Fragmental modeling of human glutamate transporter EAAT1 and analysis of its binding modes by docking and pharmacophore mapping.

Abstract:

:The objective of the study was to generate a reliable model of the homotrimeric structure for the human glutamate transporter EAAT1, based on experimental folding of transporter homologue from Pyrococcus horikoshii. The monomer structure was derived using a fragmental approach and the homotrimer was assembled using protein-protein docking. The interaction capacities of the EAAT1 model were explored by docking a set of 32 known ligands including both substrates and blockers. Docking results unveiled that the substrates' bioactivity is strongly influenced by a precise fitting between the ligand and the EAAT1 binding site, wheras the blockers' activity depends on a set of apolar contacts that ligands can realize in an adjacent hydrophobic subpocket. The docking results were further verified by generating two pharmacophore models (the first for substrates and the latter for blockers) which revealed the features necessary for high EAAT1 activity. The consistency of docking results and the agreement with pharmacophore models afford an encouraging validation for the EAAT1 model and emphasize the soundness of the fragmental approach to model any transmembrane protein.

journal_name

ChemMedChem

journal_title

ChemMedChem

authors

Pedretti A,De Luca L,Sciarrillo C,Vistoli G

doi

10.1002/cmdc.200700197

subject

Has Abstract

pub_date

2008-01-01 00:00:00

pages

79-90

issue

1

eissn

1860-7179

issn

1860-7187

journal_volume

3

pub_type

杂志文章
  • Are MAP kinases drug targets? Yes, but difficult ones.

    abstract::Pharmaceutical companies are facing an increasing interest in new target identification and validation. In particular, extensive efforts are being made in the field of protein kinase inhibitors research and development, and the past ten years of effort in this field have altered our perception of the potential of kina...

    journal_title:ChemMedChem

    pub_type: 杂志文章,评审

    doi:10.1002/cmdc.200600271

    authors: Margutti S,Laufer SA

    更新日期:2007-08-01 00:00:00

  • Synthesis and Biological Evaluation of Glycyrrhetic Acid Derivatives as Potential VEGFR2 Inhibitors.

    abstract::Vascular endothelial growth factor receptor 2 (VEGFR2) has been proven to play a major role in the regulation of tumor angiogenesis. A series of novel glycyrrhetic acid derivatives were synthesized and evaluated for their VEGFR2 inhibitory activity as well as their antiproliferative properties against four cancer cell...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201700271

    authors: Yan TL,Bai LF,Zhu HL,Zhang WM,Lv PC

    更新日期:2017-07-06 00:00:00

  • Organoruthenium Prodrugs as a New Class of Cholinesterase and Glutathione-S-Transferase Inhibitors.

    abstract::A small library of 17 organoruthenium compounds with the general formula [RuII (fcl)(chel)(L)]n+ (in which fcl=face capping ligand, chel=chelating bidentate ligand, and L=monodentate ligand) were screened for inhibitory activity against cholinesterases and glutathione-S-transferases of human and animal origins. Compou...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201800432

    authors: Ristovski S,Uzelac M,Kljun J,Lipec T,Uršič M,Zemljič Jokhadar Š,Žužek MC,Trobec T,Frangež R,Sepčić K,Turel I

    更新日期:2018-10-22 00:00:00

  • Binding Mode and Structure-Activity Relationships of ITE as an Aryl Hydrocarbon Receptor (AhR) Agonist.

    abstract::Discovered as a modulator of the toxic response to environmental pollutants, aryl hydrocarbon receptor (AhR) has recently gained attention for its involvement in various physiological and pathological pathways. AhR is a ligand-dependent transcription factor activated by a large array of chemical compounds, which inclu...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201700669

    authors: Dolciami D,Gargaro M,Cerra B,Scalisi G,Bagnoli L,Servillo G,Fazia MAD,Puccetti P,Quintana FJ,Fallarino F,Macchiarulo A

    更新日期:2018-02-06 00:00:00

  • Dinuclear platinum complexes containing planar aromatic ligands to enhance stacking interactions with proteins.

