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org/JPCL Letter

Immune Escape Mechanisms of SARS-CoV‑2 Delta and Omicron


Variants against Two Monoclonal Antibodies That Received
Emergency Use Authorization
Danyang Xiong, Xiaoyu Zhao, Song Luo, Yalong Cong, John Z. H. Zhang,* and Lili Duan*
Cite This: J. Phys. Chem. Lett. 2022, 13, 6064−6073 Read Online

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ABSTRACT: Multiple-site mutated SARS-CoV-2 Delta and Omicron variants may trigger
immune escape against existing monoclonal antibodies. Here, molecular dynamics
simulations combined with the interaction entropy method reveal the escape mechanism
of Delta/Omicron variants to Bamlanivimab/Etesevimab. The result shows the
significantly reduced binding affinity of the Omicron variant for both antibodies, due to
the introduction of positively charged residues that greatly weaken their electrostatic
interactions. Meanwhile, significant structural deflection induces fewer atomic contacts and
an unstable binding mode. As for the Delta variant, the reduced binding affinity for
Bamlanivimab is owing to the alienation of the receptor-binding domain to the main part
of this antibody, and the binding mode of the Delta variant to Etesevimab is similar to that
of the wild type, suggesting that Etesevimab could still be effective against the Delta
variant. We hope this work will provide timely theoretical insights into developing
antibodies to prevalent and possible future variants of SARS-CoV-2.

C oronavirus disease 2019 (COVID-19), caused by the


severe acute respiratory syndrome coronavirus 2 (SARS-
CoV-2), is spreading globally, with more than 520 million
human body and change epitopes. Many variants exhibit
stronger virulence and infectivity6,14−16 and even produce
immune escape.17−22 It is urgent to investigate whether the
confirmed cases and 6 million deaths as of June 2022.1 As a current epidemic lineages can escape existing antibodies.
member of the coronavirus family, SARS-CoV-2 belongs to the As the two most popular mutation strains recently, Delta
β genus single-stranded RNA viruses, and its surface (lineage B.1.617.2) and Omicron (lineage B.1.1.529) have
transmembrane spike glycoprotein (S-protein) can specifically become the focus of many researchers.17,23−28 Since its
recognize the host cell receptor angiotensin-converting enzyme appearance in India in October 2020, the Delta variant has
2 (ACE2) through the receptor-binding domain (RBD) to spread to more than 185 countries and was listed as a variant
mediate virus invasion.2−4 This process has been identified as a of concern (VOC) by the World Health Organization (WHO)
critical step of viral infection in the body, and the RBD has also on May 11, 2021.29 There are two mutations, L452R and T478
become a significant target for drug and antibody research.5,6 K, on its RBD (Figure 1C), which can enhance the affinity
Currently, monoclonal antibodies (mAbs) are promising for between the virus and ACE2 and trigger immune escape.30−32
treating and preventing COVID-19, and the effectiveness of Compared with the Delta variant, the Omicron variant
various mAbs has been validated. 7−11 Among them, appeared much later, but this did not affect its rapid spread.
Bamlanivimab (LY-CoV555) and Etesevimab (LY-CoV016) Since the Omicron variant was first detected on November 9,
have received emergency use authorization (EUA) from the 2021, it was classified as a VOC by the WHO in just half a
U.S. Food and Drug Administration (FDA) for the treatment month, and it has become prevalent in most regions of the
of patients with mild to moderate symptoms due to their good world.29 More importantly, it has an astonishing 15 mutations
response in clinical trials.12,13 They are both RBD-targeting on its RBD (G339D, S371L, S373P, S375F, K417N, N440K,
G446S, S477N, T478K, E484A, Q493R, G496S, Q498R,
antibodies and can specifically bind to the RBD and interfere
N501Y, and Y505H) (Figure 1C). As for other VOCs, only
with the regular recognition between the S-protein and ACE2,
preventing the virus from invading host cells (Figure 1A and
B). Received: March 30, 2022
However, most antibodies are designed against early strains, Accepted: June 23, 2022
and the persistent mutation of SARS-CoV-2 poses challenges
for antibody efficacy and novel antibody development. As a key
site for receptor binding and antibody targeting, mutations in
the RBD can directly affect the ability of the virus to invade the

