Identification of cell cycle-regulated genes by convolutional neural network.
Abstract BACKGROUND: The cell cycle-regulated genes express periodically with the cell cycle stages, and the identification and study of these genes can provide a deep understanding of the cell cycle process. Large false positives and low overlaps are big problems in cell cycle-regulated gene detection. METHODS: Here, a computational framework called DLGene was proposed for cell cycle-regulated gene detection. It is based on the convolutional neural network, a deep learning algorithm representing raw form of data pattern without assumption of their distribution. First, the expression data was transformed to c...
Source: Combinatorial Chemistry and High Throughput Screening - April 17, 2017 Category: Chemistry Authors: Liu C, Cui P, Huang T Tags: Comb Chem High Throughput Screen Source Type: research

The safety of ovarian preservation in stage I endometrioid adenocarcinoma based on propensity score matching.
Abstract Most patients with early stage endometrioid adenocarcinoma are treated with hysterectomy and bilateral oophorectomy to prevent ovarian metastasis. But this surgical menopause leads to some long-term sequelae for premenopausal women, especially for young women of childbearing age. This population-based study was to evaluate the safety of ovarian preservation in young women with stage I endometrioid adenocarcinoma.Patients of age 50 or younger than 50 with stage I endometrioid adenocarcinoma were explored from the Surveillance, Epidemiology, and End Results program database during 2004 to 2013. Propensity s...
Source: Combinatorial Chemistry and High Throughput Screening - April 17, 2017 Category: Chemistry Authors: Hou T, Wang Z, Sun Y, Liu C, Li J, Li Y Tags: Comb Chem High Throughput Screen Source Type: research

Docking-related survey on Natural-product-based new monoamine oxidase inhibitors and their therapeutic potential.
The objective of this review is to identify and critically discuss the computational development of multi-target natural and related ligand-MAO protein docking approaches in the study of monoamine oxidase (MAO) enzymes. Computational development of the new compounds form natural and related synthetic origin, active as MAO inhibitors (MAOIs) were discussed in some detail. The docking studies related to the alkaloids and their various categories secondary metabolites from plants like alkaloids, flavonoids and xanthones class of compounds specially caffeine, β-carboline, naphthoquinone, morpholine, piperine, amphetamine ...
Source: Combinatorial Chemistry and High Throughput Screening - April 14, 2017 Category: Chemistry Authors: Dhiman P, Malik N, Khatkar A Tags: Comb Chem High Throughput Screen Source Type: research

Combined Approach of QSAR and Docking Studies for the Design of Local Anaesthetic Agents.
CONCLUSION: Further GRIP docking with the pentameric ligand gated ion channel, 2XQ3 facilitated the mechanistic analysis of interactions of the test molecules active site residues. PMID: 28412906 [PubMed - as supplied by publisher] (Source: Combinatorial Chemistry and High Throughput Screening)
Source: Combinatorial Chemistry and High Throughput Screening - April 13, 2017 Category: Chemistry Authors: Zheng S Tags: Comb Chem High Throughput Screen Source Type: research

Validation of TZD Scaffold as Potential ARIs: Pharmacophore Modelling, Atom-based 3D QSAR and Docking Studies.
Abstract Metabolic disorders associated with diabetic patients are a serious concern. Aldose reductase (ALR2) has been identified as first rate-limiting enzyme in the polyol pathway which catalyzes the reduction of glucose to sorbitol. It represents one of the validated targets to develop potential new chemical entities for the prevention and subsequent progression of microvascular diabetic complications. In order to further understand the intricate structural prerequisites of molecules to act as ALR2 inhibitors, ligand-based pharmacophore model, atom-based 3D-QSAR and structure based drug design studies have been...
Source: Combinatorial Chemistry and High Throughput Screening - March 15, 2017 Category: Chemistry Authors: Dahiya L, Mahapatra MK, Kaur R, Kumar V, Kumar M Tags: Comb Chem High Throughput Screen Source Type: research

Targeting pyrimidine pathway of Plasmodium knowlesi: new strategies towards identification of novel antimalarial chemotherapeutic agents.
Abstract Plasmodium knowlesi has been recently recognized as a human malarial parasite, particularly in the region of south-east Asia. The effective prevention and treatment of this disease is increasingly bound to fail due to the emergence of drug resistance. Hence, design of new drugs against known targets is gaining importance. Pyrimidine pathway is a crucial metabolic pathway in P. knowlesi, and the enzymes involved are also unique in terms of their structure and function as compared to its human counterpart. Thus targeting Dihydroorotase, an enzyme involved in the pyrimidine pathway, provides a promising rout...
Source: Combinatorial Chemistry and High Throughput Screening - March 15, 2017 Category: Chemistry Authors: Rashmi M, Yadav MK, Swati D Tags: Comb Chem High Throughput Screen Source Type: research

