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Journal of Biomolecular Structure & Dynamics

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https://www.readbyqxmd.com/read/29676661/atomistic-mechanisms-of-the-double-proton-transfer-in-the-h-bonded-nucleobase-pairs-qm-qtaim-computational-lessons
#1
Ol'ha O Brovarets', Dmytro M Hovorun
In this Review we have summarized and generalized the results of the investigation of the microstructural mechanisms of the tautomerisation by the counter movement of the protons along the neighboring intermolecular H-bonds in 22 biologically important pairs of nucleotide bases in the framework of the original method, which allows to trace the evolution of the physico-chemical parameters, that characterize these processes along the intrinsic reaction coordinate (IRC). It was demonstrated the performance of the introduction of the conception of the key points (KPs) (from nine to five, depending on the symmetry and nature of system), which exhaustively characterize the flow of the tautomerisation processes...
April 20, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29676660/new-tailored-substituted%C3%A2-benzothiazole-schiff-base-cu-ii-zn-ii-antitumor-drug-entities-effect-of-substituents-on-dna-binding-profile-antimicrobial-and-cytotoxic-activity
#2
Siffeen Zehra, Mohammad Shavez Khan, Iqbal Ahmad, Farukh Arjmand
New tailored Cu(II) & Zn(II) metal-based antitumor drug entities were synthesized from substituted benzothiazole o‒vanillin Schiff base ligands. The complexes were thoroughly characterized by elemental analysis, spectroscopic studies {IR, 1 H & 13 C NMR, ESI-MS, EPR} and magnetic susceptibility measurements. The structure activity relationship (SAR) studies of benzothiazole Cu(II) & Zn(II) complexes having molecular formulas [C30 H22 CuN5 O7 S2 ], [C30 H20 Cl2 CuN5 O7 S2 ], [C30 H20 CuF2 N5 O7 S2 ], [C30 H22 N4 O4 S2 Zn], [C30 H20 Cl2 N4 O4 S2 Zn] and [C30 H20 F2 N5 O7 S2 Zn], with CT‒DNA were performed by employing absorption, emission titrations and hydrodynamic measurements...
April 20, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29671687/exploring-the-interactional-details-between-aldose-reductase-akr1b1-and-3-mercapto-5h-1-2-4-triazino-5-6-b-indole-5-acetic-acid-through-molecular-dynamics-simulations
#3
Jiu-Yu Zhan, Ke Ma, Qing-Chuan Zheng, Guang-Hui Yang, Hong-Xing Zhang
Aldose reductase (AKR1B1) has been considered as a significant target for designing drugs to counteract the development of diabetic complications. In the present study, molecular dynamics (MD) simulations and molecular mechanics generalized Born surface area (MM-GB/SA) calculations were performed to make sure which tautomer is the preferred one among three tautomeric forms (Mtia1, Mtia2, and Mtia3) of 3-Mercapto-5H-1,2,4-triazino[5,6-b]indole-5-acetic acid (Mtia) for binding to AKR1B1. The overall structural features and the results of calculated binding free energies indicate that Mtia1 and Mtia2 have more superiority than Mtia3 in terms of binding to AKR1B1...
April 19, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29669491/biophysical-insights-into-the-interaction-of-clofazimine-with-human-alpha-1-acid-glycoprotein-a-multitechnique-approach
#4
Mohammad Rehan Ajmal, Fahad Almutairi, Nida Zaidi, Parvez Alam, Mohammad Khursheed Siddiqi, MohsinVahid Khan, Masih Uzzaman, Mohd Ishtikhar, Rizwan Hasan Khan
Alpha1-acid glycoprotein (AAG) is a major acute phase protein of human plasma. Binding of clofazimine to AAG is investigated using optical spectroscopy and molecular docking tools. We found significant quenching of intrinsic fluorescence of AAG upon the binding of clofazimine, binding mode is static with binding constant of 3.52x104 at 298K. The Gibbs free energy change is found to be negative for the interaction of clofazimine with AAG indicating spontaneity of the binding process. Binding of clofazimine induced ordered structure in protein and lead to molecular compaction...
April 19, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29667536/simulation-of-protein-diffusion-a-sensitive-probe-of-protein-solvent-interactions
#5
Valerio Ferrario, Jürgen Pleiss
Aqueous solutions of Candida antarctica lipase B (CALB) were simulated considering three different water models (SPC/E, TIP3P, TIP4P) by a series of molecular dynamics (MD) simulations of three different box sizes (L = 9, 14, and 19 nm) to determine the diffusion coefficient, the water viscosity, and the protein density. The protein-water systems were equilibrated for 500 ns, followed by 100 ns production runs which were analyzed. The diffusional properties of CALB were characterized by the Stokes radius (RS ), which was derived from the diffusion coefficient and the viscosity...
