A computationally designed ACE2 decoy has broad efficacy against SARS-CoV-2 omicron variants and related viruses in vitro and in vivo

SARS-CoV-2, especially B.1.1.529/omicron and its sublineages, continues to mutate to evade monoclonal antibodies and antibodies elicited by vaccination. Affinity-enhanced soluble ACE2 (sACE2) is an alternative strategy that works by binding the SARS-CoV-2 S protein, acting as a ‘decoy’ to block the...

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Published inCommunications Biology Vol. 6; no. 1; pp. 513 - 16
Main Authors Havranek, Brandon, Lindsey, Graeme Walker, Higuchi, Yusuke, Itoh, Yumi, Suzuki, Tatsuya, Okamoto, Toru, Hoshino, Atsushi, Procko, Erik, Islam, Shahidul M.
Format Journal Article
LanguageEnglish
Published London Springer Science and Business Media LLC 12.05.2023
Nature Publishing Group UK
Nature Publishing Group
Nature Portfolio
Subjects
631/114/469
631/154/51/2314
631/57/2266
82
82/80
82/81
82/83
96
96/31
ACE2
Affinity
Angiotensin-converting enzyme 2
Angiotensin-Converting Enzyme 2 - genetics
Angiotensin-Converting Enzyme 2 - therapeutic use
antibodies
Antibodies, Monoclonal
Biology
Biology (General)
Biomedical and Life Sciences
Computer applications
COVID-19
Design
Humans
Life Sciences
Medical Biochemistry
Medical Sciences
Medicine and Health Sciences
monoclonal
Monoclonal antibodies
Protein Engineering
QH301-705.5
SARS-CoV-2
SARS-CoV-2 - genetics
Severe acute respiratory syndrome coronavirus 2
Vaccination
Online AccessGet full text

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Abstract SARS-CoV-2, especially B.1.1.529/omicron and its sublineages, continues to mutate to evade monoclonal antibodies and antibodies elicited by vaccination. Affinity-enhanced soluble ACE2 (sACE2) is an alternative strategy that works by binding the SARS-CoV-2 S protein, acting as a ‘decoy’ to block the interaction between the S and human ACE2. Using a computational design strategy, we designed an affinity-enhanced ACE2 decoy, FLIF , that exhibited tight binding to SARS-CoV-2 delta and omicron variants. Our computationally calculated absolute binding free energies (ABFE) between sACE2:SARS-CoV-2 S proteins and their variants showed excellent agreement to binding experiments. FLIF displayed robust therapeutic utility against a broad range of SARS-CoV-2 variants and sarbecoviruses, and neutralized omicron BA.5 in vitro and in vivo. Furthermore, we directly compared the in vivo therapeutic efficacy of wild-type ACE2 (non-affinity enhanced ACE2) against FLIF . A few wild-type sACE2 decoys have shown to be effective against early circulating variants such as Wuhan in vivo. Our data suggest that moving forward, affinity-enhanced ACE2 decoys like FLIF may be required to combat evolving SARS-CoV-2 variants. The approach described herein emphasizes how computational methods have become sufficiently accurate for the design of therapeutics against viral protein targets. Affinity-enhanced ACE2 decoys remain highly effective at neutralizing omicron subvariants. A computational design strategy is used to develop an affinity-enhanced ACE2 decoy, which is shown to be effective at neutralizing omicron subvariants in vitro and in vivo.
AbstractList SARS-CoV-2, especially B.1.1.529/omicron and its sublineages, continues to mutate to evade monoclonal antibodies and antibodies elicited by vaccination. Affinity-enhanced soluble ACE2 (sACE2) is an alternative strategy that works by binding the SARS-CoV-2 S protein, acting as a ‘decoy’ to block the interaction between the S and human ACE2. Using a computational design strategy, we designed an affinity-enhanced ACE2 decoy, FLIF , that exhibited tight binding to SARS-CoV-2 delta and omicron variants. Our computationally calculated absolute binding free energies (ABFE) between sACE2:SARS-CoV-2 S proteins and their variants showed excellent agreement to binding experiments. FLIF displayed robust therapeutic utility against a broad range of SARS-CoV-2 variants and sarbecoviruses, and neutralized omicron BA.5 in vitro and in vivo. Furthermore, we directly compared the in vivo therapeutic efficacy of wild-type ACE2 (non-affinity enhanced ACE2) against FLIF . A few wild-type sACE2 decoys have shown to be effective against early circulating variants such as Wuhan in vivo. Our data suggest that moving forward, affinity-enhanced ACE2 decoys like FLIF may be required to combat evolving SARS-CoV-2 variants. The approach described herein emphasizes how computational methods have become sufficiently accurate for the design of therapeutics against viral protein targets. Affinity-enhanced ACE2 decoys remain highly effective at neutralizing omicron subvariants. A computational design strategy is used to develop an affinity-enhanced ACE2 decoy, which is shown to be effective at neutralizing omicron subvariants in vitro and in vivo.
SARS-CoV-2, especially B.1.1.529/omicron and its sublineages, continues to mutate to evade monoclonal antibodies and antibodies elicited by vaccination. Affinity-enhanced soluble ACE2 (sACE2) is an alternative strategy that works by binding the SARS-CoV-2 S protein, acting as a ‘decoy’ to block the interaction between the S and human ACE2. Using a computational design strategy, we designed an affinity-enhanced ACE2 decoy, FLIF , that exhibited tight binding to SARS-CoV-2 delta and omicron variants. Our computationally calculated absolute binding free energies (ABFE) between sACE2:SARS-CoV-2 S proteins and their variants showed excellent agreement to binding experiments. FLIF displayed robust therapeutic utility against a broad range of SARS-CoV-2 variants and sarbecoviruses, and neutralized omicron BA.5 in vitro and in vivo. Furthermore, we directly compared the in vivo therapeutic efficacy of wild-type ACE2 (non-affinity enhanced ACE2) against FLIF . A few wild-type sACE2 decoys have shown to be effective against early circulating variants such as Wuhan in vivo. Our data suggest that moving forward, affinity-enhanced ACE2 decoys like FLIF may be required to combat evolving SARS-CoV-2 variants. The approach described herein emphasizes how computational methods have become sufficiently accurate for the design of therapeutics against viral protein targets. Affinity-enhanced ACE2 decoys remain highly effective at neutralizing omicron subvariants.
SARS-CoV-2, especially B.1.1.529/omicron and its sublineages, continues to mutate to evade monoclonal antibodies and antibodies elicited by vaccination. Affinity-enhanced soluble ACE2 (sACE2) is an alternative strategy that works by binding the SARS-CoV-2 S protein, acting as a 'decoy' to block the interaction between the S and human ACE2. Using a computational design strategy, we designed an affinity-enhanced ACE2 decoy, FLIF, that exhibited tight binding to SARS-CoV-2 delta and omicron variants. Our computationally calculated absolute binding free energies (ABFE) between sACE2:SARS-CoV-2 S proteins and their variants showed excellent agreement to binding experiments. FLIF displayed robust therapeutic utility against a broad range of SARS-CoV-2 variants and sarbecoviruses, and neutralized omicron BA.5 in vitro and in vivo. Furthermore, we directly compared the in vivo therapeutic efficacy of wild-type ACE2 (non-affinity enhanced ACE2) against FLIF. A few wild-type sACE2 decoys have shown to be effective against early circulating variants such as Wuhan in vivo. Our data suggest that moving forward, affinity-enhanced ACE2 decoys like FLIF may be required to combat evolving SARS-CoV-2 variants. The approach described herein emphasizes how computational methods have become sufficiently accurate for the design of therapeutics against viral protein targets. Affinity-enhanced ACE2 decoys remain highly effective at neutralizing omicron subvariants.SARS-CoV-2, especially B.1.1.529/omicron and its sublineages, continues to mutate to evade monoclonal antibodies and antibodies elicited by vaccination. Affinity-enhanced soluble ACE2 (sACE2) is an alternative strategy that works by binding the SARS-CoV-2 S protein, acting as a 'decoy' to block the interaction between the S and human ACE2. Using a computational design strategy, we designed an affinity-enhanced ACE2 decoy, FLIF, that exhibited tight binding to SARS-CoV-2 delta and omicron variants. Our computationally calculated absolute binding free energies (ABFE) between sACE2:SARS-CoV-2 S proteins and their variants showed excellent agreement to binding experiments. FLIF displayed robust therapeutic utility against a broad range of SARS-CoV-2 variants and sarbecoviruses, and neutralized omicron BA.5 in vitro and in vivo. Furthermore, we directly compared the in vivo therapeutic efficacy of wild-type ACE2 (non-affinity enhanced ACE2) against FLIF. A few wild-type sACE2 decoys have shown to be effective against early circulating variants such as Wuhan in vivo. Our data suggest that moving forward, affinity-enhanced ACE2 decoys like FLIF may be required to combat evolving SARS-CoV-2 variants. The approach described herein emphasizes how computational methods have become sufficiently accurate for the design of therapeutics against viral protein targets. Affinity-enhanced ACE2 decoys remain highly effective at neutralizing omicron subvariants.
