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Journal of Biomolecular Structure & Dynamics

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https://www.readbyqxmd.com/read/29216799/flavonoids-as-potent-allosteric-inhibitors-of-protein-tyrosine-phosphatase-1b-molecular-dynamics-simulation-and-free-energy-calculation
#1
Farshid Zargari, Maryam Lotfi, Omolbanin Shahraki, Zahra Nikfarjam, Jafar Shahraki
Protein tyrosine phosphatase 1B (PTP1B) is a member of the PTP superfamily which is considered to be a negative regulator of insulin receptor (IR) signalling pathway. PTP1B is a promising drug target for the treatment of type 2 diabetes, obesity and cancer. The existence of allosteric site in PTP1B has turned the researcher's attention to an alternate strategy for inhibition of this enzyme. Herein, the molecular interactions between the allosteric site of PTP1B with three non-competitive flavonoids, (MOR), (MOK), and (DPO) have been investigated...
December 7, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29210603/an-unexpected-switch-in-peptide-binding-mode-from-simulation-to-substrate-specificity
#2
Ursula Kahler, Julian E Fuchs, Peter Goettig, Klaus R Liedl
A ten microsecond molecular dynamics simulation of a kallikrein-related peptidase 7 peptide complex revealed an unexpected change in binding mode. After more than two microseconds unrestrained sampling we observe a spontaneous transition of the binding pose including a 180 degree rotation around the P1 residue. Subsequently, the substrate peptide occupies the prime side region rather than the cognate non-prime side in a stable conformation. We characterize the unexpected binding mode in terms of contacts, solvent-accessible surface area, molecular interactions and energetic properties...
December 6, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29210342/antibiotics-potentiating-potential-of-catharanthine-against-superbug-pseudomonas-aeruginosa
#3
Gaurav Raj Dwivedi, Rekha Tyagi, Sanchita Gupta, Shubhandra Tripathi, Sanghamitra Pati, Santosh K Srivastava, Mahendra P Darokar, Ashok Sharma
Multidrug resistance (MDR) put an alarming situation like preantibiotic era which compels us to invigorate the basic science of anti-infective chemotherapy. Hence the drug resistant genes/proteins were explored as promising drug targets. Keeping this thing in mind, proteome of Pseudomonas aeruginosa PA01 was explored, which resulted in the identification of tripartite protein complexes (MexA, MexB and OprM) as promising drug target for the screening of natural and synthetic inhibitors. The purpose of present investigation was to explore the drug resistance reversal potential mechanism of catharanthine isolated from the leaves of Catharanthus roseous...
December 6, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29199524/metal-complexes-of-naphthoquinone-based-ligand-synthesis-characterization-protein-binding-dna-binding-cleavage-and-cytotoxicity-studies
#4
A Kosiha, C Parthiban, Samuele Ciattini, Laura Chelazzi, Kuppanagounder P Elango
Protein binding, DNA binding/cleavage and in vitro cytotoxicity studies of 2-((3-(dimethylamino)propyl)amino)naphthalene-1,4-dione (L) and its four coordinated M(II) complexes [M(II) = Co(II), Cu(II), Ni(II) and Zn(II)] have been investigated using various spectral techniques. The structure of the ligand was confirmed by spectral and single crystal XRD studies. The geometry of the complexes has been established using analytical and spectral investigations. These complexes show good binding tendency to bovine serum albumin (BSA) exhibiting high binding constant values (105 M-1) when compared to free ligand...
December 4, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29199545/the-inhibitory-performance-of-flavonoid-cyanidin-3-sambubiocide-against-h274y-mutation-in-h1n1-influenza-virus
#5
S Kannan, P Kolandaivel
Oseltamivir (Tamiflu) is the most accepted antiviral drug that targets the neuraminidase (NA) protein to inhibit the viral release from the host cell. Few H1N1 influenza strains with the H274Y mutation creates drug-resistance to oseltamivir. In this study, we reported flavonoid cyanidin-3-sambubiocide (C3S) compound acts as a potential inhibitor against H274Y mutation. The drug-resistance mechanism and inhibitory activity of C3S and oseltamivir against wild type (WT) and H274Y mutant type (MT) have been studied and compared based on the results of molecular docking, molecular dynamics and quantum chemical methods...
