Map of SARS-CoV-2 spike epitopes not shielded by glycans

The severity of the COVID-19 pandemic, caused by the SARS-CoV-2 coronavirus, calls for the urgent development of a vaccine. The primary immunological target is the SARS-CoV-2 spike (S) protein. S is exposed on the viral surface to mediate viral entry into the host cell. To identify possible antibody binding sites not shielded by glycans, we performed multi-microsecond molecular dynamics simulations of a 4.1 million atom system containing a patch of viral membrane with four full-length, fully glycosylated and palmitoylated S proteins. By mapping steric accessibility, structural rigidity, sequence conservation and generic antibody binding signatures, we recover known epitopes on S and reveal promising epitope candidates for vaccine development. We find that the extensive and inherently flexible glycan coat shields a surface area larger than expected from static structures, highlighting the importance of structural dynamics in epitope mapping.

[1]  Yiwei Cao,et al.  Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane , 2020, The journal of physical chemistry. B.

[2]  Alexander D. MacKerell,et al.  CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses. , 2009, Journal of chemical theory and computation.

[3]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997 .

[4]  Nicholas C. Wu,et al.  A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV , 2020, Science.

[5]  Jaap Goudsmit,et al.  Human Monoclonal Antibody Combination against SARS Coronavirus: Synergy and Coverage of Escape Mutants , 2006, PLoS medicine.

[6]  Gerhard Hummer,et al.  Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding. , 2008, Journal of Molecular Biology.

[7]  B. L. de Groot,et al.  CHARMM36m: an improved force field for folded and intrinsically disordered proteins , 2016, Nature Methods.

[8]  Structural basis for neutralization of SARS-CoV-2 and SARS-CoV by a potent therapeutic antibody , 2020, Science.

[9]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using Modeller , 2006, Current protocols in bioinformatics.

[10]  P. Masters,et al.  The Molecular Biology of Coronaviruses , 2006, Advances in Virus Research.

[11]  A. Lupas,et al.  Predicting coiled coils from protein sequences , 1991, Science.

[12]  W. Im,et al.  Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations , 2007, PloS one.

[13]  C. Broder,et al.  A Cryptic Site of Vulnerability on the Receptor Binding Domain of the SARS-CoV-2 Spike Glycoprotein , 2020, bioRxiv.

[14]  Alexander D. MacKerell,et al.  CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field , 2015, Journal of chemical theory and computation.

[15]  F. Rey,et al.  Common Features of Enveloped Viruses and Implications for Immunogen Design for Next-Generation Vaccines , 2018, Cell.

[16]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[17]  Ralf Bartenschlager,et al.  SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography , 2020, Nature Communications.

[18]  E. Holmes,et al.  The proximal origin of SARS-CoV-2 , 2020, Nature Medicine.

[19]  T. Gallagher,et al.  Ready, Set, Fuse! The Coronavirus Spike Protein and Acquisition of Fusion Competence , 2012, Viruses.

[20]  Amalio Telenti,et al.  Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody , 2020, Nature.

[21]  Berk Hess,et al.  GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .

[22]  T. D. Schneider,et al.  Sequence logos: a new way to display consensus sequences. , 1990, Nucleic acids research.

[23]  Daniel Wrapp,et al.  Site-specific glycan analysis of the SARS-CoV-2 spike , 2020, Science.

[24]  Taehoon Kim,et al.  CHARMM‐GUI: A web‐based graphical user interface for CHARMM , 2008, J. Comput. Chem..

[25]  B. Roux,et al.  Simulation of Osmotic Pressure in Concentrated Aqueous Salt Solutions , 2010 .

[26]  Thomas L. Vincent,et al.  LOGICOIL - multi-state prediction of coiled-coil oligomeric state , 2013, Bioinform..

[27]  Zachary T. Berndsen,et al.  Vulnerabilities in coronavirus glycan shields despite extensive glycosylation , 2020, Nature Communications.

[28]  Z. Rao,et al.  Structural basis for neutralization of SARS-CoV-2 and SARS-CoV by a potent therapeutic antibody , 2020, Science.

[29]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[30]  Rose E Goodchild,et al.  The ins and outs of endoplasmic reticulum‐controlled lipid biosynthesis , 2017, EMBO reports.

