Structural and functional aspects of P-glycoprotein and its
inhibitors
Shirin Mollazadeh, Amirhossein Sahebkar, Farzin Hadizadeh,
Javad Behravan, Sepideh Arabzadeh
PII: S0024-3205(18)30673-8
DOI: https://doi.org/10.1016/j.lfs.2018.10.048
Reference: LFS 16028
To appear in: Life Sciences
Received date: 9 September 2018
Revised date: 12 October 2018
Accepted date: 23 October 2018
Please cite this article as: Shirin Mollazadeh, Amirhossein Sahebkar, Farzin Hadizadeh,
Javad Behravan, Sepideh Arabzadeh , Structural and functional aspects of P-glycoprotein
and its inhibitors. Lfs (2018), https://doi.org/10.1016/j.lfs.2018.10.048
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Structural and functional aspects of P-glycoprotein and its inhibitors
Shirin Mollazadeha,b, Amirhossein Sahebkarb,c,d, Farzin Hadizadeha,b *
, Javad Behravanb,d*
Sepideh Arabzadehb
Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences,
Mashhad, Iran.
Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical
Sciences, Mashhad, Iran
cNeurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad,
Iran
School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
*Corrsponding author:
Professor Farzin Hadizadeha, Professor Javad Behravan
Biotechnology Research Center, Mashhad University of medical Sciences, Mashhad, Iran
Tel: +98-51-38823255
Email: [email protected], [email protected]
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Abstract
P-glycoprotein (P-gp) is a member of ATP-binding cassette (ABC) superfamily which
extrudes chemotherapeutic agents out of the cell. Suppression of this efflux activity has been the
subject of numerous attempts to develop P-gp inhibitors. The aim of this review is to present up￾to-date information on the structural and functional aspects of P-gp and its known inhibitors. The
data presented also provide some information on drug discovery approaches for candidate P-gp
inhibitors. Nucleotide-binding domains (NBDs) and drug-binding domains (DBDs) have been
extensively studied to gain more information about P-gp inhibition and it looks that the ATPase
activity of this pump has been the most attractive target for designing inhibitors. Hydrophobic
and π-π (aromatic) interactions between P-gp binding domains and inhibitors are dominant
intermolecular forces that have been reported in many studies using different methods. Many
synthetic and natural products have been found to possess inhibitory or modulatory effects on
drug transporter proteins. Log P value is an important factor in studying these inhibitors and has
a crucial role on absorption, distribution, metabolism, and excretion (ADME) properties of
candidate P-gp inhibitors.
Keywords: Multidrug resistance; Drug transporter; P-glycoprotein; inhibitor
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1. Introduction
P-gp is an ABC transporter which belongs to the multidrug resistance (MDR) pump
superfamily. The function of ABC drug transporters is intricate (Gillet and Gottesman, 2010). In
physiological conditions, xenobiotics are effluxed from the normal cells by these membrane
proteins while in tumor cells , where there is an overexpression of P-gp, anticancer drugs are
transported to the extracellular matrix by these pumps. This phenomenon keeps the intracellular
drug concentration in tumor cells below a therapeutic threshold that can lead to suboptimal
cytotoxic effect of anti-tumor drugs (Persidis, 1999). The function of efflux pumps requires
energy that is produced by ATP hydrolysis (Szöllősi et al. , 2017). Since protein function
depends on its structure and conformational change, any information about the structure of the
protein and ligand would benefit the rational design of MDR inhibitors [5]. Many
crystallographic structures of bacterial and mouse P-gp from Protein Data Bank (PDB) website
have been used to obtain insights into the binding mode between ligand and protein which
contains a few binding sites (Condic-Jurkic et al. , 2018, Min et al. , 2017, Sachs et al. , 2018).
Many synthetic and naturally occurring compounds have been found to possess inhibitory or
modulatory effects on MDR proteins (Liu et al. , 2013). Elucidation of chemical and physical
characteristics of these compounds are integral to gain knowledge on the optimal parameters for
designing novel inhibitors (Wang et al. , 2003).
