A channel blocker is the biological mechanism in which a particular molecule is used to prevent the opening of ion channels in order to produce a physiological response in a cell. Channel blocking is conducted by different types of molecules, such as cations, anions, amino acids, and other chemicals. These blockers act as ion channel antagonists, preventing the response that is normally provided by the opening of the channel.

Ion channels permit the selective passage of ions through cell membranes by utilizing proteins that function as pores, which allow for the passage of electrical charge in and out of the cell. These ion channels are most often gated, meaning they require a specific stimulus to cause the channel to open and close. These ion channel types regulate the flow of charged ions across the membrane and therefore mediate membrane potential of the cell.

Molecules that act as channel blockers are important in the field of pharmacology, as a large portion of drug design is the use of ion channel antagonists in regulating physiological response. The specificity of channel block molecules on certain channels makes it a valuable tool in the treatment of numerous disorders.

To comprehend the mechanism of channel blockers, it is critical to understand the composition of ion channels. Their main function is to contribute to the resting membrane potential of a cell via the flow of ions through a cell membrane. To accomplish this task, ions must be able to cross the hydrophobic region of a lipid bilayer membrane, an unfavorable process. To assist in ion transport, ion channels form a hydrophilic pore through the membrane which allows for the usually unfavorable transfer of hydrophilic molecules. Various ion channels have varying mechanisms of function. They include:

Molecules that act as ion channel blockers can be used in relation to any of these various channels. For example, sodium channels, which are essential to the production of action potentials, are affected by many different toxins. Tetrodotoxin (TTX), a toxin found in pufferfish, completely blocks sodium ion transportation by blocking the selectivity filter region of the channel. Much of the structure of the pores of ion channels has been elucidated from studies that used toxins to inhibit channel function.

Tools such as X-ray crystallography and electrophysiology have been essential in locating the binding sites of open channel block molecules. By studying the biological and chemical makeup of ion channels, researchers can determine the makeup of the molecules that bind to certain regions. X-ray crystallography provides a structural image of the channel and molecule in question. Determining the hydrophobicity of channel domains through hydrophobicity plots also provides clues to the chemical makeup of the molecule and why it binds to a certain region. For example, if a protein binds to a hydrophobic region of the channel (and therefore, has a transmembrane region), the molecule in question might be composed of the amino acids alanine, leucine, or phenylalanine, as they are all hydrophobic themselves. Electrophysiology is also an important tool in identifying channel structure, as analyzing the ionic factors that lead to channel activation can be critical to understanding the inhibiting actions of open channel block molecules.

Channel blockers are antagonists for the respective ion channels. Many channels have binding spots for regulatory elements which can promote or repress normal function depending on the requirements within the cell and organism. The normal function of agonist binding is the generation of cellular changes leading to various downstream effects; these effects range from altering membrane potential to initiation of signaling cascades. Conversely, when open channel blockers bind to the cell they prevent the normal function of agonist binding. For example, voltage-gated channels open and close based on membrane potential and are critical in the generation of action potentials by their allowance of ions to flow down established gradients. However, open channel blockers can bind to these channels to prevent ions from flowing, thus inhibiting the initiation of an action potential.

Many different organic compounds can act as channel blockers despite channel specificity. Channels have evolved structures that, due to their membrane spanning regions, can discriminate between various ions or compounds. For example, some objects are too large for to fit into channels that are structurally specified to transport smaller objects, such as a potassium ion attempting to fit into a sodium channel. Conversely, some objects are too small to be properly stabilized by certain channel pores, such as a sodium ion attempting to pass through a potassium channel. In both cases, channel flux is not permitted. However, as long as a particular compound possesses adequate chemical affinity to a channel, that compound may be able to bind and block the channel pore. For example, TTX can bind and inactivate voltage-gated sodium channels, despite the fact that TTX is much larger and chemically different than sodium ions. Given the disparities in size and chemical properties between TTX and a sodium ion, this is an example of structure being used to block usually specific channels.