As noted before, bromodomains are a "hot" area of drug discovery. Dan mentioned last year that PFI-1 was being released as a tool compound by the SGC. In this paper, Fish et al. describe its discovery (Supplemental Information here). They started their discovery with potential fragment-sized acetyl-lysine mimics (DMSO need not apply!), like others have described. In particular, 3,4-dihydro-3-methyl-2(1H)-quinazolinones like Cpd 7 and its bromoequivalent. These two compounds had sub-30uM potency and thus LE>0.45. The efforts of Conway et al. and Chung et al. were highly instructive to the Pfizer group. Crystallography was a key driver of confirming the binding modes seen by Conway are possible and that the quinazolinones are a viable acetyl-lysine mimic.
The crystallography pointed out that the bromine is pointing towards solvent and thus the appropriate place to start doing chemistry. Based upon the structures, a "bent" substituent at the 6 position appeared to be promising; sulfonamides were chosen for this role. Compounds 9 and 11 were also noted as attractive, novel compounds in their own right. These were used for very limited library construction. The compounds derived from 9 were profiled first. While better than the parent bromide, subsequent structural analysis showed that they were not making good interactions with the sites intended (WPF shelf). The sulfonamides derived from 11 on the other hand showed significantly improved activity. The SAR was relatively insensitive to the substitution of the aryl group, due to the optimized placement on the shelf and the reversed sulfonamide.
PFI-1 has 0.22uM activity against BRD4 and it was nominated as the probe molecule. They further investigated its binding via X-ray. They also looked at it in a much broader array of assays: broader pharmacological selectivity, a cell-based inflammatory end-point assay, and rodent pharmacokinetics. It had < 50% inhibition against 15 targets at 10uM (GPCR, ion channels, enzymes) and < 20% inhibition against 50 kinases. It fits the criteria for a good probe.
As the authors state, it was designed in a little over 250 molecules from an efficient fragment starting point covering only two design cycles. I think this is an excellent example of probe design/discovery.