Table 1.
Nanobody binding and neutralization characterization; related to Figure 2.
| Group# | Nano-body | wildtype# | Delta | Omicron BA.1 | Omicron BA.4/5 | Omicron XBB | Omicron BQ.1.1 | ||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Kon | Koff | KD | PSV | Kon | Koff | KD | PSV | IC50 fold change | Kon | Koff | KD | PSV | IC50 fold change | Kon | Koff | KD | IC50 | Kon | Koff | KD | Kon | Koff | KD | ||
| (M−1s−1) | (s−1) | (M) | IC50 (s.e.m) (nm) | (M−1s−1) | (s−1) | (M) | IC50 (s.e.m) (nm) | Wildtype\Delta | (M−1s−1) | (s−1) | (M) | IC50 (s.e.m) (nm) | Wildtype\Omicron BA.1 | (M−1s−1) | (s−1) | (M) | (nm) | (M−1s−1) | (s−1) | (M) | (M−1s−1) | (s−1) | (M) | ||
|
| |||||||||||||||||||||||||
| 1 | S1-1 | 6.50E+05 | 5.98E-07 | 9.20E-12 | 6.7(1.0) | 1.27E+06 | 1.00E-06 | 7.87E-13 | 2.3(0.5) | 2.91 | No binding | NA | No binding | Nottested | Nottested | ||||||||||
|
| |||||||||||||||||||||||||
| S1-RBD-9 | 2.85E+05 | 1.23E-04 | 4.30E-10 | 235(97.5) | (1)3.93E+05 (2)1.76E-03 |
(1)1.00E-03 (2)5.04E-04 |
5.69E-10* | 85.2 (24.3) |
2.76 | 6.05E+03 | 1.82E-04 | 3.01E-08 | 323 (20.8) |
0.73 | 4.36E+05 | 5.49E-03 | 1.26E-08 | 966 (220) |
6.31DE+05 | 5.41E-03 | 8.58E-09 | 2.65E+06 | 1.08E-02 | 4.06E-09 | |
|
| |||||||||||||||||||||||||
| S1-RBD-15 | 7.52E+06 | 4.95E-04 | 6.58E-11 | 4.6(1.2) | 2.55E+06 | 1.08E-04 | 4.25E-11 | 2(0.9) | 2.30 | 1.95E+06 | 1.32E-02 | 6.79E-09 | 617(87) | 0.01 | No binding | Not tested | Not tested | ||||||||
|
| |||||||||||||||||||||||||
| S1-RBD-22 | 9.24E+05 | 4.42E-04 | 4.78E-10 | 100(0.1) | (1)1.07E+06 (2)9.10E-04 |
(1)6.25E-04 (2)4.15E-04 |
1.83E-10* | 46.4(12) | 2.16 | 7.30E+05 | 1.91E-04 | 2.62E-10 | 179(68) | 0.56 | 1.07E+06 | 1.05E-02 | 9.80E-09 | 976 (285) |
4.22E+05 | 3.61E-03 | 8.57E-09 | 5.66E+05 | 3.09E-03 | 5.46E-09 | |
|
| |||||||||||||||||||||||||
| S1-RBD-24 | 2.12E+06 | 1.22E-03 | 5.75E-10 | 221(4) | (1)5.74E+05 (2)1.61E-03 |
(1)2.62E-03 (2)9.00E-04 |
1.64E-09* | 85.5 (13.5) |
2.58 | (1)2.66E+05 (2)2.63E-03 |
(1)1.49E-02 (2)8.24E-04 |
1.34E-08* | 2382 (878) |
0.09 | 9.25E+05 | 1.62E-02 | 1.75E-08 | Not tested | Not tested | ||||||
|
| |||||||||||||||||||||||||
| 2 | S1-6 | 5.92E+05 | 3.69E-04 | 6.22E-10 | 56.1(20.7) | 3.19E+05 | 2.48E-04 | 7.77E-10 | 37.3(14.7) | 1.50 | No binding | No binding | Not tested | Not tested | |||||||||||
|
| |||||||||||||||||||||||||
| SI-35 | 2.70E+06 | 9.77E-05 | 3.62E-11 | 12.5(0.1) | 5.83E+05 | 1.48E-05 | 2.54E-11 | 28(5.2) | 0.45 | 5.20E+05 | 7.56E-05 | 1.45E-10 | 49(13.6) | 0.25 | 1.02E+06 | 4.35E-05 | 4.27E-11 | 182(55) | 9.29E+05 | 2.85E-04 | 3.07E-10 | 1.21E+06 | 7.45E-05 | 6.17E-11 | |
|
| |||||||||||||||||||||||||
| SI-39 | 1.68E+06 | 1.06E-03 | 6.30E-10 | 111(4.0) | 2.30E+06 | 6.73E-04 | 2.92E-10 | 236(3.8) | 0.47 | (1)1.14E+05 (2)5.04E-03 |
