Identification of Dipeptidyl peptidase-4 (DPP-4) inhibitors as Potential Antidiabetic agents using Molecular docking study

Ankita¹, Keerti Bhardwaj², Navneet Khurana³, Ashish Sutte⁴, Gopal Khatik¹*

¹Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar- Delhi G.T. Road, Phagwara, Punjab, India (144411).

²Department of Pharmaceutics, School of Pharmaceutical Sciences, Lovely Professional University,

Jalandhar- Delhi G.T. Road, Phagwara, Punjab, India (144411).

³Department of Pharmacology, School of Pharmaceutical Sciences, Lovely Professional University,

Jalandhar- Delhi G.T. Road, Phagwara, Punjab, India (144411).

⁴Department of Pharmacognosy, School of Pharmaceutical Sciences, Lovely Professional University,

Jalandhar- Delhi G.T. Road, Phagwara, Punjab, India (144411).

*Corresponding Author E-mail: gopal.16803@lpu.co.in

ABSTRACT:

Diabetes is a heterogeneous disease of carbohydrates metabolism that occurs owing to a deficiency of discharge of insulin or resistance to it. Type 2 Diabetes Mellitus is very common and is a major concern. A patient over the age of 40 years mainly suffers from this and it is also increased with the increase in age and increase in obesity. Targeting to the disease progressing enzyme or protein is a valuable tool to alleviate the disease. Among several targets for diabetes, DPP-4 is recognized to control glucose metabolism. It degrades the GLP-1 or incretin which is supposed to be involved in glucagon release inhibition as well as augmented insulin secretion. Thus DPP-4 inhibitors like saxagliptin and sitagliptin are inhibiting DDP-4 leads to improve glycemic control. Therefore we have designed different novel DPP-4 inhibitors based on alogliptin which act as an antidiabetic agent with the help of Autodock vina molecular docking software. Among studies designed molecules, ANK4 showed good binding affinity (-10.7 kcal\mol) which is better than alogliptin (-9.6 kcal/mol).

KEYWORDS: Diabetes, DPP-4 inhibitor, Alogliptin, Molecular docking.

INTRODUCTION:

Diabetes is a heterogeneous disease of carbohydrates metabolism that occurs owing to a deficiency of discharge of insulin or resistance to it. Due to this, it may result in acute and chronic complications. So patient need to get the proper treatment during the initial period of time¹. Type 2 Diabetes Mellitus is very common and a major threat currently. Patient over the age of 40 years mainly suffers from this and it is also increased with the increase in age and increase in obesity. Different synthetic and natural antidiabetic agents are currently used as monotherapy (singly used), or in combinations (two or three drugs used) for the management of type 2 diabetes mellitus. The antidiabetic agents are classified based on teri structure or mechanism of action the target which includes insulin, metformin, meglitinides, sulphonylureas, thiazolidinediones (TZD), alpha-glucosidase inhibitors, glucagon-like peptide-1 (GLP-1) agonists etc.²

Dipeptidyl peptidase-4(DPP-4) is the new and potential target for antidiabetic drugs. It is present on the surface of cells and also present in circulation. Its inhibitors are also known as gliptin, which is active orally and inhibits the enzyme DPP-4 which degrades the GLP-1.³ It reduces glucagon and blood glucose level, while increases incretin level which inhibits glucagon release and increased insulin secretion,^4,5 furthermore found that DPP-4 protein is the significant one which was engaged with control of this incretin hormone.^6,7 When these DPP-4 inhibitors tested on animals, it was observed that there was an increase in the level of GLP-1.⁸ Numerous DPP-4 inhibitors are established and accepted for the management of Type 2 diabetes mellitus which includes Vildagliptin, Sitagliptin, Saxagliptin, Alogliptin, Linagliptin, Gemiglaptin, Dutogliptin etc. (Figure 1).⁹

Figure 1: Dipeptidyl peptidase-4 (DPP-4) inhibitors.

There are some adverse effects observed in the existing DPP-4 inhibitors like nasopharyngitis, headache, dizziness, arthralgia, nausea, and constipation¹⁰. Also, they show a hypoglycemic effect and weight gain when combined with sulfonylurea¹¹. Therefore search for a new drug is needed to overcome such side effects. In recent years alogliptin was observed to be the key scaffold for studying the modified analog with better antidiabetic action (Figure 2).¹²,¹³,¹⁴,¹⁵

Figure 2: Recent modifications of alogliptin.