SARS-CoV-2, especially B.1.1.529/omicron and its sublineages, continues to mutate to evade monoclonal antibodies and antibodies elicited by vaccination. Affinity-enhanced soluble ACE2 (sACE2) is an alternative strategy that works by binding the SARS-CoV-2 S protein, acting as a 'decoy' to block the interaction between the S and human ACE2. Using a computational design strategy, we designed an affinity-enhanced ACE2 decoy, FLIF, that exhibited tight binding to SARS-CoV-2 delta and omicron variants. Our computationally calculated absolute binding free energies (ABFE) between sACE2:SARS-CoV-2 S proteins and their variants showed excellent agreement to binding experiments. FLIF displayed robust therapeutic utility against a broad range of SARS-CoV-2 variants and sarbecoviruses, and neutralized omicron BA.5 in vitro and in vivo. Furthermore, we directly compared the in vivo therapeutic efficacy of wild-type ACE2 (non-affinity enhanced ACE2) against FLIF. A few wild-type sACE2 decoys have shown to be effective against early circulating variants such as Wuhan in vivo. Our data suggest that moving forward, affinity-enhanced ACE2 decoys like FLIF may be required to combat evolving SARS-CoV-2 variants. The approach described herein emphasizes how computational methods have become sufficiently accurate for the design of therapeutics against viral protein targets. Affinity-enhanced ACE2 decoys remain highly effective at neutralizing omicron subvariants.
Abstract SARS-CoV-2, especially B.1.1.529/omicron and its sublineages, continues to mutate to evade monoclonal antibodies and antibodies elicited by vaccination. Affinity-enhanced soluble ACE2 (sACE2) is an alternative strategy that works by binding the SARS-CoV-2 S protein, acting as a ‘decoy’ to block the interaction between the S and human ACE2. Using a computational design strategy, we designed an affinity-enhanced ACE2 decoy, FLIF, that exhibited tight binding to SARS-CoV-2 delta and omicron variants. Our computationally calculated absolute binding free energies (ABFE) between sACE2:SARS-CoV-2 S proteins and their variants showed excellent agreement to binding experiments. FLIF displayed robust therapeutic utility against a broad range of SARS-CoV-2 variants and sarbecoviruses, and neutralized omicron BA.5 in vitro and in vivo. Furthermore, we directly compared the in vivo therapeutic efficacy of wild-type ACE2 (non-affinity enhanced ACE2) against FLIF. A few wild-type sACE2 decoys have shown to be effective against early circulating variants such as Wuhan in vivo. Our data suggest that moving forward, affinity-enhanced ACE2 decoys like FLIF may be required to combat evolving SARS-CoV-2 variants. The approach described herein emphasizes how computational methods have become sufficiently accurate for the design of therapeutics against viral protein targets. Affinity-enhanced ACE2 decoys remain highly effective at neutralizing omicron subvariants.
SARS-CoV-2, especially B.1.1.529/omicron and its sublineages, continues to mutate to evade monoclonal antibodies and antibodies elicited by vaccination. Affinity-enhanced soluble ACE2 (sACE2) is an alternative strategy that works by binding the SARS-CoV-2 S protein, acting as a ‘decoy’ to block the interaction between the S and human ACE2. Using a computational design strategy, we designed an affinity-enhanced ACE2 decoy, FLIF, that exhibited tight binding to SARS-CoV-2 delta and omicron variants. Our computationally calculated absolute binding free energies (ABFE) between sACE2:SARS-CoV-2 S proteins and their variants showed excellent agreement to binding experiments. FLIF displayed robust therapeutic utility against a broad range of SARS-CoV-2 variants and sarbecoviruses, and neutralized omicron BA.5 in vitro and in vivo. Furthermore, we directly compared the in vivo therapeutic efficacy of wild-type ACE2 (non-affinity enhanced ACE2) against FLIF. A few wild-type sACE2 decoys have shown to be effective against early circulating variants such as Wuhan in vivo. Our data suggest that moving forward, affinity-enhanced ACE2 decoys like FLIF may be required to combat evolving SARS-CoV-2 variants. The approach described herein emphasizes how computational methods have become sufficiently accurate for the design of therapeutics against viral protein targets. Affinity-enhanced ACE2 decoys remain highly effective at neutralizing omicron subvariants.A computational design strategy is used to develop an affinity-enhanced ACE2 decoy, which is shown to be effective at neutralizing omicron subvariants in vitro and in vivo.
ArticleNumber 513
Author Brandon Havranek
Graeme Walker Lindsey
Toru Okamoto
Yumi Itoh
Shahidul M. Islam
Atsushi Hoshino
Erik Procko
Yusuke Higuchi
Tatsuya Suzuki
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BackLink https://cir.nii.ac.jp/crid/1871709542673354880$$DView record in CiNii
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Cites_doi 10.1101/gr.849004
10.1038/s41591-021-01678-y
10.1021/acs.jcim.1c00269
10.1371/journal.pcbi.1004335
10.1038/s41467-022-28528-w
10.3389/fmolb.2021.671633
10.1038/s41467-021-21972-0
10.1073/pnas.1708727114
10.1016/j.csbj.2023.01.014
10.1073/pnas.2016093117
10.1038/s42003-021-01736-8
10.15252/emmm.202216109
10.1021/jz501780a
10.1038/s41586-021-03398-2
10.1021/ar300087y
10.1002/jcc.20290
10.1126/sciadv.abn4188
10.1038/s41586-021-04386-2
10.1371/journal.ppat.1009501
10.1016/j.clim.2020.108634
10.1038/s41467-021-27097-8
10.1021/acs.jpcb.7b11367
10.1016/j.isci.2021.103670
10.1038/s41421-021-00302-0
10.1038/s41586-022-04474-x
10.1371/journal.ppat.1009328
10.1021/ct3008099
10.1126/science.abn7760
10.1517/17460441.2015.1032936
10.1016/j.bpj.2021.11.664
10.1126/science.abo7896
10.1128/mBio.02451-20
10.1093/glycob/cwaa101
10.1038/s41586-020-2180-5
10.1021/acs.jpcb.1c00869
10.1186/s12929-022-00852-9
10.1038/s41589-021-00965-6
10.1038/s41586-021-03777-9
10.1038/s41392-021-00756-4
10.1021/acs.jctc.9b00725
10.3389/fmolb.2022.1080964
10.1063/1.432526
10.1002/jcc.20289
10.1371/journal.ppat.1010022
10.1016/j.tmaid.2020.101830
10.1038/s41598-021-91809-9
10.1021/acs.jctc.9b00591
10.1126/scitranslmed.abn7737
10.1016/j.cell.2022.01.001
10.1063/1.470117
10.1038/s41591-021-01294-w
10.1126/science.abn8863
10.1021/acs.jpcb.2c01048
10.1038/s42003-020-01470-7
10.1038/d41586-022-03445-6
10.1038/s41586-022-04441-6
10.1186/s12916-022-02312-5
10.1073/pnas.0409005102
10.1016/j.cell.2022.05.014
10.1002/jcc.20945
10.1016/S1473-3099(20)30120-1
10.1073/pnas.1517719113
10.1038/s41467-020-16048-4
10.1038/s41586-022-04594-4
10.1038/s41586-022-05053-w
10.1038/s41586-022-04980-y
10.1021/acs.jcim.1c00783
