49 research outputs found
Predicting Drug-Induced Cholestasis with the Help of Hepatic Transportersî—¸An <i>in Silico</i> Modeling Approach
Cholestasis represents
one out of three types of drug induced liver
injury (DILI), which comprises a major challenge in drug development.
In this study we applied a two-class classification scheme based on <i>k</i>-nearest neighbors in order to predict cholestasis, using
a set of 93 two-dimensional (2D) physicochemical descriptors and predictions
of selected hepatic transporters’ inhibition (BSEP, BCRP, P-gp,
OATP1B1, and OATP1B3). In order to assess the potential contribution
of transporter inhibition, we compared whether the inclusion of the
transporters’ inhibition predictions contributes to a significant
increase in model performance in comparison to the plain use of the
93 2D physicochemical descriptors. Our findings were in agreement
with literature findings, indicating a contribution not only from
BSEP inhibition but a rather synergistic effect deriving from the
whole set of transporters. The final optimal model was validated via
both 10-fold cross validation and external validation. It performs
quite satisfactorily resulting in 0.686 ± 0.013 for accuracy
and 0.722 ± 0.014 for area under the receiver operating characteristic
curve (AUC) for 10-fold cross-validation (mean ± standard deviation
from 50 iterations)
Ligand and Structure-Based Classification Models for Prediction of P‑Glycoprotein Inhibitors
The
ABC transporter P-glycoprotein (P-gp) actively transports a
wide range of drugs and toxins out of cells, and is therefore related
to multidrug resistance and the ADME profile of therapeutics. Thus,
development of predictive in silico models for the identification
of P-gp inhibitors is of great interest in the field of drug discovery
and development. So far in silico P-gp inhibitor prediction was dominated
by ligand-based approaches because of the lack of high-quality structural
information about P-gp. The present study aims at comparing the P-gp
inhibitor/noninhibitor classification performance obtained by docking
into a homology model of P-gp, to supervised machine learning methods,
such as Kappa nearest neighbor, support vector machine (SVM), random
fores,t and binary QSAR, by using a large, structurally diverse data
set. In addition, the applicability domain of the models was assessed
using an algorithm based on Euclidean distance. Results show that
random forest and SVM performed best for classification of P-gp inhibitors
and noninhibitors, correctly predicting 73/75% of the external test
set compounds. Classification based on the docking experiments using
the scoring function ChemScore resulted in the correct prediction
of 61% of the external test set. This demonstrates that ligand-based
models currently remain the methods of choice for accurately predicting
P-gp inhibitors. However, structure-based classification offers information
about possible drug/protein interactions, which helps in understanding
the molecular basis of ligand-transporter interaction and could therefore
also support lead optimization
Identification of Novel Inhibitors of Organic Anion Transporting Polypeptides 1B1 and 1B3 (OATP1B1 and OATP1B3) Using a Consensus Vote of Six Classification Models
Organic anion transporting polypeptides
1B1 and 1B3 are transporters
selectively expressed on the basolateral membrane of the hepatocyte.
Several studies reveal that they are involved in drug–drug
interactions, cancer, and hyperbilirubinemia. In this study, we developed
a set of classification models for OATP1B1 and 1B3 inhibition based
on more than 1700 carefully curated compounds from literature, which
were validated via cross-validation and by use of an external test
set. After combining several sets of descriptors and classifiers,
the 6 best models were selected according to their statistical performance
and were used for virtual screening of DrugBank. Consensus scoring
of the screened compounds resulted in the selection and purchase of
nine compounds as potential dual inhibitors and of one compound as
potential selective OATP1B3 inhibitor. Biological testing of the compounds
confirmed the validity of the models, yielding an accuracy of 90%
for OATP1B1 and 80% for OATP1B3, respectively. Moreover, at least
half of the new identified inhibitors are associated with hyperbilirubinemia
or hepatotoxicity, implying a relationship between OATP inhibition
and these severe side effects
Identification of Novel Inhibitors of Organic Anion Transporting Polypeptides 1B1 and 1B3 (OATP1B1 and OATP1B3) Using a Consensus Vote of Six Classification Models
Organic anion transporting polypeptides
1B1 and 1B3 are transporters
selectively expressed on the basolateral membrane of the hepatocyte.
