5 research outputs found
Predicting Electrophoretic Mobility of ProteinâLigand Complexes for Ligands from DNA-Encoded Libraries of Small Molecules
Selection
of target-binding ligands from DNA-encoded libraries
of small molecules (DELSMs) is a rapidly developing approach in drug-lead
discovery. Methods of kinetic capillary electrophoresis (KCE) may
facilitate highly efficient homogeneous selection of ligands from
DELSMs. However, KCE methods require accurate prediction of electrophoretic
mobilities of proteinâligand complexes. Such prediction, in
turn, requires a theory that would be applicable to DNA tags of different
structures used in different DELSMs. Here we present such a theory.
It utilizes a model of a globular protein connected, through a single
point (small molecule), to a linear DNA tag containing a combination
of alternating double-stranded and single-stranded DNA (dsDNA and
ssDNA) regions of varying lengths. The theory links the unknown electrophoretic
mobility of proteinâDNA complex with experimentally determined
electrophoretic mobilities of the protein and DNA. Mobility prediction
was initially tested by using a protein interacting with 18 ligands
of various combinations of dsDNA and ssDNA regions, which mimicked
different DELSMs. For all studied ligands, deviation of the predicted
mobility from the experimentally determined value was within 11%.
Finally, the prediction was tested for two proteins and two ligands
with a DNA tag identical to those of DELSM manufactured by GlaxoSmithKline.
Deviation between the predicted and experimentally determined mobilities
did not exceed 5%. These results confirm the accuracy and robustness
of our model, which makes KCE methods one step closer to their practical
use in selection of drug leads, and diagnostic probes from DELSMs
Orally Active Fumagillin Analogues: Transformations of a Reactive Warhead in the Gastric Environment
Semisynthetic
analogues of fumagillin, <b>1</b>, inhibit methionine aminopeptidase-2
(MetAP2) and have entered the clinic for the treatment of cancer.
An optimized fumagillin analogue, <b>3</b> (PPI-2458), was found
to be orally active, despite containing a spiroepoxide function that
formed a covalent linkage to the target protein. In aqueous acid, <b>3</b> underwent ring-opening addition of water and HCl, leading
to four products, <b>4â7</b>, which were characterized
in detail. The chlorohydrin, but not the diol, products inhibited
MetAP2 under weakly basic conditions, suggesting reversion to epoxide
as a step in the mechanism. In agreement, chlorohydrin <b>6</b> was shown to revert rapidly to <b>3</b> in rat plasma. In
an ex vivo assay, rats treated with purified acid degradants demonstrated
inhibition of MetAP2 that correlated with the biochemical activity
of the compounds. Taken together, the results indicate that degradation
of the parent compound was compensated by the formation of active
equivalents leading to a pharmacologically useful level of MetAP2
inhibition
Discovery and Optimization of Potent, Selective, and <i>in Vivo</i> Efficacious 2âAryl Benzimidazole BCATm Inhibitors
To
identify BCATm inhibitors suitable for <i>in vivo</i> study,
Encoded Library Technology (ELT) was used to affinity screen
a 117 million member benzimidazole based DNA encoded library, which
identified an inhibitor series with both biochemical and cellular
activities. Subsequent SAR studies led to the discovery of a highly
potent and selective compound, 1-(3-(5-bromothiophene-2-carboxamido)Âcyclohexyl)-<i>N</i>-methyl-2-(pyridin-2-yl)-1<i>H</i>-benzoÂ[d]Âimidazole-5-carboxamide
(<b>8b</b>) with much improved PK properties. X-ray structure
revealed that <b>8b</b> binds to the active site of BACTm in
a unique mode via multiple H-bond and van der Waals interactions.
After oral administration, <b>8b</b> raised mouse blood levels
of all three branched chain amino acids as a consequence of BCATm
inhibition
Discovery of Highly Potent and Selective Small Molecule ADAMTSâ5 Inhibitors That Inhibit Human Cartilage Degradation via Encoded Library Technology (ELT)
The metalloprotease ADAMTS-5 is considered a potential
target for
the treatment of osteoarthritis. To identify selective inhibitors
of ADAMTS-5, we employed encoded library technology (ELT), which enables
affinity selection of small molecule binders from complex mixtures
by DNA tagging. Selection of ADAMTS-5 against a four-billion member
ELT library led to a novel inhibitor scaffold not containing a classical
zinc-binding functionality. One exemplar, (<i>R</i>)-<i>N</i>-((1-(4-(but-3-en-1-ylamino)-6-(((2-(thiophen-2-yl)Âthiazol-4-yl)Âmethyl)Âamino)-1,3,5-triazin-2-yl)Âpyrrolidin-2-yl)Âmethyl)-4-propylbenzenesulfonamide
(<b>8)</b>, inhibited ADAMTS-5 with IC<sub>50</sub> = 30 nM,
showing >50-fold selectivity against ADAMTS-4 and >1000-fold
selectivity
against ADAMTS-1, ADAMTS-13, MMP-13, and TACE. Extensive SAR studies
showed that potency and physicochemical properties of the scaffold
could be further improved. Furthermore, in a human osteoarthritis
cartilage explant study, compounds <b>8</b> and <b>15f</b> inhibited aggrecanase-mediated <sup>374</sup>ARGS neoepitope release
from aggrecan and glycosaminoglycan in response to IL-1β/OSM
stimulation. This study provides the first small molecule evidence
for the critical role of ADAMTS-5 in human cartilage degradation
Encoded Library Technology as a Source of Hits for the Discovery and Lead Optimization of a Potent and Selective Class of Bactericidal Direct Inhibitors of <i>Mycobacterium tuberculosis</i> InhA
Tuberculosis
(TB) is one of the worldâs oldest and deadliest
diseases, killing a person every 20 s. InhA, the enoyl-ACP reductase
from <i>Mycobacterium tuberculosis</i>, is the target of
the frontline antitubercular drug isoniazid (INH). Compounds that
directly target InhA and do not require activation by mycobacterial
catalase peroxidase KatG are promising candidates for treating infections
caused by INH resistant strains. The application of the encoded library
technology (ELT) to the discovery of direct InhA inhibitors yielded
compound <b>7</b> endowed with good enzymatic potency but with
low antitubercular potency. This work reports the hit identification,
the selected strategy for potency optimization, the structureâactivity
relationships of a hundred analogues synthesized, and the results
of the in vivo efficacy studies performed with the lead compound <b>65</b>