Oct 17 2013

PPMOs – The New Antibiotic?

People generally worry too much and about the wrong things. The media exploits dramatic risks for sensational headlines and exciting narratives, but rarely put risks into a useful context.

Meanwhile, there are some real things to be worried about out there. One thing that has long been on my short list is the coming post-antibiotic era.

Antibiotics have dramatically improved human life and life-expectancy. I know many people who would likely be dead without them. The are one of modern medicines greatest success stories. But they have a critical weakness – evolution.

The antibiotic era started an evolutionary arms race with the pathogenic bacteria they kill or inhibit – and the bacteria are winning. Antibiotics work through a number of mechanisms that interfere with the cellular function of prokaryotes, but not eukaryotes, so bacteria are affected while host cells are unharmed.

These antibiotics create selective pressure, however, and because bacteria reproduce so quickly, there are lots of opportunities for beneficial mutations to arise. In addition bacteria often have part of the genetic code in the form of plasmids – self-contained DNA strands that can be shared between different species of bacteria.

This means that if one strain of bacteria evolves resistance to a specific antibiotic, it can share that resistance to other strains and even other species through plasmids. Resistance can therefore spread, and does not have to re-evolve in each strain.

Plasmids can even contain mutations for resistance to multiple different antibiotics, the use of any one of which can result in the spread of multi-drug resistance.

We already are dealing with highly resistant strains of bacteria, which is an increasingly difficult problem. There are several partial solutions to limit resistance – avoid overuse of antibiotics, avoid broad-spectrum antibiotics, and complete courses of antibiotics when taken. It may also become necessary at some point to retire specific antibiotics for a number of years to allow resistance to wane over time.

Developing new antibiotics that work through entirely new mechanisms would also be welcome, but then it is only a matter of time before resistance develops to those new antibiotics. What is really needed is entirely new approaches to bacterial infection.

One emerging technology may be a significant new weapon is our war against bacteria – PPMOs, or Peptide phosphorodiamidate morpholino oligomers. PPMOs are synthetic DNA strands that bind to cRNA because they have the complementary, or antisense, pattern of base-pairs. They are therefore like a lock and key, and will specifically bind together.

PPMOs can be created to match RNA strands of specific bacterial genes – so they can be very specific, not just to bacteria, or even a specific species of bacteria, but to a specific gene. Once they bind they block the functioning of that RNA by blocking access to the cells machinery, called stearic hindrance. In this way they block the expression of the targeted gene. Turn off the right gene, and you can stop the bacteria’s life cycle.

This technology is still developing, but already there are animal studies showing that PPMOs have activity against bacteria and enhance survival from bacterial infections. They still need to be tested in humans.

PPMOs are also useful for more than bacterial infections. They can be targeted against genetic diseases, where the mutant gene produces an abnormal protein that causes or worsens the disease. The expression of the abnormal gene can be blocked by a targeted PPMO.

Unfortunately, there is already evidence that bacteria can develop resistance to PPMOs by evolving mutations. However, with PPMOs we can simply adjust the PPMO sequence to match the mutation.

It remains to be seen how powerful PPMOs will be in our ongoing fight against pathogenic bacteria. It does look like they have the potential to be a significant new weapon. There is not likely to be a single solution to the problem of bacterial resistance. Rather we will likely need as many different strategies as possible to keep one step ahead of rapidly evolving bacteria.

19 responses so far

19 thoughts on “PPMOs – The New Antibiotic?”

  1. locutusbrg says:

    Another factor you missed in the slowing resistance is regulating more tightly the current overuse of “preventative” antibiotics in the animal farming process.

  2. NeuroTrumpeter says:

    Hopefully, given that the specter of resistance is now well-known, we will be more prudent in our implementation of these potential new drugs

  3. MWSletten says:

    Another promising technology is bacteriophages.



