Selectio Selection and and st structural analy analysis is of of - PowerPoint PPT Presentation

Selectio Selection and and st structural analy analysis is of of sybodies bodies neutr neutralizing lizing SAR SARS ‐ CoV CoV ‐ 2 T. Custódio, H. Das, D. Sheward, L. Hanke, S. Pazicky, J.Pieprzyk, M. Sorgenfrei, M. Schroer, A. Gruzinov, C. Jeffries, M. Graewert, D. Svergun, N. Dobrev, K. Remans, M. Seeger, G. McInerney, B. Murrell, B. M. Hällberg and C. Löw  Centre for Structural Systems Biology (CSSB), and European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Notkestrasse 85, Hamburg, Germany.  Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.  Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.  Division of Virology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa.  Institute of Medical Microbiology, University of Zurich, Switzerland.  European Molecular Biology Laboratory, Protein Expression and Purification Core Facility, 69117 Heidelberg, Germany

SARS ‐ CoV SARS CoV ‐ 2 Vi Viral ral Spike Spike and and relevant relevant proteins proteins ACE2, angiotensin converting enzyme 2 Adapted from UT Austin, TMPRSS2, transmembrane serine McLellan Lab protease 2

Mechanism of Me of viral viral entry entry SARS-CoV-2 1. Binding to ACE2: TMPRSS2 cleaves the spike into viral RBD binds to S1 and S2 subunits, promoting ACE2 enzyme membrane fusion. 2. Membrane fusion TMPRSS2 ACE2

Se Sele lection ction of of ne neutr utralizing lizing nanobodies nanobodies ag agains ainst SAR SARS ‐ CoV CoV ‐ 2 Single domain antibodies (nanobodies) are antibody fragments consisting of a single monomeric variable antibody domain. They are potent reagents for the stabilization of membrane proteins. An in vitro selection platform based on VHH synthetic antibodies is developed (Zimmermann, et al, Elife (2018) doi:10.7554/eLife.34317) Here, nanobodies from the synthetic library, sybodies (Sb), to target the RBD TMPRSS2 ACE2 of the SARS-CoV-2 spike protein are rapidly selected and characterized. Sybody selections on biotinylated RBD were carried out with the thee libraries (concave, loop, convex). 62 unique sybodies were expressed, purified and characterized.

Nanobodies for HT ‐ SAXS analysis (8/5/2020), Quality control (buffer PBS)

Nanobodies for HT ‐ SAXS analysis (8/5/2020), Quality control (buffer PBS) Χ 2 Nr. MW, Da c, mg/ml R g , nm MW SAXS Vfr (mon/dim) Probable state/comment 2.1 13 Largely monomeric 1 15563.04 0.624170832 0.87/0.13 1.09 2.2 15 Largely monomeric 4 15740.29 0.726381875 0.8/0.2 1.1 2.2 17 Largely monomeric 7 15642.19 1.383658425 0.8/0.2 1.19 2.9 23 9 15928.57 1.238969189 0.48/0.52 2.36 Mon/Dim plus long (unspecific) aggregates 2.1 10 Largely monomeric 12 15966.57 0.481692335 0.84/0.16 1.12 2.2 11 Largely monomeric 15 15708.31 1.007458545 0.85/0.15 1.13 17 15584.28 2.310170221 2.5 20 0.61/0.39 1.62 Monomer/dimer equilibrium Largely monomeric 22 15584.28 1.663551226 2.1 15 0.85/0.15 1.29 2.2 16 2.3 Largely monomeric 23 15748.32 1.833179385 0.81/0.19 9.9 86 27 15652.36 1.433618484 0.65/0.35 8.67 Mon/Dim plus large (specific) aggregates 2.4 18 30 15854.49 1.17029019 0.7/0.3 1.28 Monomer/dimer equilibrium 10.4 479 33 15633.32 1.178573185 0.21/0.79 48.26 Mon/Dim plus large (specific) aggregates 16 38 16532.16 0.615295516 2.4 0.59/0.41 1.17 Monomer/dimer equilibrium Biolayer interferometry, 22 42 16772.42 0.895659391 2.7 0.52/0.48 2.25 Mon/Dim plus long (unspecific) aggregates 19 43 16594.19 1.091047267 2.4 0.64/0.36 1.35 Monomer/dimer equilibrium concave library 17 46 16437.19 1.653220266 2.2 0.69/0.31 3.35 Mon/Dim plus long (unspecific) aggregates 18 50 16718.38 1.810420691 2.3 0.72/0.28 1.38 Monomer/dimer equilibrium 20 54 16678.26 0.878722995 2.6 0.55/0.45 1.19 Monomer/dimer equilibrium 25 56 16579.33 1.856029685 2.8 0.39/0.61 2.36 Monomer/dimer equilibrium 24 57 16490.13 1.352340812 2.6 0.42/0.58 3.84 Monomer/dimer equilibrium 19 61 16783.4 1.097412818 2.4 0.67/0.33 1.33 Monomer/dimer equilibrium 16 62 16670.24 0.536295805 2.8 0.31/0.69 2.24 Mon/Dim plus long (unspecific) aggregates 35 67 16529.22 1.478203966 3.4 0.03/0.97 6.25 Mon/Dim plus long (unspecific) aggregates 15 Largely monomeric 68 16662.35 2.096041201 2.2 0.79/0.21 1.23 17 71 16744.4 2.033805247 2.4 0.64/0.36 2.82 Mon/Dim plus long (unspecific) aggregates 15 75 16813.56 2.903799277 2.6 0.6/0.4 1.21 Monomer/dimer equilibrium 20 76 17034.67 1.025215834 2.5 0.45/0.55 2.78 Mon/Dim plus long (unspecific) aggregates 53 78 16811.58 1.398091412 10.3 0.17/0.83 34.38 Mon/Dim plus large (specific) aggregates 12 83 16740.55 0.636167451 2.6 0.55/0.45 1.32 Mon/Dim plus long (unspecific) aggregates] 20 86 16646.34 2.138284755 2.5 0.62/0.38 1.4 Monomer/dimer equilibrium 24 90 16847.6 1.767520997 3.2 0.36/0.64 2.89 Mon/Dim plus long (unspecific) aggregates 19 93 16750.46 2.194328018 2.6 0.53/0.47 2.77 Mon/Dim plus long (unspecific) aggregates 15 94 16822.52 1.595226357 2.7 0.55/0.45 2.02 Mon/Dim plus long (unspecific) aggregates 13 Largely monomeric 95 16626.35 0.838997398 2.1 0.82/0.18 1.06 12 97 16921.6 1.044573482 2.4 0.67/0.33 1.46 Mon/Dim plus long (unspecific) aggregates 100 16740.35 2.350144374 2.3 15 0.7/0.3 2.2 Mon/Dim plus long (unspecific) aggregates

