Structural and energetic profiling of SARS-CoV-2 antibody recognition and the impact of circulating variants (original) (raw)
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Currently, SARS-CoV-2 causing coronavirus disease 2019 (COVID-19) is responsible for one of the most deleterious pandemics of our time. The interaction between the ACE2 receptors at the surface of human cells and the viral Spike (S) protein triggers the infection, making the receptor-binding domain (RBD) of the SARS-CoV-2 S-protein a focal target for the neutralizing antibodies (Abs). Despite the recent progress in the development and deployment of vaccines, the emergence of novel variants of SARS-CoV-2 insensitive to Abs produced in response to the vaccine administration and/or monoclonal ones represent a potential danger. Here, we analyzed the diversity of neutralizing Ab epitopes and assessed the possible effects of single and multiple mutations in the RBD of SARS-CoV-2 S-protein on its binding affinity to various antibodies and the human ACE2 receptor using bioinformatics approaches. The RBD-Ab complexes with experimentally resolved structures were grouped into four clusters wit...
Vaccines
Coronavirus disease-2019 (COVID-19) is a pandemic with a high morbidity rate occurring over recent years. COVID-19 is caused by the severe acute respiratory syndrome causing coronavirus type-2 (SARS-CoV-2). COVID-19 not only challenged mankind but also gave scope to the evolution of various vaccine design technologies. Although these vaccines protected and saved many lives, with the emerging viral strains, some of the strains may pose a threat to the currently existing vaccine design that is primarily based on the wild type spike protein of SARS-CoV-2. To evaluate the risk involved from such mutant viral strains, we performed a systematic in silico amino acid substitution of critical residues in the receptor binding domain (RBD) of the spike protein. Our molecular modeling analysis revealed significant topological changes in the RBD of spike protein suggesting that they could potentially contribute to the loss of antigen specificity for the currently existing therapeutic antibodies/...
Uncovering a conserved vulnerability site in SARS‐CoV‐2 by a human antibody
EMBO Molecular Medicine, 2021
An essential step for SARS-CoV-2 infection is the attachment to the host cell receptor by its Spike receptor-binding domain (RBD). Most of the existing RBD-targeting neutralizing antibodies block the receptor-binding motif (RBM), a mutable region with the potential to generate neutralization escape mutants. Here, we isolated and structurally characterized a non-RBMtargeting monoclonal antibody (FD20) from convalescent patients. FD20 engages the RBD at an epitope distal to the RBM with a K D of 5.6 nM, neutralizes SARS-CoV-2 including the current Variants of Concern such as B.1.1.7, B.1.351, P.1, and B.1.617.2 (Delta), displays modest cross-reactivity against SARS-CoV, and reduces viral replication in hamsters. The epitope coincides with a predicted "ideal" vulnerability site with high functional and structural constraints. Mutation of the residues of the conserved epitope variably affects FD20-binding but confers little or no resistance to neutralization. Finally, in vitro mode-of-action characterization and negative-stain electron microscopy suggest a neutralization mechanism by which FD20 destructs the Spike. Our results reveal a conserved vulnerability site in the SARS-CoV-2 Spike for the development of potential antiviral drugs.
Journal of Chemical Information and Modeling
The SARS-CoV-2 spike (S) protein is exposed on the viral surface and is the first point of contact between the virus and the host. For these reasons it represents the prime target for Covid-19 vaccines. In recent months, variants of this protein have started to emerge. Their ability to reduce or evade recognition by S-targeting antibodies poses a threat to immunological treatments and raises concerns for their consequences on vaccine efficacy. To develop a model able to predict the potential impact of S-protein mutations on antibody binding sites, we performed unbiased multi-microsecond molecular dynamics of several glycosylated S-protein variants and applied a straightforward structure-dynamics-energy based strategy to predict potential changes in immunogenic regions on each variant. We recover known epitopes on the reference D614G sequence. By comparing our results, obtained on isolated S-proteins in solution, to recently published data on antibody binding and reactivity in new S variants, we directly show that modifications in the S-protein consistently translate into the loss of potentially immunoreactive regions. Our findings can thus be qualitatively reconnected to the experimentally characterized decreased ability of some of the Abs elicited against the dominant Ssequence to recognize variants. While based on the study of SARS-CoV-2 spike variants, our computational epitope-prediction strategy is portable and could be applied to study immunoreactivity in mutants of proteins of interest whose structures have been characterized, helping the development/selection of vaccines and antibodies able to control emerging variants.