  4. Draal says:

    Without looking into the details, I am drawing a comparison to siRNA. One frequent issue is that knockdown of RNA is only temporary.
    Other issues include the strength of the promoter producing the mRNA, the stability of the mRNA, the resistance of the bacteria to foreign DNA (um… endonucleases?), etc.

    Bacteria have been fighting viruses which use RNA, dsDNA and ssDNA. Nature has already found a way to defeat this strategy.

  5. ccbowers says:

    Interesting topic. I don’t know much about them, but 2 things come to mind: PPMO delivery to specific sites, and level of specificity. I will have to look into these at a later date.

    Bacteriophages are an interesting alternative example because they are on one end of the specificity spectrum, which has advantages (e.g. less effects on host and nonpathogenic bacteria), but some disadvantages as well for having high specificity (may be more suceptible to changes/different strains)

  6. ccbowers says:


    I might be wrong, but I believe that the molecules are altered to not be degraded by nucleases.

    “Bacteria have been fighting viruses which use RNA, dsDNA and ssDNA. Nature has already found a way to defeat this strategy.”

    I would not use this argument to dismiss the approach. You could use this argument for nearly any approach, including antibiotics themselves, yet I think we can agree that antibiotics have had a huge impact in medicine and have saved many many lives. I don’t take the “post-antibiotic era” literally… it’s just getting more and more complicated.

  7. Jon Moulton says:

    The Acinetobacter work is based on a body of work using Morphlinos to target bacterial RNA, mustly from Bruce Geller’s lab. http://www.gene-tools.com/node/45

  8. Draal says:

    I understand your point. Don’t dismiss an experiment until you’ve tried it. However, I put it context relative to the invention and distribution of antibiotics in which drug resistance was not known/considered. I have been surprised numerous times by biology to do things that were once thought to not happen in Nature. It is important to test, within reason, as many possible hypotheses as possible.

    There are many different ways bacteria can overcome the silencing of mRNA by short DNA analogs. After reading the abstract, this approach relies on membrane penetrating peptides to deliver the DNA analogs (which should not be degraded by nucleases as ccbowers points out). Mutations that prevent transport across the membrane would nullify this strategy. Also, DNA repair enzymes like MUTY for example use a different mechanism that endo/exo-nucleases. Does it work in Gram positive bacteria? Are bacteria that form biofilms affected?

    It is interesting and creative research no doubt. I am skeptical of the broader applicability though.

  9. Draal says:

    My guess was right… mutations to membrane transporters result in resistance
    Google: Bacterial Resistance to Antisense Peptide Phosphorodiamidate Morpholino Oligomers

  10. Draal says:

    A few red flags went up when I started looking at the citation history. For one, very few people are working on this based on the number of citations since 2007.
    This research is being developed by Sarepta Technologies since early 2000s. As an antibacterial, PPO technology hasn’t moved from Discovery. www dot sareptatherapeutics.com/our-programs/

  11. Gojira74 says:

    “which should not be degraded by nucleases as ccbowers points out”

    This is actually pretty old technology. Using LNAs (locked nucleic acids), where certain bases are modified to form a ring, that can nucleases (this is used in the new miRNA treatment for HVC). You can also use thiol-phosphates as well.

    It’s good to be skeptical about new research, but none of the issues raised here cannot be overcome by fine tuning and additional studies. This is far from a clinical trial, but it is promising and interesting. The ability to abuse RNA silencing is huge right now. Another point was made about how RNAi isn’t always 100%, that isn’t as big a deal when you only need to slow bacterial growth to allow your immune system to work. This is why most antibiotics are effective.

  12. tmac57 says:

    What do ya’ll think about the rotation of antibiotics as an approach to blocking resistance?
    This popped up on the science news radar about a month ago,although the idea apparently has been around for awhile.


  13. starik says:

    When we wonder why we haven’t received any alien messages yet, we speculate that maybe we’re the first intelligent life to evolve in our galaxy. What if life on earth has just had an unusually successful run in staving off the inevitable domination of single celled organisms?

