5-chloro-3-(2-(2,4-dinitrophenyl) hydrazono)indolin-2-one: synthesis, characterization, biochemical and computational screening against SARS-CoV-2

Abstract

Chemical prototypes with broad-spectrum antiviral activity are important toward developing new therapies that can act on both existing and emerging viruses. Binding of the SARS-CoV-2 spike protein to the host angiotensin-converting enzyme 2 (ACE2) receptor is required for cellular entry of SARS-CoV-2. Toward identifying new chemical leads that can disrupt this interaction, including in the presence of SARS-CoV-2 adaptive mutations found in variants like omicron that can circumvent vaccine, immune, and therapeutic antibody responses, we synthesized 5-chloro-3-(2-(2,4-dinitrophenyl)hydrazono)indolin-2-one (H₂L) from the condensation reaction of 5-chloroisatin and 2,4-dinitrophenylhydrazine in good yield. H₂L was characterised by elemental and spectral (IR, electronic, Mass) analyses. The NMR spectrum of H₂L indicated a keto-enol tautomerism, with the keto form being more abundant in solution. H₂L was found to selectively interfere with binding of the SARS-CoV-2 spike receptor-binding domain (RBD) to the host angiotensin-converting enzyme 2 receptor with a 50% inhibitory concentration (IC₅₀) of 0.26 μM, compared to an unrelated PD-1/PD-L1 ligand-receptor-binding pair with an IC₅₀ of 2.06 μM in vitro (Selectivity index = 7.9). Molecular docking studies revealed that the synthesized ligand preferentially binds within the ACE2 receptor-binding site in a region distinct from where spike mutations in SARS-CoV-2 variants occur. Consistent with these models, H₂L was able to disrupt ACE2 interactions with the RBDs from beta, delta, lambda, and omicron variants with similar activities. These studies indicate that H₂L-derived compounds are potential inhibitors of multiple SARS-CoV-2 variants, including those capable of circumventing vaccine and immune responses.

Supplementary information: The online version contains supplementary material available at 10.1007/s11696-023-03274-5.

Keywords: Angiotensin-converting enzyme 2 receptor; Antivirals; Coronavirus; Isatin hydrazine; Molecular docking; SARS-CoV-2 spike.

Fig. 1

Isatin

Scheme 1

Synthesis of target compound

Fig. 2

¹H NMR of H₂L showing keto–enol forms in DMSO

Fig. 3

Proposed structure of H₂L

Fig. 4

Dose–response curves denoting ability of H₂L to disrupt luminescence due to SARS-CoV-2 spike RBD–host ACE2 protein-binding (circles) and PD-1-PD-L1-binding (triangles) AlphaScreen assay. Results denote the mean ± S.D. from 3 independent experiments

Fig. 5

A View of the ACE2-Spike RBD complex. The ACE2 protein backbone is shown as green cartoon, while the spike RBD is shown as orange ribbon. Mutation residues are depicted as lincorice-sticks. The ACE2-Spike RBD domain interface and the preferential ACE2 binding site are shown as purple egg sphere and red rectangle, respectively. B Close view of the proposed binding mode of the ligand (brown) within the ACE2 binding site. Key residues within the site are shown as green sticks. C Proposed binding mode of the ligand (cyan) docked at the interface between PD-1 (light blue) and PD-L1 (grey). For all figures, H-bond interactions are shown as magenta dashed-lines