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Dr Trevor Marshall
Research Team
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Posted: Thu May 15th, 2008 19:33 |
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A new paper is out on the PXR - a detailed in-vitro study of agonists.
Download the PDF from http://www.biomedcentral.com/content/pdf/1471-2148-8-103.pdf
or browse the main text at http://www.biomedcentral.com/1471-2148/8/103
Of note is confirmation of Hyperforin (St John's Wort) and new ones (to me) like TCDD (Dioxin).
I note that this paper saves me the bother of checking out Lithocholic acid, which is now confirmed as a PXR target. There are many Pubmed papers saying that the VDR is a target for Lithocholic Acid, but I have previously said that my modelling does not show that, and I suspected it was an error introduced by these wet-biology studies not contemplating the existence of PXR, or its key role in the VDR metabolism.
Although many steroid agonists were identified, it is unclear to me whether they would exist in-vivo at the concentrations identified in this study.
Of interest is that they found that 1,25-D and 25-D were not agonists. Since my in-silico work has identified the very high affinity they have for the PXR, it follows that they must be antagonists, which is what I had deduced and published in our recent paper "VDR discovery outpaces .. etc" (figs 1,2 of my paper).
Anyway - I have printed out this article and will read it in my spare time  over the next few days... Let me know if you find anything significant...
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Lottis
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Posted: Fri May 16th, 2008 15:46 |
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| Is it a antagonist with what kind of noncovalent binding? Last edited on Fri May 16th, 2008 15:53 by Lottis
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Dr Trevor Marshall
Research Team
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Posted: Fri May 16th, 2008 17:04 |
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Lottis, please see Fig 2 of my "Vitamin D Discovery outpaces... " paper:
http://TrevorMarshall.com/BioEssays-Feb08-Marshall-Preprint.pdf
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Lottis
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Posted: Sat May 17th, 2008 14:08 |
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Ok, I will have to think deeper.  Thank you for helping me understand! 
I am very excited about these findings and the consequences it has to the metabolism of everything that we are exposed to. I can hardly think about anything else, these days! We can do so much based on these results!
I have already drawn a lot of conclusions from this, that I am astonished about, which is of course affecting understanding the development of my own sickness and response to medicines and food. I would have to enrole back to university and get a doctors degree based on your findings, so that I do not waste my precious time on learning your discoveries just for myself!
I have copied a part here from your BioEssay paper. I hope it is OK and that you don' t mind that I put my questions right inside;
from page 3...Now it gets more complicated
The rest of the D metabolism is less well defined. Nevertheless,
the aim of this essay is to explore the challenges we face as we try to translate the molecular complexities of the D metabolism into a clinical environment. It is therefore important to identify a consensus model from the jumble of published Murine, human, and in-silico studies.
This is the thrilling part, new doors are being opened up if we look at it closely. This is a subject for a lot more explanation and research to come. Could you please make a list of the few missing links for further research.
The observation has been made that the enzyme CYP3A4(26) [EC:1.14.14.1] is more active than CYP24A1 in the human intestine and liver(27).
This enzyme was therefore added to the model (Fig. 1).
CYP3A4 is a metaboliser of a huge amount ob substrates, and is being regulated by a lot of our common foods. Getting the understanding on how it interacts with the VDR mission, is like reading a spy novel! This is exciting!
The VDR is a member of the NR1I subfamily of type 1 nuclear receptors(28). For Homo sapiens,
the other members of this family are the pregnane X receptor (PXR, SXR) and the constitutive androstane receptor (CAR).
This might be the Royal family of the human body! They certainly control the army of defence. What could possibly be more decisiv.
PXR has been shown to induce transcription of CYP27A1(29). PXR has also been reported to competitively down-regulate the VDR-induced expression of CYP24A1(27,30). PXR is an unusual transcription factor, with an LBP which enlarges to allow activation by large molecules, such as rifampicin, or shrinks to accommodate smaller molecules, such as the steroids.
It is not yet known which endogenous ligand(s) modulate PXR expression of either CYP27A1 or CYP24A1.
Rifampicin was used as the agonist during the CYP27A1 study(29), but it is clear there must also be endogenous ligands. CYP 24A1 inactivates/decreases the amount of 1,25 D and CYP 27B1 transforms 25-D to 1,25 which increases 1,25 D, and we do not yet know what it is that modulates the PXR to do this. Could it be bacteria, prions and even electromagnetic fields? Could healing or mental control be a part of this?
A structural model of the PXR with the smaller LBP has just been published(31), as [PDB], and we have used our nuclear receptor modeling methodology(32,33) to show that 1,25-D binds into this PXR structure, as an antagonist, with very high affinity (unpublished work).
It almost certainly will competitively displace the native ligand(s) at physiologic concentrations. Fig. 2 shows the minimum energy conformation of 1,25-D superimposed upon the T1317 agonist from [PDB].
How does this bond replace the native ligands? Why would nature want it to be in that way? Could this be the most important environmental factor?
The mathematical modeling also shows that 25-D and 1,25-D have similar affinities for the PXR LBP, as their antagonistic potential is largely independent of the 1-alpha hydroxylation. This would suggest that
feedback mechanisms dependent upon the concentrations of 25-D and 1,25-D, in addition to those from VDR activation, can modulate the expression of CYP27A1 and CYP24A1,
and therefore regulate the concentrations of both 25-D and 1,25-D. I see a balance board before me, with a mummy on one side and the daddy on the other, rocking the child up and down to stimulate and make him happy. Could the pulsing effect be of meaning?
