Fosfatase Cdc25B: Interações transientes intramoleculares e complexação com pequenos ligantes / Cdc25B phosphatase: Transient intramolecular interactions and small molecules complexation

Proteínas tirosina-fosfatase (PTPs) possuem papel fundamental na regulação da transdução de sinais e estão envolvidas em diversos processos fundamentais do ciclo celular. As Cdc25 (Cell Division Cycle 25) são fosfatases duais encontradas em todos os organismos eucarióticos e atuam em checkpoints do ciclo celular, permitindo ou inibindo o prosseguimento deste. Este grupo de proteínas pertence à classe de PTPs com atividade baseada em cisteína, apresenta domínio catalítico altamente conservado assim como o motivo catalítico, P-loop. Devido sua função, as Cdc25 são consideradas possíveis alvos terapêuticos para tratamento de câncer e sua interação com pequenas moléculas e inibidores tem sido investigada de forma que análises estruturais e de ligação das Cdc25 com inibidores podem elucidar aspectos importantes do mecanismo de ação destes além de direcionar para o desenho racional de fármacos. Interações cátion-π são interações intra ou intermoleculares não-covalentes que ocorrem entre uma espécie química catiônica, como o grupo guanidino de argininas, e uma das faces de um sistema π rico em elétrons, como dos anéis indólicos de triptofanos. Apesar de pouco discutidas na literatura, quando em comparação às interações não-covalentes mais convencionais, do ponto de vista energético as interações cátion-π são tão importantes na estruturação de proteínas quanto às ligações de hidrogênio ou pontes salinas. De fato estas interações são observadas com frequência em estruturas proteicas resolvidas. O domínio catalítico da Cdc25B possui diversas argininas expostas em sua superfície e um único resíduo de triptofano localizado na região C-terminal flexível, muito próximo do sítio catalítico da proteína. A flexibilidade de proteínas ou de regiões proteicas apresenta importante papel no reconhecimento entre biomoléculas participantes de vias de sinalização e tem sido muito estudada atualmente. Aqui, simulações de dinâmica molecular, experimentos de 1H-15N HSQC RMN, ensaios de cinética de inibição e de ancoragem molecular, evidenciam a existência de contatos cátion-π transientes na superfície de um importante membro da família das Cdc25, a Cdc25B, e de sítios de interação entre inibidores testados e a proteína com destaque a sítios na proximidades do P-loop, região próxima ao C-terminal desordenado, onde se demonstra estabilidade da interação com os pequenos ligantes

Protein tyrosine phosphatase (PTPs) play a fundamental role in the regulation of signal transduction and are involved in several fundamental processes of the cell cycle. Cdc25 (Cell Division Cycle 25) are dual phosphatases found in all eukaryotic organisms and act at checkpoints of the cell cycle, allowing or inhibiting its progression. This group of proteins belongs to the class of PTPs with cysteine-based activity, presenting a highly conserved catalytic domain as well as the catalytic motif, P-loop. Due to their function, Cdc25 are considered possible therapeutic targets for cancer treatment and their interaction with small molecules and inhibitors has been investigated so that structural and binding analyzes of Cdc25 with inhibitors can elucidate important aspects of their mechanism of action besides directing to rational drug design. Cation-π interactions are non-covalent intra- or intermolecular interactions that occur between a cationic chemical species, such as the guanidino group of arginines, and one of the faces of an electron-rich system, such as the indole rings of tryptophans. Although little discussed in the literature, when compared to more conventional non-covalent interactions, from the energetic point of view, cation-π interactions are as important in the structuring of proteins as hydrogen bonds or salt bridges. In fact, these interactions are frequently observed in solved protein structures. The catalytic domain of Cdc25B has several arginines exposed on its surface and a single tryptophan residue located in the flexible C-terminal region, very close to the catalytic site of the protein. The flexibility of proteins or protein regions plays an important role in the recognition between biomolecules participating in signaling pathways and has been extensively studied today. Here, molecular dynamics simulations, 1H-15N HSQC NMR experiments, inhibition kinetics and molecular anchoring assays, evidence the existence of transient cation-π contacts on the surface of an important member of the Cdc25 family, Cdc25B, and of sites of interaction between tested inhibitors and the protein, with emphasis on sites in the vicinity of the P-loop, a region close to the disordered C-terminus, where stability of the interaction with the small ligands is demonstrated

