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Journal of Biomolecular Structure & Dynamics

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https://www.readbyqxmd.com/read/30332914/the-systematic-modeling-studies-and-free-energy-calculations-of-the-phenazine-compounds-as-anti-tuberculosis-agents
#1
Yueqi Wang, Abbas Khan, Aman Chandra Kaushik, Muhammad Junaid, Xuehong Zhang, Dong-Qing Wei
Phenazine compounds have good activity against Mycobacterium tuberculosis. Based on the reported activities that were obtained in Mycobacterium tuberculosis H37Rv, a three-dimensional quantitative structure-activity relationship (3D-QSAR) model was built to design novel compounds against MTB. A 5-fold cross-validation method and external validation were used to analyze the accuracy of forecasting. The model has a cross-validation coefficient q2 =0.7 and a non-cross-validation coefficient r2 =0.903, indicating that the model has good predictive possibility...
October 17, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30328798/structural-dynamic-insights-into-the-h-pylori-cytotoxin-associated-gene-a-caga-and-its-abrogation-to-interact-with-the-tumor-suppressor-protein-aspp2-using-decoy-peptides
#2
Muhammad Junaid, Masaud Shah, Abbas Khan, Cheng-Dong Li, Muhammad Tahir Khan, Aman Chandra Kaushik, Arif Ali, Aamir Mehmood, Asma Sindhoo Nangraj, Sangdun Choi, Dong-Qing Wei
Helicobacter pylori (H. pylori) is one of the most extensively studied gram-negative bacteria due to its implication in gastric cancer. The oncogenicity of H. pylori is associated with cytotoxin-associated gene A (CagA), which is injected into epithelial cells lining the stomach. Both the C- and N-termini of CagA are involved in the interaction with several host proteins, thereby disrupting vital cellular functions, such as cell adhesion, cell cycle, intracellular signal transduction, and cytoskeletal structure...
October 17, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30319053/dissolution-of-cellulose-in-ionic-liquid-and-water-mixtures-as-revealed-by-molecular-dynamics-simulations
#3
Bharat Manna, Amit Ghosh
Increasing population growth and industrialization are continuously oppressing the existing energy resources, elevating the pollution and global fuel demand. Various alternate energy resources can be utilized to cope with these problems in an environment-friendly fashion. Currently, bioethanol (sugarcane, corn-derived) is one of the most widely consumed biofuels in the world. Lignocellulosic biomass is yet another attractive resource for sustainable bioethanol production. Pretreatment step plays a crucial role in the lignocellulose to bioethanol conversion by enhancing cellulose susceptibility to enzymatic hydrolysis...
October 15, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30319074/corrigendum
#4
(no author information available yet)
No abstract text is available yet for this article.
October 13, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30314416/an-insight-into-the-binding-of-6-hydroxyflavone-with-hen-egg-white-lysozyme-a-combined-approach-of-multi-spectroscopic-and-computational-studies
#5
Sourav Das, Santanu Santra, Mostofa Ataur Rohman, Mahuah Ray, Madhurima Jana, Atanu Singha Roy
The interaction of 6-Hydroxyflavone (6HF) with hen egg white lysozyme (HEWL) has been executed using multi-spectroscopic and computational methods. Steady state fluorescence studies indicated that static quenching mechanism is involved in the binding of 6HF with HEWL, which was further supported by excited state lifetime and UV-vis absorption studies. The binding constant (Kb ) of the HEWL-6HF complex was observed to be 6.44±0.09 ×104 M-1 at 293 K, which decreases with the increase in temperature. The calculation of the thermodynamic quantities showed that the binding is exothermic in nature with a negative enthalpy change (ΔH= -11...
