Mutations in the SARS-CoV-2 spike RBD are responsible for stronger ACE2 binding and poor anti-SARS-CoV mAbs cross-neutralization

Computational and Structural Biotechnology Journal - Tập 18 - Trang 3402-3414 - 2020
Masaud Shah1, Bilal Ahmad2, Sangdun Choi2, Hyun Goo Woo1
1Department of Physiology, Ajou University School of Medicine, Suwon, Republic of Korea
2Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea

Tài liệu tham khảo

WHO. Coronavirus disease 2019 (COVID-19) Situation Report – 46 6 March 2020. 2020. Behzadi, 2019, Overview of current therapeutics and novel candidates against influenza, respiratory syncytial virus, and middle east respiratory syndrome coronavirus infections, Front Microbiol., 10, 1327, 10.3389/fmicb.2019.01327 Worobey, 2020, The emergence of SARS-CoV-2 in Europe and North America, Science, 10.1126/science.abc8169 Wu, 2020, A new coronavirus associated with human respiratory disease in China, Nature, 10.1038/s41586-020-2008-3 Zhou, 2020, A pneumonia outbreak associated with a new coronavirus of probable bat origin, Nature, 10.1038/s41586-020-2951-z Zhu, 2020, A Novel Coronavirus from Patients with Pneumonia in China, 2019, N Engl J Med., 382, 727, 10.1056/NEJMoa2001017 Paraskevis, 2020, Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event, Infect Genet Evol., 79, 10.1016/j.meegid.2020.104212 Kandimalla, 2020, Current Status of Multiple Drug Molecules, and Vaccines: An Update in SARS-CoV-2 Therapeutics, Mol Neurobiol., 57, 4106, 10.1007/s12035-020-02022-0 Gallagher, 2001, Coronavirus spike proteins in viral entry and pathogenesis, Virology, 279, 371, 10.1006/viro.2000.0757 Letko, 2020, Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses, Nat Microbiol., 10.1038/s41564-020-0688-y Wrapp, 2020, Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation, Science, 10.1126/science.abb2507 Yuan, 2017, Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains, Nat Commun., 8, 15092, 10.1038/ncomms15092 Wrapp, 2020, Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation, Science, 367, 1260, 10.1126/science.abb2507 Mansbach, 2020, The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational State, bioRxiv. Zhang, 2020, The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity, bioRxiv. Shah, 2015, In silico mechanistic analysis of IRF3 inactivation and high-risk HPV E6 species-dependent drug response, Sci Rep., 5, 13446, 10.1038/srep13446 Park, 2017, TLR4/MD2 specific peptides stalled in vivo LPS-induced immune exacerbation, Biomaterials, 126, 49, 10.1016/j.biomaterials.2017.02.023 Junaid, 2019, Extraction of molecular features for the drug discovery targeting protein-protein interaction of Helicobacter pylori CagA and tumor suppressor protein ASSP2, Proteins., 87, 837, 10.1002/prot.25748 Achek, 2019, Linear and rationally designed stapled peptides abrogate TLR4 pathway and relieve inflammatory symptoms in rheumatoid arthritis rat model, J Med Chem., 62, 6495, 10.1021/acs.jmedchem.9b00061 Narayanan, 2009, Energy-based analysis and prediction of the orientation between light- and heavy-chain antibody variable domains, J Mol Biol., 388, 941, 10.1016/j.jmb.2009.03.043 Chothia, 1987, Canonical structures for the hypervariable regions of immunoglobulins, J Mol Biol., 196, 901, 10.1016/0022-2836(87)90412-8 Murzin, 1995, SCOP: a structural classification of proteins database for the investigation of sequences and structures, J Mol Biol., 247, 536, 10.1016/S0022-2836(05)80134-2 Hwang, 2006, Structural basis of neutralization by a human anti-severe acute respiratory syndrome spike protein antibody, 80R, J Biol Chem., 281, 34610, 10.1074/jbc.M603275200 Pak, 2009, Structural insights into immune recognition of the severe acute respiratory syndrome coronavirus S protein receptor binding domain, J Mol Biol., 388, 815, 10.1016/j.jmb.2009.03.042 Prabakaran, 2006, Structure of severe acute respiratory syndrome coronavirus receptor-binding domain complexed with neutralizing