A clinical reference mapping every cofactor and nutrient dependency extracted from the 27 core pathway files in this vault. Use this during patient consultations to trace symptoms back to biochemical bottlenecks and identify upstream nutritional interventions.
| Cofactor / Nutrient | Pathways Dependent On It | Clinical Consequence of Deficiency |
|---|---|---|
| BH4 (tetrahydrobiopterin) | Catecholamine synthesis (tyrosine hydroxylase), Serotonin (tryptophan hydroxylase), Dopamine (tyrosine hydroxylase), nitric oxide synthase (all isoforms) | Impaired Dopamine + Serotonin + nitric oxide synthesis simultaneously. Presents as anhedonia, Depression, low motivation, vascular dysfunction, endothelial dysfunction. Depleted by Oxidative Stress and inflammation (oxidised to inactive BH2). Regeneration requires NADPH and is linked to the Methylation Cycle. |
| iron (Fe2+) | Catecholamine synthesis (tyrosine hydroxylase), Serotonin (tryptophan hydroxylase), Dopamine (tyrosine hydroxylase), Oxidative Phosphorylation (ETC complexes I-III), TCA cycle (aconitase Fe-S cluster), HPT axis (thyroid peroxidase, deiodinases), HIF-1 regulation (prolyl hydroxylases), kynurenine pathway (Fenton chemistry with QUIN) | Fatigue beyond anaemia, low motivation, cognitive decline, impaired thyroid hormone synthesis, reduced Oxidative Phosphorylation. Sequestered during inflammation via Hepcidin ("nutritional immunity"), creating functional deficiency even with adequate stores. |
| Vitamin B6 (PLP, pyridoxal phosphate) | Catecholamine synthesis (AADC/DOPA decarboxylase), Serotonin (AADC: 5-HTP to 5-HT), Dopamine (AADC: L-DOPA to DA), kynurenine pathway (KAT for KYNA, kynureninase for 3-HK processing), Transsulfuration pathway (CBS and CSE), Methylation Cycle (SHMT in folate cycle), Glycolysis (glycogen phosphorylase) | Impaired monoamine synthesis (both Serotonin and Dopamine), shift of kynurenine pathway toward neurotoxic branch (less KYNA, more QUIN), elevated Homocysteine (blocked transsulfuration), reduced glutathione production, impaired GABA synthesis. Depleted by inflammation via kynurenine pathway B6 consumption -- creates a vicious cycle. |
| Vitamin B12 (cobalamin) | Methylation Cycle (methionine synthase as methylcobalamin), Catecholamine synthesis (indirectly via SAMe for PNMT) | "Methylfolate trap" -- 5-MTHF accumulates, functional folate deficiency despite adequate intake. Elevated Homocysteine, impaired DNA methylation, impaired Epinephrine synthesis, megaloblastic anaemia, peripheral neuropathy, cognitive decline, Depression. |
| folate / 5-MTHF | Methylation Cycle (methionine synthase -- 5-MTHF donates methyl group), Catecholamine synthesis (indirectly via SAMe), nucleotide synthesis (thymidylate synthase) | Elevated Homocysteine, impaired DNA methylation, impaired epigenetic regulation, neural tube defects (embryonic), megaloblastic anaemia, impaired Adrenaline synthesis (via reduced SAMe). MTHFR polymorphisms (C677T, A1298C) increase folate requirement. |
| SAMe | Catecholamine synthesis (PNMT: norepinephrine to Epinephrine), Methylation Cycle (>200 methyltransferases), COMT (dopamine/catecholamine degradation), DNA methylation (DNMTs), Histone Methylation (HMTs), Creatine synthesis (GAMT), phosphatidylcholine synthesis (PEMT), Serotonin to melatonin conversion (HIOMT) | Impaired Epinephrine production, dysregulated catecholamine metabolism, impaired DNA methylation and epigenetic programming, reduced Creatine synthesis, impaired melatonin production. SAMe is produced by MAT from Methionine + ATP, requiring Magnesium. |
| NAD+ / NADH | Glycolysis (GAPDH requires NAD+), TCA cycle (three dehydrogenases produce NADH), Oxidative Phosphorylation (Complex I accepts NADH), Beta-oxidation (3-hydroxyacyl-CoA dehydrogenase produces NADH), kynurenine pathway (terminal product is NAD+ de novo), Sirtuin function, PARP-mediated DNA repair, Polyol Mechanism (sorbitol dehydrogenase consumes NAD+) | Impaired energy production across all mitochondrial pathways, impaired Sirtuin function (anti-inflammatory, metabolic regulation), impaired DNA repair. Depleted by the Polyol Mechanism in hyperglycaemia ("pseudohypoxia"). Derived from Vitamin B3 (niacin/nicotinamide). |
