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