Medicinal chemists spend a lot of time thinking about how to make protein-ligand interactions stronger. Surprisingly, most protein-ligand interactions are actually weak. Intuitively, one would think that to make a strongly bound protein-ligand complex you should form strong interactions. Further, H-bonds make up almost 80% of the interactions between proteins and ligands. It follows that medicinal chemists should focus on strong hydrogen bonds. While this intuition has a lot of merit, strong interactions only represent a third of all observed H-bonds between ligands and protein. Surprisingly, two thirds of protein-ligand H-bonds are weak CH-interactions.
the strong, the weak and the mismatched
To classify something as strong or weak a reference point needs to be set. For the gas phase this reference is set to zero but drug design does not occur in the gas phase. In the case of drug design the reference is water. The water H-bonds with protein and ligand in the unbound state must be competed against to form the desired protein-ligand complex.
Throughout this work, the strength of water as a H-bond donor and H-bond acceptor will be used as a reference to determine whether a H-bond acceptor or donor is strong or weak. This leads to three types H-bond types referenced to water strength (see picture below).
- Strong H-bonds occur in quadrant B where both alpha and beta are stronger than water
- Weak H-bonds occur in quadrant C where both alpha and beta are weakerthan water
- Mismatched H-bonds occur in quadrants A and C where alpha is stronger and beta is weaker than water or vise versa
competing with water
Quantitative scales describing H-bond acceptor (HBA) and H-bond donor (HBD) strengths have been developed by Abrahams.
- Hydrogen bond structural group constants
- Hydrogen bonding. 31. Construction of a scale of solute effective or summation hydrogen‐bond basicity
- Scales of solute hydrogen-bonding: their construction and application to physicochemical and biochemical processes
This concept has been extended by Hunter to include influence of solvent on solution phase equilibria between H-bonded solutes.
- Quantifying intermolecular interactions: guidelines for the molecular recognition toolbox
- Solvent effects on hydrogen bonding
This extension by Hunter is particularly important for drug design as this occurs in the aqueous phase and H-Bond donors and acceptors are always in competition with water (see graphic below). The equilibrium between the free and bound states can be taken, at approximation, to the level of individual H-bonds. The free state consists of the acceptor and donor of the two solutes being solvated by water. The bound state consists of the desired H-bond formed between the two solutes (ligand and protein in the drug design case) and a water-water dimer returned to bulk due to water displacement (ie desolvation of ligand and protein).
winning and losing to water
In order for a given H-bond to be enthalpically favourable it needs to reside in quadrants B or C (see below). Strong H-bonds constitute quadrant B whereby both acceptor and donor are stronger than water. In quadrant B the protein-ligand interation dominates the enthalpic contributions to binding (I sometimes call this the win-win H-bond strategy). Weak H-bonds reside in quadrant C where both acceptor and donor are weaker than water. The newly formed water-water interations from desolvation dominate the enthalpic term in quadrant C (I refer to this as the lose-lose H-bond strategy). It is intuitive that for quadrant B the stronger the acceptor and donor strengths relative to water the greater the enthalpy of binding. It is less intuitive that in quadrant C, the weaker the acceptor and donor strengths relative to water the greater the enthalpy of binding due to destablization of the free states.
Importantly, mismatched H-bonds, regardless of whether they reside in quadrants A or D, lead to a stabilization of the free-state and not the desired bound state. The message here for molecular designers is clear: there is no point increasing the strength of a H-bond acceptor or donor when the respective H-bond partner is weaker than water.
Given the plethora of H-bonds and their high tunability, any generalization is fraught with danger. Despite this, below is a generalisation of the types of H-bonds belonging to the desired quadrants B and C. The strong H-bonds belonging to quadrant B are classical H-bonds (neutral H-bonds between strong HBA and HBD) and weak H-bonds belonging to quadrant C are largely CH-pi interactions.
It is clearly important to tune the strength (or weakness) of both H-bond partners in a given H-bond. It is also important to remember that this refers only to the enthalpic component and disregards entropy. Also this only applies to electrostatically dominated interactions (e.g. H-bonds).
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The Six Molecular Interactions – McConnell’s Medchem (mcconnellsmedchem.com)
