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Journal of Biomolecular Structure & Dynamics

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https://www.readbyqxmd.com/read/28539091/in-silico-identification-of-potential-drug-compound-against-peroxisome-proliferator-activated-receptor-gamma-by-virtual-screening-and-toxicity-studies-for-treatment-of-diabetic-nephropathy
#1
Smrita Singh, Aparajita Mohanty
Diabetic Nephropathy is a serious complication of Diabetes Mellitus. Current therapeutic strategies of Diabetic Nephropathy are based on control of modifiable risks like hypertension, glucose levels, and dyslipidemia. Peroxisome proliferator activated receptor-gamma (PPAR-γ) is implicated in several metabolic syndromes including Diabetic Nephropathy, besides obesity, insulin insensitivity, dislipidemia, inflammation and hypertension. In the present study, virtual screening of 617 compounds from two different public databases was done against PPAR- γ with an objective to find a possible lead compound...
May 24, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28537217/effect-of-the-sulphur-atom-on-geometry-and-spectra-of-the-biomolecule-2-thiouracil-and-in-the-wc-base-pair-2-thiouridine-adenosine-influence-of-water-in-the-first-hydration-shell
#2
M Alcolea Palafox, V K Rastogi, S P Singh
The effect of the sulphur atom on 2-thiouracil (2TU) and 2-thiouridine molecules, as compared with uracil and uridine molecules, respectively, was carried out in several environments. The predicted IR spectrum of 2TU in the isolated state was compared with that obtained for uracil molecule and with those reported experimentally in matrix isolation. Its crystal unit cell in the solid state was simulated through a tetramer form using DFT methods for the first time. The calculated Raman spectrum was compared to the experimental ones in the solid state...
May 24, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28537197/saffron-carotenoids-crocin-and-crocetin-binding-to-human-serum-albumin-as-investigated-by-different-spectroscopic-methods-and-molecular-docking
#3
Moslem Jafarisani, S Zahra Bathaie, Mir F Mousavi
Therapeutic effects of saffron ingredients were studied in some diseases. The pharmacokinetics and pharmacodynamics of these ingredients were also studied, but their transport mechanism is not clearly known. Serum albumin has been known as the most important transporter of many drugs in the body that affects their disposition, transportation and bioavailability. Here, we investigated the interaction of crocin (Cro) with HSA, for the first time, and compared with the crocetin (Crt)-HSA interaction. UV and fluorescence spectroscopy, circular dichroism (CD) and molecular docking was applied to investigate the possibility and mechanism of binding of HSA with these natural carotenoids...
May 24, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28537193/isolated-potato-virus-a-coat-protein-possesses-unusual-properties-and-forms-different-short-virus-like-particles
#4
Alexander L Ksenofontov, Eugeny N Dobrov, Natalia V Fedorova, Marina V Serebryakova, Andrei N Prusov, Ludmila A Baratova, Viiu Paalme, Lilian Järvekülg, Eleonora V Shtykova
In our previous study, we have observed that the isolated coat proteins (CP) of the Potyvirus Potato Virus A (PVA) virions exhibit an intrinsic tendency of to self-associate into various multimeric forms containing some fractions of cross-β-structure. In this report, we studied the effect of solution conditions on the structure and dissociation of isolated PVA CP using a number of complementary physicochemical methods. Analysis of the structure of PVA CP in solution was performed by limited proteolysis with MALDI-TOF Mass Spectrometry analysis, transmission electron microscopy, intrinsic fluorescence spectroscopy and synchrotron small angle X-ray scattering (SAXS)...
May 24, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28532244/virucidal-activity-of-cell-penetrating-peptides-of-viral-origin
#5
Nawal Abd El-Baky, Vladimir N Uversky, Elrashdy M Redwan
No abstract text is available yet for this article.
May 23, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28531373/identification-of-potential-inhibitors-for-hcv-ns3-genotype-4a-by-combining-protein-ligand-interaction-fingerprint-3d-pharmacophore-docking-and-dynamic-simulation
#6
Mahmoud Abd El-Monem El-Hasab, Eman Esmat El-Bastawissy, Tarek Faathy El-Moselhy
HCV NS3 protease domain has been one of the most attractive targets for developing new drugs for HCV infection and many drugs were successfully developed, but all of them were designed for targeting HCV genotype 1 infection. HCV genotype 4a dominant in Egypt has paid less attention. Here we describe our protocol of virtual screening in identification of novel potential potent inhibitors for HCV NS3 of genotype 4a using homology modelling, PLIF (protein ligand interaction fingerprint), docking, pharmacophore and dynamic simulation...
