Pharmacology Flashcards
Orthosteric vs allosteric ligands?
Orthosteric Ligands:
* Definition: These ligands bind to the active (orthosteric) site of a receptor.
* Mechanism: They directly compete with the endogenous ligand for binding to the receptor’s active site.
* Effect: Can either activate or inhibit the receptor, depending on whether they mimic or block the action of the endogenous ligand.
Allosteric Ligands:
* Definition: These ligands bind to a site on the receptor that is different from the active site (allosteric site).
* Mechanism: Binding of allosteric ligands induces a conformational change in the receptor, influencing its response to the orthosteric ligand.
* Effect: Can modulate the activity of the receptor, either enhancing (PAMs) or reducing (NAMs) the response to the orthosteric ligand.
PAMs vs NAMs?
Positive Allosteric Modulators (PAMs):
* Function: Enhance the effect of the orthosteric ligand.
* Mechanism: Bind to the allosteric site and facilitate the binding of the orthosteric ligand, increasing its efficacy.
* Effect: Amplify the response to endogenous ligands without directly activating the receptor on their own.
Negative Allosteric Modulators (NAMs):
* Function: Reduce the effect of the orthosteric ligand.
* Mechanism: Bind to the allosteric site and inhibit the binding or efficacy of the orthosteric ligand.
* Effect: Diminish the response to endogenous ligands without directly inhibiting the receptor.
Which binding sites have been defined for Navs?
Seven binding sites for toxins and drugs were defined on the primary sequence of Nav channels based on rigorous functional characterizations:
1) VSD
* V2EP – voltage sensing domain extracellular side, pore domain
* V4EM – voltage sensing domain extracellular side, membrane
* V4EC – voltage sensing domain extracellular side, cavity
2) PD (pore domain) – E – extracellular loops
3) PD (pore domain) – S – selectivity filter
4) PD (pore domain) – C – central cavity
5) PD (pore domain) – G – intracellular gate
6) PD (pore domain) – BIG – beneath the intracellular gate
7) PD (pore domain) – F – fenestrations
8) Site I – inactivation site
Which drugs bind to site E on Navs and how?
Site E:
- Highly glycosylated, stabilized by disulfide bonds.
- μ-conotoxin KIIIA, a 16-residue peptidic toxin with three disulfide bonds binds here.
- KIIIA: Blocks Nav1.2, Nav1.4, Nav1.7; less potent on Nav1.5, minimal effect on Nav1.8.
- Nav1.2-KIIIA structure: Reveals interactions between extracellular loops (ECLs) and toxin.
- Lys7 in KIIIA: Acts as a “cork,” obstructing Na+ entrance to the selectivity filter.
Which drugs bind to site S on Navs and how?
- Entrance to the SF vestibule below ECLs constitutes receptor site 1, redefined as site S for TTX and STX.
- TTX and STX are guanidinium neurotoxins, prototypical pore blockers for pharmacological characterization of Nav channels.
- Nav1.5, Nav1.8, and Nav1.9 are TTX-resistant (TTX-R), requiring micromolar concentrations for blocking; others are TTX-sensitive (TTX-S) at nanomolar range.
- STX competes with TTX, showing lower affinity for Nav1.7 compared to other isoforms.
- TTX and STX form extensive electrostatic interactions with the SF, obstructing the ion entrance pathway.
- Sequence alignment and structural information highlight the role of Tyr or Phe on repeat I for TTX sensitivity, while TTX-R has Cys or Ser.
Which drugs bind to site C on Navs and how?
- Central cavity in Nav channels provides ample space, with pseudo-symmetric architecture offering unique docking sites.
- Site C is located between SF, intracellular gate, and connected to fenestrations.
- Quinidine, a class Ia antiarrhythmic drug, obstructs Nav1.5 ion conductance by binding to site C. –> Nav1.5-quinidine structure reveals positioning beneath SF in PD, coordinated by residues from S6I, S6III, and S6IV.
- Flecainide, a class Ic antiarrhythmic agent, also binds to site C with a different pose compared to quinidine.
- Propafenone, another class Ic antiarrhythmic agent, binds to site C surrounded by S6I and S6IV in a distinct manner.
- Nav1.7-IN2, a pain relief aryl carboxamide derivative, exhibits a U-shaped structure in the central cavity.
- Riluzole (RLZ), a drug for motor neuron diseases, resides in the central cavity.
- Site C is divided into UC (upper cavity) and LC (lower cavity) based on a plane perpendicular to the ion permeation path. Plane is derived from conserved Phe on S6IV, dividing site C into CC (central cavity). The plane can be divided into four zones (1, 2, 3, 4) emphasizing asymmetry, annotated with repeat numbers in parentheses.
