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Computational Biology and Chemistry

Mayasah Al-Nema, Anand Gaurav, Gabriel Akowuah
The major complaint that most of the schizophrenic patients' face is the cognitive impairment which affects the patient's quality of life. The current antipsychotic drugs treat only the positive symptoms without alleviating the negative or cognitive symptoms of the disease. In addition, the existing therapies are known to produce extrapyramidal side effects that affect the patient adherence to the treatment. PDE10A inhibitor is the new therapeutic approach which has been proven to be effective in alleviating the negative and cognitive symptoms of the disease...
September 8, 2018: Computational Biology and Chemistry
Ajit Kumar Dhal, Alok Pani, Rajani Kanta Mahapatra, Soon-Il Yun
Cryptosporidium parvum is a protozoan parasite which causes waterborne diseases known as Cryptosporidiosis. It is an acute enteric diarrheal disease being severe in the case of immunocompromised individuals and children. C. parvum mainly depends on the glycolysis process for energy production and LDH (Lactate Dehydrogenase) is a key controller of this process. In this study from different in-silico approaches such as structure-based, ligand-based and de novo drug design; a total of 40 compounds were selected for docking studies against LDH...
September 8, 2018: Computational Biology and Chemistry
Valliyammai Natarajan, Priya Ramanathan, Gopal Gopisetty, Balaji Ramachandran, Rajkumar Thangarajan, Sabitha Kesavan
Synovial sarcoma (SS) is characterized by a tumour specific chromosomal translocation t(X;18) (p11;q11) which results in the formation of SYT-SSX1 fusion protein. This fusion protein represents a clear therapeutic target and molecules specifically targeting SYT-SSX1 fusion protein are currently not available. In this study, SYT-SSX1 fusion protein sequence was retrieved from Uniprot and 3D structure was generated using I-TASSER modeling program. A structure based computational screening approach has been employed using Glide docking software to identify potential SYT-SSX1 small molecule inhibitors that bind to the junction region of the fusion protein...
September 6, 2018: Computational Biology and Chemistry
Muhammad Arba, Andry Nur-Hidayat, Slamet Ibrahim Surantaadmaja, Daryono H Tjahjono
Proteasomal system plays an important role in maintaining cell homeostatis. Overexpression of proteasomes leads to several major diseases, such as cancer and autoimmune disorder. The β5 subunit of proteasome is a crucial active site in proteolysis, and targeting proteasome β5 subunit is essential for proteasome inhibition. In the present study, a pharmacophore-based virtual screening and molecular docking were employed to identify ligands as inhibitors of β5 subunit of proteasome. The pharmacophore features were built with one hydrogen bond donor, two hydrogen bond acceptors, and one hydrophobic feature using native ligand of proteasome (HU10), which was then used to screen ZINC database using ZINCPharmer...
August 28, 2018: Computational Biology and Chemistry
Atanu Maity, Sarmistha Majumdar, Shubhra Ghosh Dastidar
The proteins of Bcl-2 family, which are promising anti-cancer-drug targets, have substantial similarity in primary sequence and share homologous domains as well as similar structural folds. In spite of similarities in sequence and structures, the members of its pro- and anti- apoptotic subgroups form complexes with different type of partners with discriminating binding affinities. Understanding the origin of this discrimination is very important for designing ligands that can either selectively target a protein or could be made broad ranged as necessary...
August 23, 2018: Computational Biology and Chemistry
Rajnish Kumar, Tapobrata Lahiri
Circular RNAs are new class of stable non-coding RNAs, whose expressions are specific to tissues as well as developmental stages and reported to act as gene regulators. Conspicuous presences of some of them as biomarkers for cancers, aging etc. are well reported. Biogenesis of circular RNA competes with Pre-mRNA splicing using the same splicing machinery and gene loci. Also, some circular RNAs are reported to have open reading frames and internal ribosome entry site for ribosome binding, which increases the chance of overlapping features among circular and mRNA transcripts...
August 19, 2018: Computational Biology and Chemistry
Rajkumar Chakraborty, Himani Gupta, Razia Rahman, Yasha Hasija
Breast cancer is one of the most common cancers among women and increased expression of some polymorphic genes, which is rare within families, enhances the risk of breast cancer incidence. The correct identification of the functional SNPs of such genes is important for characterizing the functional aspect of these SNPs which can be assessed by evaluating their significant influence on the structure and function of proteins. Since the presence of SNPs in these genes affects the quality of life of a breast cancer patient, thus, the associated diagnostic markers have a reliable potential for assessing the prognosis of breast cancer...
