Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity
Tài liệu tham khảo
Pahari, 2020, SAAMBE-3D: predicting effect of mutations on protein-protein interactions, Int J Mol Sci, 21, 2563, 10.3390/ijms21072563
Pires, 2014, mCSM: predicting the effects of mutations in proteins using graph-based signatures, Bioinformatics, 30, 335, 10.1093/bioinformatics/btt691
Rodrigues, 2019, mCSM-PPI2: predicting the effects of mutations on protein-protein interactions, Nucleic Acids Res, 47, W338, 10.1093/nar/gkz383
Li, 2016, MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions, Nucleic Acids Res, 44, W494, 10.1093/nar/gkw374
Zhang, 2020, MutaBind2: predicting the impacts of single and multiple mutations on protein-protein interactions, iScience, 23
Dehouck, 2013, BeAtMuSiC: prediction of changes in protein-protein binding affinity on mutations, Nucleic Acids Res, 41, W333, 10.1093/nar/gkt450
Barlow, 2018, Flex ddG: rosetta ensemble-based estimation of changes in protein-protein binding affinity upon mutation, J Phys Chem B, 122, 5389, 10.1021/acs.jpcb.7b11367
Clark, 2017, Free energy perturbation calculation of relative binding free energy between broadly neutralizing antibodies and the gp120 glycoprotein of HIV-1, J Mol Biol, 429, 930, 10.1016/j.jmb.2016.11.021
Clark, 2019, Relative binding affinity prediction of charge-changing sequence mutations with FEP in protein-protein interfaces, J Mol Biol, 431, 1481, 10.1016/j.jmb.2019.02.003
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
Schymkowitz, 2005, The FoldX web server: an online force field, Nucleic Acids Res, 33, W382, 10.1093/nar/gki387
Geng, 2019, Finding the ΔΔG spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it?, WIREs Comput Mol Sci, 9, e1410, 10.1002/wcms.1410
Geng, 2016, Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes, Protein Eng Design Select, 29, 291, 10.1093/protein/gzw020
Abel, 2017, Advancing drug discovery through enhanced free energy calculations, Acc Chem Res, 50, 1625, 10.1021/acs.accounts.7b00083
Katz, 2021, Potency- and selectivity-enhancing mutations of conotoxins for nicotinic acetylcholine receptors can be predicted using accurate free-energy calculations, Mar Drugs, 19, 10.3390/md19070367
Katz, 2021, Potency-enhancing mutations of gating modifier toxins for the voltage-gated sodium channel NaV1.7 can be predicted using accurate free-energy calculations, Toxins (Basel), 13
La Serra, 2022, Alchemical free energy calculations to investigate protein-protein interactions: the case of the CDC42/PAK1 complex, J Chem Inf Model, 62, 3023, 10.1021/acs.jcim.2c00348
Nandigrami, 2022, Computational assessment of protein-protein binding specificity within a family of synaptic surface receptors, J Phys Chem B, 126, 7510, 10.1021/acs.jpcb.2c02173
Patel, 2021, Implementing and assessing an alchemical method for calculating protein-protein binding free energy, J Chem Theory Comput, 17, 2457, 10.1021/acs.jctc.0c01045
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
McCallum, 2021, SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern, Science, 373, 648, 10.1126/science.abi7994
McCallum, 2021, Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants, Science, 374, 1621, 10.1126/science.abl8506
Deshpande, 2021, Epitope classification and RBD binding properties of neutralizing antibodies against SARS-CoV-2 variants of concern, Front Immunol, 12, 10.3389/fimmu.2021.691715
Thomson, 2021, Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity, Cell, 184, 1171, 10.1016/j.cell.2021.01.037
Tian, 2021, N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2, Elife, 10
Gobeil, 2021, Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity, Science, 373, 10.1126/science.abi6226
Laffeber, 2021, Experimental evidence for enhanced receptor binding by rapidly spreading SARS-CoV-2 variants, J Mol Biol, 433, 10.1016/j.jmb.2021.167058
Liu, 2021, 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro, MAbs, 13, 1919285, 10.1080/19420862.2021.1919285
Liu, 2021, The basis of a more contagious 501Y.V1 variant of SARS-CoV-2, Cell Res, 31, 720, 10.1038/s41422-021-00496-8
Barton, 2021, Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics, Elife, 10
Raghu, 2021, Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants, J Pharm Anal
Han, 2021, Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants, Nat Commun, 12, 6103, 10.1038/s41467-021-26401-w
