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Marilia N N Lima, Cleber C Melo-Filho, Gustavo C Cassiano, Bruno J Neves, Vinicius M Alves, Rodolpho C Braga, Pedro V L Cravo, Eugene N Muratov, Juliana Calit, Daniel Y Bargieri, Fabio T M Costa, Carolina H Andrade
Malaria is a life-threatening infectious disease caused by parasites of the genus Plasmodium , affecting more than 200 million people worldwide every year and leading to about a half million deaths. Malaria parasites of humans have evolved resistance to all current antimalarial drugs, urging for the discovery of new effective compounds. Given that the inhibition of deoxyuridine triphosphatase of Plasmodium falciparum ( Pf dUTPase) induces wrong insertions in plasmodial DNA and consequently leading the parasite to death, this enzyme is considered an attractive antimalarial drug target...
2018: Frontiers in Pharmacology
Apeng Wang, Yang Yang, Yangsheng Jun, Bin Wang, Kai Lv, Mingliang Liu, Huiyuan Guo, Yu Lu
A series of novel nitrofuranyl methyl N-heterocycles based on the structure of IIIM-MCD-211 were designed and synthesized. Compounds 6d, 8b and 12a show excellent activity against MTB H37Rv strain (MIC: 0.031-0.062 μg/mL) roughly comparable to INH and IIIM-MCD-211. In addition, a three-dimensional quantitative structure-activity relationship (3D-QSAR) study was performed on the above mentioned chemical series employing comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) techniques...
March 3, 2018: Bioorganic & Medicinal Chemistry
Deepak Reddy Gade, Amareswararao Makkapati, Rajesh Babu Yarlagadda, Godefridus J Peters, B S Sastry, V V S Rajendra Prasad
Overexpression of P-glycoprotein (P-gp) leads to the emergence of multidrug resistance (MDR) in cancer treatment. Acridones have the potential to reverse MDR and sensitize cells. In the present study, we aimed to elucidate the chemosensitization potential of acridones by employing various molecular modelling techniques. Pharmacophore modeling was performed for the dataset of chemosensitizing acridones earlier proved for cytotoxic activity against MCF7 breast cancer cell line. Gaussian-based QSAR studies also performed to predict the favored and disfavored region of the acridone molecules...
February 24, 2018: Computational Biology and Chemistry
Samiul M Ansari, David S Palmer
Recently, Güssregen et al. used solute-solvent distribution functions calculated by the 3D Reference Interaction Site Model (3DRISM) in a 3D-QSAR approach to model activity data for a set of serine protease inhibitors; this approach was referred to as Comparative Analysis of 3D RISM MAps (CARMa). [J. Chem. Inf. MODEL: , 2017, 57, 1652-1666] Here we extend this idea by introducing probe atoms into the 3DRISM solvent model in order to directly capture other molecular interactions in addition to those related to hydration/dehydration...
March 15, 2018: Journal of Chemical Information and Modeling
Akhil Kumar, Ashish Tiwari, Ashok Sharma
Alzheimer disease (AD) is now considered as a multifactorial neurodegenerative disorder and rapidly increasing to an alarming situation and causing higher death rate. One target one ligand hypothesis is not able to provide complete solution of AD due to multifactorial nature of disease and one target one drug seems to fail to provide better treatment against AD. Moreover, current available treatments are limited and most of the upcoming treatments under clinical trials are based on modulating single target...
March 15, 2018: Current Neuropharmacology
Yunsong Mu, Zhen Wang, Fengchang Wu, Buqing Zhong, Mingru Yang, Fuhong Sun, Chenglian Feng, Xiaowei Jin, Kenneth M Y Leung, John P Giesy
Metals can pose hazards to marine species and can adversely affect structures and functions of communities of marine species. However, little is known about how structural properties of metal atoms combined with current geographical and climatic conditions affect their toxic potencies. A mathematical model, based on quantitative structure-activity relationships and species sensitivity distributions (QSAR-SSD) was developed by use of acute toxicities of six metals (Cd, Cr, Cu, Hg, Ni, and Zn) to eight marine species and accessory environmental conditions...
March 14, 2018: Environmental Science & Technology
Rajesh B Patil, Euzebio G Barbosa, Jaiprakash N Sangshetti, Vishal P Zambre, Sanjay D Sawant
Dipeptidyl peptidase-IV (DPP-IV) inhibitors are promising antidiabetic agents. Currently, several DPP-IV inhibitors have been approved for therapeutic use in diabetes mellitus. Receptor-dependent 4D-QSAR is comparatively a new approach which uses molecular dynamics simulations to generate conformational ensemble profiles of compounds representing a dynamic state of compounds at a target's binding site. This work describes a receptor-dependent 4D-QSAR study on triazolopiperazine derivatives. QSARINS multiple linear regression method was adopted to generate 4D-QSAR models...
