Unbinding of hACE2 and inhibitors from the receptor binding domain of SARS-CoV-2 spike protein

References

• Ali, A., & Vijayan, R. (2020). Dynamics of the ACE2-SARS-CoV-2/SARS-CoV spike protein interface reveal unique mechanisms. Scientific Reports, 10(1), 14214. https://doi.org/10.1038/s41598-020-71188-3
   PubMed Web of Science ®Google Scholar
• Anandakrishnan, R., Aguilar, B., & Onufriev, A. V. (2012). H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Research, 40(Web Server issue), W537–W541. https://doi.org/10.1093/nar/gks375
   PubMed Web of Science ®Google Scholar
• Arya, R., Kumari, S., Pandey, B., Mistry, H., Bihani, S. C., Das, A., Prashar, V., Gupta, G. D., Panicker, L., & Kumar, M. (2021). Structural insights into SARS-CoV-2 proteins. Journal of Molecular Biology, 433(2), 166725. https://doi.org/10.1016/j.jmb.2020.11.024
   PubMed Web of Science ®Google Scholar
• Bai, C., & Warshel, A. (2020). Critical differences between the binding features of the spike proteins of SARS-CoV-2 and SARS-CoV. The Journal of Physical Chemistry. B, 124(28), 5907–5912. https://doi.org/10.1021/acs.jpcb.0c04317
   PubMed Web of Science ®Google Scholar
• Barducci, A., Bussi, G., & Parrinello, M. (2008). Well-tempered metadynamics: A smoothly converging and tunable free-energy method. Physical Review Letters, 100(2), 020603. https://doi.org/10.1103/PhysRevLett.100.020603
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• Bodier-Montagutelli, E., Mayor, A., Vecellio, L., Respaud, R., & Heuzé-Vourc'h, N. (2018). Designing inhaled protein therapeutics for topical lung delivery: what are the next steps? Expert Opinion on Drug Delivery, 15(8), 729–736. https://doi.org/10.1080/17425247.2018.1503251
   PubMed Web of Science ®Google Scholar
• Bonomi, M., Branduardi, D., Bussi, G., Camilloni, C., Provasi, D., Raiteri, P., Donadio, D., Marinelli, F., Pietrucci, F., Broglia, R. A., & Parrinello, M. (2009). PLUMED: A portable plugin for free-energy calculations with molecular dynamics. Computer Physics Communications, 180(10), 1961–1972. https://doi.org/10.1016/j.cpc.2009.05.011
   Web of Science ®Google Scholar
• Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. The Journal of Chemical Physics, 126(1), 014101. https://doi.org/10.1063/1.2408420
   PubMed Web of Science ®Google Scholar
• Cao, Y., Su, B., Guo, X., Sun, W., Deng, Y., Bao, L., Zhu, Q., Zhang, X., Zheng, Y., Geng, C., Chai, X., He, R., Li, X., Lv, Q., Zhu, H., Deng, W., Xu, Y., Wang, Y., Qiao, L., … Xie, X. S. (2020). Potent neutralizing antibodies against SARS-CoV-2 identified by high-throughput single-cell sequencing of convalescent patients' B cells. Cell, 182(1), 73–84. https://doi.org/10.1016/j.cell.2020.05.025
   PubMed Web of Science ®Google Scholar
• Casalino, L., Gaieb, Z., Goldsmith, J. A., Hjorth, C. K., Dommer, A. C., Harbison, A. M., Fogarty, C. A., Barros, E. P., Taylor, B. C., McLellan, J. S., Fadda, E., & Amaro, R. E. (2020). Beyond shielding: The roles of glycans in the SARS-CoV-2 spike protein. ACS Central Science, 6(10), 1722–1734. https://doi.org/10.1021/acscentsci.0c01056
   PubMed Web of Science ®Google Scholar
• Chan, J. F.-W., Yuan, S., Kok, K.-H., To, K. K.-W., Chu, H., Yang, J., Xing, F., Liu, J., Yip, C. C.-Y., Poon, R. W.-S., Tsoi, H.-W., Lo, S. K.-F., Chan, K.-H., Poon, V. K.-M., Chan, W.-M., Ip, J. D., Cai, J.-P., Cheng, V. C.-C., Chen, H., Hui, C. K.-M., & Yuen, K.-Y. (2020). A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: A study of a family cluster. The Lancet, 395(10223), 514–523. https://doi.org/10.1016/S0140-6736(20)30154-9
   PubMed Web of Science ®Google Scholar
