Computer-aided aptamers screening technologies: a review / 生物工程学报

The computer information technology that has penetrated into every aspect of our lives, can not only assist the screening of drugs, but also simulate the effect of drugs. At present, computer-aided technologies have been used to screen aptamers, which play an important role in improving the screening efficiency and screening high affinity binding aptamers. This review summarized the screening methods of aptamers through computer-aided sequence evaluation, structural analysis and molecular docking.

Aptamers as a promising approach for the control of parasitic diseases

ABSTRACT Aptamers are short single-stranded RNA or DNA oligonucleotides that are capable of binding various biological targets with high affinity and specificity. Their identification initially relies on a molecular process named SELEX (Systematic Evolution of Ligands by EXponential enrichment) that has been later modified in order to improve aptamer sensitivity, minimize duration and cost of the assay, as well as increase target types. Several biochemical modifications can help to enhance aptamer stability without affecting significantly target interaction. As a result, aptamers have generated a large interest as promising tools to compete with monoclonal antibodies for detection and inhibition of specific markers of human diseases. One aptamer-based drug is currently authorized and several others are being clinically evaluated. Despite advances in the knowledge of parasite biology and host-parasite interactions from "omics" data, protozoan parasites still affect millions of people around the world and there is an urgent need for drug target discovery and novel therapeutic concepts. In this context, aptamers represent promising tools for pathogen identification and control. Recent studies have reported the identification of "aptasensors" for parasite diagnosis, and "intramers" targeting intracellular proteins. Here we discuss various strategies that have been employed for intracellular expression of aptamers and expansion of their possible application, and propose that they may be suitable for the clinical use of aptamers in parasitic infections.

Metabolismo de triptofano em melanomas: o que dizem as células do microambiente? / Tryptophan metabolism in melanomas: what do microenvironment cells can say?

O melanoma é composto por células malignas e também por um estroma de sustentação que inclui fibroblastos, células imunológicas, endoteliais, matriz extracelular, dentre outros fatores. Assim, os tumores não são entidades independentes, eles interagem ativamente com o microambiente adjacente de forma bidirecional através de sinais moleculares que modulam o fenótipo maligno. Um dos sinais bioquímicos para desenvolvimento desse fenótipo se dá pelo catabolismo de Trp pela via das quinureninas, que gera compostos com diversas atividades biológicas, que no tumor estão envolvidas com tolerância e imunoescape e, logo, com prognóstico ruim para os pacientes. Até o presente momento apenas o consumo de Trp e a formação de um único metabólito, a quinurenina (KYN), tem sido associada a malignidade dos melanomas. A fim de ampliar e elucidar os mecanismos bioquímicos do metabolismo desse aminoácido em melanomas, estudamos mais de quinze compostos de todas as rotas catabólicas de Trp em células da pele, células imunológicas, linhagens tumorais e amostras clínicas de melanoma. De forma inédita pudemos observar que as células da pele tem maior habilidade de sintetizar KYN quando comparadas às linhagens tumorais, demonstrando que o catabolismo de Trp peritumoral pode ser responsável pelos fenômenos de imunotolerância e escape. Além disso, o metabolismo de Trp pode estar envolvido nos mecanismos de homeostasia da pele, já que especificamente essas células produzem compostos com atividade biológica nesse órgão. As células imunológicas possuem um perfil metabólico completamente diferente umas das outras: monócitos, macrófagos e dendríticas possuem maior ativação da via KYN enquanto linfócitos e neutrófilos possuem maior indução da rota que gera serotonina e melatonina. Mesmo nos diferentes fenótipos de macrófagos, M1 e M2a, foram observadas marcações especificas de metabolismo, que podem estar relacionadas às atividades anti- ou pró-tumoral dessas células no microambiente. Em amostras clínicas, apesar da principal diferença entre nevos e melanomas ser a concentração de KYN, diversas outras alterações no metabolismo de tiptofano foram observadas, o que mostra a complexa magnitude deste metabolismo na fisiopatologia da pele