| NADPH | Pentose phosphate pathway (primary source via G6PD), glutathione regeneration (glutathione reductase), nitric oxide synthase (electron donor), Catecholamine synthesis (BH4 recycling via DHBR), fatty acid synthesis, CYP enzymes (Phase I detoxification), Polyol Mechanism (consumed by aldose reductase), Methylation Cycle (MTHFR uses FAD but cycle requires NADPH for DHFR) | Impaired glutathione regeneration (oxidative vulnerability), uncoupled nitric oxide synthase (produces superoxide instead of NO), impaired BH4 recycling. Depleted by the Polyol Mechanism during hyperglycaemia, competing with glutathione defence and NO production. G6PD deficiency (400M people) reduces baseline NADPH. |
| FAD / FADH2 (Vitamin B2, riboflavin) | TCA cycle (succinate dehydrogenase/Complex II produces FADH2), Beta-oxidation (acyl-CoA dehydrogenase produces FADH2), Methylation Cycle (MTHFR requires FAD), Oxidative Phosphorylation (Complex II accepts FADH2), kynurenine pathway (KMO is flavin-dependent) | Impaired MTHFR activity (particularly devastating in C677T carriers), reduced energy production, impaired Beta-oxidation. Riboflavin deficiency worsens methylation impairment and elevates Homocysteine. |
| Vitamin B1 (thiamine, TPP) | TCA cycle (alpha-ketoglutarate dehydrogenase and pyruvate dehydrogenase complex), Pentose phosphate pathway (Transketolase), pyruvate dehydrogenase (glycolysis to TCA link) | Wernicke's encephalopathy (confusion, ataxia, ophthalmoplegia), impaired TCA cycle flux, impaired PPP non-oxidative phase, reduced NADPH recycling, beriberi. Common in alcohol use disorder. Erythrocyte Transketolase activity is the functional biomarker. |
| Vitamin B3 (niacin) | NAD+ / NADH pool (precursor), TCA cycle (NAD+ required), Glycolysis (NAD+ required), Beta-oxidation (NAD+ required), Oxidative Phosphorylation (Complex I), Sirtuin function, kynurenine pathway (terminal product is NAD+) | Pellagra (dermatitis, diarrhoea, dementia), impaired energy production across all pathways, impaired Sirtuin function. Supplementing niacin or nicotinamide riboside reduces metabolic drive for kynurenine pathway-derived NAD+. |
| Vitamin B5 (pantothenic acid) | TCA cycle (CoA is derived from B5; acetyl-CoA, succinyl-CoA), Beta-oxidation (CoA required), Catecholamine synthesis (acetyl-CoA), fatty acid synthesis | Impaired CoA production, impaired TCA cycle, impaired fatty acid metabolism. Deficiency is rare but contributes to fatigue and impaired energy production. |
| Vitamin C (ascorbic acid) | Catecholamine synthesis (DBH: dopamine to norepinephrine), TCA cycle cataplerosis (alpha-ketoglutarate-dependent hydroxylases for collagen), Oxidative Phosphorylation (indirectly via collagen-dependent wound healing), HPT axis (indirectly, antioxidant protection of thyroid), BH4 recycling (antioxidant protection) | Impaired norepinephrine synthesis (adrenal glands have highest vitamin C in body), impaired collagen synthesis (scurvy), fatigue, depression/lethargy, impaired wound healing, impaired iron absorption. |
| Zinc | Methylation Cycle (methionine synthase function), Oxidative Phosphorylation (cofactor), HPT axis (thyroid function), antioxidant defence (Cu/Zn-SOD), NMDA receptor modulation, ACE (zinc-dependent metallopeptidase in Renin-angiotensin-aldosterone system) | Impaired methylation (elevated Homocysteine), impaired thyroid function, reduced antioxidant capacity, impaired immune function (T-cell maturation), impaired wound healing, altered NMDA receptor function. |
| Copper (Cu2+) | Catecholamine synthesis (DBH: dopamine to norepinephrine), Oxidative Phosphorylation (Complex IV / cytochrome c oxidase), antioxidant defence (Cu/Zn-SOD) | Impaired norepinephrine synthesis, impaired mitochondrial electron transport, anaemia (ceruloplasmin-dependent iron mobilisation). |
