scholarly journals In Silico Studies on Compounds Derived from Calceolaria: Phenylethanoid Glycosides as Potential Multitarget Inhibitors for the Development of Pesticides

Biomolecules ◽  
2018 ◽  
Vol 8 (4) ◽  
pp. 121 ◽  
Author(s):  
Marco Loza-Mejía ◽  
Juan Salazar ◽  
Juan Sánchez-Tejeda
Keyword(s):  
In Silico ◽  
Large Scale ◽  
Insect Pests ◽  
Insect Growth Regulator ◽  
Mechanisms Of Action ◽  
Ecdysone Receptor ◽  
Phenylethanoid Glycosides ◽  
In Silico Studies ◽  
In Silico Study ◽  
Potential Applications

An increasing occurrence of resistance in insect pests and high mammal toxicity exhibited by common pesticides increase the need for new alternative molecules. Among these alternatives, bioinsecticides are considered to be environmentally friendly and safer than synthetic insecticides. Particularly, plant extracts have shown great potential in laboratory conditions. However, the lack of studies that confirm their mechanisms of action diminishes their potential applications on a large scale. Previously, we have reported the insect growth regulator and insecticidal activities of secondary metabolites isolated from plants of the Calceolaria genus. Herein, we report an in silico study of compounds isolated from Calceolaria against acetylcholinesterase, prophenoloxidase, and ecdysone receptor. The molecular docking results are consistent with the previously reported experimental results, which were obtained during the bioevaluation of Calceolaria extracts. Among the compounds, phenylethanoid glycosides, such as verbascoside, exhibited good theoretical affinity to all the analyzed targets. In light of these results, we developed an index to evaluate potential multitarget insecticides based on docking scores.

scholarly journals In silico study of azithromycin, chloroquine and hydroxychloroquine and their potential mechanisms of action against SARS-CoV-2 infection

2020 ◽  
Vol 56 (3) ◽  
pp. 106119 ◽  
Author(s):  
Helyson Lucas Bezerra Braz ◽  
João Alison de Moraes Silveira ◽  
Aline Diogo Marinho ◽  
Maria Elisabete Amaral de Moraes ◽  
Manoel Odorico de Moraes Filho ◽  
...  
Keyword(s):  
In Silico ◽  
Mechanisms Of Action ◽  
In Silico Study

Phytochemicals as Therapeutics Against COVID-19: An In-Silico Study

2020 ◽  
Author(s):  
Debraj Koiri ◽  
Ditam Chakraborty ◽  
Pranotosh Das ◽  
Rajkumar Rana ◽  
Soumyanil Chatterjee ◽  
...  
Keyword(s):  
In Silico ◽  
Therapeutic Agents ◽  
Binding Energies ◽  
Daily Lives ◽  
Lab Experiments ◽  
In Silico Studies ◽  
In Silico Study ◽  
The World ◽  
Wet Lab ◽  
Low Costs

Since December 2019, the worldwide spread of COVID-19 has brought the majority of the world to a standstill, affecting daily lives as well as economy. Under these conditions, it is imperative to develop a cure as soon as possible. On account of some of the adverse side effects of the existing conventional drugs, researchers all around the world are screening natural antiviral phytochemicals as potential therapeutic agents against COVID-19. This paper aims to review interactions of some specific phytochemicals with the receptor binding domain (RBD) of the Spike glycoprotein of SARS-CoV-2 and suggest their possible therapeutic applications. Literature search was done based on the wide array of in-silico studies conducted using broad spectrum phytochemicals against SARS-CoV-2 and other viruses. We shortlisted 26 such phytochemicals specifically targeting the S protein and its interactions with host receptors. To validate the previously published results, we also conducted molecular docking using the AutoDockVina application and identified 6 high potential phytochemicals for therapeutic use based on their binding energies. Besides this, availability of these compounds, their mode of action, toxicity data and cost-effectiveness were also taken into consideration. Our review specifically identifies 6 phytochemicals that can be used as potential treatments for COVID-19 based on their availability, toxicology results and low costs of production. However, all these compounds need to be further validated by wet lab experiments and should be approved for clinical use only after appropriate trials.

