2
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Javanmardi K, Segall-Shapiro TH, Chou CW, Boutz DR, Olsen RJ, Xie X, Xia H, Shi PY, Johnson CD, Annapareddy A, Weaver S, Musser JM, Ellington AD, Finkelstein IJ, Gollihar JD. Antibody escape and cryptic cross-domain stabilization in the SARS-CoV-2 Omicron spike protein. Cell Host Microbe 2022; 30:1242-1254.e6. [PMID: 35988543 PMCID: PMC9350683 DOI: 10.1016/j.chom.2022.07.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/17/2022] [Accepted: 07/27/2022] [Indexed: 12/03/2022]
Abstract
The worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the repeated emergence of variants of concern. For the Omicron variant, sub-lineages BA.1 and BA.2, respectively, contain 33 and 29 nonsynonymous and indel spike protein mutations. These amino acid substitutions and indels are implicated in increased transmissibility and enhanced immune evasion. By reverting individual spike mutations of BA.1 or BA.2, we characterize the molecular effects of the Omicron spike mutations on expression, ACE2 receptor affinity, and neutralizing antibody recognition. We identified key mutations enabling escape from neutralizing antibodies at a variety of epitopes. Stabilizing mutations in the N-terminal and S2 domains of the spike protein can compensate for destabilizing mutations in the receptor binding domain, enabling the record number of mutations in Omicron. Our results provide a comprehensive account of the mutational effects in the Omicron spike protein and illustrate previously uncharacterized mechanisms of host evasion.
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Affiliation(s)
- Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
| | - Thomas H Segall-Shapiro
- Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Daniel R Boutz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Randall J Olsen
- Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA; Laboratory of Molecular and Translational Human Infectious Diseases Research, Center for Infectious Diseases, HMRI and Department of Pathology and Genomic Medicine, HMH, Houston, TX, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Charlie D Johnson
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Ankur Annapareddy
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Scott Weaver
- University of Texas Medical Branch, World Reference Center for Emerging Viruses and Arboviruses, Galveston, TX, USA
| | - James M Musser
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Center for Infectious Diseases, HMRI and Department of Pathology and Genomic Medicine, HMH, Houston, TX, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Andrew D Ellington
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA.
| | - Jimmy D Gollihar
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA.
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3
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Javanmardi K, Chou CW, Terrace CI, Annapareddy A, Kaoud TS, Guo Q, Lutgens J, Zorkic H, Horton AP, Gardner EC, Nguyen G, Boutz DR, Goike J, Voss WN, Kuo HC, Dalby KN, Gollihar JD, Finkelstein IJ. Rapid characterization of spike variants via mammalian cell surface display. Mol Cell 2021; 81:5099-5111.e8. [PMID: 34919820 PMCID: PMC8675084 DOI: 10.1016/j.molcel.2021.11.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/16/2021] [Accepted: 11/19/2021] [Indexed: 12/21/2022]
Abstract
The SARS-CoV-2 spike protein is a critical component of vaccines and a target for neutralizing monoclonal antibodies (nAbs). Spike is also undergoing immunogenic selection with variants that increase infectivity and partially escape convalescent plasma. Here, we describe Spike Display, a high-throughput platform to rapidly characterize glycosylated spike ectodomains across multiple coronavirus-family proteins. We assayed ∼200 variant SARS-CoV-2 spikes for their expression, ACE2 binding, and recognition by 13 nAbs. An alanine scan of all five N-terminal domain (NTD) loops highlights a public epitope in the N1, N3, and N5 loops recognized by most NTD-binding nAbs. NTD mutations in variants of concern B.1.1.7 (alpha), B.1.351 (beta), B.1.1.28 (gamma), B.1.427/B.1.429 (epsilon), and B.1.617.2 (delta) impact spike expression and escape most NTD-targeting nAbs. Finally, B.1.351 and B.1.1.28 completely escape a potent ACE2 mimic. We anticipate that Spike Display will accelerate antigen design, deep scanning mutagenesis, and antibody epitope mapping for SARS-CoV-2 and other emerging viral threats.
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Affiliation(s)
- Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | - Ankur Annapareddy
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Tamer S Kaoud
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Qingqing Guo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Josh Lutgens
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hayley Zorkic
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Andrew P Horton
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Elizabeth C Gardner
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Giaochau Nguyen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | | | - Jule Goike
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - William N Voss
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Jimmy D Gollihar
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; CCDC Army Research Laboratory-South, Austin, TX, USA; Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA.
