25 research outputs found
Uncertainty Quantification in Alchemical Free Energy Methods
Alchemical
free energy methods have gained much importance recently
from several reports of improved ligandāprotein binding affinity
predictions based on their implementation using molecular dynamics
simulations. A large number of variants of such methods implementing
different accelerated sampling techniques and free energy estimators
are available, each claimed to be better than the others in its own
way. However, the key features of reproducibility and quantification
of associated uncertainties in such methods have barely been discussed.
Here, we apply a systematic protocol for uncertainty quantification
to a number of popular alchemical free energy methods, covering both
absolute and relative free energy predictions. We show that a reliable
measure of error estimation is provided by ensemble simulationīøan
ensemble of independent MD simulationsīøwhich applies irrespective
of the free energy method. The need to use ensemble methods is fundamental
and holds regardless of the duration of time of the molecular dynamics
simulations performed
Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration
We report the implementation
of the thermodynamic integration method
on the pmemd module of the AMBER 16 package on GPUs (pmemdGTI). The
pmemdGTI code typically delivers over 2 orders of magnitude of speed-up
relative to a single CPU core for the calculation of ligandāprotein
binding affinities with no statistically significant numerical differences
and thus provides a powerful new tool for drug discovery applications
<em>De novo</em> design of protein kinase inhibitors by<em> in silico</em> identification of hinge region-binding fragments
[Image: see text] Protein kinases constitute an attractive family of enzyme targets with high relevance to cell and disease biology. Small molecule inhibitors are powerful tools to dissect and elucidate the function of kinases in chemical biology research and to serve as potential starting points for drug discovery. However, the discovery and development of novel inhibitors remains challenging. Here, we describe a structure-based de novo design approach that generates novel, hinge-binding fragments that are synthetically feasible and can be elaborated to small molecule libraries. Starting from commercially available compounds, core fragments were extracted, filtered for pharmacophoric properties compatible with hinge-region binding, and docked into a panel of protein kinases. Fragments with a high consensus score were subsequently short-listed for synthesis. Application of this strategy led to a number of core fragments with no previously reported activity against kinases. Small libraries around the core fragments were synthesized, and representative compounds were tested against a large panel of protein kinases and subjected to co-crystallization experiments. Each of the tested compounds was active against at least one kinase, but not all kinases in the panel were inhibited. A number of compounds showed high ligand efficiencies for therapeutically relevant kinases; among them were MAPKAP-K3, SRPK1, SGK1, TAK1, and GCK for which only few inhibitors are reported in the literature
Evaluation of human intestinal absorption data and subsequent derivation of a quantitative structure-activity relationship (QSAR) with the Abraham descriptors
The human intestinal absorption of 241 drugs was evaluated. Three main methods were used to determine the human intestinal absorption: bioavailability, percentage of urinary excretion of drug-related material following oral administration, and the ratio of cumulative urinary excretion of drug-related material following oral and intravenous administration. The general solvation equation developed by Abraham's group was used to model the human intestinal absorption data of 169 drugs we considered to have reliable data. The model contains five Abraham descriptors calculated by the ABSOLV program. The results show that Abraham descriptors can successfully predict human intestinal absorption if the human absorption data is carefully classified based on solubility and administration dose to humans
<i>De Novo</i> Design of Protein Kinase Inhibitors by <i>in Silico</i> Identification of Hinge Region-Binding Fragments
Protein kinases constitute an attractive
family of enzyme targets
with high relevance to cell and disease biology. Small molecule inhibitors
are powerful tools to dissect and elucidate the function of kinases
in chemical biology research and to serve as potential starting points
for drug discovery. However, the discovery and development of novel
inhibitors remains challenging. Here, we describe a structure-based <i>de novo</i> design approach that generates novel, hinge-binding
fragments that are synthetically feasible and can be elaborated to
small molecule libraries. Starting from commercially available compounds,
core fragments were extracted, filtered for pharmacophoric properties