10.1038/s41467-021-24013-y
10.1021/acs.chemrev.9b00055
10.1126/sciadv.abf1738
10.1371/journal.ppat.1009544
10.2147/IDR.S307374
10.1002/prot.20033
10.3390/vaccines10050743
10.7554/eLife.73641
10.3389/fpubh.2021.632043
10.1126/science.abn8939
10.1038/s41392-021-00863-2
10.1038/s41422-022-00644-8
10.3390/clinpract11040093
10.1002/(SICI)1096-987X(199808)19:11<1278::AID-JCC7>3.0.CO;2-H
10.1038/s41586-020-2169-0
10.1016/j.cell.2020.08.012
10.1038/nmeth.4067
10.1021/acs.jctc.2c00604
10.1038/s41586-021-03720-y
10.1021/jp003020w
10.1016/0263-7855(96)00018-5
10.1101/2022.03.28.486075
10.1021/acs.jpclett.2c01490
10.1021/ja9738539
10.1101/2022.09.15.507787
10.1056/NEJMc2206576
10.1016/j.cell.2022.06.005
10.1101/2020.08.12.247940
10.1126/science.abd9909
10.1101/2022.02.14.480335
10.1101/2022.05.21.492554
10.1101/2021.12.22.473804
10.1021/jacs.1c11554
10.1126/science.abc0870
10.2210/pdb7xnr/pdb
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References Starr (CR69) 2022; 377
Coderc de Lacam, Blazhynska, Chen, Gumbart, Chipot (CR66) 2022; 18
Wettstein (CR47) 2021; 12
CR38
Cao (CR65) 2022; 608
CR36
Izadi, Anandakrishnan, Onufriev (CR96) 2014; 5
Mark, Nilsson (CR104) 2001; 105
CR34
CR31
Wang (CR55) 2022; 13
Islam, Havranek, Procko, Chan (CR30) 2022; 121
Iwanaga (CR81) 2022; 25
Shang, Li, Zhang (CR2) 2021; 9
Chen (CR76) 2022; 8
Wang (CR43) 2019; 119
Woo, Roux (CR48) 2005; 102
Essmann (CR99) 1995; 103
Zhang (CR82) 2021; 7
Lam (CR72) 2020; 583
Karoyan (CR24) 2021; 4
Onufriev, Bashford, Case (CR101) 2004; 55
Lan (CR59) 2022; 32
Shiehzadegan, Alaghemand, Fox, Venketaraman (CR10) 2021; 11
Mou (CR78) 2021; 17
Barlow (CR41) 2018; 122
Iketani (CR15) 2022; 604
Glasgow (CR33) 2020; 117
Nutalai (CR93) 2022; 185
Curreli (CR23) 2020; 11
Meng (CR60) 2022; 603
Phillips (CR102) 2005; 26
CR56
Starr (CR73) 2020; 182
Han (CR51) 2022; 185
Yamaguchi (CR86) 2021; 12
CR50
Axelsen, Li (CR98) 1998
Tanaka (CR39) 2021; 11
Maschietto (CR87) 2023; 21
Chatterjee (CR22) 2020; 3
Fu, Chen, Cai, Shao, Chipot (CR64) 2021; 61
Ye (CR79) 2021; 6
Fredericks (CR88) 2022; 9
Ollikainen, de Jong, Kortemme (CR40) 2015; 11
CR68
CR67
CR63
Izda, Jeffries, Sawalha (CR3) 2021; 222
Yao (CR26) 2021; 17
Wu (CR57) 2022; 7
Capraz (CR77) 2021; 10
Chan, Tan, Narayanan, Procko (CR35) 2021; 7
Dong (CR1) 2020; 20
Humphrey, Dalke, Schulten (CR100) 1996; 14
Min, Sun (CR25) 2021; 8
Davis (CR12) 2021; 17
Jo, Kim, Iyer, Im (CR92) 2008; 29
Nguyen, Thai, Nguyen, Li (CR46) 2022; 126
CR74
Higuchi (CR32) 2021; 12
Lan (CR62) 2020; 581
Gumbart, Roux, Chipot (CR49) 2013; 9
Menachery (CR71) 2016; 113
Mannar (CR53) 2022; 375
Zhang (CR37) 2022; 18
Genheden, Ryde (CR44) 2015; 10
Ikemura (CR13) 2022; 14
CR9
Crooks, Hon, Chandonia, Brenner (CR105) 2004; 14
Yin (CR61) 2022; 375
Williams, Zhan (CR28) 2021; 125
Wang (CR70) 2022; 608
Kumari (CR4) 2022; 29
Case (CR91) 2005; 26
Cameroni (CR52) 2022; 602
Vogt (CR54) 2022; 10
Lei (CR85) 2020; 11
Jo, Kim, Iyer, Im (CR94) 2008; 29
Huang (CR103) 2016; 14
CR16
CR14
Kelta Wabalo, Dukessa Dubiwak, Welde Senbetu, Sime Gizaw (CR5) 2021; 14
Adelman, Doll (CR97) 1976; 64
VanBlargan (CR7) 2022; 28
Havranek, Chan, Wu, Procko, Islam (CR29) 2021; 61
Yuan (CR83) 2022; 377
Sims (CR75) 2021; 17
CR90
Planas (CR11) 2021; 596
Chen (CR6) 2021; 596
Chen (CR8) 2021; 27
Dhama (CR18) 2020; 37
Zondlo (CR42) 2013; 46
Wang (CR27) 2021; 593
Tian (CR95) 2020; 16
Callaway (CR17) 2022; 611
CR21
Halfmann (CR84) 2022; 603
CR20
Ruiz-Blanco, Sanchez-Garcia (CR45) 2020; 16
Schubert (CR58) 2022; 20
Walls (CR19) 2017; 114
Zhang (CR80) 2022; 14
Shajahan (CR89) 2021; 31
JJ Sims (4860_CR75) 2021; 17
F Maschietto (4860_CR87) 2023; 21
RE Chen (4860_CR8) 2021; 27
JC Phillips (4860_CR102) 2005; 26
KA Barlow (4860_CR41) 2018; 122
Q Wang (4860_CR70) 2022; 608
Z Zhang (4860_CR82) 2021; 7
J Lan (4860_CR59) 2022; 32
R Nutalai (4860_CR93) 2022; 185
L Zhang (4860_CR37) 2022; 18
4860_CR74
U Essmann (4860_CR99) 1995; 103
W Yin (4860_CR61) 2022; 375
TN Starr (4860_CR73) 2020; 182
PH Axelsen (4860_CR98) 1998
AH Williams (4860_CR28) 2021; 125
4860_CR68
4860_CR67
Y Higuchi (4860_CR32) 2021; 12
E Cameroni (4860_CR52) 2022; 602
AM Fredericks (4860_CR88) 2022; 9
S Jo (4860_CR94) 2008; 29
F Curreli (4860_CR23) 2020; 11
L Min (4860_CR25) 2021; 8
4860_CR63
4860_CR9
A Shajahan (4860_CR89) 2021; 31
DA Case (4860_CR91) 2005; 26
RE Chen (4860_CR6) 2021; 596
SA Adelman (4860_CR97) 1976; 64
B Havranek (4860_CR29) 2021; 61
E Wang (4860_CR43) 2019; 119
TN Starr (4860_CR69) 2022; 377
4860_CR56
E Callaway (4860_CR17) 2022; 611
J Lan (4860_CR62) 2020; 581
M Schubert (4860_CR58) 2022; 20
4860_CR50
Y Wang (4860_CR55) 2022; 13
S Yuan (4860_CR83) 2022; 377
YB Ruiz-Blanco (4860_CR45) 2020; 16
C Lei (4860_CR85) 2020; 11
A-CS Vogt (4860_CR54) 2022; 10
T Yamaguchi (4860_CR86) 2021; 12
N Ikemura (4860_CR13) 2022; 14
EG Coderc de Lacam (4860_CR66) 2022; 18
PJ Halfmann (4860_CR84) 2022; 603
S Genheden (4860_CR44) 2015; 10
H-J Woo (4860_CR48) 2005; 102
LA VanBlargan (4860_CR7) 2022; 28
H Yao (4860_CR26) 2021; 17
NJ Zondlo (4860_CR42) 2013; 46
V Izda (4860_CR3) 2021; 222
D Planas (4860_CR11) 2021; 596
S Jo (4860_CR92) 2008; 29
HL Nguyen (4860_CR46) 2022; 126
P Mark (4860_CR104) 2001; 105
S Iketani (4860_CR15) 2022; 604
GE Crooks (4860_CR105) 2004; 14
4860_CR36
4860_CR34
KK Chan (4860_CR35) 2021; 7
T Capraz (4860_CR77) 2021; 10
4860_CR38
Y Chen (4860_CR76) 2022; 8
4860_CR31
N Iwanaga (4860_CR81) 2022; 25
E Kelta Wabalo (4860_CR5) 2021; 14
C Tian (4860_CR95) 2020; 16
P Wang (4860_CR27) 2021; 593
L Zhang (4860_CR80) 2022; 14
A Glasgow (4860_CR33) 2020; 117
M Kumari (4860_CR4) 2022; 29
VD Menachery (4860_CR71) 2016; 113
Y Shang (4860_CR2) 2021; 9
4860_CR21
4860_CR20
H Fu (4860_CR64) 2021; 61
H Mou (4860_CR78) 2021; 17
E Dong (4860_CR1) 2020; 20
AC Walls (4860_CR19) 2017; 114
P Han (4860_CR51) 2022; 185
L Wu (4860_CR57) 2022; 7
L Wettstein (4860_CR47) 2021; 12
S Izadi (4860_CR96) 2014; 5
4860_CR14
MS Islam (4860_CR30) 2022; 121
A Onufriev (4860_CR101) 2004; 55
F Ye (4860_CR79) 2021; 6
4860_CR16
N Ollikainen (4860_CR40) 2015; 11
W Humphrey (4860_CR100) 1996; 14
B Meng (4860_CR60) 2022; 603
TT-Y Lam (4860_CR72) 2020; 583
S Shiehzadegan (4860_CR10) 2021; 11
P Karoyan (4860_CR24) 2021; 4
K Dhama (4860_CR18) 2020; 37
J Huang (4860_CR103) 2016; 14
4860_CR90
Y Cao (4860_CR65) 2022; 608
P Chatterjee (4860_CR22) 2020; 3
C Davis (4860_CR12) 2021; 17
S Tanaka (4860_CR39) 2021; 11
D Mannar (4860_CR53) 2022; 375
JC Gumbart (4860_CR49) 2013; 9
References_xml – ident: CR68
– ident: CR74
– volume: 14
  start-page: 1188
  year: 2004
  end-page: 1190
  ident: CR105
  article-title: WebLogo: a sequence logo generator: Fig. 1
  publication-title: Genome Res.
