Novel chalcones derivatives with potential antineoplastic activity investigated by docking and molecular dynamics simulations

Neto, Raimundo de Almeida Mira; Santos, Cleydson Breno Rodrigues dos; Henriques, Shayanne Vanessa Correia; Machado, Letícia de O; Cruz, Jorddy Neves; Silva, Carlos H. T. de P. da; Federico, Leonardo Bruno; Oliveira, Edivaldo Herculano Corrêa de; Souza, Michel Platini Caldas de; Silva, Patrícia N. B. da; Taft, Carlton A.; Ferreira, Irlon M.; Gomes, Madson Ralide Fonseca

doi:10.1080/07391102.2020.1839562

Cited by 55 publications

(25 citation statements)

References 46 publications

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“…Validation of molecular docking was performed for all of the executed experiments by comparing the alignments of the highly stable docking poses of the lead compound with the lead conformer co-crystallized with the respective enzyme from pdb. The RMSD (Root Mean Square Deviation) value was used to confirm the validity of the docking experiment, which in turn reflects the ability to predict the binding affinity of new ligands [23,24].…”

Section: In Silico Studies 281 Validation Of Molecular Docking Studie...mentioning

confidence: 99%

“…They showed RMSD values of 0.84, 1.11 and 1.83 Å for β-lactamase, DNA-gyrase and dihydrofolate reductase, respectively. Thus, it greatly ensured the validity of the docking experiment since RMSD was less than 2 angstroms [23,24] (Figure 4).…”

Section: Antimicrobial Activitymentioning

confidence: 99%

“…It is potentially valuable for reducing the level of colonization of chicks and could ultimately aid in decreasing the number of contaminated eggs in the food supply (4). QSAR studies indicated that activity against Gram-positive bacteria was controlled by the lipophilicity of the compound, while the topological steric nature of the molecule was a determining factor for antifungal activity [24,65].…”

Section: Molecular Docking Studiesmentioning

confidence: 99%

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Lobularia libyca: Phytochemical Profiling, Antioxidant and Antimicrobial Activity Using In Vitro and In Silico Studies

et al. 2022

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Lobularia libyca (L. libyca) is a traditional plant that is popular for its richness in phenolic compounds and flavonoids. The aim of this study was to comprehensively investigate the phytochemical profile by liquid chromatography, electrospray ionization and tandem mass spectrometry (LC-ESI-MS), the mineral contents and the biological properties of L. libyca methanol extract. L. libyca contains significant amounts of phenolic compounds and flavonoids. Thirteen compounds classified as flavonoids were identified. L. libyca is rich in nutrients such as Na, Fe and Ca. Moreover, the methanol extract of L. libyca showed significant antioxidant activity without cytotoxic activity on HCT116 cells (human colon cancer cell line) and HepG2 cells (human hepatoma), showing an inhibition zone of 13 mm in diameter. In silico studies showed that decanoic acid ethyl ester exhibited the best fit in β-lactamase and DNA gyrase active sites; meanwhile, oleic acid showed the best fit in reductase binding sites. Thus, it can be concluded that L. libyca can serve as a beneficial nutraceutical agent, owing to its significant antioxidant and antibacterial potential and due to its richness in iron, calcium and potassium, which are essential for maintaining a healthy lifestyle.

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Section: In Silico Studies 281 Validation Of Molecular Docking Studie...mentioning

confidence: 99%

Section: Antimicrobial Activitymentioning

confidence: 99%

Section: Molecular Docking Studiesmentioning

confidence: 99%

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Lobularia libyca: Phytochemical Profiling, Antioxidant and Antimicrobial Activity Using In Vitro and In Silico Studies

et al. 2022

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“…In this paper, we utilize molecular modeling approaches to fill the gap related to the molecular investigation of the structure of gelatin biofilms impregnated with bioactive compounds. This methodology has been used to investigate molecular systems of different types [25][26][27][28][29]. As a basis for our studies, we used the structure proposed by Hanani et al (2014) [30] to build the gelatin, and the work of Albuquerque et al (2020) [31] inspired us to carry out our molecular investigations.…”

