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Journal of Biomolecular Structure & Dynamics

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https://www.readbyqxmd.com/read/30101692/example-of-two-novel-thiocyanato-bridged-copper-ii-complexes-derived-from-substituted-thiosemicarbazone-ligand-structural-elucidation-dna-albumin-binding-biological-profile-analysis-and-molecular-docking-study
#1
Niladri Biswas, Sandeepta Saha, Sumit Khanra, Arnab Sarkar, Deba Prasad Mandal, Shamee Bhattacharjee, Ankur Chaudhuri, Sibani Chakraborty, Chirantan Roy Choudhury
Two novel copper (II) substituted thiosemicarbazone Schiff base complexes [Cu(L1 )(µ-SCN)]n (NO3 )2 (1) and [Cu2 (µ-SCN)(SCN)(L2 )2 ](NO3 ) (2) have been synthesized by condensing substituted thiosemicarbazides like 4-methyl-3-thiosemicarbazide or 4-ethyl-3-thiosemicarbazide with 2-acetylpyridine. Both the metal complexes 1 and 2 are characterized by different spectroscopic techniques like IR, UV-Vis, ESR spectroscopy followed by elemental analysis, cyclic voltammetric measurement and single crystal X-ray structure analysis...
August 13, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30101656/effects-of-secondary-structures-of-dna-templates-on-the-quantification-of-qpcr
#2
Huijun Fan, Jing Wang, Makoto Komiyama, Xingguo Liang
In the current design of qPCR systems, the sequences of primers are the primary concerns. The secondary structures of DNA templates have not been much considered, although they should be also critically important. In this paper, various hairpins with different stem lengths and loop sizes are placed near primer-binding sites, and their effects on the amplification efficiency of qPCR are systematically investigated. When a hairpin is formed either in the inside of the amplicon or in its outside, the amplification is notably suppressed...
August 13, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30101645/effect-of-epicatechin-3-gallate-and-epigallocatechin-3-gallate-on-the-binding-of-tegafur-to-human-serum-albumin-as-determined-by-spectroscopy-isothermal-titration-calorimetry-and-molecular-docking
#3
Lixia Yuan, Min Liu, Yabo Shi, Hui Yan, Jun Han, Liying Liu
Green tea has attracted great interest as a cancer prevention agent. Interactions of tea polyphenols with serum albumin may influence the efficacy of drugs. The interactions of (-)-epigallocatechin-3-gallate (EGCG), (-)-epicatechin-3-gallate (ECG), and tegafur (TF) alone or in combination with human serum albumin (HSA) at pH 7.4 and different temperatures were investigated by spectroscopic methods, isothermal titration calorimetry (ITC), and molecular docking. The binding affinities to HSA were ranked in the order of EGCG > ECG > TF, and the interactions were spontaneous and exothermic...
August 13, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30099932/in-silico-studies-and-the-design-of-novel-agents-for-the-treatment-of-systemic-tuberculosis
#4
Vanja P Ničković, Zorica N Vujnović-Živković, Rada Trajković, Dane Krtinić, Lidija Ristić, Milan Radović, Zorica Ćirić, Dušan Sokolović, Aleksandar M Veselinović
Tuberculosis is an ancient infectious disease, which re-emerged with the appearance of multidrug-resistant strains and Acquired Immune Deficiency Syndrome. Enoyl-acyl-carrier protein reductase (InhA) has emerged as a promising target for the development of antituberculosis therapeutics. The present study aims to develop quantitative structure-activity relationship (QSAR) models for a series of arylcarboxamides as InhA inhibitors. The QSAR models were calculated on the basis of optimal molecular descriptors based on the simplified molecular-input line-entry system (SMILES) notation with the Monte Carlo method as a model developer...