Avaliação in vitro e in silico da atividade do S-(-)-Álcool Perílico sobre linhagens celulares do Carcinoma Epidermóide de Língua / In vitro and in silico evaluation of the activity of S-(-)-Peryllic Alcohol on Tongue Squamous Carcinoma cell lines

O carcinoma epidermóide oral (CEO) é a neoplasia maligna mais frequente da cavidade oral e constitui um problema de saúde pública devido a sua alta taxa de incidência e mortalidade devido em muitos casos ao fracasso terapêutico e a resistência tumoral. Assim sendo, destaca-se a busca por novas moléculas biologicamente ativas, como as encontradas nos produtos de origem natural. Este trabalho tem como objetivo avaliar a atividade antineoplásica do S-(-)-álcool perílico (POH) em culturas de células de CEO de língua e predizer sua afinidade através de modelo computacional sobre proteínas que regulam o ciclo celular. Para isso, foram utilizadas duas linhagens celulares de CEO de língua, HSC-3 e SCC-25. Os seguintes grupos foram analisados: G0 (controle; células cultivadas na ausência de POH), G1 (células tratadas com cisplatina a 40 µM), G2 (células tratadas com POH a 0,5 mM), G3 (células tratadas com POH a 1,0 mM), G4 (células tratadas com POH a 1,5 mM) e G5 (células tratadas com POH a 3,0 mM). Diferenças entre estes grupos foram investigadas através dos seguintes ensaios: viabilidade celular (Alamar Blue e Live/Dead assay) e atividade migratória (Wound healing). Foi também realizada a predição de afinidade entre o POH e as moléculas de controle do ciclo celular utilizando a docagem molecular com emprego do software Molegro Virtual Docker, v. 6.0.1. Os dados foram tratados estatisticamente pelo GraphPad Prism 6.0 (GraphPad Software, EUA), análises paramétricas utilizando teste Anova, pós-teste de Tukey e teste estatístico não-paramétricos de Kruskal-Wallis, seguido pelo teste t de estudent foram adotados para determinação de diferenças entre os grupos experimentais. O índice de significância considerado neste trabalho foi de 5%. Para ambas as técnicas de avaliação da viabilidade celular (Alamar Blue e Live/dead assay) analisadas neste trabalho, o POH foi capaz de reduzir a viabilidade celular de linhagens do CEO de língua de maneira dosedependente e tempo-dependente (p<0,05). As concentrações de 1,5 mM e 3 mM do POH obtiveram resultados melhores ou semelhantes aos encontrados na cisplatina 40 µM, para as duas linhagens, na avaliação da viabilidade celular (p<0,05). Os valores de IC50 do POH foram de 1,5 mM para a célula SCC-25 em todos os intervalos de tempo (24 h, 48 h e 72 h), uma vez que, para a linhagem HSC-3, foram de 3 mM para os tempos de 24 h e 48 h e de 1,5 mM para o intervalo de 72 h. O POH foi capaz de inibir a migração das duas linhagens celulares de CEO de maneira dependente da concentração (p≤0,05), comparados ao grupo controle. A habilidade da molécula POH se ligar a proteínas responsáveis pela ativação do ciclo celular foi avaliada usando docking models. Dentre elas, a proteína GTPase Kras mostrou a melhor energia de ligação (-86.70 kcal/mol), apresentando ligações de hidrogênio com os resíduos THR58 (A) e ASP57 (A) e ligações estéricas com os resíduos TRY32 (A) e ALA18 (A). As evidências deste estudo corroboram a ideia de que o POH possui atividade sobre o CEO, sugerindo que essa molécula possa ser uma forte candidata para o desenvolvimento de medicamentos direcionados ao tratamento desta patologia (AU).

