Metabolic profiling indicates impaired pyruvate dehydrogenase function in myalgic encephalopathy/CFS (Fluge et al., 2016)

[alex3619]

Something we need to consider is that while alternative paths exist to provide energy via oxidation, they do not all have the same capacity for increasing rate. I do not know the kinetics of all these paths, but that would have an impact. Also, if I recall correctly, beta oxidation of fats can increase oxygen utilization, though I could be wrong since its been a very long time since I looked at beta oxidation. However I think the word oxidation is a clue.

 

[alicec]

At least from my perspective, we may have a problem of semantics

I don't think it is semantics, I think you are missing a few key points.

I'd clarify that Acetyl-CoA can't supply energy per se; it just supplies itself

See this post. Acetyl-CoA contains a high energy thioester bond, it does supply energy. The reaction of acetyl-CoA with oxaloacetate, the initiation of the cycle, is highly exergonic.

We are perhaps more familiar with ATP and how the cell couples the many endergonic reactions which power the cell with the exergonic hydroysis of ATP, thus harvesting the energy stored in the chemical bonds of the molecule.

Acetyl-CoA is another such molecule.

It carries energy derived from breakdown of carbohydrates, fats and proteins into the Kreb's cycle. Oxidation of the acetyl portion of acetyl-CoA in the cycle produces CO2 and water and the energy released is captured in high energy GTP (or ATP depending on the cell) and high energy electrons captured in NADH and FADH2. These electrons are used to produce the energy currency of the cell, ATP, via oxidative phosphorylation.

All of the cycle intermediates are regenerated by the cycle. This does not apply to acetyl-CoA which is not actually part of the cycle, but rather is an initiator. It is consumed with each turn of the cycle; it is not regenerated by the cycle.

The oxidation of acetyl-CoA is the point of the cycle and the overall reaction of the cycle can be written as
Acetyl-CoA + 3 NAD+ + FAD + GDP + Pi + 2 H2O → CoA-SH + 3 NADH + 3 H+ + FADH2 + GTP + 2 CO2

Acetyl-CoA is the limiting factor for the cycle. Anapleurotic substances can feed in and in effect increase the amount of all intermediates as one is converted to another, but this is dependent on newly formed acetyl-CoA being available to react with oxaloacetate and initiate the cycle.

There is nothing weird about the statement

Acetyl-CoA, on the other hand, derived from pyruvate oxidation, or from the beta-oxidation of fatty acids, is the only fuel to enter the citric acid cycle.

As far as I am aware, acetyl-CoA is the only high energy molecule to enter the Kreb's cycle. Perhaps there is some loose language in places with "fuel" which may or may not mean the same thing as a high energy bond.

That particular statement doesn't mention amino acids for which you appear to be trying to make a special case, but that may be just the context in which the statement was made.

The text you quote about amino acids being oxidised to generate metabolic energy goes on to say in the next sentence

Most of their carbon and hydrogen atoms eventually form CO2 or H2O, whereas their nitrogen atoms are shuttled through various forms and eventually appear as urea, which is excreted.

Formation of CO2 and H20 is of course done by the oxidation of acetylCoA.

 

[Hip]

OK @JaimeS, I have just been taking my best brain fog-clearing supplements, in order to try to think this issue through! As a result, I think that you are likely right: I think that anaplerotically adding to the Krebs cycle intermediates can in some (but not all) cases supply energy to the Krebs cycle (although I suspect this is not a very efficient process, so you won't get much energy throughput via this route).


What I have realized is that from the energy perspective, the Krebs cycle is not really a cycle at all, but is best thought of as a cascade of events, starting at the top and ending at the bottom — a cascade analogous to water flowing down a mountain stream, or a ball rolling down a hill.

The diagram below is very instructive: it displays the energy levels associated with each of the 8 steps of the Krebs cycle — or the "Krebs cascade," which I think would be a better name for the Krebs cycle, when you look at it from the energy angle.