2022
ABSTRACTA highly efficient and robust multiple scales in silico protocol, consisting of atomistic constant charge Molecular Dynamics (MD), constant-charge coarse-grain (CG) MD and constant-pH CG Monte Carlo (MC), has been used to study the binding affinities, the free energy of complexation of selected antigen-binding fragments of the monoclonal antibody (mAbs) CR3022 (originally derived from SARS-CoV-1 patients almost two decades ago) and 11 SARS-CoV-2 variants including the wild type. CR3022 binds strongly to the receptor-binding domain (RBD) of SARS-CoV-2 spike protein, but chooses a different site rather than the receptor-binding motif (RBM) of RBD, allowing its combined use with other mAbs against new emerging virus variants. Totally 235,000 mAbs structures were generated using the RosettaAntibodyDesign software, resulting in top 10 scored CR3022-RBD complexes with critical mutations and compared to the native one, all having the potential to block virus-host cell interaction. ...
In silico analysis of SARS-CoV-2 spike glycoprotein and insights into antibody binding
Research Ideas and Outcomes
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China in December 2019. Since then, COVID-19, the disease caused by SARS-CoV-2, has become a rapidly spreading pandemic that has reached most countries in the world. So far, there are no vaccines or therapeutics to fight this virus. Here, I present an in silico analysis of the virus spike glycoprotein (recently determined at atomic resolution) and provide insights into how antibodies against the 2002 virus SARS-CoV might be modified to neutralize SARS-CoV-2. I ran docking experiments with Rosetta Dock to determine which substitutions in the 80R and m396 antibodies might improve the binding of these to SARS-CoV-2 and used molecular visualization and analysis software, including UCSF Chimera and Rosetta Dock, as well as other bioinformatics tools, including SWISS-MODEL. Supercomputers, including Bridges Large, Stampede and Frontera, were used for macromolecular assemblies and large scale analysis and visual...
Frontiers in Molecular Biosciences, 2022
The COVID-19 pandemic resulting from the spread of SARS-CoV-2 spurred devastating health and economic crises around the world. Neutralizing antibodies and licensed vaccines were developed to combat COVID-19, but progress was slow. In addition, variants of the receptor-binding domain (RBD) of the spike protein confer resistance of SARS-CoV-2 to neutralizing antibodies, nullifying the possibility of human immunity. Therefore, investigations into the RBD mutations that disrupt neutralization through convalescent antibodies are urgently required. In this study, we comprehensively and systematically investigated the binding stability of RBD variants targeting convalescent antibodies and revealed that the RBD residues F456, F490, L452, L455, and K417 are immune-escaping hotspots, and E484, F486, and N501 are destabilizing residues. Our study also explored the possible modes of actions of emerging SARS-CoV-2 variants. All results are consistent with experimental observations of attenuated ...
SARS-CoV-2 antibodies recognize 23 distinct epitopic sites on the receptor binding domain
Research Square (Research Square), 2023
The COVID-19 pandemic and SARS-CoV-2 variants have dramatically illustrated the need for a better understanding of antigen (epitope)-antibody (paratope) interactions. To gain insight into the immunogenic characteristics of epitopic sites (ES), we systematically investigated the structures of 340 Abs and 83 nanobodies (Nbs) complexed with the Receptor Binding Domain (RBD) of the SARS-CoV-2 spike protein. We identified 23 distinct ES on the RBD surface and determined the frequencies of amino acid usage in the corresponding CDR paratopes. We describe a clustering method for analysis of ES similarities that reveals binding motifs of the paratopes and that provides insights for vaccine design and therapies for SARS-CoV-2, as well as a broader understanding of the structural basis of Ab-protein antigen (Ag) interactions.
