7 research outputs found
PPARĪ³ non-covalent antagonists exhibit mutable binding modes with a similar free energy of binding: a case study
<p>The structural and dynamical properties of PPARĪ³ receptor in a complex with either partial or full agonists have been intensively studied but little is known about the receptor antagonistic conformation. A composition of microsecond accelerated molecular dynamics (aMD) simulation show that like partial agonists a non-covalent PPARĪ³ full antagonist can bind in different modes of similar population size and free energies of binding. Four different and periodically exchanging ligand conformations are detected and described. The studied antagonist interacts with different receptor substructures and affects both the co-activator and the Cdk5 phosphorylation sites and, presumably, the natural complex with the DNA. However, no significant changes in the conformational states of the activation helix 12, and in particular an antagonist orientation, have been recorded. Finally, our results show also that the aMD approach can be successfully used in recovering the possible binding modes, considering fully the receptor flexibility, and is not dependent on the starting conformation.</p
Prediction of Accurate Binding Modes Using Combination of Classical and Accelerated Molecular Dynamics and Free-Energy Perturbation Calculations: An Application to Toxicity Studies
Estimating the correct
binding modes of ligands in proteināligand
complexes is crucial not only in the drug discovery process but also
for elucidating potential toxicity mechanisms. In the current paper,
we propose a computational modeling workflow using the combination
of docking, classical molecular dynamics (cMD), accelerated molecular
dynamics (aMD) and free-energy perturbation (FEP+ protocol) for identification
of possible ligand binding modes. It was applied for investigation
of selected perfluorocarboxyl acids (PFCAs) in the PPARĪ³ nuclear
receptor. Although both regular and induced fit docking failed to
reproduce the experimentally determined binding mode of the ligands
when docked into a non-native X-ray structure, cMD and aMD simulations
successfully identified the most probable binding conformations. Moreover,
multiple binding modes were identified for all of these compounds
and the shorter-chain PFCAs continuously moved between a few energetically
favorable binding conformations. On the basis of MD predictions of
binding conformations, we applied the default and also redesigned
FEP+ sampling protocols, which accurately reproduced experimental
differences in the binding energies. Thus, the preliminary MD simulations
can also provide helpful information about correct setup of the FEP+
calculations. These results show that the PFCA binding modes were
accurately predicted and that the FEP+ protocol can be used to estimate
free energies of binding of flexible ligands that are not typical
druglike compounds. Our in silico workflow revealed the specific ligandāresidue
interactions within the ligand binding domain and the main characteristics
of the PFCAs, and it was concluded that these compounds are week PPARĪ³
partial agonists. This work also suggests a common pipeline for identification
of ligand binding modes, ligandāprotein dynamics description,
and relative free-energy calculations
Combination of Genetic Screening and Molecular Dynamics as a Useful Tool for Identification of Disease-Related Mutations: ZASP PDZ Domain G54S Mutation Case
Cypher/ZASP
(<i>LDB3</i> gene) is known to interact with
a network of proteins. It binds to Ī±-actinin and the calcium
voltage channels (LTCC) via its PDZ domain. Here we report the identification
of a highly conserved ZASP G54S mutation classified as a variant of
unknown significance in a sample of an adult with hypertrophic cardiomyopathy
(HCM). The initial bioinformatics calculations strongly evaluated
G54S as damaging. Furthermore, we employed accelerated and classical
molecular dynamics and free energy calculations to study the structural
impact of this mutation on the ZASP apo form and to address the question
of whether it can be linked to HCM. Seventeen independent MD runs
and simulations of 2.5 Ī¼s total were performed and showed that
G54S perturbs the Ī±2 helix position via destabilization of the
adjacent loop linked to the Ī²5 sheet. This also leads to the
formation of a strong H-bond between peptide target residues Leu17
and Gln66, thus restricting both the Ī±-actinin2 and LTCC C-terminal
peptides to access their natural binding site and reducing in this
way their binding capacity. On the basis of these observations and
the adultās clinical data, we propose that ZASP<sup>G54S</sup> and presumably other ZASP PDZ domain mutations can cause HCM. To
the best of our knowledge, this is the first reported ZASP PDZ domain
mutation that might be linked to HCM. The integrated workflow used
in this study can be applied for the identification and description
of other mutations that might be related to particular diseases
Prediction of Accurate Binding Modes Using Combination of Classical and Accelerated Molecular Dynamics and Free-Energy Perturbation Calculations: An Application to Toxicity Studies
Estimating the correct
binding modes of ligands in proteināligand
complexes is crucial not only in the drug discovery process but also
for elucidating potential toxicity mechanisms. In the current paper,
we propose a computational modeling workflow using the combination
of docking, classical molecular dynamics (cMD), accelerated molecular
dynamics (aMD) and free-energy perturbation (FEP+ protocol) for identification
of possible ligand binding modes. It was applied for investigation
of selected perfluorocarboxyl acids (PFCAs) in the PPARĪ³ nuclear
receptor. Although both regular and induced fit docking failed to
reproduce the experimentally determined binding mode of the ligands
when docked into a non-native X-ray structure, cMD and aMD simulations
successfully identified the most probable binding conformations. Moreover,
multiple binding modes were identified for all of these compounds
and the shorter-chain PFCAs continuously moved between a few energetically
favorable binding conformations. On the basis of MD predictions of
binding conformations, we applied the default and also redesigned
FEP+ sampling protocols, which accurately reproduced experimental
differences in the binding energies. Thus, the preliminary MD simulations
can also provide helpful information about correct setup of the FEP+