May 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28531371/wing-1-of-protein-hop2-is-as-important-as-helix-3-in-dna-binding-by-md-simulation
#7
Hem Moktan, Donghua H Zhou
The repair of programmed DNA double-strand breaks through recombination is required for proper association and disjunction of the meiotic homologous chromosomes. Meiosis specific protein HOP2 plays essential roles in recombination by promoting recombinase activities. The N-terminal domain of HOP2 interacts with DNA through helix 3 (H3) and wing 1 (W1). Mutations in wing 1 (Y65A/K67A/Q68A) slightly weakened the binding but mutations in helices 2 and 3 (Q30A/K44A/K49A) nearly abolished the binding. To better understand such differential effects at atomic level, molecular dynamics simulations were employed...
May 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28521603/in-silico-binding-mechanism-prediction-of-benzimidazole-based-corticotropin-releasing-factor-1-receptor-antagonists-by-quantitative-structure-activity-relationship-molecular-docking-and-pharmacokinetic-parameters-calculation
#8
Neeraj Kumar, Shashank Shekhar Mishra, Chandra Shekhar Sharma, Hamendra Pratap Singh, Sourav Kalra
Despite the various research efforts towards the treatment of stress related disorders, the drug has not yet launched last 20 years. Corticotropin releasing factor-1 receptor antagonists have been point of great interest in stress related disorders. In the present study, we have selected benzazole scaffold based compounds as corticotropin releasing factor-1 antagonists and performed 2D and 3D QSAR studies to identify the structural features to elucidating the binding mechanism prediction. The best 2D QSAR model was obtained through multiple linear regression method with r(2) value of 0...
May 19, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28521571/milk-caseins-as-useful-vehicle-for-delivery-of-dipyridamole-drug
#9
Hamid Dezhampanah, Masoomeh Esmaili, Leila Hasani
The interaction of bovine milk α- and β-caseins as an efficient drug carrier system with Dipyridamole (DIP) was investigated using spectroscopy and molecular docking studies at different temperatures (20-37(o)C). FTIR, CD and fluorescence spectroscopy methods demonstrated that α- and β-caseins interact with DIP molecule mainly via hydrophobic and hydrophilic interactions and change in secondary structure of α- and β-caseins. DIP showed a higher quenching efficiency and binding constant of α-casein than β-casein...
May 18, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28514900/a-qm-qtaim-detailed-look-at-the-watson-crick%C3%A2-wobble-tautomeric-transformations-of-the-2-aminopurine%C3%A2-pyrimidine-mispairs
#10
Ol'ha O Brovarets', Ivan S Voiteshenko, Horacio Pérez-Sánchez, Dmytro M Hovorun
This work is devoted to the careful QM/QTAIM analysis of the evolution of the basic physico-chemical parameters along the intrinsic reaction coordinate (IRC) of the biologically important 2AP∙T(WC)↔2AP∙T*(w) and 2AP·C*(WC)↔2AP·C(w) Watson-Crick(WC)↔wobble(w) tautomeric transformations obtained at each point of the IRC using original authors' methodology. Established profiles reflect the high similarity between the courses of these processes. Basing on the scrupulous analysis of the profiles of their geometric and electron-topological parameters it was established that the dipole-active WC↔w tautomerisations of the Watson-Crick-like 2AP∙T(WC) / 2AP·C*(WC) mispairs, stabilized by the two classical N3H···N1, N2H···O2 and one weak C6H···O4/N4 H-bonds, into the wobble 2AP∙T*(w)/ 2AP·C(w) base pairs, respectively, joined by the two classical N2H···N3 and O4/N4H···N1 H-bonds, proceed via the concerted stepwise mechanism through the sequential intrapair proton transfer and subsequent large-scale shifting of the bases relative each other, through the planar, highly stable, zwitterionic transition states stabilized by the participation of the four H-bonds - N1(+)H···O4(-)/N4(-), N1(+)H···N3(-), N2(+)H···N3(-) and N2(+)H···O2(-)...
