6 research outputs found
Knowledge-Based Strategy to Improve Ligand Pose Prediction Accuracy for Lead Optimization
Accurately predicting how a small
molecule binds to its target
protein is an essential requirement for structure-based drug design
(SBDD) efforts. In structurally enabled medicinal chemistry programs,
binding pose prediction is often applied to ligands after a related
compound’s crystal structure bound to the target protein has
been solved. In this article, we present an automated pose prediction
protocol that makes extensive use of existing X-ray ligand information.
It uses spatial restraints during docking based on maximum common
substructure (MCS) overlap between candidate molecule and existing
X-ray coordinates of the related compound. For a validation data set
of 8784 docking runs, our protocol’s pose prediction accuracy
(80–82%) is almost two times higher than that of one unbiased
docking method software (43%). To demonstrate the utility of this
protocol in a project setting, we show its application in a chronological
manner for a number of internal drug discovery efforts. The accuracy
and applicability of this algorithm (>70% of cases) to medicinal
chemistry
efforts make this the approach of choice for pose prediction in lead
optimization programs
Beyond PAINs: Chemotype Sensitivity of Protein Methyltransferases in Screens
Screening of the relatively new target
class, the lysine and arginine
methyltransferases (MTases), presents unique challenges in the identification
and confirmation of active chemical matter. Examination of high throughput
screening data generated using Scintillation Proximity Assay (SPA)
format for a number of protein MTase targets reveals sensitivity to
both the known pan assay interference compounds (PAINS) and also other
scaffolds not currently precedented as assay interferers. We find
that, in general, true actives show significant selectivity within
the MTase family. With the exception of slight modifications of SAM-like
compounds, scaffolds that are observed frequently in multiple MTase
assays should be viewed with caution and should be carefully validated
before following up
Predicting the Conformational Variability of Abl Tyrosine Kinase using Molecular Dynamics Simulations and Markov State Models
Understanding protein conformational
variability remains a challenge
in drug discovery. The issue arises in protein kinases, whose multiple
conformational states can affect the binding of small-molecule inhibitors.
To overcome this challenge, we propose a comprehensive computational
framework based on Markov state models (MSMs). Our framework integrates
the information from explicit-solvent molecular dynamics simulations
to accurately rank-order the accessible conformational variants of
a target protein. We tested the methodology using Abl kinase with
a reference and blind-test set. Only half of the Abl conformational
variants discovered by our approach are present in the disclosed X-ray
structures. The approach successfully identified a protein conformational
state not previously observed in public structures but evident in
a retrospective analysis of Lilly in-house structures: the X-ray structure
of Abl with WHI-P154. Using a MSM-derived model, the free energy landscape
and kinetic profile of Abl was analyzed in detail highlighting opportunities
for targeting the unique metastable states
Selectivity Data: Assessment, Predictions, Concordance, and Implications
Could
high-quality in silico predictions in drug discovery eventually
replace part or most of experimental testing? To evaluate the agreement
of selectivity data from different experimental or predictive sources,
we introduce the new metric concordance minimum significant ratio
(cMSR). Empowered by cMSR, we find the overall level of agreement
between predicted and experimental data to be comparable to that found
between experimental results from different sources. However, for
molecules that are either highly selective or potent, the concordance
between different experimental sources is significantly higher than
the concordance between experimental and predicted values. We also
show that computational models built from one data set are less predictive
for other data sources and highlight the importance of bias correction
for assessing selectivity data. Finally, we show that small-molecule
target space relationships derived from different data sources and
predictive models share overall similarity but can significantly differ
in details
Exploiting an Allosteric Binding Site of PRMT3 Yields Potent and Selective Inhibitors
Protein arginine
methyltransferases (PRMTs) play an important role
in diverse biological processes. Among the nine known human PRMTs,
PRMT3 has been implicated in ribosomal biosynthesis via asymmetric
dimethylation of the 40S ribosomal protein S2 and in cancer via interaction
with the DAL-1 tumor suppressor protein. However, few selective inhibitors
of PRMTs have been discovered. We recently disclosed the first selective
PRMT3 inhibitor, which occupies a novel allosteric binding site and
is noncompetitive with both the peptide substrate and cofactor. Here
we report comprehensive structure–activity relationship studies
of this series, which resulted in the discovery of multiple PRMT3
inhibitors with submicromolar potencies. An X-ray crystal structure
of compound <b>14u</b> in complex with PRMT3 confirmed that
this inhibitor occupied the same allosteric binding site as our initial
lead compound. These studies provide the first experimental evidence
that potent and selective inhibitors can be created by exploiting
the allosteric binding site of PRMT3
An Orally Bioavailable Chemical Probe of the Lysine Methyltransferases EZH2 and EZH1
EZH2 or EZH1 is the catalytic subunit
of the polycomb repressive
complex 2 that catalyzes methylation of histone H3 lysine 27 (H3K27).
The trimethylation of H3K27 (H3K27me3) is a transcriptionally repressive
post-translational modification. Overexpression of EZH2 and hypertrimethylation
of H3K27 have been implicated in a number of cancers. Several selective
inhibitors of EZH2 have been reported recently. Herein we disclose
UNC1999, the first orally bioavailable inhibitor that has high <i>in vitro</i> potency for wild-type and mutant EZH2 as well as
EZH1, a closely related H3K27 methyltransferase that shares 96% sequence
identity with EZH2 in their respective catalytic domains. UNC1999
was highly selective for EZH2 and EZH1 over a broad range of epigenetic
and non-epigenetic targets, competitive with the cofactor SAM and
non-competitive with the peptide substrate. This inhibitor potently
reduced H3K27me3 levels in cells and selectively killed diffused large
B cell lymphoma cell lines harboring the EZH2<sup>Y641N</sup> mutant.
Importantly, UNC1999 was orally bioavailable in mice, making this
inhibitor a valuable tool for investigating the role of EZH2 and EZH1
in chronic animal studies. We also designed and synthesized UNC2400,
a close analogue of UNC1999 with potency >1,000-fold lower than
that
of UNC1999 as a negative control for cell-based studies. Finally,
we created a biotin-tagged UNC1999 (UNC2399), which enriched EZH2
in pull-down studies, and a UNC1999–dye conjugate (UNC2239)
for co-localization studies with EZH2 in live cells. Taken together,
these compounds represent a set of useful tools for the biomedical
community to investigate the role of EZH2 and EZH1 in health and disease