Scripps-led analysis of tiny marine organisms indicates early promise in areas ranging from inflammation to skin conditions.

Darkly colored cyanobacteria overtake a Hawaiian coral reef.

A seaweed considered a threat to the healthy growth of coral reefs in Hawaii may possess the ability to produce substances that could one day treat human diseases, a new study led by scientists at Scripps Institution of Oceanography at UC San Diego has revealed.

An analysis led by Hyukjae Choi, a postdoctoral researcher in William Gerwick’s laboratory at Scripps, has shown that the seaweed, a tiny photosynthetic organism known as a “cyanobacterium,” produces chemical compounds that exhibit promise as anti-inflammatory agents and in combatting bacterial infections. The study is published in the May 25 issue of the journal Chemistry & Biology.

“In different arenas these compounds could be helpful, such as treating chronic inflammatory conditions for which we currently don’t have really good medicines,” said Gerwick, a professor of oceanography and pharmaceutical sciences at the Center for Marine Biotechnology and Biomedicine at Scripps and UC San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences.

Scientists identified the “nuisance” organism in 2008 on the reefs directly adjacent to the National Park Pu‘uhonua o H’onaunau off the Kona coast of Hawaii. The cyanobacterium is believed to be native to Hawaii and is usually inconspicuous, said Jennifer Smith, a Scripps assistant professor in the Scripps Center for Marine Biodiversity and Conservation and a paper coauthor.

“When we first found the bloom during routine surveys with the University of Hawaii we were concerned as it was clearly smothering the corals at one of the most popular dive sites in Hawaii,” said Smith. “Observations in the field even suggested that the cyanobacteria may have been releasing some chemical that was causing the coral to bleach.”

When Smith and her colleagues found the seaweed blooming it was clear that it was overgrowing and negatively affecting the underlying corals. Samples were retrieved in 2009 and transferred to Scripps for analysis.

Choi, Gerwick and their colleagues conducted various laboratory experiments and discovered that the seaweed (the cyanobacterium Leptolyngbya crossbyana) generates natural products known as honaucins with potent anti-inflammation and bacteria-controlling properties.

Specifically, the substances hamper bacteria’s ability to “swarm” over surfaces. For example, when overtaking a new area, bacteria secrete small amounts of a substance known as a quorum sensing factor, which tests to see if the new surface is safe for colonization. Halting a quorum sensing factor could one day translate to a treatment for bacterial infections. For instance, this could be critical, Gerwick said, in the development of drugs to prevent infection in patients who require catheters to deliver vital nutrients to key areas such as arteries, as well the development of new treatments for acne and other skin conditions.

“I think this finding is a nice illustration of how we need to look more deeply in our environment because even nuisance pests, as it turns out, are not just pests,” said Gerwick. “It’s a long road to go from this early-stage discovery to application in the clinic but it’s the only road if we want new and more efficacious medicines.”

“These organisms have been on the planet for millions of years and so it is not surprising that they have evolved numerous strategies for competing with neighboring species, including chemical warfare,” said Smith. “Several species of cyanobacteria and algae are known to produce novel compounds, many that have promising use in drug development for human and other uses.”

Other co-authors of the paper include Samantha Mascuch, Francisco Villa, Tara Byrum and Lena Gerwick of Scripps Institution of Oceanography; Margaret Teasdale and David Rowley of the University of Rhode Island; and Linda Preskitt of the University of Hawaii, Manoa.

UC San Diego and the National Institutes of Health supported the research.

UCSF, UC San Diego team finds approved drug that could block key cause of dysentery.

James McKerrow, UC San Francisco

>>Related: UC San Diego release

A team of researchers from UC San Francisco and UC San Diego has identified an approved arthritis drug that is effective against amoebas in lab and animal studies, suggesting it could offer a low-dose, low cost treatment for the amoebic infections that cause human dysentery throughout the world.

Based on these results, the team has received Orphan Drug Status for the drug, known as auranofin, from the U.S. Food and Drug Administration (FDA), and has applied for approval to start clinical trials to treat both amebiasis and the parasite Giardia intestinalis in humans.

The findings, which showed that auranofin inhibited growth of the parasite Entamoeba histolytica in lab tests as well as two rodent models of the disease, highlight the importance of screening existing drugs for new purposes, especially for neglected diseases, the researchers said. Findings will be reported in the June 2012 issue of Nature Medicine and were selected for advance online publication on the Nature website.

The combination of an off-patent drug and decades of clinical safety data offers the possibility of providing a lower-cost solution worldwide with fewer side effects or risks of bacterial resistance than the current therapy, according to co-senior author James McKerrow, M.D., Ph.D., a professor of pathology in the UCSF Sandler Center for Drug Discovery.

Sharon Reed, UC San Diego

“When we’re looking for new treatments for the developing world, we start with drugs that have already been approved,” said McKerrow, who co-authored the paper with Sharon Reed, M.D., of UC San Diego and first author Anjan Debnath, Ph.D., of UCSF. “If we can find an approved drug that happens to kill these organisms, we’ve leapfrogged the development process that goes into assessing whether they are safe, which also makes them affordable throughout the world.”

Each year, 50 million people worldwide contract amebiasis through contaminated food or water, making it the third leading cause of illness and fourth leading cause of death due to protozoan infections worldwide. Most of the 70,000 deaths each year are in developing countries, where children are at greatest risk of severe illness. While less deadly than amoebas, Giardia is the most frequent parasitic agent of intestinal disease worldwide, causing an estimated 280 million cases annually, including also infects between 6 percent and 8 percent of all children in developing countries, and more than 19,000 Americans.

Both amebiasis and giardiasis are currently treated with the antibiotic metronidazole, which has side effects that include nausea, vomiting, dizziness and headache.

