Molecular dynamics simulation study of PTP1B with allosteric inhibitor and its application in receptor based pharmacophore modeling

Allosteric inhibition of protein tyrosine phosphatase 1B (PTP1B), has paved a new path to design specific inhibitors for PTP1B, which is an important drug target for the treatment of type II diabetes and obesity. The PTP1B_1–282-allosteric inhibitor complex crystal structure lacks α7 (287–298) and moreover there is no available 3D structure of PTP1B_1–298 in open form. As the interaction between α7 and α6–α3 helices plays a crucial role in allosteric inhibition, α7 was modeled to the PTP1B_1–282 in open form complexed with an allosteric inhibitor (compound-2) and a 5 ns MD simulation was performed to investigate the relative orientation of the α7–α6–α3 helices. The simulation conformational space was statistically sampled by clustering analyses. This approach was helpful to reveal certain clues on PTP1B allosteric inhibition. The simulation was also utilized in the generation of receptor based pharmacophore models to include the conformational flexibility of the protein-inhibitor complex. Three cluster representative structures of the highly populated clusters were selected for pharmacophore model generation. The three pharmacophore models were subsequently utilized for screening databases to retrieve molecules containing the features that complement the allosteric site. The retrieved hits were filtered based on certain drug-like properties and molecular docking simulations were performed in two different conformations of protein. Thus, performing MD simulation with α7 to investigate the changes at the allosteric site, then developing receptor based pharmacophore models and finally docking the retrieved hits into two distinct conformations will be a reliable methodology in identifying PTP1B allosteric inhibitors. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Pharmacophore modelling,virtual screening and molecular docking studies on PLD1 inhibitors

Lipid metabolism plays a significant role in influenza virus replication and subsequent infection. The regulatory mechanism governing lipid metabolism and viral replication is not properly understood to date, but both Phospholipase D (PLD1 and PLD2) activities are stimulated in viral infection. In vitro studies indicate that chemical inhibition of PLD1 delays viral entry and reduction of viral loads. The current study reports a three-dimensional pharmacophore model based on 35 known PLD1 inhibitors. A sub-set of 25 compounds was selected as the training set and the remaining 10 compounds were kept in the test set. One hundred and twelve pharmacophore models were generated; a six-featured pharmacophore model (AADDHR.57) with survival score (2.69) produced a statistically significant three-dimensional quantitative structure–activity relationship model with r² = 0.97 (internal training set), r² = 0.71 (internal test set) and Q² = 0.64. The predictive power of the pharmacophore model was validated with an external test set (r² = 0.73) and a systematic virtual screening work-flow was employed showing an enrichment factor of 23.68 at the top 2% of the dataset (active and decoys). Finally, the model was used for screening of the filtered PubChem database to fetch molecules which can be proposed as potential PLD1 inhibitors for blocking influenza infection.     

Rational Design and Identification of a Non‐Peptidic Aggregation Inhibitor of Amyloid‐β Based on a Pharmacophore Motif Obtained from cyclo[‐Lys‐Leu‐Val‐Phe‐Phe‐]

Inhibition of pathogenic protein aggregation may be an important and straightforward therapeutic strategy for curing amyloid diseases. Small‐molecule aggregation inhibitors of Alzheimer’s amyloid‐β (Aβ) are extremely scarce, however, and are mainly restricted to dye‐ and polyphenol‐type compounds that lack drug‐likeness. Based on the structure‐activity relationship of cyclic Aβ16–20 (cyclo‐[KLVFF]), we identified unique pharmacophore motifs comprising side‐chains of Leu², Val³, Phe⁴, and Phe⁵ residues without involvement of the backbone amide bonds to inhibit Aβ aggregation. This finding allowed us to design non‐peptidic, small‐molecule aggregation inhibitors that possess potent activity. These molecules are the first successful non‐peptidic, small‐molecule aggregation inhibitors of amyloids based on rational molecular design.     

