A Hybrid Approach Combining Shape-Based and Docking Methods to Identify Novel Potential P2X7 Antagonists from Natural Product Databases.

P2X7 is an ATP-activated purinergic receptor implicated in pro-inflammatory responses. It is associated with the development of several diseases, including inflammatory and neurodegenerative conditions. Although several P2X7 receptor antagonists have recently been reported in the literature, none of them is approved for clinical use. However, the structure of the known antagonists can serve as a scaffold for discovering effective compounds in clinical therapy. This study aimed to propose an improved virtual screening methodology for the identification of novel potential P2X7 receptor antagonists from natural products through the combination of shape-based and docking approaches. First, a shape-based screening was performed based on the structure of JNJ-47965567, a P2X7 antagonist, using two natural product compound databases, MEGx (~5.8 × 103 compounds) and NATx (~32 × 103 compounds). Then, the compounds selected by the proposed shape-based model, with Shape-Tanimoto score values ranging between 0.624 and 0.799, were filtered for drug-like properties. Finally, the compounds that met the drug-like filter criteria were docked into the P2X7 allosteric binding site, using the docking programs GOLD and DockThor. The docking poses with the best score values were submitted to careful visual inspection of the P2X7 allosteric binding site. Based on our established visual inspection criteria, four compounds from the MEGx database and four from the NATx database were finally selected as potential P2X7 receptor antagonists. The selected compounds are structurally different from known P2X7 antagonists, have drug-like properties, and are predicted to interact with key P2X7 allosteric binding pocket residues, including F88, F92, F95, F103, M105, F108, Y295, Y298, and I310. Therefore, the combination of shape-based screening and docking approaches proposed in our study has proven useful in selecting potential novel P2X7 antagonist candidates from natural-product-derived compounds databases. This approach could also be useful for selecting potential inhibitors/antagonists of other receptors and/or biological targets.

Physiologic roles of P2 receptors in leukocytes.

Since their discovery in the 1970s, purinergic receptors have been shown to play key roles in a wide variety of biologic systems and cell types. In the immune system, purinergic receptors participate in innate immunity and in the modulation of the adaptive immune response. In particular, P2 receptors, which respond to extracellular nucleotides, are widely expressed on leukocytes, causing the release of cytokines and chemokines and the formation of inflammatory mediators, and inducing phagocytosis, degranulation, and cell death. The activity of these receptors is regulated by ectonucleotidases-expressed in these same cell types-which regulate the availability of nucleotides in the extracellular environment. In this article, we review the characteristics of the main purinergic receptor subtypes present in the immune system, focusing on the P2 family. In addition, we describe the physiologic roles of the P2 receptors already identified in leukocytes and how they can positively or negatively modulate the development of infectious diseases, inflammation, and pain.

Virtual immunology: an educational software to encourage antigen-antibody interaction learning.

Immunology is a knowledge area of paramount importance in life sciences and health care professional education with diverse applications, as well as for a general public understanding of issues related to vaccination. However, many concepts are complex and difficult to understand based only on conventional classes or static images. The use of tools, such as educational software, may enhance the learning of dynamic molecular phenomena that occur in our bodies. Virtual Immunology is a software that aims to facilitate the learning of certain complex immunology concepts. Herein, we present the "Antigen-antibody interactions" module that was used and evaluated by 127 students and 3 teachers from medical schools from 2 universities, 1 public and 1 private, both in the state of Rio de Janeiro, Brazil. The pretest/posttest research design was used to assess student learning in a randomized sample. To evaluate user perceptions concerning software quality, 14 statements were analyzed using a Likert scale. Results indicate suitable evaluations from both students and teachers concerning the "Antigen-antibody module" as an auxiliary tool in immunology teaching. The software was well rated as an educational resource since it allows dynamically viewing immunological phenomena. In addition, its ease of use and immunological process visualization were the best-evaluated parameters by the students, who recommended this software module as an auxiliary learning tool. The use of the evaluated software may motivate students and aid in the understanding of immunology-related concepts, becoming a complementary tool that may enhance the teaching-learning process.