The new drug, auranofin, has been used as a twice-daily oral therapy for adults with rheumatoid arthritis since 1985, and has been shown to be safe at that dosage. The researchers’ laboratory studies indicated that auranofin would be about ten times more potent than the current treatment for dysentery, meaning it could be given at low dose, and on a one-time or limited basis.

“This is a drug that you can find in every country,” said Debnath, a postdoctoral fellow at UCSF who led the research and is first author on the paper. “Based on the dosage we’re seeing in the lab, this treatment could be sold at about $2.50 per dose, or lower. That cost savings could make a big difference to the people who need it the most.”

The research stemmed from a joint effort among several labs at UCSF that are affiliated with the California Institute for Quantitative Biosciences (QB3) on UCSF’s Mission Bay campus, as well as with the pathology departments in UC San Diego and in the Instituto Politecnico Nacional, in Mexico.

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Findings could mean good news for protein-based therapeutics.

Heather Maynard, UCLA

Proteins are widely used as drugs — insulin for diabetics is the best known example — and as reagents in research laboratories, but they react poorly to fluctuations in temperature and are known to degrade in storage.

Because of this instability, proteins must be shipped and stored at regulated temperatures, resulting in increased costs, and sometimes must be discarded because their “active” properties have been lost. Manufacturers of protein drugs will generally add substances known as excipients, like polyethylene glycol, to the proteins to prolong their activity.

In a new study published in the Journal of the American Society of Chemistry (DOI: 10.1021/ja2120234), investigators from the UCLA Department of Chemistry and Biochemistry and the California NanoSystems Institute at UCLA (CNSI) describe how they synthesized polymers to attach to proteins in order to stabilize them during shipping, storage and other activities. The study findings suggest that these polymers could be useful in stabilizing protein formulations.

The polymers consist of a polystyrene backbone and side chains of trehalose, a disaccharide found various plants and animals that can live for long periods with very little or no water. An example many people will recognize is Sea-Monkeys — the ‘novelty aquarium pet’ introduced in 1962. Sea-Monkeys can be purchased as kits that contain a white powder; when water is added, the powder becomes small shrimp whose long tails are said to resemble those of monkeys.

Trehalose is known to stabilize proteins when water is removed, and as a result, it is an additive in several protein drug formulations approved by the Food and Drug Administration (FDA) to treat cancer and other conditions.

“Our polymers were synthesized by a controlled radical polymerization technique called reversible addition-fragmentation chain transfer (RAFT) polymerization in order to have end groups that can attach to proteins to form what is called a protein-polymer conjugate,” said Heather Maynard, a UCLA associate professor of chemistry and  biochemistry and a member of the CNSI. “We found that the polymers significantly stabilized the protein we used — lysozyme — better to lyophilization (freeze-drying, in which water is removed from the protein) and to heat than did the protein with no additives.”

The research team found that attaching the polymer covalently to the protein — that is, forming a protein-polymer conjugate — stabilized the protein to lyophilization better than adding the non-conjugated polymer at the same concentration.

The team also found that the polymers stabilized lysozyme significantly better than the currently used excipients trehalose and polyethylene glycol, depending on the stress and conditions used.

The Maynard research group is currently exploring the use of their polymer as a stabilizer by attaching it or adding it to FDA–approved protein therapeutics. In addition, they are investigating the mechanism of how the polymer stabilizes proteins.

The research team included Rock J. Mancini and Juneyoung Lee, both graduate students of chemistry and biochemistry in the Maynard research group.

The research is supported by the National Science Foundation.

The paper is available at http://pubs.acs.org/doi/abs/10.1021/ja2120234.

Copper transporter carries anti-cancer drug into cancer cells to help kill them.

A team of University of California, San Diego, researchers has made new discoveries about a copper-transporting protein in the membranes of human cells that drug-discovery scientists can co-opt for the development of new anti-cancer drugs.

The findings, published May 9 as an online-first paper in Cell Biochemistry and Biophysics, describe how the copper transporter works as a biochemical pump to seize copper atoms outside of a cell and whisks the atoms through the otherwise impervious cell membrane into the cell cytoplasm. The same pump transports the platinum-containing drug cisplatin into cancer cells to help kill them. Igor Tsigelny, a research scientist at the university’s San Diego Supercomputer Center and Department of Neurosciences, is lead author of the paper.

The body needs only a tiny amount of copper, but the little that is needed acts as a key component of vital cellular enzymes, including superoxide dismutase, cytochrome c oxidase, lysyl oxidase and dopamine β-hydrolase.

Researchers have shown before that that human copper transporter 1 (hCTR1) protein also participates in transport of the platinum-containing cisplatin, one of the most widely used anti-cancer drugs. Once platinum-containing cisplatin molecules enter a tumor cell, the molecules interact with the cell’s DNA and kill it in a process that has been extensively studied by Stephen B. Howell, a professor of medicine at the UC San Diego Moores Cancer Center.

The way that hCTR1 works is a focus of research by Howell and other cancer researchers because cisplatin and similar drugs somehow lose their punch: they are effective anti-cancer drugs when first administered, but lose much of their effectiveness during cancer relapses. Some researchers theorize that the diminished effect of cisplatin could be due to a change in hCTR1 in cancer cells.

New insights derived by the UC San Diego team is leading to a better understanding of what happens to the protein transporter and that knowledge could possibly be used to design a better version of cisplatin or an entirely new drug to take advantage of the new information.

In addition to cancer researchers, the hCTR1 has been a mystery to cell biologists. Until recently, they didn’t know whether the transporter protein formed dimers, or trimers. In a 2006 breakthrough that was refined in 2009, scientists confirmed that the trimer is the predominant structure, which was confirmed by the pioneering work of Northwestern University professor Vincenz Unger.

Unger’s team identified the structure of the part of the hCTR1 transporter protein that spans the cell membrane. But they were not able to determine the structure of the part of the protein that extends to the outside of the membrane. Because of that gap in knowledge, they were not able to obtain a high-resolution 3-D map of the protein’s structure.