In silico methods have been increasingly applied in drug discovery studies (Brewer et al. , 2014).
Structure-based methods such as MD (molecular dynamics) and molecular docking could help
identify structural changes, binding sites (DBD and NBDs) and ATPase activity (at the time of
efflux) of P-gp as well as discovering the nature of interactions with this protein. (McCormick et
al. , 2015, Prajapati et al. , 2013, Shahraki et al. , 2017). Ligand-based methods such as
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QSAR(quantitative structure-activity relationship) and pharmacophore modeling could be used
to distinguish important features of drug candidates and to compare them with potent
inhibitors(Pajeva et al. , 2009).
Potency and pharmacodynamics aspects as well as pharmacokinetic features of structures are
important factors that need to be taken into consideration for the design of protein inhibitors. One
obstacle against development of P-gp inhibitors to clinical setting is potential interaction of these
inhibitors with CYP 450 isoenzymes. Inhibitors of these two protein families (drug transporters
and CYP450 enzymes) have many common features. Computational calculations are used to
obtain information on substrates and inhibitors of CYP450 isoenzymes. Exploring the
interactions P-gp inhibitors with CYP 450 isoenzymes would be necessary in drug design
experiments in order to minimize adverse reactions(Vasanthanathan et al. , 2009).
2. Conformational changes affecting protein function
2.1 Different structures from conformational changes
P-gp is a 170 kD protein containing two amino acid chains, each chain consists of six
transmembrane domains (TMDs) and a nucleotide-binding domain (NBD). The flexible structure
of P-gp is responsible for its translational and rotational motions during the efflux mechanism,
which also includes simultaneous variation in the NBD distance, and is related to the entrance of
a molecule suitable for efflux. These conformational changes seem to be very important in the
alteration of the ligand affinity. In molecular dynamic studies the Root mean square deviations
(RMSDs) plot gives valuable supposal about the changes in atomic positions of TM helices
along the simulation and other information about conformational changes in different TMs
(Ferreira et al. , 2012, Prajapati et al., 2013) . Different crystallization conditions, such as
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presence or absence of substrates, inhibitors, nucleotides and different detergents result in
obtaining a spectrum of various conformations of these proteins. Apo-P-gp structures have an
inward-facing conformation as inverted “V” shape for substrate entry, and the outward-facing
conformation for the efflux of substrate to the extracellular space (Palmeira et al. , 2012). A
series of conformational shapes between these two conformations have been assumed to be
involved in the transport mechanism for P-gp molecule (Subramanian et al. , 2016a). However,
based on experimental observations, the secondary structure of P-gp does not change during its
catalytic function (Pan and Aller, 2015). This structure has been shown in figure 1.
2.2 The Drug-Binding Domain (DBD )
In silico findings have revealed similar protein-ligand binding patterns for mouse, rat and
human P-gp in DBD (Jain et al. , 2018). One proposed structure of P-gp in open conformation is
based on the crystal structure of mouse P-gp with the NBDs apart was used for mapping the
binding site of the P-gp inhibitors.
2.2.1 Predicted tariquidar-binding sites 1,2,3 are shown in green, yellow, and red respectively
in figure 1 that are obtained from mutation studies by Loo and Clarke (Loo and Clarke, 2015).
To obtain more information about the above mentioned three different binding sites, molecular
dynamic simulations were implemented based on crystal structures of homologous ABCB1 (P￾gp) proteins. Result from molecular docking analysis was used to determine these binding
pockets and study the transport properties for tariquidar. The predominant intermolecular force
would be Vander Waals interaction, while other characters of these areas (site1 in green, site 2 in
yellow and site 3 in red) are not identical .The average movement of the center of mass for six
independent simulations for each site has been calculated.
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Figure 1- Three sites (DBDs) in the efflux process using molecular dynamic simulation for
tariquidar indicates that site 1 with highest binding energy (−10.1 kcal/mol, color green) could
be more effective than site 2 (-9.1 kcal/mol, color yellow) and site 3 (-8.4 kcal/mol, color red).