October 12, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30309295/tris-chelated-complexes-of-nickel-ii-with-bipyridine-derivatives-dna-binding-and-cleavage-bsa-binding-molecular-docking-and-cytotoxicity
#6
Marzieh Anjomshoa, Masoud Torkzadeh-Mahani, Mehdi Sahihi, Corrado Rizzoli, Mehdi Ansari, Jan Janczak, Sheila Sherafat Esfahani, Farangis Ataei, Monireh Dehkhodaei, Bagher Amirheidari
Two nickel(II) complexes with substituted bipyridine ligand of the type [Ni(NN)3 ](ClO4 )2 , where NN is 4,4'-dimethyl-2,2'-bipyridine (dimethylbpy) (1) and 4,4'-dimethoxy-2,2'-bipyridine (dimethoxybpy) (2) have been synthesized, characterized, and their interaction with DNA and BSA studied by different physical methods. X-ray crystal structure of 1 shows a six-coordinate complex in a distorted octahedral geometry. DNA binding studies of 1 and 2 reveal that both complexes sit in DNA groove and then interact with neighboring nucleotides differently; 2 undergoes a partial intercalation...
October 11, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30304999/crystal-structure-of-a-dimerization-domain-of-human-caprin-2-similar-overall-dimeric-fold-but-different-molecular-surface-properties-to-that-of-human-caprin-1
#7
Yuhong Wu, Jiang Zhu, Xiaolan Huang, Xia Zhou, Zhihua Du
Human Caprin-1 and Caprin-2 are prototypic members of the caprin (cytoplasmic activation/proliferation-associated protein) protein family. Vertebrate caprin proteins contain two highly conserved homologous regions (HR1 and HR2) and C-terminal RGG motifs. Drosophila caprin (dCaprin) shares HR1 and RGG motifs but lacks HR2. Caprin-1 and Caprin-2 have important and non-redundant functions. The detailed molecular mechanism s of their actions remain largely unknown. Previously, we determined the crystal structure of a ∼120-residue fragment of Caprin-1 within the HR1 region...
October 11, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30301423/investigation-of-activation-mechanism-and-conformational-stability-of-n-4-chloro-3-trifluoromethyl-phenyl-2-ethoxybenzamide-and-n-4-chloro-3-trifluoromethyl-phenyl-2-ethoxy-6-pentadecyl-benzamidein-the-active-site-of-p300-histone-acetyl-transferase-enzyme-by
#8
Magudeeswaran Sivanandam, Saravanan Manjula, Poomani Kumaradhas
The CBP (CREB binding protein) and p300 are related to transcriptional coactivator family and are involves several post translational modifications; in which the acetylation is an important factor because it commences the transcription process. Experimental studies report that CTPB [N-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-6-pentadecyl-benzamide] and CTB [N-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxybenzamide] are good activators of p300 HAT enzyme, but yet the molecular mechanism of their activation is not explored...
October 9, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30301411/an-overview-about-the-impact-of-hinge-region-towards-the-anticancer-binding-affinity-of-the-ck2-ligands-a-quantum-chemical-analysis
#9
P Deepa, D Thirumeignanam, P Kolandaivel
Casein Kinase 2 (CK2) is extremely preserved and universally uttered serine/threonine kinase, vital for cellular feasibility. The present study was aimed to analyse the binding strength of CK2 ligands specifically in the hinge region, as it is aware that most of the existing drugs are targeted to bind the hinge of the corresponding protein. The analysis will give a clear picture about the role of hinge region with ligand, which will be useful for scientist community in drug designing. To predict the binding strength of CK2 ligands, the role of halogen bond, hydrogen bond interaction at the hinge region was depicted in detail through interaction energy calculations at M062Z/def2-QZVP level of theory...
October 9, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30296922/novel-insights-into-the-dynamics-behavior-of-glucagon-like-peptide-1-receptor-with-its-small-molecule-agonists
#10
Khyati Girdhar, Budheswar Dehury, Mahender Kumar Singh, Vineeth P Daniel, Abhinav Choubey, Surbhi Dogra, Sunil Kumar, Prosenjit Mondal
The glucagon-like peptide-1 receptor (GLP-1R) is a well-known target of therapeutics industries for the treatment of various metabolic diseases like Type2 Diabetes and Obesity. The structural-functional relationships of small molecule agonists and GLP-1R are yet to be understood. Therefore, an attempt was made on structurally known GLP-1R agonists (Compound 1, Compound 2, Compound A, Compound B, and (S)-8) to study their interaction with the extracellular domain of GLP-1R. In this study, we explored the dynamics, intrinsic stability and binding mechanisms of these molecules through computational modeling, docking, molecular dynamics (MD) simulations and MM/PBSA binding free energy estimation...
