Literature DB >> 34874007

Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape.

Fred D Mast1, Peter C Fridy2, Natalia E Ketaren2, Junjie Wang3, Erica Y Jacobs3,4, Jean Paul Olivier1, Tanmoy Sanyal5, Kelly R Molloy3, Fabian Schmidt6, Magdalena Rutkowska6, Yiska Weisblum6, Lucille M Rich7, Elizabeth R Vanderwall7, Nicholas Dambrauskas1, Vladimir Vigdorovich1, Sarah Keegan8, Jacob B Jiler2, Milana E Stein2, Paul Dominic B Olinares3, Louis Herlands9, Theodora Hatziioannou6, D Noah Sather1,10, Jason S Debley7,10,11, David Fenyö8, Andrej Sali5, Paul D Bieniasz6,12, John D Aitchison1,10,13, Brian T Chait3, Michael P Rout2.   

Abstract

The emergence of SARS-CoV-2 variants threatens current vaccines and therapeutic antibodies and urgently demands powerful new therapeutics that can resist viral escape. We therefore generated a large nanobody repertoire to saturate the distinct and highly conserved available epitope space of SARS-CoV-2 spike, including the S1 receptor binding domain, N-terminal domain, and the S2 subunit, to identify new nanobody binding sites that may reflect novel mechanisms of viral neutralization. Structural mapping and functional assays show that indeed these highly stable monovalent nanobodies potently inhibit SARS-CoV-2 infection, display numerous neutralization mechanisms, are effective against emerging variants of concern, and are resistant to mutational escape. Rational combinations of these nanobodies that bind to distinct sites within and between spike subunits exhibit extraordinary synergy and suggest multiple tailored therapeutic and prophylactic strategies.
© 2021, Mast et al.

Entities:  

Keywords:  SARS-CoV-2; human; infectious disease; microbiology; nanobodies; single-domain antibodies; spike glycoprotein; synergy; variants of concern

Mesh:

Substances:

Year:  2021        PMID: 34874007      PMCID: PMC8651292          DOI: 10.7554/eLife.73027

Source DB:  PubMed          Journal:  Elife        ISSN: 2050-084X            Impact factor:   8.140


  150 in total

1.  Protein Structure Modeling with MODELLER.

Authors:  Benjamin Webb; Andrej Sali
Journal:  Methods Mol Biol       Date:  2021

2.  Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies.

Authors:  Yufei Xiang; Zhe Sang; Lirane Bitton; Jianquan Xu; Yang Liu; Dina Schneidman-Duhovny; Yi Shi
Journal:  Cell Syst       Date:  2021-02-15       Impact factor: 10.304

3.  Inhalable Nanobody (PiN-21) prevents and treats SARS-CoV-2 infections in Syrian hamsters at ultra-low doses.

Authors:  Sham Nambulli; Yufei Xiang; Natasha L Tilston-Lunel; Linda J Rennick; Zhe Sang; William B Klimstra; Douglas S Reed; Nicholas A Crossland; Yi Shi; W Paul Duprex
Journal:  Sci Adv       Date:  2021-05-26       Impact factor: 14.136

4.  A pneumonia outbreak associated with a new coronavirus of probable bat origin.

Authors:  Peng Zhou; Xing-Lou Yang; Xian-Guang Wang; Ben Hu; Lei Zhang; Wei Zhang; Hao-Rui Si; Yan Zhu; Bei Li; Chao-Lin Huang; Hui-Dong Chen; Jing Chen; Yun Luo; Hua Guo; Ren-Di Jiang; Mei-Qin Liu; Ying Chen; Xu-Rui Shen; Xi Wang; Xiao-Shuang Zheng; Kai Zhao; Quan-Jiao Chen; Fei Deng; Lin-Lin Liu; Bing Yan; Fa-Xian Zhan; Yan-Yi Wang; Geng-Fu Xiao; Zheng-Li Shi
Journal:  Nature       Date:  2020-02-03       Impact factor: 69.504

5.  Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation.

Authors:  Daniel Wrapp; Nianshuang Wang; Kizzmekia S Corbett; Jory A Goldsmith; Ching-Lin Hsieh; Olubukola Abiona; Barney S Graham; Jason S McLellan
Journal:  Science       Date:  2020-02-19       Impact factor: 47.728

6.  Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants.

Authors:  Yiska Weisblum; Fabian Schmidt; Fengwen Zhang; Justin DaSilva; Daniel Poston; Julio Cc Lorenzi; Frauke Muecksch; Magdalena Rutkowska; Hans-Heinrich Hoffmann; Eleftherios Michailidis; Christian Gaebler; Marianna Agudelo; Alice Cho; Zijun Wang; Anna Gazumyan; Melissa Cipolla; Larry Luchsinger; Christopher D Hillyer; Marina Caskey; Davide F Robbiani; Charles M Rice; Michel C Nussenzweig; Theodora Hatziioannou; Paul D Bieniasz
Journal:  Elife       Date:  2020-10-28       Impact factor: 8.140

7.  Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021.

Authors:  Finlay Campbell; Brett Archer; Henry Laurenson-Schafer; Yuka Jinnai; Franck Konings; Neale Batra; Boris Pavlin; Katelijn Vandemaele; Maria D Van Kerkhove; Thibaut Jombart; Oliver Morgan; Olivier le Polain de Waroux
Journal:  Euro Surveill       Date:  2021-06

8.  Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition.