Harmony Search as a Powerful Tool for Feature Selection in QSPR Study of the Drugs Lipophilicity.
Abstract Lipophilicity represents one of the most studied and most frequently used fundamental physicochemical properties. In the present work harmony search (HS) algorithm is suggested to feature selection in quantitative structure-property relationship (QSPR) modeling to predict lipophilicity of neutral, acidic, basic and amphotheric drugs that were determined by UHPLC. Harmony search is a music-based metaheuristic optimization algorithm. It was affected by the observation that the aim of music is to search for a perfect state of harmony. Semi-empirical quantum-chemical calculations at AM1 level were used to fin...
Source: Combinatorial Chemistry and High Throughput Screening - March 15, 2017 Category: Chemistry Authors: Bahadori B, Atabati M Tags: Comb Chem High Throughput Screen Source Type: research

The Breakthroughs in Cancer Immune Checkpoint Based Therapy: a review of development in immune checkpoint study and its application.
Abstract Recently, immunotherapy has attracted more attentions to fight cancer due to its selectivity, long lasting effects, and demonstrated better overall survival and tolerance, when compared to patients treated with conventional chemotherapy or radiotherapy alone. The anti-tumor response of patient with cancer is improved either by increasing the effector cell number, the production of soluble mediators, or by modulating the host's immune checkpoint. Over the last decades, many new approaches in immunotherapy have been developed, such as immune checkpoint inhibitors, chimeric antigen receptor T cells (CART), s...
Source: Combinatorial Chemistry and High Throughput Screening - March 15, 2017 Category: Chemistry Authors: Huang Y, Liang D, Liu J, Zeng J, Zeng Y Tags: Comb Chem High Throughput Screen Source Type: research

A feature and algorithm selection method for improving the prediction of protein structural class.
In this study, a feature and algorithm selection method was presented for improving the accuracy of protein structural class prediction. The amino acid compositions and physiochemical features were adopted to represent features and thirty-eight machine learning algorithms collected in Weka were employed. All features were first analyzed by a feature selection method, minimum redundancy maximum relevance (mRMR), producing a feature list. Then, several feature sets were constructed by adding features in the list one by one. For each feature set, thirty-eight algorithms were executed on a dataset, in which proteins were repre...
Source: Combinatorial Chemistry and High Throughput Screening - March 14, 2017 Category: Chemistry Authors: Ni Q, Chen L Tags: Comb Chem High Throughput Screen Source Type: research

Prediction of Lysine Malonylation Sites Based on Pseudo Amino Acid Compositions.
Abstract Protein malonylation is a newly discovered post-translational modification. Due to the limitations of experimental techniques, it is a great challenge to fast and accurately identify malonylation sites. We proposed a computational method to address the problem by extracting protein segments so that the lysine is at the center of each segment, which were further coded by the pseudo amino acid compositions. Then a support vector machine classifier trained by a training dataset was built to distinguish malonylation sites from non-malonylation ones. The leave-one-out test on the training dataset reached the a...
Source: Combinatorial Chemistry and High Throughput Screening - March 14, 2017 Category: Chemistry Authors: Xiang Q, Feng K, Liao B, Liu Y, Huang G Tags: Comb Chem High Throughput Screen Source Type: research

Computational prediction of protein epsilon lysine acetylation sites based on a feature selection method.
In this study, we developed a position-specific method for epsilon lysine acetylation site prediction. Various kinds of features such as position specific scoring matrix (PSSM), amino acid factors (AAF), and disorders were incorporated. A feature selection method based on mRMR (Maximum Relevance Minimum Redundancy) and IFS (Incremental Feature Selection) was employed. Finally, 319 optimal features were selected from total 541 features. Using the 319 optimal features to encode peptides, a predictor was constructed based on dagging. As a result, an accuracy of 69.56% with MCC of 0.2792 was achieved. We analyzed the optimal f...
Source: Combinatorial Chemistry and High Throughput Screening - March 13, 2017 Category: Chemistry Authors: Gao J, Tao XW, Zhao J, Feng YM, Cai YD, Zhang N Tags: Comb Chem High Throughput Screen Source Type: research

Prediction and Identification of Kr üppel-like transcription factors by machine learning method.
In conclusion, we have built two-class classification models for KLFs prediction by novel machine learning methods. PMID: 28292252 [PubMed - as supplied by publisher] (Source: Combinatorial Chemistry and High Throughput Screening)
Source: Combinatorial Chemistry and High Throughput Screening - March 13, 2017 Category: Chemistry Authors: Liao Z, Wang X, Chend X, Zoub Q Tags: Comb Chem High Throughput Screen Source Type: research

Therapeutic, molecular and computational aspects of novel monoamine oxidase (MAO) inhibitors.
Abstract Due to the limited number of MAOs inhibitors in the clinic and several research efforts are aimed at the discovery of novel MAOs inhibitors. At present, high specificity and a reversible mode of inhibition of MAO-A/B are cited as desirable traits in drug discovery process. This will help to reduce the probability of causing target disruption and may increase the duration of action. Most of the existing MAO inhibitors lead to side effects due to lack of affinity and selectivity. Therefore, there is an urgent need to design novel, potent, reversible and selective inhibitors for MAO-A/B. Selective inhibition...
Source: Combinatorial Chemistry and High Throughput Screening - March 10, 2017 Category: Chemistry Authors: Ramesh M, Dokurugu YM, Thompson MD, Soliman M Tags: Comb Chem High Throughput Screen Source Type: research

