Biomedical Engineering Reference
In-Depth Information
circulatory half-life and superior imaging performance with respect to the parental
compounds [64].
ESAC dual-pharmacophore libraries (see Section 11.2.3) have led to the identi-
fication of novel inhibitors of stromelysin-1 (MMP-3), a matrix metalloproteinase
involved in both physiological and pathological tissue remodeling processes (entry
10, Table 11.1) [94]. Initially, a 550-memebred ESAC sublibrary was panned on
human MMP-3 covalently coupled to CNBr-activated Sepharose resin. Microarray-
based decoding enabled the identification of a lead binding structure, which was
subsequently conjugated to the amino-modified 3
-extremity of a 24-mer oligonu-
cleotide capable of pairing with the previous ESAC sublibrary and used as a lead in
a further affinity maturation selection experiment. Eventually, decoding and chem-
ical conjugation of synergistically binding molecules in the absence of the DNA
appendage yielded a MMP3 inhibitor with an IC
50
value as high as 9.9
M [94].
The advent of high-throughput-sequencing technologies for decoding of DNA-
encoded chemical libraries enormously facilitates the identification of bioactive
molecules from libraries of unprecedented size (see Section 11.3.2) [54]. Indeed,
shortly afterward, Philochem in collaboration with MedImmune (formerly Cam-
bridge Antibody Technology) described the implementation of high-throughput
sequencing for the discovery of protein-protein interaction inhibitors. Selections
against Bcl-xL, an antiapoptotic target protein for cancer therapy, using a 4000-
member DNA-encoded library (two building blocks single pharmacophore format;
see Section 11.2.2.1) allowed for the identification of several structurally related bind-
ing compounds with dissociation constants ranging between 60 and 0.93
M (entry
17, Table 11.1) [65]. The highest-affinity binder was able to compete with a Bak-
derived BH3 peptide (an antagonist of Bcl-xL function) and to induce cell death in Raji
cells with an EC
50
value of 77
M [65]. Notably, the newly discovered compound
displayed an indomethacin moiety, a previously reported anti-inflammatory com-
pound capable of inducing apoptosis in various cancer cell lines [117-119], probably
by suppression of the STATs/Bcl-xL signaling pathway [120] and the simultaneous
inhibition of multidrug-resistance protein 1 function [121].
In 2009, together with ETH Zurich, Philochem described a selection against tumor
necrosis factor (TNF) deploying a 4000-compound library based on Diels-Alder
cycloaddition reactions (see Section 11.2.2.1; entry 14, Table 11.1) [56]. Among
the selected structures, the best ligand displayed a dissociation constant of 20
M.
Medicinal chemistry optimization yielded a compound able to completely inhibit
TNF-mediated killing of L-M fibroblast at concentrations as high as 300
M [56].
Diels-Alder cycloaddition reaction has been explored further by Buller et al. in
the construction of a 1-million DNA-encoded library based on the combinatorial
assembly of three different sets of building blocks and corresponding DNA-coding
fragments [55]. This library facilitated the isolation of several inhibitors against the
tumor-associated antigen carbonic anhydrase IX [97], with IC
50
as potent as 240
nM (entry 20, Table 11.1) [55]. A fluorescently labeled derivative of one of the
most potent compounds revealed an in vitro specific accumulation in hypoxic tumor
tissues overexpressing carbonic anhydrase IX and in vivo tumor targeting of human
colorectal adenocarcinoma and human renal cell carcinoma xenograft models [55].
