Picomolar beta-lactamase inhibitors with help from fragments

In 2009 Practical Fragments highlighted a computational fragment screen against AmpC beta lactamase, a challenging antibacterial target. That paper described several millimolar fragments, and at the time we noted, “it remains to be seen whether these fragments can be advanced to low nanomolar inhibitors, but at least fragment-screening has provided many new starting points.” In a new paper in PNAS, Brian Shoichet and colleagues at UCSF, along with collaborators in Italy and France, have used the fragments to discover not just nanomolar, but picomolar inhibitors.

The researchers had previously identified reversible covalent inhibitors containing boronic acids, some of which were quite potent. However, they had reached an affinity plateau, and the compounds had only modest activity against bacteria in vitro. By examining the crystal structures of some of these molecules bound to AmpC, and superimposing these on the crystal structures of some of the fragments bound to the protein, they were able to come up with new ideas. For example, adding the tetrazole of fragment F3 to their previously reported compound 9 led to a low nanomolar inhibitor, and adding a small hydrophobic substituent improved the potency to an impressive 50 picomolar. Similar strategies worked with other fragment-inhibitor combinations.

AmpC beta lactamase degrades cephalosporin antibiotics, and the researchers demonstrated that many of their new molecules were effective at restoring sensitivity to otherwise resistant bacterial strains in vitro and, in the one case tested, in a mouse survival model.

This paper also addresses Teddy’s recent question, what is FBDD? Although the fragments described in 2009 were not themselves advanced, the information they provided was essential to moving the project forward. As the researchers note:

Whereas fragments are widely used to nucleate early discovery, this study suggests that they also may be used to guide late-stage optimiziation into chemotypes and geometries that would be hard to systematically sample by other methods.

This is all the more impressive given the relatively low ligand efficiency of the initial fragments. So though purists may argue whether this work is technically FBDD, it is certainly a nice example of fragment-assisted drug discovery, in this case merging parts of fragments with other molecules.