Omicron: Emergence, detection, and response

COVID-19 pandemic emerged in December 2019, and it is still a global threat with quite a few variants. The B.1.1.529, Omicron, identified in South Africa in 2021, was one of the most notorious variants due to its high infection and mutability capacity. The Omicron variant had mutations in the S region of the key RBD which boosted the transmission ability of the virus. Resistance to antibodies and vaccines has been the key features of this variant. The rise of antibody-evading variants has reached alarming proportions and discovery of small molecule inhibitors has been thought to be a solution to this problem. Presently scientific attention has been substantially directed towards computational drug design performing molecular simulations to generate effective chemical agents to tackle the Omicron variant. © 2023 Nova Science Publishers, Inc. All rights reserved.

Could boron compounds be effective against SARS-CoV-2?

BACKGROUND: Seven dioxaborole compounds are investigated in this study. Structural and spectral characterization is done at M062X/6-31+G(d,p) level in the water. Active sites of these compounds are determined using molecular electrostatic potential (MEP) maps. Electrophilic and nucleophilic attack regions are determined. AIM: We aimed to determine whether Boron-Containing Compounds (BCCs) inhibitor used in the treatment of COVID-19 are effective against SARS Cov-2 in silico. RESULTS AND CONCLUSION: Since SARS-CoV-2 is a worldwide health problem, anti-viral properties of studied boron-containing compounds were investigated by molecular docking calculations. In addition to these calculations, MM/PSBA calculations were performed. It was found that boron compounds can be good drug candidate against SARS-CoV-2 and the best compound is ((R)-1-((S)-3-(4-(aminomethyl)phenyl)-2-benzamidopropanamido)-4-guanidinobutyl)boronic acid (C26) (Tab. 2, Fig. 6, Ref. 29). Text in PDF www.elis.sk Keywords: boronate ester, dioxaborole, in silico, SARS-CoV-2, MD calculations.

Could Peganum harmala be effective in the treatment of COVID-19?

BACKGROUND: Predominant molecules in Peganum harmala leaves were detected using gas chromatography-mass spectrometry (GC-MS). Based on the results of this analysis, most alkaloids, flavonoids and triterpenoids in found P. harmala was compiled from the literature in order to develop and lead the production of effective inhibitor drugs for ACE2, main protease, and RNA dependent RNA polymerase (RdRp) proteins of SARS-CoV-2 virus, which is today's most contagious and deadly disease. AIM: By comparing FDA-approved drugs used in the treatment of COVID-19, we aimed to determine whether the molecules in P. harmala are effective against SARS CoV-2 in silico. RESULTS AND CONCLUSION: P. harmala molecules were selected as drug candidates from the PubChem web tool. Afterwards, molecular docking calculations of these inhibitor molecules were made with Maestro Molecular modeling program by Schrödinger. The comparison of molecules with high inhibitory activities with FDA-approved drugs was made. With molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations, docking calculations of molecules that have high inhibitory activity, were tried to be verified by calculations in the range of 0-100 nanoseconds (Tab. 4, Fig. 6, Ref. 53).

Determination of inhibitor activity of drugs against the COVID-19.

BACKGROUND: It is the SARS-CoV-2 virus, one of the most significant diseases of today's world. Due to the high transmission of this disease, studies are ongoing to discover an inhibitor drug that can stop this disease. In this study, inhibitory drugs used for many diseases were tried to stop the SARS-CoV-2 virus. AIM: In the calculations made, inhibitor molecules for the SARS-CoV-2 virus were calculated by molecular docking method. RESULTS AND CONCLUSION: Inhibitory activities of SARS-CoV-2 virus against spike glycoprotein (PDB ID: 6M0J, 6LZG), main protease (PDB ID: 5RGG, 6WTT), and RNA dependent RNA polymerase (RdRp) (PDB ID: 6YYT, 7BV2) proteins were compared. Then, docking calculations were supported by calculations by MM-PSBA of the inhibitor with the highest activity. Afterwards, it was compared with FDA approved drugs for the SARS-CoV-2 virus. It was found that the Carvedilol molecule was the best against RNA dependent RNA polymerase (RdRp) protein of SARS-CoV-2 (Tab. 4, Fig. 9, Ref. 42).

