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Computational Biology and Chemistry

Seyed Mahmoud Sadjjadi, Mohammad Ebrahimipour, Fatemeh Sadat Sadjjadi
BACKGROUND: Cystic echinococcosis (CE) as a zoonotic parasitic disease, remains a health challenge in many parts of the world. There are different species of Echinococcus granulosus sensu lato with different pathogenicity and host preferences.Different procedures have been applied for characterization of Echinococcus taxa in which two mitochondrial genes, cox1 and nad1 have been used more common. They have been able to differentiate E. granulosus sensu stricto and E. canadensis species in different hosts...
February 5, 2019: Computational Biology and Chemistry
Neetu Agrawal, Pradeep Mishra
Monoamine oxidase (MAO) enzymes are one of the most promising targets for the treatment of neurological disorders. A series of phenylisoxazole carbohydrazides was designed, synthesized and screened for both MAO-A and MAO-B inhibition using Amplex Red assays. None of the compounds inhibited the MAO-A activity while most of them significantly inhibited MAO-B in the micromolar to nanomolar range. Among them, the compound N'-(4-methylbenzylidene)-5-phenylisoxazole-3-carbohydrazide (6c) exhibited the most potent inhibitory activity towards MAO-B...
January 29, 2019: Computational Biology and Chemistry
S Murugavel, C Ravikumar, G Jaabil, Ponnuswamy Alagusundaram
Computational quantum chemical study and biological evaluation of a synthesized novel sulfur heterocyclic thiophene derivative containing 1,2,3-triazole and pyridine moieties namely BTPT [2-(1-benzyl-5-methyl-1H-1,2,3-triazol-4-yl)-6-methoxy-4-(thiophen-2-yl) pyridine] was presented in this study. The crystal structure was determined by SCXRD method. For the title compound BTPT, spectroscopic characterization like 1 H NMR, 13 C NMR, FTIR, UV-vis were carried out theoretically by computational DFT method and compared with experimental data...
January 28, 2019: Computational Biology and Chemistry
Reaz Uddin, Noor-Ul-Ain Zahra, Syed Sikander Azam
Tuberculosis (TB) is a major global health challenge. It has been afflicting human for thousands of years and is still severely affecting a huge population. The etiological agent of the disease is Mycobacterium tuberculosis (MTB) that survives in the human host in latent, dormant, and non-replicative state by evading the immune system. It is one of the leading causes of infection related death worldwide. The situation is exacerbated by the massive increase in the resistant strains such as multi-drug resistant TB (MDR-TB) and extensive drug-resistant TB (XDR-TB)...
January 24, 2019: Computational Biology and Chemistry
Manoj Kumar Gupta, Ramakrishna Vadde
Diabetes mellitus is clinically characterized by hyperglycemia. Though many studies have been done to understand the mechanism of Type 2 Diabetes (T2D), however, the complete network of diabetes and its associated disorders through polygenic involvement is still under debate. The present study designed to re-analyze publicly available T2D related microarray raw datasets present in GEO database and T2D genes information present in GWAS catalog for screening out differentially expressed genes (DEGs) and identify key hub genes associated with T2D...
January 24, 2019: Computational Biology and Chemistry
Vinícius Guimarães da Paixão, Samuel Silva da Rocha Pita
Trypanosoma cruzi Trypanothione Reductase (TcTR) is one of the therapeutic targets studied in the development of new drugs against Chagas' disease. Due to its biodiversity, Brazil has several compounds of natural origin that were not yet properly explored in drug discovery. Therefore, we employed the Virtual Screening against TcTR aiming to discover new inhibitors from the Natural Products Database of the Bahia Semi-Arid region (NatProDB). This database has a wide chemical diversity favoring the discovery of new chemical entities...
January 22, 2019: Computational Biology and Chemistry
Snezana Ćirić Zdravković, Milan Pavlović, Svetlana Apostlović, Goran Koraćević, Sonja Šalinger Martinović, Dragana Stanojević, Dušan Sokolović, Aleksandar M Veselinović
Rho kinases, one of the best-known members of the serine/threonine (Ser/Thr) protein kinase family, can be used as target enzymes for the treatment of many diseases such as cancer or multiple sclerosis, and especially for the treatment of cardiovascular diseases. This study presents QSAR modeling for a series of 41 chemical compounds as Rho kinase inhibitors based on the Monte Carlo method. QSAR models were developed for three random splits into the training and test set. Molecular descriptors used for QSAR modeling were based on the SMILES notation and local invariants of the molecular graph...