• Chen, Q., Allot, A., & Lu, Z. (2021). LitCovid: An open database of COVID-19 literature. Nucleic Acids Research, 49(D1), D1534–D1540. https://doi.org/10.1093/nar/gkaa952
   PubMed Web of Science ®Google Scholar
• Chen, R. E., Zhang, X., Case, J. B., Winkler, E. S., Liu, Y., VanBlargan, L. A., Liu, J., Errico, J. M., Xie, X., Suryadevara, N., Gilchuk, P., Zost, S. J., Tahan, S., Droit, L., Turner, J. S., Kim, W., Schmitz, A. J., Thapa, M., Wang, D., … Diamond, M. S. (2021). Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Nature Medicine, 27(4), 717–726. https://doi.org/10.1038/s41591-021-01294-w
   PubMed Web of Science ®Google Scholar
• Chowdhury, S. M., Talukder, S. A., Khan, A. M., Afrin, N., Ali, M. A., Islam, R., Parves, R., Al Mamun, A., Sufian, M. A., Hossain, M. N., Hossain, M. A., & Halim, M. A. (2020). Antiviral peptides as promising therapeutics against SARS-CoV-2. The Journal of Physical Chemistry B, 124(44), 9785–9792. https://doi.org/10.1021/acs.jpcb.0c05621
   PubMed Web of Science ®Google Scholar
• Constantinos Kurt, W., Frances, A., Tandile, H., Mashudu, M., Prudence, K., Brent, O., Bronwen, E. L., Tulio de, O., Marion, V., Karin van der, B., Theresa, R., Michael, B., Veronica, U., Susan, M., Anne von, G., Cheryl, C., Lynn, M., Jinal, N. B., & Penny, L. M. (2021) . SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma. Nature Medicine, 27, 622–625.
   Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• DeFrancesco, L. (2020). COVID-19 antibodies on trial. Nature Biotechnology, 38(11), 1242–1252. https://doi.org/10.1038/s41587-020-0732-8
   PubMed Web of Science ®Google Scholar
• Donoghue, M., Wakimoto, H., Maguire, C. T., Acton, S., Hales, P., Stagliano, N., Fairchild-Huntress, V., Xu, J., Lorenz, J. N., Kadambi, V., Berul, C. I., & Breitbart, R. E. (2003). Heart block, ventricular tachycardia, and sudden death in ACE2 transgenic mice with downregulated connexins. Journal of Molecular and Cellular Cardiology, 35(9), 1043–1053. https://doi.org/10.1016/S0022-2828(03)00177-9
   PubMed Web of Science ®Google Scholar
• Du, L., He, Y., Zhou, Y., Liu, S., Zheng, B.-J., & Jiang, S. (2009). The spike protein of SARS-CoV-a target for vaccine and therapeutic development. Nature Reviews. Microbiology, 7(3), 226–236. https://doi.org/10.1038/nrmicro2090
   PubMed Web of Science ®Google Scholar
• Duan, K., Liu, B., Li, C., Zhang, H., Yu, T., Qu, J., Zhou, M., Chen, L., Meng, S., Hu, Y., Peng, C., Yuan, M., Huang, J., Wang, Z., Yu, J., Gao, X., Wang, D., Yu, X., Li, L., … Yang, X. (2020). Effectiveness of convalescent plasma therapy in severe COVID-19 patients. Proceedings of the National Academy of Sciences of the United States of America, 117(17), 9490–9496. https://doi.org/10.1073/pnas.2004168117
   PubMed Web of Science ®Google Scholar
• Eastman, P., Swails, J., Chodera, J. D., McGibbon, R. T., Zhao, Y., Beauchamp, K. A., Wang, L.-P., Simmonett, A. C., Harrigan, M. P., Stern, C. D., Wiewiora, R. P., Brooks, B. R., & Pande, V. S. (2017). OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLoS Computational Biology, 13(7), e1005659. https://doi.org/10.1371/journal.pcbi.1005659
   PubMed Web of Science ®Google Scholar
• Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/10.1063/1.470117
   Web of Science ®Google Scholar
• Forni, G., Mantovani, A., Forni, G., Mantovani, A., Moretta, L., Rappuoli, R., Rezza, G., Bagnasco, A., Barsacchi, G., Bussolati, G., Cacciari, M., Cappuccinelli, P., Cheli, E., Guarini, R., Bacci, M. L., Mancini, M., Marcuzzo, C., Morrone, M. C., Parisi, G., … COVID-19 Commission of Accademia Nazionale dei Lincei, Rome. (2021). COVID-19 vaccines: Where we stand and challenges ahead. Cell Death and Differentiation, 28(2), 626–639.