(1)5.48 E-03 (2)4.12 E-04 |
3.62E-09* | NA | 7.59E+04 | 7.30E-04 | 9.61E-09 | No binding | No binding | |||||||
|
| |||||||||||||||||||||||||
| 3 | S1-23 | 1.09E+06 | 1.07E-04 | 9.78E-11 | 5.7(2.2) | 2.33E+05 | 2.85E-03 | 1.23E-08 | NA | No binding | NA | No binding | Nobinding | Nobinding | |||||||||||
|
| |||||||||||||||||||||||||
| S1-36 | 7.87E+06 | 1.72E-03 | 2.18E-10 | 48.5(21.1) | (1)7.90E+05 (2)2.11E- 03 |
(1)2.28E-02(2)9.57E-04 | 9.00E-09* | 1387 (209) | 0.03 | (1)1.19E+06 (2)2.02E-03 |
(1)1.64E-02 (2)6.80E-04 |
3.47E-09* | NA | No binding | Not tested | Not tested | |||||||||
|
| |||||||||||||||||||||||||
| S1-RBD-40 | 7.47E+05 | 2.77E-05 | 3.71E-11 | 25.6(5.9) | No binding | NA | 2.25E+05 | 3.71E-05 | 1.65E-10 | 46.1 (4.7) |
0.55 | (1)2.54E+04 (2)6.23E-03 |
(1)3.07 E-01 (2)3.29 E-03 |
4.17E-06* | NA<10uM | 4.35E+05 | 1.24E-02 | 2.86E-08 | 1.24E+06 | 6.11E-03 | 4.92E-09 | ||||
|
| |||||||||||||||||||||||||
| S1-37 | 4.03E+06 | 2.75E-04 | 6.82E-11 | 6.8(0.7) | 1.18E+05 | 1.35E-03 | 1.14E-08 | NA | 1.38E+06 | 1.99E-02 | 1.44E-08 | NA | No binding | Not tested | Not tested | ||||||||||
|
| |||||||||||||||||||||||||
| S1-48 | 2.61E+06 | 6.22E-05 | 2.39E-11 | 5.82(0.5) | 5.74E+05 | 3.54E-03 | 6.18E-09 | 145(5) | 0.04 | No binding | NA | No binding | Not tested | Not tested | |||||||||||
|
| |||||||||||||||||||||||||
| 4 | S1-RBD-21 | 3.15E+06 | 1.71E-03 | 5.45E-10 | 17.3(3.1) | (1)1.82E+06 (2)8.40E-04 |
(1)1.98E-03 (2)3.48E-04 |
3.18E-10* | 21(1.3) | 0.82 | (1)1.90E+05 (2)2.17E-03 |
(1)3.16 E-03 (2)1.16E-03 |
5.80E-09* | 113(14) | 0.15 | No binding | Not tested | Not tested | |||||||
|
| |||||||||||||||||||||||||
| S1-RBD-27 | 6.19E+06 | 1.24E-02 | 2.00E-09 | 163(71.4) | (1)4.06E+05 (2)5.17E-03 |
(1)1.48E-02 (2)1.51E-03 |
8.24E-09* | 1390(198) | 0.12 | No binding | NA | No binding | Not tested | Not tested | |||||||||||
|
| |||||||||||||||||||||||||
| S1-RBD-29 | 5.36E+05 | 1.35E-03 | 2.51E-09 | 9.53(1.0) | (1)1.80E+05 (2)9.46E-04 |
(1)6.99E-03 (2)7 .32 E-04 |
1.69E-08* | 564(332) | 0.02 | 3.30E+04 | 1.20E-04 | 3.63E-09 | NA | No binding | Not tested | Not tested | |||||||||
|
| |||||||||||||||||||||||||
| S1-RBD-43 | 6.21E+05 | 1.82E-04 | 2.92E-10 | 33.6(1.3) | 5.39E+06 | 1.19E-03 | 2.21E-10 | NA | 4.79E+05 | 4.23E-04 | 8.83E-10 | 1032(543) | 0.03 | No binding | Not tested | Not tested | |||||||||
|
| |||||||||||||||||||||||||
| S1-RBD-46 | 4.69E+05 | 5.79E-04 | 1.23E-09 | 48 | 1.11E+06 | 3.12E-04 | 2.81E-10 | 8.7(3) | 5.52 | No binding | NA | (1)2.17E+05 (2)1.60E-02 |
(1)1.38E-01 (2)4.15E-03 |
1.31E-07* | 1020 | 2.84E+05 | 5.06E-02 | 1.78E-07 | 1.90E+05 | 3.65E-02 | 1.92E-07 | ||||
|
|
|
||||||||||||||||||||||||
|
| |||||||||||||||||||||||||
| S1-RBD-49 | 3.15E+05 | 5.34E-04 | 1.69E-09 | 37.6(5.6) | No binding | 2.54E+05 | 3.48E-04 | 1.37E-09 | 404(145) | 0.09 | No binding | Not tested | Not tested | ||||||||||||
