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Trypanosoma cruzi (T. cruzi) causes Chagas, which is a neglected tropical disease (NTD). WHO estimates that 6 to 7 million people are infected worldwide. Current treatment is done with benznidazole (BZN), which is very toxic and effective only in the acute phase of the disease. In this work, we designed, synthesized, and characterized thirteen new phenoxyhydrazine-thiazole compounds and applied molecular docking and in vitro methods to investigate cell cytotoxicity, trypanocide activity, nitric oxide (NO) production, cell death, and immunomodulation. We observed a higher predicted affinity of the compounds for the squalene synthase and 14-alpha demethylase enzymes of T. cruzi. Moreover, the compounds displayed a higher predicted affinity for human TLR2 and TLR4, were mildly toxic in vitro for most mammalian cell types tested, and LIZ531 (IC50 2.8 µM) was highly toxic for epimastigotes, LIZ311 (IC50 8.6 µM) for trypomastigotes, and LIZ331 (IC50 1.9 µM) for amastigotes. We observed that LIZ311 (IC50 2.5 µM), LIZ431 (IC50 4.1 µM) and LIZ531 (IC50 5 µM) induced 200 µg/mL of NO and JM14 induced NO production in three different concentrations tested. The compound LIZ331 induced the production of TNF and IL-6. LIZ311 induced the secretion of TNF, IFNγ, IL-2, IL-4, IL-10, and IL-17, cell death by apoptosis, decreased acidic compartment formation, and induced changes in the mitochondrial membrane potential. Taken together, LIZ311 is a promising anti-T. cruzi compound is not toxic to mammalian cells and has increased antiparasitic activity and immunomodulatory properties.
Assuntos
Doença de Chagas , Simulação de Acoplamento Molecular , Óxido Nítrico , Tiazóis , Tripanossomicidas , Trypanosoma cruzi , Trypanosoma cruzi/efeitos dos fármacos , Tiazóis/farmacologia , Tiazóis/química , Doença de Chagas/tratamento farmacológico , Doença de Chagas/imunologia , Humanos , Animais , Camundongos , Óxido Nítrico/metabolismo , Óxido Nítrico/biossíntese , Tripanossomicidas/farmacologia , Tripanossomicidas/química , Concentração Inibidora 50 , Potencial da Membrana Mitocondrial/efeitos dos fármacos , Hidrazinas/farmacologia , Hidrazinas/química , Citocinas/metabolismo , Camundongos Endogâmicos BALB CRESUMO
The COVID-19 pandemic is already considered one of the biggest global health crises. In Rio Grande do Norte, a Brazilian state, the RegulaRN platform was the health information system used to regulate beds for patients with COVID-19. This article explored machine learning and deep learning techniques with RegulaRN data in order to identify the best models and parameters to predict the outcome of a hospitalized patient. A total of 25,366 bed regulations for COVID-19 patients were analyzed. The data analyzed comes from the RegulaRN Platform database from April 2020 to August 2022. From these data, the nine most pertinent characteristics were selected from the twenty available, and blank or inconclusive data were excluded. This was followed by the following steps: data pre-processing, database balancing, training, and test. The results showed better performance in terms of accuracy (84.01%), precision (79.57%), and F1-score (81.00%) for the Multilayer Perceptron model with Stochastic Gradient Descent optimizer. The best results for recall (84.67%), specificity (84.67%), and ROC-AUC (91.6%) were achieved by Root Mean Squared Propagation. This study compared different computational methods of machine and deep learning whose objective was to classify bed regulation data for patients with COVID-19 from the RegulaRN Platform. The results have made it possible to identify the best model to help health professionals during the process of regulating beds for patients with COVID-19. The scientific findings of this article demonstrate that the computational methods used applied through a digital health solution, can assist in the decision-making of medical regulators and government institutions in situations of public health crisis.
