Literature DB >> 32409444

De novo protein design enables the precise induction of RSV-neutralizing antibodies.

Fabian Sesterhenn1,2, Che Yang1,2, Jaume Bonet1,2, Johannes T Cramer3, Xiaolin Wen4, Yimeng Wang5, Chi-I Chiang5, Luciano A Abriata1,2, Iga Kucharska6,7, Giacomo Castoro3, Sabrina S Vollers1,2, Marie Galloux8, Elie Dheilly9, Stéphane Rosset1,2, Patricia Corthésy1,2, Sandrine Georgeon1,2, Mélanie Villard1,2, Charles-Adrien Richard8, Delphyne Descamps8, Teresa Delgado10, Elisa Oricchio9, Marie-Anne Rameix-Welti11, Vicente Más10, Sean Ervin12, Jean-François Eléouët8, Sabine Riffault8, John T Bates13, Jean-Philippe Julien6,7, Yuxing Li5,14, Theodore Jardetzky4, Thomas Krey3,15,16,17,18, Bruno E Correia19,2.   

Abstract

De novo protein design has been successful in expanding the natural protein repertoire. However, most de novo proteins lack biological function, presenting a major methodological challenge. In vaccinology, the induction of precise antibody responses remains a cornerstone for next-generation vaccines. Here, we present a protein design algorithm called TopoBuilder, with which we engineered epitope-focused immunogens displaying complex structural motifs. In both mice and nonhuman primates, cocktails of three de novo-designed immunogens induced robust neutralizing responses against the respiratory syncytial virus. Furthermore, the immunogens refocused preexisting antibody responses toward defined neutralization epitopes. Overall, our design approach opens the possibility of targeting specific epitopes for the development of vaccines and therapeutic antibodies and, more generally, will be applicable to the design of de novo proteins displaying complex functional motifs.
Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

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Year:  2020        PMID: 32409444      PMCID: PMC7391827          DOI: 10.1126/science.aay5051

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   63.714


  81 in total

1.  Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space.

Authors:  Daniel Gottstein; Donata K Kirchner; Peter Güntert
Journal:  J Biomol NMR       Date:  2012-02-22       Impact factor: 2.835

2.  Linking crystallographic model and data quality.

Authors:  P Andrew Karplus; Kay Diederichs
Journal:  Science       Date:  2012-05-25       Impact factor: 47.728

Review 3.  The coming of age of de novo protein design.

Authors:  Po-Ssu Huang; Scott E Boyken; David Baker
Journal:  Nature       Date:  2016-09-15       Impact factor: 49.962

4.  HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen.

Authors:  Joseph G Jardine; Daniel W Kulp; Colin Havenar-Daughton; Anita Sarkar; Bryan Briney; Devin Sok; Fabian Sesterhenn; June Ereño-Orbea; Oleksandr Kalyuzhniy; Isaiah Deresa; Xiaozhen Hu; Skye Spencer; Meaghan Jones; Erik Georgeson; Yumiko Adachi; Michael Kubitz; Allan C deCamp; Jean-Philippe Julien; Ian A Wilson; Dennis R Burton; Shane Crotty; William R Schief
Journal:  Science       Date:  2016-03-25       Impact factor: 47.728

5.  Design and characterization of epitope-scaffold immunogens that present the motavizumab epitope from respiratory syncytial virus.

Authors:  Jason S McLellan; Bruno E Correia; Man Chen; Yongping Yang; Barney S Graham; William R Schief; Peter D Kwong
Journal:  J Mol Biol       Date:  2011-04-27       Impact factor: 5.469

6.  Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope.

Authors:  Bruno E Correia; Yih-En Andrew Ban; Margaret A Holmes; Hengyu Xu; Katharine Ellingson; Zane Kraft; Chris Carrico; Erica Boni; D Noah Sather; Camille Zenobia; Katherine Y Burke; Tyler Bradley-Hewitt; Jessica F Bruhn-Johannsen; Oleksandr Kalyuzhniy; David Baker; Roland K Strong; Leonidas Stamatatos; William R Schief
Journal:  Structure       Date:  2010-09-08       Impact factor: 5.006

7.  A proof of concept for structure-based vaccine design targeting RSV in humans.

Authors:  Michelle C Crank; Tracy J Ruckwardt; Man Chen; Kaitlyn M Morabito; Emily Phung; Pamela J Costner; LaSonji A Holman; Somia P Hickman; Nina M Berkowitz; Ingelise J Gordon; Galina V Yamshchikov; Martin R Gaudinski; Azad Kumar; Lauren A Chang; Syed M Moin; Juliane P Hill; Anthony T DiPiazza; Richard M Schwartz; Lisa Kueltzo; Jonathan W Cooper; Peifeng Chen; Judith A Stein; Kevin Carlton; Jason G Gall; Martha C Nason; Peter D Kwong; Grace L Chen; John R Mascola; Jason S McLellan; Julie E Ledgerwood; Barney S Graham
Journal:  Science       Date:  2019-08-02       Impact factor: 47.728

8.  Structural basis of potent Zika-dengue virus antibody cross-neutralization.

Authors:  Giovanna Barba-Spaeth; Wanwisa Dejnirattisai; Alexander Rouvinski; Marie-Christine Vaney; Iris Medits; Arvind Sharma; Etienne Simon-Lorière; Anavaj Sakuntabhai; Van-Mai Cao-Lormeau; Ahmed Haouz; Patrick England; Karin Stiasny; Juthathip Mongkolsapaya; Franz X Heinz; Gavin R Screaton; Félix A Rey
Journal:  Nature       Date:  2016-06-23       Impact factor: 49.962

