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Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection

https://doi.org/10.1038/srep06356
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
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Verification of protein structures: Patterns of nonbonded atomic interactions
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Similarity networks of protein binding sites
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Binding similarity network of ligand
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AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR
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The molecular surface package
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Valproic acid as a promising agent to combat Alzheimer's disease
inferredcites →https://doi.org/10.1016/j.jsb.2007.09.005openalex-snapshot
PocketDepth: A new depth based algorithm for identification of ligand binding sites in proteins
inferredcites →https://doi.org/10.1016/j.pharmthera.2013.01.016openalex-snapshot
Structure and dynamics of molecular networks: A novel paradigm of drug discovery
inferredcites →https://doi.org/10.1016/j.phrs.2009.04.002openalex-snapshot
Cooperative N-methyl-d-aspartate (NMDA) receptor antagonism and μ-opioid receptor agonism mediate the methadone inhibition of the spinal neuron pain-related hyperactivity in a rat model of neuropathic pain
inferredcites →https://doi.org/10.1016/j.socnet.2011.07.001openalex-snapshot
Triadic closure in two-mode networks: Redefining the global and local clustering coefficients
inferredcites →https://doi.org/10.1016/j.str.2004.02.027openalex-snapshot
Cofactors in Fatty Acid Biosynthesis—Active Site Organizers and Drug Targets
inferredcites →https://doi.org/10.1016/j.tube.2010.09.008openalex-snapshot
TubercuList – 10 years after
inferredcites →https://doi.org/10.1016/s0924-977x(99)00055-3openalex-snapshot
Clozapine blocks dopamine, 5-HT2 and 5-HT3 responses in the medial prefrontal cortex: an in vivo microiontophoretic study
inferredcites →https://doi.org/10.1021/bi061874mopenalex-snapshot
Proteome-wide Profiling of Isoniazid Targets in Mycobacterium tuberculosis
inferredcites →https://doi.org/10.1021/ci200132zopenalex-snapshot
PocketAlign A Novel Algorithm for Aligning Binding Sites in Protein Structures
inferredcites →https://doi.org/10.1038/nature11691openalex-snapshot
Automated design of ligands to polypharmacological profiles
inferredcites →https://doi.org/10.1038/nchembio.118openalex-snapshot
Network pharmacology: the next paradigm in drug discovery
inferredcites →https://doi.org/10.1038/ng.2747openalex-snapshot
Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis
inferredcites →https://doi.org/10.1038/nmeth.1938openalex-snapshot
Detecting overlapping protein complexes in protein-protein interaction networks
inferredcites →https://doi.org/10.1038/nrd2684openalex-snapshot
Genomic-scale prioritization of drug targets: the TDR Targets database
inferredcites →https://doi.org/10.1038/nrd4001openalex-snapshot
Advances in the development of new tuberculosis drugs and treatment regimens
inferredcites →https://doi.org/10.1038/nsmb1089openalex-snapshot
Mycobacterium tuberculosis dihydrofolate reductase is a target for isoniazid
inferredcites →https://doi.org/10.1039/c2cc33415aopenalex-snapshot
Polypharmacology of sulfonamides: pazopanib, a multitargeted receptor tyrosine kinase inhibitor in clinical use, potently inhibits several mammalian carbonic anhydrases
inferredcites →https://doi.org/10.1073/pnas.231275498openalex-snapshot
Comprehensive identification of conditionally essential genes in mycobacteria
inferredcites →https://doi.org/10.1074/jbc.m109.057836openalex-snapshot
Histone Deacetylase Inhibitor Valproic Acid Inhibits Cancer Cell Proliferation via Down-regulation of the Alzheimer Amyloid Precursor Protein
inferredcites →https://doi.org/10.1074/jbc.m113.475798openalex-snapshot
para-Aminosalicylic Acid Is a Prodrug Targeting Dihydrofolate Reductase in Mycobacterium tuberculosis
inferredcites →https://doi.org/10.1074/mcp.m400159-mcp200openalex-snapshot
Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes
inferredcites →https://doi.org/10.1080/15257770903051031openalex-snapshot
The Rationale for Targeting the NAD/NADH Cofactor Binding Site of Parasitic S-Adenosyl-L-Homocysteine Hydrolase for the Design of Anti-Parasitic Drugs
