This document discusses an in silico discovery approach to identify selective and high affinity inhibitors of the metabotropic glutamate receptor 3 (mGluR3). The researchers created a pharmacophore model of mGluR3 and used it to screen over 18 million drug-like compounds from the ZINC database. Compounds matching the model were docked into the receptor using Autodock Vina software. Over 3 million compounds were tested, with more than 130 having a predicted binding energy below -9.6 kcal/mol. The top 18 compounds below -10 kcal/mol were selected for further analysis in a bioassay to determine potency and selectivity for mGluR3. Preliminary results suggest this in silico
In Silico discovery of Metabotropic Glutamate Receptor-3 (mGluR-3) inhibitorsmaldjuan
This study developed an in silico drug discovery strategy to identify selective inhibitors of the metabotropic glutamate receptor 3 (mGluR3). The researchers created three pharmacophore models of mGluR3 based on known inhibitors and docking simulations. They screened over 18 million drug-like compounds from the ZINC database using the models, identifying over 130 compounds with predicted binding energies below -9.6 kcal/mol. The top 18 compounds below -10.0 kcal/mol were selected for further analysis in a bioassay to determine potency and selectivity for mGluR3. This in silico approach successfully identified several candidate mGluR3 inhibitor compounds for future experimental testing.
In Silico discovery of Metabotropic Glutamate Receptor-3 (mGluR-3) inhibitors...maldjuan
This document summarizes research aiming to discover novel inhibitors of the metabotropic glutamate receptor 3 (mGluR3) using an in silico drug discovery strategy. A pharmacophore model was generated based on a known inhibitor and used to screen a drug-like compound database. Compounds with high predicted binding energies were identified as potential leads. The top hits will be validated experimentally. If successful, this in silico approach could facilitate the development of new therapeutics targeting mGluR3-associated disorders.
This document summarizes a presentation on discovering inhibitors for the histone-lysine N-methyltransferase SETD2 using an in silico approach. It discusses methyltransferases and histone methyltransferases as a potential target. The hypothesis is that selective, high-affinity SETD2 inhibitors can be identified by targeting its SAM binding site. The methodology involves generating pharmacophore models using software and screening databases of compounds. Results show two pharmacophore models and top-hit compounds identified. The conclusions are that the SETD2 binding site is a potential drug target and compounds with high predicted binding energies were identified. Future work involves refining models and testing top compounds in assays.
This report analyzes differential RNA methylation between wild type and FTO knockout mouse midbrain cell lines using MeRIP-Seq data. The study found that FTO targets m6A sites mainly around stop codons and in coding sequences. Differential expression analysis found no significant changes, indicating FTO may not regulate gene expression levels. Gene ontology analysis revealed FTO could regulate mRNAs related to neuronal signal transduction. The study developed an interactive web application using Shiny to allow custom analysis of the data.
Mascot is a software package from Matrix Science that interprets mass spectral data into protein identities.
In this presentation we will study about MASCOT and also on how to use it.
This document provides information on various computational tools and methods for protein identification, characterization, and structure prediction. It discusses tools that use amino acid composition, sequence alignment, peptide mass fingerprinting, and physico-chemical properties to identify proteins. It also describes methods such as Chou-Fasman, GOR, and neural networks that predict protein secondary structure and properties based on amino acid order, propensities, and probabilities.
Mascot is a software search engine that uses mass spectrometry data to identify proteins by comparing observed peptide molecular weights to known peptide databases. It was originally developed in 1993 and improved over time to integrate multiple search methods and databases. Mascot identifies proteins by in silico digesting database proteins with trypsin, comparing resulting peptide masses to experimental data, and calculating probability-based scores to match peptides to the most likely source protein.
In silico discovery of histone methyltranferase 1juancarlosrise
This study investigated potential inhibitors of the histone methyltransferase SETD2 using in silico methods. Two pharmacophore models were generated and used to screen a database of 150,000 compounds, filtering it to 31,669 potential leads. Molecular docking ranked these by predicted binding energy, identifying 58 compounds with binding energies from -9.7 to -9.0 kcal/mol. Further refinement of the models and testing of top-scoring compounds may reveal inhibitors of histone methylation and cancer progression.
In Silico discovery of Metabotropic Glutamate Receptor-3 (mGluR-3) inhibitorsmaldjuan
This study developed an in silico drug discovery strategy to identify selective inhibitors of the metabotropic glutamate receptor 3 (mGluR3). The researchers created three pharmacophore models of mGluR3 based on known inhibitors and docking simulations. They screened over 18 million drug-like compounds from the ZINC database using the models, identifying over 130 compounds with predicted binding energies below -9.6 kcal/mol. The top 18 compounds below -10.0 kcal/mol were selected for further analysis in a bioassay to determine potency and selectivity for mGluR3. This in silico approach successfully identified several candidate mGluR3 inhibitor compounds for future experimental testing.
In Silico discovery of Metabotropic Glutamate Receptor-3 (mGluR-3) inhibitors...maldjuan
This document summarizes research aiming to discover novel inhibitors of the metabotropic glutamate receptor 3 (mGluR3) using an in silico drug discovery strategy. A pharmacophore model was generated based on a known inhibitor and used to screen a drug-like compound database. Compounds with high predicted binding energies were identified as potential leads. The top hits will be validated experimentally. If successful, this in silico approach could facilitate the development of new therapeutics targeting mGluR3-associated disorders.
This document summarizes a presentation on discovering inhibitors for the histone-lysine N-methyltransferase SETD2 using an in silico approach. It discusses methyltransferases and histone methyltransferases as a potential target. The hypothesis is that selective, high-affinity SETD2 inhibitors can be identified by targeting its SAM binding site. The methodology involves generating pharmacophore models using software and screening databases of compounds. Results show two pharmacophore models and top-hit compounds identified. The conclusions are that the SETD2 binding site is a potential drug target and compounds with high predicted binding energies were identified. Future work involves refining models and testing top compounds in assays.
This report analyzes differential RNA methylation between wild type and FTO knockout mouse midbrain cell lines using MeRIP-Seq data. The study found that FTO targets m6A sites mainly around stop codons and in coding sequences. Differential expression analysis found no significant changes, indicating FTO may not regulate gene expression levels. Gene ontology analysis revealed FTO could regulate mRNAs related to neuronal signal transduction. The study developed an interactive web application using Shiny to allow custom analysis of the data.
Mascot is a software package from Matrix Science that interprets mass spectral data into protein identities.
In this presentation we will study about MASCOT and also on how to use it.
This document provides information on various computational tools and methods for protein identification, characterization, and structure prediction. It discusses tools that use amino acid composition, sequence alignment, peptide mass fingerprinting, and physico-chemical properties to identify proteins. It also describes methods such as Chou-Fasman, GOR, and neural networks that predict protein secondary structure and properties based on amino acid order, propensities, and probabilities.
Mascot is a software search engine that uses mass spectrometry data to identify proteins by comparing observed peptide molecular weights to known peptide databases. It was originally developed in 1993 and improved over time to integrate multiple search methods and databases. Mascot identifies proteins by in silico digesting database proteins with trypsin, comparing resulting peptide masses to experimental data, and calculating probability-based scores to match peptides to the most likely source protein.
In silico discovery of histone methyltranferase 1juancarlosrise
This study investigated potential inhibitors of the histone methyltransferase SETD2 using in silico methods. Two pharmacophore models were generated and used to screen a database of 150,000 compounds, filtering it to 31,669 potential leads. Molecular docking ranked these by predicted binding energy, identifying 58 compounds with binding energies from -9.7 to -9.0 kcal/mol. Further refinement of the models and testing of top-scoring compounds may reveal inhibitors of histone methylation and cancer progression.
If you want to know more, please visit https://www.creative-proteomics.com/s...
Stable isotope labeling using amino acids in cell culture (SILAC) is a powerful method based on mass spectrometry that identifies and quantifies relative differential changes in protein abundance. First used in quantitative proteomics in 2002, it provides accurate relative quantification without any chemical derivatization or manipulation.
This document describes a novel database search algorithm for identifying proteins from data independent acquisitions where multiple precursor ions are fragmented simultaneously. The algorithm uses an iterative process to incrementally increase selectivity, specificity, and sensitivity. It accounts for peptide retention time, ion intensities, charge states, and accurate masses of precursors and products. The algorithm was tested on simple and complex protein mixtures and validated independently, demonstrating its ability to correctly identify proteins across a wide dynamic range with high sensitivity and specificity.
