4.5 Physicochemical properties

Properties affecting drug absorption

Absorption is the process by which a drug moves from its site of administration into the bloodstream. The physicochemical properties of a molecule largely dictate how well it gets absorbed, so understanding these properties is central to designing drugs with good oral bioavailability.

Lipophilicity vs hydrophilicity

Every drug sits somewhere on a spectrum between lipophilic (fat-loving) and hydrophilic (water-loving), and where it falls has major consequences for absorption.

• Lipophilic drugs cross biological membranes more easily because cell membranes are lipid bilayers. But if a drug is too lipophilic, it won't dissolve well in the aqueous environment of the GI tract, which limits absorption from the other direction.
• Hydrophilic drugs dissolve readily in water and GI fluids but struggle to permeate lipid-rich membranes.

The challenge in drug design is finding the sweet spot: enough lipophilicity to cross membranes, enough hydrophilicity to dissolve in biological fluids.

Solubility in biological fluids

A drug must dissolve before it can be absorbed. Solubility is the maximum concentration of drug that can dissolve in a given volume of solvent at a specific temperature.

• Drugs need to be soluble in the aqueous environment of the GI tract to reach the intestinal epithelium.
• Poorly soluble drugs may precipitate in the gut, drastically reducing bioavailability.
• Common strategies to improve solubility:
  • Salt formation: reacting the drug with an acid or base to create a more water-soluble ionic form
  • Prodrug approaches: masking hydrophobic groups with solubilizing moieties
  • Formulation techniques: micronization (reducing particle size), solid dispersions (dispersing drug in a hydrophilic matrix), and cyclodextrin complexation

Ionization of drugs

Most drugs are weak acids or weak bases, meaning they exist in equilibrium between ionized and unionized forms depending on the surrounding pH.

• The unionized form is more lipophilic and crosses membranes more readily via passive diffusion.
• The ionized form is more water-soluble but has poor membrane permeability.
• The Henderson-Hasselbalch equation lets you calculate the ratio of ionized to unionized drug at any given pH:

$pH = pKa + \log\left(\frac{[A^-]}{[HA]}\right)$

This is written for a weak acid. For a weak base, the equation uses $\frac{[B]}{[BH^+]}$. Knowing a drug's $pKa$ and the pH of the environment (stomach ~1.5, small intestine ~6.5, blood ~7.4) lets you predict where absorption will be favored.

Partition coefficient

The partition coefficient (log P) quantifies lipophilicity. It's defined as the ratio of a drug's concentration in octanol to its concentration in water at equilibrium:

$\log P = \log\left(\frac{[drug]_{octanol}}{[drug]_{water}}\right)$

• Higher log P = more lipophilic = generally better membrane permeability.
• The optimal log P range for oral drugs is typically 1 to 5.
• Extremely high log P values (above 5) bring problems: poor aqueous solubility, increased metabolic liability, and a tendency to accumulate in fatty tissues.

Note that log P measures the partitioning of the unionized form only. Log D is the distribution coefficient measured at a specific pH and accounts for ionization, making it more physiologically relevant.

Drug permeability

Permeability is a drug's ability to cross biological membranes such as the intestinal epithelium or the blood-brain barrier.

• Passive diffusion is the dominant mechanism for most drugs and favors small, lipophilic, uncharged molecules.
• Active transport (e.g., via amino acid or peptide transporters) can carry drugs that wouldn't cross membranes well on their own.
• Efflux transporters like P-glycoprotein (P-gp) actively pump drugs out of cells, reducing effective permeability. This is a common reason drugs fail to reach adequate concentrations at their target.

Key factors affecting permeability: lipophilicity, molecular size, hydrogen bonding capacity, charge state, and transporter interactions.

Properties affecting drug distribution

Once a drug reaches the bloodstream, it distributes into tissues and organs. The extent of distribution depends on the drug's physicochemical properties and how it interacts with blood and tissue components.

Plasma protein binding

Many drugs bind reversibly to plasma proteins, primarily albumin (which tends to bind acidic drugs) and alpha-1-acid glycoprotein (which tends to bind basic drugs).

• Only the unbound (free) fraction can diffuse into tissues and exert pharmacological effects.
• High protein binding can limit the volume of distribution and slow clearance, but it also prolongs half-life by creating a circulating reservoir.
• Clinically, protein binding matters most for drugs with a narrow therapeutic index, where small changes in free fraction can cause toxicity.

