A computational evaluation of structural stability of omicron and delta mutations of SARS-CoV-2 spike proteins and human ACE-2 interactions

Ganeshpurkar, 2018, RNA-dependent RNA polymerases and their emerging roles in antiviral therapy, 1 World Health Organization Mlcochova, 2021, SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion, Nature, 10.1038/s41586-021-03944-y World Health Organizations, 2021 World Health Organizations, 2022 2021, 1 2021 Kumar, 2021, Omicron and Delta variant of SARS‐CoV‐2: a comparative computational study of spike protein, J Med Virol, 94, 1641 Gowrisankar, 2022, Omicron: a mysterious variant of concern, Europ. phy. j. plus, 137, 100, 10.1140/epjp/s13360-021-02321-y Pulliam, 2022, Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa, Science, 10.1126/science.abn4947 Brandal, 2021, Outbreak caused by the SARS-CoV-2 omicron variant in Norway, november to december 2021, Euro Surveill: bullet. Europ. sur les malad. transmis = Europ. commun. dis. bullet., 26, 10.2807/1560-7917.ES.2021.26.50.2101147 Espenhain, 2021, Epidemiological characterisation of the first 785 SARS-CoV-2 Omicron variant cases in Denmark, December 2021, Euro Surveill: bullet. Europ. sur les malad. transmis = Europ. commun. dis. bullet., 26, 10.2807/1560-7917.ES.2021.26.50.2101146 Lupala, 2022, Mutations on RBD of SARS-CoV-2 Omicron variant result in stronger binding to human ACE2 receptor, Biochem Biophys Res Commun, 590, 34, 10.1016/j.bbrc.2021.12.079 Elbe, 2017, Data, disease, and diplomacy: GISAID's innovative contribution to global health, Glob. challeng. (Hoboken, NJ), 1, 33, 10.1002/gch2.1018 Cerutti, 2022, Cryo-EM structure of the SARS-CoV-2 Omicron spike, Cell Rep, 38, 10.1016/j.celrep.2022.110428 Cui, 2022, Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron, Cell, 185, 860, 10.1016/j.cell.2022.01.019 Sabiu, 2021, An insight on the nature of biochemical interactions between glycyrrhizin, myricetin and CYP3A4 isoform, J Food Biochem, 2, 232 Uhomoibhi, 2022, Molecular modelling identification of phytocompounds from selected African botanicals as promising therapeutics against druggable human host cell targets of SARS-CoV-2, J Mol Graph Model, 10.1016/j.jmgm.2022.108185 Idowu, 2022, Inhibitory mechanism of ambroxol and bromhexine hydrochlorides as potent blockers of molecular interaction between SARS-CoV-2 spike protein and human angiotensin-converting enzyme-2, J Mol Graphic and dyn Obakachi, V. A., Idowu, K, Narva Deshwar Kushwaha, Olayinka I. Akinpelu, Babita Kushwaha, Srinivas Reddy Merugu, Rajshekhar Karpoormath. “Structural based investigation of novel pyrazole-thiazole hybrids as dual CDK-1 and CDK-2 inhibitors for cancer chemotherapy” molecular simulation, DOI: 10.1080/08927022.2022.2045016. Xu, 2021, Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM, Sci Adv, 7, 10.1126/sciadv.abe5575 Shapovalov, 2011, A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions, Structure (London, England, 19, 844, 10.1016/j.str.2011.03.019 Yang, 2012, UCSF chimera, MODELLER, and IMP: an integrated modeling system, J Struct Biol, 179, 269, 10.1016/j.jsb.2011.09.006 Dominguez, 2003, HADDOCK: a protein-protein docking approach based on biochemical or biophysical information, J Am Chem Soc 2003, 125, 1731 Case, 2021 Nair, 2014, Molecular dynamics simulations: from structure function relationships to drug discovery, Silico Pharm, 2, 1, 10.1186/s40203-014-0004-8 Jorgensen, 1983, Comparison of simple potential functions for simulating liquid water, J Chem Phys, 79, 926, 10.1063/1.445869 Gonnet, 2007, P-SHAKE: a quadratically convergent SHAKE in O(n2), J Comput Phys, 220, 740, 10.1016/j.jcp.2006.05.032 Basconi, 2013, Effects of temperature control algorithms on transport properties and kinetics in molecular dynamics simulations, J Chem Theor Comput, 9, 2887, 10.1021/ct400109a Ryckaert, 1977, Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes, J Comput Phys, 23, 327, 10.1016/0021-9991(77)90098-5 Izaguirre, 2001, Langevin stabilization of molecular dynamics, J Chem Phys, 114, 2090, 10.1063/1.1332996 Ylilauri, 2013, MMGBSA as a tool to understand the binding affinities of filamin-peptide interactions, J Chem Inf Model, 53, 2626, 10.1021/ci4002475 Idowu, 2020, Molecular dynamic mechanism(s) of inhibition of bioactive antiviral phytochemical compounds targeting cytochrome P450 3A4 and P-glycoprotein, J Biomol Struct Dyn, 1 Abdullahi, 2018, Allosteric inhibition abrogates dysregulated LFA-1 activation: structural insight into mechanisms of diminished immunologic disease, Comput Biol Chem, 73, 49, 10.1016/j.compbiolchem.2018.02.002 Hwang, 2022, Interaction analysis of the spike protein of delta and omicron variants of SARS-CoV-2 with hACE2 and eight monoclonal antibodies using the fragment molecular orbital method, J Chem Inf Model 2022, 62, 1771, 10.1021/acs.jcim.2c00100 Lan, 2022, Structural and computational insights into the SARS-CoV2 omicron RBD-ACE2 interaction, bioRxiv Costa, 2022, Assessment of mutations on RBD in the spike protein of SARS-CoV-2 alpha, delta and omicron variants, Research Square Kehinde, 2019, The pharmacokinetic properties of HIV-1 protease inhibitors: a computational perspective on herbal phytochemicals, Heliyon, 5, 10.1016/j.heliyon.2019.e02565 Vincent, 2021, Design and synthesis of pyrazolone-based compounds as potent blockers of SARS-CoV-2 viral entry into the host cells, J Mol Struct, 1241 Sindhu, 2015, Exploring the binding properties of agonists interacting with human TGR5 using structural modelling, molecular docking and dynamics simulations, RSC Adv, 5, 14202, 10.1039/C4RA16617E Aribisala, 2021, Astaxanthin-mediated bacterial lethality: evidence from oxidative stress contribution and molecular dynamics simulation, Oxid Med Cell Longev, 10.1155/2021/7159652 John, 2022, Molecular modelling identification of potential drug candidates from selected African plants against SARS-CoV-2 key druggable proteins, Scientific African Hess, 2002, Convergence of sampling in protein simulations, Phys Rev, 65 Idowu, 2022, Inhibitory mechanism of clioquinol and its derivatives at the exopeptidase site of human angiotensin-converting enzyme-2 and receptor binding domain of SARS-CoV-2 viral spike protein, J Biomol Struct Dyn Kumar, 2014, Computational analysis reveals the association of threonine 118 methionine mutation in PMP22 resulting in CMT-1A”. Advan, Bioinformatics, 2014, 1, 10.1155/2014/502618 Ogidigo Sinyani, 2022, A molecular dynamics perspective into estrogen receptor inhibition by selective flavonoids as alternative therapeutic options, J Biomol Struct Dyn, 10.1080/07391102.2022.2062786 Joseph, 2022 Lindsey