利用自然获得的免疫反应对严重急性呼吸综合征冠状病毒2(SARS-CoV-2)刺突蛋白进行表位作图以开发单克隆抗体。
Epitope mapping of SARS-CoV-2 Spike protein using naturally-acquired immune responses to develop monoclonal antibodies.
作者信息
López-Aladid Rubén, Bueno-Freire Leticia, Farriol-Duran Roc, Porta-Pardo Eduard, Aguilar Ruth, Vidal Marta, Jiménez Alfons, Cabrera Roberto, Vázquez Nil, López-Gavín Alexandre, Moncunill Gemma, Carrascal Montserrat, García Teresa, Lozano Miquel, García-Basteiro Alberto L, Dobaño Carlota, Pazos Martalu D, Estevez M-Carmen, Lechuga Laura M, Torres Antoni, Fernández-Barat Laia
机构信息
Cellex Laboratory, Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES, 06/06/0028), Fundació de Recerca Clínic Barcelona-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), School of Medicine, Universitat de Barcelona, Barcelona, Spain.
Pulmonology Service, Hospital Clínic de Barcelona, Barcelona, Spain.
出版信息
Sci Rep. 2025 May 9;15(1):16269. doi: 10.1038/s41598-025-00555-9.
COVID-19 vaccination strategies are already available almost worldwide. However, it is also crucial to develop new therapeutic approaches, especially for vulnerable populations that may not fully respond to vaccination, such as the immunocompromised. In this project, we predicted 25 B-cell epitopes in silico in the SARS-CoV-2 Spike (S) protein and screened these against serum and plasma samples from 509 COVID-19 convalescent patients. The aim was to identify those epitopes with the highest IgG reactivity to produce monoclonal antibodies against them for COVID-19 treatment. We implemented Brewpitopes, a computational pipeline based on B-cell epitope prediction tools, such as BepiPred v2.0 and Discotope v2.0, and a series of antibody-epitope accessibility filters. We mapped the SARS-CoV-2 S protein epitopes most likely to be recognised by human neutralizing antibodies. Linear and structural epitope predictions were included and were further refined considering accessibility factors influencing their binding to antibodies like glycosylation status, localization in the viral membrane and accessibility on the 3D-surface of S. Blood samples were collected from 509 COVID-19 patients prospectively recruited 35 days after symptoms initiation, positive RT-qPCR or hospital/ICU discharge. Presence of IgG against SARS-CoV-2 was confirmed by lateral flow immunoassays. Epitopes immunogenicity was tested through the analysis of IgG levels and seropositivity in the convalescent serum and plasma samples and 126 pre-pandemic negative controls by Luminex to identify those with the highest reactivity. The seropositivity cut-offs for each epitope were calculated using a set of 126 pre-pandemic samples as negative controls (NC). Twenty-five SARS-CoV-2 S epitopes were predicted in silico as potentially the most immunogenic. These were synthesized and tested in a multiplex immunoassay against sera/plasmas from convalescent COVID-19 patients (5.7% asymptomatic, 35.6% mild, 13.8% moderate, 23% severe and 22% unknown because of anonymous donation). Among the 25 epitopes tested, 3 exhibited significantly higher IgG reactivity compared to the rest. The proportion of seropositive patients towards these 3 epitopes, based on median fluorescence intensity (MFI or Log MFI) above that from NC, ranged between 11 and 48%. Two out of the three most immunogenic epitopes were scaled up, resulting in the generation of two monoclonal antibodies (mAbs). These two mAbs exhibited comparable levels of S protein affinity to commercialized mAbs. Our data shows that the candidate S epitopes predicted in silico are recognised by IgG present in convalescent serum and plasma. This evidence suggests that our computational and experimental pipeline is able to yield immunogenic epitopes against SARS-CoV-2 S. These epitopes are suitable for the development of novel antibodies for preventive or therapeutic approaches against COVID-19.
几乎在全球范围内,新冠病毒(COVID-19)疫苗接种策略均已出台。然而,开发新的治疗方法也至关重要,特别是针对那些可能对疫苗接种反应不完全的弱势群体,如免疫功能低下者。在本项目中,我们通过计算机模拟预测了严重急性呼吸综合征冠状病毒2(SARS-CoV-2)刺突(S)蛋白中的25个B细胞表位,并使用509例COVID-19康复患者的血清和血浆样本对其进行筛选。目的是识别那些具有最高IgG反应性的表位,以生产针对它们的单克隆抗体用于COVID-19治疗。我们采用了Brewpitopes,这是一种基于B细胞表位预测工具(如BepiPred v2.0和Discotope v2.0)以及一系列抗体-表位可及性过滤器的计算流程。我们绘制了最有可能被人类中和抗体识别的SARS-CoV-2 S蛋白表位。其中包括线性和结构表位预测,并根据影响其与抗体结合的可及性因素(如糖基化状态、在病毒膜中的定位以及S蛋白三维表面的可及性)进行了进一步优化。从症状出现、逆转录定量聚合酶链反应(RT-qPCR)检测呈阳性或出院/重症监护病房(ICU)出院35天后前瞻性招募的509例COVID-19患者中采集血样。通过侧向流动免疫测定法确认了针对SARS-CoV-2的IgG的存在。通过分析康复期血清和血浆样本以及126份大流行前阴性对照中的IgG水平和血清阳性率,测试表位的免疫原性,以识别那些具有最高反应性的表位。使用一组126份大流行前样本作为阴性对照(NC)计算每个表位的血清阳性阈值。通过计算机模拟预测了25个SARS-CoV-2 S表位可能是最具免疫原性的。将这些表位合成后,在多重免疫测定中针对COVID-19康复患者的血清/血浆进行测试(5.7%无症状、35.6%轻症、13.8%中症、23%重症以及22%因匿名捐赠情况不明)。在测试的25个表位中,有3个表位的IgG反应性明显高于其他表位。基于高于NC的中位荧光强度(MFI或Log MFI),血清阳性患者针对这3个表位的比例在11%至48%之间。扩大了三个免疫原性最强的表位中的两个的规模,从而产生了两种单克隆抗体(mAb)。这两种mAb对S蛋白的亲和力水平与商业化mAb相当。我们的数据表明,通过计算机模拟预测的候选S表位可被康复期血清和血浆中的IgG识别。这一证据表明,我们的计算和实验流程能够产生针对SARS-CoV-2 S的免疫原性表位。这些表位适用于开发针对COVID-19的预防或治疗方法的新型抗体。