Prediction of the Ebola virus infection related human genes using protein-protein interaction network.
Abstract Ebola hemorrhagic fever (EHF) is caused by Ebola virus (EBOV). It is reported that human could be infected by EBOV with a high fatality rate. However, association factors between EBOV and host still tend to be ambiguous. According to the "guilt by association" (GBA) principle, proteins interacting with each other are very likely to function similarly or the same. Based on this assumption, we tried to obtain EBOV infection-related human genes in a protein-protein interaction network using Dijkstra algorithm. We hope it could contribute to the discovery of novel effective treatments. Finally, 15 g...
Source: Combinatorial Chemistry and High Throughput Screening - March 10, 2017 Category: Chemistry Authors: Cao H, Zhang Y, Zhao J, Zhu L, Wang Y, Li J, Feng Y, Zhang N Tags: Comb Chem High Throughput Screen Source Type: research

ZnO-nanorods as an efficient heterogeneous catalyst for the synthesis of thiazole derivatives in water.
Abstract Thiazole derivatives are produced by using one-pot multicomponent reactions of acid chlorides, potassium thiocyanate, amino acids, alkyl bromides and ZnO nanorods (NR-ZnO) as the catalyst in water at ambient temperature. These reactions were not performed without using NR-ZnO as the catalyst. Nanorods of ZnO have been prepared by reflux procedure using sodium dodecylsulfate (SDS). Nanorods of ZnO showed a considerable improvement in the field of the product and displayed significant reusable activity. PMID: 28294057 [PubMed - as supplied by publisher] (Source: Combinatorial Chemistry and High Throughput Screening)
Source: Combinatorial Chemistry and High Throughput Screening - March 10, 2017 Category: Chemistry Authors: Shams-Najafi SJ, Gholizadeh M, Ahmadpour A, Rostami-Charati F Tags: Comb Chem High Throughput Screen Source Type: research

Recognizing and predicting thioether bridges formed by lanthionine and β-methyllanthionine in lantibiotics using a random forest approach with feature selection.
Recognizing and predicting thioether bridges formed by lanthionine and β-methyllanthionine in lantibiotics using a random forest approach with feature selection. Comb Chem High Throughput Screen. 2017 Mar 10;: Authors: Wang S, Zhang YH, Zhang N, Chen L, Huang T, Cai YD Abstract Lantibiotics, which are usually produced from Gram-positive bacteria, are regarded as one type of special bacteriocins. Lantibiotics have unsaturated amino acid residues formed by lanthionine (Lan) and β-methyllanthionine (MeLan) residues as a ring structure in the peptide. They are derived from the serine and threoni...
Source: Combinatorial Chemistry and High Throughput Screening - March 10, 2017 Category: Chemistry Authors: Wang S, Zhang YH, Zhang N, Chen L, Huang T, Cai YD Tags: Comb Chem High Throughput Screen Source Type: research

The metabolomic strategy in tuberculosis therapy.
Abstract Tuberculosis causes around 1.4 million deaths every year remaining to be a major cause of morbidity and mortality. Mycobacterium tuberculosis is adept at surviving the assault of our immune system, which has perplexed many researchers. Not only are they difficult to treat, but also difficult to detect accurately. The current reservoir of drugs and method to diagnose them is depleting faster than we are able to replace them with newer one. The advances made in the field of metabolomic have opened up a window of opportunities such as identification of new drug and druggable site, prediction of drug toxicity...
Source: Combinatorial Chemistry and High Throughput Screening - March 9, 2017 Category: Chemistry Authors: Kumar N, Shreshtha AK, Patra S Tags: Comb Chem High Throughput Screen Source Type: research

Structural Exploration of Synthetic Chromones as Selective MAO-B Inhibitors: A Mini Review.
Abstract Specific inhibitors of monoamine oxidase (MAO)-B are considered useful therapeutic agents in targeting of neurological disorders like Alzheimer's and Parkinson's diseases. Due to the academic challenge of designing new hMAO-B inhibitors and the possibility of discovering compounds with improved properties compared to existing MAO-B inhibitors, a number of research groups are searching for new classes of chemical compounds that may act as selective hMAO-B inhibitors. Among these, chromone (4H-1-benzopyran-4-one) derivatives have recently emerged as a chemotype with specific and high potency MAO-B inhibitio...
Source: Combinatorial Chemistry and High Throughput Screening - February 27, 2017 Category: Chemistry Authors: Mathew B, Mathew GE, Petzer JP, Petzer A Tags: Comb Chem High Throughput Screen Source Type: research

