Chen said. Using a lock (binding pocket, or receptor) and key (drug) analogy, “GC-376 was by far the key with the best, or tightest, fit,” he added. “Our modeling shows how the inhibitor can mimic the original peptide substrate when it binds to the active site on the surface of the SARS-CoV-2 main protease.”

Instead of promoting the activity of viral enzyme, like the substrate normally does, the inhibitor significantly decreases the activity of the enzyme that helps SARS-CoV-2 make copies of itself.

Visualizing 3-D interactions between the antiviral compounds and the viral protein provides a clearer understanding of how the M^pro complex works and, in the long-term, can lead to the design of new COVID-19 drugs, Dr. Chen said. In the meantime, he added, researchers focus on getting targeted antiviral treatments to the frontlines more quickly by tweaking existing coronavirus drug candidates to improve their stability and performance.

Two viral protein images generated by Yu Chen, University of South Florida Health, using X-ray crystallography. Above: The protein dimer (one molecule is blue and the other orange) shows the overall structure of the COVID-19 virus’s main protease (M^pro), the researchers’ drug target. Below: Three configurations of active sites where inhibitor GC-376 binds with the M^pro viral enzyme, as depicted by 3D computer modeling.

Dr. Chen worked with lead investigator Jun Wang, PhD, UA assistant professor of pharmacology and toxicology, on the study. The work was supported in part by grants from the National Institutes of Health.

-Photos by Torie Doll, USF Health Communications and Marketing

From designing 3D printed test swabs, to researching antibody responses and engaging in leading clinical trials, USF Health scientists rapidly team up to help fight COVID-19

While the world waits for therapies to reduce death rates and a widely available vaccine to prevent COVID 19, team science at USF Health and other academic medical centers continues to take on an unprecedented sense of urgency.

Globally, scientists across disciplines are publicly sharing their ideas, expertise and data like never before – all singularly focused on finding solutions to a highly contagious and potentially life-threatening new virus known as severe acute respiratory syndrome coronavirus 2, or SARS-CoV-2.

Since the pandemic began, the number of studies posted by researchers worldwide to open-access repositories like bioRxiv and medRxiv has skyrocketed. These preprints – papers written after a study concludes but made available before peer review – let scientists disseminate their findings more quickly and obtain instant feedback on their work. Researchers also continue to identify and share viral genome sequences, protein structures, and COVID-19 related epidemiological and clinical data through online databases.

Meanwhile, thousands of clinical trials have been launched as academic medical centers, hospitals and laboratories join forces with government and industry in the search for optimal diagnostics and therapies. At USF Health, more than 65 COVID-19 related laboratory, clinical and epidemiological projects are underway or in final stages of the approval process. These represent unique research efforts by the faculty of all four USF Health colleges, as well as joint efforts with pharmaceutical firms and biotechnical and software companies. Many of the patient-related studies are conducted by USF Health faculty physicians at Tampa General Hospital.  USF Health is also working with Tampa General to create a biorepository that collects, processes and stores health data and residual specimens from patients who test positive or negative for COVID-19 to use in future biomedical research.

“The need for rapid and accurate basic and clinical results has never been greater. The scientific community has risen to the challenge of a lifetime and continues to push forward,” said Stephen Liggett, MD, associate vice president for USF Health Research and vice dean for research in the Morsani College of Medicine. “Without a doubt we are still in the early stages of understanding this new coronavirus – in knowing who should be tested and how often, and which tests work best; in knowing how to treat patients and how effective vaccines will be in conferring immunity.”

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View the interview with Stephen Liggett, MD, associate vice president for research at USF Health, who discusses how the COVID-19 pandemic has changed research here.

USF faculty and student researchers have been quick to mobilize their talent and resources, Dr. Liggett said. “They want to do whatever they can to find answers — both to help fight this pandemic and to prepare for future outbreaks.”

How are some key scientific areas contributing to the pandemic response?  Below are just a few examples provided by USF Health scientists:

Epidemiology:  Containing the spread of the virus

From the start, epidemiologists have been at the forefront of efforts to understand how fast and why SARS-CoV-2 is spreading. Also known as disease detectives or virus hunters, epidemiologists and the models using data they gather are instrumental in tracking and predicting the patterns of disease transmission in populations, said Thomas Unnasch, PhD, distinguished professor in the USF College of Public Health and codirector of the Center for Global Health Infectious Disease Research. Their work had been critical for both guiding policymakers’ plans to curb the pandemic and helping evaluate whether countermeasures to contain the virus are working.

“We’ve been hunkered down in the midst of a pandemic wildfire and testing only the symptomatic people most likely to be infected” — largely to prevent surges of sick patients from overwhelming the health care system, Dr. Unnasch said. “We’re still missing about 90 percent of the population with COVID-19 infections exhibiting mild or no symptoms.”

USF College of Public Health’s Thomas Unnasch, PhD, oversees the COVID-19 symptom surveillance network for Tampa Bay.

Dr. Unnasch oversees a symptom-based surveillance network launched in mid-April to help identify and map COVID-19 hotspots across the Tampa Bay region. USF College of Public Health researchers worked with the Hillsborough, Pinellas, Pasco and Polk County Health Departments to create the Tampa Bay symptom surveillance survey, adapting existing COVID-19 surveillance technology developed by the Puerto Rico Sciences Trust and deployed in Puerto Rico and, more recently, the Boston area through Harvard University.

The anonymous survey asks Tampa Bay residents questions about potential exposure and symptoms consistent with COVID-19. The information collected, which drills down to the zip code level, is provided to the local health departments and hospital groups.

Surveillance – a tool commonly used by public health agencies to identify and prevent the spread of HIV, tuberculosis, anthrax and other infectious diseases – can help fill in the gaps created by limitations inherent in a complex society, such as a lack of uniform testing, Dr. Unnasch said.

COVID-19 cases in Pinellas and Hillsborough County broken down by zip code, as tracked and entered by the Hillsborough County Health Department on April 16, 2020. Pasco and Polk counties have since been added to the symptom surveillance system.

“So far the only way to prevent the disease is to prevent transmission of the virus. That has meant everyone doing the right thing — staying at home, social distancing face masks, and hygiene,” Dr. Unnasch said.  “As we reopen our communities, surveillance can help us do that safely by detecting clusters of new cases early at a very targeted level, so we can stomp out the embers before they reignite COVID-19 outbreaks.”

Real-time mapping of suspected COVID-19 hotspots can be used to strategically direct Tampa Bay’s public health resources to specific areas where testing, contact tracing and isolation are most likely needed, he said.

“The more data we get and the more accurate the information, the more powerful the tool will be.”

Biostatisticians: Keeping the bias at bay

The data collected by epidemiologists or other health researchers can be fed into mathematical models that predict how fast COVID-19 infections may spread or the number of deaths expected in an overall population. At the community/clinical level, predictive models can help hospitals and medical staff triage patients and allocate limited health care resources (like ICU beds or ventilators) by estimating the risk of people being infected or having a poor disease outcome.

While they can be useful to prepare for worst-case scenarios, predictive models have differed widely in their forecasts – and sometimes they can cause more harm than benefit in guiding policy or clinical decisions, said Ambuj Kumar, MD, MPH, director of the Research Methodology and Biostatistics Core, USF Health Office of Research.

Dr. Kumar, a biostatistician and associate professor of internal medicine, points to a recently published systematic review analyzing studies of prediction models for the diagnosis and prognosis of patients with COVID-19. This review concluded that all 31 clinical models were poor quality, at high risk of bias, and their reported performance was likely overly optimistic.

