Detox/Biotransformation Pathways Overview

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Description Of The Various Biotransformation/Detox Systems In The Body

Links to detailed descriptions of  these systems are on the Detox/Biotransformation Pathways page.  A beginners guide to what detoxing is will be found there also.


Phase I Biotransformation

Phase I transformation of most chemical toxins involves a group of isoenzymes.  Phase I enzymes are our first defense against toxins. Although they are in all cells of the body, they are in great number in the endoplasmic reticulum of the liver cells. You will hear them called microsomal enzymes. Although there are several types of phase I enzymes, the most common enzymes are the cytochrome P450 (CYP450). Usually when people talk about Phase I enzymes, they are talking about the CYP450 system enzymes. The CYP450 enzymes are also essential for the production of numerous agents including cholesterol and steroids. There is so much known now about CYP450 enzymes and their activity that even a cursory explanation needs its own page. Please see the detailed explanation of CYP450 System here.

Phase II Transformation

The enzymes involved in phase II reactions are mainly located in the cytosol, except glucuronidation enzyme, which is also a microsomal enzyme similar to the phase I enzymes. Phase II transformation typically involves conjugation in which various enzymes in the liver cells (or other cells at lesser amounts) attach small chemicals to the toxin. This conjugation reaction either neutralizes the toxin, or makes the toxin more easily excreted through the urine or bile. Phase II enzymes act on some compounds directly. Examples would be ciprofloxacin, propranolol, bilirubin, diflunisal, acetaminophen, and thyroxin. Other compounds must first be activated by the phase I enzymes to add a functional group before conjugation can take place. There are essentially six phase II transformation pathways.

Conjugation reactions generally serve as a detoxifying step in metabolism of drugs and other xenobiotics as well as endogenous substrates. However, these conjugations can add to toxicity due to the metabolic formation of toxic metabolites such as reactive electrophiles.

In order to work, both Phase I and II enzyme systems need nutrients. In addition, they utilize metabolic energy to function and to synthesize some of the small conjugating molecules. Thus, mitochondrial dysfunction, a magnesium deficiency or physical inactivity, can cause phase II detoxification to slow down, allowing the build-up of toxic intermediates. Phase II is especially affected by inadequate energy in the form of ATP to carry out conjugation.

The 6 transformation pathways of Phase II

Below are short synopsis of each conjugation reaction. For more details on each one go to glucuronidation, sulfation, conjugation with amino acids, conjugation with glutathione, methylation and acetylation.

Some of the conjugation pathways seem to share phase III transporter proteins that move the conjugated items out of the cells. The multidrug resistance protein (MRP) 1 (encoded by ABCC1) and the related MRP2 (ABCC2) are adenosine triphosphate (ATP)-binding cassette transporter proteins that can work synergistically with phase II conjugation pathways to reduce the accumulation of a broad range of glutathione- (GSH/GS−, γ-Glu-Cys-Gly), glucuronide- and sulfate-conjugated organic anions. In addition, MRP1 and MRP2 require GSH for the transport of certain unconjugated and conjugated compounds.

Glutathione conjugation

A primary phase II transformation route is conjugation with glutathione (a tripeptide composed of three amino acids—cysteine, glutamine, and glycine). Through direct conjugation, it detoxifies many xenobiotics (foreign compounds) and carcinogens, both organic and inorganic. This includes heavy metals, such as mercury, lead, and arsenic. Glutathione conjugation is probably the most important detoxification pathway for industrial toxins and carcinogens and 60% of toxins excreted in the bile are excreted in this way. Glutathione conjugation also produces water-soluble mercaptates which are excreted via the kidneys. The elimination of heavy metals like mercury and lead, is dependent upon adequate levels of glutathione, which in turn is dependent upon adequate levels of methionine and cysteine. When increased levels of toxic compounds are present, more methionine is utilized to make cysteine and ultimately glutathione synthesis. Methionine and cysteine have a protective effect on glutathione and prevent depletion during toxic overload. (See the methylation cycle diagram to understand how they are necessary in the creation of glutathione.) This, in turn, protects the liver from the damaging effects of toxic compounds and promotes their elimination.

Glutathione is also an important antioxidant. This combination of detoxification and free radical protection, results in glutathione being one of the most important anticarcinogens and antioxidants in our cells, which means that a deficiency is cause of serious liver dysfunction and damage. Exposure to high levels of toxins depletes glutathione faster than it can be produced or absorbed from the diet. This results in increased susceptibility to toxin-induced diseases, such as cancer, especially if phase I detoxification system is highly active and Phase II can't keep up. Disease states due to glutathione deficiency are not uncommon. Health conditions like mold susceptibility (CIRS due to water-damaged buildings), Parkinson's and Alzheimer's have been linked to glutathione deficiency. Glutathione is needed to protect us from damage due to cigarette smoke, radiation exposure, and alcohol to name a few issues. Glutathione provides the major intracellular defense against mercury-induced neurotoxicity. High levels of mercury will use up glutathione.

For details on glutathione, including how to increase glutathione in the body: See more data on Glutathione here.


