Abstract:
:The limited clinical success of therapeutics targeting cellular signaling processes is due to multiple factors, including off-target effects and complex feedback regulation encoded within the signaling network. To understand these effects, chemical proteomics and chemical genetics tools have been developed to map the direct targets of kinase inhibitors, determine the network-level response to inhibitor treatment, and to infer network topology. Here we provide an overview of chemical phosphoproteomic and chemical genetic methods, including specific examples where these methods have been applied to yield biological insight regarding network structure and the system-wide effects of targeted therapeutics. The challenges and caveats associated with each method are described, along with approaches being used to resolve some of these issues. With the broad array of available techniques the next decade should see a rapid improvement in our understanding of signaling networks regulation and response to targeted perturbations, leading to more efficacious therapeutic strategies.
journal_name
ACS Chem Bioljournal_title
ACS chemical biologyauthors
Carlson SM,White FMdoi
10.1021/cb1002834subject
Has Abstractpub_date
2011-01-21 00:00:00pages
75-85issue
1eissn
1554-8929issn
1554-8937journal_volume
6pub_type
杂志文章,评审abstract::The endoplasmic reticulum (ER) is the initial site of biogenesis of secretory pathway proteins, including proteins localized to the ER, Golgi, lysosomes, intracellular vesicles, plasma membrane, and extracellular compartments. Proteins within the secretory pathway contain a high abundance of disulfide bonds to protect...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.9b01014
更新日期:2020-02-21 00:00:00
abstract::Gaussia luciferase (GLUC) is a bioluminescent reporter protein of increasing importance. As a secretory protein, it has increased sensitivity in vitro and in vivo (∼20 000-fold, and ∼1000-fold, respectively) over its competitor, secreted alkaline phosphatase. Unfortunately, this same advantageous secretory nature of G...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.7b00454
更新日期:2017-09-15 00:00:00
abstract::The ubiquity of microorganisms is unparalleled in any other known organism. These creatures surround our outsides and colonize our insides, a fact that has been known for centuries. However, despite their prevalence and long study, many of their characteristics still remain largely unexplained, including how proteins ...
journal_title:ACS chemical biology
pub_type: 传,历史文章,杂志文章
doi:10.1021/cb100179t
更新日期:2010-07-16 00:00:00
abstract::Simocyclinone D8 (1, SD8) has attracted attention due to its highly complex hybrid structure and the unusual way it inhibits bacterial DNA gyrase by preventing DNA binding to the enzyme. Although a hypothesis explaining simocyclinone biosynthesis has been previously proposed, little was proven in vivo due to the genet...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.5b00669
更新日期:2016-01-15 00:00:00
abstract::Aldehydes are key intermediates in many cellular processes, from endogenous metabolic pathways like glycolysis to undesired exogenously induced processes such as lipid peroxidation and DNA interstrand cross-linking. Alkyl aldehydes are well documented to be cytotoxic, affecting the functions of DNA and protein, and th...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.6b00269
更新日期:2016-08-19 00:00:00
abstract::We have developed an improved tool for imaging acidic tumors by reporting the insertion of a transmembrane helix: the pHLIP-Fluorescence Insertion REporter (pHLIP-FIRE). In acidic tissues, such as tumors, peptides in the pHLIP family insert as α-helices across cell membranes. The cell-inserting end of the pHLIP-FIRE p...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb500388m
更新日期:2014-11-21 00:00:00
abstract::The Akt kinase family, consisting of three isoforms in humans, is a well-validated class of drug target. Through various screening campaigns in academics and pharmaceutical industries, several promising inhibitors have been developed to date. However, due to the mechanistic and structural similarities of Akt kinases, ...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb200388k
更新日期:2012-03-16 00:00:00
abstract::In urodele amphibians, an early step in limb regeneration is skeletal muscle fiber dedifferentiation into a cellulate that proliferates to contribute new limb tissue. However, mammalian muscle cannot dedifferentiate after injury. We have developed a novel, small-molecule-based method to induce dedifferentiation in mam...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb200532v
