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Proteins or substances you find interesting/cool

Neuroprotection

Bluelighter
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Apr 18, 2015
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Hi everyone. in this thread, I hope to hear about your favourite natural substances or proteins, especially enzymes of biological relevance.
I’ll share some examples in my next post but it can be anything you think is pretty cool or something you think doesn’t get much attention
 
My recent favourites are actually quite surprising given that most of my life, I've been incredibly obsessed with pro-survival pathways like PI3K/AKT ERK1/2 and JAK2/STAT3. fingers, once I understood how these worked I discovered that The substances and enzymes normally implicated in cell death and neurodegeneration have some rather fascinating and cool biological effects independence of their cell killing mechanisms. furthermore, they generally only kill cells when highly activated for a long period of time.
These enzymes are; PTEN, P53, protein phosphatase2A(PP2A) and GSK3. an example of. A proapoptotic small molecule i've come to admire is ceramide which is a powerful activator of many protein phosphatases but especially PP2A. scientists have long thought about blocking these proteins and substances to treat neurodegeneration but never seem to get there, probably because these things have vital and amazing biological functions which are needed for the body and brain to function properly.
What are these amazing properties?:
Most relevant to the brain, protein phosphatases like PTEN and PP2A as well as GSK3 are needed to carry out long-term depression LTD which is the weakening of synaptic strength by removing glutamate receptors from the surface. most importantly, this helps protect against seizures and protects against development of epilepsy. secondly, it prevents saturation of synapses, thus allowing less useful or even harmful memories to be removed and replaced with new relevant ones. interestingly, many forms of autism including severe intellectual disability could be linked to a lack of these phosphatase protein activity.
In terms of neurotransmitter effects, PP2A and downstream GSK3 activity are needed for the behavioural effects of dopamine. I once read an article that warned about the unintended negative affects of using pro-survival strategies like PTEN inhibitors for Parkinson's disease. this is because, whilst switching off. PTEN could theoretically protect dopaminergic neurons, it could also prevent The dopamine D2 receptor from carrying out its downstream functions like stimulating movements in response to dopamine.
In terms of biological effects outside the body, PTEN and many other protein phosphatases are needed to switch off excessive insulin signalling. yes, under conditions of obesity this does lead to insulin resistance and possibly diabetes. however, many people may not realise that insulin resistance is actually a protective mechanism that protects individual cells against nutrients overload and also spares glucose for the brain, thus preventing potentially deadly hypoglycaemia. actually, many researchers have been pushing for the development of drugs that block ceramide production, because apparently doing so can completely prevent insulin resistance even in the face of extremely high fat and sugar diets. yet again, this has never gone beyond lab testing in animals. that's probably because these drugs would have many unintended toxic effects and I imagine they would carry the risk of severe hypoglycaemia. they would also probably promote massive fat storage by enhancing insulin signalling. Note that ceramide works by activating protein phosphatases to switch off AKT which in tern switches off insulin signalling. many may not know this, but insulin resistance can actually promote fat loss because fat cells are less likely to take up glucose and are more likely to release fatty acids into the bloodstream. how long as you exercise, these fatty acids will be burnt off and harm should be minimised. This might be one of the reasons why weight loss is quite easy when starting a weight loss program, but slows down as you lose weight.
These next two points are closely related. Firstly, traditionally proapoptotic proteins like P 53 and above mentioned protein phosphatases can have pro-survival functions by helping cells to adapt to extreme environments. for example, they can enhance fatty acid oxidation as an alternative source of energy, induce antioxidant enzyme expression, slowdown nutrient uptake to prevent nutrient overload and slow down. or halt cell division under conditions of extreme starvation or stress when there is a risk that dividing could actually kill both cells.
Finally, it should be noted that all the proapoptotic proteins I have mentioned generally kill cells when strongly activated and they do so by pretty much the same downstream mechanisms. usually this is rupture of the mitochondrial membrane and activation of CASPASES. however, the beneficial biological effects of these proteins and their small molecule activators like ceramide are actually completely separate from their proapoptotic function.
What does this mean for medical research?
Well, at least in my opinion, it means that blocking things like protein phosphatases or GSK3 is not the answer. Instead, we should focus on blocking their downstream interactions with the mitochondria, which is actually the cause of cell damage and cell death. some scientist have been investigating this, and have demonstrated that it can be done with small molecules.
 
One big concept with kinases and phosphatases, is that they are extremely promiscuous, and specificity is achieved with scaffold and adaptor proteins.

It is not hyperbole to say that common kinases (pka, akt, erk) and phosphatases (pp1, pp2a) are involved in hundreds of discrete signaling pathways, with many occurring simultaneously in a single cell.

PP1 for example doesn't directly bind most of its substrates. Instead there is a cohort of adaptor proteins which bind a small range of substrates, and PP1, thereby giving the phosphatase a measure of precision (as well as constraining the enzyme and its substrate to a precise location in the cell).

I bring this up, because many of the targets you mention would be lethal if knocked out or permanently inhibited. There are certainly pathways that could be inhibited, but global inhibition would be ugly and imprecise.

