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Journal of Biomolecular Structure & Dynamics

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https://www.readbyqxmd.com/read/30526410/molecular-dynamic-simulations-on-an-inhibitor-of-anti-apoptotic-bcl-2-proteins-for-insights-into-its-interaction-mechanism-for-anti-cancer-activity
#1
Aarti Anantram, Harish Kundaikar, Mariam Degani, Arati Prabhu
Inhibition of normal cellular apoptosis or programed cell death is the hallmark of all cancers. Apoptotic dysregulation can result in numerous pathological conditions, such as cancers, autoimmune disorders, and neurodegeneration. Members of the BCL-2 family of proteins regulate the process of apoptosis by its promotion or inhibition and overexpression of the pro-survival anti-apoptotic proteins (Bcl-2, Bcl-xL, and Mcl-1) has been associated with tumor maintenance, growth and progression Small molecules and peptides which bind the BH3 binding groove of these proteins have been explored in the recent times for their anticancer potential...
December 10, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30526398/in-vitro-cytotoxicity-studies-of-parent-and-nano-encapsulated-holmium-2-9-dimethyl-1-10-phenanthroline-complex-toward-fish-salmon-dna-binding-properties-and-antibacterial-activity
#2
Shohreh Jahani, Meissam Noroozifar, Mozhgan Khorasani-Motlagh, Masoud Torkzadeh-Mahani, Mahboubeh Adeli-Sardou
In this study, the interaction of Holmium (Ho) complex including 2, 9-dimethyl-1,10-phenanthroline, also it called Neocuproine (Neo), [Ho(Neo)2 Cl3 .H2 O], as fluorescence probe with Fish-Salmon-DNA (FS-DNA) is studied during experimental investigations. Multi-spectroscopic methods are utilized to determine the affinity binding constants (Kb ) of complex-FS-DNA. It is found that fluorescence of Ho-complex is strongly quenched by the FS-DNA through a static quenching procedure. Under optimal conditions in Tris(trishydroxymethyl-aminomethane)-HCl buffer at 25 °C with pH≈7...
December 10, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30526395/validation-of-nad-synthase-inhibitors-for-inhibiting-the-cell-viability-of-leishmania-donovani-in-silico-and-in-vitro-approach
#3
Haraprasad Mandal, Vijayakumar Saravanan, Shalini Yadav, Shubhankar Kumar Singh, Pradeep Das
NAD (nicotinamide adenine dinucleotide) synthase catalyses the biochemical synthesis of NAD, from nicotinic acid adenine dinucleotide (NaAD). NAD may be synthesized through the de novo pathways and/or the salvage pathways in cells. However, in Leishmania parasite, the synthesis of NAD solely depends on the salvage pathways. NAD synthetase is widely explored as a drug target in various microorganisms. In Bacillus anthracis, a group of sulfonamides 5599, 5617, 5824, and complex amide 5833 were reported to have activity at micromolar range against NAD synthetase...
December 10, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30526389/identification-of-new-promising-plant-based-lead-compounds-for-inhibition-of-prokaryotic-replicative-dna-polymerases-combination-of-in-silico-and-in-vitro-studies
#4
Milad Lagzian, Ali Qasemi, Pegah Kaviani, Malihe Mohammadi
Emerging widespread bacterial resistance to current antibiotics with traditional targets is one of the major global concerns. Therefore, so many investigations are exploring the potential of other druggable macromolecules of bacteria such as replication machinery components that are not addressed by previous antibiotics. DNA polymerase is the major part of this machine. However, a few studies have been done on it so far. In this respect, we report the discovery of four new plant-based leads against DNA polymerase (pol) IIIC (three leads) and pol IIIE (one lead) of Gram-positive and negative bacteria by combining a sequentially constrained high-throughput virtual screenings on Traditional Chinese Medicine Database with in vitro assays...
December 10, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30526382/molecular-dynamics-simulation-on-the-effect-of-transition-metal-binding-to-the-n-terminal-fragment-of-amyloid-%C3%AE
#5
Matthew Turner, Shaun T Mutter, James A Platts
We report molecular dynamics simulations of three possible adducts of Fe(II) to the N-terminal 1-16 fragment of the amyloid-β peptide, along with analogous simulations of Cu(II) and Zn(II) adducts. We find that multiple simulations from different starting points reach pseudo-equilibration within 100 to 300 ns, leading to over 900 ns of equilibrated trajectory data for each system. The specifics of the coordination modes for Fe(II) have only a weak effect on peptide secondary and tertiary structure, and we therefore compare one of these with analogous models of Cu(II) and Zn(II) complexes...