Integrated pharmacophore and docking‐based designing of dual inhibitors of aldose reductase (ALR2) and protein tyrosine phosphatase 1B (PTP1B) as novel therapeutics for insulin‐resistant diabetes and its complications

The dual inhibitors against aldose reductase (ALR2) and protein tyrosine phosphatase 1B (PTP1B) may present an anti‐diabetic potency in insulin resistance without risks of serious diabetic complications. Therefore, in the present study, we constructed two separate pharmacophore mapping‐based 3D quantitative structure–activity relationship models for ALR2 (AADRR.1109₃ with standard deviation 0.663, 0.719, F 22.3, root‐mean‐square error 0.705, 0.647, Pearson‐r 0.802) and PTP1B (AARR.15₅ with standard deviation 0.146, 0.945, F 82.70, root‐mean‐square error 0.351, 0.621, Pearson‐r 0.831) employing the dataset of 54 flavonoids as ALR2 inhibitors and 46 naphthoquinones as PTP1B inhibitors to identify structural features necessary for the inhibition of both enzymes. These models were subsequently used as 3D query search for hierarchical virtual screening‐based designing using the PHASE database of 1.5 million compounds. Designed dual inhibitors were further subjected to GLIDE XP docking analysis using high‐resolution 3D structures of ALR2 (1US0, at resolution of 0.66 Å) and PTP1B (2F71 at resolution of 1.55 Å) available in the Protein Data Bank to authenticate identified structural features with important binding interactions necessary for dual inhibition. Copyright © 2014 John Wiley & Sons, Ltd.     

Pharmacophore modelling,atom-based 3D-QSAR generation and virtual screening of molecules projected for mPGES-1 inhibitory activity

COX-2 inhibitors exhibit anticancer effects in various cancer models but due to the adverse side effects associated with these inhibitors, targeting molecules downstream of COX-2 (such as mPGES-1) has been suggested. Even after calls for mPGES-1 inhibitor design, to date there are only a few published inhibitors targeting the enzyme and displaying anticancer activity. In the present study, we have deployed both ligand and structure-based drug design approaches to hunt novel drug-like candidates as mPGES-1 inhibitors. Fifty-four compounds with tested mPGES-1 inhibitory value were used to develop a model with four pharmacophoric features. 3D-QSAR studies were undertaken to check the robustness of the model. Statistical parameters such as r² = 0.9924, q² = 0.5761 and F test = 1139.7 indicated significant predictive ability of the proposed model. Our QSAR model exhibits sites where a hydrogen bond donor, hydrophobic group and the aromatic ring can be substituted so as to enhance the efficacy of the inhibitor. Furthermore, we used our validated pharmacophore model as a three-dimensional query to screen the FDA-approved Lopac database. Finally, five compounds were selected as potent mPGES-1 inhibitors on the basis of their docking energy and pharmacokinetic properties such as ADME and Lipinski rule of five.     

A three-dimensional chemical phase pharmacophore mapping,QSAR modelling and electronic feature analysis of benzofuran salicylic acid derivatives as LYP inhibitors

Lymphoid tyrosine phosphatase (LYP), encoded by the PTPN22 gene, has a critical negative regulatory role in T-cell antigen receptor (TCR) and emerged as a promising drug target for human autoimmune diseases. A five-point pharmacophore with two hydrogen bond acceptors, one hydrogen bond donor and two aromatic ring features was generated for a series of benzofuran salicylic acid derivatives as LYP inhibitors in order to elucidate their anti-autoimmune activity. The generated pharmacophore yielded a significant 3D-QSAR model with r² of 0.9146 for a training set of 27 compounds. The model also showed excellent predictive power with Q² of 0.7068 for a test set of eight compounds. The investigation of the 3D-QSAR model has revealed the structural insights which could lead to more potent analogues. The most active and inactive compounds were further subjected to electronic structure analysis using density functional theory (DFT) at B3LYP/3?21^?G level to support the 3D-QSAR predictions. The results obtained from this study are expected to be useful in the proficient design and development of benzofuran salicylic acid derivatives as inhibitors of LYP.     

Synthesis of Triazole‐Linked Amino Acid‐Aryl C‐Glycoside Hybrids via Click Chemistry as Novel PTP1B Inhibitors

Triazolyl phenylalanine and tyrosine‐aryl C‐glycoside hybrids were readily synthesized via microwave‐assisted Cu(I)‐catalyzed azide‐alkyne 1,3‐dipolar cycloaddition in high yields. Successive enzymatic assay identified the synthesized glycoconjugates as novel PTP1B inhibitors with low micromole‐ranged inhibitory activity and at least several‐fold selectivity over other homologous PTPs tested. In addition, the benzyl groups on glucosyl moiety were found crucial toward PTP1B inhibition.     

