02 — Compounds & Molecules
Silo Scope
Molecular interventions spanning foundational nutraceuticals, neurochemical modulators, signaling peptides, and longevity pharmacology.
- Upward Index: 00 - Biohacking Index
- Mirrored Sourcing & COA Hub: 02 - Compounds & Molecules Sourcing MOC
- Mirrored Literature Hub: 02 - Compounds & Molecules References MOC
2.1 Foundational Supplements & Micronutrients
Essential cofactors, minerals, and lipid mediators.
- Magnesium Forms & Bioavailability — Glycinate, L-Threonate (Magtein), Taurate, Malate, Citrate
- Vitamin D3, K2 & Calcium Homeostasis — Cholecalciferol, MK-4 vs. MK-7, VDR activation, PTH regulation
- Omega-3 & Lipid Membrane Health — EPA/DHA ratios, phospholipid vs. triglyceride vs. ethyl ester forms, resolving inflammation (SPMs)
- Methylation & B-Complex — Methylfolate (5-MTHF), Methylcobalamin/Adenosylcobalamin, P5P (B6), Riboflavin (B2), TMG (Betaine), Choline
- Creatine & Phosphocreatine System — ATP buffering in muscle and brain, methylation sparing, cognitive resilience under sleep deprivation
- Amino Acids & Precursors — Taurine, Glycine, NAC (GlyNAC), L-Citrulline, Beta-Alanine, EAA profiles
2.2 Nootropics & Neurochemistry
Targeted modulation of neurotransmission, synaptic plasticity, and cerebral blood flow.
- Cholinergics (Alpha-GPC, Citicoline) — Acetylcholine synthesis, phosphatidylcholine repair, ALCAR
- Racetams & AMPAkines — Piracetam, Phenylpiracetam, Aniracetam, Noopept, allosteric AMPA/NMDA modulation
- Dopaminergics & Catecholamines — L-Tyrosine, NALT, Bromantane (tyrosine hydroxylase upregulation), Mucuna, MAO-B modulation
- Adaptogens — Rhodiola rosea (salidroside/rosavins), Ashwagandha (withanolides), Panax ginseng, Eleuthero, Cordyceps, Schisandra
- Neurotrophins (BDNF, NGF, Lion’s Mane) — Hericenones & erinacines, 7,8-DHF (4’-DMA-7,8-DHF), Polygala tenuifolia, Bacopa monnieri
- GABAergics & Anxiolytics — L-Theanine, Lemon Balm, Magnolia Bark, Picamilon, Emoxypine (Mexidol), Etifoxine
2.3 Peptides & Bioregulators
Short-chain amino acid signaling molecules, secretagogues, and tissue-specific bioregulators.
- Tissue Repair Peptides (BPC-157, TB-500, GHK-Cu) — Angiogenesis (VEGF), actin upregulation, fibroblasts, collagen remodeling, KPV
- GH Secretagogues (Ipamorelin, CJC-1295, Tesamorelin) — GHRH analogs vs. ghrelin mimetics, pulsatile GH release, visceral adipose reduction
- Cognitive & Neurogenic Peptides (Semax, Selank, Dihexa) — BDNF/trkB signaling, enkephalinase inhibition, P21, Cerebrolysin, Cortexin, PE-22-28
- Mitochondrial & Metabolic Peptides (MOTS-c, SS-31, GLP-1) — Cardiolipin stabilization (Elamipretide), AMPK activation, Retatrutide / Tirzepatide / Semaglutide, 5-Amino-1MQ
- Khavinson Bioregulators (Epitalon, Pinealon) — Telomerase activation, pineal/retinal/thymic/vascular short peptides (Thymalin, Ventfort, Bonomarlot)
- Immune & Thymic Peptides (Thymosin Alpha-1, LL-37) — T-cell maturation, TLR modulation, antimicrobial defense, VIP
2.4 Longevity & Repurposed Pharmacology
Small-molecule therapeutics targeting conserved aging and metabolic pathways.
