Computation-aided novel epitope prediction by targeting spike protein's functional dynamics in Omicron

References

[1] Cele S, Jackson L, Khoury D S, et al. Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization. Nature, 2022; 602(7898): 654-656.

[2] Qiao J, Li Y S, Zeng R, et al. SARS-CoV-2 Mpro inhibitors with antiviral activity in a transgenic mouse model. Science, 2021; 371(6536): 1374-1378.

[3] Quan B X, Shuai H, Xia A J, et al. An orally available Mpro inhibitor is effective against wild-type SARS- CoV-2 and variants including Omicron. Nat Microbiol, 2022; 7(5): 716-725.

[4] Nemet I, Kliker L, Lustig Y, et al. Third BNT162b2 vaccination neutralization of SARS-CoV-2 Omicron infection. N Engl J Med, 2022; 386(5): 492-494.

[5] Du X, Tang H, Gao L, et al. Omicron adopts a different strategy from Delta and other variants to adapt to host. Signal Transduct Target Ther, 2022; 7(1): 45.

[6] Zhou T, Tsybovsky Y, Gorman J, et al. Cryo-EM structures of SARS-CoV- 2 spike without and with ACE2 reveal a pH-Dependent switch to mediate endosomal positioning of receptor-binding domains. Cell Host Microbe, 2020; 28(6): 867-879.e5.

[7] Triveri A, Serapian S A, Marchetti F, et al. SARS-CoV-2 spike protein mutations and escape from antibodies: a computational model of epitope loss in variants of concern. J Chem Inf Model, 2021; 61(9): 4687-4700.

[8] Weisblum Y, Schmidt F, Zhang F, et al. Escape from neutralizing antibodies 1 by SARS-CoV-2 spike protein variants. Elife, 2020; 9: e61312.

[9] Wang Y, Wang L, Cao H, et al. SARS-CoV-2 S1 is superior to the RBD as a COVID-19 subunit vaccine antigen. J Med Virol, 2021; (2): 892-898.

[10] Miller N L, Clark T, Raman R, et al. Insights on the mutational landscape of the SARS-CoV-2 Omicron variant receptor-binding domain. Cell Rep Med, 2022; 3(2): 100527.

[11] Nabel K G, Clark S A, Shankar S, et al. Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain. Science, 2022; 375(6578): eabl6251.

[12] Baptista A M, Martel P J, Petersen S B. Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration. Proteins, 1997; 27(4): 523-544.

[13] Zhou Z, Yang Z, Ou J, et al. Temperature dependence of the SARS-CoV-2 affinity to human ACE2 determines COVID-19 progression and clinical outcome. Comput Struct Biotechnol J, 2021; 19: 161-167.

[14] Wei G, Xi W, Nussinov R, et al. Protein ensembles: how does nature harness thermodynamic fluctuations for life? the diverse functional roles of conformational ensembles in the cell. Chem Rev, 2016; 116(11): 6516-6551.

[15] Yao X Q, Hamelberg D. Detecting functional dynamics in proteins with comparative perturbed-ensembles analysis. Acc Chem Res, 2019; 52(12): 3455-3464

[16] Van Wart A T, Durrant J, Votapka L, et al. Weighted implementation of suboptimal paths (WISP): an optimized algorithm and tool for dynamical network analysis. J Chem Theory Comput, 2014; 10(2): 511-517.

[17] Wang P, Casner R G, Nair M S, et al. Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization. Cell Host Microbe, 2021; 29(5): 747-751.e4.

[18] Garrett M E, Galloway J G, Wolf C, et al. Comprehensive characterization of the antibody responses to SARS- CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection. Elife, 2022; 11: e73490.

[19] Serapian S A, Marchetti F, Triveri A, et al. The answer lies in the energy: how simple atomistic molecular dynamics simulations may hold the key to epitope prediction on the fully glycosylated SARS-CoV-2 spike protein. J Phys Chem Lett, 2020; 11(19): 8084-8093.

[20] Crooke S N, Ovsyannikova I G, Kennedy R B, et al. Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome. Sci Rep, 2020; 10(1): 14179.