Exploring epitope and functional diversity of anti-SARS-CoV2 antibodies using AI-based methods
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Abstract
Since the beginning of the COVID19 pandemics, an unprecedented research effort has been conducted to analyze the antibody responses in patients, and many trials based on passive immunotherapy — notably monoclonal antibodies — are ongoing. Twenty-one antibodies have entered clinical trials, 6 having reached phase 2/3, phase 3 or having received emergency authorization. These represent only the tip of the iceberg, since many more antibodies have been discovered and represent opportunities either for diagnosis purposes or as drug candidates. The main problem facing laboratories willing to develop such antibodies is the huge task of analyzing them and choosing the best candidate for exhaustive experimental validation. In this work we show how artificial intelligence-based methods can help in analyzing large sets of antibodies in order to determine in a few hours the best candidates in few hours. The MAbCluster method, which only requires knowledge of the amino acid sequences of the antibodies, allows to group the antibodies having the same epitope, considering only their amino acid sequences and their 3D structures (actual or predicted), and to infer some of their functional properties. We then use MAbTope to predict the epitopes for all antibodies for which they are not already known. This allows an exhaustive comparison of the available epitopes, but also gives a synthetic view of the possible combinations. Finally, we show how these results can be used to predict which antibodies might be affected by the different mutations arising in the circulating strains of the virus, such as the N501Y mutation that has started to spread in Great-Britain.
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SciScore for 10.1101/2020.12.23.424199: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources Antibody sequences targeting the spike protein of the different coronaviruses were collected from the database CoV-AbDab17, patent and literature mining and IMGT18. IMGT18suggested: NoneSoftware and Algorithms Sentences Resources Visualizations were made using Pymol** for 3D structures and Observable†† for maps and matrices. Pymol**suggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques …SciScore for 10.1101/2020.12.23.424199: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources Antibody sequences targeting the spike protein of the different coronaviruses were collected from the database CoV-AbDab17, patent and literature mining and IMGT18. IMGT18suggested: NoneSoftware and Algorithms Sentences Resources Visualizations were made using Pymol** for 3D structures and Observable†† for maps and matrices. Pymol**suggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on page 3. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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SciScore for 10.1101/2020.12.23.424199: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources Material and methods Antibody sequences targeting the spike protein of the different coronaviruses were collected from the database CoV-AbDab17, patent and literature mining and IMGT18. IMGT18suggested: NoneSoftware and Algorithms Sentences Resources For all the remaining antibodies amongst the 1569, epitopes were predicted using MAbTope. MAbTopesuggested: NoneVisualizat… SciScore for 10.1101/2020.12.23.424199: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources Material and methods Antibody sequences targeting the spike protein of the different coronaviruses were collected from the database CoV-AbDab17, patent and literature mining and IMGT18. IMGT18suggested: NoneSoftware and Algorithms Sentences Resources For all the remaining antibodies amongst the 1569, epitopes were predicted using MAbTope. MAbTopesuggested: NoneVisualizations were made using Pymol** for 3D structures and Observable†† for maps and matrices. Pymol**suggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: Please consider improving the rainbow (“jet”) colormap used on page 3. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
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