Download Protein–Ligand Interactions as the Basis for Drug Action

Protein–Ligand Interactions as the Basis for Drug Action
Some important terms
• Ligand – A (usually small) molecule that binds to a biological macromolecule
• Enzyme – An endogenous biocatalyst that can transform one or more substrates into one or more products
• Substrate – A ligand that is a starting material for an enzymatic reaction
• Inhibitor – A ligand that prevents the binding of a substrate either directly (competitive) or indirectly (allosteric), reversibly or irreversibly
• Receptor – A membrane-­‐bound or soluble protein (or a protein complex) that i nitiates an effect after binding an agonist
• Agonist – A receptor ligand that exhibits an intrinsic effect, that is, it causes a receptor response
• Antagonist – A receptor ligand that either directly (competitive) or indirectly (allosteric) prevents the binding of an agonist
• Partial agonist – A weak agonist that has a high affinity to the binding site, and in this manner acts as an antagonist
• Inverse agonist – A ligand that stabilizes the inactive conformation of a receptor or ion channel
• Functional antagonist
– A substance that prevents a receptor response by another mode of action
• Allosteric effector
– A ligand that influences the function of a protein by causing a change in the 3D structure of the protein
• Ion channel – A pore in a protein that allows specific ions to flow in and out across the cell membrane along a concentration gradient. Opening and closing is affected by binding a ligand or by a membrane potential change
• Transporter – A protein that transports molecules or ions across the cell membrane against the concentration gradient by consuming energy
• Antimetabolite – A substance that interferes with the biosynthesis of a central metabolic product either as a false substrate or as an inhibitor
The Lock-­‐and-­‐Key Principle
• HERMANN EMIL FISCHER (1852-­‐1919), Nobel 1902
“Um ein Bild zu gebrauchen, will ich sagen, dass Enzym und Glucosid
wie Schloss und Schlüssel zueinander passen müssen, um eine chemische Wirkung aufeinander ausüben zu können”.
” To use a picture, I want to say that enzymes and glucosides must fit
together like a lock and key to be able to exert a chemical effect upon
one another.”
1894, Berichte der Deutschen Chemischen Gesellschaft
Beyond the Lock-­‐and-­‐Key Principle
• Not all proteins/drug targets are very selective
– some are quite promiscuous while other may be extremely selective
• Ligand (the key..) is typically flexible
• Also protein is adapting a different conformation upon ligand binding
• If we know the protein target then “Structure-­‐
based design” is used (methods like docking)
• It the target is not known in details “Ligand-­‐
based” approach is used (typically pharmacophores)
The Binding Constant Ki Describes the Strength of Protein–Ligand Interactions
• The extent of the drug binding into its target characterized by the binding constant
• However, one should recognize that Ki is having NO units (it’s dimensionless)
– if it would have a dimension, like usually mentioned (typically mol/L) the following equaiton would be impossible…
Gibbs Energy of Binding
• Binding constant (or more precisely binding association constant) can be connected to the Gibbs energy of binding using the following equation
0
G = RT ln K a = RT ln(1 / K d )
• A binding constant of Ki=10-­‐9 corresponds to a Gibbs energy of 53.4 kJ/mol at body temperature. A change in Ki of one order of magnitude means a change in the Gibbs energy of 5.9 kJ/mol (or 1.4 kcal/mol)
Enthalpy and Entropy
ΔG = −RT ln K A = ΔH − TΔS
−ΔG / T = −ΔH / T + ΔS
Important Types of Protein–Ligand Interactions
• Hydrogen bonds
– typical, untypical, charge-­‐assisted, etc…
• Ionic interactions
– effect of pKa-­‐values
– local pH of the binding environment
• Hydrophobic interactions
– The hydrophobic interactions are mainly caused by the displacement, or more correctly put, the liberation of water molecules from the lipophilic environment of the binding pocket
• Cation–π interactions
The Strength of Protein–Ligand Interactions
Blame It All on Water!
• Above mentioned data would suggest that ionic interactions (and H-­‐bonds) are the dominant ones…
– This is not the case, as for example amides usually do not interact in water even though inside proteins this happens regularly!
• Aqueous environment has a major contributions to all biological processes, and especially to molecular interactions!
Water is almost everywhere…
• Proteins are solvated
– also binding cavities
• conserved water molecules are special cases!
• Ligands are solvated
– upon ligand binding waters are rearranged
Entropic Contributions to Protein–
Ligand Interactions
• Fixing/relaxing water
• Change in translational and rotational freedom
– protein
– ligand
• Change in conformational freedom
– protein
– ligand
Enthalpy and Entropy Driven Binding
• A general trend in drug design is to find “Enthalpy-­‐Driven” binders
– The dominant component if favorable enthalpy
• It is believed (and with a good reason) that enthalpy-­‐driven compounds are more water soluble, have better pharmacokinetics and are more selective compounds
• In optimal case both enthalpy and entropy are favorable (and should be if sub-­‐nanomolar
compound is needed).
What Is the Contribution of a Hydrogen Bond to the Strength of Protein–Ligand Interactions?
• Protein tyrosyl-­‐RNA synthase in complex with the substrate
• Mutant Tyr34-­‐Phe34
– binding weakened by 2 kJ/mol
• Effect of other neutral H-­‐
bonds from 2-­‐6kJ/mol
• Tyr169-­‐Phe169 (charged H-­‐bond) reduced binding by 15.6 kJ/mol!
Another example
• Fildarestat (4.1)
– aldose reductase
inhibitor
– Leu300-­‐Pro300
• effect 7.8 kJ/mol
• Sorbinil (4.2)
– Leu300-­‐Pro300
• no effect on binding!
• enthalpy-­‐entropy compensation
Is there a trend concerning H-­‐bond effects?
• A plot of the binding constants Ki of 80 crystallographically
investigated protein ligand complexes shows that Ki has no direct relationship to the number of hydrogen bonds that exist between protein and ligand
• Data based on X-­‐ray structures and indicates that H-­‐bond can increase, decrease or have no affect on binding affinity!
The Strength of Hydrophobic Protein–
Ligand Interactions
• Hydrophobic effects are due to (mainly) water replacement
• Effect can be related to the non-­‐polar interaction surface between the ligand and the protein
– Typical values are between -­‐50 to -­‐200 J/mol per Å2 of lipophilic contact area
• However, this is only a general rule and cannot be used more as a rough guideline!
Strength of the Hydrophobic Effects
• A plot of the binding constants Ki of the 80 crystallographically
investigated protein–
ligand complexes against the buried hydrophobic surface area shows that there is no simple function for this measure either
Binding and mobility
• Difference between weakly binding (millimolar) and strongly binding (nanomolar) binding is between 35-­‐55 kJ/mol
– lead optimization covers even smaller range
– typically progress in the range of 5-­‐6 orders of magnitude, corresponding to 25-­‐30 kJ/mol
• There is a great risk to have compensatoric
effects, as enthalpy variation typically exceeds 30 kJ/mol range!
Entropic/Enthalpic optimization
Entropic optimization
Enthalpic optimization
• Aims at increasing the hydrophobic surface participating to the ligand-­‐
protein interaction
• Also designing more rigid compounds to minimize penalty due to conformational entropy • Additional polar groups added to support ligand-­‐
receptor interactions
– the problem is that this will increase the penalty of ligand desolvation!
The Lessons from Enthalpy and Entropy?
• Even ligands with very similar structure may have totally different binding energetics
– this applies to Gibbs energy, enthalpy and entropy!
• It is very difficult to give any general rules how some functional groups affects on binding
• One cannot work on the basis of additive effects!