Finally, Wang, et al., have located
a possible VDR response element (VDRE) near the gene for CYP27A1(5). This element is discrete and separate from the putative PXR response elements located by Li, et al.(29), and suggests a role for the activated VDR in the expression of CYP27A1.
However, this final feedback pathway has been omitted from Fig. 1, as we currently have no evidence it is expressed, and no clinical observations which would support its presence. This CYP27A1 is thought to be involved in the the degradation of cholesterol into bile acids, and high cholesterol is common in Th1 diseases, so a inactive VDR would not help here. This is very interesting. This is already a fact in the clinical study, is it not?
Thank you for your hard work! /Lottis
Last edited on Sat May 17th, 2008 14:19 by Lottis
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Lottis
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Posted: Sat May 17th, 2008 19:23 |
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I don't know but I think this is important. 
According to how the different CYP's are classified, they seem to be some kind of cooperation or similarities within the groups, classes and families and it is not obvious on what those factors are.
So the CYP27A1 and the CYP27B1 could do more things together than what has previously been known.
Read at this web page: http://www.ebi.ac.uk/interpro/IEntry?ac=IPR002397
| Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity. |
There is a lot more here to discover! Is anyone with me? /LottisLast edited on Sat May 17th, 2008 19:24 by Lottis
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NickBowler
Member in Phase 3
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Posted: Thu May 22nd, 2008 09:43 |
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Here are some articles I found that illustrates 2 points - Firstly that there are other 'no pain no gain' treatment protocols out there, in case anybody was doubting the wisdom of following MP. The term ‘paradoxical pharmacology’ has been coined for these, and in one sense I think MP can join the list, after all it appears at first sight counter intuitive to make use of a VDR agonist (benicar) treatment when TH1 disease sufferers are already awash with a VDR agonist (1,25 D).
Secondly it shows that receptors are not just simple on/off switches. Maybe some of the vitamin D metabolite interactions with various nuclear receptors are of the 'inverse agonist' type rather than antagonists. It might explain a few of the more unusual observations.
http://www.scienceagogo.com/news/20080309193820data_trunc_sys.shtml
http://www.newscientist.com/article/mg18024185.700-what-doesnt-kill-you.html
http://en.wikipedia.org/wiki/Inverse_agonist
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wrotek
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Posted: Fri May 23rd, 2008 13:49 |
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Regarding TCDD dioxin, it's half life is 8 years in humans ! 
This makes me wonder, what if bacteria can produce a ligand that lasts for a very long time, accumulates, and exerts its VDR inhibitory effect long after the infection has been eliminated ? Hmmmm...... Is it probable ?
Dioxins accumulate in food chains in a fashion similar to other chlorinated compounds (bioaccumulate). This means that even small concentrations in contaminated water can be concentrated up a food chain to dangerous levels due to the long biological half life and low water solubility of dioxins. The estimated elimination half-life for highly chlorinated dioxins (4-8 chlorine atoms) in humans ranges from 7.8 to 132 years
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Lottis
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Posted: Sun May 25th, 2008 23:50 |
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Dr Trevor Marshall wrote: I note that this paper saves me the bother of checking out Lithocholic acid, which is now confirmed as a PXR target. There are many Pubmed papers saying that the VDR is a target for Lithocholic Acid, but I have previously said that my modelling does not show that, and I suspected it was an error introduced by these wet-biology studies not contemplating the existence of PXR, or its key role in the VDR metabolism.
Could it be like this; Lithocholic acid activates CYP 3A4, which interacts with VDR and the enzyme to metabolise lithocholic acid is created, and the danger is gone.
If I do it backwards, lithocholic acid (LCA) induces its metabolism through VDR interaction. It could be through the CYP 3A4 induction.
Lithocholic acid is a rest product from metabolization of bile acid, which has been broken down by the CYP2B6. The bile acid is a rest product from the metabolization of cholesterol, which has been initially broken down by the CYP27A1. So, the induction och inhibition of CYP 2B6 is involved in the cholesterol metabolism, Which somehow is involved in the VDR-PXR-CAR relationship.
Phenobarbitates has been noticed to dysregulate vitamin D metabolism. Even though this paper is not properly identifying the PXR effect on the CYP24, it does have some interesting points.
Phenobarbitates have earlier one been used for breaking down bilirubin in newborn babies, but nowadays it is being done by letting the baby lay under a strong UVA lamp. It seems like this have something to do with the 1,25 D?
The phenobarbitates are inducing most of the P450 cytochrome but very much inducing the CYP2B6.
Grapefruit juice is also inhibiting CYP3A4 as well as influx-(OATs) and efflux- (P-gp) Grapefruit seed extract has also recently been reported in Sweden to induce spontaneous bleeding, especially in mucous membrane. Within only three days the Pk-INR had drastically risen to dangerous levels.
The CYP2B6 is inhibited by Grapefruit juice. So, if such a powerful compound is inhibiting the CYP2B6, which creates litocholic acid, maybe we should have a closer look at this one?
/Lotus
Last edited on Sun May 25th, 2008 23:55 by Lottis
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HTN,LVH,CHF,arrhythmia,hypercholesterol,IBS? fibromyositis?e.c.t.|15feb-07 init. 1,25D 37,5,|25-D 7,8(latest 15/2-07)| Ph1 29/5-08|Med;Cardizem|Atenolol|Inspra|Lasix|Stesolid|Magnyl|NoIR's|covered up|disabled|
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