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基于结构的药物发现中具有挑战性的靶标中 X 射线自由电子激光的潜力。

Potential of X-ray free-electron lasers for challenging targets in structure-based drug discovery.

机构信息

Max Planck Institute for Medical Research, Jahnstr. 29, Heidelberg 69120, Germany.

出版信息

Drug Discov Today Technol. 2021 Dec;39:101-110. doi: 10.1016/j.ddtec.2021.08.002. Epub 2021 Aug 26.

DOI:10.1016/j.ddtec.2021.08.002
PMID:34906320
Abstract

X-ray crystallography has provided the vast majority of three-dimensional macromolecular structures. Most of these are high-resolution structures that enable a detailed understanding of the underlying molecular mechanisms. The standardized workflows and robust infrastructure of synchrotron-based macromolecular crystallography (MX) offer the high throughput essential to cost-conscious investigations in structure- and fragment-based drug discovery. Nonetheless conventional MX is limited by fundamental bottlenecks, in particular X-ray radiation damage, which limits the amount of data extractable from a crystal. While this limit can in principle be circumvented by using larger crystals, crystals of the requisite size often cannot be obtained in sufficient quality. That is especially true for membrane protein crystals, which constitute the majority of current drug targets. This conventional paradigm for MX-suitable samples changed dramatically with the advent of serial femtosecond crystallography (SFX) based on the ultra-short and extremely intense X-ray pulses of X-ray Free-Electron Lasers. SFX provides high-resolution structures from tiny crystals and does so with uniquely low levels of radiation damage. This has yielded a number of novel structures for G-protein coupled receptors, one of the most relevant membrane protein superfamilies for drug discovery, as well as tantalizing advances in time-resolved crystallography that elucidate protein dynamics. This article attempts to map the potential of SFX for drug discovery, while providing the reader with an overview of the yet remaining technical challenges associated with such a novel technique as SFX.

摘要

X 射线晶体学提供了绝大多数的三维大分子结构。这些结构大多是高分辨率的,使我们能够深入了解潜在的分子机制。基于同步加速器的大分子晶体学 (MX) 的标准化工作流程和强大的基础设施提供了高通量的必要条件,这对基于结构和基于片段的药物发现的成本意识调查至关重要。尽管如此,传统的 MX 受到一些基本瓶颈的限制,特别是 X 射线辐射损伤,这限制了从晶体中提取的数据量。虽然从理论上讲,可以通过使用更大的晶体来规避这个限制,但通常无法获得足够质量的所需大小的晶体。对于膜蛋白晶体来说尤其如此,它们构成了当前大多数药物靶点。随着基于 X 射线自由电子激光器的超短和极强 X 射线脉冲的串行 femtosecond 晶体学 (SFX) 的出现,这种适用于 MX 的传统样本的范例发生了巨大的变化。SFX 提供了来自微小晶体的高分辨率结构,而且其辐射损伤水平非常低。这为 G 蛋白偶联受体(药物发现中最相关的膜蛋白超家族之一)提供了许多新结构,并在阐明蛋白质动力学方面取得了一些有前途的时间分辨晶体学进展。本文试图绘制 SFX 在药物发现中的潜力,同时为读者提供与 SFX 等新型技术相关的技术挑战的概述。

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引用本文的文献

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A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers.一种用于在 X 射线自由电子激光上进行时间分辨连续蛋白质晶体学和化合物筛选的多储库挤出机。
Nat Commun. 2023 Dec 2;14(1):7956. doi: 10.1038/s41467-023-43523-5.
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Exploring the World of Membrane Proteins: Techniques and Methods for Understanding Structure, Function, and Dynamics.探索膜蛋白的世界:理解结构、功能和动力学的技术和方法。
Molecules. 2023 Oct 19;28(20):7176. doi: 10.3390/molecules28207176.
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Perspective: Structure determination of protein-ligand complexes at room temperature using X-ray diffraction approaches.
观点:利用X射线衍射方法在室温下测定蛋白质-配体复合物的结构
Front Mol Biosci. 2023 Jan 23;10:1113762. doi: 10.3389/fmolb.2023.1113762. eCollection 2023.