当前位置： SCI文献检索 > BIOORGANIC & MEDICINAL CHEMISTRY期刊下所有文献 > An evaluation of automated in silico ligand docking of amino acid ligands to Family C G-protein coupled receptors.

An evaluation of automated in silico ligand docking of amino acid ligands to Family C G-protein coupled receptors.

Abstract：

:Family C G-protein coupled receptors (GPCRs) consist of the metabotropic glutamate receptors (mGluRs), the calcium-sensing receptor (CaSR), the T1R taste receptors, the GABA(B) receptor, the V2R pheromone receptors, and several chemosensory receptors. A common feature of Family C receptors is the presence of an amino acid binding pocket. The objective of this study was to evaluate the ability of the automatic docking program FlexX to predict the favored amino acid ligand at several Family C GPCRs. The docking process was optimized using the crystal structure of mGluR1 and the 20 amino acids were docked into homology models of the CaSR, the 5.24 chemosensory receptor, and the GPRC6A amino acid receptor. Under optimized docking conditions, glutamate was docked in the binding pocket of mGluR1 with a root mean square deviation of 1.56 angstroms from the co-crystallized glutamate structure and was ranked as the best ligand with a significantly better FlexX score compared to all other amino acids. Ligand docking to a homology model of the 5.24 receptor gave generally correct predictions of the favored amino acids, while the results obtained with models of GPRC6A and the CaSR showed that some of the favored amino acids at these receptors were correctly predicted, while a few other top scoring amino acids appeared to be false positives. We conclude that with certain caveats, FlexX can be successfully used to predict preferred ligands at Family C GPCRs.

journal_name

Bioorg Med Chem

journal_title

Bioorganic & medicinal chemistry

authors

Wang M,Hampson DR

doi

10.1016/j.bmc.2005.10.052

subject

Has Abstract

pub_date

2006-03-15 00:00:00

pages

2032-9

issue

6

eissn

0968-0896

issn

1464-3391

pii

S0968-0896(05)01039-4

journal_volume

14

pub_type

杂志文章

相关文献

BIOORGANIC & MEDICINAL CHEMISTRY文献大全
  • New derivatives of silybin and 2,3-dehydrosilybin and their cytotoxic and P-glycoprotein modulatory activity.

    abstract：:Large series of O-alkyl derivatives (methyl and benzyl) of silybin and 2,3-dehydrosilybin was prepared. Selective alkylation of the silybin molecule was systematically investigated. For the first time we present here, for example, preparation of 19-nor-2,3-dehydrosilybin. All prepared silybin/2,3-dehydrosilybin deriva...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2006.01.035

    authors： Dzubák P,Hajdúch M,Gazák R,Svobodová A,Psotová J,Walterová D,Sedmera P,Kren V

    更新日期：2006-06-01 00:00:00

  • ORL1 and opioid receptor preferences of nociceptin and dynorphin A analogues with Dmp substituted for N-terminal aromatic residues.

    abstract：:Nociceptin (NOC) and dynorphin A (DYN) analogues containing 2',6'-dimethylphenylalanine (Dmp) in place of Phe or Tyr in position 1 and/or 4 were synthesized and their metabolic stability and receptor-binding properties were investigated. [Dmp1]NOC(1-13)-NH2 (1) possessed high ORL1 receptor affinity comparable to that ...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2005.11.021

    authors： Sasaki Y,Kawano S,Kohara H,Watanabe H,Ambo A

    更新日期：2006-04-01 00:00:00

  • Analysis of the binding specificities of oligomannoside-binding proteins using methylated monosaccharides.

    abstract：:The binding specificities of the closely related lectins from Canavalia ensiformis and Dioclea grandiflora were examined using specifically O-alkylated mono- and disaccharides. Both lectins accept any substitution at the monosaccharide C2 hydroxyl group. The binding energy of C2-alkylated ligands-concanavalin A comple...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/s0968-0896(96)00178-2

    authors： Chervenak MC,Toone EJ

    更新日期：1996-11-01 00:00:00

  • Criteria for the mode of binding of DNA binding agents.