Identifying the Main Mosquito Species in the Taiwan Strait Using DNA Barcoding.
In this study, we collected a total of 144 specimens from 42 mosquito specimens belonging to 9 genera from both sides of the Taiwan Strait during 2013 and 2014. We then applied the COI DNA Barcoding technique to classify the specimens and performed a phylogenetic analysis to infer the evolutionary history of these mosquitoes. Based on the analyses, we found that though the mosquitoes from different sides of the Taiwan Strait share a lot of commonality, they have a few regional specificities. Our results also suggested a very small divergences (1%~9%) between specimens from the same mosquito species and relatively large div...
Source: Combinatorial Chemistry and High Throughput Screening - February 17, 2017 Category: Chemistry Authors: Gao B, Fang Y, Zhang J, Wu R, Xu B, Xie L Tags: Comb Chem High Throughput Screen Source Type: research

In silico prediction of chemical toxicity profile using local lazy learning.
In this study, we carried out a research on six types of toxicities: (I) Acute Toxicity; (II) Mutagenicity; (III) Tumorigenicity; (IV) Skin and Eye Irritation; (V) Reproductive Effects; (VI) Multiple Dose Effects, using local lazy learning (LLL) method for multi-label learning. 17,120 compounds were split into the training set and the test set as a ratio of 4:1 by using the Kennard-Stone algorithm. Four types of properties, including molecular fingerprints (ECFP_4 and FCFP_4), descriptors, and chemical-chemical-interactions, were adopted for model building. The model 'ECFP_4+LLL' yielded the best performance for the test s...
Source: Combinatorial Chemistry and High Throughput Screening - February 17, 2017 Category: Chemistry Authors: Lu J, Zhang P, Zou X, Zhao X, Cheng K, Zhao Y, Bi Y, Zheng M, Luo X Tags: Comb Chem High Throughput Screen Source Type: research

A novel protein characterization based on Pseudo Amino Acids composition and Star-like graph topological indices.
Abstract In the work, a new description of proteins based on five topological indices of star-like graph representation and the occurrence frequency of 20 amino acids was proposed to compare the similarities of proteins. A phylogenetic tree of eight ND6 proteins was constructed to demonstrate the effectiveness and rationality of our approach. Analogously, we applied this method to RNA polymerase proteins of some subtypes of influenza virus to infer their phylogenetic relationship. The results showed that the phylogenetic relationship among RNA polymerase of influenza virus is closely related to distributions of sp...
Source: Combinatorial Chemistry and High Throughput Screening - February 17, 2017 Category: Chemistry Authors: He P, Tao H, Ma T, Dai Q, Yao Y Tags: Comb Chem High Throughput Screen Source Type: research

Molecular characterization and in-silico analysis of the tissue inhibitor of metalloproteinases-3 (TIMP-3) gene of canine mammary tumor.
CONCLUSIONS: The three dimensional structure of TIMP-3 was generated and its interactions with MMP-2 and MMP-9, demonstrates the role of key binding residues. Until now, no structural details were available for canine TIMP-3 proteins, hence this study will broaden the horizon towards understanding the structural and functional aspects of this proteins in canine. PMID: 28215146 [PubMed - as supplied by publisher] (Source: Combinatorial Chemistry and High Throughput Screening)
Source: Combinatorial Chemistry and High Throughput Screening - February 17, 2017 Category: Chemistry Authors: Yadav PK, Yadav BS, Panigrahi PN, Tripathi V, Chaturvedi N, Kataria M Tags: Comb Chem High Throughput Screen Source Type: research

Development of in vitro co-culture model in anti-cancer drug development cascade.
Abstract Tumour microenvironment is recognized as a major determinant of intrinsic resistance to anticancer therapies. In solid tumour types, such as breast cancer, lung cancer and pancreatic cancer, stromal components provide a fibrotic niche, which promotes stemness, EMT, chemo- and radio-resistance of tumour. However, this microenvironment is not recapitulated in the conventional cell monoculture or xenografts, hence these in vitro and in vivo preclinical models are unlikely to be predictive of clinical response; which might attribute to the poor predictivity of these preclinical drug-screening models. In this ...
Source: Combinatorial Chemistry and High Throughput Screening - February 1, 2017 Category: Chemistry Authors: Xu R Tags: Comb Chem High Throughput Screen Source Type: research

Machine learning and molecular dynamics based insights into mode of actions of insulin degrading enzyme modulators.
CONCLUSIONS: The present study shows that such in silico approaches can be effectively used to discover and select active compounds from unseen data for accelerated drug development process. The machine learning models generated in the present study were used to screen Traditional Chinese Medicine (TCM) database to identify the phytocompounds already been reported to have therapeutic effects against AD. PMID: 28137222 [PubMed - as supplied by publisher] (Source: Combinatorial Chemistry and High Throughput Screening)
Source: Combinatorial Chemistry and High Throughput Screening - January 30, 2017 Category: Chemistry Authors: Jamal S, Goyal S, Shanker A, Grover A Tags: Comb Chem High Throughput Screen Source Type: research