  doi: 10.1101/gr.849004
– ident: CR16
– volume: 28
  start-page: 490
  year: 2022
  end-page: 495
  ident: CR7
  article-title: An infectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by therapeutic monoclonal antibodies
  publication-title: Nat. Med.
  doi: 10.1038/s41591-021-01678-y
– volume: 61
  start-page: 2116
  year: 2021
  end-page: 2123
  ident: CR64
  article-title: BFEE2: automated, streamlined, and accurate absolute binding free-energy calculations
  publication-title: J. Chem. Inf. Model.
  doi: 10.1021/acs.jcim.1c00269
– volume: 11
  start-page: e1004335
  year: 2015
  ident: CR40
  article-title: Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity
  publication-title: PLOS Comput. Biol.
  doi: 10.1371/journal.pcbi.1004335
– volume: 13
  year: 2022
  ident: CR55
  article-title: Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-022-28528-w
– volume: 8
  start-page: 671633
  year: 2021
  ident: CR25
  article-title: Antibodies and vaccines target RBD of SARS-CoV-2
  publication-title: Front. Mol. Biosci.
  doi: 10.3389/fmolb.2021.671633
– volume: 12
  year: 2021
  ident: CR47
  article-title: Alpha-1 antitrypsin inhibits TMPRSS2 protease activity and SARS-CoV-2 infection
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-021-21972-0
– volume: 114
  start-page: 11157
  year: 2017
  end-page: 11162
  ident: CR19
  article-title: Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.1708727114
– volume: 21
  start-page: 1066
  year: 2023
  end-page: 1076
  ident: CR87
  article-title: Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism
  publication-title: Comput. Struct. Biotechnol. J.
  doi: 10.1016/j.csbj.2023.01.014
– volume: 117
  start-page: 28046
  year: 2020
  end-page: 28055
  ident: CR33
  article-title: Engineered ACE2 receptor traps potently neutralize SARS-CoV-2
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.2016093117
– volume: 4
  start-page: 197
  year: 2021
  ident: CR24
  article-title: Human ACE2 peptide-mimics block SARS-CoV-2 pulmonary cells infection
  publication-title: Commun. Biol.
  doi: 10.1038/s42003-021-01736-8
– volume: 14
  start-page: e16109
  year: 2022
  ident: CR80
  article-title: An ACE2 decoy can be administered by inhalation and potently targets omicron variants of SARS‐CoV‐2
  publication-title: EMBO Mol. Med.
  doi: 10.15252/emmm.202216109
– volume: 5
  start-page: 3863
  year: 2014
  end-page: 3871
  ident: CR96
  article-title: Building water models: a different approach
  publication-title: J. Phys. Chem. Lett.
  doi: 10.1021/jz501780a
– volume: 593
  start-page: 130
  year: 2021
  end-page: 135
  ident: CR27
  article-title: Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7
  publication-title: Nature
  doi: 10.1038/s41586-021-03398-2
– volume: 46
  start-page: 1039
  year: 2013
  end-page: 1049
  ident: CR42
  article-title: Aromatic–proline interactions: electronically tunable CH/π interactions
  publication-title: Acc. Chem. Res.
  doi: 10.1021/ar300087y
– volume: 26
  start-page: 1668
  year: 2005
  end-page: 1688
  ident: CR91
  article-title: The Amber biomolecular simulation programs
  publication-title: J. Comput. Chem.
  doi: 10.1002/jcc.20290
– volume: 8
  start-page: eabn4188
  year: 2022
  ident: CR76
  article-title: Engineered ACE2-Fc counters murine lethal SARS-CoV-2 infection through direct neutralization and Fc-effector activities
  publication-title: Sci. Adv.
  doi: 10.1126/sciadv.abn4188
– ident: CR36
– volume: 602
  start-page: 664
  year: 2022
  end-page: 670
  ident: CR52
  article-title: Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift
  publication-title: Nature
  doi: 10.1038/s41586-021-04386-2
– volume: 17
  start-page: e1009501
  year: 2021
  ident: CR78
  article-title: Mutations derived from horseshoe bat ACE2 orthologs enhance ACE2-Fc neutralization of SARS-CoV-2
  publication-title: PLOS Pathog.
  doi: 10.1371/journal.ppat.1009501
– volume: 222
  start-page: 108634
  year: 2021
  ident: CR3
  article-title: COVID-19: a review of therapeutic strategies and vaccine candidates
  publication-title: Clin. Immunol.
  doi: 10.1016/j.clim.2020.108634
– volume: 12
  year: 2021
  ident: CR86
  article-title: ACE2-like carboxypeptidase B38-CAP protects from SARS-CoV-2-induced lung injury
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-021-27097-8
– volume: 122
  start-page: 5389
  year: 2018
  end-page: 5399
  ident: CR41
  article-title: Flex ddG: Rosetta ensemble-based estimation of changes in protein-protein binding affinity upon mutation
  publication-title: J. Phys. Chem. B
  doi: 10.1021/acs.jpcb.7b11367
– volume: 25
  start-page: 103670
  year: 2022
  ident: CR81
  article-title: ACE2-IgG1 fusions with improved in vitro and in vivo activity against SARS-CoV-2
  publication-title: iScience
  doi: 10.1016/j.isci.2021.103670
– volume: 7
  start-page: 65
  year: 2021
  ident: CR82
  article-title: Potent prophylactic and therapeutic efficacy of recombinant human ACE2-Fc against SARS-CoV-2 infection in vivo
  publication-title: Cell Discov.
  doi: 10.1038/s41421-021-00302-0
– volume: 603
  start-page: 706
  year: 2022
  end-page: 714
  ident: CR60
  article-title: Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity
  publication-title: Nature
  doi: 10.1038/s41586-022-04474-x
– volume: 17
  start-page: e1009328
  year: 2021
  ident: CR26
  article-title: A high-affinity RBD-targeting nanobody improves fusion partner’s potency against SARS-CoV-2
  publication-title: PLOS Pathog.
  doi: 10.1371/journal.ppat.1009328
– volume: 9
  start-page: 794
  year: 2013
  end-page: 802
  ident: CR49
  article-title: Standard binding free energies from computer simulations: what is the best strategy?
  publication-title: J. Chem. Theory Comput.
