当前位置： SCI文献检索 > JOURNAL OF MOLECULAR MODELING期刊下所有文献 > Molecular modeling of noncompetitive antagonists of the NMDA receptor: proposal of a pharmacophore and a description of the interaction mode.

Molecular modeling of noncompetitive antagonists of the NMDA receptor: proposal of a pharmacophore and a description of the interaction mode.

Abstract：

:Since the three-dimensional structure of the NMDA receptor has not been determined experimentally, indirect computer-assisted molecular modeling techniques appear to be of great usefulness in the characterization of the common pharmacophore of all NMDA receptor noncompetitive antagonists, despite their structural differences. Indeed, the conformational analysis of three different chemical families (MK801, PCP, dexoxadrol and their analogues), has allowed us to visualize the different conformations and configurations of each molecule. Superimposition with configurations 1 and 2 of the MK801 molecule has allowed us to propose active conformations and thereafter a geometrical characterization of the pharmacophore, especially the determination of the orientation of the nitrogen lone pair (NLP) related to the phenyl. On the other hand, electrostatic studies, combined with geometrical features, have allowed us to schematize the interaction mode of an active conformation to the binding site. Finally, studies of the molecular lipophilic potential (MLP) have provided us information on the position of lipophilic and hydrophilic zones of the pharmacophore.

journal_name

J Mol Model

journal_title

Journal of molecular modeling

authors

Elhallaoui M,Laguerre M,Carpy A,Ouazzani FC

doi

10.1007/s00894-001-0067-4

subject

Has Abstract

pub_date

2002-02-01 00:00:00

pages

65-72

issue

2

eissn

1610-2940

issn

0948-5023

journal_volume

8

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR MODELING文献大全
  • Double-layer carbon nanocapsules with radioiodine content and its interaction with calcium, phosphorus, and strontium.

    abstract：:First principles calculations have been performed for C60@C180 carbon double-layer endofullerenes with up to: three diatomic radioiodine molecules (131I2), two potassium radio-iodide (K131I), and three sodium radio-iodide (Na131I) inside. The plane-wave pseudopotential (PP) method within the general gradient approxima...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3538-y

    authors： Valderrama A,Reynoso R,Gómez RW,Quintana M,Romero M

    更新日期：2017-12-04 00:00:00

  • A CASSCF/CASPT2 investigation on electron detachments from ScSi n- (n = 4-6) clusters.

    abstract：:In this work, the low-lying states of several isomers of ScSi n-/0 (n = 4-6) were investigated with the B3LYP functional and CASPT2 method. The ground states of the anionic clusters were predicted to be the singlet states of the trigonal bipyramid ScSi4- (A-ScSi4-), the face-capped trigonal bipyramid ScSi5- (A-ScSi5-)...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3461-2

    authors： Nguyen MT,Tran QT,Tran VT

    更新日期：2017-09-20 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

  • 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

  • Molecular insights into quorum sensing in Acidithiobacillus ferrooxidans bacteria via molecular modelling of the transcriptional regulator AfeR and of the binding mode of long-chain acyl homoserine lactones.

    abstract：:Amino acid sequence alignments of the transcriptional regulator AfeR, which is involved in type 1 quorum sensing (QS) in Acidithiobacillus ferrooxidans bacteria, with other acyl homoserine lactone (AHL)-dependent QS regulators, revealed the presence of strictly or highly conserved residues located in the active site o...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-008-0315-y

    authors： Soulère L,Guiliani N,Queneau Y,Jerez CA,Doutheau A

    更新日期：2008-07-01 00:00:00

  • Computation of multicenter overlap integrals with Slater-type orbitals using psi(alpha)-ETOs.

    abstract：:Multicenter overlap integrals appearing in the evaluation of multicenter-multielectron integrals of central and noncentral interaction potentials are calculated using complete orthonormal sets of psi(alpha)-ETOs (alpha=1, 0, -1, -2,...). The final results are expressed in terms of two-center overlap integrals between ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-003-0151-z

    authors： Guseinov I,Aydin R,Mamedov B

    更新日期：2003-10-01 00:00:00

  • In-silico studies on DegP protein of Plasmodium falciparum in search of anti-malarials.

