Antimalarial Drug Pyrimethamine Plays a Dual Role in Anti-Tumor Proliferation and Metastasis Through Targeting DHFR and TP

Home , Pyrimethamine

Author Manuscript Published OnlineFirst on January 14, 2019; DOI: 10.1158/1535-7163.MCT-18-0936 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.

Antimalarial drug pyrimethamine plays a dual role in anti-tumor

proliferation and metastasis through targeting DHFR and TP

Huijuan Liu*,#,1,2, Yuan Qin*,1,3, Denghui Zhai*1,3, Qiang Zhang*,1,3, Ju Gu1,3, Yuanhao Tang1,3, Jiahuan Yang1,3, Kun Li1,3, Lan Yang3, Shuang Chen3, Weilong Zhong1,3, Jing Meng1,3, Yanrong Liu3, Tao Sun#,1,3, Cheng Yang#,1,3

1State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy,

Nankai University, Tianjin, China

2College of Life Sciences, Nankai University, Tianjin, China

3Tianjin Key Laboratory of Molecular Drug Research, Tianjin International Joint

Academy of Biomedicine, Tianjin, China

*These authors contributed equally to this work

#Correspondence to: Cheng Yang, email: [email protected]

Tao Sun, email: [email protected]

Hui-juan Liu, email：[email protected]

Running Title: Pyrimethamine anti-tumor proliferation and metastasis

Competing interests

The authors declare no competing interests.

Abbreviations:

Pyr, Pyrimethamine; pDHFR, Plasmodium dihydrofolate reductase; MTX,

Methotrexate; hDHFR, human dihydrofolate reductase; EMT, epithelial–

Downloaded from mct.aacrjournals.org on September 24, 2021. © 2019 American Association for Cancer Research. Author Manuscript Published OnlineFirst on January 14, 2019; DOI: 10.1158/1535-7163.MCT-18-0936 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.

mesenchymal transition; TP, thymidine phosphorylase; RTCA, the real time cell

analyzer; LLC, Lewis lung cancer xenografts; 5UIR, 5-Iodouracil; 5UFR,

5-fluorouracil; MD, Molecular dynamic simulations; ΔGbind, The binding free

energies; OD, the optical density; PI, propidium iodide; TCGA, the Cancer Genome

Atlas

Abstract

Pyrimethamine (Pyr), an antimalarial drug that targeting plasmodium

dihydrofolate reductase (pDHFR), has been proved to have antitumor activity.

However, its direct target on cancer cells remains unclear. Methotrexate (MTX) is a

widely used anticancer drug that blocks human dihydrofolate reductase (hDHFR). In

this work, we examined the anticancer effects of Pyr in vitro and in vivo. Our results

showed that hDHFR and pDHFR have similar secondary and three-dimensional

structures and that Pyr can inhibit the activity of hDHFR in lung cancer cells.

Although Pyr and MTX can inhibit the proliferation of lung cancer cells by targeting

DHFR, only Pyr can inhibit the epithelial–mesenchymal transition (EMT), metastasis

and invasion of lung cancer cells. These results indicated that hDHFR is not the only

target of Pyr. We further found that thymidine phosphorylase (TP), an enzyme that is

closely associated with the EMT of cancer cells, is also a target protein of Pyr. The

data retrieved from the Cancer Genome Atlas (TCGA) database revealed that TP

overexpression is associated with poor prognosis of lung cancer patients. In

conclusion, Pyr plays a dual role in anti-tumor proliferation and metastasis by

targeting DHFR and TP. Pyr may have potential clinical applications for the treatment

of lung cancer.

Key Words

Pyrimethamine, dihydrofolate reductase, thymidine phosphorylase, epithelial–

mesenchymal transition

Introduction

Pyrimethamine (2,4-diamino-5-p-chlorophenyl-6-ethyl-pyrimidine, Pyr) has

been clinically used as antimalarial drugs (1). Pyr exerts its antimalarial effect by

targeting plasmodium dihydrofolate reductase (pDHFR) (2). DHFR is an essential

enzyme in the synthesis of folic acid, which is a cofactor required for DNA synthesis.

In addition to its antimalarial effects, Pyr exhibits the activity of inducing apoptosis of

tumor cells through cathepsin B‐dependent and caspase‐dependent apoptotic

pathways (3, 4). Pyr can also inhibit the STAT3 pathway in breast cancer cells (5).

Pyr also has a broad range of effects in non-small cell lung cancers (6). However, the

target of Pyr has not been elucidated before.

Human DHFR (hDHFR) is a core enzyme in folate metabolism. It plays a key

role in the biosynthesis of nucleic acids and is closely associated with thymidylate

synthase in purine and pyrimidine production (7-9). Given these characteristics,

hDHFR is a crucial target in anticancer drug development. In fact, DHFR inhibitors,

such as methotrexate (MTX), have been applied in cancer treatment (10). The effect

of Pyr on hDHFR has not been previously reported.

MTX is extensively used in chemotherapy for several cancer types, including

lung cancer, leukemia, lymphoma, breast cancer, and head and neck cancers (11-13).

Previous studies showed that MTX treatment may also result in undesirable

side-effects. For example, MTX might induce lethal interstitial lung diseases,

including pulmonary fibrosis in some cases (14). High doses of MTX can also inflict

structural and functional injury to the gastrointestinal tract (15), cause inflammatory

response, and alter absorptive capacity (16-18). Some in vitro studies have shown that

MTX may induce EMT of epithelial cells. MTX can promote the migration and

invasion of RLE/Abca3 cells and increase the expression of TGF-β (19). MTX can

also inflict damage on alveolar epithelial cells and promote the epithelial–

mesenchymal transition (EMT) of epithelial cells (20, 21). During EMT, cells lose

their typical epithelial characteristics and acquire mesenchymal traits (22). Cancer

cells undergoing EMT lose their cell–cell connection, cell–matrix contact, and normal

epithelial polarity while gaining mesenchymal characteristics. These modifications

may enhance the migratory and invasive ability of cancer cells.

