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.
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