Molecular dynamics and pharmacophore modelling studies of different subtype (ALK and EGFR (T790M)) inhibitors in NSCLC

Extensively validated 3D pharmacophore models for ALK (anaplastic lymphoma kinase) and EGFR (T790M) (epithelial growth factor receptor with acquired secondary mutation) were developed. The pharmacophore model for ALK (r² = 0.96, q² = 0.692) suggested that two hydrogen bond acceptors and three hydrophobic groups arranged in 3-D space are essential for the binding affinity of ALK inhibitors. Similarly, the pharmacophore model for EGFR (T790M) (r² = 0.92, q² = 0.72) suggested that the presence of a hydrogen bond acceptor, two hydrogen bond donors and a hydrophobic group plays vital role in binding of an inhibitor of EGFR (T790M). These pharmacophore models allowed searches for novel ALK and EGFR (T790M) dual inhibitors from multiconformer 3D databases (Asinex, Chembridge and Maybridge). Finally, the eight best hits were selected for molecular dynamics simulation, to study the stability of their complexes with both proteins and final binding orientations of these molecules. After molecular dynamics simulations, one hit has been predicted to possess good binding affinity for both ALK and EGFR (T790M), which can be further investigated for its experimental in-vitro/in-vivo activities.     

Simultaneous quantitation of IC87114, roflumilast and its active metabolite roflumilast N‐oxide in plasma by LC‐MS/MS: application for a pharmacokinetic study

A sensitive and reliable high‐performance liquid chromatography–mass spectrometry (LC–MS/MS) was developed and validated for simultaneous quantification IC87114, roflumilast (RFM), and its active metabolite roflumilast N‐oxide (RFN) using tolbutamide as an internal standard. The analytes were extracted by using liquid–liquid extraction and separated on a reverse phase C₁₈ column (50 mm × 3 mm i.d., 4.6 µ) using methanol: 2 mM ammonium acetate buffer, pH 4.0 as mobile phase at a flow rate 1 mL/min in gradient mode. Selective reaction monitoring was performed using the transitions m/z 398.3 > 145.9, 403.1 >186.9, 419.1 > 187.0 and 271.1 > 155.0 to quantify quantification IC87114, RFM, RFN and tolbutamide, respectively. The method was validated over the concentration range of 0.1–60 ng.mL^?1 for RFM and RFN and 6 to 2980 ng.mL^?1 for IC87114. Intra‐ and inter‐day accuracy and precision of validated method were within the acceptable limits of <15% at all concentrations. Coefficients of correlation (r²) for the calibration curves were >0.99 for all analytes. The quantitation method was successfully applied for simultaneous estimation of IC87114, RFM and RFN in a pharmacokinetic drug–drug interaction study in Wistar rats. Copyright © 2012 John Wiley & Sons, Ltd.     

Pharmacophore Modeling and Virtual Screening of Novel Inhibitors for c-Kit Kinase

The stem cell factor receptor (c‐Kit) has been known to play critical roles in regulating numerous aspects of cellular behavior including cell growth, differentiation, migration and metabolism. In this investigation, a three‐dimensional pharmacophore model of c‐Kit inhibitors has been established by using the HypoGen algorithms implemented in the catalyst software package. The best quantitative pharmacophore model, hypothesis 1, which has the highest correlation coefficient (0.989), consists of one hydrogen bond acceptor, two hydrogen bond donors and one hydrophobic feature. To our knowledge, this is the first report on the pharmacophore modeling study of c‐Kit inhibitors. The best hypothesis, hypothesis 1, was used to screen molecular structural databases, including Specs and China Natural Products Database for potential lead compounds. The hit compounds were subsequently subjected to filtering by Lipinski's rules and docking study to refine the retrieved hits and as a result to reduce the rate of false positive. Finally 28 compounds were purchased or synthesized for further in vitro assay against several human tumour cell lines including A549, MCF‐7, HepG2 and PC‐3, in which c‐Kit is overexpressed. Two compounds show very low micromolar inhibition potency against the PC‐3 and HepG2 cell lines respectively. And they were selected for further modification and testing.     

Simultaneous Quantitation of Tetrahydropalmatine and Protopine in Rabbit Plasma by HPLC–PAD, and Application to Pharmacokinetic Studies

A reversed-phase high-performance liquid chromatographic method coupled with photodiode-array detection (HPLC–PAD) has been developed and validated for simultaneous quantitation of dl-tetrahydropalmatine (dl-THP) and protopine (PTP), two active constituents of the herbal medicine Rhizoma Corydalis, in rabbit plasma. The pharmacokinetics of dl-THP and PTP were researched in rabbits after oral administration of extracts of Rhizoma Corydalis. Optimum separation was achieved on a reversed-phase column with methanol–phosphate buffer (pH 7.75, 65:35, v/v) as mobile phase. The experimental results showed the intra-day and inter-day precision and accuracy of the method were satisfactory for simultaneous determination of dl-THP and PTP at low, middle, and high concentrations. The lower limits of quantitation were 2.05 ng mL^?1 for dl-THP and 2.10 ng mL^?1 for PTP. Plasma concentration–time data for dl-THP were best fitted by the two-compartment linear pharmacokinetic model whereas data for PTP were best fitted by the one-compartment model.     

