19 Jul 2008
By this point, people familiar with the Marshall pathogenesis realize that the Vitamin D Receptor plays an extremely important role in activating immune function and keeping the chronic, intraphagocytic bacteria that cause inflammatory disease under control.
But when the vitamin D feedback pathways fleshed out by Marshall in a recent BioEssays paper are examined, another important receptor enters the picture.[1] It goes by the name of the Pregane X Receptor (PXR), and like the VDR, the PXR is also a nuclear receptor. Mainstream researchers generally understand that the PXR plays an important role in regulating the metabolism, transport, and excretion of exogenous compounds, steroid hormones, vitamins, bile salts, and xenobiotics (chemicals that are foreign to the body). However, they are only recently beginning to understand that the receptor is also intricately connected to VDR function, vitamin D metabolism, and proper regulation of the vitamin D metabolites.
The PXR is unique in the sense that its ligand binding pocket (the place where other molecules can dock into the receptor) enlarges to allow for activation by large molecules or shrinks to accommodate smaller molecules such as the steroids.
Marshall’s model of vitamin D metabolism predicts that blockage of the VDR will cause problems with the feedback pathways that keep levels of the vitamin D metabolites 25-D and 1,25-D in the correct range. To be more specific, when the VDR is blocked by bacterial substances and 25-D, it can not longer transcribe an important gene that under normal circumstances allows for the transcription of CYP24A1, an enzyme whose role is to inactivate excess 1,25-D. However, while it is the VDR’s job to transcribe the gene for CYP24A1, the PXR actually induces transcription, or actual creation, of the enzyme. This means that any molecule capable of slowing the activity of the PXR also allows for less production of CYP24A1.
The consequences of the above are two-fold. If the VDR is blocked, it will transcribe the gene for CYP24A1 at a greatly reduced rate. If the PXR is blocked, the actual creation of the enzyme will be thwarted as well. Under such circumstances, the amount of CYP24A1 in the tissues drops significantly, meaning that 1,25-D is able to reach unnaturally high levels without any system to keep it in check.
But what blocks the PXR? After deriving data from a structural model of the PXR that has just been published, Marshall used nuclear receptor modeling to show that 1,25-D binds the PXR and slows its activity, acting as a strong antagonist. According to Marshall, “[1,25-D] almost certainly will competitively displaces the native ligand(s) [of the PXR] at psysiologic concentrations.” This means that high levels of 1,25-D slow PXR activity, blocking production of the CYP24A1 that would otherwise cause 1,25-D to be broken down to other forms of vitamin D.
Still, a skeptic might ask, “Besides Marshall’s in silico data, how do we know that 1,25-D inactivates the PXR causing a drop in the production of CYP24A1?”
In a study recently published in BMC Evolutionary Biology researchers performed a detailed analysis of molecules that activate the PXR. They ended up detecting numerous compounds that activate (serve as agonists) of the receptor. Interestingly, 25-D and 1,25-D were not among the compounds that they found to be PXR agonists. This strongly suggests that, as Marshall puts forth, the vitamins D do indeed serve as antagonists of the PXR.
“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 figures 1 and 2 of my paper [BioEssays 2008],” states Marshall.
One of the PXR agonists detected by the team was Hyperforin, or St John’s Wort. Now that it is confirmed as a PXR target, Marshall warns against its use, essentially because any molecule that interferes with the receptors that control the vitamin D receptors is likely to dysregulate immune function.The team also noted that another primary target of the PXR is rifampicin. Since rifampicin (a drug often used to treat infections) is derived from streptococcal bacteria, one could say that the PXR is essentially activated by a pathogen, a reality compatible with the fact that pathogens themselves can directly affect the body’s receptors and feedback pathways. Furthermore, the PXR is also strongly activated by dioxin, a compound that has been linked to an increased risk of cancer. According to Marshall, the fact that dioxin binds the PXR with such a high affinity provides a possible pathway for how the substance causes damage to the immune system.