December 10, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30526379/ordering-a-selected-zn-ii-cu-ii-pd-ii-and-co-iii-complex-compounds-their-separately-and-combinedly-antibacterial-therapy-and-dna-binding-studies
#6
Hassan Mansouri-Torshizi, Fatemeh Khosravi, Khatereh Abdi, Sareh Zareian-Jahromi
In this study, four Co(III)-, Cu(II)-, Zn(II)- and Pd(II)- based potent antibacterial complexes of formula K3 [Co(ox)3 ]·3H2 O (I), [Cu(phen)2 Cl]Cl·6.5H2 O (II), [Zn(phen)3 ]Cl2 (III) and [Pd(phen)2 ](NO3 )2 (IV) (where ox is oxalato and phen is 1,10-phenanthroline) were synthesized. They were characterized by elemental analysis, molar conductivity measurements, UV-Vis, FT-IR and 1 H-NMR techniques. These metal complexes were ordered in three combination series of I+II, I+II+III and I+II+III+IV. Antibacterial screening for each metal complex and their combinations against Gram positive and Gram negative bacteria revealed that all compounds were more potent antibacterial agents against the Gram negative than those of the Gram positive bacteria...
December 10, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30526403/the-design-of-potent-hiv-1-integrase-inhibitors-by-a-combined-approach-of-structure-based-virtual-screening-and-molecular-dynamics-simulation
#7
Augustine S Samorlu, Kemal Yelekçi, Abdullahi Ibrahim Uba
No abstract text is available yet for this article.
December 8, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30518311/comparing-protein-structures-and-inferring-functions-with-a-novel-three-dimensional-yau-hausdorff-method
#8
Kun Tian, Xin Zhao, Yuning Zhang, Stephen Yau
Structures and functions of proteins play various essential roles in biological processes. The functions of newly discovered proteins can be predicted by comparing their structures with that of known-functional proteins. Many approaches have been proposed for measuring the protein structure similarity, such as the template-modeling (TM)-score method, GRaphlet (GR)-Align method as well as the commonly used root-mean-square deviation (RMSD) measures. However, the alignment comparisons between the similarity of protein structure cost much time on large dataset, and the accuracy still have room to improve...
December 5, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30517053/study-on-the-interaction-of-amprolium-hcl-and-dinitolmide-in-animal-derived-food-products-with-bsa-by-multiple-spectroscopies-and-molecular-modeling-techniques
#9
Xiao-Yue Sun, Shu-Yun Bi, Jun Wu, Rui Zhao
No abstract text is available yet for this article.
December 5, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30516448/evaluation-of-maltose-on-conformation-and-activity-parameters-of-trypsin
#10
Mina Rajabi, Behzad Shareghi, Sadegh Farhadian, Lida Momeni
No abstract text is available yet for this article.
December 5, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30513263/side-projections-of-double-helical-dna-example-of-binding-patterns-of-dna-in-the-complex-with-factor-tfiiia
#11
Y N Chirgadze, E A Boshkova, A V Yakovlev, V V Ivanov
No abstract text is available yet for this article.
December 4, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30499387/insight-into-binding-mechanisms-of-egfr-allosteric-inhibitors-using-molecular-dynamics-simulations-and-free-energy-calculations
#12
Shanhe Wan, Ruohong Yan, Ying Jiang, Zhonghuang Li, Xiaoyun Wu
Lung cancer is the leading cause of cancer death, and EGFR kinase domain mutations are a common cause of NSCLCs, a major subtype of lung cancers. Patients harboring most of these mutations respond well to the EGFR inhibitors Gefitinib and Erlotinib initially, but soon develop resistance to them due to the emergence of the gatekeeper mutation T790M. The new-generation inhibitors such as AZD9291, HM61713, CO-1686, and WZ4002 can overcome T790M through covalent binding to Cys 797, but ultimately lose their efficacy upon the emergence of the C797S mutation that abolishes the covalent bonding...
November 30, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30489230/structural-and-biological-study-of-synthesized-anthraquinone-series-of-compounds-with-sulfonamide-feature
#13
Pamita Awasthi, Manu Vatsal, Anjali Sharma
1, 4 and 5, 8- positions as well as type of functionalities on these positions at anthraquinone-9, 10-dione are proposed to be significant for anticancer activity. Therefore, keeping this in to consideration, series of 1-substituted anthraquinone based compounds are designed, synthesized, characterized and biologically evaluated for anticancer activity. The structure of synthesized compounds are confirmed by spectroscopic analysis i.e. 1D (1 H and 13 C) NMR, ESI-MS studies, FT-IR tools. Synthesized 1-substituted anthraquinone compounds showed cytotoxic effect against MCF-7, PC-3 and Hep2C (Hela derivative) cell lines...
November 29, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30488782/side-chain-torsion-dictates-planarity-and-ionizability-of-green-fluorescent-protein-s-chromophore-leading-to-spectral-perturbations
#14
S Sriram Raghavan, Ayyadurai Niraikulam, Krishnasamy Gunasekaran
Spectral characteristics of Fluorescent Proteins (FP) are well studied and through protein engineering, several FP variants constituting entire visible spectrum have been created. One of the most common mechanisms attributed to spectral shifts in FP are excited state proton transfer (ESPT), hydroxyl moiety protonation and deprotonation, along with chromophore Cis-Trans isomerism. Most widely studied FPs are those derived from avGFP (Aequorea victoria GFP) and Dsred (Discosoma coral). Apart from the above mechanism, certain interacting residues are said to play a vital role in altering the proton transfer pathway leading to numerous spectral variants...