The estimated binding energy for highest affinity binding site 1 (intracellular loop) for tariquidar
was found to be −10.1 kcal/mol. These binding energies for verapamil and daunorubicin were -
7.4 and -7.6 kcal/mol respectively. The second docking site for tariquidar was investigated as the
site 2 had an approximated binding energy of −9.1 kcal/mol. These experiments in the third
docking site (site 3) showed a binding energy of −8.4 kcal/mol. This study also emphasized
importance of role of the NBD in the mechanism of tariquidar inhibition (McCormick et al.,
2015). It can be said that the site 1 with highest binding energy to inhibitor (−10.1 kcal/mol)
could be more effective than other sites for inhibitory function. The modulator bound to this site
does not extrude out of the cell in the efflux process and it is not a P-gp substrate.
2.2.2 The intrinsic affinity of P-gp for binding to substrate in the lipid bilayer (Kdlip) can be
approximated by the parameters of Klip (lipid–water partition coefficient) and Kd (apparent
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binding affinity) (equation 1). Figure 2 shows that compounds (yellow shapes) accumulate in the
lipid bilayer because of its high lipid–water partition coefficient in spite of low apparent binding
affinity, (Sharom, 2015) causing increased P-gp binding. Based on Figure 1, inhibitors which act
through DBDs (specially site 1), with high klip (log p) values could be trapped in the lipid bilayer
and not excreted from the cell.
equation [1]
Figure 2.The intrinsic affinity of P-gp for compounds from the lipid bilayer. Compounds (yellow
shapes) containing high Log p value have more accumulation in the lipid bilayer causing to increase P-gp
binding rather than compounds ( pink shapes) with low Log p value.(The figure reproduced with
permission)
2.3 Nucleotide-binding domains (NBD)
Conformational changes of P-gp start at the nucleotide-binding domains once a substrate or
inhibitor enters the different binding domains (figure 3) (Zoghbi et al. , 2017). Function of a
membrane transporter depends on the energy from ATP hydrolysis. It is suggested that binding
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of ATP to the NBD and dimerization of the NBD is a driving force for this function (Scian et al. ,
2014, Szöllősi et al. , 2018). The energy from hydrolysis causes complete conformational
changes in the TMD and catalyzes the efflux of substrate through the TMD and lipid bilayer
(Nagao et al. , 2011). However, in molecular dynamic studies time-frame, the NBDs do not fully
dimerize. This energy also must be used to reset the membrane transporter into its original
conformation (Ferreira et al., 2012). Any ATPase activity of P-gp requires the presence of
phospholipid bilayer (Loo and Clarke, 2015).
Figure 3. Proximity of two NBDs in the P-gp structure during MD simulation as the start of
conformational changes is related to the docked inhibitor (1,4-dihydropyridine) in the drug
binding site.
2.4 ATPase activity
Zosuquidar, elacridar and tariquidar have been reported to inhibit ATP hydrolysis activity of
P-gp and are considered as third generation modulators of P-gp that inhibit drug transport and its
ATPase activity. They are effective at nano molar concentrations. It can be demonstrated that
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inhibition of ATPase activity, by zosuquidar is greater than tariquidar and elacridar (Chufan et al.
, 2016).
It has also been reported that tariquidar inhibits the cross-linking between Cys-431 and Cys-1074
in the two mutant nucleotide-binding sites which are structurally very close and capable of
generation catalytic function so that out-ward shape will not be produced (Loo and Clarke, 2015,
Urbatsch et al. , 2001).
Distance between two cysteine residues, for example Cys607 and Cys1252, in different
conformations of P-gp has been analyzed to obtain more information about NBD changes
(Zoghbi et al., 2017).
Mutagenesis and molecular docking studies- by means of the flexible receptor were utilized and
two structural motifs recognized that were necessary for inhibition of basal ATP hydrolysis.
Formation of these motifs as T-shape aromatic-aromatic interaction by phenylalanines with aid
of tyrosine is interesting (Chufan et al., 2016).
