Antioxidants — the dark side

There was (and probably still is) quite a vogue for antioxidants.  They were supposed to counteract aging, vascular disease, and prevent cancer.  So much so that 25 years ago, they were given in a trial to prevent lung cancer.  It didn’t work.  Here are the gory details

[ New England J. Med. vol. 330 pp. 1029 – 1035 ’94 ] The Alpha-Tocopherol, Beta-Carotene Trial (ATBC trial)  randomized double blind placebo controlled of daily supplementation with alpha-tocopherol (a form of vitamin E), beta carotene or both to see if it reduced the incidence of lung cancer was done in 29000 Finnish male smokers ages 50 – 69 (when most of the damage had been done).  They received either alpha tocopherol 50 mg/day, beta carotene 20 mg/day or both.   There was a high incidence of lung cancer (876/29000) during the 5 – 8 year period of followup.  Alpha tocopherol didn’t decrease the incidence of lung cancer, and there was a higher incidence among the men receiving beta carotene (by 18%).    Alpha tocopherol had no benefit on mortality (although there were more deaths from hemorrhagic stroke among the men receiving the supplement).   Total mortality was 8% higher among the participants on beta carotene (more deaths from lung cancer and ischemic heart disease).  It is unlikely that the dose was too low, since it was much higher than the estimated intake thought to be protective in the uncontrolled dietaryt studies.   The trial organizers were so baffled by the results that they even wondered whether the beta-carotene pills used in the study had become contaminated with some known carcinogen during the manufacturing process.  However, tests have ruled out that possibility.

Needless to say investigators in other beta carotene clinical trials (the Women’s Health Study, the Carotene and Retinoid Efficacy Trial) are upset.  [ Science vol. 264 pp. 501 – 502 ’94 ]  “In our heart of hearts, we don’t believe [ beta carotene is ] toxic”  says one researcher.

This is not science.

On to the present [ Cell vol. 178 pp. 265 – 267, 316 – 329, 330 – 345 ’19 ] in which the following appears “Recent evidence ‘suggests’ that antioxidants can also promote tumor formation”

The work concerns an animal model of nonsmallcell lung cancer (NSCLC).  I’m always wary of animal models, as they have been so useless in pointing to a useful therapy for stroke.  But the model is worth studying as it provides a mechanism by which antioxidants promote metastases of the primary tumor.  It is also worth studying because it shows the fiendish complexity of cellular biochemistry and physiology.

The only way you can appreciate complexity is by being buried in details. So let’s begin.  The actual details aren’t that important, just the number and the intricacy of them.

30% of humans with NSCLC have mutations in two genes (NFEL2L2, KEAP1).  The mutation in NFEL2L2 produces mutated NRF2 (a transcriptional activator of the antioxidant response gene set). The mutation doesn’t inactivate NRF2, but leaves it in a hyperactivated state.  KEAP1 normally inactivates NRF2, but not the mutated forms found in NSCLC.

One gene turned on by activated NRF2 is HO1 (heme oxidase).  During oxidative stress heme is released from heme containing resulting elevated intracellular heme lever resulting in the creation of free radicals which are inherently oxidative.  HO1 destroys heme. So this is one mechanisms of NRF2’s antioxidative activity.

Heme isn’t all bad, as it destabilizes BACH1 (not the composer)which is a prometastatic transcription factor.  Antioxidants (N-acetyl-cysteine, tocopherol [ vitamin E to you ] reduce heme levels stabilizing BACH1 (hence promoting metastasis).  Genes activated by BACH1 include glycolytic enzymes (hexokinase2, GAPDH).  So what?  Cancer cells use a lot of glycolytic enzymes even when oxygen is available — this is called aerobic glycolysis.  This is the Warburg effect.

I’m sure there’s far more to discover, but this should be enough to convince you that things are pretty complicated inside us.

It’s probably too good to be true

SR9009 and SR9011 are drugs which selectively kill cancer cells by an entirely new mechanism.  They mess with DNA but don’t mutate it.  http://www.nature.com/articles/nature25170 [ Nature vol. 553 pp. 351 – 355 ’18 ] has the details.

First a bit of background.  How do the classic hormones (estrogen, androgen, thyroid, adrenal steroids) do what they do?  Clearly they change the expression of many many genes as any post-pubertal woman will attest.  They bind to proteins called nuclear hormone receptors, changing their shape so they can bind to DNA and change gene expression.   We have 48 of them in our genome.  For a long time we didn’t know what the natural ligands of many actually were.  These were called orphan nuclear hormone receptors.  I’m not sure how many orphans are left.