Melanoma is composed of malignant cells and also by a stromal support that includes fibroblasts, immune cells, endothelial cells, extracellular matrix, among other factors. Thus, tumors are not separate entities; they actively interact with the surrounding microenvironment bi-directionally through molecular signals that modulate the malignant phenotype. One of biochemical signals for the development of this phenotype occurs by Trp catabolism through kynurenine pathway, that generates compounds with diverse biological activities, which in tumors are involved with tolerance and imunoescape and therefore with poor prognosis for patients. To date only the consumption of Trp and formation of a single metabolite, kynurenine (KYN), has been associated with malignant melanomas. In order to enlarge and clarify the biochemical mechanisms of this amino acid metabolism in melanomas, we have studied more than fifteen compounds of all catabolic routes of Trp in skin cells, immune cells, tumor cell lines and clinical samples of melanoma. In an unique way we could observe that the skin cells has superior ability to synthesize KYN when compared to tumor cell lines, demonstrating that the peritumoral catabolism of Trp may be responsible for the phenomena of immune tolerance and escape. Furthermore, the Trp metabolism may be involved in skin homeostasis mechanisms, since these cells produce specific compounds with biological activity in this organ. The immune cells have a completely different metabolic profile among them: monocytes, macrophages and dendritic cells have greater KYN pathway activation, and lymphocytes and neutrophils possess greater induction of the route that generates serotonin and melatonin. Even in different macrophages phenotypes, M1 and M2a, we observed specific metabolic marks, which may be related to the anti- or pro-tumoral activity of these cells in the tumor microenvironment. In clinical samples, although the main difference between nevi and melanomas is the concentration of KYN, a range of other changes in Trp metabolism were observed, which shows the complex magnitude of this metabolism in the skin pathophysiology

DNA aptamer selection in vitro for determining ketamine by FluMag-SELEX / 法医学杂志

OBJECTIVE@#To select specific DNA aptamer for determining ketamine by FluMag-SELEX.@*METHODS@#Based on magnetic beads with tosyl surface modification as solid carrier and ketamine as target, a random ssDNA library with total length of 78 bp in vitro was compounded. After 13 rounds screening, DNA cloning and sequencing were done. Primary and secondary, structures were analyzed. The affinity, specificity and Kd values of selected aptamer were measured by monitoring the fluorescence intensity.@*RESULTS@#Two ssDNA aptamers (Apt#4 and Apt#8) were successfully selected with high and specific abilities to bind ketamine as target with Kd value of 0.59 and 0.66 μmol/L. The prediction of secondary structure was main stem-loop and G-tetramer. The stem was the basis of stability of aptamer's structure. And loop and G-tetramer was the key of specific binding of ketamine.@*CONCLUSION@#FluMag-SELEX can greatly improve the selection efficiency of the aptamer, obtain the ketamine-binding DNA aptamer, and develop a new method for rapid detection of ketamine.

Seleção de aptâmeros que se ligam ao receptor humano para o gosto doce / Screening for aptamers that bind to the human sweet taste receptor (hT1R2/hT1R3)

Foi demonstrado que o gosto doce é transduzido por receptores acoplados a proteína G classe III (GPCRs), T1R2 e T1R3. Essas proteínas exibem longas extremidades amino-terminais que formam um domínio de ligação globular extracelular. Elas são expressas em células associadas ao gosto (células epiteliais que constituem os botões gustativos nas papilas gustativas), que respondem a moléculas associadas ao gosto doce. Quando T1R2 e T1R3 são co-expressas em células heterólogas, elas respondem, como heterômeros, a uma série de açúcares, alguns D-aminoácidos, edulcorantes artificiais e proteínas doces. Foi também demonstrado que o receptor humano T1R2/T1R3 para o gosto doce apresenta múltiplos sítios de ligação. Para melhor compreender a estrutura desse receptor e responder à pergunta de como um único quimiorreceptor pode ser responsivo a uma variedade de ligantes, foi utilizada a abordagem denominada evolução sistemática de ligantes por enriquecimento exponencial (SELEX) para isolar, a partir de uma biblioteca combinatória de oligonucleotídeos, aptâmeros de RNA resistentes a nuclease que se ligam ao receptor humano para o gosto doce com alta afinidade. Após um enriquecimento de doze ciclos do pool original de RNA contendo em torno de 1013 sequências diferentes (contra preparações de membrana de células HEK293T que expressam hT1R2/hT1R3) e outros ciclos de contrasseleção negativa (para eliminar moléculas de RNA que se ligam de forma inespecífica à membrana de nitrocelulose e a outras proteínas diferentes do alvo, ou seja, proteínas de membrana de células HEK293T selvagem), realizou-se a transcrição reversa do RNA seguida de amplificação por PCR e sequenciamento. Aptâmeros do ciclo 12 com sequências consenso foram selecionados, e a ligação de alguns deles com hT1R2/hT1R3 foi então avaliada. Cinco desses aptâmeros mostram claramente uma maior afinidade por células HEK293T que expressam hT1R2/hT1R3. Como segunda parte desta tese, estudamos outro receptor, denominado CD36, que, como o receptor T1R2/T1R3, é expresso na língua. Estudos indicam que ele age como receptor gustativo de gordura. Neste trabalho, verificamos que essa proteína é expressa em uma subpopulação de neurônios olfatórios presentes no epitélio olfatório, indicando que ela pode ter também uma função olfatória, ainda não caracterizada