antibody, J Biol Chem., 281, 15829, 10.1074/jbc.M600697200 Walls, 2019, Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion, Cell, 176, 1026, 10.1016/j.cell.2018.12.028 Dunbar, 2016, SAbPred: a structure-based antibody prediction server, Nucleic Acids Res., 44, W474, 10.1093/nar/gkw361 Krawczyk, 2014, Improving B-cell epitope prediction and its application to global antibody-antigen docking, Bioinformatics, 30, 2288, 10.1093/bioinformatics/btu190 Huang, 2017, CHARMM36m: an improved force field for folded and intrinsically disordered proteins, Nat Methods., 14, 71, 10.1038/nmeth.4067 Pronk, 2013, GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit, Bioinformatics, 29, 845, 10.1093/bioinformatics/btt055 Wang, 2010, Optimizing working parameters of the smooth particle mesh Ewald algorithm in terms of accuracy and efficiency, J Chem Phys, 133, 10.1063/1.3446812 Hess, 1997, LINCS: a linear constraint solver for molecular simulations, J Comput Chem, 18, 1463, 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H Kumari, 2014, Open Source Drug Discovery C, Lynn A. g_mmpbsa–a GROMACS tool for high-throughput MM-PBSA calculations, J Chem Inf Model., 54, 1951, 10.1021/ci500020m Anwar, 2015, Insights into the species-specific TLR4 signaling mechanism in response to Rhodobacter sphaeroides lipid A detection, Sci Rep., 5, 7657, 10.1038/srep07657 Monteil, 2020, Inhibition of SARS-CoV-2 Infections in Engineered Human Tissues Using Clinical-Grade Soluble Human ACE2, Cell, 181, 905, 10.1016/j.cell.2020.04.004 Andre Watson, Leonardo Ferreira, Peter Hwang, Jinbo Xu, Stroud R. Peptide Antidotes to SARS-CoV-2 (COVID-19). biorxiv. 2020. Yan, 2020, Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2, Science, 10.1126/science.abb2762 Shang, 2020, Structural basis for receptor recognition by the novel coronavirus from Wuhan, Research Square. Wang, 2020, Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2, Cell, 181, 894, 10.1016/j.cell.2020.03.045 Walls, 2020, Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein, Cell press. Tian, 2020, Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody, Emerg Microbes Infect., 9, 382, 10.1080/22221751.2020.1729069 Wang, 2020, Enhanced receptor binding of SARS-CoV-2 through networks of hydrogen-bonding and hydrophobic interactions, Proc Natl Acad Sci USA, 117, 13967, 10.1073/pnas.2008209117 He, 2020, Molecular Mechanism of Evolution and Human Infection with SARS-CoV-2, Viruses., 12, 10.3390/v12040428 Hu, 2005, Screening and identification of linear B-cell epitopes and entry-blocking peptide of severe acute respiratory syndrome (SARS)-associated coronavirus using synthetic overlapping peptide library, J Comb Chem., 7, 648, 10.1021/cc0500607 Han, 2006, Identification of critical determinants on ACE2 for SARS-CoV entry and development of a potent entry inhibitor, Virology, 350, 15, 10.1016/j.virol.2006.01.029 Zhang, 2020, Investigation of ACE2 N-terminal fragments binding to SARS-CoV-2 Spike RBD, biorxiv. Cao, 2020, De novo design of picomolar SARS-CoV-2 miniprotein inhibitors, Science, 10.1126/science.abd9909 ter Meulen, 2006, Human monoclonal antibody combination against SARS coronavirus: synergy and coverage of escape mutants, PLoS Med., 3, 10.1371/journal.pmed.0030237 Park, 2020, Spike protein binding prediction with neutralizing antibodies of SARS-CoV-2, bioRxiv. Chen, 2013, Crystal structure of the receptor-binding domain from newly emerged Middle East respiratory syndrome coronavirus, J Virol., 87, 10777, 10.1128/JVI.01756-13 Yuan, 2020, A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV, bioRxive. Hansen, 2020, Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail, Science, 369, 1010, 10.1126/science.abd0827 Du, 2020, Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy, Cell, 10.1016/j.cell.2020.09.035 Shah, 2020, Sequence variation of SARS-CoV-2 spike protein may facilitate stronger interaction with ACE2 promoting high infectivity, ResearchSquare.