当前位置： SCI文献检索 > JOURNAL OF MOLECULAR MODELING期刊下所有文献 > Homology modeling and in silico screening of inhibitors for the substrate binding domain of human Siah2: implications for hypoxia-induced cancers.

Homology modeling and in silico screening of inhibitors for the substrate binding domain of human Siah2: implications for hypoxia-induced cancers.

Abstract：

:The three-dimensional (3D) structure of the substrate binding domain (SBD) of human ubiquitin ligase Siah2 (seven in absentia homolog) was constructed based on the homology modeling approach using the Modeller 9v7 program. The molecular dynamics method was utilized to refine the model and it was further assessed by ProSA, three-dimensional structural superposition (3d-SS) and PROCHEK in order to analyze the quality and reliability of the generated model. Furthermore, we predicted the binding pocket of Siah2 and also validated it by both blind and normal docking using a known functional inhibitor, menadione. Using structure-based high-throughput virtual screening, we identified five lead drug-like molecules against the modeled SBD of Siah2 and analyzed its pharmacokinetic properties to identify the potential inhibitors for Siah2. The docking results for menadione and the lead molecules at the ligand binding site of SBD of Siah2 revealed that the residue Ser39 (corresponding to Ser167 in the full-length protein) is consistently involved in strong hydrogen bonding, and plays an important role in phosphorylation and the enhanced activity of Siah2.

journal_name

J Mol Model

journal_title

Journal of molecular modeling

authors

Anupriya G,Roopa K,Basappa S,Chong YS,Annamalai L

doi

10.1007/s00894-011-1025-4

subject

Has Abstract

pub_date

2011-12-01 00:00:00

pages

3325-32

issue

12

eissn

1610-2940

issn

0948-5023

journal_volume

17

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR MODELING文献大全
  • Exploring 3D structure of human gonadotropin hormone receptor at antagonist state using homology modeling, molecular dynamic simulation, and cross-docking studies.

    abstract：:Human gonadotropin hormone receptor, a G-protein coupled receptor, is the target of many medications used in fertility disorders. Obtaining more structural information about the receptor could be useful in many studies related to drug design. In this study, the structure of human gonadotropin receptor was subjected to...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-016-3091-0

    authors： Sakhteman A,Khoddami M,Negahdaripour M,Mehdizadeh A,Tatar M,Ghasemi Y

    更新日期：2016-09-01 00:00:00

  • Molecular modeling and dynamics studies of cytidylate kinase from Mycobacterium tuberculosis H37Rv.

    abstract：:Bacterial cytidylate kinase or cytidine monophosphate kinase (CMP kinase) catalyses the phosphoryl transfer from ATP to CMP and dCMP, resulting in the formation nucleoside diphosphates. In eukaryotes, CMP/UMP kinase catalyses the conversion of UMP and CMP to, respectively, UDP and CDP with high efficiency. This work d...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-008-0291-2

    authors： Caceres RA,Macedo Timmers LF,Vivan AL,Schneider CZ,Basso LA,De Azevedo WF Jr,Santos DS

    更新日期：2008-05-01 00:00:00

  • Effect of partial atomic charges on the calculated free energy of solvation of poly(vinyl alcohol) in selected solvents.

    abstract：:It is well-known that properties of poly(vinyl alcohol) (PVA) in the pure and solution states depend largely on the hydrogen bonding networks formed. In the context of molecular simulation, such networks are handled through the Coulombic interactions. Therefore, a good set of partial atom charges (PACs) for simulation...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2554-4

    authors： Noorjahan A,Choi P

    更新日期：2015-03-01 00:00:00

  • G2, G3, and complete basis set calculations of the thermodynamic properties of cis- and trans-triazene.

    abstract：:Following our recent study on triazane, we present a follow-up study on the thermodynamic properties of triazane's unsaturated analog, triazene. We predict optimized structural parameters, vibrational frequencies, enthalpies of formation, enthalpies of combustion, specific enthalpies of combustion, and proton affiniti...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-007-0248-x

    authors： Richard RM,Ball DW

    更新日期：2008-01-01 00:00:00

  • Insights into the structural function of the complex of HIV-1 protease with TMC-126: molecular dynamics simulations and free-energy calculations.

    abstract：:The binding properties of the protein-inhibitor complex of human immunodeficiency virus type 1 (HIV-1) protease with the inhibitor TMC-126 are investigated by combining computational alanine scanning (CAS) mutagenesis with binding free-energy decomposition (BFED). The calculated results demonstrate that the flap regio...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-011-1205-2

    authors： Li D,Han JG,Chen H,Li L,Zhao RN,Liu G,Duan Y

    更新日期：2012-05-01 00:00:00

  • Targeting imidazoline site on monoamine oxidase B through molecular docking simulations.