This document provides an overview of plant proteomics techniques, including 2D gel electrophoresis, mass spectrometry, and software analysis. 2D gel electrophoresis separates proteins by isoelectric focusing based on pH in the first dimension, followed by SDS-PAGE based on size in the second dimension. Spots are visualized, excised, digested, and identified using mass spectrometry. Software performs matching, detection, quantitation, and annotation of protein spots across gels to identify differentially expressed proteins.
Metabolomics aims to quantify all metabolites in a cellular system. The challenges are chemical complexity and heterogeneity of metabolites, dynamic range of measurements, and throughput. Metabolites can be analyzed using spectroscopy and mass spectrometry coupled with gas or liquid chromatography. NMR provides information on metabolites directly from biofluids with little sample preparation. GC-MS and LC-MS are commonly used, with LC-MS measuring a broader range of primary and secondary metabolites. Data integration and identification of specific metabolites remain challenges.
Peptide Mass Fingerprinting (PMF) and Isotope Coded Affinity Tags (ICAT)Suresh Antre
Analytical technique for identifying unknown protein. The peptide mass are compared to database containing the theoretical peptide masses of all known protein sequences.
Mass Spectrometry-Based Proteomics Quantification: iTRAQ Creative Proteomics
This document discusses iTRAQ (isobaric tag for relative and absolute quantitation), a method for determining the amount of proteins from different sources in a single experiment. It describes the basic structure of iTRAQ reagents, which consist of a unique reporter group, peptide reactive group, and neutral balance group. The principle and workflow of iTRAQ is explained, involving labeling samples with iTRAQ tags, combining samples, performing MS/MS for identification and quantitation. Factors affecting iTRAQ results and its advantages/disadvantages are briefly covered. An example application of iTRAQ to identify tyrosine phosphorylation sites is provided.
Molecular Modeling of Metalloreductase STEAP2 Protein and Docking Interaction...BRNSS Publication Hub
This gene is an individual from the STEAP family and encodes a multipass film protein that confines to the Golgi complex, the plasma layer, and the vesicular cylindrical structures in the cytosol. A very comparative protein in mouse has both ferrireductase and cupric reductase action and invigorates the cell take-up of both iron and copper in vitro. Expanded transcriptional articulation of the human quality is related with prostate malignant growth movement. Substitute transcriptional graft variations, encoding distinctive isoforms, have been described. Therefore, in the present study, we generated a precise three-dimensional (3D) model of metalloreductase STEAP2 protein using MODELLER 9.21 and validated its structure using PROCHECK software. Modeled protein contains more than 94.5% of amino acids in core region. We interpreted the action of natural compounds docking against the modeled metalloreductase STEAP2 protein. Three compounds (ginkgetin, medicagenin, and erybraedin A) showed lower binding affinity values toward metalloreductase STEAP2 protein compared to mitoxantrone, abiraterone acetate, apalutamide, enzalutamide, and flutamide. Ginkgetin exhibited the lowest binding energy of −9.10 kcal/mol with interacting Trp212 and Thr210. All the 17 compounds showed excellent binding energies than standard drugs for the modeled metalloreductase STEAP2 protein. These computational studies can be helpful to discover novel drug candidates.
For more information, you can visit https://www.creative-proteomics.com/services/protein-post-translational-modification-analysis.htm. In this video, we introduce some commonly used methods to detect PPIs and techniques for proteome-scale interactome maps.
A brief introfuction of label-free protein quantification methodsCreative Proteomics
If you want to know more about our services, please visit https://www.creative-proteomics.com/services/label-free-quantification.htm.
Label-free protein quantification is a mass spectrometry-based method for identifying and quantifying relative changes in two or more biological samples instead of using a stable isotope-containing compound to label proteins.
Peptide mass fingerprinting is a technique to identify proteins by breaking them into peptides via enzymatic digestion, measuring the peptide masses using mass spectrometry, and comparing the results to theoretical peptide masses from protein sequence databases to find a match. The key steps are isolating the protein, digesting it into peptides, using MALDI or ESI mass spectrometry to determine peptide masses, running an in silico digestion of protein databases to generate theoretical peptide masses, and comparing the experimental and theoretical masses to identify the protein.
The document discusses peptide mass fingerprinting (PMF), a technique used to identify proteins. PMF involves breaking proteins down into peptides using enzymes like trypsin, then using mass spectrometry to measure the peptides' masses and compare them to theoretical masses from a database to identify the original protein. The key steps are protein digestion, mass measurement using MALDI or ESI, and computational analysis comparing experimental results to databases to output matching protein IDs. PMF allows rapid protein identification and has applications in fields like identifying materials in cultural artifacts by comparing collagen peptide masses to a reference database.
This document discusses various bioinformatics approaches for analyzing molecular interactions, including protein-protein interaction, protein-ligand interaction, docking, pharmacophore, and virtual screening. It provides details on each topic, describing things like how protein-protein interactions occur and are classified, common methods for studying protein-ligand interactions, the basic process and types of docking, and the definition of a pharmacophore. The key topics covered are protein-protein interaction, protein-ligand interaction analysis through methods like docking, and virtual screening using pharmacophore models.
Proteomics is the large-scale study of proteins and how they function. [1] It uses techniques like mass spectrometry and protein chips to study post-translational modifications and interactions that cannot be predicted from genomic data alone. [2] Proteomics provides insights into biological processes by identifying proteins, analyzing modifications, detecting interactions, and comparing expression levels between cell states. [3] Studying proteomics is necessary to understand how genes are functionally expressed at the protein level.
Application of proteomics for identification of abiotic stress tolerance in c...Vivek Zinzala
It is the study of “Proteome”.
The word "proteome" is a blend of "protein" and "genome”.
Large scale study of Proteins.
Particularly their structures and functions.
Study of full set of proteins in a cell type or tissue, and changes during various conditions
The document discusses metabolomics data analysis and issues for biostatistics. It describes the metabolomics pipeline from experimental design and data acquisition to statistical analysis and biological interpretation. Key aspects covered include data preprocessing methods, exploratory and supervised multivariate analysis, and biological interpretation tools like metabolic network inference and pathway analysis. Specific statistical challenges in metabolomics like handling non-detects and exploring variable importance are also addressed.
Unveiling the role of network and systems biology in drug discoverychengcheng zhou
This document reviews recent advances in network and systems biology applied to human health and drug discovery. It discusses how these approaches consider biological targets in their physiological context without losing molecular details. Network biology will be central to developing polypharmacology strategies for complex multi-factorial diseases by altering entire pathways rather than single proteins. Predictive toxicology and drug repurposing are areas where network and systems biology strategies could have an immediate impact on drug discovery.
METABOLOMICS is the systematic study of the small molecular metabolites in a cell, tissue, biofluid, or cell culture media that are the tangible result of cellular processes or responses to an environmental stress.
Simplified receptor based pharmacophore approach to retrieve potent ptp lar i...rajmaha9
Simplified Receptor Based Pharmacophore Approach to Retrieve Potent PTP-LAR Inhibitors Using Apoenzyme
M. Elizabeth Sobhia*
Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S.
Nagar, Punjab 160062, India
Abstract: The design of biological active compounds from the apoenzyme is still a challenging task. Herein a simple yet efficient technique is reported to generate a receptor based pharmacophore solely using a ligand-free protein crystal structure. Human leukocyte antigen-related phosphatase (PTP-LAR) is an apoenzyme and a receptor like transmembrane phosphatase that has emerged as a drug target for diabetes, obesity and cancer. The prior knowledge of the active residues responsible for the mechanism of action of the protein was used to generate the LUDI interaction map. Then, the complement negative image of the binding site was used to generate the pharmacophore features. A unique strategy was
followed to design a pharmacophore query maintaining crucial interactions with all the active residues, essential for the enzyme inhibition. The same query was used to screen several databases consisting of the Specs, IBS, iniMaybridge, NCI and an in-house PTP inhibitor databases. In order to overcome the common bioavailability problem associated with phosphatases, the hits obtained were filtered by Lipinski’s Rule of Five, SADMET properties and validated by docking studies in Glide and GOLD. These docking studies not only suggest the essential ligand binding interactions but also the binding patterns necessary for the LAR inhibition. The ligand pharmacophore mapping studies further validated the
screened protocol and supported that the final screened molecules, presumably, showed potent inhibitory activity.
Subsequently, these molecules were subjected to Derek toxicity predictions and nine new molecules with different
scaffold were obtained as non-toxic PTP-LAR inhibitors. The present prospective strategy is a powerful technique to
identify potent inhibitors using the protein 3D structure alone and is a valid alternative to other structure-based and
random docking approaches.
