Enhancing and initiating phage-based therapies

Abstract

D rug development has typically been a primary foundation of strategy for systematic, long-range management of pathogenic cells. However, drug development is limited in speed and flexibility when response is needed to changes in pathogenic cells, especially changes that produce drug-resistance. The high replication speed and high diversity of phages are potentially useful for increasing both response speed and response flexibility when changes occur in either drug resistance or other aspects of pathogenic cells. We present strategy, with some empirical details, for (1) using modern molecular biology and biophysics to access these advantages during the phage therapy of bacterial infections, and (2) initiating use of phage capsid-based drug delivery vehicles (DDVs) with procedures that potentially overcome both drug resistance and other present limitations in the use of DDVs for the therapy of neoplasms. The discussion of phage therapy includes (a) historical considerations, (b) changes that appear to be needed in clinical tests if use of phage therapy is to be expanded, (c) recent work on novel phages and its potential use for expanding the capabilities of phage therapy and (d) an outline for a strategy that encompasses both theory and practice for expanding the applications of phage therapy. The discussion of DDVs starts by reviewing current work on DDVs, including work on both liposomal and viral DDVs. The discussion concludes with some details of the potential use of permeability constrained phage capsids as DDVs.

ATP-Driven Contraction of Phage T3 Capsids with DNA Incompletely Packaged In Vivo

“…We purified WT NLD capsid II using procedures previously described, finishing with buoyant density centrifugation in a Nycodenz density gradient [3]. …”

In-Gel Isolation and Characterization of Large (and Other) Phages

“…Phage size increases as the slope of this plot increases, as seen by comparing the plot for near-jumbo myophage T4 (168.903 Kb genome [35]; Figure 1 [36]) to the plot for myophage G (626 Kb genome [6]; Figure 1) and podophage T3 (38.208 Kb genome [37]); the latter plot is horizontal (not shown in Figure 1). However, when comparing jumbo myophage G to jumbo myophage 0305phi8-36 (218.948 Kb genome [38]; Figure 1 [36]), this relationship is lost in that one visually observes no significant difference in slope, even though (1) the surface area of phage G (cryo-EM data in [6]) is over 2x the surface area of phage 0305phi8-36 (cryo-EM data in [39]) and (2) gel sieving is best correlated with particle surface area [40]. Thus, we conclude that at least one factor beyond sieving has a significant effect on data for jumbo phages.…”

“…This is the theoretical source of the above hypothesis. The empirical sources are the plot of Figure 1 and the observation that the 453 nm long phage G tail [4] is about the same length as the 486 nm long [39] phage 0305phi8-36 tail.…”

“…As previously mentioned [39], phage isolation/propagation exclusively in dilute agarose gels has additional advantages. These advantages are derived, in part, from isolation procedure that includes (1) flooding a dry environmental sample with a molten agarose-host cell mixture (no filtration, centrifugation or chloroform treatment), (2) gelling this mixture and (3) incubating until clear regions appear within the lawn formed by the bacteria (detailed illustration: [47]).…”

States of phage T3/T7 capsids: buoyant density centrifugation and cryo-EM

“…The obscuring effect of the car hood is analogous to the obscuring effect of not knowing the DNA packaging intermediates. Intermediates-based strategy also can produce opportunities for practical uses of isolated intermediates (for example, see Serwer et al 2014b). This strategy is projected to complement (not to replace) the various procedures of real-time single-molecule analysis.…”