Given that hDHFR is a target of antitumor drug development and pDHFR is a

target of Pyr in plasmodium, we firstly investigated whether Pyr demonstrates

antitumor activity by inhibiting hDHFR in tumor cells. We found that Pyr not only

inhibits the proliferation of cancer cells but also suppresses the migration of lung

cancer cells, while MTX could only inhibit the proliferation of cancer cells. These

results suggested that DHFR isn’t the only target of Pyr. We found that Pyr might

play a dual role in anti-tumor proliferation and migration by synergistic targeting

DHFR and thymidine phosphorylase (TP). TP is a nucleoside-metabolizing enzyme

that has a crucial association with tumor migration and invasion (23).

Materials and Methods

Protein sequence alignment and structural analysis

ClustalX was used to blast the primary structure of Human dihydrofolate

reductase (hDHFR) and Plasmodium falciparum Dihydrofolate Reductase (pDHFR).

The secondary structure elements alignment of pDHFR and hDHFR was generated by

the Esprint 3.0 server. Three-dimensional structures were aligned by using PYMOL.

The crystal structures of the hDHFR–MTX complex (PDB code 1u72) and pDHFR–

Pyr complex (PDB code 1j3j) were downloaded from the Protein Data Bank.

Molecular docking was performed using Schrodinger software. MTX in

hDHFR-MTX complex was extracted from crystal structures, and the pocket was used

as the central docking location.

MD simulation

Energy minimizations and MD simulations were performed with the Pmemd

module of the Amber 14 package. To simulate the normal physiological reaction

temperature, the entire MD system was gradually heated to 310 K. Periodic boundary

conditions were used in the NPT ensemble and the SHAKE algorithm was applied to

constrain all covalent bonds that involved hydrogen atoms. The cutoff values for

nonbonded interactions were set at 10 Å. Finally, the RMSD of the initial structure

from the simulated positions was used to evaluate the stability of the entire

simulation.

Binding free energy calculations

The binding free energies (ΔGbind) of the ligands with proteins were calculated

through the MM–PBSA procedure in AMBER14. The binding free energy for each

molecular species (complex, protein, and ligand) was computed by using the

equation ΔGbind = Gcomplex − (Gprotein + Gligand).

Cell culture

The cancer cell lines NCI-H460, NCI-H446, A549, HepG2, MHCC97L, LLC,

MCF-7, ASPC-1, PCNA-1, SGC-7901, HT-29, SW480 and PC-3 were obtained from

KeyGen Biotech (Nanjing, China) in 2013 and authenticated by STR genotyping.

Mycoplasma was analyzed using Mycoplasma qPCR Detection Kit (Sigma) before

experiment. Cells were grown in medium supplemented with 10% fetal bovine serum

(Hyclone, USA) and maintained at 37 °C in a humidified atmosphere containing 5%

CO2.

Cell viability assay

The effects of Pyr and MTX on cell viability were determined through the

MTT（3-(4,5)-dimethylthiahiazo (-z-y1)-3,5-di- phenytetrazoliumromide）assay. Pyr

and MTX were purchased from Meilun Biotechnology Co.,LTD. (Dalian, China), and

the chemical structures of them were showed in Supplementary materials (Fig. S1). A

total of 5×103 cells were seeded in 96-well culture plates. Then, the cells were treated

with various concentrations MTX and Pyr (0-200 µM). After 24, 48, and 72 h of

incubation, the cells were stained with MTT. Then, the culture medium was removed,

and cells were lysed using DMSO. Finally, the optical density (OD) values of the

solution were determined at 570 nm by using a microplate reader (Multiskan™ FC,

Thermo Scientific). Data were analyzed using Graphpad and a log plot of cell viability

(%) against the concentrations of drugs was constructed. The half-maximal inhibitory

concentration was also calculated from the plot.

Real-time cell proliferation monitoring

Cell proliferation assays were performed with the real time cell analyzer (RTCA).

Background impedance was measured with 50 μL of culture medium. NCI-H460 and

A549 cells were seeded into plates (E-plate 16, ACEA Biosciences) with 100 μL of

medium per well. Subsequently, the plates were monitored on the xCELLigence

RTCA Dual Plate instrument (ACEA Biosciences) at 37 °C in a humidified

atmosphere with 5% CO2. Pyr (15 µM) and MTX (30 µM) were added to the plate

after the cells entered the logarithmic growth period. The experiments were repeated

three times.

Live/dead and apoptosis analyses

Live/dead fixable dead cell stain kits (Invitrogen, USA) were used to evaluate

the effect of Pyr on cells in accordance with the manufacturer’s instructions. Cell

viability was analyzed through flow cytometry (Millipore guava easyCyte™).

An Annexin V-FITC/PI apoptosis detection kit（Nanjing Kaiji Biotechnology

Development Co., Ltd.）was also used to evaluate the effect of Pyr on cell apoptosis in

accordance with the manufacturer’s protocol. The cells (1×106) were evenly spread in

a 6-well plate and the drug was added after adherence. After 24 hours, the cells were

collected, Annexin V-FITC and PI were sequentially added according to the

instructions. Experiments were repeated three times.