© XXXX American Chemical Society https://doi.org/10.1021/acs.jpclett.2c00912


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Figure 1. (A) The action mode of monoclonal antibodies (mAbs) hinders SARS-CoV-2 invasion into host cells. (B) Binding sites of the two mAbs
(Bamlanivimab and Etesevimab) to RBD. (C) The mutation residues of the SARS-CoV-2 Delta and Omicron variants in the RBD are green and
orange, respectively, and the binding sites of mAbs to the RBD are marked with dashed ellipses.

one (N501Y) in the Alpha variant, three (K417N, E484K, and individual residues to the binding affinity for key site
N501Y) in the Beta variant, three (K417T, E484K, and prediction.40−42 It is hoped that our work will provide timely
N501Y) in the Gamma variant, and two (L452R and T478K) theoretical insights into the development of vaccines and
in the Delta variant, the Omicron variants essentially contain antibodies against Delta or Omicron and future novel variants.
their mutation sites except for L452. This suggests that To complement the existing experimental results from the
Omicron variants may have unprecedented infection and molecular level, a total of six systems (Bamlanivimab−WT/
immune evasion capabilities, further accelerating the spread of Delta/Omicron and Etesevimab−WT/Delta/Omicron) were
the epidemic. used for the MD simulations. All systems were in a stable
Through the tireless efforts of scientists, some recent studies binding state during the simulation with the root mean square
have evaluated the effects of the Delta and Omicron variants deviation (RMSD) fluctuating almost below the 4 Å range
on Bamlanivimab and Etesevimab. The results show that the (Figure S1A). When binding to Bamlanivimab, both variants
Delta variant can escape Bamlanivimab but is still inhibited by exhibited higher flexibility compared to the wild type (WT),
Etesevimab, while the Omicron variant has obvious immune especially the Bamlanivimab−Omicron system, which was
escape to both antibodies.33−36 These studies provide significantly more flexible at the binding interface than the
experimental guidance for the subsequent use and research other two systems (Figure S1B). When binding to Etesevimab,
of mAbs. However, the molecular mechanism of their all systems exhibited similar flexibility in the binding interface
interaction and escape remains to be improved, especially (Figure S1C). The slightly higher flexibility is reflected in the
the identification of the key sites where the antibody-binding binding interface of the antibody in the Etesevimab−Omicron
epitope changes due to mutation, which is helpful for the complex.
improvement of the design of mAbs. Then, the binding free energy of each system was calculated
In our work, molecular dynamics (MD) simulations were by MM/GBSA and IE methods (Table S1), and the results
used to study the binding and escape mechanisms of the Delta were consistent with recently reported experimental evidence.
and Omicron variants to Bamlanivimab and Etesevimab. Taking the randomness into account, two repeated simulations
Detailed energetic and conformational analyses were used to were performed additionally for each system, and the binding
determine the origin of the binding differences caused by the affinity was calculated by the same method. showing that three
mutations. For the binding free energy calculation, the independent simulations obtained similar results. That is, the
enthalpy term was calculated by the molecular mechanics/ Omicron variant has significantly weaker binding free energy
generalized Born surface area (MM/GBSA) method,37,38 and with both mAbs compared to the WT, while the Delta variant
the entropy was obtained by the interaction entropy (IE) only exhibits lower binding affinity to Bamlanivimab, and its
method.39 In addition, alanine scanning combined with the IE binding affinity with Etesevimab has no significant change
(ASIE) method was used to calculate the contribution of compared to WT. In addition, the standard error of the mean
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Figure 2. (A) Two-dimensional eigenvector projections and (B) characteristic dynamic fluctuations of the Bamlanivimab−RBD and Etesevimab−
RBD complexes. The WT, Delta, and Omicron systems are shown in blue, green, and orange, respectively.

