Wednesday, March 25, 2020

From Yeasts to Chloroquine

This paper is from Hughes and Gottschling

An early age increase in vacuolar pH limits mitochondrial function and lifespan in yeast

It got a mention in the blog back in 2012 when it was freshly published. The group have gone on to study yeasts, ageing and the lysosome-like vacuole of yeasts. Their core finding is that vacuolar pH controls mitochondrial "health" which controls ageing, at least in their model.

The group has been very busy and earlier this year this paper was published from Hughes' lab:

Cysteine Toxicity Drives Age-Related Mitochondrial Decline by Altering Iron Homeostasis

The paper describes a very long series (way too many to detail here) of experiments aimed at adjusting vacuolar pH upwards and downwards and observing the effect on the survival of mother yeast cells through repeated cell divisions (replicative age rather than chronological age, there are arguments about which matters most).

Bottom line: Acidifying vacuolar pH extends lifespan, reducing its acidity shortens it.

Why should that be?

Their next series of experiments demonstrated that cysteine toxicity was the driver of early mitochondrial functional decline secondary to loss of vacuolar acidity. Cysteine is normally harmless and essential for life. Your cells love it, just so long as it is within the vacuole (or lysosome in humans), not in the cytoplasm. It's kept there by a vacuolar amino acid transporter driven by the vacuole proton gradient. The pH gradient is generated using a vacuolar vATP-ase to pump protons from the cytoplasm in to the vacuole, using ATP. It's related to the mitochondrial ATP synthase but normally runs in reverse.

If, on a long term basis, vacuolar pH rises (ie the vATP-ase fails), cysteine is released from the vacuole in to the cytoplasm where it auto-oxidises, generating much too much hydrogen peroxide. This reacts with the iron-sulphur clusters of complex I and many other crucial enzymes in the mitochondria. In old age cysteine becomes toxic through vacuolar failure.

I've been interested in this for some time because Barja and Sinclair have both intimated that they are tending to avoid animal proteins in favour of low cysteine/methionine plant proteins. Cysteine is the cellular executioner when vacuole pH rises during the old age of yeasts or lysosomal pH rises in ageing mammalian cells. It's interesting because methionine restriction (which reduces cysteine levels) appears to core to the longevity promotion seen with caloric restriction or protein restriction in mice fed on crapinabag.

You have to wonder whether we are looking at this the wrong way round. What if crapinanbag, based on starch and sucrose, causes early onset lysosomal failure which can be ameliorated by removing the cysteine, which is the cellular execution mechanism?

This would make methionine restriction's longevity extension rather specific to glucose based metabolism. My biases would tend to favour this point of view. There are no data, yet.

As an aside:

Now, I have speculated that both influenza and corona viruses need anabolic processes generated by mTOR activation. This requires acute acidification of the lysosome. Blocking acute lysosomal acidification is one technique currently being investigated for treating the life threatening pneumonia which develops in susceptible individuals during the current COVID-19 pandemic. There are suggestions that chloroquine, a suppressor of lysosomal acidification, might be an effective treatment. My guess is because it blocks anabolism.

There is probably a fine line between suppressing anabolism and releasing a mitochondrial-executing concentration of cysteine.

Neither Hughes nor Gottschling were considering therapeutic inhibition of vacuolar acidification as a stratagem for anything. They were more interested in avoiding long term loss of vacuolar acidity to delay mitochondrial function decline. But blunting anabolism without causing catastrophic cysteine release is a current anti-viral/anti-neoplastic therapeutic target.

You can see that the drug chloroquine a) might work and b) might be very toxic in overdose.

It does currently appear that it might work but we should never forget that "clinical experience is no guarantee of therapeutic efficacy".

However it would be great if it really did work.



  1. Does this suggest fasting as a potential flu/corona therapy?

  2. Chloriquine supposedly a quinine analogue, wonder if that has similar effects?

    One more gin and tonic can't hurt much. Or a Dubonnet.

  3. @Richard
    Feed a cold and starve a fever?

  4. Hi Richard and David,

    Activating AMPK increases vacuolar pH, so yes. Unless starving releases a ton of linoleic acid from your adipocytes and aims you for ARDS on a ventilator...

    Pass, quite possibly so...


  5. This comment has been removed by the author.

  6. peter... do you believe the pkd notion that FASTING = STARVING? ... inst that kinda reductionist ? with good nutrition if you fast lets say 24 hrs you are not really starving at all, having access to all the nutrients, aminos, fats, from previous meals , PLUS your own glycogen and fat stores, calling this privileged situation "starvation" is kinda silly honestly... when i see a sleeping lion after a feast i dont think... the poor guy is starving!
    question: unsweetened cocoa powder interferes with ROS production? what about unsweetened shredded coconut? first one has a bit of stearic acid in it, but maybe the antioxidants are not that good after all? its my only daily source of magnesium
    .thanks ! pablo

  7. Pablo, Starving/fasting. At some point one transitions to the other. I suspect starting with 100kg of adipose tissue might delay the transition but you can also keep AMPK activated by eating a ketogenic diet. I'm more interested in the mechanisms than the labels.