SDSC’s Tsigelny and his colleagues set out to create a complete, detailed 3-D model of the transporter. “There is no magic bullet in protein modeling, especially when we do not have a direct homologous template of another protein crystal structure,” Tsigelny said. “We predicted the structure of the protein on the level of information available at the current time, but this model needed to be checked with actual experimental results.”

Any model that Tsigelny’s team came up with would have to answer questions that had evaded scientists for years. For example, why is the extracellular end of the transporter so flexible? While the flexibility frustrated Unger’s ability to determine its 3-D structure, was the flexible tip of the protein stable enough to support its copper-transporting function?

Would the positively charged metal ions be transported electrostatically? And how does the transporter initially corral metal ions at pick-up points on the cell exterior and drop them off inside?

Tsigelny’s team used a computationally rigorous approach to find the answers.

So-called molecular dynamics modeling studies showed that the path the metal ions take through the intra-membrane transporter channel is stable despite the innate flexibility of the protein. In addition, while electrostatic forces worked well to hold positively charged metal ions like magnets at the extracellular and intracellular ends of the transporter protein, the passage of the metal atoms through an interior channel in the protein must be caused by another means.

Searching the Protein Data Bank

To help to understand the metals’ interaction with protein, Tsigelny’s team invented a new programming tool called METBIND, which works like a chemistry search engine. The program tried to find the possible binding sites of copper and platinum (along with other metal ions) as they interact with the hCTR1 protein and then move along it.

They checked the validity of their METBIND program with all possible copper-protein binding arrangements reported in the 74,000 proteins in the Protein Data Bank.

To the Tsigelny team’s surprise, the METBIND program correctly predicted 80 percent of all known copper binding sites in all 636 copper-binding proteins in the Protein Data Bank. They then focused the METBIND search engine on hCTR1.

They looked for individual atoms in the protein that could be placed within 3.5 Angstrom units of a hypothetical copper ion. One Angstrom unit is equal to one hundred-millionth (10 -8) of a centimeter. They identified six histidine residues in the protein that bind copper (and probably platinum) as the first step in the metal transport process.

They identified nine negatively charged amino acids in the part of the hCTR1 protein that stick out into the extracellular medium waiting for oppositely charged copper or platinum ions to pass by. When the ions arrive, the hCTR1 protein grabs them firmly.

They also found that the hCTR1 trimer creates a neutral channel with a set of triads of methionine amino acids. The triads shepherd copper or platinum ions through the cell membrane into the interior cytoplasm. Each of the methionines is important: if one is lost, copper transport is inhibited. The same effect of methionines has been reported for yeast copper transporter (yCTR).

“Drug developers are interested in the selective transport of platinum and other metal ions into cells to invoke a desired effect, and this study provides a blue print for how they could search for drugs to enhance those effects,” Tsigelny said.

Tsigelny’s research team included Yuriy Sharikov, with SDSC and UC San Diego’s Department of Neurosciences; Jerry P. Greenberg, Mark A. Miller, Valentina L. Kouzentsova, Christopher A. Larson, all with SDSC; and Stephen B. Howell, a professor of medicine at the UC San Diego School of Medicine and associate director for clinical research at the UC San Diego Moores Cancer Center.

The research was funded by grant # W81XWH-08-1-0135 from the National Institutes of Health, as well as grants from the Department of Defense and the Clayton Medical Research Foundation. Computational resources were provided by SDSC and additional support was provided by the UC San Diego Neuroscience Microscopy Shared Facility and the UC San Diego Moores Cancer Center.

About SDSC
As an Organized Research Unit of UC San Diego, SDSC is considered a leader in data-intensive computing and all aspects of ‘big data’, which includes data integration, performance modeling, data mining, software development, workflow automation, and more. SDSC supports hundreds of multidisciplinary programs spanning a wide variety of domains, from earth sciences and biology to astrophysics, bioinformatics and health IT. With its two newest supercomputer systems, Trestles and Gordon, SDSC is a partner in XSEDE (Extreme Science and Engineering Discovery Environment), the most advanced collection of integrated digital resources and services in the world.

Initial tests show potential to treat diseases involving inflammation, such as asthma, stroke.

Dimitrios Morikis, UC Riverside

Pursuing a relatively untapped route for regulating the immune system, an international team of researchers has designed and conducted initial tests on molecules that have the potential to treat diseases involving inflammation, such as asthma, rheumatoid arthritis, stroke and sepsis.

The team, which included Dimitrios Morikis, professor of bioengineering at UC Riverside’s Bourns College of Engineering, started by creating a dynamic three-dimensional map of the structure of a protein called the C3a receptor, which sits on the surface of human cells and plays a critical role in regulating a branch of the immune system called the complement system.

They then used computational techniques to design short portions of protein molecules, known as peptides, that they predicted would interact with the receptor and either block or enhance aspects of its activity.

Finally, experimentalists validated the theoretical predictions by synthesizing the peptides and testing them in animal and human cells.

The researchers – a collaboration of teams at four institutions on three continents – published their results May 10 in the Journal of Medicinal Chemistry.

In addition to Morikis, the team included Christodoulos Floudas, the Stephen C. Macaleer ’63 Professor of Engineering and Applied Science in the Department of Chemical and Biological Engineering at Princeton University; Peter Monk of the Department of Infection and Immunity at the University of Sheffield Medical School, U.K.; and Trent Woodruff of the School of Biomedical Sciences at the University of Queensland, Australia.

The regulation of the complement system – so called because it complements the body’s central system of immune cells and antibodies – is thought to be a possible route to controlling over-active or mistaken immune responses that cause damage.

However, few drugs directly target complement proteins, and none targets the C3a receptor, in part because of the complexity of the complement system. In some cases complement activity can help downplay immune responses while in other cases it can stoke even stronger reactions.

