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    Design and in silico study of the novel coumarin derivatives against SARS-CoV-2 main enzymes
    (Taylor and Francis Ltd., 2020) Özdemir, Mücahit; Köksoy, Baybars; Ceyhan, Deniz; Sayın, Koray; Erçağ, Erol; Bulut, Mustafa; Yalçın, Bahattin
    The novel coronavirus (SARS-CoV-2) causes severe acute respiratory syndrome and can be fatal. In particular, antiviral drugs that are currently available to treat infection in the respiratory tract have been experienced, but there is a need for new antiviral drugs that are targeted and inhibit coronavirus. The antiviral properties of organic compounds found in nature, especially coumarins, are known and widely studied. Coumarins, which are also metabolites in many medicinal drugs, should be investigated as inhibitors against coronavirus due to their pharmacophore properties (low toxicity and high pharmacokinetic properties). The easy addition of substituents to the chemical structures of coumarins makes these structures unique for the drug design. This study focuses on factors that increase the molecular binding and antiviral properties of coumarins. Molecular docking studies have been carried out to five different proteins (Spike S1-subunit, NSP5, NSP12, NSP15, and NSP16) of the SARS-CoV-2 and two proteins (ACE2 and VKORC1) of human. The best binding scores for 17 coumarins were determined for NSP12 (NonStructural Protein-12). The highest score (–10.01 kcal/mol) in the coumarin group is 2-morpholinoethan-1-amine substituted coumarin. Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analyses of selected ligand-protein complexes were performed. The binding energies in each 5 ns were calculated and it was found that the interaction between ligand and target protein were stable. Communicated by Ramaswamy H. Sarma. © 2020 Informa UK Limited, trading as Taylor & Francis Group.
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    In silico, 6lu7 protein inhibition using dihydroxy-3-phenyl coumarin derivatives for SARS-CoV-2
    (Turkish Chemical Society, 2020) Özdemir, Mücahit; Köksoy, Baybars; Ceyhan, Deniz; Bulut, Mustafa; Yalçın, Bahattin
    The new emerging coronavirus (SARS-CoV-2) has become a global health problem with very rapid transmission from person to person, causing severe acute respiratory problems. In the circumstance, the discovery of vaccines or drugs to eradicate or reduce the impact of the COVID-19 has made it imperative to develop new approaches. In the current situation, many drugs on the drug bank have been researched computationally, and there has not been an emphasis on synthetic effort. We tested 42 coumarin derivatives (1a-14c) containing 14 different substituents, which are secondary metabolites of plants, and the anticoagulant Coumadin (warfarin) drug as a reference by Molecular Docking calculation technique on 6LU7 main protease of the coronavirus. Optimized geometries, electron motions and energy values of all coumarins were also determined using the Density Functional Theory (DFT) method. The drug properties of coumarins were estimated using the ADME-Tox test method. Coumarins formed strong interactions with HIS41, CYS145, and other amino acids in the active site of the main protease. In general, 6,7-dihydroxy-3-phenylcoumarin derivatives gave relatively higher scores, and for all coumarins, biphenyl (for 10a,-8.6 kcal/mol; 10b,-8.3 kcal/mol; 10c,-7.9 kcal/mol) and 4-trifluoromethylphenyl (for 13a,-8.1 kcal/mol; 13b,-8.1 kcal/mol; 13c-8.3 kcal/mol) substituted coumarin had the highest score. The coumarins data reported in this study serves as a stepping stone for in vitro and in vivo experimental research for vaccine development purposes. © 2020, Turkish Chemical Society. All rights reserved.