Molecular Knowledge Base

Overview

Superoxide dismutase (SOD) is a metalloenzyme that catalyzes the conversion of the superoxide radical into oxygen and hydrogen peroxide, forming the primary cellular defense against reactive oxygen species. Three isoforms exist: cytoplasmic CuZn-SOD, mitochondrial Mn-SOD, and extracellular EC-SOD.

Mechanism of action

Superoxide Dismutase (SOD) is a metalloenzyme that catalyzes the dismutation of superoxide anion (O₂•⁻) into oxygen and hydrogen peroxide. This reaction proceeds via the redox cycling of copper (Cu,Zn-SOD) or manganese (Mn-SOD) ions at the active site. SOD constitutes the primary tier of intracellular antioxidant defense.

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Overview

Catalase is one of the most catalytically efficient enzymes known, decomposing millions of hydrogen peroxide molecules per second. Present predominantly in peroxisomes, it limits H2O2 accumulation, a source of oxidative damage, and works together with SOD.

Mechanism of action

Catalase is a heme-enzyme that catalyzes the reaction 2H₂O₂ → 2H₂O + O₂. The reaction proceeds when H₂O₂ oxidizes the enzyme's iron center to Compound I, a high-valent iron intermediate; a second H₂O₂ molecule then reduces this intermediate. Operating at an exceptionally high turnover, catalase limits accumulation of H₂O₂, which could otherwise generate hydroxyl radicals.

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Glutathione peroxidase (GPx) is a selenium-containing enzyme family that reduces lipid hydroperoxides and H2O2 using glutathione as the electron donor. GPx acts on membrane lipid hydroperoxides and contributes to intracellular redox balance.

Mechanism of action

Glutathione Peroxidase (GPx) is a selenoprotein containing selenocysteine at its active site. It reduces H₂O₂ and lipid hydroperoxides to their corresponding alcohols, using glutathione (GSH) as the reducing agent. The GPx4 isoform directly reduces complex lipid peroxides and has been identified as a regulator of ferroptosis.

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Bromelain is a cysteine protease complex derived from pineapple stem (Ananas comosus). It inhibits NF-κB and COX-2 pathways (anti-inflammatory activity in experimental models), displays fibrinolytic activity and has proteolytic digestive activity.

Mechanism of action

Bromelain is a cysteine protease complex derived from pineapple stem (Ananas comosus). It inhibits NF-κB and MAPK signaling pathways, suppressing iNOS and COX-2 expression and reducing production of pro-inflammatory cytokines. It also modulates the arachidonate cascade, inhibits platelet aggregation, and displays fibrinolytic activity.

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Lysozyme (muramidase) is a glycoside hydrolase enzyme that disrupts bacterial peptidoglycan layers, causing bacterial lysis. Abundantly present in tears, saliva, and human milk, it is a key antimicrobial component of the innate immune system.

Mechanism of action

Lysozyme (muramidase) is a glycoside hydrolase enzyme that cleaves β-(1,4)-glycosidic bonds between N-acetylmuramic acid and N-acetylglucosamine. This disrupts bacterial peptidoglycan layers, compromising cell wall integrity and causing bacterial lysis. As a cationic antimicrobial peptide, it also provides a second defense mechanism independent of its muramidase activity.

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Glutathione-S-Transferase (GST) is an enzyme family that conjugates glutathione to electrophilic xenobiotics, increasing their water solubility and facilitating excretion. It is studied in xenobiotic metabolism and multidrug resistance research.

Mechanism of action

Glutathione-S-Transferase (GST) is a family of enzymes that catalyze the conjugation of glutathione (GSH) to electrophilic xenobiotics generated by cytochrome P450 metabolism. An active-site residue activates GSH to the nucleophilic GS⁻ form; this nucleophile forms conjugates with reactive xenobiotics and environmental pollutants, increasing water solubility and facilitating excretion.

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Telomerase is a ribonucleoprotein complex consisting of the TERT reverse transcriptase subunit and the RNA component TERC. It maintains telomere length by adding TTAGGG repeats to chromosome ends; it is active in progenitor cells, and its activity is investigated in cellular-senescence biology.

