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从分子对接和分子动力学模拟洞察深海真菌代谢产物中SIRT3调节化合物的鉴定

Identification of SIRT3 modulating compounds in deep-sea fungi metabolites: Insights from molecular docking and MD simulations.

作者信息

Alanzi Abdullah R, Alhaidhal Bayan Abdullah, Aloatibi Raghad Mohammad

机构信息

Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia.

出版信息

PLoS One. 2025 May 8;20(5):e0323107. doi: 10.1371/journal.pone.0323107. eCollection 2025.

Abstract

SIRT3, a crucial deacetylase that plays a key role in regulating mitochondrial acetylation, is tightly linked to metabolic processes and is essential for the maintenance of eukaryotic life. SIRT3 is a potential therapeutic target due to its key role in various diseases, including ageing, heart disease, cancer, and metabolic disorders. In this work, we aimed to identify potential SIRT3 inhibitors from the deep-sea fungal metabolites by employing molecular docking and ADMET analysis. Based on the binding affinities, ten compounds were selected whose docking scores were in the range of -9.693 to -8.327 kcal/mol. Further, four compounds Penipanoid C, Penicillactam, Quinolonimide, and Brevianamide R were selected based on the ADMET properties and subjected to Molecular dynamics simulations to assess the stability of these molecules with target. The stability analysis indicated that the selected compounds could act as lead compounds during in vitro assays to advance these drug candidates towards clinical drug development.

摘要

SIRT3是一种关键的去乙酰化酶,在调节线粒体乙酰化过程中发挥着关键作用,它与代谢过程紧密相连,对维持真核生物的生命至关重要。由于SIRT3在包括衰老、心脏病、癌症和代谢紊乱在内的各种疾病中发挥关键作用,它是一个潜在的治疗靶点。在这项工作中,我们旨在通过分子对接和ADMET分析,从深海真菌代谢产物中鉴定潜在的SIRT3抑制剂。基于结合亲和力,选择了10种对接分数在-9.693至-8.327千卡/摩尔范围内的化合物。此外,根据ADMET性质选择了四种化合物Penipanoid C、Penicillactam、Quinolonimide和Brevianamide R,并进行分子动力学模拟,以评估这些分子与靶点的稳定性。稳定性分析表明,所选化合物在体外试验中可作为先导化合物,推动这些候选药物向临床药物开发迈进。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f00/12061134/04561525c7f0/pone.0323107.g001.jpg

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