Aldose reductase from Schistosoma japonicum: crystallization and structure-based inhibitor screening for discovering antischistosomal lead compounds
© Liu et al.; licensee BioMed Central Ltd. 2013
Received: 18 December 2012
Accepted: 22 May 2013
Published: 5 June 2013
Schistosomiasis is a neglected tropical disease with high morbidity and mortality in the world. Currently, the treatment of this disease depends almost exclusively on praziquantel (PZQ); however, the emergence of drug resistance to PZQ in schistosomes makes the development of novel drugs an urgent task. Aldose reductase (AR), an important component that may be involved in the schistosome antioxidant defense system, is predicted as a potential drug target.
The tertiary structure of Schistosoma japonicum AR (Sj AR) was obtained through X-ray diffraction method and then its potential inhibitors were identified from the Maybridge HitFinder library by virtual screening based on this structural model. The effects of these identified compounds on cultured adult worms were evaluated by observing mobility, morphological changes and mortality. To verify that Sj AR was indeed the target of these identified compounds, their effects on recombinant Sj AR (rSj AR) enzymatic activity were assessed. The cytotoxicity analysis was performed with three types of human cell lines using a Cell Counting Kit-8.
We firstly resolved the Sj AR structure and identified 10 potential inhibitors based on this structural model. Further in vitro experiments showed that one of the compounds, renamed as AR9, exhibited significant inhibition in the activity of cultured worms as well as inhibition of enzymatic activity of rSj AR protein. Cytotoxicity analysis revealed that AR9 had relatively low toxicity towards host cells.
The work presented here bridges the gap between virtual screening and experimental validation, providing an effective and economical strategy for the development of new anti-parasitic drugs. Additionally, this study also found that AR9 may become a new potential lead compound for developing novel antischistosomal drugs against parasite AR.
Schistosomiasis is a major tropical disease in developing countries. It is estimated that over 200 million people from 76 countries and territories are suffering from this disease . The disease is usually caused by one of three schistosome species: Schistosoma japonicum, Schistosoma mansoni and Schistosoma haematobium. In China, S. japonicum is the primary pathogen of this disease . Currently, the treatment of schistosomiasis depends almost exclusively on praziquantel (PZQ), and this drug has been widely used for nearly 40 years because of its high efficacy but low cost . However, the long-term utilization of one drug can result in drug-resistant parasites. Decreased susceptibility of S. mansoni and S. haematobium to PZQ has already been identified in previous studies [4, 5]. Although no reduced susceptibility of S. japonicum has been proven to date, the efficacy of this drug is found to vary in different strains within this species . Therefore there is an urgent need to develop novel antischistosomal lead compounds, and the identification of ideal drug targets is an important step toward this goal.
Antioxidant defense is an essential mechanism for schistosomes to cope with damage from host immune- and self-generated reactive oxygen species (ROS) . Many redox-associated proteins such as thioredoxin glutathione reductase (TGR), peroxiredoxin (Prx) and thioredoxin (Trx) have been demonstrated to be involved in this system in previous studies [8–11]. Most of these proteins are considered as potential drug targets, as one example, two recently discovered prospective antischistosomal compounds, auranofin and oxadiazoles, were developed with TGR as drug target [9, 12]. Although no research has shown that S. japonicum AR participates in the antioxidant pathway, in other organisms, AR is believed to be an important antioxidant component. Spycher et al. found that the levels of AR mRNA were up-regulated under oxidative stress in rat smooth muscle cells. Furthermore, the levels of AR expression as well as its activity were increased during hyperglycemia and other oxidative stress-induced diseases in humans [14, 15]. Additionally, many byproducts of oxidative stress, such as methylglyoxal and 3-deoxyglucosone, have been shown to be excellent substrates of AR . Considering both these conclusions and the antioxidant requirement of schistosomes, it is reasonable to speculate that Sj AR might also participate in the antioxidant pathway and protect the worms from host ROS attack. In addition to the above, AR has also been demonstrated to play an important role in aldehyde detoxification, steroid metabolism, energy supply, cellular proliferation, apoptosis and senescence [17–20]. Its multiple functions suggest that it may represent a key enzyme in schistosomes.
In the present study, we successfully resolved the tertiary structure of recombinant Sj AR and identified 10 inhibitor candidates through molecular docking based on the obtained structural model. We then assessed the activity inhibition of these compounds on cultured worms. To further confirm that the Sj AR protein was indeed the target of the selected compounds, we investigated the effect of the identified compounds on the enzymatic activity of recombinant Sj AR (rSj AR). The cytotoxicity of the active compounds towards the host cell was evaluated as well. Finally, one compound, renamed as AR9, was determined to effectively inhibit the activity of cultured worms but show relatively low cytotoxicity against host cells, which suggests its potential use as a lead compound from the selected candidate inhibitors. The work presented here bridges the gap between virtual screening and experimental validation, providing an effective and economical strategy to develop novel anti-parasitic drugs.
