Combinatorial Chemistry & High Throughput Screening - Volume 19, Issue 10, 2016

Background: Docking allows to predict ligand binding to proteins, since the 3D-structure for the target is available. Several docking studies have been carried out to identify potential ligands for drug targets. Many of these studies resulted in the leads that were later developed as drugs. Objective: Our goal here is to describe the development of an integrated computational tool to assess docking accuracy and build new scoring functions to predict ligandbinding affinity. Method: We carried out docking simulations using MVD program for a data set available on CSAR 2014 database (coagulation factor Xa) for which ligand-binding information and structures are available. These docking results were analyzed using SAnDReS available at www.sandres.net. Machine learning methods were applied to build new scoring functions and our results were compared with previously published benchmarks. Results: Our integrated docking strategy generated poses with docking accuracy higher than previously published benchmarks. In addition, the new scoring function developed using SAnDReS shows better performance than well-established scoring functions such the ones available in Autodock, Autodock- Vina, Gold, Glide, and MVD. Conclusion: The big data generated during docking lacked an integrated computational tool for statistical analysis of the influence of structural parameters on docking and scoring function performance. Here we describe methods to evaluate docking results using SAnDReS, a computational environment for statistical analysis of docking results and development of scoring functions. We believe that SAnDReS is a computational tool with potential to improve accuracy in docking projects.

Background: Visceral leishmaniasis (VL) is a tropical neglected disease, which encounters poorest of poor people living in Asia, Africa and Latin America; causing the mortality of more than 30,000 people worldwide. The armamentarium for the treatment of VL cases is limited and continuously facing decreasing of efficacy for existing drugs. Ornithine decarboxylase (ODC) is one of the interesting drug targets in Leishmania donovani, due to its association with redox metabolism. Objective: To search an antileishmanial compound showing the inhibitory effect against ornithine decarboxylase of Leishmania donovani Method: In this study, we have modelled the three dimensional structure of ODC using Phyre2 (Protein Homology/analog Y Recognition Engine V 2.0), followed by validation using VADAR (Volume, Area, Dihedral Angle Reporter), RAMPAGE, ERRAT, Verify3D and ProSA (Protein Structure Analysis). In order to develop potential antileishmanial, we conducted a high throughput virtual screening of ZINC database ligands comprising of 135,966 compounds. Furthermore, QikProp, ADMET predictor and MM-GBSA was performed for ADME (Absorption, Distribution, Metabolism and Elimination), toxicity and binding energy prediction for top ligands, respectively. Finally, molecular dynamics simulation was performed to get potential antileishmanial compounds. Result: Screening of zinc database compounds using high throughput virtual screening has given twelve compounds with good inhibition activity against ornithine decarboxylase. Furthermore, the molecular dynamics simulation work reveals that ZINC67909154 could be a potent inhibitor and this compound can be used to combat VL disease Conclusion: This study concludes that ZINC67909154 has the great potential to inhibit L. donovani ODC and would add to the drug discovery process against visceral leishmaniasis.

Background: Rather than a Janus Kinase 2 inhibitor (ruxolitinib), a specific thrombopoietin receptor (TpoR) inhibitor would be more specific for the treatment of myeloproliferative neoplasms due to TpoR mutations. Objective: A cell-based phenotypic approach to identify specific TpoR inhibitors was implemented and a library of 505,483 small molecules was screened for inhibitory effects on cells transformed by TpoR mutants. Results: Among the identified hits are two analogs of 3-(4-piperidinyl) indole. The analogs showed about five-fold preferential inhibition of cell viability towards Ba/F3 cells expressing the TpoR W515L mutation compared to the parental cells. There was no significant difference in inhibition of cell viability between the TpoR wild type and the TpoR W515L mutant cells. Preferential inhibition of viability was observed in Ba/F3 cells expressing erythropoietin receptor (EpoR) when stimulated with Epo compared to stimulation with interleukin-3 (IL3). The indole analog inhibited ex vivo colony formations of primary bone marrow cells from heterozygous JAK2 V617F knock-in mice. Drug combination treatment study was performed using ruxolitinib and the indole analog. Drug synergistic effects were observed when cells were stimulated to proliferate through both the IL3 and TpoR pathways. Our compound specifically targets monoamine receptors in the rhodopsin-like receptor family of G protein-coupled receptor. Conclusion: This screen has identified a monoamine receptor inhibitor that can inhibit viability of cells with active TpoR or EpoR signalings. Drug synergism with ruxolitib is demonstrated.

