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Activity-based protein profiling for mapping and pharmacologically interrogating proteome-wide ligandable hotspots
2017
Current Opinion in Biotechnology
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Here, we discuss modern methods for activitybased protein profiling-based chemoproteomic strategies to map 'ligandable' hotspots in proteomes using activity and reactivity-based chemical probes to allow ...
Despite the completion of human genome sequencing efforts nearly 15 years ago that brought with it the promise of genomebased discoveries that would cure human diseases, most protein targets that control ...
Acknowledgements We thank the members of the Nomura Research Group for critical reading of the manuscript. ...
doi:10.1016/j.copbio.2016.08.003
pmid:27568596
pmcid:PMC5305418
fatcat:zl6riwnrinc2zbujhsjjz2mr6u
Target Identification of Bioactive Covalently Acting Natural Products
[chapter]
2018
Current Topics in Microbiology and Immunology
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chemical probes to profile proteome-wide reactive, functional, and ligandable hotspots directly in complex proteomes (Fig. 5b, c) . ...
probes to profile proteome-wide reactive and ligandable hotspots in complex proteomes. ...
doi:10.1007/82_2018_121
pmid:30105423
fatcat:7qxfb5snvzfrbawauylxlb6ekm
Druggable Targets and Targeted Drugs: Enhancing the Development of New Therapeutics
2008
Pharmacology
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The convergence of novel druggable targets with new chemical entities that can be specifically targeted to disease-causing sites and genes represents one means of creating highly efficacious and specific ...
In spite of these advances, the gross measure of approvable drug output is declining, with only 17 new chemical entities approved by the FDA in 2007. ...
Small molecule chemical libraries are often coupled with high-throughput screening of defined protein targets to profile 'chemical space'; this approach has led to the identification of lead compounds ...
doi:10.1159/000157624
pmid:18802381
fatcat:dnenvnh3qnclfmawgarweqz2gm
Multiscale Modelling of Relationships between Protein Classes and Drug Behavior Across all Diseases Using the CANDO Platform
2015
Mini-Reviews in Medical Chemistry
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The first version of the CANDO platform utilizes a matrix of predicted interactions between 48278 proteins and 3733 human ingestible compounds (including FDA approved drugs and supplements) that map to ...
Keywords Druggable proteins; protein drug interactions; protein folds; protein classes; proteome drug discovery; drug discovery benchmark; multiscale modeling; polypharmacology Sethi et al. ...
The study was supported by a NIH Director's Pioneer Award (1DP1OD006779-01) to Ram Samudrala and a JDRF fellowship to Gaurav Chopra. ...
doi:10.2174/1389557515666150219145148
pmid:25694071
pmcid:PMC5903852
fatcat:lt2qtjtq7fhdplgt7jttmow5rm
A practical view of 'druggability'
2006
Current Opinion in Chemical Biology
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This is best explained using the cartoon representation of chemical space introduced by Lipinski and Hopkins (Figure 1 ) [23 ] where compounds are mapped onto coordinates of chemical descriptors of ...
A close-up of the cartoon in Figure 1 that shows the chemical space occupied by active site serine protease inhibitors. ...
Interestingly, the impact of druggability on these attrition rates is not discussed.
2. Lipinski CA: Lead-and drug-like compounds: the rule-of-five revolution. Drug Discov Today: ...
doi:10.1016/j.cbpa.2006.06.014
pmid:16814592
fatcat:e3cq6546vjdjroqxafx5wjnt6e
The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications
2010
PLoS Computational Biology
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The TB-drugome reveals that approximately one-third of the drugs examined have the potential to be repositioned to treat tuberculosis and that many currently unexploited M.tb receptors may be chemically ...
druggable and could serve as novel anti-tubercular targets. ...
Acknowledgments We appreciate the constructive suggestions of the anonymous reviewers and the editor in improving the manuscript. We thank Dr. ...
doi:10.1371/journal.pcbi.1000976
pmid:21079673
pmcid:PMC2973814
fatcat:434vr2sbgjhfzk5qfub7m3aofi
Biomolecular NMR: a chaperone to drug discovery
2006
Current Opinion in Chemical Biology
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Biomolecular NMR now contributes routinely to every step in the development of new chemical entities ahead of clinical trials. ...
The versatility of NMR--from detection of ligand binding over a wide range of affinities and a wide range of drug targets with its wealth of molecular information, to metabolomic profiling, both ex vivo ...
Acknowledgement Work supported by the Center for Biomolecular Magnetic Resonance through a grant of the state of Hesse. ...
doi:10.1016/j.cbpa.2006.04.006
pmid:16679046
pmcid:PMC7185745
fatcat:tnl33hakmjaunn6nm65o6y7wfu
Predicting Selectivity and Druggability in Drug Discovery
[chapter]
2008
Annual Reports in Computational Chemistry
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Some have pointed out that the much larger "druggable proteome" or "druggable targetome" is more relevant than the "druggable genome" [67] . ...