Metabolomics is the newest hype in the 'omics' family. Although defined as highly important to recent biological research, the analytical science applied is far from acceptable for the majority of publications that appear nowadays. Take a look at our approach to tackle the metabolomics issue, which remains a new name for an old science.
Proteomics is the large-scale study of proteins, including their structures, functions, and interactions. It has become an important technology for understanding biological systems on a global scale. Mass spectrometry plays a key role in proteomic analysis by allowing researchers to identify and characterize proteins and their post-translational modifications like phosphorylation. There are challenges in analyzing post-translational modifications since proteins exist in multiple modified forms, but methods like affinity enrichment and tandem mass spectrometry are used to map modifications and locate them on protein sequences.
cell communications and cellular signalling systems vishnuvishnu priya
This document provides a seminar report on cell communications and cellular signaling systems. It contains an introduction to cellular communication and signaling, different forms of communication between cells, types of signaling, targets of drug action including receptors, ion channels, enzymes and carriers. It discusses cellular aspects related to excitation, contraction and secretion involving calcium regulation and release mechanisms. Finally, it covers conclusions and references. The document provides a comprehensive overview of the key topics in cellular communication and signaling in 3 pages with figures and content organized under headings.
This document discusses signal transduction in cells. It explains that membrane proteins in bacterial cells detect environmental changes and generate signals to trigger responses. In multicellular organisms, cells exchange various signals, such as plant cells responding to growth hormones and sunlight. The document then provides details on the specific and sensitive nature of signal transduction pathways, including different types of receptors and some important signal transduction pathways like G protein-coupled receptors and receptor tyrosine kinases. It also discusses two-component regulatory systems in bacteria and plants.
If you want to know more, please visit https://www.creative-proteomics.com/s...
Stable isotope labeling using amino acids in cell culture (SILAC) is a powerful method based on mass spectrometry that identifies and quantifies relative differential changes in protein abundance. First used in quantitative proteomics in 2002, it provides accurate relative quantification without any chemical derivatization or manipulation.
This document describes a novel database search algorithm for identifying proteins from data independent acquisitions where multiple precursor ions are fragmented simultaneously. The algorithm uses an iterative process to incrementally increase selectivity, specificity, and sensitivity. It accounts for peptide retention time, ion intensities, charge states, and accurate masses of precursors and products. The algorithm was tested on simple and complex protein mixtures and validated independently, demonstrating its ability to correctly identify proteins across a wide dynamic range with high sensitivity and specificity.
This document provides an overview of plant proteomics techniques, including 2D gel electrophoresis, mass spectrometry, and software analysis. 2D gel electrophoresis separates proteins by isoelectric focusing based on pH in the first dimension, followed by SDS-PAGE based on size in the second dimension. Spots are visualized, excised, digested, and identified using mass spectrometry. Software performs matching, detection, quantitation, and annotation of protein spots across gels to identify differentially expressed proteins.
Metabolomics aims to quantify all metabolites in a cellular system. The challenges are chemical complexity and heterogeneity of metabolites, dynamic range of measurements, and throughput. Metabolites can be analyzed using spectroscopy and mass spectrometry coupled with gas or liquid chromatography. NMR provides information on metabolites directly from biofluids with little sample preparation. GC-MS and LC-MS are commonly used, with LC-MS measuring a broader range of primary and secondary metabolites. Data integration and identification of specific metabolites remain challenges.
Peptide Mass Fingerprinting (PMF) and Isotope Coded Affinity Tags (ICAT)Suresh Antre
Analytical technique for identifying unknown protein. The peptide mass are compared to database containing the theoretical peptide masses of all known protein sequences.
Mass Spectrometry-Based Proteomics Quantification: iTRAQ Creative Proteomics
This document discusses iTRAQ (isobaric tag for relative and absolute quantitation), a method for determining the amount of proteins from different sources in a single experiment. It describes the basic structure of iTRAQ reagents, which consist of a unique reporter group, peptide reactive group, and neutral balance group. The principle and workflow of iTRAQ is explained, involving labeling samples with iTRAQ tags, combining samples, performing MS/MS for identification and quantitation. Factors affecting iTRAQ results and its advantages/disadvantages are briefly covered. An example application of iTRAQ to identify tyrosine phosphorylation sites is provided.
Molecular Modeling of Metalloreductase STEAP2 Protein and Docking Interaction...BRNSS Publication Hub
This gene is an individual from the STEAP family and encodes a multipass film protein that confines to the Golgi complex, the plasma layer, and the vesicular cylindrical structures in the cytosol. A very comparative protein in mouse has both ferrireductase and cupric reductase action and invigorates the cell take-up of both iron and copper in vitro. Expanded transcriptional articulation of the human quality is related with prostate malignant growth movement. Substitute transcriptional graft variations, encoding distinctive isoforms, have been described. Therefore, in the present study, we generated a precise three-dimensional (3D) model of metalloreductase STEAP2 protein using MODELLER 9.21 and validated its structure using PROCHECK software. Modeled protein contains more than 94.5% of amino acids in core region. We interpreted the action of natural compounds docking against the modeled metalloreductase STEAP2 protein. Three compounds (ginkgetin, medicagenin, and erybraedin A) showed lower binding affinity values toward metalloreductase STEAP2 protein compared to mitoxantrone, abiraterone acetate, apalutamide, enzalutamide, and flutamide. Ginkgetin exhibited the lowest binding energy of −9.10 kcal/mol with interacting Trp212 and Thr210. All the 17 compounds showed excellent binding energies than standard drugs for the modeled metalloreductase STEAP2 protein. These computational studies can be helpful to discover novel drug candidates.
For more information, you can visit https://www.creative-proteomics.com/services/protein-post-translational-modification-analysis.htm. In this video, we introduce some commonly used methods to detect PPIs and techniques for proteome-scale interactome maps.
A brief introfuction of label-free protein quantification methodsCreative Proteomics
If you want to know more about our services, please visit https://www.creative-proteomics.com/services/label-free-quantification.htm.
Label-free protein quantification is a mass spectrometry-based method for identifying and quantifying relative changes in two or more biological samples instead of using a stable isotope-containing compound to label proteins.
Peptide mass fingerprinting is a technique to identify proteins by breaking them into peptides via enzymatic digestion, measuring the peptide masses using mass spectrometry, and comparing the results to theoretical peptide masses from protein sequence databases to find a match. The key steps are isolating the protein, digesting it into peptides, using MALDI or ESI mass spectrometry to determine peptide masses, running an in silico digestion of protein databases to generate theoretical peptide masses, and comparing the experimental and theoretical masses to identify the protein.
The document discusses peptide mass fingerprinting (PMF), a technique used to identify proteins. PMF involves breaking proteins down into peptides using enzymes like trypsin, then using mass spectrometry to measure the peptides' masses and compare them to theoretical masses from a database to identify the original protein. The key steps are protein digestion, mass measurement using MALDI or ESI, and computational analysis comparing experimental results to databases to output matching protein IDs. PMF allows rapid protein identification and has applications in fields like identifying materials in cultural artifacts by comparing collagen peptide masses to a reference database.
This document discusses various bioinformatics approaches for analyzing molecular interactions, including protein-protein interaction, protein-ligand interaction, docking, pharmacophore, and virtual screening. It provides details on each topic, describing things like how protein-protein interactions occur and are classified, common methods for studying protein-ligand interactions, the basic process and types of docking, and the definition of a pharmacophore. The key topics covered are protein-protein interaction, protein-ligand interaction analysis through methods like docking, and virtual screening using pharmacophore models.
Proteomics is the large-scale study of proteins and how they function. [1] It uses techniques like mass spectrometry and protein chips to study post-translational modifications and interactions that cannot be predicted from genomic data alone. [2] Proteomics provides insights into biological processes by identifying proteins, analyzing modifications, detecting interactions, and comparing expression levels between cell states. [3] Studying proteomics is necessary to understand how genes are functionally expressed at the protein level.
Application of proteomics for identification of abiotic stress tolerance in c...Vivek Zinzala
It is the study of “Proteome”.
The word "proteome" is a blend of "protein" and "genome”.
Large scale study of Proteins.
Particularly their structures and functions.
Study of full set of proteins in a cell type or tissue, and changes during various conditions
The document discusses metabolomics data analysis and issues for biostatistics. It describes the metabolomics pipeline from experimental design and data acquisition to statistical analysis and biological interpretation. Key aspects covered include data preprocessing methods, exploratory and supervised multivariate analysis, and biological interpretation tools like metabolic network inference and pathway analysis. Specific statistical challenges in metabolomics like handling non-detects and exploring variable importance are also addressed.