Aim and objective: Rheumatoid Arthritis (RA) is a progressing autoimmune inflammatory disease of joint, hallmarked by inflammation, pain and atrophy of bones. Toll-like receptor 5 (TLR5) is a novel inflammatory mediator in RA, and TLR5 inhibitors are speculated to have a therapeutic potential for the treatment of RA. Material and method: Here we applied fragment pharmacophore-based virtual screening to identify novel TLR5 ligands. Results: Among compounds collected from Otava peptidomimetic compounds, Maybridge fragment and ZINC libraries, 3355 compounds were selected for docking into the flagellin-binding site of TLR5. 16 compounds with the required interaction, critical amino acid residues and the binding free energies <-7 kcal/mol were identified as potential TLR5 inhibitors, one of which was followed up by molecular dynamics simulation. Conclusion: These compounds open a possibility to discover novel TLR5 inhibitors for the treatment of RA.

Aim and objective: This study aimed to quantify phenolic compounds in ethyl acetate and n-butanol extract of Centaurea choulettiana Pomel (Asteraceae) leaves and flowers; compare the antioxidant activity of their extracts, identification and quantification of their phenolic acids. Materials and methods: Both organs extracts of Centaurea choulettiana Pomel were investigated and evaluated for their potential antioxidant properties using total phenolics and flavonoids content, DPPH radical scavenging and lipid peroxidation inhibition assays. HPLC-TOF/MS analyses were carried out to identify and quantify some phenolic acids. Results: The amounts of phenolic and flavonoid content were higher in ethyl acetate extract of leaves (325.81 ± 0.038 mgGAE and 263.73 ± 0.004 mgQE /g of extract) respectively. Besides, this extract exhibited the most powerful effect on the DPPH radical scavenging activity with (96.54%), on lipid peroxydation inhibition (64.17%). Ethyl acetate extract of leaves and flowers were found to contain almost the same phenolic compounds, with the leaves having the highest values. Chlorogenic acid was detected in the n-butanol extract of flowers with the highest concentration 17.78 mg/kg plant. Conclusion: The ethyl acetate extract of leaves of Centaurea choulettiana possesses strong antioxidative properties in vitro. They are confirmed by high polyphenols and flavonoids content. The HPLC-TOF/MS analysis reveals the presence of 4-hydroxybenzoic acid, gentisic acid, chlorogenic acid, caffeic acid, vanillic acid, p-Coumaric acid, ferulic acid, salicylic acid and protocatechuic acid.

Background: Selenocyanate derivatives have been recently presented as potent anti-leishmanial agents. Objective: In this research, thirty five selenocyanate and diselenide compounds were subjected to docking studies and compared to Edelfosine and Miltefosine as reference drugs and then molecular dynamics (MD) simulation analysis. Methods: Desired Selenocyanates were built using the HyperChem program and docking calculations were performed on the crystal structure of trypanothione reductase from Leishmania infantum. Then, MD simulation analysis was performed to explore the interaction stability of selected compound during structural motions of the interacting molecules. Results: Based on the binding energy, all of the aryl rings were more potent than Edelfosine and Miltefosine as reference drug. The best compound base on hydrogen bonding, π-π interactions and orientation within the active site with high binding energy was selected for MD simulation analysis. The selected compound is known as high-affinity selective inhibitor for trypanothione reductase. Conclusion: These results can be used for future synthesis of new antileishmanial agents with better potency.

Background: Tuberculosis (TB) kills over 1.5 million people per year despite the available anti-TB drugs. The long duration needed to treat TB by the current TB drugs, which target the essential cellular activities, inevitably leads to the emergence of drug-resistance. The emergence of drug-resistant TB prompts for an urgent need for new and more effective drugs. Objective: The response regulator PhoP, an essential virulence factor of Mycobacterium tuberculosis (MTB), is an attractive target for developing novel anti- TB drugs. This study aims to develop a robust high-throughput screening assay to identify PhoP inhibitors that disrupt the PhoP-DNA binding. Method: Guided by the crystal structure of the PhoP-DNA complex, we designed and developed an assay based on Foster resonance energy transfer (FRET) by labeling Cy3 on the DNA and Cy5 on PhoP. We screened compound libraries for inhibitors that dissociated the PhoP-DNA complex by detection of the FRET signal. Hits were confirmed for their direct binding to PhoP by thermal shift assays. Results: From a test screening of ~6,000 bioactive compounds and approved drugs, three active compounds were identified that directly bound to PhoP and inhibited the PhoP-DNA interactions. These three PhoP inhibitors can be further developed to improve potency and are useful to study the mechanism of inhibition. Conclusion: Our results demonstrated that this FRET-based PhoP-DNA binding assay is valid for additional compound library screening to identify new leads for developing novel TB drugs that target the virulence of MTB.

