Abstract:
:Since the advent of high-throughput DNA sequencing technologies, the ever-increasing rate at which genomes have been published has generated new challenges notably at the level of genome annotation. Even if gene predictors and annotation softwares are more and more efficient, the ultimate validation is still in the observation of predicted gene product( s). Mass-spectrometry based proteomics provides the necessary high throughput technology to show evidences of protein presence and, from the identified sequences, confirmation or invalidation of predicted annotations. We review here different strategies used to perform a MS-based proteogenomics experiment with a bottom-up approach. We start from the strengths and weaknesses of the different database construction strategies, based on different genomic information (whole genome, ORF, cDNA, EST or RNA-Seq data), which are then used for matching mass spectra to peptides and proteins. We also review the important points to be considered for a correct statistical assessment of the peptide identifications. Finally, we provide references for tools used to map and visualize the peptide identifications back to the original genomic information.
journal_name
Curr Top Med Chemjournal_title
Current topics in medicinal chemistryauthors
Hernandez C,Waridel P,Quadroni Mdoi
10.2174/1568026613666131204105652subject
Has Abstractpub_date
2014-01-01 00:00:00pages
425-34issue
3eissn
1568-0266issn
1873-4294pii
CTMC-EPUB-57843journal_volume
14pub_type
杂志文章,评审abstract::The vesicular acetylcholine transporter (VAChT) is a glycoprotein responsible for the accumulation of acetylcholine into pre-synaptic vesicules of cholinergic neurons. Cholinergic innervation has been shown to be decreased at the earlier stages of Alzheimer's disease (AD). Thus, the expression of VAChT has been correl...
journal_title:Current topics in medicinal chemistry
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journal_title:Current topics in medicinal chemistry
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abstract::Two general aspects which need to be considered for the successful application of dendrimers for biomedical purposes are their availability at an acceptable cost and their suitability as regards their pharmacodynamic and pharmacokinetic properties. These two aspects are covered in this review. In the first part, synth...
journal_title:Current topics in medicinal chemistry
pub_type: 杂志文章,评审
doi:10.2174/156802608785849012
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abstract::Our understanding of glutamatergic transmission in the central nervous system has been greatly expanded with the discovery and investigation of the metabotropic glutamate receptor family. Complementing the ionotropic glutamate-gated ion channels, these G-protein coupled receptors play critical roles in neuronal and gl...
journal_title:Current topics in medicinal chemistry
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更新日期:2005-01-01 00:00:00
abstract::Artemisinin is isolated from Artemisia annua L. with peroxide-containing sesquiterpene lactone structure. Because of its unique structural characteristics and promising anticancer, antivirus activities, it has recently received increasing attention. The aim of this review is to summarize recent discoveries of artemisi...
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abstract::Autoimmune diseases are characterized by the production of autoantibodies directed against specific organs of own organism. Additional common traits of autoimmune diseases are chronic inflammation due to generation of inflammatory mediators, and disorders of redox processes. The pathogenesis of autoimmune diseases is ...
journal_title:Current topics in medicinal chemistry
pub_type: 杂志文章,评审
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abstract::Chemical genomics combines chemistry with molecular biology as a means of exploring the function of unknown proteins or identifying the proteins responsible for a particular phenotype induced by a small cell-permeable bioactive molecule. Chemical genomics therefore has the potential to identify and validate therapeuti...
journal_title:Current topics in medicinal chemistry
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abstract::The development of computational tools for the prediction of passive transport is reviewed with particular reference to four diverse approaches: the rule-of-5, polar surface area, Volsurf and Abraham's General Solvation Equation. To illustrate the current state of the art, several examples of the application of in sil...
journal_title:Current topics in medicinal chemistry
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更新日期:2003-01-01 00:00:00
abstract::Release of somatostatin into the circulation from the activated TRPV1-expressing nociceptors revealed by antidromic stimulation of dorsal roots in the rat pinpointed to a novel potential drug target on these nociceptors. The review summarizes the functional, biochemical and pharmacological evidence for a novel somatos...