| Magnesium | Methylation Cycle (MAT: methionine to SAMe), Glycolysis (hexokinase, PFK-1, pyruvate kinase all use Mg-ATP), TCA cycle (isocitrate dehydrogenase), Oxidative Phosphorylation (ATP synthase), COMT (cofactor for catecholamine degradation), NMDA receptor (physiological channel blocker), kynurenine pathway (NMDA modulation -- magnesium as downstream protectant) | Impaired SAMe production (first step of methylation), impaired energy production, NMDA receptor hyperexcitability (increased excitotoxicity from quinolinic acid), muscle cramps, cardiac arrhythmias, impaired Insulin sensitivity. |
| Selenium | HPT axis (all three deiodinases D1/D2/D3 are selenoenzymes; glutathione peroxidase protects thyroid from H2O2), glutathione peroxidase (selenium-dependent), thioredoxin reductase | Impaired T4-to-T3 conversion (functional hypothyroidism), impaired thyroid peroxidase protection (thyroid damage), reduced antioxidant capacity. 200 mcg/day reduces anti-TPO antibodies by 30-50% in Hashimoto's thyroiditis. |
| CoQ10 (ubiquinone) | Oxidative Phosphorylation (electron carrier between Complex I/II and Complex III in ETC), TCA cycle (SDH/Complex II transfers electrons to CoQ10) | Impaired mitochondrial ATP production, fatigue, muscle weakness, chronic fatigue, statin-induced myopathy (statins inhibit CoQ10 synthesis via HMG-CoA reductase pathway). |
| Acetyl-CoA | TCA cycle (entry substrate via citrate synthase), Beta-oxidation (product), fatty acid synthesis, histone acetylation (epigenetic regulation), Catecholamine synthesis (indirectly) | Impaired TCA cycle entry, impaired energy production, impaired epigenetic regulation (histone acetylation). Generated from pyruvate (via PDH), fatty acids (via Beta-oxidation), and amino acids. |
| ATP | Methylation Cycle (MAT: methionine activation to SAMe), Glycolysis (hexokinase and PFK-1 investment), Transsulfuration pathway (gamma-GCL for glutathione synthesis), mTOR (energy status via AMPK), all active transport, muscle contraction, biosynthesis | Universal energy currency. Deficiency = cellular energy crisis. Produced by Glycolysis (2 net), TCA cycle + Oxidative Phosphorylation (~30-32 per glucose), Beta-oxidation (~106 per palmitate). |
| glutathione (GSH) | Transsulfuration pathway (product), Pentose phosphate pathway (regeneration via NADPH), Phase II detoxification (GST conjugation), antioxidant defence (glutathione peroxidase) | Impaired antioxidant defence, impaired detoxification, increased Oxidative Stress, impaired immune function. Depleted in chronic inflammation, aging, insulin resistance, Depression. Requires cysteine (from transsulfuration or NAC), glutamate, glycine, ATP, and NADPH for regeneration. |
| Omega-3 fatty acids (EPA/DHA) | Eicosanoid Class Switch (substrate for Resolvins, Protectins, Maresins), inflammatory resolution (SPM production via 15-LOX) | Failed Eicosanoid Class Switch, impaired inflammatory resolution, chronic unresolved inflammation. Requires omega-6:omega-3 ratio <4:1 for efficient switching. EPA specifically reduces IDO1 induction. |
| Vitamin D | HPT axis (immune modulation, autoimmune thyroid risk), kynurenine pathway (modulates IDO1 expression in dendritic cells), immune regulation (T-cell differentiation, antimicrobial peptides) | Increased autoimmune thyroid disease risk, impaired immune regulation, impaired IDO1 modulation, increased susceptibility to infections. Not a direct enzyme cofactor in the 27 pathways but a critical immunomodulator. |
| Iodine | HPT axis (structural component of T4 and T3; NIS-mediated uptake, TPO-mediated organification) | Goitre, hypothyroidism, impaired metabolic rate, cognitive impairment, cretinism (severe prenatal deficiency). |
| Tyrosine | Catecholamine synthesis (substrate for tyrosine hydroxylase), Dopamine (precursor), HPT axis (thyroglobulin tyrosine residues are iodinated) | Impaired catecholamine production, reduced Dopamine, norepinephrine, Epinephrine. Non-essential amino acid (synthesised from phenylalanine via BH4-dependent phenylalanine hydroxylase), but becomes conditionally essential when BH4 or phenylalanine is limiting. |
