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  • Review Article
  • Published:

Bacterial proteolytic complexes as therapeutic targets

Nature Reviews Drug Discovery volume 11, pages 777–789 (2012)Cite this article

Subjects

Key Points

  • Bacteria encode a conserved set of proteolytic complexes: Clp, FtsH, Lon, HslUV, high-temperature requirement A serine protease (HtrA) and the prokaryotic proteasome.

  • These enzymes consist of two major components: a recognition element that recognizes particular proteins to facilitate targeted protein turnover, and a compartmentalized degradative chamber that ensures efficient and complete destruction of proteins delivered by the recognition elements.

  • The bacterial proteolytic complexes are crucially required for normal bacterial growth and virulence in numerous pathogenic bacterial species, thus highlighting their potential therapeutic relevance.

  • The enzymes were initially identified to have important roles in regulating protein quality control through the degradation of misfolded, mislocalized or aberrant protein products.

  • We now know that they also coordinate several important cell processes through the targeted degradation of key regulator and effector proteins. Their biological significance has been extensively studied. Some of the key areas of bacterial physiology they are involved in include the regulation of stress responses, cellular replication and division, and virulence.

  • No clinically available antibiotics currently target the protease complexes in bacteria. With the development of bortezomib, the inhibitor of the human proteasome, many tools currently exist to facilitate a targeted development of bacterial protease modulators.

  • The Clp protease represents the most validated therapeutic target among the bacterial complexes, with specific small molecules recently developed that either inhibit or activate the enzyme and result in abrogation of virulence or cell death, respectively.

  • Key differences in the structure of the human proteasome and the proteasome of Mycobacterium tuberculosis (the causative agent of tuberculosis) have been exploited to yield a small molecule that specifically targets the prokaryotic homologue of the enzyme.

  • Inhibition of HtrA protease has been utilized to inhibit the growth of Helicobacter pylori in the context of infection. Inhibition of bacterial HtrA is also specific and does not interfere with host HTRA function.

  • Drug discovery efforts utilizing the bacterial proteolytic complexes remain in their infancy, but the tools that exist for protease-based drug discovery and the critical role that these enzymes have in bacterial physiology mandate a more concerted exploration of their therapeutic potential.

Abstract

Proteases have been successfully targeted for the treatment of several diseases, including hypertension, type 2 diabetes, multiple myeloma, HIV and hepatitis C virus infections. Given the demonstrated pharmacological tractability of this enzyme family and the pressing need for novel drugs to combat antibiotic resistance, proteases have also attracted interest as antibacterial targets — particularly the widely conserved intracellular bacterial degradative proteases, which are often indispensable for normal bacterial growth or virulence. This Review summarizes the roles of the key prokaryotic degradative proteases, with a focus on the initial efforts and associated challenges in developing specific therapeutic modulators of these enzymes as novel classes of antibacterial drugs.

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Figure 1: Role of proteolysis in regulation of RpoS.
Figure 2: Targeted whole-cell screens to identify modulators of proteolysis.
Figure 3: Crystal structure of the M. tuberculosis 20S proteasome after exposure to the oxathiazol-2-one inhibitor, HT1171, shows modification of the active site threonine (Thr1), and conformational changes in a non-conserved, M. tuberculosis-specific portion of the β-subunit.

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Acknowledgements

We would like to thank S. Sieber and V. Dartois for personal communications that aided the impact of this work. Additionally, we thank M. Chao, K. Guinn, A. Trauner and J. Zhang for valuable editorial input during the revision process.

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Authors and Affiliations

  1. Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, 02138, Massachusetts, USA

    Ravikiran M. Raju & Eric J. Rubin

  2. Department of Cell Biology, Harvard Medical School, Boston, 02138, Massachusetts, USA

    Alfred L. Goldberg

Authors
  1. Ravikiran M. Raju
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  2. Alfred L. Goldberg
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  3. Eric J. Rubin
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Corresponding author

Correspondence to Eric J. Rubin.

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FURTHER INFORMATION

Protein Data Bank

Glossary

Bacterial proteolytic complexes

A conserved set of bacterial enzymes that are responsible for the degradation of whole proteins into smaller, inactive polypeptides and amino acids.

AAA+ enzymes

ATPases associated with diverse cellular activities; a broad class of enzymes that share the ability to hydrolyse ATP.

Chaperones

Single-subunit proteins or complexes that interact with other proteins to promote proper folding or re-folding and inhibit aggregation of aberrant protein-folding variants.

Trans-translation

A conserved mechanism that allows for the recycling of ribosomes that have stalled in the process of reading an mRNA template, and enables the subsequent degradation of the aborted protein product produced by the incomplete translation.

Unfolded protein stress response

An inducible response that enables the cell to eliminate misfolded and denatured proteins via chaperone-dependent re-folding and protease-dependent degradation.

Type III secretion system

A specialized secretory apparatus used by Gram-negative bacteria that directly injects bacterial virulence factors into the host cytoplasm.

Anti-virulence antibiotics

Antibiotics that interfere with the ability of a pathogenic bacteria to establish infection, but are not bacteriostatic or bactericidal.

Suicide inhibitors

Small molecules that react irreversibly with an enzyme to produce a stable enzyme–molecule compound that is incapable of catalysing further reactions.

Substrate scanning

The use of large peptide libraries to determine the amino acid residues that are preferentially hydrolysed by a protease.

Walker box ATP-binding domains

Protein sequence motifs that have been shown to interact with ATP.

Partition coefficients

Ratios that define the concentration of a compound in two phases of a mixture of octanol and water.

Structure-based virtual screening

A method of in silico drug discovery that uses structural information about a target protein to find small molecules that are complementary to the modelled protein active site.

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Raju, R., Goldberg, A. & Rubin, E. Bacterial proteolytic complexes as therapeutic targets. Nat Rev Drug Discov 11, 777–789 (2012). https://doi.org/10.1038/nrd3846

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