- mTOR & Autophagy Modulators (Rapamycin) — Intermittent mTORC1 inhibition vs. mTORC2 off-target effects, dosing schedules
- AMPK & Glycemic Agents (Metformin, Berberine, Acarbose) — Complex I inhibition, SGLT2 inhibitors (Canagliflozin/Empagliflozin), blunting postprandial glucose spikes
- PDE5 Inhibitors & Endothelial Function — Tadalafil, nitric oxide-cGMP signaling, microvascular perfusion, endothelial protection
- Methylene Blue & Electron Transport Chain — Alternative electron carrier (Complex I–III bypass), hormetic dose curve (0.5–4 mg/kg), MAO-A considerations
Tracked Compounds in Vault
| Compound / Class | Category | Mechanism | Standard Dose | Evidence Tier |
|---|---|---|---|---|
| Sleep Supplementation & Pharmacology | Sleep & Circadian Biology | Synergistic modulation of GABA-A allosteric sites, NMDA receptor blockade, SCN NMDA-mediated peripheral vasodilation, and dual orexin receptor (OX1R/OX2R) antagonism to promote sleep initiation and preserve N3/REM architecture. | Magnesium L-Threonate (144 mg elemental) or Bisglycinate (200-400 mg); Glycine (3 g); Apigenin (50 mg); L-Theanine (100-200 mg); Myo-Inositol (900 mg) | 🟢 Tier 1 |
| AMPK & Glycemic Agents (Metformin, Berberine, Acarbose) | Longevity & Repurposed Pharmacology | Mild mitochondrial Complex I & mGPDH inhibition elevating AMP:ATP ratios to activate AMPK (Metformin/Berberine), brush-border alpha-glucosidase blockade (Acarbose), and renal SGLT2 glucosuria | Metformin ER 500–1,500 mg/day; Dihydroberberine 100–200 mg 2x/day (or Berberine HCl 500 mg 2–3x/day); Acarbose 25–50 mg with first bite of starch meals; Empagliflozin 10 mg/day | 🟢 Tier 1 |
| Adaptogens | Nootropics & Neurochemistry | HPA-axis cortisol modulation, Heat Shock Protein 70 (Hsp70) & Neuropeptide Y (NPY) chaperone induction, and AMPK/mitochondrial stress-response hormesis | Rhodiola rosea 200–400 mg/day; Ashwagandha 300–600 mg/day; Panax ginseng 200–400 mg/day; Cordyceps militaris 1,000–3,000 mg/day | 🟢 Tier 1 |
| Amino Acids & Precursors | Foundational Supplements & Micronutrients | Intracellular glutathione restoration (GlyNAC), mitochondrial tRNA taurine-modification, urea/eNOS nitric oxide cycling (L-Citrulline), and carnosine H+ buffering | Taurine 2–6 g/day; Glycine 3–10 g/day; NAC 600–2,400 mg/day; L-Citrulline 4–8 g/day; Beta-Alanine 3.2–6.4 g/day | 🟢 Tier 1 |
| Cholinergics (Alpha-GPC, Citicoline) | Nootropics & Neurochemistry | Blood-brain barrier choline and cytidine/uridine delivery driving Choline Acetyltransferase (ChAT) acetylcholine synthesis and Kennedy Pathway phospholipid repair | Alpha-GPC 300–600 mg/day; Citicoline (CDP-Choline) 250–500 mg/day; ALCAR 500–1,500 mg/day | 🟢 Tier 1 |