Phytochemical Constituents, ChEs and Urease Inhibition, Antiproliferative and Antioxidant Properties of Elaeagnus umbellata Thunb.
Abstract Due to the common ethnopharmacological used or scientifically examined biochemical properties, Elaeagnaceae family, Elaeagnus umbellata Thunb. (autumn olive) was worth investigated. In this investigation, we revealed antioxidant, antiproliferative and enzyme inhibition activities of the water, methanol, ethanol, acetone, ethyl acetate and hexane extracts of E. umbellata as well as contents of their phenolic, flavonoid, anthocyanin, ascorbic acid, lycopene and b-carotene. The antioxidant activity was screened by phosphomolybdenum assay. The scavenging activities of the extracts were determined against 1,1...
Source: Combinatorial Chemistry and High Throughput Screening - January 27, 2017 Category: Chemistry Authors: Ozen T, Yenigun S, Altun M, Demirtas I Tags: Comb Chem High Throughput Screen Source Type: research

A novel gene selection method based on sparse representation and Max-Relevance and Min-Redundancy.
This article proposes a new method based on sparse representation and MRMR algorithm(SRCMRMR), using the sparse representation coefficient to represent the relevance of genes and correlation between genes and categories. The SRCMRMR algorithm contains two steps. Firstly,the genes irrelevant to the classification target are removed by using sparse representation coefficient. Secondly, sparse representation coefficient is used to calculate the correlation between genes and the most representative gene with the highest evaluation. The former ones are under the influence of other genes, while the latter is selected throu...
Source: Combinatorial Chemistry and High Throughput Screening - January 26, 2017 Category: Chemistry Authors: Chen M, He X, Duan SB, Deng YW Tags: Comb Chem High Throughput Screen Source Type: research

Exploration of new and potent lead molecules against CAAX prenyl protease I of Leishmania donovani through Pharmacophore based virtual screening approach.
This study mainly focuses on developing new and potent inhibitors against CAXX prenyl protease I of Leishmania donovani. MATERIALS AND METHODS: Pharmacophore based virtual screening was carried out using derivatives of bi-substrate analog farnesyl transferase inhibitors reported against CAAX prenyl proteases I. On the basis of ligand based pharmacophore model we have obtained 5 point pharmacophore AAADR with three hydrogen bond acceptors (A), one hydrogen bond donor (D) and one aromatic ring. The newly identified hits through pharmacophore model were further docked into the active site of the modeled protein. To get f...
Source: Combinatorial Chemistry and High Throughput Screening - January 20, 2017 Category: Chemistry Authors: Prabhu SV, Tiwari K, Suryanarayanan V, Dubey VK, Singh SK Tags: Comb Chem High Throughput Screen Source Type: research

Anticancer Properties of Traditional Chinese Medicine.
Abstract Cancer is a systemic disease. Cancer occurrence is associated with several factors, including cell proliferation, apoptosis, metastasis, tumor microenvironment and immune system. Traditional Chinese medicine (TCM) has been widely used for thousands of years in China for its anti-cancer therapeutic effect. The advantage of using TCM is related to its action on multiple signaling pathways and molecular targets related to cancer, whilst causing few adverse effects. TCM exerts its anticancer effects through multiple mechanisms, including apoptosis induction, proliferation inhibition, metastasis suppression, m...
Source: Combinatorial Chemistry and High Throughput Screening - January 16, 2017 Category: Chemistry Authors: Yan Z, Lai Z, Lin J Tags: Comb Chem High Throughput Screen Source Type: research

Molecular modeling and dynamics simulation analysis of KATNAL1 for identification of novel inhibitor of sperm maturation.
In conclusion, our results 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. PMID: 28093975 [PubMed - as supplied by publisher] (Source: Combinatorial Chemistry and High Throughput Screening)
Source: Combinatorial Chemistry and High Throughput Screening - January 16, 2017 Category: Chemistry Authors: Sarma K, Roychoudhury S, Bora SS, Dehury B, Parida P, Das S, Das R, Dohutia C, Nath S, Deb B, Modi MK Tags: Comb Chem High Throughput Screen Source Type: research

Recent advances in developing photosensitizers for photodynamic cancer therapy.
Abstract Photosensitizers are key molecules used in photodynamic cancer therapy (PDT), which is an effective therapeutic modality option for several diseases and non-oncological disorders. Due to its lower systemic toxicity and its ability to destroy tumors selectively, PDT has been considered clinical avenue for the treatment of several cancers. Three essential elements are involved in a PDT procedure: a photosensitizer, light of a specific wavelength, and singlet oxygen. However, the properties of conventional photosensitizers exhibit some drawbacks that may limit their use. Nanoparticles can provide significant...
Source: Combinatorial Chemistry and High Throughput Screening - January 13, 2017 Category: Chemistry Authors: Chen C, Wang J, Li X, Liu X, Han X Tags: Comb Chem High Throughput Screen Source Type: research

