The antibacterial lead discovery challengeA recent report provides a rare example of a potential new class of antibiotics. Dan Jones investigates the difficulties of finding such drugs.

Researchers at GlaxoSmithKline (GSK) recently described a novel class of antibacterial agents that target type IIA topoisomerases, an important group of targets in treating bacterial infections, through a new mechanism of action (Nature 466, 935–940; 2010). “This is a target that matters, and if you can hit it in a different way you can avoid current resistant mechanisms,” says Christopher Walsh, Professor of Biological Chemistry and Molecular Pharmacology at Harvard Medical School, Massachusetts, USA. “Developing new chemical classes for old targets is a great idea.”

Type IIA topoisomerases, such as DNA gyrase, cleave and re-join DNA, and are essential for bacterial cells to function. Although antibacterials that bind to and inhibit these topoisomerases — most notably the quinolones and the fluoroquinolone derivatives — have been in use since the 1960s, the development of resistance to these compounds has become an increasing problem, spurring the search for new classes of topoisomerase inhibitors.

The GSK team had previously identified such a class through whole-cell antibacterial screens of their chemical libraries, which led to GSK299423 — the focus of the new paper. GSK299423 is structurally distinct from the fluoroquinolones, it potently inhibits DNA gyrase in both Staphylococcus aureus and Escherichia coli, and it has antibacterial activity against a broad spectrum of Gram-positive and Gram-negative bacterial pathogens, including clinical isolates with fluoroquinolone resistance.

Crystallographic studies revealed that GSK299423 binds to a different site on DNA gyrase than fluoroquinolones and acts by a different mechanism. In addition, mutations that convert serine 83 to leucine in DNA gyrase, which are a common route to fluoroquinolone resistance, have no effect on GSK299423’s inhibitory activity. These mechanistic and structural insights may, in turn, lead to further novel antibacterials. “These structures provide us with a springboard to design other novel classes

against this target,” says David Payne, Vice President of GSK’s Antibacterial Drug Discovery Unit.

Leads like this are particularly welcome given what John Rex, Vice President and Head of Clinical Infection at AstraZeneca, calls a “quiet, but very real, crisis” in our capacity to treat bacterial infections. “We have very few good drug choices for some classes of pathogen,” he says. This brewing public health crisis has been driven by two key factors: the emergence of antibacterial resistance in important pathogenic species — a recent example being bacterial strains producing a metallo-β-lactamase that neutralizes carbapenems (Lancet Infect. Dis. 10, 597–602; 2010), an important class of antibiotics — and a downturn in the number of new antibacterial agents coming through company pipelines.

This shortage of new antibiotics, particularly those that could combat resistant bacteria, has been exacerbated by the exit of many companies from the field in the past decade owing to a range of scientific, commercial, development and regulatory challenges (Box 1). Indeed, at present, just five major pharmaceutical companies have active antibacterial discovery programmes: GSK, Novartis, AstraZeneca, Merck and Pfizer (Clin. Infect. Dis. 48, 1–12; 2009).

Historically, the main route to discovering new antibacterials has been to modify existing classes of drugs that inhibit validated bacterial targets and to conduct whole-cell screening to evaluate their antibacterial activity. The basic idea has been to retain the core scaffold of a chemical class and then to change the chemical groups attached to this scaffold — an approach that Walsh says has been productive for the past 70 years. “The virtue is that you already know that these molecules are active,” says Walsh. “You’re trying to retain this activity, and defeat the current generation of resistant microbes that have arisen from extensive use of antibiotics”.

Although this is still a path that a number of companies are taking, there are questions

about how many more generations of modified molecules can be squeezed out of the known scaffolds, and whether subsequent generations will offer diminishing improvements as they encounter the pre-existing resistance mechanisms.

The advent of genomics in the early 1990s also failed to herald in a new era of antibacterial discovery as hoped for, even though it did open up a new range of novel drug targets. Between 1995 and 2001, researchers at GSK evaluated more than 300 bacterial genes as potential targets, and identified more than 160 of them as essential to bacterial function (Nature Rev. Drug Discov. 6, 29–40; 2007). Yet screening chemical libraries against these targets produced very few leads, leading to disappointment with this approach.

“We’re not short of targets,” says Payne, so the issues lay elsewhere. One problem is that the genomics-derived targets have frequently been studied initially in isolated assays rather than in whole-cell screens, which throws up new challenges. For example, compounds active in an isolated assay may not have the properties needed to pass through the cytoplasmic membrane of Gram-positive bacteria — and an additional outer membrane in the case of Gram-negative species — to reach an intracellular target. “Targets by themselves don’t even begin to describe the complexity of what’s needed to get antimicrobial drugs to work,” says Barry Eisenstein, Senior Vice President for Scientific Affairs at Cubist Pharmaceuticals.

These difficulties have led to a return to whole-cell screens, because any compounds that show antibacterial activity must already have what it takes to hit their target, says Eisenstein. Another advantage of whole-cell screens, exploited by Cubist, is that bacteria can be engineered to carry the most common antibiotic-resistance genes, so that any leads that emerge from screening campaigns will not be susceptible to these resistance mechanisms.