Ambuj Kumar, MD, MPH, directs USF Health’s Research Methodology and Biostatistics Core.

Methodologist/biostatisticians like Dr. Kumar are trained to recognize the issues and complications arising from the analysis of human health data. They play a key role in any team designing and executing a model, providing the statistical methodology needed to draw meaningful conclusions or make predictions. These data scientists help reduce bias in selecting sample populations, observing or reporting findings, and measurement. They are attuned to factors that can interfere with an accurate estimate of cause-and-effect.

Requiring frequent updates, projections are only as good as the model’s underlying assumptions and the reliability and standardization of the data applied to the model, Dr. Kumar said.

For instance, the commonly cited Institute for Health Metrics and Evaluation model assumes social distancing and other strong voluntary measures to control viral spread will stay in place, but predicting how people will behave as the U.S. reopens in phases is tricky. And, the death data relied upon by many models may be confounded a lack of consistency in the way COVID-19 deaths are reported and counted by hospitals and health departments. (Public health experts have suggested that deaths are undercounted.)

Predictive modeling uses existing data and reasonable assumptions to forecast how an infectious disease spreads in the real world. As more data becomes available, it triggers adjustment of the model, resulting in different outcomes.

Many people understandably want to know now what to expect during this pandemic: How many more cases? How long will it last? When can I safely return to work, or school? Will there be a second wave?

But, many uncertainties about testing, immunity, susceptibility and treatments still influence the variables that make up the algorithms forecasting COVID-19 outcomes, Dr. Kumar said. As the reliability and accuracy of rapidly accumulating data improves, so should the models, he added.

“Predicting the future is particularly challenging when we’re dealing with a virus new to the entire world,” Dr. Kumar said.  “Whether you’re battling COVID-19 or another crisis, you can’t compromise on the systematic, standardized approach needed to create a useful model, or study. If you want accurate results, there’s no substitute for good, rigorous science.”

Virology:  Studying how SARS-CoV-2 works

To develop effective therapies and vaccines to combat COVID-19, scientists need to understand how the virus functions, including its interaction with human immune response. That’s the role of virologists like Michael Teng, PhD, associate professor of internal medicine in the USF Health Morsani College of Medicine.

Dr. Teng has spent many years working with the National Institutes of Health and other groups on research and development of a vaccine for respiratory syncytial virus, or RSV. While RSV was discovered over 60 years ago, researchers continue to work on a vaccine for this common respiratory virus that infects virtually every child by age 2.

Like many other scientists, USF Health virologist Michael Teng, PhD, quickly pivoted from his usual research activities to respond to the new global health threat.

Scientists and companies now testing a myriad of SARS-CoV-2 vaccines in the pipeline have benefited from the extensive RSV research, Dr. Teng said. “They’ve learned a lot from RSV about what works and what pitfalls to avoid in vaccine development.”

Like many other scientists, Dr. Teng quickly pivoted from his usual research activities to respond to the new global health threat. In mid-March his laboratory studied the durability and effectiveness of the 3D-printed nasal swabs successfully created for COVID-19 testing by a team at USF Health Radiology and its innovative 3D Clinical Applications Division, directed by  associate professor Summer Decker, PhD.  Faculty with expertise  in anatomy and infectious diseases as well as radiology contributed to the effort. The ambitious 3D design, modeling and printing project teamed USF Health with Formlabs, a 3D printer manufacturer, and Northwell Health, the largest hospital system in New York, the pandemic’s U.S. epicenter.

An integral part of coronavirus test kits that detect the RNA virus’s genetic code, swabs were in extremely short supply as the pandemic escalated. The slender, flexible device collects a sample from the nasal passages or throat, and that sample goes into a test tube containing transport media for preservation until the specimen is processed by a hospital or commercial laboratory. Using RSV as a proxy for a SARS-CoV-2, synthetic respiratory tract mucous (made by USF Health’s Sophie Darch, PhD), and a World Health Organization recipe for transport media, Dr. Teng demonstrated that the 3D-printed alternative swabs worked as well as conventional commercial swabs to safely collect enough of the sample, without leeching into transport media or interfering with the nucleic acid test’s ability to detect virus particles.

Top:  A USF Health Radiology-led team successfully designed, tested and produced a prototype 3D printed nasopharyngeal swab in record time. As of late May, more than 50,000 of the nasal swabs had been mass produced and were being used worldwide by health care providers to alleviate bottlenecks in COVID-19 testing. Bottom: Jonathan Ford, PhD, a biomedical engineer in USF Health Radiology, holds a cube of the 3D diagnostic nasal swabs.

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The 3D printed swabs, fabricated with FDA-approved, nontoxic materials, also passed performance benchmarks when clinically validated in hospitalized patients undergoing COVID-19 screening at Tampa General Hospital and Northwell Health sites. (A larger-scale multisite clinical trial, led by USF Health Infectious Disease Division Director Kami Kim, MD, is further evaluating the performance of the investigational 3D swabs for diagnostic testing.) Meanwhile, several hundred hospitals and academic medical centers across the country, many state governments, and international agencies and health care facilities are already using the USF-patented swabs to alleviate bottlenecks in COVID-19 testing.

The team worked late nights, taking only about a week from swab prototype design and bench testing to the start of clinical validation. “That’s an incredibly fast turnaround time,” Dr. Teng said.

Dr. Teng is also a coinvestigator for a Morsani College of Medicine-College of Public Health project led by Dr. Kim, which is working to find and map epitopes, the parts of SARS-CoV-2 proteins recognized by the immune system. Antibodies are made by the immune system in response to a threat from a specific virus, bacteria and other harmful pathogen. Some epitopes are associated with protective antibody responses that neutralize (inactivate) a virus when that pathogen is recognized by the immune system again. Others may actually lead to a harmful immune response when a person is exposed to the same virus a second time. The USF Health team wants to identify specific epitopes triggering strong protective antibodies to help researchers design vaccines that mimic a beneficial immune response against COVID-19.

“The data we gather may also be useful in screening (convalescent) plasma for specific antibodies that may best be used to treat critically ill COVID-19 patients,” Dr. Teng said.

Thomas McDonald, MD, USF Health professor of cardiovascular sciences, is investigating whether genetic, physiological or medication-interaction factors may contribute to racial and ethnic disparities in COVID-19 infection rates and cardiovascular complications.

A coronavirus “pseudotype” created by Dr. Teng’s laboratory is being used by the team working on finding neutralizing antibodies and a second USF Health team investigating what factors may affect who suffers worse COVID outcomes.

The second team, led by Thomas McDonald, MD, professor of cardiovascular sciences at the USF Health Heart Institute, wants to know if socioeconomic differences alone account for racial and ethnic disparities in who gets sicker and dies from COVID-19, or if genetic, physiological, or even medication-interaction factors contribute to disproportionate infection rates and cardiovascular complications.

Human pluripotent stem cells grown in Dr. McDonald’s laboratory are prodded to become lung, immune, and heart cells in a petri dish. The stem cells come from blood samples donated by many patient volunteers of different ages, genders and races, as well as various pre-existing cardiovascular conditions. These tissue samples will be infected with the COVID-19 proxy virus engineered by Dr. Teng.

