An experimental antibiotic fights resistant bacteria

The work was part-funded by the Wellcome Trust’s Seeding Drug Discovery initiative and the US Defense Threat Reduction Agency, a sign of the growing importance of public–private partnerships in antibacterial discovery.

It is estimated that in 2007 about 25 000 people in the EU died as a result of infections caused by multi-drug-resistant bacteria. Also, infections due to antibiotic-resistant bacteria resulted in approximately 2.5 million extra hospital days at a cost of more than ¤900 m (European Centre for Disease Control and Prevention, 2009).

Topoisomerase inhibitors, called quinolones, are commonly used antibiotics with reported worldwide annual sales of $7.1 bn in 2009 (B Hamad, 2010). Quinolones have been used as antibiotics since the 1960s, but bacteria are developing resistance. The GSK researchers have shown that a new class of “novel bacterial topoisomerase inhibitors” (NBTIs) work via a mechanism that is distinct from the quinolones (B D Bax, 2010). Both the new NBTIs and the well established quinolones target bacterial type IIA topoisomerases, trapping the enzyme in complexes with DNA, but they do this in different ways (B D Bax, 2010 and A Wohlkonig, 2010). Stopping this enzyme and trapping it in a complex with DNA is highly lethal to bacteria and prevents them from reproducing.

Using the structural biology beamlines at the ESRF, the scientists could see how the new experimental compound, called GSK299423, latched on to the enzyme topoisomerase in a different place to quinolones, enabling it to stop the same bacteria that are resistant to the older treatment (B D Bax, 2010). The new compound targets a binding site that has not previously been characterised structurally or exploited by available drugs, giving a structural basis for the action of a new class of antibacterial agents against a well validated drug target.

GSK299423 was approximately 70 times more potent against the topoisomerase enzyme from Staphylococus aureus than another NBTI that progressed to human trials. “The structure was difficult to solve because the topoisomerase enzymes are inherently flexible, making it difficult to grow well ordered crystals. We had to make many different truncated forms of the enzyme, try many different DNA sequences and test hundreds of crystals in order to obtain a good high-resolution structure. However, when we had grown the ‘right crystal’, the high flux, low divergence and well collimated beams available at the ESRF made it relatively straightforward to collect a 2.1  Å dataset (on crystals that had a 93 × 93 × 410  Å cell, with one 170 kDa complex in the asymmetric unit),” explains Ben Bax, a member of the GSK team.

The new compound class is still at an early stage of drug development, and could become important for attacking antibiotic-resistant strains of bacteria, such as methicillin resistant Staphylococcus aureus (MRSA), and against Gram-negative bacteria like Escherichia coli, Pseudomonas, Klebsiella and Acinetobacter. An added problem arises with Gram-negative bacteria, as they have an outer membrane surrounding the bacterial cell wall, which interferes with drug penetration. New medicines must not only be toxic to the pathogen, but must first overcome the entry barriers that stop the bacterial cell being reached.

References
B D Bax et al. 2010 Nature 466 935–940.
European Centre for Disease Control and Prevention/European Medicines Agency Joint Working Group 2009 The bacterial challenge: time to react. B Hamad 2010 Nature Rev. Drug Discov. 9 675–676.
A Wohlkonig et al. 2010 Nature Struc. Mol. Biol. 17 1152–1153.

M Capellas

This article appeared in ESRFnews, December 2010. 

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Top image: DNA gyrase can cut DNA (blue/green) into two pieces and separate the cleaved DNA to allow passage of another DNA segment. The NBTI (yellow solid) inhibits this process – sitting half way between the two active sites (red spheres). (Credit: B. Bax.)