Coronavirus Disease 2019 (COVID-19). Structural and Pharmacophore mapping of RNA dependent RNA polymerase (RdRp)

Research Paper (undergraduate) from the year 2021 in the subject Biology - Virology, grade: A+, Governament College University Faisalabad (Department of Bioinformatics and Biotechnology), course: Bioinformatics, language: English, abstract: The present study will be designed to execute a rational screening of natural compounds against SARS COV-2 to cure COVID-19. For this purpose, firstly protein and structure conservation analysis of SARS COV-2 RdRp was performed to check the mutations. Secondly, a library of 15,000 phytochemicals were developed from literature search, PubChem, zinc database and MPD3 database. This library was employed for molecular docking and simulation studies against SARS-COV-2 RdRp. The top-ranked natural compounds were subsequently be subjected to In-silico pharmacokinetic and pharmacological study. Top seven natural compounds (Monotropein, Docetaxel, Daphnodorin M, Spinasaponin A, Neohesperidoee, Paucin, Saikosaponin B2) were selected based on their interaction with binding pocket residues (618,619,759-761,811-814)), Energy function score (-16.38, -17.83, -16.15, - 17.65, -15.80, -20.03, -18.11) and their ADMET properties. Coronavirus Disease 2019 (COVID-19) is a highly contagious disease, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which can be transmitted from person to person. Currently, no vaccine and antiviral treatment available to control this deadly virus but preventive measures and a few re-purposed drugs are available to combat COVID-19. RNA dependent RNA polymerase (RdRp) also named as nsp12 has key role in the replication or transcription of the viral machinery. Anti-viral drug such as Remdesivir (approved drug) has been shown the inhibiting activity against SARS-COV-2 RdRp.