The collaborators were able to create peptides that blocked activity of C3a (antagonists) and others that stimulated it (agonists) with unprecedented potency and precision.

Their success stems from a novel optimization-based approach, developed in the Floudas lab, for computing how a protein’s three-dimensional structure will change when changes are made in the protein’s chemical sequence. This ability to design peptides of a desired shape, allowed them to target the C3a receptor in precise ways.

Morikis and his graduate students Chris Kieslich and Li Zhang provided the collaborators 3-D structures, derived from molecular dynamics simulations, of the naturally occurring peptide that normally regulates the C3a receptor in human cells.

Using a portion of the structures as a flexible templates, Floudas and graduate students Meghan Bellows-Peterson and Ho Ki Fung designed new peptides that were predicted either to enhance or block C3a. Monk and postdoctoral fellow Kathryn Wareham tested the predictions in rat cells, while Woodruff and student Owen Hawksworth tested them in human cells. The Morikis group also performed physicochemical analysis of the structures that implicates electric fields generated by peptide charges as discriminating factors for agonist and antagonist activities.

Among the conditions potentially treatable through complement regulation is reperfusion injury, which occurs when blood flow is temporarily cut off to some part of the body, as in a heart attack or stroke, and then an inflammatory response develops when the blood returns.

Another possible use would be in organ transplantation, in which the body often mounts a destructive immune response against the newly introduced organ. Other common conditions affected by the complement system are rheumatoid arthritis and sepsis.

As next steps, the team will seek to test their peptides in live animal models of inflammation. They also plan to explore more generally the dual role of C3a in inflammation, with an eye toward developing further drug candidates.

The work was funded in part by the National Science Foundation, National Institutes of Health, University of California Tobacco-Related Disease Research Program, Beckman Initiative for Macular Research, US Environmental Protection Agency, British Heart Foundation, and the US Department of Defense.

Often-fatal form of cancer currently has no reliable method for early detection.

Jonathan Kelber, UC San Diego

Researchers at the University of California, San Diego, School of Medicine and Moores Cancer Center have identified a new biomarker and therapeutic target for pancreatic cancer, an often-fatal disease for which there is currently no reliable method for early detection or therapeutic intervention.  The paper will be published today (May 15) in Cancer Research.

Pancreatic ductal adenocarcinoma, or PDAC, is the fourth-leading cause of cancer-related death.  Newly diagnosed patients have a median survival of less than one year, and a 5-year survival rate of only 3 to 5 percent. Therefore, biomarkers that can identify early onset of PDAC and which could be viable drug targets are desperately needed.

“We found that a kinase called PEAK1 is turned on very early in pancreatic cancer,” said first author Jonathan Kelber, Ph.D., a postdoctoral researcher in the UCSD Department of Pathology and Moores Cancer Center.  “This protein was clearly detected in biopsies of malignant tumors from human patients – at the gene and the protein levels – as well as in mouse models.”

PEAK1 is a type of tyrosine kinase – an enzyme, or type of protein, that speeds up chemical reactions and acts as an “on” or “off” switch in many cellular functions.  The fact that PEAK1 expression is increased in human PDAC and that its catalytic activity is important for PDAC cell proliferation makes it an important candidate as a biomarker and therapeutic target for small molecule drug discovery.

In addition to showing that levels of PEAK1 are increased during PDAC progression, the scientists found that PEAK1 is necessary for the cancer to grow and metastasize.

“PEAK1 is a critical signaling hub, regulating cell migration and proliferation,” said Kelber. “We found that if you knock it out in PDAC cells, they form significantly smaller tumors in preclinical mouse models and fail to metastasize efficiently.”

The research team, led by principal investigator Richard Klemke, Ph.D., UCSD professor of pathology, studied a large, online data base of gene expression profiles to uncover the presence of PEAK1 in PDAC.  These findings were corroborated at the protein level in patient biopsy samples from co-investigator Michael Bouvet, M.D., and in mouse models developed by Andrew M. Lowy, M.D., both of the UCSD Department of Surgery at Moores Cancer Center.

While many proteins are upregulated in cancers of the pancreas, there has been limited success in identifying candidates that, when inhibited, have potential as clinically approved therapeutics. However, the researchers found that inhibition of PEAK1-dependent signaling sensitized PDAC cells to existing chemotherapies such as gemitabine, and immunotherapies such as trastuzumab.

“Survival rates for patients with pancreatic cancer remain low,” said Bouvet. “Therefore, earlier detection and novel treatment strategies are very important if we are going to make any progress against pancreatic cancer. Since current therapies are often ineffective, our hope is that the findings from this research will open up a new line of investigation to bring a PEAK1 inhibitor to the clinic.”

Additional contributors to the study include Theresa Reno, Sharmeela Kaushal, Cristina Metildi,Tracy Wright, Konstantin Stoletov, Jessica M. Weems, Frederick D. Park, Evangeline Mose, UC San Diego; Yingchun Wang, Chinese Academy of Science, Beijing; and Robert M. Hoffman, UC San Diego and AntiCancer Inc., San Diego.

The study was supported by the National Institutes of Health.

UC San Diego researchers announce two new clinical trials.

Michael Rafii, UC San Diego

Researchers at the Comprehensive Alzheimer’s Program at the University of California, San Diego, School of Medicine have announced two new clinical trials for patients with either mild to moderate Alzheimer’s disease (AD) and one trial for mild cognitive impairment.

“Two of these studies represent an exciting new approach to treating Alzheimer’s, focusing on improving memory in patients with early symptoms of impaired memory and possibly slowing down  the disease progression long before symptoms appear,” said Michael Rafii, M.D., Ph.D., assistant professor of neurosciences and director of the Memory Disorders Clinic at UC San Diego .