It has been shown that sweet taste is transduced by the Class III G Protein-Coupled Receptors (GPCRs) T1R2 and T1R3, which show long N-termini that form a globular extracellular ligand-binding domain. These receptors are expressed in the taste cells (epithelial cells that constitute the taste buds in taste papillae) that respond to sweet tastants, and when T1R2 and T1R3 are coexpressed in heterologous cells, they respond, as heteromers, to a series of sugars, some D-amino acids, artificial sweeteners and sweet proteins. It has also been demonstrated that the sweet taste receptor has multiple binding sites. In order to better understand the structure of this receptor and answer the question of how a single chemoreceptor can respond to a variety of ligands, we used the combinatorial oligonucleotide library screening approach, denominated Systematic Evolution of Ligands by Exponential Enrichment (SELEX), to isolate nuclease-resistant RNA aptamers that bind to the human sweet taste receptor with high affinity. Following a twelve round enrichment of the previous random RNA pool containing around 1013 different sequences (against membrane preparations of hT1R2/hT1R3-expressing HEK293T cells) and negative counterselection cycles (to eliminate RNA molecules that bind nonspecifically to the nitrocellulose membrane and to proteins other than the target, that is, HEK293T cells membrane proteins), the RNA was reverse-transcribed for DNA sequencing. Aptamers from cycle 12 with consensus sequences were selected, and the binding of some of them to the human sweet taste receptor was then evaluated. Five out of the aptamers clearly show greater affinity for hT1R2/hT1R3-expressing HEK293T cells than for hT1R2/hT1R3-non-expressing HEK293T cells. In this thesis we have also analyzed another receptor, denominated CD36, which is also expressed in the tongue. Studies indicate that it acts as a receptor for fat. In this work, we found that CD36 is expressed in a subset of the olfactory neurons localized in the olfactory epithelium, indicating that it may also have an as yet uncharacterized olfactory function

Purificação de células troco de lipoaspirado humano por aptâmeros de DNA, seguida da caracterização dos fenótipos obtidos da diferenciação neuronal / Human adipose mesechymal stem cell separation by DNA aptamers followed by the characterization of the obtained phenotypes from neuronal differentiation

Células tronco mesenquimais de tecido adiposo, são uma promissora ferramenta para aplicações clínicas em terapias celular e regenerativa, em vista da facilidade de sua extração e da maior quantidade de células por unidade de massa de tecido quando comparado a outras fontes clássicas de células mesenquimais como medula óssea. O protocolo clássico de extração e purificação dessas células, depende de sua adesão em plástico e xeno-materiais demandando muito tempo para ser utilizado por médicos para auxiliar pacientes em procedimentos de emergência. Estas células são capazes se diferenciar em diversos tipos celulares, o que as torna boas candidatas para terapia celular, embora sua capacidade de transdiferenciação para fenótipos neuronais seja ainda discutida. Neste trabalho demonstramos um novo processo para isolar essas células na base de epitopos específicos expressos (assinatura molecular de superfície) utilizando aptâmeros como ligantes de alta afinidade para estes sitios. Aptâmeros, moléculas de DNA simples fita identificadas a partir de uma biblioteca combinatória de sequencias de DNA simples-fita foram identificados por ciclos reiterativos de seleção in vitro (SELEX) utilizando células tronco do lipoaspirado como alvo. Dois aptâmeros isolados, denominados APT9 e APT11, foram capazes de identificar subpopulações (15,8 e 23,7% respectivamente) dentre as células tronco mesenquimais (classicamente CD29+/CD90+/CD45-) e separá-las usando nano-partículas magnéticas acopladas aos aptâmeros. Além disso, seguindo uma indução para diferenciação neuronal, as células tronco mesenquimais passam a apresentar morfologia neuronal e apresentam expressão e atividade de diversos receptores de neurotransmissores, avaliados por PCR real-time e imageamento de variações da concentração de cálcio intracelular ápos stimulação com vários agonistas de receptores metatrópicos e ionotrópicos. Ao longo da diferenciação, os níveis transcricionais de mRNA de receptores de cininas (B1 e B2), nicotínicos (alfa 7), muscarínicos (M1, M3 e M4), glutamatérgicos (AMPA2 e mGluR2), purinérgicos (P2Y1 e P2Y4) e GABAergicos (GABA-A, subunidade 3) e da óxido nítrico sintase neural aumentaram quando comparados aos níveis das células não diferenciadas, enquanto que os níveis de expressão de outros receptores incluindo purinérgicos P2X1, P3X4, P2X7 e P2Y6 e muscarínico M5 diminuíram. Os níveis de atividade das classes dos receptores estudados, por imageamento de variações da concentração de cálcio intrac, aumentaram para a maioria dos agonistas analisados durante a diferenciação neuronal com exceção para respostas induzidas por glutamato e NMDA. Células diferenciadas expressavam altos níveis de antígenos específicos de neurônios como ß3-tubulina, NF-H, NeuN e MAP-2 indicando uma diferenciação em fenótipo neuronal bem sucedida. Desta maneira, esta tese, ao identificar aptâmeros, prove uma inovadora solução para médicos usarem as células tronco mesenquimais dentro de uma sala de cirurgia, através de um método que é capaz de purificar essas células em um tempo clínico viável, com pureza e sem contato com contaminantes. Além disso, nós mostramos aqui que com um protocolo como o proposto para diferenciação neuronal, nós poderíamos induzir essas células para se diferenciar em neurônios, através da ativação de fatores de transcrição específicos, levando às células tronco mesenquimais a serem possivelmente utilizadas em terapias celulares de reparo neuronal