Click Synthesis of Triazolyl Phenylalaninyl and Tyrosinyl Derivatives as New Protein Tyrosine Phosphatase Inhibitors

The efficient construction of triazolyl peptidomimetics via the powerful click chemistry for the discovery of small molecule‐based chemotherapeutic agents represents a promising strategy in drug development today. Herein, the synthesis of novel mono‐triazolyl or bis‐triazolyl amino acid derivatives was rapidly achieved via microwave‐assisted Cu(I)‐catalyzed azide‐alkyne 1,3‐dipolar cycloaddition (CuAAC). Subsequent in vitro enzymatic assay on several homologous protein tyrosine phosphatases (PTPs) identified the triazolyl dimers as new specific inhibitors of Cell Cycle Division 25B (CDC25B) phosphatase and Protein Tyrosine Phosphatase 1B (PTP1B).     

Organoruthenium Antagonists of Human A3 Adenosine Receptors

Human A₃ adenosine receptor (hA₃AR) is a membrane‐bound G protein‐coupled receptor implicated in a number of severe pathological conditions, including cancer, in which it acts as a potential therapeutic target. To derive structure–activity relationships on pyrazolo–triazolo–pyrimidine (PTP)‐based A₃AR antagonists, we developed a new class of organometallic inhibitors through replacement of the triazolo moiety with an organoruthenium fragment. The objective was to introduce by design structural diversity into the PTP scaffold in order to tune their binding efficacy toward the target receptor. These novel organoruthenium antagonists displayed good aquatic stability and moderate binding affinity toward the hA₃ receptor in the low micromolar range. The assembly of these complexes through a template‐driven approach with selective ligand replacement at the metal center to control their steric and receptor‐binding properties is discussed.     

A sensitive and high‐throughput LC‐MS/MS method for inhibition assay of seven major cytochrome P450s in human liver microsomes using an in vitro cocktail of probe substrates

A sensitive and high‐throughput LC‐MS/MS method was established and validated for the simultaneous quantification of seven probe substrate‐derived metabolites (cocktail assay) for assessing the in vitro inhibition of cytochrome P450 (CYP) enzymes in pooled human liver microsomes. The metabolites acetaminophen (CYP1A2), hydroxy‐bupropion (CYP2B6), n‐desethyl‐amodiaquine (CYP2C8), 4′‐hydroxy‐diclofenac (CYP2C9), 4′‐hydroxy‐mephenytoin (CYP2C19), dextrorphan (CYP2D6) and 1′‐hydroxy‐midazolam (CYP3A4/5), together with the internal standard verapamil, were eluted on an Agilent 1200 series liquid chromatograph in <7 min. All metabolites were detected by an Agilent 6410B tandem mass spectrometer. The concentration of each probe substrate was selected by substrate inhibition assay that reduced potential substrate interactions. CYP inhibition of seven well‐known inhibitors was confirmed by comparing a single probe substrate assay with cocktail assay. The IC₅₀ values of these inhibitors determined on this cocktail assay were highly correlated (R² > 0.99 for each individual probe substrate) with those on single assay. The method was selective and showed good accuracy (85.89–113.35%) and between‐day (RSD <13.95%) and within‐day (RSD <9.90%) precision. The sample incubation extracts were stable at 25 °C for 48 h and after three freeze–thaw cycles. This seven‐CYP inhibition cocktail assay significantly increased the efficiency of accurately assessing compounds’ potential inhibition of the seven major CYPs in drug development settings. Copyright © 2014 John Wiley & Sons, Ltd.     