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Modulation of the CXCL12-CXCR4 signaling axis is of the utmost importance due to its central involvement in several pathological disorders, including inflammatory diseases and cancer. Among the different currently available drugs that inhibit CXCR4 activation, motixafortide-a best-in-class antagonist of this GPCR receptor-has exhibited promising results in preclinical studies of pancreatic, breast, and lung cancers. However, detailed information on the interaction mechanism of motixafortide is still lacking. Here, we characterize the motixafortide/CXCR4 and CXCL12/CXCR4 protein complexes by using computational techniques including unbiased all-atom molecular dynamics simulations. Our microsecond-long simulations of the protein systems indicate that the agonist triggers changes associated with active-like GPCR conformations, while the antagonist favors inactive conformations of CXCR4. Detailed ligand-protein analysis indicates the importance of motixafortide's six cationic residues, all of which established charge-charge interactions with acidic CXCR4 residues. Furthermore, two synthetic bulky chemical moieties of motixafortide work in tandem to restrict the conformations of important residues associated with CXCR4 activation. Our results not only elucidate the molecular mechanism by which motixafortide interacts with the CXCR4 receptor and stabilizes its inactive states, but also provide essential information to rationally design CXCR4 inhibitors that preserve the outstanding pharmacological features of motixafortide.
Assuntos
Antineoplásicos , Receptores CXCR4 , Receptores CXCR4/metabolismo , Ligação Proteica , Peptídeos/metabolismo , Quimiocina CXCL12/metabolismoRESUMO
Organophosphorus compounds (OP) make up an important class of inhibitors, mostly employed as pesticides, even as chemical weapons. These toxic substances act through the inhibition of the acetylcholinesterase (AChE) enzyme, which results in elevated synaptic acetylcholine (ACh) levels, leading to serious adverse effects under the cholinergic syndrome. Many reactivators have been developed to combat the toxic effects of these AChE inhibitors. In this line, the oximes highlight because of their good reactivating power of cholinesterase enzymes. To date, no universal antidotes can reactivate AChE inhibited by any OP agent. This review summarizes the intoxication process by neurotoxic OP agents, along with the development of reactivators capable of reversing their effects, approaching aspects like the therapeutic and toxicological profile of these antidotes. Computational methods and conscious in vitro studies, capable of significantly predicting the toxicological profile of these drug candidates, might support the process of development of these reactivators before entering in vivo studies in animals, and then clinical trials. These approaches can assist in the design of safer and more effective molecules, reducing related cost and time for the process.
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Antídotos , Reativadores da Colinesterase , Animais , Antídotos/farmacologia , Antídotos/uso terapêutico , Antídotos/química , Acetilcolinesterase/química , Reativadores da Colinesterase/uso terapêutico , Reativadores da Colinesterase/toxicidade , Compostos Organofosforados , Oximas/uso terapêutico , Oximas/toxicidade , Inibidores da Colinesterase/toxicidadeRESUMO
A rapid, efficient, and original synthesis of novel pyrido[3,2,1-de]phenanthridin-6-ones is reported. First, the key cinnamamide intermediates 8a-f were easily prepared from commercial substituted anilines, cinnamic acid, and 2-bromobenzylbromide in a tandem amidation and N-alkylation protocol. Then, these N-aryl-N-(2-bromobenzyl) cinnamamides 8a-f were subjected to a TFA-mediated intramolecular Friedel-Crafts alkylation followed by a Pd-catalyzed direct C-H arylation to obtain a series of potentially bioactive 4-phenyl-4,5-dihydro-6H,8H-pyrido[3,2,1-de]phenanthridin-6-one derivatives 4a-f in good yields. Finally, the toxicological profile of the prepared final compounds, including their corresponding intermediates, was explored through in silico computational methods, while the acute toxicity toward zebrafish embryos (96 hpf-LC50, 50% lethal concentration) was also determined in the present study.
