Week 1 Flashcards
What is Molecular Pharmacology?
Molecular pharmacology is the study of understanding how cells respond to hormones or pharmacologic agents, and how chemical structure correlates with biological activity through understanding interactions between drug molecules and the cell.
What types of molecules act as drugs?
Drugs alter the physiological state by modulating the activity of a molecular target.
Molecules that can act as a drug include:
- Guide RNA
- asRNA, siRNA, miRNA
- RNA aptamer
- Antibodies
- Small molecules
What type of molecules act as drug receptors?
A target/receptor is the molecular recognition site in the body to which a drug binds to produce a therapeutic effect.
Molecules that can act as drug targets are:
- DNA
- RNA (mRNA and ncRNA)
- Proteins
What are the defining characteristics of each drug receptor class?
Ligand-Gated Ion Channels
- Located in the cellular membrane
- Binding of a ligand or a change in membrane voltage results in conformational change that opens the channel
- Ions are then able to pass through causing a change in membrane potential and a cellular response (signal)
- Cations that pass through travel down their electrochemical gradient
- Milliseconds
Transporters
- Located in the cellular membrane
- Primary active transporters require ATP to overcome the energy barrier
- Secondary active transporters
- Pump cations against their electrochemical gradient
- Involved in absorption, distribution and elimination of drugs
- Responsible for resistance seen with some drugs as they actively pump drugs out of target cells
Catalytic Receptors
- Found in the cellular membrane
- Consist of a binding domain, a transmembrane domain and a catalytic domain
- Must be dimerised to be activated
- Hours
Nuclear Receptors
- Located in the cytoplasm and move into the nucleus once activated
- Bind inhibitory proteins in the inactive state where agonist binding causes conformational change, resulting in corepressor dissociation and coactivator recruitment
- Increase gene expression
- Hours
G Protein-Coupled Receptors (GPCRs)
- Located in the cellular membrane
- Typically consist of 7 transmembrane domains, an extracellular N terminus and intracellular C terminus
- Ligand binding activates signalling cascades
- Seconds
What methods are used to investigate interactions between drugs and drug targets?
Organ Baths
Electrophysiology
Cloning and Expression of Genes
Site-Directed Mutagenesis
- PCR-based method to mutate specific nucleotides of a DNA sequence within a plasmid vector
- Allows the replacement of individual amino acids to then examine how this affects protein function and drug binding
In silico Methods
- Pharmacophore models
- Molecular docking simulations
What are the families of GPCRs?
The names of the GPCR families based on the phylogenetic origin are GRAFS (glutamate, rhodopsin, adhesion, frizzled and secretin).
What are the differences in the structure of the N termini of each GPCR family?
Glutamate
- Very large N terminus
- Has Venus fly trap and cysteine-rich domains located in N terminus
Rhodopsin
- Small N terminus
Adhesion
- Varied N terminus, typically intermediate
Frizzled
- Intermediate N terminus (larger than rhodopsin)
Secretin
- Rod-like N terminus that sticks out into the extracellular space
What are the different site and modes of ligand binding for each GPCR family?
Glutamate
- Orthosteric site in the N-terminus
- Multiple allosteric sites in the transmembrane domain
Rhodopsin
- Four sub-branches (alpha, beta, delta, gamma)
- Variety of orthosteric binding sites, mainly in the top half of transmembrane domains
- Differences in ECL2 lead to either an open binding pocket or one in which access is restricted to a small channel
Adhesion
- Ligand binding and signalling partners highly contentious (unknown)
Frizzled
- Smoothened: transmembrane binding site that antagonists bind to
- Frizzled: binding sites in the cysteine-rich domain of N-terminus
Secretin
- Binding sites located in the N-terminus and top of the transmembrane bundle
What is the molecular basis for GPCR activation for the glutamate and rhodopsin family receptors?
Glutamate
- If an agonist is binds to the orthosteric site, then there is complete closure of the Venus fly trap and there is a change in orientation that is transmitted down the cysteine-rich domain which leads to the spinning of transmembrane domains and g protein signalling
- If a negative allosteric modulator (NAM) binds to an allosteric site in the transmembrane domain, rotation occurs in the opposite direction to the agonist binding which pushes the homodimer further into an inactive state
Rhodopsin
- Minor movements in the binding pocket causes rotation of the connector region which is magnified in TM6 causing a large swing (35 degrees)
- TM6 moves closer to TM5 and away from TM3 which causes hydrogen bonds to break between E/DRY motif and E6.30 with new bonds forming. Y7.53 from NPxxY swings into the vacated space
- This allows a G protein to enter the enlarged pocket at the bottom of the receptor via its C-terminal alpha5-helix
What is the effect of receptor activity-modifying proteins (RAMPs) on receptor pharmacology?
RAMPs are single membrane-spanning accessory proteins that interact with many different GPCRs. They stabilise the ECD of the receptor which alters how peptides interact with the transmembrane core. Interactions between 3 different RAMPs and the calcitonin receptor or calcitonin-like receptor gives rise to 7 receptors with differing pharmacological profiles which alters the potency rank of each receptor.
