Wrangling with resistance

September 2018

Early in his career at McMaster University Medical Centre in Hamilton, Ont., while on his way to the cafeteria for coffee, Justin Nodwell regularly walked past the unit for premature babies, watching as jaundiced infants were wheeled into the sunlight for phototherapy treatment. The route also took him past the paediatric oncology unit, filled with the threat of young lives being cut all too short. The sight of all those ill children nurtured within him a fundamental desire, to “do something that had the potential to lead to cures for things.”

 Justin Nodwell

Justin Nodwell, chair, Department of Biochemistry, University of Toronto. Photo credit: Justin Nodwell

As he advanced from researcher to chair of the Department of Biochemistry at the University of Toronto, that “something” turned out to be the search for solutions to the growing menace of antimicrobial resistance (AMR). Before antibiotics like penicillin and streptomycin entered the public-health arena in the 20th century, more than 30% of all deaths occurred among children under five, most of them stricken down by bacterial diseases like pneumonia, tuberculosis, diarrhea, enteritis, and diphtheria, according to the Centers for Disease Control and Prevention in the United States. Thanks in part to improved hygiene — but especially because of antibiotic research that blossomed in the 1950s and 1960s — that grim statistic tumbled to 1.4% by the end of the 20th century. 

But the bacteria that cause these diseases never went away, and they are slowly but surely adapting to the chemical arsenal we use to keep them in check. According to Nodwell, it’s not an exaggeration to say that the world is on the cusp of a post-antibiotic era. While deaths from antibiotic resistant bacteria still lag behind other major killers such as cancer and heart disease, the prevalence of AMR pathogens is increasing in a way that he calls “really worrisome.”

This past spring, Jim O’Neill, a British economist and former chairman of Goldman Sachs Asset Management, released a book he co-wrote, Superbugs: an Arms Race Against Bacteria, which outlines the global policies needed to fight AMR. O’Neill pointed to the enormity of the crisis, predicting that 10 million people around the globe could die yearly by 2050, costing the world economy upwards of $100 trillion in lost productivity.

The struggle is rooted in evolution itself, with bacteria hardwired by hundreds of millions of years of adaptation to defend themselves from other bacteria trying to wipe them out. Our ongoing challenge is the search for new drugs to fight bacteria that are developing or have already developed resistance, such as Mycobacterium tuberculosis, which infects two billion people and kills 1.7 million every year, according to the World Health Organization.

Back to basics

The overwhelming importance of AMR demands cooperation between academia, government, and Big Pharma, says Nodwell. The government should be responsible for funding basic research, allowing academic labs to undertake research that is too risky for a pharmaceutical company to do.

“If we discover something new, we’re relatively happy,” he explains. “If pharma spends three years studying something and it doesn’t turn into a drug, that’s a disappointment for them.”

And an expensive one at that: multinational drug firms can spend between $1 billion and $2 billion to bring a new medication to market. In contrast, Nodwell’s search for antimicrobial agents focuses on new molecules that can either kill bacterial cells or inhibit their ability to grow and reproduce.

“We’re going full tilt trying to find antimicrobials at the moment,” he says, referring to his 13-person team that focuses on Streptomyces. These filamentous bacteria are the largest antibiotic-producing genus, having generated such workhorse drugs as tetracycline and vancomycin in the mid-20th century. Unfortunately, there have been few additions to the list since then, as today’s investigators try to keep pace with AMR mainly by making new versions of old drugs like penicillin.

Nodwell maintains that Streptomyces still holds enormous promise, since these bacteria produce significant numbers of molecules known as secondary metabolites. Many of these are cryptic, which means they are only expressed under certain conditions that can be hard to replicate in a lab. Such molecules used to be discarded during the course of discovery because they were too difficult to synthesize or purify to the levels needed for drug formulations. Now, he observes, “we don’t have that luxury anymore.”

Streptomyces already has a track record of success when it comes to re-examining these cryptic secondary metabolites. The antibiotic daptomycin, produced from the microorganism Streptomyces roseosporus, was developed in the late 1980s to fight Staphylococcus aureus infections. Adverse side effects derailed the drug’s clinical trial results, but in 1997 a company called Cubist Pharmaceuticals eliminated the problem with an innovative new method for administering this agent. That accomplishment represented the only completely new class of antibiotic to be put on the market in the past two decades.

Finding the next daptomycin is not expected to be easy, says Nodwell. “The low-hanging fruit of secondary metabolism has been discovered and so we’re trying to go further up the tree and discover new ways to find the interesting apples.”

