An oral xanthine based DPP-4 inhibitor used for treating diabetes. dpp4 inhibitor, tradjenta, antidiabetic drug



Oral anti-diabetic drug


Dipeptidyl peptidase-4 (DPP-4)



Commercial Name

Tradjenta® (United States, Canada)

Combination Drug(s)

Glyxambi® (linagliptin & empagliflozin)

Other Synonyms

BI-1356, Ondero



Ligand Code in PDB


3D Structure of linagliptin bound to target protein DPP-4

PDB ID 2rgu

Table 1.  Basic profile of linagliptin

Figure 1. 2D and 3D structure of linagliptin

Drug Information: 

Chemical Formula


Molecular Weight

472.23 g/mol

Calculated Predicted Partition Coefficient: cLogP


Calculated Predicted Aqueous Solubility: cLogS


Solubility (in water)

0.0502 mg/mL (sparingly soluble)

Predicted Topological Polar Surface Area (TPSA)

113.48 Å2

Table 2. Chemical and physical properties (DrugBank).

*Note: Predicted values may slightly vary from source to source. 

Drug Target: 

Linagliptin is an orally active, antidiabetic drug that works by inhibiting the enzyme dipeptidyl peptidase-4 (DPP-4) (Eckhardt et al., 2007). In response to food intake, endocrine cells in the gastrointestinal tract release incretin hormones, GLP-1 and GIP, to stimulate insulin secretion. Normally, DPP-4 degrades the incretin hormones within a few minutes of their release, thereby playing a key role in regulating the duration of incretin hormone function. Linagliptin, is a xanthine-based, non-substrate-like inhibitor of DPP-4. By blocking DPP-4 enzymatic activity, linagliptin increases the half-life of the incretin hormones, which in turn stimulates increased secretion of insulin by pancreatic β-cells and reduces secretion of glucagon by pancreatic α-cells. Collectively, these functions lower blood glucose levels. Since the incretins, GLP-1 and GIP, are only released after eating, DPP-4 inhibitors typically do not induce hypoglycemia (Aschner et al., 2006).

Learn more about DPP-4 here.

Drug-Target Complex: 

Each molecule of the DPP-4 enzyme is a transmembrane glycoprotein made up of 766 amino acids and consists of five regions: 

  • a cytoplasmic region (residues 1–6) not crystallized/not shown
  • a trans-membrane region (residues 7–28) not crystallized/not shown
  • a highly-glycosylated region (residues 29–323) colored cyan
  • a cysteine-rich region (residues 324–551) colored pink
  • a catalytic region (residues 552–766) colored orange

The overall structure of the extracellular portion of the enzyme, showing the highly glycosylated, cysteine-rich, and catalytic regions can be seen in Figure 2.

Figure 2. Overall structure of human DPP-4 monomer, complexed with linagliptin. The enzyme is shown in ribbon representation highlighting the N- and C-termini and various regions of the protein - cysteine-rich region (pink), highly glycosylated region (cyan) and catalytic domain (orange). Linagliptin is shown in ball-and-stick representation (PDB ID: 2rgu; Eckhardt et al., 2007).


The DPP-4 enzyme functions as a dimer, composed of two copies of the same protein (Figure 3).Linagliptin has been structurally derived from the xanthine scaffold (Deacon et al. 2010). It is a non-substrate-like inhibitor of DPP-4. This class of DPP-4 inhibitors does not mimic the dipeptidic nature of the DPP-4 substrates. Instead, it binds non-covalently to DPP-4 through hydrophobic and hydrogen-bonding interactions, and an aromatic group usually occupies the S1 hydrophobic sub-pocket of the active site of DPP-4.

Figure 3. X-ray crystal structure of the DPP-4 dimer (ribbons), with bound linagliptin (ball-and-stick). The DPP-4 monomer on the right is color-coded by region as in Figure 2 and the monomer on the left is shown as a grey ribbon (PDB ID: 2rgu; Eckhardt et al., 2007). The surface of the active site of DPP-4 is shown in the inset. Linagliptin is shown in a ball-and-stick representation, color-coded by atom type (C: gray; N: blue; O: red). Selected residues in the active sites are shown as stick figures.