The arrangement of a “cage” of aromatic residues around the ligand, hydrophobic packing and
hydrogen bonding are important interactions that are reported by mutagenesis and molecular
modeling studies (Jagodinsky and Akgun, 2015). These inhibitors interact with P-gp via its DBD
but the NBD site has an important role as the hydrolysis site of the molecule and is related to the
formation of special shapes by aromatic (phenylalanine) residues. Proximity of two NBDs in the
P-gp structure occurs but it is limited by the factors such as steric effect in the presence of potent
inhibitor which should keep conformational change from reaching the outward shape.
Molecular dynamic simulation (our unpublished work) and its analysis showed that seventy￾three percent of residues in the active site were hydrophobic type such phenylalanine. It looks
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like displacement and dynamic of phenylalanine residues around ligand during simulation time
scale is considerable.
2.5 The composition of lipid bilayer membrane
The thickness of the membrane and its other properties such as phospholipid and cholesterol
content have crucial roles in the ATPase activity of P-gp. The 3D structure of these membrane￾embedded proteins are available through crystallographic procedures, and when these membrane
proteins are not embedded in the lipid bilayer, usually perfect information about structural
deformation will not be gained (Ferreira et al., 2012, Prajapati and Sangamwar, 2014). The
presence of cholesterol is also essential for the activity of the P-gp pump (Sharom, 2015).
Molecular dynamic simulation analysis suggested that enhanced activity of P-gp for transporting
substrates can be related to the cholesterol-rich domain of the membrane as accumulation of
substrates occurs in this domain (Subramanian et al. , 2016b). Coarse-grained molecular
dynamics simulation was used to evaluate the effects of bilayer on the function of P-gp. Based
on the results, POPC and POPE lipids from the lower leaflet affect the entrance of substrates to
the cavity of transporter. Positively charged residues have also been recognized to play a key role
in the access of lipids to the cavity of P-gp (Barreto-Ojeda et al. , 2018).
Many deliberations have been reported about the importance of structures such as linker
sequence connecting two P-gp chains and lipid bilayer in maintaining stability of the protein
(Ferreira et al., 2012, Prajapati et al., 2013).
3. Protein-ligand interaction
Data suggest that aromatic/hydrophobic interactions could be the key features in specification
of the binding affinity for substrates/modulators within the drug binding pocket of P-gp.
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These interactions are prominently responsible for ligand binding in most of the cases (Wang et
al. , 2018). The RMSD plot reveals that these interactions remain during molecular dynamic
simulations (Prajapati et al., 2013).
The ability to organize a greater number of hydrophobic and aromatic contacts within the
binding pocket is one of the major features that permit a molecule to block the substrate binding
site competitively. These findings predict that Van der Waals contributions are more favorable
than electrostatic contribution for ligand binding (Ferreira et al., 2012, Prajapati and Sangamwar,
2014, Prajapati et al., 2013), and hydrophobic residues such as PHE have a crucial role in the
stability of the protein-ligand complex at the drug binding site.
Induced fit docking (IFD) analysis has also showed that each compound captures the binding site
in the hydrophobic cavity of P-gp. Jabeen and co-workers reported two important hydrophobic
binding cavities, generated by the amino acid residues of TMDs (Jabeen et al. , 2012).
4. Ligand properties
4.1 General properties
A molecule must be hydrophobic in order to enter into hydrophobic drug binding pocket and
pass the membrane. The binding free energy calculation has also demonstrated that ligand
binding is mainly contributed by hydrophobic terms. Many studies suggest that lipophilicity is
crucial in designing pump inhibitors. In contrast hydrophilic features within the molecule
structure could help in bypassing P-gp efflux (Prajapati et al., 2013).
Recent studies indicate that inhibitors with potential for clinical use should bear several
properties:
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(a) High log P value (defined by the lipid–water partition coefficient for the drug). This
parameter for the compound should be at least 2.92 or higher which is required for formation of
hydrophobic/Vander Waals interaction with P-gp binding site.
(b) A considerable molecular weight is essential and the molecule should have 18 or a higher
number of atoms to cover more than one P-gp binding region.