November 29, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30488780/reliable-structural-information-for-rational-design-of-benzoxazole-type-potential-cholesteryl-ester-transfer-protein-cetp-inhibitors-through-multiple-validated-modelling-techniques
#15
Sk Abdul Amin, Nilanjan Adhikari, Shovanlal Gayen, Tarun Jha
The drug design and discovery of lipid modulators is very demanding as no new molecule has entered into the market in the last 35 years. Cholesteryl ester transfer protein (CETP) is a promising target as lipid modulators. Inhibition of the CETP enzyme reduces the risk of cardiovascular events. The first CETP inhibitor torcetrapib and related drug candidates failed in the clinical trial due to the off target effects leading to high toxicity. Thus, newer ETP inhibitors have now paramount importance to accelerate the drug discovery efforts in the field of cardiovascular disease (CVD)...
November 29, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30488779/transient-protein-protein-complexes-in-base-excision-repair
#16
Anton V Endutkin, Anna V Yudkina, Viktoriya S Sidorenko, Dmitry O Zharkov
Transient protein-protein complexes are of great importance for organizing multiple enzymatic reactions into productive reaction pathways. Base excision repair, a process of critical importance for maintaining genome stability against a plethora of DNA-damaging factors, involves several enzymes, including DNA glycosylases, AP endonucleases, DNA polymerases, DNA ligases, and accessory proteins acting sequentially on the same damaged site in DNA. Rather than being assembled into one stable multisubunit complex, these enzymes pass the repair intermediates between them in a highly coordinated manner...
November 29, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30488775/elucidation-of-conformational-diversity-of-druggable-enzymes-and-classification-of-chemical-modulators-based-on-inhibitor-bound-structures
#17
Sravani Akula, Venkata Krishna Vanamamalai, Vishnu Prasad Nair Ru, Dashavantha Reddy Vudem, Rama Krishna Kancha
Proteins are remarkably flexible and exhibit multiple conformations each of which may be modulated or stabilized by natural/synthetic ligands. Analysis of conformational diversity of an enzyme helps in understanding its function and has implications in biochemical and pharmacological applications. The variation observed among an array of structures of a particular enzyme can be indicative of its conformational diversity. In the present study, a large scale superposition analysis of enzyme-ligand co-crystal structures was performed revealing the presence of higher conformational diversity in the kinome than that of the non-kinome...
November 29, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30488774/comparative-study-of-the-bindings-between-3-phenyl-1h-indazole-and-five-proteins-by-isothermal-titration-calorimetry-spectroscopy-and-docking-methods
#18
Ning Wang, Xinxin Han, Junya Li, Ying Wang, Wenquan Yu, Ruiyong Wang, Junbiao Chang
In this study, the interaction between 3-phenyl-1H-indazole (1a) and the fat mass and obesity-associated (FTO) protein was confirmed by isothermal titration calorimetry. The structure feature of 1a was differently from our previously reported FTO inhibitors (radicicol, N-CDPCB and CHTB), the Cl and diol group in structure motif is critical for inhibitors to bind to FTO. In order to test whether there is specificity for the interaction between FTO and 1a, the interactions between 1a and four important proteins (human serum albumin, pepsin, catalase and trypsin) were investigated by isothermal titration calorimetry, spectroscopy and molecular docking methods...
November 29, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30488773/binding-mechanism-of-caffeic-acid-and-simvastatin-to-the-integrin-linked-kinase-for-therapeutic-implications-a-comparative-docking-and-md-simulation-studies
#19
Mehak Gulzar, Shahid Ali, Faez Iqbal Khan, Parvez Khan, Pankaj Taneja, Imtaiyaz Hassan
Integrin linked kinase (ILK) is a Ser/Thr kinase which regulates various integrin mediated signaling pathways, and is involved in cell adhesion, migration and differentiation. Alteration in the ILK is responsible for abnormal functioning of the cell system, which may lead to the cancer progression and metastasis. On the other hand, caffeic acid (CA) and simvastatin are used as antioxidants and possesses anticancer properties. Thus, inhibiting the kinase activity of ILK by CA and simvastatin may be implicated in the cancer therapy...
November 29, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/30488771/aerobic-respiration-proof-of-concept-for-the-oxygen-centric-murburn-perspective
#20
Kelath Murali Manoj, Abhinav Parashar, Vivian David Jacob, Surjith Ramasamy
The inner mitochondrial membrane protein Complexes (I - V) and prokaryotic respiratory machinery are examined for a deeper understanding of their structure-function correlations and dynamics. In silico analysis of the structure of complexes I-IV, docking studies and erstwhile literature confirm that they carry ADP binding sites which are in close proximity to DROS (diffusible reactive oxygen species) generating redox centers. These findings provide supportive evidence for the newly proposed oxygen-centric chemical-coupling mechanism (murburn concept), wherein DROS catalyzes the esterification of inorganic phosphate to ADP...
November 29, 2018: Journal of Biomolecular Structure & Dynamics
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