Phage Therapy in the Era of Synthetic Biology

Abstract

For more than a century, bacteriophage (or phage) research has enabled some of the most important discoveries in biological sciences and has equipped scientists with many of the molecular biology tools that have advanced our understanding of replication, maintenance, and expression of genetic material. Phages have also been recognized and exploited as natural antimicrobial agents and nanovectors for gene therapy, but their potential as therapeutics has not been fully exploited in Western medicine because of challenges such as narrow host range, bacterial resistance, and unique pharmacokinetics. However, increasing concern related to the emergence of bacteria resistant to multiple antibiotics has heightened interest in phage therapy and the development of strategies to overcome hurdles associated with bacteriophage therapeutics. Recent progress in sequencing technologies, DNA manipulation, and synthetic biology allowed scientists to refactor the entire bacterial genome of Mycoplasma mycoides, thereby creating the first synthetic cell. These new strategies for engineering genomes may have the potential to accelerate the construction of designer phage genomes with superior therapeutic potential. Here, we discuss the use of phage as therapeutics, as well as how synthetic biology can create bacteriophage with desirable attributes.

Figure 1.

Lytic cycle of bacteriophage. Schematic representation of virulent phage infection, replication, and lysis of bacterial host cells.

Figure 2.

Synthetic assembly of bacteriophage genomes. Step-by-step construction of phage genomes starting from overlapping nucleotides and recovery of functional phage particles from host cells following transformation. (Left) Chemical assembly of DNA fragments synthesized from overlapping nucleotides using Gibson assembly. (Right) Assembly of DNA fragments synthesized from overlapping nucleotides in yeast artificial chromosome (YAC, in purple).

Figure 3.

Iterative engineering of phage genomes to create phages with superior therapeutic potential. Phage B V1.0 represents a phage with enhanced host range (includes the host range specific to phage A). Phage B V2.0 delineates iterative engineering of phage B V1.0 to include moieties aiding in biofilm disruption. Similarly, phage B V3.0 captures the properties of phage B V2.0 and is engineered to express antimicrobial payloads that may aid in elimination of bacterial subpopulation that lost susceptibility to phage.

Figure 4.

Phage therapy approaches. Classical (or Eastern European approach) relies on extensive banks of phages that can be used for treatment on a case-by-case basis by a physician specializing in phage therapy and adjusted based on clinical assessment. The synthetic phage therapy approach aims to develop phage with drug-like properties that can be used, much like antibiotics, in standardized Western treatment approaches. cGMP, Current good manufacturing practice.