The substitute virus combines the well-studied vesicular stomatitis virus (VSV) with an outer shell containing the spike protein on the surface of SARS-CoV-2 that allows the coronavirus to enter human cells. This non-replicating virus is “a sheep in wolf’s clothing,” invading cells like the COVID-19 virus without harming scientists working with the pathogen, Dr. McDonald said. VSV also expresses the same enzyme, luciferase, that gives fireflies their glow. When hit with a chemical, this “firefly luciferase” lights up the virus so researchers can trace how much invades cells and which cell types are vulnerable.

“With a machine we can image the range of light, which is the level of infection coming out of the cells,” Dr. Teng said.

For the Dr. Kim-led study evaluating the ability of different serum antibodies to block the virus from entering human cells, less light would indicate that the antibodies protected against infection, he added.

Luciferase, the same enzyme that gives fireflies their glow, is helping USF Health researchers track how much proxy COVID-virus invades human cells and which cells are most vulnerable.

Structural biology: A key to drug discovery

Unraveling the structure of viral proteins and identifying the receptors they use to enter cells can help guide discovery and design of potential antiviral treatments.

Yu Chen, PhD, is a USF Health associate professor of molecular medicine with a background in structural biology and biochemistry. Dr. Chen applies his expertise in structure-based drug design using advanced techniques — including X-ray crystallography and molecular docking — to help develop inhibitors (drug compounds) that target bacterial enzymes causing resistance to certain commonly prescribed antibiotics such as penicillin.

Now he’s turned his attention toward looking for new or existing drugs to stop SARS-CoV-2.

Yu Chen, PhD, an associate professor of molecular medicine who has expertise in structure-based drug design, has turned toward looking for new or existing drugs to stop SARS-CoV-2.

One way to do this would be to block the virus’s main protease, known as M^pro, an enzyme that cuts out proteins from a long strand that the virus produces when it invades a cell. Without it, the virus cannot replicate. Dr. Chen works with colleagues at the University of Arizona College of Pharmacy (Jun Wang, PhD) and the USF Department of Chemistry (James Leahy, PhD) on this project.

“M^pro represents a promising target for drug development against COVID-19 because of the enzyme’s essential role in viral replication and the absence of a similar protease in humans,” Dr. Chen said. Since people do not have the enzyme, drugs targeting this protein are less likely to cause side effects, he explained.

This winter, an international team of scientists shared their description of the complex crystal structure of M^pro and in April published their discovery of its inhibitors, a half-dozen leading drug candidates identified by targeting the viral enzyme. Taking advantage of the breakthrough, Dr. Chen and other scientists worldwide hope to add more candidates to the drug discovery pipeline soon.

Together with the scientists from University of Arizona, Dr. Chen has found that several known protease inhibitors, including an FDA-approved hepatitis C (HCV) drug boceprevir and an investigational veterinary antiviral drug GC376, showed potent inhibition of the viral protein, and were more active than the previously identified inhibitors. Dr. Chen and his doctoral student, Michael Sacco, have recently determined the first structure of GC376 bound by M^pro, and characterized the molecular interactions between the compound and the viral enzyme.  Their paper describing these results will soon be published in the prestigious scientific journal Cell Research.

Generated by X-ray crystallograhy, this image depicts the overall structure of the COVID-19 virus’s main protease (Mpro), which plays a key role in viral replication. Dr. Chen and colleagues recently found two new protease inhibitors that offer promise in blocking the drug target. –Photo courtesy of Yu Chen.

Dr. Chen and colleagues are also looking for small molecules that can effectively stop the M^pro enzyme from working or last long enough in the body to kill the COVID-19 virus.

The researchers use the latest computer software to visualize and predict how different drug candidates (M^pro inhibitors) bind with the viral proteins. This 3D structural analysis of “binding hotspots” can help in designing and chemically modifying other types of protease inhibiting-drugs with improved activity against SARS-CoV-2, Dr. Chen said.

The most potent antiviral compounds would be tested in human respiratory cell cultures growing the virus. Only then can a drug candidate move to animal models, and, eventually, human trials.

Genomics: Linking genetic variations to outcomes

Why do some individuals get so ill from the COVID-19 virus, while others barely notice symptoms? Why do certain countries and populations have higher death rates than others? Age, underlying medical conditions, socioeconomic and environmental factors play a role – but genetic variation, both in the virus itself and the humans it invades, are likely part of the equation.

“This virus has swept across the world, and some differences in immune response, virulence and disease outcomes of people infected with SARS-CoV-2 could be due to various strains of the virus yet to be defined,” USF Health’s Dr. Liggett said.

Differences in immune response, virulence and disease outcomes of people infected with SARS-CoV-2 could be due to various strains of the virus not yet defined, Dr.  Liggett says.

Sequencing all genes that make up the COVID-19 virus — not just certain sections of the virus’s genome — will be key to uncovering genetic changes that could make a difference in patient susceptibility and outcomes, Dr. Liggett said. More than a decade ago, a team led by Dr. Liggett sequenced for the first time all known genomes of the human rhinovirus, providing a framework for antiviral treatments or vaccine development for this common respiratory virus implicated in asthma flare-ups.

“All parts of a virus’s genome work together for its existence, reproduction and infectivity,” he said. “So, to sequence only one part would be like looking at just the spark plugs, instead of the whole engine, when your car is not running well.”

The data gathered so far indicates that SARS-CoV-2 mutates slowly in the population. Most people have only 10 or so genetic variations in the 30,0000 nucleotide viral genome compared to the reference standard, Dr. Liggett said. “This may be a good sign that antibodies developed from an infection, a vaccine, or derived from an infusion, will provide long-lived immunity. This lower level of mutations also allows us to track a viral strain, potentially knowing how a community became infected.”

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Noting where genetic variation does not occur is also important, since this may represent a “soft-spot” in the virus’s genome that cannot tolerate change because it is so vital, he added. “That might offer a clue about where to target a vaccine or therapy.”

As for human genetic variations that might influence whether certain individuals or subgroups of patients with COVID-19 fare better or worse, Dr. Liggett says the scientific community understands many human genes responsible for mounting an immune defense against this SARS-CoV-2 virus, and other respiratory viruses.

“With enough samples and epidemiology, we may be able to identify patients at genetic risk for serious, life-threatening outcomes,” he said. “However, it will be extremely challenging to find those needles in this big haystack.”

Clinical Trials: Testing treatments that attack on several fronts

As clinicians cared for more patients, one thing became increasingly clear – COVID-19 is more than a respiratory disease that injures the lungs.

It can strike many cell types and organs throughout the body including the brain, heart, blood vessels and kidneys; destroy taste and smell; cause life-threatening blood clots; and trigger a dangerous inflammatory cytokine storm. People with weakened immune systems are more vulnerable to severe illness – including the elderly and those with heart or lung diseases, diabetes, obesity or other underlying medical conditions. Black and Latino populations are disproportionately more likely to die from the virus. And while children are largely spared, a rare inflammatory pediatric syndrome with cardiac complications has been associated with COVID-19.

USF Health, working with Tampa General Hospital, had been at the forefront of a wide range of COVID-19 clinical trials in the Tampa Bay region.

Physicians and scientists are exploring many possible treatments to increase survival and improve prognoses for critically ill patients. Some target the virus itself or human cellular pathways that the virus exploits to replicate. Others aim to prevent collateral inflammatory damage in the human host. A disease affecting so many parts of the body will need drugs, or combinations of drugs, to attack on several fronts, said USF Health infectious disease physician-scientist Dr. Kim.

