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C₆₀ fullerene against SARS-CoV-2 coronavirus: an in silico insight.

ABSTRACT: Based on WHO reports the new SARS-CoV-2 coronavirus is currently widespread all over the world. So far > 162 million cases have been confirmed, including > 3 million deaths. Because of the pandemic still spreading across the globe the accomplishment of computational methods to find new potential mechanisms of virus inhibitions is necessary. According to the fact that C₆₀ fullerene (a sphere-shaped molecule consisting of carbon) has shown inhibitory activity against various protein targets, here the analysis of the potential binding mechanism between SARS-CoV-2 proteins 3CLpro and RdRp with C₆₀ fullerene was done; it has resulted in one and two possible binding mechanisms, respectively. In the case of 3CLpro, C₆₀ fullerene interacts in the catalytic binding pocket. And for RdRp in the first model C₆₀ fullerene blocks RNA synthesis pore and in the second one it prevents binding with Nsp8 co-factor (without this complex formation, RdRp can't perform its initial functions). Then the molecular dynamics simulation confirmed the stability of created complexes. The obtained results might be a basis for other computational studies of 3CLPro and RdRp potential inhibition ways as well as the potential usage of C₆₀ fullerene in the fight against COVID-19 disease.

SUBMITTER: Hurmach VV

PROVIDER: S-EPMC8423725 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The photodynamic action mechanism sensitized by a non-charged porphyrin-fullerene C60 dyad (TCP-C60) and its tetracationic analogue (TCP-C60 4+) was investigated in solution and in Staphylococcus aureus cells. The ability of both dyads to form a photoinduced charge-separated state was evidenced by the reduction of methyl viologen in N,N-dimethylformamide (DMF). Moreover, the formation of superoxide anion radicals induced by these dyads was detected by the reduction of nitro blue tetrazolium. Also, photosensitized decomposition of l-tryptophan (Trp) was investigated in the presence of reactive oxygen species (ROS) scavengers. The addition of β-carotene and sodium azide had a slight effect on reaction rate. However, photooxidation of Trp mediated by TCP-C60 was negligible in the presence of d-mannitol, while no protection was found using TCP-C60 4+. In a polar medium, these dyads mainly act by a contribution of type I pathway with low generation of singlet molecular oxygen, O2(1Δg). In S. aureus cell suspensions, an aerobic atmosphere was required for the photokilling of this bacterium. The photocytotoxicity induced by TCP-C60 was increased in D2O with respect to water, while a small effect was found using TCP-C60 4+. Furthermore, photoinactivation of microbial cells was negligible in the presence of sodium azide. The addition of d-mannitol did not affect the photoinactivation induced by TCP-C60. In contrast, S. aureus cells were protected by d-mannitol when TCP-C60 4+ was used as a photosensitizer. Also, generation of O2(1Δg) in the S. aureus cells was higher for TCP-C60 than TCP-C60 4+. Therefore, TCP-C60 appears to act in microbial cells mainly through the mediation of O2(1Δg). Although, a contribution of the type I mechanism was found for cell death induced by TCP-C60 4+. Therefore, these dyads with high capacity to produce photoinduced charge-separated state represent interesting photosensitizers to inactivate microorganisms by type I or type II mechanisms. In particular, TCP-C60 may be located in a non-polar microenvironment in the cells favoring a type II pathway, while a contribution of the type I mechanism was produced using the cationic TCP-C60 4+.

Project description:The human body contains 60-70% water, depending on age. As a body fluid, it is not only a medium in which physical and chemical processes take place, but it is also one of the active mediators. Water is the richest substance with non-covalent hydrogen bonds. Water molecules, by themselves (in vacuum), are diamagnetic but when organized into clusters, they become diamagnetic or paramagnetic. Also, biomolecules (DNA, collagen, clathrin, and other proteins) have non-covalent hydrogen bonds in their structure. The interaction, as well as signal transmission, between water and biomolecules is achieved through the vibrations of covalent and non-covalent hydrogen bonds, which determine the state and dynamics of conformational changes in biomolecules. Disruptive conformational changes in biomolecules, cells, and tissues lead to their dysfunctionality, so they are a frequent cause of many disorders and diseases. For example, the rearrangement of hydrogen bonding due to mitochondrial disease mutation in cytochrome bc1 disturbs heme bH redox potential and spin state. In order to prevent and repair the dysfunctional conformational changes, a liquid substance was developed based on the second derivative of the C60 molecule (SD-C60), which has classical and quantum properties. The characterization of SD-C60 by UV-VIS-NIR, FTIR, TEM, and AFM/MFM was performed and it is shown that SD-C60 water layers generate vibrations with near-zero phase dispersion which are transmitted through Fibonacci's water chains to biomolecules. In comparison with previously published SD-C60 derivate (3HFWC, size until 10 nm, and 1-5 water layers), the improved formulation (3HFWC-W, size 10-25 nm, and 6-9 water layers) showed multiplied cytotoxic activity against melanoma cell lines of different aggressiveness. Apart from this, the mode of action was preserved and based on an induction of senescence rather than cell death. Importantly, high selectivity towards malignant phenotypes was detected. Observed effects can be ascribed to a machinery of hydrogen bonds, which are generated in SD-C60 and transmitted through water to biomolecules. This approach may open a new field in science and healthcare-a "water-based nanomedicine".

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C₆₀ fullerene against SARS-CoV-2 coronavirus: an in silico insight.

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C60 fullerene against SARS-CoV-2 coronavirus: an in silico insight.

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OmicsDI is part of the ELIXIR infrastructure

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C₆₀ fullerene against SARS-CoV-2 coronavirus: an in silico insight.