Fragment merging vs bacterial SAICAR synthetase

People living with cystic fibrosis are susceptible to lung infections from a rogues’ gallery of bacterial species, one of which is Mycobacterium abscessus. It is often antibiotic resistant, and even when it responds, a course of antibiotics can take two years to resolve the infection. In a recent ACS Infect. Dis. paper Tom Blundell, Anthony Coyne, and collaborators at University of Cambridge and elsewhere describe progress against this organism.

 

The researchers chose to target a protein called SAICAR synthetase, or PurC, which is essential for purine biosynthesis and thus bacterial growth, as shown by genetic knockout studies. The enzyme is significantly different from the human ortholog, but similar to the Mycobacterium tuberculosis ortholog, giving the potential for a twofer.

 

Fragment screening was conducted both in-house using thermal shift assays as well as at XChem using crystallography; we discussed the differing outputs of these screens in this 2019 post. Compound 1, from the in-house screen, was found crystallographically to bind in the ATP-binding site, and ITC studies revealed it to have high micromolar affinity for the protein. Meanwhile, compound 2 was identified from the crystallographic screen, and while the affinity wasn’t measured, the pyridyl ring is located a short distance from where compound 1 binds.

 

Initial SAR around fragment 1 revealed that growing toward the binding site of compound 2 would be possible, as illustrated by compound 9. Appending a pyridyl ring onto this molecule led to compound 16, with low micromolar affinity. The pyridyl moiety stacks onto an arginine side chain, and improving this interaction by replacing the pyridyl with a phenyl appended with electron-withdrawing fluorine atoms led to compound 27, with submicromolar activity. Overlaying the crystal structures of compounds 1 (cyan), 2 (magenta), and 27 (gray) reveals that the merged molecule does indeed bind in a similar manner to the component fragments.

Unfortunately, despite good biochemical activity against PurC, none of the compounds were particularly effective at inhibiting growth of either M. abscessus or M. tuberculosis. Such disconnects between biochemical and cell potency are unfortunately all too common, particularly for antimicrobial targets, as we wrote about here. The researchers suggest possible reasons including efflux and physicochemical properties. The paper ends by noting that work is continuing, and we look forward to hearing more.