Synthesis,characterization, and in vitro degradation of thermotropic polyesters and copolyesters based on terephthalic acid, 3‐(4‐hydroxyphenyl)propionic acid,and glycols

A new series of thermotropic liquid‐crystalline (LC) polyesters were prepared from a diacyl chloride derivative of 4,4′‐(terephthaloyldioxy)‐di‐4‐phenylpropionic acid (PTP) and glycols with a different number of methylene groups (n) [HO(CH₂)_n OH, n = 6–10, 12] by high‐temperature solution polycondensation in diphenyl oxide. PTP6/10 and PTP6/hydroquinone (H) LC copolyesters were also prepared according to a similar procedure. The chemical structure, LC, phase‐transition behaviors, thermal stability, and solubility were characterized by elemental analysis, Fourier transform infrared spectroscopy, ¹H and ¹³C NMR spectra, differential scanning calorimetry (DSC), thermogravimetric analysis, and a polarizing light microscope. The melting and isotropization temperatures decreased in a zigzag manner as the number of n increased. All of the polyesters formed a nematic phase with the exception of PTP8. The temperature ranges of the mesophase (ΔT) were much wider for the polyesters with an odd number of n's than those with an even number. ΔT increased markedly for the PTP6/10 and PTP6/H copolyesters. The in vitro degradations of the polymers were ascertained by enzymatic hydrolysis and alkaline hydrolysis. The model compound, PTP dihexylester, was synthesized and found to be degraded into terephthalic acid, 3‐(4‐hydroxyphenyl)propionic acid, and 1‐hexanol by Rhizopus delemar lipase, but PTPn homopolyesters and PTP6/10 and PTP6/H copolyesters were resistant to Rhizopus delemar hydrolysis. They were degradable in a sodium hydroxide buffer solution of pH 12 at 60 °C, depending on the number of n's and the copolymer composition. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 3043–3051, 2001     

Quantitation of acotiamide in rat plasma by UHPLC‐Q‐TOF‐MS: method development,validation and application to pharmacokinetics

A novel, sensitive and selective ultra‐high‐performance liquid chromatography–electrospray ionization mass spectrometry method was developed and validated for the quantification of acotiamide (ACT), a first‐in‐class drug used in functional dyspepsia, in rat plasma. A simple protein precipitation method with acetonitrile as precipitating solvent was used to extract ACT from rat plasma. ACT and an internal standard (mirabegron, IS) were separated on an Agilent poroshell EC C₁₈ column (50 × 3.0 mm, 2.7 µm) using methanol–10 mM ammonium acetate binary gradient mobile phase at a flow rate of 0.4 mL/min over 4 min run time. Detection was performed using target ions of [M + H]⁺ at m/z 451.2010 for ACT and m/z 397.1693 for IS in selective ion mode. The method was validated in the calibration range of 1.31–1000 ng/mL. All the validation parameters were well within the limits. The method demonstrated good performances in terms of intra‐ and inter‐day precision (3.27–12.60% CV) and accuracy (87.96–104.94%). Thus the present ultra‐high‐pressure liquid chromatograhy–high‐resolution mass spectrometry method for determination of ACT in rat plasma, is highly sensitive and rapid with a short run‐time of 4 min, can be suitable for high sample throughput and for large batches of biological samples in pharmacokinetic studies. This method can be extended to measure plasma concentrations of ACT in humans to understand drug metabolism, drug interaction and adverse effects. Copyright © 2015 John Wiley & Sons, Ltd.     

Development of a sensitive LC‐MS/MS method for simultaneous quantification of eleven constituents in rat serum and its application to a pharmacokinetic study of a Chinese medicine Shengmai injection

A sensitive LC‐MS/MS method was developed and validated for simultaneous quantification of 11 constituents, ginsenoside Rg1, Re, Rf, Rg2, Rb1, Rd, Rc, ophiopogonin D, schisandrin, schisandrol B and schizandrin B, in rat serum using digoxin as the internal standard (IS). The serum samples were pretreated and extracted with a two‐step liquid–liquid extraction. Chromatographic separation was achieved on a C₁₈ analytical column with a proper gradient elution using 0.02% acetic acid aqueous solution and 0.02% acetic acid–acetonitrile as mobile phase at a flow rate of 0.5 mL/min. MS detection was performed using multiple reaction monitoring via an electrospray ionization source. Good linearity was observed in the validated concentration range for every analyte (r² ≥0.9929), and the lower limits of quantitation of the analytes were in the range of 0.044–1.190 ng/mL in rat serum. Intra‐ and inter‐day precisions were <14.2%. The accuracy expressed as recovery was within the range of 85.1–112.8%. The extraction recoveries were >75.8%.The validated method was successfully applied to a pharmacokinetic study of all analytes in rats after single intravenous administration of Shengmai injection. Copyright © 2014 John Wiley & Sons, Ltd.     