The VDR and PXR work in such a symbiotic fashion that the two receptors likely evolved from the same base structures. Such PXR/VDR homology fits nicely with Marshall’s view of the immune system. When asked about the immune system, Marshall emphasizes that it was not designed in order to accomplish specific tasks – its creation was never planned. Rather, it simply evolved. Because evolutionary processes are ruled by chance, not everything a particular receptor or cell type does is necessarily beneficial. Yet, it can be assumed that those components of the immune system that remain with us today exist because the bulk of what they do is useful. Certainly the majority of functions performed by the VDR and the PXR are critical to our well being.
9 Responses for "Laboratory study on PXR supports Marshall’s in silico model of Vitamin D metabolism"
I have 2 thoughts on this interesting article:
I find it curious (perhaps preposterous) that the very molecule that the PXR is supposed to eliminate can itself block that action! The creator must have been asleep at the switch when that system was designed.
Why do we assume that if a molecule is not an agonist, then it must be an antagonist? Maybe its the Switzerland of microbiology, a neutral entity.
Phil
@phil
The mechanism needn’t be perfect. It just needs to work long enough for the organism to successfully reproduce.
I, too, often wonder why a non-agonist must automatically be an antagonist. There seems to be a lot of this sort thing going on in the Marshall Theory. Apparently the general medical assumption is that a chemical is assumed to be an antagonist if it will chemically interact with one of the receptors. All of this ligand-receptor business is about homeostasis and it appears that most of the ligand-receptors are there for negative feedback (to slow something) and it’s a rare case when they cause positive feedback.
I think in this case since the Ds will plug in there at all we have to assume they will cause negative feedback or just disrupt the system entirely because the authors would have mentioned the fact that they saw agonist behavior by the Ds.
It may be that the theory is still evolving and a cogent layman-friendly version can’t easily be produced. Every time I think I have it I discover that I have missed some key element and I really have no clue what I’m talking about…as I’m sure the next commenter will point out.
Phil, Douglas,
I believe that when a molecule binds a receptor it inevitably changes the activity of the receptor, at least to a certain degree.
I am guilty of referring to receptors as switches, which I do in order to help the average person understand agonism and antagonism.
But in reality a receptor isn’t very much like a switch. Rather, it’s a molecule with a certain shape and it has a binding pocket where molecules with other various shapes and sizes can fit. Myriad molecules will pass by a receptor in the matter of a second but only a few might actually dock into the binding pocket. If they do, it’s because their shape is in some way compatible with the binding pocket – sort of a lock and key effect.
Then, when a molecule with a certain shape binds the receptor binding pocket the fact that a fit is established elicits a change in the shape of the receptor/ligand complex – a change in conformation. This change in shape is then going to affect what DNA the receptor transcribes.
So if a ligand binds a receptor it does so because it has evolved a shape that correlates with the receptor’s shape. It probably wouldn’t have evolved such a shape if it didn’t have some purpose for having the shape. So when it binds the receptor, a change is bound to take place.
So no, I don’t think that there are ligand/receptor interactions that don’t result in antagonism or antagonism at least to a small degree. If there are molecules that do bind receptors with no purpose then I would assume they would gradually be eliminated by evolutionary forces and are thus rare.
Best,
Amy
What I find amazing Amy is that the molecular modeling finally allows to start to fully understand the action (and the important side-effects) of many dugs that were before just empirically explained and observed on mice and groups of volunteers. We can arive to shocking dicoveries yet. Dr. Marshall showed us already how to shake the pharm industry and FDA… (statins, sartans). They will have to be much more careful form now, as this new wind arrives to this industry.
Hi Petr,
Yes, a molecular model is capable of discerning interactions and relationships that sometimes simply cannot be determined by a clinical trial. It’s hard to argue with accurate mathematical data, although of course, there is always some degree of uncertainty even when it comes to modeling.
