Comparison of the unbinding process of RBD-ACE2 complex between SARS-CoV-2 variants (Delta, delta plus, and Lambda): A steered molecular dynamics simulation

References

• Huynh T, Wang H, Cornell W, et al. In Silico Exploration of Repurposing and Optimizing Traditional Chinese Medicine Rutin for Possibly Inhibiting SARS-CoV-2’s Main Protease. J.Phys.Chem.Lett. 2020;11:4413–4420. https://doi.org/10.26434/chemrxiv.12281078.
   PubMed Web of Science ®Google Scholar
• Nami B, Ghanaeian A, Ghanaeian K, et al. The interaction of the severe acute respiratory syndrome coronavirus 2 spike protein with drug-inhibited angiotensin converting enzyme 2 studied by molecular dynamics simulation. J Hypertens. 2021;39:1705–1716. https://doi.org/10.1097/HJH.0000000000002829.
   PubMed Web of Science ®Google Scholar
• Ngo ST, Quynh Anh Pham N, Thi Le L, et al. Computational Determination of Potential Inhibitors of SARS-CoV-2 Main Protease. J. Chem. Inf. Model. 2020;60:5771–5780. https://doi.org/10.1021/acs.jcim.0c00491.
   PubMed Web of Science ®Google Scholar
• Gamakaranage CSK, Hettiarachchi D, Ediriweera D, et al. Symptomatology of Coronavirus Disease 2019 (COVID-19) - Lessons from A Meta-Analysis Across 13 Countries. ChemRxiv. 2020 https://doi.org/10.21203/rs.3.rs-39412.
   Google Scholar
• Abdelhafiz AS, Mohammed Z, Ibrahim ME, et al. Knowledge, Perceptions, and Attitude of Egyptians Towards the Novel Coronavirus Disease (COVID-19). J. Community Health. 2020;45:881–890. https://doi.org/10.1007/s10900-020-00827-7.
   PubMed Web of Science ®Google Scholar
• Paderno A, Schreiber A, Grammatica A, et al. Smell and taste alterations in COVID-19: a cross-sectional analysis of different cohorts. Int. Forum Allergy Rhinol. 2020;10:955–962. https://doi.org/10.1002/alr.22610.
   PubMed Web of Science ®Google Scholar
• Gioia M, Ciaccio C, Calligari P, et al. Role of proteolytic enzymes in the COVID-19 infection and promising therapeutic approaches. Biochem. Pharmacol. 2020;182:114225, https://doi.org/10.1016/j.bcp.2020.114225.
   PubMed Web of Science ®Google Scholar
• Gur M, Taka E, Yilmaz SZ, et al. Conformational transition of SARS-CoV-2 spike glycoprotein between its closed and open states. J Chem Phys. 2020;153:075101, https://doi.org/10.1063/5.0011141.
   PubMed Web of Science ®Google Scholar
• Nguyen HL, Lan PD, Thai NQ, et al. Does SARS-CoV-2 Bind to Human ACE2 Stronger Than SARS-CoV ? Phys. Chem. 2020;124:7336–7347. https://doi.org/10.1021/acs.jpcb.0c04511.
   PubMed Web of Science ®Google Scholar
• Qiao B, De La Cruz MO. Enhanced binding of SARS-CoV-2 spike protein to receptor by distal polybasic cleavage sites. ACS Nano. 2020;14:10616–10623. https://doi.org/10.1021/acsnano.0c04798.
   PubMed Web of Science ®Google Scholar
• Banerjee AK, Ray U. Mutation hot spots in Spike protein of COVID-19 virus: Mutation in spike protein. Proc. Indian Natl. Sci. Acad. 2020;86:1–10. https://doi.org/10.16943/ptinsa/2020/155490.
   Google Scholar
• Ou J, Zhou Z, Dai R, et al. V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Virol. 2021;95:e00617–21. https://doi.org/10.1128/JVI.00617-21.
   Web of Science ®Google Scholar
• Becerra-Flores M, Cardozo T. SARS-CoV-2 viral spike G614 mutation exhibits higher case fatality rate. Int. J. Clin. Pract. 2020;74:13525, https://doi.org/10.1111/ijcp.13525.
   PubMed Web of Science ®Google Scholar
• Saha P, Majumder R, Chakraborty S, et al. Mutations in Spike protein of SARS-CoV-2 modulate receptor binding, membrane fusion and immunogenicity: an insight into viral tropism and pathogenesis of COVID-19. ChemRxiv. 2020 https://doi.org/10.26434/chemrxiv.12320567.v1.