Wound-healing assay

For the wound-healing assay, NCI-H460 and A549 cells were grown on 24-well

plates to 100% confluence. A 100 μm wound was scratched using sterile pipette tips,

and the exfoliated cells were washed off three times with PBS, and then Pyr (7.5 or 15

μM) or MTX (15 μM) was added to cells cultured in serum-free medium. Cell

migration ability was assessed by measuring the movement of cells in the scratches in

the wells. The wound closure rate after 24 and 48 hours was measured and normalized

to length at 0 hours. After 48 h, images of the wounds were acquired under light

microscopy (Nikon, Japan). The relative length values of the individual wounds were

counted according to the normalized length of 0 hours.

Invasion assays

In this assay, 24-transwell plates (Corning, USA) were used. A total of 5×104

cells were placed on the top chamber inserts, which were coated with Matrigel (BD

Biosciences, New Jersey, USA). After incubation with Pyr (7.5 or 15 μM) or MTX

(15 μM) for 24 h, the cells were stained with 0.1% crystal violet. Invading cells were

visualized and counted in six randomly selected fields under an inverted microscope

(100×).

Western blot analysis

After treatment with different drugs, proteins were extracted from NCI-H460

cells and analyzed through western blot analysis. After the culture medium was

aspirated, each dish was washed with PBS, and protein lysis buffer was added

(containing protease and phosphatase inhibitors) to extract the proteins. The proteins

were separated by 10% polyacrylamide gel electrophoresis, transferred to a

polyvinylidene fluoride (PVDF) membrane (the PVDF membrane was activated by

methanol), and blocked with 5% skim milk. Proteins were incubated with primary

antibodies against β-actin (Affinity, 1:5000), E-cadherin (Affinity, 1:1000), Vimentin

(Affinity, 1:1000 dilution), Ki-67 (Affinity, 1:1000), MEK2 (Affinity, 1:1000), ERK2

(Affinity, 1:1000), and GAPDH (Affinity, 1:5000). The samples were incubated with

primary antibody overnight in a rotator at 4˚C. Blots were further incubated with

HRP-labeled secondary antibodies (Affinity, 1:5000). Finally, target proteins were

visualized using ECL substrate reagents (Millipore, USA).

Immunofluorescent staining

NCI-H460 cells seeded on a cell-climbing slice were incubated for 24 h with Pyr

(7.5 or 15 μM) or MTX (15 μM) in 24-well culture plates. The cells were fixed in 3.7%

paraformaldehyde for 15 min and then treated with 0.1% Triton X-100 for 10 min,

after which the cells were incubated with 3% BSA for 30 min. The cells were then

incubated overnight with primary antibodies at 4 °C. Cells were washed four times

with PBS and incubated for 30 min with secondary antibodies. Finally, the cells were

covered with DAPI for 15 min. Proteins were visualized through confocal microscopy

(Nikon, Japan).

Animal studies

C57BL/6J mice (male, 5-6 weeks old) were maintained in a specific

pathogen-free animal care facility. The mice were allowed to acclimate for 7 days

before the experiment. All animal studies were carried out in accordance with

National Institutes of Health Animal Use Guidelines and the current Chinese

Regulations and Standards for the Use of Laboratory Animals. All animal procedures

were approved on the basis of guidelines of the Animal Ethics Committee of the

Tianjin International Joint Academy of Biotechnology and Medicine. Lung cancer

xenografts were established by subcutaneously injecting 1×107 cells (suspended in

saline) into the flanks of the mice. After the tumors volume reached approximate 100

mm3, the mice were randomly divided into four groups (n = 5). Pyr (7.5 or 15 mg/kg),

MTX (7.5 mg/kg) or saline were orally administered to the mice once a day. Tumor

volume and body weight were measured daily after tumor inoculation. Tumor

volumes were calculated in accordance with the formula V = ab2/2 (a = length, b =

width). After 2 weeks of treatment, all mice were euthanized. The xenografts and

lungs were resected and measured. Metastases in lung tissues were observed by using

a stereoscopic microscope and detected through hematoxylin/eosin staining.

Hematoxylin/eosin staining

Tumor and lung tissues were fixed in 10% formaldehyde, dehydrated, and

embedded in paraffin wax. Then, 4 μm sections of the tissues were stained with

hematoxylin and eosin. Digital images were acquired under microscopy (Nikon,

Japan).

Immunohistochemical analysis

Tissues were deparaffinized and rehydrated through incubation with xylene and

decreasing concentrations of ethanol. Endogenous peroxidase activity was blocked

with 3% hydrogen peroxide. The microwave antigen retrieval technique was used for

antigen retrieval. Samples were incubated overnight with primary antibodies at 4 °C

after blocking with rabbit polyclonal anti-E-cadherin, rabbit polyclonal anti-vimentin,

rabbit polyclonal anti-MMP2, and rabbit polyclonal anti-MMP9. All antibodies were

obtained from Affinity and diluted at the rate of 1:50. Brown-stained cytoplasm,

nuclei, or membranes in cells were considered positive. Staining intensity was scored

as follows: none (0), weak brown (1+), moderate brown (2+), and strong brown (3+).

The percentage of stained cells was divided into five classes: 0 for negative cells, 1

for 1%–25%, 2 for 25%–50%, 3 for 50%–75%, and 4 for >75%.

Biacore assay and protein thermal shift assay (TSA)

Biacore 3000 instrument (GE Healthcare, Piscataway, NJ, USA) was used in the

experiment. TP was immobilized on CM5 sensor chips in accordance with the

instructions provided with the Biacore Amini Coupling Kit. Pyr was diluted in

running buffer at different concentrations and injected into TP-immobilized CM5

sensor chips. The concentrations of Pyr were 0, 0.25, 0.5, 1, 2, 4, and 8 μM. The

surface of the control chip was prepared in the same manner for data correction. BIA

evaluation software was adopted for data analysis.