Several studies reveal that they are involved in drug–drug
interactions, cancer, and hyperbilirubinemia. In this study, we developed
a set of classification models for OATP1B1 and 1B3 inhibition based
on more than 1700 carefully curated compounds from literature, which
were validated via cross-validation and by use of an external test
set. After combining several sets of descriptors and classifiers,
the 6 best models were selected according to their statistical performance
and were used for virtual screening of DrugBank. Consensus scoring
of the screened compounds resulted in the selection and purchase of
nine compounds as potential dual inhibitors and of one compound as
potential selective OATP1B3 inhibitor. Biological testing of the compounds
confirmed the validity of the models, yielding an accuracy of 90%
for OATP1B1 and 80% for OATP1B3, respectively. Moreover, at least
half of the new identified inhibitors are associated with hyperbilirubinemia
or hepatotoxicity, implying a relationship between OATP inhibition
and these severe side effects
Structure–Activity Relationships, Ligand Efficiency, and Lipophilic Efficiency Profiles of Benzophenone-Type Inhibitors of the Multidrug Transporter P-Glycoprotein
The drug efflux pump P-glycoprotein (P-gp) has been shown
to promote
multidrug resistance (MDR) in tumors as well as to influence ADME
properties of drug candidates. Here we synthesized and tested a series
of benzophenone derivatives structurally analogous to propafenone-type
inhibitors of P-gp. Some of the compounds showed ligand efficiency
and lipophilic efficiency (LipE) values in the range of compounds
which entered clinical trials as MDR modulators. Interestingly, although
lipophilicity plays a dominant role for P-gp inhibitors, all compounds
investigated showed LipE values below the threshold for promising
drug candidates. Docking studies of selected analogues into a homology
model of P-glycoprotein suggest that benzophenones show an interaction
pattern similar to that previously identified for propafenone-type
inhibitors
A Binding Mode Hypothesis of Tiagabine Confirms Liothyronine Effect on γ‑Aminobutyric Acid Transporter 1 (GAT1)
Elevating
GABA levels in the synaptic cleft by inhibiting its reuptake
carrier GAT1 is an established approach for the treatment of CNS disorders
like epilepsy. With the increasing availability of crystal structures
of transmembrane transporters, structure-based approaches to elucidate
the molecular basis of ligand–transporter interaction also
become feasible. Experimental data guided docking of derivatives of
the GAT1 inhibitor tiagabine into a protein homology model of GAT1
allowed derivation of a common binding mode for this class of inhibitors
that is able to account for the distinct structure–activity
relationship pattern of the data set. Translating essential binding
features into a pharmacophore model followed by in silico screening
of the DrugBank identified liothyronine as a drug potentially exerting
a similar effect on GAT1. Experimental testing further confirmed the
GAT1 inhibiting properties of this thyroid hormone
A Binding Mode Hypothesis of Tiagabine Confirms Liothyronine Effect on γ‑Aminobutyric Acid Transporter 1 (GAT1)
Elevating
GABA levels in the synaptic cleft by inhibiting its reuptake
carrier GAT1 is an established approach for the treatment of CNS disorders
like epilepsy. With the increasing availability of crystal structures
of transmembrane transporters, structure-based approaches to elucidate
the molecular basis of ligand–transporter interaction also
become feasible. Experimental data guided docking of derivatives of
the GAT1 inhibitor tiagabine into a protein homology model of GAT1
allowed derivation of a common binding mode for this class of inhibitors
that is able to account for the distinct structure–activity
relationship pattern of the data set. Translating essential binding
features into a pharmacophore model followed by in silico screening
of the DrugBank identified liothyronine as a drug potentially exerting
a similar effect on GAT1. Experimental testing further confirmed the
GAT1 inhibiting properties of this thyroid hormone
A Binding Mode Hypothesis of Tiagabine Confirms Liothyronine Effect on γ‑Aminobutyric Acid Transporter 1 (GAT1)
Elevating
GABA levels in the synaptic cleft by inhibiting its reuptake
carrier GAT1 is an established approach for the treatment of CNS disorders
like epilepsy. With the increasing availability of crystal structures
of transmembrane transporters, structure-based approaches to elucidate
the molecular basis of ligand–transporter interaction also
become feasible. Experimental data guided docking of derivatives of
the GAT1 inhibitor tiagabine into a protein homology model of GAT1
allowed derivation of a common binding mode for this class of inhibitors
that is able to account for the distinct structure–activity
relationship pattern of the data set. Translating essential binding
features into a pharmacophore model followed by in silico screening
of the DrugBank identified liothyronine as a drug potentially exerting
a similar effect on GAT1. Experimental testing further confirmed the
GAT1 inhibiting properties of this thyroid hormone
Mutational Analysis of the High-Affinity Zinc Binding Site Validates a Refined Human Dopamine Transporter Homology Model
<div><p>The high-resolution crystal structure of the leucine transporter (LeuT) is frequently used as a template for homology models of the dopamine transporter (DAT). Although similar in structure, DAT differs considerably from LeuT in a number of ways: (i) when compared to LeuT, DAT has very long intracellular amino and carboxyl termini; (ii) LeuT and DAT share a rather low overall sequence identity (22%) and (iii) the extracellular loop 2 (EL2) of DAT is substantially longer than that of LeuT. Extracellular zinc binds to DAT and restricts the transporter‚s movement through the conformational cycle, thereby resulting in a decrease in substrate uptake. Residue H293 in EL2 praticipates in zinc binding and must be modelled correctly to allow for a full understanding of its effects. We exploited the high-affinity zinc binding site endogenously present in DAT to create a model of the complete transmemberane domain of DAT. The zinc binding site provided a DAT-specific molecular ruler for calibration of the model. Our DAT model places EL2 at the transporter lipid interface in the vicinity of the zinc binding site. Based on the model, D206 was predicted to represent a fourth co-ordinating residue, in addition to the three previously described zinc binding residues H193, H375 and E396. This prediction was confirmed by mutagenesis: substitution of D206 by lysine and cysteine affected the inhibitory potency of zinc and the maximum inhibition exerted by zinc, respectively. Conversely, the structural changes observed in the model allowed for rationalizing the zinc-dependent regulation of DAT: upon binding, zinc stabilizes the outward-facing state, because its first coordination shell can only be completed in this conformation. Thus, the model provides a validated solution to the long extracellular loop and may be useful to address other aspects of the transport cycle.</p> </div
Salt bridges and water in the substrate permeation pathway.
<p>A) Time evolution of the salt bridge in the outer vestibule between R85 in transmembrane helix 1 and D476 in transmembrane helix 10. The structure of the salt bridge is shown in the insert. The distance is measured between the Cζ carbon of the guanidium group of R85 and the Cγ carbon of D476. B) Time evolution of the salt bridge between R60 and D436 in the inner vestibule. The structure of the salt bridge is shown in the insert. The distance is measured between the Cζ carbon of the guanidium group of R60 and the Cγ carbon of D436. C–E) A slice through the DAT showing an overlay of average water density (black hash) with a respective representative snapshot for simulation 1 (panel C), simulation 2 (panel D) and simulation 3 (panel E). Several residues in the S1 binding site and at the outer gate are shown for orientation.</p