What is it about?
The receptor binding domain of SARS-CoV-2 (the virus of the Covid-19 pandemic) attaches to the human cell via a protein called angiotensin-converting enzyme 2 (ACE2). Exposing the properties of this attachment process is crucial for the development of vaccines and drugs. From this viewpoint, the authors computed the binding energies between the human ACE2 and and SARS-CoV-2 using an accurate tool called density functional theory (DFT). The original strain, delta variant and the omicron variant of SARS-CoV-2 are considered for the computations. The DFT computations are performed without fragmenting the interfaces to involve longer-range interactions for improved accuracy, which is one of the primary features of the approach used in this study. The binding energies of the original strain, delta and omicron variants to the human ACE2 are computed as -4.76 eV, -6.68 eV and -11.77 eV, respectively. These binding energy values imply that the binding of the omicron variant to the ACE2 is much more favorable than the binding of the original strain and the delta variant, which may constitute a molecular reason for the takeover of the omicron variant.
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Why is it important?
The results of this paper are important as the binding energies of the delta and omicron variants to the human cell are computed employing density functional theory for the first time. The roots of the differences of the binding energies are explained using energy decomposition which may be helpful for the analysis of the attachment processes leading to Covid-19 infections.
Perspectives
Computational approaches are vital for a lot of research areas and its importance has also been demonstrated during the pandemic for the global fight against SARS-CoV-2. The atomic level model of viruses can be obtained using various physical techniques and the virtual model of these viruses can be inspected and processed in computational environments. As usual, there is a trade-off between the size of the model and the computational cost. Fortunately, state of the art computational algorithms combined with fast simulation servers finally enables us to compute various properties of biological molecules and their interactions in an acceptable accuracy level. The future will probably offer much more possibilities and maybe one day, we will hopefully be able to simulate the molecular dynamics and interactions of complete models of pathogens and human cells in real time.
Serhan Yamacli
Nuh Naci Yazgan Universitesi
Read the Original
This page is a summary of: Computation of the Binding Energies between Human ACE2 and Spike RBDs of the Original Strain, Delta and Omicron Variants of the SARS‐CoV‐2: A DFT Simulation Approach, Advanced Theory and Simulations, September 2022, Wiley,
DOI: 10.1002/adts.202200337.
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