| Cognitive & Neurogenic Peptides (Semax, Selank, Dihexa) | Peptides & Bioregulators | Intranasal olfactory-trigeminal delivery driving hippocampal BDNF/TrkB upregulation (Semax), enkephalinase inhibition & GABAA modulation (Selank), and HGF/c-Met synaptogenesis (Dihexa) | Semax (or NA-Semax-Amidate) 200–600 mcg/day intranasal; Selank (or NA-Selank-Amidate) 250–750 mcg/day intranasal; Dihexa 2–5 mg transdermal/oral (1–2x/week); P21 500–1,000 mcg/day | 🟡 Tier 2 |
| Creatine & Phosphocreatine System | Foundational Supplements & Micronutrients | Reversible creatine kinase (CK) phosphagen buffering of ADP to ATP, mitochondrial creatine shuttle optimization, and GAMT methylation sparing | 5 g/day Creatine Monohydrate (myocyte saturation); 10–20 g/day for cerebral saturation or acute sleep deprivation | 🟢 Tier 1 |
| Dopaminergics & Catecholamines | Nootropics & Neurochemistry | Rate-limiting Tyrosine Hydroxylase (TH) substrate saturation and epigenetic upregulation (Bromantane) driving prefrontal and striatal dopamine/norepinephrine synthesis | L-Tyrosine 500–2,000 mg; N-Acetyl-L-Tyrosine (NALT) 350–700 mg; Bromantane 25–100 mg/day; Mucuna Pruriens (L-DOPA) 50–150 mg (acute only) | 🟢 Tier 1 |
| GABAergics & Anxiolytics | Nootropics & Neurochemistry | Allosteric GABAA modulation, Glutamate Decarboxylase (GAD) upregulation, GABA Transaminase (GABA-T) inhibition, and TSPO neurosteroid synthesis | L-Theanine 100–400 mg; Lemon Balm (Cyracos) 300–600 mg; Magnolia Bark 200–400 mg; Emoxypine (Mexidol) 125–250 mg; Apigenin 50 mg | 🟢 Tier 1 |
| GH Secretagogues (Ipamorelin, CJC-1295, Tesamorelin) | Peptides & Bioregulators | Dual activation of pituitary GHRH receptors (cAMP/PKA) and Ghrelin/GHS-R1a receptors (PLC/IP3/Ca2+) to amplify endogenous pulsatile Growth Hormone and hepatic IGF-1 secretion | Ipamorelin 100–300 mcg + CJC-1295 (No DAC / Mod GRF 1-29) 100–200 mcg SubQ; Tesamorelin 1.0–2.0 mg/day SubQ | 🟢 Tier 1 |
| Immune & Thymic Peptides (Thymosin Alpha-1, LL-37) | Peptides & Bioregulators | Toll-Like Receptor (TLR2/4/9) dendritic cell priming & CD4+/CD8+/Treg immunosenescence reversal (Thymosin Alpha-1) alongside cationic amphipathic bacterial/biofilm membrane disruption (LL-37) | Thymosin Alpha-1 1.5–1.6 mg SubQ 2x/week (longevity/prophylaxis) or 1.6 mg/day for 5–7 days (acute viral); LL-37 100–125 mcg/day SubQ for 2–4 weeks | 🟢 Tier 1 |
| Khavinson Bioregulators (Epitalon, Pinealon) | Peptides & Bioregulators | Sequence-specific DNA minor-groove binding and histone H1/H4 epigenetic decondensation driving hTERT telomerase expression and pineal AANAT melatonin synthesis | Epitalon 1–5 mg/day SubQ for 10–20 days (or 10 mg every 3 days for 5 doses); Pinealon 1–2 mg/day SubQ/intranasal or 10–20 mg/day oral for 10–20 days | 🟡 Tier 2 |
| Magnesium Forms & Bioavailability | Foundational Supplements & Micronutrients | Obligate divalent cation cofactor for >600 enzymatic reactions, ATP-Mg2+ chelation, voltage-dependent NMDA receptor blockade, and L-type Ca2+ channel antagonism | 300–500 mg/day elemental Mg (144–200 mg elemental from 2,000 mg Mg L-Threonate) | 🟢 Tier 1 |