January 21, 2019: Computational Biology and Chemistry
Laurent Soulère, Yves Queneau
A method aiming at investigating possible bioactive conformations of acyl homoserine lactone (AHL) quorum sensing (QS) modulators is established. The method relies on the exhaustive conformational analysis of AHLs by varying torsion angles around the amide group then on the selection of the closest conformation to those known from co-crystallized XRD data of AHL-receptor complexes. These latter are then docked as rigid ligand within the receptor binding site, leading to interactions with binding site residues which are highly consistent as compared with the data arising from XRD studies...
January 19, 2019: Computational Biology and Chemistry
Md Lisul Islam, Swakkhar Shatabda, Mahmood A Rashid, M G M Khan, M Sohel Rahman
Nuclear Magnetic Resonance Spectroscopy (most commonly known as NMR Spectroscopy) is used to generate approximate and partial distances between pairs of atoms of the native structure of a protein. To predict protein structure from these partial distances by solving the Euclidean distance geometry problem from the partial distances obtained from NMR Spectroscopy, we can predict three-dimensional (3D) structure of a protein. In this paper, a new genetic algorithm is proposed to efficiently address the Euclidean distance geometry problem towards building 3D structure of a given protein applying NMR's sparse data...
January 19, 2019: Computational Biology and Chemistry
Surabhi Johari, Ashwani Sharma, Subrata Sinha, Aparoop Das
AIM: An integrated protocol of virtual screening involving molecular docking, pharmacophore probing, and simulations was established to identify small novel molecules targeting crucial residues involved in the variant apoE ε4 to mimic its behavior as apoE2 thereby eliminating the amyloid plaque accumulation and facilitating its clearance. MATERIALS AND METHODS: An excellent ligand-based and structure-based approach was made to identify common pharmacophoric features involving structure-based docking with respect to apoE ε4 leading to the development of apoE ε4 inhibitors possessing new scaffolds...
January 11, 2019: Computational Biology and Chemistry
Muchun Zhu, Xiaoping Song, Peng Chen, Wenyan Wang, Bing Wang
Protein-ligand complexes perform specific functions, most of which are related to human diseases. The database, called as human disease-related protein-ligand structures (dbHDPLS), collected 8833 structures which were extracted from protein data bank (PDB) and other related databases. The database is annotated with comprehensive information involving ligands and drugs, related human diseases and protein-ligand interaction information, with the information of protein structures. The database may be a reliable resource for structure-based drug target discoveries and druggability predictions of protein-ligand binding sites, drug-disease relationships based on protein-ligand complex structures...
January 11, 2019: Computational Biology and Chemistry
Kasmika Borah, Sanchita Sharma, Yumnam Silla
Plant based lead compounds have been historically incredible as a source of therapeutic agents for various complex disorders including Alzheimer's disease (AD). AD is one of the leading neurodegenerative disorder in which the underlying risk factors remain largely unclear and presently, there is no disease modifying treatment available. Despite its potential, to date only few compounds have entered for clinical trials. Herein, we described the identification of plant based lead compounds for treatment of AD through an integrative approach of pharmacokinetics and structure bioinformatics approach...
January 8, 2019: Computational Biology and Chemistry
Virendra R Mishra, Chaitannya W Ghanavatkar, Suraj N Mali, Shahnawaz I Qureshi, Hemchandra K Chaudhari, Nagaiyan Sekar
Novel azo linked substituted benzimidazole, benzoxazole, and benzothiazole were synthesized by diazo coupling and characterized by 1 H NMR, elemental analysis, FTIR and UV-vis spectroscopy. The newly synthesized compounds were evaluated for invitro antibacterial activity against Staphylococcus aureus and Escherichia Coli strains by Resazurin microtiter assay method (REMA). The minimum inhibitory concentration (MIC in μg/mL) were used to express the antibacterial activities. The azo linked compounds exhibited good to moderate or high antibacterial activities in vitro...
January 7, 2019: Computational Biology and Chemistry
Mona Shafaghi, Ali Akbar Shabani, Zarrin Minuchehr
Glycoengineering is a recently used approach to extend serum half-life of valuable protein therapeutics. One aspect of glycoengineering is to introduce new N-glycosylation site (Asn-X-Thr/Ser, where X ≠ Pro) into desirable positions in the peptide backbone, resulting in the generation of hyper-glycosylated protein. In this study, human luteinizing hormone (LH) was considered for identification of the suitable positions for the addition of new N-linked glycosylation sites. A rational in silico approach was applied for prediction of structural and functional alterations caused by changes in amino acid sequence...