His group has found ways to selectively turn on secondary metabolic genes. One strategy is to use a collection of molecules called “elicitors”, synthetic compounds that trigger the expression of cryptic secondary metabolites. Streptomyces strains grown either in the presence or absence of these elicitors appear to activate different biochemical mechanisms, leading to what Nodwell calls “weirder, stranger and more exotic sources of molecules.” So far, the team has found more than half a dozen new compounds that he dubs “of pretty significant interest”.

Moreover, the elicitors themselves can sometimes yield new antibiotic strategies. Streptomyces, while not pathogenic itself, uses the same reproductive mechanisms as many pathogenic bacteria. Nodwell and his team have found molecules that can prevent sporulation, the development of dormant forms that enable bacteria to survive hostile conditions. This same strategy could head off such resistance in Staphylococcus aureus, a prospect that was raised when these findings were recently accepted for publication in ACS Chemical Biology. He also points to new chemical inhibition strategies that have been identified, including what he tantalizingly calls “the first true novel antibiotic” in decades, which he declines to reveal pending publication of these results later this year.

Emphasizing enzymes and elegant, efficacious RiPPs

Nodwell isn’t the only researcher looking into unique approaches to AMR mitigation.

Christopher Thibodeaux, an assistant professor in McGill University’s Department of Chemistry, is addressing AMR from an entirely different perspective — enzymes that are involved in natural product biosynthesis. What makes such products reactive — and possibly good antibiotics — are unusual chemical functional groups, which have become the targets for Thibodeaux and his McGill team of about half a dozen graduate and undergraduate students. They are seeking antibiotics in some entirely new molecules, rather than relying upon existing compound libraries, which have given up virtually all their secrets.

Christopher Thibodeaux, assistant professor, Department of Chemistry, McGill University

Christopher Thibodeaux, assistant professor, Department of Chemistry, McGill University. Photo credit: Christopher Thibodeaux

Part of their work focuses on genome sequencing in bacteria to find unique gene clusters that look like they might behave in an unusual manner. These are then characterized to determine whether or not they might act as antibiotics. Genes that are needed to make antibiotics are often clustered together; depending on their setting in the genome, these clusters can be identified as making something that is toxic. Thibodeaux then looks for similarities between such genes and those known to make antibiotics. It may not be as daunting as finding a needle in a haystack, but he acknowledges the process to be a “cat-and-mouse game”.

Thibodeaux has zeroed in on a family of molecules called ribosomally synthesized and post-translationally modified peptides (RiPPs). These functionally diverse molecules include some that are already well known, such as nisin, a potent antibiotic made by lactic acid bacteria that was first isolated in the 1930s and has been used to prevent spoilage in dairy products since the 1960s.

For Thibodeaux, what makes RiPPs elegant is that unlike many other types of biomolecules, their structure can be fairly well predicted from the genes that encode them. This means they can be hunted down by analyzing genome data, which today is relatively inexpensive to obtain. Once they find the precursor peptide that will become the antibiotic, they can easily synthesize it, analyze it, and test its effectiveness as an antibiotic.

“The key biosynthetic features that many of these RiPP enzymes have are that they’re multifunctional, with very relaxed substrate specificity,” says Thibodeaux. That offers to employ these enzymes to build structures not found in nature, which could give these researchers an edge in the evolutionary arms race with pathogenic bacteria.

Battling bacterial biofilms

Another main area of research for Thibodeaux is the study of bacterial biofilms. These extracellular excretions form a protective barrier around organisms such as Clostridium difficile, which can cause fatal infections in hospitals, Pseudomonas aeruginosa, which affects the lungs of those with cystic fibrosis, and Helicobacter pylori, which contribute to certain gastric cancers. If such biofilms can be disrupted, antibiotics stand a better chance of getting to their target.

The tendency of biofilms to form within an organism has been linked to the presence of a key biomolecule, cyclic di-GMP. Using mass spectrometry, Thibodeaux’s group is studying how certain protein complexes undergo large structural transitions when they bind to cyclic di-GMP and then participate in signaling networks that help to establish the biofilm. Although this work is in its early stages, it is exploring the possibility of disrupting biofilm formation by perturbing the protein/protein interactions within these signaling complexes.

With the spectre of widespread AMR becoming ever more dire, public health concerns are exacerbated by the idea that breakthroughs — large or small — will take years. But Thibodeaux points out that even if a raft of new drugs were to be discovered, the natural phenomenon of adaptation and evolution will eventually take its toll on these products too.

“This problem is not going to go away,” he concludes. “Even if we come up with new drugs, it’s just a matter of time before they are ineffective, so we’re going to have to continuously replenish that pipeline.”