inferredcites →https://doi.org/10.1088/1367-2630/10/5/053039openalex-snapshot
Analysis of the structure of complex networks at different resolution levels
inferredcites →https://doi.org/10.1093/bioinformatics/btp562openalex-snapshot
E asy MIF s and S ite H ound : a toolkit for the identification of ligand-binding sites in protein structures
inferredcites →https://doi.org/10.1093/bioinformatics/btq442openalex-snapshot
The CoFactor database: organic cofactors in enzyme catalysis
inferredcites →https://doi.org/10.1093/jn/137.6.1518sopenalex-snapshot
c-Abl Tyrosine Kinase and Inhibition by the Cancer Drug Imatinib (Gleevec/STI-571)
inferredcites →https://doi.org/10.1093/nar/27.1.29openalex-snapshot
KEGG: Kyoto Encyclopedia of Genes and Genomes
inferredcites →https://doi.org/10.1093/nar/28.1.27openalex-snapshot
KEGG: Kyoto Encyclopedia of Genes and Genomes
inferredcites →https://doi.org/10.1093/nar/gkh063openalex-snapshot
The KEGG resource for deciphering the genome
inferredcites →https://doi.org/10.1093/nar/gki070openalex-snapshot
The Universal Protein Resource (UniProt)
inferredcites →https://doi.org/10.1093/nar/gki524openalex-snapshot
TM-align: a protein structure alignment algorithm based on the TM-score
inferredcites →https://doi.org/10.1093/nar/gkm611openalex-snapshot
PROCOGNATE: a cognate ligand domain mapping for enzymes
inferredcites →https://doi.org/10.1093/nar/gkm911openalex-snapshot
Binding MOAD, a high-quality protein ligand database
inferredcites →https://doi.org/10.1093/nar/gkq1126openalex-snapshot
DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs
inferredcites →https://doi.org/10.1093/nar/gks1067openalex-snapshot
New and continuing developments at PROSITE
inferredcites →https://doi.org/10.1093/nar/gks421openalex-snapshot
PocketAnnotate: towards site-based function annotation
inferredcites →https://doi.org/10.1093/nar/gkt1076openalex-snapshot
Data, information, knowledge and principle: back to metabolism in KEGG
inferredcites →https://doi.org/10.1093/nar/gkt1223openalex-snapshot
Pfam: the protein families database
inferredcites →https://doi.org/10.1101/gr.1239303openalex-snapshot
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
inferredcites →https://doi.org/10.1110/ps.062416606openalex-snapshot
Statistical potential for assessment and prediction of protein structures
inferredcites →https://doi.org/10.1111/j.1574-6968.1999.tb13575.xopenalex-snapshot
BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences
inferredcites →https://doi.org/10.1126/science.1228980openalex-snapshot
Para -Aminosalicylic Acid Acts as an Alternative Substrate of Folate Metabolism in Mycobacterium tuberculosis
inferredcites →https://doi.org/10.1126/scisignal.2001950openalex-snapshot
Network-Based Tools for the Identification of Novel Drug TargetsAdapted from the opening presentation at the International Conference on Systems Biology of Human Disease (SBHD) in Boston, Massachusetts, 16 to 18 June 2010.
inferredcites →https://doi.org/10.1126/scitranslmed.3006548openalex-snapshot
Systems Pharmacology of Adverse Event Mitigation by Drug Combinations
inferredcites →https://doi.org/10.1128/aac.01696-12openalex-snapshot
Anthelmintic Avermectins Kill Mycobacterium tuberculosis, Including Multidrug-Resistant Clinical Strains
inferredcites →https://doi.org/10.1128/aac.01775-13openalex-snapshot
Binding Pocket Alterations in Dihydrofolate Synthase Confer Resistance to para -Aminosalicylic Acid in Clinical Isolates of Mycobacterium tuberculosis
inferredcites →https://doi.org/10.1146/annurev-pharmtox-010611-134520openalex-snapshot
Systems Pharmacology: Network Analysis to Identify Multiscale Mechanisms of Drug Action
inferredcites →https://doi.org/10.1186/1471-2105-12-436openalex-snapshot
clusterMaker: a multi-algorithm clustering plugin for Cytoscape
inferredcites →https://doi.org/10.1186/1471-2105-4-2openalex-snapshot
An automated method for finding molecular complexes in large protein interaction networks
inferredcites →https://doi.org/10.1186/1471-2105-9-543openalex-snapshot
PocketMatch: A new algorithm to compare binding sites in protein structures
inferredcites →https://doi.org/10.1186/1471-2105-9-66openalex-snapshot
Validation of protein models by a neural network approach
inferredcites →https://doi.org/10.1186/1472-6807-6-19openalex-snapshot
LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation.
