Opportunities for synthetic biology in antibiotics: expanding glycopeptide chemical diversity

Abstract

Synthetic biology offers a new path for the exploitation and improvement of natural products to address the growing crisis in antibiotic resistance. All antibiotics in clinical use are facing eventual obsolesce as a result of the evolution and dissemination of resistance mechanisms, yet there are few new drug leads forthcoming from the pharmaceutical sector. Natural products of microbial origin have proven over the past 70 years to be the wellspring of antimicrobial drugs. Harnessing synthetic biology thinking and strategies can provide new molecules and expand chemical diversity of known antibiotic scaffolds to provide much needed new drug leads. The glycopeptide antibiotics offer paradigmatic scaffolds suitable for such an approach. We review these strategies here using the glycopeptides as an example and demonstrate how synthetic biology can expand antibiotic chemical diversity to help address the growing resistance crisis.

Keywords: antibiotic scaffold; glycopeptides; heterologous host; resistance; synthetic biology; tailoring enzymes.

Figure 1

Chemical diversity and complexity of antibiotics in nature. Antibiotics derived from microbial sources are rich in chiral centers and hydrogen bond donors and acceptors and span an order of magnitude in molecular weight.

Figure 2

Representative model for the application of synthetic biology to expand antibiotic chemical diversity. Various tailoring enzymes and backbones (parts) can be assembled in biosynthetic circuits (devices) in a versatile host (chasis) to generate novel compounds. Synthetic chemistry can expand chemical diversity orthogonally to further increase diversity.

Figure 3

GPAs: a structurally diverse class of bacterially produced antibiotics.

Figure 4

The maturation of GPAs includes a number of distinct enzyme activities and chemical modifications. The maturation of teicoplanin is shown as an example. In a series of enzymatic steps, the linear heptapeptide is cross-linked via the activity of monooxygenases followed by a tandem action of scaffold modifying enzymes to create the final teicoplanin antibiotic.

Figure 5

Examples of GPA biosynthetic gene clusters. Scaffold biosynthesis is encoded by nonribosomal peptide synthetases (orange) producing peptides that are cross-linked by P450 monooxygenases (black). Tailoring enzyme are encoded by genes for glycosylation (red), halogenation (green), sulfation (yellow), methylation (blue), and acylation (pink) are shown.

Figure 6

The diversity of GPA modifications offers tremendous opportunity for chemical diversification. The GPA heptapeptide backbone is numbered, and arcs represent regions of cross-linking. (A) Sites of primary modification of the backbone in the form of halogenation, glycosylation, methylation, and sulfation. Homologues of the modifying enzymes act on one or more different amino acid as indicated. (B) Secondary modifications are confined to the Hpg₄ sugar (glucose or GlcNAc) in the form of methylation, acylation, or glycosylation.