TSA was performed using SYPRO Orange (Life Sciences) as the shift reporter

dye. Briefly, 11.4 μg of protein was incubated with Pyr at a ratio of 1:10 or 1:20 for

20 minutes, dye was added, and the reactions were monitored in real time (Bio-Rad

MiniOpticon; excitation, 490; emission, 575 nm) from 29°C to 95°C with a rate of

change of 1°C/minute. The melt curve is represented as normalized data and

calculated as d(fluorescence)/d (temperature).

TP activity assay

TP activity was reflected by intercellular thymine concentration, which was

detected through LC–MS–MS (24). NCI-H460 cells were incubated for 24 h with Pyr

(30 μM), 5UIR (30 μM), and MTX (30 μM). Next, 1×107 cells were lysed with

13 15 ice-cold 80% methanol. After centrifugation, 0.05 μg of U- C10 and U- N2

thymidine (Sigma, USA) were added to the supernatant as the internal control. The

polar metabolites in the supernatant were separated, dried, and reconstituted with the

LC mobile phase. Intercellular thymidine level was measured through LC–MS–MS in

the positive-ion mode and expressed as ng/1×107 cells. All experiments were repeated

independently at least twice.

Effect of Pyr on TP induced EMT

The methods of wound-healing assay, invasion assays and westernblot were

same as mentioned above. A549 cells were used in the experiments. Cells were

divided into four groups: control (treated with solvent), TP (treated with TP 10

ng/mL), Pyr (treated with Pyr 15 μM) and Pyr+TP (Pyr 15 μM combined with TP 10

ng/mL).

Proteomics analysis

Proteomics analysis was used to identify the differentially expressed proteins of

A549 cells treated versus non-treated with Pyr (7.5 μM)，which were significantly

regulated (|logFC|>1.5) in the samples treated with Pyr. In order to initially explore

which functions and pathways have changed in the Pyr groups, we used metascape

website (http://metascape.org/) to perform GO and KEGG enrichment analysis.

Protein-protein interaction (PPI) network was analyzed using STRING website

(www.string-db.org/) and Cytoscape software. In order to get more reliable data, we

only chose the interactions of the combination score >0.9. To further study which

proteins play a greater role in the PPI network, CentiScape 2.2 plug-in module of

Cytoscape was performed to calculate the degree of connectivity in the PPI network.

To better understand the biological significance of the PPI network, MCODE plug-in

module was used to select most significant (MCODE score > 10) sub-modules.

DHFR activity assay

Commercially available Human DHFR ELISA Kit (Wuhan Elabscience

Biotechnology Co., Ltd.) was used for assaying of the activity of the DHFR in lung

cancer cells. NCI-H460 cells were used to test the activity of DHFR. The cells (1×106)

were evenly spread in a 6-well plate and the drug was added after adherence. After 24

hours, the cell supernatant was collected, centrifuged at 1000×g for 20 minutes to

remove impurities and cell debris, and the supernatant was collected. Then the activity

of DHFR was tested according to the product manual.

TCGA data analysis

The data of DHFR expression levels was obtained from “Human Protein Atlas”

database (https://www.proteinatlas.org/ENSG00000228716-DHFR/cell). Survival

data of lung cancer patients was downloaded from TCGA. There are 982 lung cancer

patients and 12 normal ones. Overall survival and disease-free survival was analyzed

according to the expression of TP or DHFR in 982 cases of lung cancer patient (using

the KaplanMeier method and evaluated using the log-rank test). According to the data,

the FPKM（fragments per kilobase of exon per million fragments mapped）value of

more than 2.8 is classified as "high", and the FPKM value of less than 2.8 is classified

as “low”. Graphpad was used for mapping.

Results

Pyr exerts an inhibitory effect on lung cancer cells

Pyr is a known inhibitor of pDHFR. However, its effect on hDHFR has not been

verified. We used DHFR assay kits to test the effect of Pyr on hDHFR in lung cancer

cells. Our results showed that both MTX and Pyr could inhibit the activity of DHFR

in lung cancer cells (Fig. 1A). MTX, a clinically used chemotherapy drug targeting

DHFR, exerts an inhibitory effect on different tumor cells. So we detected the

inhibitory effect of Pyr on different tumors cells. Figs 1B and 1C showed the

inhibitory effects of MTX and Pyr on various types of tumor cells in vitro. Our

findings showed that Pyr showed inhibitory activity to a variety of cell lines, such as

MCF-7, NCI-H460, NCI-H446 and so on. The expression levels of DHFR in several

cell lines from the Human Protein Atlas Database are displayed in Fig. 1D. The results

of correlation analysis showed that the half-maximal inhibitory concentration (IC50)

values of MTX and Pyr for cancer cells were positively correlated with the expression

level of DHFR (Figs. 1E and 1F).

pDHFR and hDHFR possess similar three-dimensional structures

We aligned orthologous pDHFR and hDHFR sequences (downloaded from

UniProt) to identify the residues and secondary structures that were shared by these

enzymes. pDHFR and hDHFR shared low amino acid sequence identity (Fig. 2A).