inferredcites →https://doi.org/10.1186/1752-0509-2-109openalex-snapshot
targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis
inferredcites →https://doi.org/10.1186/1752-0509-7-132openalex-snapshot
A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis
inferredcites →https://doi.org/10.1186/1758-2946-3-33openalex-snapshot
Open Babel: An open chemical toolbox
inferredcites →https://doi.org/10.1371/journal.pcbi.0020061openalex-snapshot
Prioritizing Genomic Drug Targets in Pathogens: Application to Mycobacterium tuberculosis
inferredcites →https://doi.org/10.1371/journal.pcbi.1000976openalex-snapshot
The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications
inferredcites →https://doi.org/10.1371/journal.pcbi.1003253openalex-snapshot
Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis
inferredcites →https://doi.org/10.1371/journal.pntd.0000804openalex-snapshot
Identification of Attractive Drug Targets in Neglected-Disease Pathogens Using an In Silico Approach
inferredcites →https://doi.org/10.1371/journal.pone.0027044openalex-snapshot
Structural Annotation of Mycobacterium tuberculosis Proteome
inferredcites →https://doi.org/10.1371/journal.ppat.1002251openalex-snapshot
High-Resolution Phenotypic Profiling Defines Genes Essential for Mycobacterial Growth and Cholesterol Catabolism
inferredcites →https://doi.org/10.1517/17460441.2013.741119openalex-snapshot
Network approaches to drug discovery
inferredcites →https://doi.org/10.2174/138945010790030965openalex-snapshot
The Role of Pemetrexed Combined with Targeted Agents for Non-Small Cell Lung Cancer

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Resolving protein structure‐function‐binding site relationships from a binding site similarity network perspective
inferred← citeshttps://doi.org/10.1007/978-94-024-1069-3_10openalex-snapshot
Function Prediction Using Patches, Pockets and Other Surface Properties
inferred← citeshttps://doi.org/10.1016/b978-0-12-816125-8.00008-0openalex-snapshot
Data-Driven Systems Level Approaches for Drug Repurposing: Combating Drug Resistance in Priority Pathogens
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Biophysical and biochemical characterization of Rv3405c, a tetracycline repressor protein from Mycobacterium tuberculosis
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Collaborative drug discovery for More Medicines for Tuberculosis (MM4TB)
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Bioinformatics approach to prioritize known drugs towards repurposing for tuberculosis
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A whole genome bioinformatic approach to determine potential latent phase specific targets in Mycobacterium tuberculosis
inferred← citeshttps://doi.org/10.1038/s41598-017-12471-8openalex-snapshot
A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis
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PPE50 variants as novel phylogeographic signatures of host-pathogen co-evolution in tuberculosis
inferred← citeshttps://doi.org/10.1039/c5mb00476dopenalex-snapshot
Recognizing drug targets using evolutionary information: implications for repurposing FDA-approved drugs against Mycobacterium tuberculosis H37Rv
inferred← citeshttps://doi.org/10.1039/d6md00029kopenalex-snapshot
Polypharmacology in multi-drug-resistant tuberculosis: current scenario and future promise
inferred← citeshttps://doi.org/10.1093/database/bav060openalex-snapshot
SInCRe—structural interactome computational resource forMycobacterium tuberculosis
inferred← citeshttps://doi.org/10.1093/gigascience/giy091openalex-snapshot
eModel-BDB: a database of comparative structure models of drug-target interactions from the Binding Database
inferred← citeshttps://doi.org/10.1101/535856openalex-snapshot
Analysis of metabolic pathways in mycobacteria to aid drug-target identification
inferred← citeshttps://doi.org/10.1128/spectrum.02315-21openalex-snapshot
In Silico Drug Discovery Strategies Identified ADMET Properties of Decoquinate RMB041 and Its Potential Drug Targets against Mycobacterium tuberculosis
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Towards a comprehensive view of the pocketome universe—biological implications and algorithmic challenges
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Multitargeting: An Alternative Approach to Tackle Multidrug Resistance in Tuberculosis
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Transcriptional Profile of Mycobacterium tuberculosis in an in vitro Model of Intraocular Tuberculosis
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Two-Component Signal Transduction Systems of Pathogenic Bacteria As Targets for Antimicrobial Therapy: An Overview
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Structure-Guided Computational Approaches to Unravel Druggable Proteomic Landscape of Mycobacterium leprae
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Two Component Regulatory Systems and Antibiotic Resistance in Gram-Negative Pathogens
inferred← citeshttps://doi.org/10.3390/molecules25051239openalex-snapshot
Multitargeting Compounds: A Promising Strategy to Overcome Multi-Drug Resistant Tuberculosis
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Faculty Opinions recommendation of Two-Component Signal Transduction Systems of Pathogenic Bacteria As Targets for Antimicrobial Therapy: An Overview.
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A novel ensemble based recommendation approach using network based analysis for identification of effective drugs for Tuberculosis
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The aspartate metabolism pathway
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Docking-based virtual screening of known drugs against murE of Mycobacterium tuberculosis towards repurposing for TB
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