Química combinatória de materiais com análise por microdifração de raios X. Primeira parte: fundamentos

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Translated abstract

Combinatorial chemistry refers to techniques to rapidly fabricate tens, hundreds or even thousands of different micro samples. The analysis of the large number of samples generated by combinatorial methods requires highly efficient analytical methods. In this case, the challenges are due not only to the large number of samples to be analyzed, but also to the small amount of sample available for analysis. This paper describes the fundamentals of combinatorial chemical methods applied to discover of materials and the development in x-ray diffraction to analyze micro samples.

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Designing chemically modified oligonucleotides for targeted gene silencing.

Glen F. Deleavey, Masad J. Damha (2012)

Oligonucleotides (ONs), and their chemically modified mimics, are now routinely used in the laboratory as a means to control the expression of fundamentally interesting or therapeutically relevant genes. ONs are also under active investigation in the clinic, with many expressing cautious optimism that at least some ON-based therapies will succeed in the coming years. In this review, we will discuss several classes of ONs used for controlling gene expression, with an emphasis on antisense ONs (AONs), small interfering RNAs (siRNAs), and microRNA-targeting ONs (anti-miRNAs). This review provides a current and detailed account of ON chemical modification strategies for the optimization of biological activity and therapeutic application, while clarifying the biological pathways, chemical properties, benefits, and limitations of oligonucleotide analogs used in nucleic acids research. Copyright © 2012 Elsevier Ltd. All rights reserved.

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Developing irreversible inhibitors of the protein kinase cysteinome.

Qingsong Liu, Yogesh Sabnis, Zheng Zhao … (2013)

Protein kinases are a large family of approximately 530 highly conserved enzymes that transfer a γ-phosphate group from ATP to a variety of amino acid residues, such as tyrosine, serine, and threonine, that serves as a ubiquitous mechanism for cellular signal transduction. The clinical success of a number of kinase-directed drugs and the frequent observation of disease causing mutations in protein kinases suggest that a large number of kinases may represent therapeutically relevant targets. To date, the majority of clinical and preclinical kinase inhibitors are ATP competitive, noncovalent inhibitors that achieve selectivity through recognition of unique features of particular protein kinases. Recently, there has been renewed interest in the development of irreversible inhibitors that form covalent bonds with cysteine or other nucleophilic residues in the ATP-binding pocket. Irreversible kinase inhibitors have a number of potential advantages including prolonged pharmacodynamics, suitability for rational design, high potency, and ability to validate pharmacological specificity through mutation of the reactive cysteine residue. Here, we review recent efforts to develop cysteine-targeted irreversible protein kinase inhibitors and discuss their modes of recognizing the ATP-binding pocket and their biological activity profiles. In addition, we provided an informatics assessment of the potential "kinase cysteinome" and discuss strategies for the efficient development of new covalent inhibitors. Copyright © 2013 Elsevier Ltd. All rights reserved.

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Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N(epsilon)-(o-azidobenzyloxycarbonyl) lysine for site-specific protein modification.

Tatsuo Yanagisawa, Ryohei Ishii, Ryuya Fukunaga … (2008)

Pyrrolysyl-tRNA synthetase (PylRS) esterifies pyrrolysine to tRNA(Pyl). In this study, N(epsilon)-(tert-butyloxycarbonyl)-L-lysine (BocLys) and N(epsilon)-allyloxycarbonyl-L-lysine (AlocLys) were esterified to tRNA(Pyl) by PylRS. Crystal structures of a PylRS catalytic fragment complexed with BocLys and an ATP analog and with AlocLys-AMP revealed that PylRS requires an N(epsilon)-carbonyl group bearing a substituent with a certain size. A PylRS(Y384F) mutant obtained by random screening exhibited higher in vitro aminoacylation and in vivo amber suppression activities with BocLys, AlocLys, and pyrrolysine than those of the wild-type PylRS. Furthermore, the structure-based Y306A mutation of PylRS drastically increased the in vitro aminoacylation activity for N(epsilon)-benzyloxycarbonyl-L-lysine (ZLys). A PylRS with both the Y306A and Y384F mutations enabled the large-scale preparation (>10 mg per liter medium) of proteins site-specifically containing N(epsilon)-(o-azidobenzyloxycarbonyl)-L-lysine (AzZLys). The AzZLys-containing protein was labeled with a fluorescent probe, by Staudinger ligation.

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Author and article information

Contributors

Najla Maroun Estrada: Role: ND

Francisco Manoel dos Santos Garrido: Role: ND

Marta Eloisa Medeiros: Role: ND

Sérgio de Paula Machado: Role: ND

Journal

Journal ID (publisher): qn

Title: Química Nova

Abbreviated Title: Quím. Nova

Publisher: Sociedade Brasileira de Química (São Paulo )

ISSN: 1678-7064

Publication date (Print): August 2005

Volume: 28

Issue: 4

Pages: 670-677

Affiliations

[1 ] Centro de Pesquisas da Petrobras

[2 ] Universidade Federal do Rio de Janeiro Brazil

Article

Publisher ID: S0100-40422005000400021

DOI: 10.1590/S0100-40422005000400021

SO-VID: e15a6939-17fd-470f-93db-7fd3c9b56955

License:

http://creativecommons.org/licenses/by/4.0/

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SciELO Brazil

Self URI (journal page): http://www.scielo.br/scielo.php?script=sci_serial&pid=0100-4042&lng=en

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Química combinatória de materiais com análise por microdifração de raios X. Primeira parte: fundamentos Translated title: Combinatorial chemistry of materials with analysis by X-ray microdiffraction. Part I: fundamentals

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Translated abstract

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SciELO Brazil

Most cited references 79

Designing chemically modified oligonucleotides for targeted gene silencing.

Developing irreversible inhibitors of the protein kinase cysteinome.

Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N(epsilon)-(o-azidobenzyloxycarbonyl) lysine for site-specific protein modification.

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