| Tryptophan | Serotonin (substrate for TPH), kynurenine pathway (substrate for IDO/TDO), melatonin (via serotonin), NAD+ de novo synthesis (via kynurenine pathway terminus) | Impaired Serotonin and melatonin synthesis, Depression, sleep disruption, Circadian rhythm disturbance. Competes with other large neutral amino acids (BCAAs, tyrosine) for LAT1 transporter at the blood-brain barrier. 95% metabolised via kynurenine pathway, only 1-3% becomes serotonin. |
| Cholesterol | HPG Axis (precursor for sex steroids: oestrogen, Progesterone, Testosterone), HPA axis (precursor for Cortisol), Renin-angiotensin-aldosterone system (precursor for Aldosterone), Wingless/Wnt signaling (vesicle production), cell membrane integrity, Vitamin D synthesis | Impaired steroid hormone synthesis across all axes, impaired cell membrane function, impaired vesicular communication for Wnt signaling. |
| Carnitine | Beta-oxidation (carnitine shuttle for fatty acid transport into mitochondria via CPT1) | Impaired fatty acid entry into mitochondria, impaired Beta-oxidation, metabolic inflexibility, fatigue, exercise intolerance. Endogenous synthesis requires Vitamin C, iron, B6, niacin. |
| Methionine | Methylation Cycle (essential amino acid substrate activated to SAMe by MAT), Transsulfuration pathway (via homocysteine) | Impaired methylation capacity, reduced SAMe availability, impaired epigenetic regulation. Must come from dietary protein. |
| Leucine | mTOR (most potent amino acid activator via Sestrin2/GATOR2), Notch signaling (supports satellite cell activation via mTOR) | Impaired mTORC1 activation for muscle protein synthesis, impaired post-exercise recovery. Threshold ~2-3g per meal (~25-30g high-quality protein). |
| Arginine | mTOR (activator via CASTOR1/GATOR), nitric oxide synthase (substrate for NO production), Renin-angiotensin-aldosterone system (NO counter-regulation) | Impaired mTORC1 signaling, impaired nitric oxide production, endothelial dysfunction, impaired immune function. |
| Glutamine | TCA cycle (major anaplerotic substrate via glutaminolysis to alpha-ketoglutarate), mTOR (activator via glutaminolysis), glutathione synthesis (glutamate component) | Impaired TCA cycle anaplerosis (especially in immune cells), impaired immune cell function, impaired glutathione synthesis. Conditionally essential during inflammation and critical illness. |
| Choline / betaine | Methylation Cycle (BHMT pathway: betaine-homocysteine methyltransferase for folate-independent remethylation), phosphatidylcholine synthesis (PEMT) | Impaired alternative homocysteine remethylation, Fatty Liver Disease (impaired VLDL secretion), impaired membrane integrity. Betaine from dietary sources or choline oxidation. |
| Alpha-lipoic acid | TCA cycle (lipoic acid is cofactor for alpha-ketoglutarate dehydrogenase and pyruvate dehydrogenase complexes), glutathione regeneration | Impaired TCA cycle flux at two dehydrogenase complexes. Therapeutic use: regenerates glutathione, improves nerve conduction in Diabetic neuropathy (ALADIN/SYDNEY trials). |
| Manganese | TCA cycle (cofactor), mitochondrial SOD (MnSOD/SOD2) | Impaired mitochondrial antioxidant defence, impaired TCA cycle enzyme function. |
| Vitamin B7 (biotin) | TCA cycle anaplerosis (pyruvate carboxylase: pyruvate to oxaloacetate), Gluconeogenesis, fatty acid synthesis (acetyl-CoA carboxylase) | Impaired anaplerotic replenishment of TCA cycle, impaired Gluconeogenesis, dermatitis, hair loss. |
| Molecular oxygen (O2) | Catecholamine synthesis (tyrosine hydroxylase co-substrate), Serotonin (tryptophan hydroxylase co-substrate), Oxidative Phosphorylation (final electron acceptor), HIF-1 regulation (prolyl hydroxylases) | Hypoxia shifts metabolism to Aerobic Glycolysis, stabilises HIF-1, impairs monoamine synthesis, activates inflammatory metabolic programmes. Tissue oxygenation critical for wound healing (collagen hydroxylation). |
| Pathway | Required Cofactors / Nutrients |
|---|---|
| Catecholamine synthesis | BH4, iron (Fe2+), O2, Vitamin B6 (PLP), Vitamin C, Copper (Cu2+), SAMe, Tyrosine (substrate) |
| Serotonin | BH4, iron (Fe2+), O2, Vitamin B6 (PLP), Tryptophan (substrate), SAMe (for melatonin conversion via HIOMT) |