    Where did you get the idea that antioxidants are good? I consider them to be worse than useless. You need ROS signalling. If your liver didn't get rid of exogenous antioxidants they would cause havoc, though some specifically mitochondrially targeted drugs do appear to really do some good, MitoQ for example. I've never really thought much about coconut back when I ate plants. A lot of people seem to get on okay with them, as far as they know...


  8. Peter, would it be fair to say that after around a decade of LCHF eating and avoiding seed oils, and dropping about 17kg in that time, that the risks of high linoleic acid release during fasting is quite low?

    I've been a fan of this blog since about 2010...but I have never been able to work out why high protein is a problem. You mentioned once that you do not like the idea of proteins feeding into the TCA. Running through the Protons thread more than once, I still could not fathom where the problem is. Now that carnivore is a Thing and some of these guys are putting away 200g plus per day, the question is more relevant than ever.

  9. Hi Richard,

    My concern was always about increasing GH secretion with subsequent rise in IGF-1, which is an insulin mimetic and agonist for the IGF-1 receptors that multiple tumour cell types express on their surface. Seemed like a good thing to avoid. However the production of IGF-1 in response to GH is regulated by insulin. If insulin is low enough for ketosis the production of IGF-1 in response to GH is blunted. That's good enough for me to worry less about protein intake. The set of blog posts about the control of IGF-1 by insulin never actually got written!


  10. Thanks Peter - long standing source of confusion resolved!

  11. Peter, since antioxidants were brought up, how do you feel about supplementing Vitamin C, especially in gram to several gram/day doses? This seems to have gained ground even in keto circles, and was promoted recently as good policy against the Corona almost everywhere.

    I have been taking a 1000 mg slow release somewhat regularly for a while but always felt uneasy because it is an antioxidant.

    When Malcolm Kendrick brought it up recently, I asked about my concerns, and he acknowledged they might be relevant, but to him, the beneficial effect on the endothelium is what is decisive against ARDS.

    Others are not so nuanced, e.g. He is recommending 5 g/day, increasing to 1g/h with symptoms, in addition to promoting iodine once again. Somewhere in the comments, he even labelled IV Vit C along with IV ozone and IV peroxide as oxidative treatments.


    According to Sally Norton, oxalates are in the urine at higher doses of c-vitamin..

  13. found the blanket statement by DrB that was bothering me

    right in the very first comments

    18 Mar 2020
    I think we should maintein our iodine levels. But insted of using antioxidants, we should use oxidants. Our defensive system use oxidation to destroid parasites. Also our body works using conbustion, this is create energy from oxidation of glucose. In that sense we can use chlorine dioxide (CDS) as a powerfull tool. The CDS have two good properties, it oxidates whole kind of unicelular parasites and provide the body whit more oxigen.

    Author Icon
    David Brownstein, M.D.
    18 Mar 2020
    YOU GO! Hydrogen peroxide, ozone and IV vitamin C therapies are all oxidant therapies!!

  14. peter maybe i dint express myself correctly, i know antioxidants are not good for ros, thats why i asked about unsweetened cocoa powder... your guess is? btw i do more protein that the regular keto / pkd but there is a reason, in fact 2: i kinda exercise a bit, and fasting. regarding this last one (fasting) old but good

    Efficient adaptation to famine was important for survival during rough times in our evolution. Lowering metabolic rate during starvation allowed us to live longer, increasing the possibility that we might come across something to eat. Starvation literally means starvation. It doesn’t mean skipping a meal not eating for 24 hours. Or not eating for three days even. The belief that meal skipping or short-term fasting causes “starvation mode” is so completely ridiculous and absurd that it makes me want to jump out the window.

    Looking at the numerous studies I’ve read, the earliest evidence for lowered metabolic rate in response to fasting occurred after 60 hours (-8% in resting metabolic rate). Other studies show metabolic rate is not impacted until 72-96 hours have passed (George Cahill has contributed a lot on this topic).

    Seemingly paradoxical, metabolic rate is actually increased in short-term fasting. For some concrete numbers, studies have shown an increase of 3.6% – 10% after 36-48 hours (Mansell PI, et al, and Zauner C, et al). This makes sense from an evolutionary perspective. Epinephrine and norepinephrine (adrenaline/noradrenaline) sharpens the mind and makes us want to move around. Desirable traits that encouraged us to seek for food, or for the hunter to kill his prey, increasing survival. At some point, after several days of no eating, this benefit would confer no benefit to survival and probably would have done more harm than good; instead, an adaptation that favored conservation of energy turned out to be advantageous. Thus metabolic rate is increased in short-term fasting (up to 60 hours).