As you can see in the diagram, citrate is the first molecule of the Krebs cascade, and has the highest energy. In our mountain stream analogy, you can think of citrate as like a certain quantity of water placed at the source of a mountain stream: this quantity of water at the top of the stream has a lot of potential energy, by virtue of the fact it is so high up. And as that water starts flowing down the mountain stream, you can harness the energy in its flow by means of a series of water mills, placed at different locations along the mountain stream.

This "mountain stream with watermills" is useful analogy to understand energy in the Krebs cycle, or the Krebs cascade as I am going to call it here. In the Krebs cascade, you don't have water, but a series of molecules (intermediates) that are sequentially converted from one to another, with each subsequent molecule being lower down on the energy hill than the previous molecule. Energetically, as these Krebs molecules convert from one to the next, it is like water flowing down a hill.

At various points in the Krebs cycle / Krebs cascade you have "water mills" that extract the energy: these "water mills" extract the energy from the Krebs cascade in the form of NADH, FADH2 or ATP (these "water mill" points of energy extraction are marked with arrows in the diagram below).

Energy Levels for the 8 Steps of the Krebs Cycle (Right in Blue),
and the 10 Steps of Glycolysis (Left in orange)
The vertical axis indicates how much energy is contained in each of the
8 intermediates of the Krebs cascade. Citrate is the first molecule of the
Krebs cascade, and this contains the highest amount of energy.

Source: here​

The Krebs cascade ends up with oxaloacetate, the final product of the 8 steps of the Krebs cycle. Oxaloacetate contains no usable energy, because it is like water that has flowed down to the lowest point of the stream: sea level.

However, this is where acetyl-CoA comes in: acetyl-CoA is like a bucket that picks up water from sea level at the lowest point of the stream, and brings that water back to the top and source of the mountain stream, so that the water can once again flow down the mountainside.

Acetyl-CoA acts like such a bucket in the Krebs cascade, because acetyl-CoA converts oxaloacetate back to citrate. And this is why acetyl-CoA supplies so much energy to the Krebs cycle, because in one fell swoop, it acts to convert the lowest energy molecule, oxaloacetate, back to the highest energy molecule, citrate.



Viewing the Krebs cycle in this way, in terms of an energy level cascade, helps understand how adding intermediates to the Krebs cascade can supply energy. The eight Krebs intermediates are, in their correct order:

Eight Krebs intermediates:

1. Citrate
2. Isocitrate
3. Alpha-ketoglutarate (aka: oxoglutarate)
4. Succinyl-CoA
5. Succinate
6. Fumarate
7. Malate
8. Oxaloacetate

In terms of inputs to the Krebs cycle, where you can add to and replenish the Krebs intermediates, there are only 4 such inputs, and these 4 are shown in green above. See: Anaplerotic reactions - Wikipedia.

Now, if you added some alpha-ketoglutarate to the Krebs cycle, that I think would add energy, because it would be like carrying a bucket of water from sea level, and placing that water not very far down from the source of mountain stream (since alpha-ketoglutarate is in the 3rd position down from the source of the mountain stream, with citrate being in the 1st position, at the very top and source of the stream).

But if you added some fumarate to the Krebs cycle, that would supply less energy, because fumarate is quite a long way down the mountain stream, in 6th position. It would be like unloading your bucket of water in the stream at a position already quite a long way down the mountain, close to the end of the stream.

And if you added oxaloacetate to the Krebs cycle, that would not supply any energy at all, as oxaloacetate is at the very bottom sea level position of the stream, so cannot provide any energy.



So as far as I can see (and assuming my analysis is correct), the answer seems to be that replenishing the Krebs intermediates can provide energy to the Krebs cycle, but you get more energy if you replenish the intermediates that are higher up on the Krebs cascade.