May 18, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28514875/identification-of-novel-nicotinamide-phosphoribosyltransferase-nampt-inhibitors-using-computational-approaches
#11
Manish Kesherwani, Sriram Raghavan, Krishnasamy Gunasekaran, Devadasan Velmurugan
Nicotinamide Phosphoribosyltransferase (NAMPT) is a rate-limiting enzyme in the biosynthesis of NAD. Cancer cells have elevated poly [ADP-Ribose] polymerase 1 (PARP) activity as well as the immense necessity of ATP: thereby consuming NAD at a higher rate than normal tissues. The perturbation of these intracellular processes is more sensitive and highly dependent on NAMPT to maintain the required NAD levels. Functional inhibition of NAMPT is, therefore, a promising drug target in therapeutic oncology. In this study, the importance of intermolecular contacts was realized based on contact occupancy and favorable energetic from molecular dynamic simulation to discern non-critical contacts of four different classes of potential NAMPT inhibitor bound complexes...
May 17, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28511583/deciphering-the-crucial-residues-involved-in-heterodimerization-of-bak-peptide-and-anti-apoptotic-proteins-for-apoptosis
#12
Parthiban Marimuthu, Kalaimathy Singaravelu
B-cell lymphoma 2 (Bcl-2) family proteins are the central regulators of apoptosis, function via mitochondrial outer membrane permeabilization. The family members are involved in several stages of apoptosis regulation. The overexpression of the anti-apoptotic proteins leads to several cancer pathological conditions. This overexpression is modulated or inhibited by heterodimerization of pro-apoptotic BH3 domain or BH3-only peptides to the hydrophobic groove present at the surface of anti-apoptotic proteins. Additionally, the heterodimerization displayed differences in binding affinity profile among the pro-apoptotic peptides binding to anti-apoptotic proteins...
May 16, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28504004/experimental-and-computational-studies-on-the-binding-of-diazinon-to-human-serum-albumin
#13
Fataneh Jafari, Setareh Samadi, Amin Nowroozi, Komail Sadrjavadi, Sajad Moradi, Mohammad Reza Ashrafi-Kooshk, Mohsen Shahlaei
In the present research, the binding properties of Diazinon (DZN), as an organophosphorus herbicide, to human serum albumin (HSA) were investigated using combination of spectroscopic, electrochemistry and molecular modeling techniques. Changes in the UV-Vis and FT-IR spectra were observed upon ligand binding along with a significant degree of tryptophan fluorescence quenching on complex formation. The obtained results from spectroscopic and electrochemistry experiments along with the computational studies suggest that DZN binds to residues located in subdomains IIA of HSA with binding constant about 1410...
May 15, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28504081/dissecting-physical-structure-of-calreticulin-an-intrinsically-disordered-ca-2-buffering-chaperone-from-endoplasmic-reticulum
#14
Anna Rita Migliaccio, Vladimir N Uversky
Calreticulin (CALR) is a Ca(2+) binding multifunctional protein that mostly resides in the endoplasmic reticulum (ER) and plays a number of important roles in various physiological and pathological processes. Although the major functions ascribed to CALR are controlling the Ca(2+) homeostasis in ER and acting as a lectin-like ER chaperon for many glycoproteins, this moonlighting protein can be found in various cellular compartments where it has many non-ER functions. To shed more light on the mechanisms underlying polyfunctionality of this moonlighting protein that can be found in different cellular compartments and that possesses a wide spectrum of unrelated biological activities, being able to interact with Ca(2+) (and potentially other metal ions), RNA, oligosaccharides, and numerous proteins, we used a set of experimental and computational tools to evaluate the intrinsic disorder status of CALR and the role of calcium binding on structural properties and conformational stability of the full-length CALR and its isolated P- and C-domains...
