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There is a daunting public health emergency due to the emergence and rapid global spread of the new omicron variants of SARS-CoV-2. The variants differ in many characteristics, such as transmissibility, antigenicity and the immune system of the human hosts' shifting responses. This change in characteristics raises concern, as it leads to unknown consequences and also raises doubts about the efficacy of the currently available vaccines. As of March 2022, there are five variants of SARS-CoV-2 disseminating: the alpha, the beta, the gamma, the delta and the omicron variant. The omicron variant has more than 30 mutations on the spike protein, which is used by the virus to enter the host cell and is also used as a target for the vaccines. In this work, we studied the possible anti-COVID-19 effect of two molecules by molecular docking using Autodock Vina and molecular dynamic simulations using Gromacs 2020 software. We docked amoxicillin and clavulanate to the main protease (M pro ), the RNA-dependent RNA polymerase (RdRp) and the spike protein receptor-binding domain (SRBD) of the wild type with the two variants (delta and omicron) of SARS-CoV-2. The docking results show that the ligands bound tightly with the SRBD of the omicron variant, while the dynamic simulation revealed the ability of amoxicillin to bind to the SRBD of both variants' delta and omicron. The high number of mutations that occurred in both variants increases the affinity of amoxicillin towards them.Communicated by Ramaswamy H. Sarma.

The black fungus is a SARS-CoV-2-associated fungal co-infection. Mechanisms by which antifungal drugs act against Mucormycosis are by inhibition of enzymes implicated in ergosterol biosynthesis or cell wall formation or the drug interaction directly with ergosterol. Since it has been shown that the reduction of ergosterol biosynthesis prevents this infection, we carried out a virtual screening with molecular docking analysis and tested a dataset of 880 molecules for its effects on an enzyme involved in ergosterol biosynthesis (CYP51) and fungal infection (lipase), as well as ADMET and toxicity properties of the studied molecules. We calculated the stability of the complex's inhibitor-enzyme throughout the time using molecular dynamics simulations. From this, initial screening indicated that 600 out of a total of 880 compounds have a good affinity towards sterol 14α-demethylase. The two compounds ZINC95486139 and ZINC33833639 were determined as safe and have good drug-likeness properties, and have binding energies of −75.07 and −83.89 kcal/mol, respectively by MMGBSA and create strong and stable interactions with the residues of the active site of the enzyme. To the best of our knowledge, ZINC95486139 and ZINC33833639 have not yet been described in the literature as anti-sterol 14α-demethylase inhibitors or evaluated for their anti-fungal activity. [ABSTRACT FROM AUTHOR]