for the binding free energy of each system was calculated first two eigenvectors (Figure 2A), and it is clear that the
(Table S1), and the results showed that the error was too small Bamlanivimab−Delta, Bamlanivimab−Omicron, and Etesevi-
compared to the energy change caused by the mutations to mab−Omicron complexes have a more dispersed distribution
affect the conclusion. From each energy term, we found that than the WT system, suggesting that they have lower structural
both the Delta and Omicron variants can significantly weaken stability affected by the mutation. Then, the characteristic
the electrostatic interaction between the RBD and mAbs. This dynamic fluctuations of each complex are depicted by the
may be due to the mutations introducing plenty of positively maximum and minimum eigenvalues of the lowest frequency
charged amino acids (L452R and T478K for Delta; N440K, principal component (Figure 2B). The result shows that all
T478K, Q493R, Q498R, and Y505H for Omicron) while complexes are deflected to varying degrees around the
reducing the number of negatively charged amino acids interaction interface; the deflection angle is determined by
(E484A for Omicron) so that more positive charges the center of mass of the mAb of the structure corresponding
accumulated in the binding interface (Figure S2), which
to the maximum/minimum eigenvalue and the center of mass
enhanced the electrostatic repulsion between the RBD and
of the RBD. The Omicron variant has the highest rotational
mAbs. In addition, the Omicron variant can weaken the van
degrees of freedom of all systems, while the Delta variant
der Waals (vdW) interaction energy between the RBD and
mAbs. This may be due to the obvious changes in the exhibits greater torsion than the WT only when bound to
conformation and binding mode caused by the multisite Bamlanivimab. These changes further indicate that the
mutation of the Omicron variant, leading to fewer atomic structural stabilities of the Bamlanivimab−Delta, Bamlanivi-
contacts at the binding interface. The heavy-atom contacts mab−Omicron, and Etesevimab−Omicron systems were
between the RBD and mAbs for different distance cutoffs in reduced, supporting the results of the energy calculations.
each system are calculated and support this speculation (Figure Following the assessment of the global motion patterns, the
S3). local conformational transitions at the binding interface are
Quantitative calculation initially reveals the energy origin of discussed via changes in the distances of each residue between
the affinity change of each system, and the subsequent analysis the RBD and the antibody (Figure S4). We define ΔD as the
of essential dynamics was used for the in-depth exploration of difference between the average distance for the Cα atoms of
mutation-induced changes in the binding mode. The dynamic each residue in the equilibrium phase of the MD simulation
conformational sampling of each system is projected onto the and the original distance in the initial structure. Negative and
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Figure 3. (A) Number and occupancy of the hydrogen bonds formed at the interaction interface. (B) Stable hydrogen bonds (occupancy ≥70%) of
each complex, marked with green dashed lines.

positive values indicate closer or farther motion between binding of the two, further reducing the potency of the
residues, colored blue and red, respectively. antibody. As for the Bamlanivimab−Omicron complex, it
In the Bamlanivimab−RBD system, the distance change of showed more red patches in the image than the WT (Figure
the Delta variant is significantly different from that of the WT S4C), especially in the region corresponding to the RBD and
(Figure S4A and B). In the regions corresponding to 444− the antibody heavy chain, indicating that more residues
455@RBD (the region where the L452R mutation is located) separated from each other at the binding interface. This may
and 488−501@RBD, the Delta variant has closer contact with result in fewer atomic contacts between the RBD and the
the light chain and residues 100−110 of the heavy chain of antibody (Figure S3A), thereby exacerbating the escape of the
Bamlanivimab than the WT, but the distance from residues Omicron variant to Bamlanivimab.
28−65 of the heavy chain of Bamlanivimab is farther than that The Etesevimab−Delta and Etesevimab−WT systems
of the WT. Through the structural observation of the showed similar distance changes (Figure S4D and E), which
Bamlanivimab−RBD complex (Figure S5A), we found that was consistent with the results of energy calculations that their
100−110@Bamlanivimab is an independent region extending binding free energies are similar. This implies that the
from the heavy chain, located between the light chain and the Etesevimab work with the virus is less affected by the Delta
RBD. The Delta variant is close to this region while being away variant and can still exert a neutralizing effect. As for the
from the main part of the heavy chain (residues 28−65), which Etesevimab−Omicron system (Figure S4F), more large-area
may reduce the contact area of the heavy chain with the RBD, red patches appear compared to the WT. Although the part of
resulting in a more unstable binding state. region corresponding to 453−493@RBD appears blue, most of
In addition, residues 444−455 and 488−501 of the Delta the other residues show a tendency to move away from the
variant were close to the light chain of Bamlanivimab, but the binding interface, resulting in fewer atomic contacts between
minor changes did not play a significant role compared to the Etesevimab and the Omicron RBD (Figure S3B). Through
greater distance between them. For the region near the T478K structural analysis of the complex (Figure S5B), we found that
mutation, the area closest to the light chain of Bamlanivimab 453−493@RBD is a long loop region close to Etesevimab,
on the RBD, the Delta variant showed a tendency to move while other regions of the RBD show a trend away from
away from the light chain in this region. This would impair the Etesevimab. This may cause these regions away from the
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Figure 4. Binding free energy contribution of the important sites of the (A) Bamlanivimab−RBD and (B) Etesevimab−RBD complexes obtained
by the ASIE method. The energy difference between the mutant system and the WT system (ΔΔGVar−WT) is projected on the protein structure and
residues with |ΔΔGVar−WT| ≥ 1 are labeled in the images.

