Persistent Laplacian projected Omicron BA.4 and BA.5 to become new dominating variants

Computers in Biology and Medicine - Tập 151 - Trang 106262 - 2022
Jiahui Chen1, Yuchi Qiu1, Rui Wang1, Guo-Wei Wei2,3
1Department of Mathematics, Michigan State University, East Lansing, MI 48824 USA
2Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824 USA
3Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA

Tài liệu tham khảo

Li, 2005, Bats are natural reservoirs of SARS-like coronaviruses, Science, 310, 676, 10.1126/science.1118391 Qu, 2005, Identification of two critical amino acid residues of the severe acute respiratory syndrome coronavirus spike protein for its variation in zoonotic tropism transition via a double substitution strategy, J. Biol. Chem., 280, 29588, 10.1074/jbc.M500662200 Song, 2005, Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human, Proc. Natl. Acad. Sci., 102, 2430, 10.1073/pnas.0409608102 Hoffmann, 2020, SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor, Cell, 181, 271, 10.1016/j.cell.2020.02.052 Walls, 2020, Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein, Cell, 10.1016/j.cell.2020.02.058 Chen, 2020, Mutations strengthened SARS-CoV-2 infectivity, J. Mol. Biol., 432, 5212, 10.1016/j.jmb.2020.07.009 Wang, 2021, Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries, Genomics, 113, 2158, 10.1016/j.ygeno.2021.05.006 Wang, 2020, A human monoclonal antibody blocking SARS-CoV-2 infection, Nature Commun., 11, 1 Yu, 2020, Receptor-binding domain-specific human neutralizing monoclonal antibodies against SARS-CoV and SARS-CoV-2, Signal Transduct. Target. Ther., 5, 1 Li, 2021, The impact of receptor-binding domain natural mutations on antibody recognition of SARS-CoV-2, Signal Transduct. Target. Ther., 6, 1 Wang, 2021, Mechanisms of sars-cov-2 evolution revealing vaccine-resistant mutations in europe and america, J. Phys. Chem. Lett., 12, 11850, 10.1021/acs.jpclett.1c03380 Wang, 2022, Emerging vaccine-breakthrough SARS-CoV-2 variants, ACS Infect. Dis., 8, 546, 10.1021/acsinfecdis.1c00557 Chen, 2022, Omicron ba. 2 (b.1.1. 529.2) high potential for becoming the next dominant variant, J. Phys. Chem. Lett., 13, 3840, 10.1021/acs.jpclett.2c00469 Guerois, 2002, Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations, J. Mol. Biol., 320, 369, 10.1016/S0022-2836(02)00442-4 Petukh, 2016, Saambe: webserver to predict the charge of binding free energy caused by amino acids mutations, Int. J. Mol. Sci., 17, 547, 10.3390/ijms17040547 Pires, 2016, Mcsm-ab: a web server for predicting antibody–antigen affinity changes upon mutation with graph-based signatures, Nucleic Acids Res., 44, W469, 10.1093/nar/gkw458 Rodrigues, 2019, Mcsm-ppi2: predicting the effects of mutations on protein–protein interactions, Nucleic Acids Res., 47, W338, 10.1093/nar/gkz383 Xiong, 2017, Bindprofx: assessing mutation-induced binding affinity change by protein interface profiles with pseudo-counts, J. Mol. Biol., 429, 426, 10.1016/j.jmb.2016.11.022 Wang, 2020, A topology-based network tree for the prediction of protein–protein binding affinity changes following mutation, Nat. Mach. Intell., 2, 116, 10.1038/s42256-020-0149-6 Frosini, 1992, Measuring shapes by size functions, 122 Edelsbrunner, 2000, Topological persistence and simplification, 454 Zomorodian, 2005, Computing persistent homology, Discrete Comput. Geom., 33, 249, 10.1007/s00454-004-1146-y Carlsson, 2009, Topology and data, Bull. Amer. Math. Soc., 46, 255, 10.1090/S0273-0979-09-01249-X Mischaikow, 2013, Morse theory for filtrations and efficient computation of persistent homology, Discrete Comput. Geom., 50, 330, 10.1007/s00454-013-9529-6 Xia, 2014, Persistent homology analysis of protein structure, flexibility and folding, Int. J. Numer. Methods Biomed. Eng., 30, 814, 10.1002/cnm.2655 De Silva, 2007, Coverage in sensor networks via persistent homology, Algebr. Geom. Topol., 7, 339, 10.2140/agt.2007.7.339 Yao, 2009, Topological methods for exploring low-density states in