Determination of sparstolonin B by ultra‐high performance liquid chromatography coupled with triple quadrupole mass spectrometry: application to pharmacokinetic study of sparstolonin B in rat plasma

Sparstolonin B (SsnB), a spontaneous isocoumarin compound isolated from the tuber of Scirpus yagara Ohwi. (Cyperaceae), possesses potent anti‐inflammatory and antitumor activity. In the present study, a rapid and simple UHPLC/MS/MS method for determination of SsnB in rat plasma was developed and validated. Plasma samples were pretreated by liquid–liquid extraction with ethyl acetate containing rhein as an internal standard and separated on a C₁₈ column at 35 °C, with a gradient mobile phase consisting of acetonitrile and water containing 0.2% (v/v) formic acid within 2.1 min. MS/MS detection was accomplished in multiple reaction monitoring mode with negative electrospray ionization. The precursor–product ion transitions were m/z 266.9 [M–H]^? → m/z 211.0 for SsnB and m/z 283.2 [M–H]^? → m/z 239.0 for IS. The intra‐ and inter‐day precision (RSD) was <8.98% and the accuracy (RE) ranged from ?7.40 to 4.50%. The extraction recoveries ranged from 96.28 to 97.30%. The pharmacokinetic parameters were calculated using Win Nonlin53 software. The absolute bioavailability of SsnB was estimated to be 6.98%. The proposed method was successfully applied to a pharmacokinetic study of SsnB in rats after intravenous administration with a dose of 0.5 mg/kg and oral administration at a dose of 5 mg/kg. Copyright © 2015 John Wiley & Sons, Ltd.     

Simultaneous determination of six C21 steroids of Xiao‐Ai‐Ping injection in rat plasma by LC‐MS/MS

Xiao‐Ai‐Ping injection (XAPI) is a traditional Chinese medicine that has been widely used to treat cancer. Modern pharmacological studies have demonstrated that C₂₁ steroids are the main active compounds in XAPI. In this study, a sensitive and specific liquid chromatography tandem mass spectrometry (LC‐MS/MS) method was developed and validated the first time for simultanenous determination of three isomeric pregnane genins (17β‐tenacigenin B, tenacigenin B and tenacigenin A) and their corresponding glycosides (tenacigenoside A, tenacissoside F and marsdenoside I) from XAPI in rat plasma. A simple liquid–liquid extraction technique was used after the addition of dexamethasone acetate as internal standard. The chromatography separation of analytes was achieved on an Agilent Zorbax Eclipse XDB‐C₁₈ column (3.5 µm, 150 × 3 mm i.d.) using methanol–water as mobile phase in a gradient elution program. Detection was performed in multiple reaction monitoring mode using electrospray ionization in the negative ion mode. The method showed satisfactory linearity over a concentration range 5.00–2000.00 ng/mL for tenacigenin B, tenacigenin A, marsdenoside I and tenacissoside F (r² > 0.99), 10.00–4000.00 ng/mL for 17β‐tenacigenin B and tenacigenoside A (r² > 0.99). Intra‐ and inter‐day precisions (valued as relative standard deviation) were <9.00% and accuracies (as relative error) in the range ?6.31 to 7.23%. Finally, this validated method was successfully applied to the pharmacokinetic study of XAPI after intravenous administration to rats. Copyright © 2013 John Wiley & Sons, Ltd.     

Identification of novel PfDHODH inhibitors as antimalarial agents via pharmacophore-based virtual screening followed by molecular docking and in vivo antimalarial activity

Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) catalyses the fourth reaction of de novo pyrimidine biosynthesis in parasites, and represents an important target for the treatment of malaria. In this study, we describe pharmacophore-based virtual screening combined with docking study and biological evaluation as a rational strategy for identification of novel hits as antimalarial agents. Pharmacophore models were established from known PfDHODH inhibitors using the GALAHAD module with IC₅₀ values ranging from 0.033 μM to 142 μM. The best pharmacophore model consisted of three hydrogen bond acceptor, one hydrogen bond donor and one hydrophobic features. The pharmacophore models were validated through receiver operating characteristic and Günere–Henry scoring methods. The best pharmacophore model as a 3D search query was searched against the IBS database. Several compounds with different structures (scaffolds) were retrieved as hit molecules. Among these compounds, those with a Q_FIT value of more than 81 were docked in the PfDHODH enzyme to further explore the binding modes of these compounds. In silico pharmacokinetic and toxicities were predicted for the best docked molecules. Finally, the identified hits were evaluated in vivo for their antimalarial activity in a parasite inhibition assay. The hits reported here showed good potential to become novel antimalarial agents.