7: Ligand-Target Interactions 1

Question 1

what is a ligand?

Answer 1

a substance that binds to a receptor or enzyme to trigger a biological response
- agonists (for receptors)
- antagonists (for receptors)
- inhibitors (for enzymes)
- substrates (for enzymes)

Question 2

what determines the strength of the bond between a ligand and receptor?

Answer 2

the balance between k1 and k2
k1 - association
k2 - dissociation

Question 3

when do you have competition for a receptor?

Answer 3

• when you have an agonist AND antagonist, you will have competition for the receptor
• when you have an inhibitor that competes with a substrate to prevent it from binding

Question 4

ligands can be:

Answer 4

• small organic molecules
• proteins/peptides
• gases

Question 5

how does Raloxifene function against estrogen binding?

Answer 5

Raloxifene competes with estrogen to bind to its receptor.
- halts estrogen functions bc of this competition
- causes conformational change

Question 6

describe characteristics of ligand-target interactions

Answer 6

• targets can be proteins, nucleic acids, etc..
• the strength of the ligand-target bond is going to determine how long the interaction lasts

Question 7

how do ligands bind to their target?

Answer 7

non-covalent bonds - you can get dissociation (rate of dissociation is going to be determined by strength of bond)
ion-dipole, hydrogen bonding, dipole-dipole, ion-induced dipole, dipole-induced dipole, van der waals

Question 8

how does enthalpy relate to ligand binding?

Answer 8

enthalpy (deltaH) is the difference in bond energies (broken - formed)
- the energy difference between breaking and forming ligand-target complexes

Question 9

how does entropy relate to ligand binding?

Answer 9

entropy (deltaS) is the the measurement of disorder
- the presence of a ligand can trap water molecules in one position –> reduce disorder –> reduce entropy –> unfavorable

Question 10

what significance does water have on ligand binding?

Answer 10

• water can facilitate interactions through hydrogen bonding
• energy (enthalpy) may be required to remove water molecules from the ligand or target to allow for binding
• energy (entropy) may be gained or lost by changes in dynamic behavior of water molecules

Question 11

what is Kd? how do you calculate it?

Answer 11

Kd is the equilibrium dissociation constant (M)
Kd = [A][B]/[AB]
the lower the number, the tighter the association
in irreversible reactions, Kd = 0

Question 12

what is Ka? how do you calculate it?

Answer 12

Ka is the equilibrium association constant (M)
Ka = [AB]/[A][B]
the higher the number, the tighter the association

Question 13

how is Kd experimentally determined?

Answer 13

radioligand binding assay
- mix radiolabeled ligand with unlabeled protein
- filter and measure the amount of unbound ligand
- you can solve for Kd

Question 14

explain what IC50 is.

Answer 14

IC50 is the concentration of drug that blocks 50% of binding of the known standard
- concentration that inhibits 50% of the endogenous ligand

Question 15

what is Ki?

Answer 15

Ki is the equilibrium dissociation constant for the unlabeled drug in the absence of a competitive binder.