Aligning the secondary and three-dimensional structures of hDHFR and pDHFR

revealed that the structures of the two enzymes are mainly differentiated by an α-helix

(circled in red), which is consistent with previous report (25). The root-mean-square

deviation (RMSD) obtained by aligning the three-dimensional structures of the

proteins was 0.679 (Fig. 2B). On the basis of the alignment results, we docked Pyr

into the active sites of hDHFR and pDHFR. The conformations and orientations

exhibited by Pyr in the active centers of hDHFR and pDHFR are almost identical. The

docking score of Pyr and hDHFR is -7.483, and the docking score of Pyr and pDHFR

is -7.140 (Fig. 2B). Therefore, Pyr may have similar binding capacities for hDHFR

and pDHFR. We ran 50 ns molecular dynamics (MD) simulations for the

complexation of hDHFR with Pyr, pDHFR with Pyr, and hDHFR with MTX. We

analyzed the RMSD values provided by the simulations to illustrate the dynamic

stability of the three complexes and to ensure the rationality of the following analysis

(Fig. 2C). The RMSD of each system tended to converge. This tendency indicated

that the systems are stable and in equilibrium. To further compare the binding of Pyr 16

to hDHFR and pDHFR, we calculated the binding free energies of all three systems

by using the MM-PBSA program in AMBER. As shown in Fig. 2D, the binding

capacities of Pyr for hDHFR and pDHFR are almost the same. The binding capacity

of Pyr-hDHFR complex was weaker than MTX-hDHFR complex. The hydrogen bond

interactions that occur between the drug and protein play an important role in the

binding of the inhibitor to kinase in the three protein–inhibitor systems. Our results

showed that Pyr and MTX formed stable hydrogen bonds with Ile 7, Tyr 121, and Val

115 in hDHFR. The above results suggested that similar to MTX, Pyr can act as a

hDHFR inhibitor.

Pyr inhibits the proliferation of lung cancer cells in vitro

We used the MTT assay to detect the effect of Pyr on cell viability at 24, 48, and

72 h. As shown in Fig. 3A, the IC50 values of Pyr for NCI-H460 cells at 24, 48, and 72

h treatment are 98.17, 64.31, and 37.60 μM, respectively. As shown in Fig. 3B, the

IC50 values of Pyr for A549 cells at 24, 48, and 72 h treatment are 83.37, 40.57, and

28.07 μM, respectively. Next, we used a real-time cell analyzer (RTCA) to

demonstrate the effects of Pyr on the proliferation of NCI-H460 and A549 cells. We

found that Pyr inhibited the proliferation of NCI-H460 and A549 cells in a

dose-dependent manner (Figs. 3C and 3E). We also used the live/dead assay to

explore the effect of Pyr (15 and 30 μM) on NCI-H460 and A549 cells. The

percentage of cell death increased in a dose-dependent manner (Figs. 3D and 3F). We

used an Annexin V-FITC/propidium iodide (PI) kit to examine the effect of Pyr on

cell apoptosis and found that Pyr can effectively induce apoptosis in the NCI-H460 17

and A549 cells in a dose-dependent manner (Figs. 3G and H). The western blot

analysis results also showed that Pyr treatment decreased the expression level of Ki67,

which is a marker of cell proliferation (Fig. 3I).

Pyr can inhibit the migration, invasion, and EMT of lung cancer cell lines

We performed the wound-healing assay to investigate the ability of Pyr to inhibit

the migration of NCI-H460 (Fig. 4A) and A549 (Fig. 4B) cells. The migration ability

of cells increased after 48 h of treatment with MTX. By contrast, wounds were

widened under Pyr treatment. This behavior indicated that Pyr treatment inhibited the

migration of cancer cells. We also detected the effect of Pyr on cell invasiveness (Fig.

4C). The number of cells that invaded through the matrigel-coated filter decreased

under Pyr treatment relative to the control. We used western blot analysis and

immunofluorescent staining to detect the effect of Pyr and MTX on the expression of

EMT markers E-cadherin and vimentin. We found that Pyr decreased the expression

of vimentin and increased the expression of E-cadherin in NCI-H460 cells (Figs. 4D

and 4E), whereas MTX exerted the opposite effect. The same results were observed in

A549 cell lines (Figs. S2 and S3).

Pyr inhibits tumor growth and metastasis in vivo

We examined the effect of Pyr on Lewis lung cancer (LLC) xenografts in

C57BL/6J mice. The body weights of mice in the MTX treatment group decreased

relative to those of mice in the model group. No significant change was noted

between the model group and Pyr treatment group (Fig. 5A). Tumor growth was

suppressed in the MTX and Pyr treatment groups relative to that in the model group

(Figs. 5B and 5C). As shown in Figs. 5D–5F, the number of metastatic tumor nodes

on lung surfaces drastically decreased after Pyr treatment. Meanwhile, the extent of

lung metastasis increased after MTX treatment. Immunohistochemical results of

tumor tissues revealed that E-cadherin expression levels were higher in the Pyr

treatment group than those in the control groups and the expression levels of vimentin,

MMP2, and MMP9 decreased in the Pyr treatment groups (Figs. 5G). Western-blot

analysis showed the same results (Fig. S4).

Pyr targets thymidine phosphorylase (TP) and inhibits its activity

Pyr could not only inhibit the proliferation of lung cancer cells like MTX, but

also inhibit EMT, migration, and invasion of lung cancer cells. Thus, we speculated

that Pyr may have another EMT-associated target in tumor cells. Pyr is a pyrimidine

analog. Thymidine phosphorylase (TP) plays an important role in tumor migration,

and invasion. The chemical structures of Pyr and thymidine were similar. So we

hypothesized that TP may be another target of Pyr. We performed molecular docking

simulations to compare the binding scores of the TP inhibitors (TPI, 5-Iodouracil, and

5-fluorouracil), Pyr, and MTX. We found that Pyr and TP inhibitors have similar

docking scores and that MTX cannot enter the active center of TP (Fig. 6A and Fig.