Tissue binding

Drugs can also bind to components within tissues: proteins, lipids, nucleic acids, or other macromolecules.

• Tissue binding can cause drug accumulation in specific organs (e.g., aminoglycosides in the kidney, tetracyclines in bone).
• Highly lipophilic drugs tend to accumulate in adipose tissue.
• Extensive tissue binding results in a large volume of distribution and a prolonged elimination half-life, since the drug is sequestered away from the bloodstream where clearance occurs.
• Tissue accumulation can also drive organ-specific toxicity.

Blood-brain barrier penetration

The blood-brain barrier (BBB) is a tightly regulated barrier formed by endothelial cells with tight junctions, limiting what enters the CNS.

To cross the BBB, a drug generally needs to be:

• Lipophilic
• Low molecular weight (typically < 500 Da)
• Not heavily bound to plasma proteins
• Not a substrate for efflux transporters like P-gp (which is highly expressed at the BBB)

This creates a design tension: drugs for CNS disorders (antidepressants, antipsychotics, anti-epileptics) must penetrate the BBB, while drugs for peripheral targets should ideally not penetrate it to avoid central side effects.

Properties affecting drug metabolism

Metabolism is the enzymatic modification of drugs, occurring primarily in the liver. A drug's chemical structure determines which enzymes act on it and how quickly it's transformed.

Metabolic stability

Metabolic stability describes how resistant a drug is to enzymatic biotransformation.

• High metabolic stability = longer duration of action, less frequent dosing.
• Too much stability can lead to accumulation and toxicity.
• The goal is a balance: enough stability for adequate exposure, enough clearance to prevent buildup.

Cytochrome P450 interactions

The cytochrome P450 (CYP) enzymes are the most important drug-metabolizing enzyme family. Key isoforms include CYP3A4, CYP2D6, CYP2C9, and CYP1A2.

• CYP inhibition by one drug can increase plasma levels of another drug metabolized by the same enzyme, raising toxicity risk.
• CYP induction increases enzyme expression, accelerating metabolism of co-administered drugs and potentially reducing their efficacy.
• Medicinal chemists try to minimize CYP interactions during optimization by modifying structures to avoid strong inhibition or induction of major CYP isoforms.

Phase I vs Phase II metabolism

Drug metabolism occurs in two phases:

1. Phase I (functionalization): Introduces or exposes polar functional groups through oxidation, reduction, or hydrolysis. Primarily mediated by CYP enzymes. These reactions often create a "handle" for Phase II conjugation.
2. Phase II (conjugation): Attaches highly polar moieties (glucuronic acid, sulfate, glutathione, acetyl groups) to the drug or its Phase I metabolite. This dramatically increases water solubility and facilitates renal or biliary excretion.

The balance between Phase I and Phase II metabolism influences bioavailability, half-life, and whether toxic intermediates are formed.

Prodrugs and active metabolites

A prodrug is an inactive compound that undergoes metabolic conversion to release the active drug in vivo. Prodrug strategies are used to overcome specific physicochemical limitations:

• Ester prodrugs improve lipophilicity and permeability (e.g., oseltamivir phosphate is converted to the active oseltamivir carboxylate by esterases).
• Phosphate ester prodrugs improve aqueous solubility (e.g., fosamprenavir releases amprenavir after phosphatase cleavage).

Some drugs also generate active metabolites that contribute to the therapeutic effect. Codeine is O-demethylated by CYP2D6 to morphine, and tamoxifen is converted to the more potent endoxifen. These metabolic pathways must be considered during drug design.

Properties affecting drug excretion

Excretion is the removal of drugs and metabolites from the body. The two major routes are renal (urine) and biliary (feces).

Renal clearance

Renal clearance is the volume of blood completely cleared of a drug by the kidneys per unit time. Three processes in the nephron determine renal clearance:

1. Glomerular filtration: Unbound drug is passively filtered at the glomerulus. Protein-bound drug is not filtered.
2. Tubular secretion: Active transporters in the proximal tubule pump drug from blood into the tubular fluid.
3. Tubular reabsorption: Lipophilic, unionized drug can be passively reabsorbed from the tubular fluid back into the blood, reducing net clearance.