- Quinidine’s specific binding site referred to as UC(1,3,4) situated above conserved Phe and close to repeats I, III, and IV.
- Propafenone resides in CC(1,4) based on this nomenclature system.
- No reported chemicals binding to LC.
Which drugs bind to site I on Navs and how?
- Cannabidiol (CBD), derived from cannabis plants, is known for its potential therapeutic properties and common usage as an antiepileptic Binds two places
o IV-I fenestration
o Right next to the fast inactivation site, designated as site I for inactivation - CBD stabilizes inactivated state
Which drugs bind to site BIG on Navs and how?
- The structures of Nav1.7 in the presence of bupivacaine (BPV), carbamazepine (CBZ), lacosamide (LCM), and lamotrigine (LTG) demonstrated that these four drugs bind to a common shallow pocket located beneath the intracellular gate (BIG).
- Site BIG consists of cytosolic residues located beneath the intracellular gate and is enveloped by the four S6 helices. While BPV, CBZ, LCM, and LTG all bind to site BIG, the surrounding residues vary. BPV and LTG reside in site BIG enclosed by hydrophobic residues, and LCM and CBZ form additional hydrogen bonds. these four clinical drugs share a conserved binding pattern, wherein the aromatic ring extends into the central pore, leaving the flexible tail toward the inner side of the membrane. These structures demonstrate that drugs with a similar chemical skeleton can exhibit a comparable binding pose.
Which drugs bind to site F on Navs and how?
- Allow drugs to directly access the receptor pocket from the membrane phase rather than passing through the pore of the channel
- Substitution of small side chain residues to large ones in fenestration sites would block drug access pathway,
Which drugs bind to VSD on Navs and how?
- Each VSD contains a set of highly conserved positively charged residues located at every three positions on the S4 segment, which are essential for voltage sensing
- Gating modifier toxins (GMTs) target the VSDs and allosterically modulate the function of Nav channels
Which ligand blocks of the ion channel pore of Cavs and how?
Cadmium (Cd2+): Nonselective inhibitor of all CaVs.
* Mechanism: Binds to the selectivity filter in the pore.
* Details: Cd2+ binds specifically to a ring of four glutamate residues in the selectivity filter of the pore. This interaction occurs with much higher affinity than Ca2+ itself. By binding to these glutamate residues, Cd2+ effectively blocks the ion flow through the pore.
Which allosteric modulator binds to Cavs and how?
Dihydropyridines: Selectively affect CaV1 family.
* Mechanism: Modifies the gating characteristics of the channel.
* Details: Dihydropyridines act as allosteric modulators by influencing the way the channel opens and closes. They selectively impact members of the CaV1 family, altering the dynamics of channel activation and inactivation.
Which drugs are known to block Cav1 and how?
Organic Calcium Blockers (e.g., Verapamil, Diltiazem, Nifedipine):
* Binding Sites: High-affinity binding to α1 subunits of CaV1. The amino acid residues important for the binding of these compounds have been identified through mutagenesis studies and are located in the S5 and S6 segments of domains III and IV of the α1 subunit.
* Allosteric Modulation: Act as allosteric modulators.
* Use-Dependent Inhibition: Exhibits higher affinity for inactivated conformations of CaVs. This property is termed “use-dependent” because the inhibition increases with the frequency of channel activation.
Which drugs are known to block Cav2 and how?
N-type channel is inhibited by peptide toxins from fish-eating marine snails.
ω-Conotoxin GVIA and ω-Conotoxin MVIIA:
* Binding Site: ω-Conotoxin GVIA binds with high affinity to residues in the pore loop region of domain III.
* Blocker
Which drugs are known to block Cav3 and how?
Mibefradil:
* Selectivity: Moderately selective blocker of CaV3.
* Use-Dependent Inhibition: Inhibits CaV3.1–CaV3.3 channels in a use-dependent manner, showing ~10-fold selectivity over CaV1.2 channels.
Gabapentin:
* Selectivity: Binds with extremely high affinity to the α2δ subunit of CaVs.
* Mechanism: This impairs the trafficking function of α2δ subunit which normally increases CaV channel cell surface expression. Thereby, gabapentin partially decreases the amplitude of calcium currents without producing the complete blockade seen with CaV inhibitors targeting the α1 subunit. Both CaV2.1 and CaV2.2 are involved in mediating the effects of gabapentin/pregabalin. Both drugs are nontoxic which may be related to their partial blocking effect.