9.  De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy.

Authors:  Po-Ssu Huang; Kaspar Feldmeier; Fabio Parmeggiani; D Alejandro Fernandez Velasco; Birte Höcker; David Baker
Journal:  Nat Chem Biol       Date:  2015-11-23       Impact factor: 15.040

10.  A computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells.

Authors:  Erik Procko; Geoffrey Y Berguig; Betty W Shen; Yifan Song; Shani Frayo; Anthony J Convertine; Daciana Margineantu; Garrett Booth; Bruno E Correia; Yuanhua Cheng; William R Schief; David M Hockenbery; Oliver W Press; Barry L Stoddard; Patrick S Stayton; David Baker
Journal:  Cell       Date:  2014-06-19       Impact factor: 41.582

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  37 in total

Review 1.  Rationalizing Random Walks: Replicating Protective Antibody Trajectories.

Authors:  Jennifer L Remmel; Margaret E Ackerman
Journal:  Trends Immunol       Date:  2021-01-26       Impact factor: 16.687

Review 2.  Subdominance in Antibody Responses: Implications for Vaccine Development.

Authors:  Gunnar Lindahl
Journal:  Microbiol Mol Biol Rev       Date:  2020-11-25       Impact factor: 11.056

3.  The register shift rules for βαβ-motifs for de novo protein design.

Authors:  Hiroto Murata; Hayao Imakawa; Nobuyasu Koga; George Chikenji
Journal:  PLoS One       Date:  2021-08-30       Impact factor: 3.240

4.  Structural basis for broad coronavirus neutralization.

Authors:  Maximilian M Sauer; M Alejandra Tortorici; Young-Jun Park; Alexandra C Walls; Leah Homad; Oliver J Acton; John E Bowen; Chunyan Wang; Xiaoli Xiong; Willem de van der Schueren; Joel Quispe; Benjamin G Hoffstrom; Berend-Jan Bosch; Andrew T McGuire; David Veesler
Journal:  Nat Struct Mol Biol       Date:  2021-05-12       Impact factor: 15.369

Review 5.  Toward complete rational control over protein structure and function through computational design.

Authors:  Jared Adolf-Bryfogle; Frank D Teets; Christopher D Bahl
Journal:  Curr Opin Struct Biol       Date:  2020-12-01       Impact factor: 6.809

Review 6.  Can We AlphaFold Our Way Out of the Next Pandemic?

Authors:  Matthew K Higgins
Journal:  J Mol Biol       Date:  2021-06-08       Impact factor: 5.469

7.  Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design.

Authors:  Clara T Schoeder; Samuel Schmitz; Jared Adolf-Bryfogle; Alexander M Sevy; Jessica A Finn; Marion F Sauer; Nina G Bozhanova; Benjamin K Mueller; Amandeep K Sangha; Jaume Bonet; Jonathan H Sheehan; Georg Kuenze; Brennica Marlow; Shannon T Smith; Hope Woods; Brian J Bender; Cristina E Martina; Diego Del Alamo; Pranav Kodali; Alican Gulsevin; William R Schief; Bruno E Correia; James E Crowe; Jens Meiler; Rocco Moretti
Journal:  Biochemistry       Date:  2021-03-11       Impact factor: 3.162

Review 8.  The Status and Prospects of Epstein-Barr Virus Prophylactic Vaccine Development.

Authors:  Cong Sun; Xin-Chun Chen; Yin-Feng Kang; Mu-Sheng Zeng
Journal:  Front Immunol       Date:  2021-06-08       Impact factor: 7.561

9.  Hyper-Enriched Anti-RSV Immunoglobulins Nasally Administered: A Promising Approach for Respiratory Syncytial Virus Prophylaxis.

Authors:  Emilie Jacque; Claire Chottin; Daphné Laubreton; Michel Nogre; Cécile Ferret; Sandrine de Marcos; Linda Baptista; Carole Drajac; Philippe Mondon; Christophe De Romeuf; Marie-Anne Rameix-Welti; Jean-François Eléouët; Sami Chtourou; Sabine Riffault; Gérald Perret; Delphyne Descamps
Journal:  Front Immunol       Date:  2021-06-07       Impact factor: 7.561

10.  Protective neutralizing antibodies from human survivors of Crimean-Congo hemorrhagic fever.

Authors:  J Maximilian Fels; Daniel P Maurer; Andrew S Herbert; Ariel S Wirchnianski; Olivia Vergnolle; Robert W Cross; Dafna M Abelson; Crystal L Moyer; Akaash K Mishra; Jennifer T Aguilan; Ana I Kuehne; Noel T Pauli; Russell R Bakken; Elisabeth K Nyakatura; Jan Hellert; Gregory Quevedo; Leslie Lobel; Stephen Balinandi; Julius J Lutwama; Larry Zeitlin; Thomas W Geisbert; Felix A Rey; Simone Sidoli; Jason S McLellan; Jonathan R Lai; Zachary A Bornholdt; John M Dye; Laura M Walker; Kartik Chandran
Journal:  Cell       Date:  2021-06-01       Impact factor: 66.850

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