Protein Targets for Drug Binding Lecture 3 PDF

# PROTEIN TARGETS FOR DRUG BINDING 1. **Receptors** - Type 1: ligand-gated ion channels (ionotropic receptors) - Type 2: G-protein-coupled receptors (GPCRs, metabotropic receptors) - Type 3: kinase-linked and related receptors - Type 4: nuclear receptors 2. **Ion channels** 3. **Enz...

# PROTEIN TARGETS FOR DRUG BINDING 1. **Receptors** - Type 1: ligand-gated ion channels (ionotropic receptors) - Type 2: G-protein-coupled receptors (GPCRs, metabotropic receptors) - Type 3: kinase-linked and related receptors - Type 4: nuclear receptors 2. **Ion channels** 3. **Enzymes** 4. **Transporters** (carrier molecules) ## Ion Channels in General Ion Channels are gateways in cell membranes that selectively allow the passage of particular ions and that are induced to open or close by various mechanisms: - Ligand-gated channels (open only when one or more agonist molecules are bound and are properly classified as receptors) and - Voltage-gated channels (gated by changes in the transmembrane potential) Drugs can affect ion channel function in several ways: - **By binding to the channel protein itself**, either to the - Ligand-binding (orthosteric) site of ligand-gated channels (adrenaline) - Other (allosteric) sites (benzodiazepines to GABA receptor) - Plug the channel physically (anesthetics on Na+ channel) - **Indirect interaction**, involving a G protein and other downstream intermediaries. - **Altering the level of expression** of ion channels on the cell surface. ## Ligand-gated ion channels (AKA ionotropic receptors) - Ions can cross the fatty barrier of the cell membrane by moving through these hydrophilic channels or tunnels. - The lock gate is controlled by a receptor protein sensitive to an external chemical messenger. ## Ligand-gated ion channels - **Ion channels are specific for certain ions:** - Cationic ion channels for sodium (Na+), potassium (K+), and calcium (Ca2+) ions; - Anionic ion channels for the chloride ion (Cl-). - Typically, these are the receptors on which fast neurotransmitters act. - These are membrane proteins, they incorporate a ligand-binding (receptor) site, usually in the extracellular domain. - The up to five protein subunits that make up an ion channel are glycoproteins. - Examples include the nicotinic acetylcholine receptor (nAChR); GABAA, glutamate receptor, and glycine receptor. ## Ligand-gated ion channels - The ion channel controlled by the nicotinic acetylcholine receptor is made up of five subunits of four different types [a (x2) β, γ, δ] - The ion channel controlled by the glycine receptor is made up of five subunits of two different types [α (×3), β (×2)] ## Ligand-gated ion channels - **Nicotinic acetylcholine receptor (nAChR), heteropentameric structure** = five receptor subunits (α₂, β, γ, δ) form a cluster surrounding a central transmembrane pore - **Two ACh binding sites** at the a-δ and α-γ subunit interfaces ## Nicotinic acetylcholine receptor - The lining of a transmembrane pore is formed by the M₂ helical segments (containing hydrophobic leucine and valine residues) of each subunit. These contain a preponderance of negatively charged amino acids which makes the pore cation selective - **Permeable mainly to Na+ and K+** - **There are two acetylcholine binding sites** in the extracellular portion of the receptor at the interface between the a and the adjoining subunits. - When acetylcholine binds, the twisted a helices either straighten out or swing out of the way, thus opening the channel pore ## Nicotinic acetylcholine receptor - Receptors of this type control the fastest synaptic events in the nervous system, in which a neurotransmitter acts on the postsynaptic membrane of a nerve or muscle cell and transiently increases its permeability to particular ions. - Most excitatory neurotransmitters, such as acetylcholine at the neuromuscular junction or glutamate in the central nervous system, cause an increase in Na+, K+, and sometimes Ca2+ permeability. This results in a net inward current carried mainly by Na+, which depolarises the cell and increases the probability that it will generate an action potential. - The action of the transmitter reaches a peak in a fraction of a millisecond, and usually decays within a few milliseconds. - The speed of this response implies that the coupling between the receptor and the ionic channel is a direct one, and the molecular structure of the receptor-channel complex agrees with this. - In contrast to some other receptor families, no intermediate biochemical steps are involved in the transduction process. ## Nicotinic acetylcholine receptor - Patch clamp technique: Single acetylcholine-operated ion channel at the frog motor endplate (note the speed!) ## Occupation & Activation - **The conformation R**, representing the open state of the ion channel, is the same for all agonists, accounting for the finding that the channel conductance does not vary. - **Kinetically, the mean open time** is determined mainly by the closing rate constant, a, and this varies from one drug to another. - **An agonist of high efficacy** that activates a large proportion of the receptors that it occupies will be characterized by β/α >> 1, whereas for a drug of low efficacy β/α has a lower value. ## Other ligand-gated ion channels - **Cys-loop type** - Examples: nAChR, GABAA, 5-HT3 - (pentameric assembly) - **Ionotropic glutamate type** - Examples: NMDA - (tetrameric assembly) - **P2X type** - Example: P2XR - (trimeric assembly) - **Calcium release type** - Example: IP3R, RyR - (tetrameric assembly) ## Summary: Ligand-gated ion channels - They are involved mainly in **fast synaptic transmission.** - There are several structural families, the commonest being **heteromeric assemblies of four or five subunits,** with transmembrane helices arranged around a central aqueous channel. - **Ligand binding and channel opening** occur on a millisecond timescale. - **Examples** include the nicotinic acetylcholine, GABA type A (GABA), glutamate (NMDA), and ATP (P2X) receptors.