In the Tampa Bay region, USF Health, working with Tampa General Hospital, is at the forefront of a wide range of COVID-19 clinical trials. Creating drugs from scratch can take years, so several trials are investigating medications already prescribed for other infectious or inflammatory diseases to determine their effectiveness against SARS-CoV-2. For instance, Dr. Kim is local lead investigator for a multisite randomized controlled trial testing the safety and effectiveness of sarilumab in blocking acute lung damage in hospitalized COVID-19 patients. Sarilumab, approved for treating rheumatoid arthritis, is a monoclonal antibody targeting the proinflammatory cytokine receptor interleukin 6. Another trial will evaluate the ability of nitazoxanide, originally developed as an antiparasitic drug for gastrointestinal infections, to prevent respiratory virus replication in health care workers.

Dr. Kim is also working with Tampa General’s laboratory to analyze and validate the reliability of commercial tests that test patient blood samples for antibodies, proteins that provide evidence of past COVID-19 infection and recovery.

Kami Kim, MD, director of the Division of Infectious Disease and International Medicine at USF Health, leads a study evaluating the accuracy of antibody testing.

The accuracy of the antibody testing – different from the nasopharynx swab or saliva tests used to diagnose a current active infections – is important because it can give health officials a clearer picture of how widely COVID-19 has spread in the community and the extent of asymptomatic cases. Based on past experience with other coronaviruses like SARS and MERS, a positive SARS-CoV-2 antibody test would typically indicate some level of immunity. Researchers like Dr. Kim want to confirm that and hope to define the concentration of antibodies needed to confer immunity as well as how long that immunity lasts.

(In late May, the Centers for Disease Control and Prevention released new guidelines cautioning that some antibody tests have high false positive rates, and more definitive data is needed before they can be used to make decisions about returning to work, school or other public places.)

“We need to know if people who have the antibodies are actually protected against another infection,” Dr. Kim said. “It’s not yet clear… but, preliminary data indicates that a fairly large proportion of those people who recover from COVID-19 infection will have what are the protective (neutralizing) antibodies.”

SARS-CoV-2 shares genetic and some clinical similarities with the first SARS virus (SARS-CoV) — which caused a smaller scale global outbreak and has not re-emerged since the last reported case in 2004. But the new coronavirus is both more highly contagious and more apt to spread asymptomatically.

Based on past experience with other coronaviruses like SARS and MERS, a positive SARS-CoV-2 antibody test would typically indicate some level of immunity. Scientists are working to figure out how much immunity and how long it lasts.

“It’s the thing that has kept all of us in public health and infectious diseases up at night – a completely new pathogen that explodes before we had a real chance to get a handle on what was happening,” Dr. Kim said. “We’re learning more as we go, but teamwork is essential. No one will be able to solve all the pieces of this pandemic puzzle by themselves,” she added.

It will take time for scientists to fully understand the COVID-19 virus and how genetics, the environment, medications, lifestyle and public health measures impact the course of the disease.

“COVID-19 has essentially shut down the entire world,” added Dr. Kim, who as a clinical infectious diseases fellow at the University of California San Francisco in the 1980s witnessed firsthand the devastating consequences of the domestic HIV/AIDS epidemic. “A lesson we need to learn is the importance of maintaining preventive public health infrastructures — not only in our local communities, but globally, so that we can efficiently combat any future pandemics.”

His team searches beyond the hallmark Alzheimer’s disease proteins for alternative treatments

//www.youtube.com/watch?v=Hbl6gGddYpM

In his laboratory at the USF Health Byrd Alzheimer’s Center, neuroscientist David Kang, PhD, focuses on how different types of proteins damage the brain when they accumulate there. In the case of Alzheimer’s disease, decades of good science has zeroed in on amyloid and tau, as the two types of hallmark proteins driving the disease process that ultimately kills brain cells.

Dr. Kang and his team investigate molecular pathways leading to the formation large, sticky amyloid plaques between brain cells, and to the tau neurofibrillary tangles inside brain cells –including the interplay between the two proteins. But, he is quick to point out that amyloid and tau are “not the full story” in the quest to understand how normally aging brains go bad.

“Our goal is to understand as much of the entire Alzheimer’s disease process as possible and then target specific molecules that are either overactive or underactive, which is part of the drug discovery program we’re working on,” said Dr. Kang, professor of molecular medicine and director of basic research for the Byrd Alzheimer’s Center, which anchors the USF Health Neuroscience Institute.

Neuroscientist David Kang, PhD, (third from left)  stands with his team in his laboratory at the Byrd Alzheimer’s Center, which anchors the USF Health Neuroscience Institute.

Attacking dementia from different angles 

Dr. Kang’s group takes a multifaceted approach to studying the biological brain changes that impair thinking and memory in people with Alzheimer’s, the most common type of dementia, as well as Lewy body, vascular and frontotemporal dementias.

That includes examining how damaged mitochondria, the energy-producing power plants of the cell, contribute to pathology in all neurodegenerative diseases. “Sick mitochondria leak a lot of toxins that do widespread damage to neurons and other cells,” Dr. Kang said.

Dr. Kang’s team was the first to identify how mutations of a gene, called CHCHD10, which contributes to both frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS), cause both mitochondrial dysfunction and protein pathology called TDP-43. Their findings on the newly identified mitochondrial link to both neurodegenerative diseases were published in Nature Communications in 2017.

The role of selective degradation in ridding cells of abnormal proteins, old or damaged organelles (including mitochondria) and other debris is another key line of research pursued by Dr. Kang and colleagues.

A single stained nerve cell | Microscopic image courtesy of Kang lab

“We believe something more fundamental is going wrong in the brain during the aging process to tip the balance toward Alzheimer’s disease – beyond what we call proteinopathy” or deposits of malformed proteins like toxic amyloid and tau, said Dr. Kang, whose work is bolstered by nearly $8 million in grant funding from the National Institutes of Health (NIH), the Veterans Administration (VA merit awards) and the Florida Department of Health.

“I think one of the fundamental things happening is that the (cellular) plumbing system isn’t working to clear out all the accumulating junk,” he said. “That’s why we’re looking at the protective clearance mechanisms (autophagy and mitophagy) that would normally quickly remove misfolded proteins and dysfunctional mitochondria.”

Unfortunately, pharmaceutical trials to date have yielded no effective treatments for Alzheimer’s disease, the sixth leading cause of death in the U.S.  Most clinical studies have centered on developing medications to block or destroy the amyloid protein plaque formation, and a few have targeted the tau-containing neurofibrillary tangles. The five Alzheimer’s drugs currently available may provide temporary relief of symptoms, such as memory loss and confusion. But, they do not prevent or delay the mind-robbing disease as toxic proteins continue to build up and dismantle the brain’s communication network.

Lesson learned: The critical importance of intervening earlier

Some scientists argue that the “amyloid hypothesis” approach is not working. Dr. Kang is among those who maintain that amyloid plays a key role in initiating the disease process that leads to brain atrophy in Alzheimer’s – but that amyloid accumulation happens very early, as much as 10 to 20 years before people experience memory problems or other signs of dementia.

Early detection and treatment are key, Dr. Kang says, because as protein plaques and other lesions continue to accumulate in the brain, reversing the damage may not be possible.

“One reason we’ve been disappointed in the clinical trials is because so far they have primarily targeted patients who are already symptomatic,” Dr. Kang said. “Over the last decade we’ve learned that by the time someone is diagnosed with early Alzheimer’s disease, or even mild cognitive impairment, the brain has degenerated a lot. And once those nerve cells are gone they do not, for the most part, regenerate… The amyloid cascade has run its course.”