 

SR9009 and SR9011 bind to REV-ERBalpha and REV-ERBbeta which are nuclear hormone receptors. They are agonists (e.g. they cause SR9009 and 11 to do what they do)  Their natural ligand is heme (which isn’t a hormone) and they are involved in the circadian clock.   However they also act as repressors of processes involved in tumorigenesis, including metabolism, proliferation and inflammation.

So the authors threw the agonists at a variety of tumor cells (brain cancer, leukaemia, breast cancer, colon cancer and melanoma) and watched them commit suicide (apoptosis).  They had no effect on normal cells !

How do they work?  There is only speculation at this point.  It is known that SR90xx’s inhibit autophagy, something cancer cells depend on for nourishment.  Normal cells only use autophagy under starvation conditions. They also repress several lipogenic enzymes (fatty acid synthase etc. etc) and cancer cells are said to be dependent on de novo lipogenesis (if they want to proliferate, they got to make a lot of membrane).

It’s almost too good to be true.  Stay tuned.

The uses of disorder

There was a lot of shock and awe about a report showing how seemingly minor changes in an aliphatic group on benzene led to markedly different conformations in its protein target (lysozyme from bacteriophage T4) http://pipeline.corante.com/archives/2015/06/18/tiny_and_not_so_tiny_changes.php.

Our noses are being rubbed in just how floppy proteins are, in contrast to the first glimpses of protein structure obtained by Xray crystallography. Back then we knew so little about proteins, that seeing all the atoms laid out in alpha helices and beta sheets was incredibly compelling. We talked about the structure of a protein rather than a structure. Even back then, with hemoglobin (one of the first solved proteins) it was obvious that proteins had to have more than one structure. The porphyrin ring in heme that oxygen binds to is buried deep in hemoglobin, and the initial structure had to move in some way to allow oxygen to find its way in (because the initial structure showed no obvious channel for oxygen). So hemoglobin had to breathe.

We now know that many proteins have intrinsically disordered segments. Amazingly, the most recent estimate I could find in my notes (or in Wikipedia) is this — It is estimated that over 30% of eukaryotic proteins have stretches of over 30 amino acids that are intrinsically disordered [ J. Mol. Biol. vol. 337 pp. 635 – 645 ’04 ]. Does anyone out there know of more recent data?

We’re a lot smarter now — here’s a comment on Derek’s post — “I have always thought crystal structures of proteins/enzymes are more a guide than actually useful. You are crystallizing a protein first-proteins don’t pack like that in vivo. Then you are settling on the conformation that freezes out- is this the lowest energy form? Then you are ignoring hte fact that these are highly dynamic structures that are constantly moving, sliding, shaking, adjusting. Then if you put a ligand in there you get the lowest energy form-which is what it would look like after reaction and before ligand dissociation- this is quite different from what it can look like at other stages of the reaction.”

Here is an interesting example of the uses of protein disorder going on right now in just about every neuron in your body. Most neurons have long processes, far too long for diffusion to move a needed protein to their ends. For that purpose we have microtubules (aka neurotubules in neurons) stretching the length of the processes, onto which two types of motors attach (dyneins which moves things to negative end of the microtubule and kinesins which move things to the positive end).

The microtubule is built from a heterodimer of two proteins (alpha and beta tubulin). Each contains about 450 amino acids and forms a globule 40 Angstroms (4 nanoMeters) in diameter. The heterodimers pack end to end to form a protofilament. 13 protofilaments line up side by side to form the microtubule, a hollow structure about 250 Angstroms in diameter. In cells microtubules are 1 to 10 microns long, but in nerve process they can be ‘up to’ 100 microns in length. Even at 1 micron (1,000 nanoMeters) that’s 13 * 250 heterodimers in a microtubule.

Any protein structure this important has a lot of modifications imposed on it to alter structure and function. Examples include phosphorylation and the addition of glutamic acid chains (polyglutamylation). The carboxy terminal tails of alpha and beta tubulin are flexible and stick out from the tubulin rod (which is why they aren’t seen on Xray crystallography). The carboxy terminal tail is the site of post-translational glutamylation. The enzyme polyglutamylating the carboxy terminal tail of beta tubular is TTLL7 (you don’t want to know what the acronym stands for). It binds to the alpha/beta tubular heterodimer by an intrinsically disordered region of its own (becoming structured in the process), then it binds to the intrinsically disordered carboxyl terminal tails, structuring them and modifying them. It’s basically a mating dance. There is a precedent for this — see https://luysii.wordpress.com/2013/12/29/the-mating-dance-of-a-promiscuous-protein/

So disordered regions of proteins although structureless are far from functionless