Here Today Gone Tomorrow - Drug Discovery and Development

Cover Story

James Netterwald, PhD, MT (ASCP)
Senior Editor

Emerging pathogens are still a threat, but their lack of staying power has caused big drug companies to lose interest in combating them.

Ebola, anthrax, bubonic plague, MRSA—these words strike fear into the hearts of all of us. They are some of the deadliest diseases known to man, and some of the toughest diseases to treat, mainly because people who get them die quickly. These are emerging diseases—those that have either recently become known or have re-emerged as a result of antibiotic resistance or the threat of bioterrorism. But don’t take my word for it.

“There are two ways to think about emerging pathogens,”says Joseph Blondeau, PhD, head of clinical microbiology at Royal University Hospital, Saskatoon,

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Source: Tufts Center for the Study of Drug Development

Saskatchewan, Canada. One way is to look at the emergence of infectious microorganisms that had not previously been recognized as problems, he says. And a second way is to look at pathogens that have become a problem as a result of a number of conditions, including antibiotic resistance. It’s the latter kind that interests Blondeau.

Some of the pathogens Blondeau studies include methicillin-resistant Staphylococcus aureus (MRSA); penicillin- and multidrug-resistant Streptococcus pneumoniae; and Pseudomonas aeruginosa. Although Blondeau is not developing drugs against these bugs, his lab does test a lot of drugs already developed by pharma.

One of the tests he has set up is an in vitro system for assessing the likelihood that a pathogen will become resistant to a certain antibiotic. Specifically, the system determines the mutant prevention concentration—the threshold of a drug necessary to inhibit the growth of the most resistant organism present in a high-density population. This new technology is being groomed

Signature biodefense
Government labs, such as the Lawrence Livermore National Laboratory (LLNL) in Livermore, Calif., are also working on the biodefense bugs present on all of the threat lists, including Bacillus anthracis (the causative agent of anthrax) and Yersenia pestis (the causative agent of bubonic plague). “Our main focus is in designing diagnostic signatures,”says Tom Slezak, associate program leader for informatics and assays of the Chembio National Security Program at the LLNL. “We’re looking to see if environmental samples—and for us, it’s primarily air samples—contain biothreat agents. “The system of detection, which started development in 2000, is based on computational techniques to predict the regions of a pathogen’s genome that appear to be conserved among the known sequenced strains of the bug, but are unique when compared with other species.

This is a large computational task, to say the least, considering that the B. anthracis genome is five million bases long, and the bug exists in at least one dozen strains. “What we have here at Livermore are very efficient ways of eliminating regions of the genome that are not good to mine from for unique signatures,”says Slezak. Once the not-so-useful sequences are eliminated, Slezak can then build candidate signatures from the remaining sequences. Candidate signatures yielded by in silico analyses are subjected to rigorous wet-lab testing against a panel of over 2,000 backgrounds, including air samples from around the country, soil samples, and human DNA to check them for cross-reactivity. They also test each signature against as many of the target organisms’ near neighbors as possible to further ensure its specificity.

The ultimate customer of these signatures is the US Centers for Disease Control, Atlanta, Ga., who put them through rigorous testing of their own. By the end of this process, the signatures are very specific, very sensitive, and in the words of Tom Slezak: “ready to be pushed out into the world for use.”

to improve antibiotic-susceptibility testing in clinical labs. Current assays focus on testing the susceptibility of a bacterial inoculum of 1 x 10⁵ cells. “This number may not reflect what actually happens in bacterial populations present in infections, where the number of organisms might be 10¹⁰,”says Blondeau.

He will also be investigating how bacteria develop drug resistance, in the hopes of developing new antibiotics. “Most of the intracellular targets for antibiotics are known, but there may be some novel targets,”he says. “In the absence of novel targets, we may have to realize that the antibiotic era as we know it could be ending. And that is a scary prospect.”

But are drug companies concerned about developing new antimicrobials?

In and out
In 2003, Wyeth Research terminated all of its drug-discovery efforts for antimicrobials, says Steve Projans, PhD, vice president of biological technologies, Wyeth Research, Cambridge, Mass. “We are making a very heavy investment in vaccine development, antibacterial development, and antiviral agents, but what we are not doing much of is trying to discover new vaccines, antibacterials, and antivirals.”He concludes by saying that there are already good drugs on the market for bacterial infection, and that if it weren’t for resistance, there would be no need to develop any more.

So Wyeth is out of the front end (discovery) but in the back end (development). Is this a trend in the industry? “Actually, what is pretty much common now is to be out of the front and the back end—out of discovery and development [of antimicrobials],”says Projans. And there are many reasons for this trend, he says. Wyeth Research felt a degree of futility prior to closing down their antimicrobials program. “We have not really discovered any great new [antimicrobial] drugs to put into development.”And this is a major reason many companies shut their antimicrobial programs down, he says.

Another reason, according to Projans, is that after antimicrobials are discovered, they are much more difficult than other types of therapeutics to develop. And this, he says, is due to the fact that the regulatory hurdles for bringing these drugs to market keep getting “higher and higher.”The hurdles are so high that drugs approved 20 years ago would not be approved under the current US Food and Drug Administration regulations.

More than regulation
There is more to the story than just regulatory hurdles and feelings of futility. And there are some companies working on new antimicrobials; one of them is SRI, Menlo Park, Calif. SRI is an independent research and development (R&D) company contracted by businesses and government agencies to do R&D. Jon Mirsalis, PhD, DABT, director of preclinical development, Biosciences Division at SRI, says that the company has a long history of developing drugs for infectious diseases. “Halofantrine for malaria was discovered by SRI in the 1970s, and AraA, an antiviral, is also an SRI drug,”he says.

