molecular recognition Flashcards
what is the affinity of a ligand for its receptor
equilibrium between unbound ligand protein complex and unbound ligand and protein/equilibrium measurement equal to the free energy difference (∆G=-RTlnKa)
explain the things in ∆G=-RTlnKa
∆G=free energy
R=gas constant (8.315 j/k/mol)
T=temperature in k
Ka=[complex]/[ligand][receptor]
what is the equation for Ka
[complex]/[ligand][receptor]
what is the equation for Kd
1/Ka
what is the equation for ∆G when using Kd
∆G=RTlnKd
what is Kd
inhibition constant=Ki
what is IC50 and what does it depend on
IC50=concentration of an inhibitor required to displace 50% of another ligand
-depends on the affinity of the displaced ligand to the receptor
what is the equation for Ki that relates to IC50
Ki=IC50/(1+[L]/Kd)
[L]=ligand being displaced
in ∆G = ∆H – T∆S what would a more negative ∆G mean
higher affinity, smaller Ki
what is Kon and Koff
rates going in and out of the bound state
(Ka and Kd are the ratio of these rates)
how to calculate Ka and Kd from Kon and Koff
Ka=Kon/Koff
Kd=Koff/Kon
what does a higher and lower Koff mean
higher=faster unbinding so it doesnt bind as tightly
lower=slower unbinding, stronger binding, reaches higher saturation
half life equation
t/2 or ln(2)k
what are the main components of partitioning of ∆G when splitting the free energy difference and whats the equation
main components=electrostatic interactions, lipophilicity/hydrophobicity, shape complementarity
∆G=∆G (trans+rot) + ∆G (conf) +∆G (polar) +∆G (hydrophob) + ∆G (vdw)
explain ∆G (trans+rot)
-describe the movement of ligands in unbound and bound states
-in free unbound state, both receptor and ligand are able to rotate and translate freely, free movement reduced/inhibited when binding
-loss of freedom unfavourable, ∆S lowered, ∆G increased
-∆G trans+rot always present, cant be reduced by ligand design
-entropic cost of binding only counts once in drugs with multiple binding sites in receptor (multivalent avidity) (?)
-if drug has multiple binding sites to multiple sites in receptor then the entropic cost of binding only counts once
explain ∆G (conf)
-what is it, describe the rotations/conformations of a ligand, how to avoid large conformational penalties on binding
∆G (conf)=conformational changes of ligand and receptors
-ligands are flexible and constantly change conformation by rotations around a single bond, rotations are frozen when binding
-possible to design ligand to reduce energy costs (1-6 kj/mol/rotation) by reducing flexibility eg, replace single bonds by double bonds)
-rearrangement of ligand from global energy minimum conformation to its bioactive conformation (?)
-to avoid large conformational penalties on binding, make the ligand rigid
-conformation rearrangements in ligands also have to occur in receptor
explain ∆G polar
-what is the free energy due to
-free energy due to interactions of polar side chain atoms, of C=O and NH backbone atoms and indirect interactions mediated by water
-electrostatic interactions and hydrogen bonding
strength of any electrostatic interaction:
Epolar=q1 q2 / ε r0
q1 and q2= ion-ion interactions or partial charges
ε= dielectric constant
r0= distance between the charges
-hydrogen bond is also electrostatic interaction between a H atom bound to an electronegative atom and an electronegative hydrogen bnod acceptor atom (X-H-A), hydrogen bonds are highly orientation dependent, max 180 degrees
-a ligand that hydrogen bonds the water but does not hydrogen bond to the protein when buried is unfavourable, an unpaired hydrogen bond for a neutral substituent costs around 4 kJ/mol, and around 16 kJ/mol for a charged one
-successful H-bonding in the cavity contributes between 2 and 6.5 kJ/mol for a neutral substituent, and 10 to 20 kJ/mol for a charge assisted bond or salt bridge
+ve atom will interact favourably at aromatic parts, delocalised electrons can interact with other pi electrons in other rings (pi pi interactions)
how to calculate the strength of any electrostatic interaction
Epolar=q1 q2 / ε r0
q1 and q2= ion-ion interactions or partial charges
ε= dielectric constant
r0= distance between the charges
explain ∆G hydrophob
-what is the hydrophobic effect, what happens when lipophilic compound interacts with water
-the hydrophobic effect=tendency of nonpolar compounds to transfer from water to an organic phase
-when lipophilic compound interacts with water an interface is created around compound and water at this interface is more ordered, this decreases entropy/increases enthalpy
-formation of complex displaces both water from around ligand and from binding site, its now free, increased entropy and decreases enthalpy and increased affinity
explain ∆G vdw
-equation, what happens if a methyl group is introduced
-non polar interactions between atoms can be calculatd by
EvdW = A/r^12 – B/r^6
r=distance between atoms
A and B=atom specific repulsive and attractive terms
-introduction of a methyl group may be expected to increase affinity due to hydrophobic effect but only if it fits
-if methyl group doesnt fit then VDW repulsion can decrease affinity
-adding methyl group at various positions may be a useful strategy to map out the size of the binding pocket