antibody to drag 453−493@RBD and, thus, prevent it from thereby reducing the stability of the hydrogen bond network.
approaching Etesevimab in subsequent movements, further Interestingly, more stable hydrogen bonds were formed
promoting the escape of the Omicron variant to Etesevimab. between residues S494@RBD and E102@Bamlanivimab in
Next, hydrogen bond network analysis was used to further the Bamlanivimab−Delta complex compared to the WT.
evaluate the differences in binding modes resulting from the According to the above analysis, this is due to the fact that
mutation-induced conformational changes (Figure 3A and B).
residue E102 is located in the region where the heavy chain of
Bamlanivimab−Delta and Bamlanivimab−Omicron have more
Bamlanivimab extends (100−110@Bamlanivimab), and the
low-occupancy hydrogen bonds (occupancy <70%) but fewer
high-occupancy hydrogen bonds (occupancy ≥70%) com- Delta variant has closer contacts to this region. But with the
pared to the WT, especially for the Omicron variant, which has separation between the RBD and the Bamlanivimab heavy
only one stable hydrogen bond. This may be since the chain main part, the occupancy of hydrogen bonds between
conformational transition induced by the mutation interferes residues E484@RBD and R50, R96@Bamlanivimab decreases.
with the normal contact between Bamlanivimab and the RBD, The Delta variant still has fewer high-occupancy hydrogen
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Figure 5. (A) Binding free energy calculated by the MM/GBSA and IE methods. (B) Average number of heavy-atom contacts between the RBD
and mAb when the distance cutoff is set to 4−10 Å. (C and D) Superposition of the average structure of the complexes with the initial structure for
Bamlanivimab/Etesevimab−WT/Omicron systems in the equilibrium phase of the 1.5 μs MD simulation.