All three are randomized, double-blind, placebo-controlled studies:

The first is a national clinical trial examining the effects of resveratrol – a compound found in red grapes or juice, red wine, chocolate, tomatoes and peanuts – on participants with mild to moderate dementia due to Alzheimer’s disease. Preclinical and pilot clinical research studies suggest that resveratrol may prevent diabetes, act as a natural cancer fighter, ward off cardiovascular disease and prevent memory loss, but there has been no large definitive study of its effects in humans.

“The risk of all of these diseases increases with aging,” said Rafii. “Most resveratrol studies showing any health benefits have been conducted in animal models such as mice, and with doses that far exceed intake from sipping wine or nibbling on chocolate. With this clinical trial, we hope to find out if daily doses of pure resveratrol can delay or alter memory deterioration and daily functioning in people with mild to moderate dementia due to Alzheimer’s.”

The second trial is a phase-two study employing an immunotherapeutic drug developed by Roche called gantenerumab to remove beta-amyloid, a protein that is deposited into plaques found in the brains of patients with Alzheimer’s disease.  Beta-amyloid is neurotoxic and believed to be the main cause of neuronal degeneration in AD. This trial is for patients with what is called prodromal Alzheimer’s disease, or mild cognitive impairment that represents the earliest state of the disease.

The third study involves a drug called crenezumab , which Rafii says has been shown to be one of the more potent amyloid-lowering compounds yet developed.  This drug, from Genentech, is a monoclonal antibody, which means that it very specifically binds only to beta-amyloid.

“By using antibodies against beta-amyloid we hope to reduce its neurotoxic effects on the brain,” Rafii said. “There is a lot of evidence that beta-amyloid molecules cause damaging effects in the brain perhaps as much as ten years before they deposit to form plaques and result in symptoms of memory loss. The aim of these two studies is to see if we can remove beta-amyloid before it causes damage and forms the plaques that result in Alzheimer’s.”

According to the National Institute of Aging, more than 5.3 million people in the United States are suffering from Alzheimer’s, and every 70 seconds, another person develops the disease. Currently, there are no drugs to treat prodomal AD.

The UC San Diego research is sponsored by the Alzheimer’s Disease Cooperative Study through a grant from the National Institute on Aging, as well as by Hoffman La Roche and Genentech. For more information on enrolling at the UC San Diego site, contact the Comprehensive Alzheimer’s Program at (858) 246-1300 or email CAPmemory@ucsd.edu.

T1 Catalyst Award supports crucial next step in development.

Adti Bhargava, UC San Francisco

Chronic pain affects an estimated 116 million Americans and costs $635 billion each year in medical treatment and lost productivity.

Aditi Bhargava, Ph.D., associate professor at UC San Francisco’s School of Medicine, is using a technique known as RNA interference (RNAi) to develop a gene therapy system that sends specific commands to certain neurons, or nerve cells, telling them to turn off pain, or stop inflammation.

“The current treatments for pain dull everything,” Bhargava said. “You have a little fire in the kitchen, but your only solution is a fire hose that floods the entire house. You put out the fire, but you’re affecting the whole house in the process — a huge negative side effect.”

Likening her method to a Trojan horse, Bhargava’s novel therapeutic approach essentially hides the pain-silencing commands, carried by distinct proteins that affect cellular function, inside other proteins which bind only to the troublemaker cells. Once attached, they release their hidden power.

“We want to target the small or medium neurons that sense pain, while leaving other neurons unaffected,” she said. “We’re hoping that while you reduce pain, for example, you’ll still be able to chew or not drool.”

The data from her proof-of-concept animal studies look promising, Bhargava said. “I believe that this project has tremendous translational potential to turn what we learn into concrete benefits for patients.”

Targeted pain and inflammation relief could also be used to treat illnesses, such as Inflammatory Bowel Disease (IBD), an autoimmune condition. This approach has potential to not only minimize unwanted side effects, but save costs, as it sends very small amounts of drug therapies to the targeted cells.

Targeted delivery of drug would reduce the dose required to treat, reduce cost, and most importantly, reduce unwanted side effects.

However, Bhargava’s work is in the early stages, and she’s now facing the critical next steps of moving from animal models to studies with humans, a phase she describes as complex and challenging.

Customized support to develop early-stage ideas

To get help tailored to her individual needs, Bhargava applied for a T1 Translational Catalyst Award, granted by UCSF’s Clinical and Translational Science Institute (CTSI). The award is designed to help drive promising, early-stage research through the lengthy and complex process of translating promising ideas into patient benefit.

The CTSI T1 Catalyst Award works with a tiered model that provides increasing benefit at each of three phases, beginning with feedback and analysis of all proposals. In the second phase, a selected number of awardees are chosen to receive expert consultation from a customized panel of technical, clinical, and business experts.

During this consultation period, applicants are also eligible to apply for a pilot award of up to $15,000 to be used toward a critical experiment or study that may strengthen the proposal. In the final phase, funds of up to $100,000 are awarded to one or more applicants to develop proposals further.

“Many recipients point to individualized consultation with industry, legal, and regulatory experts as the most valuable element of the T1 Catalyst award process,” said Ruben Rathnasingham, Ph.D., a senior program manager with CTSI’s Early Translational Research program, which administers the award. “Applicants have found that expert advice that steers their research toward greater commercial and clinical utility often opens new doors to funding opportunities that were previously unavailable.”

“For researchers who have a well-developed idea with promising data, yet struggle to breach the gap between early research and clinical practice, the T1 Catalyst Award offers an indispensable opportunity,” he added.

In the case of Bhargava, “her work was very innovative and we immediately saw its potential clinical relevance,” Rathnasingham said. “Connecting her with an industry veteran has helped her tap into the full capabilities of her innovation, as well as provide a clear path forward.”

Bhargava was matched with Alex Bajamonde, then a biostatistician at Genentech, who suggested she focus on developing the method for wider applications, including delivering therapies.

“The advice was illuminating,” Bhargava said. “Working with someone who has done this is much better than reinventing the wheel. We obviously needed help scaling it up.”

