## 3 Results and Discussion  
The structure of the YTH domain of YTHDC1 in the complex with the ligand 6 MZ was first analyzed to determine the critical amino acids involved in the recognition of m6A (Figure 2A). Notably, the 6 MZ engages the binding site that primarily contains hydrophobic residues. YTHDC1's YTH domain contains an aromatic cage that has evolved precisely to bind m6A [27]. The methyl group of m6A interacts strongly with aromatic residues TRP377, TRP428, and hydrophobic residues LEU439. Notably, both residues TRP377 and TRP428 are conserved in YTH domain family proteins. The mutation in TRP377 and TRP428 residues completely disrupts the binding of 6 MZ to m6A RNA [43]. Moreover, the adenine ring of m6A forms three hydrogen bonds with residues SER378, ASN363, and ASN367. This study [43] screened and identified 30 fragments representing 10 different chemotypes. Key interactions in most of the 30 fragments included hydrogen bonds with SER378 and van der Waals contacts within an aromatic cage. One study [44] found that the YTHDC1 aromatic cage recognizes the m6A nucleoside. Three residues (SER378, ASN363, and ASN367) form hydrogen bonds with the nucleobase. The ligand-protein binding is further strengthened by the methyl group with van der Waals interactions with the lipophilic binding site. This recognition was also confirmed by another study [45] that found that m6A's methyl group contributed to binding by interacting with two residues (TRP377 and TRP428) that also form an aromatic cage. The study [46] designed a potent ligand that interacted strongly with YTHDC1 through TRP377, TRP428, and LEU439.  
Most residues directly connected to m6A do not undertake apparent changes in the YTHDC1 holo and apo forms [27]. This observation was also found in the new complex of  
Figure 2: **(A)** The critical amino acids that recognize m6A are labeled in black. The methylated residue (6 MZ) is shown in Licorice representation with carbon atoms in orange, nitrogen atoms in blue, and oxygen atoms in red. PDB accession code 4R3I has been used to generate the figures. **(B)** Structural comparison between apo-state YTHDC1 (2 YUD) and YTHDC1 in the complex with 6 MZ (4R3I).  
m6A-YTHDC1 (PDB ID: 6 ZCN) [45]. We checked whether the binding of a ligand with the YTHDC1 domain affects the structure. The structural comparison was carried out between the apo state of YTHDC1 (2 YUD) and the complex upon ligand binding (Figure 2B). The overall RMSD between the two structures was 1.10 A. The conserved residues TRP377, TRP428, and LEU439 are critical residues for binding, forming an aromatic cage for the binding of m6A. These residues and their side-chain orientations are conserved and do not undergo considerable changes. However, the side chain of residue ASN363 is slightly different. One study [45] found a different conformation for the binding residues in a new apo YTHDC1 structure with two YTH domains in an asymmetric unit (PDB ID: 6 ZD9). 6 ZD9's chains, A and B, showed different orientations for the MET438 residue. The conformation of Chain A more closely resembled the canonical one. However, in chain B, a side chain flipping of the MET438 residue from the solvent into the binding pocket was observed, which resulted in one impeded aromatic cage to bind m6A. We also performed a docking study of the native ligand m6A using the same pipeline and parameters as employed for our virtual screening (Figure S7). The score obtained is 9.11 kcal/mol, which serves as a reference to compare the binding affinities of our top candidate ligands, which had docking scores ranging from \(-\)11.03 to \(-\)9.6 kcal/mol. The docking score of m6A falls within this range, indicating that our identified ligands exhibit comparable or better binding affinities to the YTHDC1 protein than the native m6A ligand.