December 3, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29198175/new-semicarbazones-as-gorge-spanning-ligands-of-acetylcholinesterase-and-potential-new-drugs-against-alzheimer-s-disease-synthesis-molecular-modeling-nmr-and-biological-evaluation
#6
Denise Cristian Ferreira Neto, Josélia Alencar Lima, Joyce Sobreiro Francisco Diz de Almeida, Tanos Celmar Costa França, Claudia Jorge do Nascimento, José Daniel Figueroa Villar
Two new compounds (E)-2-(5,7-dibromo-3,3-dimethyl-3,4-dihydroacridin-1(2H)-ylidene)hydrazinecarbothiomide (3) and (E)-2-(5,7-dibromo-3,3-dimethyl-3,4-dhihydroacridin-1(2H)-ylidene)hydrazinecarboxamide (4) were synthesized and evaluated for their anticholinesterase activities. In vitro tests performed by NMR and Ellman's tests, pointed to a mixed kinetic mechanism for the inhibition of acetylcholinesterase (AChE). This result was corroborated through further docking and molecular dynamics studies, suggesting that the new compounds can work as gorge-spanning ligands by interacting with two different binding sites inside AChE...
December 3, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29195491/ros-mediated-heme-degradation-and-cytotoxicity-induced-by-iron-nanoparticles-hemoglobin-and-lymphocyte-cells-as-targets
#7
Sepideh Mirzaei, Zari Hadadi, Farnoosh Attar, Seyyedeh Elaheh Mousavi, Seyed Shahaboddin Zargar, Aida Tajik, Ali Akbar Saboury, Seyed Mahdi Rezayat, Mojtaba Falahati
Nanoparticles (NPs) due to their small size and high surface area induce remarkable adverse effects on the biological systems. However, the exact mechanism by which NPs interacted with biological system and induce their adverse effects is still an enigma. Herein, the interaction of zero valent iron NPs (ZVFe NPs) with human hemoglobin (Hb) was evaluated using a variety of techniques including circular dichroism (CD), fluorescence, and UV-visible (UV-vis) spectroscopy methods. Also, the cytotoxicity of ZVFe NPs on the human lymphocyte cell line as a model of blood system cell line was investigated by reactive oxygen species (ROS), caspase-9 and caspase-3 activities assays...
December 1, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29188757/folate-receptor-targeted-multimodal-fluorescence-mesosilica-nanoparticles-for-imaging-delivery-palladium-complex-and-in-vitro-g-quadruplex-dna-interaction
#8
Marziyeh Poshteh Shirani, Behzad Rezaei, Taghi Khayamian, Mohammad Dinari, Kazem Karami, Zohreh Mehri-Lighvan, Fazileh Hosseini Shamili, Mohammd Ramezani, Mona Alibolandi
New folic acid-conjugated mesoporous silica nanoparticles were synthesized. The effect of calcination at 400°C on the fluorescence characteristics of mesoporous silica nanoparticles was studied in this work. The formed carbon dots (CDs) from calcination was used as the source of fluorescence. 3-Aminopropyltriethoxysilane was then used to amine-functionalized the fluorescent surface of mesoporous silica nanoparticles. The amine fluorescence mesoporous silica nanoparticles (amine-FMSNs) were coupled with folic acid (FA) as the target ligand (FA-amine-FMSNs)...
November 30, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29187070/loading-efficacy-and-binding-analysis-of-retinoids-with-milk-proteins-a-short-review
#9
D Agudelo, P Bourassa, J Bariyanga, H A Tajmir-Riahi
In this review, the loading efficacies of retinoids with milk proteins are investigated. It has been shown that milk proteins β-lactoglobulin, α- and β-caseins bind retinol and retinoic acid via hydrophobic, hydrophilic and H-bonding contacts causing minor alterations of protein secondary structure. Hydrophobic contact is predominant in retinoid-protein conjugation and several amino acids are involved in complex formation, stabilized by H-bonding network. Loading efficacy of retinoid was about 30 to 50% with retinol forming more stable protein conjugates...
