De novo design of bioactive phenol and chromone derivatives for inhibitors of Spike glycoprotein of SARS-CoV-2 in silico

• Published in: 3 Biotech 2023-09, Vol.13 (9), p.301, Article 301
• Main Authors: Lima, Joan Petrus Oliveira, da Fonseca, Aluísio Marques, Marinho, Gabrielle Silva, da Rocha, Matheus Nunes, Marinho, Emanuelle Machado, dos Santos, Helcio Silva, Freire, Rafael Melo, Marinho, Emmanuel Silva, de Lima-Neto, Pedro, Fechine, Pierre Basílio Almeida
• Format: Article
• Language: English
• Subjects: Agriculture; Artificial intelligence; Bioinformatics; Biomaterials; Biotechnology; Cancer Research; Chemistry; Chemistry and Materials Science; COVID-19; Drug development; Dynamic stability; Glycoproteins; Macromolecules; Molecular dynamics; Molecular structure; Original; Original Article; Pandemics; Phenols; Severe acute respiratory syndrome coronavirus 2; Spike glycoprotein; Stem Cells
• ISSN: 2190-572X; 2190-5738
• DOI: 10.1007/s13205-023-03695-9

This work presents the synthesis of 12 phenol and chromone derivatives, prepared by the analogs, and the possibility of conducting an in silico study of its derivatives as a therapeutic alternative to combat the SARS-CoV-2, pathogen responsible for COVID-19 pandemic, using its S-glycoprotein as a macromolecular target. After the initial screening for the ranking of the products, it was chosen which structure presented the best energy bond with the target. As a result, derivative 4 was submitted to a molecular growth study using artificial intelligence, where 8436 initial structures were obtained that passed through the interaction filters and similarity to the active glycoprotein pocket through the MolAICal computational package. Thus, 557 Hits with active configuration were generated, which is very promising compared to the BLA reference link for inhibiting the biological target. Molecular dynamics also simulated these compounds to verify their stability within the active protein site to seek new therapeutic propositions to fight against the pandemic. The Hit 48 and 250 are the most active compounds against SARS-CoV-2. In summary, the results show that the Hit 250 would be more active than the natural compound, which could be further developed for further testing against SARS-CoV-2. The study employs the de novo approach to design new drugs, combining artificial intelligence and molecular dynamics simulations to create efficient molecular structures. This research aims to contribute to the development of effective therapeutic strategies against the pandemic.