    abstract::In an approach to design drugs with higher affinity for π-π stacking and electrostatic interactions with targeted biomolecules, complexes of the type [{cis-Pt(A)2 (L)}2 -μ-{trans-1,4-dach}](NO3 )4 ((A)2 =(NH3 )2 or ethylenediamine (en), L=quinoline (quin) or benzothiazole (bztz), dach=trans-1,4-diaminocyclohexane) wer...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201402052

    authors: Ma ES,Daniel AG,Farrell NP

    更新日期:2014-06-01 00:00:00

  • A Novel Prodrug of a γ-Glutamylcyclotransferase Inhibitor Suppresses Cancer Cell Proliferation in vitro and Inhibits Tumor Growth in a Xenograft Mouse Model of Prostate Cancer.

    abstract::γ-Glutamylcyclotransferase (GGCT) depletion inhibits cancer cell proliferation. However, whether the enzymatic activity of GGCT is critical for the regulation of cancer cell growth remains unclear. In this study, a novel diester-type cell-permeable prodrug, pro-GA, was developed based on the structure of N-glutaryl-l-...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201700660

    authors: Ii H,Yoshiya T,Nakata S,Taniguchi K,Hidaka K,Tsuda S,Mochizuki M,Nishiuchi Y,Tsuda Y,Ito K,Kageyama S,Yoshiki T

    更新日期:2018-01-22 00:00:00

  • 18F-Labeled FAUC 346 and BP 897 derivatives as subtype-selective potential PET radioligands for the dopamine D3 receptor.

    abstract::Disturbances of neutrotransmission at the dopamine D3 receptor are related to several neuropsychiatric diseases and in particular to drug addiction. Herein, we report the computer-assisted prediction of D3 selectivities of new fluoroalkoxy-substituted receptor ligands by means of 3D-QSAR analysis. As close analogues o...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.200700327

    authors: Hocke C,Prante O,Salama I,Hübner H,Löber S,Kuwert T,Gmeiner P

    更新日期:2008-05-01 00:00:00

  • Acyclic Cucurbit[n]uril-Type Molecular Containers: Influence of Linker Length on Their Function as Solubilizing Agents.

    abstract::Two acyclic cucurbit[n]uril (CB[n])-type molecular containers that differ in the length of the (CH2 )n linker (M2C2: n=2, M2C4: n=4) between their aromatic sidewalls and sulfonate solubilizing groups were prepared and studied. The inherent solubilities of M2C2 (68 mm) and M2C4 (196 mm) are higher than the analogue wit...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201600090

    authors: Sigwalt D,Moncelet D,Falcinelli S,Mandadapu V,Zavalij PY,Day A,Briken V,Isaacs L

    更新日期:2016-05-06 00:00:00

  • Promiscuity and the conformational rearrangement of drug-like molecules: insight from the protein data bank.

    abstract::Selectivity is a central aspect of lead optimization in the drug discovery process. Medicinal chemists often try to decrease molecular flexibility to improve selectivity, given the common belief that the two are interdependent. To investigate the relationship between polypharmacology and conformational flexibility, we...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201402389

    authors: He MW,Lee PS,Sweeney ZK

    更新日期:2015-02-01 00:00:00

  • Discovery and Mechanistic Elucidation of a Class of Protein Disulfide Isomerase Inhibitors for the Treatment of Glioblastoma.

    abstract::Protein disulfide isomerase (PDI) is overexpressed in glioblastoma, the most aggressive form of brain cancer, and folds nascent proteins responsible for the progression and spread of the disease. Herein we describe a novel nanomolar PDI inhibitor, pyrimidotriazinedione 35G8, that is toxic in a panel of human glioblast...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201700629

    authors: Kyani A,Tamura S,Yang S,Shergalis A,Samanta S,Kuang Y,Ljungman M,Neamati N

    更新日期:2018-01-22 00:00:00

  • The potential of P1 site alterations in peptidomimetic protease inhibitors as suggested by virtual screening and explored by the use of C-C-coupling reagents.