   PubMed Web of Science ®Google Scholar
• Garber, K. (2021). Hunt for improved monoclonals against coronavirus gathers pace. Nature Biotechnology, 39(1), 9–12. https://doi.org/10.1038/s41587-020-00791-6
   PubMed Web of Science ®Google Scholar
• García-Iriepa, C., Hognon, C., Francés-Monerris, A., Iriepa, I., Miclot, T., Barone, G., Monari, A., & Marazzi, M. (2020). Thermodynamics of the interaction between the spike protein of severe acute respiratory syndrome coronavirus-2 and the receptor of human angiotensin-converting enzyme 2. Effects of possible ligands. The Journal of Physical Chemistry Letters, 11(21), 9272–9281. https://doi.org/10.1021/acs.jpclett.0c02203
   PubMed Web of Science ®Google Scholar
• Gervasio, F. L., Laio, A., & Parrinello, M. (2005). Flexible docking in solution using metadynamics. Journal of the American Chemical Society, 127(8), 2600–2607. https://doi.org/10.1021/ja0445950
   PubMed Web of Science ®Google Scholar
• Ghorbani, M., Brooks, B. R., & Klauda, J. B. (2020). Critical sequence hotspots for binding of novel coronavirus to angiotensin converter enzyme as evaluated by molecular simulations. The Journal of Physical Chemistry. B, 124(45), 10034–10047. https://doi.org/10.1021/acs.jpcb.0c05994
   PubMed Web of Science ®Google Scholar
• Glasgow, A., Glasgow, J., Limonta, D., Solomon, P., Lui, I., Zhang, Y., Nix, M. A., Rettko, N. J., Zha, S., Yamin, R., Kao, K., Rosenberg, O. S., Ravetch, J. V., Wiita, A. P., Leung, K. K., Lim, S. A., Zhou, X. X., Hobman, T. C., Kortemme, T., & Wells, J. A. (2020). Engineered ACE2 receptor traps potently neutralize SARS-CoV-2. Proceedings of the National Academy of Sciences of the United States of America, 117(45), 28046–28055. https://doi.org/10.1073/pnas.2016093117
   PubMed Web of Science ®Google Scholar
• Han, Y., & Král, P. (2020). Computational design of ACE2-based peptide inhibitors of SARS-CoV-2. ACS Nano, 14(4), 5143–5147. https://doi.org/10.1021/acsnano.0c02857
   PubMed Web of Science ®Google Scholar
• Hanke, L., Vidakovics Perez, L., Sheward, D. J., Das, H., Schulte, T., Moliner-Morro, A., Corcoran, M., Achour, A., Karlsson Hedestam, G. B., Hällberg, B. M., Murrell, B., & McInerney, G. M. (2020). An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction. Nature Communications, 11(1), 4420. https://doi.org/10.1038/s41467-020-18174-5
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen Herman, J. C., & Fraaije Johannes, G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
   Web of Science ®Google Scholar
• Jiang, S., Zhang, X., Yang, Y., Hotez, P. J., & Du, L. (2020). Neutralizing antibodies for the treatment of COVID-19. Nature Biomedical Engineering, 4(12), 1134–1139. https://doi.org/10.1038/s41551-020-00660-2
   PubMed Web of Science ®Google Scholar
• Jianliang, X., Kai, X., Seolkyoung, J., Andrea, C., Jenna, L., Frauke, M., Julio Cesar Cetrulo, L., Solji, P., Fabian, S., Zijun, W., Yaoxing, H., Yang, L., Manoj, N., Pengfei, W., Jonathan, E. S., Lino, T., Tatsiana, B., Gwo-Yu, C., Adam, S. O., … Rafael, C. (2021). Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. Nature, 595, 278–282. https://doi.org/10.1038/s41586-021-03676-z.