    abstract：:Despite encouraging progress over the past decade, malaria caused by the Plasmodium parasite continues to pose an enormous disease burden and is one of the major global health problems. The extreme challenge in malaria management is the resistance of parasites to traditional monochemotherapies like chloroquine and sul...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-016-3064-3

    authors： Sharma D,Soni R,Patel S,Joshi D,Bhatt TK

    更新日期：2016-09-01 00:00:00

  • Three applications of path integrals: equilibrium and kinetic isotope effects, and the temperature dependence of the rate constant of the [1,5] sigmatropic hydrogen shift in (Z)-1,3-pentadiene.

    abstract：:Recent experiments have confirmed the importance of nuclear quantum effects even in large biomolecules at physiological temperature. Here we describe how the path integral formalism can be used to describe rigorously the nuclear quantum effects on equilibrium and kinetic properties of molecules. Specifically, we expla...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-010-0711-y

    authors： Zimmermann T,Vaníček J

    更新日期：2010-11-01 00:00:00

  • In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV.

    abstract：:ORF 3a of human severe acute respiratory syndrome corona virus (SARS-CoV) has been identified as a 274 amino acid membrane protein. When expressed in Xenopus oocytes the protein forms channels. Based on bioinformatics approaches the topology has been identified to include three transmembrane domains (TMDs). Since stru...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-011-1092-6

    authors： Hsu HJ,Fischer WB

    更新日期：2012-02-01 00:00:00

  • Fractional kinetics on thermal analysis: application to lumefantrine thermal decomposition.

    abstract：:The fractional derivative concept to treat non-isothermal solid state thermal decomposition was employed in this work. Simulated data were compared with the exact solutions for the method validation. Calculated fractional kinetics data for four heating rates were initially considered and the Kissinger-Akahira-Sunose (...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-020-04360-1

    authors： Carvalho FS,Braga JP,Marques MBF,Sebastião RCO

    更新日期：2020-06-10 00:00:00

  • Electron density reactivity indexes of the tautomeric/ionization forms of thiamin diphosphate.

    abstract：:The generation of the highly reactive ylide in thiamin diphosphate catalysis is analyzed in terms of the nucleophilicity of key atoms, by means of density functional calculations at X3LYP/6-31++G(d,p) level of theory. The Fukui functions of all tautomeric/ionization forms are calculated in order to assess their reacti...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1908-7

    authors： Jaña GA,Delgado EJ

    更新日期：2013-09-01 00:00:00

  • Effects of water content on the tetrahedral intermediate of chymotrypsin - trifluoromethylketone in polar and non-polar media: observations from molecular dynamics simulation.

    abstract：:The work uses MD simulation to study effects of five water contents (3 %, 10 %, 20 %, 50 %, 100 % v/v) on the tetrahedral intermediate of chymotrypsin - trifluoromethyl ketone in polar acetonitrile and non-polar hexane media. The water content induced changes in the structure of the intermediate, solvent distribution ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1807-y

    authors： Tian X,Jiang L,Yuan Y,Wang M,Guo Y,Zeng X,Li M,Pu X

    更新日期：2013-06-01 00:00:00

  • Identification of novel, less toxic PTP-LAR inhibitors using in silico strategies: pharmacophore modeling, SADMET-based virtual screening and docking.

    abstract：:Human leukocyte antigen-related (PTP-LAR) is a receptor-like transmembrane phosphatase and a potential target for diabetes, obesity and cancer. In the present study, a sequence of in silico strategies (pharmacophore mapping, a 3D database searching, SADMET screening, and docking and toxicity studies) was performed to ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-011-1037-0

    authors： Ajay D,Sobhia ME

    更新日期：2012-01-01 00:00:00

  • Bloch Oscillations in Fibonacci lattices: polaron formation.

    abstract：:We investigated the dynamics of an electron subjected to a uniform electric field in the scope of a tight-binding electron-phonon interacting approach. We aimed at describing the transport in a one-dimensional lattice in which the on-site energies are distributed according to a Fibonacci sequence. Within this physical...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-019-3972-0

    authors： de Brito PE,Enders BG,Ribeiro LA Jr,Nazareno HN

    更新日期：2019-03-28 00:00:00

  • The role of hydrogen bonds in an aqueous solution of acetylsalicylic acid: a molecular dynamics simulation study.