Oral squamous cell carcinoma (OSCC) is the most frequent malignant neoplasm of the oral cavity and constitutes a public health problem due to its high incidence and mortality rate caused in many cases by therapeutic failure and tumor resistance. Therefore, the search for new biologically active molecules stands out, such as those found in products of natural origin. This work aims to evaluate the antineoplastic activity of S-(-)-perillyl alcohol (POH) in cell cultures of tongue CEO and to predict its affinity through a computer model on proteins that regulate the cell cycle. For this purpose, two cell lines of tongue CEO were used, HSC-3 and SCC-25. The following groups were analyzed: G0 (control; cells cultured in the absence of POH), G1 (cells treated with 40 µM cisplatin), G2 (cells treated with 0.5 mM POH), G3 (cells treated with 1 .0 mM), G4 (cells treated with 1.5 mM POH) and G5 (cells treated with 3.0 mM POH). Differences between these groups were investigated through the following assays: cell viability (Alamar Blue and Live/Dead assay) and migratory activity (Wound healing). Affinity prediction between POH and cell cycle control molecules were also performed using molecular docking using Molegro Virtual Docker, v. 6.0.1. The data was statistically treated by GraphPad Prism 6.0 (GraphPad Software, USA), parametric analysis using Anova test, Tukey post-test and Kruskal-Wallis non-parametric statistical test, followed by t student test were adopted for determination of differences between the experimental groups. The significance index considered in this work was 5%. For both cell viability assessment techniques (Alamar Blue and Live/dead assay) analyzed in this work, POH was able to reduce the cell viability of tongue CEO lines in a dose-dependent and time-dependent manner (p<0 .05). The concentrations of 1.5 mM and 3 mM of POH obtained better or similar results to those found in 40 µM cisplatin, for the two strains, in the evaluation of cell viability (p<0.05). The IC50 values of POH were 1.5 mM for the SCC-25 cell at all time intervals (24 h, 48 h and 72 h), since for the HSC-3 line they were 3 mM for 24 h and 48 h times and 1.5 mM for the 72 h interval. POH was able to inhibit the migration of the two DSC cell lines in a concentration-dependent manner (p≤0.05), compared to the control group. The ability of the POH molecule to bind to proteins responsible for cell cycle activation was evaluated using docking models. Among them, the protein GTPase Kras showed the best binding energy (-86.70 kcal/mol), featuring hydrogen bonds with residues THR58 (A) and ASP57 (A) and steric bonds with residues TRY32 (A) and ALA18 ( THE). The evidence from this study supports the idea that POH has antineoplastic activity on the CEO, suggesting that this molecule may be a strong candidate for the development of drugs aimed at the treatment of this pathology (AU).

Antibacterial effect of isoeugenol against Pseudomonas aeruginosa

Abatsract Pseudomonas aeruginosa is an important nosocomial pathogen and its clinical importance is mainly related to nosocomial infections. Increased rates of bacterial resistance in recent years has led WHO to publish a global priority list to guide research and discovery of new antibiotics, where P. aeruginosa is among the group of bacteria for which there is a critical level of priority for new drugs to be discovered. In this context, isoeugenol appears as an interesting alternative and the objective of this study was to investigate its action against P. aeruginosa. Isoeugenol presented significant antibacterial activity, with minimum inhibitory concentration (MIC) of 64µg/mL and minimum bactericidal concentration (MBC) of 128µg/mL, and was considered bactericidal against this species. Molecular docking revealed interactions that suggest that isoeugenol may bind to the enzyme Penicillin-Binding Protein 3 and interfere with the bacterial cell wall synthesis process. This study reinforces the antibacterial potential of this compound and emphasizes that more studies are needed in order to better investigate its mechanism of antibacterial action.