| Methylation & B-Complex | Foundational Supplements & Micronutrients | One-carbon metabolism cofactor supply for S-Adenosylmethionine (SAMe) synthesis, homocysteine remethylation (MTHFR/MTR/BHMT), and transsulfuration (CBS) | 400–800 mcg L-5-MTHF + 500–1,000 mcg Methyl/Adenosyl/Hydroxocobalamin + 10–25 mg P5P + 10–25 mg Riboflavin-5-Phosphate + 1,000–2,000 mg TMG | 🟢 Tier 1 |
| Methylene Blue & Electron Transport Chain | Longevity & Repurposed Pharmacology | Reversible redox cycling (MB ←> Leucomethylene Blue) acting as an alternative mitochondrial electron carrier bypassing Complex I/III to Cytochrome c (Complex IV) and upregulating Cytochrome c Oxidase | Low-dose hormetic window: 0.5–1.0 mg/kg/day (typically 5–25 mg/day for routine neuro-bioenergetics; max 0.5–2.0 mg/kg in clinical fMRI memory studies) | 🟢 Tier 1 |
| Mitochondrial & Metabolic Peptides (MOTS-c, SS-31, GLP-1) | Peptides & Bioregulators | Inner mitochondrial membrane cardiolipin stabilization (SS-31), folate-AICAR-AMPK nuclear retro-signaling (MOTS-c), and incretin GLP-1/GIP/Glucagon receptor agonism (Retatrutide/Tirzepatide) | MOTS-c 5 mg SubQ 2–3x/week; SS-31 (Elamipretide) 2–5 mg/day SubQ; Semaglutide 0.25–2.4 mg/week; Tirzepatide 2.5–15 mg/week; Retatrutide 1–8 mg/week | 🟢 Tier 1 |
| Neurotrophins (BDNF, NGF, Lion’s Mane) | Nootropics & Neurochemistry | Induction of Nerve Growth Factor (NGF) and Brain-Derived Neurotrophic Factor (BDNF) synthesis alongside direct Tropomyosin Receptor Kinase B (TrkB) agonism | Lion’s Mane (fruiting body + erinacine mycelium) 1,000–3,000 mg/day; 7,8-DHF 15–30 mg/day (4’-DMA-7,8-DHF 8–10 mg); Bacopa monnieri 300 mg/day; Polygala tenuifolia 100–300 mg/day | 🟢 Tier 1 |
| Omega-3 & Lipid Membrane Health | Foundational Supplements & Micronutrients | Cell membrane phospholipid incorporation, competitive COX/LOX eicosanoid shifting, PPAR-alpha/gamma activation, and synthesis of Specialized Pro-resolving Mediators (SPMs) | 2,000–4,000 mg/day combined EPA + DHA (targeting an RBC Omega-3 Index of 8–12%) | 🟢 Tier 1 |
| PDE5 Inhibitors & Endothelial Function | Longevity & Repurposed Pharmacology | Selective inhibition of Phosphodiesterase Type 5 (PDE5), preventing cyclic GMP (cGMP) hydrolysis to amplify endothelial nitric oxide (eNOS-NO-sGC-PKG) microvascular perfusion | Tadalafil 2.5–5.0 mg/day (microvascular longevity & endothelial protocol); Sildenafil 20–50 mg as needed | 🟢 Tier 1 |
| Racetams & AMPAkines | Nootropics & Neurochemistry | Positive allosteric modulation of AMPA glutamate receptors, neuronal phospholipid membrane fluidization, and hippocampal high-affinity choline uptake (HACU) acceleration | Piracetam 2,400–4,800 mg/day; Aniracetam 750–1,500 mg/day; Oxiracetam 750–1,500 mg/day; Phenylpiracetam 100–200 mg; Noopept 10–30 mg/day | 🟢 Tier 1 |
