A few months ago we described a fragment linking approach
against the protein EthR, a transcriptional repressor from Mycobacterium tubercuolosis responsible for resistance to the
second-line tuberculosis drug ethionamide. In a new paper in J. Med. Chem., a different team led by
Benoit Deprez and Nicolas Willand (Université Lille Nord de France and Institut
Pasteur) describe work on the same target using fragment growing and merging.
The researchers started with a fragment (compound 3) they
had previously made as part of an in-situ click chemistry effort. A thermal shift assay revealed that this compound marginally stabilized EthR. More
convincingly, it displayed mid-micromolar inhibition of EthR binding to DNA,
with respectable ligand efficiency.
Interestingly, when compound 3 was cocrystallized with the
protein, it bound at two different locations within the binding site. (In the
work we highlighted previously this year, a different fragment also bound at
two sites, and in that case the researchers linked fragments bound at each site to create a tighter binder.) In the current paper, the researchers
focused on fragment growing.
Compound 3 is a sulfonamide that can be readily constructed
from amines and sulfonyl chlorides, and the researchers started by constructing
a 976-member virtual library of larger sulfonamides. These were then screened
in silico against the protein, and many of the top-scoring hits resulted from
an isopentylamine building block (such as compound 4). Ten of these were made
and tested, and indeed, compounds 4 and 8 were more effective than compound 3 at
stabilizing EthR in the thermal shift assay. Moreover, not only did compound 8
show low micromolar activity in the DNA-binding assay (IC50 = 4.9
µM), it also showed low micromolar activity in sensitizing M. tubercuolosis to ethionamide (EC50 = 5.7 µM).
Crystallography of compound 8 bound to EthR revealed that
the isopentyl substituent was binding in a hydrophobic part of the pocket, and
adding a few fluorine atoms (compound 17) gave a satisfying increase in potency
as well as solubility. Replacing the sulfonamide with an amide (compound 19)
further improved potency.
The researchers also made a couple compounds in which a
second copy of compound 3 was merged with compound 19, and although this
approach did produce a compound with nearly the same potency, it was also
larger and less soluble.
This team has been pursuing EthR for some time, and
they were able to use information from previous structures both in the
computational screening as well as in the optimization. In that sense, this is
an example of fragment-assisted drug discovery. It is also another nice example
of fragment work in academia.
2 comments:
I find it interesting that adding fluorines in a hydrophobic pocket increased affinity and SOLUBILITY.
Also, Cpd 3 has a big ole Iodine on it, I assume that is filing a HB pocket?
The increase in solubility is nice, though just to be clear they are replacing two methyl groups with fluorine atoms, so perhaps not too surprising; the ClogP also decreases.
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