Fragment linking vs IMPDH (with a little help from the literature)

Mycobacterium tuberculosis (Mtb), the cause of its eponymous disease, is making an unwelcome comeback. Current treatments are lengthy, and highly resistant strains are emerging – and spreading. Chris Abell’s lab at the University of Cambridge has been working on multiple tuberculosis targets, and his latest results – in collaboration with Tom Blundell, David Ascher, and collaborators at the University of Cape Town and the University of Melbourne – has just published open access in J. Med. Chem.

The researchers were interested in inosine-5’-monophosphate dehydrogenase, or IMPDH, which is important for the synthesis of guanine nucleotides and is essential for every pathogen examined. They started by screening 960 fragments at 1 mM in a biochemical (spectrophotometric) assay. The IMPDH enzyme from a related organism was used due to its better expression and higher diffracting crystals; selected compounds were cross-checked with the Mtb enzyme and showed similar behavior.

This screen identified 18 molecules that gave at least 50% inhibition. IC₅₀ values were determined for the six most active, and these ranged from 325-675 µM. These molecules were soaked into crystals of IMPDH, but only compound 2 produced a structure. As if to compensate, two molecules of compound 2 bound in the active site. Moreover, these two fragments bound in the same region as a previously reported molecule, compound 1.

Initial attempts at fragment growing yielded only modest improvements in potency, so the researchers tried to link the two copies of compound 2. One linking attempt failed outright, a second gave a 58 µM inhibitor, but a breakthrough came when the linker taken from compound 1 was used. The (S) enantiomer of compound 31 is 2500 times more active than the starting fragment, and crystallography revealed that it binds as designed. Unfortunately, and in contrast to compound 1, compound 31 showed no activity against Mtb in culture. The researchers hope to figure out why.

This paper illustrates several points. First, fragment linking can be quite effective. Second, consistent with our poll from a few years ago, this is not necessarily easy. Indeed, given the reliance on the structure of compound 1, this study can be considered an example of fragment-assisted drug discovery as much as fragment linking. And finally, as we’ve said before, biochemical potency all too often does not translate to cell-based activity – let alone good pharmacokinetic properties. Potency is just the first step in the long march to a drug.