DNA-encoded libraries (DEL) are collections of peptides or small molecules attached to DNA tags. In a typical application, libraries are mixed with a protein of interest, non-binders are washed away and those that remain are identified by using PCR to amplify the DNA tags. Two years ago we highlighted an article in which previously identified fragments were merged with molecules identified from DEL. However, because fragments typically have low affinities, screening fragments directly by DEL would seem to be difficult. In a new open-access RSC Medicinal Chemistry paper, Rod Hubbard and collaborators at Vernalis and HitGen describe how to do so. (Rod presented some of this work in April at the CHI DDC meeting.)
To identify weak binders, the researchers turned to photoactivatable fragments that – in the presence of UV light – would bind irreversibly to a nearby protein. Specifically, they used the diazirine tag, which has proven useful in both cell-based screening as well as screens of isolated proteins. Here, the researchers generated two libraries of fragments bound to DNA, with each library member also containing a diazirine tag. The libraries were built using different chemistries and consisted of 15,804 and 23,905 members, small by DEL standards (which often range in the millions) but large by fragment standards.
The PAC-FragmentDEL libraries were incubated against two proteins: the kinase PAK4 and the bacterial enzyme 2-epimerase. Each protein was incubated with both libraries for one hour at room temperature and then treated with ultraviolet light for 10 minutes on ice. Next, the proteins were captured on an affinity resin and washed extensively under denaturing conditions to remove any non-covalently bound library members. Finally, the DNA was amplified by PCR and quantified; any library members that bind to the protein stand out over background.
Of course, there is plenty of opportunity for non-specific binding, so the researchers incorporated several controls, such as omitting the UV-crosslinking step or protein. Moreover, they repeated the experiment in the presence of known high-affinity binders and looked for fragments that were competed.
In the case of PAK4, the researchers identified 301 fragments that could be competed. Eleven of these were further examined (without the DNA tags), all of which demonstrated binding by ligand-observed NMR, and ten of them yielded crystal structures bound to the protein. The examples shown in the paper occupy the hinge-binding site, which the researchers acknowledge is a low bar for fragment screens.
The second target, 2-epimerase, has a more challenging active site, and indeed the hit rate was lower: just 21 competitive fragments were found. But all 9 of those selected for further testing confirmed by ligand-observed NMR, and 5 of them yielded crystal structures.
This paper demonstrates that DEL can be used to identify fragment hits with a fairly low false-positive rate. But do we need yet another fragment-finding method? The researchers point out that PAC-FragmentDEL is fast, with screening and sequencing analysis taking just a few weeks. This also means that fragment libraries can be much larger than for most techniques. Protein requirements are also modest, at around 250 pmol (12.5 mg for a 50 kD protein). They also note that – because of the DNA tag – less intrinsically soluble fragments can be screened, increasing chemical diversity, though one might counter that this could lead to problems down the road.
On the downside, it is not clear whether affinity information can be obtained from the primary screen. Also, the need for a competitive tool molecule could limit choice of targets, as some of the most interesting targets lack any chemical probes. Still, as the researchers note, the competitor could be a peptide or protein, and in a pinch the site of interest could be mutated.
In summary, this looks to be an interesting approach, and I look forward to seeing more applications.