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., & Jenson, C. (1998). Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density. Journal of Computational Chemistry, 19(10), 1179–1186. https://doi.org/10.1002/(SICI)1096-987X(19980730)19:10<1179::AID-JCC6>3.0.CO;2-J
   Web of Science ®Google Scholar
• Ju, B., Zhang, Q., Ge, J., Wang, R., Sun, J., Ge, X., Yu, J., Shan, S., Zhou, B., Song, S., Tang, X., Yu, J., Lan, J., Yuan, J., Wang, H., Zhao, J., Zhang, S., Wang, Y., Shi, X., … Zhang, L. (2020). Human neutralizing antibodies elicited by SARS-CoV-2 infection. Nature, 584(7819), 115–119. https://doi.org/10.1038/s41586-020-2380-z
   PubMed Web of Science ®Google Scholar
• Khan, A., Zia, T., Suleman, M., Khan, T., Ali, S. S., Abbasi, A. A., Mohammad, A., & Wei, D.-Q. (2021). Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Journal of Cellular Physiology, 236(10), 7045–7013. https://doi.org/10.1002/jcp.30367
   PubMed Web of Science ®Google Scholar
• Kumawat, A., Namsani, S., Pramanik, D., Roy, S., & Singh, J. K. (2021). Integrated docking and enhanced sampling-based selection of repurposing drugs for SARS-CoV-2 by targeting host dependent factors. Journal of Biomolecular Structure and Dynamics, 1–12. https://doi.org/10.1080/07391102.2021.1937319
   Google Scholar
• Lan, J., Ge, J., Yu, J., Shan, S., Zhou, H., Fan, S., Zhang, Q., Shi, X., Wang, Q., Zhang, L., & Wang, X. (2020). Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature, 581(7807), 215–220. https://doi.org/10.1038/s41586-020-2180-5
   PubMed Web of Science ®Google Scholar
• Laurini, E., Marson, D., Aulic, S., Fermeglia, A., & Pricl, S. (2021). Computational mutagenesis at the SARS-CoV-2 spike protein/angiotensin-converting enzyme 2 binding interface: Comparison with experimental evidence. ACS Nano, 15(4), 6929–6948. https://doi.org/10.1021/acsnano.0c10833
   PubMed Web of Science ®Google Scholar
• Laurini, E., Marson, D., Aulic, S., Fermeglia, M., & Pricl, S. (2020). Computational alanine scanning and structural analysis of the SARS-CoV-2 spike protein/angiotensin-converting enzyme 2 complex. ACS Nano, 14(9), 11821–11830. https://doi.org/10.1021/acsnano.0c04674
   PubMed Web of Science ®Google Scholar
• Leader, B., Baca, Q. J., & Golan, D. E. (2008). Protein therapeutics: A summary and pharmacological classification. Nature Reviews. Drug Discovery, 7(1), 21–39. https://doi.org/10.1038/nrd2399
   PubMed Web of Science ®Google Scholar
• Li, Y., Wan, Y., Liu, P., Zhao, J., Lu, G., Qi, J., Wang, Q., Lu, X., Wu, Y., Liu, W., Zhang, B., Yuen, K.-Y., Perlman, S., Gao, G. F., & Yan, J. (2015). A humanized neutralizing antibody against MERS-CoV targeting the receptor-binding domain of the spike protein. Cell Research, 25(11), 1237–1249. https://doi.org/10.1038/cr.2015.113
   PubMed Web of Science ®Google Scholar
• Lindorff-Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J. L., Dror, R. O., & Shaw, D. E. (2010). Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins, 78(8), 1950–1958. https://doi.org/10.1002/prot.22711
   PubMed Web of Science ®Google Scholar
• Ling, R., Dai, Y., Huang, B., Huang, W., Yu, J., Lu, X., & Jiang, Y. (2020). In silico design of antiviral peptides targeting the spike protein of SARS-CoV-2. Peptides, 130, 170328. https://doi.org/10.1016/j.peptides.2020.170328
   PubMed Web of Science ®Google Scholar
• Lu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., Wang, W., Song, H., Huang, B., Zhu, N., Bi, Y., Ma, X., Zhan, F., Wang, L., Hu, T., Zhou, H., Hu, Z., Zhou, W., Zhao, L., … Tan, W. (2020). Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding. The Lancet, 395(10224), 565–574. https://doi.org/10.1016/S0140-6736(20)30251-8