S5). We used LC–MS–MS to detect thymine concentration in cells treated with 5UIR

and Pyr, which can reflect TP activity,. The results showed that Pyr inhibited the

activity of TP (Fig. 6B). Moreover, we verified the interaction between Pyr and TP

through the Biacore assay (Kd=6.19 ± 0.78 μM) (Fig. 6C). The TSA assay also 19

showed that Pyr could bind with TP (Figure S6).

To further explore the inhibitory effect of Pyr on TP, we conducted a

wound-healing assay. Our results showed that TP induces the migration and invasion

of lung cancer cells. Pyr inhibited the TP-induced migration and invasion of cancer

cells (Figs. 6D and 6E). Compared with the control treatment, TP promoted the

expression of ERK2 and MEK2, whereas Pyr suppressed the expression of ERK2 and

MEK2 (Fig. 6F). TP increased the expression of vimentin and decreased the

expression of E-cadherin, and Pyr reversed the changes of EMT markers, which

showed that Pyr inhibited the EMT induced by TP (Fig. 6F).

Effects of Pyr on proteomics profiles of lung cancer cells

Proteomics analysis was used to identify the differentially expressed proteins of

A549 cells treated or non-treated with Pyr. Gene Ontology (GO) analysis results

showed that the differential proteins were enriched in the functions of pyridine

nucleotide metabolic process, apoptotic signaling pathway, regulation of cell cycle

G2/M phase transition, cell cycle phase transition, and extracellular matrix

organization. The KEGG pathway analysis revealed that the differential proteins were

mainly involved in several pathways, including Programmed Cell Death, Focal

adhesion, Extracellular matrix organization, Collagen formation, Collagen

degradation, and Cell cycle pathway. Protein-protein interaction (PPI) network was

shown in Fig. 7B. The hub proteins were marked in red, such as HSP90AA1, CKAP5,

NEDD4L, and CPSF1. The sub-networks (MCODE score > 10) from PPI network

were shown in Figs. 7C-E. The functions of the sub-networks mainly associated with

cell cycle phase transition, protein ubiquitination, collagen degradation, and nucleic

acid binding. These results indicated that Pyr affected not only the

proliferation-related pathways (eg. pyridine nucleotide metabolic process, apoptotic

signaling pathway, and Cell cycle pathway) of tumor cells, but also migration and

invasion-related pathways (eg. Focal adhesion, Extracellular matrix organization,

Collagen formation, and Collagen degradation) of tumor cells, which is consistent

with the functions of Pyr observed in vivo and in vitro.

DHFR and TP are associated with lung cancer malignancy

We analyzed the expression of DHFR and TP in tissues from 982 patients with

lung cancer included in the TCGA database. We found that the expression levels of

DHFR and TP in lung cancer tissues were significantly higher than that in normal

human lung tissues (Figs. 8A and 8B). The results from the ULCAN database

revealed that the mRNA levels of the two proteins in lung cancer tissues were

elevated relative to those in normal lung tissues (Fig. 8C). We also analyzed the

samples in the TCGA database on the basis of pathology grade and clinical stage. The

mRNA expression of DHFR was positively correlated with clinical phase I, clinical

phase II, and clinical phase III. And the mRNA expression of TP was positively

correlated with clinical phase II and clinical phase III (Fig. 8D). We analyzed the

effect of DHFR and TP expression on survival status. DHFR and TP overexpression

were associated with poor prognosis (Figs. 8E–G). To further investigate the

relationship between DHFR/TP expression and EMT, we analyzed the correlation 21

between the mRNA expression levels of DHFR/TP and EMT markers E-cadherin

(gene name: CDH1) and vimentin (gene name: VIM). We found that TP was

positively correlated with vimentin expression and negatively correlated with

E-cadherin expression. However, the expression levels of DHFR and EMT markers

were not correlated (Fig. 8H).

Discussion

Pyrimethamine (Pyr) is a pyrimidine derivative, which interferes with the

regeneration of tetrahydrofolic acid from dihydrofolate by targeting DHFR of the

plasmodium. Because pDHFR and hDHFR possess similar three-dimensional

structures, so Pyr was used for anti-cancer drug research. Our results showed that Pyr

could bind to hDHFR, but the binding capacities of Pyr and hDHFR was weaker than

MTX and hDHFR. We found that Pyr could effectively inhibit the proliferation of

many cancer cell lines, and the effect is equivalent to MTX in vitro, which suggested

that DHFR was a driving force for tumor cell proliferation, and even mild inhibition

could significantly affect the proliferation of cells. Besides, we found that Pyr

inhibited the EMT, migration, and invasion of lung cancer cells. We further

demonstrated that TP might be another target protein of Pyr, which plays an important

role in EMT.

DHFR, a folate-dependent enzyme that is related to DNA synthesis in cancer

cells, has become a crucial target enzyme of antitumor drugs (26). DHFR positively

regulates the proliferation of tumor cells, and its expression is markedly elevated in

tumor cells. MTX is an antitumor drug that targets DHFR and exhibits inhibitory

activity against lung cancer, breast cancer, acute leukemia, and other malignancies

(27-30). Pyr is an antimalarial drug targeting plasmodium dihydrofolate reductase

(pDHFR). It can induce tumor cell apoptosis through the bilateral mechanisms of

caspases and cathepsins (3). Pyr can also inhibit tumor growth by regulating the

activity of matrix metalloproteinases (MMPs) and telomerase (4, 31). Pyr can

influence the activity of STAT3 in TUBO and TM40D-MB metastatic breast cancer

cells (5). The target protein of Pyr in human cancer cells has not been reported. Our

results showed that the tertiary structure of pDHFR is highly similar to that of hDHFR.