compatible with hinge-region binding, and docked into a panel of protein
kinases. Fragments with a high consensus score were subsequently short-listed
for synthesis. Application of this strategy led to a number of core
fragments with no previously reported activity against kinases. Small
libraries around the core fragments were synthesized, and representative
compounds were tested against a large panel of protein kinases and
subjected to co-crystallization experiments. Each of the tested compounds
was active against at least one kinase, but not all kinases in the
panel were inhibited. A number of compounds showed high ligand efficiencies
for therapeutically relevant kinases; among them were MAPKAP-K3, SRPK1,
SGK1, TAK1, and GCK for which only few inhibitors are reported in
the literature
Discovery and Structure Enabled Synthesis of 2,6-Diaminopyrimidin-4-one IRAK4 Inhibitors
We
report the identification and synthesis of a series of aminopyrimidin-4-one
IRAK4 inhibitors. Through high throughput screening, an aminopyrimidine
hit was identified and modified via structure enabled design to generate
a new, potent, and kinase selective pyrimidin-4-one chemotype. This
chemotype is exemplified by compound <b>16</b>, which has potent
IRAK4 inhibition activity (IC<sub>50</sub> = 27 nM) and excellent
kinase selectivity (>100-fold against 99% of 111 tested kinases),
and compound <b>31</b>, which displays potent IRAK4 activity
(IC<sub>50</sub> = 93 nM) and good rat bioavailability (<i>F</i> = 42%)
Incorporation of Putative Helix-Breaking Amino Acids in the Design of Novel Stapled Peptides: Exploring Biophysical and Cellular Permeability Properties
Stapled α-helical peptides represent an emerging superclass of macrocyclic molecules with drug-like properties, including high-affinity target binding, protease resistance, and membrane permeability. As a model system for probing the chemical space available for optimizing these properties, we focused on dual Mdm2/MdmX antagonist stapled peptides related to the p53 N-terminus. Specifically, we first generated a library of ATSP-7041 (Chang et al., 2013) analogs iteratively modified by L-Ala and D-amino acids. Single L-Ala substitutions beyond the Mdm2/(X) binding interfacial residues (i.e., Phe3, Trp7, and Cba10) had minimal effects on target binding, α-helical content, and cellular activity. Similar binding affinities and cellular activities were noted at non-interfacial positions when the template residues were substituted with their d-amino acid counterparts, despite the fact that d-amino acid residues typically ‘break’ right-handed α-helices. d-amino acid substitutions at the interfacial residues Phe3 and Cba10 resulted in the expected decreases in binding affinity and cellular activity. Surprisingly, substitution at the remaining interfacial position with its d-amino acid equivalent (i.e., Trp7 to d-Trp7) was fully tolerated, both in terms of its binding affinity and cellular activity. An X-ray structure of the d-Trp7-modified peptide was determined and revealed that the indole side chain was able to interact optimally with its Mdm2 binding site by a slight global re-orientation of the stapled peptide. To further investigate the comparative effects of d-amino acid substitutions we used linear analogs of ATSP-7041, where we replaced the stapling amino acids by Aib (i.e., R84 to Aib4 and S511 to Aib11) to retain the helix-inducing properties of α-methylation. The resultant analog sequence Ac–Leu–Thr–Phe–Aib–Glu–Tyr–Trp–Gln–Leu–Cba–Aib–Ser–Ala–Ala–NH2 exhibited high-affinity target binding (Mdm2 Kd = 43 nM) and significant α-helicity in circular dichroism studies. Relative to this linear ATSP-7041 analog, several d-amino acid substitutions at Mdm2(X) non-binding residues (e.g., d-Glu5, d-Gln8, and d-Leu9) demonstrated decreased binding and α-helicity. Importantly, circular dichroism (CD) spectroscopy showed that although helicity was indeed disrupted by d-amino acids in linear versions of our template sequence, stapled molecules tolerated these residues well. Further studies on stapled peptides incorporating N-methylated amino acids, l-Pro, or Gly substitutions showed that despite some positional dependence, these helix-breaking residues were also generally tolerated in terms of secondary structure, binding affinity, and cellular activity. Overall, macrocyclization by hydrocarbon stapling appears to overcome the destabilization of α-helicity by helix breaking residues and, in the specific case of d-Trp7-modification, a highly potent ATSP-7041 analog (Mdm2 Kd = 30 nM; cellular EC50 = 600 nM) was identified. Our findings provide incentive for future studies to expand the chemical diversity of macrocyclic α-helical peptides (e.g., d-amino acid modifications) to explore their biophysical properties and cellular permeability. Indeed, using the library of 50 peptides generated in this study, a good correlation between cellular permeability and lipophilicity was observed