August 11, 2018: Computational Biology and Chemistry
Dhayalan Pavithra, Kesavan Sabitha, Thangarajan Rajkumar
Gastric cancer is a common cancer in the world with higher incidence rates. Micro RNAs (miRNAs) are known to control biological processes and are also involved in the initiation and progression of numerous cancers. The aim of this study was to identify small molecule inhibitors using bioinformatics methods for over-expressed miRNAs that are known to play a major role in the genesis of gastric cancer. Our study included three datasets from Gene expression omnibus (GEO) database and we used bioinformatics tool to identify differentially expressed miRNAs in all the three datasets...
July 21, 2018: Computational Biology and Chemistry
Hui Liu, Zhuoming Li, Lang Li
No abstract text is available yet for this article.
July 12, 2018: Computational Biology and Chemistry
Mourad Ounissi, Abdelkrim Kameli, Chafia Tigrine, Fatma Zohra Rachedi
In order to find more natural lead-compounds as inhibitors for Cyclooxygenase-2, the essential structural features for human cyclooxygenase-2 inhibitors and 3D-Quantitative structure activity relationship (3D-QSAR) model were carried out based on dataset from three confirmatory bioassays using Phase program. Six point pharmacophore (AAHRRR) of COX-2 selective inhibitors was generated from training set of 52 compounds. The 3D-QSAR model was selected as having favourable statistic measures (R2  = 0.93, Q2 ext  = 0...
July 4, 2018: Computational Biology and Chemistry
M A Zayed, M El-Desawy, A A Eladly
In the present work novel para chloro, para fluoro and para nitro maleanilic acid derivatives were prepared and investigated using FT-IR, thermal analyses (TA) measurements (TGA/DTG and DTA) in comparison with mass spectral (MS) fragmentation at 70 eV. The crystallographic structures of studied compounds were investigated by X-ray diffraction (XRD). The vibrational frequencies and the corresponding normal modes were evaluated at the optimized geometry. Vibrational modes were analyzed using GAUSSVIEW software...
October 2018: Computational Biology and Chemistry
Burçin Türkmenoğlu, Yahya Güzel
By using the molecular docking and 4D-QSAR analysis, it is aimed to find the interaction points in the receptor binding site of transforming growth factor-beta (TGF-beta) used to inhibit invasion and metastasis. To elucidate the interaction points of receptor, different types of local reactive descriptor (LRD) of ligands have been used. Activity values related to interaction energy between the ligand-receptor (L-R) were determined by nonlinear least squares (NLLS) using the Levenberg-Marquardt (LM) algorithm...
October 2018: Computational Biology and Chemistry
Wei Zhou, Ziyi Chen, Zhigang Liu, Yonghua Wang
MicroRNAs (miRNAs) play a critical role in regulating the signaling network such as the extracellular signal regulated kinase (ERK) pathway. However, the mechanisms of miRNA-mediated posttranscriptional regulations with regard to their impacts on signaling require further investigation from a systematic level. Therefore, we develop a mathematical model by analyzing the precise dynamic mechanisms with a bevy of miRNAs involved in the Ras/Raf/MEK/ERK pathway. A systems-based analysis approach is introduced into this model and the dynamics have been implemented deterministically and stochastically...
October 2018: Computational Biology and Chemistry
Muhammad Shakil Shah, Muhammad Najam-Ul-Haq, Hamid Saeed Shah, Syed Umar Farooq Rizvi, Jamshed Iqbal
Cholinesterases (ChEs) play a vital role in regulating cholinergic transmission. Inhibition of ChEs is thought to be an emerging and useful therapeutic target for neurodegenerative disorders through restoration of acetylcholine (ACh) levels in the brain (e.g. Alzheimer's disease). To increase the chemical diversity of cholinesterase inhibitors, a series of quinoline chalcones derivatives were tested against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) isoenzymes. All tested compounds (4a-1; 5a-s) exhibited inhibitory activities against AChE and BChE to a considerable extent...