    abstract：:A complete characterization of DNA binding agents requires that their mode of binding to DNA be established. In the absence of high resolution structural data, the mode of binding is, of necessity, usually inferred indirectly from various solution studies. The purpose of this study is to show that only certain methods...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/0968-0896(95)00053-j

    authors： Suh D,Chaires JB

    更新日期：1995-06-01 00:00:00

  • Modification at the C9 position of the marine natural product isoaaptamine and the impact on HIV-1, mycobacterial, and tumor cell activity.

    abstract：:As part of an investigation to generate optimized drug leads from marine natural pharmacophores for the treatment of neoplastic and infectious diseases, a series of novel isoaaptamine analogs were prepared by coupling acyl halides to the C9 position of isoaaptamine (2) isolated from the Aaptos sponge. This library of ...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2006.08.042

    authors： Gul W,Hammond NL,Yousaf M,Bowling JJ,Schinazi RF,Wirtz SS,de Castro Andrews G,Cuevas C,Hamann MT

    更新日期：2006-12-15 00:00:00

  • 4-Fluoro-N-butylphenylacetamide (H6) inhibits cell growth via cell-cycle arrest and apoptosis in human cervical cancer cells.

    abstract：:Phenylacetate induced tumor cytostasis and differentiation. The chemotherapeutic function of the compound in lung cancer has been previously reported, however, whether or not phenylacetate performs other activities is not known. In this study, the potential usage of synthetic phenylacetate derivatives, 4-fluoro-N-buty...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2008.11.028

    authors： Liu CH,Huang LJ,Kuo SC,Lee TH,Tsai KJ,Chan HC

    更新日期：2009-01-01 00:00:00

  • Synthesis and evaluation of 4- and 5-pyridazin-3-one phenoxypropylamine analogues as histamine-3 receptor antagonists.

    abstract：:A novel series of 4-pyridazin-3-one and 5-pyridazin-3-one analogues were designed and synthesized as H(3)R antagonists. Structure-activity relationship revealed the 5-pyridazin-3-ones 8a and S-methyl 8b had excellent human and rat H(3)R affinities, and acceptable pharmacokinetic properties. In vivo evaluation of 8a sh...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2012.04.028

    authors： Becknell NC,Lyons JA,Aimone LD,Huang Z,Gruner JA,Raddatz R,Hudkins RL

    更新日期：2012-06-15 00:00:00

  • Bioluminescence probe for γ-glutamyl transpeptidase detection in vivo.

    abstract：:To detect γ-Glutamyl Transpeptidase (GGT) activity in vitro and in vivo, a bioluminescence probe with high sensitivity and specificity was well designed and synthesized. This probe can be recognized by GGT and release strong bioluminescence with its further reaction with luciferase. The performance of this probe was d...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2017.11.025

    authors： Lin Y,Gao Y,Ma Z,Jiang T,Zhou X,Li Z,Qin X,Huang Y,Du L,Li M

    更新日期：2018-01-01 00:00:00

  • Characterization of a transglycosylase domain of Streptococcus pneumoniae PBP1b.

    abstract：:Inhibitors of transglycosylases may serve as potent antibiotics that are less prone to resistance development in bacterial pathogens. To facilitate the search of such compounds, a transglycosylase (TGase) domain of the membrane integral multidomain Streptococcus pneumoniae PBP1b was cloned and expressed. This TGase do...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2006.06.058

    authors： Liu H,Wong CH

    更新日期：2006-11-01 00:00:00

  • Docking and hydropathic scoring of polysubstituted pyrrole compounds with antitubulin activity.

    abstract：:Compounds that bind at the colchicine site of tubulin have drawn considerable attention with studies indicating that these agents suppress microtubule dynamics and inhibit tubulin polymerization. Data for 18 polysubstituted pyrrole compounds are reported, including antiproliferative activity against human MDA-MB-435 c...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2007.11.076

    authors： Tripathi A,Fornabaio M,Kellogg GE,Gupton JT,Gewirtz DA,Yeudall WA,Vega NE,Mooberry SL

    更新日期：2008-03-01 00:00:00

  • Scutione, a new bioactive norquinonemethide triterpene from Maytenus scutioides (Celastraceae).

