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https://www.readbyqxmd.com/read/29147824/an-integrated-qsar-modeling-approach-to-explore-the-structure-property-and-selectivity-relationships-of-n-benzoyl-l-biphenylalanines-as-integrin-antagonists
#1
Sk Abdul Amin, Nilanjan Adhikari, Sonam Bhargava, Shovanlal Gayen, Tarun Jha
Integrins [Formula: see text] and [Formula: see text] are important targets to treat different inflammatory diseases, such as multiple sclerosis, inflammatory bowel diseases, rheumatoid arthritis, atherosclerosis, and asthma. Despite being valuable targets, only a few work has been reported to date regarding molecular modeling studies on these integrins. Not only that, none of these reports addressed the selectivity issue between integrins [Formula: see text] and [Formula: see text]. Therefore, a major challenge regarding the design and discovery of selective integrin antagonists remains...
November 17, 2017: Molecular Diversity
https://www.readbyqxmd.com/read/29143468/predictive-qsar-modeling-study-on-berberine-derivatives-with-hypolipidemic-activity
#2
Pan Yu, Dongdong Li, Junjun Ni, Linguo Zhao, Gang Ding, Zhenzhong Wang, Wei Xiao
Berberine (BBR) isolated from a Chinese herb, is identified as a new cholesterol-lowering small molecule, and hundreds of berberine derivatives have been obtained for optimization of their hypolipidemic activities in recent years. However, so far there is no available quantitative structure-activity relationship (QSAR) model used for the development of novel BBR analogs with hypolipidemic activities, mainly due to lack of lipid-lowering molecular mechanisms and target identification of BBR. In this paper, the tactics using ligand efficiency indices instead of pIC50 as the activity could be adopted for the development of BBR QSAR models...
November 16, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/29141777/design-synthesis-and-biological-evaluation-of-novel-oseltamivir-derivatives-as-potent-neuraminidase-inhibitors
#3
Zhen Wang, Li Ping Cheng, Xing Hua Zhang, Wan Pang, Liang Li, Jin Long Zhao
Neuraminidase (NA) is one of the particular potential targets for novel antiviral therapy. In this work, a series of neuraminidase inhibitors with the cyclohexene scaffold were studied based upon the combination of 3D-QSAR, molecular docking, and molecular dynamics techniques. The results indicate that the built 3D-QSAR models yield reliable statistical information: the correlation coefficient (r(2)) and cross-validation coefficient (q(2)) of CoMFA (comparative molecular field analysis) are 0.992 and 0.819; the r(2) and q(2) of CoMSIA (comparative molecular similarity analysis) are 0...
November 4, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/29139200/allosteric-mechanism-of-quinoline-inhibitors-for-hiv-rt-associated-rnase-with-md-simulation-and-dynamics-fluctuation-network
#4
Yi Cai, Hao Liu, Haifeng Chen
The human immunodeficiency virus (HIV) is a retrovirus which infects T lymphocyte of human body and causes Immunodeficiency. Reverse transcriptase inhibitors (RTIs) can inhibit some functions of RT, preventing virus synthesis (double-stranded DNA), so that HIV virus replication can be reduced. Experimental results indicate a series of benzimidazole-based inhibitors which target HIV RT-associate RNase to inhibit the reverse transcription of HIV virus. However, the allosteric mechanism is still unclear. Here, molecular dynamics simulations and dynamics fluctuation network analysis were used to reveal the binding mode between the inhibitors and RT-associate RNase...
November 15, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/29137937/design-synthesis-and-evaluation-of-3-arylidene-azetidin-2-ones-as-potential-antifungal-agents-against-alternaria-solani-sorauer
#5
Wang Delong, Wu Yongling, Wang Lanying, Feng Juntao, Zhang Xing
A new concise and facile method was explored to synthesize a collection of new 3-arylidene azetidin-2-ones, which could be regarded as the derivatives of the hybrid scaffold of bioactive natural cinnamamide and heterocycle azetidi-2-one. The structures of the synthesized compounds were characterized by (1)H, (13)C NMR, and MS; and their antifungal activity were evaluated against Alternaria solani Sorauer. These antifungal data were subjected to a quantitative structure-activity relationship (QSAR) analysis using Codessa software on the basis of the results from B3LYP/6-31G(d,p) quantum calculations...
