Assessing the interaction between hemoglobin and the receptor binding domain of SARS-CoV-2 spike protein through MARTINI coarse-grained molecular dynamics

The emergence of different coronavirus-related diseases in the 2000's (SARS, MERS, and Covid-19) warrants the need of a complete understanding of the pathological, biological, and biochemical behavior of this class of pathogens. Great attention has been paid to the SARS-CoV-2 Spike protein, and its interaction with the human ACE2 has been thoroughly investigated. Recent findings suggested that the SARS-CoV-2 components may interact with different human proteins, and hemoglobin has very recently been demonstrated as a potential target for the Spike protein. Here we have investigated the interaction between either adult or fetal hemoglobin and the receptor binding domain of the Spike protein at molecular level through advanced molecular dynamics techniques and proposed rational binding modes and energy estimations. Our results agree with biochemical data previously reported in literature. We also demonstrated that co-incubation of pulmonary epithelial cells with hemoglobin strongly reduces the pro-inflammatory effects exerted by the concomitant administration of Spike protein.

Spike-specific humoral and cellular immune responses after COVID-19 mRNA vaccination in patients with cirrhosis: A prospective single center study

BACKGROUND AND AIMS

COVID-19 mRNA vaccines were approved to prevent severe forms of the disease, but their immunogenicity and safety in cirrhosis is poorly known.

METHOD

In this prospective single-center study enrolling patients with cirrhosis undergoing COVID-19 vaccination (BNT162b2 and mRNA-1273), we assessed humoral and cellular responses vs healthy controls, the incidence of breakthrough infections and adverse events (AEs). Antibodies against spike- and nucleocapsid-protein (anti-S and anti-N) and Spike-specific T-cells responses were quantified at baseline, 21 days after the first and second doses and during follow-up.

RESULTS

182 cirrhotics (85% SARS-CoV-2-naïve) and 38 controls were enrolled. After 2 doses of vaccine, anti-S titres were significantly lower in cirrhotics vs controls [1,751 (0.4-25,000) U/mL vs 4,523 (259-25,000) U/mL, p=0.012] and in SARS-CoV-2-naïve vs previously infected cirrhotics [999 (0.4-17,329) U/mL vs 7,500 (12.5-25,000) U/mL, (p<0.001)]. T-cell responses in cirrhotics were similar to controls, although with different kinetics. In SARS-CoV-2-naïve cirrhotics, HCC, Child-Pugh B/C and BNT162b2 were independent predictors of low response. Neither unexpected nor severe AEs emerged. During follow-up, 2% turned SARS-CoV-2 positive, all asymptomatic.

CONCLUSION

Humoral response to COVID-19 vaccines appeared suboptimal in patients with cirrhosis, particularly in SARS-CoV-2-naïve decompensated cirrhotics, although cellular response appeared preserved, and low breakthrough infections rate was registered.

Stability and expression of SARS-CoV-2 spike-protein mutations

Protein fold stability likely plays a role in SARS-CoV-2 S-protein evolution, together with ACE2 binding and antibody evasion. While few thermodynamic stability data are available for S-protein mutants, many systematic experimental data exist for their expression. In this paper, we explore whether such expression levels relate to the thermodynamic stability of the mutants. We studied mutation-induced SARS-CoV-2 S-protein fold stability, as computed by three very distinct methods and eight different protein structures to account for method- and structure-dependencies. For all methods and structures used (24 comparisons), computed stability changes correlate significantly (99% confidence level) with experimental yeast expression from the literature, such that higher expression is associated with relatively higher fold stability. Also significant, albeit weaker, correlations were seen between stability and ACE2 binding effects. The effect of thermodynamic fold stability may be direct or a correlate of amino acid or site properties, notably the solvent exposure of the site. Correlation between computed stability and experimental expression and ACE2 binding suggests that functional properties of the SARS-CoV-2 S-protein mutant space are largely determined by a few simple features, due to underlying correlations. Our study lends promise to the development of computational tools that may ideally aid in understanding and predicting SARS-CoV-2 S-protein evolution.

