Inside Job

“Infectious disease is a kind of natural mortar, binding one creature to another, one species to another, within the elaborate biophysical edifices we call ecosystems.” — David Quammen, Spillover: Animal Infections and the Next Human Pandemic

Carnivores eat their prey from the outside, author David Quammen writes in his 2012 book Spillover. Pathogens attack from within and are no less deadly. They enter our bodies unseen when we breathe, have sex, take a drink of water or just walk in the woods.

And they are relentlessly opportunistic. Pathogens that cause about six out of 10 human diseases — including AIDS, influenza, cholera, malaria, tuberculosis and Ebola — infect animals such as birds, bats, cattle, monkeys, camels and other species. These microbes bring humans and animals together in a deadly exchange driven in part by shifting environmental conditions. Through a global initiative known as One Health, veterinary and human health organizations are coordinating research and sharing results. They are tracking pathogens wherever they go.

Researchers at Oregon State University take a multipronged approach to these diseases. They are delving into the social and historical dimensions of disease transmission and medical science. In the face of growing resistance to antibiotics, they are developing new drugs, including antivirals. They are helping public-health agencies get the most from vaccination campaigns and efforts to combat outbreaks.

While the nearly complete eradication of smallpox, polio and other diseases stands as a triumph of medicine and science, new threats are emerging. For example, climate change raises the possibility that malaria, eradicated in the United States in the early 1950s, could come back. And as the footprint of human development expands, pathogens such as the bacteria that cause Lyme disease proliferate along with their preferred host, the blacklegged tick.

“It’s a race that humans cannot win,” says Luiz Bermudez, Oregon State professor of Veterinary Medicine. “Microbes grow too fast. They modify too fast. There are billions of them.” Our best chance, he says, is to disarm them without promoting resistance.

Customized Medicine

As Patrick Iversen tells it, the push for a new Ebola drug got started with a kick from a laboratory mouse. On a Friday in 2004, the senior vice president for research at AVI BioPharma (now Sarepta Therapeutics) was having lunch with Alan Timmins, AVI’s president, when Iversen received a call from a colleague at the U.S. Army Medical Research Institute for Infectious Diseases (USAMRIID) in Maryland. A lab worker was injecting Ebola into a mouse when the animal kicked and sent the virus-filled needle into the researcher’s double-gloved hand.

Iversen, now a research professor at Oregon State University, had just returned from USAMRIID. He had talked up AVI’s success in treating two deadly viral infections: West Nile in penguins at the Milwaukee Zoo and feline calicivirus in Eugene and Atlanta.

“‘It takes only one particle (of Ebola virus) for this woman to be killed,’” Iversen says the caller told him. “‘We’re going to try everything. What can you do?’”

Iversen turned to Timmins. “I asked him, ‘What do you think? Is this something we can try?’ He made the decision immediately. ‘Yeah, let’s do it,’” Iversen recalls.

“The whole company became Ebola for the weekend in 24-hour shifts,” he explains. “We had designed the compound by 2:30 or 3 and (sent it) over to the chemistry group by 4. They started assembling their reagents, and that evening they were synthesizing it. On Monday we got authorization (from the U.S. Food and Drug Administration) that we could use this in the patient.”

Ultimately, the lab worker didn’t test positive for Ebola, so doctors didn’t administer the drug. However, the three days in which scientists created the compound — in contrast to the decade or more it normally takes to develop a new pharmaceutical — shows the power of a biomedical technology that owes much to Corvallis-area scientists.

AVI Biopharma emerged from another company, Antivirals, which was founded to develop technology created by OSU professors Jim Summerton and Dwight Weller. Today Summerton runs Gene Tools LLC in Philomath, which also grew out of Antivirals.

At the heart of these efforts are advances in the ability to probe the genes and proteins that make infectious agents such as Ebola, influenza, HIV, tuberculosis and malaria so deadly. By knowing how bacteria and viruses replicate, navigate through the human body and enter a cell, researchers are learning to outsmart and disarm the invaders.

Tuberculosis and malaria kill more than 2 million people a year, mostly in low-income countries. Although death rates have been falling for decades, progress is slowing. Front-line antibiotics are losing their effectiveness. According to the World Health Organization, about 500,000 cases of multidrug resistant TB were reported in 2013. Resistance to antimalarial drugs has been growing since the 1970s.

These trends worry Taifo Mahmud, a medicinal chemist in the Oregon State College of Pharmacy. The son of an Indonesian doctor who treated people with TB and malaria, Mahmud is developing new drugs by turning to the bacteria that produce them. Since they are made in nature, such compounds are known as “natural products.” In his lab, colorful microbial colonies produce the compounds that he pits against TB and malaria pathogens.

To find a new malaria treatment, Mahmud is focusing on pactamycin, a powerful broad-spectrum antibiotic that is so toxic to human cells that it is unfit for medical use. In search of a way to modify pactamycin, Mahmud deleted genes from the bacteria that make the compound. He has shown that, in cell culture, the altered form of the drug retains its potency against the malarial parasite but is about 30 times less toxic to human cells. Additional tests are underway.