|
| |||||||||||||||||||||||||
| 5 | S1-RBD-16 | 1.68E+04 | 6.25E-05 | 3.73E-09 | 79.2(4.2) | 3.13E+04 | 3.04E-04 | 9.74E-09 | 688(72.6) | 0.12 | No binding | 690(150) | 0.11 | No binding | 8500(2300) | Not tested | Not tested | ||||||||
|
| |||||||||||||||||||||||||
| S1-RBD-23 | 2.89E+06 | 4.61E-05 | 1.59E-11 | 7.31(0.4) | No binding | NA | 7.91E+05 | 5.43E-05 | 6.87E-11 | 91.7(5.2) | 0.08 | No binding | Not tested | Not tested | |||||||||||
|
| |||||||||||||||||||||||||
| S1-RBD-38 | 1.12E+06 | 9.84E-04 | 8.79E-10 | 84.6(22.7) | No binding | NA | 2.37E+05 | 7.06E-04 | 2.98E-09 | 790(146) | 0.11 | No binding | NA<10uM | Not tested | Not tested | ||||||||||
|
| |||||||||||||||||||||||||
| 6 | S1-RBD-35 | 1.33E+06 | 2.50E-04 | 1.88E-10 | 12.3(2.4) | No binding | No binding | No binding | Not tested | Not tested | |||||||||||||||
|
| |||||||||||||||||||||||||
| 7 | S1-46 | 2.22E+05 | 1.70E-04 | 7.66E-10 | 312(14.0) | 6.93E+04 | 4.05E-05 | 5.85E-10 | 210.2(26) | 1.49 | 2.12E+05 | 1.24E-04 | 5.85E-10 | 412(116) | 0.76 | 1.27E+05 | 1.07E-04 | 8.46E-10 | NA<10uM | 5.01E+04 | 1.88E-04 | 3.75E-09 | 5.44E+04 | 1.99E-04 | 3.65E-09 |
|
| |||||||||||||||||||||||||
| 8 | S1-65 | 1.06E+06 | 1.67E-04 | 1.57E-10 | 7.3(6.0) | Not tested | NA | 3.42E+05 | 1.05E-03 | 3.07E-09 | 517(218) | 0.01 | No binding | Not tested | Not tested | ||||||||||
|
| |||||||||||||||||||||||||
| 1/2 | S1-4 | 1.26E+06 | 1.26E-04 | 1.37E-10 | 41.5(3.7) | 1.38E+06 | 4.83E-05 | 3.51E-11 | 10.7(0.4) | 3.88 | 6.00E+05 | 7.98E-05 | 1.33E-10 | 58.6(9.2) | 0.71 | 1.32E+06 | 1.32E-03 | 1.00E-09 | 148.6(37.6) | 1.27 E+04 | 1.10 E-06 | 8.66 E-10 | 1.30 E+06 | 1.38 E-04 | 1.06 E-03 |
|
| |||||||||||||||||||||||||
| 1/4 | S1-RBD-3 | 5.12E+05 | 1.01E-02 | 1.98E-08 | 384(18.7) | (1)3.27 E+05 (2)1.62 E- 03 |
(1)5.54 E-03 (2)7.42 E-04 |
5.32E-09* | 83.9 | 4.58 | No binding | Not tested | Not tested | Not tested | |||||||||||
|
| |||||||||||||||||||||||||
| S1-RBD-5 | 7.21E+06 | 1.05E-03 | 1.45E-10 | 174(3.3) | 1.49E+06 | 3.29E-04 | 2.20E-10 | 280 | 0.62 | (1)1.18E+05 (2)2.95E-03 |
(1)4.32E-03 (2)7.96E-04 |
7.75E-09* | 204(24.6) | 0.85 | 1.19E+06 | 9.71E-03 | 8.19E-09 | 2.06E+06 | 3.97E-03 | 1.93E-09 | 2.33E+06 | 5.69E-03 | 2.44E-09 | ||
|
| |||||||||||||||||||||||||
| S1-RBD-6 | 3.48E+06 | 1.13E-03 | 3.24E-10 | 77.2(21.8) | (1)6.68E+05 (2)1.08E-03 |
(1)5.04E-04 (2)3.85E-04 |
1.99E-10* | 542.3(155) | 0.14 | (1)1.43E+05 (2)3.37E-03 |
(1)3.44E-03 (2)9.96E-04 |
5.49E-9* | 233.8(23) | 0.33 | 8.72E+05 | 5.71E-03 | 6.55E-09 | 2.25E+05 | 5.52E-03 | 2.46E-08 | 2.25E+05 | 4.94E-03 | 2.19E-08 | ||
#
Values taken from (Mast, Fridy et a . 2021)
*
Fit to a two-state mode
§
S1-RBD-16 showed binding to omicron BA.1 and omicron BA.4/5 using ELISA