Strain Wars: Competitive interactions between SARS-CoV-2 strains are explained by Gibbs energy of antigen-receptor binding

Abstract

Since the beginning of the COVID-19 pandemic, SARS-CoV-2 has mutated several times into new strains, with an increased infectivity. Infectivity of SARS-CoV-2 strains depends on binding affinity of the virus to its host cell receptor. In this paper, we quantified the binding affinity using Gibbs energy of binding and analyzed the competition between SARS-CoV-2 strains as an interference phenomenon. Gibbs energies of binding were calculated for several SARS-SoV-2 strains, including Hu-1 (wild type), B.1.1.7 (alpha), B.1.351 (beta), P.1 (Gamma), B.1.36 and B.1.617 (Delta). The least negative Gibbs energy of binding is that of Hu-1 strain, -37.97 kJ/mol. On the other hand, the most negative Gibbs energy of binding is that of the Delta strain, -49.50 kJ/mol. We used the more negative Gibbs energy of binding to explain the increased infectivity of newer SARS-CoV-2 strains compared to the wild type. Gibbs energies of binding was found to decrease chronologically, with appearance of new strains. The ratio of Gibbs energies of binding of mutated strains and wild type was used to define a susceptibility coefficient, which is an indicator of viral interference, where a virus can prevent or partially inhibit infection with another virus.

Strain wars 2: Binding constants, enthalpies, entropies, Gibbs energies and rates of binding of SARS-CoV-2 variants

“…Antigen-receptor binding is a simple process, similar to protein-ligand binding ( Du et al, 2016 ; Popovic and Popovic, 2022 ). It occurs in only one step, which can be described using reaction (1) ( Du et al, 2016 ; Popovic and Popovic, 2022 ).…”

“…Antigen-receptor binding is a simple process, similar to protein-ligand binding ( Du et al, 2016 ; Popovic and Popovic, 2022 ). It occurs in only one step, which can be described using reaction (1) ( Du et al, 2016 ; Popovic and Popovic, 2022 ). Thus, analogously to protein-ligand binding, antigen-receptor binding is characterized by a set of thermodynamic properties of binding, including standard enthalpy of binding, Δ B H⁰ , standard entropy of binding, Δ B S⁰ , and standard Gibbs energy of binding, Δ B G⁰ ( Gale, 2021 , 2020 , 2019 ).…”

“…Thus, analogously to protein-ligand binding, antigen-receptor binding is characterized by a set of thermodynamic properties of binding, including standard enthalpy of binding, Δ B H⁰ , standard entropy of binding, Δ B S⁰ , and standard Gibbs energy of binding, Δ B G⁰ ( Gale, 2021 , 2020 , 2019 ). A particular set of thermodynamic properties of binding is characteristic of every virus species or strain ( Popovic and Popovic, 2022 ). Since the binding process is a simple process, it is not coupled to other processes such as ATP hydrolysis ( Gale, 2021 , 2020 , 2019 ).…”

“…Thus, equation (10c) simplifies into the binding phenomenological equation where L B is the binding phenomenological coefficient and T is temperature ( Demirel, 2014 ; Popovic and Popovic, 2022 ; Popovic and Minceva, 2021). Thus, the rate of the antigen-receptor binding reaction, r B , is a linear function of Gibbs energy of binding, Δ B G , given by the binding phenomenological equation.…”

“…Gibbs energy of growth is the driving force of growth of organisms ( Von Stockar, 2013a , 2013b ; Demirel, 2014 ; Hellingwerf et al, 1982 ; Westerhoff et al, 1982 ). Gibbs energy of binding represents the driving force for virus attachment and entry into host cell (Popovic and Minceva, 2021; Popovic and Popovic, 2022 ; Gale, 2021 , 2020 , 2019 ).…”