Unveiling the role of network and systems biology in drug discoverychengcheng zhou
This document reviews recent advances in network and systems biology applied to human health and drug discovery. It discusses how these approaches consider biological targets in their physiological context without losing molecular details. Network biology will be central to developing polypharmacology strategies for complex multi-factorial diseases by altering entire pathways rather than single proteins. Predictive toxicology and drug repurposing are areas where network and systems biology strategies could have an immediate impact on drug discovery.
METABOLOMICS is the systematic study of the small molecular metabolites in a cell, tissue, biofluid, or cell culture media that are the tangible result of cellular processes or responses to an environmental stress.
Simplified receptor based pharmacophore approach to retrieve potent ptp lar i...rajmaha9
Simplified Receptor Based Pharmacophore Approach to Retrieve Potent PTP-LAR Inhibitors Using Apoenzyme
M. Elizabeth Sobhia*
Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S.
Nagar, Punjab 160062, India
Abstract: The design of biological active compounds from the apoenzyme is still a challenging task. Herein a simple yet efficient technique is reported to generate a receptor based pharmacophore solely using a ligand-free protein crystal structure. Human leukocyte antigen-related phosphatase (PTP-LAR) is an apoenzyme and a receptor like transmembrane phosphatase that has emerged as a drug target for diabetes, obesity and cancer. The prior knowledge of the active residues responsible for the mechanism of action of the protein was used to generate the LUDI interaction map. Then, the complement negative image of the binding site was used to generate the pharmacophore features. A unique strategy was
followed to design a pharmacophore query maintaining crucial interactions with all the active residues, essential for the enzyme inhibition. The same query was used to screen several databases consisting of the Specs, IBS, iniMaybridge, NCI and an in-house PTP inhibitor databases. In order to overcome the common bioavailability problem associated with phosphatases, the hits obtained were filtered by Lipinski’s Rule of Five, SADMET properties and validated by docking studies in Glide and GOLD. These docking studies not only suggest the essential ligand binding interactions but also the binding patterns necessary for the LAR inhibition. The ligand pharmacophore mapping studies further validated the
screened protocol and supported that the final screened molecules, presumably, showed potent inhibitory activity.
Subsequently, these molecules were subjected to Derek toxicity predictions and nine new molecules with different
scaffold were obtained as non-toxic PTP-LAR inhibitors. The present prospective strategy is a powerful technique to
identify potent inhibitors using the protein 3D structure alone and is a valid alternative to other structure-based and
random docking approaches.
Metabolomics is the newest hype in the 'omics' family. Although defined as highly important to recent biological research, the analytical science applied is far from acceptable for the majority of publications that appear nowadays. Take a look at our approach to tackle the metabolomics issue, which remains a new name for an old science.
Proteomics is the large-scale study of proteins, including their structures, functions, and interactions. It has become an important technology for understanding biological systems on a global scale. Mass spectrometry plays a key role in proteomic analysis by allowing researchers to identify and characterize proteins and their post-translational modifications like phosphorylation. There are challenges in analyzing post-translational modifications since proteins exist in multiple modified forms, but methods like affinity enrichment and tandem mass spectrometry are used to map modifications and locate them on protein sequences.
cell communications and cellular signalling systems vishnuvishnu priya
This document provides a seminar report on cell communications and cellular signaling systems. It contains an introduction to cellular communication and signaling, different forms of communication between cells, types of signaling, targets of drug action including receptors, ion channels, enzymes and carriers. It discusses cellular aspects related to excitation, contraction and secretion involving calcium regulation and release mechanisms. Finally, it covers conclusions and references. The document provides a comprehensive overview of the key topics in cellular communication and signaling in 3 pages with figures and content organized under headings.
This document discusses signal transduction in cells. It explains that membrane proteins in bacterial cells detect environmental changes and generate signals to trigger responses. In multicellular organisms, cells exchange various signals, such as plant cells responding to growth hormones and sunlight. The document then provides details on the specific and sensitive nature of signal transduction pathways, including different types of receptors and some important signal transduction pathways like G protein-coupled receptors and receptor tyrosine kinases. It also discusses two-component regulatory systems in bacteria and plants.
The document is a presentation on pharmacodynamics given by Megh Vithalkar. It discusses the history of receptor theory, defines receptors and describes the main types - ion channel receptors, G-protein coupled receptors, kinase-linked receptors and intracellular receptors. It also covers the classification of receptor subtypes based on pharmacological criteria, tissue distribution, ligand binding, transducer pathways and molecular cloning. The key difference between drug action and drug effect is explained. The presentation provides an overview of important concepts in receptor pharmacology.
1. Toxicology is the study of the biochemical and physiological effects of toxicants on the body and their mechanisms of action, focusing on interactions with target sites. Two factors that determine effect are affinity, how tightly a toxicant binds to a receptor, and intrinsic activity, its ability to activate the receptor and produce a cellular response.
2. Receptors are membrane proteins that toxicants bind to in order to produce effects. There are four main classes of receptors: ligand-gated ion channels, G-protein coupled receptors, enzymatic receptors, and receptors that regulate DNA transcription.
3. G-protein coupled receptors are the largest family and activate distinct effector proteins through G-proteins. Their activation
Shubham Sharma presented on the principles of pharmacodynamics at G.H.G Khalsa College of Pharmacy. Pharmacodynamics is the study of how drugs act on the body, including their biochemical and physiological effects. Drugs can act at the molecular, cellular, tissue and system levels. The main types of molecular drug targets include receptors, enzymes, ion channels, and nucleic acids. Drugs typically work by either directly binding to receptors or altering the activity of enzymes and ion channels. The main classes of receptors that drugs can target are ligand-gated ion channels, G-protein coupled receptors, enzyme-linked receptors, and nuclear receptors.
The document discusses drug receptors and their interactions. It provides an overview of receptor occupation theory and the two-state receptor model. It describes the different types of receptors including physiological, orphan, and silent receptors. It outlines the criteria used to classify receptors such as pharmacological, tissue distribution, ligand binding, transducer pathways, and molecular cloning. The major transducer mechanisms are ligand gated ion channels, G-protein coupled receptors, kinase-linked receptors, and nuclear receptors. Specific examples like nicotinic acetylcholine receptors and their mechanisms and clinical significance are explained.
This presentation is about the functioning of G-Protein coupled receptors. It also gives necessary information about the G-protein and it functions. It ends by explaining some of the faults associated with GPCR (G-PROTEIN COUPLED RECEPTORS).
Receptors are macromolecular components of cells that interact with drugs and initiate biochemical events leading to the drug's effects. The main types are ligand-gated ion channels, G protein-coupled receptors, kinase-linked receptors, and nuclear receptors. Ligand-gated ion channels allow ion flow in response to ligand binding. G protein-coupled receptors signal via intracellular G proteins and second messengers. Kinase-linked receptors activate intracellular kinase cascades. Nuclear receptors regulate gene transcription as ligand-activated transcription factors in the nucleus. Together these receptor types mediate diverse drug actions in important physiological systems.
This document discusses different types of receptors and how they transmit signals. It describes two main domains of receptors - a recognition domain that binds hormones and a coupling domain that generates an intracellular signal. It also discusses three types of cell surface receptors - ion channel receptors, transmembrane receptors, and receptors that are kinases or bind kinases. Steroid hormones can directly activate genes by diffusing into the cell and binding intracellular receptors, which then bind DNA and activate transcription.
This document provides an overview of signal transduction mechanisms. It discusses various types of receptors including G protein-coupled receptors, receptor tyrosine kinases, integrins, toll-like receptors and ligand-gated ion channels. It describes how extracellular ligands bind to cell surface receptors and initiate intracellular signaling pathways such as the cAMP pathway and phosphatidylinositol pathway. Defects in these signaling pathways can lead to diseases. The document provides details on the mechanisms of G protein-coupled receptor signaling and downstream effects.
In biology, cell signaling is part of any communication process that governs basic activities of cells and coordinates multiple-cell actions. The ability of cells to perceive and correctly respond to their microenvironment is the basis of development, tissue repair, and immunity, as well as normal tissue homeostasis.
RECEPTORS AS BIOLOGCAL DRUG TARGETS ppt.pptxosmanshaheen
Receptors are biological molecules that bind to specific ligands or drugs to produce a cellular response. There are several types of receptors including cell surface receptors like G-protein coupled receptors and receptor tyrosine kinases, as well as intracellular receptors. When a ligand binds to a receptor, it causes a conformational change in the receptor that propagates a signal through various pathways to produce an effect in the cell. Agonists mimic endogenous ligands to activate receptors, while antagonists bind receptors but prevent activation. The binding of ligands is influenced by various chemical forces including covalent, electrostatic, and hydrophobic interactions. Receptors are important drug targets, and understanding their functions and binding properties is essential for drug development.
