Anti-Inflammatory Diet

All health care starts with diet. My recommendations for a healthy diet are here:
Anti-Inflammatory Diet and Lifestyle.
There are over 190 articles on diet, inflammation and disease on this blog
(find topics using search [upper left] or index [lower right]), and
more articles by Prof. Ayers on Suite101 .

Friday, May 4, 2012

New Antibiotics, Biofilm Inhibitors, Vitamin Deficiency

I was not expecting my recent reading of an article on femtosecond reaction kinetics to produce another discussion of quorum sensing, biofilms and vitamins. The idea behind the article was to identify new targets for drug design based on the ephemeral transition states that occur as enzymes bind substrates, stabilize transition states and yield product molecules. Drugs that mimic the transition states make good enzyme inhibitors. One of the target enzymes for the control of disease is an enzyme, MTAN, involved in the synthesis of quorum sensing molecules that orchestrate the construction of common biofilms. The idea is to inhibit MTAN and also avoid selection for antibiotic resistance. Unfortunately, targeting quorum sensing molecules also may produce vitamin deficiencies, since many of these molecules, in this case vitamin K, are also quorum sensing molecules.

Drugs have too many Side Effects
Specificity in the binding of molecules to the thousands of proteins that are coded by the ca. 20,000 human genes depends on a very tight fit between the molecular "key" and the binding site "lock" of the protein. Just as in physical world, a small key/drug molecule with limited surface detail is not as safe/specific as a larger key with many surface features, and a larger lock/enzyme active site that is harder to pick/has fewer interactions with random enzymes. Unfortunately, most drugs are small molecules with limited surface features that make them like molecular skeleton keys that produce many side effects by interacting with unintended proteins/enzymes.

Transition States are more Specific
A recent focus on drug research is to exploit molecular computation and modeling to design molecules that will bind to the part of an enzyme that actually participates in binding substrates and catalyzing chemical reactions. These designed molecules can interact with an expanded region of the enzyme and bind more strongly than the normal substrate. The designed molecules can be very effective inhibitors that will not react as nonspecifically as inhibitors identified by trial an error, e.g. statins.

Biofilm Inhibitors are Targets for Antibiotic Development
The enzymes involved in the synthetic pathways of biofilm quorum sensing signals have been identified and powerful inhibitors of some of these enzymes have now been designed and synthesized. These inhibitors are very effective in inhibiting biofilm formation by some common bacterial pathogens (and essential gut flora.)

Biofilm Inhibitors will also Block Vitamin Production in Gut Biofilms
The new biofilm inhibitor antibiotics may have enhanced specificity, but they target enzymes that also provide essential functions in biofilms that are needed for healthy gut and immune system function. Many of the vitamins that are produced by gut flora are also quorum sensing signal molecules in healthy gut biofilms. Thus, blocking MTAN to block biofilm formation of a pathogen, will also block gut synthesis of vitamin K, which is made in gut bacteria using the MTAN pathway. These inhibitors would be expected to be particularly damaging to the specialized gut flora of breastfed babies, since these gut bacteria are known producers of vitamin K.


Anonymous said...

Dr. Ayers. I have quit taking antibiotics and eat much better now thanks to your diet protocols. I feel much better now, but I still have a lot of flatulence.

I was wondering what this might mean about my GI health. Does this mean that my gut flora is still incomplete and the flatulence should go down as my gut flora improves? Or is this something that is just natural and not indicative of a bad gut?

This seems to be a problem no matter what I eat. Do you have any suggestions?

Anonymous said...

ive read GM food pass their genes onto gut bacteria in a single meal. This makes them produce similar antibiotics as that programmed in the genes of the food.

24x7 antibiotic/pesticide production in the body now plus antibiotic resistant gut bacteria!

Any thoughts?

sweetlady said...

This is why I'm not into antibiotics as well. Vitamin K, especially its K2 form, is indeed essential to the body.

Greg Davis said...

Dr. Ayers,

I have been put on a course of antibiotics for a MRSA/staph skin infection.

Any advice for minimizing the gut biota damage? I know it's not ideal but I am going to try probiotics at the tail end of the treatment..

Levi said...

Dear Dr. Ayers,

I like your blod so much that I read almost all the year's articles from 2009 to today. In this post, you make the point that there are also healthy biofilms in the gut, which you mention also in

Now, taking this point, I wonder if treatments such as reommended in:
- such as EDTA, vinegar, etc. do not do also a lot of harm? So I understand, they are effective in disrupting biofilms, but will they disrupt only the bad biofilms or also the good ones?

Formulating the same question in another way: Apart from consisting of good bacteria, what distinguishes good from bad biofilms? Are both made in similar ways of divalent cations, ..., fibrin?

The optimum would be to find such things among the list of EDTA, vinegar, pectin etc that exploint a structural difference of good and bad biofilms - if there is any. But if there is none, then we must learn that disrupting the bad biofilms will also disrupt the good biofilms and in the end its a bit like antibiotics in the reagard that good canot be done without harm at the same time. ok, I understand one difference, which is that the EDTA & co will not kill the bacteria in the "seed reservoir", the appendix, as you write here
but are there more differences?

- I am full with curiosity...! :)

Tanya said...

Seems they have proved your point about biolfilms...this one a combo of bacteria and fungus that creates slime!