March 13, 2018: Molecular Diversity
Fangyou Yan, Wensi He, Qingzhu Jia, Shuqian Xia, Qiang Wang
The quantitative structure-activity relationship (QSAR) model is an effective alternative to traditional experimental toxicity testing, which is undoubtedly important for modern environmental risk assessment and property prediction. Based on this background, the toxicological effects of ionic liquids (ILs) against Candida albicans (C. albicans) were studied via the QSAR method. A large diverse group of 141 and 85 ILs that have a minimal inhibitory concentration (MIC) and a minimum fungicidal concentration (MBC) against C...
February 26, 2018: Chemosphere
Zaheer Ul-Haq, Sajda Ashraf, Majdi M Bkhaitan
Casein kinase-II, a member of protein kinase family, plays significant role in different cellular processes such as cell growth, differentiation, proliferation, gene expression and embryogenesis. Being a potent suppressor of apoptosis, it serves as a significant link for its association with various types of malignancies such as colorectal and breast cancer. To overcome its pathological role in various cancerous diseases, CK-II procures great consideration as a therapeutic target. This study aimed at understanding the binding mechanism and structural properties of benzimidazole derivatives by utilizing various computational tools including docking simulation, 3-dimensional quantitative structure activity relationships and molecular dynamic simulation...
March 12, 2018: Journal of Biomolecular Structure & Dynamics
Sujith Rajan, Sabbu Satish, Kripa Shankar, Sukanya Pandeti, Salil Varshney, Ankita Srivastava, Durgesh Kumar, Abhishek Gupta, Sanchita Gupta, Rakhi Choudhary, Vishal M Balaramnavar, Tadigoppula Narender, Anil N Gaikwad
BACKGROUND AND PURPOSE: In our drug discovery program of natural product, earlier we have reported Aegeline that is N-acylated-1-amino-2- alcohol, which was isolated from the leaves of Aeglemarmelos showed anti-hyperlipidemic activity for which the QSAR studies predicted the compound to be the β3-AR agonist, but the mechanism of its action was not elucidated. In our present study, we have evaluated the β3-AR activity of novel N-acyl-1-amino-3-arylopropanol synthetic mimics of aegeline and its beneficial effect in insulin resistance...
March 7, 2018: Metabolism: Clinical and Experimental
Miriam Moreno-Montoro, Paula Jauregi, Miguel Navarro-Alarcón, Manuel Olalla-Herrera, Rafael Giménez-Martínez, Lourdes Amigo, Beatriz Miralles
In this study, ultrafiltered goat milks fermented with the classical starter bacteria Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus salivarus subsp. thermophilus or with the classical starter plus the Lactobacillus plantarum C4 probiotic strain were analyzed using ultra-high performance liquid chromatography-quadrupole-time-of-flight tandem mass spectrometry (UPLC-Q-TOF-MS/MS) and/or high performance liquid chromatography-ion trap (HPLC-IT-MS/MS). Partial overlapping of the identified sequences with regard to fermentation culture was observed...
March 10, 2018: Analytical and Bioanalytical Chemistry
Kai He, Erika Okuta, José Andres Cordero, Shinya Echigo, Yasuhiro Asada, Sadahiko Itoh
Anthropogenic compounds accidentally released to the environment could be important precursors of disinfection byproducts (DBPs) in drinking water treatment processes. In this study, the haloacetic acid formation potentials (HAAFPs) of 155 anthropogenic compounds listed on the Japanese pollutant release and transfer register (PRTR) system were evaluated. The results showed that phenolic and aromatic amine compounds were important HAA precursors, and chlorinated phenols showed high HAAFPs (>400 μg/mgC)...
February 19, 2018: Journal of Hazardous Materials
Vladimir Potemkin, Maria Grishina
Various techniques for rational drug design are presented in the paper. The methods are based on a substitution of antipharmacophore atoms of the molecules of training dataset by new atoms and/or group of atoms increasing the atomic bioactivity increments obtained at a SAR study. Furthermore, a design methodology based on the genetic algorithm DesPot for discrete optimization and generation of new drug candidate structures is described. Additionally, wide spectra of SAR approaches (3D/4D QSAR interior and exterior-based methods - BiS, CiS, ConGO, CoMIn, high-quality docking method - ReDock) using MERA force field and/or AlteQ quantum chemical method for correct prognosis of bioactivity and bioactive probability is described...