Amino Acid Conjugation

Several amino acids are needed for amino acid conjugation. Glycine, taurine, glutamine, arginine, and ornithine are used to combine with and neutralize toxins. Of these, glycine is the most commonly utilized in phase II amino acid detoxification. Patients suffering from hepatitis, alcoholic liver disorders, carcinomas, chronic arthritis, hypothyroidism, toxemia of pregnancy, and excessive chemical exposure are commonly found to have a poorly functioning amino acid conjugation system. For example, using the benzoate clearance test (a measure of the rate at which the body detoxifies benzoate by conjugating it with glycine to form hippuric acid, which is excreted by the kidneys), the rate of clearance in those with liver disease is 50% of that in healthy adults.

Even in normal adults, a wide variation exists in the activity of the glycine conjugation pathway. This is due to genetic variation, as well as the availability of glycine in the liver. Glycine, and the other amino acids used for conjugation, become deficient on a low-protein diet. Of course chronic exposure to toxins results in depletion also.

Adequate dietary protein is necessary for availability of these 5 amino acids.


Methylation involves conjugating methyl groups to toxins. Most of the methyl groups used for detoxification come from S-adenosylmethionine (SAM). SAM is synthesized from the amino acid methionine, a process which requires the nutrients choline, vitamin B12, and active folate. SAM is able to inactivate estrogens (through methylation), supporting the use of methionine in conditions of estrogen excess. Its effects in preventing estrogen-induced cholestasis (stagnation of bile in the gall bladder) have been demonstrated in pregnant women and those on oral contraceptives. In addition to its role in promoting estrogen excretion, methionine has been shown to increase the membrane fluidity that is typically decreased by estrogens, thereby restoring several factors that promote bile flow. Methionine also promotes the flow of lipids to and from the liver in humans. Methionine is a major source of numerous sulfur-containing compounds, including the amino acids cysteine and taurine and is involved in createion of the antioxidant glutathione. Methylation has been studied extensively and it is known that some various genetic mutations can cause methylation issues. A common one is the inability to create active folate from folic acid.

Substrates that are used for methylation: choline, methionine, betaine, folate, vitamin B 6, B12, Riboflavin. methyltransferases are zinc dependent enzymes

Thorne has a nice product called Methyl-Guard Plus used to enhance methylation.


Sulfation is involved in a variety of biological processes, including detoxification, hormone regulation, molecular recognition, cell signaling, and viral entry into cells.

Sulfation has been shown to be an important pathway in the biotransformation of numerous xenobiotics such as drugs, and endogenous compounds such as hormones, bile acids, neurotransmitters, peptides, and lipids. Sulfation is the conjugation of toxins with sulfur-containing compounds. This process is catalyzed by the super-family of sulfotranferases (SULTs). The sulfation system is important for detoxifying industrial and environmental chemicals, several drugs, neurotransmitters, steroids, food additives, and toxins from intestinal bacteria. In addition, sulfation is also used to detoxify some normal body chemicals and is the main pathway for the elimination of steroid hormones such as thyroid hormones. Since sulfation is also the primary route for the elimination of neurotransmitters, dysfunction in this system may contribute to the development of some nervous system disorders. Additionally sulfation is important in the biosynthesis of proteins, petptides, gycosaminoglycans (GAGs) and intestinal mucins.

Many factors influence the activity of sulfate conjugation. For example, a diet low in methionine and cysteine has been shown to reduce sulfation.

When sulfation is inhibited a person is unable to detoxify and eliminate tylenol (acetaminophen) as well as adrenaline and dopamine (catecholamines) from the brain and phenols in herbs (high in some essenatial oils) and foods.

Substrates that may be used for sulfation and sulfoxidation: Sulfur containing foods in general, sulfate, taurine, methionine, cysteine, glutathione, molybdenum and B2.

Inhibitors of Sulfation
Non-steroidal anti-inflammatory drugs (e.g. aspirin), tartrazine (yellow food dye)


Acetylation is a reaction, where an acetyl chemical group (CH3C=O) is added to another compound. This is a common reaction used in the metabolism of drugs. Conjugation of toxins with acetyl-CoA is the primary method by which the body eliminates sulfa drugs. This system appears to be especially sensitive to genetic variation, with those having a poor acetylation system being far more susceptible to sulfa drugs and other antibiotics. When salicylic acid is acetylated it becomes aspirin. While not much is known about how to directly improve the activity of this system, it is known that acetylation is dependent on thiamine, pantothenic acid, and vitamin C.

People with CIRS often have problems with sleep. We know that melatonin is necessary for good sleep and acetylation is necessary to make melatonin from serotonin. Serotonin is converted to melatonin by three steps involving a series of enzymes that add an acetyl, methyl and finally a hydroxyl group to the indole ring.