Pharmacodynamics (PD) is the study of the biochemical and physiologic effects of drugs (especially pharmaceutical drugs). The effects can include those manifested within animals (including humans), microorganisms, or combinations of organisms (for example, infection).
Pharmacodynamics and pharmacokinetics are the main branches of pharmacology, being itself a topic of biology interested in the study of the interactions between both endogenous and exogenous chemical substances with living organisms.
Mechanism of drug action, Relationship between drug conc & effect, Receptors, Structural & families of receptors, Quantitation of drug receptor interaction & elicited effects
The document discusses how immunologists have recently rediscovered the importance of metabolism in immune cell function. Technological advances like metabolomics have allowed researchers to better understand how metabolic pathways are directly linked to immune cell effector functions. The review will provide an overview of six major metabolic pathways (glycolysis, TCA cycle, pentose phosphate pathway, fatty acid oxidation, fatty acid synthesis, amino acid metabolism) and their roles in immune cells like T cells, macrophages, and dendritic cells. It aims to encourage immunologists to incorporate the perspective of immunometabolism into their research.
Cell signaling(signaling through g protien coupled receptors,signal transduct...Senthura Pandi
Cell signaling involves the communication between cells through chemical signals or direct cell contact. There are four main types of chemical signaling: paracrine (between nearby cells), autocrine (a cell signaling itself), endocrine (over long distances via hormones), and direct contact signaling through structures like gap junctions. G-protein coupled receptors (GPCRs) are the largest family of receptors and detect extracellular molecules, activating intracellular signaling pathways. Upon ligand binding, GPCRs activate G proteins which function as molecular switches to transmit signals within the cell via second messengers like cAMP, IP3 and calcium. This leads to functional changes in the target cell.
Our cells are filled with intracellular and surface cell receptors (.docxaman341480
Our cells are filled with intracellular and surface cell receptors (Berg & Clarke, 2018). These receptor proteins are delineated by structure and bind to a variety of substances responsible for creating a reaction or lack thereof. When a ligand binds to the appropriate receptor, signal transduction activates the receptor and produces a biological response ( Berg & Clarke, 2018). Changes in shape or activity after binding allow signal transmission outside the cell or significant changes within the cell, creating an altered chemical when binding to a ligand-gated-ion channel ( Berg & Clarke, 2018). This post will discuss the agonist/ antagonist spectrum of psychopharmacological agents, G-proteins and ion-gated channels, and epigenetics and their relevance to practice.
Agonists act like ligands, binding to receptors and causing action (Berg & Clarke, 2018). Ligands or agonists consist of pharmaceuticals, drugs, light, hormones, and nerve impulses. Ligands and agonists jump in and out of receptors, increasing signaling or changes in the cell. Antagonists block the standard action of ligands, preventing a response from the receptor (Berg & Clarke, 2018). Competitive antagonists bind to receptors and prevent ligands from attaching to its preferred receptor, inhibiting stimulation, and leaving the receptor unchanged (Berg & Clarke, 2018). Naloxone is a competitive antagonist to opiate receptors London, 2017). The naloxone has a stronger affinity for the receptor, making it more desirable. The medication discontinues the effects of the opiates by taking their place on the receptor. The higher the dose of opiates circulating the more naloxone required. Due to the excess amount of continued competition for receptors, some patients require multiple doses of naloxone before regaining the ability to breath or regain consciousness (London, 2017).
G-protein coupled receptors (GPCRs) target 30-50% of psychotropic medications (Stahl, 2013). As the most abundant protein family, GPCR ligands include neurotransmitters such as serotonin, norepinepherine, and dopamine. After aligand binds to a GPCR, the GPCR undergoes a conformational change (London, 2017). Alpha subunit exchanges Guanyl nucleotide phosphates, GTP, GPP, and Alpha unit disassociates and regulates target proteins (London, 2017). Regulation of neurotransmission is imperative in medication management (London, 2017). The target proteins can then relay signals via a second messenger, and GTP is finally hydrolyzed to GPP (Lambert, 2004). G-protein receptors tend to have a delay in effect due to a requirement for the accumulation of changed cellular function (London, 2017).
Ion gated channel linked receptors open and close in response to a chemical message changing signal transduction in the synaptic cleft. These ion channels act like pores in the cellular membrane to allow ion passage (Stahl, 2013). Transmembrane ion channels open and close in response to the binding of a ligand, dif.
The document discusses different types of receptors and how they function. It describes transmembrane receptors like G protein-coupled receptors and ionotropic receptors. It also discusses intracellular receptors like nuclear receptors and receptor tyrosine kinases. The key concepts covered are how ligands bind to receptors and the downstream cell signaling pathways that are activated, including G proteins, second messengers like cAMP and IP3/DAG, and transcriptional regulation. Receptor properties like affinity, efficacy, desensitization, and regulation are also summarized.
The document discusses three types of cell signaling:
1) Autocrine signaling occurs when a cell produces a messenger that stimulates receptors on its own surface.
2) Paracrine signaling involves messenger molecules that travel short distances to stimulate nearby cells.
3) Endocrine signaling uses messenger molecules that travel long distances through the bloodstream to target distant cells.
Similar to In Silico discovery of Metabotropic Glutamate Receptor-3 (mGluR-3) inhibitors Report (20)
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Juan Enrique Maldonado Weng is a biology major pursuing a PhD in Neuroscience. He has experience with cell cultures, biological assays, and virtual drug discovery from his undergraduate research. This includes work with an in silico drug discovery team and conducting cell culture work and assays as an intern. He has presented a poster on his research at the Annual Biomedical Research Conference for Minority Students.
1) The document discusses using in silico research to inhibit the methyltransferase enzyme of dengue virus, which is essential for viral replication.
2) Through virtual screening of chemical databases, the researchers identified 25 compounds predicted to bind tightly to the enzyme's GTP binding site with higher affinity than GTP.
3) The top 3 compounds were selected for testing, with DENV-M2_1 showing the highest binding affinity and occupying the active site similarly to how GTP binds. This supports inhibiting the enzyme's function through competitive binding, validating the hypothesis.
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This document contains summaries of three laboratory assignments from a biomedical techniques course at the University of Puerto Rico - Cayey. The first summary describes learning about nanotechnology and observing nano fibers using an electron microscope. The second discusses using nanoparticles and affinity chromatography to isolate specific proteins, then using SDS-Page gel electrophoresis to measure the results. The third summary explains how computer programs help researchers visualize proteins and compare them to databases to understand protein-protein interactions and design new drugs.
This document contains summaries from three laboratory workshops:
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1. Korean researchers used a new technique called rRT-PCR to test for the presence of Borna Disease Virus (BDV) antibodies or RNA in the blood cells of 198 psychiatric patients and 60 healthy controls.
2. The study found that none of the patients tested positive for BDV using this method.
3. However, the results were inconclusive due to uncertainties in the methodology, such as the researchers' experience with the new technique and a lack of validation or follow up testing. More research is still needed to fully understand the potential relationship between BDV and schizophrenia.
1. Korean researchers used rRT-PCR to test for Borna Disease Virus (BDV) antibodies and RNA in peripheral blood mononuclear cells of 60 healthy and 198 psychiatric patients, including 60 with schizophrenia and 138 with other conditions.
2. All patients tested negative for BDV. However, the results were inconclusive due to uncertainties in the methodology, such as success rate and the researchers' experience with the new rRT-PCR technique.
3. More research is needed using improved methods to track the virus in order to determine if BDV could be linked to schizophrenia or other psychiatric conditions.
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1) Korean researchers used rRT-PCR to test for Borna Disease Virus (BDV) antibodies and RNA in peripheral blood mononuclear cells of 60 healthy and 198 psychiatric patients, including 60 with schizophrenia and 138 with other conditions.
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3) More research is needed using improved methods to trace the virus in patients in order to determine if BDV could be linked to schizophrenia or other psychiatric conditions.
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This summary provides the key details from the annotated bibliography in 3 sentences:
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EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...Sérgio Sacani
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
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were carried out using the ACIS-Extract software.
