Systems analysis shows that thermodynamic physiological and pharmacological fundamentals drive COVID-19 and response to treatment

The valley of death: why Australia failed to develop clinically effective drugs in COVID-19

There is a paucity of public discussion of costs spent on drug trials during coronavirus disease 2019 (COVID-19) and their value, and of large public outlay on research funding for vaccine and drug development that did not deliver medicines nor vaccines for Australians. This oversight left us at the behest of global supply chains, politics and commercial cost-plus pricing for vaccines. It is possible that these outcomes were the result of some major cognitive biases and the failure of a clinical pharmacologist's voice in the leadership teams. Biases included unawareness of the complexities of taking interesting chemicals in vitro to development into therapeutic use that can be tolerated, show efficacy and have appropriate disposition in humans; lack of a systems approach to therapeutic development; and an understanding of the relevance and translatability of pharmacology, physiology and clinical drug development. We believe that reflecting on and addressing these biases will help Australia reposition itself better with a therapeutics and clinical trial strategy for future pandemics, built into the strategy of a Centre for Disease Control.

SARS-CoV-2 strain wars continues: Chemical and thermodynamic characterization of live matter and biosynthesis of Omicron BN.1, CH.1.1 and XBC variants

SARS-CoV-2 has during the last 3 years mutated several dozen times. Most mutations in the newly formed variants have been chemically and thermodynamically characterized. New variants have been declared as variants under monitoring. The European Centre for Disease Prevention and Control has suggested the hypothesis that the new BN.1, CH.1.1 and XBC variants could have properties similar to those of VOC. Thermodynamic properties of new variants have been reported in this manuscript for the first time. Gibbs energy of biosynthesis, as the driving force for viral multiplication, is less negative for the new variants than for the earlier variants. This indicates that the virus has evolved towards decrease in pathogenicity, which leads to less severe forms of COVID-19.

Ghosts of the past: Elemental composition, biosynthesis reactions and thermodynamic properties of Zeta P.2, Eta B.1.525, Theta P.3, Kappa B.1.617.1, Iota B.1.526, Lambda C.37 and Mu B.1.621 variants of SARS-CoV-2

From the perspectives of molecular biology, genetics and biothermodynamics, SARS-CoV-2 is the among the best characterized viruses. Research on SARS-CoV-2 has shed a new light onto driving forces and molecular mechanisms of viral evolution. This paper reports results on empirical formulas, biosynthesis reactions and thermodynamic properties of biosynthesis (multiplication) for the Zeta P.2, Eta B.1.525, Theta P.3, Kappa B.1.617.1, Iota B.1.526, Lambda C.37 and Mu B.1.621 variants of SARS-CoV-2. Thermodynamic analysis has shown that the physical driving forces for evolution of SARS-CoV-2 are Gibbs energy of biosynthesis and Gibbs energy of binding. The driving forces have led SARS-CoV-2 through the evolution process from the original Hu-1 to the newest variants in accordance with the expectations of the evolution theory.

XBB.1.5 Kraken cracked: Gibbs energies of binding and biosynthesis of the XBB.1.5 variant of SARS-CoV-2

The SARS-CoV-2 Hydra with many heads (variants) has been causing the COVID-19 pandemic for 3 years. The appearance of every new head (SARS-CoV-2 variant) causes a new pandemic wave. The last in the series is the XBB.1.5 "Kraken" variant. In the general public (social media) and in the scientific community (scientific journals), during the last several weeks since the variant has appeared, the question was raised of whether the infectivity of the new variant will be greater. This article attempts to provide the answer. Analysis of thermodynamic driving forces of binding and biosynthesis leads to the conclusion that infectivity of the XBB.1.5 variant could be increased to a certain extent. The pathogenicity of the XBB.1.5 variant seems to be unchanged compared to the other Omicron variants.