November 30, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29183268/potential-natural-mtor-inhibitors-screened-by-in-silico-approach-and-suppress-hepatic-stellate-cells-activation
#10
Varadharajan Thiyagarajan, Kuan-Wei Lee, Max K Leong, Ching-Feng Weng
The mammalian target of rapamycin (mTOR), an atypical serine/threonine kinase, plays a central role in the regulation of cell proliferation, growth, differentiation, migration, and survival. In this study, the 3D structure of the mTOR (PDB ID: 2FAP) was used for the docking of 47 natural compounds and compared with pharmacophore model of 14 known mTOR inhibitors to identify the novel and specific natural inhibitor. The top four compounds, rutin, curcumin, antroquinonol, and benzyl cinnamate, have been selected based on their PLP score and further validated with hepatic stellate cells NHSC and THSC...
November 28, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29183267/in-silico-evaluation-of-the-resistance-of-the-t790m-variant-of-epidermal-growth-factor-receptor-kinase-to-cancer-drug-erlotinib
#11
Inderpal Singh, Shashank Singh, Vijeshwar Verma, Vladimir N Uversky, Ratna Chandra
Epidermal growth factor receptor (EGFR) kinase is implicated in cancer development due to either overexpression or activation variants in its functional intracellular kinase domain. Threonine to Methionine (Thr 790 Met) is one such variant observed commonly in patients showing resistance to kinase inhibitor drug Erlotinib. Two mechanisms for resistance have been proposed (1) steric hindrance and (2) enhanced binding to ATP. In this study, we employed molecular dynamics simulations and studied both the mechanisms...
November 28, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29182450/infrared-studies-of-deformation-and-docking-in-hydrogen-bonded-molecular-systems
#12
Md Mozzammel Haque
No abstract text is available yet for this article.
November 28, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29182104/steered-molecular-dynamics-for-studying-ligand-unbinding-of-ecdysone-receptor
#13
Xueping Hu, Song Hu, Jiazhe Wang, Yawen Dong, Li Zhang, Yanhong Dong
Ecdysone receptor (EcR) is an important target for pesticide design. Ligand binding regulates EcR transcriptional activity similar to other nuclear receptors; however, the pathways by which ligands enter and leave the EcR remain poorly understood. Here, we performed computational studies to identify unbinding pathways of an ecdysone agonist [the selective ecdysone agonist, BYI06830] from the EcR ligand binding domain (EcR LBD). BYI06830 can dissociate from EcR LBD via four different pathways with little effect on receptor structure...
November 28, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29182053/identification-of-potential-pkc-inhibitors-through-pharmacophore-designing-3d-qsar-and-molecular-dynamics-simulations-targeting-alzheimer-s-disease
#14
Saleem Iqbal, Dhanabalan Anantha Krishnan, Krishnasamy Gunasekaran
Protein kinases are ubiquitously expressed as Serine/Threonine kinases, and play a crucial role in cellular activities. Protein kinases have evolved through stringent regulation mechanisms. Protein kinase are also involved in tauopathy, thus are important targets for developing Anti-Alzheimer's disease compounds. Structures with an indole scaffold turned out to be potent new leads. With the aim of developing new inhibitors for human protein kinase C, here we report the generation of four point 3D geometric featured pharmacophore model...
November 28, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29173031/probing-the-interaction-of-silver-nanoparticles-with-tau-protein-and-neuroblastoma-cell-line-as-nervous-system-models
#15
Sara Rahmani, Leila Mogharizadeh, Farnoosh Attar, Seyed Mahdi Rezayat, Seyyedeh Elaheh Mousavi, Mojtaba Falahati
Interestingly pharmaceutical sciences are using nanoparticles (NPs) to design and develop nanomaterials-based drugs. However, up to recently, it has not been well realized that NPs themselves may impose risks to the biological systems. In this study, the interaction of silver nanoparticles (AgNPs) with tau protein and SH-SY5Y neuroblastoma cell line, as potential nervous system models, was examined with a range of techniques including intrinsic fluorescence spectroscopy, circular dichroism (CD) spectroscopy, 3-(4,5-dimethylthiazol-2-Yl)-2,5-diphenyltetrazolium bromide (MTT) assay, and acridine orange/ethidium bromide (AO/EB) dual staining method...