See details on glucuronidation here.
Glucuronidation, the combining of glucuronic acid with toxins, requires the enzyme UDP-glucuronyl transferase (UDPGT). This is the most common conjugation process for many of the drugs and other xenobiotics. Glucuronidation processes potentially carcinogenic environmental toxins such as polycyclic aromatic hydrocarbons and nitrosamines, as well as excess steroid hormones. During glucuronidation, the enzyme glucuronosyl transferase catalyzes the conjugation of free carcinogens and steroid hormones to glucuronic acid. The glucuronide-bound toxins and hormones are then safely excreted in the bile and the urine. Many of the commonly prescribed drugs are detoxified through this pathway. It also helps to detoxify aspirin, acetaminophen, menthol, vanillin (synthetic vanilla), benzodiazepines, phenols, pesticides, food additives such as benzoates, and some hormones. Glucuronidation is thought to work well, except for those with Gilbert’s Syndrome. Gilbert's Syndrome is now known to affect as much as 5% of the general population. I think it has issues more often than thought by general opinion.


Evaluating transformation/detoxification abilities of the Various Enzymes

Testing of these systems is available to some degree. Challenge tests are usually the most helpful. A probe substance is ingested and their metabolites are measure in the urine, blood or saliva. Here are some tests available at the time of writing this article.

Cytochrome P450 Testing - Phase I
  • CYP1A2: The probe used here is caffeine. Elevation of depression of the rate of caffeine clearance suggests upregulation or downregulation of this enzyme.
  • CYP2C9: The probe is Tolbutamide
  • CYP2C19 The probes are mephenytoin or proguanil
  • CYP2D6: The probes are sparteine, dextromethorphan, or debrisoquine
  • CYP2E1: The probe is chlorzoxazone
  • CYP3A4: The probes are erythromycin(breath test), midazolam, 6Beta-hydroxycortisol
Conjugation Testing - Phase II
  • N-acetyl transferase: The probes are sulphadimidine, Isoniazid, or caffeine
  • Glucuronyl transferase: The probes are oxazepam, acetaminophen
  • Sulfation: The probe is acetaminophen
  • Glycination: The probes are benzoic acid or salicylate

Testing of common toxic elements such as mercury, arsenic, lead, aluminum, cadmium and nickel is important as they can impair these transformational pathways, besides causing metabolic toxicity on their own.

Links To Additional Articles On The Detox/Biotransformation System

For an explanation of what detoxing is, the process, details on where toxins come from, how the body reacts, and a few ideas of how the body can be supported in detoxin, read the article "Detox and Biotransformation - What Is It?"

If you are looking for data on individual biotransformation pathways, the links to each pathway can be found at Detox/Biotransformation Pathways

For information on how these biotransformation systems are supported in see the article "Supporting The Detox - Biotransformation System in mold related illness (other toxins too)".



Endogenous: Produced originating inside of the organism.

Exogenous: Produced or originating outside of the organism.

Ferritin: Binding of free iron to prevent its reaction with superoxide to produce hydroxyl radical.

Glutathione: A predominant intracellular sulfur-containing direct antioxidant. Essential in function of Glutathione peroxidase and reduced glutathione for redox balance and detoxification.

Glutathione-S-transferase: A Phase II detoxifying enzyme with broad spectrum of activity, depending on subclass. Best known for catalyzing conjugation of the reduced form of glutathione to xenobiotics for removal from the body.

Hemoxygenase-1: Redox-regulating, broad protection against oxidative stress.  Metabolises haem, also producing bilirubin which scavenges peroxyl radicals.  Anti-inflammatory and immune-modulating properties.

Metallothionein: Helps removal of heavy metals such as mercury and cadmium.

NADPH regenerative enzymes: Restores reducing equivalents and reduces oxidized GSH to its reduced form.

Nuclear factor erythroid 2-related factor 2: Nrf2 induces its own synthesis. It can be inuced by many substances.

Peroxisome proliferator-activated receptor: Regulator of adipogenesis and central integrator of glucose metabolism, energy homeostasis and skeletal metabolism.

Quinone oxidoreductase - NAD(P)H:Quinone oxido-reductase has a protective function for cells against the toxicity of electrophiles and reactive forms of oxygen. In addition, its induction protects cells against carcinogenesis. Therefore, quinone reductase is acknowledged as belonging to the group of enzymes classified as phase 2 detoxification enzymes.

Quinone oxidoreductase catalyzes the beneficial two-electron reduction of quinones to hydroquinones, preventing the one-electron reduction of quinones by other quinone reductases that would result in the production of radical species.

A multifunctional redox-regulating and detoxifying enzyme, including protection against oestrogen quinone metabolites. Directly scavenges superoxide but less efficiently than SOD.  Stabilises the p53 tumor suppressor protein, especially under exposure from γ-irradiation or other oxidative stress. Protective against dopamine cytotoxicity where SOD and Catalase were not. Upregulation of its activity by Nrf2 induction is described as an avenue for maintaining cellular defenses with advancing age.

Thioredoxin (non-enzyme): Ubiquitous intracellular sulfur-rich protein. Singlet oxygen quencher and hydroxyl radical scavenger.

Thioredoxin reductase: An oxido-reductase which regenerates thioredoxin and GSH.

Xenobiotic: In relattion to the human or animal body, a xenobiotic is a foregin compound that originates externally to the body in sources such as environmental toxins or drugs.

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