Repurposing dye ligands as antivirals via a docking approach on viral membrane and globular proteins – SARS-CoV-2 and HPV-16

• Published in: Biochimica et biophysica acta. Biomembranes 2024-01, Vol.1866 (1), p.184220-184220, Article 184220
• Main Authors: Chen, Yi-Ming, Lu, Ching-Tai, Wang, Chia-Wen, Fischer, Wolfgang B.
• Format: Article
• Language: English
• Subjects: Antivirals; Dyes; Globular protein; Ligand docking; Repurposing ligands; SARS-CoV-2 and HPV16; Viral channel forming proteins
• ISSN: 0005-2736; 1879-2642
• DOI: 10.1016/j.bbamem.2023.184220

A series of dye ligands are docked to three different proteins, E and 3a of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) and E6 of human papilloma virus type 16 (HPV-16) using three different software. A four-level selection algorithm is used based on nonparametric statistics of numerical key values such as the “rank” derived from (i) averaged estimated binding energies (EBEs) and (ii) absolute EBE value of each of the software, (iii) frequency of ranking and (iv) rank of the area-under-curve values (AUCs) from decoy docking. A series of repurposing drugs and known antivirals used in experimental studies are docked for comparison. One dye ligand is ranked best for all proteins using the selection algorithm levels i - iii. Another three dye ligands are ranked top for the proteins individually when using all four levels. [Display omitted] •Repurposing dye ligands for E and 3a proteins of SARS-CoV-2 and E6 of HPV-16•A four-level selection algorithm based on nonparametric statistics is proposed.•Application of three different docking software•Three dye ligands are ranked top.•Comparison with other repurposing ligands and antivirals