    abstract::A synthetic concept is presented that allows the construction of peptide isostere libraries through polymer-supported C-acylation reactions. A phosphorane linker reagent is used as a carbanion equivalent; by employing MSNT as a coupling reagent, the C-acylation can be conducted without racemization. Diastereoselective...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.200500027

    authors: Weik S,Luksch T,Evers A,Böttcher J,Sotriffer CA,Hasilik A,Löffler HG,Klebe G,Rademann J

    更新日期:2006-04-01 00:00:00

  • Evaluating p97 inhibitor analogues for their domain selectivity and potency against the p97-p47 complex.

    abstract::We previously found that p97 ATPase inhibitors 2-(2-amino-1H-benzo[d]imidazol-1-yl)-N-benzyl-8-methoxyquinazolin-4-amine (ML240) and 2-(2H-benzo[b][1,4]oxazin-4(3H)-yl)-N-benzyl-5,6,7,8-tetrahydroquinazolin-4-amine (ML241) specifically target the D2 domain of wild-type p97. In addition, one of the major p97 cofactors,...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201402420

    authors: Fang CJ,Gui L,Zhang X,Moen DR,Li K,Frankowski KJ,Lin HJ,Schoenen FJ,Chou TF

    更新日期:2015-01-01 00:00:00

  • Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors.

    abstract::Lysine-specific demethylase 1 (LSD1) is a flavin adenine dinucleotide (FAD)-dependent enzyme that catalyzes the demethylation of histone H3 and regulates gene expression. Because it is implicated in the regulation of diseases such as acute myeloid leukemia, potent LSD1-specific inhibitors have been pursued. Trans-2-ph...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.202000014

    authors: Niwa H,Sato S,Handa N,Sengoku T,Umehara T,Yokoyama S

    更新日期:2020-05-06 00:00:00

  • Screening for the drug-phospholipid interaction: correlation to phospholipidosis.

    abstract::Phospholipid bilayers represent a complex, anisotropic environment fundamentally different from bulk oil or octanol, for instance. Even "simple" drug association to phospholipid bilayers can only be fully understood if the slab-of-hydrocarbon approach is abandoned and the complex, anisotropic properties of lipid bilay...

    journal_title:ChemMedChem

    pub_type: 杂志文章,评审

    doi:10.1002/cmdc.200900052

    authors: Alakoskela JM,Vitovic P,Kinnunen PK

    更新日期:2009-08-01 00:00:00

  • Structure-activity relationships and mechanism of action of Eph-ephrin antagonists: interaction of cholanic acid with the EphA2 receptor.

    abstract::The Eph-ephrin system, including the EphA2 receptor and the ephrinA1 ligand, plays a critical role in tumor and vascular functions during carcinogenesis. We previously identified (3α,5β)-3-hydroxycholan-24-oic acid (lithocholic acid) as an Eph-ephrin antagonist that is able to inhibit EphA2 receptor activation; it is ...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201200102

    authors: Tognolini M,Incerti M,Hassan-Mohamed I,Giorgio C,Russo S,Bruni R,Lelli B,Bracci L,Noberini R,Pasquale EB,Barocelli E,Vicini P,Mor M,Lodola A

    更新日期:2012-06-01 00:00:00

  • Approaching 'Kit-Type' Labelling with (68)Ga: The DATA Chelators.

    abstract::The DATA chelators are a novel class of tri-anionic ligands based on 6-amino-1,4-diazepine-triacetic acid, which have been introduced recently for the chelation of (68)Ga. Compared with macrocyclic chelators based on the cyclen scaffold (i.e., DOTA, DO3A, and DO2A derivatives), DATA chelators undergo quantitative radi...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201500092

    authors: Seemann J,Waldron BP,Roesch F,Parker D

    更新日期:2015-06-01 00:00:00

  • Fragmenting the S100B-p53 interaction: combined virtual/biophysical screening approaches to identify ligands.

    abstract::S100B contributes to cell proliferation by binding the C terminus of p53 and inhibiting its tumor suppressor function. The use of multiple computational approaches to screen fragment libraries targeting the human S100B-p53 interaction site is reported. This in silico screening led to the identification of 280 novel pr...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.200900393

    authors: Agamennone M,Cesari L,Lalli D,Turlizzi E,Del Conte R,Turano P,Mangani S,Padova A