    abstract：:This work focuses on the role of the dynamic hydrogen bonds (HB) formed in an aqueous solution of aspirin using molecular dynamics simulation. The statistics reveal the existence of internal HB that inhibit the rotational movements of the acetyl and the carboxylic acid groups, forcing the molecule to adopt a closed co...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-010-0930-2

    authors： Donnamaria MC,de Xammar Oro JR

    更新日期：2011-10-01 00:00:00

  • Structure and localisation of drug binding sites on neurotransmitter transporters.

    abstract：:The dopamine (DAT), serotontin (SERT) and noradrenalin (NET) transporters are molecular targets for different classes of psychotropic drugs. The crystal structure of Aquifex aeolicus LeuT(Aa) was used as a template for molecular modeling of DAT, SERT and NET, and two putative drug binding sites (pocket 1 and 2) in eac...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-009-0478-1

    authors： Ravna AW,Sylte I,Dahl SG

    更新日期：2009-10-01 00:00:00

  • A comparative theoretical investigation into the strength of the trigger-bond in the Na⁺, Mg²⁺ and HF complexes involving the nitro group of R-NO₂ (R = -CH₃, -NH₂ and -OCH₃) or the C = C bond of (E)-O₂N-CH = CH-NO₂.

    abstract：:A comparative theoretical investigation into the change in strength of the trigger-bond upon formation of the Na(+), Mg(2+) and HF complexes involving the nitro group of RNO₂ (R = -CH₃, -NH₂, -OCH₃) or the C = C bond of (E)-O₂N-CH = CH-NO₂ was carried out using the B3LYP and MP2(full) methods with the 6-311++G**, 6-31...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1793-0

    authors： Zhang L,Ren FD,Cao DL,Wang JL,Gao JF

    更新日期：2013-06-01 00:00:00

  • A density functional theory study on oxygen reduction reaction on nitrogen-doped graphene.

    abstract：:Nitrogen (N)-doped carbons reportedly exhibit good electrocatalytic activity for the oxygen reduction reaction (ORR) of fuel cells. This work provides theoretical insights into the ORR mechanism of N-doped graphene by using density functional theory calculations. All possible reaction pathways were investigated, and t...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-2047-x

    authors： Zhang J,Wang Z,Zhu Z

    更新日期：2013-12-01 00:00:00

  • Trapping N5 rings and N3 chains on the outer surface of fullerene C60: a theoretical study.

    abstract：:The capture of N3-chains and N5-rings on the outer surface of C60 was studied using density functional calculations. For the neutral N5-ring, it was found that a N5-ring trapped by a C60 cage becomes more stable than an isolated N5-ring radical, and a C60-N5 compound with a C-N bond at an exohedral position of C60 is ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-015-2811-1

    authors： Liang Y,Gao X,Li N,Zhang X

    更新日期：2015-10-01 00:00:00

  • On the origin of internal rotation in ammonia borane.

    abstract：:The internal rotation in ammonia borane (AB) was studied on the basis of natural orbitals for chemical valence (NOCV) and eigenvectors for Pauli repulsion (NOPR). We found that the total hyperconjugation stabilization (ca. 5 kcal mol(-1)), based on the charge transfer from the occupied σ (B-H) orbitals into the empty ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2272-y

    authors： Parafiniuk M,Mitoraj MP

    更新日期：2014-06-01 00:00:00

  • Ab initio study of electron transport in 4-(3-nitro-4-tetrafluorophenylthiolate-ethynyl, phenylethynyl) benzenethiolate.

    abstract：:The electron transport of the 4-(3-nitro-4-tetrafluorophenylthiolate-ethynyl, phenylethynyl) benzenethiolate (S-FNPPB-o) molecule assembled in two Au (111) electrodes, was studied using two approaches: in the first approximate approach an electric field was applied to the pure molecule attached to two thiolate ends fi...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-011-1106-4

    authors： Serrato-Villegas L,Gallo M,Delgado-Ríos M,Romero MT,Glossman-Mitnik D

    更新日期：2012-02-01 00:00:00

  • Mechanism of antioxidant properties of quercetin and quercetin-DNA complex.

