Screening of Preferential Binding Affinity of Selected Natural Compounds to SARS-CoV-2 Proteins Using in Silico Methods
Nikolina Tomic1, Lejla Pojskic1, Abdurahim Kalajdzic1, Jasmin Ramic1, Naida Lojo Kadric1, Tarik Ikanovic2, Milka Maksimovic1, Naris Pojskic11University of Sarajevo – Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and Herzegovina, 2Faculty of Science-University of Sarajevo, Sarajevo, Bosnia and Herzegovina,
Objectives: The global burden of the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the corona virus disease-19 (COVID-19) is enormous. No definitive treatment and prophylactic guidelines for COVID-19 currently exist except for physical distancing and aerial barriers between individuals. This work explored the natural compound-binding efficiency of SARS-CoV-2 proteins essential for host cell interaction and infection. Methods: The binding activity of artemisinin to SARS-CoV-2 spike glycoprotein (Protein Data Bank (PDB) ID: 6VYB), SARS-CoV-2 main protease (3C-like main protease (3CLpro); PDB ID: 6Y84) and SARS-CoV-2 papain-like protease (PLpro; PDB ID: 6W9C), were tested using in silico methods. Moreover, chloroquine and hesperidin were used as the positive control of binding affinity and proven therapeutic effect, respectively. Results: The highest affinities for binding to all tested SARS-CoV-2 proteins are observed for hesperidin (?5.8,?10.0, and ?8.1 kcal/mol), then for artemisinin (?4.8,?8.3, and ?6.0 kcal/mol), and the lowest for chloroquine (?4.1,?8.2, and ?4.8 kcal/mol). Artemisinin, hesperidin, and chloroquine had similar positioning toward targeted proteins at specific sites when these interactions were visualized. Conclusion: This study shows that artemisinin has the potential to bind and inhibit the SARS-CoV-2 spike protein, the 3CLpro main protease, and PLpro proteinase similar to hesperidin and chloroquine that have been proven as antivirals in previous preclinical and clinical studies. Keywords: Artemisinin, molecular docking study, SARS-CoV-2 proteins
Cite This Article
Tomic N, Pojskic L, Kalajdzic A, Ramic J, Kadric N, Ikanovic T, et al. Screening of Preferential Binding Affinity of Selected Natural Compounds to SARS-CoV-2 Proteins Using in Silico Methods. EJMO. 2020; 4(4): 319-323
Corresponding Author: Lejla Pojskic