For tuberculosis, Mahmud turns to rifampin, a TB drug-of-choice since the 1960s. By throwing a switch in its genes, Mycobacterium tuberculosis, the pathogen that causes the disease, has learned to shrug off rifampin like a bad joke. So Mahmud and his team have re-engineered the bacteria that make the compound, essentially giving it a new punch line. In cell culture experiments, they found that the new drug kills resistant TB bacteria. The M.J. Murdock Charitable Trust and the Medical Research Foundation of Oregon provided funding.

Worldwide Killers

A new tuberculosis treatment is also under study in Luiz Bermudez’s lab in the College of Veterinary Medicine. With support from the National Institutes of Health, he has confirmed that a compound never before used as an antibiotic kills M. tuberculosis cells. However, in what could be a setback, he also found that it triggers resistance and enables some bacteria to survive.

Bermudez and his team have identified an enzyme that plays a key role in this process. In cell cultures, they administer the drug together with an enzyme inhibitor. As a result, they have cut the time it takes to kill TB cells from six days to two. Since treating TB now takes as long as six months, faster recovery could cut costs and curtail the development of resistance to new drugs.

Dead Giveaway

Even among resistant microbes, Neisseria gonorrhoeae is a star. It has thwarted a host of antibiotics including sulfas, penicillin, tetracycline and fluoroquinolones. About 106 million new cases of this sexually transmitted disease are reported around the globe every year, and it is the second most commonly reported infectious disease in the United States. For treatment, only compounds known as cephalosporins are still effective, but their days are numbered. Bacterial strains resistant to these antimicrobials are beginning to appear.

Among the consequences of infection are pelvic inflammatory disease, ectopic pregnancy and infertility. Furthermore, repeated infection facilitates the acquisition and spread of HIV.

In her lab in the College of Pharmacy, Aleksandra Sikora is looking for new ways to outwit N. gonorrhoeae. “Unfortunately, no gonorrhea vaccine exists and surprisingly little work has been done to develop such a vaccine,” Sikora says.

Sikora’s group is the first to use the science of proteomics — the comprehensive analysis of protein composition and structure — to identify potential targets for gonorrhea vaccines. In the journal Molecular and Cellular Proteomics, Sikora and colleagues at Seattle’s Fred Hutchinson Cancer Research Center reported the discovery of novel proteins in the bacterial cell envelope and in the naturally released vesicles — small pouches within the cells.

Sikora also collaborates with Ann Jerse, a professor at the Uniformed Services University in Bethesda, Maryland, who has developed a mouse genital tract infection model for testing candidate vaccines.

Spoils of War

In 2003, when a multidrug-resistant pathogen started showing up in U.S. troops wounded in Iraq, it was nicknamed “Iraqibacter.” Its scientific name — Acinetobacter baumanii — doesn’t exactly roll off the tongue.

Soldiers were coming down with hard-to-treat infections in field hospitals. Major facilities such as the Walter Reed National Military Medical Center in Washington, D.C., weren’t spared. In 2009, the Public Broadcasting Service (PBS) reported that A. baumanii infections affected as many as 20 percent of all wounded soldiers in military hospitals. Health authorities referred to Iraqibacter as a “superbug.”

So when Oregon State microbiologist Bruce Geller was considering a practical target for a new approach to pathogen control, this one seemed like a good choice. Geller had been collaborating with Patrick Iversen and other researchers at AVI Biopharma on a gene-based treatment for bacterial diseases. Working with E. coli as a model organism, the researchers succeeded in delivering a synthetic compound known as a “Morpholino oligomer” — a string of genetic building blocks designed to bind to specific sequences of mRNA, a major component of cells — into E. coli and killing them. Morpholinos work by blocking the expression of genes that are necessary for microbes to survive.

Experiments with Acinetobacter infected mice show promise. In 2013, Geller and co-authors at Sarepta Therapeutics and the University of Texas reported in The Journal of Infectious Diseases that treatment with a Morpholino tailored to Acinetobacter genes increased the survival of infected mice. Moreover, as doses were raised, symptoms of inflammation decreased and survival rates grew accordingly.

A significant challenge, says Geller, was finding a way to deliver Morpholinos into the cell. As antibiotic molecules go, Morpholinos are large. Hong Moulton, director of drug delivery research and development at AVI, solved that problem by attaching the compound to a smaller molecule known as a peptide. She designed peptides that were able to burrow through the cell wall, dragging the Morpholino along with them.

Now a senior research associate professor in the College of Veterinary Medicine, Moulton continues to investigate methods for delivering these gene-based drugs where they can do the most good. An important benefit of this technology, she adds, is that it can respond quickly to mutations that render pathogens resistant to antibiotics. “With Morpholinos, we can quickly sequence the DNA, design a compound to accommodate the mutation, make the compound and put the right delivery component on it in about three weeks,” she told Lyn Smith-Gloria, a publicist in the college.

Success with Acinetobacter was followed by another milestone in 2014. Iversen and his colleagues at Sarepta Therapeutics reported in the journal Antimicrobial Agents and Chemotherapy that Morpholinos customized to Ebola genes protected laboratory monkeys against the disease.

The future of molecular medicine is bright, says Geller. “It’s expanding exponentially with the sequencing of the human genome. And now over 5,000 bacterial genomes have been sequenced. The data that is available is enormous, and we’re only now learning what to do with that information.”