biomolecular folding pathways, J. Chem. Phys., 130, 10.1063/1.3103496 Bubenik, 2014, Categorification of persistent homology, Discrete Comput. Geom., 51, 600, 10.1007/s00454-014-9573-x Dey, 2014, Computing topological persistence for simplicial maps, 345 Cang, 2017, Topologynet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions, PLoS Comput. Biol., 13, 10.1371/journal.pcbi.1005690 Cang, 2018, Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening, PLoS Comput. Biol., 14, 10.1371/journal.pcbi.1005929 Nguyen, 2019, Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand challenges, J. Comput. Aided Mol. Des., 33, 71, 10.1007/s10822-018-0146-6 Chen, 2021, Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies, Chem. Sci., 12, 6929, 10.1039/D1SC01203G Chen, 2021, Revealing the threat of emerging SARS-CoV-2 mutations to antibody therapies, J. Mol. Biol., 433 Alenquer, 2021, Signatures in sars-cov-2 spike protein conferring escape to neutralizing antibodies, PLoS Pathog., 17, 10.1371/journal.ppat.1009772 Dupont, 2021, Neutralizing antibody activity in convalescent sera from infection in humans with sars-cov-2 and variants of concern, Nat. Microbiol., 1 Linsky, 2020, De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2, Science, 370, 1208, 10.1126/science.abe0075 Starr, 2020, Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding, Cell, 182, 1295, 10.1016/j.cell.2020.08.012 Chen, 2022, Omicron variant (b, 1.1. 529) infectivity, vaccine breakthrough, and antibody resistance, J. Chem. Inf. Model., 62, 412, 10.1021/acs.jcim.1c01451 Wang, 2020, Persistent spectral graph, Int. J. Numer. Methods Biomed. Eng., 36, 10.1002/cnm.3376 Mémoli, 2020 Wang, 2021, Hermes: Persistent spectral graph software, Found. Data Sci. (Springfield, Mo.), 3, 67, 10.3934/fods.2021006 Meng, 2021, Persistent spectral–based machine learning (perspect ml) for protein-ligand binding affinity prediction, Sci. Adv., 7, 10.1126/sciadv.abc5329 Wee, 2022, Persistent spectral based ensemble learning (perspect-el) for protein–protein binding affinity prediction, Brief. Bioinform., 23, 10.1093/bib/bbac024 Sirin, 2016, AB-Bind: antibody binding mutational database for computational affinity predictions, Prot. Sci., 25, 393, 10.1002/pro.2829 Moal, 2012, SKEMPI: a structural kinetic and energetic database of mutant protein interactions and its use in empirical models, Bioinformatics, 28, 2600, 10.1093/bioinformatics/bts489 Jankauskaitė, 2019, SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation, Bioinformatics, 35, 462, 10.1093/bioinformatics/bty635 Chen, 2022 Mannar, 2021, Sars-cov-2 omicron variant: Ace2 binding, cryo-em structure of spike protein-ace2 complex and antibody evasion, BioRxiv BA2 reinfection, 0000. https://www.timesofisrael.com/several-cases-of-omicron-reinfection-said-detected-in-israel-with-new-ba2-strain/. Lyngse, 2022, Transmission of sars-cov-2 omicron voc subvariants ba. 1 and ba. 2: Evidence from danish households, MedRxiv Jemimah, 2017, Proximate: a database of mutant protein–protein complex thermodynamics and kinetics, Bioinformatics, 33, 2787, 10.1093/bioinformatics/btx312 Liu, 2018, Dbmpikt: a database of kinetic and thermodynamic mutant protein interactions, BMC Bioinformatics, 19, 1, 10.1186/s12859-018-2493-7 Procko, 2020, The sequence of human ace2 is suboptimal for binding the s spike protein of sars coronavirus 2, BioRxiv Serrano, 2019 Maletić, 2014, Consensus formation on a simplicial complex of opinions, Phys. A, 397, 111, 10.1016/j.physa.2013.12.001 Hernández Serrano, 2021 Goldberg, 2002 Horak, 2013, Spectra of combinatorial laplace operators on simplicial complexes, Adv. Math., 244, 303, 10.1016/j.aim.2013.05.007 Paszke, 2019, Pytorch: An imperative style, high-performance deep learning library, Adv. Neural Inf. Process. Syst., 32 Pedregosa, 2011, Scikit-learn: Machine learning in python, J. Mach. Learn. Res., 12, 2825 Wang, 2021, Emerging vaccine-breakthrough SARS-CoV-2 variants, ACS Infect. Dis., 8, 546, 10.1021/acsinfecdis.1c00557