So if you are thinking of replenishing the Krebs intermediates in order to boost energy, I think you'd want to go for the intermediates that are towards the top of the Krebs cascade, such as alpha-ketoglutarate (alpha-ketoglutarate replenishment is achieved in the mitochondria by the reaction of glutamate and NAD+, and is catalyzed by glutamate dehydrogenase).

As far as I am aware, the alpha-ketoglutarate supplements that you can buy cannot be directly utilized by the mitochondria, so I suspect these will not work to replenish the Krebs alpha-ketoglutarate intermediate.


If in ME/CFS, alpha-ketoglutarate is being used in order to supply energy to the Krebs cycle, it could explain why in an Australian study, glutamate was found to be low in ME/CFS. Cort wrote an article about this.

 

[JaimeS]

Great explanation @Hip ! I do think of it like you said initially, like water that flows downhill. <--- visual person!

Not to derail, but just saw this interesting comment on the article at #MEAction:

seb says:
January 8, 2017 at 1:20 pm (Edit)
Sorry for my english:
there are 2 inhibitors of pdk1, dichloroacetate but seems to be dangerous for nerve in high dose. Thiamine ( vit B1) in high dose has the same capability… (25mg/kg in study)…..

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3963161/

” Inhibition of PDKs by dichloracetate (DCA) exhibits a growth suppressive effect in many cancers. Recently it has been shown that the thiamine co-enzyme, thiamine pyrophosphate reduces PDK mediated phosphorylation of PDH.”

I replied

Reply

Jaime S says:
January 8, 2017 at 10:51 pm (Edit)
Thanks for mentioning this, seb!

We are now talking about inhibiting an inhibitor that inhibits PDH! So let’s explain for the folks at home before continuing.

Seb is talking about inhibiting PDK1. PDK1 suppresses the function of PDH because it is an inhibitor of PDH. If we were to suppress PDK1, this would (presumably) allow PDH to function better, and glycolysis to work more effectively. Seb is focusing on PDK1 because (I assume!) it’s the one that directly relates to illness severity, even though 1, 2, and 4 all apparently have elevated expression.

I went searching to see if I could find out about any other PDK1 inhibitors, on reading Seb’s comment.

The first thing I noticed is that PDK1 is (unfortunately) used for two different chemicals:

— Phosphoinositide-dependent kinase 1
— Pyruvate dehydrogenase kinase 1

We’re talking here about the latter. If you just search PubMed for PDK1 you’ll get both, so consider using the full name. Seb has the correct chemical in hir post!

There is a very similar chemical to the one that Seb mentions referenced in this study, though it refers to inhibiting PDK4: https://www.ncbi.nlm.nih.gov/pubmed/24865588

Selected bits of the abstract: “Severe influenza is characterized by cytokine storm and multiorgan failure with metabolic energy disorders and vascular hyperpermeability. In the regulation of energy homeostasis, the pyruvate dehydrogenase (PDH) complex plays an important role by catalyzing oxidative decarboxylation of pyruvate, linking glycolysis to the tricarboxylic acid cycle and fatty acid synthesis, and thus its activity is linked to energy homeostasis. The present study tested the effects of diisopropylamine dichloroacetate (DADA), a new PDH kinase 4 (PDK4) inhibitor, in mice with severe influenza.”

Sounds familiar!

Will Fluge and Mella try this, or a similar but perhaps less toxic chemical, next? If we’ve found this information they likely have as well. Moreover, since they work in oncology, this may have been the very thing they were looking to find. Seb, you might well have anticipated their next clinical trial!

Just in case they haven’t seen it, though, I emailed the abstract to them.

Jaime

 

[temple88]

Formation of CO2 and H20 is of course done by the oxidation of acetylCoA.

I find this interesting because I have CO2 values below normal ranges consistently and I don't hyperventilate.

 

[JaimeS]

I find this interesting because I have CO2 values below normal ranges consistently and I don't hyperventilate.

It's considered a marker of metabolic dysfunction by some.

 

[alicec]

citrate is the first molecule of the Krebs cascade, and has the highest energy.