The Potency of Catechin from Gambir (Uncaria gambir Roxb.) as a Natural Inhibitor of MurA (1UAE) Enzyme: In vitro and In silico studies

2020 ◽  
Vol 17 (12) ◽  
pp. 1531-1537
Author(s):  
Bella Riyana ◽  
Desi Harneti Putri Huspa ◽  
Mieke Hemiawati Satari ◽  
Dikdik Kurnia
Keyword(s):  
Cell Wall ◽  
Bacterial Cell ◽  
In Silico ◽  
Bacterial Activity ◽  
Bacterial Cell Wall ◽  
Resistant Bacteria ◽  
In Silico Studies ◽  
In Silico Study ◽  
Natural Inhibitor

Background: Currently, infectious diseases caused by pathogenic and resistant bacteria are more challenging for anti-bacterial drug discovery. The discovery of new anti-bacterial agents developed in many mechanisms includes disruption of the bacterial cell wall formations. The MurA is a key enzyme contributing to the first step of bacterial peptidoglycan biosynthesis and is, therefore, proposed as an effective bactericidal target. Objective: The purpose of this research is to identify anti-bacterial compounds from U. gambir Roxb and to predict the potential inhibitory activities against murA enzyme by in silico study. Materials and Methods: Investigation and discovery of new inhibitors of MurA enzyme were conducted on the medicinal plant of Gambir (Uncaria gambir Roxb) and those that reportedly contained anti-bacterial agents. The anti-bacterial compounds were isolated by combinations of chromatography methods guided by anti-bacterial activity against bacteria of E. faecalis, S. mutans, and S. sanguinis. The structures of active compounds were characterized by spectroscopic methods, and the anti-bacterial activity was evaluated by the microdilution method (in vitro) combined with molecular docking of the MurA enzyme (in silico). Results: The anti-bacterial flavonoids of catechin were isolated from U. gambir Roxb with MIC values of 6250 and 12500 ppm, respectively, against S. sanguinis and E. faecalis. The in silico study showed that catechin has a binding affinity of -8.5 Kcal/mol to MurA which is higher than fosfomycin as a positive control. Conclusions: The catechin is predicted to have potential as a new natural inhibitor of the MurA enzyme to inhibit bacterial cell wall biosynthesis.

Multi-Target Drugs Against Metabolic Disorders

2019 ◽  
Vol 19 (4) ◽  
pp. 402-418 ◽  
Author(s):  
Luciana Scotti ◽  
Alex France Messias Monteiro ◽  
Jéssika de Oliveira Viana ◽  
Francisco Jaime Bezerra Mendonça Junior ◽  
Hamilton M. Ishiki ◽  
...  
Keyword(s):  
In Silico ◽  
Metabolic Disorders ◽  
The Body ◽  
Target Drug ◽  
Body Tissues ◽  
In Silico Studies ◽  
Hybrid Molecules ◽  
In Silico Study ◽  
Diabetes And Obesity ◽  
New Strategies

Background: Metabolic disorders are a major cause of illness and death worldwide. Metabolism is the process by which the body makes energy from proteins, carbohydrates, and fats; chemically breaking these down in the digestive system towards sugars and acids which constitute the human body's fuel for immediate use, or to store in body tissues, such as the liver, muscles, and body fat. Objective: The efficiency of treatments for multifactor diseases has not been proved. It is accepted that to manage multifactor diseases, simultaneous modulation of multiple targets is required leading to the development of new strategies for discovery and development of drugs against metabolic disorders. Methods: In silico studies are increasingly being applied by researchers due to reductions in time and costs for new prototype synthesis; obtaining substances that present better therapeutic profiles. Discussion: In the present work, in addition to discussing multi-target drug discovery and the contributions of in silico studies to rational bioactive planning against metabolic disorders such as diabetes and obesity, we review various in silico study contributions to the fight against human metabolic pathologies. Conclusion: In this review, we have presented various studies involved in the treatment of metabolic disorders; attempting to obtain hybrid molecules with pharmacological activity against various targets and expanding biological activity by using different mechanisms of action to treat a single pathology.

scholarly journals Global In-Silico Scenario of tRNA Genes and Their Organization in Virus Genomes

Viruses ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 180 ◽  
Author(s):  
Sergio Morgado ◽  
Ana Vicente
Keyword(s):  
In Silico ◽  
Large Scale ◽  
Trna Gene ◽  
Gene Clusters ◽  
Trna Genes ◽  
Genome Survey ◽  
In Silico Study ◽  
Domains Of Life ◽  
Dsdna Viruses ◽  
Virus Genomes

Viruses are known to be highly dependent on the host translation machinery for their protein synthesis. However, tRNA genes are occasionally identified in such organisms, and in addition, few of them harbor tRNA gene clusters comprising dozens of genes. Recently, tRNA gene clusters have been shown to occur among the three domains of life. In such a scenario, the viruses could play a role in the dispersion of such structures among these organisms. Thus, in order to reveal the prevalence of tRNA genes as well as tRNA gene clusters in viruses, we performed an unbiased large-scale genome survey. Interestingly, tRNA genes were predicted in ssDNA (single-stranded DNA) and ssRNA (single-stranded RNA) viruses as well in many other dsDNA viruses of families from Caudovirales order. In the latter group, tRNA gene clusters composed of 15 to 37 tRNA genes were characterized, mainly in bacteriophages, enlarging the occurrence of such structures within viruses. These bacteriophages were from hosts that encompass five phyla and 34 genera. This in-silico study presents the current global scenario of tRNA genes and their organization in virus genomes, contributing and opening questions to be explored in further studies concerning the role of the translation apparatus in these organisms.

