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Computational Biology and Chemistry

Haneesh Jasuja, Navriti Chadha, Pankaj Kumar Singh, Maninder Kaur, Malkeet Singh Bahia, Om Silakari
Janus kinase 1 and 3 are non-receptor protein tyrosine kinases, involved in the regulation of various cytokines implicated in the pathogenesis of autoimmune and inflammatory disease conditions. Thus, they serve as therapeutic targets for the designing of multi-targeted agents for the treatment of inflammatory-mediated pathological conditions. In the present study, diverse inhibitors of JAK1 and JAK3 were considered for the development of ligand-based pharmacophore models, followed by docking analysis to design putative dual inhibitors...
July 5, 2018: Computational Biology and Chemistry
Mingshun Yuan, Zijiang Yang, Guangzao Huang, Guoli Ji
Integrating various features from different protein properties helps to improve the prediction accuracy of protein structural class but need to deal with the corresponding integrated high-dimensional data. Thus, the feature selection process used to select the informative features from the integrated features also becomes an indispensable key step. This paper proposes a novel feature selection method, Partial-Maximum-Correlation-Information based Recursive Feature Elimination (PMCI-RFE), to quickly select the best feature subset from the integrated high-dimensional protein features set to improve the prediction performance of protein structural class...
July 2, 2018: Computational Biology and Chemistry
Ikrormi Rungsung, Muthukumaran Rajagopalan, Amutha Ramaswamy
LKB1 protein is involved in the regulation of cell polarity by phosphorylating the AMPK under energetic stress conditions. LKB1 protein is expressed in both cytoplasm and nucleus. In the nucleus, LKB1 interacts with orphan nuclear receptor protein Nur77. It is reported that the interaction of LKB1 with Nur77 is disrupted by the small molecular ligand TMPA (ethyl 2-[2,3,4-trimethoxy-6-(1-octanoyl)phenyl]acetate), such that the LKB1 is enabled to play its role in cytoplasm and further to regulate/reduce the blood glucose level...
June 30, 2018: Computational Biology and Chemistry
Didem Şöhretoğlu, Suat Sari, Burak Barut, Arzu Özel
Neolignans are a large group of polyphenols found in plants and exhibit a wide range of bioactivities including cytotoxicity, apoptosis inducer, antimalarial and antifungal effects, acetylcholinesterase, tyrosinase, and α-glucosidase inhibition. In this study we tested acetylcholinesterase (AChE), butyrylcholinesterase (BuChE), tyrosinase, and α-glucosidase inhibitory effects of a rare neolignan, (-)-4-O-methyldehydrodiconiferyl alcohol 9'-O-β-glucopyranoside (1) in search for its new pharmaceutical effects...
June 20, 2018: Computational Biology and Chemistry
Navaneethan Palanisamy
Tropheryma whipplei (T. whipplei) is the causative agent of Whipple's disease and blood culture-negative endocarditis. Due to the variability of symptoms, the disease is often poorly diagnosed. Treatment for this bacterial infection is often lengthy, and improper uptake of antibiotics has resulted in relapses in many patients. In the present study, using available bioinformatic tools and databases such as the Cluster Database at High Identity with Tolerance (CD-HIT), the Basic Local Alignment Search Tool for proteins (BLASTp), the Database of Essential Genes (DEG), and the DrugBank database, 13 putative drug targets were identified in T...
June 9, 2018: Computational Biology and Chemistry
Sajjad Farashi, Pezhman Sasanpour, Hashem Rafii-Tabar
The TRPM5 channels are transient receptor potential channels whose presence in the human pancreatic β-cell has been confirmed. The sensitivity of these channels to membrane voltage, temperature and intracellular calcium concentration and their possible role in insulin secretion has made them a focal point in research in the past decade. While experimental researches have confirmed the role of the TRPM5 channels in insulin secretion, but the underlying mechanism is still unclear. In this study, based on the experimental results of other studies, a mathematical description of the TRPM5 channel activity has been proposed which correlates the TRPM5 electrical activity to the voltage and intracellular calcium concentration...
June 6, 2018: Computational Biology and Chemistry
Yaping Li, Jiale Peng, Yeheng Zhou, Penghua Li, Yingying Li, Xingyong Liu, Abu Nasar Siddique, Li Zhang, Zhili Zuo
Checkpoint kinase 1 (Chk1), a serine/threonine protein kinase, plays an important role in G2/M checkpoint, which is a key regulator in response to DNA damage. In this study, the structure-based drug design approach and molecular dynamics (MD) simulations were used to explore potent Chk1 inhibitors. A series of the best fitting candidates were picked out from the Specs database. Out of these, five candidates were submitted for MD simulations to explore the stability of complex. The result indicates that these five candidates could be considered potential Chk1 inhibitors and represents a promising starting point for developing potent inhibitors of Chk1 for the treatment of tumor...