Mechanism of action

Telomerase is a ribonucleoprotein complex consisting of the TERT (reverse transcriptase subunit) and the RNA component TERC. It maintains telomere length by adding TTAGGG repeats to chromosome ends, thereby delaying cellular senescence. Regulation of TERT expression, including through promoter mutations or epigenetic activation, is investigated in cell-proliferation research.

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Vitamin C (L-ascorbic acid) is an essential micronutrient with wide-ranging physiological roles. As a water-soluble antioxidant it scavenges reactive oxygen species and recycles vitamin E; as an enzyme cofactor it is indispensable for collagen hydroxylation, carnitine synthesis, and catecholamine biosynthesis.

Mechanism of action

Vitamin C (ascorbic acid) acts as an essential cofactor for prolyl hydroxylase and lysyl hydroxylase enzymes, hydroxylating proline and lysine residues in procollagen to enable proper folding of the stable collagen triple helix. As an electron donor, it neutralizes superoxide, hydroxyl, and peroxyl radicals and reduces vitamin E radicals back to vitamin E.

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Vitamin B12 (cobalamin) is a water-soluble vitamin essential for two key enzymes: methionine synthase, involved in DNA methylation and homocysteine regulation, and L-methylmalonyl-CoA mutase, involved in fatty acid metabolism. Deficiency is associated with megaloblastic anaemia and neurological changes.

Mechanism of action

Vitamin B12 (cobalamin) is a cofactor for methionine synthase, catalyzing the synthesis of methionine from homocysteine and thereby contributing to production of S-adenosylmethionine (SAM), the universal methyl donor. SAM is essential for virtually all transmethylation reactions including DNA, RNA, histone, and neurotransmitter methylation.

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Vitamin D3 (cholecalciferol) is a fat-soluble prohormone synthesized endogenously upon UV-B exposure. After hydroxylation in the liver and other tissues to active calcitriol, it functions as a steroid hormone binding nuclear vitamin D receptors and regulating expression of over 1,000 genes across virtually all tissues.

Mechanism of action

Vitamin D3 (cholecalciferol) is converted in the liver to 25(OH)D3, then in other tissues, including immune cells, to the active form 1,25(OH)₂D3 (calcitriol). Calcitriol binds the vitamin D receptor (VDR), heterodimerizes with the retinoid X receptor, and regulates transcription of thousands of genes; it increases intestinal calcium absorption and modulates immune pathways.

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The B-complex encompasses eight water-soluble vitamins — B1, B2, B3, B5, B6, B7, B9, and B12 — that collectively act as coenzymes in cellular energy metabolism, DNA synthesis, neurotransmitter production, and one-carbon metabolic pathways.

Mechanism of action

The B vitamin complex (B1, B2, B3, B5, B6, B7, B9, B12) is a group of water-soluble vitamins functioning as coenzymes in mitochondrial aerobic respiration. Their active forms (thiamine pyrophosphate, FAD, NAD+, coenzyme A) catalyze critical steps in the citric acid cycle and electron transport chain for ATP production.

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Vitamin A regulates cell differentiation and proliferation genes through its active form all-trans retinoic acid (atRA) via RAR/RXR nuclear receptors. In its 11-cis-retinal form it is essential for photoreceptor function, and it plays critical roles in immune development and epithelial integrity.

Mechanism of action

Vitamin A regulates gene expression through its active form all-trans retinoic acid (atRA) via nuclear receptors (RAR/RXR heterodimers). This complex binds retinoic acid response elements in DNA to modulate transcription of genes governing cell differentiation and proliferation. Retinol in its 11-cis-retinal form is also essential for photoreceptor function.

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Vitamin E (α-tocopherol) acts as a chain-breaking antioxidant within lipophilic biological membranes and lipoproteins. It terminates lipid peroxidation chain reactions and is recycled by vitamin C or glutathione, completing the antioxidant cycle.

Mechanism of action

Vitamin E (α-tocopherol) acts as a chain-breaking antioxidant within lipophilic biological membranes and lipoproteins. It terminates lipid peroxidation chain reactions by donating a hydrogen atom to lipid peroxyl radicals; the resulting tocopheroxyl radical is recycled by vitamin C or glutathione.

