Fig 2: Interactions of compounds I4 and I5 from the Enamine PPI library. 3D model of interacting residues of INTS3 (green) with the overlaid structures of compounds I4 (pink) and I5 (yellow).

Fig 3: Binding mode of screened compounds to the INTS3 pocket. The representative frame from the top cluster from the MD simulations of (a) compounds I4 (pink) and I5 (yellow) overlaid at the binding site of INTS3 (green ribbon) shows interaction with amino acid residues at two binding grooves, and (b) the terminal N-naphthaloyl ring of I4 and p-fluoro benzoyl ring of I5 share the same binding pocket as the aromatic ring of Phe98 of hSSB1 (blue); (c) compound I2 also shares similar binding pockets as I4 and I5; however, pocket 2 is shallow. (d) Compounds I1 (salmon) and I3 (purple) wrap around α-helix 1 from the residue (Pro307–Ser318).

Fig 4: Targeting the INTS3-hSSB1 interface with small molecule inhibitors.(a) PPI residues between INTS3 and hSSB1 from the crystal structure, PDB ID: 4OWW, generated by PDBsum indicate the involvement of interaction via formation of the salt bridge, H-bonds, and nonbonded interaction. (b) Ligand binding cavity on the N-terminus of INTS3 predicted by the CASTp 3.0 server. (c) Overlaid binding poses of the five top-scoring ligands (green: I4 - Z826681950, pink: I3 - Z336696716, orange: I5 - Z978928456, blue: I1 - Z1033202002, and salmon: I2 - Z30413849) with INTS3 from virtual screening using Autodock Vina. (d) Co-immunoprecipitation assay (n = 3) of endogenous INTS3 with hSSB1 from U2OS cell lysates after compound (I1–I5) treatment for 36 h.

Fig 5: Crystal structure of the SOSS1 complex bound to ssDNA. The crystal structure of SOSS1 deposited in the Protein Data Bank (PDB ID: 4OWW) shows a ternary protein complex wherein 6-nucleotide ssDNA (dT6, represented in blue) binds to the OB-fold of SOSSB1 (hSSB1) at a site distinct from the SOSSA (INTS3) binding interfaces. The PPI interfaces of INTS3, interface I and II, bear loop and helical structures, respectively, at the N-terminus of INTS3, separating it from the SOSSC binding interface.