Discovery of a new class of inhibitors for the protein arginine deiminase type 4 (PAD4) by structure-based virtual screening
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Rheumatoid arthritis (RA) is an autoimmune disease with unknown etiology. Anticitrullinated protein autoantibody has been documented as a highly specific autoantibody associated with RA. Protein arginine deiminase type 4 (PAD4) is the enzyme responsible for catalyzing the conversion of peptidylarginine into peptidylcitrulline. PAD4 is a new therapeutic target for RA treatment. In order to search for inhibitors of PAD4, structure-based virtual screening was performed using LIDAEUS (Ligand discovery at Edinburgh university). Potential inhibitors were screened experimentally by inhibition assays.
Twenty two of the top-ranked water-soluble compounds were selected for inhibitory screening against PAD4. Three compounds showed significant inhibition of PAD4 and their IC50 values were investigated. The structures of the three compounds show no resemblance with previously discovered PAD4 inhibitors, nor with existing drugs for RA treatment.
Three compounds were discovered as potential inhibitors of PAD4 by virtual screening. The compounds are commercially available and can be used as scaffolds to design more potent inhibitors against PAD4.
KeywordsRheumatoid Arthritis Citrulline Virtual Screening Chlortetracycline Rheumatoid Arthritis Treatment
List of abbreviations used
benzoyl arginine ethyl ester
disease modifying anti rheumatic drugs
protein arginine deiminase type 4.
Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic inflammation of the joints and surrounding tissues. About 0.5-1.0% of the adult population is affected by the disease . It is the second most common type of arthritis which often starts after 40 years of age and before 60 years of age [2, 3]. In common with multiple sclerosis and type-1 diabetes, RA is an autoimmune disease with unknown etiology. The factors leading to the development of RA remain unknown, although environmental factors, such as smoking and diet have been implicated . Autoimmune diseases are caused when the immune system attacks the body's own tissues. For RA, the tissues under attack are the synovial membranes around joints which become swollen, stiff, red and painful leading to joint destruction and functional disability.
The first written reference to arthritis, dated 123 AD described symptoms very similar to what we know now as rheumatoid arthritis. An ancient Indian text, Caraka Samhita describes a disease where swollen, painful joints initially strike the hands and feet, then spreads to the body, causing loss of appetite, and occasionally fever . In 1800, a French physician, A.J. Landré-Beauvais wrote the first recognized description of rheumatoid arthritis . The clinical term 'rheumatoid arthritis' was coined by Alfred Garrod, the London rheumatologist, making the first reference in medical literature .
Many autoantibodies that react against various autoantigens are detectable in the sera of RA patients  and are useful in diagnosis of the disease. Diagnosis at the early stage of the disease can prevent irreversible joint damage, reducing signs and symptoms of erosion and improving physical function . Historically, rheumatoid factor is an important serological marker for the diagnosis of RA and is still used as one of the criteria for the classification of the disease . It can be found in most of the RA patients, but it is not a specific marker for RA. It can also be seen in other bacterial, viral, parasitic diseases and other inflammatory conditions . For disease diagnosis, it is a good but not ideal marker for RA and better markers are needed.
Studies have been performed by several research groups to explore the connection of PAD4 with the disease based on ethnicity. Polymorphism in PADI4, the gene encoding PAD4, is found to be associated with RA. Studies show that the gene is associated with RA susceptibility in Asians including Koreans, Japanese, and Chinese [13, 14, 15]. Most of the studies demonstrated the association of PADI4 with RA among Asian populations but not the Caucasian population . In a study carried out by Iwamoto et al. , they found a positive association between PADI4 and RA in population of European descent. Chang et al.,  showed that the expression of PADI4 in the synovial fluid of RA patients is higher than patients of another two types of arthritis, osteoarthritis and ankylosing spondylitis.
To date, there is no known cure for RA. Current available treatments are mainly focused on pain relief. Current treatments available for RA can be classified into three groups: non-steroidal anti-inflammatory drugs (NSAIDs), corticosteroids, and disease modifying anti-rheumatic drugs (DMARDs) . The most common and useful DMARD is methotrexate (MTX). It is the preferred drug for current RA treatment but causes side effects such as nausea, mouth ulcers and hair loss. With hope of curing the disease, PAD4 has become the new therapeutic target for RA. PAD4 catalyzes the citrullination process which generates the epitope for RA. By inhibiting the activity of PAD4 it should be possible to control the development of RA.