Based on consultant feedback, and supported by a $15,000 Pilot Award from the T1 Catalyst Program, she revised her proposal to test her method with other localized diseases, such as inflammatory bowel disease, one of her areas of expertise. She used it to send a proven bowel disease antibody that blocks inflammation directly to the affected part of the intestine. “We found a dramatic reduction in inflammation, and we think the side effects will be much less,” she said.

While her investigation is on stronger footing than before the consultation, Bhargava cautions that far more research is needed. With the support of new data, she’s now working to get a patent on her innovation.

In another indication that she’s on a promising path, Bhargava, and her collaborator, Peter Ohara, Ph.D., UCSF professor of anatomy, recently secured an additional $100,000 in funding from a private donor and the Painless Research Foundation.

CTSI is a member of the National Institutes of Health-funded Clinical and Translational Science Awards network. Under the banner of “Accelerating Research to Improve Health,” it provides a wide range of services for researchers, and promotes online collaboration and networking tools such as UCSF Profiles.

Janet Woodcock gives lecture at UCSF.

U.S. Food and Drug Administration (FDA) officials are being assailed by the citizenry they serve. Some attack them for slowing down or impeding drug approvals, while others accuse them of safety lapses.

According to FDA official Janet Woodcock, M.D., the agency is blamed — unfairly — for losing jobs and stifling innovation on one hand, and for letting too many unsafe drugs onto the market on the other. “I hear this every day from both sides,” Woodcock said during a lecture on the UC San Francisco Mission Bay campus on April 26.

Janet Woodcock, FDA, and Regis Kelly, QB3

Woodcock, director of the agency’s Center for Drug Evaluation and Research (CDER) — which is responsible for ensuring the availability of safe and effective drugs — said the FDA is not the cause of slow drug development.

The expense of shepherding drugs through clinical trials may be driving down investment in some quarters, Woodcock said. Meanwhile, instances of serious drug side effects coming to light only after drugs have reached the market have led to complaints about the agency’s alleged failures to safeguard the public.

Drug approval often comes at a high cost

Woodcock and her CDER staff oversee clinical trials and evaluate drugs before they can be sold by prescription or over the counter. They provide caregivers and patients with information for the safe use of drugs, and they target the illegal sale of drugs that are unapproved, contaminated or fraudulent.

“I don’t think you can say FDA review times are a barrier, although our standards may be difficult to meet,” Woodcock said. A significant number of new drugs continue to gain approval. “In 2011, the FDA approved 30 new molecular entities, and that’s more than we have seen in a while,” she said.

Still, ten drugs enter Phase I trials for every one that is approved, according to Woodcock. And to bring an innovative drug to market often requires a decade and a billion dollars of investment. Companies “cannot afford to invest that in research and development and get so few drugs out at the other end,” Woodcock said.

Some of the costs are driven by growing expectations in recent decades for the pre-marketing evaluation of drug performance, both for safety and efficacy, Woodcock said. “There has been a decreased tolerance of uncertainty,” she said — particularly evident beginning in the 1990s — and regulators have responded with additional testing requirements. Pharmaceutical companies have in many cases decided that costs associated with conducting studies to eliminate uncertainty are unfeasible, according to Woodcock.

Evaluating the effectiveness of drugs remains a “huge challenge,” she said. “You can’t predict if a drug is going to work or not,” she added, and half of drugs in Phase III clinical trials fail to prove effective. There is a need for better tools, techniques and strategies to identify winners, minimize costs and reduce failures during drug development, according to Woodcock.

Academic medical centers’ input sought

Woodcock outlined how academic medical centers can play a larger role in helping to meet today’s heightened expectations related to drug development and testing.

Many scientists at academic medical centers are experts in molecular biology, capable not only of discovering the nuts-and-bolts mechanisms of how diseases arise and progress, but also of identifying molecular targets for drug development within biochemical pathways that contribute to disease, Woodcock said. Academic scientists have developed many animal and in-vitro models for disease, in which drugs can be tested before human studies begin.

But university researchers also can make greater contributions to methods and technologies that can be used in pre-clinical studies and clinical trials, she said. For instance, academic scientists can develop biomarkers that may serve as indicators of early success or failure in clinical trials, or as a way to identify patients who may be the most likely to benefit from a new, targeted therapies.

In addition, academic scientists should be encouraged to conduct more applied as well as basic research, according to Woodcock. “We have all these great evaluation tools for reductionist science down at the molecular level, but there is a tremendous need for scholarly work on drug manufacturing and scale-up,” she said.

In some cases university scientists will be following through with drug development, rather than handing it off early to industry partners, according to Woodcock. Building on expertise related to identifying biochemical pathways that drive disease, proof of disease-fighting concepts, and how the body handles drugs, researchers at academic medical centers will increasingly take the lead in developing drugs to fight so-called “orphan” diseases that are not a priority for pharmaceutical companies, she said.

Clinical trials innovation

Woodcock added that physician-scientists at academic medical centers also are playing a driving role in developing and implementing new ways to conduct clinical trials, and she specifically cited the I-SPY breast-cancer clinical trials led by UCSF breast surgeon Laura Esserman, M.D., M.B.A. and colleagues. In I-SPY trials information on biomarkers gathered at earlier stages of a trial is used to more quickly identify patients who might be the most likely to benefit from specific therapies being tested.

An important goal in designing clinical trials ought to be to develop faster, smaller clinical studies to gain important information more quickly, Woodcock said.

Woodcock also envisions academic medical centers as hubs for new clinical-trials networks. These networks would have the capacity to incorporate sophisticated laboratory science into clinical trials and would include medical practices in surrounding communities and regions, so that patients would not need to travel far for promising experimental treatments, she said.

Many clinical trials fail to enroll an adequate number of patients, leading to drug-development failures. “Ninety-five percent of cancer patients are never asked to participant in a clinical trial,” Woodcock say. “Most patients are out in communities, not in the places where trials are being run.”

