Computer-aided design, synthesis, and biological evaluation of 4-chloro-N-(2-oxo-3-(2-pyridin-4-yl)hydrazineylidene)indolin-5yl)benzamide and 1-(4-bromobenzyl)-5-indoline-2,3-dione against SARS-CoV-2 spike/ACE2

Abstract

The emergence of the severe acute respiratory syndrome 2 (SARS-CoV-2) as a global threat has driven the urgent need for the identification of bioactive molecules capable of controlling or completely eradicating this virus. Our group has been investigating isatin hybrids that block the binding of the human angiotensin-converting enzyme 2 (ACE2) and the viral spike protein. This work describes the synthesis and biological evaluation of two derivatives of isatin (indol-2,3-dione) based on a computational approach. Isatin, a secondary metabolite of tryptophan, has been used as the core structure and is a versatile and favorable precursor and as a privileged scaffold against this enzyme complex. The new compound scaffolds AVS-01 and AVS-02 were designed by modifications at the C-3 and N-1 positions, respectively, according to the various reagents available in our lab. Molecular docking of the designed compounds was used to explore their interactions with the target protein complex. The two designed compound scaffolds shown in this article showed quite distinct docking glide scores (GScore = −3.657 and −4.534 for AVS-01 and AVS-02, respectively). Several analogs were synthesized and tested in the quest to find a plausible scaffold for further synthesis. While compound AVS-02 showed inhibition of spike/ACE2 binding with an IC₅₀ value of 8.8 µM, the reference compound hopeaphenol inhibited the interaction with an IC₅₀ of 0.3 µM. Compound AVS-01 rather showed no inhibition of the SARS-CoV-2 spike/host ACE2 interaction with an IC₅₀ > 32 µM. An estimation of their binding free energy (ΔG_bind), and free energy of solvation (ΔG_solv) MM-GBSA calculations was carried out to re-evaluate the affinity to the target protein to gain further insights into the observed activity and non-activity. MM-GBSA calculation showed that ΔG_bind = −35.91 kcal/mol and-25.32 kcal/mol for AVS-01 and AVS-02, respectively, and ΔG_solv = 25.56 kcal/mol and 16.92 kcal/mol for AVS-01 and AVS-02, respectively. This leads to the conclusion that the N-1 position of the indole-2,3-dione moiety favors the blockage of SARS-CoV-2 spike/ACE2 interactions compared to the C-3 position. Analysis of GScores, per-residue interaction energies, and free energies of binding and solvation showed that van der Waals interactions should favor the binding towards the spike/ACE2 complex.