Traditional Chinese medicine network pharmacology study on exploring the mechanism of Xuebijing Injection in the treatment of coronavirus disease 2019 / 中国天然药物

As a representative drug for the treatment of severe community-acquired pneumonia and sepsis, Xuebijing (XBJ) injection is also one of the recommended drugs for the prevention and treatment of coronavirus disease 2019 (COVID-19), but its treatment mechanism for COVID-19 is still unclear. Therefore, this study aims to explore the potential mechanism of XBJ injection in the treatment of COVID-19 employing network pharmacology and molecular docking methods. The corresponding target genes of 45 main active ingredients in XBJ injection and COVID-19 were obtained by using multiple database retrieval and literature mining. 102 overlapping targets of them were screened as the core targets for analysis. Then built the PPI network, TCM-compound-target-disease, and disease-target-pathway networks with the help of Cytoscape 3.6.1 software. After that, utilized DAVID to perform gene ontology (GO) function enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis to predict the action mechanism of overlapping targets. Finally, by applying molecular docking technology, all compounds were docked with COVID-19 3 CL protease(3CLpro), spike protein (S protein), and angiotensin-converting enzyme II (ACE2). The results indicated that quercetin, luteolin, apigenin and other compounds in XBJ injection could affect TNF, MAPK1, IL6 and other overlapping targets. Meanwhile, anhydrosafflor yellow B (AHSYB), salvianolic acid B (SAB), and rutin could combine with COVID-19 crucial proteins, and then played the role of anti-inflammatory, antiviral and immune response to treat COVID-19. This study revealed the multiple active components, multiple targets, and multiple pathways of XBJ injection in the treatment of COVID-19, which provided a new perspective for the study of the mechanism of traditional Chinese medicine (TCM) in the treatment of COVID-19.

Identificación in silico de moléculas potencialmente inhibidoras de CDK5, proteína relacionada con la enfermedad de Alzheimer / Identification in silico of potentially inhibitive molecules of CDK5, protein related with the Alzheimer´s disease

Introducción: La enfermedad de Alzheimer exhibe un compromiso neurodegenerativo e irreversible. Hoy, numerosas investigaciones promueven la inhibición de algunas quinasas para su tratamiento, de especial mención la CDK5. Objetivo: Identificación de nuevas moléculas con posibilidad de interactuar con la proteína quinasa dependiente de ciclina 5, CDK5, inhibiendo su función. Material y Métodos: Se realizó un estudio in silico, para lo cual se extrajeron 911 moléculas de pubchem, y mediante AutoDock Vina se hicieron acoplamientos moleculares con la proteína CDK5 extraída de Protein Data Bank y con un inhibidor conocido para la proteína. Además se realizó un acoplamiento inverso para la identificación de otros posibles blancos moleculares con los mejores ligandos seleccionados. Resultados: Con los resultados obtenidos fueron identificadas cinco moléculas con valores de afinidad entre -11,6 hasta -17,7 Kcal/mol que se unen en el sitio activo de la proteína, de igual forma que lo hace el inhibidor conocido de la misma, e interactúan con los residuos cisteína 83 y glutamina 81. Conclusiones: Las moléculas identificadas pueden interactuar con la CDK5 a nivel de su sitio activo, por lo que podrían actuar como inhibidores de esta quinasa. Esto abre una futura ventana terapéutica en el tratamiento de la enfermedad de Alzheimer)AU)

Introduction: The illness of Alzheimer exhibits a neurodegenerative and irreversible commitment. Today, numerous investigations promote the inhibition of some kinases to the treatment, of special mention the CDK5. Objective: Identification of new molecules witch are able to interact with the cicline dependent kinase protein 5, CDK5, inhibiting their function. Material and Methods: it was carried out a study in silico, for that 911 pubchem molecules were extracted, and by means of AutoDock Vina molecular joining were made with the protein CDK5 extracted from the Protein Data Bank and with a well-known inhibitor for the protein. It was also carried out an inverse joining for the identification of other possible molecular targets with the best selected ligands. Results: With the obtained results five molecules were identified with values of likeness among -11,6 until -17,7 Kcal/mol that joins in the active site of the protein, in the same form that makes it the well-known inhibitor of the CDK5, and interact with the residuals cysteine 83 and glutamine 81. Conclusions: The identified molecules can interact with the CDK5 at level of their active place, for what you/they could act as inhibitors of this quinasa. This opens a future therapeutic window in the treatment of the illness of Alzheimer(AU)

Structural analysis and molecular docking of potential ligands with chorismate synthase of Listeria monocytogenes: A novel antibacterial drug target.

