Deciphering the mechanism and binding interactions of Pemetrexed with dsDNA with DNA-targeted chemotherapeutics via spectroscopic, analytical, and simulation studies

Şenel, Pelin; Agar, Soykan; İş, Yusuf Serhat; Altay, Filiz; Gölcü, Ayşegül; Yurtsever, Mine

doi:10.1016/j.jpba.2021.114490

Cited by 6 publications

(4 citation statements)

References 31 publications

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“…This binding significantly increases the thermal denaturation temperature of dsDNA. In contrast, groove-binding agents cannot raise the denaturation temperature of dsDNA much, which we have confirmed in several studies [ 26 , 27 , 28 , 29 ]. Table 2 shows T m values based on the interaction of dsDNA with different agents.…”

Section: Resultssupporting

confidence: 86%

Elucidation of DNA-Eltrombopag Binding: Electrochemical, Spectroscopic and Molecular Docking Techniques

et al. 2023

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Eltrombopag is a powerful adjuvant anticancer drug used in treating MS (myelodysplastic syndrome) and AML (acute myeloid leukemia) diseases. In this study, the interaction mechanism between eltrombopag and DNA was studied by voltammetry, spectroscopic techniques, and viscosity measurements. We developed a DNA-based biosensor and nano-biosensor using reduced graphene oxide-modified glassy carbon electrode to detect DNA-eltrombopag binding. The reduction of desoxyguanosine (dGuo) and desoxyadenosine (dAdo) oxidation signals in the presence of the drug demonstrated that a strong interaction could be established between the eltrombopag and dsDNA. The eltrombopag-DNA interaction was further investigated by UV absorption and fluorescence emission spectroscopy to gain more quantitative insight on binding. Viscosity measurements were utilized to characterize the binding mode of the drug. To shed light on the noncovalent interactions and binding mechanism of eltrombopag molecular docking and molecular dynamics (MD), simulations were performed. Through simultaneously carried out experimental and in silico studies, it was established that the eltrombopag binds onto the DNA via intercalation.

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Section: Resultssupporting

confidence: 86%

Elucidation of DNA-Eltrombopag Binding: Electrochemical, Spectroscopic and Molecular Docking Techniques

et al. 2023

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“…The initial structures for the MD simulations were chosen based on the docking poses with the most favorable binding energies (15)(16)(17)(18), as previously reported in scientific literature. The molecular dynamics (MD) simulations were conducted using Schrödinger's Maestro Desmond software (19), each spanning 50 ns with 5000 poses at 10 ps intervals.…”

Section: Molecular Dynamics (Md) Simulationsmentioning

confidence: 99%

New Drug Design to Suppress Nonalcoholic Steatohepatitis

Agar,

Akkurt,

Ulukaya

2024

Journal of the Turkish Chemical Society Section A: Chemistry

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A de novo designed biomolecule called INASHD was utilized through computer-aided drug design techniques to specifically target β2-spectrin, effectively suppressing and preventing NASH disease. Advanced computational software tools concerning the technologies of molecular docking and molecular dynamics (MD), were employed to showcase the drug's remarkable ability to efficiently suppress and control the α-helical topology of β2-spectrin. This protein is a vital component within the disease pathway. We successfully devised an effective design suppressing β2-spectrin, exhibiting an inhibition score surpassing any other molecule documented in scientific literature. With robust support from validated computational software, this bioorganic structure holds significant value and can be applied for a patent due to its innovative design. It shows promising potential for delivering positive outcomes in various stages, including in vitro, in vivo, ex vivo, and human phase studies.

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“…The docking poses possessing the best and most favorable binding energy concerning the docking results were used as the initial structure for the MD simulations (42,43). Utilizing Schrödinger's Maestro Desmond software (44), all the ligands were run for molecular dynamics (MD) simulations with 50 ns total time periods per each new seeded run, including 5000 poses with 10 ps time intervals, respectively.…”

Section: Molecular Dynamics (Md) Simulationsmentioning

confidence: 99%

De novo Drug Design to Suppress Coronavirus RNA-Glycoprotein via PNA-Calcitonin

Agar,

Akkurt,

Alparslan

2024

Journal of the Turkish Chemical Society Section A: Chemistry

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De novo drug design has been studied utilizing the organic chemical structures of Salmon Calcitonin 9 - 19 and Peptide Nucleic Acid (PNA) to suppress Coronavirus Ribonucleic Acid (RNA)-Glycoprotein complex. PNA has a polyamide backbone and Thymine pendant groups to selectively bind and inhibit Adenine domains of the RNA-Glycoprotein complex. While doing so, molecular docking and molecular dynamics studies revealed that there is great inhibition docking energy (-12.1 kcal/mol) with significantly good inhibition constant (124.1 µM) values confirming the efficient nucleotide-specific silencing of Coronavirus RNA-Glycoprotein complex.

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Deciphering the mechanism and binding interactions of Pemetrexed with dsDNA with DNA-targeted chemotherapeutics via spectroscopic, analytical, and simulation studies

Cited by 6 publications

References 31 publications

Elucidation of DNA-Eltrombopag Binding: Electrochemical, Spectroscopic and Molecular Docking Techniques

Elucidation of DNA-Eltrombopag Binding: Electrochemical, Spectroscopic and Molecular Docking Techniques

New Drug Design to Suppress Nonalcoholic Steatohepatitis

De novo Drug Design to Suppress Coronavirus RNA-Glycoprotein via PNA-Calcitonin

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