    Again, I have choosen extreme examples to show how absurd the myth of “starvation mode” is – especially when you consider that the exact opposite is true in the context of how the term is thrown around.

  15. Only in prolonged fasting does protein catabolism become an issue. This happens when stored liver glycogen becomes depleted. In order to maintain blood glucose, conversion of amino acids into glucose must occur (DNG: de novo glucogenesis). This happens gradually and if amino acids are not available from food, protein must be taken from bodily stores such as muscle. Cahill looked at the contribution of amino acids to DNG after a 100 gram glucose load. He found that amino acids from muscle contributed 50% to glucose maintenance after 16 hours and almost 100% after 28 hours (when stored liver glycogen was fully depleted). Obviously, for someone who eats a high protein meal before fasting, this is a moot point as you will have plenty of aminos available from food during the fast.

  16. Hi Eric,

    To me my white blood cells are not generating ROS on exposure to a pathogen for the fun of it. In terms of immediate response to any pathogen such as in COVID-19 I suspect that this oxidative burst may be what makes most people innately immune to the virus (assuming most of Wuhan was exposed and maybe 3% became ill). Bit if I was in the ITU and looking to die from an excess of inflammatory mediators then I would seriously consider high dose C as an approach to limiting the damage, though of course for cancer treatment you need to be looking at doses high enough to have ascorbate act as a pro-oxidant, which it can be. ROS are needed to kill cancer cells, not ROS scavenging. Currently I take no vitamin C. But then I am never hyperglycaemic, rarely hyperinsulinaemic and have been largely avoiding linoleic acid for decades.

    Sadly that is not the case for the majority of people.

    It looks like the virus targets metabolic syndrome, rather than age per se.

    You have to wonder what will happen in the USA, maybe not the world leader for metabolic syndrome but certainly working at this title. In terms of sheer numbers with metabolic syndrome, maybe the USA wins? I’ve never looked at comparative numbers.

    Kajus, no surprise there. Interesting re oxalates, I have vague memories of this from the period that I tried megadosing vit C. There is a paper somewhere on my hard drive that demonstrated guineapigs getting stifle arthritis from high dose oral ascorbate. I wonder if this was the mechanism.


    Addendum to Eric. I think I can simply sum up my stance as: don’t have metabolic syndrome. Everything else might, or might not, help you survive while living on doughnuts (or their equivalent wherever you live).

  17. btw, it goes beyond labels, ists proper understanding the difference.... intermittent fasting ALONE, is a MUCH powerful tool than, atkins, keto, pkd, any other bs diet interventions, combined? trust me autophagy / atp/ mitocondria thrives under that mix... i have the feeling people that dont get fasting are doing something wrong... is just natural... xo

  18. Hi Peter,

    I certainly understand your point, and had come across that previously, that Vitamin C will modulate a runaway immune reaction.

    My question was more about maintenance doses which have been advocated to maintain endthelial health, protect against cancer, and support the immune system, and that are now advocated even more in the context of the CoViD2 pandemic.

    I take it you are rather sceptical?

    Re oxalates, there are several studies out there that seem to conclude that kidney stones from ascorbate are a myth, even if oxalates are generated.

    Edit: the antioxidant vs. pro-oxidant story doesn't seem to be that simple:

  19. Maybe vitamin C here is a little like antibiotics: a cure for certain things, but not a preventative.

    Some things need to get oxidized. I've read articles saying COVID-19 is vulnerable to oxidation; taking megadoses of vitamin C doesn't sound like a good idea with that in mind.

  20. The 'anti-oxidant' view of nutrients has always seemed a bit dim to me. What can be oxidised can be reduced given the right circumstance, acid versus salt etc, not to mention zwitterions. Referring back to the Palaeomedicina link above from Kajus, what are the animal stored forms of vitamin C as opposed to 'vegetable sources'??? If ascorbate is a co-factor in connective tissue building and repair then consuming plenty of collagen should reduce the demand for it but does that mean that skin 'contains' vitamin C???

    For people on a sad diet, vegetable sources of C might be almost obligatory, but maybe not mega. That will be most people. I find that if I have a minor throat infection, chewing a piece of a vit C tablet and gargling with it clears it up for a while. It's a useful topical medication, probably acting as an oxidant. If your diet is otherwise going to hell a bit of C might be an essential nutrient (= conditionally essential).

    What the PK interviewee seems to be saying is 1) vitamin C is important and animal parts contain it and you should eat them to get some so you can store it yourself BUT 2) You shouldn't consume any, it won't do you any good.