Graph Neural Networks as a Potential Tool in Improving Virtual Screening Programs.

Despite the increasing number of pharmaceutical companies, university laboratories and funding, less than one percent of initially researched drugs enter the commercial market. In this context, virtual screening (VS) has gained much attention due to several advantages, including timesaving, reduced reagent and consumable costs and the performance of selective analyses regarding the affinity between test molecules and pharmacological targets. Currently, VS is based mainly on algorithms that apply physical and chemistry principles and quantum mechanics to estimate molecule affinities and conformations, among others. Nevertheless, VS has not reached the expected results concerning the improvement of market-approved drugs, comprising less than twenty drugs that have reached this goal to date. In this context, graph neural networks (GNN), a recent deep-learning subtype, may comprise a powerful tool to improve VS results concerning natural products that may be used both simultaneously with standard algorithms or isolated. This review discusses the pros and cons of GNN applied to VS and the future perspectives of this learnable algorithm, which may revolutionize drug discovery if certain obstacles concerning spatial coordinates and adequate datasets, among others, can be overcome.

New Insights in Purinergic Therapy: Novel Antagonists for Uridine 5'-Triphosphate-Activated P2Y Receptors from Brazilian Flora.

P2Y2 and P2Y4 receptors are physiologically activated by uridine 5'-triphosphate (UTP) and are widely expressed in many cell types in humans. P2Y2 plays an important role in inflammation and proliferation of tumor cells, which could be attenuated with the use of antagonists. However, little is known about the physiological functions related to P2Y4, due to the lack of selective ligands for these receptors. This can be solved through the search for novel compounds with antagonistic activity. The aim of this study was to discover new potential antagonist candidates for P2Y2 and P2Y4 receptors from natural products. We applied a calcium measurement methodology to identify new antagonist candidates for these receptors. First, we established optimal conditions for the calcium assay using J774.G8, a murine macrophage cell line, which expresses functional P2Y2 and P2Y4 receptors and then, we performed the screening of plant extracts at a cutoff concentration of 50 µg/mL. ATP and ionomycin, known intracellular calcium inductors, were used to stimulate cells. The calculated EC50 were 11 µM and 103 nM, respectively. These cells also responded to the UTP stimulation with an EC50 of 1.021 µM. Screening assays were performed and a total of 100 extracts from Brazilian plants were tested. Joannesia princeps Vell. (stem) and Peixotoa A. Juss (flower and leaf) extracts stood out due to their ability to inhibit UTP-induced responses without causing cytotoxicity, and presented an IC50 of 32.32, 14.99, and 12.98 µg/mL, respectively. Collectively, our results point to the discovery of potential antagonist candidates from Brazilian flora for UTP-activated receptors.

Identificação de novos antagonistas para receptores purinérgicos P2 / Identification of new antagonists for P2 purinergic receptors

Os receptores purinérgicos P2 são receptores expressos na membrana plasmática de diversos tipos celulares humanos, nos quais exercem importantes funções fisiológicas . Eles são divididos em duas classes, de acordo com a estrutura apresentad a . A classe P2X comp reende os subtipos de receptores ionotrópicos que são ativados fisiologicamente pelo ATP. Dentre os receptores P2X, o P2X7 destaca se por suas funções associadas à dor e à inflamação. Já a classe P2Y compreende os subtipos de receptores metabotrópicos, os quais são ativados por diferentes nucleotídeos extracelulares. Nes s a última classe, o subtipo P2Y2 destaca se p elos seus papeis desempenhados na inflamação e no câncer, enquanto o P 2Y4 se sobressai pela escassez de informações acerca de suas funções fisiol ógicas devido a limitações de caráter farmacológico . Apesar de serem considerados importantes alvos terapêuticos , ainda não existe m fármacos com atuação sobre ess es receptores que sejam aprovados para uso clínico , o que encoraja a busca por novas moléculas com atividade antagonista. Ness e contexto, o objetivo des t e estudo foi identificar novos antagonistas para receptores P2 (P2X7, P2Y2 e P2Y4) e averiguar se eles exercem algum papel n a atenuação da dor e inflamação Na primeira part e dess e trabalho foi identificada a atividade antagonista d o extrato galhos de Joannesia princeps Vell. após a realização de uma mini campanha de triagem. Utilizando a técnica de mensuração de cálcio intracelular, foi demonstrado que esse extrato foi capaz de inibir a mobiliza ção de cálcio induzida por UTP de forma concentração dependente, sendo que esse efeito não foi provocado por citotoxicidade ou fenômeno quenching. (AU)

