key: cord-0718879-os1wyb6w authors: Ranjan, Prashant; Neha,; Devi, Chandra; Devar, Kaviyapriya Arulmozhi; Das, Parimal title: The influence of new SARS-CoV-2 variant Omicron (B.1.1.529) on vaccine efficacy, its correlation to Delta Variants: a computational approach date: 2021-12-08 journal: bioRxiv DOI: 10.1101/2021.12.06.471215 sha: 702bacdc056f1ffb368dac74655537c1d57d8a87 doc_id: 718879 cord_uid: os1wyb6w The newly discovered COVID variant B.1.1.529 in Botswana has more than 30 mutations in spike and many other in non-spike proteins, far more than any other SARS-CoV-2 variant accepted as a variant of concern by the WHO and officially named Omicron, and has sparked concern among scientists and the general public. Our findings provide insights into structural modification caused by the mutations in the Omicrons receptor-binding domain and look into the effects on interaction with the hosts neutralising antibodies CR3022, B38, CB6, P2B-2F6, and REGN, as well as ACE2R using an in silico approach. We have employed secondary structure prediction, structural superimposition, protein disorderness, molecular docking, and MD simulation to investigate host-pathogen interactions, immune evasion, and transmissibility caused by mutations in the RBD region of the spike protein of the Omicron variant and compared it to the Delta variants (AY.1, AY.2, & AY.3) and wild type. Computational analysis revealed that the Omicron variant has a higher binding affinity for the human ACE2 receptor than the wild and Delta (AY.1 and AY.2 strains), but lower than the Delta AY.3 strain. MD simulation and docking analysis suggest that the omicron and Delta AY.3 were found to have relatively unstable and compact RBD structures and hampered interactions with antibodies more than wild and Delta (AY.1 and AY.2), which may lead to relatively more pathogenicity and antibody escape. In addition, we observed lower binding affinity of Omicron for human monoclonal antibodies (CR3022, B38, CB6, and P2B2F6) when compared to wild and Delta (AY.1 & AY.2). However, the binding affinity of Omicron RBD variants for CR3022, B38, and P2B2F6 antibodies is lower as compared to Delta AY.3, which might promote immune evasion and reinfection and needs further experimental investigation. Viruses naturally have the ability to change their genetic makeup with time, which does not affect it drastically, but these changes may affect host range, disease severity, transmissibility, diagnosis, re-infection, the performance of vaccines and other therapeutics, etc. 1 The coronavirus spike (S) protein located throughout the virus surface is important for interaction with the host cell. The S protein (1273aa) is composed of signal peptide (amino acids 1-13), the S1 subunit (14-685aa), and the S2 subunit (686-1273aa). S1 and S2 mainly mediate host angiotensin-converting enzyme-2 (ACE2) receptor recognition and binding, followed by membrane fusion [4] [5] [6] [7] . To be precise, it is the RBD domain (319-541aa residues) located in the S1 subunit that binds to the host cell ACE2 receptor 6 . After binding with ACE2, a serine protease TMPRSS2 located on the host cell membrane is essentially required for S protein priming and helps viral spread. This TMPRSS2 (transmembrane protease, serine-2) proteolytically cleaves the peptide bond Arg685-Ser686 of the S1/S2 site and separates the two subunits. The S2 subunit, which remains within the viral envelop, ultimately attaches to the host membrane. The process of fusion and infection is further enhanced due to irreversible conformational changes of S protein by the second proteolysis at the S2' site (Arg815-Ser816). TMPRSS2 also cleaves ACE2 and promotes uptake of SARS-CoV and likely SARS-CoV-2 virions as well. In the secretory pathway of the infected host cell, SARS-CoV-2 S protein is preactivated by furin-mediated proteolysis, which requires a single bond cleavage for the fusion process activation and subsequent entry into the cell 8,9 . Mutations in the spike region may affect the way the virus interacts with the host or responds to antibodies. The D614G mutation in spike protein enabled higher ACE2 binding affinity and was correlated with higher transmission and increased viral loads in COVID-19 patients 7,10 . The Delta variant (B.1.617.2) of SARS-CoV-2 with higher infectivity was the leading factor in the third wave of the COVID-19 pandemic 11 . Multiple sub-lineages of Delta variants were observed to be circulated among populations. From data submitted in Nextstrain database, the PANGO lineage AY .1 contains T19R, T95I, G142D, E156-, F157-, R158G, W258L, K417N, L452R, T478K, D614G, P681R, D950N and PANGO AY.2 contains