The energy comes from acetylCoA.

if you are thinking of replenishing the Krebs intermediates in order to boost energy, I think you'd want to go for the intermediates that are towards the top of the Krebs cascade,

This strategy will always be limited by the availability of acetylCoA which is needed to react with oxalacetate and form citrate, thus providing another turn of the cycle.

Without sufficient acetylCoA no amount of anaplerotic amino acids will cause another turn of the cycle.

 

[Hip]

This strategy will always be limited by the availability of acetylCoA which is needed to react with oxalacetate and form citrate, thus providing another turn of the cycle.

I am still learning about this, but I don't think you need to start with citrate to derive energy. I think that you can start at any point in the Krebs cascade, and still obtain some energy.

If you insert any of the Krebs intermediates into the mitochondria, they are automatically converted by the Krebs enzymes into the next intermediate down in the sequence, and then that next intermediate is itself converted into the following intermediate, etc, until you reach oxaloacetate, which is the last intermediate in the Krebs sequence.

So say you inserted some alpha-ketoglutarate into the mitochondria: that would commence the Krebs cascade from alpha-ketoglutarate onwards, which would follow these energy-yielding steps:

Alpha-ketoglutarate ➤ succinyl-CoA ➤ succinate ➤ fumarate ➤ malate ➤ oxaloacetate

So you would get a tiny bit of energy out of the inserted alpha-ketoglutarate — but very little, because I agree with you that the acetyl-CoA is crucial, and without the acetyl-CoA, you would only get a "one shot" single run of the Krebs cascade, and the cascade would then stop with oxaloacetate.

As you indicate, acetyl-CoA facilitates a continuous Krebs cycle, because it recycles the oxaloacetate back into citrate, which then starts a new Krebs cascade.


So for all intents and purposes, acetyl-CoA is the only real fuel for the Krebs cycle.



Though insertion of more Krebs intermediates into the Krebs cycle would be effective for increasing Krebs energy generation in cases where there are low levels of these intermediates in the mitochondria. In the case of low levels of these intermediates, even if you have lots of acetyl-CoA, there will not be enough intermediates available and thus not enough oxaloacetate for the acetyl-CoA to recycle. So you get a shortfall in Krebs energy generation not due to lack of acetyl-CoA, but due to a shortage of intermediates.

In my earlier mountain stream analogy of the Krebs cycle, acetyl-CoA is the bucket that brings the water from the bottom of the stream, back to the top and source of the stream. But if you don't have enough water in your stream (= the Krebs intermediates), there will not be enough water for the bucket to pick up and carry, and so the bucket will not be effective.

In the Myhill, Booth and McLaren-Howard (MBM) studies, they think that in some patients, the energy metabolism dysfunction in ME/CFS involves a lack of Krebs intermediates. MBM think that the Group A2 ME/CFS patients are short of Krebs intermediates (also called Krebs substrates), and find that these Group A2 patients can benefit from supplements which boost levels of the Krebs intermediates.

The groups that MBM use to classify ME/CFS patients are detailed in this post.

 

[Hip]

@JaimeS
Dichloroacetate (DCA) was mentioned earlier in this thread; I am thinking of trying it. I read that DCA's side effects are all reversible if caught early, and the neuropathy side effect may be preventable if you take vitamin B1 and a few other supplements with your DCA. See this post.

 

[gregh286]

I am still learning about this, but I don't think you need to start with citrate to derive energy. I think that you can start at any point in the Krebs cascade, and still obtain some energy.

If you insert any of the Krebs intermediates into the mitochondria, they are automatically converted by the Krebs enzymes into the next intermediate down in the sequence, and then that next intermediate is itself converted into the following intermediate, etc, until you reach oxaloacetate, which is the last intermediate in the Krebs sequence.