With the discovery of PAD4 as a promising target for the treatment of RA, structure-based drug design can be carried out to search for new potential drug leads . The cost of the process is relatively low, not requiring high initial outlays or complex synthesis efforts . In this research, inhibitors of PAD4 were searched for using a high-throughput virtual screening program - LIDAEUS (ligand discovery at Edinburgh university) . This program screened approximately 1 million commercially available compounds against the active site of PAD4. Potential compounds were then screened experimentally using an enzyme inhibition assay. From computer-aided virtual screening, a number of compounds were identified as weak inhibitors of the enzyme, PAD4.
Expression and purification of PAD4
The majority of the protein expressed by the E. coli system was in inclusion bodies . There are 18 cysteines in PAD4 that cause the correct folding of the enzyme, this presented difficulties as random disulfide bonds formation between cysteins induces incorrect protein folding and aggregation, often producing insoluble and inactive protein. Therefore, the medium used for PAD4 expression was altered in order to produce properly folded protein. Studier media , which provides milder conditions for protein expression without the use of IPTG yielded more soluble protein compared to the conventional protein expression system. PAD4 consists of 663 amino acids and the theoretical molecular weight of the enzyme is 74.1 kDa. The PAD4 expressed from the system was attached with Trx-His-S-tags. The molecular weight of the tagged PAD4 was approximately 91 kDa as shown by SDS-PAGE analysis. The purity of the obtained enzyme was high, approximately 90% after one step of purification, with recovery of 79% activity. About 3 mg of PAD4 was isolated from 100 ml of culture after purification. The enzymatic activity of purified PAD4 was determined by citrulline colorimetric assay and the protein content was checked by Bradford protein assay. One unit of PAD4 was defined as the amount of PAD4 needed to produce 1 μM of Nα-benzoylcitrulline ethyl ester from N-α-benzoylarginine ethyl ester (BAEE) per hour .
High-throughput virtual screening using LIDAEUS
LIDAEUS was utilized to search for inhibitors of PAD4. LIDAEUS searched for inhibitors using a structure-based approach. Sitepoints and energy maps were generated and used to fit and score around 1 million commercially available small molecules into the active site of PAD4. The top 500 compounds obtained after docking by LIDAEUS were extracted and re-docked with the more exhaustive docking software AutoDock .
Initially LIDAEUS performed the docking using a course-grained approach that is essentially rigid body docking (rigid protein and rigid ligand) , which enables the screening of large datasets. To get around the rigid-rigid limitation, LIDAEUS docks the small molecules into the active site using multiple pre-generated conformations (number determined by the flexibility of the molecule). After LIDAEUS identified potential inhibitors of PAD4 from the database, more accurate analysis was carried out using AutoDock for flexible ligand docking. The compounds were ranked again after docking using AutoDock according to their predicted binding affinity to PAD4.
The active site of PAD4 has been studied by many research groups [28, 29, 30, 31, 32] with the goal of understanding the catalytic mechanism of the enzyme. Knuckley et al.,  suggested that PAD4 utilizes a reverse protonation mechanism. They claimed that Cys645 and His471 are essential for substrate binding. Inhibitors proposed by Luo et al. [34, 35] were designed to block Cys645 from binding with the substrate.
Potential inhibitors obtained from LIDAEUS were not targeted to any specific amino acid of the active site. Site points generated in the active site are used to define energetically favourable locations for specific atom types, taking into account contributions from van der Waals, hydrophobic and hydrogen bonding interactions. Potential inhibitors were indentified using LIDAEUS as a course grained (rigid protein-rigid ligand) docking technique, followed by a more rigorous treatment with AutoDock.
Inhibitory activity of hits
After potential in-silico hit identification, a quick experimental screen was carried out. One of the criteria for a drug is that it has to be soluble in aqueous medium. Drugs with poor aqueous solubility are likely to have absorption problems since the flux of drugs across the intestinal membrane is proportional to concentration gradients between the intestine lumen and blood . From the top 100 compounds obtained after molecular docking, 22 aqueous soluble compounds were selected for quick screening. To perform quick screening, an inhibition assay was carried out and the activity of PAD4 after inhibition was compared with a negative control. Compound concentration was fixed at 100 μM and the percentage of PAD4 activity remaining after adding inhibitor calculated. Additional File 1: Table S1 shows the IDs, rankings, structures, and binding affinities of the compounds tested in this work.