June 4, 2018: Computational Biology and Chemistry
Akram Vasighizaker, Saeed Jalili
Disease gene detection is an important stage in the understanding disease processes and treatment. Some candidate disease genes are identified using many machine learning methods Although there are some differences in these methods including feature vector of genes, the method used to selecting reliable negative data (non-disease genes), and the classification method, the lack of negative data is the most significant challenge of them. Recently, candidate disease genes are identified by semi-supervised learning methods based on positive and unlabeled data...
June 1, 2018: Computational Biology and Chemistry
Mostafa Herajy, Fei Liu, Christian Rohr, Monika Heiner
Coloured Petri nets are an excellent choice for exploring large biological models, particularly when there are repetitions of components. Such models can be easily adapted by slight modifications of parameter values related to colours. Similarly, multi-scale models could involve multiple spatial scales in addition to multiple time scales. Thus, they require the full interplay between stochastic as well as deterministic processes. In this paper we take these two aspects into account and present a modelling and simulation approach for multi-scale biochemical networks using Coloured Generalised Hybrid Petri Nets (GHPNC )...
May 28, 2018: Computational Biology and Chemistry
Rajesh Kumar Pathak, Ayushi Gupta, Rohit Shukla, Mamta Baunthiyal
Xanthine oxidoreductase plays an important role in formation of uric acid and its regulation during purine catabolism. Uncontrolled expression of this enzyme is responsible for overproduction and deposition of uric acid in blood that is potentially injurious because it can breakdown DNA and protein molecules, triggering many diseases. Human Xanthine oxidoreductase (HsXOR) is considered to be a pharmacological target for the treatment of hyperuricemia. Many of the HsXOR-inhibitor drugs such as Febuxostat and Allopurinol are known to have significant adverse effects...
May 28, 2018: Computational Biology and Chemistry
Felipe Valenzuela-Riffo, Patricio Ramos, Luis Morales-Quintana
Changes in the cellulose-hemicellulose fraction take place during ripening of strawberry fruit and are associated with the activity of a set of proteins and hydrolytic enzymes. Expansins are proteins located in the cell wall with no catalytic activity. In this context, FaEXPA1 was previously reported to have a high accumulation rate during fruit ripening in three different strawberry cultivars. In order to understand at the molecular level the expansin mechanism mode, a 3D model of FaEXPA1 protein was built by comparative modeling...
May 26, 2018: Computational Biology and Chemistry
Diana F Rojas-Rengifo, Maria Camila Alvarez-Silva, Cindy P Ulloa-Guerrero, Vanessa Lucía Nuñez-Velez, Maria Del Pilar Delgado, Sonia Milena Aguilera, Harold Castro, Carlos Alberto Jaramillo, Andrés Fernando González Barrios
The Helicobacter pylori cytotoxin-associated gene A (CagA) is known for causing gastroduodenal diseases, such as atrophic gastritis and peptic ulcerations. Furthermore Helicobacter pylori CagA positive strains has been reported as one of the main risk factors for gastric cancer (Parsonnet et al., 1997). Structural variations in the CagA structure can alter its affinity with the host proteins, inducing differences in the pathogenicity of H. pylori. CagA N-terminal region is characterized for be conserved among all H...
May 25, 2018: Computational Biology and Chemistry
Ritika Srivastava, Sunil K Gupta, Farha Naaz, Anuradha Singh, Vishal K Singh, Rajesh Verma, Nidhi Singh, Ramendra K Singh
A series of 2-Cl-benzimidazole derivatives was synthesized and assessed for antibacterial activity. Antibacterial results indicated that compounds 2d, 2e, 3a, 3b, 3c, 4d and 4e showed promising activity against B. cerus, S. aureus and P. aeruginosa (MIC: 6.2 μg/mL) and excellent efficacy against E. coli (MIC: 3.1 μg/mL). Furthermore, compounds 3d and 3e displayed better activity (MIC: 3.1 μg/mL) than the reference drugs chloramphenicol and cycloheximide against gram positive and gram negative bacterial strains...