Adipose mesenchymal stem cells are promising tools for clinical applications in cellular and regeneration therapies, in view of easiness of extraction and higher amount of isolated stem cells per mass of tissue when compared to other classical mesenchymal stem cell sources including bone marrow. The classical protocol to extract and purify these cells, depending on plastic adherence and xeno-materials, is too time consuming to be used by physicians to help patients at emergency procedures. These cells are able to differentiate into various cell types, making them good candidates for cell therapy, however their capability for transdifferentiation into neural phenotypes is yet discussed. Here we show a novel process to isolate these cells using their surface molecular signature and aptamers, ssDNA molecules identified through the SELEX technique, denominated APT9 and APT11 that are able to identify subpopulations (15,8 and 23,7% respectively) within the mesenchymal stem cells (classically CD29+/CD90+/CD45-) and separate them using magnetic nano-particles attached to the aptamers. Moreover, following induction to neural differentiation, mesenchymal cells presents neuronal morphology and present expression and activity of several neurotransmitter receptors, as evaluated by real-time PCR and calcium imaging. During this process, mRNA transcription levels of bradykinin (B1 and B2), cholinergic (alpha 7), muscarinic (M1, M3 and M4), glutamatergic (AMPA2 and mGlu2), purinergic (P2Y1 and P2Y4) and GABAergic (GABA-A, subunit 3) receptors and neuronal nitric oxide synthase were augmented when compared to levels of undifferentiated cells, while the expression levels of other receptors including purinergic P2X1, P2X4, P2X7 and P2Y6 and muscarinic M5 receptors were down-regulated. Activity levels of the studied receptor classes, as studied by calcium imaging, increased for most of the agonists analyzed during the neuronal differentiation with the exception for glutamate- and NMDA-induced receptor responses. Differentiated cells expressed high levels of neuron-specific antigens such as ß3-tubulin, NF-H, NeuN and MAP-2, indicating a successful differentiation into neuronal phenotypes. This thesis, by identifying aptamers, provides a novel solution for physicians to use mesenchymal stem cells inside a surgery room, by using a method that are able to purify the cells in a clinical viable time, with purity and no contact with contaminats. Furthermore, we show here that with a protocol as provided for neuronal differentiation, we could induce these cells to differentiate into neurons, by activating specific transcription factors,making mesenchymal stem cells to possibly be used in neuronal repair cell therapies

Antibodies are challenged.

Studies on antibody were documented as early as in 1890. They are proteins found in blood or other body fluid of vertebrates, and are used by the immune system to identify and neutralize antigens (like foreign objects, pathogens like bacteria and virus etc). Antibodies are dominating the biomedical research field especially detection, imaging and inhibition of biological target molecules, and therapeutics so far. However, recently aptamer has been seen to compete with antibodies in all the above areas. Aptamers are single stranded oligonucleotides or peptides that fold into well defined three dimensional shapes, allowing them to bind their targets with high affinity and specificity. Aptamer technology is relatively new and discovered only in 1990. Because of synthetic origin and similar function as antibodies, they are often termed as chemical antibody. Within 25 years of discovery, the first generation of aptamer drug "Macugen" is already marketed and available for public use. The Global market for aptamer was $236 million in 2010 and is expected to be valued at nearly $1.8 billion by 2014, with a growing compound annual growth rate of 67.5%. Various drugs being on the pipeline for clinical trials this emerging field of medical biotechnology is raising significant interest. This article gives an overview how aptamers are similar yet distinctly different from antibodies in terms of synthesis, handling, and applicability.