November 4, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/29137864/synthesis-molecular-docking-and-qsar-study-of-sulfonamide-based-indoles-as-aromatase-inhibitors
#6
Ratchanok Pingaew, Prasit Mandi, Veda Prachayasittikul, Supaluk Prachayasittikul, Somsak Ruchirawat, Virapong Prachayasittikul
Thirty four of indoles bearing sulfonamides (11-44) were synthesized and evaluated for their anti-aromatase activities. Interestingly, all indole derivatives inhibited the aromatase with IC50 range of 0.7-15.3 μM. Indoles (27-36) exerted higher aromatase inhibitory activity than that of ketoconazole. The phenoxy analogs 28 and 34 with methoxy group were shown to be the most potent compounds with sub-micromolar IC50 values (i.e., 0.7 and 0.8 μM, respectively) without affecting to the normal cell line. Molecular docking demonstrated that the indoles 28, 30 and 34 could occupy the same binding site on the aromatase pocket and share several binding residues with those of the natural substrate (androstenedione), which suggested the competitive binding could be the mode of inhibition of the compounds...
October 20, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29135323/impact-assessment-of-the-rational-selection-of-training-and-test-sets-on-the-predictive-ability-of-qsar-models
#7
M F Andrada, E G Vega-Hissi, M R Estrada, J C Garro Martinez
This study performed an analysis of the influence of the training and test set rational selection on the quality and predictively of the quantitative structure-activity relationship (QSAR) model. The study was carried out on three different datasets of Influenza Neuraminidase (H1N1) inhibitors. The three datasets were divided into training and test sets using three rational selection methods: based on k-means, Kennard-Stone algorithm and Activity and the results were compared with Random selection. Then, a total of 31,490 mathematical models were developed and those models that presented a determination coefficient higher than: r(2)train > 0...
November 14, 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/29135084/identification-of-bioactive-scaffolds-based-on-qsar-models
#8
Tomoki Nakagawa, Tomoyuki Miyao, Kimito Funatsu
In medicinal chemistry, the molecular scaffolds commonly found in compounds with preferable biological activities are called bioactive scaffolds. They are important because if present in a structure, it is more likely that the compound will be bioactive. Traditionally, medicinal chemists use their knowledge to identify bioactive scaffolds from a given data set after systematic extraction of all candidate scaffolds. However, manually sorting all the scaffolds is not practical as the number of compounds in a data set is often very large...
November 14, 2017: Molecular Informatics
https://www.readbyqxmd.com/read/29134756/development-of-predictive-qsar-models-of-4-thiazolidinones-antitrypanosomal-activity-using-modern-machine-learning-algorithms
#9
Anna Kryshchyshyn, Oleg Devinyak, Danylo Kaminskyy, Philippe Grellier, Roman Lesyk
This paper presents novel QSAR models for the prediction of antitrypanosomal activity among thiazolidines and related heterocycles. The performance of four machine learning algorithms: Random Forest regression, Stochastic gradient boosting, Multivariate adaptive regression splines and Gaussian processes regression have been studied in order to reach better levels of predictivity. The results for Random Forest and Gaussian processes regression are comparable and outperform other studied methods. The preliminary descriptor selection with Boruta method improved the outcome of machine learning methods...
November 14, 2017: Molecular Informatics
https://www.readbyqxmd.com/read/29134510/drug-design-for-alk-positive-nsclc-an-integrated-pharmacophore-based-3d-qsar-and-virtual-screening-strategy
#10
Nivya James, V Shanthi, K Ramanathan
The increasing death rates related to anaplastic lymphoma kinase (ALK)-positive lung cancer culminated in a significant interest in the discovery of novel inhibitors for ALK. In the present research work, pharmacophore-based 3D QSAR modeling and virtual screening strategy have been carried out to address these issues. Initially, a five-point pharmacophore model was developed using the biological data of 50 compounds which includes an FDA-approved ALK inhibitor, crizotinib. Using the generated pharmacophore, a 3D QSAR model was developed and used as a query to screen the DrugBank database...