bonds compared to the WT; this results in the reduction of the relatively obvious energy change, which is due to its mutation
binding stability between the RBD and Bamlanivimab. from neutral threonine to positively charged lysine, enhancing
Both the Etesevimab−Delta and Etesevimab−Omicron the electrostatic repulsion between the antibody and the RBD.
systems have more low-occupancy hydrogen bonds than the Residues Q493 and S494 in Bamlanivimab−Delta are also
Etesevimab−WT system. For high-occupancy hydrogen bonds, more sensitive to mutation, which may be related to their
the stable hydrogen bond originally formed between residues proximity to the 100−110@Bamlanivimab region.
R457@RBD and S53@Etesevimab in the WT system has For the Bamlanivimab−Omicron system, it has more hot-
decreased occupancy in the Delta system, but this phenom- spot residues than Bamlanivimab−Delta, probably due to the
enon is compensated by the hydrogen bond formed between larger number of mutation sites of the Omicron variant.
residues R403@RBD and Y92@Etesevimab so that Etesevi- According to the results, these hot-spot residues mainly come
mab−Delta and Etesevimab−WT have the same number of from those that involve the mutation of charged amino acids,
high-occupancy hydrogen bonds. As for the Omicron variant, such as K417N, N440K, T478K, E484A, Q493R, and Q498R.
the two hydrogen bonds involving residues R403@RBD and The residues mutated to positively charged amino acids can
Y473@RBD become more unstable compared to the WT. This induce attenuated electrostatic interaction energy, whereas
implies that the Delta variant may have less effect on the mutations to negative do the opposite. In addition, residues
hydrogen bond network between Etesevimab and the RBD, V483 and F490 exhibit significant energy reduction; the former
while the more unstable hydrogen bond network exhibited by is mainly due to weakened electrostatic energy and enhanced
the Omicron variant may facilitate its escape from Etesevimab. polar solvation energy, and the latter comes from weakened
Then, the contributions of binding free energy for these vdW energy.
residues near the binding interface were calculated using the Etesevimab−Delta and Etesevimab−WT have similar bind-
ASIE method (Figure 4 and Table S2), and they are generally ing modes, differing only slightly in residues 403 and 478. This
considered important sites for mutation-induced changes in may be since the charged residues introduced by the mutation
the binding affinity of the system. We define these residues are not close to the binding interface and do not cause a
with an absolute value of the binding free energy difference significant effect on the binding affinity. For the Etesevimab−
from the WT system ≥1 kcal/mol as hot-spot residues. In the Omicron complex, residues 417 and 478 have obvious energy
Bamlanivimab−Delta complex, mutated residue 478 has a changes among the mutated residues, both of which have
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weakened electrostatic interaction energy after mutation, with minor differences, which are not sufficient to affect the
which is not conducive to their interaction with the mAbs. sustained stabilization of the mAbs against the WT. In contrast,
Other residues involved in the mutation also have changes in for the Bamlanivimab/Etesevimab−Omicron complexes, there
the electrostatic interaction energy, but they are offset by the is a significant deflection from the initial structure. The
polar solvation energy, resulting in no obvious change in the conformational change leads to an open hinge-like angle
affinity of these residues with the antibody. Furthermore, between the binding interface of the mAbs and the RBD, with
residues E406, R408, Y421, and N460 show obvious sensitivity one side of the mAbs gradually moving away from the RBD
to mutation. They clustered in a similar region, suggesting that while the other side is temporarily immobile or slightly closer
large conformational changes may have occurred in this region, to the RBD. This explains why the Omicron variant shows a
leading to significant energy changes in nearby residues. large number of red patches but still retains a few blue patches
As the epidemic progresses, the Omicron variant gradually (Figure S8). However, with a gradual increase of the opening