   PubMed Web of Science ®Google Scholar
• Luan, B., & Huynh, T. (2020). In silico antibody mutagenesis for optimizing its binding to spike protein of severe acute respiratory syndrome coronavirus 2. The Journal of Physical Chemistry Letters, 11(22), 9781–9787. https://doi.org/10.1021/acs.jpclett.0c02706
   PubMed Web of Science ®Google Scholar
• McKee, M., & Stuckler, D. (2020). If the world fails to protect the economy, COVID-19 will damage health not just now but also in the future. Nature Medicine, 26(5), 640–642. https://doi.org/10.1038/s41591-020-0863-y
   PubMed Web of Science ®Google Scholar
• Moreira, R. A., Chwastyk, M., Baker, J. L., Guzman, H. V., & Poma, A. B. (2020). Quantitative determination of mechanical stability in the novel coronavirus spike protein. Nanoscale, 12(31), 16409–16413. https://doi.org/10.1039/d0nr03969a
   PubMed Web of Science ®Google Scholar
• Namsani, S., Pramanik, D., Khan, M. A., Roy, S., & Singh, J. K. (2021). Metadynamics-based enhanced sampling protocol for virtual screening: Case study for 3CLpro protein for SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 1–16. https://doi.org/10.1080/07391102.2021.1892530
   Google Scholar
• Nguyen, H. L., Lan, P. D., Thai, N. Q., Nissley, D. A., O'Brien, E. P., & Li, M. S. (2020). Does SARS-CoV-2 bind to human ACE2 more strongly than does SARS-CoV? The Journal of Physical Chemistry B, 124(34), 7336–7347. https://doi.org/10.1021/acs.jpcb.0c04511
   PubMed Web of Science ®Google Scholar
• Peng, C., Zhu, Z., Shi, Y., Wang, X., Mu, K., Yang, Y., Zhang, X., Xu, Z., & Zhu, W. (2020). Computational insights into the conformational accessibility and binding strength of SARS-CoV-2 spike protein to human angiotensin-converting enzyme 2. The Journal of Physical Chemistry Letters, 11(24), 10482–10488. https://doi.org/10.1021/acs.jpclett.0c02958
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Pramanik, D., Smith, Z., Kells, A., & Tiwary, P. (2019). Can one trust kinetic and thermodynamic observables from biased metadynamics simulations?: Detailed quantitative benchmarks on millimolar drug fragment dissociation. The Journal of Physical Chemistry B, 123(17), 3672–3678. https://doi.org/10.1021/acs.jpcb.9b01813
   PubMed Web of Science ®Google Scholar
• Pronk, S., Páll, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., Shirts, M. R., Smith, J. C., Kasson, P. M., van der Spoel, D., Hess, B., & Lindahl, E. (2013). GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (Oxford, England), 29(7), 845–854. https://doi.org/10.1093/bioinformatics/btt055
   PubMed Web of Science ®Google Scholar
• Qiao, B., & Olvera de la Cruz, M. (2020). Enhanced binding of SARS-CoV-2 spike protein to receptor by distal polybasic cleavage sites. ACS Nano, 14(8), 10616–10623. https://doi.org/10.1021/acsnano.0c04798
   PubMed Web of Science ®Google Scholar
• Serapian, S. A., Marchetti, F., Triveri, A., Morra, G., Meli, M., Moroni, E., Sautto, G. A., Rasola, A., & Colombo, G. (2020). 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. The Journal of Physical Chemistry Letters, 11(19), 8084–8093. https://doi.org/10.1021/acs.jpclett.0c02341
   PubMed Web of Science ®Google Scholar
• Shang, J., Wan, Y., Luo, C., Ye, G., Geng, Q., Auerbach, A., & Li, F. (2020). Cell entry mechanisms of SARS-CoV-2. Proceedings of the National Academy of Sciences of the United States of America, 117(21), 11727–11734. https://doi.org/10.1073/pnas.2003138117
   PubMed Web of Science ®Google Scholar
