Bacterial Type I Signal Peptidases as Antibiotic Targets

Smitha Rao CV; Jozef Anné

Disclosures

Future Microbiol. 2011;6(11):1279-1296. 

In This Article

Future Perspective

The target-based HTS of SPase inhibitors has so far identified only two good hits, the 5S-penems (GlaxoSmithKline, Essex, UK) and lipoglycopeptides (Eli Lilly and Company, Indianapolis, USA). The penem-type inhibitor could not make it to a lead compound, but then this inhibitor has played a pivotal role in our understanding of the SPases as drug targets. The limited success of HTS has unveiled a number of issues with regard to the screening method, the compound library and the target itself used for screening for new antibiotics. These issues are discussed in greater detail later.

The most common assays for HTS of SPase inhibitors are the in vitro assays based on fluorescence resonance energy transfer. While these assays are rapid, sensitive and indispensible for mode-of-action studies, the drawbacks are the use of artificial or small-model substrates and incompatibility with some compounds that are autofluorescent or have quenching effects. Whole-cell assays are relatively time consuming but have the advantage of preselecting hits, based on their permeability across the bacterial cell envelope. A combination of a robust biochemical assay and a whole-cell assay that allows measurement of SPase activity in intact cells is needed to improve screening efficiency, thereby increasing the chances of success. Furthermore, other detection methods whose sensitivities and throughput have significantly improved over the years, such as NMR and surface-plasmon resonance (SPR) could be employed in complementation or for hit validation.

With regard to the quality of the compound library for screening, there is a now general awareness that the characteristics of antibiotics differ in important aspects from those of drugs in other therapeutic sectors. In particular, parenteral antibiotics do not follow the Lipinski's "rule of five".[73] Payne et al., based on GlaxoSmithKline's experience with HTS-campaigns, point out the importance of proper and sufficient molecular diversity of compounds for screening and the need to revamp libraries to better suit antibacterial targets.[8] Natural products, such as secondary metabolites from microbial sources, are attractive candidates due to their complex architecture that is tailored to inhibit antibacterial targets inside the cells, as also exemplified in the case of SPases by arylomycins and lipoglycopeptides. While natural products from easily culturable microorganisms are handy, newer natural products from micro-organisms surviving in extreme conditions are sought. On the other hand, synthetic molecules need not be excluded as these also have the potential to make it to successful antibiotics.

Given the extremely low hit rates in random screening of SPase inhibitors, the alternative or parallel routes include:

  • Fragment-based method, which involves screening fragments or scaffolds smaller in size (MW <250 Da) than the molecules that are typically found in high-throughput compound collections, followed by optimization of hits often using structure-guided medicinal chemistry (see review[74]);

  • Rational inhibitor design based on natural SPase substrates has already proved to be potent in vitro, but needs to be optimized for efficacy in vivo;

  • Virtual screening or structure-based inhibitor design using the template provided by the SPase co-structure with different inhibitors.

Although, the 3D structure is currently confined to E. coli LepB, when the structure of SPase from Gram-positive bacteria is available, it will significantly boost this line of work.

From the genomic through to the post-genomic era, SPases have been successfully evaluated as suitable targets in many bacterial pathogens and the future does hold some promise. SPases are broad-spectrum targets. Although drugs based on SPases have a long way to go, taking into account the time required for obtaining regulatory approval before they can make it to the clinic, they have a potential application in monotherapy as well as in combination therapy, as they do not only inhibit but also weaken several microbial defenses. Analogous to the current clinical use of clavulanic acid (a β-lactamase inhibitor) and amoxicillin (a β-lactam drug), drugs based on SPases could also be used in combination with other antibiotics. The potential of SPases as drug targets also remains to be explored in other important pathogens, such as M. tuberculosis.

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