The physical studies and interaction with anti-apoptotic proteins of 2-(bis(cyanomethyl)amino)-2-oxoethyl methacrylate molecule

Yalçın, Serap; Sas, E.B.; Çankaya, Nevin; Ercan, Filiz; Kurt, Mustafa

doi:10.5488/cmp.22.33301

Condens. Matter Phys.

2019

DOI: 10.5488/cmp.22.33301

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The physical studies and interaction with anti-apoptotic proteins of 2-(bis(cyanomethyl)amino)-2-oxoethyl methacrylate molecule

Serap Yalçın¹,

E.B. Sas²,

Nevin Çankaya³

et al.

Abstract: In this work 2-(bis(cyanomethyl)amino)-2-oxoethyl methacrylate (CMA2OEM) molecule has been characterized theoretically. First, the potential energy surface has been calculated to find the lowest energy state of the molecule. After the most stable state of the molecule, Mulliken atomic charge and nonlinear-optical properties were investigated. Also in the study, binding poses of CMA2OEM molecule and anti-apoptotic proteins, such as BCL-2, BCL-w, MCL-1, AKT1 and BRAF were investigated. The molecular docking resu… Show more

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Cited by 3 publications

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Determination of Potential Drug Candidate Molecules of the Hypericum perforatum for COVID-19 Treatment

2021

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The novel human coronavirus was firstly emerged in December 2019 in Wuhan, China, and has spread rapidly around the world. There is no known specific effective treatment of COVID-19. The most commonly used agents against this disease both in Turkey and around the world include chloroquine, hydroxychloroquine, lopinavir/ritonavir, favipiravir, and remdesivir. In the study, we investigated the drug potential of molecules that the components of an important medicinal plant Hypericum perforatum by using molecular docking and drug possibility properties of these molecules. The molecular docking results showed that the most stable complex was obtained with COVID-19 main protease and hypericin/isohypericin ligands with − 11 kcal/mol binding energy. Furthermore, ADMET, drug-likeness features of compounds of H. perforatum were investigated using the rules of Lipinski, Veber, and Ghose. According to the results obtained, it has been shown that H. perforatum has the potential to be an effective drug in the COVID-19 pandemic. In the next stage, it is necessary to carry out the clinically necessary reliability studies of these components. It is thought that it can be used for the treatment of COVID-19 if our molecular docking results are found to be in high correlation with clinical studies. Supplementary Information The online version contains supplementary material available at 10.1007/s40495-021-00254-9.

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Determination of Potential Drug Candidate Molecules of the Hypericum perforatum for COVID-19 Treatment

2021

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In silico detection of inhibitor potential of Passiflora compounds against SARS-Cov-2(Covid-19) main protease by using molecular docking and dynamic analyses

Yalçın

Yalçınkaya

Ercan

2021

Journal of Molecular Structure

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The Determination of Molecular and Toxicological Mechanisms of Cucurbitacin E in Model Organism Drosophila melanogaster and Various Cancer Cell Lines: Molecular Modelling, Docking and Dynamic Simulation Studies

Tunçbilek

Azarkan

Ercan

2023

CAD

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Introduction: Cucurbitacins are one of the most important components of Ecballium elaterium. Among the cucurbitacins, Cucurbitacin E was the first to be isolated. This study focused on screening the anticancer and insecticidal potential of Cucurbitacin E by the in-vitro, in-vivo, and in-silico methods. Methods: In the study, toxicity analysis of Cucurbitacin E were determined on HeLa, Caco 2 cancer cell lines and D. melanogaster. While the expression levels of the BAD, BCL-2, AKT-1 and H-purine genes of cancer cell lines were determined, the CG15530, BUFFY, AKT-1 and Purine genes of D. melanogaster were determined by RT-PCR. Besides, molecular docking and dynamic properties of Cucurbitacin E with human and insectoid enzymes were presented in silico. Results: The IC50 value of Cucurbitacin E in the HeLa ovarian and Caco 2 colon cancer cell lines was determined to be 42 ug/ml and 85 ug/ml, respectively. The LC50 and LC99 doses for fruit flies were determined to be 47,693 µg/ml and 133,251 µg/ml, respectively. Gene expression analysis revealed that Cucurbitacin E showed the greatest effect on Purine and AKT-1 genes in D. melanogaster. We analyzed all genes by Western blot, but we did not detect significant changes in genes other than H-purine. In silico studies revealed that the Purine protein of D. melanogaster had the highest bonding energy with Cucurbitacin E as a ligand. Similarly, Cucurbitacin E showed great affinity towards H-purine (-10.2 kcal/mol). Molecular dynamics simulation studies were also performed to determine the stability of the dynamic process. Conclusion: Conclusion: As a result of our in vivo, in vitro and bioinformatic analyzes, it has been seen that Cucurbitacine E is effective against the cancer types and model insect studied.

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The physical studies and interaction with anti-apoptotic proteins of 2-(bis(cyanomethyl)amino)-2-oxoethyl methacrylate molecule

Cited by 3 publications

References 15 publications

Determination of Potential Drug Candidate Molecules of the Hypericum perforatum for COVID-19 Treatment

Determination of Potential Drug Candidate Molecules of the Hypericum perforatum for COVID-19 Treatment

In silico detection of inhibitor potential of Passiflora compounds against SARS-Cov-2(Covid-19) main protease by using molecular docking and dynamic analyses

The Determination of Molecular and Toxicological Mechanisms of Cucurbitacin E in Model Organism Drosophila melanogaster and Various Cancer Cell Lines: Molecular Modelling, Docking and Dynamic Simulation Studies

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