T19R, G142D, E156-, F157-, R158G, A222V, K417N, L452R, T478K, D614G, P681R, D950N and PANGO lineage AY.3 contains T19R, E156-, F157-, R158G, L452R, T478K, Delta variant mutation Del157-158 in the NTD of the S protein is considered to be associated with antibody escape 12, 13 . The Delta variant has been shown to have a higher replication rate, transmissibility, viral load as well as immune evasion [14] [15] [16] The crystal structure of different human neutralizing monoclonal antibodies CR3022 6W41 20 , B38 7BZ5 21 , CB6 7C01 22 , P2B-2F6 7BWJ 23 ,and REGN 6XDG 24 were retrieved from PDB RCSB database. In addition, the crystal structure of the hACE2 receptor (PDB ID: 7A97) and S protein (7AD1) was also retrieved 25 . The Swiss model was used to create the RBD mutants (Omicron, Delta AY.1, AY.2, and AY.3) 26 . In the Swiss model, 7AD1 was used as a template for homology modelling of mutations. A Modrefiner was also employed to reduce the energy of the mutant structure 27 . PDB-Sum was used to evaluate the simulated structure 28 .The structure of the spike glycoprotein was preprocessed by eliminating all nonstandard residues, including water molecules, and replacing them with hydrogen atoms using the Discovery studio programme 29 . In addition, the monomeric structure of the protein was examined for further research. By eliminating the spike glycoprotein chain from the complex and other nonstandard residues with the discovery studio, other antibodies-based complex structures were retrieved. The structure of the ACE2R was similarly constructed and preprocessed. The Psipred online server 30 predicted the physicochemical characteristics and secondary structure of Omicron and wild RBD as well as the protein disorderness of wild, Omicron, and Delta variants. By using multalign, a chimaera tool was used to superimpose wild and mutant RBD structures. The distance matrix of the wild and mutant structures was calculated by the superpose tool 31 . The difference distance matrix algorithm was used to visually discover substantial differences between any two structures. The PatchDock server 32,33 was used to dock RBD mutant variants with specified targets (ACE2R and distinct five monoclonal antibody structures), with an RMSD of 4.0 and complex type as default. The geometric form complementarity score was used to conduct the docking investigation. A higher score suggests a stronger affinity for binding. The docking scores and interaction at the RBD areas determine the outcome of the results. LigPlot plus v2.2 was used to view protein-protein and antibody-protein interactions 34 . Antibody scripts under the antibody loop numbering scheme, i.e., the KABAT Scheme and the DIMPLOT script algorithm package integrated into LigPlot plus v2.2, were used to perform molecular interactions of antibodies and ACE2R with RBD variants. GROMACS was used to investigate the molecular dynamics of wild-type and mutant RBD Spike variants. On the basis of protein dynamics, MD simulation was used to produce time-dependent conformational alterations and protein modifications. The GROMACS96 54a7 force field 35 was used for the MD simulation study. To cope with dissolvable water surrounding protein, The XMGRACE application was used to visualise the MD trajectory data 36 . The docking analysis of the RBD region of Omicron and Delta variants (AY.1, AY.2, & AY. 3) with ACE2R showed differences in binding affinity when compared with the wild SARS-CoV-2 (original strain) spike-RBD region. The binding score determines the binding affinity. The higher the binding score, the higher the binding affinity. The binding score of ACE2R-Omicron RBD is higher (18208) than that of ACE2R-wild RBD, which is 17910, but it is less than ACE2R-Delta AY. 3 (19084) . The ACE2R-Delta AY.1 & 2 binding score 16886 is the lowest of all (Table 1) The RMSD values of wild-type and mutant proteins were compared to better understand the impact of mutations on protein structure. We calculated the RMSD for all proteins' backbones with reference to their original structures during the molecular dynamics simulation. The structure of Omicron and Delta AY.3 swings more than wild and Delta AY. In summary this study anticipated more binding affinity of Omicron variant with ACE2R while lower affinity for neutralizing antibodies in contrast to wild type and Delta variant AY.1 & 2. However, Delta AY.3 shows highest binding affinity for ACE2R in contrast to Omicron variant. In addition Delta AY.3 and Omicron variant is likely to be relatively unstable and highly compact protein structure that may lead to more pathogenicity as well as antibody escape than wild and N764K, D796Y, N856K, Q954H) in the fusion region. This