    更新日期:2010-03-01 00:00:00

  • Chemerin and vaspin: possible targets to treat obesity?

    abstract::Obesity is one of the main human epidemics today. The increase in fat accumulation, which is associated with obesity, may significantly change the expression of several bioactive molecules known as adipokines. These adipokines interact not only with adipose tissue, but also with metabolically relevant organs such as l...

    journal_title:ChemMedChem

    pub_type: 杂志文章,评审

    doi:10.1002/cmdc.201200448

    authors: Schultz S,Beck-Sickinger AG

    更新日期:2013-04-01 00:00:00

  • Identification of the binding site of an allosteric ligand using STD-NMR, docking, and CORCEMA-ST calculations.

    abstract::Singling out the truth: A combined application of STD-NMR, molecular docking, and CORCEMA-ST calculations is described as an attractive, easily applicable tool for the identification and validation of the binding site for allosteric ligands, with potential application as an aid in drug discovery research. ...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201300267

    authors: Zhang W,Li R,Shin R,Wang Y,Padmalayam I,Zhai L,Krishna NR

    更新日期:2013-10-01 00:00:00

  • Selective and brain-permeable polo-like kinase-2 (Plk-2) inhibitors that reduce α-synuclein phosphorylation in rat brain.

    abstract::Polo-like kinase-2 (Plk-2) has been implicated as the dominant kinase involved in the phosphorylation of α-synuclein in Lewy bodies, which are one of the hallmarks of Parkinson's disease neuropathology. Potent, selective, brain-penetrant inhibitors of Plk-2 were obtained from a structure-guided drug discovery approach...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201300166

    authors: Aubele DL,Hom RK,Adler M,Galemmo RA Jr,Bowers S,Truong AP,Pan H,Beroza P,Neitz RJ,Yao N,Lin M,Tonn G,Zhang H,Bova MP,Ren Z,Tam D,Ruslim L,Baker J,Diep L,Fitzgerald K,Hoffman J,Motter R,Fauss D,Tanaka P,Dap

    更新日期:2013-08-01 00:00:00

  • Efficient stacking on protein amide fragments.

    abstract::The less polar π-surface of protein amide groups is exposed in many receptor binding sites, either as part of the backbone or in Gln/Asn side chains. Using quantum chemical calculations and Protein Data Bank (PDB) searches on model systems, we investigate the energetics and geometric preferences for the stacking on am...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201200512

    authors: Harder M,Kuhn B,Diederich F

    更新日期:2013-03-01 00:00:00

  • Improved bioactivity of antimicrobial peptides by addition of amino-terminal copper and nickel (ATCUN) binding motifs.

    abstract::Antimicrobial peptides (AMPs) are promising candidates to help circumvent antibiotic resistance, which is an increasing clinical problem. Amino-terminal copper and nickel (ATCUN) binding motifs are known to actively form reactive oxygen species (ROS) upon metal binding. The combination of these two peptidic constructs...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201402033

    authors: Libardo MD,Cervantes JL,Salazar JC,Angeles-Boza AM

    更新日期:2014-08-01 00:00:00

  • Tranylcypromine-Based LSD1 Inhibitors: Structure-Activity Relationships, Antiproliferative Effects in Leukemia, and Gene Target Modulation.

    abstract::LSD1 is a lysine demethylase highly involved in initiation and development of cancer. To design highly effective covalent inhibitors, a strategy is to fill its large catalytic cleft by designing tranylcypromine (TCP) analogs decorated with long, hindered substituents. We prepared three series of TCP analogs, carrying ...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201900730

    authors: Fioravanti R,Romanelli A,Mautone N,Di Bello E,Rovere A,Corinti D,Zwergel C,Valente S,Rotili D,Botrugno OA,Dessanti P,Vultaggio S,Vianello P,Cappa A,Binda C,Mattevi A,Minucci S,Mercurio C,Varasi M,Mai A

    更新日期:2020-04-03 00:00:00

  • 50 Years European Federation for Medicinal Chemistry (EFMC) - The Ascent of Medicinal Chemistry in Europe.