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Vitamin K2 (menaquinone, especially MK-7) activates osteocalcin and matrix Gla protein as a cofactor for gamma-glutamyl carboxylase. Osteocalcin binds calcium in the bone matrix while matrix Gla protein inhibits calcification of soft-tissue matrices.

Mechanism of action

Vitamin K2 (menaquinone, especially MK-7) is a cofactor for gamma-glutamyl carboxylase, which γ-carboxylates glutamate residues of vitamin K-dependent proteins. This carboxylation activates the calcium-binding capacity of osteocalcin and matrix Gla protein; osteocalcin binds calcium in the bone matrix, while matrix Gla protein inhibits calcification of soft-tissue matrices.

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Folate (vitamin B9) is the central cofactor of one-carbon metabolism. Its tetrahydrofolate form participates in purine and thymidine synthesis and methionine recycling, providing methyl groups for DNA and histone methylation via SAM production.

Mechanism of action

Folate (vitamin B9) is the central cofactor of one-carbon metabolism. Its tetrahydrofolate (THF) form carries single-carbon units used in thymidine and purine synthesis and methionine recycling, thereby generating SAM to provide methyl groups for DNA and histone methylation. Inadequate folate disrupts the nucleotide pool and leads to DNA hypomethylation.

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L-Glutamine is the most abundant free amino acid in circulation, becoming conditionally essential during catabolic states such as illness, surgery, or intense exercise. It is the principal fuel for rapidly dividing cells including intestinal enterocytes and immune cells.

Mechanism of action

Glutamine is the most abundant free amino acid in the human body and the primary energy substrate for small intestinal enterocytes. It maintains gut barrier integrity by regulating tight junction protein expression. In immune cells it serves as a critical nitrogen source for proliferation and cytokine production, and provides the precursor amino acid for glutathione synthesis.

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L-Arginine is a semi-essential amino acid and the exclusive precursor for nitric oxide synthesis via nitric oxide synthase enzymes. NO regulates vascular tone, platelet aggregation, and immune function. Arginine also stimulates growth hormone secretion and serves as a key intermediate in the urea cycle.

Mechanism of action

L-Arginine is the direct precursor for nitric oxide (NO) synthesis as the substrate for endothelial nitric oxide synthase (eNOS). eNOS converts L-arginine to L-citrulline, generating NO; NO activates guanylate cyclase to increase cGMP, leading to smooth muscle relaxation. It also inhibits platelet aggregation and participates in the urea cycle.

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Taurine is a conditionally essential sulfur-containing amino acid abundantly present in skeletal muscle, the retina and the central nervous system. It regulates intracellular calcium signaling, osmotic balance, and bile acid conjugation, while exerting broad antioxidant and anti-inflammatory effects.

Mechanism of action

Taurine participates in mitochondrial protein synthesis by forming 5-taurinomethyluridine on mitochondrial tRNA, which influences electron transport chain activity. It scavenges hypochlorous acid directly, modulates intracellular calcium, and has been studied for effects on nitric oxide bioavailability.

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Glycine is the simplest amino acid, constituting approximately 33% of all collagen residues. It acts as an inhibitory neurotransmitter at glycine receptors in the brainstem and spinal cord, and plays essential roles in glutathione synthesis, one-carbon metabolism, and bile acid and xenobiotic conjugation.

Mechanism of action

Glycine is the dominant amino acid in the collagen Gly-X-Y repeat motif, determining triple helix stability; adequate glycine is essential for cartilage and connective tissue synthesis. It also acts as a co-agonist at NMDA receptors and, as an inhibitory neurotransmitter, participates in spinal cord inhibition.

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Carnosine is an endogenous dipeptide (beta-alanine + L-histidine) highly concentrated in muscle and brain. It serves as an intracellular pH buffer during high-intensity exercise, a carbonyl scavenger inhibiting advanced glycation end-product formation, and a zinc and copper chelator.

Mechanism of action

Carnosine (β-alanyl-L-histidine) is a dipeptide found at high concentrations in skeletal muscle. The pKa of histidine's imidazole ring provides muscle pH buffering, buffering pH changes during intense exercise. Through non-enzymatic reaction with protein carbonyl groups it inhibits advanced glycation end product (AGE) formation and chelates metal ions.