How do arbidol and its analogs inhibit the SARS-CoV-2?

BACKGROUND: COVID-19 is not fully known and causes severe inflammation and cytokine storm. It has many symptoms, such as: fever, sore throat, headache, dyspnoea, and diarrhoea. Arbidol was used in the treatment of COVID19, which was the most critical health problem in the world. However, the desired recovery was not achieved with Arbidol. Many countries still use this drug in the treatment of COVID19. AIM: We aimed to determine whether Arbidol, the hemagglutinin esterase inhibitor used in the treatment of COVID-19, was effective against SARS Cov-2 in silico. RESULTS AND CONCLUSION: The similarity between hemagglutinin and spike proteins were reported due to the fact that inhibition properties of Arbidol and its 39 analogues were examined in detail against hemagglutinin esterase and spike glycoproteins. CID 1070884 and CID 1207786 were found to be more active against hemagglutinin esterase than in Arbidol, while these compounds were inactive against spike glycoproteins. The interaction mechanism was clarified between arbidol and spike proteins. Phenylalanine, tyrosine, glycine, lysine, and aspartic acid were found to be the headliner amino acids in the interactions between Arbidol and binding domains of spike glycoproteins in the SARS-CoV2 (Tab. 3, Fig. 8, Ref. 28).

Could boron-containing compounds (BCCs) be effective against SARS-CoV-2 as anti-viral agent?

BACKGROUND: Seven dioxaborole compounds are investigated in this study. Structural and spectral characterizations are done at the M062X/6-31+G(d,p) level in water. Active sites of these compounds are determined by contour plots of frontier molecular orbital and molecular electrostatic potential (MEP) maps. Electrophilic and nucleophilic attack regions are determined. Since SARS-CoV-2 is a worldwide health problem, antiviral properties of studied boron-containing compounds are investigated by molecular docking calculations. In addition to these calculations, MM/PSBA calculations are performed. RESULTS AND CONCLUSION: It is found that the studied boron compounds can be good drug candidates against the main protease of SARS-CoV-2, while the best of them is 4,6-di-tert-butyl-2-(4-methoxyphenyl)benzo[d][1,3,2] dioxaborole (B2) (Tab. 3, Fig. 8, Ref. 23).

Are clarithromycin, azithromycin and their analogues effective in the treatment of COVID19?

BACKGROUND: SARS-CoV-2, which started in Wuhan and later affected the whole world, is the most important disease of the world today. Many ways to inhibit SARS-CoV-2 virus are sought to prevent the spread of this virus. Azithromycin and clarithromycin are considered for the treatment of the SARS-CoV-2 virus, which has a high similarity to previous colonic diseases. AIM: We aimed to determine whether azithromycin and clarithromycin, the RNA-dependent RNA polymerase protein inhibitor used in the treatment of COVID-19, is effective against SARS Cov-2 in silico. RESULTS AND CONCLUSION: The 503 analogues of azithromycin and clarithromycin were studied to target SARS-CoV-2 the RNA-dependent RNA polymerase protein inhibition. Maestro program was used to compare the inhibition activities of these analogues. A detailed comparison was made using the numerical value of many parameters obtained. ADME / T properties were then examined to determine the effects and reactions of analogues on human metabolism. In this study, the SARS-CoV2 virus is 6NUR and 6NUS, which is the RNA-dependent RNA polymerase protein. Among these proteins, the best inhibitor among the 503 analogues according to the docking score parameter was 9851445 with a great difference. This analogue was an analogue of azithromycin (Tab. 3, Fig. 6, Ref. 58).