  doi: 10.1021/ct3008099
– ident: CR63
– volume: 375
  start-page: 760
  year: 2022
  end-page: 764
  ident: CR53
  article-title: SARS-CoV-2 Omicron variant: antibody evasion and cryo-EM structure of spike protein–ACE2 complex
  publication-title: Science
  doi: 10.1126/science.abn7760
– volume: 10
  start-page: 449
  year: 2015
  end-page: 461
  ident: CR44
  article-title: The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
  publication-title: Expert Opin. Drug Discov.
  doi: 10.1517/17460441.2015.1032936
– volume: 121
  start-page: 422a
  year: 2022
  ident: CR30
  article-title: Computationally engineered ACE2 decoy binds with nanomolar affinity with the SARS-CoV-2 spike protein
  publication-title: Biophys. J.
  doi: 10.1016/j.bpj.2021.11.664
– volume: 377
  start-page: 420
  year: 2022
  end-page: 424
  ident: CR69
  article-title: Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution
  publication-title: Science
  doi: 10.1126/science.abo7896
– volume: 11
  start-page: e02451
  year: 2020
  end-page: 20
  ident: CR23
  article-title: Stapled peptides based on human angiotensin-converting enzyme 2 (ACE2) potently Inhibit SARS-CoV-2 infection in vitro
  publication-title: MBio
  doi: 10.1128/mBio.02451-20
– ident: CR38
– volume: 31
  start-page: 410
  year: 2021
  end-page: 424
  ident: CR89
  article-title: Comprehensive characterization of N- and O- glycosylation of SARS-CoV-2 human receptor angiotensin converting enzyme 2
  publication-title: Glycobiology
  doi: 10.1093/glycob/cwaa101
– volume: 581
  start-page: 215
  year: 2020
  end-page: 220
  ident: CR62
  article-title: Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor
  publication-title: Nature
  doi: 10.1038/s41586-020-2180-5
– volume: 125
  start-page: 4330
  year: 2021
  end-page: 4336
  ident: CR28
  article-title: Fast prediction of binding affinities of the SARS-CoV-2 spike protein mutant N501Y (UK Variant) with ACE2 and miniprotein drug candidates
  publication-title: J. Phys. Chem. B
  doi: 10.1021/acs.jpcb.1c00869
– volume: 29
  start-page: 68
  year: 2022
  ident: CR4
  article-title: A critical overview of current progress for COVID-19: development of vaccines, antiviral drugs, and therapeutic antibodies
  publication-title: J. Biomed. Sci.
  doi: 10.1186/s12929-022-00852-9
– volume: 18
  start-page: 342
  year: 2022
  end-page: 351
  ident: CR37
  article-title: Engineered ACE2 decoy mitigates lung injury and death induced by SARS-CoV-2 variants
  publication-title: Nat. Chem. Biol.
  doi: 10.1038/s41589-021-00965-6
– volume: 596
  start-page: 276
  year: 2021
  end-page: 280
  ident: CR11
  article-title: Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization
  publication-title: Nature
  doi: 10.1038/s41586-021-03777-9
– volume: 6
  start-page: 343
  year: 2021
  ident: CR79
  article-title: S19W, T27W, and N330Y mutations in ACE2 enhance SARS-CoV-2 S-RBD binding toward both wild-type and antibody-resistant viruses and its molecular basis
  publication-title: Signal Transduct. Target. Ther.
  doi: 10.1038/s41392-021-00756-4
– volume: 16
  start-page: 1396
  year: 2020
  end-page: 1410
  ident: CR45
  article-title: CL-FEP: an end-state free energy perturbation approach
  publication-title: J. Chem. Theory Comput.
  doi: 10.1021/acs.jctc.9b00725
– volume: 9
  start-page: 1080964
  year: 2022
  ident: CR88
  article-title: Identification and mechanistic basis of non-ACE2 blocking neutralizing antibodies from COVID-19 patients with deep RNA sequencing and molecular dynamics simulations
  publication-title: Front. Mol. Biosci.
  doi: 10.3389/fmolb.2022.1080964
– volume: 64
  start-page: 2375
  year: 1976
  ident: CR97
  article-title: Generalized Langevin equation approach for atom/solid-surface scattering: general formulation for classical scattering off harmonic solids
  publication-title: J. Chem. Phys.
  doi: 10.1063/1.432526
– volume: 26
  start-page: 1781
  year: 2005
  end-page: 1802
  ident: CR102
  article-title: Scalable molecular dynamics with NAMD
  publication-title: J. Comput. Chem.
  doi: 10.1002/jcc.20289
– volume: 17
  start-page: e1010022
  year: 2021
  ident: CR12
  article-title: Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination
  publication-title: PLOS Pathog.
  doi: 10.1371/journal.ppat.1010022
– volume: 37
  start-page: 101830
  year: 2020
  ident: CR18
  article-title: SARS-CoV-2 jumping the species barrier: Zoonotic lessons from SARS, MERS and recent advances to combat this pandemic virus
  publication-title: Travel Med. Infect. Dis.
  doi: 10.1016/j.tmaid.2020.101830
– volume: 11
  year: 2021
  ident: CR39
  article-title: An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants
  publication-title: Sci. Rep.
  doi: 10.1038/s41598-021-91809-9
– volume: 16
  start-page: 528
  year: 2020
  end-page: 552
  ident: CR95
  article-title: ff19SB: amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution
  publication-title: J. Chem. Theory Comput.
  doi: 10.1021/acs.jctc.9b00591
– volume: 14
  start-page: eabn7737
  year: 2022
  ident: CR13
  article-title: An engineered ACE2 decoy neutralizes the SARS-CoV-2 Omicron variant and confers protection against infection in vivo
  publication-title: Sci. Transl. Med.
  doi: 10.1126/scitranslmed.abn7737
– volume: 185
  start-page: 630
  year: 2022
  end-page: 640.e10
  ident: CR51
  article-title: Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2
  publication-title: Cell
  doi: 10.1016/j.cell.2022.01.001
– volume: 103
  start-page: 8577
  year: 1995
  end-page: 8593
  ident: CR99
  article-title: A smooth particle mesh Ewald method
  publication-title: J. Chem. Phys.
  doi: 10.1063/1.470117
– volume: 27
  start-page: 717
  year: 2021
  end-page: 726
  ident: CR8
  article-title: Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies
  publication-title: Nat. Med.
  doi: 10.1038/s41591-021-01294-w
– volume: 375
  start-page: 1048
  year: 2022
  end-page: 1053
  ident: CR61
  article-title: Structures of the Omicron spike trimer with ACE2 and an anti-Omicron antibody
  publication-title: Science
  doi: 10.1126/science.abn8863
– volume: 126
  start-page: 4669
  year: 2022
  end-page: 4678
  ident: CR46
  article-title: SARS-CoV-2 Omicron variant binds to human cells more strongly than the wild type: evidence from molecular dynamics simulation
  publication-title: J. Phys. Chem. B
  doi: 10.1021/acs.jpcb.2c01048
– ident: CR21
– volume: 3
  start-page: 715
  year: 2020
  ident: CR22
  article-title: Targeted intracellular degradation of SARS-CoV-2 via computationally optimized peptide fusions
  publication-title: Commun. Biol.
  doi: 10.1038/s42003-020-01470-7
– volume: 611
  start-page: 213
  year: 2022
  end-page: 214
  ident: CR17
  article-title: COVID ‘variant soup’ is making winter surges hard to predict
  publication-title: Nature
  doi: 10.1038/d41586-022-03445-6
– ident: CR67
– volume: 603
  start-page: 687
  year: 2022
  end-page: 692
  ident: CR84
  article-title: SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamsters
  publication-title: Nature
  doi: 10.1038/s41586-022-04441-6
– volume: 20
  year: 2022
  ident: CR58
  article-title: Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant
  publication-title: BMC Med.
  doi: 10.1186/s12916-022-02312-5
– ident: CR50
– volume: 102
  start-page: 6825
  year: 2005
  end-page: 6830
  ident: CR48
  article-title: Calculation of absolute protein–ligand binding free energy from computer simulations
  publication-title: Proc. Natl Acad. Sci.
  doi: 10.1073/pnas.0409005102
– volume: 185
  start-page: 2116
  year: 2022
  end-page: 2131.e18
  ident: CR93
  article-title: Potent cross-reactive antibodies following Omicron breakthrough in vaccinees
  publication-title: Cell
  doi: 10.1016/j.cell.2022.05.014
– volume: 29
  start-page: 1859
  year: 2008
  end-page: 1865
  ident: CR92
  article-title: CHARMM-GUI: a web-based graphical user interface for CHARMM
  publication-title: J. Comput. Chem.