In the original SARAH idea, experimentally measured affinities for a diverse set of compounds represent an "affinity fingerprint" for a target, and similar pharmacological profiles would indicate target ...
doi:10.1016/s1574-1400(08)00002-9
fatcat:23tyvzeezrfy5pmom3tooj7yta
Bioinformatics in translational drug discovery
2017
Bioscience Reports
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Competing interests The authors declare that there are no competing interests associated with the manuscript. ...
; GWAS, genome-wide association studies; HCV, hepatitis C virus; HR, homologous recombination; PSA, polar surface area; SSBR, single-strand break repair; SSL, synthetically sensitive or lethal; TCGA, The ...
Alternatively, it is possible to map the gene expression profile that is associated with disease and compare it with pre-existing profiles that are associated with drugs [65] . ...
doi:10.1042/bsr20160180
pmid:28487472
fatcat:iffd7elku5b5fbnrggvpwzbqn4
Hydrazines as versatile chemical biology probes and drug-discovery tools for cofactor-dependent enzymes
[article]
2020
biorxiv/medrxiv
pre-print
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Here, we have innovated a versatile class of chemoproteomic probes for this less charted hemisphere of the proteome by using hydrazine as the common chemical warhead. ...
The capacity of substituted hydrazines to profile, discover and inhibit diverse cofactor-dependent enzymes enables cell and tissue imaging and makes this platform useful for enzyme and drug discovery. ...
It should be possible to further elaborate probe molecules to develop more selective compounds that enable spatially resolved activity maps for existing histological samples and chemical druggability maps ...
doi:10.1101/2020.06.17.154864
fatcat:7ukltv6u4zagtpzy2t62ikt4gq
Multi-Omics Technologies Applied to Tuberculosis Drug Discovery
2020
Applied Sciences
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Firstly, in a discovery biology approach, to find new targets in druggable pathways for target-based investigation, advancing from target to lead compound. ...
This review summarizes the application of Mycobacterium tuberculosis omics technologies to the early stages of tuberculosis antimicrobial drug discovery. ...
MmpL3 is an integral inner membrane transporter, with a role in the export of mycolic acids to the periplasmic space in the biosynthesis of the mycobacterial cell wall. ...
doi:10.3390/app10134629
fatcat:nz63bhm635fkbmbokv3aux7pqa
Interrogating the druggable genome with structural informatics
2006
Molecular diversity
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We report here a detailed analysis of the structural coverage for the set of druggable human targets, highlighting drug target families where the level of structural knowledge is currently quite high, ...
In this paper, we present the Target Informatics Platform (TIP), a novel structural informatics approach for amplifying the rapidly expanding body of experimental protein structure information to enhance ...
Structural coverage for druggable target space To define the space of known and potential druggable targets in the human genome, we used a sequence-domain based approach for annotation and retrieval of ...
doi:10.1007/s11030-006-9035-3
pmid:17031532
fatcat:xjdq6lzlh5ht3jsnuxen4eqqrq
canSAR: an integrated cancer public translational research and drug discovery resource
2011
Nucleic Acids Research
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canSAR is a fully integrated cancer research and drug discovery resource developed to utilize the growing publicly available biological annotation, chemical screening, RNA interference screening, expression ...
This allows easy access to the multidisciplinary data within, including target and compound synopses, bioactivity views and expert tools for chemogenomic, expression and protein interaction network data ...
ACKNOWLEDGEMENTS The authors acknowledge data providers (ChEMBL, BindingDB, ArrayExpress, ...
doi:10.1093/nar/gkr881
pmid:22013161
pmcid:PMC3245005
fatcat:xdiuj2msgnep5hltiov6qp3qoe
Development of a chemogenomics library for phenotypic screening
2021
Journal of Cheminformatics
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However, phenotypic screening does not rely on knowledge of specific drug targets and needs to be combined with chemical biology approaches to identify therapeutic targets and mechanisms of actions induced ...
phenotypic profiling assay known as "Cell Painting". ...
Acknowledgements We would like to thank the doctoral school "Pierre Louis de santé publique" and the pharmaceutical company Servier for their support on this study. ...
doi:10.1186/s13321-021-00569-1
pmid:34819133
pmcid:PMC8611952
fatcat:k5ze5hfad5ehtokoq7qguzkzoa
Visualizing the drug target landscape
2010
Drug Discovery Today
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A retrospective on how the application of data integration and visualisation has been used to connect disparate information sources into a drug-discovery focused, decision making environment. ...
Acknowledgements The authors acknowledge the guidance of Enoch Huang and substantial input from Robert Hernandez, Markella Skempri, Dave ...
This can be achieved using the filter mechanism to display the scores calculated for any data component as a heat map across the proteome. ...
doi:10.1016/j.drudis.2009.09.011
pmid:19840866
fatcat:csd4hsaokjgbjjbq4azwdnf24q
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