Drugs with high renal clearance are eliminated quickly. In patients with impaired kidney function, drugs with significant renal clearance can accumulate to toxic levels, requiring dose adjustment.

Biliary excretion

In biliary excretion, drugs are actively transported from hepatocytes into bile canaliculi by transporters such as P-gp and BCRP, then excreted into the intestine via bile.

• Biliary excretion tends to favor larger, more polar molecules (molecular weight > 500 Da for many species).
• Some drugs undergo enterohepatic recirculation: after biliary excretion into the intestine, they're reabsorbed and returned to the liver via the portal circulation. This recycling prolongs the drug's half-life and can create a secondary peak in plasma concentration.

Half-life and elimination rate

The elimination half-life ($t_{1/2}$) is the time for plasma drug concentration to fall by 50% during the elimination phase.

$t_{1/2} = \frac{\ln(2)}{k_e} \approx \frac{0.693}{k_e}$

where $k_e$ is the elimination rate constant (fraction of drug eliminated per unit time).

• Short half-life drugs require more frequent dosing to stay within the therapeutic window.
• Long half-life drugs can be dosed less often but take longer to reach steady state (approximately 4-5 half-lives).
• Half-life is determined by both clearance (CL) and volume of distribution ($V_d$):

$t_{1/2} = \frac{0.693 \times V_d}{CL}$

This means a drug's half-life can be long either because it's slowly cleared or because it's widely distributed into tissues.

Structure-property relationships

Structure-property relationships (SPRs) connect a drug's chemical structure to its physicochemical and pharmacokinetic behavior. These relationships are the foundation of rational drug design: if you understand how structural changes affect properties, you can systematically optimize a molecule.

Functional groups and properties

Functional groups are specific atomic arrangements that confer characteristic chemical behavior. Changing even a single functional group can dramatically alter a drug's profile.

• Hydroxyl (-OH): Increases water solubility and hydrogen bonding capacity, but may introduce a metabolic soft spot (glucuronidation site).
• Amino (-NH₂): Introduces basicity, affects ionization state, and can participate in hydrogen bonding.
• Carboxyl (-COOH): Makes the molecule acidic, increases polarity and water solubility, but reduces membrane permeability.
• Ester (-COO-): Increases lipophilicity relative to the free acid, but esters are often rapidly hydrolyzed by esterases in vivo.

The art of medicinal chemistry lies in choosing functional group modifications that improve one property without wrecking another.

Molecular size and shape

• Smaller molecules (MW < 500 Da) generally have better oral bioavailability and membrane permeability.
• Very small molecules (MW < 200 Da) may lack sufficient complexity to bind selectively to a target, leading to off-target effects.
• Molecular shape and conformational flexibility matter too: rigid molecules may bind more tightly to a specific target (lower entropic penalty), while flexible molecules can adopt multiple conformations but may lose selectivity.

Stereochemistry and drug properties

Stereochemistry refers to the 3D arrangement of atoms in a molecule. Because biological targets (receptors, enzymes) are chiral, stereoisomers of a drug can have very different activities.

• (S)-ibuprofen is the pharmacologically active enantiomer; the (R)-enantiomer is largely inactive (though it's slowly converted to the S-form in vivo).
• (R)-thalidomide was considered the safe sedative enantiomer, while (S)-thalidomide is teratogenic. However, the enantiomers interconvert in vivo, so administering a single enantiomer doesn't solve the problem.

These examples illustrate why stereochemistry must be carefully considered during drug design and why regulatory agencies now require characterization of individual enantiomers.

Quantitative structure-activity relationships (QSAR)

QSAR uses mathematical models to correlate molecular descriptors with biological activity or physicochemical properties.

The general workflow:

1. Assemble a dataset of structurally related compounds with measured activity data.
2. Calculate molecular descriptors for each compound (e.g., log P, molecular weight, topological indices, hydrogen bond counts).
3. Build a statistical model (multiple linear regression, partial least squares, or machine learning methods) relating descriptors to activity.
4. Validate the model using test set compounds not included in model building.
5. Use the model to predict properties of untested compounds and guide synthesis priorities.

QSAR is widely used to predict ADME properties, identify key structural features driving activity, and prioritize compounds during lead optimization.

Optimization of drug properties

Drug optimization is the iterative process of improving a lead compound's efficacy, safety, and pharmacokinetic profile to produce a viable drug candidate. The physicochemical properties discussed throughout this guide are the levers medicinal chemists pull during optimization.