Xue, 2021, Single point mutations can potentially enhance infectivity of SARS-CoV-2 revealed by in silico affinity maturation and SPR assay, RSC Adv, 11, 14737, 10.1039/D1RA00426C
Mannar, 2021, Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding, Cell Rep, 37, 10.1016/j.celrep.2021.110156
Saville, 2022, Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants, Nat Commun, 13, 742, 10.1038/s41467-022-28324-6
Zhu, 2021, Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies, PLoS Biol, 19, e3001237, 10.1371/journal.pbio.3001237
Cai, 2021, Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants, Science, 373, 642, 10.1126/science.abi9745
Zhang, 2021, Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant, Science, 374, 1353, 10.1126/science.abl9463
Yang, 2021, Structure-activity relationships of B.1.617 and other SARS-CoV-2 spike variants, bioRxiv
Bayarri-Olmos, 2021, Functional effects of receptor-binding domain mutations of SARS-CoV-2 B.1.351 and P.1 variants, Front Immunol, 12, 10.3389/fimmu.2021.757197
Bayarri-Olmos, 2021, The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice, Elife, 10
Bayarri-Olmos, 2021, The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization, J Biol Chem, 296, 10.1016/j.jbc.2021.100536
Supasa, 2021, Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera, Cell, 184, e7
Yuan, 2021, Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants, Science, 373, 818, 10.1126/science.abh1139
Lopez, 2021, Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay, JCI Insight, 6
Collier, 2021, Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies, Nature, 593, 136, 10.1038/s41586-021-03412-7
Chen, 2021, Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2, Proc Natl Acad Sci U S A, 118, 10.1073/pnas.2106480118
Liu, 2021, Deep geometric representations for modeling effects of mutations on protein-protein binding affinity, PLoS Comput Biol, 17, e1009284, 10.1371/journal.pcbi.1009284
Chen, 2020, Mutations Strengthened SARS-CoV-2 Infectivity, J Mol Biol, 432, 5212, 10.1016/j.jmb.2020.07.009
Strokach, 2021, ELASPIC2 (EL2): Combining contextualized language models and graph neural networks to predict effects of mutations, J Mol Biol, 433, 10.1016/j.jmb.2021.166810
Laurini, 2021, Computational mutagenesis at the SARS-CoV-2 spike protein/angiotensin-converting enzyme 2 binding interface: comparison with experimental evidence, ACS Nano, 15, 6929, 10.1021/acsnano.0c10833
Laurini, 2020, Computational alanine scanning and structural analysis of the SARS-CoV-2 spike protein/angiotensin-converting enzyme 2 complex, ACS Nano, 14, 11821, 10.1021/acsnano.0c04674
Fratev, 2021, N501Y and K417N mutations in the spike protein of SARS-CoV-2 alter the interactions with both hACE2 and human-derived antibody: a free energy of perturbation retrospective study, J Chem Inf Model, 61, 6079, 10.1021/acs.jcim.1c01242
Fratev, 2021, The High transmission of SARS-CoV-2 Omicron (B.1.1.529) variant is not only due to its hACE2 binding: a free energy of perturbation study, bioRxiv
Pavlova, 2021, Machine learning reveals the critical interactions for SARS-CoV-2 spike protein binding to ACE2, J Phys Chem Lett, 12, 5494, 10.1021/acs.jpclett.1c01494
Luan, 2021, Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations, FEBS Lett, 595, 1454, 10.1002/1873-3468.14076
Khan, 2021, Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data, J Cell Physiol, 236, 7045, 10.1002/jcp.30367
Cheng, 2022, Impact of new variants on SARS-CoV-2 infectivity and neutralization: A molecular assessment of the alterations in the spike-host protein interactions, iScience, 25, 10.1016/j.isci.2022.103939
Buratto, 2021, Rapid assessment of binding affinity of SARS-COV-2 spike protein to the human angiotensin-converting enzyme 2 receptor and to neutralizing biomolecules based on computer simulations, Front Immunol, 12, 10.3389/fimmu.2021.730099
Villoutreix, 2021, In silico investigation of the new UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 variants with a focus at the ACE2-spike RBD interface, Int J Mol Sci, 22
Wu, 2022, SARS-CoV-2 Omicron RBD shows weaker binding affinity than the currently dominant Delta variant to human ACE2, Signal Transduct Target Ther, 7, 8, 10.1038/s41392-021-00863-2