Além disso, esse extrato também foi capaz de inibir parcialmente a mobilização de cálcio induzida por UDP . Co m isso , os resultados sugerem uma possível seletividade quanto à ação antagonista desse extrato sobre os receptores P2Y ativados por nucleotídeos derivados da uridina. Enquanto isso, na segunda parte do trabalho foi identificada a atividade antagonista d a molécula CS 15 sobre o receptor P2X7 durante a realização de uma mini campanha de triagem . A molécula CS 15 , um triterpeno isolado da planta Clusia studartiana C. M. Vieira & Gomes da Silva foi capaz de inibir a captação do corante YO PRO 1 em ensaios de permeabilização celular de forma concentração dependente e apresentou um IC 50 na faixa de nanomolar. A demais , ess a molécula não demonstrou toxicidade in vitro e ainda foi capaz de aliviar os sintomas de nocicepção em modelo experimental animal. Coletivamen te, os resultados apontam para a descoberta de novos antagonistas para receptores P2 de origem natural , os quais podem contribuir no futuro para o escasso campo da terapia associada aos receptores purinérgicos. (AU)

Brilliant Blue Dyes in Daily Food: How Could Purinergic System Be Affected?

Dyes were first obtained from the extraction of plant sources in the Neolithic period to produce dyed clothes. At the beginning of the 19th century, synthetic dyes were produced to color clothes on a large scale. Other applications for synthetic dyes include the pharmaceutical and food industries, which are important interference factors in our lives and health. Herein, we analyzed the possible implications of some dyes that are already described as antagonists of purinergic receptors, including special Brilliant Blue G and its derivative FD&C Blue No. 1. Purinergic receptor family is widely expressed in the body and is critical to relate to much cellular homeostasis maintenance as well as inflammation and cell death. In this review, we discuss previous studies and show purinergic signaling as an important issue to be aware of in food additives development and their correlations with the physiological functions.

An Improved Method for P2X7R Antagonist Screening.

ATP physiologically activates the P2X7 receptor (P2X7R), a member of the P2X ionotropic receptor family. When activated by high concentrations of ATP (i.e., at inflammation sites), this receptor is capable of forming a pore that allows molecules of up to 900 Da to pass through. This receptor is upregulated in several diseases, particularly leukemia, rheumatoid arthritis and Alzheimer's disease. A selective antagonist of this receptor could be useful in the treatment of P2X7R activation-related diseases. In the present study, we have evaluated several parameters using in vitro protocols to validate a high-throughput screening (HTS) method to identify P2X7R antagonists. We generated dose-response curves to determine the EC50 value of the known agonist ATP and the ICs50 values for the known antagonists Brilliant Blue G (BBG) and oxidized ATP (OATP). The values obtained were consistent with those found in the literature (0.7 ± 0.07 mM, 1.3-2.6 µM and 173-285 µM for ATP, BBG and OATP, respectively) [corrected].The Z-factor, an important statistical tool that can be used to validate the robustness and suitability of an HTS assay, was 0.635 for PI uptake and 0.867 for LY uptake. No inter-operator variation was observed, and the results obtained using our improved method were reproducible. Our data indicate that our assay is suitable for the selective and reliable evaluation of P2X7 activity in multiwell plates using spectrophotometry-based methodology. This method might improve the high-throughput screening of conventional chemical or natural product libraries for possible candidate P2X7R antagonist or agonist.