Phytochemicals - A Novel and Prominent Source of Anti-cancer Drugs against Colorectal Cancer.
Abstract Colorectal cancer (CRC) is a malignant disease whose incidence and mortality rates are greatly influenced by environmental factors. Under-treatment of CRC such as a poor diagnostic evaluation, less aggressive surgery, less intensive chemotherapy results in metastasizing of the primary tumor cells and recurrence of cancer. Prolonged chemotherapy treatment against cancer is hazardous to the patients, which also limits its use in cancer therapy. Current research in developing a novel anti-cancer agent, direct towards finding a better anti-metastatic and an anti-invasive drug with reduced side effects. In thi...
Source: Combinatorial Chemistry and High Throughput Screening - January 12, 2017 Category: Chemistry Authors: Mahadevappa R, Kwok HF Tags: Comb Chem High Throughput Screen Source Type: research

New imidazole-based compounds active against Trypanosoma cruzi.
This study screened several imidazole-based compounds for anti-Trypanosoma potential. Using 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. All test compounds demonstrated interesting trypanocidal potential with IC50 values in the µM range (1amplt; 1C50 amplt;8 µM). The activities of the test compounds compared favorably with BZN, which had an IC50 value ca. 30 ...
Source: Combinatorial Chemistry and High Throughput Screening - January 10, 2017 Category: Chemistry Authors: Adeyemi OS, Molina MT, Eseola AO, Fonseca-Berzal C, Gomez-Barrio A Tags: Comb Chem High Throughput Screen Source Type: research

Cystic Fibrosis Mutation Detection with SPR Biosensor in Real Samples via Multiple Surfaces Binding Method.
Abstract Surface Plasmon Resonance (SPR) based biosensor system was developed for the detection of Delta F508 (DF508del) Cystic Fibrosis (CF) mutation in both synthetic and real samples. 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 a...
Source: Combinatorial Chemistry and High Throughput Screening - January 3, 2017 Category: Chemistry Authors: Kayran YU, Ozkan-Ariksoysal D, Topkaya SN, Kaymaz BT, Can BK Tags: Comb Chem High Throughput Screen Source Type: research

Probing into the Molecular Requirements for Antioxidant Activity in Plant Phenolic Compounds Utilizing a Combined Strategy of PCA and ANN.
This study investigates molecular structural requirements that are responsible for the antioxidant activity in phenolic compounds. Antioxidant activity 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. Both models agreed that structural characteristics of phenolic compounds responsible for the antioxidant activity include: (1) number and position of alco...
Source: Combinatorial Chemistry and High Throughput Screening - January 2, 2017 Category: Chemistry Authors: Agatonovic-Kustrin S, Morton DW, Ristivojevic P Tags: Comb Chem High Throughput Screen Source Type: research

DephosSitePred: a high accuracy predictor for protein dephosphorylation sites.
In this study, we developed a novel PTP site prediction model, DephosSitePred, based on bi-profile sequence features. Weight parameters in the support vector machine were applied to improve the low sensitivity due to extremelyimbalanced datasets.DephosSitePred yielded Matthews correlation coefficientsof 0.686 for proteintyrosine phosphatase 1B (PTP1B), 0.668 for Src homology region 2 domain-containing phosphatase (SHP)-1,and 0.748 for SHP-2substrate sites, whichsignificantly outperformed other existing predictors. Moreover, 30 times of 5-fold cross-validations showed that DephosSitePred achieved average area under the curv...
Source: Combinatorial Chemistry and High Throughput Screening - December 28, 2016 Category: Chemistry Authors: Jia C, He W, Zou Q Tags: Comb Chem High Throughput Screen Source Type: research

Synthesis of spiro indole-2-ons using three component reactions of N-alkylisatins and triphenylphosphonium intermediates.
Abstract A simple and efficient procedure is achieved for the synthesis of indole-2-on derivatives via three-component reaction of N-alkylisatin, activated acetylenic compounds and alkyl bromide in the presence of triphenylphosphine in water under two conditions of room temperature and microwave irradiation. The yields of reaction in cavity of microwave were good and the reaction time was decreased in contrast to the other method. The method recommends several advantages involving high yields of products and an easy work-up procedure. PMID: 28031012 [PubMed - as supplied by publisher] (Source: Combinatorial C...
Source: Combinatorial Chemistry and High Throughput Screening - December 28, 2016 Category: Chemistry Authors: Moradi AV Tags: Comb Chem High Throughput Screen Source Type: research

Development of a Web-enabled SVR-based Machine Learning Platform and Its Application on Modeling Transgene Expression Activity of Aminoglycoside-derived Polycations.
Abstract 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 material...
Source: Combinatorial Chemistry and High Throughput Screening - December 28, 2016 Category: Chemistry Authors: Zhen Z, Potta T, Lanzillo NA, Rege K, Breneman CM Tags: Comb Chem High Throughput Screen Source Type: research