    abstract：:Monoamine oxidase (MAO) is an enzyme of major importance in neurochemistry, because it catalyzes the inactivation pathway for the catecholamine neurotransmitters, noradrenaline, adrenaline and dopamine. In the last decade it was demonstrated that imidazoline derivatives were able to inhibit MAO activity. Furthermore, ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1390-7

    authors： Moraes FP,de Azevedo WF Jr

    更新日期：2012-08-01 00:00:00

  • Bonding analysis of the donor-acceptor sandwiches CpE-MCp (E = B, Al, Ga; M = Li, Na, K; Cp = η⁵-C₅H₅).

    abstract：:The nature of E-M bonds in CpE-MCp (E = B, Al, Ga; M = Li, Na, K; Cp = η (5)-C5H5) donor-acceptor sandwiches was studied using the atoms in molecules (AIM) theory, electron localization function (ELF), energy decomposition analysis (EDA), and natural bond orbital analysis (NBO) methods. Both topological and orbital an...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2455-6

    authors： Huo S,Meng D,Zhang X,Meng L,Li X

    更新日期：2014-10-01 00:00:00

  • Elimination of the azeotropic point of acetone and methanol by 1,3-dimethylimidazolium dimethylphosphate: an ab initio calculation study.

    abstract：:1,3-Dimethylimidazolium dimethylphosphate ([C1mim][DMP]) was observed experimentally to be able to eliminate the atmospheric azeotropic point of acetone and methanol, which is an important azeotrope generally encountered in furfural production and the Fischer-Tropsch process. Here, we employed ab initio calculation to...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3218-y

    authors： Yu G,Liu X,Zhang X,Chen X,Liu Z,Abdeltawab AA

    更新日期：2017-03-01 00:00:00

  • Molecular basis of the beta-lactamase protein using comparative modelling, drug screening and molecular dynamics studies to understand the resistance of β-lactam antibiotics.

    abstract：:Beta-lactamase (ampC) in general causes the onset of antibiotic resistance in pathogenic bacteria against the β-lactam antibiotics. Morganella morganii which belongs to the Proteae tribe of the Enterobacteriaceae family is a Gram-negative bacillus. Gram-negative bacteria are the key problematic agents among the human ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-020-04459-5

    authors： Alazmi M

    更新日期：2020-07-07 00:00:00

  • Computational simulations of structural role of the active-site W374C mutation of acetyl-coenzyme-A carboxylase: multi-drug resistance mechanism.

    abstract：:Herbicides targeting grass plastidic acetyl-CoA carboxylase (ACCase, EC 6.4.1.2) are selectively effective against graminicides. The intensive worldwide use of this herbicide family has selected for resistance genes in a number of grass weed species. Recently, the active-site W374C mutation was found to confer multi-d...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-010-0742-4

    authors： Zhu XL,Yang WC,Yu NX,Yang SG,Yang GF

    更新日期：2011-03-01 00:00:00

  • Theoretical study of photophysical properties of 1,4-dihydropyrrolo[3,2-b]pyrrole-cored branched molecules with thienylenevinylene arms toward broad absorption spectra for solar cells.

    abstract：:A series of oligo(thienylenevinylene) derivatives with 1,4-dihydropyrrolo[3,2-b]pyrrole as core has been investigated at the PBE0/6-31G(d) and the TD-PBE0/6-31+G(d,p) levels to design materials with high performances such as broad absorption spectra and higher balance transfer property. The results show that position ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1920-y

    authors： Tang S,Tang B,Liang D,Chen G,Jin R

    更新日期：2013-09-01 00:00:00

  • A novel dimerization interface of cyclic nucleotide binding domain, which is disrupted in presence of cAMP: implications for CNG channels gating.

    abstract：:Cyclic nucleotide binding domain (CNBD) is a ubiquitous domain of effector proteins involved in signalling cascades of prokaryota and eukaryota. CNBD activation by cyclic nucleotide monophosphate (cNMP) is studied well in the case of several proteins. However, this knowledge is hardly applicable to cNMP-modulated cati...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1404-5

    authors： Gushchin IY,Gordeliy VI,Grudinin S

    更新日期：2012-09-01 00:00:00

  • Theoretical determination of the effects of various linkages between trinitrobenzenes on energetic properties and sensitivity.

    abstract：:Density functional theory (DFT) has been applied to understand the influence of various linkages on the energetic properties and stability of the polynitro-biphenyl compounds. Structures were optimized using the B3PW91/6-31G(d,p) level, and the heats of formation (HOFs) were computed by employing the selected isodesmi...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-019-4201-6

    authors： Nirwan A,Devi A,Ghule VD

    更新日期：2019-09-15 00:00:00

  • Modeling the pore structure of voltage-gated sodium channels in closed, open, and fast-inactivated conformation reveals details of site 1 toxin and local anesthetic binding.

