Combinatorial Chemistry & High Throughput Screening - Volume 20, Issue 1, 2017

Aim and Objective: Actinomycetes produce structurally unique secondary metabolites with pharmaceutically essential bioactivities. Salinispora, an obligate marine actinomycete, produces structurally varied and unique secondary metabolites. There is plenty of scope for development of drugs from the novel compounds isolated from Salinispora. Anticancer, antibacterial and anti-protozoa activities have been shown for Salinosporamides A, B and C, the secondary metabolites identified from Salinispora, which make them interesting subjects for further extended biological activity prediction. Material and Methods: An in silico ligand based-pharmacophore approach was used for the prediction of extended biological targets for salinosporamide A, B and C. Pharmacophore models of salinosporamide A, B and C were generated individually and screened against known drug databases. The drugs with best fitness score were shortlisted, and their respective targets pertaining to their bioactivity were retrieved. The predicted biological drug targets were docked with salinosporamide A, B and C for validation. Results: The glucocorticoid receptor and methionine aminopeptidase 2 showed good docking score and binding energy with salinosporamide A, B and C. Molecular dynamics studies of the protein-ligand complexes showed stable interactions suggesting that the predicted new targets for salinosporamides might be promising. Conclusions: The glucocorticoid receptor and methionine aminopeptidase 2 could be possible new drug targets of bioactivity of salinosporamides. These proteins could be the druggable targets for antiinflammatory and anticancer activity of salinosporamides.

Background: Current drugs available for the treatment of Chagas disease are fraught with several challenges including severe toxicity and limited efficacy. These factors coupled with the absence of effective drugs for treating the chronic stage of the disease have rendered the development of new drugs against Chagas disease a priority. Objective: This study screened several imidazole-based compounds for anti-Trypanosoma potential. Method: Using an in vitro experimental infection model, several imidazole-based compounds were screened for anti-proliferative effect on Trypanosoma cruzi epimastigotes. Additionally, all test compounds were evaluated for unspecific cytotoxicity on L929 murine fibroblasts. Benznidazole (BZN) served as reference drug. Results: All test compounds demonstrated interesting trypanocidal potential with IC50 values in the μM range (1< 1C50 <8 μM). The activities of the test compounds compared favorably with BZN, which had an IC50 value ca. 30 μM. Conversely, most of the test compounds were highly cytotoxic, resulting in selectivity lower than that of BZN (SI > 9.42). Conclusion: We provide evidence which implicate the imidazole-based compounds as potential prototypes for the development of anti-parasitic agents. Findings have far-reaching relevance to drug discovery efforts for trypanosomiasis.

Aim and Objective: This study investigates molecular structural requirements that are responsible for the antioxidant activity in phenolic compounds. Method: Antioxidant activity of compounds was determined with a 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical assay. Principal component analysis (PCA) was used to classify phenolic antioxidants according to the key molecular features that contribute to their antioxidant activity. Artificial neutral networks (ANNs) was used to develop a predictive QSAR model. Results: Both models agreed that structural characteristics of phenolic compounds responsible for the antioxidant activity include: (1) number and position of alcohol groups on the aromatic ring; (2) molecular size; (3) flexibility/bulkiness; and (4) water solubility. PCA has classified data into phenolic acids and flavonoids, suggesting two distinct mechanisms of action. ANN has confirmed different mechanisms of action for flavonoids and polyphenolic acids, i.e. breaking of free radical chain reactions by donation of a hydrogen atom to neutralise a free radical and the chelating ability of polyphenolic acids. Conclusion: Although two phenolic acids may have the same relative polarity, their different functional groups may drastically change the nature of their interactions with free radicals, and their antioxidant activity.