Padronização da triagem de alto desempenho de antagonistas para receptores purinérgicos ativados por UTP a partir da mensuração de cálcio intracelular / Standardization of the screening of high performance antagonists For receivers purinergic activated by UTP from Measurement of calcium intracellular

Os receptores purinérgicos são proteínas expressas na membrana plasmática de diversos tiposcelulares e são ativadas por purinas e pirimidinas extracelulares. Eles são classificados emreceptores P1 e P2, de acordo com o tipo de ligante fisiológico, entretanto, os P2R são aindasubdivididos nas classes: P2XR, que abrange os subtipos ionotrópicos e P2YR, que agrupa ossubtipos acoplados à proteína G. Dentre os P2YR, os subtipos P2Y2 e P2Y4 vem sendoamplamente estudados em virtude de suas funções sobre diversos sistemas biológicos. Umavez ativados pelo UTP, estes receptores promovem a ativação e inibição de canais iônicos,controlam o fluxo de íons através da membrana, induzem um aumento de cálcio intracelular,além de estimular a proliferação celular. Em vista disso, muitos grupos de pesquisa já vemestudando o P2Y2 e o P2Y4 como alvos terapêuticos para o tratamento de diversas doenças,tais como fibrose cística, doença do olho seco, doença de Alzheimer, entre outras. Entretanto,a escassez de moléculas com propriedade antagonista seletiva sobre estes receptores dificultao avanço da caracterização de novos papéis funcionais associados a eles, e neste contexto, osprodutos naturais podem atuar como uma importante fonte para a descoberta de compostosque apresentem a característica almejada. Por isso, o objetivo deste trabalho foi padronizaruma metodologia de mensuração de cálcio intracelular induzido pelo UTP em células dalinhagem de macrófagos murinos J774.G8 e realizar a triagem de extratos oriundos deprodutos naturais a fim de identificar compostos com atividade antagonista sobre o P2Y2R eo P2Y4R. Para isso, foi padronizado um protocolo de carregamento celular com o indicadorde cálcio Fluo-4AM com posterior leitura dos sinais de cálcio no FlexStation III em células J774.G8...

The purinergic receptors are proteins expressed in plasma membrane of many cell types thatare activated by extracellular purines and pyrimidines. They are classified in P1 and P2receptors, according to physiological ligand. However, the P2R are further subdivided in twoclasses: P2X for ionotropic subtypes and P2Y for G-protein coupled ones. Among P2YR, theP2Y2 and P2Y4 subtypes has been widely studied due to their functions in many biologicalsystems. Once activated by UTP, these receptors promote the activation and inhibition of ionchannels, control the flow of ions through the membrane, induce an increase of intracellularcalcium and stimulate the cell proliferation. In view of this, many research groups have beenstudying the P2Y2 and P2Y4 as therapeutic targets for the treatment of several diseases likeCystic Fibrosis, Dry Eye Disease, Alzheimer, among others. However, the lack of moleculeswith selective antagonist property on these receptors difficults the advancement ofcharacterization of new functional roles associated with them, and in this context, naturalproducts may act as an important source for the discovery of compounds that present thisdesired feature. Therefore, the aim of this study was to standardize a methodology formeasurement of intracellular calcium mobilization induced by UTP in a murine macrophagecell line J774.G8 and perform the screening of extracts derived from natural products in orderto identify compounds with antagonist activity on the P2Y2R and P2Y4R. For this, it wasstandardized a protocol of cell labeling with calcium indicator Fluo-4AM in J774.G8 cellswith subsequent detection of calcium signals in FlexStation III...