    abstract：:Scutione (1), a new norquinonemethide triterpene with a netzahualcoyene type skeleton, has been isolated from the root bark of Maytenus scutioides (Celastraceae) by bioactivity-directed fractionation. The structure of 1 has been elucidated by means of 1H and 13C NMR spectroscopic studies, including 1H-13C heteronuclea...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/0968-0896(96)00078-8

    authors： González AG,Alvarenga NL,Ravelo AG,Bazzocchi IL,Ferro EA,Navarro AG,Moujir LM

    更新日期：1996-06-01 00:00:00

  • A new structural alternative in benzo[b]furans for antimicrobial activity.

    abstract：:Two series of 2-substituted and three new diacetyl benzofurans were synthesized through palladium-catalyzed reactions and their in vitro antimicrobial spectra were assessed. The compounds demonstrated mild to significant growth inhibition against antibiotic-susceptible standard and clinically isolated strains of Gram-...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2005.05.009

    authors： Wahab Khan M,Jahangir Alam M,Rashid MA,Chowdhury R

    更新日期：2005-08-15 00:00:00

  • An altered zinc-binding site confers resistance to a covalent inactivator of New Delhi metallo-beta-lactamase-1 (NDM-1) discovered by high-throughput screening.

    abstract：:Due to the global threat of antibiotic resistance mediated by New Delhi metallo-beta-lactamase-1 (NDM-1) and the lack of structurally diverse inhibitors reported for this enzyme, we developed screening and counter-screening assays for manual and automated formats. The manual assay is a trans-well absorbance-based endp...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2013.03.031

    authors： Thomas PW,Spicer T,Cammarata M,Brodbelt JS,Hodder P,Fast W

    更新日期：2013-06-01 00:00:00

  • Structural interrogation of benzosuberene-based inhibitors of tubulin polymerization.

    abstract：:The discovery of 3-methoxy-9-(30,40,50-trimethoxyphenyl)-6,7-dihydro-5H-benzo[7]annulen-4-ol (a benzosuberene-based analogue referred to as KGP18) was originally inspired by the natural products colchicine and combretastatin A-4 (CA4). The relative structural simplicity and ease of synthesis of KGP18, coupled with its...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2015.10.012

    authors： Herdman CA,Devkota L,Lin CM,Niu H,Strecker TE,Lopez R,Liu L,George CS,Tanpure RP,Hamel E,Chaplin DJ,Mason RP,Trawick ML,Pinney KG

    更新日期：2015-12-15 00:00:00

  • Click synthesis of estradiol-cyclodextrin conjugates as cell compartment selective estrogens.

    abstract：:Cyclodextrin (CD) is a well known drug carrier and excipient for enhancing aqueous solubility. CDs themselves are anticipated to have low membrane permeability because of relatively high hydrophilicity and molecular weight. CD derivatization with 17-beta estradiol (E(2)) was explored extensively using a number of diff...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2009.11.046

    authors： Kim HY,Sohn J,Wijewickrama GT,Edirisinghe P,Gherezghiher T,Hemachandra M,Lu PY,Chandrasena RE,Molloy ME,Tonetti DA,Thatcher GR

    更新日期：2010-01-15 00:00:00

  • Pyrazolo[1',5':1,6]pyrimido[4,5-d]pyridazin-4(3H)-ones as selective human A(1) adenosine receptor ligands.

    abstract：:A series of pyrazolo[1',5':1,6]pyrimido[4,5-d]pyridazin-4(3H)-ones was synthesized and tested in radioligand binding assays to determine their affinities for the human adenosine A(1), A(2A), A(2B) and A(3) receptors. Results indicated that this scaffold is appropriate for adenosine receptor subtype A(1) ligands and th...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2010.09.043

    authors： Giovannoni MP,Vergelli C,Cilibrizzi A,Crocetti L,Biancalani C,Graziano A,Dal Piaz V,Loza MI,Cadavid MI,Díaz JL,Gavaldà A

    更新日期：2010-11-15 00:00:00

  • Quantitative structure-activity relationships of 1,3,4-thiadiazol-2(3H)-ones and 1,3,4-oxadiazol-2(3H)-ones as human protoporphyrinogen oxidase inhibitors.