However, Eisenstein acknowledges that, so far, this has not been a dramatic success either. The fundamental reason why these approaches have failed to deliver a bounty of new lead compounds is the nature of the chemical libraries that were used in the screens, says Rex. These often lacked the requisite diversity for finding promising antibacterial leads. Drugs developed for other therapeutic areas generally share a number of physicochemical properties related to oral bioavailability (for example, as highlighted by Lipinski’s ‘rule of

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five’), but antibacterials, says Rex, look very different: they are typically larger and have more polar surfaces. As such, standard libraries have not been the best starting point in screens for new antibacterials.

To tackle this problem, companies are developing libraries in which members are more like typical antibacterials. Another tool that is gaining popularity is fragment-based screening, in which small chemical ‘fragments’ that bind (usually weakly) to the target are identified using techniques such as X-ray crystallography and nuclear magnetic resonance (Nature Rev. Drug Discov. 6, 211–219; 2007). These are then optimized using structural information to build up a drug-like compound that has greater potency in inhibiting the target. “It’s an approach we’re finding to be productive,” says Rex, “and has led to the discovery of a new class called the pyrrolamides that bind to DNA gyrase in a way that’s different to the quinolones and different to the GSK molecule.”

Efforts are also underway to develop libraries based on novel chemistries. GSK, for example, has an alliance with Anacor Pharmaceuticals to develop antibacterial leads identified through Anacor’s boron chemistry platform. Such compounds, the companies say, confer molecules with certain drug-like properties, specifically geometries and reactivities that enhance their capacity to interact with biological targets. Earlier this year, Anacor and GSK reported proof-of-concept studies for GSK2251052 (formerly AN3365), a first-in-class antibacterial developed with the boron platform, which shows activity against a range of resistant bacterial species.

Attempts are also underway to breathe new life into old antibiotics by administering them with ‘potentiators’ that enhance their effects by blocking various bacterial defences — an approach that can also be coupled with new generations of old drug classes. GSK has partnered with Mpex

Pharmaceuticals to develop efflux-pump inhibitors to prevent bacteria pumping out the active antibacterial; AstraZeneca and Forest Pharmaceuticals are pursuing novel β-lactamase inhibitors to protect β-lactam drugs, which as a class include the cephalosporins and carbapenems; Cubist is also pursuing a similar potentiation strategy, coupling β-lactamase inhibitors with next-generation β-lactams.

Ideally, companies would like to find brand new chemical classes against novel targets, as that would reduce the likelihood of resistance emerging rapidly. “That’s the dream,” says Eisenstein, although the difficulty of the task might make other approaches more attractive. “The challenges of finding completely novel mechanisms is such that much industry effort still exploits existing antibacterial classes,” says Michael Gwynn, Director of GSK’s Antibacterial Discovery Performance Unit, who led the development of GSK299423.

And there is still life in well-known targets, says Gwynn: “A good target is better than a simply new target”. In fact, as GSK299423 binds to a new and different region of DNA gyrase compared with the quinolones, it could be said to hit a new ‘target’. In any case, the structural studies on the mechanism of action of GSK299423 open the door for new strategies to inhibit this important target, with AstraZeneca’s pyrrolamides offering a further potential avenue of attack.

Yet there is widespread concern that there is insufficient investment in — and public financial support for — getting new antibiotics to the market. “The fundamental challenge is that as a society we undervalue antibiotics,” says Rex. It might take something dramatic to make people take notice, says Walsh. “I’m worried that in the absence of some disaster, such as an epidemic of drug-resistant bacteria, people will go about ignoring the problem”.

Box 1 | Challenges beyond antibacterial lead discovery

The scientific challenges of identifying suitable lead compounds are not the only problems that companies face in the development of new antibacterial drugs. Once approved for use, antibiotics are usually prescribed as short-duration courses, and the emergence of resistance truncates their commercial life span, all of which can diminish return on investment. In addition to these concerns, a range of development and regulatory issues have turned companies away from the field.

“The clinical, regulatory and commercial issues surrounding the generation of new antibiotics have as much to do with the challenges of getting new antibiotics to the market as the biological aspects of discovery,” says Barry Eisenstein, Senior Vice President for Scientific Affairs at Cubist Pharmaceuticals. A recent survey confirms that this is a widely held view (Clin. Infect. Dis. 48, 1–12; 2009). Industry leaders reported concerns about the costs of carrying out the large studies that are required for regulatory approval, as well as uncertainty about the precise regulatory demands for getting new agents approved.

In addition, there are ongoing discussions between industry representatives and government agencies around the world about how antibacterial drug discovery and development can be made more commercially viable — whether that be through tax credits, granting enhanced patent protection or market exclusivity (similar to that afforded to orphan drugs), or the involvement of public–private partnerships. These themes were reiterated in calls for global action aired at an international meeting called “The Global Need for Effective Antibiotics — Moving Towards Concerted Action” hosted in September this year in Uppsala, Sweden, by ReAct (Action on Antibiotic Resistance).

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