journal_title:Current topics in medicinal chemistry
pub_type: 杂志文章,评审
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journal_title:Current topics in medicinal chemistry
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doi:
更新日期:2017-01-01 00:00:00
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journal_title:Current topics in medicinal chemistry
pub_type: 杂志文章,评审
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更新日期:2013-01-01 00:00:00
abstract::Recent advances in DNA microarray technology have great impact on many areas of biomedical research and pharmacogenomics: discovering novel targets and genes, elucidating signatures of complex diseases, transcriptional profiling of models for diseases, and the development of individually optimized drugs based on diffe...
journal_title:Current topics in medicinal chemistry
pub_type: 杂志文章,评审
doi:10.2174/1568026043387773
更新日期:2004-01-01 00:00:00
abstract::Hepatitis C virus (HCV) is a major cause of acute hepatitis and chronic liver disease, including cirrhosis and hepatocellular carcinoma (HCC). No vaccine is currently available to prevent hepatitis C, and the current standard of care (SOC) - pegylated interferon-α (PEG-IFN-α) in combination with ribavirin (RBV) - is o...
journal_title:Current topics in medicinal chemistry
pub_type: 杂志文章,评审
doi:10.2174/156802610792232051
更新日期:2010-01-01 00:00:00
abstract::Imidazo[1,2-a]pyridine has been shown to be an important biologically active moiety. This review is a compilation of the scattered output of results of the anticancer activities of the imidazo[1,2-a]pyridine system since 2001, which have been classified as inhibition of CDK, VEGFR, PI3K, EGFR, RGGT etc. along with inh...
journal_title:Current topics in medicinal chemistry
pub_type: 杂志文章
doi:10.2174/1568026616666160414122644
更新日期:2016-01-01 00:00:00
abstract::Alpha-particles are of considerable growing interest for Targeted Alpha Therapy (TAT). TAT gains more attention as new targets, chemical labeling techniques and α-particle emitters are developed but translation of TAT into the clinic has been slow, in part because of the limited availability and the short physical hal...
journal_title:Current topics in medicinal chemistry
pub_type: 杂志文章,评审
doi:10.2174/1568026611212230002
更新日期:2012-01-01 00:00:00
abstract::Over activation of the NMDA receptor complex has been implicated in a number of neurological conditions. The use of NMDA antagonists as therapeutic agents has been limited by serious cognitive and motor side effects. Significant efforts have been reported in the development of NR2B subtype-selective antagonists, which...
journal_title:Current topics in medicinal chemistry
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更新日期:2006-01-01 00:00:00
abstract::Notwithstanding the functional role that the aggregates of some amyloidogenic proteins can play in different organisms, protein aggregation plays a pivotal role in the pathogenesis of a large number of human diseases. One of such diseases is Alzheimer's disease (AD), where the overproduction and aggregation of the β-a...
journal_title:Current topics in medicinal chemistry
pub_type: 杂志文章,评审
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更新日期:2013-01-01 00:00:00
abstract::This review mainly covers last five year literature on CCK1R agonists and antagonists. These CCK1R ligands have been found following the two usual and complementary strategies for drug discovery: rational design based on structure activity relationships on the CCK-7 and CCK-4 peptide sequences of the endogenous ligand...
journal_title:Current topics in medicinal chemistry
pub_type: 杂志文章,评审
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更新日期:2007-01-01 00:00:00
abstract::In the last few years, there has been a great increase in our understanding of pain mechanisms. Given the complexity of the mechanisms involved in pain modulation, it is surprising that the pharmacological control of pain through the application of relatively simple analgesics can be effective. Nevertheless, the appli...
