ADME Data¶
Warning
This page offers a concise overview of ADME data for reference purposes on how synthbiodata generates datasets for molecular properties. It is not intended to be a comprehensive educational resource or a detailed scientific guide.
When developing and testing new drugs, it is essential to understand how a compound behaves within the body to evaluate its safety and potential toxicity.
ADME stands for Absorption, Distribution, Metabolism, and Excretion. These studies focus on how a substance (such as a drug candidate) is taken up, processed, and eliminated by a living organism.
Absorption¶
Absorption refers to the process by which a chemical enters the body, specifically the movement of a substance from the site of administration into the bloodstream.
There are four primary ways a substance can be administered:
- Ingestion (through the digestive tract)
- Inhalation (via the respiratory system)
- Dermal application (to the skin or eyes)
- Injection (directly into the bloodstream)
Of these, only injection delivers the compound straight into systemic circulation. For drugs given by ingestion, inhalation, or dermal routes, the substance must first cross a biological membrane before reaching the bloodstream.
The rate and extent of absorption depend on several factors:
- Physicochemical properties of the compound (molecular weight, lipophilicity, ionization)
- Route of administration and formulation
- Physiological factors (pH, blood flow, surface area)
- First-pass metabolism in the liver or gut wall
SynthBioData - Absortion¶
How does synthbiodata generates data for absortion?
| Feature | Description |
|---|---|
| Statistical Modeling | Uses normal distributions with configurable mean and standard deviation parameters (absorption_mean, absorption_std) |
| Realistic Ranges | Default values (70% ± 20%) based on typical oral drug absorption patterns |
| Percentage Format | Values generated as percentages (0-100%) representing bioavailability |
| Binary Classification | Creates binary labels for "bioavailable" vs "non-bioavailable" based on absorption thresholds |
| Reproducible Generation | Uses seeded random number generation for consistent results |
Distribution¶
Distribution describes the reversible transfer of a drug from one location to another within the body. Once a drug enters the bloodstream, it is distributed throughout the body via the circulatory system.
Key Distribution Concepts¶
Volume of Distribution (Vd): The theoretical volume that would be required to contain the total amount of drug in the body at the same concentration as in plasma. It indicates how extensively a drug is distributed in tissues.
Plasma Protein Binding: Many drugs bind to plasma proteins (primarily albumin and α1-acid glycoprotein), which affects their distribution and activity. Only unbound (free) drug can cross membranes and exert pharmacological effects.
Tissue Distribution: Drugs distribute differently across various tissues based on: - Blood flow to the tissue - Tissue composition and pH - Drug lipophilicity and molecular size - Presence of specific transporters or receptors
Distribution Barriers¶
- Blood-Brain Barrier: Highly selective barrier that protects the central nervous system
- Placental Barrier: Regulates drug transfer between mother and fetus
- Mammary Gland: Can concentrate certain drugs in breast milk
SynthBioData - Distribution¶
SynthBioData generates synthetic distribution with:
| Feature | Description |
|---|---|
| Plasma Protein Binding | Uses normal distributions (plasma_protein_binding_mean, plasma_protein_binding_std) with realistic ranges (85% ± 15%) |
| Percentage Format | Values generated as percentages (0-100%) representing protein binding affinity |
| Validation | Ensures values stay within biologically meaningful ranges (0-100%) |
| Statistical Consistency | Maintains realistic distribution patterns based on drug-like molecule properties |
| Configurable Parameters | Allows customization of mean and standard deviation for different drug classes |
Metabolism¶
Metabolism (biotransformation) is the chemical alteration of a drug by the body, primarily in the liver. The main purpose is to make drugs more water-soluble for easier elimination.
Factors Affecting Metabolism¶
- Age: Metabolic capacity changes throughout life
- Genetics: Genetic polymorphisms in drug-metabolizing enzymes
- Disease states: Liver disease significantly affects metabolism
- Drug interactions: One drug can inhibit or induce another's metabolism
- Environmental factors: Diet, smoking, alcohol consumption
SynthBioData - Metabolism¶
SynthBioData generates synthetic metabolism data by:
| Feature | Description |
|---|---|
| Clearance Rate | Uses normal distributions (clearance_mean, clearance_std) with realistic pharmacokinetic ranges (5.0 ± 2.0 L/h) |
| Half-Life | Generates half-life values (half_life_mean, half_life_std) in hours (12.0 ± 6.0 hours) |
| Positive Values | Ensures all clearance and half-life values are positive (no negative or zero values) |
| Realistic Ranges | Based on typical drug metabolism patterns for small molecules |
| Statistical Validation | Validates standard deviations are positive to maintain proper distribution shapes |
| Configurable Parameters | Allows adjustment of metabolic parameters for different drug types |
Excretion¶
Excretion is the elimination of drugs and their metabolites from the body. The primary routes are renal (kidney) and biliary (liver), with minor contributions from other routes.
Renal Excretion¶
The kidneys are the most important organs for drug elimination. Renal excretion involves:
Glomerular Filtration: Passive filtration of small, unbound molecules through the glomerulus.
Active Tubular Secretion: Active transport of drugs from blood into urine via specific transporters (OAT, OCT, P-gp).
Tubular Reabsorption: Passive reabsorption of lipophilic drugs back into the bloodstream.
Clearance¶
Clearance is the volume of plasma from which a drug is completely removed per unit time. It's a key parameter that determines:
- How quickly a drug is eliminated
- Dosing frequency requirements
- Drug accumulation potential
Total Clearance = Renal Clearance + Hepatic Clearance + Other Clearances
Synthbiodata - Excretion¶
SynthBioData generates synthetic excretion data with:
| Feature/Aspect | Description |
|---|---|
| Renal Clearance Ratio | Uses a fixed ratio parameter (renal_clearance_ratio) with default value of 0.3 (30% of total clearance) |
| Ratio Validation | Ensures the renal clearance ratio is between 0 and 1 (0-100%) |
| Realistic Proportions | Based on typical drug elimination patterns where renal excretion accounts for 20-40% of total clearance |
| Mathematical Consistency | Maintains proper relationships between total clearance and renal clearance |
| Configurable Parameters | Allows adjustment of renal clearance ratios for different drug classes |
| Binary Classification | Creates bioavailability labels based on overall ADME profile integration |