April 18, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29663870/identification-of-some-novel-pyrazolo-1-5-a-pyrimidine-derivatives-as-inha-inhibitors-through-pharmacophore-based-virtual-screening-and-molecular-docking
#6
Palmi Modi, Shivani Patel, Mahesh T Chhabria
The InhA inhibitors play key role in mycolic acid synthesis by preventing the fatty acid biosynthesis pathway. In this present article Pharmacophore modelling and molecular docking study followed by in silico virtual screening could be considered as effective strategy to identify newer enoyl-ACP reductase inhibitors. Pyrrolidine carboxamide derivatives were opted to generate pharmacophore models using HypoGen algorithm in Discovery studio 2.1. Further it was employed to screen Zinc and Minimaybridge databases to identify and design newer potent hit molecules...
April 17, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29663862/dynamics-and-structural-stability-effects-of-germline-pten-mutations-associated-with-cancer-versus-autism-phenotypes
#7
Iris Nira Smith, Stetson Thacker, Ritika Jaini, Charis Eng
Individuals with germline mutations in the tumor suppressor gene phosphatase and tensin homolog (PTEN), irrespective of clinical presentation, are diagnosed with PTEN hamartoma tumor syndrome (PHTS). PHTS confers a high risk of breast, thyroid, and other cancers or autism spectrum disorder (ASD) with macrocephaly. It remains unclear why mutations in one gene can lead to seemingly disparate phenotypes. Thus, we sought to identify differences in ASD vs. cancer-associated germline PTEN missense mutations by investigating putative structural effects induced by each mutation...
April 17, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29663860/novel-coumarin-derivatives-as-potent-acetylcholinesterase-inhibitors-insight-into-efficacy-mode-and-site-of-inhibition
#8
Prayasee Baruah, Grace Basumatary, Semen O Yesylevskyy, Kripamoy Aguan, Ghanashyam Bez, Sivaprasad Mitra
The inhibitory efficacy of two substituted coumarin derivatives on the activity of neurodegenerative enzyme acetylcholinesterase (AChE) was assessed in aqueous buffer as well as in the presence of human serum albumin (HSA) and compared against standard cholinergic AD drug, Donepezil (DON). The experimental data revealed the inhibition to be of non-competitive type with both the systems showing substantial inhibitory activity on AChE. In fact, one of the tested compounds Chromenyl Coumarate (CC) was found to be better inhibitor (IC50 = 48...
April 17, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29663856/computational-insights-into-the-interaction-of-small-molecule-inhibitors-with-hri-kinase-domain
#9
Sourabh Palrecha, Dushant Lakade, Abhijeet Kulkarni, Jayanta K Pal, Manali Joshi
The heme-regulated inhibitor (HRI) kinase regulates globin synthesis in a heme-dependent manner in reticulocytes and erythroid cells in bone marrow. Inhibitors of HRI have been proposed to lead to an increased amount of hemoglobin, benefitting anemia patients. A series of indeno[1,2-c]pyrazoles were discovered to be the first known in vitro inhibitors of HRI. However, the structural mechanism of inhibition is yet to be understood. The aim of this study was to unravel the binding mechanism of these inhibitors using molecular dynamic simulations and docking...
April 17, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29663850/oxidative-dna-damage-is-associated-more-with-genome-accessibility-than-spatial-positioning-in-the-nucleus
#10
Gang Xue, Xin-Yi Chu, Hong-Yu Zhang
No abstract text is available yet for this article.
April 17, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29658431/in-silico-identification-and-screening-of-cyp24a1-inhibitors-3d-qsar-pharmacophore-mapping-and-molecular-dynamics-analysis
#11
Jayaraj John Marshal, Gopinath Krishnasamy, Jung-Kul Lee, Karthikeyan Muthusamy
Vitamin D is a key signalling molecule that plays a vital role in the regulation of calcium-phosphate homeostasis and bone remodelling. The circulating biologically active form of vitamin D is regulated by the catabolic mechanism of cytochrome P450 24-hydroxylase (CYP24A1) enzyme. The over-expression of CYP24A1 negatively regulates the vitamin D level, which is the causative agent of chronic kidney disease, osteoporosis, and several types of cancers. In this study, we found three potential lead molecules adverse to CYP24A1 through structure-based, atom-based pharmacophore and e-pharmacophore-based screening methods...
April 16, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29658387/identification-of-avian-vasotocin-receptor-subtype-specific-antagonists-involved-in-the-stress-response-of-the-chicken-gallus-gallus
#12
Seong W Kang, Srinivas Jayanthi, Gurueswar Nagarajan, Thallapuranam Krishnaswamy Suresh Kumar, Wayne J Kuenzel
Vasotocin 1a and 1b receptors (V1aR and V1bR) have been shown to play important roles in the neuroendocrine regulation of stress responses via the anterior pituitary (AP) of birds. To identify effective subtype-specific antagonists for the chicken V1aR (cV1aR) and cV1bR, potential antagonists to the mammalian V1R were screened against the cV1aR and cV1bR 3D structural models by molecular docking analysis with determination of binding pocket / amino acid residues involved in the interaction. The antagonistic effects of the selected ligands were examined by measuring pro-opiomelanocortin (POMC) heteronuclear RNA (hnPOMC) levels following the in vitro stress administration to primary chicken AP cells...