As protein plaques and other lesions continue to accumulate, becoming apparent with MRI imaging, reversing the damage may not be possible.  So, for anti-amyloid therapies – or even those targeting downstream tau – to work, patients at risk of Alzheimer’s need to be identified and treated very early, Dr. Kang said.

USF Health is recruiting healthy older adults with no signs of memory problems for a few prevention trials. A pair of Generation Program studies will test the effectiveness of investigational anti-Alzheimer’s drugs on those at high genetic risk for the disease before symptoms start. And, the NIH-sponsored Preventing Alzheimer’s with Cognitive Training (PACT) study is examining whether a specific type of computerized brain training can reduce the risk of mild cognitive impairment and dementias like Alzheimer’s disease in those age 65 and older.

To accelerate early intervention initiatives, more definitive tests are needed to pinpoint biomarkers that will predict Alzheimer’s disease development in genetically susceptible people. Dr. Kang is hopeful about the prospects.  His own team investigates how exosomes, in particular the lipid vesicles that shuttle proteins and other molecules from the brain into the circulating bloodstream, might be isolated and used to detect people at risk of proteinopathy.

“I think within the next five years, some type of diagnostic blood test will be available that can accurately identify people with early Alzheimer’s brain pathology, but not yet experiencing symptoms,” he said.

Graduate research assistant Yan Yan, a member of Dr. Kang’s research team, works at a cell culture hood.

Searching for alternative treatment targets

Meanwhile, Dr. Kang’s laboratory continues searching for other treatment targets in addition to amyloid and tau — including the enzyme SSH1, which regulates the internal infrastructure of nerve cells, called the actin cytoskeleton. SSHI, also known as slingshot, is needed for amyloid activation of cofilin, a protein identified by the USF Health neuroscientists in a recent study published in Communications Biology as a possible early culprit in the tauopathy process.

“Cofilin is overactive in the brains of Alzheimer’s patients so if we can inhibit cofilin by targeting slingshot, it may lead to a promising treatment,” Dr. Kang said.

Ultimately, as with other complex chronic diseases, Alzheimer’s may not be eliminated by a single silver-bullet cure.  Rather, Dr. Kang said, a combination of approaches will likely be needed to successfully combat the neurodegenerative disorder, which afflicts 5.8 million Americans.

“I think prevention through healthy living is definitely key, because brain aging is modifiable based on things like your diet as well as physical activity and brain exercises,” he said.  “Also, we need to focus on earlier diagnosis, before people become symptomatic, and develop next-generation drugs that can attack the disease on multiple fronts.”

Xingyu Zhao, PhD, a research associate in the Department of Molecular Medicine, is among the scientists in Dr. Kang’s laboratory studying the basic biology of the aging brain.

Fascinated by how the brain works — and malfunctions

Dr. Kang came to USF Health in 2012 after nearly 20 years as a brain researcher at the University of California San Diego, where he earned M.S. and PhD degrees in neurosciences and completed NIH National Research Service Award fellowships in the neuroplasticity of aging.

As an undergraduate Dr. Kang switched from studying engineering to a dual major in science/psychology. He began focusing on neurosciences in graduate school, he said, because tackling how the brain works and malfunctions was fascinating and always challenged him.

“With every small step forward, we learn something else about the basic biology of the aging brain,” said Dr. Kang, “It’s not just helpful in discovering what therapeutic approaches may work best against Alzheimer’s disease – we’re also learning more about other neurodegenerative conditions affecting the brain.”

In addition to leading day-to-day research operations at the Byrd Center and helping to recruit new Alzheimer’s investigators, Dr. Kang holds the Mary and Louis Fleming Endowed Chair in Alzheimer’s Research and serves as a research neurobiologist at the James A. Haley Veterans Haley Veterans’ Hospital.

He has authored more than 50 peer-reviewed journal articles on brain aging and Alzheimer’s disease research. A member of the NIH Clinical Neuroscience and Neurodegeneration Study Section since 2016, he has served on multiple national and international editorial boards, scientific panels and advisory boards.

Dr. Kang sits next to a computer monitor depicting stained microscopic images — a single neuron (far left) and the two hallmark pathological proteins for Alzheimer’s disease, tau tangles (center) and amyloid plaques (right).

Some things you may not know about Dr. Kang

• His parents were Presbyterian missionaries in Africa, so he spent nine years of his early life (third through 10^th grade) in Nigeria.
• Dr. Kang practices intermittent fasting, often forgoing breakfast and eating only within an 8-hour window. Animal studies indicate the practice may contribute to lifespan and brain health by improving cellular repair through the process of autophagy, he said. “Autophagy really kicks your cells’ plumbing system into gear to clear out all the waste.”

-Video and photos by Allison Long, USF Health Communications and Marketing

//www.youtube.com/watch?v=8EGW58Uq-Yk

Patients have always been the center of the yearly scientific symposium hosted by the Friedreich’s Ataxia Research Alliance (FARA) and the University of South Florida Ataxia Research Center.

But, for the 8^th annual symposium held Sept. 15 at USF’s Gibbons Alumni Center, patients took on an even more prominent role. The panel discussion in which they share their stories about living with the rare, but devastating, progressive neurodegenerative disease, including patient participation in clinical trials, was moved up in the program format.

The 8th annual scientific symposium hosted by FARA and USF was held in the USF Gibbons Alumni Center.  More than 750 in the FA community listened to the latest perspectives on ataxia research from patients and scientists, in person and internationally via live-stream.

And this year, led by FARA spokesperson Kyle Bryant as moderator, the four patient panelists were the ones driving the conversation with leading researchers from academia and industry who sat onstage beside these young adults to discuss the latest advances in the search for effective treatments and, ultimately, a cure.

More than 250 attendees gathered at the USF Gibbons Alumni Center for the symposium, which was also live-streamed and viewed worldwide by those in the FA community, over 500 people in eight countries. The symposium “Understanding Energy for a Cure” kicked off a series of events in Tampa Bay to raise awareness about FA, culminating Sept. 17 with the FARA Energy Ball gala, which this year raised $2 million to benefit innovative ataxia research.

The patient panel, moderated by FARA spokesperson Kyle Bryant (far left), helped drive the conversation with leading researchers. Participants were, from left, Alex Fielding, Sean Baumstark, Alison Avery and Anna Gordon.

“My parents and sister never really let me believe that Friedreich’s ataxia was going to stop me,” said panelist Alison Avery, 22, diagnosed with Friedreich’s ataxia at age 18, who is interning with the National Football League’s social responsibility department in NYC following college graduation. “It may have changed the way that I do certain things, but right now I’m living on my own in New York City, and that’s something not everyone would do, whether or not they have FA.”

Alison participates in the “Cardiac MRI and Biomarkers in Friedreich’s Ataxia” study at Children’s Hospital of Philadelphia and another evaluating the relationship between exercise performance and neurological/cardiac status and overall functioning in children and adults with FA. “I’m excited to be able to share my perspective on being involved in different research studies,” she said. “I feel like that’s something more people should know, especially the researchers — about how patients actually feel about trials and studies.”

USF System President Judy Genshaft said USF has made neurosciences, including ataxia research, a high institutional research priority.