Predicting citrullination sites in protein sequences using mRMR method and random forest algorithm.
In this study, we investigated the peptide segments that contain the citrullination sites in the centers, which were encoded into numeric digits from four aspects. A reliable feature selection technique, maximum-relevance-minimum-redundancy (mRMR), was applied to analyze these features, and four algorithms, including random forest (RF), Dagging, nearest neighbor algorithm (NNA), and support vector machine (SVM), together with the incremental feature selection (IFS) method were adopted to extract important features, by which an optimal classifier derived from RF algorithm was constructed to predict citrullination sites. 44 ...
Source: Combinatorial Chemistry and High Throughput Screening - December 27, 2016 Category: Chemistry Authors: Zhang Q, Sun X, Feng K, Wang S, Zhang YH, Wang S, Lu L, Cai YD Tags: Comb Chem High Throughput Screen Source Type: research

Drug repurposing in anticancer reagent development.
Abstract The development process for cancer drugs is risky, lengthy and costly. Exploration of the anticancer potential of listed non-cancer drugs has become a popular research field in the pharmaceutical industry. The efficacy of various drugs are tested in multiple cancer types and the mechanisms underlying their effect were investigated. In this review, we have summarized the drug relocation instances for different cancer types in recent years and discussed the future direction of drug repurposing. PMID: 28025934 [PubMed - as supplied by publisher] (Source: Combinatorial Chemistry and High Throughput Screening)
Source: Combinatorial Chemistry and High Throughput Screening - December 26, 2016 Category: Chemistry Authors: Chen PC, Liu X, Lin Y Tags: Comb Chem High Throughput Screen Source Type: research

Developmental Phases of Anticancer Screening Models.
Abstract The development of new screening models for cancer therapy is indispensable for the improvement of cancer treatment, and for the creation of alternative possibilities in the field of chemotherapy. Screening models are routinely used to reduce the cost and resources involved in anticancer drug development. The value of any screening model will ultimately be ascertained by its ability to reliably predict the clinical response. Traditional in vivo screening models have been replaced with cell-based screening assays, and these cell-based models are under constant development to better mimic in vivo conditions...
Source: Combinatorial Chemistry and High Throughput Screening - December 26, 2016 Category: Chemistry Authors: Alsamman K, El-Masry OS Tags: Comb Chem High Throughput Screen Source Type: research

Recoverable nanocatalyst for the preparation of 2-amino-5,10-dihydro-5,10-dioxo-4H-benzo[g]chromenes and tetrahydrobenzo[g]quinoline-5,10-diones.
Abstract In this research an advanced and effective approach for the three-component reactions of malononitrile, 2-hydroxynaphthalene-1,4-dione and diverse aromatic aldehydes has been described using amino-functionalized Fe3O4@SiO2 as catalyst under reflux conditions. In addition, Fe3O4@SiO2-NH2 nanocomposite catalyzed four-component synthesis of tetrahydrobenzo[g]quinolines. The structure of nanocatalyst was determined by FT-IR, SEM, XRD, EDX and VSM analysis. The remarkable advantages of the presented method are environmentally friendly, low cost, excellent yields and absent of hazardous and toxic catalysts. ...
Source: Combinatorial Chemistry and High Throughput Screening - December 23, 2016 Category: Chemistry Authors: Ghasemzadeh MA, Elyasi Z, Azimi-Nasrabad M, Mirhosseini-Eshkevari B Tags: Comb Chem High Throughput Screen Source Type: research

Protein modeling and molecular dynamics simulation of cloned Regucalcin (RGN) gene from Bubalus bubalis.
Abstract Regucalcin (RGN), a calcium regulating protein having anti prolific, anti-apoptotic functions, plays important part in the biosynthesis of ascorbic acid. It is a highly conserved protein that has been reported from many tissue types of various vertebrate species. Employing its effect of regulating enzyme activities through reaction with sulfhydryl group (-SH) and calcium, structural level study is believed to offer a better understanding of its binding properties along with information exploited as part of the regulatory mechanisms of RGN. After successfully achieving amplification corresponding to reguca...
Source: Combinatorial Chemistry and High Throughput Screening - December 20, 2016 Category: Chemistry Authors: Pillai H, Yadav BS, Chaturvedi N, Jan AT, Gupta GK, Baig MH, Bhure SK Tags: Comb Chem High Throughput Screen Source Type: research

Synchronized Fast SPE and UFLC Methods for the Analyses of Eight Antidiabetic Drugs in Human Plasma.
Abstract The number of the diabetic patients is increasing rapidly globally. The treatment of these patients is a complex phenomenon due to the use of the different drugs. The present article reports a synchronized fast SPE-UFLC separation of eight antidiabetic drugs in human plasma. The separated drugs include metformin HCl, vildagliptin, gliclazide, linagliptin, sitagliptin, pioglitazone, glimepiride and repaglinide. The column used was Sunshell C18 (150 x 4.6 mm, 2.6 µm) with mobile phase of acetate buffer (0.05% TEA in 0.05 M ammonium acetate of pH 7.0 with H 3PO4)-acetonitrile (60:40, v/v). The flow rat...
Source: Combinatorial Chemistry and High Throughput Screening - December 20, 2016 Category: Chemistry Authors: Ali I, Dutta K, Jain AK Tags: Comb Chem High Throughput Screen Source Type: research