Woodcock previously served as the FDA’s deputy commissioner and chief medical officer. She also led CDER as director from 1994–2005. Prior to joining CDER, Woodcock oversaw approval of the first biotechnology-based treatments for multiple sclerosis and cystic fibrosis in her position as director of the Office of Therapeutics Research and Review in FDA’s Center for Biologics Evaluation and Research (CBER). Woodcock has held teaching appointments at Pennsylvania State University and at UCSF. She joined the FDA in 1986.

Study finds anti-smoking drug decreases alcohol consumption in heavy-drinking smokers.

Howard Fields and Jennifer Mitchell

The smoking cessation drug varenicline significantly reduced alcohol consumption in a group of heavy-drinking smokers, in a study carried out by researchers at the Ernest Gallo Clinic and Research Center at the University of California, San Francisco.

“Alcohol abuse is a huge problem, and this is a big step forward in identifying a potential new treatment,” said senior author Howard L. Fields, M.D., Ph.D., professor of neurology and director of the Wheeler Center for the Neurobiology of Addiction at UCSF.

The study was published on May 1 in the journal Psychopharmacology.

Study participants, who were seeking treatment for smoking and not for drinking, were randomly assigned to take either varenicline or a placebo. By the end of the study, participants assigned to varenicline had reduced their average number of drinks per week by 36 percent compared to those taking placebo.

The scientists found no correlation between the average number of drinks consumed per week by each subject and the average number of cigarettes they smoked, indicating that varenicline’s effects on drinking behavior were separate from its effects on smoking.

While they cautioned that additional study was needed to further examine potential side effects, the scientists said they are optimistic about the potential of varenicline as a treatment for heavy drinking. “The drug is already widely used by smokers to help them quit,” said Fields. “Many heavy drinkers also smoke, and this study indicated that, in this group, varenicline was effective in reducing both the number of cigarettes smoked and the number of drinks consumed.”

Interestingly, in the study, varenicline did not change the number of times per week that subjects drank, said lead author Jennifer Mitchell, PhD, clinical project director at the Gallo Center and an adjunct assistant professor of neurology at UCSF. “People initiated drinking at the same rate, but they drank less once they started,” she said. “If your usual pattern was to come home and have a few beers, you would still do that, but you might have one or two instead of four or five.”

A medication that reliably decreases alcohol consumption would be of immense value in reducing the harm caused by alcohol abuse, Mitchell said. “If you currently drink seven drinks a night, and we can turn that into two or three, then you’re not only drinking at a level that’s going to harm you less, you’re less likely to harm others, as well. If we could lower the rates of drunk driving, spousal and child abuse and other secondary effects of alcoholism, that would be tremendous.”

They noted that the study corroborates earlier Gallo Center research indicating that alcohol and nicotine act through a common pathway in regions of the brain that provide a sense of pleasure and reward. Varenicline acts as a smoking cessation aid by blocking the pleasant effects of nicotine in the brain.

Few unpleasant or serious side effects were reported, suggesting that the drug can be well tolerated, said Fields. However, the scientists cautioned that the absence of significant side effects might have occurred because subjects were rigorously screened for mental health disorders such as depression, anxiety and suicidal ideation, as well as alcoholism, before the study began. They recommended that the drug be tested for safety and effectiveness in populations with comorbid psychiatric conditions, as well as in treatment-seeking alcohol abusers who do not smoke.

Varenicline is marketed by Pfizer Inc. under the brand name Chantix. The company donated the drug for the study, but did not fund or participate in any part of the research. The scientists have no conflicts of interest with the company.

Co-authors are Candice H. Teague of the Gallo Center and Andrew S. Kayser, M.D., and Selena E. Bartlett, PhD, of the Gallo Center and UCSF.

The study was supported by funds from the National Institutes of Health and by funds provided by the State of California for medical research on alcohol and substance abuse through UCSF.

The UCSF-affiliated Ernest Gallo Clinic and Research Center is one of the world’s preeminent academic centers for the study of the biological basis of alcohol and substance use disorders. Gallo Center discoveries of potential molecular targets for the development of therapeutic medications are extended through preclinical and proof-of-concept clinical studies.

UCSF is a leading university dedicated to promoting health worldwide through advanced biomedical research, graduate-level education in the life sciences and health professions, and excellence in patient care.

Important new target for those diagnosing, treating and studying the disease.

(From left) Jitka Petrlova, Robin Altman, Izumi Maezawa, Lee-Way Jin and John Voss in the Alzheimer's disease research lab

UC Davis researchers have found novel compounds that disrupt the formation of amyloid, the clumps of protein in the brains of people with Alzheimer’s disease believed to be important in causing the disease’s characteristic mental decline. The so-called “spin-labeled fluorene compounds” are an important new target for researchers and physicians focused on diagnosing, treating and studying the disease.

The study, published today in the online journal PLoS ONE, is entitled “The influence of spin-labeled fluorene compounds on the assembly and toxicity of the Aβ peptide.”

“We have found these small molecules to have significant beneficial effects on cultured neurons, from protecting against toxic compounds that form in neurons to reducing inflammatory factors,” said John C. Voss, professor of biochemistry and molecular medicine at the UC Davis School of Medicine and the principal investigator of the study. “As a result, they have great potential as a therapeutic agent to prevent or delay injury in individuals in the earliest stages of Alzheimer’s disease, before significant damage to the brain occurs.”

Amyloid is an accumulation of proteins and peptides that are otherwise found naturally in the body. One component of amyloid — the amyloid beta (Aβ) peptide — is believed to be primarily responsible for destroying neurons in the brain. Fluorene compounds, which are small three-ringed molecules, originally were developed as imaging agents to detect amyloid with PET imaging. In addition to being excellent for detecting amyloid, fluorenes bind and destabilize Aβ peptide and thereby reduce amyloid formation, according to previous findings in mice by Lee-Way Jin, another study author and associate professor in the UC Davis MIND Institute and Department of Medical Pathology and Laboratory Medicine.

