The concept of bioisosterism is central to medicinal chemistry. Essentially, one functional group is replaced by another which has similar activity but a different chemical structure. This might be done for a variety of reasons: improving pharmaceutical properties, enabling new analogs, or inventing around existing intellectual property. Most medicinal chemists are familiar with common bioisosteres, such as replacing a carboxylic acid with an acyl sulfonamide. But what about replacing a carboxylic acid with an amidine? This and other surprising examples are provided in a new Angew. Chem. paper by Gerhard Klebe and colleagues at Philipps Universität Marburg.
The researchers focused on fragments binding to the hinge region of protein kinase A (PKA), a well-characterized and easily crystallized kinase. As we noted a couple weeks ago, most kinase inhibitors bind to the so-called hinge region, where the adenine ring of ATP normally sits. Protein backbone amides typically make one to three hydrogen bonds with inhibitors. The researchers chose 19 simple fragments, each containing an aromatic ring and various substituents, soaked these into crystals of PKA, and obtained high-resolution (between 1.12 and 1.82 Å) structures. They also experimentally measured the pKa values of each fragment.
All except two of the fragments made one or two hydrogen bonds to a backbone amide NH and/or carbonyl oxygen, but the moieties that did so varied dramatically. Benzamide, with its hydrogen bond accepting carbonyl oxygen and hydrogen bond donating primary amide, is a quintessential hinge-binder, but surprisingly benzoic acid bound in a similar fashion. The measured pKa of this carboxylic acid is 4.01, yet the acid serves as a hydrogen bond donor, suggesting that it is protonated in the active site of the enzyme.
On the other end of the acidity spectrum, a substituted benzamidine fragment with a pKa of 10.78 bound in the neutral form, with a normally charged nitrogen atom serving as a hydrogen bond acceptor. In fact, the binding mode it assumes is identical to that of benzoic acid.
These and several other examples illustrate that protonation states of ligands in active sites can be very different from what one would predict based on calculated or even measured pKa values. There are of course limits: an amidine with a measured pKa of 11.32 avoids the hinge and instead interacts with an aspartic acid side chain.
One quibble is that the researchers did not seem to consider hydrogens on carbon atoms as potential acceptors; these are increasingly recognized as important, including in kinases. One pyridine fragment shown may have a CH in close proximity to a carbonyl, but it is difficult to tell from the figures, and the coordinates have not yet been released.
Another omission is the lack of quantitative information about binding energies. Just because benzoic acid and a benzamidine bind identically does not mean they have the same affinities. That said, Gerhard Klebe warned last year of the dangers of putting too much stock in thermodynamic measurements.
These issues aside, this is a nice analysis and should serve as a useful reminder to medicinal chemists that bioisoteres can be quite unexpected. And once the structures are released in the pdb, they will provide a useful resource for modelers seeking to recapitulate crystallographic data.