Aim and objective: Tetrahydrobenzo[b]pyran derivatives are considered as a special class in drug research because of their various biological and pharmacological benefiting usages. In the current work, we developed new synthetic methods for the preperation of tetrahydrobenzo[b]pyran derivatives using arylaldehydes 1, malononitrile 2 and dimedonein 3 in the presence of caffeine as catalyst as a cheap, easily accessible, biodegradable and green catalyst. Moreover, for the first time, we have described kinetic results together along with detailed mechanistic studies of the synthetic reaction of a derivative of 4Htetrahydrobenzo[ b]pyran based on a global kinetic analysis methodology using UVvis spectrophotometry apparatus. Material and method: Products were characterized by comparison of physical data with authentic samples and spectroscopic data (IR and NMR). Infrared (IR) spectra were recorded on a JASCO FT- IR-460 plus spectrometer. 1H nuclear magnetic resonance (NMR) spectra were obtained with a Bruker DRX-400 Advance spectrometer and using deuterated dimethylsulfoxide (DMSO) and acetone as solvents. Thin-layer chromatography (TLC) was performed on Silica–gel polygram SILG/UV 254 plates. Rate constants are presented as an average of several kinetic runs (at least 6-10) and are reproducible within ± 3%. The overall rate of reaction is followed by monitoring the absorbance changes of the products versus time on a Varian (Model Cary Bio-300) UV-vis spectrophotometer with a 10 mm light-path cell. Results: For optimization, the reaction of benzaldehyde (1 mmol), malonitrile (1 mmol) and dimedone (1 mmol) was investigated. The desired results were obtained at 70 °C in the presence of (20 mol %) caffeine in H2O: EtOH (2:1). Moreover, the overall order of reaction for the formation of a 4Htetrahydrobenzo[ b]pyran derivative in the presence of caffeine followed second-order kinetics and the partial orders with regard to 4-nitrobenzaldehyde 1, malononitrile 2 and dimedone 3 were one, one and zero, respectively. Conclusion: It was observed that the yield was a function of temperature, as the yield increased, the reaction temperature rose. At 70 ºC, the product was obtained with an excellent yield and higher temperatures did not increase the reaction yield any more. Also, 20 mol% was elected as a suitable amount of catalyst for this reaction. It is understood from the result that the rate of reaction speeds up in a solvent with a high dielectric constant (H2O/EtOH, 2:1) compared to those with a low dielectric constant (Ethanol and methanol) at all temperatures. In the studied temperature range, the second-order rate constant of the reaction was inversely proportional to the temperature, which was in agreement with the Arrhenius and Eyring equations. It was obvious that the high positive values of the activation parameters leads to a stiff reaction progress. The first step of the proposed mechanism was identified as a rate-determining step (k1) and this was confirmed based on the steady-state approximation.

Background: The Rab family proteins are involved in membrane trafficking, cell growth and differentiation. Rab38 is implicated in the biogenesis of melanosomes that help in the synthesis, storage and transport of melanin pigments. The Rab38 protein is overexpressed at the RNA level in melanoma cancer. Aim and objective: The protein Rab38 is targeted for identification of novel antagonists as cancer drug candidates. Materials and methods: The 3D structure of Rab38 was generated using homology modelling method. The 3D model was validated. The active site was identified by using standard computational prediction tools like CASTp, efindsite and SiteMap. The study of protein-protein docking was performed between Rab38 and its natural substrate BLOC-3 using patchDock server tool. Virtual screening protocols were carried out using glide module. Various informatics tools like 1) Schrodinger Suite 2) Modeller 3) Accelrys Discovery Studio 4) PyMOL 5) SPDBV etc. are applied for the identification of novel inhibitors of Rab38. Results: The residues from SER35 to LEU63 of Rab38 protein are important for binding to ligands. The nineteen docked structures were obtained as an output of virtual screening. The compounds obtained show good glide score, and a common binding pattern at the active site. Conclusion: The benzosulfonamide and heterocyclic nitrogen moieties may be considered as pharmacophores for designing new anticancer leads with better docking score and admissible ADME properties. Our study helps in the identification of potential inhibitors against Rab38 and melanoma cancer.