May 24, 2018: Computational Biology and Chemistry
Yu Song, Yi Gan, Liangyu Liu, Richard T Corlett
Machilus yunnanensis Lecomte is an important Chinese timber species in the family Lauraceae, subclass Magnoliidae. To understand the genetic and molecular basis of flowering in M. yunnanensis, we applied RNA-seq for transcriptome analysis of young and mature flowers and compared these with the transcriptome of leaves. From approximately 26 Gb Illumina clean reads, we obtained a total of 85 823 high-quality transcripts using Trinity software. Comparisons of gene expression in young and mature flowers showed that 37 877 genes were differentially expressed...
May 12, 2018: Computational Biology and Chemistry
Tahmeena Khan, Rumana Ahmad, Iqbal Azad, Saman Raza, Seema Joshi, Abdul Rahman Khan
The present paper deals with in silico evaluation of 32 virtually designed transition metal complexes of 2-butanone thiosemicarbazone and N,S,O containing donor hetero-ligands namely py, bpy, furan, thiophene, 2-picoline, 1,10-phenanthroline, piperazine and liquid ammonia. The complexes were designed with a view to assess their potential anticancer, antioxidant and antibacterial activity. The absorption, distribution, metabolism, excretion and toxicity (ADMET) properties of the chosen ligands were calculated by admetSAR software...
May 8, 2018: Computational Biology and Chemistry
Alireza Salimi Chirani, Mona Ghazi, Mehdi Goudarzi, Shahin Najar Peerayeh, Hoorieh Soleimanjahi, Masoud Dadashi, Bahareh Hajikhani
Helicobacter pylori (H. pylori) as microaerophilic, Gram-negative bacterium colonize the human gastric milieu, where it impetuses chronic disorders. Vaccination is a complementary plan, along with antibiotic therapy, for clearance of H. pylori. Today, Computer based tools are essential for the evaluation, design, and experiment for novel chimeric targets for immunological administration. The purpose of this experiment was immunoinformatic analysis of UreB and HpaA molecules in a fusion arrangement and also, construction and expression of recombinant protein containing chimeric sequences...
May 5, 2018: Computational Biology and Chemistry
T Murlidharan Nair
Preeclampsia is a pregnancy associated disease. It is characterized by high blood pressure and symptoms that are indicative of damage to other organ systems, most often involving the liver and kidneys. If left untreated, the condition could be fatal to mother and baby. This makes it important to delineate the complexities associated with the disease at a molecular level that would help develop methods for early diagnosis. In microarray-based studies, Textoris et al. and Mirzakhani et al. have analyzed the transcriptome with a view to identify biomarkers for preeclampsia...
August 2018: Computational Biology and Chemistry
Abdullahi Ibrahim Uba, Kemal Yelekçi
Human histone deacetylase 6 (HDAC6) has been shown to play a major role in oncogenic cell transformation via deacetylation of α-tubulin, making it a viable target of anticancer drug design and development. The crystal structure of HDAC6 catalytic domain 2 has been recently made available, providing avenues for structure-based drug design campaign. Here, in our continuous effort to identify potentially selective HDAC6 inhibitors, structure-based virtual screening of ∼72 461 compounds was carried out using Autodock Vina...
August 2018: Computational Biology and Chemistry
Ramesh Kheirabadi, Mohammad Izadyar
The mechanism of action of the selenenamide 1 as a mimic of the glutathione peroxidase (GPx) was investigated by the density functional theory. The solvent-assisted proton exchange procedure was applied to model the catalytic behavior and antioxidant activity of this mimic. To have an insight into the charge transfer effect, different aromatic thiols, including electron donating substituents on the phenyl ring were considered. The catalytic behavior of the selenenamide was modeled in a four-step mechanism, described by the oxidation of the mimic, the reduction of the obtained product, selenoxide, the reduction of the selenenylsulfide and dehydration of selenenic acid...
August 2018: Computational Biology and Chemistry
Mahmoud Kandeel, Abdulla Al-Taher, Huifang Li, Udo Schwingenschlogl, Mohamed Al-Nazawi
Structural studies related to Middle East Respiratory Syndrome Coronavirus (MERS CoV) infection process are so limited. In this study, molecular dynamics (MD) simulations were carried out to unravel changes in the MERS CoV heptad repeat domains (HRs) and factors affecting fusion state HR stability. Results indicated that HR trimer is more rapidly stabilized, having stable system energy and lower root mean square deviations (RMSDs). While trimers were the predominant active form of CoVs HRs, monomers were also discovered in both of viral and cellular membranes...
August 2018: Computational Biology and Chemistry
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