March 8, 2018: Current Medicinal Chemistry
Kai Lin, Lan-Wei Zhang, Xue Han, Zhao-Xu Meng, Yi-Fan Wu, Jian-Ming Zhang, Da-You Cheng
In this study, Qula casein derived from yak milk casein was hydrolyzed using a two-enzyme combination approach and high angiotensin I-converting enzyme (ACE) inhibitory activity peptides were screened by quantitative structure-activity relationship (QSAR) modeling integrate with molecular docking analysis. Hydrolysates (< 3 kDa) derived from combinations of thermolysin+alcalase and thermolysin+proteinase K demonstrated high ACE inhibitory activities. Peptide sequences in hydrolysates derived from these two combinations were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS)...
March 9, 2018: Journal of Agricultural and Food Chemistry
Ségolène De Vaugelade, Edith Nicol, Svetlana Vujovic, Sophie Bourcier, Stéphane Pirnay, Stéphane Bouchonnet
RATIONALE: The present work is devoted to the structural elucidation of by-products issued from the direct UV-visible irradiation of dehydroacetic acid (DHA) in solution and in cosmetic emulsion. METHODS: Analyses were carried out using a gas chromatography coupled with an ion trap mass spectrometer and by a high performance liquid chromatography coupled with ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (LC-UHRMS). The potential toxicities of by-products were estimated by in silico calculations based on a QSAR (Quantitative Structure-Activity Relationship) approach and by in vitro bioassays conducted on Vibrio fischeri bacteria...
March 8, 2018: Rapid Communications in Mass Spectrometry: RCM
Kamel Mansouri, Chris M Grulke, Richard S Judson, Antony J Williams
The collection of chemical structure information and associated experimental data for quantitative structure-activity/property relationship (QSAR/QSPR) modeling is facilitated by an increasing number of public databases containing large amounts of useful data. However, the performance of QSAR models highly depends on the quality of the data and modeling methodology used. This study aims to develop robust QSAR/QSPR models for chemical properties of environmental interest that can be used for regulatory purposes...
March 8, 2018: Journal of Cheminformatics
Davy Guan, Kevin Fan, Ian Spence, Slade Matthews
Five datasets were constructed from ligand and bioassay result data from the literature. These datasets include bioassay results from the Ames mutagenicity assay, Greenscreen GADD-45a-GFP assay, Syrian Hamster Embryo (SHE) assay, and 2 year rat carcinogenicity assay results. These datasets provide information about chemical mutagenicity, genotoxicity and carcinogenicity.
April 2018: Data in Brief
I Luque Ruiz, M Á Gómez-Nieto
The development of robust QSAR models to predict the activity of molecules of β-secretase inhibitors is an area of interest due to the increase of Alzheimer's disease in patients in the global population. In this paper, we present a proposal based on the use of relative distance matrices as input data to the QSAR algorithms. These matrices store measurements of distances between the structural characteristics of pairs of molecules and between the molecules and a structural pattern extracted from the whole data set, thus efficiently representing a correlation between structural changes and activity...
March 7, 2018: SAR and QSAR in Environmental Research
Lili Dong, Ruirui Feng, Jiawei Bi, Shengqiang Shen, Huizhe Lu, Jianjun Zhang
Human sodium-dependent glucose co-transporter 2 (hSGLT2) is a crucial therapeutic target in the treatment of type 2 diabetes. In this study, both comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were applied to generate three-dimensional quantitative structure-activity relationship (3D-QSAR) models. In the most accurate CoMFA-based and CoMSIA-based QSAR models, the cross-validated coefficients (r2 cv ) were 0.646 and 0.577, respectively, while the non-cross-validated coefficients (r2 ) were 0...
March 6, 2018: Journal of Molecular Modeling
Anukrati Goel, Kishore Gajula, Rakesh Gupta, Beena Rai
Quantitative structure activity relationship (QSAR) models appear to be an ideal tool for quick screening of promising candidates from a vast library of molecules, which can then be further designed, synthesized and tested using a combination of rigorous first principle simulations, such as molecular docking, molecular dynamics simulation and experiments. In this study, QSAR models have been built with an extensive dataset of 487 compounds to predict the sweetness potency relative to sucrose (ranging 0.2-220,000)...
July 1, 2018: Food Chemistry
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