October 2018: Computational Biology and Chemistry
Praveen Kumar Guttula, Anushka Agarwal, Usharani Maharana, Mukesh Kumar Gupta
Germline stem cells (GSCs) are known to transmit genetic information from parents to offspring. These GSCs can undergo reprogramming to transform themselves into pluripotent stem cells, called as Multipotent adult Germline stem cells (maGSCs). The mechanism of the reprogramming of GSCs to maGSCs is elusive. To investigate novel factors that may govern the process of reprogramming, the RNA-seq data of both GSCs and maGSCs were retrieved and subjected to Tuxedo protocol using Galaxy server. Total 1558 differentially expressed genes were identified from the analysis...
October 2018: Computational Biology and Chemistry
Mohit Yadav, Jitendra Singh Rathore
Here we report the first essentially complete TAome analysis for type II toxin-antitoxin (TA) system, a major class of TA modules found in bacterial system, from entomopathogenic bacterium Xenorhabdus nematophila ATCC 19061 (NCBI RefSeq NC_014228). We summarize this analysis in terms of TA locus, accession identifier, hits in conserved domain database, toxin superfamily, antitoxin superfamily and chromosomal/mobile genome/plasmid occurrences. Moreover, for TA context analyses we use six different specifications namely virulence factors, mobile genetic elements (MGE), antibiotic resistance genes, secretion systems, prophage and a classification of mobile genetic elements (ACLAME); among these hits are found for only MGE, ACLAME and prophage...
October 2018: Computational Biology and Chemistry
M Asadollahi-Baboli, S Dehnavi
The α-glucosidase inhibitors are considered as important agents in drug discovery against diabetes mellitus. Molecular docking and quantitative structure-activity relationship (QSAR) were performed based on a series of tetracyclic oxindole derivatives to elucidate key structural properties affecting inhibitory activity and support the design of new α-glucosidase inhibitors. The molecular docking results demonstrate that at least two hydrogen bonds between Thr681 and Arg676 residues and the oxygen atoms in amid groups have an important role in the optimum binding of inhibitors...
October 2018: Computational Biology and Chemistry
Yuanxin Tian, Yunci Ma, Shaoyu Wu, Tingting Zhang, Zhonghuang Li, Guangfa Wang, Jiajie Zhang
Receptor Tyrosine Kinase inhibitors are the most popular anti-cancer drug types. But the resistance is the major challenge. Our study on the network with 1334 proteins and their 2623 interactions which retrieved from 52 RTKs indicated that most RTKs proteins were the key controllers of the protein-protein network. Direct or indirect interactions with RTKs (shortest path of 2) were often associated with resistance to RTKs inhibitors in the literature. The results based on the KEGG pathway analysis demonstrated the Rap1 signal pathway would also contribute to the resistance of RTKs inhibitor as well as the known Ras pathway and PI3K/Akt pathway...
October 2018: Computational Biology and Chemistry
Vatsal M Patel, Navin B Patel, Manuel J Chan-Bacab, Gildardo Rivera
The present work highlightsthe synthesis of a newer biologically active Mannich bases contributing 4-((4-fluorobenzylidene)amino)-5-(pyridin-4-yl)-4H-1,2,4-triazole-3-thiol and various heterocyclic amines via N-Mannich reaction by the conventional method as well as microwave heating approach as a part of an environmentally benign synthetic protocol. All the synthesized compounds were characterized by spectral analysis and were screened for in vitro antimicrobial, antitubercular and antiprotozoal activity. The compound 4k was found to be most active respectively against S...
October 2018: Computational Biology and Chemistry
Gokalp Ozmen Guler, Gokhan Zengin, Firat Karadag, Adriano Mollica, Carene Marie Nancy Picot, Mohamad Fawzi Mahomoodally
Onobrychis argyrea Boiss. subsp. Isaurica (Fabaceae), endemic to the eastern Mediterranean region, is a poorly studied medicinal plant. This study sets out to investigate into antioxidant and inhibitory activities of O. argyrea extracts (ethyl acetate, methanol, and water) against key enzymes linked to diabetes (α-amylase, α-glucosidase), Alzheimer's disease (acetylcholinesterase, butyrylcholinesterase), and skin hyperpigmentation (tyrosinase). Phytochemical composition was determined by HPLC-DAD and in silico approach used to provide additional insight of the possible interaction of the identified phenolic compounds with the studied enzymes...
October 2018: Computational Biology and Chemistry
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