[31]  John A.G. Briggs,et al.  Structures, conformations and distributions of SARS-CoV-2 spike protein trimers on intact virions , 2020, bioRxiv.

[32]  Gary R. Whittaker,et al.  Host cell proteases: Critical determinants of coronavirus tropism and pathogenesis , 2014, Virus Research.

[33]  Beata Turoňová,et al.  In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges , 2020, Science.

[34]  Daniel Wrapp,et al.  Site-specific analysis of the SARS-CoV-2 glycan shield , 2020, bioRxiv.

[35]  K. Shi,et al.  Structural basis of receptor recognition by SARS-CoV-2 , 2020, Nature.

[36]  Qiang Zhou,et al.  Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2 , 2020, Science.

[37]  John D. Chodera,et al.  SARS-CoV-2 Simulations go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome , 2021, Biophysical Journal.

[38]  Sunhwan Jo,et al.  CHARMM‐GUI Membrane Builder toward realistic biological membrane simulations , 2014, J. Comput. Chem..

[39]  Anton Andonov,et al.  Architecture of the SARS coronavirus prefusion spike , 2006, Nature Structural &Molecular Biology.

[40]  Gerhard Hummer,et al.  MDBenchmark: A toolkit to optimize the performance of molecular dynamics simulations. , 2020, The Journal of chemical physics.

[41]  M. Parrinello,et al.  Polymorphic transitions in single crystals: A new molecular dynamics method , 1981 .

[42]  A. Walls,et al.  Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein , 2020, Cell.

[43]  Qiang Zhou,et al.  A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2 , 2020, Science.

[44]  M. Parrinello,et al.  Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.

[45]  D. Agard,et al.  A molecular pore spans the double membrane of the coronavirus replication organelle , 2020, Science.

[46]  Sunhwan Jo,et al.  CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates , 2019, Glycobiology.

[47]  B. Neuman,et al.  Supramolecular Architecture of the Coronavirus Particle , 2016, Advances in Virus Research.

[48]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2007, Current protocols in protein science.

[49]  John D. Chodera,et al.  SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome , 2020, bioRxiv.

[50]  Asif Shajahan,et al.  Deducing the N- and O-glycosylation profile of the spike protein of novel coronavirus SARS-CoV-2 , 2020, bioRxiv.

[51]  Jeffery B. Klauda,et al.  CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. , 2009, Biophysical journal.

[52]  Derek N Woolfson,et al.  CCBuilder 2.0: Powerful and accessible coiled‐coil modeling , 2017, Protein science : a publication of the Protein Society.

[53]  B. Graham,et al.  Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation , 2020, Science.

[54]  Kathryn L. Schornberg,et al.  Structures and Mechanisms of Viral Membrane Fusion Proteins: Multiple Variations on a Common Theme , 2008 .

[55]  Austin G. Meyer,et al.  Maximum Allowed Solvent Accessibilites of Residues in Proteins , 2012, PloS one.

[56]  Bjoern Peters,et al.  BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes , 2017, Nucleic Acids Res..

[57]  Young Do Kwon,et al.  Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9 , 2011, Nature.

[58]  William J. Liu,et al.  A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2 , 2020, Nature.

[59]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[60]  D. Burton,et al.  Rational Vaccine Design in the Time of COVID-19 , 2020, Cell Host & Microbe.

[61]  Rommie E. Amaro,et al.  Beyond Shielding: The Roles of Glycans in SARS-CoV-2 Spike Protein , 2020, bioRxiv.

[62]  D. Sheward,et al.  An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction , 2020, Nature Communications.

[63]  S. Harrison,et al.  Viral membrane fusion. , 2015, Virology.

[64]  Linqi Zhang,et al.  Human neutralizing antibodies elicited by SARS-CoV-2 infection , 2020, Nature.

[65]  B. Haynes,et al.  Glycans on the SARS-CoV-2 Spike Control the Receptor Binding Domain Conformation , 2020, bioRxiv.

[66]  Lijun Rong,et al.  Solution Structure of the Severe Acute Respiratory Syndrome-Coronavirus Heptad Repeat 2 Domain in the Prefusion State , 2006, Journal of Biological Chemistry.