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Microbial genetics

Genetic strategies for antibacterial drug discovery

Nature Reviews Genetics volume 4, pages 442–456 (2003)Cite this article

Key Points

  • The emergence of antibiotic resistance among important bacterial pathogens has generated the need to develop new and more effective therapies.

  • All classes of antibiotics in use at present were identified using simple screens that identified compounds by their ability to inhibit bacterial growth. However, the usefulness of this strategy has been limited, more recently, by the difficulty of identifying cellular targets of compounds that act by new mechanisms.

  • Genomic strategies are now being used to discover new antibacterials. Proteins are being validated as targets on the basis of their sequence conservation among pathogens and their genetic requirement for bacterial life.

  • Genetic approaches that modify the classical whole-cell screening strategy are being used to identify new compounds that act by inhibiting selected target enzymes or biochemical pathways.

  • Genetic approaches include: the use of conditional lethal mutants to identify compounds with synergistic effects; the use of resistance mutations to identify the cellular targets of antimicrobial compounds; and gene-expression assays, such as DNA microarrays, that identify compounds that elicit specific stress responses.

  • These approaches have made an outstanding impact on antibacterial drug discovery. It is anticipated that the appropriate combination of these strategies, and the insights and research directions they inspire, will give rise to the discovery of new antibacterial agents.

Abstract

The availability of genome sequences is revolutionizing the field of microbiology. Genetic methods are being modified to facilitate rapid analysis at a genome-wide level and are blossoming for human pathogens that were previously considered intractable. This revolution coincided with a growing concern about the emergence of microbial drug resistance, compelling the pharmaceutical industry to search for new antimicrobial agents. The availability of the new technologies, combined with many genetic strategies, has changed the way that researchers approach antibacterial drug discovery.

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Figure 1: An approach for developing new antibacterial compounds.
Figure 2: Transposon footprinting in Escherichia coli.

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Acknowledgements

We thank Y. Xu, P. McNicholas, S. Fenster and two anonymous reviewers for their insightful comments and critical review of this manuscript. We also thank G. Foulkes and T. Kenney for providing unpublished data. L.M. is grateful to D. Biek, J. DeVito, M. Schmid, K. Shaw, P. Youngman and Y. Zhengyu for helpful discussions and for providing references. This work was supported by the Schering–Plough Research Institute.

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  1. Department of Antimicrobial Therapy, Schering–Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, 07033-0530, New Jersey, USA

    Lynn Miesel, Jonathan Greene & Todd A. Black

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  1. Lynn Miesel
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DATABASES

BioCyc

def

EF-Tu

FabA

fabI

FabI

fmt

MurA

NadB

nadD

nadE

smf

tufA

FURTHER INFORMATION

COGs database

Comprehensive annotations of select genomes

E. coli Genome Center

Entrez microbial genomes

GOLD Genomes Online Database

Protein Data Bank

Sanger Institute microbial sequencing effort

TIGR Comprehensive Microbial Resource

Glossary

METHICILLIN AND VANCOMYCIN

Antibiotics that are used against serious Gram-positive pathogens; resistance to these drugs is an important medical concern.

OXAZOLIDINONES

A group of antibiotics that affect protein biosynthesis.

BACTERICIDAL

An antimicrobial agent or condition that kills a bacterial cell.

BACTERIOSTATIC

An antimicrobial agent or condition that halts bacterial growth but does not kill the cell.

DNA GYRASE

A topoisomerase that maintains a state of negative supercoiling in the bacterial chromosome, which is essential for DNA replication and transcription.

TOPOISOMERASE IV

A topoisomerase that is required for the progression of the DNA replication fork and for daughter chromosome segregation.

ORTHOLOGUES

Sequences or genes in different organisms that are direct evolutionary counterparts; that is, they are related by descent from a common ancestor. Orthologous genes normally have the same cellular function.

HOMOLOGY MODELLING

The process in which an algorithm, such as Modeller, constructs a model of the three-dimensional structures of aligned protein sequences, using a related protein with a known structure as a template.

GRAM-POSITIVE BACTERIA

A lineage of bacteria that is differentiated by having a thick peptidoglycan cell wall that contains long-chain polymers called teichoic acids. These organisms are identified by their retention of a crystal violet dye (Gram stain).

GRAM-NEGATIVE BACTERIA

A lineage of bacteria that is distinguished by having a thinner cell wall than Gram-positives and has an outer membrane that consists of lipopolysaccharide. The outermembrane serves as a permeability barrier for small molecules such as antibiotics.

ANALOGOUS ENZYMES

Structurally unrelated enzymes that catalyse the same reaction.

PLASMID SUICIDE VECTOR

A plasmid that cannot replicate in a particular host.

TRANSFORMATION

The process in which bacteria take up DNA from a medium.

NATURALLY COMPETENT

Bacteria that have efficient transformation and recombination systems, and can take up homologous DNA from the environment and integrate it into the chromosome by homologous recombination. Bacillus subtilis, Haemophilus influenzae, Neisseria gonorrhoeae, Streptococcus pneumoniae and Helicobacter pylori are naturally competent.

POLAR EFFECT

Many bacterial genes are located in operons in which they are transcribed in a single polycistronic mRNA. A mutation that prevents the transcription or translation of one gene can prevent the transcription of promoter-distal genes in the same operon.

THERMOLABILE

A protein that is unstable and, therefore, inactive at an elevated temperature.

METABOLIC LABELLING

The process in which bacterial cells are grown in the presence of radiolabelled precursors of macromolecule synthesis (DNA, protein, fatty acids and peptidoglycan). Blocks to radiolabel incorporation can identify a mutant defect or the cellular target of an antimicrobial compound.

K i

The dissociation constant of an enzyme–inhibitor complex. This value represents the affinity of an enzyme–inhibitor interaction — a potent inhibitor has a small Ki value.

HETERO-MULTIMERIC ENZYME

A multi-subunit enzyme that comprises two or more different proteins.

MYCOLIC ACID

Long fatty acids (C50–C80) that are a main component of the mycobacterial cell envelope.

PCR AMPLICONS

DNA that is generated by PCR amplification.

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Miesel, L., Greene, J. & Black, T. Genetic strategies for antibacterial drug discovery. Nat Rev Genet 4, 442–456 (2003). https://doi.org/10.1038/nrg1086

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