    abstract：:In this work molecular modeling was applied to generate homology models of the pore region of the Na(v)1.2 and Na(v)1.8 isoforms of human voltage-gated sodium channels. The models represent the channels in the resting, open, and fast-inactivated states. The transmembrane portions of the channels were based on the equi...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-005-0066-y

    authors： Scheib H,McLay I,Guex N,Clare JJ,Blaney FE,Dale TJ,Tate SN,Robertson GM

    更新日期：2006-09-01 00:00:00

  • 3D-QSAR studies of orvinol analogs as kappa-opioid agonists.

    abstract：:Orvinols are potent analgesics that target opioid receptors. However, their analgesic mechanism remains unclear and no significant preference for subtype opioid receptor has been achieved. In order to find new orvinols that target the kappa-receptor, comparative 3D-QSAR studies were performed on 26 orvinol analogs usi...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-005-0084-9

    authors： Li W,Tang Y,Xie Q,Sheng W,Qiu ZB

    更新日期：2006-09-01 00:00:00

  • An insight into paracetamol and its metabolites using molecular docking and molecular dynamics simulation.

    abstract：:Paracetamol is a relatively safe analgesia/antipyretic drug without the risks of addiction, dependence, tolerance, and withdrawal when used alone. However, when administrated in an opioid/paracetamol combination product, which often contains a large quantity of paracetamol, it can be potentially dangerous due to the r...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-018-3790-9

    authors： Wang Y,Lin W,Wu N,He X,Wang J,Feng Z,Xie XQ

    更新日期：2018-08-18 00:00:00

  • Structural analysis and molecular dynamics simulations of novel δ-endotoxin Cry1Id from Bacillus thuringiensis to pave the way for development of novel fusion proteins against insect pests of crops.

    abstract：:The theoretical three-dimensional structure of a novel δ-endotoxin Cry1Id (81 kDa) belonging to Cry1I class, toxic to many of the lepidopteran pests has been investigated through comparative modeling. Molecular dynamics (MD) simulations was carried out to characterize its structural and dynamical features at 10 ns in ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-2010-x

    authors： Dehury B,Sahu M,Sahu J,Sarma K,Sen P,Modi MK,Barooah M,Choudhury MD

    更新日期：2013-12-01 00:00:00

  • Charge localization and charge transfer in the Bebq2 monomer and dimer.

    abstract：:The geometrical structure and electronic properties of bis(10-hydroxybenzo[h]quinolinato)beryllium (Bebq2) molecule and its dimer both in the neutral and in the positively and negatively charged states were studied using quantum-chemical calculations. It is found that the excess charge in the charged systems is locali...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2397-z

    authors： Safonov AA,Bagaturyants AA

    更新日期：2014-08-01 00:00:00

  • A computational study on the role of noncovalent interactions in the stability of polymer/graphene nanocomposites.

    abstract：:Understanding the interaction between graphene and polymers is of essential interest when designing novel nanocomposites with reinforced mechanical and electrical properties. In this computational study, the interaction of pristine graphene (PG) and graphene oxide (GO) with a series of functional groups, representativ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3214-2

    authors： Güryel S,Alonso M,Hajgató B,Dauphin Y,Van Lier G,Geerlings P,De Proft F

    更新日期：2017-02-01 00:00:00

  • Chlorine gas reaction with ZnO wurtzoid nanocrystals as a function of temperature: a DFT study.

    abstract：:In the present work, we applied density functional theory and temperature-dependent Gibbs free energy calculations to wurtzoid structures to explain the sensitivity of ZnO nanocrystals towards chlorine molecules. In agreement with experimental findings, our results revealed that chlorine sensing under ambient conditio...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3309-9

    authors： Abdulsattar MA

    更新日期：2017-04-01 00:00:00

  • Spectroscopic and quantum mechanical investigation of N,N'-bisarylmalonamides: solvent and structural effects.

    abstract：:The UV absorption spectra of ten N,N'-bisarylmalonamides have been recorded in the range 200-400 nm in a set of selected solvents. The solute-solvent interactions have been analyzed on the basis of the linear solvation energy relationship (LSER) concept proposed by Kamlet and Taft. The effects of substituents on the a...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2384-4

    authors： Arsovski VM,Božić BĐ,Mirković JM,Vitnik VD,Vitnik ZJ,Fabian WM,Petrović SD,Mijin DZ

    更新日期：2014-08-01 00:00:00

  • Application of the PM6 method to modeling proteins.