| Dopamine | BH4, iron (Fe2+), O2, Vitamin B6 (PLP), Tyrosine (substrate), Magnesium (COMT cofactor), SAMe (COMT methyl donor) |
| kynurenine pathway | Vitamin B6 (KAT, kynureninase), Vitamin B2 (KMO is flavin-dependent), iron (Fenton chemistry), Vitamin B3 / NAD+ (terminal product) |
| Methylation Cycle | folate / 5-MTHF, Vitamin B12, Vitamin B6 (SHMT, transsulfuration), Vitamin B2 (MTHFR FAD cofactor), Magnesium (MAT), Zinc (methionine synthase), ATP, Choline / betaine (BHMT pathway) |
| Transsulfuration pathway | Vitamin B6 (CBS and CSE), SAMe (allosteric activator of CBS), ATP (gamma-GCL), glutamate, glycine (glutathione synthesis) |
| Glycolysis | NAD+ (GAPDH), Magnesium (Mg-ATP for kinases), ATP (investment phase) |
| TCA cycle | Vitamin B1 (thiamine/TPP), Vitamin B2 (FAD), Vitamin B3 (NAD+), Vitamin B5 (CoA), iron (aconitase Fe-S cluster), Magnesium, Manganese, Alpha-lipoic acid, Vitamin B7 (biotin, for anaplerotic pyruvate carboxylase), Vitamin C (alpha-KG-dependent hydroxylases) |
| Oxidative Phosphorylation | iron (ETC complexes), CoQ10 (electron carrier), Copper (Complex IV), Vitamin B2 (FAD/Complex II), Vitamin B3 (NAD+/Complex I), Zinc, O2 (final electron acceptor) |
| Beta-oxidation | Carnitine (CPT1 shuttle), NAD+ (NADH production), FAD (FADH2 production), CoA (from Vitamin B5) |
| Pentose phosphate pathway | Vitamin B1 (thiamine for Transketolase), NADP+ (substrate for G6PD) |
| Polyol Mechanism | NADPH (consumed by aldose reductase), NAD+ (consumed by SDH) -- this pathway depletes cofactors rather than requiring them |
| HPT axis | Iodine (T4/T3 structural), Selenium (deiodinases D1/D2/D3, glutathione peroxidase), Zinc, iron (thyroid peroxidase), Vitamin D (autoimmune protection) |
| HPA axis | Cholesterol (cortisol precursor), Vitamin C (adrenal steroidogenesis) |
| HPG Axis | Cholesterol (sex steroid precursor), Zinc (testosterone synthesis) |
| GH-IGF-1 axis | Zinc (GH signaling), adequate protein/Leucine (IGF-1 production), sleep (GH pulsatility) |
| Renin-angiotensin-aldosterone system | Zinc (ACE is zinc-dependent metallopeptidase), Cholesterol (aldosterone precursor) |
| Eicosanoid Class Switch | Omega-3 fatty acids (EPA/DHA substrates), Arachidonic acid (omega-6 substrate for initiation phase) |
| Lipoxins | Arachidonic acid (omega-6 substrate), 15-LOX and 5-LOX enzymes |
| Complement System | No specific vitamin/mineral cofactors identified; protein-dependent cascade |
| JAK-STAT pathway | ATP (phosphorylation energy), no specific vitamin/mineral cofactors; impaired by SOCS from chronic inflammation |
| TLR-NF-kappaB pathway | No specific vitamin/mineral cofactors; inhibited by Omega-3 fatty acids, Polyphenols, Vitamin D |
| Notch signaling | No specific vitamin/mineral cofactors identified; supported by Leucine (via mTOR), Omega-3 fatty acids (resolution restores signaling) |
| mTOR | Leucine (primary activator), Arginine (activator), Glutamine (activator), ATP (energy status via AMPK), Insulin / IGF-1 (growth factor input) |
| PI3K-Akt signaling | ATP (phosphorylation), Insulin / IGF-1 (ligand input) |
| MAPK pathway | ATP (phosphorylation cascades) |
| Wingless / Wnt signaling | Dietary lipids, vitamins, metal ions, Cholesterol (vesicle production) |
These cofactors appear in 3 or more pathways and represent critical clinical chokepoints. When depleted, multiple systems fail simultaneously.
Pathways: Catecholamine synthesis (TH), Serotonin (TPH), Dopamine (TH), nitric oxide synthase (all isoforms)
Why it matters: BH4 is the single most devastating bottleneck in cPNI because its depletion simultaneously impairs three neurotransmitter systems and vascular function. Inflammation oxidises BH4 to inactive BH2 via reactive oxygen species. BH2 then competitively inhibits the enzymes, making the problem worse than simple depletion. When BH4 is insufficient, NOS becomes "uncoupled" and produces superoxide instead of NO, further amplifying Oxidative Stress in a vicious cycle. The net result of chronic BH4 depletion: low Dopamine (anhedonia, amotivation), low Serotonin (depression, sleep disruption), low NO (endothelial dysfunction, hypertension), and increased oxidative damage.
