DNA-encoded chemical libraries are one of the sexier new
approaches for lead discovery. Typically, small molecules are synthesized while
covalently linked to DNA and then screened for binding to a target. The structure
of the molecule is encoded in the sequence of the DNA, and since incredibly
tiny amounts of DNA can be sequenced (wooly mammoth genome, anyone?) you can
fit massive libraries into a single Eppendorf tube. Indeed, some companies
boast 100-billion compound libraries, nearly three orders of magnitude more
than the number of molecules indexed by Chemical Abstract Service.
One might think this has no relevance for fragments. Indeed,
the only mention of DNA-encoded libraries I recall on Practical Fragments was a comment by Teddy back in 2012 that the
approach is “as opposite from FBDD as you can go”. A recent paper by Dario
Neri, Filippo Sladojevich, and their collaborators at the ETH Zürich and
Philochem in ChemMedChem suggests
otherwise.
The researchers have developed an approach called
DNA-encoded self-assembling chemical (ESAC) libraries (see also their earlier paper in Nat. Chem.). Rather than
synthesizing a single molecule on each strand of DNA, this approach involves
assembling two separate sub-libraries of DNA-linked molecules, one attached to
the 5’-end and the other attached to the 3’-end. These are then mixed together,
allowed to hybridize in a combinatorial mixture, and screened against the
target; if a specific combination of fragments is identified (through elegant
PCR experiments), this indicates that the two fragments bind to the target in
close proximity.
The researchers have focused on the protein alpha-1-acid
glycoprotein (AGP), a prominent plasma protein whose function is poorly
understood. In their Nat. Chem.
paper, a library of 111,100 members (550 x 202 fragments) identified fragments
A-117 and B-113. Neither of these fragments showed any binding themselves, but
when linked together the resulting compound 1 bound with low micromolar
affinity as assessed by isothermal titration calorimetry (ITC).
The linker connecting the two fragments is long, flexible,
and not particularly drug-like; its improvement is the focus of the ChemMedChem paper. The researchers
increased the size of their second fragment library from 202 to 428 elements,
and an ESAC screen revealed that the pair of fragments A-117 and B-217 – both
still attached to DNA – had a dissociation constant of 110 nM; B-217 itself (attached
to DNA) was around 9900 nM.
To find out how these fragments could be productively
linked, the researchers coupled them to 11 different scaffolds, each of which
was attached to DNA. All of these bound to AGP, with dissociation constants ranging
from 9.9 to 1300 nM. The moment of truth came when the researchers
resynthesized some of the molecules no longer attached to DNA. Compound A117-L1-B217
bound with a Kd of 76 nM as assessed by SPR, while the weakest on-DNA
binder (Kd = 1300 nM) showed no binding by itself. Although no
explanation is provided for this discrepancy, it could be due to low
solubility.
This is an interesting approach, though the molecules
reported do tend towards molecular obesity (A117-L1-B217 weighs 765 Da and
has a ClogP approaching 8). Indeed, this may be an inherent liability – the
minimum allowable distance between two fragments that are each attached to DNA
may be larger than desirable for most targets. Still, it will be fun to watch
this develop.
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