9 research outputs found
3D imaging of colorectal cancer organoids identifies responses to Tankyrase inhibitors
Aberrant activation of the Wnt signalling pathway is required for tumour initiation and survival in the majority of colorectal cancers. The development of inhibitors of Wnt signalling has been the focus of multiple drug discovery programs targeting colorectal cancer and other malignancies associated with aberrant pathway activation. However, progression of new clinical entities targeting the Wnt pathway has been slow. One challenge lies with the limited predictive power of 2D cancer cell lines because they fail to fully recapitulate intratumoural phenotypic heterogeneity. In particular, the relationship between 2D cancer cell biology and cancer stem cell function is poorly understood. By contrast, 3D tumour organoids provide a platform in which complex cell-cell interactions can be studied. However, complex 3D models provide a challenging platform for the quantitative analysis of drug responses of therapies that have differential effects on tumour cell subpopulations. Here, we generated tumour organoids from colorectal cancer patients and tested their responses to inhibitors of Tankyrase (TNKSi) which are known to modulate Wnt signalling. Using compounds with 3 orders of magnitude difference in cellular mechanistic potency together with image-based assays, we demonstrate that morphometric analyses can capture subtle alterations in organoid responses to Wnt inhibitors that are consistent with activity against a cancer stem cell subpopulation. Overall our study highlights the value of phenotypic readouts as a quantitative method to asses drug-induced effects in a relevant preclinical model
Ligand Desolvation Steers On-Rate and Impacts Drug Residence Time of Heat Shock Protein 90 (Hsp90) Inhibitors
Residence
time and more recently the association rate constant <i>k</i><sub>on</sub> are increasingly acknowledged as important parameters
for in vivo efficacy
and safety of drugs. However, their broader consideration in drug
development is limited by a lack of knowledge of how to optimize these
parameters. In this study on a set of 176 heat shock protein 90 inhibitors,
structure–kinetic relationships, X-ray crystallography, and
molecular dynamics simulations were combined to retrieve a concrete
scheme of how to rationally slow down on-rates. We discovered that
an increased ligand desolvation barrier by introducing polar substituents
resulted in a significant <i>k</i><sub>on</sub> decrease.
The slowdown was accomplished by introducing polar moieties to those
parts of the ligand that point toward a hydrophobic cavity. We validated
this scheme by increasing polarity of three Hsp90 inhibitors and observed
a 9-, 13-, and 45-fold slowdown of on-rates and a 9-fold prolongation
in residence time. This prolongation was driven by transition state
destabilization rather than ground state stabilization
Ligand Desolvation Steers On-Rate and Impacts Drug Residence Time of Heat Shock Protein 90 (Hsp90) Inhibitors
Residence
time and more recently the association rate constant <i>k</i><sub>on</sub> are increasingly acknowledged as important parameters
for in vivo efficacy
and safety of drugs. However, their broader consideration in drug
development is limited by a lack of knowledge of how to optimize these
parameters. In this study on a set of 176 heat shock protein 90 inhibitors,
structure–kinetic relationships, X-ray crystallography, and
molecular dynamics simulations were combined to retrieve a concrete
scheme of how to rationally slow down on-rates. We discovered that
an increased ligand desolvation barrier by introducing polar substituents
resulted in a significant <i>k</i><sub>on</sub> decrease.
The slowdown was accomplished by introducing polar moieties to those
parts of the ligand that point toward a hydrophobic cavity. We validated
this scheme by increasing polarity of three Hsp90 inhibitors and observed
a 9-, 13-, and 45-fold slowdown of on-rates and a 9-fold prolongation
in residence time. This prolongation was driven by transition state
destabilization rather than ground state stabilization
Ligand Desolvation Steers On-Rate and Impacts Drug Residence Time of Heat Shock Protein 90 (Hsp90) Inhibitors
Residence
time and more recently the association rate constant <i>k</i><sub>on</sub> are increasingly acknowledged as important parameters
for in vivo efficacy
and safety of drugs. However, their broader consideration in drug
development is limited by a lack of knowledge of how to optimize these
parameters. In this study on a set of 176 heat shock protein 90 inhibitors,
structure–kinetic relationships, X-ray crystallography, and
molecular dynamics simulations were combined to retrieve a concrete
scheme of how to rationally slow down on-rates. We discovered that
an increased ligand desolvation barrier by introducing polar substituents
resulted in a significant <i>k</i><sub>on</sub> decrease.
