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通过分子动力学模拟对 FDA 批准的药物进行再利用及其针对潜在药物靶点的验证。

Repurposing of FDA approved drugs and their validation against potential drug targets for through molecular dynamics simulation.

机构信息

Centre of Bioinformatics, IIDS, University of Allahabad, Prayagraj, Uttar Pradesh, India.

Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, New Delhi, India.

出版信息

J Biomol Struct Dyn. 2022 Sep;40(14):6255-6271. doi: 10.1080/07391102.2021.1880482. Epub 2021 Feb 2.

Abstract

is a widely distributed pathogen causing infection of intestinal tract, typhoid, and paratyphoid fever. Number of drugs was developed against salmonella, but in the last few decades due to the emergence of drug resistant strains, most of these drugs became dormant. As a result Salmonellosis emerges as a trivial cause of human mortality worldwide; therefore, there is an urgent need for unexploited drug targets and drugs to treat Salmonellosis. As development of new drug molecules is very time consuming and costly, drug repurposing is in consideration as a better alternative. With the aim to identify a new drug molecule against the through repurposing approach, we utilized 14 well reported druggable targets known to play a vital role in the life cycle of pathogens. These targets were used to screen DrugBank and got 53 FDA approved drugs against them. To find the interaction between considered target proteins and screened drugs, molecular docking was performed. Fourteen docked drug-target complexes with reasonable binding affinities were subjected to Molecular Dynamics Simulation (MDS) at 150 ns, using Amber18. At the end MMPBSA and MMGBSA calculations were performed for all stable complexes and finally, got 3 precise and favourable complexes, i.e. ArcB-Cefpiramide, MrcB-Cefoperazone, and PhoQ-Carindacillin. Rigorous structural and energetic analysis for these complexes validates the potential of drug molecules to act as therapeutic drugs against . With this study we hypothesize that the drugs Cefpiramide (DB00430), Cefoperazone (DB01329) and Carindacillin (DB09319) will be the good repurposed-drugs for the treatment of Salmonellosis. Communicated by Ramaswamy H. Sarma.

摘要

是一种广泛分布的病原体,可引起肠道感染、伤寒和副伤寒。已经开发出了许多针对沙门氏菌的药物,但在过去几十年中,由于耐药菌株的出现,大多数这些药物已经失效。因此,沙门氏菌感染成为了全球人类死亡的一个微不足道的原因;因此,迫切需要寻找未被开发的药物靶点和药物来治疗沙门氏菌感染。由于开发新的药物分子非常耗时且昂贵,因此药物再利用被认为是一种更好的替代方法。为了通过再利用方法来确定针对 的新药分子,我们利用了 14 个已知在病原体生命周期中发挥重要作用的有报道的可成药靶点。这些靶点被用于筛选 DrugBank,并获得了针对它们的 53 种 FDA 批准的药物。为了找到考虑的靶蛋白和筛选出的药物之间的相互作用,进行了分子对接。对 14 个对接的药物-靶复合物进行了分子动力学模拟(MDS),模拟时间为 150ns,使用的是 Amber18。最后,对所有稳定的复合物进行了 MMPBSA 和 MMGBSA 计算,最终得到了 3 个精确和有利的复合物,即 ArcB-Cefpiramide、MrcB-Cefoperazone 和 PhoQ-Carindacillin。对这些复合物进行严格的结构和能量分析验证了药物分子作为治疗沙门氏菌感染的潜在治疗药物的潜力。通过这项研究,我们假设药物 Cefpiramide(DB00430)、Cefoperazone(DB01329)和 Carindacillin(DB09319)将成为治疗沙门氏菌感染的良好再利用药物。

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