Strategies for improving solubility

• Salt formation: React the drug with a counterion to form a more soluble salt. For example, the sodium salt of ibuprofen dissolves much faster than the free acid.
• Prodrugs: Attach a solubilizing group that's cleaved in vivo. Fosamprenavir is a phosphate ester prodrug of amprenavir with greatly improved aqueous solubility.
• Formulation approaches: These don't change the molecule itself but improve its dissolution behavior. Examples include micronization, amorphous solid dispersions, nanoparticle formulations, and cyclodextrin complexation.

Enhancing permeability and absorption

• Increase lipophilicity by adding nonpolar groups or reducing hydrogen bond donors (each H-bond donor lost can meaningfully improve passive permeability).
• Reduce polar surface area (PSA): Compounds with PSA < 140 Ų tend to have better oral absorption. For BBB penetration, PSA < 90 Ų is often targeted.
• Reduce molecular size where possible.
• Target uptake transporters (e.g., PEPT1 for peptide-like drugs, LAT1 for amino acid analogs) to achieve active absorption when passive diffusion is insufficient.

Reducing metabolic liability

1. Identify metabolic soft spots using in vitro microsomal assays or in silico prediction tools.

2. Block or replace vulnerable groups:

   • Replace metabolically labile esters with more stable amides.
   • Substitute hydrogen atoms at oxidation-prone positions with fluorine or deuterium to slow CYP-mediated metabolism.
   • Reduce overall lipophilicity, since highly lipophilic compounds tend to have higher CYP affinity.

3. Verify that structural changes maintain potency at the target.

Prolonging half-life and duration of action

• Increase plasma protein binding to create a circulating drug reservoir (though this reduces the free fraction available for activity).
• Design prodrugs with slow bioactivation to extend exposure to the active species.
• Reduce renal clearance by increasing molecular size or adjusting polarity to minimize glomerular filtration and tubular secretion.
• Reduce hepatic clearance by improving metabolic stability as described above.

Physicochemical profiling in drug discovery

Physicochemical profiling is the systematic measurement and prediction of a compound's properties throughout the discovery pipeline. Early profiling helps identify liabilities before significant resources are invested.

High-throughput screening assays

High-throughput screening (HTS) assays evaluate properties of large compound libraries rapidly:

• Solubility assays: Measure compound concentration in aqueous buffer using UV/Vis spectroscopy or nephelometry (light scattering by undissolved particles).
• Permeability assays: PAMPA (parallel artificial membrane permeability assay) uses a synthetic lipid membrane for fast passive permeability screening. Caco-2 cell monolayers provide a more physiologically relevant model that also captures transporter-mediated effects.
• Metabolic stability assays: Incubate compounds with liver microsomes or hepatocytes and measure the rate of parent compound disappearance over time.

In vitro ADME studies

These provide more detailed pharmacokinetic data than HTS:

• Plasma protein binding: Measured by equilibrium dialysis or ultrafiltration.
• BBB penetration models: MDCK or LLC-PK1 cell lines, often transfected with efflux transporters like P-gp, estimate CNS penetration potential.
• CYP inhibition/induction: Tested using human liver microsomes (for inhibition) or hepatocytes (for induction) to flag drug-drug interaction risks.

In silico property prediction

Computational methods predict properties from chemical structure alone, saving time and resources:

• QSPR models (quantitative structure-property relationships) correlate molecular descriptors with experimental data using regression or machine learning.
• Molecular docking predicts binding affinity to specific targets, including metabolic enzymes and transporters.
• PBPK modeling (physiologically based pharmacokinetic modeling) integrates in vitro and in silico data into a whole-body simulation to predict human PK before clinical trials.

Druglikeness and lead optimization

Druglikeness describes the set of molecular properties associated with successful oral drugs. Several rule sets help assess it:

These are guidelines, not hard rules. Many successful drugs violate one or more criteria (especially in areas like oncology or natural product-derived drugs). Still, compounds that satisfy these filters have a statistically higher chance of good oral bioavailability.

Lead optimization is the iterative cycle of designing, synthesizing, testing, and refining compounds to improve druglike properties while maintaining potency and selectivity at the target. The physicochemical principles covered in this guide are applied at every step of that cycle.