    abstract：:The applicability of the newly developed PM6 method for modeling proteins is investigated. In order to allow the geometries of such large systems to be optimized rapidly, three modifications were made to the conventional semiempirical procedure: the matrix algebra method for solving the self-consistent field (SCF) equ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-008-0420-y

    authors： Stewart JJ

    更新日期：2009-07-01 00:00:00

  • Insights into ET(A) subtype selectivity of benzodiazepine endothelin receptor antagonists by 3D-QSAR approaches.

    abstract：:ET(A) subtype selective antagonists constitute a novel and potentially important class of agents for the treatment of pulmonary hypertension, heart failure, and other pathological conditions. In this paper, 60 benzodiazepine derivatives displaying potent activities against ET(A) and ET(B) subtypes of endothelin recept...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-011-1153-x

    authors： Xia J,Li J,Sun H

    更新日期：2012-04-01 00:00:00

  • Dual-inhibitors of STAT5 and STAT3: studies from molecular docking and molecular dynamics simulations.

    abstract：:Although molecularly targeted therapy with imatinib has improved treatments of chronic myeloid leukemia (CML), clinical resistance gradually develops in patients with accelerated or blast phase CML. The inability of imatinib to cure CML suggests that inactivation of BCR-ABL kinase activity alone is not sufficient to c...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2399-x

    authors： Shao S,Yu R,Yu Y,Li Y

    更新日期：2014-08-01 00:00:00

  • Benchmarking and optimization of molecular simulation models of zinc dialkyldithiophosphate and calcium sulfonate oil additives.

    abstract：:We present an ab initio based molecular mechanics model for prominent additives used in lubricants to moderate oil-steel interfaces. The force field is created for zinc dialkyldithiophosphate and calcium sulfonate charge neutral ligand-ion-ligand complexes and benchmarked to the widely spread generalized amber force f...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-019-3980-0

    authors： Ectors P,Zahn D

    更新日期：2019-03-25 00:00:00

  • Bonding analysis of telluroketones H₂A = Te (A = C, Si, Ge).

    abstract：:Quantum chemical calculations using density functional theory BP86/def2-TZVPP and ab initio methods at CCSD(T)/def2-TZVPP have been carried for the telluroketones H2A=Te (A = C, Si, Ge). DFT calculations have also been carried out for the ketones H2C=E (E = O, S, Se, Te) and for the complexes NHC → [H2A=Te] → B(C6F5)3...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2433-z

    authors： Jaufeerally NB,Ramasami P,Jerabek P,Frenking G

    更新日期：2014-10-01 00:00:00

  • Structure analysis of montmorillonite intercalated with rhodamine B: modeling and experiment.

    abstract：:The intercalation process and the structure of montmorillonite intercalated with [rhodamine B]+ cations have been investigated using molecular modeling (molecular mechanics and molecular dynamics simulations), X-ray powder diffraction and IR spectroscopy. The structure of the intercalate depends strongly on the concen...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-002-0107-8

    authors： Pospísil M,Capková P,Weissmannová H,Klika Z,Trchová M,Chmielová M,Weiss Z

    更新日期：2003-02-01 00:00:00

  • A theoretical study of the inhibition effect of PAMAM molecule on silica scale.

    abstract：:In this work, the molecular modeling method was performed to study adsorption interaction between PAMAM molecules of different generations and silicic acid molecules, and the inhibition effect on silica scale were discussed. The results show that adsorption energies of PAMAM molecule of generation 1.0 with amine-termi...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3208-0

    authors： Chen C,Bai N,Zhang Y,Jiao L,Xia M,Chen G

    更新日期：2017-01-01 00:00:00

  • Effects of local protein environment on the binding of diatomic molecules to heme in myoglobins. DFT and dispersion-corrected DFT studies.

    abstract：:The heme-AB binding energies (AB = CO, O2) in a wild-type myoglobin (Mb) and two mutants (H64L, V68N) of Mb have been investigated in detail with both DFT and dispersion-corrected DFT methods, where H64L and V68N represent two different, opposite situations. Several dispersion correction approaches were tested in the ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1864-2

    authors： Liao MS,Huang MJ,Watts JD

    更新日期：2013-08-01 00:00:00

  • Investigation of the binding network of IGF-I on the cavity surface of IGFBP4.

    abstract：:Insulin-like growth factor-binding proteins (IGFBPs) control bioactivity and distribution of insulin-like growth factors (IGFs) through high-affinity complex of IGFBP and IGF. To get more insight into the binding interaction of IGF system, the site-directed mutagenesis and force-driving desorption methods were employe...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-2020-8

    authors： Chen X,Zhu S,Duan D,Wu T,Wang Q

    更新日期：2013-12-01 00:00:00