In Silico Study of Organic Compounds from Dipteryx odorata with SARS-COV-2 Targets by Molecular Docking and ADME-TOX Analysis

Abstract

Introduction: The new coronavirus SARS-CoV-2, identified in December 2019 as the cause of COVID-19, has triggered an outbreak of potentially fatal atypical pneumonia. The constant search for new molecules or strategies to combat this disease continues. Thus, the objective of this work was to evaluate, using in silico methods, the compounds present in Dipteryx odorata as inhibitors of crucial targets of SARS-COV-2.
 Methodology: The methodology included the selection of plant compounds from the Pubchem database and obtaining the structures of SARS-COV-2 proteins (6vxx, 6lu7, 1R42) from the Protein Data Bank (PDB). The molecular docking analysis was performed using the Autodock Tools 1.5.6 and Autodock Vina programs, LigPlus to obtain amino acids, and Chimera v.13.1 to generate 3D images. The absorption, distribution, metabolism, excretion and toxicity (ADME-TOX) properties of the most promising compounds were evaluated with the pkCSM tool.
 Results: In total, 672 molecular dockings were carried out, tested with 168 ligands, resulting in 17 compounds with binding energies lower than -7.9 kcal.mol-¹. A highlight was the exceptional interaction of the vouacapenic acid compound with the Spike protein, recording an energy of -9.9 kcal.mol-¹. The study revealed that compounds such as vouacapenic acid, taraxasterol and luteolin showed notable interactions with the Spike protein, in addition to positive results in the ADMET-TOX profile.
 Conclusion: These findings indicate the potential of these compounds and point to the need for in vivo and in vitro studies to validate their antiviral efficacy as therapeutic agents against SARS-COV-2.