May 13, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28504057/molecular-dynamic-modeling-of-cyp51b-in-complex-with-azole-inhibitors
#15
Pan Gao, Yinglu Cui, Rongling Wu
Cytochrome P450 14α-sterol demethylase (CYP51), the key enzyme in sterol biosynthesis pathway, is an important target protein of cholesterol-lowering agents, antifungal drugs and herbicides. CYP51B enzyme is one of the CYP51 family members. In the present study, we have chosen four representative inhibitors of CYP51B: diniconazole(Din), fluconazole(Flu), tebuconazole(Teb), voriconazole(Vor) and launched to investigate the binding features of CYP51B-inhibitor and gating characteristics via molecular docking and molecular dynamics(MD) simulations...
May 13, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28492103/amphipathic-secondary-structure-elements-and-putative-cholesterol-recognizing-amino-acid-consensus-crac-motifs-as-governing-factors-of-highly-specific-matrix-protein-interactions-with-raft-type-membranes-in-enveloped-viruses
#16
Victor A Radyukhin, Liubov A Dadinova, Ivan A Orlov, Ludmila A Baratova
No abstract text is available yet for this article.
May 11, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28490275/genome-wide-sequential-evolutionary-organizational-and-expression-analyses-of-phenylpropanoid-biosynthesis-associated-myb-domain-transcription-factors-in-arabidopsis
#17
Sunil Kanti Mondal, Sujit Roy
The MYB gene family represents one of the largest groups of transcription factors in plants. Recent evidences have also demonstrated key role of MYB transcription factors in regulating the expression of major genes involved in the biosynthesis of phenylpropanoid compounds which confer biotic and abiotic stress tolerance in plant species. However, no comprehensive genome-wide analysis of the phenylpropanoid pathway associated MYB transcription factors has been reported thus far. In this study, 11 Arabidopsis MYB proteins, such as MYB3, MYB4, MYB7, MYB11, MYB12, MYB32, MYB75, MYB90, MYB111, MYB113 and MYB114 were initially identified considering their reported regulatory function in phenylpropanoid biosynthesis pathway...
May 10, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28490269/investigations-of-fak-inhibitors-a-combination-of-3d-qsar-docking-and-molecular-dynamics-simulations-studies
#18
Peng Cheng, Jiaojiao Li, Juan Wang, Xiaoyun Zhang, Honglin Zhai
Focal adhesion kinase (FAK) is one kind of tyrosine kinases that modulates integrin and growth factor signaling pathways, which is a promising therapeutic target because of involving in cancer cell migration, proliferation and survival. To investigate the mechanism between FAK and triazinic inhibitors and design high activity inhibitors, a molecular modeling integrated with 3D-QSAR, molecular docking, molecular dynamics simulations and binding free energy calculations was performed. The optimum CoMFA and CoMSIA modeles showed good reliability and satisfactory predictability (with Q(2)=0...
May 10, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28490248/sodium-louroyl-sarcosinate-sarkosyl-modulate-amyloid-fibril-formation-in-hen-egg-white-lysozyme-hewl-at-alkaline-ph-a-molecular-insight-study
#19
Javed Masood Khan, Mohd Shahnawaz Khan, Mohammad Abdurehman Alsenaidy, Anwar Ahmed, Priyankar Sen, Mohammad Oves, Nasser Abdulatif Al-Shabib, Rizwan Hasan Khan
Amyloid fibril formation is responsible for several neurodegenerative diseases and are formed when native proteins misfold and stick together with different interactive forces. In the present study, we have determined the mode of interaction of the anionic surfactant sarkosyl with hen egg white lysozyme (HEWL) [EC no. 3.2.1.17] at two pHs (9.0 and 13.0) and investigated its impact on fibrillogenesis. Our data suggested that sarkosyl is promoting amyloid fibril formation in HEWL at the concentration range between 0...
May 10, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28482755/3d-qsar-molecular-docking-and-molecular-dynamic-simulations-to-prediction-of-new-hsp90-inhibitors-based-on-isoxazole-scaffold
#20
Maryam Abbasi, Hojjat Sadeghi-Aliabadi, Massoud Amanlou
Heat shock protein 90(Hsp90), as a molecular chaperone, play a crucial role in folding and proper function of many proteins. Hsp90 inhibitors containing isoxazole scaffold are currently being used in the treatment of cancer as tumor suppressers. Here in the present studies, new compounds based on isoxazole scaffold were predicted using a combination of molecular modeling techniques including three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamic (MD) simulations...
May 9, 2017: Journal of Biomolecular Structure & Dynamics
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