That’s why the best molecular models are, in my opinion, those that hold true in a clinical setting. And the MP is does exactly that. The treatment has allowed Dr. Marshall’s in silico model to be confirmed by the reactions of human subjects, making it even harder to contest.
Best,
Amy
Amy,
I have some basic questions regarding ligands and their interactions with receptors. We know from TM’s tables that different ligands have different binding energies with various receptors. So…
1. Can ligands with higher binding energies displace others after the others “got there first”?
2. How long must a ligand dock with a receptor before DNA transcription is affected?
3. Once a high binding ligand docks with a receptor does it remain docked until the cell dies?
4. How many PXR’s or VDR’s does a cell have? One of each? Thousands of each? Variable of each?
5. Are these receptors located in the nucleus of the cell? (Or as W would say, the newculus, or new clueless).
Finally, you state that “So if a ligand binds a receptor it does so because it has evolved a shape that correlates with the receptor’s shape. It probably wouldn’t have evolved such a shape if it didn’t have some purpose for having the shape.”
This makes it sound as if a specific shape is developed for a specific binding pocket. Yet we know that a specific shape will bind with a variety of pocket shapes, each with a different level of attraction. There doesn’t seem to be a perfect ligand/receptor match, but a full range of good, fairly good, doggone good, and very strong matches.
This raises the disturbing question of a ligand that has a strong attraction to two different receptors (Or two ligands having a strong attraction for the same receptor). Could you get a situation where one pair would be a desirable effect, while the other pair produced undesirable consequences?
Thanks for suffering these questions,
Phil
Hi Phil,
Good questions! Here are my answers. I’m not sure these are completely right, these are just my impressions:
1. I believe the answer is yes. The ligand with a higher affinity will have a more compatible shape for the receptor and may try to squeeze in, displacing another ligand.
2. I think DNA transcription happens quite soon after a particular ligands docks into a receptor, probably starting immediately.
3. Absolutely not. Ligands are always jostling with each other for binding supremacy, no matter what their affinities is for a particular receptors. A ligand with a high affinity may spend more time in a receptor but it is never there permanently.
4. Around hundreds or thousands. I’m not sure of the exact number and it definitely depends on cell type. At first researchers thought the vitamin D was only produced in the skin cells. Now they know the VDR is also present in many other tissue types including cells of the bone marrow and the endometrium. For all we know every cell type may express the VDR, it’s just that not enough research has tested for its presence in specific tissues.
5. In the nucleus. That’s why the VDR is a type 1 NUCLEAR receptor.
You’re right, most ligands can bind many different receptors. For example, 25-D binds the VDR, PPAR gamma, the alpha/beta thyroid receptors, the androgen receptor, the progesterone receptor, the glucoccorticoid receptor and others. Ligand and receptor binding is always a balancing act, with ligands constantly moving and binding into new sites.
It’s definitely possible that a ligand could bind one receptor and elicit a positive effect and bind another and elicit a negative effect. Evolutionary forces do not result in perfection. Yet as I stated at the end of the piece:
“Because evolutionary processes are ruled by chance, not everything a particular receptor or cell type does is necessarily beneficial. Yet, it can be assumed that those components of the immune system that remain with us today exist because the bulk of what they do is useful.”
Nevertheless, when deciding to use a drug for a certain purpose, it’s important to know that that same drug does not bind other receptors (besides its intended target) and produce a negative effect. That’s why molecular modeling data is so useful. Such information can simply not be obtained from a clinical trial.
Hope this helps!
Amy
Hi Amy,
In the text I think there is a typo, instead of
“CYP27A1, an enzyme whose role is to inactivate excess 1,25-D.”
Should be
“CYP24A1, an enzyme..”
According to Marshalls paper “Vitamin D Discovery outpaces FDA decision making”
Isn´t it?
best regards,
Alex
Hi Alex,
You are absolutely right. Thanks very much for pointing that out. Good work interpreting Trevor’s Bioessay!
Best,
Paul