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Lysine is an essential amino acid that contributes to the indispensable post-translational modification enabling collagen fibril formation by generating hydroxylysine in procollagen. It is also the precursor for carnitine synthesis; carnitine transports fatty acids for mitochondrial oxidation.

Mechanism of action

Lysine serves as the substrate for prolyl hydroxylase and lysyl hydroxylase enzymes, generating hydroxylysine in procollagen; this post-translational modification is essential for collagen cross-linking and fibril formation. Lysine is also a precursor amino acid for carnitine synthesis; carnitine transports fatty acids for mitochondrial oxidation.

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Cysteine is the rate-limiting amino acid for glutathione biosynthesis; its N-acetylcysteine (NAC) form is widely used in research as a cysteine source for glutathione synthesis. Through the redox state of protein thiol groups it regulates enzyme activities, signaling pathways, and cellular redox homeostasis.

Mechanism of action

Cysteine is the rate-limiting amino acid for glutathione biosynthesis. The enzyme glutamate-cysteine ligase combines cysteine with glutamate to form γ-glutamylcysteine; GSH synthase then adds glycine to produce glutathione (GSH). The redox state of protein thiol groups determines their tertiary structure and function.

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Tyrosine is the central precursor for catecholamine neurotransmitter synthesis, converted by tyrosine hydroxylase to dopamine, then norepinephrine and epinephrine. It also serves as the building block for thyroid hormone synthesis.

Mechanism of action

Tyrosine is the central precursor for catecholamine neurotransmitter synthesis, converted by tyrosine hydroxylase to L-DOPA and then to dopamine, norepinephrine, and epinephrine. It is also used in thyroid hormone synthesis; iodination forms the building blocks of thyroxine (T4) and triiodothyronine (T3).

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Tryptophan is the sole dietary precursor for serotonin and melatonin biosynthesis. It is also converted to NAD+ precursor nicotinamide nucleotides via the kynurenine pathway; it participates in gut-brain axis signalling and immune responses.

Mechanism of action

Tryptophan converts a portion of dietary intake to serotonin (5-HT) and then melatonin via the serotonin/melatonin pathway, and the majority to nicotinamide nucleotides (NAD+ precursors) via the kynurenine pathway. Serotonin signalling is involved in the gut-brain axis and gut motility.

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Proline frequently occupies the X and Y positions of the Gly-X-Y motif in collagen and is converted to hydroxyproline by prolyl 4-hydroxylase to increase collagen triple helix thermal stability. It also modulates oxidative stress responses via the proline cycle.

Mechanism of action

Proline frequently occupies the X and Y positions of the Gly-X-Y motif in collagen and is converted to hydroxyproline in procollagen by prolyl 4-hydroxylase. This hydroxylation increases the thermal stability of the collagen triple helix and reinforces tissue integrity. Proline also modulates cellular responses to oxidative stress via the 'proline cycle.'

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Nicotinamide adenine dinucleotide (NAD+) is a coenzyme found in all living cells and central to oxidative phosphorylation and the TCA cycle. Beyond redox chemistry, NAD+ is a critical substrate for sirtuins, PARP enzymes, and CD38, linking cellular energy status to DNA repair, epigenetic regulation and cellular signalling.

Mechanism of action

NAD+ (nicotinamide adenine dinucleotide) serves a dual function as an electron-carrying coenzyme in redox reactions and as a substrate for NAD+-consuming enzymes (sirtuins SIRT1-7, PARPs, CD38). Sirtuins consume NAD+ in deacylation reactions to deacetylate histones and transcription factors; NAD+ availability depends on the balance between biosynthesis and consumption.

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Flavin adenine dinucleotide (FAD) is a redox-active coenzyme synthesized from riboflavin (vitamin B2). It serves as a prosthetic group for flavoproteins and participates in the mitochondrial electron transport chain, beta-oxidation of fatty acids, and the TCA cycle.

Mechanism of action

FAD (flavin adenine dinucleotide) is a riboflavin (B2)-derived coenzyme that catalyzes single- or two-electron redox reactions via its isoalloxazine ring. As a component of mitochondrial Complex II, it catalyzes the oxidation of succinate to fumarate and transfers electrons to coenzyme Q10, linking fatty acid β-oxidation to the respiratory chain.