  14. tmac – that might be inevitable. If resistance continues to grow, we may have no choice but to rotate our certain antibiotics for a period of time.

  15. ccbowers says:


    As Steve says, there will be no choice as resistance increases. In some sense this is already being done as certain antibiotics are not being used as resistance increases. The more specific question is how will this be done in a more formal way, utilizing knowledge and evidence to determine which agents will be rotated when and for how long. Some healthcare systems have already tried doing this, mostly in a limited fashion within hospital systems. There is also the issue of resistance being a regional issue, which would require different recommendations for different areas, and (ideally) there would need to be a way to coordinate rotations between regions for best effect. I would think that the sharing and using of antiograms in different areas to coordinate rotations would be needed to do this effectively. This is a big topic, I think, and one that will need many solutions. The rotation of antibiotics would just be one of them.

  16. ccbowers says:

    *antibiograms. Typo

  17. Ceeps says:

    What other strategies are there to counter antibiotic resistant bacteria? Phage based therapeutics? Designing bacteria that will crowd out and out compete the resistant strains?

    If we were to implement a rotation of antibiotics, at what point would it be appropriate to switch to another kind of antibiotic, and how long would administration of the new antibiotic last? Months? Years?

    Is the specific nature of the PPMO playing a role for resistance to PPMO’s? How many codons does the RNA strand need to be, to be specific? Could the problem of resistance be avoided if they were to anticipate all mutations in that region that would code for the same proteins (For example, how CGA and CGG both code for arginine)?

  18. tmac57 says:

    Hmmm…I think by “rotating” antibiotics, we might be talking about two different things here based on some of the answers. I was referring to the new approach by some Danish researchers who tested rotating drugs (3 or 4) on the same strain sequentially to utilize the ‘collateral sensitivity’ effect :

    Published in Science Translational Medicine, the Danish duo’s approach depends upon a principle termed “collateral sensitivity”.

    Put simply, in order to become resistant to one class of antibiotic drugs – call it drug A, bacteria often have to drop their guard and become super-sensitised to another antibiotic – drug B. This can happen because the clusters of genes that are activated to defend against A can switch off the very genes needed to fortify the bacteria against B. And thus, the first bugs to die when exposed to drug B would actually be the very ones that were showing resistance to drug A.

    So, Imamovic and Sommer reasoned, if the right antibiotics are administered in the right order, it should be possible to prevent the establishment drug-resistant bugs in the first place.

    To test this theory, cultures of E. coli bacteria that were individually resistant to one of 23 different antibiotics were tested against the other 22 antibiotics to see which, if any, of the drugs they were more or less sensitive to.

    Seventeen of the 23 drugs tested showed the theorised collateral sensitivity to a second antibiotic ranging from them being two- to eight-fold more vulnerable to the drug compared with non-resistant bugs.

    Using this information, the researchers were able to draw up over 200 drug cycles – sequences of 2, 3 or 4 antibiotics – that if administered successively over a short period to bugs with resistance to a given drug should destroy those bugs and thus prevent further resistance developing.

    Tested on two clinical strains of E. coli that were resistant to 8 of the 23 antibiotics studied, the drug cycles successfully destroyed all of the bugs as predicted.

    According to the researchers, “This study provides proof of principle that an underappreciated side effect of resistance, collateral sensitivity, can be used to target drug resistance when selected drugs are cycled optimally.”

    I think the idea is to treat the individual patient with a sequence of different antibiotics to fool the resistant bugs into dropping their guard.

  19. ccbowers says:


    Yes that is something a bit different. I would think that an approach like that may be useful in a few select situations, but I’m not sure that it is clear what situations those might be. First we would need to identify in which situations collateral sensitivity takes place (which organisms and which antibiotics), and then we would need to know that it actually worked in practice. I imagine that it may have fairly narrow applications, but you never know until the proof-of-concept is further studied.

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