Clinical strategy: Address upstream inflammation first. Support BH4 regeneration with NADPH (adequate Pentose phosphate pathway function), reduce oxidative BH2 accumulation, ensure adequate GTP (BH4 synthesised de novo from GTP via GTPCH). Vitamin C and folate support BH4 stability.
Pathways: Methylation Cycle (>200 methyltransferases), Catecholamine synthesis (PNMT), COMT (catecholamine degradation), DNA methylation (DNMTs), Histone Methylation (HMTs), Serotonin-to-melatonin conversion (HIOMT), Creatine synthesis (GAMT), phosphatidylcholine synthesis (PEMT), Transsulfuration pathway (CBS allosteric activator)
Why it matters: SAMe is the universal methyl donor for over 200 reactions. Creatine synthesis alone consumes ~40% of all SAMe-derived methyl groups. SAMe availability determines methylation capacity, epigenetic programming, neurotransmitter metabolism, and the switch between methylation and glutathione production (via transsulfuration). The SAMe:SAH ratio -- not absolute SAMe -- is the true indicator of methylation capacity.
Clinical strategy: Ensure adequate Methionine (dietary protein), folate/5-MTHF, Vitamin B12, Vitamin B2 (MTHFR cofactor), Magnesium (MAT cofactor), Zinc (methionine synthase). Consider Creatine supplementation to spare methyl groups. Address Oxidative Stress (which inactivates MAT and methionine synthase).
Pathways: Glycolysis (GAPDH), TCA cycle (3 dehydrogenases), Oxidative Phosphorylation (Complex I), Beta-oxidation (dehydrogenase), kynurenine pathway (terminal product), Sirtuin function, PARP DNA repair, Polyol Mechanism (depleted by SDH)
Why it matters: NAD+ is required by hundreds of enzymes across energy metabolism, DNA repair, and epigenetic regulation. The kynurenine pathway exists evolutionarily to produce NAD+ de novo from Tryptophan, but the neurotoxic intermediates generated along the way are the price. The Polyol Mechanism in hyperglycaemia depletes NAD+ ("pseudohypoxia"), impairing Sirtuin function and energy metabolism. NAD+ decline with aging contributes to inflammaging and metabolic dysfunction.
Clinical strategy: Supplement Vitamin B3 (niacin, nicotinamide riboside, NMN) to provide preformed NAD+ and reduce metabolic drive for kynurenine pathway-derived NAD+. Address hyperglycaemia to prevent polyol pathway NAD+ depletion. physical activity and Intermittent fasting support NAD+ levels via AMPK/Sirtuin activation.
Pathways: Pentose phosphate pathway (source), glutathione regeneration, nitric oxide synthase, BH4 recycling (DHBR), fatty acid synthesis, CYP enzymes (detoxification), Polyol Mechanism (depleted by aldose reductase)
Why it matters: NADPH is the dedicated reducing currency for biosynthesis and redox defence -- distinct from NADH (energy metabolism). The Polyol Mechanism during hyperglycaemia creates an NADPH crisis by consuming it for sorbitol production while simultaneously increasing oxidative stress that demands more NADPH for glutathione recycling. G6PD deficiency (most common enzymopathy, ~400M people) reduces baseline NADPH capacity, compounding all downstream vulnerabilities.
Clinical strategy: Screen for G6PD deficiency. Support Pentose phosphate pathway function. Prevent hyperglycaemia (lifestyle interventions to reduce polyol pathway activation). Ensure adequate Vitamin B2 (supports glutathione reductase as FAD cofactor).
Pathways: Catecholamine synthesis (TH), Serotonin (TPH), Dopamine (TH), Oxidative Phosphorylation (ETC complexes I-III, cytochrome c), TCA cycle (aconitase Fe-S cluster), HPT axis (thyroid peroxidase), HIF regulation (prolyl hydroxylases)
Why it matters: Most common nutritional deficiency worldwide. Beyond anaemia, iron deficiency directly impairs catecholamine and serotonin synthesis (explaining fatigue, low motivation, cognitive impairment beyond what haemoglobin explains), impairs mitochondrial energy production, and disrupts thyroid function. During inflammation, Hepcidin sequesters iron into macrophages and blocks intestinal absorption ("nutritional immunity"), creating functional iron deficiency even when ferritin appears adequate.
