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A benchmarking study on virtual ligand screening against homology models of human GPCRs [article]

Victor Jun Yu Lim, Weina Du, Yu Zong Chen, Hao Fan
2018 bioRxiv   pre-print
models can be the optimal option in practical applications where X-ray structure is not available and the performance of each model cannot be estimated.  ...  Among the 19 GPCRs involved in this study, we observed that 10 GPCRs have homology models that have better or comparable performance with respect to the corresponding X-ray structures, making homology  ...  Acknowledgement The work was supported by Biomedical Research Council of A*STAR (to Hao Fan and Weina Du), and by the Singapore Academic Research Fund R-148-000-230-112 and R-148-000-239-112 (to Yu Zong  ... 
doi:10.1101/284075 fatcat:55cjl57v4zb25nfyg3cr4kenyy

A benchmarking study on virtual ligand screening against homology models of human GPCRs

Victor Jun Yu Lim, Weina Du, Yu Zong Chen, Hao Fan
2018 Proteins: Structure, Function, and Bioinformatics  
Among the 19 GPCRs involved in this study, we observed that 10 GPCRs have homology models that have better or comparable performance with respect to the corresponding X-ray structures, making homology  ...  However, being a membrane protein, it is difficult to obtain the 3D crystal structures of GPCRs for virtual screening of ligands by molecular docking.  ...  Acknowledgement The work was supported by Biomedical Research Council of A*STAR (to Hao Fan and Weina Du), and by the Singapore Academic Research Fund R-148-000-230-112 and R-148-000-239-112 (to Yu Zong  ... 
doi:10.1002/prot.25533 pmid:30051928 fatcat:ktmqex4vxrh7hgjfa7ouwnr7ga

A Brief View of Molecular Modeling Approaches to P2 Receptors [chapter]

Anael V.P. Alberto, Lucianna H.S. Santos, Rafael Ferreira, Dinarte N.M. Ferreira, Luiz A. Alves
2019 Receptors p1 and p2 as Targets for Drug Therapy in Humans [Working Title]  
Alternatively, in the last 20 years, molecular modeling has emerged as an exciting tool for the design of new drugs, in less time and at low costs.  ...  The general approach applied in the discovery of new drugs is expensive and lengthy.  ...  and two subtypes have been resolved by X-ray crystallography, P2Y1 and P2Y12 [1-3].  ... 
doi:10.5772/intechopen.86862 fatcat:nl6wwutc2zfqha6nl2bfpvbbii

Application of GPCR Structures for Modelling of Free Fatty Acid Receptors [chapter]

Irina G. Tikhonova
2016 Handbook of Experimental Pharmacology  
The recent progress in crystallography of GPCRs has now enabled the elucidation of the structure of FFA1 and provided reliable templates for homology modelling of other FFA receptors.  ...  Analysis of the crystal structure and improved homology models, along with mutagenesis data and structure activity, highlighted an unusual arginine charge pairing interaction in FFA1-3 for receptor modulation  ...  The use of X-ray structural data is now able to provide greater insight into ligand recognition than earlier approaches.  ... 
doi:10.1007/164_2016_52 pmid:27757764 fatcat:2vno7b6omfbobjdq2vdifqsb74

Sequence, Structure and Ligand Binding Evolution of Rhodopsin-Like G Protein-Coupled Receptors: A Crystal Structure-Based Phylogenetic Analysis

Steffen Wolf, Stefan Grünewald, Atsuko Yamashita
2015 PLoS ONE  
So far, 24 receptors have been structurally determined by x-ray protein crystallization .  ...  Furthermore, four receptor structures of non-rhodopsin GPCRs are available as structural models, of which two receptors are from the secretin family [23, 25] , one receptor from the frizzled/taste family  ...  Calculations were performed on the PICB high-performance computing cluster. The Evolutionary Trace Baylor code was kindly provided by Angela Wilkins, Oliver Lichtarge, and Baylor College of Medicine.  ... 
doi:10.1371/journal.pone.0123533 pmid:25881057 pmcid:PMC4399913 fatcat:5gv4ncuq55bu7abxh6ldxgeawy

Identification of Determinants Required for Agonistic and Inverse Agonistic Ligand Properties at the ADP Receptor P2Y12