The current research studied the effects of fluorene compounds by attaching a special molecule to make their activity evident using electron paramagnetic resonance (EPR) spectroscopy. This technology allows researchers to observe very specific activities of molecules of interest because biological tissues do not emit signals detectable by EPR. Since Voss was interested in the activity of fluorenes, he added a nitroxide “spin label,” a chemical species with a unique signal that can be measured by EPR.

The group found that spin-labeled compounds disrupted Aβ peptide formation even more effectively than did non-labeled fluorenes. In addition, the antioxidant properties of the nitroxide, which scavenge reactive oxygen species known to damage neurons and increase inflammation, significantly contributed to the protective effects on neurons.

“The spin-labeled fluorenes demonstrated a number of extremely important qualities: They are excellent for detecting amyloid in imaging studies, they disrupt Aβ formation, and they reduce inflammation,” said Voss. “This makes them potentially useful in the areas of research, diagnostics and treatment of Alzheimer’s disease.”

Alzheimer’s disease is the most common form of dementia and affects some 5 million Americans. Current medications used to fight the disease usually have only small and temporary benefits, and commonly have many side effects.

A major obstacle in developing Alzheimer’s disease therapy is that most molecules will not cross the blood-brain barrier, so that potential treatments given orally or injected into the bloodstream cannot enter the brain where they are needed. Fluorene compounds are small molecules that have been shown to penetrate the brain well.

“We have brought together expertise from diverse fields to get to this point, and what was once a side interest has become a major focus,” said Voss. “We are very excited and hopeful that these unique compounds can become extremely important.”

Voss’ group next plans to study the safety of spin-labeled fluorene compounds as well as their efficacy for treating models of Alzheimer’s disease in small animals.

Other UC Davis study authors include Jitka Petrlova and Robin Altman, also of the Department of Biochemistry and Molecular Medicine; Izumi Maezawa and Seok Hong of the MIND Institute and the Department of Pathology and Laboratory Medicine; and Daniel A. Bricarello and Atul N. Parikh of the Department of Applied Science. Other authors are Tamás Kálai and Kálmán Hideg of the University of Pecs, Institute of Organic and Medicinal Chemistry in Hungary, and Ghimire Harishchandra and Gary A. Lorigan of the Department of Chemistry and Biochemistry at Miami University in Oxford, Ohio.

This work was funded by grants from the U.S. National Institutes of Health (R01 AG029246) and the Hungarian National Research Fund OTKA T81123.

UC Davis Health System is improving lives and transforming health care by providing excellent patient care, conducting groundbreaking research, fostering innovative, interprofessional education, and creating dynamic, productive partnerships with the community. The academic health system includes one of the country’s best medical schools, a 631-bed acute-care teaching hospital, an 800-member physician’s practice group and the new Betty Irene Moore School of Nursing. It is home to a National Cancer Institute-designated comprehensive cancer center, an international neurodevelopmental institute, a stem cell institute and a comprehensive children’s hospital. Other nationally prominent centers focus on advancing telemedicine, improving vascular care, eliminating health disparities and translating research findings into new treatments for patients. Together, they make UC Davis a hub of innovation that is transforming health for all. For more information, visit healthsystem.ucdavis.edu.

Hunt on at UC San Diego for drug candidates that block ring formation in neuron membranes.

This image shows a construction of a possible ring oligomer position in the cell membrane after four nanoseconds of molecular dynamics simulations.

University of California, San Diego, scientists have used powerful computational tools and laboratory tests to discover new support for a once-marginalized theory about the underlying cause of Parkinson’s disease.

The new results conflict with an older theory that insoluble intracellular fibrils called amyloids cause Parkinson’s disease and other neurodegenerative diseases. Instead, the new findings provide a step-by-step explanation of how a “protein-run-amok” aggregates within the membranes of neurons and punctures holes in them to cause the symptoms of Parkinson’s disease.

The discovery, published in the March issue of the FEBS Journal, describes how α-synuclein (a-syn), can turn against us, particularly as we age. Modeling results explain how α-syn monomers penetrate cell membranes, become coiled and aggregate in a matter of nanoseconds into dangerous ring structures that spell trouble for neurons.

“The main point is that we think we can create drugs to give us an anti-Parkinson’s effect by slowing the formation and growth of these ring structures,” said Igor Tsigelny, lead author of the study and a research scientist at the San Diego Supercomputer Center and Department of Neurosciences, both at UC San Diego.

Familial Parkinson’s disease is caused in many cases by a limited number of protein mutations. One of the most toxic is A53T. Tsigelny’s team showed that the mutant form of α-syn not only penetrates neuronal membranes faster than normal α-syn, but the mutant protein also accelerates ring formation.

“The most dangerous assault on the neurons of Parkinson’s patients appears to be the relatively small α-syn ring structures themselves,” said Tsigelny. “It was once heretical to suggest that these ring structures, rather than long fibrils found in neurons of people having Parkinson’s disease, were responsible for the symptoms of the disease; however, the ring theory is becoming more and more accepted for this neurodegenerative disease and others such as Alzheimer’s disease. Our results support this shift in thinking.”

The modeling results also are consistent with the electron microscopy images of neurons in Parkinson’s disease patients; the damaged neurons are riddled with ring structures.

Wasting no time, the modeling discoveries have spawned an intense hunt at UC San Diego for drug candidates that block ring formation in neuron membranes. The sophisticated modeling required involves a complex realm of science at the intersection of chemistry, physics and statistical probabilities. A kaleidoscope of interacting forces in this realm makes α-syn proteins bump and tremble like they’re in an earthquake, coil and uncoil, and join together in pairs or larger groups of inventive ballroom dancers.

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