Engineered SARS-CoV-2 receptor binding domain improves manufacturability in yeast and immunogenicity in mice

Neil C. Dalvie; Sergio A. Rodriguez-Aponte; Brittany L. Hartwell; Lisa H. Tostanoski; Andrew M. Biedermann; Laura E. Crowell; Kawaljit Kaur; Ozan S. Kumru; Lauren Carter; Jingyou Yu; Aiquan Chang; Katherine McMahan; Thomas Courant; Celia Lebas; Ashley A. Lemnios; Kristen A. Rodrigues; Murillo Silva; Ryan S. Johnston; Christopher A. Naranjo; Mary Kate Tracey; Joseph R. Brady; Charles A. Whittaker; Dongsoo Yun; Natalie Brunette; Jing Yang Wang; Carl Walkey; Brooke Fiala; Swagata Kar; Maciel Porto; Megan Lok; Hanne Andersen; Mark G. Lewis; Kerry R. Love; Danielle L. Camp; Judith Maxwell Silverman; Harry Kleanthous; Sangeeta B. Joshi; David B. Volkin; Patrice M. Dubois; Nicolas Collin; Neil P. King; Dan H. Barouch; Darrell J. Irvine; J. Christopher Love

doi:10.1073/pnas.2106845118

Engineered SARS-CoV-2 receptor binding domain improves manufacturability in yeast and immunogenicity in mice

Neil C. Dalvie, Sergio A. Rodriguez-Aponte, Brittany L. Hartwell, Lisa H. Tostanoski, Andrew M. Biedermann, Laura E. Crowell, Kawaljit Kaur, Ozan S. Kumru, Lauren Carter, Jingyou Yu, Aiquan Chang, Katherine McMahan, Thomas Courant, Celia Lebas, Ashley A. Lemnios, Kristen A. Rodrigues, Murillo Silva, Ryan S. Johnston, Christopher A. Naranjo, Mary Kate TraceyJoseph R. Brady, Charles A. Whittaker, Dongsoo Yun, Natalie Brunette, Jing Yang Wang, Carl Walkey, Brooke Fiala, Swagata Kar, Maciel Porto, Megan Lok, Hanne Andersen, Mark G. Lewis, Kerry R. Love, Danielle L. Camp, Judith Maxwell Silverman, Harry Kleanthous, Sangeeta B. Joshi, David B. Volkin, Patrice M. Dubois, Nicolas Collin, Neil P. King, Dan H. Barouch, Darrell J. Irvine, J. Christopher Love

Research output: Contribution to journal › Article › peer-review

62 Scopus citations

Abstract

Global containment of COVID-19 still requires accessible and affordable vaccines for low- and middle-income countries (LMICs). Recently approved vaccines provide needed interventions, albeit at prices that may limit their global access. Subunit vaccines based on recombinant proteins are suited for large-volume microbial manufacturing to yield billions of doses annually, minimizing their manufacturing cost. These types of vaccines are well-established, proven interventions with multiple safe and efficacious commercial examples. Many vaccine candidates of this type for SARS-CoV-2 rely on sequences containing the receptor-binding domain (RBD), which mediates viral entry to cells via ACE2. Here we report an engineered sequence variant of RBD that exhibits high-yield manufacturability, high-affinity binding to ACE2, and enhanced immunogenicity after a single dose in mice compared to the Wuhan-Hu-1 variant used in current vaccines. Antibodies raised against the engineered protein exhibited heterotypic binding to the RBD from two recently reported SARS-CoV-2 variants of concern (501Y.V1/V2). Presentation of the engineered RBD on a designed virus-like particle (VLP) also reduced weight loss in hamsters upon viral challenge.

Original language	English (US)
Article number	e2106845118
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	118
Issue number	38
DOIs	https://doi.org/10.1073/pnas.2106845118
State	Published - Sep 21 2021
Externally published	Yes