Molecular docking analysis of hits
To date, the therapies available for RA treatment are merely treating its symptoms . The discovery of anticitrullinated protein autoantibody as a specific autoantibody to RA has led to the discovery of PAD4 as a new therapeutic target for RA. It is hoped that inhibitors of PAD4 can treat the underlying cause of the disease. The catalytic mechanism of PAD4 was investigated  in order to identify important features that could be exploited for inhibitor development.
The discovery of drugs can be accelerated by the use of computational methods in lead identification and optimization. High-Throughput Screening (HTS) is a conventional experimental method which identifies leads by carrying out individual biochemical assays with more than millions compounds. It is a good method for the identification of leads but is costly and time consuming. This leads to the integration of another computational methodology, namely virtual high throughput screening (vHTS) . vHTS is a computational screening method widely used to screen in-silico collections of compounds and predict binding affinities of library compounds to the target receptor. vHTS aims to operate on millions of compounds in a short period of time. HTS and vHTS are complementary methods; HTS confirms the accuracy of vHTS predictions.
vHTS has been performed in many projects searching for therapeutics - for example, nuclear hormone receptor antagonists for cancer, diabetes and neurological diseases , CK2 inhibitors as antitumor agents , 17β-hydroxysteroid dehyrogenase type 1 inhibitors for breast cancer , and tyrosine phosphorylation regulated kinase 1A inhibitors for Down's syndrome . LIDAEUS, the structure-based vHTS program utilized in this work has been previously employed in drug discovery efforts searching for CDK inhibitors (targeting cancer cells) , cyclophilins inhibitors for HIV infection , and NS5 methyltransferase for dengue fever .
Nevertheless, we have identified several compounds as potential therapeutics for RA. By comparing the compounds with reported inhibitors [34, 35, 46, 47, 48, 49], there is no similarity between reported inhibitor structures and potential inhibitors discovered in this work. Luo et al. [34, 35] proposed amidine inhibitors containing halogens capable of forming a stable thiother adduct between the inhibitor and Cys645, which has been suggested as an essential amino acid in the citrullination process . Initially, it was thought that ideal PAD4 inhibitors must be able to penetrate deeply into the active site of PAD4 where Cys645 is located, this scenario is only possible if the inhibitors mimic the structure of an arginine side chain. Amidine derivatives were discovered by mimicking the structure of benzoylarginine amide, an arginine-containing PAD4 substrate. However, later findings show that there are compounds without any similarity with arginine show significant inhibition against PAD4 in micromolar scale, such as streptomycin, minocycline, chlortetracycline, and streptonigrin that shows multiple fold higher inhibitory activity against PAD4 than that of amidine compounds [46, 47]. These facts suggest that potential PAD4 inhibitors may be identified by the presence of a warhead that protrudes into the deep binding site of PAD4 and subsequently forms a stable bond with Cys645, thus completely blocking the action of PAD4; however, that is not an absolute prerequisite for a PAD4 inhibitor as has been show by the efficacy of larger molecules such as streptomycin, minocycline, chlortetracycline, and streptonigrin in inhibiting PAD4 activity.
In this work we found few compounds that inhibit the activity of PAD4. None of these compounds mimic the structure of arginine or previously discovered PAD4 inhibitors. Compound 9 and 59 contain five-membered rings while compound 10 contains furan (a cyclic ether) and thiazolidine rings. Furan rings are found in many natural products and synthetic drug molecules . Zeni et al.,  synthesized a series of compounds containing furan rings and studied their anti-inflammatory behavior. They tested the compounds using the carrageenin-induced paw edema method, and discovered that several compounds exhibited greater potency than classical anti-inflammatory agents in inhibiting paw edema formation. A furan-containing compound synthesized by Closse et al. , 5-chloro-6-cyclohexyl-2,3-dihydrobenzofuran-2-one, was more active than the reference compounds, indomethacin and diclofenac in inhibiting the acute inflammation and the adjuvant-induced arthritis. Wakimoto et al.,  proposed that furan fatty acids could be potential antioxidants which may prevent chronic inflammatory diseases.