Protein crystallization kits were purchased from Hampton Research Corporation (USA). NADPH was obtained from Roche (Switzerland). DL-glyceraldehyde and PZQ came from Sigma (USA). Small molecules identified by virtual screening were purchased from Maybridge HitFinder library (USA). RPMI 1640, DMEM and bovine serum (Newborn calf serum and fetal bovine serum) came from Invitrogen (USA). The recombinant Sj AR-pET28a plasmid was constructed previously and stored in our laboratory. BL21 (DE3) and Hep G2 cells were also stored in our laboratory. 293T and HeLa cell lines were kindly provided by Hongyan Wang (School of Life Sciences, Fudan University, China). S. japonicum cercaria was provided by the pathogen biology laboratory of the National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention. Specific pathogen-free Kunming female mice were purchased from the Shanghai Experimental Animal Center, Chinese Academy of Sciences (China).
Expression and purification of rSj AR
The recombinant plasmid Sj AR-pET28a was transformed into E. coli BL21 (DE3) cells and cultured in Luria-Bertani (LB) medium plus 50 μg/ml kanamycin. Isopropylthio-β-D-galactoside (IPTG), 1 mM, was added to the medium to induce protein expression, and then the cells were cultured for an additional 6 h. The cells were harvested by centrifugation, and pellets were resuspended in lysis buffer (20 mM Tris–HCl, 500 mM NaCl, 1 mM PMSF, pH 8.0). Subsequently, the cells were disrupted by ultrasonic waves for 5 min in 2 s pulses at 160 W. The whole cell lysate was clarified by centrifugation at 10,000 × g for 30 min at 4°C. The resulting supernatant was purified sequentially using immobilized metal ion affinity chromatography, anion-exchange chromatography, and finally, size-exclusion chromatography. The purified protein was stored in 20 mM Tris–HCl (pH 6.2), 100 mM NaCl, 5 mM DTT. The rSj AR protein was concentrated by ultrafiltration using Millipore Ultrafiltration System with a molecular weight cut off at 10 KDa. Protein concentration was determined by a Bradford Protein Assay Kit (Glory, USA).
Initial crystallization conditions were screened in Tissue Culture Test Plates 24 (TPP) by the hanging-drop method at 291 K, using the sparse-matrix method  implemented in the Crystallization Screens Kits (included Index, Crystal Screen, Crystal Screen 2, PEG/Ion Screen and PEG/Ion 2 Screen and SaltRx) from Hampton Research. Three protein concentrations were adopted: 24 mg/ml, 12 mg/ml and 6 mg/ml. A total of 1 μl protein solution was mixed with 1 μl well solution and equilibrated against 200 μl reservoir solution. Crystallization leads were identified in over 10 of these conditions. One initial condition (PEG/Ion Screen: 0.2 M Sodium fluoride, 20% w/v Polyethylene glycol 3,350, pH 7.3), which produced single crystals, was optimized to obtain crystals suitable for diffraction analysis. The final optimal conditions were 12 mg/ml protein and a reservoir solution consisting of 0.2 M Sodium fluoride, 30% w/v, Polyethylene glycol 3,350 (pH 7.1).
Data collection and processing
Crystals were flash-cooled in liquid nitrogen with a cryoprotectant containing only reservoir solution. Diffraction data were collected at Beamline BL17U at the Shanghai Synchrotron Radiation Facility and processed with the package HKL-2000 using routine procedures . The initial phases were calculated in the program PHASER , from the CCP4 suites, using a structure known H. sapiens AR (Hsa AR, PDB ID: 1ZUA) as a search model. The final model was manually built with COOT . All computational refinements were performed using the refinement module phenix.refine of the PHENIX package . The model quality was checked with the PROCHECK program, which showed good stereochemistry according to the Ramachandran plot for the structure.
To identify potential inhibitors of Sj AR, the Maybridge HitFinder library, which contains approximately 80,000 compounds, was chosen for in-silico screening with the model of the rSj AR protein. Molecular docking was firstly performed with Sybyl v8.0 Surflex-Dock (http://www.tripos.com) followed by docking the top 5% hits with AutoDock 4.2 (http://autodock.scripps.edu/). The top 100 scoring compounds were selected out and exported to an Excel spreadsheet. To increase the selectivity of these compounds, they were also docked into the Hsa AR protein. The final obtained compounds conformed to the following principles: 1) the Sj AR protein-compound binding free energy was lower than −9 kCal/mol; and 2) the compound showed a greater binding preference to the Sj AR protein than to Hsa AR (the difference of binding free energy was higher than 2 kCal/mol).