Friedreich’s ataxia typically strikes in childhood or adolescence and leads to a progressive loss of coordination and muscle strength, eventually robbing young people of their energy and ability to walk. While the neurological symptoms are most visible, FA is a multisystem disease that can adversely affect cardiac function, metabolism, vision, hearing and the skeletal system. There is currently no approved treatment for FA.

“Throughout the history of this event, the one constant has been how incredibly motivating and inspiring it is to hear from patients and their families who never fail to share one valuable message: ‘Live life to its fullest despite the challenges of Friedreich’s ataxia,’” said USF System President Judy Genshaft in her symposium welcome remarks.

FARA Executive Director Jennifer Farmer introduced the patients and provided insights on their participation in studies and clinical trials.

The USF Health Morsani College of Medicine is one of 10 sites in the international FARA Collaborative Clinical Research Network, all working to discover treatments that can attack FA on different fronts and improve the quality of life for patients.

“We’ve made this a high research priority within the institution,” President Genshaft said. “Over the last 20 years FARA’s international collaborative of researchers has increased the pace in the fight against FA. Today more than 20 drugs are in the treatment pipeline and ongoing studies are working toward the discovery of new therapies… We have every reason to be hopeful, but we do know there is more work to be done.”

Theresa Zesiewicz, MD, professor of neurology and director of the USF Ataxia Research Center, presented promising preliminary results from two clinical trials conducted at USF, among other sites. – Photo by Kent Ross

Theresa Zesiewicz, MD, professor of neurology and director of the USF Ataxia Research Center, updated attendees on the center’s initiatives.

“We started out at USF with one clinical trial eight years ago, and now we have five or six clinical trials and each (investigational) drug works differently,” Dr. Zesiewicz said. “Some drugs work to increase frataxin (the protein depleted in those with FA), some drugs work on inflammation, some work as strong antioxidants. So, there may not be one magic bullet to stop this disease; rather, it may require a cocktail of therapies, a conglomerate of different compounds to help delay or stop the disease process.”

David Lynch, MD, PhD, (center) lead investigator for the FA Natural History Study at Children’s Hospital of Philadelphia, responds to a patient question. He was joined in the discussion of clinical trials by Martin Delatycki, PhD, (far left) of Murdoch Children’s Research Institute, Melbourne, Australia.

Some promising preliminary results for two clinical trials conducted at USF, among other sites, were announced by lead investigator Dr. Zesiewicz. Both studies were done in collaboration with FARA.

• EPI-743 Safety and Effectiveness Study: The Phase 2 open-label extension study, sponsored by Edison Pharmaceuticals, tested the effectiveness of the potent antioxidant EPI 743 primarily on vision, and secondarily, on neurological function in adult patients with FA. After two years of study and a year of data analysis, the researchers found that patients taking EPI-743 from the study’s start demonstrated markedly less disease progression than would be expected in the natural history of the disease. The improvement in neurological function was dose-dependent, and although the last 18 months of the study were open-label, patients and investigators were blinded to the drug dose allocation. Additional studies of EPI-743 are planned in pediatric patients and those with point mutations.

FARA President Ron Bartek thanked everyone in the room, including researchers, pharmaceutical partners and patients and their families, for working together to advance discoveries to “slow, stop and reverse” Friedreich’s ataxia.

• Retrotope RT001 Phase 1/2: The randomized double-blind, placebo-controlled trial evaluated the safety, tolerability and early effectiveness of the stabilized fatty acid RT001 in adult patients with FA. In the small, 28-day study, researchers found that the drug was safe, well tolerated at high doses and rapidly absorbed to target levels, with early signs of effectiveness. Earlier this year, the FDA granted Retrotope orphan drug designation for RT001 in FA.

The scientist and physician panelists at the symposium covered four areas of FA research:

• Basic and Discovery Science: Helene Puccio, PhD; Marek Napierala, PhD; and Jordi Magrane, PhD
• Drug Development and Advancing Treatments: Mark Payne, MD; and Barry Byrne, MD, PhD.
• FA Biomarkers: Kimberly Lee Lin, MD; Angel Martin, PhD student; and Christophe Lenglet, PhD.
• Clinical Trials and Translating Treatments to Improved Care: Martin Delatycki, PhD; and David Lynch, MD, PhD.

The researchers discussed their scholarly work, progress beyond their laboratories and its relevance to advancing treatments. They also emphasized their passion for FA science and personal commitment to patients.

Scientists participating in the Basic and Discovery Science panel discussion were, from left, Jordi Magrane, PhD, of the Brain and Mind Research Institute, Weill Cornell Medical College; Marek Napierala, PhD, of the University of Alabama; and Helene Puccio, PhD, of the Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg.

Moving from treating symptoms to slowing and stopping progression to reversing disease is “not an overnight event,” said David Lynch, MD, PhD, lead investigator for the FARA Natural History Study at Children’s Hospital of Philadelphia. “So, in 15 years we may look back and talk not about the advance but about the 15 advances from each of 15 clinical trials superimposed on top of one another, eventually leading to that four letter word — cure.”

Answering patient questions on drug development and advancing treatments were physician-scientists Barry Byrne, MD, PhD, (left) of the University of Florida College of Medicine; and R. Mark Payne, MD, of Indiana University School of Medicine.

Despite the challenges, the researchers agreed that the steadfast determination and resilience of patients and their families energizes them to keep working toward a cure.

“Everything we do is for the patients, and we are all in this together trying to find a treatment and cure for Friedreich’s ataxia,” said USF’s Dr. Zesiewicz. “That’s the only reason we’re here.”

Participants in the FA BioMarkers panel discussion were, from left, Kimberly Lee Lin, MD, of Children’s Hospital of Philadelphia; Christophe Lenglet, PhD, of the Institute for Translational Neuroscience, University of Minnesota; and Angel Martin, a PhD candidate at Duke University.

Alison Avery, second from right, credits her family — sister Laurel Avery (left) and parents Paul and Suzanne Avery — with “never really letting me believe that Friedreich’s ataxia is going to stop me.”

Dr. Zesiewicz with members of the USF Ataxia Research Center, one of 10 sites in the international FARA Collaborative Clinical Research Network. – Photo by Kent Ross

Photos by Eric Younghans and video by Sandra C. Roa, USF Health Communications and Marketing

University of South Florida researchers continue to hone the high-volume screening of compounds that may lead to optimal drugs to combat the rare but deadly infection caused by the brain-eating amoeba Naegleria fowleri.

Distinguished USF Health Professor Dennis Kyle, PhD, who has studied the parasite since the early 1980s, was a featured speaker Sept. 9 at the Second Annual Amoeba Summit in Orlando, FL. The summit brings together health care professionals to spread awareness about risk, diagnosis and the need for research to find effective treatments against primary amebic meningoencephalitis (PAM). The infection is caused by Naegleria fowleri, which flourishes in warm freshwater lakes. Florida, Texas and California are states with the most reported cases of PAM.

Distinguished USF Health Professor Dennis Kyle, PhD, is among a select group of researchers across the country focusing on drug discovery for the rare but deadly infection caused by Naegleria fowleri, commonly known as the brain-eating amoeba. – Photo by Christopher Rice

Dr. Kyle, a member of the USF College of Public Health Global Infectious Diseases Research group, leads a National Institutes of Health-funded study to find faster-acting drugs that might be combined with existing therapies to significantly increase survival rates of patients who contract infections from these pathogenic free-living amoebae. He is among a select group of researchers across the country who focus on this neglected infectious disease.

