Fragments vs a Pseudomonas aeruginosa virulence factor

The world is understandably focused on SARS-CoV-2; see for example last week’s post. But there are many other threats out there, including infectious Pseudomonas aeruginosa, which is particularly problematic for immunocompromised people. A recent (open access!) ChemMedChem paper by Martin Empting and collaborators at the Helmholtz Centre for Infection Research and elsewhere describes a clever approach to tackle this pathogen.

An age-old problem for antibiotics is that they provoke resistance: nothing like death to kick evolution into high gear. One way to sidestep this is to develop drugs that target virulence rather than essential microbial pathways. The protein PqsR is part of the Pseudomonas Quinolone Signal Quorum Sensing system, and is important for pathogenicity.

A previously published screen of 720 fragments by SPR yielded about 40 hits, including compound 3. Not only does this compound have impressive ligand efficiency, it also has high enthalpic efficiency; the binding is largely enthalpy-driven. Although the utility of thermodynamics for lead optimization is questionable, the researchers were cognizant of the hydrophobic nature of the ligand binding site for PqsR, and sought molecules that would make polar interactions from the start rather than having to engineer them; a similar strategy proved successful for Astex.

Crystallography with compound 3 was unsuccessful, but SAR by catalog led to compound 7, which has higher affinity for PqsR as assessed by isothermal titration calorimetry (ITC) and also shows activity in a reporter gene assay. Fragment growing led to compound 11, which the researchers were able to characterize crystallographically. The two aromatic rings are at a sharp angle to one another, and attempts at rigidifying the linker proved unsuccessful. But further growing led to compound 20, with submicromolar activity in the reporter assay. This molecule also reduced release of a toxic virulence factor from a clinical isolate of P. aeruginosa.

Interestingly, despite the increased activity of compound 20 over compound 11 in the reporter assay, it seems to have lower affinity for PqsR by ITC. The researchers suggest that the full protein in cells likely behaves differently than the truncated version studied in the biophysical assays.

The researchers also emphasize that flexible linkers were more successful than rigid linkers in improving potency – a phenomenon we’ve previously highlighted here and here. Intuitively a more flexible linker is likely to be more forgiving, as a fraction of an ångström can make the difference between binding or not.

There is still much to do: in particular, activity will need to be improved further, and no pharmacokinetic or other animal data are provided. Moreover, a clinical trial with an anti-virulence strategy would be difficult to design. Still, this is an interesting approach, and I hope the authors or others will follow up on it.