    abstract：:Protoporphyrinogen oxidase (Protox, EC 1.3.3.4) has attracted great interest during the last decades due to its unique biochemical characteristics and biomedical significance. As a continuation of our research work on the development of new PPO inhibitors, 23 new 1,3,4-thiadiazol-2(3H)-ones bearing benzothiazole subst...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2011.10.079

    authors： Zuo Y,Yang SG,Jiang LL,Hao GF,Wang ZF,Wu QY,Xi Z,Yang GF

    更新日期：2012-01-01 00:00:00

  • Design and synthesis of novel androgen receptor antagonists with sterically bulky icosahedral carboranes.

    abstract：:Carboranes (dicarba-closo-dodecaboranes) are a class of carbon-containing polyhedral boron-cluster compounds having remarkable chemical and thermal stability, and hydrophobic character. These features may allow application of carboranes as a new hydrophobic core structure in biologically active molecules that interact...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2005.06.061

    authors： Goto T,Ohta K,Suzuki T,Ohta S,Endo Y

    更新日期：2005-12-01 00:00:00

  • Synthesis of indomethacin analogues for evaluation as modulators of MRP activity.

    abstract：:Synthesis of a range of indomethacin analogues, required for investigation in combination toxicity assays, bearing both N-benzyl and N-benzoyl groups, is described. ...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/s0968-0896(00)00292-3

    authors： Maguire AR,Plunkett SJ,Papot S,Clynes M,O'Connor R,Touhey S

    更新日期：2001-03-01 00:00:00

  • Synthesis and biological evaluation of epothilone A dimeric compounds.

    abstract：:The preparation and biological evaluation of a novel series of dimeric epothilone A derivatives (1-6) are described. Two types of diacyl spacers were introduced to establish the various dimeric epothilone A constructs. The effect of these compounds on tubulin polymerization and their cytotoxicity against four differen...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2009.09.032

    authors： Passarella D,Comi D,Cappelletti G,Cartelli D,Gertsch J,Quesada AR,Borlak J,Altmann KH

    更新日期：2009-11-01 00:00:00

  • Synthesis and antimalarial evaluation of a screening library based on a tetrahydroanthraquinone natural product scaffold.

    abstract：:As part of a research program aimed at discovering new antimalarial leads from Australian macrofungi a unique fungi-derived prefractionated library was screened against a chloroquine-sensitive Plasmodium falciparum line (3D7) using a radiometric growth inhibition assay. A library fraction derived from a Cortinarius sp...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2012.09.052

    authors： Choomuenwai V,Andrews KT,Davis RA

    更新日期：2012-12-15 00:00:00

  • Recreating ancient metabolic pathways before enzymes.

    abstract：:The biochemistry of all living organisms uses complex, enzyme-catalyzed metabolic reaction networks. Yet, at life's origins, enzymes had not yet evolved. Therefore, it has been postulated that non-enzymatic metabolic pathways predated their enzymatic counterparts. In this account article, we describe our recent work t...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章,评审

    doi：10.1016/j.bmc.2019.03.012

    authors： Muchowska KB,Chevallot-Beroux E,Moran J

    更新日期：2019-06-15 00:00:00

  • Synthesis and cytotoxic activities of goniothalamins and derivatives.

    abstract：:Substituted goniothalamins containing cyclopropane-groups were efficiently prepared in high yields and good selectivity. Antiproliferative activity was measured on three human cancer cell lines (A549, MCF-7, HBL-100), to show which of the structural elements of goniothalamins is mandatory for cytotoxicity. We found th...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2017.02.004

    authors： Weber A,Döhl K,Sachs J,Nordschild ACM,Schröder D,Kulik A,Fischer T,Schmitt L,Teusch N,Pietruszka J

    更新日期：2017-11-15 00:00:00

  • An unusual functional group interaction and its potential to reproduce steric and electrostatic features of the transition states of peptidolysis.

    abstract：:The donor-acceptor interaction between a tertiary amine and an aldehyde, first observed among a select class of alkaloids, was deliberately established in a peptidomimetic (1a-c) to mimic features of the two principal transition states of peptide hydrolysis. Compounds 1a-c show preferential adoption in methanol and wa...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2006.01.031

    authors： Gautier A,Pitrat D,Hasserodt J

    更新日期：2006-06-01 00:00:00

  • Identification of potent farnesoid X receptor (FXR) antagonist showing favorable PK profile and distribution toward target tissues: Comprehensive understanding of structure-activity relationship of FXR antagonists.

