Ionisation: pKa at physiological pH

The structure you drew is almost certainly not the species present in the body. Most drugs carry an ionisable group, and whether it is charged decides solubility, permeability, distribution and which interactions are available at the binding site. This module makes that quantitative.

The pKa is the pH at which a group is exactly half ionised. That is the whole definition, and everything else follows from it.

For an acid, which loses a proton, the ionised form is the anion. Above its pKa an acid is ionised; below, it is neutral. For a base, which gains one, the ionised form is the cation. Below its pKa a base is ionised; above, it is neutral.

Getting that direction backwards is the commonest error in this topic, so it is worth a mnemonic: an acid gives away a proton, and it will do so when there are few protons around — that is, at high pH. A base takes one up, and it can only do that when protons are plentiful — at low pH.

The fraction ionised follows directly. For an acid at pH one unit above its pKa, the ionised form outnumbers the neutral by ten to one. Two units, a hundred to one. Three units, a thousand to one.

So a carboxylic acid with pKa 4.4 sitting in plasma at pH 7.4 — three units up — is 99.9% ionised. Not "mostly". Not "partly". Effectively all of it, all the time.

Now the same amine in the small intestine at pH 6.5.

You will not predict pKa reliably by eye, and no offline tool does it well either. But a small table of typical values will get you most of the way, and these are the ones that recur.

• Carboxylic acid — about 4. Ionised everywhere in the body except the stomach.
• Tetrazole — about 4.9. Which is why it substitutes for a carboxylic acid so well.
• Aliphatic amine — about 10. Protonated everywhere in the body.
• Phenol — about 10. Mostly neutral at pH 7.4; a few percent ionised.
• Sulfonamide (N-H) — about 10, sometimes lower. Partly ionised.
• Imidazole — about 6 to 7. The interesting one: it sits close enough to physiological pH that ordinary variation flips its charge.
• Aniline — about 4.6. Effectively neutral at pH 7.4, unlike an aliphatic amine.
• Guanidine — about 13. Permanently cationic.

Substituents move these, sometimes a long way. An electron-withdrawing group next to a carboxylic acid lowers its pKa; next to an amine, it lowers its basicity. Fluorine is used deliberately for exactly this.

A molecule with more than one ionisable group is more complicated than a list of pKa values suggests.

The values a titration gives you are macroscopic constants: they describe the loss of the first proton, then the second, without saying which group lost which. If two groups have similar pKa values, the first proton comes off both of them, in proportion — so there are two different singly ionised species present at once. Those individual species are microspecies, and their constants are microscopic.

This is not pedantry. Which microspecies dominates determines which hydrogen bonds are available and where the charge sits — and therefore which pose is right. If you protonate a ligand for docking by applying a rule to each group independently, you may produce a species that barely exists.

A zwitterion carries a positive and a negative charge at the same time. Its net charge is zero, and it behaves nothing like a neutral molecule.

The reason is that partition and permeability respond to the charges themselves, not to their sum. A zwitterion has two charged centres to desolvate before it can cross a membrane, so it is typically a very poor passive permeant despite a net charge of zero. It is also usually highly soluble, for the same reason. Amino acids are zwitterions; so are the fluoroquinolones, and so is levodopa — all of which rely on transporters rather than passive diffusion.

A drug meets several environments, and its charge is different in each.

• 1.5, the stomach. Acids are neutral here; bases are fully protonated.
• 6.5, the small intestine. Where most oral absorption happens.
• 7.4, plasma. The reference point for everything.
• 5.0, the lysosome. Where basic drugs accumulate — they diffuse in neutral, become protonated, and cannot get out again. That is lysosomal trapping, and it is behind both the very large volumes of distribution of many basic drugs and the phospholipidosis that some of them cause.

Everything downstream, which is why this module sits where it does.

• Solubility. An ionised species is far more soluble. Introducing an ionisable centre is the standard fix for a poorly soluble compound.
• Permeability. Only the neutral form crosses a membrane passively. The two requirements pull in opposite directions, which is module 13's problem.
• Distribution. Basic drugs accumulate in acidic compartments; acidic drugs bind albumin and stay in plasma.
• Binding. A salt bridge needs a charge. Whether your ligand's amine is protonated decides whether it can reach that aspartate at all — which is the question module 16's widget will keep asking you.
• Salt selection. An ionisable group is what lets you make a salt, and salt form is often what makes a compound developable.