| Tissue Repair Peptides (BPC-157, TB-500, GHK-Cu) | Peptides & Bioregulators | VEGFR2/eNOS angiogenesis, Focal Adhesion Kinase (FAK-paxillin) tendon fibroblast migration, G-actin sequestration, and TGF-beta/epigenetic ECM remodeling | BPC-157 250–500 mcg 1–2x/day; TB-500 (Thymosin Beta-4) 2.0–2.5 mg 2x/week; GHK-Cu 1–2 mg/day SubQ or 1–2% topical; KPV 250–500 mcg/day | 🟡 Tier 2 |
| Vitamin D3, K2 & Calcium Homeostasis | Foundational Supplements & Micronutrients | Nuclear Vitamin D Receptor (VDR) transcriptional activation paired with Vitamin K2-dependent gamma-carboxylation of Osteocalcin and Matrix Gla Protein (MGP) | 2,000–5,000 IU/day (50–125 mcg) Vitamin D3 + 100–200 mcg/day Vitamin K2 (MK-7) or 1.5–45 mg/day (MK-4) | 🟢 Tier 1 |
| mTOR & Autophagy Modulators (Rapamycin) | Longevity & Repurposed Pharmacology | Allosteric FKBP12-rapamycin complex binding to the FRB domain of mTORC1, suppressing S6K1/4E-BP1 hyperfunction and disinhibiting ULK1/TFEB macroautophagy | Sirolimus (Rapamycin) 3–6 mg pulsed once weekly (or 8–12 mg once every 10–14 days); Everolimus 5 mg once weekly | 🟢 Tier 1 |
| Autophagy & Mitophagy (Spermidine, Urolithin A) | Cellular Health, NAD+ & Hallmarks of Aging | Spermidine inhibits EP300 acetyltransferase and hypusinates eIF5A to translate TFEB/ATG3 (macroautophagy), while Urolithin A stabilizes PINK1/Parkin to selectively ubiquitylate and clear depolarized mitochondria (mitophagy). | Urolithin A 500–1,000 mg/day; Spermidine 6–15 mg/day (wheat germ extract or pure trihydrochloride); Trehalose 5–15 g/day | 🟢 Tier 1 |
| Cellular Senescence & Senolytics (Fisetin, Quercetin, Dasatinib) | Cellular Health, NAD+ & Hallmarks of Aging | Transient ‘hit-and-run’ inhibition of Senescent Cell Anti-Apoptotic Pathways (SCAPs: PI3K/AKT, BCL-2/BCL-xL, Src tyrosine kinases, p53/p21) to induce selective apoptosis of p16INK4a+ senescent cells and suppress SASP. | Fisetin 20 mg/kg/day (or 1,000–1,500 mg liposomal) for 2–3 consecutive days every 1–3 months; Quercetin Phytosome 500–1,000 mg/day during pulse | 🟢 Tier 1 |
| Glycation & AGEs Inhibition (Carnosine, Benfotiamine) | Cellular Health, NAD+ & Hallmarks of Aging | Benfotiamine activates transketolase to shunt glycolytic triosephosphates away from methylglyoxal formation, while L-Carnosine scavenges reactive dicarbonyls (MGO/GO) and blocks RAGE-NF-kB signaling. | L-Carnosine 1,000–1,500 mg/day (or Beta-Alanine 3.2 g/day) + Benfotiamine 300–600 mg/day + Pyridoxamine/P5P 50 mg/day | 🟢 Tier 1 |
| NAD+ Salvage Pathway (NMN, NR, CD38 Inhibition) | Cellular Health, NAD+ & Hallmarks of Aging | Upregulation of intracellular NAD+ biosynthesis via NAMPT/NRK salvage enzymes paired with CD38 ecto-NADase inhibition to fuel sirtuins (SIRT1-7) and PARPs. | NMN 500–1,000 mg/day or NR 500–1,000 mg/day + Apigenin 50–100 mg/day + TMG 500–1,000 mg/day | 🟢 Tier 1 |