更新日期:2012-04-20 00:00:00
abstract::Bacterial tRNA-guanine transglycosylase (Tgt) is involved in the biosynthesis of the modified tRNA nucleoside queuosine present in the anticodon wobble position of tRNAs specific for aspartate, asparagine, histidine, and tyrosine. Inactivation of the tgt gene leads to decreased pathogenicity of Shigella bacteria. Ther...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.0c00700
更新日期:2020-11-20 00:00:00
abstract::Ubc13 is an E2 ubiquitin conjugating enzyme that functions in nuclear DNA damage signaling and cytoplasmic NF-κB signaling. Here, we present the structures of complexes of Ubc13 with two inhibitors, NSC697923 and BAY 11-7082, which inhibit DNA damage and NF-κB signaling in human cells. NSC697923 and BAY 11-7082 both i...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.5b00222
更新日期:2015-07-17 00:00:00
abstract::Reactive oxygen species (ROS) play an important role in the onset of Parkinson's disease (PD), and deciphering protective mechanisms is a major goal for therapeutic development. Here, DJ-1 (PARK7) gained major attention when a conserved cysteine residue with a putative role in oxidative stress sensing/protection was l...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.8b00633
更新日期:2018-08-17 00:00:00
abstract::Angiogenesis, the formation of new blood vessels, is implicated in a number of important human diseases, including cancer, diabetic retinopathy, and rheumatoid arthritis. To identify clinically useful angiogenesis inhibitors, we assembled and screened a library of mostly Food and Drug Administration-approved drugs for...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb600362d
更新日期:2007-04-24 00:00:00
abstract::Development of precision therapeutics is of immense interest, particularly as applied to the treatment of cancer. By analyzing the preferred cellular RNA targets of small molecules, we discovered that 5"-azido neomycin B binds the Drosha processing site in the microRNA (miR)-525 precursor. MiR-525 confers invasive pro...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.5b00615
更新日期:2016-02-19 00:00:00
abstract::Pathogenic Yersinia spp. secrete the effector YopJ (YopP) into host cells to counteract cytokine production and to induce programmed cell death (apoptosis). YopJ achieves these aims by inactivating mitogen-activated protein kinase (MAPK) and nuclear factor kappaB signaling pathways. YopJ was shown to bind to members o...
journal_title:ACS chemical biology
pub_type: 杂志文章,评审
doi:10.1021/cb600261k
更新日期:2006-07-21 00:00:00
abstract::Various potential G-quadruplex forming sequences present in the genome offer a platform to modulate their function by means of stabilizing molecules. Though G-quadruplex structures exhibit diverse structural topologies, the presence of G-quartets as a common structural element makes the design of topology specific lig...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb5008597
更新日期:2015-03-20 00:00:00
abstract::In type-2 diabetes (T2D), islet amyloid polypeptide (IAPP) self-associates into toxic assemblies causing islet β-cell death. Therefore, preventing IAPP toxicity is a promising therapeutic strategy for T2D. The molecular tweezer CLR01 is a supramolecular tool for selective complexation of K residues in (poly)peptides. ...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.5b00146
更新日期:2015-06-19 00:00:00
abstract::The anxiolytic, anticonvulsant, muscle-relaxant, and sedative-hypnotic effects of benzodiazepine site ligands are mainly elicited by allosteric modulation of GABAA receptors via their extracellular αx+/γ2- ( x = 1, 2, 3, 5) interfaces. In addition, a low affinity binding site at the homologous α+/β- interfaces was rep...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.8b00145
更新日期:2018-08-17 00:00:00
abstract::Cutaneous leishmaniasis remains ignored in therapeutic drug discovery programs worldwide. This is mainly because cutaneous leishmaniasis is frequently a disease of impoverished populations in countries where funds are limited for research and patient care. However, the health burden of individuals in endemic areas man...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb400800q
更新日期:2014-03-21 00:00:00
abstract::The human ClpP proteolytic complex (HsClpP) is a serine protease located in the mitochondrial matrix and participates in the maintenance of the mitochondrial proteome among other cellular functions. HsClpP typically forms a multimeric complex with the AAA+ protein unfoldase HsClpX. Notably, compared to that of normal,...