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Peixe-Zebra , Animais , Alquilação , CiclizaçãoRESUMO
Ebola Virus (EBOV) is an infectious disease that mainly affects the cardiovascular system. It belongs to the Filoviridae family, consisting of filamentous envelopes and non-segmented negative RNA genome. EBOV was initially identified in Sudan and Zaire (now named the Democratic Republic of Congo) around 1967. It is transmitted mainly by contact with secretions (blood, sweat, saliva, and tears) from infected wild animals, such as non-human primates and bats. It has gained more prominence in recent years due to the recent EBOV outbreaks that occurred from 2013 to 2016, resulting in approximately 28,000 infected individuals, with a mortality rate of 40- 70%, affecting mainly Liberia, Guinea, and Sierra Leone. Despite these alarming levels, there is still no FDA-approved drug for the effective treatment of these diseases. The most advanced drug to treat EBOV is remdesivir. However, it is a high-cost drug and is available only for intravenous use. In this sense, more investments are needed in the research focused on the development of new antiviral drugs. In this context, medicinal chemistry strategies have been improving and increasingly discovering new hits that can be used in the future as a treatment against these diseases. Thus, this review will address the main advances in medicinal chemistry, such as drug discovery through computational techniques (virtual screening and virtual high throughput screening), drug repurposing, phenotypic screening assays, and employing classical medicinal chemistry, such as bioisosterism, metabolism-based drug design, and the discovery of new inhibitors through natural products, thereby presenting several promising compounds that may contain the advance of these pathogens.
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Produtos Biológicos , Ebolavirus , Doença pelo Vírus Ebola , Animais , Ebolavirus/genética , Doença pelo Vírus Ebola/tratamento farmacológico , Doença pelo Vírus Ebola/epidemiologia , Química Farmacêutica , Descoberta de Drogas , Antivirais/farmacologia , Antivirais/uso terapêutico , Antivirais/química , Produtos Biológicos/farmacologia , RNA/farmacologia , RNA/uso terapêuticoRESUMO
This chapter provides two main contributions: (1) a description of computational tools and databases used to identify and analyze transposable elements (TEs) and circRNAs in plants; and (2) data analysis on public TE and circRNA data. Our goal is to highlight the primary information available in the literature on circular noncoding RNAs and transposable elements in plants. The exploratory analysis performed on publicly available circRNA and TEs data help discuss four sequence features. Finally, we investigate the association on circRNAs:TE in plants in the model organism Arabidopsis thaliana.
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Arabidopsis , Elementos de DNA Transponíveis , Arabidopsis/genética , Biologia Computacional , Elementos de DNA Transponíveis/genética , Plantas/genética , RNA CircularRESUMO
Among the compounds of natural origin, diterpenes have proved useful as drugs for the treatment of cancer. Marine organisms, such as soft corals and algae, are a promising source of diterpenes, being a rich and unexplored source of cytotoxic agents. This study evaluated a library of 32 natural and semisynthetic marine diterpenes, including briarane, cembrane, and dolabellane nuclei, with the aim of determining their cytotoxicity against three human cancer cell lines (A549, MCF7, and PC3). The three most active compounds were submitted to a flow cytometry analysis in order to determine induction of apoptosis against the A549 cell line. An NMR analysis was conducted to determine and evaluate the interactions between active diterpenes and tubulin. These interactions were characterized by a computational study using molecular docking and MD simulations. With these results, two cembrane and one chlorinated briarane diterpenes were active against the three human cancer cell lines, induced apoptosis in the A549 cell line, and showed interactions with tubulin preferably at the taxane-binding site. This study is a starting point for the identification and optimization of the marine diterpenes selected for better antitumor activities. It also highlights the power of integrating NMR studies, computational predictions, and in vitro assays in the search for compounds with antitumor activity.