Inhibition studies on cultured worms
Mice infected with 80–100 cercariae were killed at 35 days-post-infection for worm collection. S. japonicum adult worms were obtained by perfusion and washed three times with sterile saline. Next, the worms were transferred to RPMI 1640 medium containing 300 μg/ml penicillin, 300 μg/ml streptomycin, 0.25 μg/ml amphotericin and 20% fetal bovine serum and then cultured for 2 h to make the worms discharge their gut contents. Two pairs of worms with good activity were selected and transferred to each well of a 24-well plate containing 2 ml of the preceding culture medium. Stocking solutions of compounds were prepared by dissolving 2 mg of the compounds in 0.4 ml dimethyl sulfoxide (DMSO) and then were added to a series of final concentrations (for initial screening, three concentrations of 5 μg/ml, 25 μg/ml and 50 μg/ml were assessed, while for the second screening, five concentrations of 1.25 μg/ml, 2.5 μg/ml, 5 μg/ml, 10 μg/ml, and 20 μg/ml were assessed). The worms in the control group were treated with equal amounts of the compound carrier. A PZQ treated group was also observed as a positive control. The test was repeated three times, and for each experimental condition, 12 worms in 3 wells were tested.
The worms were cultured at 37°C in an incubator with 5% CO2. The worm mobility, morphological changes and mortality were observed under an inverted microscope at 2 h, 24 h, 48 h and 72 h. Parasite death was defined as non-detectable activity in 2-minutes, accompanied by morphological and tegumental alterations . The median lethal concentration (LC50) values for the identified active compounds were calculated by the software SPSS 18.0, with a confidence interval of 95%.
Effect of compound AR9 on rSj AR enzymatic activity
The enzymatic assay was described previously . Briefly, the reaction was performed in 120 mM PBS buffer (pH 6.2), containing 1.5 mM DL-glyceraldehyde, 0.15 mM NADPH and 0.15 μM rSj AR in a final volume of 200 μl. The mixture was first incubated at 37°C for 5 min, and then the reaction was initiated by adding the substrate of NADPH. For inhibition analysis, AR9 was added to the same reaction system to final concentrations of 5 μg/ml, 10 μg/ml, 20 μg/ml and 40 μg/ml. The reaction process was determined by monitoring the absorbance reduction at 340 nm due to the depletion of NADPH using a Model 680 Microplate Reader (Bio-Rad, USA).
Scanning electron microscopy (SEM)
Schistosome samples were fixed with 2.5% glutaraldehyde in PBS buffer for 2 h and were then washed thoroughly three times with PBS buffer. The samples were fixed again in 1% osmium tetroxide in PBS buffer. After ethanol dehydration and critical point drying, they were mounted on microscope stubs, followed by gold sputtering for 3 min in an IB-3 ion-sputtering instrument. The SEM scanning was performed on an S-520 SEM (Hitachi, Japan) instrument with an accelerating voltage of 20 kV .
Cytotoxicity analysis was performed with three types of human cell lines (Hep G2, 293T and Hela cell lines) using a Cell Counting Kit-8 according to the protocol provided by the manufacturers (Beyotime, China). Briefly, the cells were cultured in a 96-well plate containing 100 μl DMEM medium (containing 10% fetal bovine serum) at a density of 5,000 cells per well at 37°C in 5% CO2. The cells were allowed to recover for 24 h and then exposed to various concentrations of compound or compound-carrier. When the cells in the negative control group (carrier alone) covered more than 90% of the surface of the well, 10 μl of WST-8 chromogenic agent was added to each well and then continuously incubated for 30 min. The absorbance at 450 nm was determined by using a Model 680 Microplate Reader (Bio-Rad, USA).
The animal work was approved by the Ethics Committee of the National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention in Shanghai, China (Ref No: 20100525–1). Animal care and all procedures involving animals were performed in strict accordance with the Guidelines for the Care and Use of Laboratory Animals of the Ministry of Science and Technology of People’s Republic of China (398). All efforts were made to minimize suffering.