August 13, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30092746/insights-on-inhibition-of-plasmodium-falciparum-plasmepsin-i-by-novel-epoxyazadiradione-derivatives-molecular-docking-and-comparative-molecular-field-analysis
#5
Mahalakshmi Thillainayagam, Kullappan Malathi, Anand Anbarasu, Harpreet Singh, Renu Bahadur, Sudha Ramaiah
In the present study, we have explored the anti-malarial potential of epoxyazadiradione, the natural entity extracted from the neem seed oil and its chemical derivatives, against Plasmodium falciparum. The Surflex dock analysis of forty one compounds against an indispensable target, plasmepsin I revealed that around 70% of the compounds are found to have good binding capacity with the Consensus score of 5 to 4 with few hydrogen bonds. To elucidate the major structural requirements, vital for binding with the plasmepsin enzyme and to develop the predictive models, 3-Dimentional Quantitative Structure Activity Relationship - Comparative Molecular Field Analysis was carried out using Sybyl X...
August 9, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30088794/interaction-and-photo-induced-cleavage-studies-of-meropenem-drug-with-human-serum-albumin-using-spectroscopic-and-molecular-docking-investigations
#6
Sabah Ahmed Abdo Esmail, Manal Shamsi, Waddhaah M Al-Asbahy
No abstract text is available yet for this article.
August 8, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30088792/in-vitro-and-in-silico-evaluation-of-fucosterol-from-sargassum-horridum-as-potential-human-acetylcholinesterase-inhibitor
#7
E S Castro-Silva, M Bello, M Hernández-Rodríguez, J Correa-Basurto, J I Murillo-Álvarez, M C Rosales-Hernández, M Muñoz-Ochoa
The fucosterol has been reported numerous biological activities. In this study, the activity in vitro of the fucosterol from Sargassum horridum as potential human acetylcholinesterase inhibitor was evaluated. The structural identification was obtained by nuclear magnetic resonance (NMR) spectroscopy and based on experimental data, we combined docking and molecular dynamics simulations coupled to the Molecular-Mechanics-Generalized-Born-Surface-Area approach to evaluating the structural and energetic basis for the molecular recognition of fucosterol and neostigmine at the binding site of acetylcholinesterase (AChE)...
August 8, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30081753/two-dimensional-ising-model-for-microarray-hybridization-cooperative-interactions-between-bound-target-molecules
#8
Y V Stirmanov, O V Matveeva, Y D Nechipurenko
The Langmuir adsorption model is widely used for description and quantification of microarray oligo-target hybridization. According to the model, the binding centers for adsorption of target molecules from solution are represented by oligo-probes. However, the Langmuir model does not consider the interactions between the targets adsorbed at the neighboring binding centers, which are possible due to high density of array-bound probes. We have shown that the two-dimensional Ising model, which takes into account the nearest neighboring target molecules interactions, better describes the experimental data of oligo-target hybridization in comparison with the Langmuir model...
August 6, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30081748/epigallocatechin-3-gallate-location-and-interaction-with-late-endosomal-and-plasma-membrane-model-membranes-by-molecular-dynamics
#9
José Villalaín
Epigallocatechin-3-gallate (EGCG) is the most abundant polyphenol in green tea and it has been reported to have many beneficial properties against many different types of illnesses and infections. However, the exact mechanism/s underlying its biological effects are unknown. It has been previously shown that EGCG is capable of binding to and disrupting the membrane, so that some of its effects on biological systems could be ascribed to its capacity to incorporate into the biological membrane and modulate its structure...
August 6, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30080442/exploring-the-binding-dynamics-of-etoricoxib-with-human-hemoglobin-a-spectroscopic-calorimetric-and-molecular-modeling-approach
#10
Paromita Seal, Jyotirmoy Sikdar, Niladri Ghosh, Payel Biswas, Rajen Haldar
Etoricoxib, widely used for the treatment of osteoarthritis, rheumatoid arthritis, ankylosing spondylitis and related conditions has ample affinity to bind with globular proteins. Here, the molecular interaction between purified human hemoglobin, a major heme protein and etoricoxib, a cyclooxygenase-2 inhibitor was studied by various spectroscopic, calorimetric and molecular modeling techniques. The binding affected hypochromic changes in the Soret band of hemoglobin and induced remarkable quenching of the intrinsic fluorescence property of protein molecules...