The thioazolidine ring, which is present in compound 10, possesses a wide range of promising biological activities. Thiazolidine has shown its importance as an antimicrobial, anti-inflammatory, anticonvulsant, antimalarial, analgesic, anti-HIV and anticancer agent . Thiazolidine dione was identified as a compound which has high potency in suppressing chronic inflammation and joint destruction . The compound has been studied for its antiarthritic activity against rat adjuvant arthritis which is a chronic T cell-dependent autoimmune disease with many similarities to rheumatoid arthritis and exhibited activity at daily oral doses between 0.01 and 1 mg/kg . Ma et al.,  synthesized a series of thiazolidene diones and examined the antiarthritic potency of the most active compound with adjuvant induced arthritis. Rats treated with thiazolidine compound did not develop severe arthritis after adjuvant injection, loss of body weight was also reduced significantly. This indicated that the compound exhibited potential immunomodulating activity.
The IC50 values of the inhibitors discovered in this work were lower compared to existing drugs for RA treatment. The most common recently used drug for RA treatment is methotrexate with an IC50 value of more than 10 mM . Paclitaxel showed inhibition to PAD isolated from bovine brain with IC50 value of approximately 5 mM. Besides methotrexate and paclitaxel, other DMARDs such as sulfamethoxazole, trimethoprim, and 5-aminosalicylic acid were also investigated for their potency in inhibiting PAD4 . Most of the DMARDs have high IC50 values. Among the tested DMARDs, chlortetracycline showed the best inhibition of PAD4 (IC50 = 100 μM). Although the three compounds discovered in this work have higher IC50 compared to chlortetracycline and amidine inhibitors, LIDAEUS has discovered a new class of compound that are able to inhibit PAD4.
We have discovered three inhibitory compounds against PAD4 through structure-based virtual screening using LIDAEUS. These compounds show IC50 values between 1.54 to 2.50 mM. The compounds have thioazolidine and cyclic ether groups in their structures, which may suggest the importance of those groups in inhibiting the enzymatic activity of PAD4. The compounds are commercially available and can be utilized as scaffold to design more potent PAD4 inhibitors. The new class of PAD4 inhibitors discovered during the course of this work provide a starting point not only for medicinal chemists, but for the future in-silico work based on molecular similarity and scaffold hopping. With binding modes predictable by virtual screening, ligand-based virtual screening techniques feeding into structure-based techniques offer the ability to explore structure-activity relationship (SAR) using commercially available small molecules, greatly focusing medicinal chemistry efforts.
Expression and purification of PAD4
PAD4 cDNA was purchased from Genecopoeia (Rockville, MD, USA) and amplified using PCR with primers designed according to the gene sequence (accession number: NM_012387). The cDNA of PAD4 consisted of 1992 base pairs nucleotides. The band size of the amplified gene was checked by agarose gel electrophoresis and the gene was purified by gel extraction using GeneAll DNA Purification Kit (GeneAll, Seoul, South Korea). The purified cDNA of PAD4 was then digested with EcoRV and Bpu1102I (Fermentas, Vilnius, Lithuania) and cloned into vector pET32b (Novagen, Madison, WI, USA). The presence of the insert in the vector was confirmed by double digestion with restriction enzymes and DNA sequencing. After that, the plasmid that produced correct band sizes after double digestion and with correct DNA sequence was transformed into E. coli BL21(DE3)pLysS (Invitrogen, Carlsbad, CA, USA) for protein expression. E.coli was grown in Studier media . The seed culture was prepared in MDG media, then inoculated at a 1:1000 dilution into ZYM-5052 media. The bacteria were grown for 5 to 6 hours at 37°C under agitation (220 rpm) until the culture appeared turbid, the temperature was then dropped to 20°C and the culture allowed to grow overnight. The cells were harvested by centrifugation at 10000 rpm for 10 minutes, then resuspended in lysis buffer (100 mM Tris pH 7.2, 500 mM NaCl, 30 mM imidazole, and 1 mg/ml lysozyme) and lysed by sonication. The cell debris were removed by centrifugation. The supernatant was passed through a Ni Sepharose™ 6 Fast Flow affinity column (GE Healthcare, Uppsala, Sweden) for purification. The column was washed with a binding buffer (100 mM Tris pH 7.2, 500 mM NaCl and 30 mM imidazole) and the His-tagged PAD4 was eluted with an elution buffer (100 mM Tris pH 7.2, 500 mM NaCl and 500 mM imidazole). The presence of the protein in specific fractions was detected by SDS-PAGE analysis. Fractions containing the protein were pooled and stored at 4°C.