Listeriosis, in particular that caused by Listeria monocytogenes, is a major foodborne pathogen, and its control is becoming difficult because of widespread emergence of drug resistance strains. Chorismate synthase (CS), an essential enzyme of shikimate pathway present only in bacteria, fungi, plant and some apicomplexan parasites, is a validated potential antimicrobial drug target. Antimicrobial development through the elucidation of essential structural features of the CS of L. monocytogenes (LmCS), identification and prioritization of potential lead compounds targeted against LmCS were done. Structure-based virtual screening and docking studies were performed using Autodock tools to retrieve potential candidates with high affinity binding against LmCS model from several ligand repositories. The potency of binding was also checked with other structurally similar CS from Streptococcus pneumoniae (SpCS) and Mycobacterium tuberculosis (MtCS). The sequence and structural studies revealed LmCS was similar to be other CS structures (1Q1L, 1QXO, 1R52, 1R53, 1SQ1, 1UM0, 1UMF, 1ZTB, 2011, 2012, 4ECD and 2G85) with each monomer presenting β-α-β sandwich topology with a central helical core. Molecular docking studies and ADME/Tox results revealed that ZINC03803450 and ZINC20149031 were most potent molecules binding into the active site of LmCS. Other two ligands ZINC13387711 and ZINC16052528 showed a strong binding affinity score against all three structures (LmCS, SpCS and MtCS) and bind to LmCS with the predicted inhibition constant (Ki) values of 22.94 nM and 35.84 nM, respectively. A reported benzofuran-3[2H]-one analog CHEMBL135212 with good ADME/Tox properties and experimental IC50 (nM) value of 7000 nM with SpCS could also be considered as a potential inhibitor of LmCS, as compared to previously reported 41 benzofuran-3[2H]-one analogs against SpCS. This information will assist in discovering those compounds that may act as potent CS inhibitors. Further experimental studies and evaluation of structure-activity relationship could help in the development of potential inhibitors against listeriosis, as well as antibacterial chemotherapy.

Haloperidol inhibits Memapsin 2: innovation by docking simulation and in vitro assay

A number of drugs exhibit unexpected pharmacological effects related to their ability to bind more than one receptor in humans. Haloperidol a typical antipsychotic drug appeared in several reports to be used in schizophrenia patients in which the significant of Alzheimer's disease has been reduced. The etiology of the disease is characterized by aggregates of amyloid plaques, largely composed of amyloid- beta peptide formed from the amyloid precursor protein cleaved by Memapsin 2. To investigate if haloperidol can bind to Memapsin 2 active site, an initial molecular docking was performed as a preliminary in-silico screening test followed by in vitro enzyme inhibition assay. Haloperidol was found to fit readily in Memapsin binding site with IC50value 250mM. Haloperidol can be considered as important lead or important target can be modified for more inhibitory activity, with the intention of protection or treatment for Alzheimer's disease

In silico analysis of the structure and interaction of COP1 protein of Arabidopsis thaliana.

Previous studies have shown that COP1 (constitutive photomorphogenic 1) protein of Arabidopsis thaliana plays a crucial role in different aspects of photomorphogenesis. Interaction of COP1 with SPA1 (suppressor of phytochrome A) and other regulatory proteins actively affect light regulatory gene expression in diverse directions. Though several studies have explained the function of COP1 protein, method of its interaction with SPA1 and cryptochromes are still not explained in detail. In this study, in silico analysis was followed to predict the tertiary structure, active site residues, functionally important regions and regular expressions of COP1 protein. Its ease of its interaction with SPA1 and seven other regulatory proteins, namely bZIP transcription factor 56 (HY5), transcription factor HY5-like (HYH), serine/threonine-protein phosphatase 7 (AtPP7), protein long hypocotyl in FAR-RED 1 (HFR1), OBP3-responsive protein 1 (OBP3), transcription factor MYC2 (MYC2/ZBF1) and Z-box binding factor 2 protein (GBF1/ZBF2) was measured using protein-protein docking. Interaction with MYC2 was found to be stronger than with others with a global energy value of -22.46. It was also found that COP1 shared three regions of regular expression with SPA1, the last expression also being present in MYC2/ZBF1 and OBP3. Taken together, the insight into structural and functional properties of COP1 protein presented in this study would be helpful in determining the role of COP1 in unknown mechanisms of photomorphogenesis.