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4
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Goike J, Hsieh CL, Horton A, Gardner EC, Bartzoka F, Wang N, Javanmardi K, Herbert A, Abbassi S, Renberg R, Johanson MJ, Cardona JA, Segall-Shapiro T, Zhou L, Nissly RH, Gontu A, Byrom M, Maranhao AC, Battenhouse AM, Gejji V, Soto-Sierra L, Foster ER, Woodard SL, Nikolov ZL, Lavinder J, Voss WN, Annapareddy A, Ippolito GC, Ellington AD, Marcotte EM, Finkelstein IJ, Hughes RA, Musser JM, Kuchipudi SV, Kapur V, Georgiou G, Dye JM, Boutz DR, McLellan JS, Gollihar JD. Synthetic repertoires derived from convalescent COVID-19 patients enable discovery of SARS-CoV-2 neutralizing antibodies and a novel quaternary binding modality. bioRxiv 2021:2021.04.07.438849. [PMID: 33851158 PMCID: PMC8043448 DOI: 10.1101/2021.04.07.438849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The ongoing evolution of SARS-CoV-2 into more easily transmissible and infectious variants has sparked concern over the continued effectiveness of existing therapeutic antibodies and vaccines. Hence, together with increased genomic surveillance, methods to rapidly develop and assess effective interventions are critically needed. Here we report the discovery of SARS-CoV-2 neutralizing antibodies isolated from COVID-19 patients using a high-throughput platform. Antibodies were identified from unpaired donor B-cell and serum repertoires using yeast surface display, proteomics, and public light chain screening. Cryo-EM and functional characterization of the antibodies identified N3-1, an antibody that binds avidly (Kd,app = 68 pM) to the receptor binding domain (RBD) of the spike protein and robustly neutralizes the virus in vitro. This antibody likely binds all three RBDs of the trimeric spike protein with a single IgG. Importantly, N3-1 equivalently binds spike proteins from emerging SARS-CoV-2 variants of concern, neutralizes UK variant B.1.1.7, and binds SARS-CoV spike with nanomolar affinity. Taken together, the strategies described herein will prove broadly applicable in interrogating adaptive immunity and developing rapid response biological countermeasures to emerging pathogens.
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Affiliation(s)
- Jule Goike
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew Horton
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Elizabeth C. Gardner
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Foteini Bartzoka
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Kamyab Javanmardi
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Shawn Abbassi
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Rebecca Renberg
- CCDC Army Research Laboratory, Biotechnology Branch, Adelphi, MD, USA
| | - Michael J. Johanson
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
| | - Jose A. Cardona
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | | | - Ling Zhou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ruth H. Nissly
- Department of Veterinary and Biomedical Science and Animal Diagnostic Laboratory, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Abhinay Gontu
- Department of Veterinary and Biomedical Science and Animal Diagnostic Laboratory, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Michelle Byrom
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andre C. Maranhao
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Anna M. Battenhouse
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Varun Gejji
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
| | - Laura Soto-Sierra
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
- Department of Agricultural and Biological Engineering, Texas A&M University, College Station, TX, USA
| | - Emma R. Foster
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
- Department of Agricultural and Biological Engineering, Texas A&M University, College Station, TX, USA
| | - Susan L. Woodard
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
| | - Zivko L. Nikolov
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
- Department of Agricultural and Biological Engineering, Texas A&M University, College Station, TX, USA
| | - Jason Lavinder
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Will N. Voss
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ankur Annapareddy
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, Austin, TX, USA
| | - Gregory C. Ippolito
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Andrew D. Ellington
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Edward M. Marcotte
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ilya J. Finkelstein
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Randall A. Hughes
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, Austin, TX, USA
| | - James M. Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Suresh V. Kuchipudi
- Department of Veterinary and Biomedical Science and Animal Diagnostic Laboratory, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Vivek Kapur
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - George Georgiou
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - John M. Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Daniel R. Boutz
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, Austin, TX, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jimmy D. Gollihar
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, Austin, TX, USA
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
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5
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Shroff R, Cole AW, Diaz DJ, Morrow BR, Donnell I, Annapareddy A, Gollihar J, Ellington AD, Thyer R. Discovery of Novel Gain-of-Function Mutations Guided by Structure-Based Deep Learning. ACS Synth Biol 2020; 9:2927-2935. [PMID: 33064458 DOI: 10.1021/acssynbio.0c00345] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite the promise of deep learning accelerated protein engineering, examples of such improved proteins are scarce. Here we report that a 3D convolutional neural network trained to associate amino acids with neighboring chemical microenvironments can guide identification of novel gain-of-function mutations that are not predicted by energetics-based approaches. Amalgamation of these mutations improved protein function in vivo across three diverse proteins by at least 5-fold. Furthermore, this model provides a means to interrogate the chemical space within protein microenvironments and identify specific chemical interactions that contribute to the gain-of-function phenotypes resulting from individual mutations.
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Affiliation(s)
- Raghav Shroff
- Center for Systems and Synthetic Biology, The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Austin W. Cole
- Center for Systems and Synthetic Biology, The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Daniel J. Diaz
- The Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Barrett R. Morrow
- Center for Systems and Synthetic Biology, The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Isaac Donnell
- Center for Systems and Synthetic Biology, The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ankur Annapareddy
- US Army Research Laboratories − South, 2506 Speedway, Austin, Texas 78712, United States
| | - Jimmy Gollihar
- US Army Research Laboratories − South, 2506 Speedway, Austin, Texas 78712, United States
| | - Andrew D. Ellington
- Center for Systems and Synthetic Biology, The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ross Thyer
- Center for Systems and Synthetic Biology, The Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
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