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photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
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In Silico discovery of Metabotropic Glutamate Receptor-3 (mGluR-3) inhibitors Report
1. In Silico discovery of Metabotropic Glutamate Receptor-3 (mGluR-3) inhibitors
Juan E. Maldonado Weng1
, Walter I. Silva, PhD.2
and Héctor M. Maldonado, PhD.3
1
Universidad de Puerto Rico, Cayey, Puerto Rico; 2
University of Puerto Rico, Medical Science Campus; 3
Universidad
Central del Caribe, Medical School
Abstract
Glutamate is an excitatory neurotransmitter associated with many important brain functions. The metabotropic glutamate receptor3
(mGluR3) is an inhibitory auto-receptor that regulates glutamate presynaptic release through the use of G proteins. Although still a
controversial topic, a large number of scientific reports have suggested that this receptor is associated with many neurological disorders,
including a variety of psychiatric conditions. Discovery of highly selective mGluR3 (small chemical compounds) antagonists could lead
to more conclusive evidence since most of the currently available inhibitors target both mGluR2 and mGluR3. Moreover, drug-like
compounds with high affinity and selectivity for this receptor will have broad potential as psychopharmacological agents that can be
useful for treatment of several psychiatric conditions. In the other hand, advances in computer hardware and software have allowed
for the rapid development of computer-aid “In Silico” methodologies for the screening of large databases of small chemical compounds.
Therefore, as part of this research project we are testing the hypothesis that: “Selective and high affinity inhibitors of mGluR-3 can be
found using our Drug Discovery Strategy based on our novel “In Silico” approach”. We employed this innovative In Silico methodology
for the screening of a massive quantity of drug-like small chemical compounds for possible candidates with high affinity for the target
receptor. To that end, the 3D structure of the target receptor was analyzed for potential for chemical interactions or features. A
pharmacophore model was created (Ligand Scout software) based on those predicted features and used to filter (ZincPharmer
pharmacophore search software; zincpharmer.csb.pitt.edu/) a large (>18 million) drug-like compounds (ZINC drug-like database;
www.zinc.org), and only compounds fulfilling all requirements imposed by the model where selected for further analysis. Docking of
the selected group of compounds where performed in a high performance computer facility (UPR-HPCf; www.hpcf.upr.edu/) with the
aid of Autodock Vina software. Results from this part of the study where organized and compounds ranked according to their predicted
binding energy. Over three million compounds where tested with >130 compounds found to have a predicted binding energy below -
9.6 kcal/mol. From this group we have selected the top 18 compounds (binding energies below -10.0 kcal/mol) for further analysis in a
bioassay for potency and selectivity for mGluR3 receptor. Based on these preliminary results we can conclude that our In Silico approach
has resulted in the identification of several compounds as candidates for metabotropic glutamate receptor 3 inhibitors. Potency and
selectivity of these compounds remains to be determined in future studies employing an appropriate bioassay.
I. Background
Glutamate
Glutamate is an important neurotransmitter that plays major roles in the Central Nervous
System. This neurotransmitter is an ionized state of glutamic acid and very abundant in human
brains. A glutamate vesicle contains a concentration of up to 100mmol/L. This release of
glutamate results in an excitatory postsynaptic potential which leads to other signal pathways
(Meldrum 2000). Additionally, glutamate is classified as an excitatory neurotransmitter for its
capacity to cause powerful responses in neurons. Its excitatory abilities are utilized in many
pathways to create fast and responsive stimuli.
Glutamate has key roles in many functions that are necessary for development such as learning
and memory (Meyer, 2013). This neurotransmitter has part in neuronal differentiation and
survival in brain development. Furthermore, this important characteristic of glutamate is the
result of permitting the entry of calcium ions (Meldrum 2000). Glutamate has also been thought
to be involved in numerous neurodegenerative conditions such as schizophrenia, Alzheimer’s,
and amyotrophic lateral sclerosis (ALS) (Meyer 2013 & O'Brien 2014).
2. Maldonado 2
Receptors
Once released into the synapsis, glutamate can activate a broad range of receptors. The two
main classifications of glutamate receptors are Ionotropic and Metabotropic. Ionotropic-type
receptors are fast acting receptors with ion channels that are modulated by the presence of
specific neurotransmitters. Glutamate receptors are usually not highly selective and can interact
with other agonists with more selectivity. Those that would be placed into this category include:
AMPA, kainate and NMDA receptors. These receptors require the selective agonist for which
they are named after, as well as glutamate. These allow Na+ to enter the cell through their ion
channel; with exception of NMDA, which permits influx of both Na+ and Ca2+ (Meyer, 2013).
Glutamate can also interact with metabotropic-type receptors. Metabotropic receptors are a
slower type of receptors that are usually associated with prolonged stimulus. Moreover, these
receptors utilize second-messenger systems, where activation of the main protein causes a G
protein to carry on the message or function. These receptors share a common particular
morphology. Metabotropic glutamate receptors have similar seven trans-membrane domains,
N-terminal, and intracellular COOH terminal such as other G protein linked receptors (Meldrum,
2000). These receptors respond to glutamate and carry out their signal functions by manner of
the G-protein reactions. A total of eight (8) metabotropic glutamate receptors (mGluR) have been
described and further sub-divided into three groups (mGluR I, II, III) based on molecular identity
and type of signal transduction system activated. Activation of members of the metabotropic
glutamate receptors Group I can result in either increases in intracellular Ca++ concentration
(mGluR1) or activation of K+ ion channels (mGluR2). Members of Group II (mGluR2 and mGluR3)
are associated with inhibition of adenylyl cyclase that can result in reductions cAMP levels.
Finally, members of Group III metabotropic glutamate receptors (mGluR4, mGluR6, mGluR7,
mGluR8), are known to activate Ca++ channels, allowing influx of calcium inside the cells.
Furthermore, some of these receptors have an inhibitory effect on glutamate release, which in
turn manipulate the amount of glutamate in the synapse. These receptors have a wide array of
functions and roles in the synapse and within neurons and therefore can modulate a wide range
of physiological effects. As they are found widely distributed throughout the brain, many more
roles have been link to the metabotropic Glutamate Receptors.
Group II metabotropic glutamate receptors are located in both presynaptic and postsynaptic
neurons serving a variety of different functions. Presynaptic receptors belonging to this group
function as glutamate release inhibitors while as post-synaptic receptors, they serve as cAMP
formation inhibitors, which in turn could affect metabolism. Furthermore, they are also known
to activate MAPK (mitogen-activated protein kinase) and phosphatidylinositol-3-kinase
pathways, which will also lead to the synthesis of transforming growth factor-β (TGF- β).
Fortunately, this synthesis protects neurons from being overly excited from neurotransmitters
(retracted). In addition, they also regulate ion channels through the liberation of Gβγ subunits
(Conn 2010). Through their many functions, mGluR II are necessary components for many
cellular mechanisms.
The metabotropic glutamate receptor 3 (mGluR3) has been found to be associated with various
mental disorders. Chemical compounds with potential to exert pharmacological actions as
3. Maldonado 3
agonists, antagonists, or allosteric modulators of this receptor are currently been evaluated for
clinical applications. Examples include agonists like LY354740 with potential in the treatment of
anxiety and drug addiction (Monn 1997), and LY341495 an antagonist with antidepressant
properties (Pilc 2008). Group II mGlu-Receptors antagonists have been found to have positive
anti-depressant effects with a yet to be fully understood mechanism. Also, a study is looking to
affect the receptor through allosteric modulation (Campo 2011). Beneficially, a more selective
compound provides a more precise understanding of each receptor.
In Silico Discovery Approach
Utilizing our technological system, the receptor will be analyzed and compared against the many
compounds in the “Zinc Pharmer” database (Koes 2012). A pharmacophore model will be
created and will represent all the chemical features of the receptor. A pharmacophore model can
utilize two different methods to recreate the receptor: ligand-based or structure-based method.
The ligand-based method utilizes a set of known ligands. Alternately, structure-based method
use protein-ligand complex from readily available files to construct the model (Vourinen 2015).
A pharmacophore modeling software will construct the receptor model based on chemical traits
and prepare it for virtual screening process. Virtual screening process will provide lists of
numerous compounds readily available for further analysis. This would provide the candidates
for the receptor. The purpose of screening in 3D databases is to find compounds or hits with
similar chemical traits (Yang 2010).
The protein-ligand interaction will be heavily studied as the database will contain several
thousands of candidates. This would require the assistance of a high performance computer to
process the heavy amount of data. With the aid of high performance computing (Scholz 2012),
drug discovery has evolved with the addition of sophisticated drug design and high throughput
statistical algorithms ranking by order of potential potency numerous candidates for testing.
II. Methodology
As stated previously, this investigation will be carried out mostly In Silico. Fundamentally,
all results and procedures will hinge on computer processing power. This research design will
focus on compounds that interact with the virtually targeted receptor.