journal_title:ACS chemical biology
pub_type: 杂志文章,评审
doi:10.1021/acschembio.9b00347
更新日期:2019-11-15 00:00:00
abstract::Pentamycin is a polyene antibiotic, registered in Switzerland for the treatment of vaginal candidiasis, trichomoniasis, and mixed infections. Chemical instability has hindered its widespread application and development as a drug. Here, we report the identification of Streptomyces sp. S816, isolated from Philippine man...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.9b00270
更新日期:2019-06-21 00:00:00
abstract::The complexity of the human proteome is greatly expanded by post-translational modifications. New tools capable of recognizing these modifications in a sequence-specific fashion provide a route to purify these modified proteins, to alter protein trafficking, and to visualize signal transduction in real time. Here, we ...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb800069c
更新日期:2008-08-15 00:00:00
abstract::Human glucosylcerebrosidase 2 (GBA2) of the CAZy family GH116 is responsible for the breakdown of glycosphingolipids on the cytoplasmic face of the endoplasmic reticulum and Golgi apparatus. Genetic defects in GBA2 result in spastic paraplegia and cerebellar ataxia, while cross-talk between GBA2 and GBA1 glucosylceram...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.6b00192
更新日期:2016-07-15 00:00:00
abstract::A Natural Compound Library containing myxobacterial secondary metabolites was screened in murine macrophages for novel activators of IL-1β maturation and secretion. The most potent of three hits in total was a so far undescribed metabolite, which was identified from the myxobacterium Hyalangium minutum strain Hym3. Wh...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.8b00659
更新日期:2018-10-19 00:00:00
abstract::Terpene synthases (TS) are classified into two broad types, Class I and II, based on the chemical strategy for initial carbocation formation and motif sequences of the catalytic site. We have recently identified a new class of enzymes, Class IB, showing the acceptability of long (C20-C35) prenyl-diphosphates as substr...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.0c00145
更新日期:2020-06-19 00:00:00
abstract::The Siglec family of sialic acid-binding proteins are differentially expressed on white blood cells of the immune system and represent an attractive class of targets for cell-directed therapy. Nanoparticles decorated with high-affinity Siglec ligands show promise for delivering cargo to Siglec-bearing cells, but this ...
journal_title:ACS chemical biology
pub_type: 信件
doi:10.1021/cb400125w
更新日期:2013-07-19 00:00:00
abstract::The Morita-Baylis-Hillman reaction forms a carbon-carbon bond between the α-carbon of a conjugated carbonyl compound and a carbon electrophile. The reaction mechanism involves Michael addition of a nucleophile catalyst at the carbonyl β-carbon, followed by bond formation with the electrophile and catalyst disassociati...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb3006227
更新日期:2013-04-19 00:00:00
abstract::We have developed a chemically controlled very long-acting delivery system to support once-monthly administration of a peptidic GLP-1R agonist. Initially, the prototypical GLP-1R agonist exenatide was covalently attached to hydrogel microspheres by a self-cleaving β-eliminative linker; after subcutaneous injection in ...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.7b00218
更新日期:2017-08-18 00:00:00
abstract::Glycosylphosphatidylinositol (GPI)-anchored proteins are abundant in the protozoan parasite Trypanosoma brucei, the causative agent of African sleeping sickness in humans and the related disease Nagana in cattle, and disruption of GPI biosynthesis is genetically and chemically validated as a drug target. Here, we exam...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb800143w
更新日期:2008-10-17 00:00:00
abstract::The ATP site of kinases displays remarkable conformational flexibility when accommodating chemically diverse small molecule inhibitors. The so-called activation segment, whose conformation controls catalytic activity and access to the substrate binding pocket, can undergo a large conformational change with the active ...
journal_title:ACS chemical biology
pub_type: 杂志文章,评审
doi:10.1021/cb500129t
更新日期:2014-06-20 00:00:00
abstract::Despite the stereospecificity of translation for l-amino acids (l-AAs) in vivo, synthetic biologists have enabled ribosomal incorporation of d-AAs in vitro toward encoding polypeptides with pharmacologically desirable properties. However, the steps in translation limiting d-AA incorporation need clarification. In this...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.8b00952
更新日期:2019-02-15 00:00:00