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In silico identification of potential SARS COV-2 2'-O-methyltransferase inhibitor: fragment-based screening approach and MM-PBSA calculations.
El Hassab, Mahmoud A; Ibrahim, Tamer M; Shoun, Aly A; Al-Rashood, Sara T; Alkahtani, Hamad M; Alharbi, Amal; Eskandrani, Razan O; Eldehna, Wagdy M.
  • El Hassab MA; Department of Pharmaceutical Chemistry, School of Pharmacy, Badr University in Cairo (BUC) Cairo Egypt mahmoud65582@pharm.tanta.edu.eg.
  • Ibrahim TM; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University Kafrelsheikh Egypt wagdy2000@gmail.com.
  • Shoun AA; Department of Microbiology & Immunology, Faculty of Pharmacy, Sinai University North Sinai Egypt.
  • Al-Rashood ST; Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University Riyadh Saudi Arabia.
  • Alkahtani HM; Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University Riyadh Saudi Arabia.
  • Alharbi A; Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University Riyadh Saudi Arabia.
  • Eskandrani RO; Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University Riyadh Saudi Arabia.
  • Eldehna WM; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University Kafrelsheikh Egypt wagdy2000@gmail.com.
RSC Adv ; 11(26): 16026-16033, 2021 Apr 26.
Article in English | MEDLINE | ID: covidwho-1236099
ABSTRACT
In the present era, there are many efforts trying to face the emerging and successive waves of the COVID-19 pandemic. This has led to considering new and unusual targets for SARS CoV-2. 2'-O-Methyltransferase (nsp16) is a key and attractive target in the SARS CoV-2 life cycle since it is responsible for the viral RNA protection via a cap formation process. In this study, we propose a new potential inhibitor for SARS COV-2 2'-O-methyltransferase (nsp16). A fragment library was screened against the co-crystal structure of the SARS COV-2 2'-O-methyltransferase complexed with Sinefungin (nsp16 - PDB ID 6WKQ), and consequently the best proposed fragments were linked via a de novo approach to build molecule AP-20. Molecule AP-20 displayed a superior docking score to Sinefungin and reproduced the key interactions in the binding site of 2'-O-methyltransferase. Three molecular dynamic simulations of the 2'-O-methyltransferase apo structure and its complexed forms with AP-20 and Sinefungin were performed for 150 nano-seconds to provide insights on the dynamic nature of such setups and to assess the stability of the proposed AP-20/enzyme complex. AP-20/enzyme complex demonstrated better stability for the ligand-enzyme complex compared to Sinefungin in a respective setup. Furthermore, MM-PBSA binding free energy calculations showed a better profile for AP-20/enzyme complex compared to Sinefungin/enzyme complex emphasizing the potential inhibitory effect of AP-20 on SARS COV-2 2'-O-methyltransferase. We endorse our designed molecule AP-20 to be further explored via experimental evaluations to confront the spread of the emerging COVID-19. Also, in silico ADME profiling has ascribed to AP-20 an excellent safety and metabolic stability profile.

Full text: Available Collection: International databases Database: MEDLINE Type of study: Experimental Studies / Prognostic study Language: English Journal: RSC Adv Year: 2021 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Experimental Studies / Prognostic study Language: English Journal: RSC Adv Year: 2021 Document Type: Article