Design, synthesis, and biochemical and computational screening of novel oxindole derivatives as inhibitors of Aurora A kinase and SARS-CoV-2 spike/host ACE2 interaction

Abstract

Isatin (indol-2,3-dione), a secondary metabolite of tryptophan, has been used as the core structure to design several compounds that have been tested and identified as potent inhibitors of apoptosis, potential antitumor agents, anticonvulsants, and antiviral agents. In this work, several analogs of isatin hybrids have been synthesized and characterized, and their activities were established as inhibitors of both Aurora A kinase and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike/host angiotensin-converting enzyme II (ACE2) interactions. Amongst the synthesized isatin hybrids, compounds 6a, 6f, 6g, and 6m exhibited Aurora A kinase inhibitory activities (with IC₅₀ values < 5 $\mu$M), with GScore values of -7.9, -7.6, -8.2 and -7.7 kcal/mol, respectively. Compounds 6g and 6i showed activities in blocking SARS-CoV-2 spike/ACE2 binding (with IC₅₀ values in the range < 30 $\mu$M), with GScore values of -6.4 and -6.6 kcal/mol, respectively. Compounds 6f, 6g, and 6i were both capable of inhibiting spike/ACE2 binding and blocking Aurora A kinase. Pharmacophore profiling indicated that compound 6g tightly fits Aurora A kinase and SARS-CoV-2 pharmacophores, while 6d fits SARS-CoV-2 and 6l fits Aurora A kinase pharmacophore. This work is a proof of concept that some existing cancer drugs may possess antiviral properties. Molecular modeling showed that the active compound for each protein adopted different binding modes, hence interacting with a different set of amino acid residues in the binding site. The weaker activities against spike/ACE2 could be explained by the small sizes of the ligands that fail to address the important interactions for binding to the ACE2 receptor site.

Keywords: ACE2; Aurora A kinase; SARS-CoV-2; spike/ACE2 interactions.

Fig. 1

Design of the target compounds

Scheme 1

Formation of intermediate 3. (i) neopentyl glycol, p-toluenesulfonic acid, n-heptane, 125 °C, 36 h in N₂ atm using Dean stark apparatus; (ii) Pd/C, H₂, ethyl acetate, r.t., 3 h

Scheme 2

Synthesis of compounds 6a – 6c. (i) acetyl chloride, K₂CO₃, ethyl acetate, 0 °C, 12 h; (ii) glacial acetic acid, concentrated hydrochloric acid, r.t., 2 h; (iii) p-tolyhydrazine hydrochloric acid, EtOH, acetic acid, 80–85 °C, 2 h; (iv) 2,4 dichlorohydrazine hydrochloric acid, EtOH, acetic acid, 80–85 °C, 2 h. (v) 4-hydrazinylpyridine, EtOH, acetic acid, 80–85 °C, 2 h

Scheme 3

Synthesis of compounds 6d – 6 f. (i) 2-(4-cholorophenyl)acetic acid, HATU, DIPEA, Dimethylformamide (DMF), N₂ atm, r.t., 1 h (ii) glacial acetic acid, concentrated hydrochloric acid, r.t., 2 h (iii) p-tolyhydrazine hydrochloric acid, EtOH, acetic acid, 80–85 °C, 2 h; (iv) 2,4 dichlorohydrazine hydrochloric acid, EtOH, acetic acid, 80–85 °C, 2 h; (v) (4-(trifluoromethyl)phenyl)hydrazine, EtOH, acetic acid, 80–85 °C, 2 h

Scheme 4

Synthesis of compounds 6 g – 6i. (i) 3-morpholinopropanoic acid, HATU, DIPEA, DMF, N₂ atm, r.t., 1 h (ii) glacial acetic acid, concentrated hydrochloric acid, r.t., 2 h (iii) p-tolyhydrazine hydrochloric acid, EtOH, acetic acid, 80–85 °C, 2 h; (iv) 2,4 dichlorohydrazine hydrochloric acid, EtOH, acetic acid, 80–85 °C, 2 h; (v) (4-(trifluoromethyl)phenyl)hydrazine, EtOH, acetic acid, 80–85 °C, 2 h

Scheme 5

Synthesis of compounds 6j – 6 l. (i) 4-chlorobenzoic acid, HATU, DIPEA, DMF, N₂ atm, r.t., 1 h (ii) glacial acetic acid, concentrated hydrochloric acid, r.t., 2 h (iii) p-tolyhydrazine hydrochloric acid, EtOH, acetic acid, 80–85 °C, 2 h; (iv) 2,4 dichlorohydrazine hydrochloric acid, EtOH, acetic acid, 80–85 °C, 2 h; (v) (4-(trifluoromethyl)phenyl)hydrazine, EtOH, acetic acid, 80–85 °C, 2 h. Synthesis of compound 6 m. (i) 4-chlorobenzoic acid, HATU, DIPEA, DMF, N₂ atm, r.t., 1 h (ii) glacial acetic acid, concentrated hydrochloric acid, r.t., 2 h (iii) 4-hydrazinylpyridine, EtOH, acetic acid, 80–85 °C, 2 h

Fig. 2

Dose-response curves for (left) Aurora A kinase inhibition of the compounds and (right) Spike RBD/ACE2 inhibition of the compounds

Fig. 3

Superposition of the docked ligands at the docking sites (top left) All docked compounds in Aurora A kinase in green (top right) All docked compounds in the spike/ACE2 in brown (B) receptor site. Active compounds in deep purple and inactive compounds in light orange; (bottom left) the most active (6l) and least active (6c) ligands in the docked sites for the Aurora A kinase and (bottom right) spike/ACE2 receptor site. The active compounds are in deep purple and the inactive in light orange

Fig. 4

Interaction of the most active of the ligands at the Aurora A kinase (in green) binding site (top left) 6d and (top right) 6a. Active ligand in deep purple, residues at the binding site in yellow and interactions in black dotted lines. (bottom left) Interaction of the most active ligands at the Spike/ACE2 receptor site (in brown) with 6 l on the left, and (bottom right) 6i. Active ligand in deep purple, residues at the binding site in yellow and interactions in black dotted lines