变构方法及其应用:促进变构药物的发现和变构机制的研究。
Allosteric Methods and Their Applications: Facilitating the Discovery of Allosteric Drugs and the Investigation of Allosteric Mechanisms.
机构信息
Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education , Shanghai Jiao Tong University, School of Medicine , Shanghai 200025 , China.
Medicinal Bioinformatics Center , Shanghai Jiao Tong University, School of Medicine , Shanghai 200025 , China.
出版信息
Acc Chem Res. 2019 Feb 19;52(2):492-500. doi: 10.1021/acs.accounts.8b00570. Epub 2019 Jan 28.
Allostery, or allosteric regulation, is the phenomenon in which protein functional activity is altered by the binding of an effector at an allosteric site that is topographically distinct from the orthosteric, active site. As one of the most direct and efficient ways to regulate protein function, allostery has played a fundamental role in innumerable biological processes of all living organisms, including enzyme catalysis, signal transduction, cell metabolism, and gene transcription. It is thus considered as "the second secret of life". The abnormality of allosteric communication networks between allosteric and orthosteric sites is associated with the pathogenesis of human diseases. Allosteric modulators, by attaching to structurally diverse allosteric sites, offer the potential for differential selectivity and improved safety compared with orthosteric drugs that bind to conserved orthosteric sites. Harnessing allostery has thus been regarded as a novel strategy for drug discovery. Despite much progress having been made in the repertoire of allostery since the turn of the millennium, the identification of allosteric drugs for therapeutic targets and the elucidation of allosteric mechanisms still present substantial challenges. These challenges are derived from the difficulties in the identification of allosteric sites and mutations, the assessment of allosteric protein-modulator interactions, the screening of allosteric modulators, and the elucidation of allosteric mechanisms in biological systems. To address these issues, we have developed a panel of allosteric services for specific allosteric applications over the past decade, including (i) the creation of the Allosteric Database, with the aim of providing comprehensive allosteric information such as allosteric proteins, modulators, sites, pathways, etc., (ii) the construction of the ASBench benchmark of high-quality allosteric sites for the development of computational methods for predicting allosteric sites, (iii) the development of Allosite and AllositePro for the prediction of the location of allosteric sites in proteins, (iv) the development of the Alloscore scoring function for the evaluation of allosteric protein-modulator interactions, (v) the development of Allosterome for evolutionary analysis of query allosteric sites/modulators within the human proteome, (vi) the development of AlloDriver for the prediction of allosteric mutagenesis, and (vii) the development of AlloFinder for the virtual screening of allosteric modulators and the investigation of allosteric mechanisms. Importantly, we have validated computationally predicted allosteric sites, mutations, and modulators in the real cases of sirtuin 6, casein kinase 2α, phosphodiesterase 10A, and signal transduction and activation of transcription 3. Furthermore, our developed allosteric methods have been widely exploited by other users around the world for allosteric research. Therefore, these allosteric services are expected to expedite the discovery of allosteric drugs and the investigation of allosteric mechanisms.
变构作用,或变构调节,是指蛋白质功能活性通过效应物与变构位点的结合而改变的现象,该变构位点在拓扑上与正位、活性位点不同。作为调节蛋白质功能最直接、最有效的方法之一,变构作用在所有生物的无数生物过程中都发挥了基础作用,包括酶催化、信号转导、细胞代谢和基因转录。因此,它被认为是“生命的第二个秘密”。变构和正位位点之间的变构通讯网络的异常与人类疾病的发病机制有关。变构调节剂通过附着在结构多样的变构位点上,与结合保守正位位点的正位药物相比,提供了更好的选择性和更高的安全性潜力。因此,利用变构作用已被视为一种新的药物发现策略。尽管自千禧年以来,在变构作用的研究中已经取得了很大的进展,但为治疗靶点寻找变构药物和阐明变构机制仍然存在很大的挑战。这些挑战源于变构位点和突变的鉴定、变构蛋白-调节剂相互作用的评估、变构调节剂的筛选以及生物系统中变构机制的阐明。为了解决这些问题,我们在过去十年中开发了一系列针对特定变构应用的变构服务,包括 (i) 创建变构数据库,旨在提供全面的变构信息,如变构蛋白、调节剂、位点、途径等,(ii) 构建用于开发预测变构位点的计算方法的高质量变构位点 ASBench 基准,(iii) 开发用于预测蛋白质中变构位点位置的 Allosite 和 AllositePro,(iv) 开发 Alloscore 评分函数用于评估变构蛋白-调节剂相互作用,(v) 开发 Allosterome 用于在人类蛋白质组内对查询变构位点/调节剂进行进化分析,(vi) 开发 AlloDriver 用于预测变构诱变,和 (vii) 开发 AlloFinder 用于虚拟筛选变构调节剂和研究变构机制。重要的是,我们已经在 sirtuin 6、casein kinase 2α、phosphodiesterase 10A 和信号转导和激活转录 3 的实际案例中验证了通过计算预测的变构位点、突变和调节剂。此外,我们开发的变构方法已被世界各地的其他用户广泛用于变构研究。因此,这些变构服务有望加速变构药物的发现和变构机制的研究。