I recall a coworker looking at the calcium kinetics of cardiomyocytes, and the drug H89, a fairly promiscuous PKA inhibitor would kill them and prevent them from beating at any dose high enough to observe an effect.
 
One big concept with kinases and phosphatases, is that they are extremely promiscuous, and specificity is achieved with scaffold and adaptor proteins.

It is not hyperbole to say that common kinases (pka, akt, erk) and phosphatases (pp1, pp2a) are involved in hundreds of discrete signaling pathways, with many occurring simultaneously in a single cell.

PP1 for example doesn't directly bind most of its substrates. Instead there is a cohort of adaptor proteins which bind a small range of substrates, and PP1, thereby giving the phosphatase a measure of precision (as well as constraining the enzyme and its substrate to a precise location in the cell).

I bring this up, because many of the targets you mention would be lethal if knocked out or permanently inhibited. There are certainly pathways that could be inhibited, but global inhibition would be ugly and imprecise.

I recall a coworker looking at the calcium kinetics of cardiomyocytes, and the drug H89, a fairly promiscuous PKA inhibitor would kill them and prevent them from beating at any dose high enough to observe an effect.


Thank you for building on that, you explained it much better than I could, well, actually, you added New details which gave a more holistic view of the topic. my overall basic point was in agreement with what you stated, trying to inhibit these supposedly proapoptotic phosphatases as well as GSK3 it’s probably going to cause more cell damage or cell death then the disease/condition one is trying to treat.
In line with what you said, my other main point was that The proteins are mentioned I only proapoptotic because of very specific, often common downstream targets which as you said often needs scaffold proteins to direct them there. Most of these targets are situated in the mitochondria or in the nucleus.
Thanks again for your reply
 
trying to avoid making another mega post so I’ll be quite briefe with this example.
P53 is most famous for causing apoptosis but this is only a Single function among a massive range of effects most of which are actually cytoprotective. P53 induced apoptosis is due to transcriptional upregulation of proapoptotic downstream proteins like PUMA, BAX and BAD. if these proteins are inhibited or knocked out, P53 accumulation will often make cells unusually resilient to environmental stresses via mechanisms like increased energy production, DNA repair, stopping the cell cycle/cell division, decreasing harmful levels of glycolysis and activating antioxidant enzymes on a large scale.
According to one study, I read the P 53 inhibitor, pifathrin Alpha and analogues offer unique benefits for neuro protection as well as protection against radiation and chemical toxicity because these inhibitors only target the proapoptotic Domain of P53 whilst leaving all of the beneficial functions intact.
 
I always wondered what the effects of 3,4-methylenedioxy-2-diphenylmethylpiperidine would be like. Otherwise I'm interested in mainly T.H.C. and substances like P.C.P.y and P.C.P. along with L.S.D. and psilocybin.
 
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Right now I'm interested in studying the Bromo-DragonFly compound. I'm wondering what would happen if you replaced the two Furan's on opposite sides of the Phenyl with two Methylene dioxy's.
 
Starting this week I decided to study what makes things stronger and last longer. I looked at MDMA and 4-methylaminorex and figured the 4-methyaminorex last longer than Methamphetamine. I was also comparing Methlene dioxy to Dioxolane which is structurally similar. Putting two and two together. I came to the conclusion that Dioxolane-4-Methylaminorex would possibly be more potent and last longer than MDMA, but thats just a hypothesis and it hasn't been tested. I how ever would like to test out my designs and see how well Dioxolane-4-Methylaminorex works. And if did turn out to be something better than MDMA then that would just make my day.
 
Starting this week I decided to study what makes things stronger and last longer. I looked at MDMA and 4-methylaminorex and figured the 4-methyaminorex last longer than Methamphetamine. I was also comparing Methlene dioxy to Dioxolane which is structurally similar. Putting two and two together. I came to the conclusion that Dioxolane-4-Methylaminorex would possibly be more potent and last longer than MDMA, but thats just a hypothesis and it hasn't been tested. I how ever would like to test out my designs and see how well Dioxolane-4-Methylaminorex works. And if did turn out to be something better than MDMA then that would just make my day.


These are interesting concepts but unfortunately, my comprehension of chemistry is extremely bad. also, whilst I don’t want to discourage you from posting your excellent knowledge, I was hoping this thread would be more for the discussion of biological pathways and how they link to effects on human behaviour or metabolism. examples would be things like transcription factors, enzymes, ion channels, receptors and Epigenetics.
What I hope to do is simplifying clarify how exactly these biological pathways lead to their impact of interest.
You are welcome to carry on posting here although it’s probably much more effective if we create a new thread for your chemistry related topic. that way, the two topics won’t get mixed up and to be honest, i’m sure you’ll get a lot of responses because many people on here have a deep interest in chemistry.
 
Well, I don't know too much about biology, but I can tell you what I'm working on right now. What I'm thinking about right now is two P.E.A.'s. One is 3,4-Dimethoxy-4-Methamphetamine and the other is 1,2,5-Oxodiazole-Methamphetamine. There not M.D.M.A., but close to it. What I'm really doing is coing up with these designs and studying them. Of course all the stuff I come up with is hypothetical.
 
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