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Coenzyme Q10 (ubiquinone) is a fat-soluble molecule present in virtually every cell. As a mobile electron carrier in the mitochondrial inner membrane it shuttles electrons between respiratory complexes; in its reduced form (ubiquinol) it is a membrane-bound antioxidant.

Mechanism of action

Coenzyme Q10 (ubiquinone/ubiquinol) is a lipophilic quinone molecule in the mitochondrial respiratory chain that transfers electrons from Complexes I and II to Complex III. The Q-cycle between its fully oxidized and fully reduced forms sustains the proton gradient to feed ATP synthase. The reduced form ubiquinol is an antioxidant that breaks membrane lipid peroxidation.

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Glutathione (GSH) is a tripeptide with a γ-glutamyl-cysteine-glycine structure. Via its thiol group it forms conjugates with electrophilic compounds, facilitating their excretion; as a cofactor for glutathione peroxidases it reduces H₂O₂ and lipid peroxides. The GSH/GSSG ratio is the primary indicator of cellular redox status.

Mechanism of action

Glutathione (GSH) is a tripeptide with a γ-glutamyl-cysteine-glycine structure. Via its thiol (-SH) group it forms conjugates with electrophilic compounds, facilitating their excretion; as a cofactor for glutathione peroxidases it reduces H₂O₂ and lipid peroxides. The oxidized GSSG form is recycled by glutathione reductase; the GSH/GSSG ratio is the primary indicator of cellular redox status.

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Alpha-lipoic acid (ALA) is a natural cofactor for mitochondrial dehydrogenase complexes and a unique antioxidant. The ALA/DHLA redox couple scavenges reactive oxygen species, recycles vitamins E and C as well as glutathione; its solubility in both fat and water earns it the title of 'universal antioxidant.'

Mechanism of action

Alpha-lipoic acid (ALA) is a natural cofactor for mitochondrial pyruvate dehydrogenase and alpha-ketoglutarate dehydrogenase complexes. The ALA/DHLA redox couple scavenges reactive oxygen species including superoxide, hydroxyl, and singlet oxygen, chelates metal ions, and recycles vitamin E, vitamin C, and glutathione. Its activity in both lipophilic and hydrophilic environments earns it recognition as the 'universal antioxidant.'

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Resveratrol is a stilbene-class polyphenolic compound synthesized in grape skins and other plants. It mimics caloric restriction through SIRT1 activation, modulates NF-κB and AMPK pathways for anti-inflammatory effects, and stimulates mitochondrial biogenesis.

Mechanism of action

Resveratrol is a stilbene-class polyphenolic compound synthesized in grape skins and other plants. It activates SIRT1, increasing NAD+-dependent deacetylase activity — an effect described as mimicking caloric restriction. It also modulates NF-κB and AMPK pathways and stimulates mitochondrial biogenesis.

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Astaxanthin is a unique carotenoid with hydroxyl and keto groups at both ends. Its membrane-spanning structure quenches singlet oxygen within the lipid bilayer and upregulates intrinsic antioxidant defense genes through Nrf2 activation.

Mechanism of action

Astaxanthin is a unique carotenoid with hydroxyl and keto groups at both ends. Its membrane-spanning structure quenches singlet oxygen and breaks peroxyl chain reactions within the lipid bilayer. It also activates the Nrf2 transcription factor, upregulating the cell's intrinsic antioxidant defense genes.

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NMN (nicotinamide mononucleotide) is a critical intermediate in the salvage pathway of NAD+ biosynthesis. After cellular uptake it is converted to NAD+ by NMNAT enzymes, raising cellular NAD+ levels; effects on sirtuin and PARP activity are studied in research settings.

Mechanism of action

NMN (nicotinamide mononucleotide) is a critical intermediate in the salvage pathway of NAD+ biosynthesis. After cellular uptake via transporter proteins, it is converted to NAD+ by NMNAT enzymes. In studies, NMN supplementation has been reported to raise tissue NAD+ levels; effects on sirtuin and PARP activity, metabolic function and mitochondrial biogenesis are under investigation.

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