Never ending story? Evolution of SARS-CoV-2 monitored through Gibbs energies of biosynthesis and antigen-receptor binding of Omicron BQ.1, BQ.1.1, XBB and XBB.1 variants

RNA viruses exhibit a great tendency to mutate. Mutations occur in the parts of the genome that encode the spike glycoprotein and less often in the rest of the genome. This is why Gibbs energy of binding changes more than that of biosynthesis. Starting from 2019, the wild type that was labeled Hu-1 has during the last 3 years evolved to produce several dozen new variants, as a consequence of mutations. Mutations cause changes in empirical formulas of new virus strains, which lead to change in thermodynamic properties of biosynthesis and binding. These changes cause changes in the rate of reactions of binding of virus antigen to the host cell receptor and the rate of virus multiplication in the host cell. Changes in thermodynamic and kinetic parameters lead to changes in biological parameters of infectivity and pathogenicity. Since the beginning of the COVID-19 pandemic, SARS-CoV-2 has been evolving towards increase in infectivity and maintaining constant pathogenicity, or for some variants a slight decrease in pathogenicity. In the case of Omicron BQ.1, BQ.1.1, XBB and XBB.1 variants pathogenicity is identical as in the Omicron BA.2.75 variant. On the other hand, infectivity of the Omicron BQ.1, BQ.1.1, XBB and XBB.1 variants is greater than those of previous variants. This will most likely result in the phenomenon of asymmetric coinfection, that is circulation of several variants in the population, some being dominant.

Why doesn't Ebola virus cause pandemics like SARS-CoV-2?

Ebola virus is among the most dangerous, contagious and deadly etiological causes of viral diseases. However, Ebola virus has never extensively spread in human population and never have led to a pandemic. Why? The mechanistic biophysical model revealing the biothermodynamic background of virus-host interaction) could help us to understand pathogenesis of Ebola virus disease (earlier known as the Ebola hemorrhagic fever). In this paper for the first time the empirical formula, thermodynamic properties of biosynthesis (including the driving force of virus multiplication in the susceptible host), binding constant and thermodynamic properties of binding are reported. Thermodynamic data for Ebola virus were compared with data for SARS-CoV-2 to explain why SARS-CoV-2 has caused a pandemic, while Ebola remains on local epidemic level. The empirical formula of the Ebola virus was found to be CH_1.569O_0.3281N_0.2786P_0.00173S_0.00258. Standard Gibbs energy of biosynthesis of the Ebola virus nucleocapsid is -151.59 kJ/C-mol.

Strain wars 3: Differences in infectivity and pathogenicity between Delta and Omicron strains of SARS-CoV-2 can be explained by thermodynamic and kinetic parameters of binding and growth

In this paper, for the first time, empirical formulas have been reported of the Delta and Omicron strains of SARS-CoV-2. The empirical formula of the Delta strain entire virion was found to be CH_1.6383O_0.2844N_0.2294P_0.0064S_0.0042, while its nucleocapsid has the formula CH_1.5692O_0.3431N_0.3106P_0.0060S_0.0043. The empirical formula of the Omicron strain entire virion was found to be CH_1.6404O_0.2842N_0.2299P_0.0064S_0.0038, while its nucleocapsid has the formula CH_1.5734O_0.3442N_0.3122P_0.0060S_0.0033. Based on the empirical formulas, standard thermodynamic properties of formation and growth have been calculated and reported for the Delta and Omicron strains. Moreover, standard thermodynamic properties of binding have been reported for Wild type (Hu-1), Alpha, Beta, Gamma, Delta and Omicron strains. For all the strains, binding phenomenological coefficients and antigen-receptor (SGP-ACE2) binding rates have been determined and compared, which are proportional to infectivity. The results show that the binding rate of the Omicron strain is between 1.5 and 2.5 times greater than that of the Delta strain. The Omicron strain is characterized by a greater infectivity, based on the epidemiological data available in the literature. The increased infectivity was explained in this paper using Gibbs energy of binding. However, no indications exist for decreased pathogenicity of the Omicron strain. Pathogenicity is proportional to the virus multiplication rate, while Gibbs energies of multiplication are very similar for the Delta and Omicron strains. Thus, multiplication rate and pathogenicity are similar for the Delta and Omicron strains. The lower number of severe cases caused by the Omicron strain can be explained by increased number of immunized people. Immunization does not influence the possibility of occurrence of infection, but influences the rate of immune response, which is much more efficient in immunized people. This leads to prevention of more severe Omicron infection cases.

