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Computational Biology and Chemistry

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https://www.readbyqxmd.com/read/29427909/allosteric-inhibition-abrogates-dysregulated-lfa-1-activation-structural-insight-into-mechanisms-of-diminished-immunologic-disease
#1
Maryam Abdullahi, Fisayo A Olotu, Mahmoud E Soliman
Lymphocyte Function Associated antigen-1(LFA-1) has been implicated severely in the pathophysiology of inflammatory and autoimmune diseases. Its active and inactive conformations correlate with its diseased and non-diseased state respectively. This is determined by its degree of affinity for its intrinsic ligand (ICAM) at the active site and accompanying synergistic coordination at the α7 helix. This potentiates the role of inhibitors in disrupting this interaction allosterically. Herein, we present a first account of the structural dynamics which characterizes the inhibitory effect of a novel LFA-1 antagonist, Lifitegrast (SAR1118), upon binding to the I-domain allosteric site (IDAS) using molecular dynamics simulation...
February 5, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29425935/molecular-dynamics-simulation-studies-suggests-unconventional-roles-of-non-secretary-laccases-from-enteropathogenic-gut-bacteria-and-cryptococcus-neoformans-serotype-d
#2
Krishna Kant Sharma, Deepti Singh, Surender Rawat
Laccase in Cryptococcus neoformans is covalently linked to the carbohydrate moiety of the cell wall, which allows it to get access to the different substrates for catalyzing their oxidation and therefore plays a vital role in the virulence. The laccase gene (3.0 kb) from C. neoformans serotype D was amplified, cloned and sequenced for protein modeling, docking and simulation studies. The three dimensional homology models of laccase protein from C. neoformans and other pathogenic gut bacteria were docked with selected biomolecules like prostaglandins (PG), membrane phospholipids, neurotransmitters (serotonin) using GOLD software...
February 3, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29428276/a-random-version-of-principal-component-analysis-in-data-clustering
#3
Luigi Leonardo Palese
Principal component analysis (PCA) is a widespread technique for data analysis that relies on the covariance/correlation matrix of the analyzed data. However, to properly work with high-dimensional data sets, PCA poses severe mathematical constraints on the minimum number of different replicates, or samples, that must be included in the analysis. Generally, improper sampling is due to a small number of data respect to the number of the degrees of freedom that characterize the ensemble. In the field of life sciences it is often important to have an algorithm that can accept poorly dimensioned data sets, including degenerated ones...
February 2, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29413812/molecular-dynamics-studies-show-solvation-structure-of-type-iii-antifreeze-protein-is-disrupted-at-low-ph
#4
Antonio Peramo
Antifreeze proteins are a class of biological molecules of interest in many research and industrial applications due to their highly specialized function, but there is little information of their stability and properties under varied pH derived from computational studies. To gain novel insights in this area, we conducted molecular dynamics (MD) simulations with the antifreeze protein 1KDF at varied temperatures and pH. Water solvation and H-bond formation around specific residues - ASN14, THR18 and GLN44 - involved in its antifreeze activity were extensively studied...
February 2, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29413814/interferon-induced-mx-protein-from-indian-snow-trout-schizothorax-richardsonii-gray-lacks-critical-functional-features-unlike-its-mammalian-homologues
#5
Ankur Saxena, Kiran Belwal, Ankita Chauhan, Amit Pande
Viral attack within host cells triggers the production of type I interferons and leads to the induction of interferon stimulated genes (ISGs). One of the ISG Mx, encodes type I interferon inducible GTPase that is responsible for the establishment of an anti-viral state within cells. Intriguingly, several isoforms of Mx have been reported in fish, but the structural analysis of fish Mx proteins remains unexplored. For the first time, we have identified and unraveled the molecular structure of Mx protein from Indian snow trout, Schizothorax richardsonii (Gray) a Coldwater fish that inhabits the water bodies in the sub-Himalayan region...
January 31, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29413811/3d-qsar-pharmacophore-based-virtual-screening-for-identification-of-potential-inhibitors-for-cdc25b
#6
Ying Ma, Hong-Lian Li, Xiu-Bo Chen, Wen-Yan Jin, Hui Zhou, Ying Ma, Run-Ling Wang
Owing to its fundamental roles in cell cycle phases, the cell division cycle 25B (CDC25B) was broadly considered as potent clinical drug target for cancers. In this study, 3D QSAR pharmacophore models for CDC25B inhibitors were developed by the module of Hypogen. Three methods (cost analysis, test set prediction, and Fisher's test) were applied to validate that the models could be used to predict the biological activities of compounds. Subsequently, 26 compounds satisfied Lipinski's rule of five were obtained by the virtual screening of the Hypo-1-CDC25B against ZINC databases...
