Most pharmaceutical drugs are small molecules which elicit a physiological response by "binding" to enzymes or receptors, causing an increase or decrease in the enzymes ability to function. The binding of a small molecule to a protein is governed by a combination of steric, or spatial considerations, in addition to various non-covalent interactions, although some drugs do covalently modify an active site (see irreversible inhibitors). Using the "lock and key model" of enzyme binding, a drug (key) must be of roughly the proper dimensions to fit the enzymes binding site (lock). Using the appropriately sized molecular scaffold, drugs must also interact with the enzyme non-covalently in order to maximize binding affinity binding constant and reduce the ability of the drug to dissociate from the binding site. This is achieved by forming various non-covalent interactions between the small molecule and amino acids in the binding site, including: hydrogen bonding, electrostatic interactions, pi stacking, van der Waals interactions, and dipole–dipole interactions.
Non-covalent metallo drugs have been developed. For example, dinuclear triple-helical compounds in which three ligand strands wrap around two metals, resulting in a roughly cylindrical tetracation have been prepared. These compounds bind to the less-common nucleic acid structures, such as duplex DNA, Y-shaped fork structures and 4-way junctions.