Strain wars 5: Gibbs energies of binding of BA.1 through BA.4 variants of SARS-CoV-2

This paper reports, for the first time, standard Gibbs energies of binding of the BA.1, BA.2, BA.3, BA.2.13, BA.2.12.1 and BA.4 Omicron variants of SARS-CoV-2, to the Human ACE2 receptor. Variants BA.1 through BA.3 exhibit a trend of decreasing standard Gibbs energy of binding and hence increased infectivity. The BA.4 variant exhibits a less negative standard Gibbs energy of binding, but also more efficient evasion of the immune response. Therefore, it was concluded that all the analyzed strains evolve in accordance with expectations of the theory of evolution, albeit using different strategies.

Strain wars 4 - Darwinian evolution through Gibbs' glasses: Gibbs energies of binding and growth explain evolution of SARS-CoV-2 from Hu-1 to BA.2

All processes in nature are driven by negative Gibbs energy. Gibbs energy is used by various viruses and their strains to hijack host cell metabolic machinery. The analysis was made by using the atom counting method to obtain elemental compositions and Gibbs energy of growth of the BA.2 strain of SARS-CoV-2. Moreover, Gibbs energy of binding was determined for the BA.2 strain. The properties of BA.2 were compared to those of Hu-1, Delta and Omicron strains. It is concluded that SARS-CoV-2 has evolved by making its Gibbs energy of binding more negative. Hence, it seems that the change in Gibbs energy of binding plays the major role in SARS-CoV-2 evolution. Therefore, Gibbs energy difference between various strains represents the possible mechanism of Darwinian evolution of viruses. In particular, a virus evolves through mutations, resulting in change in information content, elemental composition, increase in infectivity and decrease in pathogenicity.

"LONG COVID"-A hypothesis for understanding the biological basis and pharmacological treatment strategy

Infection of humans with SARS‐CoV‐2 virus causes a disease known colloquially as “COVID‐19” with symptoms ranging from asymptomatic to severe pneumonia. Initial pathology is due to the virus binding to the ACE‐2 protein on endothelial cells lining blood vessels and entering these cells in order to replicate. Viral replication causes oxidative stress due to elevated levels of reactive oxygen species. Many (~60%) of the infected people appear to have eliminated the virus from their body after 28 days and resume normal activity. However, a significant proportion (~40%) experience a variety of symptoms (loss of smell and/or taste, fatigue, cough, aching pain, “brain fog,” insomnia, shortness of breath, and tachycardia) after 12 weeks and are diagnosed with a syndrome named “LONG COVID.” Longitudinal clinical studies in a group of subjects who were infected with SARS‐CoV‐2 have been compared to a non‐infected matched group of subjects. A cohort of infected subjects can be identified by a battery of cytokine markers to have persistent, low level grade of inflammation and often self‐report two or more troubling symptoms. There is no drug that will relieve their symptoms effectively. It is hypothesized that drugs that activate the intracellular transcription factor, nuclear factor erythroid‐derived 2‐like 2 (NRF2) may increase the expression of enzymes to synthesize the intracellular antioxidant, glutathione that will quench free radicals causing oxidative stress. The hormone melatonin has been identified as an activator of NRF2 and a relatively safe chemical for most people to ingest chronically. Thus, it is an option for consideration of re‐purposing studies in “LONG COVID” subjects experiencing insomnia, depression, fatigue, and “brain fog” but not tachycardia. Appropriately designed clinical trials are required to evaluate melatonin.