P. Schmidt, L. Ritscher, E. N. Dong, T. Hermsdorf, M. Coster, D. Wittkopf, J. Meiler, T. Schoneberg
2012 Molecular Pharmacology  
Modification of the ribose within ATP can result in inverse activity of ATP-derived ligands.  ...  The ADP receptor P2Y 12 belongs to the superfamily of G protein-coupled receptors (GPCRs), and its activation triggers platelet aggregation.  ...  Wrote or contributed to the writing of the manuscript: Schmidt, Dong, Meiler, Schöneberg.  ... 
doi:10.1124/mol.112.082198 pmid:23093496 pmcid:PMC3533468 fatcat:cwnpr52t3jgohjwcy44ytqcd3e

Agonist-bound structure of the human P2Y12 receptor

Jin Zhang, Kaihua Zhang, Zhan-Guo Gao, Silvia Paoletta, Dandan Zhang, Gye Won Han, Tingting Li, Limin Ma, Wenru Zhang, Christa E. Müller, Huaiyu Yang, Hualiang Jiang (+6 others)
2014 Nature  
Supplementary Information is linked to the online version of the paper at www.nature.com/nature.  ...  Author information: Atomic coordinates and structure factors for the P2Y 12 R-2MeSADP and P2Y 12 R-2MeSATP structures have been deposited in the Protein Data Bank with identification codes 4PXZ and 4PY0  ...  Data collection, structure solution and refinement X-ray diffraction data were collected at the SPring-8 beam line 41XU, Hyogo, Japan, using a Rayonix MX225HE detector (X-ray wavelength 1.0000 Å).  ... 
doi:10.1038/nature13288 pmid:24784220 pmcid:PMC4128917 fatcat:5uv7h4snubgsjjlvf53rscbzey

The Pro-Gly or Hyp-Gly Containing Peptides from Absorbates of Fish Skin Collagen Hydrolysates Inhibit Platelet Aggregation and Target P2Y12 Receptor by Molecular Docking

Qi Tian, Shi-Ming Li, Bo Li
2021 Foods  
The molecular docking results implied that the OG-containing peptides might target the P2Y12 receptor and form hydrogen bonds with the key sites Cys97, Ser101, and Lys179.  ...  Among them, OGSA has the strongest inhibiting activities against ADP-induced platelet aggregation in vitro (IC50 = 0.63 mM), and OGSA inhibited the thrombus formation in rats at a dose of 200 μM/kg.bw  ...  The X-ray crystal structures of P 2 Y 12 (PDB ID:4PXZ), PLC β2 (PDB ID:2ZKM) and PLC β3 (PDB ID:4GNK) were downloaded from the RCSB protein database.  ... 
doi:10.3390/foods10071553 fatcat:gcbslti2lbaqxklf6iaiiy7gi4

A chemogenomic analysis of the transmembrane binding cavity of human G-protein-coupled receptors

Jean-Sebastien Surgand, Jordi Rodrigo, Esther Kellenberger, Didier Rognan
2005 Proteins: Structure, Function, and Bioinformatics  
the X-ray structure of bovine rhodopsin bound to retinal-to line the TM binding cavity of ground-state receptors.  ...  The amino acid sequences of 369 human nonolfactory G-protein-coupled receptors (GPCRs) have been aligned at the seven transmembrane domain (TM) and used to extract the nature of 30 critical residues supposed-from  ...  Clustering Human GPCRS From 30 Discontinuous Amino Acids The selection of the 30 amino acids was performed as follow: in the X-ray structure of the bovine rhodopsinretinal complex (pdb entry 1f88), 26  ... 
doi:10.1002/prot.20768 pmid:16294340 fatcat:fu3onxrzyvci3kk7tbus2gre7i

Targeting Neutrophil Adhesive Events to Address Vaso-Occlusive Crisis in Sickle Cell Patients

Vasilios A Morikis, Alfredo A Hernandez, John L Magnani, Markus Sperandio, Scott I Simon
2021 Frontiers in Immunology  
Two recently completed clinical trials of therapies targeting selectins and their effect on neutrophil activation in small blood vessels reveal the importance of mechanoregulation that in health is an  ...  of integrin bond clusters that anchor cells to the vessel wall.  ...  A molecular model of E-selectin binding sLe x under tension predicts that it adopts an extended conformation, which was verified by small-angle X-ray scattering of it bound to purified ligand (34) .  ... 
doi:10.3389/fimmu.2021.663886 pmid:33995392 pmcid:PMC8113856 fatcat:mdm6rm5ekzbpjix7rcpwemiz3e

