| CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY |
|
|
|
|
Molecular Insights into Striking Antibody Evasion of SARS-CoV-2 Omicron Variant |
| Zeng-Shuai Yan1, Yao Xu1, Hong-Ming Ding2*, and Yu-Qiang Ma1* |
1National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
2Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
|
|
| Cite this article: |
|
Zeng-Shuai Yan, Yao Xu, Hong-Ming Ding et al 2022 Chin. Phys. Lett. 39 108701 |
|
|
|
|
Abstract The SARS-CoV-2 Omicron variant has become the dominant variant in the world. Uncovering the structural basis of altered immune response and enhanced transmission of Omicron is particularly important. Here, taking twenty-five antibodies from four groups as examples, we comprehensively reveal the underlying mechanism of how mutations in Omicron induces the weak neutralization by using molecular simulations. Overall, the binding strength of 68% antibodies is weakened in Omicron, much larger than that in Delta (40%). Specifically, the percentage of the weakened antibodies vary largely in different groups. Moreover, the mutation-induced repulsion is mainly responsive for the weak neutralization in AB/CD groups but does not take effect in EF group. Significantly, we demonstrate that the disappearance of hydrophobic interaction and salt bridges due to residue deletions contributes to the decreased binding energy in NTD group. This work provides unprecedented atomistic details for the distinct neutralization of WT/Delta/Omicron, which informs prospective efforts to design antibodies/vaccines against Omicron.
|
|
|
Received: 19 July 2022
Published: 16 September 2022
|
|
| PACS: |
87.15.A-
|
(Theory, modeling, and computer simulation)
|
| |
87.15.ap
|
(Molecular dynamics simulation)
|
| |
87.15.km
|
(Protein-protein interactions)
|
| |
87.15.hg
|
(Dynamics of intermolecular interactions)
|
|
|
|
|
|
| [1] | Manfredonia I, Nithin C, Ponce-Salvatierra A, Ghosh P, Wirecki T K, Marinus T, Ogando N S, Snijder E J, van Hemert M J, and Bujnicki J M 2020 Nucl. Acids Res. 48 12436 |
| [2] | https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern |
| [3] | https://www.who.int/publications/m/item/enhancing-readiness-for-omicron-(b.1.1.529)-technical-brief-and-priority-actions-for-member-states |
| [4] | Grabowski F, Kochańczyk M, and Lipniacki T 2022 Viruses 14 294 |
| [5] | Karim S S A and Karim Q A 2021 Lancet 398 2126 |
| [6] | Hui K P, Ho J C, Cheung M C, Ng K C, Ching R H, Lai K L, Kam T T, Gu H G, Sit K Y, and Hsin M K 2022 Nature 603 715 |
| [7] | Meng B, Abdullahi A, Ferreira I A, Goonawardane N, Saito A, Kimura I, Yamasoba D, Gerber P P, Fatihi S, and Rathore S 2022 Nature 603 706 |
| [8] | Liu Y, Liu J Y, Johnson B A, Xia H J, Ku Z Q, Schindewolf C, Widen S G, An Z Q, Weaver S C, and Menachery V D 2022 Cell Rep. 39 110829 |