(c) Highest occupied molecular orbital (HOMO) energy of the molecule should have a high
extent to assure a nucleophilic interaction of the molecule with P-gp.
(d) At least one tertiary nitrogen atom is necessary and this could be an important property for
the candidate P-gp modulators, this tertiary amine generates a cation at the physiological pH and
guarantees the binding through ionic interaction (Wang et al., 2003).
Aromatic rings, molecular weight, cationic charge such as a protonable amine, and H-bond donor
/ acceptor factors are reported from many studies. In general, inhibitors have more log P values
than substrates. These inhibitors act predominantly as H-bond donors rather than H-bond
acceptors. Their HOMO energy is high (Jabeen et al., 2012, Prajapati and Sangamwar, 2014).
Functional groups including Arene, alkyl, carbonyl, ether and nitrogen are predominant moieties
for the generation of strong interactions between protein and inhibitor, thereby affecting the
efficacy and pharmacodynamics aspect of interactions (Table 1) (Gu et al. , 2018, Hu et al. ,
2018, Jain et al., 2018, Li et al. , 2018). Several structure-activity relationship studies have
suggested that lipophilicity and the log P value of the ligands (substrate and inhibitor) are
important parameters affecting pharmacokinetic aspects(Klepsch et al. , 2014).
4.2 potent inhibitorsis
Compounds such as cyclosporine A having a high affinity ranging from -7.9 kcal/mol to -
11.5kcal/mol at binding site are defined as inhibitors that can interact directly with these pumps
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through molecular docking simulation (Ferreira et al. , 2013, Palestro et al. , 2014). The function
of these transporters is disrupted by inhibitors causing accumulation of the substrates such as
rhodamin123 inside resistant tumor cells according to the results of biological assays with
verapamil as a gold standard inhibitor (Yang et al. , 2018). Characteristics of important inhibitors
are illustrated in Table 1.
4.2.1 Natural products
In addition to several synthetic compounds produced using chemical reactions, some natural
products extracted from plants, have been studied for their modulatory properties on P-gp. The
major classes of these structures include alkaloids, coumarins, flavonoids and terpenoids (Bansal
et al. , 2009, Daddam et al. , 2014).In alkaloid structure a basic nitrogen atom and two planar
aromatic rings are the two features that are supposed to be responsible for their modulator
function on P-gp pumps (Abdallah et al. , 2015). A large number of the natural products were
reported to be P-gp inhibitors by blocking of the ATPase activity through NBD which is their
major binding site (Wongrattanakamon et al. , 2016).
For this reason numerous investigations on flavonoids have been performed on this NBD site (Di
Pietro et al. , 2002). Therefore, the intermolecular interaction of these natural products with P-gp
could be different (Bahadur et al. , 2017) and side effects arising from such as interaction with
CYP450 enzymes have been reported.
4.2.2 Tariquidar analogs
Structure of Hoechst 33342 as a P-gp substrate has been used for recognition of the
pharmacophore scaffold of the drugs that bind to P-gp via hydrophobic, H bond acceptor and
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donor sites (Pajeva et al. , 2004).It has been suggested that tariquidar binds to the same binding
sites of P-gp as the P-gp substrate Hoechst 33342 .Based on the structure of Hoechst 33342, the
pharmacophores of tariquidar was proposed (Li et al. , 2015).In recent years QSAR analysis and
model interpretation have been applied to predict new potent structures for analysis of inhibitory
mechanisms (Liu et al., 2013, Wang et al., 2003).
Ekins and co-workers built three-dimensional quantitative structure activity relationship (3D￾QSAR) models using in vitro data and a Catalyst software that predicted IC50 values for P- gp
inhibitors. These inhibition results were then used to generate a new pharmacophore model that
contained a hydrogen bond acceptor, an aromatic ring, and two hydrophobic parts (Ekins et al. ,
2002). Structure and other properties of elacridar are shown in table 1.