January 26, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29414100/physical-quantity-of-residue-electrostatic-energy-in-flavin-mononucleotide-binding-protein-dimer
#7
Nadtanet Nunthaboot, Arthit Nueangaudom, Kiattisak Lugsanangarm, Somsak Pianwanit, Sirirat Kokpol, Fumio Tanaka
The electrostatic (ES) energy of each residue was for the first time quantitatively evaluated in a flavin mononucleotide binding protein (FBP). A residue electrostatic energy (RES) was obtained as the sum of the ES energies between atoms in each residue and all other atoms in the FBP dimer using atomic coordinates obtained by a molecular dynamics (MD) simulation. ES is one of the most important energies among the interaction energies in a protein. It is determined from the RES, the residues which mainly contribute to stabilize the structure of each subunit, and the binding energy between two subunits can be estimated...
January 12, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29414099/an-integrative-in-silico-approach-to-the-structure-of-omp33-36-in-acinetobacter-baumannii
#8
Abolfazl Jahangiri, Iraj Rasooli, Parviz Owlia, Abbas Ali Imani Fooladi, Jafar Salimian
Omp33-36 in A. baumannii, a bacterium causing serious nosocomial infections, is a virulence factor associated with the pathogen metabolic fitness as well as its adherence and invasion to human epithelial cells. This protein is also involved in interaction of the bacteria with host cells by binding to fibronectin. Moreover, Omp33-36 renders cytotoxicity to A. baumannii in addition to inducing apoptosis and modulation of autophagy. In the present study, an integrated strategy is launched to pierce into the 3D structure of Omp33-36 protein...
January 12, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29414097/normal-mode-analysis-of-zika-virus
#9
Byung Ho Lee, Soojin Jo, Moon-Ki Choi, Min Hyeok Kim, Jae Boong Choi, Moon Ki Kim
In recent years, Zika virus (ZIKV) caused a new pandemic due to its rapid spread and close relationship with microcephaly. As a result, ZIKV has become an obvious global health concern. Information about the fundamental viral features or the biological process of infection remains limited, despite considerable efforts. Meanwhile, the icosahedral shell structure of the mature ZIKV was recently revealed by cryo-electron microscopy. This structural information enabled us to simulate ZIKV. In this study, we analyzed the dynamic properties of ZIKV through simulation from the mechanical viewpoint...
January 12, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29358109/deepaligner-deep-encoding-of-pathways-to-align-epigenetic-signatures
#10
R Visakh, K A Abdul Nazeer
BACKGROUND AND OBJECTIVE: Recently, differential DNA Methylation is known to affect the regulatory mechanism of biological pathways. A pathway encompasses a set of interacting genes or gene products that altogether perform a given biological function. Pathways often encode strong methylation signatures that are capable of distinguishing biologically distinct subtypes. Even though Next Generation Sequencing techniques such as MeDIP-seq and MBD-isolated genome sequencing (MiGS) allow for genome-wide identification of clinical and biological subtypes, there is a pressing need for computational methods to compare epigenetic signatures across pathways...
January 11, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29310001/coral-qsar-models-for-carcinogenicity-of-organic-compounds-for-male-and-female-rats
#11
Alla P Toropova, Andrey A Toropov
Quantitative structure - activity relationships (QSARs) for carcinogenicity (rats, TD50) have been built up using the CORAL software. Different molecular features, which are extracted from simplified molecular input-line entry system (SMILES) serve as the basis for building up a model. Correlation weights for the molecular features are calculated by means of the Monte Carlo optimization. Using the numerical data on the correlation weights, one can calculate a model of carcinogenicity as a mathematical function of descriptors, which are sum of the corresponding correlation weights...
January 2, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29346071/identification-of-potential-inhibitors-against-nuclear-dam1-complex-subunit-ask1-of-candida-albicans-using-virtual-screening-and-md-simulations
#12
Himanshu Tripathi, Feroz Khan
Identification of hit compounds against specific target form the starting point for a drug discovery program. A consistent decline of new chemical entities (NCEs) in recent years prompted a challenge to explore newer approaches to discover potential hit compounds that in turn can be converted into leads, and ultimately drug with desired therapeutic efficacy. The vast amount of omics and activity data available in public databases offers an opportunity to identify novel targets and their potential inhibitors...
January 1, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29346072/synthesis-biological-evaluation-and-molecular-docking-studies-of-novel-benzimidazole-derivatives
#13
Gagandeep Singh, Amanjot Singh, Raman K Verma, Rajiv Mall, Uzma Azeem
A novel series of N-substituted-benzimidazolyl linked para substituted benzylidene based molecules containing three pharmacologically potent hydrogen bonding parts namely; 2,4-thiazolidinedione (TZD: a 2,4-dicarbonyl), diethyl malonate (DEM: a 1,3-diester and an isooxazolidinedione analog) and methyl acetoacetate (MAA: a β-ketoester) (6a-11b) were synthesized and evaluated for in vitro α-glucosidase inhibition. The structure of the novel synthesized compounds was confirmed through the spectral studies (LC-MS, 1H NMR, 13C NMR, FT-IR)...