So say you inserted some alpha-ketoglutarate into the mitochondria: that would commence the Krebs cascade from alpha-ketoglutarate onwards, which would follow these energy-yielding steps:

Alpha-ketoglutarate ➤ succinyl-CoA ➤ succinate ➤ fumarate ➤ malate ➤ oxaloacetate

So you would get a little bit of energy out of the inserted alpha-ketoglutarate — but not very much, because I agree with you that the acetyl-CoA is crucial, and without the acetyl-CoA, you would only get a "one shot" single run of the Krebs cascade, and the cascade would then stop with oxaloacetate.

As you indicate, acetyl-CoA facilitates a continuous Krebs cycle, because it recycles the oxaloacetate back into citrate, which then starts a new Krebs cascade.



Though insertion of more Krebs intermediates into the Krebs cycle would be effective for increasing Krebs energy generation in cases where there are low levels of these intermediates in the mitochondria. In the case of low levels of these intermediates, even if you have lots of acetyl-CoA, there will not be enough intermediates available and thus not enough oxaloacetate for the acetyl-CoA to recycle. So you get a shortfall in Krebs energy generation not due to lack of acetyl-CoA, but due to a shortage of intermediates.

In my earlier mountain stream analogy of the Krebs cycle, acetyl-CoA is the bucket that brings the water from the bottom of the stream, back to the top and source of the stream. But if you don't have enough water in your stream (= the Krebs intermediates), there will not be enough water for the bucket to pick up and carry, and so the bucket will not be effective.

In the Myhill, Booth and McLaren-Howard (MBM) studies, they think that in some patients, the energy metabolism dysfunction in ME/CFS involves a lack of Krebs intermediates. MBM think that the Group A2 ME/CFS patients are short of Krebs intermediates (also called Krebs substrates), and find that these Group A2 patients can benefit from supplements which boost levels of the Krebs intermediates.

The groups that MBM use to classify ME/CFS patients are detailed in this post.

Its very surprising more didnt get relief by taking AAKG from the thread i started complete symptom relief since starting NO2 black.

 

[NexusOwl]

I just recived some results from analysis and I had low lactate in blood... does that sort out a pyruvate dehidrogenase disfunction or it can happen too? It was an analysis that they made me at home, when I was just waking up.

 

[Hip]

Its very surprising more didnt get relief by taking AAKG from the thread i started complete symptom relief since starting NO2 black.

I am not sure if arginine alpha-ketoglutarate as a supplement can enter the mitochondria to supply the Krebs cycle with alpha-ketoglutarate. You can supply alpha-ketoglutarate to the Krebs cycle via glutamate, which is converted to alpha-ketoglutarate. Glutamate is found in Parmesan cheese.

 

[JaimeS]

I just recived some results from analysis and I had low lactate in blood... does that sort out a pyruvate dehidrogenase disfunction or it can happen too? It was an analysis that they made me at home, when I was just waking up.

Very normal for ME patients. It seems it's only elevated wildly after exertion. I had the same findings (in both cases -- low lactate at rest, ridiculously high lactate after activity).

I just double-checked, and yes, Armstrong et al's first paper says that there is low blood lactate in patients, both absolute and relative.

 

[Sidereal]

I just recived some results from analysis and I had low lactate in blood... does that sort out a pyruvate dehidrogenase disfunction or it can happen too? It was an analysis that they made me at home, when I was just waking up.

Low lactate at rest here too. Glycolysis is inhibited in ME/CFS according to Armstrong's paper. It's really a double whammy, we're not producing energy well through either pathway.

 

[alicec]

acetyl-CoA is like a bucket that picks up water from sea level at the lowest point of the stream, and brings that water back to the top and source of the mountain stream, so that the water can once again flow down the mountainside.

A better analogy would be that it represents the effort required to carry the bucket of water uphill.

I don't think you need to start with citrate to derive energy.

You do if you want to derive the benefit of a full turn of the cycle, ie if you want to derive the maximum energy provided by acetyl-CoA.

Of course starting further along the cycle would be of some benefit, but as you say, very small. Why not aim for getting as much as possible?