Clinical strategy: Assess ferritin, transferrin saturation, and soluble transferrin receptor (to distinguish true deficiency from inflammatory sequestration). Address underlying inflammation before aggressive iron supplementation. Consider that ferritin is an acute-phase reactant -- elevated ferritin does not exclude functional iron deficiency in inflammatory states.
Pathways: Catecholamine synthesis (AADC), Serotonin (AADC), Dopamine (AADC), kynurenine pathway (KAT, kynureninase), Transsulfuration pathway (CBS, CSE), Methylation Cycle (SHMT), GABA synthesis, haem synthesis
Why it matters: B6 is cofactor for >100 enzymatic reactions. In the kynurenine pathway, B6 determines whether kynurenine is converted to neuroprotective KYNA (via KAT) or remains available for conversion to neurotoxic quinolinic acid. B6 deficiency therefore shifts the kynurenine pathway toward neurotoxicity. Critically, inflammation depletes B6 by increasing kynurenine pathway flux (which consumes PLP) -- creating a vicious cycle where inflammation causes the very B6 depletion that worsens its neuropsychiatric consequences.
Clinical strategy: Supplement B6 (as P5P/pyridoxal-5'-phosphate for direct use), especially in patients with chronic inflammation, oral contraceptive use, alcohol use, or elevated Homocysteine despite adequate B12/folate. Monitor for neuropathy at very high doses (>200mg/day chronic).
Pathways: Methylation Cycle (MAT), Glycolysis (Mg-ATP kinases), TCA cycle (isocitrate dehydrogenase), Oxidative Phosphorylation (ATP synthase), COMT (cofactor), NMDA receptor modulation
Why it matters: Magnesium is required wherever ATP is used (as Mg-ATP is the true substrate for kinases). Deficiency impairs the very first step of the Methylation Cycle (MAT), undermining all downstream methylation. As a physiological NMDA receptor channel blocker, magnesium deficiency increases vulnerability to quinolinic acid-mediated excitotoxicity from the kynurenine pathway. Widely deficient in modern diets (depleted soils, processed foods).
Clinical strategy: Supplement (glycinate, threonate, or taurate forms for bioavailability). RBC magnesium is a better marker than serum magnesium (which reflects only 1% of total body stores).
Pathways: HPT axis (D1, D2, D3 deiodinases; glutathione peroxidase), glutathione peroxidase (selenium-dependent), thioredoxin reductase
Why it matters: All three thyroid deiodinases are selenoenzymes. Without selenium, T4 cannot be converted to active T3, regardless of thyroid gland function. Selenium deficiency also removes glutathione peroxidase protection from the thyroid gland, allowing H2O2 (generated during thyroid hormone synthesis) to damage thyroid tissue. This dual vulnerability makes selenium critical for both thyroid function and thyroid autoimmune protection.
Clinical strategy: 200 mcg/day selenomethionine. Particularly important in Hashimoto's thyroiditis (reduces anti-TPO by 30-50%), geographic regions with selenium-poor soils, and any patient with thyroid dysfunction.
iron deficiency --> impaired TH + TPH (Catecholamine synthesis, Serotonin) + impaired OXPHOS (Oxidative Phosphorylation) + impaired thyroid function (HPT axis)
Presentation: Fatigue beyond anaemia + low motivation + cognitive decline + cold intolerance + depressed mood + exercise intolerance
Key insight: Ferritin >30 ng/mL does not exclude functional iron deficiency during inflammation (Hepcidin-mediated sequestration). Assess soluble transferrin receptor. Address inflammation before supplementing.
chronic inflammation --> ROS oxidise BH4 to BH2 --> impaired TH (Catecholamine synthesis) + impaired TPH (Serotonin) + uncoupled NOS (nitric oxide)
Presentation: anhedonia + Depression + low motivation + fatigue + vascular dysfunction + hypertension + cognitive decline
Key insight: This is the core mechanism of "inflammatory depression." BH2 does not simply fail to work -- it competitively inhibits the enzymes, making the deficit worse than simple depletion. Neopterin (elevated) is a biomarker of BH4 pathway engagement. CRP >3-5 mg/L predicts this pattern.
