Tiliroside protects against diabetic nephropathy in streptozotocin-induced diabetes rats by attenuating oxidative stress and inflammation

Table 1 Predicted active sites for fibronectin, transforming growth factor-β1, interleukin-6, and tumor necrosis factor-α with the rank

No.	Biomarker name	Targets (PDB ID)	Rank	Score	Probability	Predicted active sites
1	Fibronectin	1MFN	1	2.74	0.084	HIS36, HIS37, ALA38, SER41, ARG46, ASN61, LEU62, ASN63, TYR68
2	TGF-β1	Q3UNK5	1	9.11	0.534	ARG277, THR282, ASN283, ASN292, CYS293, CYS294, TRP330, ASP333, GLN359, SER386, CYS387, CYS389, PRO99
3	IL-6	2 L3Y	1	10.37	0.597	ILE129, PHE132, ASN133, GLU135, VAL136, ILE142, LEU184, THR187, ARG188, THR27, VAL30, GLY31, LEU89, LEU90, LYS91, ILE92, SER93, LEU96
4	TNF-α	2TNF	1	8.36	0.491	PRO100, PRO102, TRP114, GLU116, LYS98, SER99

P2Rank is a machine learning tool that predicts ligand-binding sites in proteins using structural features, ranking them based on their likelihood of being active sites. TGF-β1: Transforming growth factor-β1; IL-6: Interleukin-6; TNF-α: Tumor necrosis factor-α.

Table 2 List of targets

Target name	Target PDB/UniProt ID	Binding affinity (kcal/mol)	RMSD (Å)	Type of interacted bonds
				Hydrogen bond	Hydrophobic residues	Other bonds
Fibronectin	1MFN	-7.6	2.583	ARG44, ASN61	HIS37, HIS40, SER41, GLY43, PRO45, LEU62, ASN63, THR66, TYR68,	ALA38pa, ARG46
IL-6	2 L3Y	-8.4	2.652	ILE92, SER93(2)	LYS91, LEU89, ILE142, LEU90, ASN133, PHE132, LEU139, ILE87, GLU86, GLN85, TYR83, ASN84	VAL136psa, CYC78ps, CYC88 Lps
TNF-α	2TNF	-5.4	1.816	SER99, TYR115, LYS112	GLY68, VAL97, PRO102, LYS103, PRO105, PRO106, TRP114, PRO113, GLU116,	LYS98pc, ch, CYS69pa
IL-1β	4G6M	-7.5	2.062	TYR24, LYS77(2), LEU82(2)	GLU25, THR79, SER125, MET130, VAL132	LYS74pc, PRO131pa, PHE133pps (2)
TGF-β1	Q3UNK5	-9.1	2.125	GLU96, GLU100, ARG277, LEU280, THR282, ASN283, CYS293, GLN359	PRO95, PRO99, SER274, ARG275, ARG278, ALA279, ASN292, CYS326, TRP330, SER386, CYS389,	GLU98pc, GLU100pc, ARG277ps, pa, ASN283ch, HIS276ch, ASP333ch

TGF-β1: Transforming growth factor-β1; IL-6: Interleukin-6; TNF-α: Tumor necrosis factor-α; IL-1β: Interleukin-1β.