  21. Hi Pablo,

    I have no problem with fasting. I climb better if I have not eaten that morning. So eating in a window between 3pm and 9pm is common for me. Also if I’m working I tend not to eat until I get home. I don’t think of either as fasting or starving. I have no desire to go without eating for extended periods unless I get good evidence that what I do currently can be improved on (this does happen occasionally, obviously!). I am quite convinced that we can make potentially large amounts of glucose via acetone and the methylglyoxal pathway. It doesn’t show unless the glucose is extracted from the body, as in lactation. So when muscle catabolism does start there must be a reason, reduced IGF-1 below a certain point?

    Simply infusing palmitic acid IV ups the metabolic rate in rodents. Fatty acids are essential for the function of (most? All?) uncoupling proteins.

    Enjoy your explorations.


  22. What's wrong with these numbers? Maybe enough beds at the beginning then they catch up?

    Infected 90,000
    Dead 10 000

    Infected 100,000
    Dead 1,500

  23. Hi Peter

    There is abundant wealth of information that can be obtained via the web ( also utter bs) regarding the many unique benefits of IF, im sure a privileged inquisitive mind like yours needs no help! heuristics...? i started 15 years ago, doing 24 hrs fast eating like crap, with great results, so i had time to practice in order to find out what really works for me, and how to keep things fresh and working long term, i don't relay on will power at all, i do not wait to eat, NEVER.

    its literately the first thing i do when i wake up EAT ( exercise a bit before some times) fasting comes AS A RESULT of THE DIET... my aim is to achive satiety / glucose stabilization / insulin reduction (not when breaking the fast)desire has nothing to do with this... anyway i will keep reading your blog it has proven to be a powerful source of unique insight

  24. Alta, no one has any idea how many people have been infected. I'm eagerly waiting serology testing data. Should be here soon. Then we can tell how many infections resulted in clinical signs, let alone deaths. The loss of life in the medics is tragic but the medical profession is hardly free from metabolic syndrome.

    Palbo, okay. Until recently I basically never read anything outside Pubmed. I've probably watched a few lectures recently and have indulged in twitter for about a year. I try to think for myself.


  25. Oops, sorry for the typo Pablo!!!!


  26. Peter there was an interview of Ivor Cummins by Dave Feldman a few days ago and at minute 49:10 Ivor is going on and on about how we may be able to get the most bang for the buck by going after cardiovascular disease, high blood pressure, and metabolic syndrome, vs going after lock-down and partial lock-down. Ivor is referring to this as the elephant in the room.

    Also this post at a Boston news outlet has three hyperlinks to the issue of Cell last August that helps us understand why fasting makes the immune system so much more effective when we reduce the nutrient load in the tissues and plasma:
    "'Magic Soup': How Intermittent Fasting May Enhance The Immune System"

    Did you mention something about climbing? In my earlier days there was Ben Moon and Lynn Hill and we all avoided the heinous British grit stone.( scary stuff ) Small world! I think Ivor climbs also with the holds on the background wall in some of his videos.

  27. Fred,

    I did a very small amount of climbing on Stanage Edge in the Peak District while at Uni but nowadays I boulder. Started a year and a half ago. It's sort of addictive. I just hope the climbing wall survives the COVID closure.

    Yes, I guess if you are a standard sort of person with either mild or severe metabolic syndrome just not eating for a few days might get you in to a better position to survive compared to being a hypertensive diabetic. The problem is that I can remember from pre-LC days how extremely difficult skipping even one meal was. A few weeks in to LC and a 48h fast was easy, while cooking for the rest of the family at the same time. It strikes me as difficult to make a ketogenic meal out of pasta, tinned tomatoes and toilet roll. But given how afraid a large chunk of the population is, they might try fasting if given correct information...

    Currently I'm furloughed from work and when my line manager called me to tell me we chatted a bit and my rather Peter-ish comment was that it has never crossed my mind that I might even get ill with COVID-19 let alone die. On brief reflection I suggested this could be my epitaph if I did die of it! She's quite used to me.


  28. "The problem is that I can remember from pre-LC days how extremely difficult skipping even one meal was."

    I know, right? Doing a lot of reading in these socially-distancing days (preference being science fiction), and it's striking me more and more how characters are constantly complaining that they're on the verge of death because they missed a meal or two, or, gawd forbid, a whole day. I struggle to remember pre-LC life – if I went three hours without eating I would get cold and shaky and cry easily.

  29. Oh yes! Junk lunch at 3.30pm, consults through the rest of the day/evening and raiding the biscuit tin at 5.30 between consults! Shaky and jittery. The nurses used to hide the best biscuits from me...


  30. Hi Peter,
    Thanks for all the interesting information.
    Would any of the following change your mind about oral vitamin C?
    There's also a detailed YouTube presentation.