Learning about Protein-Ligand Interactions
Professor Stephen Martin
Chemistry and Biochemistry Department
The University of Texas at Austin
28 September 2011
Freshman Research Initiative
Molecular Recognition in Biological Systems
Ka
+
Ligand
Protein
Complex
Changing structure of ligand leads to changes in binding affinity
K’a
+
Ligand
Protein
Complex
Key Question: How do changes in ligand preorganization, hydrophobicity, hydrogen bonding
capability, -cation stabilizing ability, etc. affect energetics in protein-ligand interactions?
Why Important: Optimizing protein binding affiniity is critical first step in drug discovery
General Features of Protein-Ligand Interactions
H2O H2O
H2O
H2O
Hydrogen
Bonding
H2O
H2O
H2O
H2O
H2O
H2O
C–H
C–H
H2O
C=O
H2O
H2O
H2O
H2O
H2O
–CO2–
H2O
H2O
–NH3+
H2O
H2O
H2O
H2O
H2O
H2O
H2O
+
H–N
H2O O=C
H2O
H2O
H2O
H2O
H2O
H2O
H2O
H2O
H2O
H2O
H2O
H2O
C–H H–C
C–H H–C
H2O
H2O
H2O
Kassoc
H2O
–CO2
– +H
H2O
H2O
H2O
3N
+
H2O
–NH3+ –O2C
H2O
H2O
H2O
H2O
Salt Bridges
H2O
H2O H2O
H2O
H2O
H2O
H2O
H2O
Solvated Protein-Ligand
Complex
Bulk Water
Changes in rotational and translational degrees of freedom
Shape complementarity of binding surfaces, but conformational changes occur
Hydrating water molecules around protein and ligand reorganize
and some are released to bulk water – desolvation
Formation of non-bonded interactions
Temperature
H2O
H2O
H2O
H2O
Solvated Ligand
H2O
N–H H2O O=C
H2O
H2O –O C
2
H2O
H2O
H2O H O
H2O H O
2
H
O
2
2
H2O
C=O H–N
H2O
H2O
Solvated Protein
H2O H2O
H2O
H2O
H2O +H N
3
H2O
H2O
H2O
H–C
H O
H2O 2 H–C
H2O
N–H
Hydrophobic
Contacts
Gas constant
∆G = ∆H – T∆S = –RTlnKassoc
Free energy
Enthalpy Entropy
Non-bonded interactions Order and dynamics
Kassoc =
[P–L]
[P][L]
Thermodynamics 101 – Applied to Protein-Ligand Interactions
Increasing Ligand Affinity by Preorganizing Ligands
affinity (Ka)
+
∆G
Flexible Ligand
Protein
Ligand-Protein Complex
∆G = ∆H – T∆S = –RTlnKa
affinity (K'a)
+
∆G'
more favorable
Constrained Ligand
Protein
Ligand-Protein Complex
∆G' = ∆H' – T∆S' = –RTlnK'a
∆G' should be more negative than ∆G because ∆S' less negative (more positive) than ∆S
by an estimated 2–6 eu (ca 0.6–1.5 kcal/mol at 25 °C) per fully restricted rotor
There are various benefits of preorganization in protein-ligand interactions, but no compelling
experimental evidence supporting the putative entropic advantage when we started!