• Shi, R., Shan, C., Duan, X., Chen, Z., Liu, P., Song, J., Song, T., Bi, X., Han, C., Wu, L., Gao, G., Hu, X., Zhang, Y., Tong, Z., Huang, W., Liu, W. J., Wu, G., Zhang, B., Wang, L., … Yan, J. (2020). A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2. Nature, 584(7819), 120–124. https://doi.org/10.1038/s41586-020-2381-y
   PubMed Web of Science ®Google Scholar
• Sikora, M., Florian, S. v B., Blanc, E. C., Gecht, M., Covino, R., & Hummer, G. (2021). Computational epitope map of SARS-CoV-2 spike protein. PLoS Computational Biology, 17(4), e1008790. https://doi.org/10.1371/journal.pcbi.1008790
   PubMed Web of Science ®Google Scholar
• Silva de Souza, A., Rivera, J. D., Almeida, V. M., Ge, P., de Souza, R. F., Farah, C. S., Ulrich, H., Marana, S. R., Salinas, R. K., & Guzzo, C. R. (2020). Molecular dynamics reveals complex compensatory effects of ionic strength on the severe acute respiratory syndrome coronavirus 2 spike/human angiotensin-converting enzyme 2 interaction. The Journal of Physical Chemistry Letters, 11(24), 10446–10453. https://doi.org/10.1021/acs.jpclett.0c02602
   PubMed Web of Science ®Google Scholar
• Sitthiyotha, T., & Chunsrivirot, S. (2020). Computational design of 25-mer peptide binders of SARS-CoV-2. The Journal of Physical Chemistry. B, 124(48), 10930–10942. https://doi.org/10.1021/acs.jpcb.0c07890
   PubMed Web of Science ®Google Scholar
• Spinello, A., Saltalamacchia, A., & Magistrato, A. (2020). Is the rigidity of SARS-CoV-2 spike receptor-binding motif the hallmark for its enhanced infectivity? Insights from all-atom simulations. The Journal of Physical Chemistry Letters, 11(12), 4785–4790. https://doi.org/10.1021/acs.jpclett.0c01148
   PubMed Web of Science ®Google Scholar
• Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., Mlisana, K., von Gottberg, A., Walaza, S., Allam, M., Ismail, A., Mohale, T., Glass, A. J., Engelbrecht, S., Van Zyl, G., … de Oliveira, T. (2021). Detection of a SARS-CoV-2 variant of concern in South Africa. Nature, 592(7854), 438–443. https://doi.org/10.1038/s41586-021-03402-9
   PubMed Web of Science ®Google Scholar
• Tiwary, P., & Parrinello, M. (2013). From metadynamics to dynamics. Physical Review Letters, 111(23), 230602. https://doi.org/10.1103/PhysRevLett.111.230602
   PubMed Web of Science ®Google Scholar
• Tortorici, M. A., Beltramello, M., Lempp, F. A., Pinto, D., Dang, H. V., Rosen, L. E., McCallum, M., Bowen, J., Minola, A., Jaconi, S., Zatta, F., De Marco, A., Guarino, B., Bianchi, S., Lauron, E. J., Tucker, H., Zhou, J., Peter, A., Havenar-Daughton, C., … Veesler, D. (2020). Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms. Science (New York, NY), 370(6519), 950–957. https://doi.org/10.1126/science.abe3354
   Google Scholar
• Wall, E. C., Wu, M., Harvey, R., Kelly, G., Warchal, S., Sawyer, C., Daniels, R., Hobson, P., Hatipoglu, E., Ngai, Y., Hussain, S., Nicod, J., Goldstone, R., Ambrose, K., Hindmarsh, S., Beale, R., Riddell, A., Gamblin, S., Howell, M., … Bauer, D. L. V. (2021). Neutralising antibody activity against SARS-CoV-2 VOCs B.1.617.2 and B.1.351 by BNT162b2 vaccination. The Lancet, 397(10292), 2331–2333. https://doi.org/10.1016/S0140-6736(21)01290-3
   PubMed Web of Science ®Google Scholar
• Walls, A. C., Park, Y.-J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020). Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell, 181(2), 281–292.e6. https://doi.org/10.1016/j.cell.2020.02.058
   PubMed Web of Science ®Google Scholar
• Wang, D., Ge, Y., Zhong, B., & Liu, D. (2021). Specific epitopes form extensive hydrogen-bonding networks to ensure efficient antibody binding of SARS-CoV-2: Implications for advanced antibody design. Computational and Structural Biotechnology Journal, 19, 1661–1671. https://doi.org/10.1016/j.csbj.2021.03.021
