What question did this study set out to answer?

This study aims to identify new inhibitors for the SARS-CoV-2 papain-like protease (PLᵖʳᵒ) and main protease (Mᵖʳᵒ) using molecular modeling and in-vitro evaluations.

May 7, 2026Open Access

Identification of a Quinolone-Based Scaffold as a Dual SARS-COV-2 PLᵖʳᵒ and Mᵖʳᵒ Inhibitor: An Integrated Molecular Modeling and In-vitro Evaluation Approach

Key Points

This study aims to identify new inhibitors for the SARS-CoV-2 papain-like protease (PLᵖʳᵒ) and main protease (Mᵖʳᵒ) using molecular modeling and in-vitro evaluations.
Employing virtual screening through pharmacophore modeling and molecular docking, followed by enzymatic evaluation.
Conducting molecular dynamics simulations to assess compound stability and binding affinity.
Testing 30 top candidates experimentally for efficacy against PLᵖʳᵒ and Mᵖʳᵒ.
The lead compound ST50940260 inhibited PLᵖʳᵒ with an IC50 of 69.53 ± 4.4 μM and Mᵖʳᵒ with an IC50 of 96.7 μM.
Molecular dynamics simulations indicated stable binding of ST50940260 to PLᵖʳᵒ compared to co-crystallized ligands.
The derivative Z30231927 showed an IC50 of 124.8 μM against PLᵖʳᵒ, demonstrating promising activity.

Abstract

Introduction: The papain-like protease (PLᵖʳᵒ) plays a critical role in the SARS-CoV-2 life cycle by regulating both viral replication and immune evasion, making it an attractive target for antiviral drug development. Methods: In this study, a virtual screening strategy combining pharmacophore modeling, molecular docking, enzymatic evaluation, and molecular dynamics (MD) simulations was employed to identify novel PLᵖʳᵒ inhibitors. From this process, 30 top ranked candidates were selected for experimental enzymatic evaluation. Results: Among them, a quinolone-based scaffold compound ST50940260 demonstrated the highest inhibitory activity with an IC 50 of 69.53 ± 4.4 μM, exhibiting favourable potency and lead like properties, with a docking score of − 10.215 kcal/mol. Notably, ST50940260 also showed inhibitory activity against Mᵖʳᵒ, suggesting dual target potential with an IC 50 of 96.7 μM. To further explore structure activity relationships, a 2D similarity search was conducted, resulting in the identification and testing of seven structural derivatives, among which Z30231927 emerged as the most promising analogue with an IC 50 of 124.8 μM against PLᵖʳᵒ. Molecular dynamics simulations of 100 ns revealed that the lead compound forms a stable complex with PLᵖʳᵒ, exhibiting interaction patterns comparable to those of the co-crystallized ligand. Furthermore, MM-GB/SA binding free energies were calculated from the MD trajectories for the lead (ST50940260), the derivative (Z30231927), and the co-crystallized ligand in 7JN2. The lead demonstrated favourable binding (− 27.33 kcal/mol) within a comparable range, while the derivative showed the most favourable binding (− 30.26 kcal/mol), followed closely by the co-crystallized reference (− 29.82 kcal/mol). Conclusion: Overall, these findings highlight ST50940260 as a promising lead candidate for further optimization, with potential dual inhibitory activity against both proteases. Keywords: docking, pharmacophore filtration, molecular dynamics, enzyme inhibition assay

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