    abstract：:Antagonizing transcriptional activity of farnesoid X receptor (FXR) in the intestine has been reported as an effective means for the treatment of nonalcoholic fatty liver disease, type 2 diabetes and obesity. We describe herein that the building blocks necessary to maintain the antagonism of our chemotype were investi...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2019.04.029

    authors： Teno N,Yamashita Y,Masuda A,Iguchi Y,Oda K,Fujimori K,Hiramoto T,Nishimaki-Mogami T,Une M,Gohda K

    更新日期：2019-06-01 00:00:00

  • Chemo-enzymatic synthesis of adenine substituted nicotinic acid adenine dinucleotide phosphate (NAADP) analogs.

    abstract：:Nicotinamide adenine dinucleotide phosphate (NADP) is an indispensable metabolic co-substrate and nicotinic acid adenine dinucleotide phosphate (NAADP) is an important Ca2+ releasing intracellular second messenger. Exploration of the NADP and NAADP interactome often requires the synthesis of NADP derivatives substitut...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2020.115901

    authors： Su P,Bretz JD,Gunaratne GS,Marchant JS,Walseth TF,Slama JT

    更新日期：2021-01-15 00:00:00

  • Stereoselective preparation of pyridoxal 1,2,3,4-tetrahydro-β-carboline derivatives and the influence of their absolute and relative configuration on the proliferation of the malaria parasite Plasmodium falciparum.

    abstract：:We have selectively synthesized by Pictet-Spengler condensation of tryptophan and pyridoxal the four stereoisomers of a pyridoxal β-carboline derivative that was designed to inhibit the proliferation of Plasmodium falciparum. Biological investigation of the four compounds revealed that they all inhibit the growth of P...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2014.01.057

    authors： Brokamp R,Bergmann B,Müller IB,Bienz S

    更新日期：2014-03-15 00:00:00

  • Metronidazole aryloxy, carboxy and azole derivatives: Synthesis, anti-tumor activity, QSAR, molecular docking and dynamics studies.

    abstract：:A series of novel metronidazole aryloxy, carboxy and azole derivatives has been synthesized and their cytotoxic activities on three cancer cell lines were evaluated by MTT assay. Compounds 4m, 4l and 4d showed the most potent cytotoxic activity (IC50s less than 100 µg/mL). Apoptosis was also detected for these compoun...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2018.12.003

    authors： Faghih-Mirzaei E,Sabouri S,Zeidabadinejad L,AbdolahRamazani S,Abaszadeh M,Khodadadi A,Shamsadinipour M,Jafari M,Pirhadi S

    更新日期：2019-01-15 00:00:00

  • The design of a novel near-infrared fluorescent HDAC inhibitor and image of tumor cells.

    abstract：:Histone deacetylases (HDACs) have been found to be biomarkers of cancers and the corresponding inhibitors have attracted much attention these years. Herein we reported a near-infrared fluorescent HDAC inhibitor based on vorinostat (SAHA) and a NIR fluorophore. This newly designed inhibitor showed similar inhibitory ac...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2020.115639

    authors： Huang Y,Ru HB,Bao B,Yu JH,Li J,Zang Y,Lu W

    更新日期：2020-09-01 00:00:00

  • Interaction between artemisinin and heme. A Density Functional Theory study of structures and interaction energies.

    abstract：:Malaria is an infectious disease caused by the unicellular parasite Plasmodium sp. Currently, the malaria parasite is becoming resistant to the traditional pharmacological alternatives, which are ineffective. Artemisinin is the most recent advance in the chemotherapy of malaria. Since it has been proven that artemisin...

    journal_title：Bioorganic & medicinal chemistry

    pub_type： 杂志文章

    doi：10.1016/j.bmc.2008.03.033

    authors： Araújo JQ,Carneiro JW,de Araujo MT,Leite FH,Taranto AG

    更新日期：2008-05-01 00:00:00