| [9] | Naveca F G, Nascimento V, Souza V, Corado A D L, Nascimento F, Silva G, Mejía M C, Brandão M J, Á C, and Duarte D 2022 Microbiol. Spectrum 10 e02366-21 |
| [10] | Song J S, Lee J, Kim M, Jeong H S, Kim M S, Kim S G, Yoo H N, Lee J J, Lee H Y, and Lee S E 2022 Emerging Infect. Dis. 28 756 |
| [11] | Ren S Y, Wang W B, Gao R D, and Zhou A M 2022 World J. Clin. Cases 10 1 |
| [12] | Araf Y, Akter F, Tang Y D, Fatemi R, Parvez S A, Zheng C, and Hossain G 2022 J. Med. Virol. 94 1825 |
| [13] | Zhang L, Li Q Q, Liang Z T, Li T, Liu S, Cui Q Q, Nie J H, Wu Q, Qu X W, and Huang W J 2022 Emerging Microbes Infect. 11 1 |
| [14] | Hu J, Peng P, Cao X X, Wu K, Chen J, Wang K, Tang N, and Huang A L 2022 Cell. & Mol. Immunol. 19 293 |
| [15] | Sun C, Kang Y F, Liu Y T, Kong X W, Xu H Q, Xiong D, Xie C, Liu Y H, Peng S, and Feng G K 2022 Signal Transduct. Target. Ther. 7 42 |
| [16] | Zhang X T, Wu S J, Wu B L, Yang Q R, Chen A, Li Y Z, Zhang Y W, Pan T, Zhang H, and He X 2021 Signal Transduct. Target. Ther. 6 430 |
| [17] | Carreño J M, Alshammary H, Tcheou J, Singh G, Raskin A J, Kawabata H, Sominsky L A, Clark J J, Adelsberg D C, and Bielak D A 2022 Nature 602 682 |
| [18] | Dejnirattisai W, Shaw R H, Supasa P, Liu C, Stuart A S, Pollard A J, Liu X X, Lambe T, Crook D, and Stuart D I 2022 Lancet 399 234 |
| [19] | Cameroni E, Bowen J E, Rosen L E, Saliba C, Zepeda S K, Culap K, Pinto D, VanBlargan L A, De Marco A, and di Iulio J 2022 Nature 602 664 |
| [20] | Cao Y L, Wang J, Jian F C, Xiao T H, Song W L, Yisimayi A, Huang W J, Li Q G, Wang P, and An R 2022 Nature 602 657 |
| [21] | Dejnirattisai W, Huo J D, Zhou D, Zahradník J, Supasa P, Liu C, Duyvesteyn H M, Ginn H M, Mentzer A J, and Tuekprakhon A 2022 Cell 185 467 |
| [22] | Planas D, Saunders N, Maes P, Guivel-Benhassine F, Planchais C, Buchrieser J, Bolland W H, Porrot F, Staropoli I, and Lemoine F 2022 Nature 602 671 |
| [23] | Liu L, Iketani S, Guo Y C, Chan J F W, Wang M, Liu L Y, Luo Y, Chu H, Huang Y M, and Nair M S 2022 Nature 602 676 |
| [24] | McCallum M, Czudnochowski N, Rosen L E, Zepeda S K, Bowen J E, Walls A C, Hauser K, Joshi A, Stewart C, and Dillen J R 2022 Science 375 864 |
| [25] | Yin W C, Xu Y W, Xu P Y, Cao X D, Wu C R, Gu C Y, He X H, Wang X X, Huang S J, and Yuan Q N 2022 Science 375 1048 |
| [26] | Lin S, Chen Z M, Zhang X D, Wen A, Yuan X, Yu C Z, Yang J, He B, Cao Y, and Lu G 2022 Signal Transduct. Target. Ther. 7 56 |
| [27] | Han P C, Li L J, Liu S, Wang Q S, Zhang D, Xu Z P, Han P, Li X M, Peng Q, and Su C 2022 Cell 185 630 |
| [28] | Wu L Y, Zhou L P, Mo M X, Liu T T, Wu C K, Gong C Y, Lu K, Gong L K, Zhu W L, and Xu Z J 2022 Signal Transduct. Target. Ther. 7 8 |
| [29] | Ye G, Liu B, and Li F 2022 Nat. Commun. 13 1214 |