Structure determination and description
X-ray data-collection and structure refinement statistics
Data collection and processing
Unit cell parameters a, b, c (Å, °)
a = 67.49, b = 91.00, c = 54.67
Resolution range (Å)1
Average B factor, (Å2)
RMSD from ideal geometry, bonds (Å)
RMSD from ideal geometry, angles (°)
Residues in the Ramachandran plot
Most favored region (%)
Allowed region (%)
Generously allowed region (%)
Disallowed region (%)
Structure-based virtual screening
The finally obtained 10 candidate compounds analyzed with AutoDock 4.2
Inhibition studies on cultured worms
Compound AR9 target validation
The antioxidant defense system plays a key role in the physiological functions of an organism . For schistosomes, there have been many studies showing that this system protects the worms from host ROS attack; therefore, the associated enzymes are usually considered to be potential drug-discovery targets [11, 33]. S. japonicum aldose reductase, an important enzyme involved in this system, was predicted as a potential drug target. In this study, we firstly obtained the Sj AR crystal structure through the X-ray diffraction method, on which a virtual screening and experimental validation strategy was applied to screen antischistosomal lead compounds. Finally, one compound, renamed as AR9, was determined to have effective antischistosomal activity but relatively low cytotoxicity towards host cells, which suggested that it has the potential as a lead compound from our selected candidate inhibitors for further drug development.
In this study, we also tested the enzyme inhibition for all of the 10 small molecule compounds (Compound AR8 was not analyzed because of its low solubility) and we tried to find whether there was a positive correlation between enzyme inhibition and parasite growth inhibition. The results showed that, besides AR9, compounds AR1, AR3, AR5 and AR6 also exhibited a certain degree of inhibition on rSj AR enzymatic activity (for AR1, AR3 and AR5, the IC50 values were less than 10 μg/ml, while for AR6, the IC50 value was greater than 20 μg/ml). However, none of these compounds showed significant inhibitory activity on the cultured worms, except that AR6 resulted in 75% mortality in 72 h at a concentration of 50 μg/ml. Therefore, no significant correlation was established between Sj AR inhibition and adult worm killing in vitro. The reason for this might be explained by other factors, such as compound molecular weight, solubility or their different pharmacokinetics in vivo, which could also affect the lack of correlation of the enzyme inhibition assay with activity on cultured worms.
The identified compound, AR9, has two linked anthraquinone scaffolds, and its name is bianthrone or dianthrone. Although anthraquinone scaffolds usually have multiple molecular targets which usually result in their promiscuity, there are indeed some cases that have successfully made the anthraquinone compound into drugs by introducing certain groups. Mitoxantrone, pixantrone and the anthracyclines, all of which are anthraquinone derivatives, have already been used as effective drugs for cancer treatment [36–38]. Additionally, rufigallol, another anthraquinone derivative, also exhibits significant toxic to the malaria parasite Plasmodium falciparum. Therefore, although the current structure of AR9 seems unsuitable for a drug, improved derivatives could also be designed based on this structural model. Additionally, bianthrone is actually the major active ingredient of a widely used Chinese herbal medicine named rheum palmatum, which has been demonstrated to effectively inhibit bacteria, fungi and viruses [40, 41]. These studies further support the speculation that AR9 has the potential to become a novel antischistosomal lead compound.
In this study, we have attempted to obtain the crystal structure of Sj AR complexed with compound AR9 through co-crystallization. However, this was very difficult to achieve because of the relatively lower solubility of AR9. AR9 is soluble in DMSO, but less soluble in water. When the concentration of AR9 in water was higher than 50 μg/ml, some precipitation would occur. Meanwhile, the optimized Sj AR protein crystallization concentration is 12 mg/ml (approximately 0.31 mM), so even assuming that one Sj AR protein molecule only binds to one compound molecule, the minimum concentration of AR9 should be 119 μg/ml. However, large amounts of precipitation have already occurred at that concentration. An alternative strategy is to introduce a polar group in the AR9 structure (ensuring that this change does not significantly affect its antischistosomal activity) to increase its solubility, and then attempt co-crystallization.
The majority of previous studies have focused either on the screening and designing of inhibitors of a known drug target or on the analysis of antischistosomal activity of potential drugs [12, 42, 43], while the work presented here bridges the gap between virtual screening and experimental validation, providing an effective and economical strategy to discover antischistosomal lead compounds. More work, such as in vivo experiments, the design of derivatives and optimization of complex crystallization conditions are still needed in further studies.
The work presented here developed an effective and economical strategy, which integrates virtual screening and experimental validation for the development of new anti-parasitic drugs. In this study, we firstly resolved the Sj AR structure and identified one compound, bianthrone, which may become a new potential lead compound for developing novel antischistosomal drugs based on this structural model.
The authors thank Que Lan from University of Wisconsin-Madison (USA), Jiahai Zhou from Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences and Hao Ye from East China University of Science and Technology (China) for constructive suggestions about this study. Yanhui Xu, also from Fudan University, is gratefully acknowledged for providing us the facility for protein crystallization. This research was supported by grants from The National Natural Science Foundation of China (grant no. 30400562) and The National Science and Technology Key Project on “Major Infectious Diseases such as HIV/AIDS, Viral Hepatitis Prevention and Treatment” (grant no. 2009ZX10004-302).
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