Bibliographical note

Funding Information:
We thank Prof. Ragahavan Varadarajan of the Indian Institute of Science for kindly providing the RBD sequence for SARS-CoV-2 Wuhan-Hu-1. We thank Laurent Pessaint, Dr. Adrienne Winn, Kamil Radzyminski, Andrew Faudree, Brittany Spence, Melissa Hamilton, and Natalie Figueroa Jones for advice and assistance with hamster studies. We thank Sumi Biswas of SpyBiotech for helpful discussions on SpyTag/SpyCatcher conjugations. We thank the Koch Institute's Robert A. Swanson (1969) Biotechnology Center for technical support. The following reagent was deposited by the Centers for Disease Control and Prevention and obtained through Biodefense and Emerging Infections Research Resources Repository, National Institute of Allergy and Infectious Diseases, NIH: SARS-Related Coronavirus 2, Isolate USAWA1/2020, NR-53780. This work was funded by the Bill & Melinda Gates Foundation (Investment IDs INV-002740, INV-006131, and OPP1156262). This study was also supported in part by the Koch Institute Support (core) Grant P30-CA14051 from the National Cancer Institute (NCI). L.H.T. is an NIH T32 postdoctoral fellow supported by the Multidisciplinary AIDS Training Program (Grant T32 AI007387). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NCI, the NIH, Bill & Melinda Gates Medical Research Institute, or the Bill & Melinda Gates Foundation.

Funding Information:
ACKNOWLEDGMENTS. We thank Prof. Ragahavan Varadarajan of the Indian Institute of Science for kindly providing the RBD sequence for SARS-CoV-2 Wuhan-Hu-1. We thank Laurent Pessaint, Dr. Adrienne Winn, Kamil Radzy-minski, Andrew Faudree, Brittany Spence, Melissa Hamilton, and Natalie Figueroa Jones for advice and assistance with hamster studies. We thank Sumi Biswas of SpyBiotech for helpful discussions on SpyTag/SpyCatcher conjugations. We thank the Koch Institute’s Robert A. Swanson (1969) Biotechnology Center for technical support. The following reagent was deposited by the Centers for Disease Control and Prevention and obtained through Biodefense and Emerging Infections Research Resources Repository, National Institute of Allergy and Infectious Diseases, NIH: SARS-Related Coronavirus 2, Isolate USA-WA1/2020, NR-53780. This work was funded by the Bill & Melinda Gates Foundation (Investment IDs INV-002740, INV-006131, and OPP1156262). This study was also supported in part by the Koch Institute Support (core) Grant P30-CA14051 from the National Cancer Institute (NCI). L.H.T. is an NIH T32 postdoctoral fellow supported by the Multidisciplinary AIDS Training Program (Grant T32 AI007387). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NCI, the NIH, Bill & Melinda Gates Medical Research Institute, or the Bill & Melinda Gates Foundation.

Publisher Copyright:
© 2021 National Academy of Sciences. All rights reserved.

Keywords

Manufacturability
Pichia pastoris
Protein vaccine
SARS-CoV-2

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Publisher link

10.1073/pnas.2106845118

Find It

Find It at U of M Libraries

Cite this

Dalvie, N. C., Rodriguez-Aponte, S. A., Hartwell, B. L., Tostanoski, L. H., Biedermann, A. M., Crowell, L. E., Kaur, K., Kumru, O. S., Carter, L., Yu, J., Chang, A., McMahan, K., Courant, T., Lebas, C., Lemnios, A. A., Rodrigues, K. A., Silva, M., Johnston, R. S., Naranjo, C. A., ... Love, J. C. (2021). Engineered SARS-CoV-2 receptor binding domain improves manufacturability in yeast and immunogenicity in mice. Proceedings of the National Academy of Sciences of the United States of America, 118(38), Article e2106845118. https://doi.org/10.1073/pnas.2106845118

Engineered SARS-CoV-2 receptor binding domain improves manufacturability in yeast and immunogenicity in mice. / Dalvie, Neil C.; Rodriguez-Aponte, Sergio A.; Hartwell, Brittany L. et al.
In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 118, No. 38, e2106845118, 21.09.2021.

Research output: Contribution to journal › Article › peer-review

Dalvie, NC, Rodriguez-Aponte, SA, Hartwell, BL, Tostanoski, LH, Biedermann, AM, Crowell, LE, Kaur, K, Kumru, OS, Carter, L, Yu, J, Chang, A, McMahan, K, Courant, T, Lebas, C, Lemnios, AA, Rodrigues, KA, Silva, M, Johnston, RS, Naranjo, CA, Tracey, MK, Brady, JR, Whittaker, CA, Yun, D, Brunette, N, Wang, JY, Walkey, C, Fiala, B, Kar, S, Porto, M, Lok, M, Andersen, H, Lewis, MG, Love, KR, Camp, DL, Silverman, JM, Kleanthous, H, Joshi, SB, Volkin, DB, Dubois, PM, Collin, N, King, NP, Barouch, DH, Irvine, DJ & Love, JC 2021, 'Engineered SARS-CoV-2 receptor binding domain improves manufacturability in yeast and immunogenicity in mice', Proceedings of the National Academy of Sciences of the United States of America, vol. 118, no. 38, e2106845118. https://doi.org/10.1073/pnas.2106845118

