20 July 2014

Poll: fragment linking and growing

A seminal paper in the fragment field is the 1996 SAR by NMR report in which two fragments were linked together. In theory, linking fragments can give a massive improvement in affinity beyond simple additivity, but in practice this is rare. The challenges of linking were not obvious in the early days, and led to much hair-pulling. Indeed, partially for this reason, Teddy has asserted that the 1996 paper is not just the most impactful paper in the field but also the most destructive.

Nonetheless, there are successful examples of linking, particularly for challenging targets (such as here and here). So how often does it really work?

Our latest poll has two questions: one on fragment linking, the other on fragment growing (see sidebars on right side of page). Tell us whether, in your experience, fragment linking didn’t work at all, worked marginally (ie, perhaps a modest boost in potency), worked OK (perhaps additivity), or worked well (synergy). You can vote multiple times, so if you’ve worked on multiple projects with different outcomes, please vote early and often. We’re asking the same questions for fragment growing since these two strategies are often compared.

Admittedly the categories are somewhat fungible: one person’s “OK” may be another person’s “well,” and some may see merging where others see linking. Still, hopefully we’ll get enough votes to discern some trends.

1 comment:

Luc Van Hijfte said...

I'm not all that amazed with this outcome. Though linking two fragments binding to different hot spots within a given binding site may appear conceptually beguiling, it is more likely to fail. First, the optimal orientation of the two independent fragments may be perturbed upon linking. Second, induced fit of a fragment binding with high efficiency to a specific hotspot may be disrupted when another fragment binds to an adjacent hotspot. So I would predict quite a bit of negative cooperation .