November 13, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/29133058/design-and-synthesis-of-thienopyrimidine-urea-derivatives-with-potential-cytotoxic-and-pro-apoptotic-activity-against-breast-cancer-cell-line-mcf-7
#11
Eman F Abdelhaleem, Mohammed K Abdelhameid, Asmaa E Kassab, Manal M Kandeel
A series of novel tetrahydrobenzothieno[2,3-d]pyrimidine urea derivatives was synthesized according to fragment-based design strategy. They were evaluated for their anticancer activity against MCF-7 cell line. Three compounds 9c, 9d and 11b showed 1.5-1.03 folds more potent anticancer activity than doxorubicin. In this study, a promising multi-sited enzyme small molecule inhibitor 9c, which showed the most potent anti-proliferative activity, was identified. The anti-proliferative activity of this compound appears to correlate well with its ability to inhibit topoisomerase II (IC50 = 9...
October 28, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29133041/design-synthesis-and-biological-evaluation-of-novel-aryldiketo-acids-with-enhanced-antibacterial-activity-against-multidrug-resistant-bacterial-strains
#12
Ilija N Cvijetić, Tatjana Ž Verbić, Pedro Ernesto de Resende, Paul Stapleton, Simon Gibbons, Ivan O Juranić, Branko J Drakulić, Mire Zloh
Antimicrobial resistance (AMR) is a major health problem worldwide, because of ability of bacteria, fungi and viruses to evade known therapeutic agents used in treatment of infections. Aryldiketo acids (ADK) have shown antimicrobial activity against several resistant strains including Gram-positive Staphylococcus aureus bacteria. Our previous studies revealed that ADK analogues having bulky alkyl group in ortho position on a phenyl ring have up to ten times better activity than norfloxacin against the same strains...
November 10, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29132751/synthesis-biological-activities-and-sar-studies-of-new-3-substitutedphenyl-4-substitutedbenzylideneamino-1-2-4-triazole-mannich-bases-and-bis-mannich-bases-as-ketol-acid-reductoisomerase-inhibitors
#13
Bao-Lei Wang, Li-Yuan Zhang, Xing-Hai Liu, Yi Ma, Yan Zhang, Zheng-Ming Li, Xiao Zhang
A series of new 3-substitutedphenyl-4-substitutedbenzylideneamino-1,2,4-triazole Mannich bases and bis-Mannich bases were synthesized through Mannich reaction with high yields. Their structures were confirmed by means of IR, (1)H NMR, (13)C NMR and elemental analysis. The preliminary bioassay indicated that compounds 7g, 7h and 7l exhibited potent in vitro inhibitory activities against ketol-acid reductoisomerase (KARI) with Ki value of (0.38 ± 0.25), (6.59 ± 2.75) and (8.46 ± 3.99) μmol/L, respectively, and were comparable with IpOHA...
November 10, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/29130688/from-classification-to-regression-multitasking-qsar-modeling-using-a-novel-modular-neural-network-simultaneous-prediction-of-anticonvulsant-activity-and-neurotoxicity-of-succinimides
#14
Davor Antanasijević, Jelena Antanasijević, Nemanja Trišović, Gordana Ušćumlić, Viktor Pocajt
Succinimides, which contain a pharmacophore responsible for anticonvulsant activity, are frequently used antiepileptic drugs and the synthesis of their new derivatives with improved efficacy and tolerability presents an important task. Nowadays, multitarget/tasking methodologies focused on quantitative-structure activity relationships (mt-QSAR/mtk-QSAR) have an important role in the rational design of drugs since they enable simultaneous prediction of several standard measures of biological activities at diverse experimental conditions and against different biological targets...
November 13, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/29130602/synthetic-piperine-amide-analogues-with-antimycobacterial-activity
#15
Irena Philipova, Violeta Valcheva, Rositsa Mihaylova, Mina Mateeva, Irini Doytchinova, Georgi Stavrakov
Piperine amide analogues are synthesized by replacement of the piperidine moiety with different types of cyclic amines, including adamantyl and monoterpene derived fragments. The compounds are screened for activity against Mycobacterium tuberculosis H37Rv. The most potent compounds are the 1-adamantyl and the monoterpene derived hybrids, which combine nanomolar antimycobacterial activity with low cytotoxicity against human cells. The presence of quaternary carbon atom as main structural requirement for anti-TB activity is pointed out by a QSAR study...