@article{af9fe5aa93104f1aa7f22f563146a28f,

title = "Engineered SARS-CoV-2 receptor binding domain improves manufacturability in yeast and immunogenicity in mice",

abstract = "Global containment of COVID-19 still requires accessible and affordable vaccines for low- and middle-income countries (LMICs). Recently approved vaccines provide needed interventions, albeit at prices that may limit their global access. Subunit vaccines based on recombinant proteins are suited for large-volume microbial manufacturing to yield billions of doses annually, minimizing their manufacturing cost. These types of vaccines are well-established, proven interventions with multiple safe and efficacious commercial examples. Many vaccine candidates of this type for SARS-CoV-2 rely on sequences containing the receptor-binding domain (RBD), which mediates viral entry to cells via ACE2. Here we report an engineered sequence variant of RBD that exhibits high-yield manufacturability, high-affinity binding to ACE2, and enhanced immunogenicity after a single dose in mice compared to the Wuhan-Hu-1 variant used in current vaccines. Antibodies raised against the engineered protein exhibited heterotypic binding to the RBD from two recently reported SARS-CoV-2 variants of concern (501Y.V1/V2). Presentation of the engineered RBD on a designed virus-like particle (VLP) also reduced weight loss in hamsters upon viral challenge.",

keywords = "Manufacturability, Pichia pastoris, Protein vaccine, SARS-CoV-2",

author = "Dalvie, {Neil C.} and Rodriguez-Aponte, {Sergio A.} and Hartwell, {Brittany L.} and Tostanoski, {Lisa H.} and Biedermann, {Andrew M.} and Crowell, {Laura E.} and Kawaljit Kaur and Kumru, {Ozan S.} and Lauren Carter and Jingyou Yu and Aiquan Chang and Katherine McMahan and Thomas Courant and Celia Lebas and Lemnios, {Ashley A.} and Rodrigues, {Kristen A.} and Murillo Silva and Johnston, {Ryan S.} and Naranjo, {Christopher A.} and Tracey, {Mary Kate} and Brady, {Joseph R.} and Whittaker, {Charles A.} and Dongsoo Yun and Natalie Brunette and Wang, {Jing Yang} and Carl Walkey and Brooke Fiala and Swagata Kar and Maciel Porto and Megan Lok and Hanne Andersen and Lewis, {Mark G.} and Love, {Kerry R.} and Camp, {Danielle L.} and Silverman, {Judith Maxwell} and Harry Kleanthous and Joshi, {Sangeeta B.} and Volkin, {David B.} and Dubois, {Patrice M.} and Nicolas Collin and King, {Neil P.} and Barouch, {Dan H.} and Irvine, {Darrell J.} and Love, {J. Christopher}",

note = "Funding Information: We thank Prof. Ragahavan Varadarajan of the Indian Institute of Science for kindly providing the RBD sequence for SARS-CoV-2 Wuhan-Hu-1. We thank Laurent Pessaint, Dr. Adrienne Winn, Kamil Radzyminski, Andrew Faudree, Brittany Spence, Melissa Hamilton, and Natalie Figueroa Jones for advice and assistance with hamster studies. We thank Sumi Biswas of SpyBiotech for helpful discussions on SpyTag/SpyCatcher conjugations. We thank the Koch Institute's Robert A. Swanson (1969) Biotechnology Center for technical support. The following reagent was deposited by the Centers for Disease Control and Prevention and obtained through Biodefense and Emerging Infections Research Resources Repository, National Institute of Allergy and Infectious Diseases, NIH: SARS-Related Coronavirus 2, Isolate USAWA1/2020, NR-53780. This work was funded by the Bill & Melinda Gates Foundation (Investment IDs INV-002740, INV-006131, and OPP1156262). This study was also supported in part by the Koch Institute Support (core) Grant P30-CA14051 from the National Cancer Institute (NCI). L.H.T. is an NIH T32 postdoctoral fellow supported by the Multidisciplinary AIDS Training Program (Grant T32 AI007387). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NCI, the NIH, Bill & Melinda Gates Medical Research Institute, or the Bill & Melinda Gates Foundation. Funding Information: ACKNOWLEDGMENTS. We thank Prof. Ragahavan Varadarajan of the Indian Institute of Science for kindly providing the RBD sequence for SARS-CoV-2 Wuhan-Hu-1. We thank Laurent Pessaint, Dr. Adrienne Winn, Kamil Radzy-minski, Andrew Faudree, Brittany Spence, Melissa Hamilton, and Natalie Figueroa Jones for advice and assistance with hamster studies. We thank Sumi Biswas of SpyBiotech for helpful discussions on SpyTag/SpyCatcher conjugations. We thank the Koch Institute{\textquoteright}s Robert A. Swanson (1969) Biotechnology Center for technical support. The following reagent was deposited by the Centers for Disease Control and Prevention and obtained through Biodefense and Emerging Infections Research Resources Repository, National Institute of Allergy and Infectious Diseases, NIH: SARS-Related Coronavirus 2, Isolate USA-WA1/2020, NR-53780. This work was funded by the Bill & Melinda Gates Foundation (Investment IDs INV-002740, INV-006131, and OPP1156262). This study was also supported in part by the Koch Institute Support (core) Grant P30-CA14051 from the National Cancer Institute (NCI). L.H.T. is an NIH T32 postdoctoral fellow supported by the Multidisciplinary AIDS Training Program (Grant T32 AI007387). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NCI, the NIH, Bill & Melinda Gates Medical Research Institute, or the Bill & Melinda Gates Foundation. Publisher Copyright: {\textcopyright} 2021 National Academy of Sciences. All rights reserved.",