may affect the host-pathogen interactions and ultimately transmissibility which need further validation from real-world data. Banaras Hindu University in Varanasi, India, supplied the internet and computer resources for this project. Prashant Ranjan, Neha are supported by the RET fellowship at BHU; Chandra Devi, DBT JRF; Kaviyapriya A. D Summer intern supported by Indian Academy of Sciences Fellowship. The authors declare that they have no any conflict of interest to more prominent structures.Thedifference distance plot i n Superpose shows six graded cutoffs. White depicts difference between 0 and 1.5 Angstroms, yellow depicts difference between 1.5 and 3.0 Angstroms, light green depictsdifference between 3.0 and 5.0 Angstroms, dark turquoise depictsdifference between 5 and 7 Angstroms, dark blue depictsdifference between 7 and 9 Angstroms, and black depicts difference between more than 9 Angstroms. Clinical characteristics of laboratory confirmed positive cases of SARS-CoV-2 infection in Wuhan, China: A retrospective single center analysis Effectiveness of Covid-19 vaccines against the B. 1.617. 2 (Delta) variant Coronaviruses: an overview of their replication and pathogenesis SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding Priming of SARS-CoV-2 S protein by several membrane-bound serine proteinases could explain enhanced viral infectivity and systemic COVID-19 infection Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus Impact of the Delta variant on vaccine efficacy and response strategies Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy Phe-157/del mutation in NTD of spike protein in B. 1.167. 2 lineage of SARS-CoV-2 leads to immune evasion through antibody escape Rapid displacement of SARS-CoV-2 variant B. 1.1. 7 by B. 1.617. 2 and P. 1 in the United States Viral infection and transmission in a large well-traced outbreak caused by the Delta SARS-CoV-2 variant SARS-CoV-2 B. 1.617. 2 Delta variant replication and immune evasion SARS-CoV-2 variants of concern and variants under investigation in England Emergence and phenotypic characterization of C. 1.2, a globally detected lineage that rapidly accumulated mutations of concern The biological and clinical significance of emerging SARS-CoV-2 variants A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV. Science (80-. ) A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2. Science (80-. ) A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2 Human neutralizing antibodies elicited by SARS-CoV-2 infection Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail. Science (80-. ) A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features The RosettaDock server for local protein-protein docking Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization PDBsum: Structural summaries of PDB entries Biovia, discovery studio modeling environment The PSIPRED protein structure prediction server SuperPose: a simple server for sophisticated structural superposition Understanding the impact of missense mutations on the structure and function of the EDA gene in X linked hypohidrotic ectodermal dysplasia: A bioinformatics approach A rational drug designing: What bioinformatics approach tells about the wisdom of practicing traditional medicines for screening the potential of Ayurvedic and natural compounds for their inhibitory effect LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions Bioinformatics analysis of SARS-CoV-2 RBD mutant variants and insights into antibody and ACE2 receptor binding Molecular dynamics simulations and principal component analysis on human laforin mutation W32G and W32G/K87A STAT3 signalling is required for leptin regulation of energy balance but not reproduction Structural studies of tau protein and Alzheimer paired helical filaments show no evidence for beta-structure Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science (80-. ) The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses Neutralization of SARS-CoV-2 lineage B. 1.1. 7 pseudovirus by BNT162b2 vaccine-elicited human sera. Science (80-. ) Antibody resistance of SARS-CoV-2 variants B. 1.351 and B. 1.1. 7 Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings SARS-CoV-2 variants, spike mutations and immune escape Emergence and expansion of the SARS-CoV-2 variant B. 1.526 identified in New York Mutation-induced changes in the receptor-binding interface of the SARS-CoV-2 Delta variant B. 1.617. 2 and implications for immune evasion Amyotrophic lateral sclerosis type 20-In Silico analysis and molecular dynamics simulation of hnRNPA1 Current updates on computer aided protein modeling and designing Hydrogen bonds in proteins: role and strength. eLS