    abstract：:Quercetin is the most abundant flavonoid with potent antioxidant activities. In the current research, the antioxidant properties of quercetin and quercetin-DNA complex were investigated theoretically and experimentally. Free radical scavenging experiments with thiobarbituric acid-reactive substances (TBARS) and 1,1-di...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-020-04356-x

    authors： Song X,Wang Y,Gao L

    更新日期：2020-05-12 00:00:00

  • Screening of functional monomers and solvents for the molecular imprinting of paclitaxel separation: a theoretical study.

    abstract：:The interactions between the template molecule paclitaxel (PTX) and seven functional monomers containing methacrylic acid (MA), acrolein (AC), 4-vinylbenzoic acid (4VA), acrylonitrile (AN), 2-vinylpyridine (2VP), 2,6-bisacrylamide pyridine (BAP) and methyl methacrylate (MM) were systematically investigated adopting th...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-019-4277-z

    authors： Wang L,Yang F,Zhao X,Li Y

    更新日期：2020-01-11 00:00:00

  • Comparative simulation study of chemical synthesis of functional DADNE material.

    abstract：:Amorphous molecular simulation to model the reaction species in the synthesis of chemically inert and energetic 1,1-diamino-2,2-dinitroethene (DADNE) explosive material was performed in this work. Nitromethane was selected as the starting reactant to undergo halogenation, nitration, deprotonation, intermolecular conde...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-016-3182-y

    authors： Liu MH,Liu CW

    更新日期：2017-01-01 00:00:00

  • 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 Pr...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-011-1025-4

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

    更新日期：2011-12-01 00:00:00

  • Force field parametrization of hydrogenoxalate and oxalate anions with scaled charges.

    abstract：:Models of the hydrogenoxalate (bioxalate, charge -1) and oxalate (charge -2) anions were developed for classical molecular dynamics (CMD) simulations and parametrized against ab initio molecular dynamics (AIMD) data from our previous study (Kroutil et al. (2016) J Mol Model 22:210). The interactions of the anions with...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3490-x

    authors： Kroutil O,Předota M,Kabeláč M

    更新日期：2017-10-28 00:00:00

  • Benchmarking coupled cluster methods on singlet excited states of nucleobases.

    abstract：:In this paper, coupled cluster methods CC2, CCSD, CCSDR(3) and EOM-CCSD(T) have been benchmarked against CC3 for the transition energies of nucleobases. Beside presenting vertical excitation energies for about 30 singlet transitions of four molecules, the results are analyzed statistically and problematic cases have b...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2503-2

    authors： Kánnár D,Szalay PG

    更新日期：2014-11-01 00:00:00

  • Acylthiocarbamates as non-nucleoside HIV-1 reverse transcriptase inhibitors: docking studies and ligand-based CoMFA and CoMSIA analyses.

    abstract：:Acylthiocarbamates (ATCs) have been identified as a class of potent non-nucleoside HIV-1 reverse transcriptase (RT) inhibitors. A computational strategy based on molecular docking studies followed by comparative molecular fields analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) was used t...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-008-0441-6

    authors： Cichero E,Cesarini S,Spallarossa A,Mosti L,Fossa P

    更新日期：2009-07-01 00:00:00

  • Theoretical study of absorption of 2,2,6,6-tetramethylpiperidine-1-oxoammonium cation (TEMPO) on TiO₂(110) rutile surface.

    abstract：:We present a theoretical study of the adsorption of 2,2,6,6-tetramethylpiperidine-1-oxoammonium cation (TEMPO) onto the TiO₂(110) surface rutile, investigating its bonding nature, electron properties and structural stability. Based on the results obtained with the PBE0/def2-SVP method, natural bond orbital (NBO) analy...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2149-0

    authors： Nieto-López I,Hernández-García L,Bonilla-Cruz J,Sanchez M

    更新日期：2014-03-01 00:00:00

  • Effect of the aminoacid composition of model α-helical peptides on the physical properties of lipid bilayers and peptide conformation: a molecular dynamics simulation.

    abstract：:The interaction of a model Lys flanked α-helical peptides K2-X24-K2, (X = A,I,L,L+A,V) with lipid bilayers composed of dimyristoylphosphatidylcholine (DMPC) and dipalmitoylphosphatidylcholine (DPPC) both, in a gel and in a liquid-crystalline state, has been studied by molecular dynamics simulations. It has been shown ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1550-9

    authors： Melicherčík M,Holúbeková A,Hianik T,Urban J

    更新日期：2013-11-01 00:00:00