| [30] | Omotuyi I, Afolabi E, Oyinloye B, Fatumo S, Femi-Oyewo M, and Bogoro S 2022 Comput. Biol. Med. 142 105226 |
| [31] | Rath S L, Padhi A K, and Mandal N 2022 Biochem. Biophys. Res. Commun. 592 18 |
| [32] | Lan J, He X H, Ren Y F, Wang Z Y, Zhou H, Fan S L, Zhu C Y, Liu D S, Shao B, and Liu T Y 2022 Cell Res. 32 593 |
| [33] | Lupala C S, Ye Y J, Chen H, Su X D, and Liu H G 2022 Biochem. Biophys. Res. Commun. 590 34 |
| [34] | Jawaid M Z, Baidya A, Mahboubi-Ardakani R, Davis R L, and Cox D L 2021 bioRxiv:10.1101/2021.12.14.472704 |
| [35] | Verma J and Subbarao N 2022 bioRxiv:2022.01.25.477671 |
| [36] | Webb B and Sali A 2016 Curr. Protoc. Bioinf. 54 5.6.1 |
| [37] | Jorgensen W L and Madura J D 1983 J. Am. Chem. Soc. 105 1407 |
| [38] | Berendsen H J, Postma J V, Van Gunsteren W F, DiNola A, and Haak J R 1984 J. Chem. Phys. 81 3684 |
| [39] | Venken T, Krnavek D, Münch J, Kirchhoff F, Henklein P, De Maeyer M, and Voet A 2011 Proteins: Struct. Funct. Bioinf. 79 3221 |
| [40] | Ding H M, Yin Y W, Sheng Y J, and Ma Y Q 2021 Chin. Phys. Lett. 38 018701 |
| [41] | Ulmschneider M B, Bagnéris C, McCusker E C, DeCaen P G, Delling M, Clapham D E, Ulmschneider J P, and Wallace B A 2013 Proc. Natl. Acad. Sci. USA 110 6364 |
| [42] | Raval A, Piana S, Eastwood M P, Dror R O, and Shaw D E 2012 Proteins: Struct. Funct. Bioinf. 80 2071 |
| [43] | Mirjalili V and Feig M 2013 J. Chem. Theory Comput. 9 1294 |
| [44] | Abraham M J, Murtola T, Schulz R, Páll S, Smith J C, Hess B, and Lindahl E 2015 SoftwareX 1–2 19 |
| [45] | Maier J A, Martinez C, Kasavajhala K, Wickstrom L, Hauser K E, and Simmerling C 2015 J. Chem. Theory Comput. 11 3696 |
| [46] | Sheng Y J, Yin Y W, Ma Y Q, and Ding H M 2021 J. Chem. Inf. Model. 61 2454 |
| [47] | Essmann U, Perera L, Berkowitz M L, Darden T, Lee H, and Pedersen L G 1995 J. Chem. Phys. 103 8577 |
| [48] | Hess B, Bekker H, Berendsen H J, and Fraaije J G 1997 J. Comput. Chem. 18 1463 |
| [49] | Wang E C, Sun H Y, Wang J M, Wang Z, Liu H, Zhang J Z, and Hou T J 2019 Chem. Rev. 119 9478 |
| [50] | Sun Z X, Yan Y N, Yang M Y, and Zhang J Z 2017 J. Chem. Phys. 146 124124 |
| [51] | Duan L L, Liu X, and Zhang J Z 2016 J. Am. Chem. Soc. 138 5722 |
| [52] | Yin Y W, Sheng Y J, Wang M, Ma Y Q, and Ding H M 2021 Nanoscale 13 12865 |
| [53] | Meenan N A, Sharma A, Fleishman S J, MacDonald C J, Morel B, Boetzel R, Moore G R, Baker D, and Kleanthous C 2010 Proc. Natl. Acad. Sci. USA 107 10080 |
| [54] | Giollo M, Martin A J, Walsh I, Ferrari C, and Tosatto S C 2014 BMC Genomics 15 S7 |
| [55] | Xu J, Gao L, Liang H, and Chen S D 2021 Nutrition 82 111049 |
| [56] | Genheden S 2011 J. Comput.-Aided Mol. Des. 25 1085 |
| [57] | Weis A, Katebzadeh K, Söderhjelm P, Nilsson I, and Ryde U 2006 J. Med. Chem. 49 6596 |
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
