Evidence map›Paper›PMID 40121330›Full record

ArticleCommunications biology2025

Structural and virological identification of neutralizing antibody footprint provides insights into therapeutic antibody design against SARS-CoV-2 variants.

Yuki Anraku, Shunsuke Kita, Taishi Onodera, Akihiko Sato, Takashi Tadokoro, Shiori Ito, Yu Adachi, Ryutaro Kotaki, Tateki Suzuki, Jiei Sasaki and 15 more

Abstract read
In one paragraph

Article in Communications biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

25 authors.

Yuki AnrakuLaboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.ORCID http://orcid.org/0000-0002-5731-0902
Shunsuke KitaLaboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan. kita@pharm.hokudai.ac.jp.ORCID http://orcid.org/0000-0003-3969-302X
Taishi OnoderaResearch Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan.
Akihiko SatoLaboratory for Drug Discovery & Disease Research, Shionogi & Co., Ltd., Osaka, Japan.
Takashi TadokoroLaboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
Shiori ItoLaboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
Yu AdachiResearch Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan.
Ryutaro KotakiResearch Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan.ORCID http://orcid.org/0000-0001-7965-1671
Tateki SuzukiLaboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
Jiei SasakiLaboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
Nozomi Shiwa-SudoDepartment of Pathology, National Institute of Infectious Diseases, Tokyo, Japan.
Naoko Iwata-YoshikawaDepartment of Pathology, National Institute of Infectious Diseases, Tokyo, Japan.
Noriyo NagataDepartment of Pathology, National Institute of Infectious Diseases, Tokyo, Japan.
Souta KobayashiLaboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
Yasuhiro KazukiChromosome Engineering Research Center, Tottori University, Tottori, Japan.
Mitsuo OshimuraTrans Chromosomics Inc., Yonago, Japan.
Takao NomuraLaboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
Michihito SasakiDivision of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
Yasuko OrbaDivision of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan.
Tadaki SuzukiDepartment of Pathology, National Institute of Infectious Diseases, Tokyo, Japan.ORCID http://orcid.org/0000-0002-3820-9542
Hirofumi SawaInstitute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan.ORCID http://orcid.org/0000-0003-2569-2755
Takao HashiguchiLaboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.ORCID http://orcid.org/0000-0001-7578-7571
Hideo FukuharaLaboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
Yoshimasa TakahashiResearch Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan. ytakahas@niid.go.jp.ORCID http://orcid.org/0000-0001-6342-4087
Katsumi MaenakaLaboratory of Biomolecular Science, and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan. maenaka@pharm.hokudai.ac.jp.ORCID http://orcid.org/0000-0002-5459-521X

Funding

MEXT | Japan Science and Technology Agency (JST) JPMJCR20H8Takeda Science Foundation Research grant
6 · The paper itself

Abstract

Medical treatments using potent neutralizing SARS-CoV-2 antibodies have achieved remarkable improvements in clinical symptoms, changing the situation for the severity of COVID-19 patients. We previously reported an antibody, NT-108 with potent neutralizing activity. However, the structural and functional basis for the neutralizing activity of NT-108 has not yet been understood. Here, we demonstrated the therapeutic effects of NT-108 in a hamster model and its protective effects at low doses. Furthermore, we determined the cryo-EM structure of NT-108 in complex with SARS-CoV-2 spike. The single-chain Fv construction of NT-108 improved the cryo-EM maps because of the prevention of preferred orientations induced by Fab orientation. The footprints of NT-108 illuminated how escape mutations such as E484K evade from class 2 antibody recognition without ACE2 affinity attenuation. The functional and structural basis for the potent neutralizing activity of NT-108 provides insights into the rational design of therapeutic antibodies.

Indexed as

Antibodies, NeutralizingAntibodies, ViralCOVID-19COVID-19 Drug TreatmentSARS-CoV-2Spike Glycoprotein, CoronavirusAngiotensin-Converting Enzyme 2AnimalsCricetinaeCryoelectron MicroscopyHumansMesocricetusAngiotensin-Converting Enzyme 2Antibodies, NeutralizingAntibodies, ViralSpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2

Identifiers

PMID40121330
PMCPMC11929858

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.