Firstly, since the method of modeling will be based on the protein-ligand complex designs,
the complex must be first obtained. The Protein Database (www.rcsb.org) will be the source for
obtaining the model. The mGluR3 receptor model that will be utilized was crystalized by
Wernimont and team (To be published). The mGluR3 is available with the compound LY341495
(Monn 1996). This compound is a known mGluR2/3 agonist. The model containing both
structures will be in a PDB format. PyMol (www.pymol.org) is the software where the model will
be first viewed. This program has the capacity to interpret all amino acids composing the
structure and the unique antagonist. This software will also separate the complex and save them
each as individual files.
Having separated the compound, the receptor is now available to be analyzed by
AutoDock (Morris 2009). This advanced software is capable computing a grid parameter file that
4. Maldonado 4
would predict ligand interactions. The UPR-High Performance Computer Facility (HPCf) systems
will execute a benzene mapping analysis utilizing the receptor file and the grid parameter
configuration file. AutoDock Vina (Trott 2009) software will carry out this function within the high
performance computer. AutoDock Vina is a successful docking program accredited for its high
accuracy and better scoring system (Trott 2010).
The result of this step would be a file containing a hundred or more different benzene
locations. These results are stored within one special file and will be retrieved from the HPCf.
These different configurations could easily be seen through PyMol. The model will be littered
with benzenes within the parameters of the grid made previously. Some benzenes will be in
clusters sharing similar locations within the receptor. The most efficient way to analyze these
results is to separate them into individual files and to choose the best benzene files that represent
those location-sharing benzene clusters. These selected benzenes will be utilized to form the
pharmacophore model.
A new file should contain the receptor and representative benzenes. This file will be used
in Ligand Scout (Wolber 2005). This software is highly utilized for creating both structure and
ligand based models. Ligand Scout will generate the pharmacophore model utilizing the receptor
and benzenes selected. A pharmacophore model is an abstract chemical representation of a
receptor (Wermuth 1998). Commonly, a pharmacophore model is constructed based on two
approaches. One approach would be to utilize training molecules, which are based on already
known ligand and interaction patterns, to guide the construction of the structure. Another, more
efficient, approach would see the model being built based on the ligand’s interaction with
another compound (Vuorinen, 2015). In this case, the model obtained from PDB will contain the
agonist structure of LY341495 interacting with the receptor. This structure-based approach
would provide accurate representation of the target as the software also analyzes the benzenes’
surrounding chemical interactions. The resulting combined model will contain all benzene
information. Visually, the pharmacophore model will be a collection of exclusion spheres that
represent the hydrophobic benzenes. The model will also contain arrows and other figures that
represent chemical bonds that could manifest chemical interactions. These spheres will be
located around a 3D space to represent the target receptor.
Next, this pharmacophore model will be uploaded unto ZINCPharmer (Koes 2012), a
virtual 3D database for compounds. This web-based search software is utilized for virtual
screening of commercially-available compounds in the ZINC database (Irwin 2005). This database
has over 35 million purchasable compounds in 3D available formats. The formats permit an
effective compound docking after the screening. ZINCPharmer interprets the parameters set by
the pharmacophore models and searches through the database. This screening software also
permits filtering compounds by molecular weight and number of rotatable bonds. After
screening, the result will be a spatial data file (SDF) containing the numerous amount of
compounds that will fit the special parameters set by the user.
This spatial data file will be translated into a Mol2 file, which is a more legible format. The
results within the newly-translated Mol2 file will be uploaded to the UPR-HPCf once more. Once
uploaded to the server within the facility, another special software will be utilized, Raccoon
5. Maldonado 5
(http://autodock.scripps.edu/resources/raccoon). As stated in the Scripps Research Institute,
“Raccoon is a graphical interface for preparing AutoDock virtual screenings”. This software is
useful for generating special computer scripts. Raccoon will convert all the results within the
Mol2 file into PDBQT files. This new file type is commonly used for AutoDock Vina’s virtual
screening hence the usefulness of Raccoon.
AutoDock Vina will run a virtual screen by docking all compounds obtained in the
ZINCPharmer screening. AutoDock Vina takes full advantage of the servers’ capabilities to run
the numerous compounds through rigorous ligand interaction analyzation of each individual
compound. The time the results will be available depends on the system capabilities and number
of compounds. With a special script, the results will be available in an easily readable table. This
permits the ranking of compounds by affinity, or binding energy. This investigation will focus on
the top five compounds in the list by affinity. These top five candidates will be extracted and
virtually compared with the 3D metabotropic Glutamate Receptor 3 structure in PyMol; this
would provide visual confirmation that this elaborate process has worked so far. The expected
model would be the newly-found compound positioned to interact with the benzenes found
within the receptor.
Further steps would include returning to the first ZINCPharmer screening and altering the
search and filter parameters. This further step would give a broader scope of the list of
compounds resulting from this screening. From previous In Silico investigations utilizing this
approach, altering search specifications will provide new compounds with higher affinity.
Another aspect to consider will be the benzenes utilized with the pharmacophore model. The
ZINCPharmer software also allows for slight modifications of the model. So another round of
tests would be to alter benzenes utilized for the search parameters. These results would all be
collected and analyzed.
III. Results
Fig1. The model obtained from the Protein Data Base. Presented are two different perspective of the receptor. The
model represents the metabotropic Glutamate receptor. The structure in green would be representative of ligand-
binding. The green structure is LY341495 antagonist and was included with the 3D model from PDB. Based on this
representation we conducted our experimentation.
6. Maldonado 6
Figure 2. Pharmacophore model representation of the target site within mGluR3 obtained from Ligandscout
software. This model is representative of the information obtained from ligand-receptor interactions from the
inhibitor LY341495 antagonist that was included in the protein database model. This model also is based on
information acquired from a benzene mapping procedure.
Analyzing the action site from the protein resulted in one hundred models each with its
own benzene. So we found four benzenes that would each be representative of those areas filled
with other benzenes, or clusters. From there, the best course of action was to find the most
favorable benzenes. This would require to understand which would yield the compounds with
most binding energy.
We performed the zinc database screening with three models. Each model derived from
the same pharmacophore model. Model A consisted in the use of the three closest benzenes
while removing the furthest (“Ben 4” from figure 2). The parameters for Model A’s screen was a
range in Molecular Weight from 350 to 450u with a range in rotatable bonds from 0 to 5 bonds.
Model B utilized all four benzenes. This model was screened with a range from 0 to 350 in
molecular weight and 0 to 5 rotatable bonds. Model C used three benzenes, removing the
benzene that was closest to the stacking benzenes (“Ben 2”). The parameters for the Zincpharmer
screen Model C were the same as with Model B.
The many compounds that have potential affinity towards the different pharmacophore
models were obtained through Zincpharmer (Wermuth, Ganellin and Lindberg) (Conn and Pin).
The number of compound are presented in table 1. This table presents the total amount of
compounds utilizing the range of molecular weight from 0 to 450u. This is to present the massive
scale of this project in terms of high input data.
Model Amount of Compounds
A 2,989,147 hits
B 197,655 hits
C 988,798 hits
Table 1. The result of screening in the Zincpharmer database. The models utilized have various alterations but are all
derivations of the mGluR3 receptor. The following parameters were utilized: [0≤Molecular Weight≤450; 0≤Rotatable
Bonds≤5] with no repeating structure.
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The second screen analyses the binding energy between receptor and ligand. This analysis
is performed mostly by the HPCf. The binding energies between compound and target are
presented in table 2.
Model
Compounds with
Leading BE
A B C
-10.4 3 0 0
-10.3 0 0 0
-10.2 2 0 0
-10.1 1 1 1
-10 8 0 0
-9.9 11 3 4
-9.8 18 2 1
-9.7 17 4 9
-9.6 40 1 7
Table 2. The amount of compounds per binding energy for every model screened.
IV. Conclusion
The results indicate the possibility of many viable compounds to study. The most
outstanding results obtained were the compounds with a binding affinity of -10.4, all of which
were from model A’s screening. As seen in table 3, the most prominent model would be A as it
has the most compounds with the highest BE. Model A had all benzenes with the removal of “Ben
4” which increased the amount of compounds compared to model B’s use of all benzenes (table
1). As well as increasing the total amount of compounds, model A also had the most compounds
with the highest BE. Further analysis would be better suited for model A as it would yield most
promising results.
Since further study is required, the potential of compounds with leading binding energy
is yet to be determined. From the group of compounds with -10.0 BE and higher, there are a total
of eighteen (18) candidates with good potential, within the confines of this study.