Effect of Delta and Omicron Mutations on the RBD-SD1 Domain of the Spike Protein in SARS-CoV-2 and the Omicron Mutations on RBD-ACE2 Interface Complex

The receptor-binding domain (RBD) is the essential part in the Spike-protein (S-protein) of SARS-CoV-2 virus that directly binds to the human ACE2 receptor, making it a key target for many vaccines and therapies. Therefore, any mutations at this domain could affect the efficacy of these treatments as well as the viral-cell entry mechanism. We introduce ab initio DFT-based computational study that mainly focuses on two parts: (1) Mutations effects of both Delta and Omicron variants in the RBD-SD1 domain. (2) Impact of Omicron RBD mutations on the structure and properties of the RBD-ACE2 interface system. The in-depth analysis is based on the novel concept of amino acid-amino acid bond pair units (AABPU) that reveal the differences between the Delta and/or Omicron mutations and its corresponding wild-type strain in terms of the role played by non-local amino acid interactions, their 3D shapes and sizes, as well as contribution to hydrogen bonding and partial charge distributions. Our results also show that the interaction of Omicron RBD with ACE2 significantly increased its bonding between amino acids at the interface providing information on the implications of penetration of S-protein into ACE2, and thus offering a possible explanation for its high infectivity. Our findings enable us to present, in more conspicuous atomic level detail, the effect of specific mutations that may help in predicting and/or mitigating the next variant of concern.

mRNA vaccines for COVID-19 and diverse diseases

Since its outbreak in late 2019, the novel coronavirus disease 2019 (COVID-19) has spread to every continent on the planet. The global pandemic has affected human health and socioeconomic status around the world. At first, the global response to the pandemic was to isolate afflicted individuals to prevent the virus from spreading, while vaccine development was ongoing. The genome sequence was first presented in early January 2020, and the phase I clinical trial of the vaccine started in March 2020 in the United States using novel lipid-based nanoparticle (LNP), encapsulated with mRNA termed as mRNA-1273. Till now, various mRNA-based vaccines are in development, while one mRNA-based vaccine got market approval from US-FDA for the prevention of COVID-19. Previously, mRNA-based vaccines were thought to be difficult to develop, but the current development is a significant accomplishment. However, widespread production and global availability of mRNA-based vaccinations to combat the COVID-19 pandemic remains a major challenge, especially when the mutations continually occur on the virus (e.g., the recent outbreaks of Omicron variant). This review elaborately discusses the COVID-19 pandemic, the biology of SARS-CoV-2 and the progress of mRNA-based vaccines. Moreover, the review also highlighted a detailed description of mRNA delivery technologies and the application potential in controlling other life-threatening diseases. Therefore, it provides a comprehensive view and multidisciplinary insights into mRNA therapy for broader audiences.

Age-dependent effects of the recombinant spike protein/SARS-CoV-2 on the M-CSF- and IL-34-differentiated macrophages in vitro

The SARS-CoV-2 virus causes elevated production of senescence-associated secretory phenotype (SASP) markers by macrophages. SARS-CoV-2 enters macrophages through its Spike-protein aided by cathepsin (Cat) B and L, which also mediate SASP production. Since M-CSF and IL-34 control macrophage differentiation, we investigated the age-dependent effects of the Spike-protein on SASP-related pro-inflammatory-cytokines and nuclear-senescence-regulatory-factors, and CatB, L and K, in mouse M-CSF- and IL-34-differentiated macrophages. The Spike-protein upregulated SASP expression in young and aged male M-CSF-macrophages. In contrast, only young and aged male IL-34-macrophages demonstrated significantly reduced pro-inflammatory cytokine expression in response to the Spike-protein in vitro. Furthermore, the S-protein elevated CatB expression in young male M-CSF-macrophages and young female IL-34-macrophages, whereas CatL was overexpressed in young male IL-34- and old male M-CSF-macrophages. Surprisingly, the S-protein increased CatK activity in young and aged male M-CSF-macrophages, indicating that CatK may be also involved in the COVID-19 pathology. Altogether, we demonstrated the age- and sex-dependent effects of the Spike-protein on M-CSF and IL-34-macrophages using a novel in vitro mouse model of SARS-CoV-2/COVID-19.

Ultra-large-scale ab initio quantum chemical computation of bio-molecular systems: The case of spike protein of SARS-CoV-2 virus

The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intra-molecular bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic bonding, partial charge distribution and the role played by hydrogen bond network are discussed. In the interaction among structural domains, we present new insights for crucial hinge-like movement and fusion process. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.