replaces other mutant strains as the overwhelmingly dominant angle, the contact between mAbs and the RBD becomes less
variant. To verify the reliability of the above findings and to and less; the RBD will get rid of the mAbs’ grasp on it, thus
further elucidate the escape mechanism of Omicron variants to producing the immune escape.
mAbs, we extend the MD simulation of the Bamlanivimab/ In summary, we dissect the impact of recently circulating
Etesevimab−Omicron systems to 1.5 μs. For comparison, the SARS-CoV-2 Delta and Omicron mutant strains on
WT systems are also extended to the same time scale. Bamlanivimab and Etesevimab, two RBD-targeting mAbs
It is found that the RMSD of each system consistently already approved for therapy. The results show that the
fluctuated within a reasonable range and eventually stabilized Omicron variant appears to be more prone to immune escape
around 4 Å (Figure S6A), indicating that the binding mode of than the Delta variant, from both the energetic and
mAbs−RBD stabilized and the systems had converged. The conformational perspectives. The Omicron variant carries
Bamlanivimab/Etesevimab−Omicron complexes have higher multiple mutations that, on the one hand, weaken the
flexibility of residues near the binding interface than the WT electrostatic interaction between the RBD and the mAbs by
systems (Figure S6B and C), suggesting that the Bamlanivi- introducing a large number of positively charged amino acids.
mab/Etesevimab−Omicron systems had undergone a pro- On the other hand, it triggers a significant conformational
nounced conformational shift that may trigger an unstable deflection resulting in less contact between the RBD and the
binding pattern between the RBD and the mAbs; this point is antibody, thus reducing the binding stability of both. As for the
also confirmed by the following computation. Delta variant, the introduction of two positively charged amino
The binding affinity of the Omicron variant to Bamlanivi- acids in the RBD also results in a weakening of the electrostatic
mab/Etesevimab remains significantly weaker than that of the interaction energy between the RBD and the mAbs, but this
WT (Figure 5A). The difference mainly arises from the change is balanced by the polar solvation energy. The real
dramatic diminution in the electrostatic and vdW energies reason for the reduced affinity of the Delta variant for
(Table S3); the former is caused by the large number of Bamlanivimab is that the mutation causes the RBD to be close
positively charged residues introduced through the mutation, to the extended region of the antibody (100−110@
and the latter comes from the unstable binding mode between banranivirumab) but away from the main part of the heavy
the mutated RBD and the mAbs with fewer atomic contacts chain (28−55@banranivirumab). This change increases the
(Figure 5B). These are consistent with the 100 ns conclusions. rotational freedom of Bamlanivimab binding to the RBD and
The lowest frequency principal component is then used to reduces the number of stable hydrogen bonds between the
describe the characteristic dynamic fluctuations of each system two, leaving the complex in an unstable binding state. In
(Figure S7). Their dynamic characteristics are found to be addition, the binding mode of the Delta variant to Etesevimab
similar to the results above; that is, the mAbs deflect on the is similar to that of the WT, which may be because the
axis of the binding interface, and the Omicron variant exhibits mutation site is far away from the binding interface and the
greater rotational freedom than the WT, suggesting unstable presence of the mutation does not cause significant conforma-
binding of the Omicron variant to the mAbs compared to the tional changes. Our work reveals the escape mechanism of
WT. mainstream SARS-CoV-2 variants against two mAbs that
Subsequently, the distance changes between residues near received EUA at the molecular level, which provides timely
the binding interface are calculated for further elaboration of theoretical insights for the improvement of existing antibodies
the escape trend of the Omicron variant toward Bamlanivi- and the development of novel antibodies.
mab/Etesevimab (Figure S8). Apparently, the distribution of
the distance changes of WT systems is similar to that of the
100 ns simulation, indicating that the WT is still stably binding