V. Discussion
This study has reached its goal to find suitable compounds with high affinity towards the
designated receptor through the in silico methodology stated. Further steps will have to be
accomplish to determine the relation between compound and receptor. Follow up studies would
include understanding how to better increase binding energy by ligand modifications. Adding
specific properties would enhance the relation. We are currently seeing the extent of molecular
weight a molecule would react towards receptor. Understanding that a compound would have
to pass through the blood brain barrier, properties such as weight, size and lipid solubility should
be considered at all times (Banks, 2009).
8. Maldonado 8
This study was the first step in finding a pharmacological candidate to treat major
neurological disorders. The metabotropic glutamate receptor is potentially very important target
for the pharmacological treatment of addiction, depression, motor neurodegenerative diseases,
and schizophrenia (Campo, 2011) (Meldrum, 2000) (Moreno, 2009). As a necessary component
in synaptic glutamate release, many conditions are caused or associated with mGluR group II
dysfunction. Many antagonist target both receptors that pertain to this group (Cleva, 2012). With
this study, an antagonist may be formed that exclusively target the mGluR3. This would progress
many current studies that cannot source that actual cause of many neurological conditions.
VI. References
Banks, William A. "Characteristics of compounds that cross the blood-brain barrier." BMC
Neurology (2009).
Campo B, Kalinichev M, Lamberg N, El Yacoubi M, Royer-Urios I, Schneider M, Legrand C, Parron
D, Girard F, Bessif A, Poli S, Vaugeois J, Le Poul E, Celanire S. 2011. Characterization of an
mGluR2/3 Negative Allosteric Modulator in Rodent Models of Depression. Journal of
Neurogenetics [Internet]. [Cited 2015 Aug 25]; 25(4): 152–166. DOI:
10.3109/01677063.2011.627485
Cleva, Richard M. and M. Foster Olive. "Metabotropic glutamate receptors and drug addiction."
WIREs Membrane Transport and Signaling (2012): 281-295.
Conn, Jeffrey P. and Jean-Philippe Pin. "PHARMACOLOGY AND FUNCTIONS OF METABOTROPIC
GLUTAMATE RECEPTORS." Annual Review Pharmacology Toxicology (1997): 205-237.
Downing A, Kinon B, Millen B, Zhang L, Liu L, Morozova M, Brenner R, Rayle T, Nisenbaum L, Zhao
F, Gomez J. 2014. A double-blind, placebo-controlled comparator study of LY2140023
monohydrate in patients with schizophrenia. BMC Psychiatry [Internet]. [cited 2015 Aug 25];
14 (351): 1471-244. DOI: 10.1186/s12888-014-0351-3
Ekins, S, J Mestres and B Testa. "In silico pharmacology for drug discovery: methods for virtual
ligand screening and profiling." British Journal of Pharmacology (2007): 9-20.
Forli S. 2010. Raccoon|AutoDock VS: an automated tool for preparing AutoDock virtual
screenings. Available from: http://autodock.scripps.edu/resources/raccoon
Irwin J J, Shoichet B K. 2006. ZINC – A Free Database of Commercially Available Compounds for
Virtual Screening. Journal of Chemical Information and Modeling. [Internet]. [Cited 2015 Oct
15]. 45(1): 177-182 DOI: 10.1021/ci049714
Koes, David Ryan and Carlos J Camacho. "ZINCPharmer: pharmacophore search of the ZINC
database." Nucleic Acids Research (2012): W409–W414. Web Server issue.
9. Maldonado 9
Matosin N, Hons BMSc, Fernandez-Enright F, Frank E, Deng C, Wong J, Huang X, Newell K. 2014.
Metabotropic glutamate receptor mGluR2/3 and mGluR5 binding in anterior cingulate
cortex in psychotic and nonpsychotic depression, bipolar disorder and schizophrenia:
implications for novel mGluR-based therapeutics. Journal of Psychiatry of Neuroscience
[Internet]. [cited 2015 Aug 25]; 39(6): 407-416. DOI: 10.1503/jpn.130242
Meldrum, Brian S. "Glutamate as a Neurotransmitter in the Brain: Review of Physiology and
Pathology." American Society for Nutritional Sciences (2000): 1007S-1015S.
Monn J, Valli M J, Massey S M, Wright R A, Salhoff C R, Johnson B G, Howe T, Alt C A, Rhodes G
A, Robey R L, Griffey K R, Tizzano J P, Kallman M J, Helton D R, Schoepp D D. 1997. Design,
Synthesis, and Pharmacological Characterization of (+)-2-Aminobicyclo[3.1.0]hexane-2,6-
dicarboxylic Acid (LY354740): A Potent, Selective, and Orally Active Group 2 Metabotropic
Glutamate Receptor Agonist Possessing Anticonvulsant and Anxiolytic Properties. Journal
of Medicinal Chemistry. [Internet]. [Cited 2015 Oct 15]. 40: 528-537 DOI:
10.1021/jm9606756
Moreno, José L., Stuart C. Sealfon and Javier González-Maeso. "Group II metabotropic glutamate
receptors and schizophrenia." Cell Molecular Life Science (2009): 3777–3785.
Morris G M, Huey R, Lindstrom W, Sanner M F, Belew R K, Goodsell D S, Olson A J 2009 Autodock4
and AutoDockTools4: automated docking with selective receptor flexibility. Journal of
Computational Chemistry [Internet]. [Cited 2015 Oct 15]. 16: 2785-91. DOI:
10.1002/jcc.21256
Niwenger, Colleen M. and P. Jeffrey Conn. "Metabotropic Glutamate Receptors: Physiology,
Pharmacology, and Disease." Anual Review Pharmacology Toxicology (2010): 295–322.
O'Brien NL, Way MJ, Kandaswamy R, Fiorentino A, Sharp SI, Quadri G, Alex J, Anjorin A, Ball D,
Cherian R, Dar K, Gormez A, Guerrini I, Heydtmann M, Hillman A, Lankappa S, Lydall G, O'Kane
A, Patel S, Quested D, Smith I, Thomson AD, Bass NJ, Morgan MY, Curtis D, McQuillin A.). The
functional GRM3 Kozak sequence variant rs148754219 affects the risk of schizophrenia and
alcohol dependence as well as bipolar disorder. Psychiatr Genet. 2014 Dec;24(6):277-8.
Profaci C, Krolikowski K, Olszewski R, Neale J. 2011. Group II mGluR agonist LY354740 and NAAG
peptidase inhibitor effects on prepulse inhibition in PCP and D-amphetamine models of
schizophrenia. Psychopharmacology [Internet]. [Cited 2015 Aug 25]; 216(2): 235–243. DOI:
10.1007/s00213-011-2200-0
Trott O, Olson A J. 2010 AutoDock Vina: improving the speed and accuracy of docking with a new
scoring function, efficient optimization and multithreading. Journal of Computational
Chemistry [Internet]. [Cited 2015 Oct 15]. 31: 455-461. DOI: 10.1002/jcc.21334
10. Maldonado 10
Vuorinen A, Schuster D. 2015. Methods for generating and applying pharmacophore models as
virtual screening filters and for bioactivity profiling. Methods. [Internet]. [Cited 2015 Oct
15]. 71 (2015): 113-134 DOI: 10.1016/j.ymeth.2014.10.013
Walker A, Wenthur C, Xiang Z, Rook J, Emmitte K, Niswender C, Lindsley C, Conn P. 2015.
Metabotropic glutamate receptor 3 activation is required for long-term depression in
medial prefrontal cortex and fear extinction. Proceedings of National Academy of Sciences
of the United States of America [Internet]. [Cited 2015 Aug 25]; 112(4):1196-1201. DOI:
10.1073/pnas.1416196112
Wermuth, C. G., et al. "Glossary of Terms used in Medicinal Chemistry." Pure and Application
Chemistry (1998): 1129-1143.
Wernimont AK, Dong A, Seitova A, Crombet L, Khutoreskaya G, Edwards AM, Arrowsmith CH,
Bountra C, Weigelt J, Cossar D, Dobrovetsky E Wernimont AK, Dong A, Seitova A, Crombet
L, Khutoreskaya G, Edwards AM, Arrowsmith CH, Bountra C, Weigelt J, Cossar D,
Dobrovetsky E Crystal Structure of Metabotropic glutamate receptor 3 precursor in
presence of LY341495 antagonist. To be published.
Yang X, Wang G, Wang Y, Yue X. 2015. Association of metabotropic glutamate receptor 3
polymorphisms with schizophrenia risk: evidence from a meta-analysis. Neuropsychiatric
Disease and Treatment [Internet]. [Cited 2015 Aug 25]; 2015(11):823–833. Doi:
10.2147/NDT.S77966