4.2.3 (cis-cis) N,N-bis(cyclohexanolamine) aryl ester (2c)
Defined molecular docking (DMD) analyses were performed on human P-gp through its DBD
or NBD. This study indicated that the compound 2c (Table 1) may block the P-gp function by
interacting with the DBD and NBD. This molecule occupied both drug and nucleotide binding
cavities so competitive binding in DBD and prevention of hydrolysis in ATP site would be
effective. It must be mentioned that verapamil (positive control) binds only to the DBD.
In this study a co-docking approach for molecular docking analysis (MDA) is used and
concludes that the compound 2c reduced strong binding of epi (epirubicin) and R123(rhodamine)
to the P-gp pocket. The representing results of the in vitro assay aren’t shown here (Kadioglu et
National Cancer Institute (NCI) has been announced new compound, NSC23925, as potent P￾gp inhibitor which extracted by screening over 2000 small molecules (Duan et al. , 2009, Duan et
al. , 2012). This compound with two chiral centers has four clear enantiomers, shown as
NSC23925a, NSC23925b, NSC23925c, and NSC23925d. Gao and co-workers showed that
NSC23925b as a P-gp inhibitor does not affect the plasma pharmacokinetic properties of the
chemotherapeutic drugs when co-administered with them (Gao et al. , 2016). Interaction with
Cyp405 iso enzymes is negligible.
New1,4-dihydropyridine derivatives containing thiophenyl substitution were also evaluated
as MDR reversing agents in tumor cells and logP value of these compounds was noticeable
(Engi et al. , 2006, Kawase et al. , 2002).
Figure 4-The structure of NSC23925b as a potent P-gp inhibitor
According to the Table 1 and figure 5, structure of P-gp inhibitors has been improved from super
molecule such as cyclosporine A to NSC23925 as a small molecule containing simple structure
with important functional groups lacking unnecessary parts. These molecules have a high
potential for inhibitory activity and less side effects such as interaction with Cyp450 enzymes.
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5. Conclusion
Computational approaches could help gaining more information for the design and synthesis
of effective P-gp inhibitors. Optimal P-gp function necessitates the proximity of two NBDs in
the protein structure. It is also suggested that binding of ATP to NBD is the driving force for P￾gp function. The energy from the hydrolysis causes complete conformational changes in the
protein structure. Three drug-binding domains have been reported for the above-mentioned
function of tariquidar analogs. These findings have suggested that Van der Waals interactions are
more favorable for ligand binding than electrostatic interactions (Jara et al. , 2013). Tariquidar
analogs have been reported to inhibit ATP hydrolysis activity of P-gp. If protein-ligand binding
energy is high (negative) and this binding is stable, the ligand will not be extruded out of the cell
and remain coupled to the pump, there by serving as a pump inhibitor owing to the occupation of
active site of the protein.
Moreover, formation of special shapes, e.g. arrangement of a “cage” of aromatic residues around
the ligand or formation of T-shape motifs by phenylalanines and tyrosine, is also another factor
that contributes to the inhibition of pump activity through steric effect of the proximity of two
NBDs in the P-gp structure. The conformational changes of P-gp after binding to tariquidar may
also lead to the inhibition of cross-linking between the two Cys residues of the two mutant NBDs
of P-gp, thereby causing inhibition of the pump function.
Blocking the pump activity of natural products proceeds only by NBD site .NBD is a general site
and is related to unwanted effects of natural products such as their interaction with CYP
isoenzymes. Inhibitors that act via DBD (and NBD) are better than those acting only on NBD.
One serious obstacle in exploring P-gp inhibitors pertains to pharmacokinetic problems and
interactions with other proteins especially CYP isoenzymes.
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Therefore, designing P-gp inhibitors that lack any interaction with CYP isoenzymes is an ideal
perspective for future research. One possible solution would be through the use of tailored
delivery systems that could release the active P-gp inhibitor in the target site without exposing
the inhibitor to the liver tissue and CYP isoenzymes. Finally, down-regulation of P-gp
expression at the gene levels still remains a viable approach that could mitigate MDR.
This research did not receive any specific grant from funding agencies in the public, commercial,
or not-for-profit sectors.
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