Vitamin B12 / folate deficiency --> impaired Methylation Cycle --> elevated Homocysteine + impaired SAMe production --> impaired Epinephrine synthesis (PNMT) + impaired DNA methylation + impaired COMT function
Presentation: Fatigue + cognitive decline + Depression + elevated cardiovascular risk + peripheral neuropathy (B12) + macrocytic anaemia + impaired catecholamine metabolism
Key insight: B12 deficiency causes the "methylfolate trap" -- folate becomes trapped as 5-MTHF. Use methylcobalamin/hydroxocobalamin (not cyanocobalamin) and 5-MTHF (not folic acid). MTHFR C677T TT carriers (10-25% of population) need methylfolate + riboflavin.
chronic inflammation --> increased kynurenine pathway flux --> B6 (PLP) consumption by KAT/kynureninase --> depleted B6 --> impaired monoamine synthesis (Serotonin, Dopamine) + shift of kynurenine toward neurotoxic branch (more QUIN, less KYNA) + impaired Transsulfuration pathway (elevated Homocysteine, reduced glutathione)
Presentation: Depression + anhedonia + increased pain sensitivity + elevated Homocysteine + reduced antioxidant capacity + cognitive impairment
Key insight: Inflammation creates a vicious cycle by consuming the very B6 needed to process kynurenine safely. Supplement as P5P (active form). physical activity independently upregulates muscle KAT (via PGC-1alpha), diverting kynurenine to neuroprotective KYNA.
Selenium deficiency --> impaired deiodinases (D1/D2/D3) + impaired thyroid peroxidase protection --> impaired T4-to-T3 conversion + thyroid oxidative damage. Combined with Iodine deficiency --> impaired T4/T3 synthesis
Presentation: fatigue + cold intolerance + cognitive decline + Depression + weight gain + dry skin + hair loss + elevated LDL cholesterol + constipation
Key insight: TSH can be "normal" despite tissue-level hypothyroidism (non-thyroidal illness syndrome). inflammation drives D3 upregulation (inactivating enzyme), producing high reverse T3. The free T3/rT3 ratio is more clinically informative than TSH alone. Assess: TSH, fT4, fT3, rT3, anti-TPO, anti-TG.
Hyperglycaemia --> Polyol Mechanism activation --> NADPH consumed by aldose reductase --> impaired glutathione regeneration + uncoupled eNOS (superoxide instead of NO) + NAD+ consumed by SDH ("pseudohypoxia") + fructose-driven AGE formation
Presentation: Diabetic neuropathy (Schwann cell damage) + Diabetic retinopathy (pericyte loss) + Cataracts (lens opacity) + endothelial dysfunction + accelerated atherosclerosis
Key insight: Operates in insulin-independent tissues (GLUT1-expressing: nerves, retina, lens, kidney). Even "prediabetic" glucose levels activate the pathway. G6PD deficiency worsens all outcomes. Interventions: glycaemic control via lifestyle, Alpha-lipoic acid, NAC for glutathione, B2/B3 for NADPH/NAD+ support.
Multiple cofactor depletion (folate + Vitamin B12 + Vitamin B6 + Vitamin B2 + Magnesium + Zinc) --> Methylation Cycle failure --> elevated Homocysteine + reduced SAMe --> impaired DNA methylation + impaired catecholamine metabolism + impaired Transsulfuration pathway --> reduced glutathione --> Oxidative Stress --> further methylation impairment (oxidative inactivation of MAT and methionine synthase)
Presentation: Elevated Homocysteine, cardiovascular disease risk, Depression, cognitive decline, Cancer risk (aberrant epigenetics), autoimmune disease susceptibility, fatigue, chemical sensitivity (impaired Phase II detoxification)
Key insight: This is a vicious cycle. Oxidative Stress impairs the methylation enzymes, which reduces glutathione (the primary antioxidant), which worsens oxidative stress. Breaking the cycle requires simultaneous multi-nutrient intervention: 5-MTHF, methylcobalamin, P5P, riboflavin, magnesium, zinc, plus antioxidant support (NAC, Vitamin C). Creatine supplementation spares 40% of methylation demand.
High omega-6:omega-3 ratio (>4:1) --> impaired Eicosanoid Class Switch --> failed production of Resolvins, Protectins, Maresins --> unresolved inflammation --> chronic low-grade inflammation
Presentation: Non-resolving inflammatory conditions, autoimmune disease, metabolic syndrome, neurodegeneration, non-healing wounds, persistent pain
Key insight: The problem is not too much inflammation but failed resolution. The same Arachidonic acid that produces pro-inflammatory prostaglandins also generates resolution mediators (Lipoxins) -- the key is enzymatic pathway switching via 15-LOX. EPA/DHA supplementation provides substrate for SPMs. Low-dose aspirin promotes aspirin-triggered lipoxins/resolvins. Obesity and insulin resistance impair the class switch.
For the cPNI practitioner, these five cofactor systems deserve assessment in virtually every chronic disease patient:
Generated from 27 pathway files in /pathways/. Cross-reference with individual pathway notes for full mechanistic detail.