calculations. These results show that the PFCA binding modes were
accurately predicted and that the FEP+ protocol can be used to estimate
free energies of binding of flexible ligands that are not typical
druglike compounds. Our in silico workflow revealed the specific ligandāresidue
interactions within the ligand binding domain and the main characteristics
of the PFCAs, and it was concluded that these compounds are week PPARĪ³
partial agonists. This work also suggests a common pipeline for identification
of ligand binding modes, ligandāprotein dynamics description,
and relative free-energy calculations
Prediction of Accurate Binding Modes Using Combination of Classical and Accelerated Molecular Dynamics and Free-Energy Perturbation Calculations: An Application to Toxicity Studies
Estimating the correct
binding modes of ligands in proteināligand
complexes is crucial not only in the drug discovery process but also
for elucidating potential toxicity mechanisms. In the current paper,
we propose a computational modeling workflow using the combination
of docking, classical molecular dynamics (cMD), accelerated molecular
dynamics (aMD) and free-energy perturbation (FEP+ protocol) for identification
of possible ligand binding modes. It was applied for investigation
of selected perfluorocarboxyl acids (PFCAs) in the PPARĪ³ nuclear
receptor. Although both regular and induced fit docking failed to
reproduce the experimentally determined binding mode of the ligands
when docked into a non-native X-ray structure, cMD and aMD simulations
successfully identified the most probable binding conformations. Moreover,
multiple binding modes were identified for all of these compounds
and the shorter-chain PFCAs continuously moved between a few energetically
favorable binding conformations. On the basis of MD predictions of
binding conformations, we applied the default and also redesigned
FEP+ sampling protocols, which accurately reproduced experimental
differences in the binding energies. Thus, the preliminary MD simulations
can also provide helpful information about correct setup of the FEP+
calculations. These results show that the PFCA binding modes were
accurately predicted and that the FEP+ protocol can be used to estimate
free energies of binding of flexible ligands that are not typical
druglike compounds. Our in silico workflow revealed the specific ligandāresidue
interactions within the ligand binding domain and the main characteristics
of the PFCAs, and it was concluded that these compounds are week PPARĪ³
partial agonists. This work also suggests a common pipeline for identification
of ligand binding modes, ligandāprotein dynamics description,
and relative free-energy calculations
Prediction of Accurate Binding Modes Using Combination of Classical and Accelerated Molecular Dynamics and Free-Energy Perturbation Calculations: An Application to Toxicity Studies
Estimating the correct
binding modes of ligands in proteināligand
complexes is crucial not only in the drug discovery process but also
for elucidating potential toxicity mechanisms. In the current paper,
we propose a computational modeling workflow using the combination
of docking, classical molecular dynamics (cMD), accelerated molecular
dynamics (aMD) and free-energy perturbation (FEP+ protocol) for identification
of possible ligand binding modes. It was applied for investigation
of selected perfluorocarboxyl acids (PFCAs) in the PPARĪ³ nuclear
receptor. Although both regular and induced fit docking failed to
reproduce the experimentally determined binding mode of the ligands
when docked into a non-native X-ray structure, cMD and aMD simulations
successfully identified the most probable binding conformations. Moreover,
multiple binding modes were identified for all of these compounds
and the shorter-chain PFCAs continuously moved between a few energetically
favorable binding conformations. On the basis of MD predictions of
binding conformations, we applied the default and also redesigned
FEP+ sampling protocols, which accurately reproduced experimental
differences in the binding energies. Thus, the preliminary MD simulations
can also provide helpful information about correct setup of the FEP+
calculations. These results show that the PFCA binding modes were
accurately predicted and that the FEP+ protocol can be used to estimate
free energies of binding of flexible ligands that are not typical
druglike compounds. Our in silico workflow revealed the specific ligandāresidue
interactions within the ligand binding domain and the main characteristics
of the PFCAs, and it was concluded that these compounds are week PPARĪ³
partial agonists. This work also suggests a common pipeline for identification
of ligand binding modes, ligandāprotein dynamics description,
and relative free-energy calculations
Discovery of a Novel Selective PPARĪ³ Ligand with Partial Agonist Binding Properties by Integrated <i>in Silico</i>/<i>in Vitro</i> Work Flow
Full agonists to the peroxisome proliferator-activated
receptor
(PPAR)ĀĪ³, such as Rosiglitazone, have been associated with a
series of undesired side effects, such as weight gain, fluid retention,
cardiac hypertrophy, and hepatotoxicity. Nevertheless, PPARĪ³
is involved in the expression of genes that control glucose and lipid
metabolism and is an important target for drugs against type 2 diabetes,
dyslipidemia, atherosclerosis, and cardiovascular disease. In an effort
to identify novel PPARĪ³ ligands with an improved pharmacological
profile, emphasis has shifted to selective ligands with partial agonist
binding properties. Toward this end we applied an integrated <i>in silico</i>/<i>in vitro</i> workflow, based on pharmacophore-
and structure-based virtual screening of the ZINC library, coupled
with competitive binding and transactivation assays, and adipocyte
differentiation and gene expression studies. Hit compound <b>9</b> was identified as the most potent ligand (IC<sub>50</sub> = 0.3
Ī¼M) and a relatively poor inducer of adipocyte differentiation.
The binding mode of compound <b>9</b> was confirmed by molecular
dynamics simulation, and the calculated free energy of binding was
ā8.4 kcal/mol. A novel functional group, the carbonitrile group,
was identified to be a key substituent in the ligandāprotein
interactions. Further studies on the transcriptional regulation properties
of compound <b>9</b> revealed a gene regulatory profile that
was to a large extent unique, however functionally closer to that
of a partial agonist