THE POTENTIAL OF CARRAGEENAN FOR THE DRUG DISCOVERY OF COVID-19 VIA MOLECULAR DOCKING WITH ANGIOTENSIN-CONVERTING ENZYME 2 (ACE2) AND THE MAIN PROTEASE (MPRO) OF SAR-COV-2
Htwe Thet, Aung, Тет Хтве Аунг, Моламьяйн, Мьянма Университет Моламьяйна
doi:10.18454/jbg.2022.18.2.001
The World Health Organization (WHO) has classified COVID-19 as a pandemic infection due to the global spread of new corona virus infections. Due to this virus infection, millions of people all around the world had to die or endure severe disease. It will be crucial to find new therapeutic treatments in order to prepare for a similar viral pandemic in the future. Carrageenans have apparently been effective against 12 viruses, including SAR-COV-2. In this investigation, angiotensin-converting enzyme 2 (ACE2) and main protease (Mpro) were used as molecular targets for virtual screening of kappa-, lambda-, and iotacarrageenans. When compared to antiviral drugs, the results show that all three carrageenans have substantial binding affinity for ACE2 and Mpro. The binding affinity of iota-carrageenan is greater than that of other compounds. The binding affinity suggests that carrageenans could be utilized to produce potent antiviral drugs.
Protein-ligand interaction The best poses of the protein-ligand complex pdb file acquired from the CB-Dock web server were submitted to the The ProteinPlus web server (http://protein.plus). PoseView [7] was used to analyze the 2D interaction diagram with hydrogen and hydrophobic contacts for the protein-ligand interaction.
Results and Discussion In order to estimate the binding sites and affinities with the Autodock Vina program, carrageenans were molecularly docked with HER2 and Mpro utilizing CB-Dock, an online application. Since 2019, the CB-Dock web server, which Autodock Vina is utilized for, has seen roughly 200 entries per day posted by academics from around the world. AutoDock Vina is an open-source, free software program that quickly determines the binding affinity (Vina scores) that roughly represent the binding energy (Kcal/mol). Affinity indicates the extent of the drug's interaction with the receptor. A low vina score denotes a high binding affinity of the protein to the ligand. Drug candidates are picked from ligands that bind firmly to the target protein because the stronger the connections, the more the ligand will influence the physiological function of the target proteins. A high affinity usually results in a reduced dose requirement [8] . Lambda-and iota-carrageenan had the lowest scores for ACE2 with vina values of -8.5, followed by kappa-carrageenan (-8.4), albeit their scores are extremely close to one another. Remdesivir and Favipiravir, the..
References
Alvarez-Vinas, Alvarez-Vinas, Souto, Florez-Fernandez, Antiviral Activity of Carrageenans and Processing Implications / M,
doi:10.3390/md19080437Aung, Proximicin A-C as prospective HER2-positive and negative breast cancer drugs: Molecular docking and in silico ADME modeling, IPS Journal of Molecular Docking Simulations,
doi:10.54117/ijmds.v1i1.9Froba, Delta, Froba, Grobe, Setz, Iota-Carrageenan Inhibits Replication of SARS-CoV-2 and the Respective Variants of Concern Alpha, Int. J. Mol. Sci,
doi:10.3390/ijms222413202Joshi, Joshi, Joshi, Sharma, European Review for Medical and Pharmacological Sciences
Liu, Liu, Yang, Gan, CB-Dock2: improved protein-ligand blind docking by integrating cavity detection, docking and homologous template fitting, Nucleic Acids Research,
doi:10.1093/nar/gkac394Padmi, Padmi, Kharisma, Ansori, Macroalgae Bioactive Compounds for the potential Antiviral of SARS-CoV-2: An In Silico Study, J Pure Appl Microbiol,
doi:10.2227/JPAM.16.2.26Stierand, Poseview-molecular interaction patterns at a glance / Stierand and Rarey, Journal of Cheminformatics
Vicidomini, In silico investigation on the interaction of Chiral phytochemicals from Opuntia ficus-indica with SARS-CoV-2 Mpro / C. Vicidomini,
doi:10.3390/sym1361041Yadav, Role of structural and Non-structural Proteins and Therapeutic Targets of SARS-CoV-2 for COVID-19
