creators_name: Das, Sudesna
creators_name: Sunnapu, Prasad
creators_name: Rafi, Mohammed
creators_name: Begum, Yasmin
creators_name: Dey, Sudip
creators_name: Joshi, Akshay
creators_name: Singh, Nittu
creators_name: Thakur, Krishan Gopal
creators_name: Jaisankar, Parasuraman
creators_name: Singh, Umesh Prasad
type: article
datestamp: 2026-02-02 07:22:32
lastmod: 2026-02-02 07:22:32
metadata_visibility: show
title: 9-fluorenone-based synthetic sulfonamide compounds as dual inhibitors of SARS-CoV-2 Main-Protease and Papain-like Protease
keywords: In-silico structure; 9-fluorenone scaffold; Based docking; Dual-protease inhibitor; FRET-based assay; High-throughput screening; Main protease (Mpro); Molecular dynamics (MD) simulation; Papain-like protease (PLpro); SARS-CoV-2; Sulfonamide derivatives; Tilorone
abstract: Tilorone, a 9-fluorenone scaffold-based molecule, is a known broad-spectrum antiviral with an IC50 of 180 nM against SARS-CoV-2, but its mechanism is not known. In the present study, we found it to have weak activity against PLpro (IC50 = 30.7 ± 7.5 μM) and was inactive against Mpro. Several sulfonamide derivatives of 9-fluorenone, having the same scaffold as tilorone, were synthesized based on our in-silico studies to enhance their protease activity. They were evaluated for their inhibitory potential for targeting SARS-CoV-2 Mpro (main protease) and PLpro (papain-like protease) using FRET-based high-throughput screening and gel-based assays. Among the derivatives, 3e exhibited dual inhibition against Mpro (IC50 = 23 ± 3.4 μM) and PLpro (IC50 = 6.33 ± 0.5 μM), while 3h selectively inhibited PLpro (IC50= 5.94 ± 1.0 μM). Both 3e and 3h suppressed SARS-CoV-2 replication with IC50 values of 13.4 ± 0.28 μM and 18.2 ± 3.2 μM, respectively. Molecular docking and dynamics studies revealed that the NO2 group in 3h enhances the rigidity of the BL2 loop of PLpro, contributing to its higher PLpro activity. Both 3e and 3h showed antiviral activity comparable with standard alpha-ketoamide inhibitor (13b-K) in cell-based assays and were non-cytotoxic with acceptable selectivity indices (S.I. > 5.5). These findings suggest that 9-fluorenone-based sulfonamides, particularly 3e and 3h, may be promising candidates as dual or selective protease inhibitors against SARS-CoV-2.
date: 2025-09
publication: Mol. Divers.
publisher: Springer Science and Business Media LLC
citation:   Das, Sudesna and Sunnapu, Prasad and Rafi, Mohammed and Begum, Yasmin and Dey, Sudip and Joshi, Akshay and Singh, Nittu and Thakur, Krishan Gopal and Jaisankar, Parasuraman and Singh, Umesh Prasad  (2025) 9-fluorenone-based synthetic sulfonamide compounds as dual inhibitors of SARS-CoV-2 Main-Protease and Papain-like Protease.  Mol. Divers..