Thermodynamic insight into viral infections 2: empirical formulas, molecular compositions and thermodynamic properties of SARS, MERS and SARS-CoV-2 (COVID-19) viruses

Abstract

The current situation with the SARS-CoV-2 pandemic indicates the importance of new approaches in vaccine design. In order to design new attenuated vaccines, to decrease virulence of virus wild types, it is important to understand what allows a virus to hijack its host cell's metabolism, a property of all viruses. RNA and protein sequences obtained from databases were used to count the number of atoms of each element in the virions of SARS, MERS and SARS-CoV-2. The number of protein copies and carbohydrate composition were taken from the literature. The number of lipid molecules was estimated from the envelope surface area. Based on elemental composition, growth equations were balanced, and thermodynamic properties of the viruses were determined using Patel-Erickson and Battley equations. Elemental and molecular compositions of SARS, MERS and SARS-CoV-2 were found, as well as their standard thermodynamic properties of formation and growth. Standard Gibbs energy of growth of virus nucleocapsids was found to be significantly more negative than that of their host tissue. The ratio of Gibbs energies of growth of virus nucleocapsids and host cell is greater than unity. The more negative Gibbs energy of growth of viruses implies that virus multiplication has a greater driving force than synthesis of host cell components, giving a physical explanation of why viruses are able to hijack their host cell's metabolism. Knowing the mechanism of viral metabolism hijacking can open new paths for vaccine design. By manipulating chemical composition of viruses, virulence can be decreased by making the Gibbs energy of their growth less negative, resulting in decreased multiplication rate, while preserving antigenic properties.

Addressing Non-linear System Dynamics of Single-Strand RNA Virus–Host Interaction

“…The described system dynamics was experimentally validated for influenza virus ( Mahmoudabadi et al, 2017 ). Results confirmed a previous theoretical assumption, showing a Gibbs free energy for virus lower than its host ( Popovic and Minceva, 2020a , b ), when virus and host cells are evaluated separately and not as a unique system as herein proposed.…”

SARS-CoV-2 spike protein detection through a plasmonic D-shaped plastic optical fiber aptasensor

“…The effect of complex biological matrix reduced by a factor of 2 the LoD of our system, maintaining a similar affinity constant (k value), encouraging its application in biomedical field. Moreover, even if our LoD is higher than that obtained using lateral flow system [ 27 ] or ELISA assay [ 14 ], considering that the virion has a molecular weight three order of magnitude higher with respect to the spike protein [ 51 ], we expect to be able to measure the virions binding.…”

Standard Thermodynamic Properties, Biosynthesis Rates, and the Driving Force of Growth of Five Agricultural Plants

“…Data for human tissues taken from Popovic and Minceva (2020c) . Data for viruses are taken from ( Popovic and Minceva, 2020a , b ).…”

“…where L is a phenomenological coefficient and T is temperature ( Hellingwerf et al, 1982 ; Westerhoff et al, 1982 ; Von Stockar, 2013c ; Demirel, 2014 ; Popovic and Minceva, 2020a , b ). The phenomenological coefficient is a proportionality constant that takes into account the kinetic factors ( Demirel, 2014 ) and can be calculated from Equation (24) if the driving force and growth rate are known.…”

“…The remaining –4,500 kJ/C-mol represents the driving force for growth ( Von Stockar et al, 2011 ). This excess driving force is required to keep the reaction sufficiently far from equilibrium for it to occur at a desired rate, since the reaction rate is proportional to distance from equilibrium ( Hellingwerf et al, 1982 ; Westerhoff et al, 1982 ; Balmer, 2011 ; Von Stockar, 2013b , c ; Demirel, 2014 ; Popovic and Minceva, 2020a , b ).…”