  doi: 10.1002/jcc.20945
– volume: 20
  start-page: 533
  year: 2020
  end-page: 534
  ident: CR1
  article-title: An interactive web-based dashboard to track COVID-19 in real time
  publication-title: Lancet Infect. Dis.
  doi: 10.1016/S1473-3099(20)30120-1
– ident: CR9
– volume: 113
  start-page: 3048
  year: 2016
  end-page: 3053
  ident: CR71
  article-title: SARS-like WIV1-CoV poised for human emergence
  publication-title: Proc. Natl Acad. Sci.
  doi: 10.1073/pnas.1517719113
– volume: 11
  year: 2020
  ident: CR85
  article-title: Neutralization of SARS-CoV-2 spike pseudotyped virus by recombinant ACE2-Ig
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-020-16048-4
– volume: 604
  start-page: 553
  year: 2022
  end-page: 556
  ident: CR15
  article-title: Antibody evasion properties of SARS-CoV-2 Omicron sublineages
  publication-title: Nature
  doi: 10.1038/s41586-022-04594-4
– volume: 608
  start-page: 603
  year: 2022
  end-page: 608
  ident: CR70
  article-title: Antibody evasion by SARS-CoV-2 Omicron subvariants BA.2.12.1, BA.4 and BA.5
  publication-title: Nature
  doi: 10.1038/s41586-022-05053-w
– volume: 608
  start-page: 593
  year: 2022
  end-page: 602
  ident: CR65
  article-title: BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection
  publication-title: Nature
  doi: 10.1038/s41586-022-04980-y
– volume: 61
  start-page: 4656
  year: 2021
  end-page: 4669
  ident: CR29
  article-title: Computationally designed ACE2 decoy receptor binds SARS-CoV-2 spike (S) protein with tight nanomolar affinity
  publication-title: J. Chem. Inf. Model.
  doi: 10.1021/acs.jcim.1c00783
– volume: 12
  year: 2021
  ident: CR32
  article-title: Engineered ACE2 receptor therapy overcomes mutational escape of SARS-CoV-2
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-021-24013-y
– volume: 119
  start-page: 9478
  year: 2019
  end-page: 9508
  ident: CR43
  article-title: End-point binding free energy calculation with MM/PBSA and MM/GBSA: strategies and applications in drug design
  publication-title: Chem. Rev.
  doi: 10.1021/acs.chemrev.9b00055
– volume: 7
  start-page: eabf1738
  year: 2021
  ident: CR35
  article-title: An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants
  publication-title: Sci. Adv.
  doi: 10.1126/sciadv.abf1738
– volume: 17
  start-page: e1009544
  year: 2021
  ident: CR75
  article-title: Intranasal gene therapy to prevent infection by SARS-CoV-2 variants
  publication-title: PLOS Pathog.
  doi: 10.1371/journal.ppat.1009544
– volume: 14
  start-page: 2187
  year: 2021
  end-page: 2192
  ident: CR5
  article-title: Effect of genomic and amino acid sequence mutation on virulence and therapeutic target of severe acute respiratory syndrome coronavirus-2 (SARS COV-2)
  publication-title: Infect. Drug Resist.
  doi: 10.2147/IDR.S307374
– volume: 55
  start-page: 383
  year: 2004
  end-page: 394
  ident: CR101
  article-title: Exploring protein native states and large-scale conformational changes with a modified generalized born model
  publication-title: Proteins Struct. Funct. Genet.
  doi: 10.1002/prot.20033
– ident: CR14
– volume: 29
  start-page: 1859
  year: 2008
  end-page: 1865
  ident: CR94
  article-title: CHARMM-GUI: a web-based graphical user interface for CHARMM
  publication-title: J. Comput. Chem.
  doi: 10.1002/jcc.20945
– volume: 10
  start-page: 743
  year: 2022
  ident: CR54
  article-title: Increased receptor affinity and reduced recognition by specific antibodies contribute to immune escape of SARS-CoV-2 variant Omicron
  publication-title: Vaccines
  doi: 10.3390/vaccines10050743
– volume: 10
  start-page: e73641
  year: 2021
  ident: CR77
  article-title: Structure-guided glyco-engineering of ACE2 for improved potency as soluble SARS-CoV-2 decoy receptor
  publication-title: Elife
  doi: 10.7554/eLife.73641
– volume: 9
  start-page: 632043
  year: 2021
  ident: CR2
  article-title: Effects of pandemic outbreak on economies: evidence from business history context
  publication-title: Front. Public Heal.
  doi: 10.3389/fpubh.2021.632043
– ident: CR56
– volume: 377
  start-page: 428
  year: 2022
  end-page: 433
  ident: CR83
  article-title: Pathogenicity, transmissibility, and fitness of SARS-CoV-2 Omicron in Syrian hamsters
  publication-title: Science
  doi: 10.1126/science.abn8939
– volume: 7
  start-page: 8
  year: 2022
  ident: CR57
  article-title: SARS-CoV-2 Omicron RBD shows weaker binding affinity than the currently dominant Delta variant to human ACE2
  publication-title: Signal Transduct. Target. Ther.
  doi: 10.1038/s41392-021-00863-2
– volume: 32
  start-page: 593
  year: 2022
  end-page: 595
  ident: CR59
  article-title: Structural insights into the SARS-CoV-2 Omicron RBD-ACE2 interaction
  publication-title: Cell Res.
  doi: 10.1038/s41422-022-00644-8
– volume: 11
  start-page: 778
  year: 2021
  end-page: 784
  ident: CR10
  article-title: Analysis of the Delta variant B.1.617.2 COVID-19
  publication-title: Clin. Pract.
  doi: 10.3390/clinpract11040093
– year: 1998
  ident: CR98
  article-title: Improved convergence in dual-topology free energy calculations through use of harmonic restraints
  publication-title: J. Comput. Chem.
  doi: 10.1002/(SICI)1096-987X(199808)19:11<1278::AID-JCC7>3.0.CO;2-H
– volume: 583
  start-page: 282
  year: 2020
  end-page: 285
  ident: CR72
  article-title: Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins
  publication-title: Nature
  doi: 10.1038/s41586-020-2169-0
– ident: CR90
– volume: 182
  start-page: 1295
  year: 2020
  end-page: 1310.e20
  ident: CR73
  article-title: Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding
  publication-title: Cell
  doi: 10.1016/j.cell.2020.08.012
– ident: CR31
– volume: 14
  start-page: 71
  year: 2016
  end-page: 73
  ident: CR103
  article-title: CHARMM36m: an improved force field for folded and intrinsically disordered proteins
  publication-title: Nat. Methods
  doi: 10.1038/nmeth.4067
– ident: CR34
– volume: 18
  start-page: 5890
  year: 2022
  end-page: 5900
  ident: CR66
  article-title: When the dust has settled: calculation of binding affinities from first principles for SARS-CoV-2 variants with quantitative accuracy
  publication-title: J. Chem. Theory Comput.
  doi: 10.1021/acs.jctc.2c00604
– volume: 596
  start-page: 103
  year: 2021
  end-page: 108
  ident: CR6
  article-title: In vivo monoclonal antibody efficacy against SARS-CoV-2 variant strains
  publication-title: Nature
  doi: 10.1038/s41586-021-03720-y
– volume: 105
  start-page: 9954
  year: 2001
  end-page: 9960
  ident: CR104
  article-title: Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K
  publication-title: J. Phys. Chem. A
  doi: 10.1021/jp003020w
– ident: CR20
– volume: 14
  start-page: 33
  year: 1996
  end-page: 38
  ident: CR100
  article-title: VMD: Visual molecular dynamics
  publication-title: J. Mol. Graph.
  doi: 10.1016/0263-7855(96)00018-5
– ident: 4860_CR90
– volume: 20
  start-page: 533
  year: 2020
  ident: 4860_CR1
  publication-title: Lancet Infect. Dis.
  doi: 10.1016/S1473-3099(20)30120-1
– volume: 32
  start-page: 593
  year: 2022
  ident: 4860_CR59
  publication-title: Cell Res.