January 3, 2019: Computational Biology and Chemistry
Vladimir Vélez-Segarra, Kelvin Carrasquillo-Carrión, Jorge J Santini-González, Yabdiel A Ramos-Valerio, Luis E Vázquez-Quiñones, Abiel Roche-Lima, José R Rodríguez-Medina, Elsie I Parés-Matos
Saccharomyces cerevisiae, the budding yeast, must remodel initial cell shape and cell wall integrity during vegetative growth and pheromone-induced morphogenesis. The cell wall remodeling is monitored and regulated by the cell wall integrity (CWI) signaling pathway. Wsc1p, together with Wsc2p and Wsc3p, belongs to a family of highly O-glycosylated cell surface proteins that function as stress sensors of the cell wall in S. cerevisiae. These cell surface proteins have the main role of activating the CWI signaling pathway by stimulating the small G-protein Rho1p, which subsequently activates protein kinase C (Pkc1p) and a mitogen activated protein (MAP) kinase cascade that activates downstream transcription factors of stress-response genes...
January 3, 2019: Computational Biology and Chemistry
Fang-Liang Huang, Yang Zhang, Lin-Ping Zhang, Shu Wang, Ye Feng, Nian-Hang Rong
Bacillus megaterium strain JX285, isolated from rhizosphere red soil sample, can solubilize inorganic phosphorus, which increases the amount of available phosphorus and promotes plant growth. To investigate the mechanisms underlying phosphate solubilization, we sequenced the entire genome of B. megaterium strain JX285 (CGMCC 1.1621), which comprises a circular chromosome of 5,066,463 bp and seven plasmids of 167,030, 128,297, 60,905, 134,795, 9,598, 37,455, and 6332 bp, respectively. The whole genome sequence includes 5948 protein-coding genes, 124 tRNAs, and 29 rRNAs, and has been deposited at Genbank/EMBL/DDBJ with accession numbers CP018874-CP018881...
December 31, 2018: Computational Biology and Chemistry
Ankush Maind, Shital Raut
Mining patterns of co-expressed genes across the subset of conditions help to narrow down the search space for the analysis of gene expression data. Identifying conditions specific key genes from the large-scale gene expression data is a challenging task. The conditions specific key gene signifies functional behavior of a group of co-expressed genes across the subset of conditions and can be act as biomarkers of the diseases. In this paper, we have propose a novel approach for identification of conditions specific key genes from Basal-Like Breast Cancer (BLBC) disease using biclustering algorithm and Gene Co-expression Network (GCN)...
December 31, 2018: Computational Biology and Chemistry
Somrak Numnark, Worasait Suwannik
The microRNA identification step is a part of a plant analytic pipeline. Researches on microRNA identification have been focused extensively on precision, recall, f-measure, and accuracy of computational techniques. However, as the database becomes larger, these computational techniques cannot reduce time complexity to handle the growth. As a result, the identification step becomes a bottleneck in the pipeline. To reduce the response time of the identification step, we proposed a new technique that can discover predictive results faster than the traditional technique...
December 27, 2018: Computational Biology and Chemistry
Jiao-Long Wang, Liang Li, Mei-Bian Hu, Bo Wu, Wen-Xiang Fan, Wei Peng, Da-Neng Wei, Chun-Jie Wu
Inhibitor of nuclear factor kappa B kinase subunit beta (IKK-β), a specific regulator of nuclear factor-κB (NF-κB), is considered a valid target to design novel candidate drugs to treat rheumatoid arthritis and various cancers. In the present study, quantitative structure-activity relationships (QSAR) and molecular docking techniques were used to screen for new IKK-β inhibitors from a series of 2-acylamino-3-aminothienopyridine analogs. During the two-dimensional QSAR phase, the statistical model partial least square was selected from among two alternatives (r2  = 0...
December 27, 2018: Computational Biology and Chemistry
Shahzaib Ahamad, Asimul Islam, Faizan Ahmad, Neeraj Dwivedi, Md Imtaiyaz Hassan
The development of multi-drug and extensively-drug resistant strains of Mycobacterium tuberculosis (Mtb) have encouraged to develop new anti-TB agents with a unique mechanism of action. FtsZ, an essential protein of bacterial cytokinesis, has emerged as a validated target for antibacterial therapy. This study describes the utility of benzimidazoles (BI) derivatives as potential FtsZ inhibitors. Through 2/3D QSAR (MLR) molecular modeling, new BI-inhibitors with improved activity have been designed. Statistically significant models from 2D-QSAR (r2  = 0...
December 27, 2018: Computational Biology and Chemistry
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