Sb23 Sb23 neutr neutralizes SAR SARS ‐ CoV CoV ‐ 2 ps pseudovi eudoviruses ruses and nd co comp mpete etes wi with AC ACE2 (a) Neutralization Assay : SARS-CoV-2 or VSV-G spike pseudotyped lentivirus was incubated with a dilution series of Sb23 or a control sybody (specific for hPepT2). (b) Biolayer interferometry (BLI) sensorgrams of immobilized SARS-CoV-2 RBD with ACE2 in the presence (blue) or absence (black) of 150 nM Sb23. (c) Microscale thermophoresis (MST) binding data of spike with fluorescently labelled Sb23, in the presence or absence of 200 nM ACE2. Affinities of spike to Sb23 in the absence of ACE2 ranged from 0.6 – 10 nM, while they were significantly lower in the presence of ACE2 (K D = 58 – 200 nM).

Ta Table 1. 1. SAXS data collection and statistics Data collection parameters Sb23 RBD Sb23+RBD Instrument EMBL P12 (PETRA III, DESY, Hamburg) Beam geometry (mm 2 ) 0.2×0.12 Wavelength (nm) 0.124 s range (nm ‐ 1 ) 0.03 ‐ 5.0 Exposure time (s) 4 (20×0.2s) Temperature (K) 293 Concentration range (mg ml ‐ 1 ) 0.37–4.0 Structural parameters R g (nm) (from P(r)) 2.2±0.1 3.2±0.2 3.7±0.2 R g (nm) (from Guinier plot) 2.1±0.1 3.1±0.2 3.5 ±0.2 D max (nm) 8.0±0.5 13±1 15±1 Porod volume estimate, V p (nm 3 ) 20±2 66±2 86±5 Molecular weight determination (kDa) From Porod volume (V p /~1.6) 13±1 37±5 54±3 From consensus Bayesian assessment 15±3 41±1 53±6 From I(0) 21±2 33±9 62±9 Calculated monomeric MW from 15.7 32.2 47.9 sequence

Modelling of Sy23 structure in solution Using the synthetic nanobody crystal structure (PDB code 5m13, chain B) with 4 dummy residues at the N terminal and 25 dummy residues at C terminal with CORAL

Modelling of RBD structure in solution A hybrid of the available crystal (6w41.pdb) and cryo-EM (6vsb.pdb) models Addition of glycans, termini and SREFLEX refinement

Two ‐ phase MONSA model of the complex

Typical hybrid SAXS models of RBP bound to Sb23 Three SASREF models yielding essentially the same fits to the scattering data from Sy23, RBD and the complex Sy23+RBD

The final consensus SAXS model of RBP bound to Sb23 (SASREF/CORAL) Sb23 is placed next to the ACE2 binding site and binds sidewise to the RBD as expected for a binder from the concave designed library

Cryo ‐ EM reconstruction of SARS ‐ CoV ‐ 2 spike bound to Sb23 Sb23 binds in the inner edge of the ACE2 interaction interface of the RBD effectively hindering ACE2 binding

Acknowledgments EMBL-Hamburg Tania Custodio Joanna Pieprzyk Samuel Pazicky Christian Löw Stefan Fiedler Karolinska Institute Ben Murrell Martin Hällberg