Pyr can block the proliferation of tumor cells by binding to hDHFR.

Although MTX can inhibit the proliferation of tumor cells, it induces some

adverse side effects. Methotrexate (MTX) can lead tco alveolar epithelial cell injury

followed by pulmonary fibrosis as a result of the recruitment and proliferation of

myofibroblasts. MTX induces the EMT-like phenotype of A549 cells accompanied by

increased interleukin-6 (IL-6) and transforming growth factor (TGF)-β1, and enhance

the migration of A549 cells (20, 21). MTX can also induce the EMT of type II

alveolar epithelial RLE/Abca3 cells like TGF-β1 in vitro (19). Our results showed that

low doses of MTX can cause the migration and invasion of lung cancer cells and

promote EMT of A549 and NCI-H460 cells in vitro. In LLC xenografts in C57BL/6J

mice, MTX increased the metastatic tumor nodes on lung tissue.

We found that Pyr not only inhibits the proliferation of lung cancer cells but also

blocks the EMT, migration, and invasion of lung cancer cells. Therefore, we 23

speculated that Pyr inhibited the EMT of lung cancer cells through other target. The

chemical structure of Pyr is similar to that of thymidine, a substrate of TP, which

indicate that TP may be a target of Pyr. The molecular docking simulations and

Biacore assay results revealed that Pyr has binding ability with TP. Pyr can also

inhibit the enzymatic activity of TP.

TP is closely related to the migration, invasion, and EMT of tumor cells and is an

important enzyme in the pyrimidine pathway. TP expression in tumor tissue is

elevated relative to that in normal tissue, and low TP expression is associated with

prolonged patient survival (32, 33). TP can stimulate the migration of human

endothelial cells by specifically activating integrins α5β1 and αVβ (34). TP exerts a

chemotactic effect on endothelial cells in vitro, induces tumor angiogenesis, and

promotes tumor cell migration in vivo (35-37). TP facilitates cell matrix degradation

and tumor invasion by promoting MMP2/9 expression. TP affects the expression of

MMPs through the MAPK/Erk2 pathway (38). Given that the activation of the Erk

pathway plays an important role in EMT (39), TP may also influence the EMT of

cancer cells. In this work, we verified that TP could induce the EMT of lung cancer

cells. Because the induction of EMT is the primary mechanism by which epithelial

cancer cells acquire malignant phenotypes that promote metastasis, TP may become a

target for the development of anti-tumor metastasis drugs. In this work, we found that

Pyr inhibits TP-induced ERK2 and MEK2 expression and that Pyr reverses the EMT

of cancer cells induced by TP. The results of the TCGA data analysis indicated that

lung cancer patients with high TP expression have poor prognoses and suggested that

TP can be a target in the development of drugs against lung cancer.

In conclusion, Pyr not only targets DHFR to repress the proliferation of lung

cancer cells but also inhibits EMT of lung cancer cells through

TP/MEK2/ERK2/MMPs pathway and thereby impeding the migration and invasion of

tumor cells (Fig. 8I). Pyr may have potential clinical applications as a novel dual

effective anti-lung cancer drug.

Acknowledgments

This study was founded by Foundation for National Natural Science Funds of

China (Grant No. 81572838 and 81703581), National Science and Technology Major

Project (Grant No. 2018ZX09736005), Tianjin science and technology innovation

system and the condition of platform construction plan (Grant No.14TXSYJC00572),

Post doctoral innovative talent support program (Grant No. BX20180150).

Author contribution

T. Sun and C. Yang developed the original hypothesis and experimental design. H.

Liu, Y. Qin, and L.Yang performed in vitro experiments. D. Zhai, J. Yang and Q.

Zhang carried out animal studies. J. Gu, Y. Tang, and W. Zhong did the molecular

docking simulation and proteomics analysis. Y. Liu and J. Meng did the

immunochemical staining and Hematoxylin/eosin staining of tissues. H. Liu, Y. Qin,

and S. Chen acquired and analyzed data. H. Liu and Y. Qin wrote the manuscript. All

read and approved the final manuscript.

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Figure Legends

Figure 1. Pyr exerts an inhibitory effect on various types of tumor cells, which is positively correlated with the expression level of DHFR. (A) DHFR activity of NCI-H460 cells under Pyr or MTX treatment. The experiment was performed in triplicate. Results are shown as means ± SD (**P < 0.01). (B) Inhibition rate of MTX (50 µM) for different cancer cell lines. (C) Inhibition rate of Pyr (50 µM) for different cancer cell lines. (D) Expression level of DHFR in different cancer cell lines obtained from the Human Protein Atlas Database. (E) Correlation between the inhibition rate of MTX and the expression level of DHFR in different cancer cell lines. (F) Correlation between the inhibition rate of Pyr and the expression level of DHFR in different cancer cell lines.

Figure 2. Pyr can bind to human DHFR (hDHFR). (A) Alignment of the hDHFR and pDHFR sequence through the Esprint 3.0 server. (B) Three-dimensional structure alignment of hDHFR and pDHFR (RMSD) and the major differences between the two proteins are marked with red circles. Binding mode of Pyr during docking in the active site of hDHFR and pDHFR ( hDHFR-Pyr are shown in blue, and pDHFR-Pyr are shown in yellow.). (C) Analysis of RMSD values of Pyr–hDHFR, Pyr–pDHFR, and MTX–DHFR complexes. (D) Binding free energies of Pyr–hDHFR, Pyr–pDHFR, and MTX–DHFR complexes calculated using the MM-PBSA program in AMBER.