  doi: 10.1038/s41422-022-00644-8
– volume: 583
  start-page: 282
  year: 2020
  ident: 4860_CR72
  publication-title: Nature
  doi: 10.1038/s41586-020-2169-0
– volume: 11
  year: 2021
  ident: 4860_CR39
  publication-title: Sci. Rep.
  doi: 10.1038/s41598-021-91809-9
– volume: 26
  start-page: 1668
  year: 2005
  ident: 4860_CR91
  publication-title: J. Comput. Chem.
  doi: 10.1002/jcc.20290
– volume: 18
  start-page: 5890
  year: 2022
  ident: 4860_CR66
  publication-title: J. Chem. Theory Comput.
  doi: 10.1021/acs.jctc.2c00604
– volume: 11
  start-page: 778
  year: 2021
  ident: 4860_CR10
  publication-title: Clin. Pract.
  doi: 10.3390/clinpract11040093
– ident: 4860_CR38
  doi: 10.1101/2022.03.28.486075
– volume: 596
  start-page: 103
  year: 2021
  ident: 4860_CR6
  publication-title: Nature
  doi: 10.1038/s41586-021-03720-y
– volume: 10
  start-page: 449
  year: 2015
  ident: 4860_CR44
  publication-title: Expert Opin. Drug Discov.
  doi: 10.1517/17460441.2015.1032936
– volume: 9
  start-page: 1080964
  year: 2022
  ident: 4860_CR88
  publication-title: Front. Mol. Biosci.
  doi: 10.3389/fmolb.2022.1080964
– volume: 611
  start-page: 213
  year: 2022
  ident: 4860_CR17
  publication-title: Nature
  doi: 10.1038/d41586-022-03445-6
– volume: 14
  start-page: 1188
  year: 2004
  ident: 4860_CR105
  publication-title: Genome Res.
  doi: 10.1101/gr.849004
– volume: 121
  start-page: 422a
  year: 2022
  ident: 4860_CR30
  publication-title: Biophys. J.
  doi: 10.1016/j.bpj.2021.11.664
– volume: 5
  start-page: 3863
  year: 2014
  ident: 4860_CR96
  publication-title: J. Phys. Chem. Lett.
  doi: 10.1021/jz501780a
– volume: 603
  start-page: 706
  year: 2022
  ident: 4860_CR60
  publication-title: Nature
  doi: 10.1038/s41586-022-04474-x
– volume: 8
  start-page: 671633
  year: 2021
  ident: 4860_CR25
  publication-title: Front. Mol. Biosci.
  doi: 10.3389/fmolb.2021.671633
– volume: 3
  start-page: 715
  year: 2020
  ident: 4860_CR22
  publication-title: Commun. Biol.
  doi: 10.1038/s42003-020-01470-7
– ident: 4860_CR9
– volume: 26
  start-page: 1781
  year: 2005
  ident: 4860_CR102
  publication-title: J. Comput. Chem.
  doi: 10.1002/jcc.20289
– volume: 61
  start-page: 2116
  year: 2021
  ident: 4860_CR64
  publication-title: J. Chem. Inf. Model.
  doi: 10.1021/acs.jcim.1c00269
– ident: 4860_CR63
  doi: 10.1021/acs.jpclett.2c01490
– volume: 113
  start-page: 3048
  year: 2016
  ident: 4860_CR71
  publication-title: Proc. Natl Acad. Sci.
  doi: 10.1073/pnas.1517719113
– volume: 7
  start-page: 8
  year: 2022
  ident: 4860_CR57
  publication-title: Signal Transduct. Target. Ther.
  doi: 10.1038/s41392-021-00863-2
– ident: 4860_CR50
  doi: 10.1021/ja9738539
– volume: 608
  start-page: 603
  year: 2022
  ident: 4860_CR70
  publication-title: Nature
  doi: 10.1038/s41586-022-05053-w
– volume: 114
  start-page: 11157
  year: 2017
  ident: 4860_CR19
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.1708727114
– volume: 9
  start-page: 794
  year: 2013
  ident: 4860_CR49
  publication-title: J. Chem. Theory Comput.
  doi: 10.1021/ct3008099
– volume: 122
  start-page: 5389
  year: 2018
  ident: 4860_CR41
  publication-title: J. Phys. Chem. B
  doi: 10.1021/acs.jpcb.7b11367
– volume: 102
  start-page: 6825
  year: 2005
  ident: 4860_CR48
  publication-title: Proc. Natl Acad. Sci.
  doi: 10.1073/pnas.0409005102
– volume: 16
  start-page: 528
  year: 2020
  ident: 4860_CR95
  publication-title: J. Chem. Theory Comput.
  doi: 10.1021/acs.jctc.9b00591
– volume: 596
  start-page: 276
  year: 2021
  ident: 4860_CR11
  publication-title: Nature
  doi: 10.1038/s41586-021-03777-9
– volume: 27
  start-page: 717
  year: 2021
  ident: 4860_CR8
  publication-title: Nat. Med.
  doi: 10.1038/s41591-021-01294-w
– volume: 12
  year: 2021
  ident: 4860_CR32
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-021-24013-y
– ident: 4860_CR16
  doi: 10.1101/2022.09.15.507787
– volume: 608
  start-page: 593
  year: 2022
  ident: 4860_CR65
  publication-title: Nature
  doi: 10.1038/s41586-022-04980-y
– volume: 25
  start-page: 103670
  year: 2022
  ident: 4860_CR81
  publication-title: iScience
  doi: 10.1016/j.isci.2021.103670
– volume: 16
  start-page: 1396
  year: 2020
  ident: 4860_CR45
  publication-title: J. Chem. Theory Comput.
  doi: 10.1021/acs.jctc.9b00725
– volume: 21
  start-page: 1066
  year: 2023
  ident: 4860_CR87
  publication-title: Comput. Struct. Biotechnol. J.
  doi: 10.1016/j.csbj.2023.01.014
– volume: 12
  year: 2021
  ident: 4860_CR47
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-021-21972-0
– volume: 377
  start-page: 420
  year: 2022
  ident: 4860_CR69
  publication-title: Science
  doi: 10.1126/science.abo7896
– volume: 593
  start-page: 130
  year: 2021
  ident: 4860_CR27
  publication-title: Nature
  doi: 10.1038/s41586-021-03398-2
– volume: 185
  start-page: 2116
  year: 2022
  ident: 4860_CR93
  publication-title: Cell
  doi: 10.1016/j.cell.2022.05.014
– ident: 4860_CR68
  doi: 10.1056/NEJMc2206576
– volume: 375
  start-page: 760
  year: 2022
  ident: 4860_CR53
  publication-title: Science
  doi: 10.1126/science.abn7760
– volume: 46
  start-page: 1039
  year: 2013
  ident: 4860_CR42
  publication-title: Acc. Chem. Res.
  doi: 10.1021/ar300087y
– volume: 29
  start-page: 68
  year: 2022
  ident: 4860_CR4
  publication-title: J. Biomed. Sci.
  doi: 10.1186/s12929-022-00852-9
– volume: 13
  year: 2022
  ident: 4860_CR55
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-022-28528-w
– ident: 4860_CR67
  doi: 10.1016/j.cell.2022.06.005
– volume: 222
  start-page: 108634
  year: 2021
  ident: 4860_CR3
  publication-title: Clin. Immunol.
  doi: 10.1016/j.clim.2020.108634
– volume: 10
  start-page: 743
  year: 2022
  ident: 4860_CR54
  publication-title: Vaccines
  doi: 10.3390/vaccines10050743
– volume: 602
  start-page: 664
  year: 2022
  ident: 4860_CR52
  publication-title: Nature
  doi: 10.1038/s41586-021-04386-2
– volume: 17
  start-page: e1010022
  year: 2021
  ident: 4860_CR12
  publication-title: PLOS Pathog.
  doi: 10.1371/journal.ppat.1010022
– volume: 126
  start-page: 4669
  year: 2022
  ident: 4860_CR46
  publication-title: J. Phys. Chem. B
  doi: 10.1021/acs.jpcb.2c01048
– volume: 11
  start-page: e02451
  year: 2020
  ident: 4860_CR23
  publication-title: MBio
  doi: 10.1128/mBio.02451-20
– volume: 64
  start-page: 2375
  year: 1976
  ident: 4860_CR97
  publication-title: J. Chem. Phys.
  doi: 10.1063/1.432526
– volume: 28
  start-page: 490
  year: 2022
  ident: 4860_CR7
  publication-title: Nat. Med.