journal_title:Current topics in medicinal chemistry
pub_type: 杂志文章
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abstract::The gradual alignment with all of drug metabolism with all aspects of drug discovery and development has led to a complete realignment of the way the work is conducted. From a background of conducting bespoke in vivo studies much of the work is now in a high throughput screening mode. Large technological advances have...
journal_title:Current topics in medicinal chemistry
pub_type: 杂志文章,评审
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journal_title:Current topics in medicinal chemistry
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journal_title:Current topics in medicinal chemistry
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doi:10.2174/156802610791384199
更新日期:2010-01-01 00:00:00
abstract::Psychiatric diagnosis has long been perceived as more of an art than a science since its foundations lie within the observation, and the self-report of the patients themselves and objective diagnostic biomarkers are lacking. Furthermore, the diagnostic tools in use not only stray away from the conventional medical fra...
journal_title:Current topics in medicinal chemistry
pub_type: 杂志文章,评审
doi:10.2174/1568026620666200131095328
更新日期:2020-01-01 00:00:00
abstract::Numerical characterization of molecular structure is a first step in many computational analysis of chemical structure data. These numerical representations, termed descriptors, come in many forms, ranging from simple atom counts and invariants of the molecular graph to distribution of properties, such as charge, acro...
journal_title:Current topics in medicinal chemistry
pub_type: 杂志文章
doi:10.2174/156802612804910278
更新日期:2012-01-01 00:00:00
abstract::In the last decade, we have been developing some gold(III) derivatives showing interesting antitumor properties and reduced systemic and renal toxicity, compared to the clinically-established reference drug cisplatin. Starting from the rationale at the base of our investigations, this review has been divided into two ...
journal_title:Current topics in medicinal chemistry
pub_type: 杂志文章,评审
doi:10.2174/1568026615666150827094500
更新日期:2016-01-01 00:00:00
abstract::Protein kinases (Ser/Thr and Tyr) play a key role in signal transduction pathways. It has been shown that deregulation of the Cdk activity is linked to cell proliferation and cancer. Inhibition of cyclin-dependent kinases (Cdks) is an important target for potential new anti-cancer drugs. Following the discovery of Olo...
journal_title:Current topics in medicinal chemistry
pub_type: 杂志文章,评审
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更新日期:2002-09-01 00:00:00
abstract::Liver cancer is the fifth (6.3% of all cancers i.e., 548,000 cases/year) and ninth (2.8% of all cancers i.e., 244,000 cases/year) most prevalent cancer worldwide in men and women, respectively. Although multiple choices of therapies are offered for Hepatocellular Carcinoma (HCC) like liver resection or transplant, rad...
journal_title:Current topics in medicinal chemistry
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doi:10.2174/1568026619666191114113048
更新日期:2020-01-01 00:00:00
abstract::Chronic hepatitis B virus (HBV) infection affects about 400 million people worldwide. The development of nucleoside analogs that inhibit HBV polymerase provides an important approach for treating HBV infection. The approval of lamivudine, adefovir and entecavir represents a cornerstone of hepatitis B therapy. However,...
journal_title:Current topics in medicinal chemistry
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更新日期:2006-01-01 00:00:00
abstract::Most drug discovery programs today originate by selection of 'hit' molecules resulting from assays against large compound screening libraries. The chemical space in which these hits reside has implications for its biological activity in vivo and likelihood of progression to a drug candidate. We have created a database...
journal_title:Current topics in medicinal chemistry
pub_type: 杂志文章,评审
doi:10.2174/156802612802652466
更新日期:2012-01-01 00:00:00
abstract::An intensive research effort during the last 25 years has generated an impressive number of alkaloids isolated from marine ascidians, which remain unique among marine invertebrates in that they overwhelmingly produce this kind of metabolites. The present review is focused on some major groups of ascidians' bioactive a...
journal_title:Current topics in medicinal chemistry
pub_type: 杂志文章,评审
doi:10.2174/1568026613666131213155813
更新日期:2014-01-01 00:00:00