    abstract::A historical overview of key events that led, 50 years ago, to the foundation of the European Federation for Medicinal Chemistry (EFMC), and the impact this had on promoting and structuring medicinal chemistry as a discipline in Europe. EFMC, together with the growing number of newly established national medicinal che...

    journal_title:ChemMedChem

    pub_type: 社论

    doi:10.1002/cmdc.202000691

    authors: Differding E

    更新日期:2020-12-15 00:00:00

  • Light-Switchable Antagonists for the Histamine H1 Receptor at the Isolated Guinea Pig Ileum.

    abstract::The histamine H1 G protein-coupled receptor (GPCR) plays an important role in allergy and inflammation. Existing drugs that address the H1 receptor differ in their chemical structure, pharmacology, and side effects. Light-controllable spatial and temporal activity regulation of photochromic H1 ligands may contribute t...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201800815

    authors: Rustler K,Pockes S,König B

    更新日期:2019-03-22 00:00:00

  • Bis-Cyclic Guanidines as a Novel Class of Compounds Potent against Clostridium difficile.

    abstract::Clostridium difficile infection (CDI) symptoms range from diarrhea to severe toxic megacolon and even death. Due to its rapid acquisition of resistance, C. difficile is listed as an urgent antibiotic-resistant threat, and has surpassed methicillin-resistant Staphylococcus aureus (MRSA) as the most common hospital-acqu...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201800240

    authors: Li C,Teng P,Peng Z,Sang P,Sun X,Cai J

    更新日期:2018-07-18 00:00:00

  • Exploiting the lactose-GM3 interaction for drug delivery.

    abstract::Protein-protein and protein-carbohydrate interactions as a means to target the cell surface for therapeutic applications have been extensively investigated. However, carbohydrate-carbohydrate interactions (CCIs) have largely been overlooked. Here, we investigate the concept of CCI-mediated drug delivery. Lactose-funct...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201500046

    authors: Murthy RV,Bavireddi H,Gade M,Kikkeri R

    更新日期:2015-05-01 00:00:00

  • A Selective Biligand Inhibitor of CK2 Increases Caspase-3 Activity in Cancer Cells and Inhibits Platelet Aggregation.

    abstract::Cancer cells express high levels of CK2, and its inhibition leads to apoptosis. CK2 has therefore emerged as a new drug target for cancer therapy. A biligand inhibitor ARC-772 was constructed by conjugating 4-(2-amino-1,3-thiazol-5-yl)benzoic acid and a carboxylate-rich peptoid. ARC-772 was found to bind CK2 with a Kd...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201700457

    authors: Rahnel H,Viht K,Lavogina D,Mazina O,Haljasorg T,Enkvist E,Uri A

    更新日期:2017-10-20 00:00:00

  • Form Matters: Stable Helical Foldamers Preferentially Target Human Monocytes and Granulocytes.

    abstract::Some hybrid foldamers of various length, all containing the (4R,5S)-4-carboxy-5-methyloxazolidin-2-one (d-Oxd) moiety alternating with an l-amino acid (l-Val, l-Lys, or l-Ala), were prepared in order to study their preferred conformations and to evaluate their biological activity. Surprisingly, only the longer oligome...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201600597

    authors: Del Secco B,Malachin G,Milli L,Zanna N,Papini E,Cornia A,Tavano R,Tomasini C

    更新日期:2017-02-20 00:00:00

  • Stable synthetic bacteriochlorins for photodynamic therapy: role of dicyano peripheral groups, central metal substitution (2H, Zn, Pd), and Cremophor EL delivery.

    abstract::A series of four stable synthetic bacteriochlorins was tested in vitro in HeLa cells for their potential in photodynamic therapy (PDT). The parent bacteriochlorin (BC), dicyano derivative (NC)(2)BC and corresponding zinc chelate (NC)(2)BC-Zn and palladium chelate (NC)(2)BC-Pd were studied. Direct dilution of a solutio...

    journal_title:ChemMedChem

    pub_type: 杂志文章

    doi:10.1002/cmdc.201200351

    authors: Huang YY,Balasubramanian T,Yang E,Luo D,Diers JR,Bocian DF,Lindsey JS,Holten D,Hamblin MR

    更新日期:2012-12-01 00:00:00