Computer-aided virtual screening
A web- based high-throughput virtual screening program, LIDAEUS http://opus.bch.ed.ac.uk/lidaeus/index.php was utilized in searching for potential inhibitors of PAD4. The three-dimensional structure of PAD4 was retrieved from the Protein Data Bank [PDB:1WDA]. The structure was prepared for structure-based virtual screening and molecular docking by removing all water molecules and Ala645 was mutated to Cys to match the human sequence using the Coot 8.04.3 program. The mutated PAD4 structure was uploaded to the LIDAEUS web service where site points were generated defining the search space to be explored within the active site of the protein. Around 1 million compounds were screened by fitting to the generated site points and subsequent scoring against pre-generated energy maps, accounting for van der Waals, hydrophobic and hydrogen bonding interactions. The top ranked top 500 compounds predicted by LIDAEUS were redocked using the more computationally expensive and exhaustive virtual screening program AutoDock . Post-docking analysis was carried out using PoseView http://poseview.zbh.uni-hamburg.de/.
Citrulline colorimetric assay
The assay was carried out based on the protocol suggested by Takahara et al., with some modifications . The reaction buffer containing 100 mM Tris (pH 7.2), 10 mM calcium chloride, 10 mM DL-dithiothreitol and 0.2 ml of the enzyme solution was incubated at 37°C for 2 minutes. The reaction was started by adding the substrate, 10 mM N-α-benzoylarginine ethyl ester (BAEE) and the reaction mixture was then incubated at 37°C for 30 minutes. The enzymatic reaction was terminated by adding 60% (w/v) perchloric acid. The reaction mixture was centrifuged to remove aggregated PAD4 after termination. Half of the reaction mixture was used for the colorimetric determination of citrulline. For color development, Redox Reagent prepared by ferrous ammonium sulfate hexahydrate and ammonium iron (III) sulfate dodecahydrate in 1 N H2SO4 was added to the reaction mixture, then boiled for 10 minutes. After cooling down to room temperature, theacid mixture (phosphoric acid, sulfuric acid and deionized water) and 12.5 mM of 2,3-butanedione monoxime solution was added. It was boiled for 20 minutes then cooled. The absorbance at 490 nm was measured and compared to a citrulline standard curve to determine the concentration of citrulline produced during the course of the reaction. The amount of protein was determined by the Bradford method with bovine serum albumin (BSA) as standard .
PAD4 inhibition assay - quick screening
The reaction buffer containing 100 mM Tris (pH 7.2), 10 mM calcium chloride, 10 mM DL-dithiothreitol, 100 μM inhibitor and 0.06 μM enzyme solution was incubated at 37°C for 15 minutes. 1 mM BAEE was added to start the enzymatic reaction and the reaction mixture was incubated at 37°C for 15 minutes. The enzymatic reaction was terminated by adding 60% (w/v) perchloric acid. Citrulline produced was determined spectrometrically as described above.
IC50 values of compounds that showed significant inhibition against PAD4 were determined by pre-incubating various concentrations of the inhibitors in the reaction buffer as described above. The enzymatic reaction was started by adding 1 mM BAEE and the reaction was allowed to occur for 15 minutes. The reaction was then terminated and the amount of citrulline produced determined as described above. IC50 values were determined by fitting the data to standard IC50 equations in the Grafit program .
The authors thank the Malaysian Ministry of Science, Technology and Innovation (MOSTI) for funding.
This article has been published as part of BMC Bioinformatics Volume 13 Supplement 17, 2012: Eleventh International Conference on Bioinformatics (InCoB2012): Bioinformatics. The full contents of the supplement are available online at http://www.biomedcentral.com/bmcbioinformatics/supplements/13/S17.
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