year = "2021",

month = sep,

day = "21",

doi = "10.1073/pnas.2106845118",

language = "English (US)",

volume = "118",

journal = "Proceedings of the National Academy of Sciences of the United States of America",

issn = "0027-8424",

publisher = "National Academy of Sciences",

number = "38",

}

TY - JOUR

T1 - Engineered SARS-CoV-2 receptor binding domain improves manufacturability in yeast and immunogenicity in mice

AU - Dalvie, Neil C.

AU - Rodriguez-Aponte, Sergio A.

AU - Hartwell, Brittany L.

AU - Tostanoski, Lisa H.

AU - Biedermann, Andrew M.

AU - Crowell, Laura E.

AU - Kaur, Kawaljit

AU - Kumru, Ozan S.

AU - Carter, Lauren

AU - Yu, Jingyou

AU - Chang, Aiquan

AU - McMahan, Katherine

AU - Courant, Thomas

AU - Lebas, Celia

AU - Lemnios, Ashley A.

AU - Rodrigues, Kristen A.

AU - Silva, Murillo

AU - Johnston, Ryan S.

AU - Naranjo, Christopher A.

AU - Tracey, Mary Kate

AU - Brady, Joseph R.

AU - Whittaker, Charles A.

AU - Yun, Dongsoo

AU - Brunette, Natalie

AU - Wang, Jing Yang

AU - Walkey, Carl

AU - Fiala, Brooke

AU - Kar, Swagata

AU - Porto, Maciel

AU - Lok, Megan

AU - Andersen, Hanne

AU - Lewis, Mark G.

AU - Love, Kerry R.

AU - Camp, Danielle L.

AU - Silverman, Judith Maxwell

AU - Kleanthous, Harry

AU - Joshi, Sangeeta B.

AU - Volkin, David B.

AU - Dubois, Patrice M.

AU - Collin, Nicolas

AU - King, Neil P.

AU - Barouch, Dan H.

AU - Irvine, Darrell J.