April 16, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29651930/molecular-insights-into-the-irreversible-mechanical-behavior-of-sickle-hemoglobin
#13
Sumith Yesudasan, Simone A Douglas, Manu O Platt, Xianqiao Wang, Rodney D Averett
Sickle cell disease is caused by the amino acid substitution of glutamic acid to valine, which leads to the polymerization of deoxygenated sickle hemoglobin (HbS) into long strands. These strands are responsible for the sickling of red blood cells (RBCs), making blood hyper-coagulable leading to an increased chance of vaso-occlusive crisis. The conformational changes in sickled RBCs traveling through narrow blood vessels in a highly viscous fluid are critical in understanding; however, there are few studies that investigate the origins of the molecular mechanical behavior of sickled RBCs...
April 13, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29633919/computational-study-of-the-binding-mechanism-between-farnesoid-x-receptor-%C3%AE-and-antagonist-n-benzyl-n-3-tertbutyl-4-hydroxyphenyl-2-6-dichloro-4-dimethylamino-benzamide-ndb
#14
Juan Du, Miaoxue Qiu, Lizhong Guo, Xiaojun Yao
No abstract text is available yet for this article.
April 10, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29633917/multiple-e-pharmacophore-modeling-to-identify-a-single-molecule-that-could-target-both-streptomycin-and-paromomycin-binding-sites-for-30s-ribosomal-subunit-inhibition
#15
Anju Cp, Sunitha Subhramanian, Natalia Sizochenko, Anu R Melge, Jerzy Leszczynski, C Gopi Mohan
The bacterial ribosome is an established target for anti-bacterial therapy since decades. Several inhibitors have already been developed targeting both defined subunits (50S and 30S) of the ribosome. Aminoglycosides and tetracyclines are two classes of antibiotics that bind to the 30S ribosomal subunit. These inhibitors can target multiple active sites on ribosome that have a complex structure. To screen putative inhibitors against 30S subunit of the ribosome, the crystal structures in complex with various known inhibitors were analyzed using pharmacophore modeling approach...
April 10, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29633916/discovery-of-novel-estrogen-related-receptor-%C3%AE-inverse-agonists-by-virtual-screening-and-biological-evaluation
#16
Hui Zhao, Chao Lin, Kaiwen Hu, Xiaoan Wen, Haoliang Yuan
No abstract text is available yet for this article.
April 10, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29633911/a-structural-comparison-of-real-and-model-calmodulin-clarified-allosteric-interactions-regulating-domain-motion
#17
Hiromitsu Shimoyama
No abstract text is available yet for this article.
April 10, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29633910/interaction-of-flavonols-with-human-serum-albumin-a-biophysical-study-showing-structure-activity-relationship-and-enhancement-when-coated-on-silver-nanoparticles
#18
Pratyusa Das, Sunil Kumar Chaudhari, Asmita Das, Somashree Kundu, Chabita Saha
Binding affinities of flavonols namely quercetin, myricetin and kaempferol to Human Serum Albumin (HSA) were determined fluorimetrically and the order was observed to be myricetin> quercetin> kaempferol demonstrating structure activity relationship. Quercetin coated silver nanoparticles (AgNPs) show higher binding affinity to HSA compared to free quercetin with binding constants 6.04×107 M-1 and 4.2×106 M-1 , respectively. Using site-specific markers it is concluded that free quercetin and that coated on AgNPs bind at different sites...
April 10, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29633908/molecular-dynamics-simulation-and-binding-free-energy-studies-of-novel-leads-belonging-to-the-benzofuran-class-inhibitors-of-mycobacterium-tuberculosis-polyketide-synthase-13
#19
Jorddy N Cruz, José F S Costa, André S Khayat, Kamil Kuca, Carlos A L Barros, A M J C Neto
No abstract text is available yet for this article.
April 10, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29633905/insights-into-the-structure-function-relationship-of-brown-plant-hopper-resistance-protein-bph14-of-rice-plant-a-computational-structural-biology-approach
#20
Manoj Kumar Gupta, Ramakrishna Vadde, Ravindra Donde, Gayatri Gouda, Jitendra Kumar, Subhashree Nayak, Mayabini Jena, Lambodar Behera
Brown plant hopper (BPH) is one of the major destructive insect pests of rice, causing severe yield loss. Thirty-two BPH resistance genes have been identified in cultivated and wild species of rice Although, molecular mechanism of rice plant resistance against BPH studied through map-based cloning, due to nonexistence of NMR/crystal structures of Bph14 protein, recognition of leucine-rich repeat(LRR) domain and its interaction with different ligands are poorly understood. Thus, in the present study, in-silico approach was adopted to predict three-dimensional structure of LRR domain of Bph14 using comparative modelling approach followed by interaction study with jasmonic and salicylic acids...
April 10, 2018: Journal of Biomolecular Structure & Dynamics
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