Yating Lei , Zihang Zhang , Xiulan Ma , Ruirui Cai , Lulu Dai , Ying Guo , Xun Tuo
{"title":"Deciphering the interaction of perampanel and calf thymus DNA: A multi-spectroscopic and computer modelling study","authors":"Yating Lei , Zihang Zhang , Xiulan Ma , Ruirui Cai , Lulu Dai , Ying Guo , Xun Tuo","doi":"10.1016/j.molstruc.2022.133900","DOIUrl":null,"url":null,"abstract":"<div><p>Perampanel (PER) is the first drug to treat epilepsy by blocking α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors. In the current study, the interaction of PER and calf thymus DNA (ctDNA) was explored through various spectroscopic techniques and computer modelling. According to the UV-vis titration results, PER combined with ctDNA via groove binding, which was also confirmed by thermal melting, salt effect, ssDNA/dsDNA quenching, and competitive experiments. The dominant forces were hydrogen bond and van der Waals force. And the binding constant obtained was 6.97 × 10<sup>3</sup> M<sup>−1</sup> at 298 K. According to the data from FTIR assays and computer modelling, PER was embedded in the minor groove of ctDNA rich in A and T bases. In the simulation of 200 ns, the PER-DNA system reached equilibrium at about 100 ns. The structure of DNA became loose when a stable binary complex with PER was formed. The energy decomposition indicated that DC-9, DT-19, and DT-20 bases played a main role in this complex-forming. In summary, this study contributed to understanding the interaction mechanism of PER and ctDNA.</p></div>","PeriodicalId":16414,"journal":{"name":"Journal of Molecular Structure","volume":null,"pages":null},"PeriodicalIF":4.0000,"publicationDate":"2022-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"1","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Molecular Structure","FirstCategoryId":"92","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S002228602201554X","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"CHEMISTRY, PHYSICAL","Score":null,"Total":0}
引用次数: 1
Abstract
Perampanel (PER) is the first drug to treat epilepsy by blocking α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors. In the current study, the interaction of PER and calf thymus DNA (ctDNA) was explored through various spectroscopic techniques and computer modelling. According to the UV-vis titration results, PER combined with ctDNA via groove binding, which was also confirmed by thermal melting, salt effect, ssDNA/dsDNA quenching, and competitive experiments. The dominant forces were hydrogen bond and van der Waals force. And the binding constant obtained was 6.97 × 103 M−1 at 298 K. According to the data from FTIR assays and computer modelling, PER was embedded in the minor groove of ctDNA rich in A and T bases. In the simulation of 200 ns, the PER-DNA system reached equilibrium at about 100 ns. The structure of DNA became loose when a stable binary complex with PER was formed. The energy decomposition indicated that DC-9, DT-19, and DT-20 bases played a main role in this complex-forming. In summary, this study contributed to understanding the interaction mechanism of PER and ctDNA.
期刊介绍:
The Journal of Molecular Structure is dedicated to the publication of full-length articles and review papers, providing important new structural information on all types of chemical species including:
• Stable and unstable molecules in all types of environments (vapour, molecular beam, liquid, solution, liquid crystal, solid state, matrix-isolated, surface-absorbed etc.)
• Chemical intermediates
• Molecules in excited states
• Biological molecules
• Polymers.
The methods used may include any combination of spectroscopic and non-spectroscopic techniques, for example:
• Infrared spectroscopy (mid, far, near)
• Raman spectroscopy and non-linear Raman methods (CARS, etc.)
• Electronic absorption spectroscopy
• Optical rotatory dispersion and circular dichroism
• Fluorescence and phosphorescence techniques
• Electron spectroscopies (PES, XPS), EXAFS, etc.
• Microwave spectroscopy
• Electron diffraction
• NMR and ESR spectroscopies
• Mössbauer spectroscopy
• X-ray crystallography
• Charge Density Analyses
• Computational Studies (supplementing experimental methods)
We encourage publications combining theoretical and experimental approaches. The structural insights gained by the studies should be correlated with the properties, activity and/ or reactivity of the molecule under investigation and the relevance of this molecule and its implications should be discussed.