December 30, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29291590/patterns-of-cation-binding-to-the-aromatic-amino-acid-r-groups-in-trp-tyr-and-phe
#14
Shelby L Scherer, Amanda L Stewart, Ryan C Fortenberry
Previous joint experimental and theoretical work demonstrates that typically soluble peptides will be rendered insoluble in the presence of saturated sodium ions in aqueous solution due to disruption of cation-π interactions between Trp and Lys. The present work utilizes quantum chemical methods including density functional theory, symmetry-adapted perturbation theory, and even coupled cluster theory to determine the strengths of cation-π interactions for the aromatic R groups of Trp, Tyr, and Phe (approximated as skatole, methyl phenol, and toluene) with both alkali and alkaline-Earth atomic cations and electron-accepting R groups from Lys, Arg, and His approximated as methyl ammonium, guanidinium, and imidazolium cations...
December 27, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29291591/proteome-scale-identification-of-leishmania-infantum-for-novel-vaccine-candidates-a-hierarchical-subtractive-approach
#15
Bahareh Vakili, Navid Nezafat, Gholam Reza Hatam, Bijan Zare, Nasrollah Erfani, Younes Ghasemi
Vaccines are one of the most significant achievements in medical science. However, vaccine design is still challenging at all stages. The selection of antigenic peptides as vaccine candidates is the first and most important step for vaccine design. Experimental selection of antigenic peptides for the design of vaccines is a time-consuming, labor-intensive and expensive procedure. More recently, in the light of computer-aided biotechnology and reverse vaccinology, the precise selection of antigenic peptides and rational vaccine design against many pathogens have developed...
December 24, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29289750/arohap-an-effective-algorithm-for-single-individual-haplotype-reconstruction-based-on-asexual-reproduction-optimization
#16
Mohammad-H Olyaee, Alireza Khanteymoori
In this paper, a method for single individual haplotype (SIH) reconstruction using Asexual reproduction optimization (ARO) is proposed. Haplotypes, as a set of genetic variations in each chromosome, contain vital information such as the relationship between human genome and diseases. Finding haplotypes in diploid organisms is a challenging task. Experimental methods are expensive and require special equipment. In SIH problem, we encounter with several fragments and each fragment covers some parts of desired haplotype...
December 14, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29277259/exciton-states-and-optical-properties-of-the-cp26-photosynthetic-protein
#17
Daniil V Khokhlov, Aleksandr S Belov, Vadim V Eremin
The photosynthetic complex CP26, one of the minor antennae of the photosystem II, plays an important role in regulation of the excitation energy transfer in the PSII. Due to instability during isolation and purification, it remained poorly studied from the viewpoint of theoretical chemistry because of the absence of X-ray crystallography data. In this work, using the recently determined three-dimensional structure of the complex we apply the quantum chemical approach to study the properties of exciton states in it...
December 13, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29248356/corrigendum-to-docking-assay-of-small-molecule-antivirals-to-p7-of-hcv-comput-biol-chem-53-2014-308-317
#18
L Bichmann, Y-T Wang, W B Fischer
No abstract text is available yet for this article.
December 13, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29274684/identification-of-novel-nt-mgam-inhibitors-for-potential-treatment-of-type-2-diabetes-virtual-screening-atom-based-3d-qsar-model-docking-analysis-and-adme-study
#19
Aicha Laoud, Fouad Ferkous, Laura Maccari, Giorgio Maccari, Youcef Saihi, Khaireddine Kraim
In this study, a virtual screening procedure was applied to identify new potential nt-MGAM inhibitors as a possible medication for type 2 diabetes. To this aim, a series of salacinol analogues were first investigated by docking analysis for their binding to the X-ray structure of the biological target nt-MGAM. Key interactions for ligand binding into the receptor active site were identified which shared common features to those found for other known inhibitors, which strengthen the results of this study. 3D QSAR model was then built and showed to be statistically significant and with a good predictive power for the training (R2 = 0...
December 12, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29290517/experimental-and-density-functional-theory-studies-on-benzalkonium-ibuprofenate-a-double-active-pharmaceutical-ingredient
#20
K P Safna Hussan, M Shahin Thayyil, Vijisha K Rajan, K Muraleedharan
Molecular aspects of a double active pharmaceutical ingredient in ionic liquid form, benzalkonium ibuprofenate (BaIb), were studied using density functional theory (DFT/B3LYP/6-31+G (d, p)). A detailed discussion on optimized geometry, energy, heat and the enthalpy of BaIb was carried out. The computed vibrational results agree well with the experimental results. The stability and biological activity were compared to the parent drugs on the basis of global descriptive parameters. The electrophilic and nucleophilic sites were pointed out in the MESP structures well evidently...
December 9, 2017: Computational Biology and Chemistry
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