Aim and Objective: Thiazol-2-imine derivatives are interested for their pharmaceutical and biologic activities. A literature survey reveals that there have been no any reports on the synthesis of thiazol-2-imine derivatives without substituents in position C-4 and C-5 via one-pot reaction. Herein we report an efficient one-pot route for synthesis of these compounds in good to high yields. Materials and Method: To a stirred mixture of amine (1 mmol) and phenylisothiocyanate (1 mmol) in EtOH (2 ml), KI (0.1 mmol) and DABCO (0.2 mmol) were added under reflux condition. Then α- chloroacetaldehyde (2 mmol) was added drop wise to the reaction mixture. After completion of the reaction, the product was purified over a silica gel short column (EtOAc/n-Hexane, 1:9). Results: One pot reaction of primary amine, phenylisocyanate, and α-chloroacetaldehyde was carried out in the presence of various base and KI in different solvents. It was found that the maximum yield was obtained when the temperature reaches to the boiling point of EtOH. Comparing the reaction results in EtOH, CH3CN, THF, CH2Cl2, and H2O at reflux in the presence of various base, demonstrate that the yield of reaction in EtOH in the presence of DABCO was the most effective. When the reaction runs at the 20 mol% of the DABCO and 10 mol% of the KI, the yield and the time of the reaction were excellent. Conclusion: One-pot procedure can be used for the synthesis of thiazol-2-imine derivatives via the reaction of primary amines, α-chloroacetaldehyde, and phenylisothiocyanate in the presence of a catalytic amount of DABCO and potassium iodide in ethanol.

Objective: Support Vector Regression (SVR) has become increasingly popular in cheminformatics modeling. As a result, SVR-based machine learning algorithms, including Fuzzy-SVR and Least Square-SVR (LS-SVR) have been developed and applied in various research areas. However, at present, few downloadable packages or public-domain software are available for these algorithms. To address this need, we developed the Support vector regression-based Online Learning Equipment (SOLE) web tool (available at http://reccr.chem.rpi.edu/SOLE/index.html) as an online learning system to support predictive cheminformatics and materials informatics studies. Results: In this work, we employed the SOLE system to model transgene expression efficacy of polymers obtained from aminoglycoside antibiotics, which allowed the results of several modeling approaches to be easily compared. All models had test set r² of 0.96-0.98 and test set R² of 0.79-0.84. Y-scrambling test showed the models were stable and not over-fitted. Conclusion: SOLE has a user-friendly interface and includes routine elements of performing QSAR/QSPR studies that can be applied in various research areas. It utilizes rational and sophisticated feature selection, model selection and model evaluation processes.

Aim and Objective: Surface Plasmon Resonance (SPR) based biosensor system was developed for the detection of Delta F508 (ΔF508del) Cystic Fibrosis (CF) mutation in both synthetic and real samples. Material and Method: In order to provide an effective hybridization between probe and the Polymerase Chain Reaction (PCR) amplicons (target), streptavidin was bound to the surface and biotin-tag probe was sent to the streptavidin-coated surface. For the target preparation, blood samples were collected from the patients who suffer from CF. Following the DNA isolation; samples were amplified with PCR with biotin-tag. Before sending the biotin-tag PCR amplicons onto the modified surface, amplicons were also interacted with the helper oligonucleotides to prevent re-annealing of the denatured DNA strands. This kind of ‘multiple surface binding’ method helps increasing the sensitivity of the detection. Results: The limit of detection (S/N= 3) was calculated as 12.24 pico-mole/ml for PCR-like synthetic long target sequence and 13x10⁵ molecules for real samples in less than half an hour. Conclusion: Using the both biotin-tag probe and the helper oligonucleotides together, hybridization was achieved much more efficiently than traditional denaturation protocols for real samples and biotinfree hybridization detection. To the best of our knowledge, the procedure described in this study is one of the simplest, rapid and sensitive methods for CF mutation detection with SPR based biosensor system in real samples.