BMC Molecular and Cell Biology, 2022
Background SARS-CoV-2, the causative agent of COVID-19 pandemic is a RNA virus prone to mutations. Formation of a stable binding interface between the Receptor Binding Domain (RBD) of SARS-CoV-2 Spike (S) protein and Angiotensin-Converting Enzyme 2 (ACE2) of host is pivotal for viral entry. RBD has been shown to mutate frequently during pandemic. Although, a few mutations in RBD exhibit enhanced transmission rates leading to rise of new variants of concern, most RBD mutations show sustained ACE2 binding and virus infectivity. Yet, how all these mutations make the binding interface constantly favourable for virus remain enigmatic. This study aims to delineate molecular rearrangements in the binding interface of SARS-CoV-2 RBD mutants. Results Here, we have generated a mutational and structural landscape of SARS-CoV-2 RBD in first six months of the pandemic. We analyzed 31,403 SARS-CoV-2 genomes randomly across the globe, and identified 444 non-synonymous mutations in RBD that cause 4...
2023
Background: The SARS-CoV-2 pandemic, caused by the novel coronavirus, has posed a significant global health threat since its emergence in late 2019. The World Health Organization declared the outbreak a pandemic on March 11, 2020, due to its rapid global spread and impact on public health. New variants have raised concerns about their potential impact on the transmission of the virus and the effectiveness of current diagnostic tools, treatments, and vaccines. This study aims to investigate the effect of new variants in Pakistani virus strains on human receptors, specifically ACE2 and NRP1. In-silico analysis provides a powerful tool to analyze the potential impact of new variants on protein structure, function, and interactions. Objectives: The SARS-CoV-2 virus is evolving quickly. After being exposed in Wuhan, SARS-CoV-2 underwent numerous mutations, leading to several variants' emergence. These variants stabilize the interaction of spike protein with human receptors ACE2 and NRP1. The study aims to check the molecular effect of these variants on human receptors using the in-silico approach. Material and methods: We use in-silico mutational tools to analyze new variants in SARS-CoV-2 and to check the molecular interaction of spike protein with human receptors (ACE2 and NRP1). Genomic sequences of 41 SARS-CoV-2 strains were sequenced using Ion Torrent (NGS) and submitted to the GISAID database. Spike protein of SARS-CoV-2 sequence trimmed and translated into a protein sequence using ExPasy. We used multiple sequence alignments to check for variants in the spike protein of strains. We utilized mutation tools such as Mupro, SIFT, SNAP2, and Mutpred2.3D structures of SARS-CoV-2 spike proteins (wild and mutated) to analyze further the mutations, ACE2 and NRP1 modelled by the ITASSER protein modelling server. Interactions of spike proteins (wild and mutant) analyzed by MD Docking, Simulation, and MMGBSA Results: Variants I210T, V213G, S371F, S373P, T478K, F486V, Y505H, and D796Y were identified in SARS-CoV-2 Pakistani strains' spike protein. Variant Y505H were found to affect protein function. MD Docking, MMGBSA and MD simulation revealed that these variants increased spike protein's binding affinity with human receptors (ACE2 and NRP1). MD simulation revealed that mutated spike protein stabilized earlier than wild when interacting with ACE2 after 40 ns and interaction with NRP1 stabilized after 30 ns for mutated spike protein compared to wild. Conclusion: These variants in Pakistani strains of SARS-CoV-2 are increasing the stability of spike protein with human receptors. These findings provide insight into how the SARS-CoV-2 virus evolves and adapts to human hosts. This information may help develop strategies to control the virus's spread and develop effective treatments and vaccines in the future.