August 6, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30079805/structure-investigation-enrichment-analysis-and-structure-based-repurposing-of-fda-approved-drugs-as-inhibitors-of-bet-brd4
#11
Wakchaure Padmaja D, Ravichandiran Velayutham, Kuldeep K Roy
We report herein detailed structural insights into the ligand recognition modes guiding bromodomain selectivity, enrichment analysis and docking-based database screening for the identification of the FDA-approved drugs that have potential to be the human BRD4 inhibitors. Analysis of multiple X-ray structures prevailed that the lysine-recognition sites are highly conserved, and apparently, the dynamic ZA loop guides the specific ligand-recognition. The protein-ligand interaction profiling revealed that both BRD2 and BRD4 shared hydrophobic interaction of bound ligands with PRO-98/PRO-82, PHE-99/PHE-83, LEU-108/LEU-92, and direct H-bonding with ASN-156/ASN-140 (BRD2/BRD4), while on the other hand the water-mediated H-bonding of bound ligands with PRO-82, GLN-85, PRO-86, VAL-87, ASP-88, LEU-92, TYR-97 and MET-132, and aromatic π - π stacking with TRP-81 prevailed as unique interaction in BRD4, and were not observed in BRD2...
August 6, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30079817/screening-for-the-selective-inhibitors-of-mmp-9-from-natural-products-based-on-pharmacophore-modeling-and-molecular-docking-in-combination-with-bioassay-experiment-hybrid-qm-mm-calculation-and-md-simulation
#12
Jiaying Hou, Qing Zou, Yijun Wang, Qi Gao, Wenhui Yao, Qizheng Yao, Ji Zhang
Matrix metalloproteinase-9 (MMP-9) has been considered as an attractive target involving cancer therapy. In this study, the 3D QSAR pharmacophore model of MMP-9 inhibitors is built, and its reliability is subsequently validated based on different methods. The built pharmacophore model consists of the four chemical features, including two hydrogen bond acceptors (HBA), one hydrophobic (HY), and one ring aromatic (RA). Among them, both HY and RA are found to be especially important features because they involve the interactions of inhibitors with the S1' pocket of MMP-9, which determines the selectivity of MMP-9 inhibitors...
August 5, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30079808/towards-a-better-understanding-of-the-interaction-between-somatostatin-receptor-2-sstr2-and-its-ligands-a-structural-characterization-study-using-molecular-dynamics-and-conceptual-density-functional-theory-dft
#13
Santhosh Kumar Nagarajan, Sathya Babu, Honglae Sohn, Panneer Devaraju, Thirumurthy Madhavan
This study is a part of the extensive research intending to provide the structural insights on somatostatin and its receptor. Herein, we have studied the structural complexity involved in the binding of Somatostatin receptor 2 (SSTR2) with its agonists and antagonist. A 3D QSAR study based on Comparative molecular field analysis (CoMFA) and Comparative molecular similarity analysis (CoMSIA) discerned that a SSTR2 ligand with electronegative, less-bulkier and hydrogen atom donating/accepting substitutions is important for their biological activity...
August 5, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30073907/a-double-edged-sword-supramolecular-complexes-of-triazavirine-display-multicenter-binding-effects-which-influence-aggregate-formation
#14
Yana A Zabrodskaya, Alexey V Shvetsov, Vladimir B Tsvetkov, Vladimir V Egorov
No abstract text is available yet for this article.
August 3, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30058457/biologically-active-compounds-from-two-members-of-the-asteraceae-family-tragopogon-dubius-scop-and-tussilago-farfara-l
#15
Sengul Uysal, Ismail Senkardes, Adriano Mollica, Gokhan Zengin, Gizem Bulut, Ahmet Dogan, Jasmina Glamočlija, Marina Soković, Devina Lobine, M Fawzi Mahomoodally
Tragopogon dubius and Tussilago farfara are consumed as vegetables and used in folk medicine to manage common diseases. Herein, the chemical compositions and biological activities of different leaf extracts (ethyl acetate, methanol, and water) of T. dubius and T. farfara were evaluated. The antibacterial, antifungal, and antioxidant abilities of the extracts were tested using different assays including free radical scavenging, reducing power, phosphomolybdenum, and metal chelating assays. Enzyme inhibitory potentials were evaluated against cholinesterases, tyrosinase, α-amylase and α-glucosidase...