Structure of the human P2Y12 receptor in complex with an antithrombotic drug

Kaihua Zhang, Jin Zhang, Zhan-Guo Gao, Dandan Zhang, Lan Zhu, Gye Won Han, Steven M. Moss, Silvia Paoletta, Evgeny Kiselev, Weizhen Lu, Gustavo Fenalti, Wenru Zhang (+9 others)
2014 Nature  
Data collection and structure solution X-ray data were collected on the 23ID-B/D beamline (GM/CA CAT) at the Advanced Photon Source using a 10 μm mini-beam (at a wavelength of 1.0330 Å) and a MarMosaic  ...  The possibility of multiple binding pockets in the P2Y 12 R structure extends our knowledge of purinoceptor family ligand recognition mechanisms, and will serve as a template for designing improved orthosteric  ... 
doi:10.1038/nature13083 pmid:24670650 pmcid:PMC4174307 fatcat:ymf4oa7xdngznogufsndeeblju

Membrane-Mediated Oligomerization of G Protein Coupled Receptors and Its Implications for GPCR Function

Stefan Gahbauer, Rainer A. Böckmann
2016 Frontiers in Physiology  
Additionally, progress in the structural analysis of GPCR-G protein and GPCR-ligand interactions allows to distinguish between actively functional and non-signaling complexes.  ...  In this review, the association of GPCRs and the role of the membrane in oligomerization will be discussed.  ...  The structure of the related serotonin 5-HT 2B receptor was recently solved using X-ray crystallography and showed a palmitoylated cysteine (Cys397) on H8 (Wacker et al., 2013) .  ... 
doi:10.3389/fphys.2016.00494 pmid:27826255 pmcid:PMC5078798 fatcat:enq3ts4k5rdubbsmojkp3fymwu

Receptor structure-based discovery of non-metabolite agonists for the succinate receptor GPR91

Mette Trauelsen, Elisabeth Rexen Ulven, Siv A. Hjorth, Matjaz Brvar, Claudia Monaco, Thomas M. Frimurer, Thue W. Schwartz
2017 Molecular Metabolism  
Through receptor modeling over the X-ray structure of the closely related P2Y1 receptor, we discovered that the binding pocket is partly occupied by a segment of an extracellular loop and that succinate  ...  All this information formed the basis for a substructure-based search query, which, combined with molecular docking, was used in virtual screening of the ZINC database to pick two serial mini-libraries  ...  The work on metabolite receptors including GPR91 is further supported by an Immunometabolism grant NNF15CC0018346 from the Novo Nordisk Foundation to Oxford University, University of Copenhagen and Karolinska  ... 
doi:10.1016/j.molmet.2017.09.005 pmid:29157600 pmcid:PMC5699910 fatcat:bcgt2owr65gurc54fdcr6iu2yu

G protein-coupled receptors--recent advances

Dorota Latek, Anna Modzelewska, Bartosz Trzaskowski, Krzysztof Palczewski, Sławomir Filipek
2012 Acta Biochimica Polonica  
In 2000 the first GPCR, bovine rhodopsin, was crystallized and the structure was solved, while in 2007 the structure of β(2)-adrenergic receptor, the first GPCR with diffusible ligands, was determined  ...  The ligands, including agonists, antagonists or inverse agonists change the structure of the receptor.  ...  Acknowledgments This work was supported by funding from the National Institutes of Health, USA (EY008061) and the National Center of Science, Poland (DEC2011/03/B/NZ1/03204). K.P. is John H.  ... 
pmid:23251911 pmcid:PMC4322417 fatcat:gagrh766r5ditpf2x3yu6jpcui

Direct and indirect cholesterol effects on membrane proteins with special focus on potassium channels

Florina Zakany, Tamas Kovacs, Gyorgy Panyi, Zoltan Varga
2020 Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids  
and receptors with different domain structures to introduce the general mechanisms of cholesterol action among membrane proteins.  ...  Early studies emphasized the importance of indirect and raft-mediated effects, but improvements in computational and structural imaging techniques allowed the definition of a wide range of functionally  ...  Cholesterol was shown to be directly bound and mediate stabilizing interactions at the dimer interface in X-ray crystallography or cryo-EM structures of A2AR [16] , P2Y12 receptors [24] and mGluR [  ... 
doi:10.1016/j.bbalip.2020.158706 pmid:32247032 fatcat:kew6vnekvbfwhjk4zmvwmbshja
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