Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 is an ongoing pandemic that causes significant health/socioeconomic burden. Variants of concern (VOCs) have emerged affecting transmissibility, disease severity and re-infection risk. Studies suggest that the Spike N-terminal domain (NTD) may have a role in facilitating virus entry via sialic-acid receptor binding. Furthermore, most VOCs include novel NTD variants. Despite global sequence and structure similarity, most NTD sialic-acid binding pockets vary across coronaviruses. Our work suggests ongoing evolutionary tuning of the sugar-binding pockets and recent analyses have shown that NTD insertions in VOCs tend to lie close to loops.

We extended the structural characterisation of these sugar-binding pockets and explored whether variants could enhance sialic acid-binding. We found that recent NTD insertions in VOCs (i.e., Gamma, Delta and Omicron variants) and emerging variants of interest (VOIs) (i.e., Iota, Lambda, Theta variants) frequently lie close to sugar-binding pockets. For some variants, including the recent Omicron VOC, we find increases in predicted sialic acid-binding energy, compared to the original SARS-CoV-2, which may contribute to increased transmission. These binding observations are supported by molecular dynamics simulations (MD).

We examined the similarity of NTD across Betacoronaviruses to determine whether the sugar-binding pockets are sufficiently similar to be exploited in drug design. Whilst most pockets are too structurally variable, we detected a previously unknown highly structurally conserved pocket which can be investigated in pursuit of a generic pan Betacoronavirus drug. Our structure-based analyses help rationalise the effects of VOCs and provide hypotheses for experiments. Our findings suggest a strong need for experimental monitoring of VOC changes in NTD.

由 SARS-CoV-2 引起的 2019 年冠状病毒病 (COVID-19) 是一种持续的大流行病，会造成重大的健康/社会经济负担。关注的变体 (VOC) 已经出现，影响传播性、疾病严重程度和再感染风险。研究表明，尖峰 N 末端结构域 (NTD) 可能在通过唾液酸受体结合促进病毒进入方面发挥作用。此外，大多数 VOC 包括新的 NTD 变体。尽管全球序列和结构相似，但大多数 NTD 唾液酸结合口袋因冠状病毒而异。我们的工作表明正在进行的糖结合口袋的进化调整，最近的分析表明，VOC 中的 NTD 插入往往靠近环路。

我们扩展了这些糖结合口袋的结构特征，并探索了变体是否可以增强唾液酸结合。我们发现最近在 VOC 中插入的 NTD（即 Gamma、Delta 和 Omicron 变体）和感兴趣的新变体 (VOI)（即 Iota、Lambda、Theta 变体）经常位于糖结合口袋附近。对于某些变体，包括最近的 Omicron VOC，我们发现与原始 SARS-CoV-2 相比，预测的唾液酸结合能增加，这可能有助于增加传播。这些具有约束力的观察得到了分子动力学模拟 (MD) 的支持。

我们检查了 NTD 在 Beta 冠状病毒中的相似性，以确定糖结合口袋是否足够相似以用于药物设计。虽然大多数口袋的结构变化太大，但我们检测到一个以前未知的结构高度保守的口袋，可以对其进行研究以寻找通用的泛 Beta 冠状病毒药物。我们基于结构的分析有助于合理化 VOC 的影响并为实验提供假设。我们的研究结果表明，强烈需要对 NTD 中的 VOC 变化进行实验监测。