In the case of low levels of these intermediates, even if you have lots of acetyl-CoA, there will not be enough intermediates available and thus not enough oxaloacetate for the acetyl-CoA to recycle.

Since each step in the cycle generates the next, this could happen in two ways.

1)There is excessive drain on some or all of the anions which leave the cycle for biosynthetic purposes - more than the defective catabolic process identified by Fluge and Mella can cope with. This could be the situation in the people with excessive consumption of anaplerotic amino acids. They are trying to compensate for the excessive drain.

2)There is a problem with one or more of the enzymes in the cycle, hence downstream intermediates are not generated.This could be due to lack of co-factors, blockage of the enzyme by an inhibitor etc.

An OAT test plus plasma and urinary amino acid analysis might give some insight into which of these possibilities is more likely and might point to the likely position of blockage/ drainage. It might then be possible to come up with a more tailored solution.

Failing this, the supplemental program proposed by @nandixon (though for somewhat different reasons) could be useful here. Leucine would help boost acetyl-CoA and glutamate would boost AKG - provided that the blockage/drainage point is not downstream of AKG.

 

[Learner1]

I think a lot of us will be interested in a dietary approach to the pyruvate issue but my impression of the keto approach, from reading the recent threads on this post, is that one could do oneself a lot of damage if one didn't have a ton of biochemical knowledge about how to do it safely (even for a healthy person), and could end up considerably worse, or stuck in some weird loop it's hard to come out of.

Are there medical practitioners with the expertise to supervise such an approach? If so, what's their specialism (including in the UK)?

I've consulted NHS dieticians on various things in the past and have been surprised at their lack of knowledge on all sorts of issues. The last one I consulted hadn't heard that certain kinds of supplemental calcium could cause arteriosclerosis and didn't know about food-related causes of migraine.

I don't feel I know enough to do this diet safely myself and don't know who to ask for help within the medical system.

This is the ketosis expert who spoke at Be n Lynch's conference:

http://alessandroferretti.com/

He's based in the UK and had the respect of the 250 or so doctors in the audience, who were a mix of MDs, NDs, and DCs, answering detailed questions.

We all are genetically unique with different environmental influences. The recent research has been showing this. So, yes, some pathways may be blocked. So, trying new treatment concepts should be lovely monitored, ideally with a good doctor, and labwork.

And this is but one intervention, an important one, but should be accompanied by others. The trouble with anecdotes is you don't always know that person's situation or what else they're also trying...

 

[alicec]

This is the ketosis expert

Who? Do you have a link?

 

[Tunguska]

What might help if mTORC1 is in fact inhibited? See my next post.

I think you can rescue it with opioids http://onlinelibrary.wiley.com/doi/10.1111/cns.12316/pdf (was it just me or do people on this forum have more problems with glutamine than opioids?)

For brain problems, on that giant Isoretinoin side effects thread on another forum, someone pointed out that ketamine - and by extension sarcosine and agmatine - are now thought to probably work by boosting mTor indirectly through AMPA receptor stimulation. Also the isoretinoin mechanisms sometimes resemble a lot some of this discussion, with FoxO activation blamed which is the other side of the coin to PI3K/Akt/mTor. But 5 years after the isoretinoin-foxo1 article no one's really connected enough dots.

(Throwing that out there with nothing else to write at this time)

 

[Learner1]

Who? Do you have a link?

Sorry, I added it above...

 

[Hip]

In his post here, @J.G points out that in acute liver failure, there is actually an anti-mitochondrial autoantibody that specifically targets the pyruvate dehydrogenase E2 subunit (as detailed in this study, and in this Wikipedia article).

And the study suggests that xenobiotic-induced and/or oxidative modification of mitochondrial autoantigens is a critical step leading to loss of tolerance, and then autoimmunity which targets pyruvate dehydrogenase.

Not sure if this might have any relevance to the Fluge and Mella findings. It certainly indicates that an autoimmune response can inhibit pyruvate dehydrogenase.