In vitro evolution predicts emerging SARS-CoV-2 mutations with high affinity for ACE2 and cross-species binding.
In vitro evolution predicts emerging SARS-CoV-2 mutations with high affinity for ACE2 and cross-species binding.
复制标题
体外进化预测新出现的SARS-CoV-2突变对ACE 2和跨物种结合具有高亲和力。
DOI：
10.1371/journal.ppat.1010733
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发表时间：
2022-07
期刊：
影响因子：
6.7
通讯作者：
中科院分区：
文献类型：
--
作者：
新出现的SARS-CoV-2变种正在给正在进行的新冠肺炎大流行带来重大挑战。能够预测SARS-CoV-2可能出现的突变，从而增加传播性或免疫逃避，对于开发广泛作用的疗法和疫苗，以及优先考虑病毒监测和遏制，将是极其有价值的。在这里，我们使用体外进化来寻找SARS-CoV-2受体结合域(RBD)中的突变，该突变将显著增加与ACE2的结合。我们发现了一个双突变，S477N和Q498H，使RBD对ACE2的亲和力增加6.5倍。这种亲和力的增加在很大程度上是由Q498H突变推动的。我们用冷冻电子显微镜测定了突变体-RBD：ACE2复合体的结构，以揭示亲和力增加的机制。在SARS-CoV-2 RBD变异体中添加Q498H可以提高其与人ACE2的结合亲和力，并赋予与大鼠ACE2高亲和力结合的新能力。然而，令人惊讶的是，在常见的N501Y突变存在的情况下，Q498H由于H498和Y501侧链之间的碰撞而抑制结合。为了实现类似于Q498H的分子间结合网络、亲和力增加和跨物种结合，具有N501Y突变的RBD变体必须获得相关的Q498R突变。因此，SARS-CoV-2 RBD可以通过涉及Q498的两条替代突变途径获得巨大的亲和力收益和跨物种结合，路径选择取决于变异体是否已经具有N501Y突变。这些突变现在出现在新出现的SARS-CoV-2变种中，它们有可能影响人与人之间和跨物种的传播。预测导致传染性增加或免疫逃避的SARS-CoV-2突变的能力，将对疫苗和治疗方法的开发以及优先监测和遏制病毒变异具有价值。通过体外快速进化，我们鉴定了SARS-CoV-2受体结合域(RBD)的突变，这些突变显著增加了RBD与ACE2的结合。特别是一个突变Q498H，导致结合亲和力大幅增加，我们通过结构测定揭示了这一机制。我们发现Q498H的加入增加了一些SARS-CoV-2变异的RBDS的结合，但发现Q498H与常见的N501Y突变不相容。带有N501Y的RBD变体可以通过获得替代的Q498R突变来获得类似的结合和亲和力增加。Q498R/N501Y组合突变和Q498H也使SARS-CoV-2 RBD与大鼠ACE2重新高亲和力结合。我们的数据显示，SARS-CoV-2 RBD可以通过涉及Q498的两条替代突变途径获得巨大的亲和力收益和跨物种结合，路径选择取决于变异株是否已经具有N501Y突变。这些突变现在出现在新的SARS-CoV-2变种中，它们有可能有助于增加变种的传播性，并有可能促进跨物种传播。
Emerging SARS-CoV-2 variants are creating major challenges in the ongoing COVID-19 pandemic. Being able to predict mutations that could arise in SARS-CoV-2 leading to increased transmissibility or immune evasion would be extremely valuable in development of broad-acting therapeutics and vaccines, and prioritising viral monitoring and containment. Here we use in vitro evolution to seek mutations in SARS-CoV-2 receptor binding domain (RBD) that would substantially increase binding to ACE2. We find a double mutation, S477N and Q498H, that increases affinity of RBD for ACE2 by 6.5-fold. This affinity gain is largely driven by the Q498H mutation. We determine the structure of the mutant-RBD:ACE2 complex by cryo-electron microscopy to reveal the mechanism for increased affinity. Addition of Q498H to SARS-CoV-2 RBD variants is found to boost binding affinity of the variants for human ACE2 and confer a new ability to bind rat ACE2 with high affinity. Surprisingly however, in the presence of the common N501Y mutation, Q498H inhibits binding, due to a clash between H498 and Y501 side chains. To achieve an intermolecular bonding network, affinity gain and cross-species binding similar to Q498H alone, RBD variants with the N501Y mutation must acquire instead the related Q498R mutation. Thus, SARS-CoV-2 RBD can access large affinity gains and cross-species binding via two alternative mutational routes involving Q498, with route selection determined by whether a variant already has the N501Y mutation. These mutations are now appearing in emerging SARS-CoV-2 variants where they have the potential to influence human-to-human and cross-species transmission. The ability to predict mutations in SARS-CoV-2 that cause increased infectivity or immune evasion would be valuable in development of vaccines and therapeutics, and prioritizing viral variants for monitoring and containment. Using rapid in vitro evolution, we identify mutations in SARS-CoV-2 receptor binding domain (RBD) that markedly increase binding of RBD to ACE2. One mutation in particular, Q498H, causes a substantial increase in binding affinity, and we uncover the mechanism for this by structural determination. We show addition of Q498H increases binding of some SARS-CoV-2 variant RBDs but find Q498H is incompatible with the common N501Y mutation. RBD variants with N501Y can instead access similar bonding and affinity increases by acquiring the alternative Q498R mutation. The Q498R/N501Y combination mutations, and Q498H, also enable de novo high affinity binding of SARS-CoV-2 RBD to rat ACE2. Our data show SARS-CoV-2 RBD can access large affinity gains and cross-species binding via two alternative mutational routes involving Q498, with route selection determined by whether a variant already has the N501Y mutation. These mutations are now appearing in new SARS-CoV-2 variants, where they have the potential to contribute to increased variant transmissibility and potentially facilitate cross-species transmission.
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影响因子：
4.6
作者：
Tanaka S;Nelson G;Olson CA;Buzko O;Higashide W;Shin A;Gonzalez M;Taft J;Patel R;Buta S;Richardson A;Bogunovic D;Spilman P;Niazi K;Rabizadeh S;Soon-Shiong P
通讯作者：
Soon-Shiong P
DOI：
10.1107/s2059798318009324
发表时间：
2018-09-01
期刊：
Acta crystallographica. Section D, Structural biology
影响因子：
--
作者：
Afonine PV;Klaholz BP;Moriarty NW;Poon BK;Sobolev OV;Terwilliger TC;Adams PD;Urzhumtsev A
通讯作者：
Urzhumtsev A
DOI：
10.1074/jbc.m113.510578
发表时间：
2013-11-15
期刊：
The Journal of biological chemistry
影响因子：
--
作者：
Brindle NP;Sale JE;Arakawa H;Buerstedde JM;Nuamchit T;Sharma S;Steele KH
通讯作者：
Steele KH
SARS-COV-2在人类和貂皮之间的貂皮农场上传播，然后回到人类。
DOI：
10.1126/science.abe5901
发表时间：
2021-01-08
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Oude Munnink BB;Sikkema RS;Nieuwenhuijse DF;Molenaar RJ;Munger E;Molenkamp R;van der Spek A;Tolsma P;Rietveld A;Brouwer M;Bouwmeester-Vincken N;Harders F;Hakze-van der Honing R;Wegdam-Blans MCA;Bouwstra RJ;GeurtsvanKessel C;van der Eijk AA;Velkers FC;Smit LAM;Stegeman A;van der Poel WHM;Koopmans MPG
通讯作者：
Koopmans MPG
影响因子：
2.9
作者：
EDELHOCH, H
通讯作者：
EDELHOCH, H