Section: Introductionmentioning

confidence: 99%

Molecular Modeling Approaches Can Reveal the Molecular Interactions Established between a Biofilm and the Bioactive Compounds of the Essential Oil of Piper divaricatum

et al. 2022

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Molecular modeling approaches are used in a versatile way to investigate the properties of diverse organic and inorganic structures such as proteins, biomolecules, nanomaterials, functionalized nanoparticles, and membranes. However, more detailed studies are needed to understand the molecular nature of interactions established in gelatin biofilms impregnated with bioactive compounds. Because of this, we used computational methods to evaluate how the major compounds of Piper divaricatum essential oil can interact with the gelatin biofilm structure. For this, we used as inspiration the paper published, where various properties of the essential oil impregnated gelatin biofilm P. divaricatum are reported. After our computer simulations, we related our molecular observations to biofilm’s structural and mechanical properties. Our results suggest that the major compounds of the essential oil were able to interrupt intermolecular interactions between the chains of the biofilm matrix. However, the compounds also established interactions with the amino acid residues of these chains. Our molecular analyses also explain changes in the structural and mechanical properties of the essential oil-impregnated biofilm. These results can support the planning of functional packaging impregnated with bioactive compounds that can protect food against microorganisms harmful to human health.

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“…A modelagem molecular permiti a criação, manipulação de modelos representativos fidedignos as estruturas reais, permitindo também a realização de cálculos físico-químicos (Araújo et al, 2020;da Silva Júnior et al, 2021;Leão et al, 2020;Neto et al, 2020;Santana de Oliveira et al, 2020). Logo, a modelagem molecular é uma ferramenta para produção direta e indireta de potencias candidatos a fármacos.…”

Section: Introductionunclassified

Estudos de SAR e Docking Molecular para o desenvolvimento de novos inibidores da Tirosinase

Tangkin

Cruz

Vale

2022

RSD

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A tirosinase é uma enzima que participa da biossíntese da melanina. Logo, é considerada uma enzima muito importante para alguns processos fisiológicos, além disso, está envolvida desde o processo de escurecimento de algumas frutas até a neurodegeneração do Parkinson. Assim, o ácido kójico é um importante metabólito que possui a propriedade de inibição da enzima tirosinase em relação a produção de melanina. Com isso, o ácido kójico é muito utilizado na medicina, caracterizando-se dessa forma como importante para certos tipos de tratamentos. Sendo assim, neste projeto utilizamos abordagens de modelagem molecular para análises de derivados do ácido kójico, alvo molecular contra a enzima tirosinase, inicialmente a otimização e parametrização foram realizadas através do método semi-empírico PM3. Posteriormente os métodos foram otimizados pelo método TFD, em seguida utilizando o programa computacional MVD foi realizado os cálculos de energia para as moléculas. Tendo como guia para a definição de parâmetros estruturais a estrutura do Tropolone para as análises computacionais visando o ácido kójico e seus derivados. Dessa forma, os resultados obtidos nas simulações chegaram à satisfação. Baseado nos valores de energia obtidos através das análises, os derivados 2,3,8 e 9 são sugeridos como moléculas potenciais candidatos a inibidores da tirosina.

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Novel chalcones derivatives with potential antineoplastic activity investigated by docking and molecular dynamics simulations

Cited by 55 publications

References 46 publications

Lobularia libyca: Phytochemical Profiling, Antioxidant and Antimicrobial Activity Using In Vitro and In Silico Studies

Lobularia libyca: Phytochemical Profiling, Antioxidant and Antimicrobial Activity Using In Vitro and In Silico Studies

Molecular Modeling Approaches Can Reveal the Molecular Interactions Established between a Biofilm and the Bioactive Compounds of the Essential Oil of Piper divaricatum

Estudos de SAR e Docking Molecular para o desenvolvimento de novos inibidores da Tirosinase

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