October 8, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30295165/developing-hispolon-based-novel-anticancer-therapeutics-against-human-nf-%C3%AE%C2%BA%C3%AE-using-in-silico-approach-of-modelling-docking-and-protein-dynamics
#11
Manish Paul, Mrunmaya Kumar Panda, Hrudayanath Thatoi
Hispolon is a polyphenolic compound derived from black hoof mushroom (Phellinus linteus) or shaggy bracket mushroom (Inonotus hispidus) which induces the inhibition of cancer promoting NF-κβ complex. To develop more potent lead molecules with enhanced anticancer efficiency, mechanism of hispolon mediated Nuclear Factor-κβ inhibition has been investigated by molecular modelling and docking. Ten derivatives of hispolon (DRG1-10) have been developed by pharmacophore based design with a view to enhance the anticancer efficacy...
October 6, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30295130/unusual-stability-exhibited-by-at-x-n-12-at-y-motif-associated-with-high-fetal-hemoglobin-levels
#12
Kapil Roy, Swati Mahendru, Ritushree Kukreti, Shrikant Kukreti
Quasi-palindromic sequences (AT)X N12 (AT)Y present in HS2 (hypersensitive site) of the human β-globin locus are known to be significantly associated with increased fetal hemoglobin (HbF) levels. High HbF levels in some adults arise due to pathological conditions such as sickle cell disease and β-thalassemia. However, elevated levels of HbF are also associated with a reducing morbidity and mortality in patients with β-thalassemia and thus ameliorate the severity of the disease. Using gel-electrophoresis, ultraviolet (UV)-thermal denaturation and circular dichroism (CD) techniques, we demonstrated that it exhibits a hairpin-duplex equilibrium...
October 6, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30286701/rational-discovery-of-a-sod1-tryptophan-oxidation-inhibitor-with-therapeutic-potential-for-amyotrophic-lateral-sclerosis
#13
Manjula Ramu, Sruthi Unni, Gareth S A Wright, Bharath M M Srinivas, Balasundaram Padmanabhan
Formation of Cu, Zn superoxide dismutase 1 (SOD1) protein inclusions within motor neurons is one of the principal characteristics of SOD1-related amyotrophic lateral sclerosis (ALS). A hypothesis as to the nature of SOD1 aggregation implicates oxidative damage to a solvent-exposed tryptophan as causative. Here, we chart discovery of a phenanthridinone based compound (Lig9) from the NCI Diversity Set III by rational methods by in silico screening and crystallographic validation. The crystal structure of the complex with SOD1, refined to 2...
October 4, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30284510/nonionic-but-water-soluble-glycine-pd-alanine-and-glycine-pd-valine-complexes-their-synthesis-characterization-antitumor-activities-and-rich-dna-hsa-interaction-studies
#14
Hassan Mansouri-Torshizi, Sareh Zareian-Jahromi, Khatereh Abdi, Maryam Saeidifar
Two novel, neutral and water soluble Pd(II) complexes of formula [Pd(Gly)(Ala)] (1) and [Pd(Gly)(Val)] (2) (Gly, Ala, and Val are anionic forms of glycine, alanine, and valine amino acids, respectively) have been synthesized and characterized by FT-IR, UV-Vis, 1 H-NMR, elemental analysis, and molar conductivity measurement. The data revealed that each amino acid binds to Pd(II) through the nitrogen of -NH2 and the oxygen of -COO- groups and acts as a bidentate chelate. These complexes have been assayed against leukemia cells (K562 ) using MTT method...
October 4, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30284504/structural-insight-into-antisense-gapmer-rna-oligomer-duplexes-through-molecular-dynamics-simulations
#15
Mallikarjunachari V N Uppuladinne, Uddhavesh B Sonavane, Ramesh Ch Deka, Rajendra R Joshi
There is an extensive research carrying out on antisense technology and the molecules entering into clinical trials are increasing rapidly. Phosphorothioate (PS) is a chemical modification in which non-bridged oxygen is replaced with a sulfur, consequently providing resistance against nuclease activity. The 2'-4' conformationaly restricted nucleoside has the structural features of both 2'-O-methoxy ethyl RNA (MOE), which shows good toxicity profile, and locked nucleic acid (LNA), which shows good binding affinity towards the target RNA...