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to the mAbs. However, a large dark red patch appears in the The Supporting Information is available free of charge at
Omicron variant systems, suggesting that it is away from the https://pubs.acs.org/doi/10.1021/acs.jpclett.2c00912.
mAbs, resulting in less atomic contact and hydrogen bonding
between the two (Figure S9). Research methods, RMSD and RMSF of each complex,
Interestingly, although the Omicron variant exhibits a more surface electrostatic potential distribution of the RBD
unfavorable binding mode to the mAbs compared to the WT, (WT, Delta, and Omicron) and mAbs (Bamlanivimab
there are still a few blue patches (Figure S8). To visualize the and Etesevimab), distribution of the number of heavy-
escape pattern of the Omicron variant toward mAbs, the atom contacts between the RBD and mAbs, distance
average conformation of the equilibrium phase is used for change between residues near the binding interface,
comparison with the initial structure (Figure 5C and D). We structural representations of the Bamlanivimab−RBD
find that the average structures of the Bamlanivimab/ and Etesevimab−RBD complexes, the RMSD, RMSF,
Etesevimab−WT systems are similar to the initial structure characteristic dynamic fluctuations, distance change, and

6070 https://doi.org/10.1021/acs.jpclett.2c00912
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■ AUTHOR INFORMATION
Corresponding Authors
X.; Tan, Y. F.; Song, L. Y.; Wang, G. P.; Du, X. X.; Gao, N.; Liu, J. N.;
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of Chemistry and Molecular Engineering, East China Normal C. Y.; Zhang, Q.; Liu, H.; Nie, L. L.; Qin, H. Y.; Wang, M.; Lu, Q.; Li,
University, Shanghai 200062, China; Shenzhen Institute of X. Y.; Sun, Q. Y.; Liu, J. K.; Zhang, L. Q.; Li, X. G.; Huang, W. J.;
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NYU Shanghai, Shanghai 200062, China; Department of W.; Song, T.; Bi, X. S.; Han, C.; Wu, L. A.; Gao, G.; Hu, X.; Zhang, Y.
Chemistry, New York University, New York, New York A.; Tong, Z.; Huang, W. J.; Liu, W. J.; Wu, G. Z.; Zhang, B.; Wang, L.;
10003, United States; orcid.org/0000-0003-4612-1863; Qi, J. X.; Feng, H.; Wang, F. S.; Wang, Q. H.; Gao, G. F.; Yuan, Z. M.;
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Normal University, Jinan 250014, China; orcid.org/
J.; Huhn, G.; Cardona, J.; Mocherla, B.; Stosor, V.; Shawa, I.; Adams,
0000-0002-1293-6784; Email: duanll@sdnu.edu.cn A. C.; Van Naarden, J.; Custer, K. L.; Shen, L.; Durante, M.; Oakley,
Authors G.; Schade, A. E.; Sabo, J.; Patel, D. R.; Klekotka, P.; Skovronsky, D.
M. Sars-Cov-2 Neutralizing Antibody Ly-Cov555 in Outpatients with
Danyang Xiong − School of Physics and Electronics, Shandong
Covid-19. N. Engl. J. Med. 2021, 384 (3), 229−237.
Normal University, Jinan 250014, China; orcid.org/ (9) Barnes, C. O.; Jette, C. A.; Abernathy, M. E.; Dam, K. M. A.;
0000-0002-0911-1888 Esswein, S. R.; Gristick, H. B.; Malyutin, A. G.; Sharaf, N. G.; Huey
Xiaoyu Zhao − School of Physics and Electronics, Shandong Tubman, K. E.; Lee, Y. E.; Robbiani, D. F.; Nussenzweig, M. C.; West,
Normal University, Jinan 250014, China A. P.; Bjorkman, P. J. Sars-Cov-2 Neutralizing Antibody Structures
Song Luo − School of Physics and Electronics, Shandong Inform Therapeutic Strategies. Nature 2020, 588 (7839), 682−687.
Normal University, Jinan 250014, China (10) Jones, B. E.; Brown-Augsburger, P. L.; Corbett, K. S.;
Yalong Cong − Shanghai Engineering Research Center of Westendorf, K.; Davies, J.; Cujec, T. P.; Wiethoff, C. M.;
Molecular Therapeutics and New Drug Development, School Blackbourne, J. L.; Heinz, B. A.; Foster, D.; Higgs, R. E.;
of Chemistry and Molecular Engineering, East China Normal Balasubramaniam, D.; Wang, L.; Zhang, Y.; Yang, E. S.; Bidshahri,
University, Shanghai 200062, China; orcid.org/0000- R.; Kraft, L.; Hwang, Y.; Ž entelis, S.; Jepson, K. R.; Goya, R.; Smith,
0002-0910-811X M. A.; Collins, D. W.; Hinshaw, S. J.; Tycho, S. A.; Pellacani, D.;
Xiang, P.; Muthuraman, K.; Sobhanifar, S.; Piper, M. H.; Triana, F. J.;
Complete contact information is available at: Hendle, J.; Pustilnik, A.; Adams, A. C.; Berens, S. J.; Baric, R. S.;
https://pubs.acs.org/10.1021/acs.jpclett.2c00912 Martinez, D. R.; Cross, R. W.; Geisbert, T. W.; Borisevich, V.; Abiona,
O.; Belli, H. M.; de Vries, M.; Mohamed, A.; Dittmann, M.;
Notes Samanovic, M. I.; Mulligan, M. J.; Goldsmith, J. A.; Hsieh, C.-L.;
The authors declare no competing financial interest. Johnson, N. V.; Wrapp, D.; McLellan, J. S.; Barnhart, B. C.; Graham,

■ ACKNOWLEDGMENTS
This work was supported by the National Natural Science
B. S.; Mascola, J. R.; Hansen, C. L.; Falconer, E. The Neutralizing
Antibody, Ly-Cov555, Protects against Sars-Cov-2 Infection in
Nonhuman Primates. Sci. Transl. Med. 2021, 13 (593), No. eabf1906.
(11) Hansen, J.; Baum, A.; Pascal Kristen, E.; Russo, V.; Giordano,
Foundation of China (Grant nos. 21933010 and 11774207) S.; Wloga, E.; Fulton Benjamin, O.; Yan, Y.; Koon, K.; Patel, K.;
and the NYU-ECNU Center for Computational Chemistry at Chung Kyung, M.; Hermann, A.; Ullman, E.; Cruz, J.; Rafique, A.;
NYU Shanghai. We thank the ECNU Public Platform for Huang, T.; Fairhurst, J.; Libertiny, C.; Malbec, M.; Lee, W. Y.; Welsh,
Innovation 001 for providing supercomputer time.


R.; Farr, G.; Pennington, S.; Deshpande, D.; Cheng, J.; Watty, A.;
Bouffard, P.; Babb, R.; Levenkova, N.; Chen, C.; Zhang, B.; Romero
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