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通过虚拟筛选和基于自由能的方法对精胺合酶二聚体的小分子稳定剂进行合理设计。

Rational design of small-molecule stabilizers of spermine synthase dimer by virtual screening and free energy-based approach.

作者信息

Zhang Zhe, Martiny Virginie, Lagorce David, Ikeguchi Yoshihiko, Alexov Emil, Miteva Maria A

机构信息

Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques In Silico, Inserm UMR-S 973, Paris, France; INSERM, U973, Paris, France; Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, United States of America.

Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques In Silico, Inserm UMR-S 973, Paris, France; INSERM, U973, Paris, France.

出版信息

PLoS One. 2014 Oct 23;9(10):e110884. doi: 10.1371/journal.pone.0110884. eCollection 2014.

Abstract

Snyder-Robinson Syndrome (SRS) is a rare mental retardation disorder which is caused by the malfunctioning of an enzyme, the spermine synthase (SMS), which functions as a homo-dimer. The malfunctioning of SMS in SRS patients is associated with several identified missense mutations that occur away from the active site. This investigation deals with a particular SRS-causing mutation, the G56S mutation, which was shown computationally and experimentally to destabilize the SMS homo-dimer and thus to abolish SMS enzymatic activity. As a proof-of-concept, we explore the possibility to restore the enzymatic activity of the malfunctioning SMS mutant G56S by stabilizing the dimer through small molecule binding at the mutant homo-dimer interface. For this purpose, we designed an in silico protocol that couples virtual screening and a free binding energy-based approach to identify potential small-molecule binders on the destabilized G56S dimer, with the goal to stabilize it and thus to increase SMS G56S mutant activity. The protocol resulted in extensive list of plausible stabilizers, among which we selected and tested 51 compounds experimentally for their capability to increase SMS G56S mutant enzymatic activity. In silico analysis of the experimentally identified stabilizers suggested five distinctive chemical scaffolds. This investigation suggests that druggable pockets exist in the vicinity of the mutation sites at protein-protein interfaces which can be used to alter the disease-causing effects by small molecule binding. The identified chemical scaffolds are drug-like and can serve as original starting points for development of lead molecules to further rescue the disease-causing effects of the Snyder-Robinson syndrome for which no efficient treatment exists up to now.

摘要

斯奈德-罗宾逊综合征(SRS)是一种罕见的智力发育迟缓疾病,由一种酶——精胺合酶(SMS)功能异常引起,SMS以同二聚体形式发挥作用。SRS患者中SMS功能异常与几个已确定的错义突变相关,这些突变发生在远离活性位点的位置。本研究涉及一种特定的导致SRS的突变,即G56S突变,计算和实验表明该突变会使SMS同二聚体不稳定,从而消除SMS的酶活性。作为概念验证,我们探索通过在突变同二聚体界面处结合小分子来稳定二聚体,从而恢复功能异常的SMS突变体G56S酶活性的可能性。为此,我们设计了一种计算机模拟方案,该方案结合虚拟筛选和基于自由结合能的方法,以识别不稳定的G56S二聚体上的潜在小分子结合剂,目的是使其稳定并从而提高SMS G56S突变体的活性。该方案产生了大量可能的稳定剂列表,我们从中选择了51种化合物进行实验测试,以检验它们提高SMS G56S突变体酶活性的能力。对实验鉴定出的稳定剂进行计算机模拟分析,提出了五种不同的化学支架。本研究表明,在蛋白质-蛋白质界面的突变位点附近存在可成药口袋,可通过小分子结合来改变致病效应。所鉴定的化学支架具有类药物性质,可作为开发先导分子的原始起点,以进一步挽救斯奈德-罗宾逊综合征的致病效应,目前尚无有效治疗方法。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/a937/4207787/535622c8e9f0/pone.0110884.g001.jpg

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