October 4, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30282523/binding-of-platinum-derivative-oxaliplatin-to-deoxyribonucleic-acid-structural-insight-into-antitumor-action
#16
Bhumika Ray, Bhumika Gupta, Ranjana Mehrotra
Platinum derived chemodrugs constitute an active class in cancer therapeutics. Besides being potent against various solid tumors, oxaliplatin has been recognized as first platinum compound to be approved for the treatment of colorectal cancer. Structurally, oxaliplatin consists of a platinum metal complexed to oxalate and diaminocyclohexane (DACH) and exert its anticancer action by inhibiting DNA replication and transcription. The present study highlights the binding properties of oxaliplatin with calf thymus DNA using spectroscopic methods to comprehend its binding mechanism at molecular level to overcome associated cellular resistance and side-effects...
October 3, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30277419/antiproliferative-activity-of-morpholine-based-compounds-on-mcf-7-breast-cancer-colon-carcinoma-c26-and-normal-fibroblast-nih-3t3-cell-lines-and-study-of-their-binding-affinity-to-calfthymus-dna-and-bovine-serum-albumin
#17
Mahboubeh Hosseini-Kharat, Rahimi Rahmatollah, Davit Zargarian, Zohreh Mehri Lighvan, Amir Abbas Momtazi-Borojeni, Tayebeh Sharifi, Elham Abdollahi, Hossein Tavakol, Tecush Mohammadi
This report describes the results of a study on the antiproliferative activity of the morpholine-based ligand 1,3-bis(1-morpholinothiocarbonyl)benzene (HL) and its nickel(II) complex (NiL) against human breast cancer cells (MCF-7), colon carcinoma cells (C26) and normal fibroblast NIH-3T3 cells. NiL showed better cytotoxicity on both cancerous cells relative to normal cells in vitro with the highest selective index of 2.22 in MCF-7 cells. The interaction of both compounds with calf thymus DNA (CT DNA) and bovine serum albumin (BSA) was studied using various spectroscopic techniques and analytical methods such as UV-vis titrations, thermal denaturation, circular dichroism, competitive fluorescent intercalator displacement assays, as well as molecular modeling...
October 2, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30261824/3d-qsar-and-docking-studies-on-ursolic-acid-derivatives-for-anticancer-activity-based-on-bladder-cell-line-t24-targeting-nf-kb-pathway-inhibition
#18
Deepika Yadav, Bhartendu Nath Mishra, Feroz Khan
Bladder cancer is the common reason for mortality worldwide and its increasing rate announces it is a significant area of research in drug designing. The side effects and toxicity of existing drugs and consequence of gradual cancer cell resistance against the available therapy make the treatment poor. Globally, there is a continuous high demand to develop new, more potent and easily affordable drugs against cancer. The current research article illustrates the application of developed 3D-QSAR based on human bladder cancer cell line T24 in vitro anticancer activity...
September 27, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30261821/in-silico-studies-on-potential-tnks-inhibitors-a-combination-of-pharmacophore-and-3d-qsar-modeling-virtual-screening-molecular-docking-and-molecular-dynamics
#19
Jianxin Liu, Kairui Feng, Yujie Ren
Maladjustment of the Wnt signalling pathway can lead to a variety of cancers. Axin can be expressed stably through the Tankyrases (TNKS) inhibitor, thus inducing the degradation of β-catenin, antagonizing the Wnt signalling pathway and consequently inhibiting tumour growth. Thus, TNKS has become a hot research target for anticancer drugs, and a systematic study of tetrazoloquinoxaline analogues as TNKS inhibitors is of considerable value. In this paper, 3D-QSAR, molecular docking and DISCOtech were applied to study a series of tetrazoloquinoxaline and establish good CoMFA (q2 =0...
September 27, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30257618/exploration-of-binding-studies-of-%C3%AE-oxalyldiamino-propionic-acid-%C3%AE-odap-a-non-protein-amino-acid-with-human-serum-albumin-biophysical-and-computational-approach
#20
Veerababu Nagati, Monika Kallubai, Dinesh Kumar Chinthapalli, Rajagopal Subramanyam
No abstract text is available yet for this article.
September 26, 2018: Journal of Biomolecular Structure & Dynamics
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