November 11, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/29127581/lessons-learned-in-induced-fit-docking-and-metadynamics-in-the-drug-design-data-resource-grand-challenge-2
#16
Matthew P Baumgartner, David A Evans
Two of the major ongoing challenges in computational drug discovery are predicting the binding pose and affinity of a compound to a protein. The Drug Design Data Resource Grand Challenge 2 was developed to address these problems and to drive development of new methods. The challenge provided the 2D structures of compounds for which the organizers help blinded data in the form of 35 X-ray crystal structures and 102 binding affinity measurements and challenged participants to predict the binding pose and affinity of the compounds...
November 10, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/29126731/synthesis-antibacterial-properties-and-2d-qsar-studies-of-quinolone-triazole-conjugates
#17
Hassan M Faidallah, Adel S Girgis, Anand D Tiwari, Hitesh H Honkanadavar, Sean J Thomas, Ahmed Samir, Atef Kalmouch, Khalid A Alamry, Khalid A Khan, Tarek S Ibrahim, Amany M M Al-Mahmoudy, Abdullah M Asiri, Siva S Panda
A set of 1,2,3-triazole incorporated quinolone antibiotic conjugates 10-15, 17-19 were synthesized via microwave assisted click chemistry technique. Some of the aryl-substituted conjugates 17-19 show promising antibacterial properties against the tested Gram-positive (S. aureus and S. pyogenes) and Gram-negative bacteria (S. typhi) with potency higher than that of the parent antibiotics 1-3. 2D-QSAR modeling supports the observed biological properties.
October 16, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29120791/identification-of-novel-dipeptidyl-peptidase-iv-dpp-iv-inhibitory-peptides-in-camel-milk-protein-hydrolysates
#18
Alice B Nongonierma, Sara Paolella, Priti Mudgil, Sajid Maqsood, Richard J FitzGerald
Nine novel dipeptidyl peptidase IV (DPP-IV) inhibitory peptides (FLQY, FQLGASPY, ILDKEGIDY, ILELA, LLQLEAIR, LPVP, LQALHQGQIV, MPVQA and SPVVPF) were identified in camel milk proteins hydrolysed with trypsin. This was achieved using a sequential approach combining liquid chromatography tandem mass spectrometry (LC-MS/MS), qualitative/quantitative structure activity relationship (QSAR) and confirmatory studies with synthetic peptides. The most potent camel milk protein-derived DPP-IV inhibitory peptides, LPVP and MPVQA, had DPP-IV half maximal inhibitory concentrations (IC50) of 87...
April 1, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29115063/corrigendum-performance-of-deep-and-shallow-neural-networks-the-universal-approximation-theorem-activity-cliffs-and-qsar
#19
David A Winkler, Tu C Le
No abstract text is available yet for this article.
November 2017: Molecular Informatics
https://www.readbyqxmd.com/read/29114443/evaluating-the-toxicity-of-tio2-based-nanoparticles-to-chinese-hamster-ovary-cells-and-escherichia-coli-a-complementary-experimental-and-computational-approach
#20
Alicja Mikolajczyk, Natalia Sizochenko, Ewa Mulkiewicz, Anna Malankowska, Michal Nischk, Przemyslaw Jurczak, Seishiro Hirano, Grzegorz Nowaczyk, Adriana Zaleska-Medynska, Jerzy Leszczynski, Agnieszka Gajewicz, Tomasz Puzyn
Titania-supported palladium, gold and bimetallic nanoparticles (second-generation nanoparticles) demonstrate promising photocatalytic properties. However, due to unusual reactivity, second-generation nanoparticles can be hazardous for living organisms. Considering the ever-growing number of new types of nanoparticles that can potentially contaminate the environment, a determination of their toxicity is extremely important. The main aim of presented study was to investigate the cytotoxic effect of surface modified TiO2-based nanoparticles, to model their quantitative nanostructure-toxicity relationships and to reveal the toxicity mechanism...
2017: Beilstein Journal of Nanotechnology
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