Fragment-based drug design using X-ray crystallography is a powerful technique to enable the development of new lead compounds, or probe molecules, against biological targets. This study addresses the need to determine fragment binding orientations for low-occupancy fragments with incomplete electron density, an essential step before further development of the molecule. Halogen atoms play multiple roles in drug discovery due to their unique combination of electronegativity, steric effects and hydrophobic properties. Fragments incorporating halogen atoms serve as promising starting points in hit-to-lead development as they often establish halogen bonds with target proteins, potentially enhancing binding affinity and selectivity, as well as counteracting drug resistance. Here, the aim was to unambiguously identify the binding orientations of fragment hits for SARS-CoV-2 nonstructural protein 1 (nsp1) which contain a combination of sulfur and/or chlorine, bromine and iodine substituents. The binding orientations of carefully selected nsp1 analogue hits were focused on by employing their anomalous scattering combined with Pan-Dataset Density Analysis (PanDDA). Anomalous difference Fourier maps derived from the diffraction data collected at both standard and long-wavelength X-rays were compared. The discrepancies observed in the maps of iodine-containing fragments collected at different energies were attributed to site-specific radiation-damage stemming from the strong X-ray absorption of I atoms, which is likely to cause cleavage of the C-I bond. A reliable and effective data-collection strategy to unambiguously determine the binding orientations of low-occupancy fragments containing sulfur and/or halogen atoms while mitigating radiation damage is presented.

中文翻译：

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使用硫和卤素原子的异常信号将低占有率碎片高置信地放置到电子密度中。


使用 X 射线晶体学进行基于片段的药物设计是一种强大的技术，可以针对生物靶标开发新的先导化合物或探针分子。这项研究解决了确定电子密度不完整的低占有率片段的片段结合方向的需要，这是进一步开发分子之前的一个重要步骤。卤素原子由于其电负性、空间效应和疏水性的独特组合，在药物发现中发挥着多种作用。包含卤素原子的片段是 hit-to-lead 开发的有希望的起点，因为它们通常与目标蛋白建立卤素键，可能增强结合亲和力和选择性，并抵消耐药性。在此，目的是明确识别 SARS-CoV-2 非结构蛋白 1 (nsp1) 片段命中的结合方向，该片段包含硫和/或氯、溴和碘取代基的组合。通过将其异常散射与泛数据集密度分析 (PanDDA) 相结合，重点关注精心选择的 nsp1 类似物命中的结合方向。对从标准 X 射线和长波长 X 射线收集的衍射数据得出的反常差分傅里叶图进行了比较。在不同能量收集的含碘碎片图中观察到的差异归因于 I 原子强烈 X 射线吸收引起的位点特异性辐射损伤，这可能导致 CI​​ 键断裂。提出了一种可靠且有效的数据收集策略，可以明确确定含有硫和/或卤素原子的低占有率碎片的结合方向，同时减轻辐射损伤。