Verbascoside A as Potent Compound of Cyperus rotundus in Cytotoxic T Lymphocyte-Associated Antigen-4 (CTLA-4) Inhibition Based on Computational Model

Abstract

Cytotoxic T lymphocyte-associated antigen-4 (CTLA-4) regulation represents a significant therapeutic target in addressing regulatory T cell (Treg) dysfunction and enhancing immune responses within the tumor microenvironment (TME). This study aimed to evaluate the inhibitory effect of compounds of Cyperus rotundus against the immune checkpoint CTLA-4 in silico. Compounds from Cyperus rotundus tubers were identified by Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS). The compounds’ toxicity was predicted using Protox 3.0 web server. In silico study was performed using molecular docking and dynamics simulations of the compounds with CTLA-4 (PDB ID: 1I8L) protein using PyRx and YASARA softwares, respectively. Fourteen compounds were identified in Cyperus rotundus tubers. All compounds were classified as safe with LD₅₀ value ranging from 740 to 26000 mg/kg. Molecular docking showed Verbascoside A and Maltopentaose as potential inhibitors of CTLA-4 with binding energies of -6.3 and -5.4 Kcal/mol, respectively. In the molecular dynamics simulation, RMSD values of all complexes exceeded 3 Å, indicating instability. However, the backbone RMSD and ligand conformation RMSD of CTLA4-Verbascoside A with values below 3 Å indicated more stability. Meanwhile, the CTLA4-maltopentaose complex exhibited higher RMSD value, indicating a change in the CTLA-4 protein structure when interacting with maltopentaose. Furthermore, the prediction of protein targets of maltopentaose and verbascoside A revealed potential direct and indirect target proteins related to cancer signaling pathways, namely; PI3K-Akt and estrogen signaling pathways. The ability of these compounds to modulate the TME-related CTLA-4 indicates their potential as anticancer drug candidates.