But much of the current infectious disease work by SRI is for the National Institutes of Health (NIH) because “infectious disease is not an area that big pharma is diving into right now because there is not much money in it.”The problem, according to Mirsalis, is that the major infectious diseases such as malaria and schistosomiasis only affect people in developing countries, who generally cannot afford to buy the therapeutic pharmaceuticals they need. And although big pharma has reluctantly worked with these countries, the pressure to make a profit there is still an issue.

Hard-to-reach targets
Drug targets for antimicrobials are tough to find, especially when they are hard-to-isolate proteins. One researcher working on finding new drug targets in emerging pathogens is Peter Henderson, BSc, PhD, professor of biochemistry and molecular biology at the Institute for Membranes and Systems Biology, University of Leeds, Leeds, UK. Henderson does not study the organism directly. Rather, he uses polymerase chain reaction (PCR) to amplify genes encoding membrane-transport proteins. Some of these proteins regulate the efflux of antibiotics, which produce drug resistance.

The genes come from the big emerging pathogens, some of which are biological weapons; they include Helicobacter pylori, Brucella mellitensis, Haemophilus influenzae, Pseudomonas aeruginosa, and Bacillus cereus. Working with these bugs is dangerous and therefore requires high biosafety level facilities. To get around this safety issue, he clones the genes and then expresses them in a benign lab bug, Escherichia coli. The proteins are then purified and put through crystallization trials, with the ultimate aim of determining their three-dimensional structure.

“Membrane [transport] proteins are very difficult to work with for several reasons,”says Henderson. The first reason: they make up less than 0.01% of the total proteome. Consequently, the only way to get enough of this protein for experimentation is to clone its gene and then overexpress the protein. A second reason is that their inherent hydrophobicity makes it difficult to solubilize the active protein intact. Detergents are used to extract the protein from the membrane. But finding the right detergent and concentration of detergent to extract the protein without denaturing it is the biggest challenge of all.

“With the 3D structure, there’s the possibility of rational design of new inhibitors that could be used as antibacterials against the original organism,”says Henderson. “The drugs themselves would be the hit and lead compounds that turned out to inhibit the activity of the membrane transport proteins.”At the moment, Henderson has 23 of these proteins purified and a number of them are going into crystallization trials. And that’s a good start.

There are some exceptions of emerging disease that big pharma and large biotech companies in the United States still care about, with MRSA and human immunodeficiency virus type 1 (HIV-1) being just a few examples. Companies care because there are still very sizable markets for these diseases in the US and Europe, where they count on making most of their profits. “The market for potential HIV vaccines is very healthy, but look at Chiron and the flu vaccine and how the bad press they got outweighed the money they made on the vaccine,”says Mirsalis. “If I were a ruthless shareholder in a pharma company, I would say ‘don’t waste your precious R&D on doing infectious disease research. Put it into cholesterol-lowering, diabetes, obesity, schizophrenia, erectile dysfunction, and GERD’ —you know, diseases of rich people.”

If the risk of losing money from developing an unprofitable drug were taken away, would bail-out drug companies consider coming back into the game? Probably not, and that’s where contract R&D companies like SRI and small biotech companies come into the picture. Most of these companies put the work in to discover and develop the drugs that they later sell or license to big pharma and big biotech.

“If we take all of the risk out, if we got the drugs through clinical trials, and solved all of the manufacturing problems, big pharma would be happy to make it and sell it for us,”says Mirsalis. And that’s the model some biotech companies are using right now to develop drugs against biodefense bugs using government funds. Their hope is to get the drugs through phase I clinical trials and then sell it to a Merck or Pfizer, he says.

Emerging pathogens: too flaky?
Obviously, the fact that big pharma and big biotech have jumped ship when it comes to antimicrobial drug discovery is not news. In fact, there are people in academia keeping track of such trends. “I don’t actually work with emerging pathogens. I keep track of what the companies are producing in terms of therapeutics; anti-infectives are a very small part of what I do,”says Janice Reichert, PhD, senior research fellow at the Tufts Center for the Study of Drug Development, Tufts University, Medford, Mass. Databases at the center track the number of ongoing clinical trials, the amount of development time, and time to approval for a given drug, even the fast-track status or orphan designation for a drug (see table).

In her job, Reichert notices all of the trends. “There was a flurry of activity when the government gave the allure of potential bioterrorism defense money,”she says. This did not come to fruition because working with the government was difficult, she says, “because they did not promise to buy anything the biotech companies were contracted to create for them.”Without a promise of an eventual purchase, companies felt they would have to sink a decade or more of work into developing anti-biodefense agents and not make any money from it, so nothing happened.

Drug discovery for some non-biodefense pathogens has also fallen by the wayside. “There is a big uproar over [these pathogens], then they fade away. A good example of this is SARS. It was big deal for a while, but then started to recede,”says Reichert. And the biotech sector is paying little attention to this bug because it’s not an issue at the moment. Reichert added this about the biotech sector: “When you’ve got an R&D timeframe of a decade, you can’t decide to work on a new anti-infective and then say ‘this pathogen has gone away, and, therefore, there is no need for the drug.’”In contrast, diseases like cancer have greater staying power, and, therefore, companies have more incentive to develop drugs against them. And of course, drug companies have their perennial favorite bugs. Pathogens like HIV-1, hepatitis B virus, and MRSA have a stable market and, thus, provide greater incentive for big pharma and small biotech companies alike to develop new anti-infectives. But of course, they won’t be the ones doing the work.

This article was published in Drug Discovery & Development magazine: Vol. 10, No. 5, May, 2007, pp. 22-25.