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Antozoários/química , Antineoplásicos/química , Produtos Biológicos/química , Misturas Complexas/química , Diterpenos/química , Bibliotecas de Moléculas Pequenas/química , Animais , Antineoplásicos/farmacologia , Apoptose/efeitos dos fármacos , Produtos Biológicos/farmacologia , Linhagem Celular Tumoral , Misturas Complexas/farmacologia , Biologia Computacional , Diterpenos/farmacologia , Ensaios de Seleção de Medicamentos Antitumorais , Halogenação , Humanos , Espectroscopia de Ressonância Magnética , Modelos Moleculares , Bibliotecas de Moléculas Pequenas/farmacologia , Relação Estrutura-AtividadeRESUMO
The construction of forest roads in Brazilian Amazon is costly and has a significant environmental impact. Several practices and principles must be observed to comply with legislation, to preserve the remaining forest, and to ensure sustainable exploitation. Road planning is complex in this context, based on the number of aspects and variables that must be considered. This research aimed to evaluate computational methods' effectiveness in planning forest roads, optimizing resources to reduce damage to the remaining forest, compared to traditional planning methods. The study area was a native forest under a sustainable forest management regime located in municipalities of Terra Santa and Oriximiná, in Pará, in Brazilian Amazon. Data obtained from area made it possible formulate six instances of different sizes. A binary integer linear programming model was used, solved using CPLEX software, and Dijkstra, Bellman-Ford, Dial, and D'Esopo-Pape shortest path algorithm, implemented in C programming language. During processing of instances, the time taken to obtain the solution increased according to size of instance, however, time difference was not significant. Among the evaluated algorithms, the D'Esopo-Pape algorithm showed the best performance. The evaluated methods were effective in obtaining an optimal solution for proposed forest road planning. The solutions obtained using computational methods more effectively considered the restrictions associated with sustainable forest management, in contrast to those derived from the traditional planning by forestry company.
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Conservação dos Recursos Naturais , Florestas , Brasil , Agricultura Florestal , Técnicas de PlanejamentoRESUMO
Trypsin inhibitors from tamarind seed have been studied in vitro and in preclinical studies for the treatment of obesity, its complications and associated comorbidities. It is still necessary to fully understand the structure and behaviour of these molecules. We purifed this inhibitor, sequenced de novo by MALDI-TOF/TOF, performed its homology modelling, and assessed the interaction with the trypsin enzyme through molecular dynamics (MD) simulation under physiological conditions. We identified additional 75 amino acid residues, reaching approximately 72% of total coverage. The four best conformations of the best homology modelling were submitted to the MD. The conformation n°287 was selected considering the RMSD analysis and interaction energy (-301.0128 kcal.mol-1). Residues Ile (54), Pro (57), Arg (59), Arg (63), and Glu (78) of pTTI presented the highest interactions with trypsin, and arginine residues were mainly involved in its binding mechanism. The results favour bioprospecting of this protein for pharmaceutical health applications.
Assuntos
Simulação de Dinâmica Molecular , Extratos Vegetais/farmacologia , Tamarindus/química , Inibidores da Tripsina/farmacologia , Tripsina/metabolismo , Relação Dose-Resposta a Droga , Estrutura Molecular , Extratos Vegetais/química , Extratos Vegetais/isolamento & purificação , Sementes/química , Relação Estrutura-Atividade , Inibidores da Tripsina/química , Inibidores da Tripsina/isolamento & purificaçãoRESUMO
Experimental methods are indispensable for the study of the function of biological macromolecules, not just as static structures, but as dynamic systems that change conformation, bind partners, perform reactions, and respond to different stimulus. However, providing a detailed structural interpretation of the results is often a very challenging task. While experimental and computational methods are often considered as two different and separate approaches, the power and utility of combining both is undeniable. The integration of the experimental data with computational techniques can assist and enrich the interpretation, providing new detailed molecular understanding of the systems. Here, we briefly describe the basic principles of how experimental data can be combined with computational methods to obtain insights into the molecular mechanism and expand the interpretation through the generation of detailed models.