In-silico analysis of heat shock protein 47 for identifying the novel therapeutic agents in the management of oral submucous fibrosis.

Background: Heat shock proteins-47 (HSP47) is a collagen specific molecular chaperone, involved in the processing and/or secretion of procollagen. It seems to be regularly upregulated in various fibrotic or collagen disorders. Hence, this protein can be a potential target for the treatment of various fibrotic diseases including oral submucous fibrosis (OSF), which is a collagen metabolic disorder of oral cavity and whose etiopathogeneic mechanism and therapeutic protocols are still not well documented. Aim: The aim of this study is to identify the novel therapeutic agents using in-silico methods for the management of OSF. Objectives: The objectives of this study are to identify the binding sites of HSP47 on the collagen molecule and to identify the lead compound with anti-HSP47 activity from the library of natural compounds, using in-silico methodology. Materials and Methods: The web-based and tool based in-silico analysis of the HSP47 and collagen molecules are used in this study. The crystal structure of collagen and HSP47 were retrieved from Protein Data Bank website. The binding site identification and the docking studies are done using Molegro Virtual Docker offline tool. Results: Out of the 104 Natural compounds, six ligands are found to possess best binding affinity to the binding amino acid residues. Silymarin binds with the 4AU2A receptor and the energy value are found to be −178.193 with four Hbonds. The other best five natural compounds are hesperidin, ginkgolides, withanolides, resveratrol, and gingerol. Our findings provide the basis for the in-vitro validation of the above specified compounds, which can possibly act as "lead" molecules in designing the drugs for OSF. Conclusion: HSP47 can be a potential candidate to target, in order to control the production of abundance collagen in OSF. Hence, the binding sites of HSP47 with collagen are identified and some natural compounds with a potential to bind with these binding receptors are also recognized. These natural compounds might act as anti-HSP47 lead molecules in designing novel therapeutic agents for OSF, which are so far unavailable.

Molecular mapping of heterocyclic diazene derivatives for estrogen receptor modulation.

Selective estrogen receptor modulators (SERMs) are effectively used in hormone replacement therapy (HRT) by reducing post-menopausal symptoms, including hormone-responsive breast cancer and osteoporosis. The present study explored the pharmacophore features of diazene derivatives for selective estrogen receptor (ER) modulation using quantitative structure activity relationship (QSAR) and space modeling approaches. The 2D-QSAR models (R2α = 0.907, Q2α = 0.700, R2pred-α = 0.735; R2β = 0.913, Q2β = 0.756, R2pred-β = 0.745) showed the importance of orbital energies, hydrophobicity, refractivity and atomic charges for selective binding affinity to ER. In 3D-QSAR, molecular field (CoMFA, R2α = 0.948, Q2 = 0.720, R2pred-α = 0.708; R2β = 0.994, Q2β = 0.541, R2pred-β = 0.721) and similarity models (CoMSIA, R2α = 0.984, Q2α = 0.793, R2pred-α = 0.738; R2β = 0.996, Q2β = 0.681, R2pred-β = 0.725) indicated that steric and hydrophobic properties were important for binding selectivity. Space modeling study (R2α = 0.885, Q2α = 0.855, R2pred-α = 0.666; R2β = 0.872, Q2β = 0.883, R2pred-β = 0.814) revealed that hydrophobic and aromatic ring features were important for both subtypes, whereas hydrogen bond (HB) acceptor and donor were crucial for β- and α-subtypes, respectively. Interactions observed between ligand and catalytic residues at the active site in docking study substantiated the developed model which may be successfully used in high throughput screening (HTS) to obtain promising lead molecules for selective estrogen therapy.