PAM usually affects healthy children and young adults who engaged in swimming, diving or other water activities that may cause contaminated water to enter the nose.  Once the parasite crosses into the sinuses, the amoeba invades the frontal brain where the infection destroys brain tissue. It kills more than 97 percent of its victims within days. An Orlando teen recently became only the fourth person known to survive an infection by Naegleria fowleri.

The amoeba moves so quickly that by the time doctors definitively identify Naegleria fowleri as the cause of meningitis, it is often too late for existing treatments to work.

“With such a high fatality rate, the odds are likely stacked against any patient who comes into the hospital with this organism,” Dr. Kyle said. “It is very important to develop rapid laboratory diagnostics and drugs that kill the amoeba quicker, so that we have more survivors.”

At the summit, Dr. Kyle highlighted the following approaches that USF is taking to discover a new drug. His laboratory collaborates on different drug discovery projects with Georgia State, USF Chemistry and the Center for Drug Discovery and Innovation, and the biotechnology company Mycosynthetix.

• Working to turn compounds that demonstrate the most promising chemical activity against the brain-eating amoeba into drugs.
• Screening libraries of small molecules and natural products to identify new “hits.” Fungi metabolites have become a promising new source.
• Repurposing drugs that may work against the amoeba — either those approved to treat a different disease or drugs tested in clinical trials but not approved.

USF Health/VA infectious diseases physician Sandra Gompf, MD, with Dr. Kyle at this year’s Amoeba Summit. After Dr. Gompf lost her 10-year-old son to amoebic meningoencephalitis, she and her husband, also a doctor, launched an Amoeba Season awareness campaign to help educate the public on ways to prevent the parasitic infection. – Photo by Christopher Rice

As they aim to shorten the timeline from discovery of a new drug to treating patients, researchers are also seeking to better understand how the brain-eating pathogen works.

Studies with mice have shown that a microscopic droplet of water containing 1,000 of the pathogenic organisms can cause the same infection as that seen in humans, Dr. Kyle said. But, researchers still don’t know why some people get sick when exposed to the amoeba and others do not.

“Is it the numbers of amoeba, or something about the person’s immune system? Nothing really ties a string between getting infected and not getting infected,” Dr. Kyle said in an interview last month with ABC News Nightline.

For the full ABC News story including comments from Dr. Kyle, click here.

For more on the Amoeba Season campaign, visit www.amoeba-season.com.

New dementia drug discovery efforts get underway this month at the University of South Florida, Tampa, Fla., thanks to £875,000 funding (approximately $1.2 million) from the Dementia Consortium. The U.S. team of academics will work with drug development experts at UK-based MRC Technology, to target the immune system in a bid to halt nerve cell damage.

The investment comes as part of the £4 million Dementia Consortium – a global partnership between Alzheimer’s Research UK, MRC Technology and the pharmaceutical companies Abbvie, Astex, Eisai and Lilly. By uniting expertise, the Consortium is bridging the gap between academic research and the pharmaceutical industry in the search for new drugs to slow neurodegenerative diseases.  The Consortium’s project with the University of South Florida marks their first contract for collaboration with an American University.

The link between the immune system and neurodegeneration is the focus of intense investigation, and a number of drug discovery efforts aimed at reducing inflammation have got underway recently. In this collaborative project, Dr. David Morgan and Dr. Kevin Nash of the USF Health Byrd Alzheimer’s Institute, University of South Florida, will explore the role of immune system regulator, fractalkine, in neurodegeneration. Their previous work in animal models of Alzheimer’s disease indicated a neuroprotective role for the protein, with increased levels of fractalkine dampening inflammation, halting nerve cell death and reducing tau deposits. The team observed similar benefits in mouse models of Parkinson’s, suggesting that fractalkine receptor agonism could be a treatment approach for a number of neurodegenerative diseases.

David Morgan, PhD, CEO of the USF Health Byrd Alzheimer’s Institute and Distinguished University Health Professor (left) and Kevin Nash, PhD, assistant professor of molecular pharmacology and physiology, with an image of neurons expressing fractalkine, an immune system regulator with a neuroprotective effect.

As no known small molecule agonists of the fractalkine receptor exist, the Dementia Consortium funding will couple Dr Morgan’s expertise in neurodegeneration and in vivo validation techniques with the MRC Technology’s extensive screening capabilities and medicinal chemistry programmes.

Talking about the new funding, Dr. David Morgan, CEO of the USF Health Byrd Alzheimer’s Institute, said:

“We’ve been exploring the role of fractalkine in Alzheimer’s and Parkinson’s disease for many years now, highlighting a neuroprotective role for the protein. Thanks to funding from the Dementia Consortium, we are now able to shift our focus from pathway characterization to drug development. We’re particularly excited that this approach could have an impact across a number of different neurodegenerative diseases and look forward to coupling our disease knowledge with drug discovery experts in the UK, to help accelerate progress towards treatments.”

Dr. Simon Ridley, Director of Research at Alzheimer’s Research UK, said:

“Dementia is our greatest medical challenge, with 46 million people worldwide living with the condition. The Dementia Consortium is one of a range of initiatives by Alzheimer’s Research UK to accelerate the ‘bench to bedside’ journey, ensuring that academic insights are translated into the clinic as rapidly as possible. The high attrition rate in drug discovery means we must invest heavily in promising early stage development projects and the Dementia Consortium provides a unique vehicle for this investment, uniting expertise across the academic, technology transfer and pharmaceutical sectors.”

Close-up of microscopic image: magnified neurons expressing fractalkine.

Dr. Justin Bryans, Director, Drug Discovery at MRC Technology, said:

“Scientists are increasingly looking at the body’s own immune system to fight some of the most challenging diseases of our time. This project will progress promising findings that fractalkine could reduce inflammation and cell death. Drug discovery expertise in our laboratories will now be applied to find small molecules to stimulate the fractalkine receptor so we can move a step closer to finding a new treatment for people with dementia.”

On forming new partnerships, Valerie McDevitt, Associate Vice President for Technology Transfer & Business Partnerships at the University of South Florida, said:

“The University of South Florida places emphasis on building new relationships like this one to help bridge the gap between academic research and industry.  Our collaboration with the Dementia Consortium provides an opportunity to positively impact the treatment of neurodegenerative diseases and aligns with our university mission to serve as a highly effective major economic engine.”

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For further information, or to speak with Dr. Morgan or Dr. Ridley, please contact Emma O’Brien, Science Communications Officer at Alzheimer’s Research UK on 0300 111 5 666, mobile or email press@alzheimersresearchuk.org.

Tampa, FL (Nov. 10, 2015) — A University of South Florida (USF) Center for Global Health & Infectious Diseases Research team has demonstrated a new screening model to classify antimalarial drugs and to identify drug targets for the most lethal strain of malaria, Plasmodium falciparum.

The National Institutes of Health-funded study appeared online Nov. 6 in the journal Scientific Reports.

Half the world’s population is at risk for malaria, a mosquito-borne disease becoming increasingly resistant to the drug artemisinin.

The malaria parasite is becoming increasingly resistant to the drug artemisinin as the front-line treatment to combat the mosquito-borne disease, even though artemisinin is given as a combination therapy with another antimalarial drug.

The USF research provides a better understanding how antimalarial drugs work, thus adding ammunition in the race to overcome the spread of multidrug-resistant malaria – a public health threat that could  potentially undermine the success of global malaria control efforts.