Authors:  Oliver C Grant; David Montgomery; Keigo Ito; Robert J Woods
Journal:  Sci Rep       Date:  2020-09-14       Impact factor: 4.379

9.  Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody.

Authors:  Xiaolong Tian; Cheng Li; Ailing Huang; Shuai Xia; Sicong Lu; Zhengli Shi; Lu Lu; Shibo Jiang; Zhenlin Yang; Yanling Wu; Tianlei Ying
Journal:  Emerg Microbes Infect       Date:  2020-02-17       Impact factor: 7.163

10.  Engineering human ACE2 to optimize binding to the spike protein of SARS coronavirus 2.

Authors:  Kui K Chan; Danielle Dorosky; Preeti Sharma; Shawn A Abbasi; John M Dye; David M Kranz; Andrew S Herbert; Erik Procko
Journal:  Science       Date:  2020-08-04       Impact factor: 47.728

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  12 in total

1.  Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library.

Authors:  Dmitri Dormeshkin; Michail Shapira; Simon Dubovik; Anton Kavaleuski; Mikalai Katsin; Alexandr Migas; Alexander Meleshko; Sergei Semyonov
Journal:  Front Immunol       Date:  2022-09-16       Impact factor: 8.786

Review 2.  Single-Domain Antibodies as Therapeutics for Respiratory RNA Virus Infections.

Authors:  Keke Huang; Tianlei Ying; Yanling Wu
Journal:  Viruses       Date:  2022-05-27       Impact factor: 5.818

3.  Anti-TRAP/SSP2 monoclonal antibodies can inhibit sporozoite infection and may enhance protection of anti-CSP monoclonal antibodies.

Authors:  Brandon K Wilder; Vladimir Vigdorovich; Sara Carbonetti; Nana Minkah; Nina Hertoghs; Andrew Raappana; Hayley Cardamone; Brian G Oliver; Olesya Trakhimets; Sudhir Kumar; Nicholas Dambrauskas; Silvia A Arredondo; Nelly Camargo; Annette M Seilie; Sean C Murphy; Stefan H I Kappe; D Noah Sather
Journal:  NPJ Vaccines       Date:  2022-05-26       Impact factor: 9.399

4.  Superimmunity by pan-sarbecovirus nanobodies.

Authors:  Yufei Xiang; Wei Huang; Hejun Liu; Zhe Sang; Sham Nambulli; Jérôme Tubiana; Kevin L Williams; W Paul Duprex; Dina Schneidman-Duhovny; Ian A Wilson; Derek J Taylor; Yi Shi
Journal:  Cell Rep       Date:  2022-06-08       Impact factor: 9.995

5.  Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant.

Authors:  Gennady Verkhivker
Journal:  Int J Mol Sci       Date:  2022-02-16       Impact factor: 5.923

6.  A potent alpaca-derived nanobody that neutralizes SARS-CoV-2 variants.

Authors:  Jules B Weinstein; Timothy A Bates; Hans C Leier; Savannah K McBride; Eric Barklis; Fikadu G Tafesse
Journal:  iScience       Date:  2022-02-22

7.  Isolation, characterization, and structure-based engineering of a neutralizing nanobody against SARS-CoV-2.

Authors:  Tingting Li; Bingjie Zhou; Yaning Li; Suqiong Huang; Zhipu Luo; Yuanze Zhou; Yanling Lai; Anupriya Gautam; Salome Bourgeau; Shurui Wang; Juan Bao; Jingquan Tan; Dimitri Lavillette; Dianfan Li
Journal:  Int J Biol Macromol       Date:  2022-04-20       Impact factor: 8.025

8.  A panel of nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants including Omicron.

Authors:  Ryota Maeda; Junso Fujita; Yoshinobu Konishi; Yasuhiro Kazuma; Hiroyuki Yamazaki; Itsuki Anzai; Tokiko Watanabe; Keishi Yamaguchi; Kazuki Kasai; Kayoko Nagata; Yutaro Yamaoka; Kei Miyakawa; Akihide Ryo; Kotaro Shirakawa; Kei Sato; Fumiaki Makino; Yoshiharu Matsuura; Tsuyoshi Inoue; Akihiro Imura; Keiichi Namba; Akifumi Takaori-Kondo
Journal:  Commun Biol       Date:  2022-07-06

9.  Evaluation of SARS-CoV-2-Neutralizing Nanobody Using Virus Receptor Binding Domain-Administered Model Mice.

Authors:  Song Liu; Guanghui Li; Lei Ding; Jin Ding; Qian Zhang; Dan Li; Xingguo Hou; Xiangxing Kong; Jing Zou; Shiming Zhang; Hongbin Han; Yakun Wan; Zhi Yang; Hua Zhu
Journal:  Research (Wash D C)       Date:  2022-07-22

Review 10.  Structural and Computational Studies of the SARS-CoV-2 Spike Protein Binding Mechanisms with Nanobodies: From Structure and Dynamics to Avidity-Driven Nanobody Engineering.

Authors:  Gennady Verkhivker
Journal:  Int J Mol Sci       Date:  2022-03-08       Impact factor: 5.923

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