Closer examination of the co-crystal structure of DPP-4 and linagliptin (Eckhardt et al., 2007) reveals multiple interactions of the drug with its pharmacological target, DPP-4 (Figure 4). The aminopiperidine motif, on one end of the drug, occupies the and S2 sub-site of the enzyme and the amine of this group forms hydrogen bonds with contributions from residues Glu205, Glu206, and Tyr662. Another hydrogen bond is formed between the carbonyl group of the xanthine scaffold and the backbone amide of residue Tyr631. The hydrophobic butynyl group of the drug occupies the S1 site (Figure 3, Figure 4), lined by several tyrosines, including Tyr662. The uracil ring of the xanthine scaffold has π-stacking interactions with Tyr547 (Figure 4), while the quinazoline ring has π-stacking interactions with Trp629 (Figure 4). Together, these interactions account for the tight binding of linagliptin with DPP-4 (IC50 < 2 nm).


Figure 4. Hydrogen bonding interactions (green lines) between linagliptin (ball-and-stick) and active site residues (stick figure) (PDB ID: 2rgu; Eckhardt et al., 2007). Figure 5. Hydrogen bonding interactions (green lines) between Diprotin A (ball-and-stick) and active site residues (stick figure) (PDB ID: 1nu8; Thoma et al., 2003).

Comparison of the co-crystal structures of DPP-4 with linagliptin (PDB ID 2rgu, Figure 4) and Diprotin A with DPP-4 (PDB ID 1nu8, Figure 5) shows that linagliptin acts by occluding the DPP-4 active site and prevents binding of incretin hormones.

Pharmacologic Properties and Safety: 




Bioavailability (%)


(Nakamura et al., 2015)

IC50 (nM)

.1-2 nM


Ki (nM)

 1 nM

(Guedes et al., 2013)

Half-life (hrs)

120-184 hours

(Capuano et al., 2013)

Duration of Action

24 hours



Human intestinal absorption



multidrug resistance protein 1



Cytochrome p450 3A4



~85% urine; ~5% feces

(Capuano et al., 2013)

AMES Test (Carcinogenic Effect)

probability 0.5444 (Non-AMES toxic)


hERG Safety Test (Cardiac Effect)

probability 0.6109 (weak inhibitor)


Liver Toxicity

In 2014, a single case of liver injury due to linagliptin was reported.


Table 3. Pharmacokinetics: ADMET of linagliptin


The half-life elimination of linagliptin is 120-184 hours, a longer persistence in comparison to that of other DPP-4 inhibitors. For instance, saxagliptin has a half-life of roughly 2.2-3.8 hours and aloglitpin is cleared from the plasma within approximately 12.4-21.4 hours (Capuano et al., 2013). Linagliptin’s longer survival time is beneficial for individuals who may accidentally skip taking their medication since the drug may remain in the system for a few days. Therefore, a once-daily dosing is appropriate since inhibition of DPP-4 activity is sustained for a long period of time. Approximately 85-90% of the drug is excreted unchanged via the enterohepatic system as feces (80%) and urine (5%), while 10% of the drug is minimally metabolized by cytochrome P450 3A4 (CYP3A4).


Drug Interactions and Side Effects: 

Hypoglycemia is uncommon with linagliptin alone (in <1% patients), but occurs in higher rates when it is combined with other oral hypoglycemic agents. Concomitant administration of single doses of linagliptin with insulin secretagogues (e.g. glyburide) or insulin may cause an elevated risk of hypoglycemia and adverse cardiovascular complications (PubChem).