scholarly journals Astrocytes as the Glucose Shunt for Glutamatergic Neurons at High Activity: An In Silico Study

2009 ◽  
Vol 101 (5) ◽  
pp. 2528-2538 ◽  
Author(s):  
Rossana Occhipinti ◽  
Erkki Somersalo ◽  
Daniela Calvetti
Keyword(s):  
High Activity ◽  
In Silico ◽  
Lactate Shuttle ◽  
Glutamatergic Neurons ◽  
Flux Balance ◽  
In Silico Studies ◽  
In Silico Study ◽  
Balance Analysis ◽  
Remarkable Agreement ◽  
Brain Energetics

The question of the preferred substrate of glutamatergic neurons at high neural activity has been vibrantly debated for over a decade since the classical hypothesis (CH) of the primacy of glucose has been challenged by the astrocyte-neuron lactate shuttle hypothesis (ANLSH), which replaces the primacy of glucose with astrocyte produced lactate. We perform Bayesian Flux Balance Analysis (BFBA) with a new mathematical model of cellular brain energetics, comprising detailed biochemical pathways in and between astrocytes and glutamatergic neurons and partitioning of each cell type into cytosol and mitochondria. Supported by the results of our in silico studies, which are in remarkable agreement with previously published results, we posit the Glucose Shunt Hypothesis (GSH) that during high activity, the inhibition of the phosphofructokinase (PFK) enzyme in neuron impairs neuronal glycolysis, enabling the process by which lactate effluxed by astrocytes is taken up by glutamatergic neurons, whereas at low activity, glucose remains the preferred substrate for neurons. We postulate that the ANLS is a shunt utilized by glutamatergic neurons to bypass their glycolysis impaired by the inhibition of PFK in connection with increased oxidative phosphorylation at high neuronal activity.

Synthesis, antineoplastic activity and in silico studies of (S)-N-(1-hydroxy-3-methylbutan-2-yl)-3-(p-tolyl)-1,2,4-oxadiazole-5-carboxamide

2021 ◽  
Vol 25 (7) ◽  
pp. 167-176
Author(s):  
Cláudia Laís Araújo Almeida Santos ◽  
Jonh Anderson Macêdo Santos ◽  
Rodrigo Ribeiro Alves Caiana ◽  
Silvia Maria Souza ◽  
Jucleiton José Rufino Freitas ◽  
...  
Keyword(s):  
In Silico ◽  
Low Cost ◽  
Docking Study ◽  
New Drugs ◽  
Molecular Docking Study ◽  
Traditional Medicines ◽  
In Silico Studies ◽  
In Silico Study ◽  
Pharmacokinetic Properties ◽  
Low Toxicity

The development of chemotherapy agents without side effects is a major challenge, since traditional medicines usually have undesirable properties such as high toxicity, resistance and low bioavailability. In this sense, computational methods play a crucial role in the discovery and optimization of new drugs, as they combine speed and efficiency with low cost. The 1,2,4-oxadiazoles are one of the main classes of heterocyclics due to their numerous biological applications. In this work, we report the synthesis, antineoplastic evaluation and in silico study of a new 1,2,4-oxadiazole. The (S)-N-(1-hydroxy-3-methylbutan-2-yl)-3-(p-toluyl)-1,2,4-oxadiazole-5-carboxamide was obtained after two reaction steps in excellent yield. Although it has shown low activity in relation to the MCF-7, HCT116 and HL60 tumor cell lines, the molecular docking study indicates that this compound acts in the colchicine site and can inhibit tubulin polymerization. From the calculation of pharmacokinetic properties by the SwissADME and Osiris Property Explorer programs, it is possible to infer that the compound meets the Lipinski rules presenting good oral bioavailability and low toxicity.

scholarly journals In silico study of wall-associated kinase family reveals large-scale genomic expansion potentially connected with functional diversification in Populus

2014 ◽  
Vol 10 (5) ◽  
pp. 1135-1147 ◽  
Author(s):  
Kévin Tocquard ◽  
Clément Lafon-Placette ◽  
Daniel Auguin ◽  
Beatriz Muries ◽  
Gisèle Bronner ◽  
...  
Keyword(s):  
In Silico ◽  
Large Scale ◽  
Functional Diversification ◽  
Kinase Family ◽  
In Silico Study ◽  
Genomic Expansion
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