The global health researchers used a collection of malaria parasite mutants that each had altered metabolism linked to defect in a single P. falciparum gene. They then screened 53 drugs and compounds against 71 of these P. falciparum piggyBac single insertion mutant parasites. Computational analysis of the response patterns linked the different antimalarial drug candidates and metabolic inhibitors to the specific gene defect.

This novel chemogenomic profiling revealed new insights into the drugs’ mechanisms of action and most importantly identified six new genes critically involved P. falciparum’s response to artemisinin, but with increased susceptibility to the drugs tested.

“That represents six new targets potentially as effective as artemisinin for killing the malaria parasite,” said the study’s co-senior author Dennis Kyle, PhD, a Distinguished USF Health Professor in the Department of Global Health, USF College of Public Health.  “There is definitely a sense of urgency for discovering new antimalarial drugs that may replace artemisinin, or work better with artemisinin, to prevent or delay drug resistance.”

From left, Dr. John Adams, Dr. Rays Jiang and Dr. Dennis Kyle are members of USF’s Center for Global Health & Infectious Diseases Research team.

The multi-faceted team of USF scientists worked with researchers from the University of Notre Dame’s Eck Institute for Global Health to undertake the chemogenomic profiling of P. falciparum for the first time.

“The methodology used in the study highlights the importance of team-based interdisciplinary research for cutting-edge scientific innovation by combining the tools of drug discovery methods with functional genomics and computational biology analysis. We are very happy to have such an important result published in the first year of a five-year NIH grant,” said co-senior author John Adams, PhD, Distinguished University Health Professor in the Department of Global Health, USF College of Public Health. “Equally important are the enormous efforts by the cadre of talented postdoctoral researchers and graduate students who were critical for making this type of challenging scientific study a success.”

“That interdisciplinary collaboration is where the power of this work comes to light,” Dr. Kyle said. “It helps us develop the tools, the molecular techniques we need to rapidly mine huge amounts of data and to discover new drug targets in ways not previously feasible.”

P. falciparum causes three-quarters of all malaria cases in Africa, and 95 percent of malaria deaths worldwide. It is transmitted to humans by the bite of an infected mosquito, which injects the one-celled malaria parasites from its salivary glands into the person’s bloodstream.

Half the world’s population is at risk of contracting malaria, so any decrease in artemisinin’s effectiveness could result in more deaths.

The USF study was supported by grants from the NIH, National Institute of Allergy and Infectious Diseases (NAID).

Microscopic image of malaria parasite P. falciparum

Article citation:
Anupam Pradhan, Geoffrey H. Siwo, Naresh Singh, Brian Martens, Bharath Balu, Katrina Button-Simons, Asako Tan, Min Zhang, Kenneth O. Udenze, Rays H.Y. Jiang, Michael T. Ferdig, John H. Adams & Dennis E. Kyle. “Chemogenomic profiling of plasmodium falciparum as a tool to aid antimalarial drug discovery.” Scientific Reports, 5, Article number 15930 (2015). doi: 10.1038/srep15930.

About USF Health
USF Health’s mission is to envision and implement the future of health. It is the partnership of the USF Health Morsani College of Medicine, the College of Nursing, the College of Public Health, the College of Pharmacy, the School of Physical Therapy and Rehabilitation Sciences, and the USF Physician’s Group. The University of South Florida is a Top 50 research university in total research expenditures among both public and private institutions nationwide, according to the National Science Foundation.  For more information, visit www.health.usf.edu

Media contact:
Anne DeLotto Baier, USF Health Communications
(813) 974-3303 or abaier@health.usf.edu

Potent compound inhibits protein synthesis at various stages of malaria parasite’s life-cycle

With the rapid emergence of multi-drug resistant strains of malaria, the need to find new drugs capable of delaying or preventing drug resistance has become even more urgent.

Now, an international team of researchers – including two from the University of South Florida – has discovered a promising new antimalarial drug that inhibits the production of a protein involved in the replication and transmission of the malaria parasite.  If successfully developed, the new drug working in combination with an existing fast-acting antimalarial may be less likely to develop rapid resistance to major strains of malaria parasites.

Dennis Kyle, PhD, Distinguished University Health Professor, and Anupam Pradhan, PhD, a research associate, both from the USF College of Public Health Department of Global Health, were among the co-authors of the multisite preclinical study published June 18 in the journal Nature.  The study was led by researchers at the University of Dundee Division of Biological Chemistry and Drug Discovery.

Dennis Kyle, PhD

The USF researchers demonstrated in a mouse model of malaria that the new drug candidate, known as DDD107498, helped block the spread of the parasitic disease with greater effectiveness than current antimalarial combination drugs. Their work was supported by a grant from Medicines for Malaria Venture.

In various preclinical studies the potent drug proved highly effective and safe while demonstrating a broad spectrum of antimalarial activity against several life-cycle stages of the malaria parasite Plasmodium falciparum.  This ability to kill parasites without harmful or bothersome side effects at all stages of a complex malaria lifecycle – after the parasites enter the bloodstream through the bite of bloodstream, once they infect the liver and as soon as the modified parasites emerge from the liver to attack red blood cells – will be critical in eradicating malaria.

DDD107498 also has the potential to be administered in less costly single doses (approximately $1 per treatment) – a major advantage since the mosquito-borne disease most often affects poor people living in developing countries, particularly children and pregnant women.

Anupam Pradhan, PhD

The researchers found that DDD107498 works by blocking a molecular target identified as translation elongation factor 2 (eEF2), which is essential for protein synthesis and expressed in various life cycle stages of malaria. Its high potency and long half-life may be well suited for both preventing malaria and offering long-term protection against re-infection.

“The discovery of eEF2 as a viable antimalarial drug target opens up new possibilities for drug discovery,” the authors concluded.

Article citation:
“A novel multiple-stage antimalarial agent that inhibits protein synthesis,” Beatriz Baragaña, Irene Hallyburton, Marcus C. S. Lee, Neil R. Norcross, Raffaella Grimaldi, Thomas D. Otto, William R. Proto, Andrew M. Blagborough, Stephan Meister, Grennady Wirjanata, Andrea Ruecker, Leanna M. Upton, Tara S. Abraham, Mariana J. Almeida, Anupam Pradhan, Achim Porzelle, María Santos Martínez, Judith M. Bolscher, Andrew Woodland, Suzanne Norval, Fabio Zuccotto, John Thomas, Frederick Simeons, Laste Stojanovski, Maria Osuna-Cabello, Paddy M. Brock, Tom S. Churcher, Katarzyna A. Sala, Sara E. Zakutansky, María Belén Jiménez-Díaz, Laura Maria Sanz, Jennifer Riley, Rajshekhar Basak, Michael Campbell, Vicky M. Avery, Robert W Sauerwein, Koen J. Dechering, Rintis Noviyanti, Brice Campo, Julie A. Frearson, Iñigo Angulo-Barturen^, Santiago Ferrer-Bazaga, Francisco Javier Gamo, Paul G. Wyatt, Didier Leroy, Peter Siegl, Michael J. Delves, Dennis E. Kyle, Sergio Wittlin, Jutta Marfurt, Ric N. Price, Robert E. Sinden, Elizabeth Winzeler, Susan A. Charman, Lidiya Bebrevska, David W. Gray, Simon Campbell, Alan H. Fairlamb, Paul Willis, Julian C. Rayner, David A. Fidock, Kevin D. Read, and Ian H. Gilbert; Nature, 522, 315-320, 18 June, 2015;  doi:10.1038/nature14451