   Google Scholar
• Zhang L, Jackson CB, Mou H, et al. The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. bioRxiv [Preprint]. 2020;11:6013, https://doi.org/10.1101/2020.06.12.148726.
   Google Scholar
• Ferreira I, Datir R, Papa G, et al. SARS-CoV-2 B.1.617 emergence and sensitivity to vaccine-elicited antibodies. bioRxiv. 2021. https://doi.org/10.1101/2021.05.08.443253.
   Google Scholar
• Hetemäki I, Kääriäinen S, Alho P, et al. An outbreak caused by the SARS-CoV-2 Delta variant (B. 1. 617. 2) in a secondary care hospital in Finland, May. Eurosurveillance. 2021;26:1–6. https://doi.org/10.2807/1560-7917.ES.2021.26.30.2100636.
   Web of Science ®Google Scholar
• Alizon S, Haim-boukobza S, Foulongne V, et al. Rapid spread of the SARS-CoV-2 Delta variant in some. Eurosurveillance. 2021;26:1–5. https://doi.org/10.2807/1560-7917.ES.2021.26.28.2100573.
   Web of Science ®Google Scholar
• Cherian S, Potdar V, Jadhav S, et al. SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R in the Second Wave of COVID-19 in Maharashtra, India. Microorganisms. 2021;2:1–11. https://doi.org/10.3390/microorganisms9071542.
   Google Scholar
• Planas D, Veyer D, Baidaliuk A, et al. Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature. 2021;596:276–280. https://doi.org/10.1038/s41586-021-03777-9.
   PubMed Web of Science ®Google Scholar
• Kannan SR, Spratt AN, Cohen AR, et al. Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Autoimmunity. 2021;124:1–5. https://doi.org/10.1016/j.jaut.2021.102715.
   Web of Science ®Google Scholar
• Pascarella S, Ciccozzi M, Bianchi M, et al. Shortening epitopes to survive: The case of sars-cov-2 lambda variant. Biomolecules. 2021;11:1–9. https://doi.org/10.3390/biom11101494.
   Web of Science ®Google Scholar
• Tian D, Sun YH, Zhou JM, et al. The global epidemic of SARS-CoV-2 variants and their mutational immune escape. J. Med. Virol. 2021;94:847–857. https://doi.org/10.1002/jmv.27376.
   PubMed Web of Science ®Google Scholar
• Baisheng Li JL, Deng A, Li K, et al. Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant. Med Rxiv. 2021;13:1–9. https://doi.org/10.1101/2021.07.07.21260122.
   Google Scholar
• Kim S, Liu Y, Lei Z, et al. Differential Interactions Between Human ACE2 and Spike RBD of SARS- CoV-2 Variants of Concern. bioRxiv. 2021;17:7972–7979. https://doi.org/10.1101/2021.07.23.453598.
   Google Scholar
• Kumar V, Singh J, Hasnain SE, et al. Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. Mol. Sci. 2021;22:1–12. https://doi.org/10.3390/ijms22179131.
   Web of Science ®Google Scholar
• Antony P, Vijayan R. Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B. 1. 617 Variant. Biomolecules. 2021;11:1–10. https://doi.org/10.3390/biom11081244.
   Web of Science ®Google Scholar
• Baral P, Bhattarai N, Hossen L, et al. Biochemical and Biophysical Research Communications Mutation-induced changes in the receptor-binding interface of the SARS-CoV-2 Delta variant B. 1. 617. 2 and implications for immune evasion. Biochem. Biophys. Res. Commun. 2021;574:14–19. https://doi.org/10.1016/j.bbrc.2021.08.036.
   PubMed Web of Science ®Google Scholar
• Upadhyay S, Kumar A, Kumar P, et al. Delta plus variant with neutral mutation is less virulent compared to wild type SARS-CoV2. Res. Sq. 2021;22:9131, https://doi.org/10.21203/rs.3.rs-805496.
   Google Scholar
• Ngo ST, Hung HM, Nguyen MT. Fast and accurate determination of the relative binding affinities of small compounds to HIV-1 protease using non-equilibrium work. J. Comput. Chem. 2016;37:2734–2742. https://doi.org/10.1002/jcc.24502.
   PubMed Web of Science ®Google Scholar