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Biologia Computacional , Substâncias Macromoleculares/ultraestrutura , Modelos Moleculares , HumanosRESUMO
Organophosphorus (OP) compounds are used as both chemical weapons and pesticides. However, these agents are very dangerous and toxic to humans, animals, and the environment. Thus, investigations with reactivators have been deeply developed in order to design new antidotes with better efficiency, as well as a greater spectrum of action in the acetylcholinesterase (AChE) reactivation process. With that in mind, in this work, we investigated the behavior of trimedoxime toward the Mus musculus acetylcholinesterase (MmAChE) inhibited by a range of nerve agents, such as chemical weapons. From experimental assays, reactivation percentages were obtained for the reactivation of different AChE-OP complexes. On the other hand, theoretical calculations were performed to assess the differences in interaction modes and the reactivity of trimedoxime within the AChE active site. Comparing theoretical and experimental data, it is possible to notice that the oxime, in most cases, showed better reactivation percentages at higher concentrations, with the best result for the reactivation of the AChE-VX adduct. From this work, it was revealed that the mechanistic process contributes most to the oxime efficiency than the interaction in the site. In this way, this study is important to better understand the reactivation process through trimedoxime, contributing to the proposal of novel antidotes.
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Reativadores da Colinesterase/química , Trimedoxima/farmacologia , Trimedoxima/uso terapêutico , Acetilcolinesterase/metabolismo , Animais , Antídotos/farmacologia , Inibidores da Colinesterase/metabolismo , Inibidores da Colinesterase/farmacologia , Reativadores da Colinesterase/farmacologia , Biologia Computacional/métodos , Humanos , Camundongos , Agentes Neurotóxicos/química , Compostos Organofosforados/química , Oximas/química , RatosRESUMO
Cancer is a complex disease caused by the accumulation of genetic alterations during the individual's life. Such alterations are called genetic mutations and can be divided into two groups: (1) Passenger mutations, which are not responsible for cancer and (2) Driver mutations, which are significant for cancer and responsible for its initiation and progression. Cancer cells undergo a large number of mutations, of which most are passengers, and few are drivers. The identification of driver mutations is a key point and one of the biggest challenges in Cancer Genomics. Many computational methods for such a purpose have been developed in Cancer Bioinformatics. Such computational methods are complex and are usually described in a high level of abstraction. This tutorial details some classical computational methods, from a computational perspective, with the transcription in an algorithmic format towards an easy access by researchers.
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Biologia Computacional/métodos , Genômica/métodos , Mutação , Neoplasias/genética , Algoritmos , Redes Reguladoras de Genes , HumanosRESUMO
Staphylococcus aureus is a notorious pathogenic bacterium causing a wide range of diseases from soft-tissue contamination, to more serious and deep-seated infections. This species is highlighted by its ability to express several kinds of virulence factors and to acquire genes related to drug resistance. Target this number of factors to design any drug is not an easy task. In this review, we discuss the importance of computational methods to impulse the development of new drugs against S. aureus. The application of docking methods to screen large libraries of natural or synthetic compounds and to provide insights into action mechanisms is demonstrated. Particularly, the studies that validated in silico results with biochemical and microbiological assays are highlighted. We also comment on the computer-aided design of new molecules using some known inhibitors. The confirmation of in silico results with biochemical and microbiological assays allowed the identification of lead molecules that could be used for drug design such as rhodomyrtone, quinuclidine, berberine (and their derivative compounds). The fast development of the computational methods is essential to improve our ability to discover new drugs, as well as to expand understanding about drug-target interactions.