Figure 3. Pyr can inhibit the viability and proliferation of lung cancer cells in vitro. (A) Survival rates of NCI-H460 cells treated for 24, 48, and 72 h with Pyr. (B) Survival rates of A549 cells treated for 24, 48, and 72 h with Pyr. (C) Real-time proliferation curve of NCI-H460 cells treated with 15 and 30 μM Pyr assayed with a real-time cell analyzer (RTCA). (D) Proportion of dead NCI-H460 cells after treatment with 15 and 30 μM Pyr detected with the live/dead assay kit. (E) Real-time proliferation curve of A549 cell under treatment with 15 and 30 μM Pyr assayed by the RTCA. (F) Proportion of dead A549 cells after treatment with 15 and 30 μM Pyr detected with the live/dead assay kit. (G & H) Effect of Pyr on cell apoptosis detected by Annexin

V-FITC/PI kit. (I) Effect of Pyr on the marker of cell proliferation Ki67 as detected through western blot analysis. Each experiment was performed in triplicate. Results are shown as means ± SD (*P < 0.05, **P < 0.01).

Figure 4. Pyr inhibits the migration, invasion, and EMT of lung cancer cells. (A) Effect of Pyr or MTX on the migration of NCI-H460 at 24 and 48 h. (B) Effects of Pyr and MTX on the migration of A549 cells at 24 and 48 h. (C) Transwell chambers were utilized for the invasion assay, and images were obtained under 200× magnification. NCI-H460 and A549 cells were treated with Pyr or MTX. (D) Changes of E-cadherin and vimentin expression in NCI-H460 cells treated with Pyr or MTX (Western blot assay). β-actin was used as the loading control. (E) Changes of E-cadherin and vimentin expression in NCI-H460 cells treated with Pyr or MTX (immunofluorescence assay). Each experiment was performed in triplicate. Results are shown as means ± SD (*P < 0.05, **P < 0.01).

Figure 5. Pyr can inhibit tumor growth and metastasis in Lewis lung cancer (LLC) xenografts, whereas MTX can only inhibit the tumor growth. (A) Body weight (g) changes in the animals with LLC xenografts after treatment with Pyr or MTX. (B) Changes in the tumor volume of LLC xenografts after treatment with Pyr or MTX. (C) Representative images of LLC xenograft tumor tissues treated with Pyr or MTX. (D & E) Number of metastatic tumor nodes in lung tissues. The metastasis of LLC xenografts is inhibited by Pyr but is promoted by MTX. (F) Pathological sections of metastatic tumor nodes in lung tissues observed through hematoxylin/eosin staining (40×). (G) Effect of Pyr and MTX on the expression of EMT markers in LLC xenograft tumor tissues, as observed through immunohistochemistry analysis (40×). Brown or yellow staining was considered as positive expression. Each experiment was performed in triplicate. The results are shown as means ± SD (*P < 0.05, **P < 0.01).

Figure 6. Pyr can bind to TP and inhibit TP-induced migration, invasion, and EMT of lung cancer cells. (A) Molecular docking results for TP and Pyr. (B) Thymine

concentration of NCI-H460 cells treated with 5-UIR, Pyr, and MTX. Intercellular thymine concentration was used as an index of TP activity. (C) Interaction between

Pyr and TP verified through Biacore assay (Kd=6.19±0.78 μM). (D) Pyr can inhibit

the TP-induced migration of cancer cells. Wound-healing assay was used in this experiment. (E) Pyr can inhibit the TP-induced invasion of cancer cells. Transwell chambers were utilized for the invasion assay, and images were obtained under 200× magnification. (F) E-cadherin, vimentin, MEK2, and ERK2 expression levels of NCI-H460 cells in different treatment groups. The GAPDH blot served as the loading control. Data are presented as the means of three experiments, and error bars represent the standard deviation (*P < 0.05, **P < 0.01)

Figure 7. The effect of Pyr on proteomics profiles of A549 cells. (A) Gene Ontology (GO) analysis and KEGG analysis results of the differentially expressed proteins in Pyr treated cells. (B) Protein-protein interaction (PPI) network of the differentially expressed proteins (the interactions of the combination score >0.9). The hub proteins were marked in red. (C-E) The three sub-networks (MCODE score > 10) obtained from PPI network.

Figure 8. TP and DHFR are associated with lung cancer prognosis. (A) Expression levels of DHFR protein in normal human lung tissues (n=6) and lung cancer tissues (n=36). (B) Expression levels of TP protein in normal human lung tissues (n=6) and lung cancer tissues (n=46). (C) mRNA expression levels of DHFR and TP in normal human lung tissues (n=12) and lung cancer tissues (n=982). (D) Relationship between the mRNA expression level of DHFR/TP and the clinical stage of lung cancer patients. (E-G) Effect of the mRNA expression levels of TP and DHFR on the median survival time of patients with lung cancer. TP and DHFR are associated with lung cancer prognosis. (H) Relationship of TP and DHFR expression level with EMT markers expression. There is a correlation between the mRNA expression of TP and EMT markers. (I) The simplified schematic diagram of Pyr and MTX anti-tumor mechanism. The data of DHFR expression levels was obtained from “Human Protein

Atlas” database. Survival data of lung cancer patients was downloaded from TCGA. Results are shown as means ± SD (*P<0.05, **P < 0.01, ***P<0.001).

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Antimalarial drug pyrimethamine plays a dual role in anti-tumor proliferation and metastasis through targeting DHFR and TP

Huijuan Liu, Yuan Qin, Denghui Zhai, et al.

Mol Cancer Ther Published OnlineFirst January 14, 2019.

Updated version Access the most recent version of this article at: doi:10.1158/1535-7163.MCT-18-0936

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