Metabolomics as a functional tool in screening gastro intestinal diseases: Where are we in high throughput screening?
Abstract Identifying novel bio markers in gastro intestinal disease is a promising method where a comprehensive analysis of the metabolome is performed. Metabolomics has evolved enormously in the past decade, paving a path in gastro intestinal disease research, especially diseases which lead to high morbidity and mortality. Metabolomics involves identifying metabolites such as anti-oxidants, and amino acids etc., which are screened in the urine, feces and tissue samples. Certain cases employ advanced tools like GC-MS, 1HNMR and GC-MS/SPME which reveal valuable information concerning disease severity and differenti...
Source: Combinatorial Chemistry and High Throughput Screening - December 20, 2016 Category: Chemistry Authors: Gundamaraju R, Vemuri R, Eri R, Ishiki HM, Coy-Barrera E, Yarla NS, Dos Santos SG, Alves MF, Filho JM, Diniz MF, Scotti MT, Scotti L Tags: Comb Chem High Throughput Screen Source Type: research

A two-layer model to identify hepatitis B virus related chronic hepatitis and liver cirrhosis based on plasma microRNA biomarkers.
CONCLUSION: Compared with previous models, the two-layer model was more consistent with the underlying pathological progress of HBV related diseases from health to chronic hepatitis and further to liver cirrhosis. It could also take the results of other diagnostic tests into account, which could be useful in both physical examination and disease diagnosis. PMID: 28000564 [PubMed - as supplied by publisher] (Source: Combinatorial Chemistry and High Throughput Screening)
Source: Combinatorial Chemistry and High Throughput Screening - December 20, 2016 Category: Chemistry Authors: Hou T, Wang Z, Jin W, Liu C, Sun X, Li N, Zhang Y, Chen Y, Zhang W, Li Y Tags: Comb Chem High Throughput Screen Source Type: research

Towards Tyrosine Metabolism in Esophageal Squamous Cell Carcinoma.
CONCLUSION: Our results reveal that tyrosine metabolism is disturbed in ESCC patients and the metabolites involved in tyrosine pathway can be used as diagnostic biomarkers of the disease. Findings of this study can help investigate pathogenesis of ESCC and facilitate understanding mechanism of the disease. PMID: 28000565 [PubMed - as supplied by publisher] (Source: Combinatorial Chemistry and High Throughput Screening)
Source: Combinatorial Chemistry and High Throughput Screening - December 20, 2016 Category: Chemistry Authors: Cheng J, Zheng G, Jin H, Gao X Tags: Comb Chem High Throughput Screen Source Type: research

Inferring Alcoholism SNPs and Regulatory Chemical Compounds Based on Ensemble Bayesian Network.
In this study, we utilized the Ensemble Bayesian Network (EBN) method to identify causal SNPs of alcoholism based on the verified GAW14 data. Thirteen out of eighteen SNPs directly connected with alcoholism were found concordance with potential risk regions of alcoholism in OMIM database. As a number of SNPs were found contributing to alteration on gene expression, known as expression quantitative trait loci (eQTLs), we further sought to identify chemical compounds acting as regulators of alcoholism genes captured by causal SNPs. Chloroprene and valproic acid were identified as the expression regulators for genes C11orf66 ...
Source: Combinatorial Chemistry and High Throughput Screening - December 20, 2016 Category: Chemistry Authors: Chen H, Sun J, Jiang H, Wang X, Wu L, Wu W, Wang Q Tags: Comb Chem High Throughput Screen Source Type: research

Analysis and prediction of myristoylation sites using the mRMR method, the IFS method and an extreme learning machine algorithm.
Abstract Myristoylation is an important hydrophobic post-translational modificationthat is covalently bound tothe amino group of Gly residueson the N-terminus of proteins. The many diversefunctions of myristoylation on proteins,such as membrane targeting, signal pathway regulation and apoptosis,are largely due to the lipid modification,whereasabnormal or irregular myristoylation on proteins can lead to several pathological changes in the cell. To better understand the function o fmyristoylated sites and to correctly identify them in protein sequences, this study conducted a novel investigation of myristoylation si...
Source: Combinatorial Chemistry and High Throughput Screening - December 20, 2016 Category: Chemistry Authors: Wang S, Zhang YH, Huang G, Chen L, Cai YD Tags: Comb Chem High Throughput Screen Source Type: research

Editorial: Beyond Pills and Needles: Delivering on New Promise.
PMID: 27966399 [PubMed - in process] (Source: Combinatorial Chemistry and High Throughput Screening)
Source: Combinatorial Chemistry and High Throughput Screening - December 16, 2016 Category: Chemistry Authors: Lushington GH Tags: Comb Chem High Throughput Screen Source Type: research

Editorial (Thematic Issue: An Update of HTS for Selected Hydrolases).
PMID: 27829342 [PubMed - in process] (Source: Combinatorial Chemistry and High Throughput Screening)
Source: Combinatorial Chemistry and High Throughput Screening - November 11, 2016 Category: Chemistry Authors: Sandoval G Tags: Comb Chem High Throughput Screen Source Type: research