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Antibacterianos/farmacologia , Simulação de Acoplamento Molecular , Staphylococcus aureus/efeitos dos fármacos , Antibacterianos/química , Antibacterianos/uso terapêutico , Proteínas de Bactérias/antagonistas & inibidores , Proteínas de Bactérias/metabolismo , Replicação do DNA/efeitos dos fármacos , Desenho de Fármacos , Humanos , Proteínas Associadas à Resistência a Múltiplos Medicamentos/antagonistas & inibidores , Proteínas Associadas à Resistência a Múltiplos Medicamentos/metabolismo , Infecções Estafilocócicas/tratamento farmacológico , Infecções Estafilocócicas/patologia , Staphylococcus aureus/genética , Staphylococcus aureus/metabolismoRESUMO
The green Brazilian bay leaf, a spice much prized in local cuisine (Aniba riparia, Lauraceae), contains chemical compounds presenting benzoyl-derivatives named riparins, which have anti-inflammatory, antimicrobial and anxiolytic properties. However, it is unclear what kind of interaction riparins perform with any molecular target. As a profitable target, human serum albumin (HSA) is one of the principal extracellular proteins, with an exceptional capacity to interact with several molecules, and it also plays a crucial role in the transport, distribution, and metabolism of a wide variety of endogenous and exogenous ligands. To outline the HSA-riparin interaction mechanism, spectroscopy and computational methods were synergistically applied. An evaluation through fluorescence spectroscopy showed that the emission, attributed to Trp 214, at 346 nm decreased with titrations of riparins. A static quenching mechanism was observed in the binding of riparins to HSA. Fluorescence experiments performed at 298, 308 and 318 K made it possible to conduct thermodynamic analysis indicating a spontaneous reaction in the complex formation (ΔG<0). The enthalpy-entropy balance experiment with a molecular modeling calculation revealed that hydrophobic, hydrogen bond and non-specific interactions are present for riparin I-III with HSA. The set of results from fractional fluorescence changes obtained through Schatchard was inconclusive in establishing what kind of cooperativity is present in the interaction. To shed light upon the HSA-riparins complex, Hill's approach was utilized to distinguish the index of affinity and the binding constant. A correspondence between the molecular structures of riparins, due to the presence of the hydroxyl group in the B-ring, with thermodynamic parameters and index of affinity were observed. Riparin III performs an intramolecular hydrogen bond, which affects the Hill coefficient and the binding constant. Therefore, the presence of hydroxyl groups is capable of modulating the interaction between riparins and HSA. Site marker competitive experiments indicated Site I as being the most suitable, and the molecular modeling tools reinforced the experimental results detailing the participation of residues.
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Benzamidas/metabolismo , Albumina Sérica Humana/metabolismo , Benzamidas/química , Humanos , Cinética , Ligantes , Modelos Moleculares , Ligação Proteica , Albumina Sérica Humana/química , Espectrometria de Fluorescência , TermodinâmicaRESUMO
Chemical weapons are a major worldwide problem, since they are inexpensive, easy to produce on a large scale and difficult to detect and control. Among the chemical warfare agents, we can highlight the organophosphorus compounds (OP), which contain the phosphorus element and that have a large number of applications. They affect the central nervous system and can lead to death, so there are a lot of works in order to design new effective antidotes for the intoxication caused by them. The standard treatment includes the use of an anticholinergic combined to a central nervous system depressor and an oxime. Oximes are compounds that reactivate Acetylcholinesterase (AChE), a regulatory enzyme responsible for the transmission of nerve impulses, which is one of the molecular targets most vulnerable to neurotoxic agents. Increasingly, enzymatic treatment becomes a promising alternative; therefore, other enzymes have been studied for the OP degradation function, such as phosphotriesterase (PTE) from bacteria, human serum paraoxonase 1 (HssPON1) and diisopropyl fluorophosphatase (DFPase) that showed significant performances in OP detoxification. The understanding of mechanisms by which enzymes act is of extreme importance for the projection of antidotes for warfare agents, and computational chemistry comes to aid and reduce the time and costs of the process. Molecular Docking, Molecular Dynamics and QM/MM (quantum-mechanics/molecular-mechanics) are techniques used to investigate the molecular interactions between ligands and proteins.
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Sea anemone neurotoxins are peptides that interact with Na(+) and K(+) channels, resulting in specific alterations on their functions. Some of these neurotoxins (1ROO, 1BGK, 2K9E, 1BEI) are important for the treatment of about 80 autoimmune disorders because of their specificity for Kv1.3 channel. The aim of this study was to identify the common residues among these neurotoxins by computational methods, and establish whether there is a pattern useful for the future generation of a treatment for autoimmune diseases. Our results showed eight new key common residues between the studied neurotoxins interacting with a histidine ring and the selectivity filter of the receptor, thus showing a possible pattern of interaction. This knowledge may serve as an input for the design of more promising drugs for autoimmune treatments.