  doi: 10.1038/s41591-021-01678-y
– volume: 117
  start-page: 28046
  year: 2020
  ident: 4860_CR33
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.2016093117
– volume: 12
  year: 2021
  ident: 4860_CR86
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-021-27097-8
– volume: 14
  start-page: 2187
  year: 2021
  ident: 4860_CR5
  publication-title: Infect. Drug Resist.
  doi: 10.2147/IDR.S307374
– volume: 29
  start-page: 1859
  year: 2008
  ident: 4860_CR92
  publication-title: J. Comput. Chem.
  doi: 10.1002/jcc.20945
– volume: 125
  start-page: 4330
  year: 2021
  ident: 4860_CR28
  publication-title: J. Phys. Chem. B
  doi: 10.1021/acs.jpcb.1c00869
– volume: 17
  start-page: e1009501
  year: 2021
  ident: 4860_CR78
  publication-title: PLOS Pathog.
  doi: 10.1371/journal.ppat.1009501
– volume: 581
  start-page: 215
  year: 2020
  ident: 4860_CR62
  publication-title: Nature
  doi: 10.1038/s41586-020-2180-5
– volume: 11
  start-page: e1004335
  year: 2015
  ident: 4860_CR40
  publication-title: PLOS Comput. Biol.
  doi: 10.1371/journal.pcbi.1004335
– volume: 37
  start-page: 101830
  year: 2020
  ident: 4860_CR18
  publication-title: Travel Med. Infect. Dis.
  doi: 10.1016/j.tmaid.2020.101830
– volume: 375
  start-page: 1048
  year: 2022
  ident: 4860_CR61
  publication-title: Science
  doi: 10.1126/science.abn8863
– volume: 17
  start-page: e1009544
  year: 2021
  ident: 4860_CR75
  publication-title: PLOS Pathog.
  doi: 10.1371/journal.ppat.1009544
– volume: 14
  start-page: 71
  year: 2016
  ident: 4860_CR103
  publication-title: Nat. Methods
  doi: 10.1038/nmeth.4067
– volume: 8
  start-page: eabn4188
  year: 2022
  ident: 4860_CR76
  publication-title: Sci. Adv.
  doi: 10.1126/sciadv.abn4188
– volume: 4
  start-page: 197
  year: 2021
  ident: 4860_CR24
  publication-title: Commun. Biol.
  doi: 10.1038/s42003-021-01736-8
– volume: 11
  year: 2020
  ident: 4860_CR85
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-020-16048-4
– ident: 4860_CR34
  doi: 10.1101/2020.08.12.247940
– volume: 377
  start-page: 428
  year: 2022
  ident: 4860_CR83
  publication-title: Science
  doi: 10.1126/science.abn8939
– volume: 603
  start-page: 687
  year: 2022
  ident: 4860_CR84
  publication-title: Nature
  doi: 10.1038/s41586-022-04441-6
– ident: 4860_CR20
  doi: 10.1126/science.abd9909
– volume: 119
  start-page: 9478
  year: 2019
  ident: 4860_CR43
  publication-title: Chem. Rev.
  doi: 10.1021/acs.chemrev.9b00055
– volume: 105
  start-page: 9954
  year: 2001
  ident: 4860_CR104
  publication-title: J. Phys. Chem. A
  doi: 10.1021/jp003020w
– ident: 4860_CR14
  doi: 10.1101/2022.02.14.480335
– volume: 185
  start-page: 630
  year: 2022
  ident: 4860_CR51
  publication-title: Cell
  doi: 10.1016/j.cell.2022.01.001
– ident: 4860_CR74
  doi: 10.1101/2022.05.21.492554
– ident: 4860_CR36
  doi: 10.1101/2021.12.22.473804
– volume: 31
  start-page: 410
  year: 2021
  ident: 4860_CR89
  publication-title: Glycobiology
  doi: 10.1093/glycob/cwaa101
– volume: 604
  start-page: 553
  year: 2022
  ident: 4860_CR15
  publication-title: Nature
  doi: 10.1038/s41586-022-04594-4
– volume: 10
  start-page: e73641
  year: 2021
  ident: 4860_CR77
  publication-title: Elife
  doi: 10.7554/eLife.73641
– volume: 103
  start-page: 8577
  year: 1995
  ident: 4860_CR99
  publication-title: J. Chem. Phys.
  doi: 10.1063/1.470117
– volume: 9
  start-page: 632043
  year: 2021
  ident: 4860_CR2
  publication-title: Front. Public Heal.
  doi: 10.3389/fpubh.2021.632043
– volume: 14
  start-page: eabn7737
  year: 2022
  ident: 4860_CR13
  publication-title: Sci. Transl. Med.
  doi: 10.1126/scitranslmed.abn7737
– volume: 55
  start-page: 383
  year: 2004
  ident: 4860_CR101
  publication-title: Proteins Struct. Funct. Genet.
  doi: 10.1002/prot.20033
– volume: 61
  start-page: 4656
  year: 2021
  ident: 4860_CR29
  publication-title: J. Chem. Inf. Model.
  doi: 10.1021/acs.jcim.1c00783
– volume: 17
  start-page: e1009328
  year: 2021
  ident: 4860_CR26
  publication-title: PLOS Pathog.
  doi: 10.1371/journal.ppat.1009328
– volume: 6
  start-page: 343
  year: 2021
  ident: 4860_CR79
  publication-title: Signal Transduct. Target. Ther.
  doi: 10.1038/s41392-021-00756-4
– ident: 4860_CR21
  doi: 10.1021/jacs.1c11554
– volume: 7
  start-page: 65
  year: 2021
  ident: 4860_CR82
  publication-title: Cell Discov.
  doi: 10.1038/s41421-021-00302-0
– volume: 20
  year: 2022
  ident: 4860_CR58
  publication-title: BMC Med.
  doi: 10.1186/s12916-022-02312-5
– volume: 7
  start-page: eabf1738
  year: 2021
  ident: 4860_CR35
  publication-title: Sci. Adv.
  doi: 10.1126/sciadv.abf1738
– year: 1998
  ident: 4860_CR98
  publication-title: J. Comput. Chem.
  doi: 10.1002/(SICI)1096-987X(199808)19:11<1278::AID-JCC7>3.0.CO;2-H
– volume: 29
  start-page: 1859
  year: 2008
  ident: 4860_CR94
  publication-title: J. Comput. Chem.
  doi: 10.1002/jcc.20945
– volume: 18
  start-page: 342
  year: 2022
  ident: 4860_CR37
  publication-title: Nat. Chem. Biol.
  doi: 10.1038/s41589-021-00965-6
– ident: 4860_CR31
  doi: 10.1126/science.abc0870
– volume: 182
  start-page: 1295
  year: 2020
  ident: 4860_CR73
  publication-title: Cell
  doi: 10.1016/j.cell.2020.08.012
– volume: 14
  start-page: 33
  year: 1996
  ident: 4860_CR100
  publication-title: J. Mol. Graph.
  doi: 10.1016/0263-7855(96)00018-5
– volume: 14
  start-page: e16109
  year: 2022
  ident: 4860_CR80
  publication-title: EMBO Mol. Med.
  doi: 10.15252/emmm.202216109
– ident: 4860_CR56
  doi: 10.2210/pdb7xnr/pdb
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Snippet SARS-CoV-2, especially B.1.1.529/omicron and its sublineages, continues to mutate to evade monoclonal antibodies and antibodies elicited by vaccination....
Abstract SARS-CoV-2, especially B.1.1.529/omicron and its sublineages, continues to mutate to evade monoclonal antibodies and antibodies elicited by...
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ACE2
Affinity
Angiotensin-converting enzyme 2
Angiotensin-Converting Enzyme 2 - genetics
Angiotensin-Converting Enzyme 2 - therapeutic use
antibodies
Antibodies, Monoclonal
Biology
Biology (General)
Biomedical and Life Sciences
Computer applications
COVID-19
Design
Humans
Life Sciences
Medical Biochemistry
Medical Sciences
Medicine and Health Sciences
monoclonal
Monoclonal antibodies
Protein Engineering
QH301-705.5
SARS-CoV-2
SARS-CoV-2 - genetics
Severe acute respiratory syndrome coronavirus 2
Vaccination
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Title A computationally designed ACE2 decoy has broad efficacy against SARS-CoV-2 omicron variants and related viruses in vitro and in vivo
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https://link.springer.com/article/10.1038/s42003-023-04860-9
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