Total Number of Drugs Interactions



Major Drug Interactions

bexarotene and gatifloxacin


Alcohol/Food Interaction(s)

moderate interaction with alcohol (ethanol)


Disease Interaction(s)

pancreatitis (major)


On-target Side Effects

abdominal pain, upper respiratory tract infection, diarrhea, constipation, urinary tract infection (UTI), pancreatitis


Off-target Side Effects

nasopharyngitis, cough, angioedema, rash, headache, depression, anxiety; blurred vision, skin exfoliation


Table 4. Drug interactions and side effects of linagliptin


Regulatory Approvals/Commercial: 

Tradjenta® (linagliptin) was developed by Boehringer Ingelheim and approved for use by the US FDA in 2011. It is prescribed as an oral medication in 5 mg tablets, taken once a day, regardless of meals (DrugBank). The cost of a 30-day supply of 5mg tablets of linagliptin is about US $243.60, which comes out to $8.12 /day.


Aschner, P., Kipnes, M. S., Lunceford, J. K., Sanchez, M., Mickel, C., and Williams-Herman, D. E. (2006) Effect of the Dipeptidyl Peptidase-4 Inhibitor Sitagliptin as Monotherapy on Glycemic Control in Patients with Type 2 Diabetes. Diabetes Care 29, 2632-2637. doi: 10.2337/dc06-0703

Capuano, A., Sportiello, L., Maiorino, M. I., Rossi, F., Giugliano, D., and Esposito, K. (2013) Dipeptidyl Peptidase-4 Inhibitors in Type 2 Diabetes Therapy – Focus on Alogliptin. Drug, Design, Development and Therapy 213, 989-1001. doi: 10.2147/DDDT.S37647

Deacon, C. F, and Holst, J. J. (2010) Linagliptin, a xanthine-based dipeptidyl peptidase-4 inhibitor with an unusual profile for the treatment of type 2 diabetes. Expert Opinion on Investigational Drugs 19, 133-140. doi: 10.1517/13543780903463862

Eckhardt, M., Langkopf, E., Mark, M., Tadayyon, M., Thomas, L., Nar, H., Pfrengle, W., Guth, B., Lotz, R., Sieger, P., Fuchs, H., and Himmelsbach, F. (2007) 8-(3-(R)-Aminopiperidin-1-Yl)-7-But-2-Ynyl-3-Methyl-1-(4-Methyl-Quinazolin-2-Ylmethyl)-3,7-Dihydropurine-2,6-Dione (BI 1356), a Highly Potent, Selective, Long-Acting, and Orally Bioavailable DPP-4 Inhibitor for the Treatment of Type 2 Diabetes. Journal of Medicinal Chemistry 50, 6450-6453. doi: 10.1021/jm701280z

Guedes, E. P., Hohl, A., de Melo, T. G., and Lauand, F. (2013) Linagliptin: Farmacology, Efficacy and Safety in Type 2 Diabetes Treatment. Diabetololgy & Metabolic Syndrome 5, 1-7. doi: 10.1186/1758-5996-5-25




Linagliptin - Affinity Data by PDB ID.

Linagliptin Uses, Side Effects & Warnings.

Nakamura, Y., Hasegawa, H., Tsuji, M., Udaka, Y., Mihara, M., Shimizu, T., Inoue, M., Goto, Y., Gotoh, H., Inagaki, M., and Oguchi, K. (2015) Diabetes Therapies in Hemodialysis Patients: Dipeptidase-4 Inhibitors. World Journal of Diabetes 6, 840-849. doi: 10.4239/wjd.v6.i6.840

Thoma, R., Loffler, B., Stihle, M., Huber, W., Ruf, A., and Hennig, M. (2003) Structural basis of proline-specific exopeptidase activity as observed in human dipeptidyl peptidase-IV. Structure 11, 947-959.  doi: 10.1016/S0969-2126(03)00160-6



September 2017, Jennifer Jiang, Dr. Sutapa Ghosh ; Reviewed by Drs. Stephen K. Burley and Kathleen Aertgeerts