Aim and Objective: This study introduces a green and effective approach for the preparation of biologically-active heterocyclic compounds including 2-amino-5,10-dihydro-5,10-dioxo-4Hbenzo[ g]chromenes and tetrahydrobenzo[g]quinoline-5,10-diones using one-pot multi-component reactions in the presence of Fe3O4@SiO2-NH2 nanocomposite. The preparation and use of aminofunctionalized Fe3O4@SiO2 as a powerful and reusable nanocatalyst is described. The catalyst was characterized by spectral techniques including FT-IR, SEM, XRD, EDX and VSM analysis. This method offers the advantages of high yields, short reaction times, comfortable work-up and reusability of the catalyst. Material and Method: The amino-functionalization silica-coated magnetite nanocomposite was prepared by three step method and the structure elucidation of the nanocatalyst has been done using various spectroscopic analyses. Then, the Fe3O4@SiO2-NH2 nanocomposite was used in the multicomponent synthesis of 2-amino-5,10-dihydro-5,10-dioxo-4H-benzo[g]chromenes and tetrahydrobenzo[g]quinoline-5,10-diones under reflux conditions. All of the products were analyzed with m.p., ¹H NMR, ¹³C NMR and FT-IR spectroscopy techniques. The study on the recoverability of the nanocatalyst showed the recovered Fe3O4@SiO2-NH2 nanocomposite could be reused sixth consecutive times with a little-decreased activity. Results: Amino-functionalized SiO2 coated Fe3O4 nanocomposite exhibited superparamagnetic behavior and strong magnetization at room temperature. The average crystallite sizes of the catalyst was about 50-60 nm. The obtained magnetic nanocomposite showed excellent catalytic activity as a new heterogeneous magnetic catalyst for the synthesis of some benzo[g]chromenes and tetrahydrobenzo[g]quinoline-5,10-diones. We propose that NH2 groups on the surfaces of nanocomposite act as the Brønsted base and cause to dehydrogenation of substrates to promote the reactions. Conclusion: It was found that Fe3O4@SiO2-NH2 nanocomposite act as an eco-friendly and efficient catalyst for one-pot synthesis of three/four component condensation reactions. In this research, aminofunctionalized Fe3O4@SiO2 was used as recoverable catalyst for the synthesis of 2-amino-5,10- dihydro-5,10-dioxo-4H-benzo[g]chromenes and tetrahydrobenzo[g]quinoline-5,10-diones under reflux conditions. The significant advantages of this method are the reasonably simple work-up, little catalyst loading, short reaction times, excellent yields, non-hygroscopic quality and reusability of the nanocatalyst which is in good agreement with green chemistry disciplines.

Objective: A simple and efficient procedure is achieved for the synthesis of indole-2-one derivatives via three-component reaction of N-alkylisatin, activated acetylenic compounds and alkyl bromide in the presence of triphenylphosphine in water under two conditions; room temperature and microwave irradiation. Materials and Methods: All chemicals used in this work were prepared from Fluka (Buchs, Switzerland) and were used without further purification. N-alkylisatin were synthesized in the laboratory in the procedure that is reported in the literature. Electrothermal 9100 apparatus is employed for measuring of melting points of products. Elemental analyses for C, H, and N were performed with Heraeus CHN-O-Rapid analyzer. Mass spectra were recorded on a FINNIGAN-MAT 8430 spectrometer operating at an ionization potential of 70 eV. Measurement of IR spectra was performed by Shimadzu IR-460 spectrometer. 1H, and 13C NMR spectra were evaluated with a BRUKER DRX- 500 AVANCE spectrometer at 500.1 and 125.8 MHz, respectively. Results: The results were demonstrated that simple mixing of N-alkylisatin, dialkyl acetylenedicarboxylate and alkyl bromides in the presence of triphenylphosphine by using of microwave condition is the efficient method for preparation of indole derivatives in good yields. In the optimized reaction conditions, water is solvent and temperature of the mixture of reaction is 80 oC. Conclusion: In this study, the reaction of activated acetylenic compounds with N-alkylisatin and alkyl bromide in the presence of triphenylphosphine is investigated which is led to a facile synthesis of some functionalized indoles.

Background: Hormone based birth control often causes various side effects. A recent study revealed that temporary infertility without changing hormone levels can be attained by inhibiting Katanin p60 ATPase-containing subunit A-like 1 protein (KATNAL1) which is critical for sperm maturation in the testes. Objective: This study aimed at attaining the most energetically stable three dimensional (3D) structure of KATNAL1 protein using comparative modeling followed by screening of a ligand library of known natural spermicidal compounds for their binding affinity with KATNAL1. This in turn may inhibit the development of mature sperm in the seminiferous epithelium. Method: A series of computational techniques were used for building the 3D structure of KATNAL1 which was further optimized by molecular dynamics (MD) simulation. For revealing the ATP binding mode of KATNAL1, docking study was carried out using the optimized model obtained from the MD simulation. The docking study was also employed to test the binding efficiency of the ligand library. Results: Molecular docking study confirmed the ATP binding of KATNAL1 with various hydrophobic and hydrogen bond interactions. Binding efficiency of the ligand library suggested that calotropin, a cardenolide of Calotropis procera showed the highest binding efficiency against the target protein without toxicity. MD simulation of the docked complex validated the results of the docking study. Conclusion: This study revealed the ATP binding mode of KATNAL1 and identified calotropin as a potential lead molecule against it showing high binding efficiency with good bioavailability and no mutagenicity. Further in vitro and in vivo bioassay of calotropin could facilitate the development of novel non-hormonal male-specific contraceptive in near future.