Free energy calculations reveal the interaction and stability of ligands in the vicinity of B-DNA dodecamer

IF 1.3 4区 化学 Q3 CHEMISTRY, MULTIDISCIPLINARY Main Group Chemistry Pub Date : 2023-04-25 DOI:10.3233/mgc-230031
Anwesh Pandey, Anupriya Adhikari
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Abstract

The double stranded Deoxyribonucleic acid (DNA) is stated as one of the idyllic targets for cancer and other various diseases. The in-depth investigation of DNA-drug interaction plays a crucial role for the recognition of drug mechanism action as well as in advance scheming of more proficient drugs with minor aftermath. Imidazoles and molecules possessing them are well known for their antimicrobial action and also possess different therapeutic properties. With the intention to improve a computational protocol towards the development of novel improvised antimicrobial agent, di-cationic molecules. Primarily, four diarylfuran derivatives having varied substituted groups have been proposed, analysed and compared for antimicrobial potential by studying their binding strength and steady complex formation with DNA. Molecular docking analysis was used to forecast the binding mode involved for DNA-drug complex and molecular dynamics was employed for studying the kinetics of interaction. The docking investigation revealed AT rich region binding for all the proposed ligands which is the preferred location for DNA minor groove binders establishing Mol-1 and Mol-3 as lead molecules. The stability of drug-DNA complexes was inferred from an analysis of the data from Molecular dynamics (MD) analysis, which showed that ligands remained coupled to the preferred binding locations of DNA without experiencing any significant changes in the minor groove.
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自由能计算揭示了B-DNA十二聚体附近配体的相互作用和稳定性
双链脱氧核糖核酸(DNA)被认为是治疗癌症和其他各种疾病的理想靶点之一。深入研究dna -药物相互作用,对于认识药物的作用机制,提前规划出更熟练、后果更小的药物具有至关重要的作用。咪唑和含有它们的分子以其抗菌作用而闻名,并且还具有不同的治疗特性。目的是改进一种用于开发新型临时抗菌剂的计算方案,双阳离子分子。首先,通过研究四种具有不同取代基的二芳基呋喃衍生物的结合强度和与DNA的稳定络合物形成,对它们的抗菌潜力进行了分析和比较。采用分子对接分析预测dna -药物复合物的结合模式,采用分子动力学研究相互作用动力学。对接研究发现,所有被提出的配体都具有丰富的AT区结合,这是DNA小凹槽结合物建立Mol-1和Mol-3作为铅分子的首选位置。从分子动力学(MD)分析数据推断药物-DNA复合物的稳定性,这表明配体仍然偶联到DNA的首选结合位置,而在次要凹槽中没有任何显着变化。
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来源期刊
Main Group Chemistry
Main Group Chemistry 化学-化学综合
CiteScore
2.00
自引率
26.70%
发文量
65
审稿时长
>12 weeks
期刊介绍: Main Group Chemistry is intended to be a primary resource for all chemistry, engineering, biological, and materials researchers in both academia and in industry with an interest in the elements from the groups 1, 2, 12–18, lanthanides and actinides. The journal is committed to maintaining a high standard for its publications. This will be ensured by a rigorous peer-review process with most articles being reviewed by at least one editorial board member. Additionally, all manuscripts will be proofread and corrected by a dedicated copy editor located at the University of Kentucky.
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