A hydrogen bond: What did it do for them? Part 1

Drug discovery is both blessed and cursed with a wealth of folklore, rules and generalisations. While these provide comfort for the timid, it can be instructive to take a closer look at the basis for some of this folklore. The focus of the previous Crapshoot was the assertion that a neutral-neutral hydrogen bond will contribute no more than 15-fold or 1.5kcal/mol to binding. This Crapshoot will examine some of the evidence.

We'll take a look at a study of binding of small N-acetylated peptides to the antibiotic ristocetin A. This paper has been cited as supporting the assertion that a neutral-neutral hydrogen bond will contribute no more than 1.5kcal/mol to binding affinity. The peptides in this study can be written as:

Ac-X-X and Ac-X

where X can be either Glycine or D-Alanine. The peptides use their NHs as donors and C-terminal carboxylates as anionic acceptors to interact with ristocetin A. Contributions of hydrogen bonds to binding affinity are estimated by comparing binding free energies for a peptide and truncated analogs, for example:

Ac-Gly-Gly/Ac-Gly , Ac-Gly/Acetate or Ac-D-Ala-D-Ala/Acetate

So far so good. But just in case you thought that you get the contribution of the hydrogen bond by just subtracting a couple of free energies, think again because you first need to account for hydrophobic interactions and the entropic cost of freezing rotatable bonds. If you overweight the importance of the hydrophobic interactions, you'll underweight the contribution of the hydrogen bonds because binding is a zero sum game from the perspective of contributions. Alert readers will recall our comments on reference states in the previous Crapshoot.

Anyway if you work your way through the results presented in the paper, you'll find (see Table 1) the contributions of amide-amide hydrogen bonds to binding range from 1.0kJ/mol to 12.5kJ/mol. The authors appear worried about the higher value which is a consequence of Ac-D-Ala-Gly binding 11kJ/mol more weakly than Ac-Gly-D-Ala despite a more favorable hydrophobic contribution. What could be causing this difference? Perhaps the methyl group of Ac-Gly-D-Ala finds a hydrophobic concavity in the binding site or somehow compromises the solvation of the carboxylate. Does Ac-D-Ala-Gly bind in a higher energy conformation than Ac-Gly-D-Ala?

We hope you're still with us. Now let's go back to the review featured in the previous Crapshoot which asserts that a neutral-neutral hydrogen bond will contribute no more than 15-fold or a maximum of 1.5kcal/mol to binding affinity. Now if you convert 1.5kcal/mol (actually equivalent to about 12-fold at 300K) to kJ/mol (1cal = 4.184J) you get a figure of 6.3kJ/mol. This is considerably less than 12.5kJ/mol and still falls short of the figure of 7.7kJ/mol that is derived from the difference in binding free energies of Ac-Gly-D-Ala and acetate.

Now if you're going to use measurements like these to set upper limits for contributions of neutral-neutral hydrogen bonds to binding, there are some questions that you'll need to address. Are the hydrogen bonds of optimal geometry? Are the bound conformations strained? How exposed are the binding partners to solvent? Does hydrogen bond formation compromise the solvation of polar atoms that do not participate in the hydrogen bond? How representative are amide-amide hydrogen bonds of all neutral-neutral hydrogen bonds?

So there you have it: 9 values for contributions of amide-amide hydrogen bonds derived from thermodynamic data. Do they support the assertion that a neutral-neutral hydrogen bond will contribute no more than 1.5kcal/mol to binding affinty? We will leave it to you, the reader, to form your own opinion.

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SMILES for Indexing
[O-]C(=O)C
CC(=O)N[C@H](C)C(=O)[O-]
CC(=O)NCC(=O)NCC(=O)[O-]
CC(=O)NCC(=O)N[C@H](C)C(=O)[O-]
CC(=O)N[C@H](C)C(=O)NCC(=O)[O-]
CC(=O)N[C@H](C)C(=O)N[C@H](C)C(=O)[O-]