Gan, 2021, Structural modeling of the SARS-CoV-2 spike/human ACE2 complex interface can identify high-affinity variants associated with increased transmissibility, J Mol Biol, 433, 10.1016/j.jmb.2021.167051
Bozdaganyan, 2022, Computational analysis of mutations in the receptor-binding domain of SARS-CoV-2 spike and their effects on antibody binding, Viruses, 14, 10.3390/v14020295
Zahradnik, 2021, SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution, Nat Microbiol, 6, 1188, 10.1038/s41564-021-00954-4
Liu, 2021, The Lambda variant of SARS-CoV-2 has a better chance than the Delta variant to escape vaccines, bioRxiv
Harder, 2016, OPLS3: A force field providing broad coverage of drug-like small molecules and proteins, J Chem Theory Comput, 12, 281, 10.1021/acs.jctc.5b00864
Roos, 2019, OPLS3e: Extending force field coverage for drug-like small molecules, J Chem Theory Comput, 15, 1863, 10.1021/acs.jctc.8b01026
Wang, 2015, Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field, J Am Chem Soc, 137, 2695, 10.1021/ja512751q
Lan, 2020, Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor, Nature, 581, 215, 10.1038/s41586-020-2180-5
Carrillo, 2015, Control of synaptic connectivity by a network of drosophila IgSF cell surface proteins, Cell, 163, 1770, 10.1016/j.cell.2015.11.022
Cosmanescu, 2018, Neuron-subtype-specific expression, interaction affinities, and specificity determinants of DIP/Dpr cell recognition proteins, Neuron, 10.1016/j.neuron.2018.10.046
Sergeeva, 2020, DIP/Dpr interactions and the evolutionary design of specificity in protein families, Nat Commun, 11, 2125, 10.1038/s41467-020-15981-8
Xu, 2022, Affinity requirements for control of synaptic targeting and neuronal cell survival by heterophilic IgSF cell adhesion molecules, Cell Rep, 39, 10.1016/j.celrep.2022.110618
Liu, 2021, The N501Y spike substitution enhances SARS-CoV-2 infection and transmission, Nature
Burkholz, 2021, Paired SARS-CoV-2 spike protein mutations observed during ongoing SARS-CoV-2 viral transfer from humans to minks and back to humans, Infect Genet Evol, 93, 10.1016/j.meegid.2021.104897
Munnink, 2021, Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans, Science, 371, 172, 10.1126/science.abe5901
Jankauskaite, 2018, SKEMPI 2.0: An updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation, Bioinformatics
Geng, 2018, iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations, Proteins
Lu, 2021, OPLS4: Improving force field accuracy on challenging regimes of chemical space, J Chem Theory Comput, 17, 4291, 10.1021/acs.jctc.1c00302
Blazhynska, 2022, Hazardous shortcuts in standard binding free energy calculations, J Phys Chem Lett, 13, 6250, 10.1021/acs.jpclett.2c01490
Fu, 2022, Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations, Nat Protoc, 17, 1114, 10.1038/s41596-021-00676-1
Wang, 2021, Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants, Commun Biol, 4, 228, 10.1038/s42003-021-01754-6
Cheng, 2019, Molecular basis of synaptic specificity by immunoglobulin superfamily receptors in Drosophila, Elife, 8, 10.7554/eLife.41028
Gotz, 2012, Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized born, J Chem Theory Comput, 8, 1542, 10.1021/ct200909j
Salomon-Ferrer, 2013, Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle mesh Ewald, J Chem Theory Comput, 9, 3878, 10.1021/ct400314y
Miller, 2012, MMPBSA.py: An efficient program for end-state free energy calculations, J Chem Theory Comput, 8, 3314, 10.1021/ct300418h
Ross, 2020, Enhancing water sampling in free energy calculations with grand canonical Monte Carlo, J Chem Theory Comput, 16, 6061, 10.1021/acs.jctc.0c00660
Chan, 2020, Engineering human ACE2 to optimize binding to the spike protein of SARS coronavirus 2, Science, 369, 1261, 10.1126/science.abc0870
Meng, 2022, Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity, Nature, 603, 706, 10.1038/s41586-022-04474-x
Zhou, 2020, Structure-based design with tag-based purification and in-process biotinylation enable streamlined development of SARS-CoV-2 spike molecular probes, Cell Rep, 33, 10.1016/j.celrep.2020.108322
Lan, 2022, Structural insights into the binding of SARS-CoV-2, SARS-CoV, and hCoV-NL63 spike receptor-binding domain to horse ACE2, Structure, 30, 1432, 10.1016/j.str.2022.07.005
Li, 2022, Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1, Cell, 185, 2952, 10.1016/j.cell.2022.06.023