November 27, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29173042/antithrombin-conformational-modulation-by-d-myo-inositol-3-4-5-6-tetrakisphosphate-tmi-a-novel-scaffold-for-the-development-of-antithrombotic-agents
#16
Pablo Ricardo Arantes, Horacio Pérez-Sánchez, Hugo Verli
Antithrombin (AT) is a serpin that inhibits mainly thrombin and fXa after being activated by binding to glycosaminoglycans as heparin and heparan sulfate. Upon binding, the native AT conformation, relatively inactive as a protease inhibitor, is converted to an activated form. Recently a new compound, named TMI, was discovered in our group with nanomolar affinity to antithrombin, and shown to be able to induce a partial activation of antithrombin. As TMI represents an original scaffold for structural optimizations aiming the development of new antithrombotic drugs, the present work demonstrated, through a series of molecular dynamics simulations, that TMI is able to modulate AT reactive center loop flexibility similarly to what is observed to heparin, as well as exposing AT P1 residue, Arg393...
November 26, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29173094/improving-efficiency-of-an-angiotensin-converting-enzyme-inhibitory-peptide-as-multifunctional-peptides
#17
Hamid Tanzadehpanah, Ahmad Asoodeh, Massoud Saidijam, Jamshidkhan Chamani, Hanie Mahaki
Bioactive peptides have been defined as specific protein fragments that have numerous biological activities. The aim of this study was to introduce three multifunctional peptides. Hence, we used rabbit lung angiotensin converting enzyme (ACE) inhibitor peptide AFKDEDTEEVPFR to prepare two analogous peptides KDEDTEEVP and KDEDTEEVH. ACE inhibitory, antioxidant and antimicrobial activities of three synthetic peptides were investigated. Among the three peptides, KDEDTEEVP exhibited the highest ACE inhibitory activity with IC50 value of 69...
November 24, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29171346/computational-and-in-vitro-insights-on-snake-venom-phospholipase-a2-inhibitor-of-phytocompound-ikshusterol3-o-glucoside-of-clematis-gouriana-roxb-ex-dc
#18
Sathishkumar Chinnasamy, Subbiah Nagarajan, Thirunavukkarasu Sivaraman, Karthikeyan Muthusamy
Ikshusterol3-O-glucoside was isolated from Clematis gouriana Roxb. ex DC root. A structure of the isolated compound was determined on the basis of various spectroscopic interpretations (UV, NMR, FTIR, and GC-MS-EI). This structure was submitted in the PubChem compound database (SID 249494133). SID 249494133 was carried out by density functional theory calculation to observe the chemical stability and electrostatic potential of this compound. The absorption, distribution, metabolism, excretion (ADME) property of this compound was predicted to evaluate the drug likeness and toxicity...
November 24, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29171343/structure-activity-relationship-on-dna-binding-and-anticancer-activities-of-a-family-of-mixed-ligand-oxidovanadium-v-hydrazone-complexes
#19
Debashis Patra, Subhabrata Paul, Nayim Sepay, Rita Kundu, Tapas Ghosh
The title family of mixed-ligand oxidovanadium(V) hydrazone complexes are [V(V)O(HL(1))(hq)] (1) and [V(V)O(HL(2))(hq)] (2), where (HL(1))(2-) and (HL(2))(2-) are the dinegative form of 2-hydroxybenzoylhydrazone of acetylacetone (H3L(1)) and benzoylacetone (H3L(2)) respectively and hq(-) is the mononegative form of 8-hydroxyquinoline (Hhq). Complexes were used to determine their binding constant with CT DNA using various spectroscopic techniques namely, electronic absorption, fluorescence and circular dichroism spectroscopy...
November 24, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29161996/computational-screening-of-fatty-acid-synthase-inhibitors-against-thioesterase-domain
#20
Wanwisa Panman, Bodee Nutho, Supakarn Chamni, Supaporn Dokmaisrijan, Nawee Kungwan, Thanyada Rungrotmongkol
Thioesterase (TE) domain of fatty acid synthase (FAS) is an attractive therapeutic target for design and development of anticancer drugs. In this present work, we search for the potential FAS inhibitors of TE domain from the ZINC database based on similarity search using three natural compounds as templates, including flavonoids, terpenoids and phenylpropanoids. Molecular docking was used to predict the interaction energy of each screened ligand compared to the reference compound, which is methyl γ-linolenylfluorophosphonate (MGLFP)...
November 21, 2017: Journal of Biomolecular Structure & Dynamics
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