AU - Love, J. Christopher

N1 - Funding Information: We thank Prof. Ragahavan Varadarajan of the Indian Institute of Science for kindly providing the RBD sequence for SARS-CoV-2 Wuhan-Hu-1. We thank Laurent Pessaint, Dr. Adrienne Winn, Kamil Radzyminski, Andrew Faudree, Brittany Spence, Melissa Hamilton, and Natalie Figueroa Jones for advice and assistance with hamster studies. We thank Sumi Biswas of SpyBiotech for helpful discussions on SpyTag/SpyCatcher conjugations. We thank the Koch Institute's Robert A. Swanson (1969) Biotechnology Center for technical support. The following reagent was deposited by the Centers for Disease Control and Prevention and obtained through Biodefense and Emerging Infections Research Resources Repository, National Institute of Allergy and Infectious Diseases, NIH: SARS-Related Coronavirus 2, Isolate USAWA1/2020, NR-53780. This work was funded by the Bill & Melinda Gates Foundation (Investment IDs INV-002740, INV-006131, and OPP1156262). This study was also supported in part by the Koch Institute Support (core) Grant P30-CA14051 from the National Cancer Institute (NCI). L.H.T. is an NIH T32 postdoctoral fellow supported by the Multidisciplinary AIDS Training Program (Grant T32 AI007387). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NCI, the NIH, Bill & Melinda Gates Medical Research Institute, or the Bill & Melinda Gates Foundation. Funding Information: ACKNOWLEDGMENTS. We thank Prof. Ragahavan Varadarajan of the Indian Institute of Science for kindly providing the RBD sequence for SARS-CoV-2 Wuhan-Hu-1. We thank Laurent Pessaint, Dr. Adrienne Winn, Kamil Radzy-minski, Andrew Faudree, Brittany Spence, Melissa Hamilton, and Natalie Figueroa Jones for advice and assistance with hamster studies. We thank Sumi Biswas of SpyBiotech for helpful discussions on SpyTag/SpyCatcher conjugations. We thank the Koch Institute’s Robert A. Swanson (1969) Biotechnology Center for technical support. The following reagent was deposited by the Centers for Disease Control and Prevention and obtained through Biodefense and Emerging Infections Research Resources Repository, National Institute of Allergy and Infectious Diseases, NIH: SARS-Related Coronavirus 2, Isolate USA-WA1/2020, NR-53780. This work was funded by the Bill & Melinda Gates Foundation (Investment IDs INV-002740, INV-006131, and OPP1156262). This study was also supported in part by the Koch Institute Support (core) Grant P30-CA14051 from the National Cancer Institute (NCI). L.H.T. is an NIH T32 postdoctoral fellow supported by the Multidisciplinary AIDS Training Program (Grant T32 AI007387). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NCI, the NIH, Bill & Melinda Gates Medical Research Institute, or the Bill & Melinda Gates Foundation. Publisher Copyright: © 2021 National Academy of Sciences. All rights reserved.

PY - 2021/9/21

Y1 - 2021/9/21

N2 - Global containment of COVID-19 still requires accessible and affordable vaccines for low- and middle-income countries (LMICs). Recently approved vaccines provide needed interventions, albeit at prices that may limit their global access. Subunit vaccines based on recombinant proteins are suited for large-volume microbial manufacturing to yield billions of doses annually, minimizing their manufacturing cost. These types of vaccines are well-established, proven interventions with multiple safe and efficacious commercial examples. Many vaccine candidates of this type for SARS-CoV-2 rely on sequences containing the receptor-binding domain (RBD), which mediates viral entry to cells via ACE2. Here we report an engineered sequence variant of RBD that exhibits high-yield manufacturability, high-affinity binding to ACE2, and enhanced immunogenicity after a single dose in mice compared to the Wuhan-Hu-1 variant used in current vaccines. Antibodies raised against the engineered protein exhibited heterotypic binding to the RBD from two recently reported SARS-CoV-2 variants of concern (501Y.V1/V2). Presentation of the engineered RBD on a designed virus-like particle (VLP) also reduced weight loss in hamsters upon viral challenge.

AB - Global containment of COVID-19 still requires accessible and affordable vaccines for low- and middle-income countries (LMICs). Recently approved vaccines provide needed interventions, albeit at prices that may limit their global access. Subunit vaccines based on recombinant proteins are suited for large-volume microbial manufacturing to yield billions of doses annually, minimizing their manufacturing cost. These types of vaccines are well-established, proven interventions with multiple safe and efficacious commercial examples. Many vaccine candidates of this type for SARS-CoV-2 rely on sequences containing the receptor-binding domain (RBD), which mediates viral entry to cells via ACE2. Here we report an engineered sequence variant of RBD that exhibits high-yield manufacturability, high-affinity binding to ACE2, and enhanced immunogenicity after a single dose in mice compared to the Wuhan-Hu-1 variant used in current vaccines. Antibodies raised against the engineered protein exhibited heterotypic binding to the RBD from two recently reported SARS-CoV-2 variants of concern (501Y.V1/V2). Presentation of the engineered RBD on a designed virus-like particle (VLP) also reduced weight loss in hamsters upon viral challenge.

KW - Manufacturability

KW - Pichia pastoris

KW - Protein vaccine

KW - SARS-CoV-2

UR - http://www.scopus.com/inward/record.url?scp=85114860752&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85114860752&partnerID=8YFLogxK

U2 - 10.1073/pnas.2106845118

DO - 10.1073/pnas.2106845118

M3 - Article

C2 - 34493582

AN - SCOPUS:85114860752

SN - 0027-8424

VL - 118

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

IS - 38

M1 - e2106845118

ER -

Engineered SARS-CoV-2 receptor binding domain improves manufacturability in yeast and immunogenicity in mice

Abstract

Bibliographical note

Keywords

UN SDGs

Publisher link

Find It

Other files and links

Fingerprint

Cite this