July 30, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30058446/molecular-dynamics-and-combined-docking-studies-for-the-identification-of-zaire-ebola-virus-inhibitors
#16
Kazeem O Sulaiman, Temitope U Kolapo, Abdulmujeeb T Onawole, Ataul Islam, Rukayat O Adegoke, Suaibu O Badmus
Ebola virus (EBOV) is a lethal human pathogen with a risk of global spread of its zoonotic infections, and Ebolavirus Zaire specifically has the highest fatality rate amongst other species. There is a need for continuous effort towards having therapies, as a single licensed treatment to neutralize the EBOV is yet to come into reality. This present study virtually screened the MCULE database containing almost 36 million compounds against the structure of a Zaire Ebola viral protein (VP) 35 and a consensus scoring of both MCULE and CLCDDW docking programs remarked five compounds as potential hits...
July 30, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30056779/insights-into-the-interaction-of-ulipristal-acetate-and-human-serum-albumin-using-multi-spectroscopic-methods-molecular-docking-and-dynamic-simulation
#17
Na Gan, Qiaomei Sun, Man Zhang, Peixiao Tang, Ludan Zhao, Tonghui Xie, Yongkui Zhang, Hui Li
Interaction between ulipristal acetate (UPA) and human serum albumin (HSA) was investigated in simulated physiological environment using multi-spectroscopic and computational methods. Fluorescence experiments showed that the quenching mechanism was static quenching, which was confirmed by the time-resolved fluorescence. Binding constants (Ka ) were found to be 1 × 105 L mol-1 , and fluorescence data showed one binding site. Thermodynamic constants suggested the binding process was mainly controlled by electrostatic interactions...
July 30, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30058445/insights-about-resveratrol-analogues-against-trypanothione-reductase-of-leishmania-braziliensis-molecular-modeling-computational-docking-and-in-vitro-antileishmanial-studies
#18
Adilson D da Silva, Juliana A Dos Santos, Patrícia A Machado, Lara A Alves, Larissa C Laque, Vinícius C de Souza, Elaine S Coimbra, Priscila V S Z Capriles
In this work, we combined molecular modeling, computational docking and in vitro analysis to explore the antileishmanial effect of some resveratrol analogues (ResAn), focusing on their pro-oxidant effect. The molecular target was the trypanothione reductase of Leishmania braziliensis (LbTryR), an essential component of the antioxidant defenses in trypanosomatid parasites. Three-dimensional structures of LbTryR were modeled and molecular docking studies of ResAn1-5 compounds showed the following affinity: ResAn1 > ResAn2 > ResAn4 > ResAn5 > ResAn3...
July 28, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30058436/molecular-mechanism-study-of-several-inhibitors-binding-to-brd9-bromodomain-based-on-molecular-simulations
#19
Li Ting Song, Jing Tu, Rui Rui Liu, Min Zhu, Ya Jie Meng, Hong Lin Zhai
Bromodomain-containing protein 9 (BRD9) has been employed as a potential target for anticancer drugs in recent years. In this work, molecular docking, molecular dynamics (MD) simulations, binding free energy calculations and per residue energy decomposition approaches were performed to elucidate the different binding modes between four pyridinone-like scaffold inhibitors and BRD9 bromodomain. Analysis results indicate that non-polar contribution mainly deriving from van der Waals energy is a critical impact on binding affinity of inhibitors against BRD9...
July 28, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30052167/evolutionary-and-structure-function-analysis-elucidates-diversification-of-prokaryotic-and-eukaryotic-trehalases
#20
Meenakshi B Tellis, Nidhi N Gujar, Rakesh S Joshi
Trehalase catalyzes the breakdown of trehalose into two glucose moieties and is ubiquitous in all organisms. Here, we provide insights into the enigmatic origin and evolution of trehalase in major species. Study of taxonomic distribution, orthology, phylogeny and functional domains indicated that trehalase possibly originates from bacteria and was transmitted to other taxa through horizontal gene transfer. Domain analysis showed that glycosyl hydrolase family 37 is present in most of the sequences and represents dominant activity during evolution...
July 27, 2018: Journal of Biomolecular Structure & Dynamics
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