The Malaria Box molecules: a source for targeting the RBD and NTD cryptic pocket of the spike glycoprotein in SARS-CoV-2

Otazu K.; Olivos-Ramirez G.E.; Fernández-Silva P.D.; Vilca-Quispe J.; Vega-Chozo K.; Jimenez-Avalos G.M.; Chenet-Zuta M.E.; Sosa-Amay F.E.; Cárdenas Cárdenas R.G.; Ropón-Palacios G.; Dattani N.; Camps I. · Journal of Molecular Modeling (2024) · DOI: 10.1007/s00894-024-06006-y

Resumen

Context: SARS-CoV-2, responsible for COVID-19, has led to over 500 million infections and more than 6 million deaths globally. There have been limited effective treatments available. The study aims to find a drug that can prevent the virus from entering host cells by targeting specific sites on the virus’s spike protein. Method: We examined 13,397 compounds from the Malaria Box library against two specific sites on the spike protein: the receptor-binding domain (RBD) and a predicted cryptic pocket. Using virtual screening, molecular docking, molecular dynamics, and MMPBSA techniques, they evaluated the stability of two compounds. TCMDC-124223 showed high stability and binding energy in the RBD, while TCMDC-133766 had better binding energy in the cryptic pocket. The study also identified that the interacting residues are conserved, which is crucial for addressing various virus variants. The findings provide insights into the potential of small molecules as drugs against the spike protein. © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2024.

Instituciones: Universidad Peruana Cayetano Heredia; Universidad Nacional de la Amazonía Peruana; Universidad Nacional Tecnológica de Lima Sur