Perhaps because it sounds like “chicken,”
when I first heard of chikungunya I thought it was a joke. But there’s nothing
funny about a disease whose name comes from a word meaning “to become contorted,”
referring to contortion caused by pain, which can last for months. The
mosquito-borne alphavirus was first identified in 1952 in West Africa, introduced
to the Americas in 2013, and is now spreading rapidly worldwide. There is no
specific treatment. In three recent papers, a large group of researchers mostly from
the Structural Genomics Consortium take the first steps towards
one.
Like many viruses, the chikungunya
genome encodes polyproteins that are cleaved by viral proteases, in this case a
domain of the nonstructural protein 2 (nsP2). This cysteine protease is essential
for viral replication, and the three papers collectively describe finding and
exploring selective probes against it.
In Proc. Nat. Acad. Sci. USA,
Kenneth Pearce (University of North Carolina at Chapel Hill) and collaborators
describe a screen of 6120 covalent fragments from Enamine against this target.
Compounds were preincubated in a FRET-based functional assay at 20 µM for 30
minutes, resulting in 153 hits that inhibited activity by at least 50%. 43 of
these were repurchased for full-dose response curves, and 20 of these had IC50
values < 20 µM. Of these, compound RA-0002034 was the most potent, with IC50
= 180 nM.
The proper way to assess
irreversible covalent inhibitors is not the time-dependent IC50, but
rather the (theoretically) invariant kinact/KI ratio. The
researchers measured this for the best hits and found the value for RA-0002034
to be 6400 M-1s-1, which is not far below that for the
approved covalent drug sotorasib for its target.
Mass spectrometry experiments
after tryptic digestion revealed the compound binds to the catalytic cysteine
of nsP2, as expected, and not to other cysteines. RA-0002034 contains a
potentially reactive vinyl sulfone warhead, but the half-life against the
biologically relevant nucleophile glutathione is a respectable 130 minutes. A
screen against 13 other cysteine proteases was also quite clean, as was chemoproteomic
profiling in human cells.
The compound was also tested in cellular
viral replication assays and found to be remarkably potent, with a low
nanomolar EC50 value. Encouragingly, it was also potent against
three other alphaviruses, Ross River virus, Venezuelan Equine Encephalitis
virus, and Mayaro virus.
RA-0002034 appears to be an
attractive chemical probe for exploring the biology of chikungunya. Best
practices are to also have an inactive control molecule, and the researchers
made a substitution off the central pyrazole ring to produce RA-0003161, which
is 500-fold less active.
The paper includes some
SAR-by-catalog, and the chemistry is more extensively explored in an open-access J. Med.
Chem. paper by Timothy Willson (UNC Chapel Hill) and collaborators. Although no
crystal structures of the compounds bound to nsP2 were available, the
researchers used modeling to guide modification of all portions of the
molecule. The most potent molecule was 8d, which is slightly more active than
RA-0002034. Also, methyl substitution near the electrophilic center is
tolerated, which could improve stability, as seen with the covalent WRN
inhibitor from Vividion which we wrote about here.
One annoying feature of
RA-0002034 is its tendency to cyclize to inactive compound 2, a process
explored in an open-access Pharmaceuticals paper by Timothy Willson and
collaborators. This occurs even at neutral pH. However, replacing the central pyrazole
with an isoxazole (compound 10) fixes this problem.
Collectively these three publications
provide new insights and tools for investigating chikungunya. RA-0002034
is a far more attractive starting point than a molecule Teddy described on Practical
Fragments back in 2015. The pharmacokinetics of RA-0002034 need to be
improved before in vivo experiments are warranted, but this seems achievable,
and I look forward to watching this story develop.
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