   PubMed Web of Science ®Google Scholar
• Wang, Q., Zhang, Y., Wu, L., Niu, S., Song, C., Zhang, Z., Lu, G., Qiao, C., Hu, Y., Yuen, K.-Y., Wang, Q., Zhou, H., Yan, J., & Qi, J. (2020a). Structural and functional basis of SARS-CoV-2 entry by using human ACE2. Cell, 181(4), 894–904. https://doi.org/10.1016/j.cell.2020.03.045
   PubMed Web of Science ®Google Scholar
• Wang, Y., Liu, M., & Gao, J. (2020b). Enhanced receptor binding of SARS-CoV-2 through networks of hydrogen-bonding and hydrophobic interactions. Proceedings of the National Academy of Sciences of the United States of America, 117(25), 13967–13974. https://doi.org/10.1073/pnas.2008209117
   PubMed Web of Science ®Google Scholar
• Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C.-L., Abiona, O., Graham, B. S., & McLellan, J. S. (2020). Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science (New York, NY), 367(6483), 1260–1263. https://doi.org/10.1126/science.abb2507
   Google Scholar
• Wu, Y., Wang, F., Shen, C., Peng, W., Li, D., Zhao, C., Li, Z., Li, S., Bi, Y., Yang, Y., Gong, Y., Xiao, H., Fan, Z., Tan, S., Wu, G., Tan, W., Lu, X., Fan, C., Wang, Q., … Liu, L. (2020). A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2. Science (New York, NY), 368(6496), 1274–1278. https://doi.org/10.1126/science.abc2241
   Google Scholar
• Xiu, S., Dick, A., Ju, H., Mirzaie, S., Abdi, F., Cocklin, S., Zhan, P., & Liu, X. (2020). Inhibitors of SARS-CoV-2 entry: Current and future opportunities. Journal of Medicinal Chemistry, 63(21), 12256–12274. https://doi.org/10.1021/acs.jmedchem.0c00502
   PubMed Web of Science ®Google Scholar
• Yan, R., Zhang, Y., Li, Y., Xia, L., Guo, Y., & Zhou, Q. (2020). Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science (New York, NY), 367(6485), 1444–14448. https://doi.org/10.1126/science.abb2762
   Google Scholar
• Yang, J., Petitjean, S. J. L., Koehler, M., Zhang, Q., Dumitru, A. C., Chen, W., Derclaye, S., Vincent, S. P., Soumillion, P., & Alsteens, D. (2020). Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor. Nature Communications, 11(1), 4541. https://doi.org/10.1038/s41467-020-18319-6
   PubMed Web of Science ®Google Scholar
• Zaki, A. M., van Boheemen, S., Bestebroer, T. M., Osterhaus, A. D. M. E., & Fouchier, R. A. M. (2012). Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. The New England Journal of Medicine, 367(19), 1814–1820. https://doi.org/10.1056/NEJMoa1211721
   PubMed Web of Science ®Google Scholar
• Zhang, Y., & Kutateladze, T. G. (2020). Molecular structure analyses suggest strategies to therapeutically target SARS-CoV-2. Nature Communications, 11(1), 2920. https://doi.org/10.1038/s41467-020-16779-4
   PubMed Web of Science ®Google Scholar
• Zimmerman, M. I., Porter, J. R., Ward, M. D., Singh, S., Vithani, N., Meller, A., Mallimadugula, U. L., Kuhn, C. E., Borowsky, J. H., Wiewiora, R. P., Hurley, M. F. D., Harbison, A. M., Fogarty, C. A., Coffland, J. E., Fadda, E., Voelz, V. A., Chodera, J. D., & Bowman, G. R. (2021). SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome. Nature Chemistry, 13(7), 651–659. https://doi.org/10.1038/s41557-021-00707-0
   PubMed Web of Science ®Google Scholar
• Zou, J., Yin, J., Fang, L., Yang, M., Wang, T., Wu, W., Bellucci, M. A., & Zhang, P. (2020). Computational prediction of mutational effects on SARS-CoV-2 binding by relative free energy calculations. Journal of Chemical Information and Modeling, 60(12), 5794–5802. https://doi.org/10.1021/acs.jcim.0c00679
   PubMed Web of Science ®Google Scholar