The slowdown was accomplished by introducing polar moieties to those
parts of the ligand that point toward a hydrophobic cavity. We validated
this scheme by increasing polarity of three Hsp90 inhibitors and observed
a 9-, 13-, and 45-fold slowdown of on-rates and a 9-fold prolongation
in residence time. This prolongation was driven by transition state
destabilization rather than ground state stabilization
Estimation of Drug-Target Residence Times by τ‑Random Acceleration Molecular Dynamics Simulations
Drug-target
residence
time (τ), one of the main determinants
of drug efficacy, remains highly challenging to predict computationally
and, therefore, is usually not considered in the early stages of drug
design. Here, we present an efficient computational method, τ-random
acceleration molecular dynamics (τRAMD), for the ranking of
drug candidates by their residence time and obtaining insights into
ligand-target dissociation mechanisms. We assessed τRAMD on
a data set of 70 diverse drug-like ligands of the N-terminal domain
of HSP90α, a pharmaceutically important target with a highly
flexible binding site, obtaining computed relative residence times
with an accuracy of about 2.3τ for 78% of the compounds and
less than 2.0τ within congeneric series. Analysis of dissociation
trajectories reveals features that affect ligand unbinding rates,
including transient polar interactions and steric hindrance. These
results suggest that τRAMD will be widely applicable as a computationally
efficient aid to improving drug residence times during lead optimization
Estimation of Drug-Target Residence Times by τ‑Random Acceleration Molecular Dynamics Simulations
Drug-target
residence
time (τ), one of the main determinants
of drug efficacy, remains highly challenging to predict computationally
and, therefore, is usually not considered in the early stages of drug
design. Here, we present an efficient computational method, τ-random
acceleration molecular dynamics (τRAMD), for the ranking of
drug candidates by their residence time and obtaining insights into
ligand-target dissociation mechanisms. We assessed τRAMD on
a data set of 70 diverse drug-like ligands of the N-terminal domain
of HSP90α, a pharmaceutically important target with a highly
flexible binding site, obtaining computed relative residence times
with an accuracy of about 2.3τ for 78% of the compounds and
less than 2.0τ within congeneric series. Analysis of dissociation
trajectories reveals features that affect ligand unbinding rates,
including transient polar interactions and steric hindrance. These
results suggest that τRAMD will be widely applicable as a computationally
efficient aid to improving drug residence times during lead optimization
Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects
Here we present an evaluation of the binding affinity prediction accuracy of the free energy calculation method FEP+ on internal active drug discovery projects and on a large new public benchmark set.<br /
Discovery of Cycloalkyl[<i>c</i>]thiophenes as Novel Scaffolds for Hypoxia-Inducible Factor-2α Inhibitors
Hypoxia-inducible factors (HIFs) are heterodimeric transcription
factors induced in diverse pathophysiological settings. Inhibition
of HIF-2α has become a strategy for cancer treatment since the
discovery that small molecules, upon binding into a small cavity of
the HIF-2α PAS B domain, can alter its conformation and disturb
the activity of the HIF dimer complex. Herein, the design, synthesis,
and systematic SAR exploration of cycloalkyl[c]thiophenes
as novel HIF-2α inhibitors are described, providing the first
chemotype featuring an alkoxy–aryl scaffold. X-ray data confirmed
the ability of these inhibitors to induce perturbation of key amino
acids by appropriately presenting key pharmacophoric elements in the
hydrophobic cavity. Selected compounds showed inhibition of VEGF-A
secretion in cancer cells and prevention of Arg1 expression and activity
in IL4-stimulated macrophages. Moreover, in vivo target gene modulation
was demonstrated with compound 35r. Thus, the disclosed
HIF-2α inhibitors represent valuable tools for investigating
selective HIF-2α inhibition and its effect on tumor biology