Identification of Novel Inhibitors against Coactivator Associated Arginine Methyltransferase 1 Based on Virtual Screening and Biological Assays

Abstract

Overexpression of coactivator associated arginine methyltransferase 1 (CARM1), a protein arginine N-methyltransferase (PRMT) family enzyme, is associated with various diseases including cancers. Consequently, the development of small-molecule inhibitors targeting PRMTs has significant value for both research and therapeutic purposes. In this study, together with structure-based virtual screening with biochemical assays, two compounds DC_C11 and DC_C66 were identified as novel inhibitors of CARM1. Cellular studies revealed that the two inhibitors are cell membrane permeable and effectively blocked proliferation of cancer cells including HELA, K562, and MCF7. We further predicted the binding mode of these inhibitors through molecular docking analysis, which indicated that the inhibitors competitively occupied the binding site of the substrate and destroyed the protein-protein interactions between CARM1 and its substrates. Overall, this study has shed light on the development of small-molecule CARM1 inhibitors with novel scaffolds.

Figure 1

Flowchart of virtual screening procedures for CARM1 inhibitors.

Figure 2

Antiproliferative effect of DC_C11 and DC_C66 on several cancer cell lines. (a–c) Time-dependent and dose-dependent inhibitory effect of DC_C11 on HELA, K562, and MCF7 within 24 hrs, 48 hrs, and 72 hrs, respectively. (d–f) Time-dependent and dose-dependent inhibitory effect of DC_C66 on HELA, K562, and MCF7 within 24 hrs, 48 hrs, and 72 hrs, respectively. (g–i) Time-dependent and dose-dependent inhibitory effect of Sinefungin on HELA, K562, and MCF7 within 24 hrs, 48 hrs, and 72 hrs, respectively.

Figure 3

Predicted binding mode of DC_C11 and DC_C66 with CARM1 from docking analysis. (a) Superimposition of the binding modes of the two compounds and substrate H3 peptide (PDB ID: 5DX0). The structure of CARM1 is displayed in vacuum electrostatics. H3 peptide is shown as gray sticks, DC_C11 is shown as magenta sticks, and DC_C66 is displayed as green sticks. (b) A close view of the interactions between DC_C66 and CARM1 in the binding pocket; the key residues are shown as sticks. (c) Schematic diagram showing putative interactions between CARM1 and DC_C66. Residues involved in the hydrophobic interactions are shown as starbursts, and hydrogen-bonding interactions are denoted by dotted green lines. (d) A close view of the interactions between DC_C11 and CARM1 in the binding pocket; the key residues are shown as sticks. (e) Schematic diagram showing putative interactions between CARM1 and DC_C11.