Methods:

The structures were designed on the basis of known DPP-4 inhibitor i.e. alogliptin (Figure 3) by varying the different functional groups at X, R₁, R_2, and R₃. The designed molecules were analyzed by molecular modeling software Autodock-vina^16,17 using the pdb or protein as selected DPP-4 protein 3g0b at the binding site.¹⁸,¹⁹ The designed molecules were drawn by ChemDraw and converted to 3D. Further energy minimizations were performed using the MM2 Interface program on ChemBio3D Ultra 12.0 and molecules were saved in pdb format.²⁰

For the identification of the most active molecule, initially the extraction of internal ligand was done and docking it in the same manner as an actual ligand T22800 (which is alogliptin) using the process as described our research group previously.^21-33

Figure 3: Design of new ligands based on alogliptin.

Results and Discussions:

DPP-4 based 3g0b protein was used for the docking study and its internal ligand T22800 (which is alogliptin) was studied via extracting and docking as showed in Figure 4. For the same polar hydrogens added with Kollman charges. The grid was optimized and validated for its output, which resulted in Figure 5 shows a good overlay of ligand before docking and after docking with 9.6 kcal/mol of binding affinity.

Figure 4: Internal ligand (T22800) and grid optimization.

After optimization and validation, all the designed ligands were studied and results were obtained as bindin affinity as showed in Table 1. The results were compared with the internal ligand as a small ligand, which is very much comparable with respect to the binding energies at the binding site of the 3g0b receptor protein.

Figure 5: Grid validation.

Table 1: Comparison of estimated binding affinity of designed ligands on DPP-4 protein.

Ligand	Structure	Binding affinity (kcal\mol)	Ligand	Structure	Binding affinity (kcal\mol)
T22800 (Alogli-ptin)		-9.6	NA	NA	NA
ANK1		-8.2	ANK13		-7.5
ANK2		-8.5	ANK14		-8.0
ANK3		-8.6	ANK15		-7.9
ANK4		-10.7	ANK16		-9.8
ANK5		-10.3	ANK17		-9.5
ANK6		-10.1	ANK18		-9.7
ANK7		-7.3	ANK19		-7.8
ANK8		-7.1	ANK20		-8.1
ANK9		-7.3	ANK21		-8.0
ANK10		-8.8	ANK22		-8.7
ANK11		-8.9	ANK23		-9.0
ANK12		-9.1	ANK24		-8.3

The designed ligands showed good affinity and comparatively better binding affinity varying from -7.5 kcal/mol to -10.7 kcal./mol to 3g0b than alogliptin -9.6 kcal/mol. The highest binding affinity was observed with ANK4 (-10.7 kcal/mol), therefore it was selected for detail interaction studies at the binding site and shown in Figure 6 and 7. There were eleven amino acid residues were found at the binding site which are TRY547, PHE357, TYR666, SER209, HIS126, GLU205, ARG125, TYR662, VAL656, SER630, and VAL111. These showed various favorable interactions with the ANK4.

Figure 6: Binding of ANK4 (Molecular surface with sky blue colour) at the binding site of 3g0b protein (ribbon structure with red colour).

Figure 7: (a) Front view and (b) side view for the binding interaction of ANK4 (Molecular surface) at the binding site of 3g0b protein (close contact).

The hydroxyl group of SER209 has a hydrogen bonding with NH of ANK4, also imidazole ring of HIS126 having another hydrogen bonding. The side chain of the acidic group (COOH) of GLU205 having hydrophilic interaction with the carbonyl group of primidone ring of ANK4. VAL657 having hydrophobic interaction with phenyl ring of ANK4, while TRY547 and PHE357 showed pi-pi interaction with the benzylamine ring of ANK4. These results suggest that ANK4 can be transformed further as a potential antidiabetic agent targetting to DPP-4 receptor, and for the same, a detailed study is further required.

Conclusion:

We have designed different novel DPP-4 inhibitors based on alogliptin and may act as an antidiabetic agent. Autodock vina molecular docking software was used for the identification of better ligand having a good binding affinity to the DPP-4 receptor. The designed ligands were transformed to pdbqt and docked at the binding site of protein 3q0b. Among these molecules, ANK4 showed the best result in having a binding affinity -10.7kcal\mol. Further studies on the same ligand were done to investigate the binding interaction which shoed two hydrogen bonding of NH to the hydroxyl group of SER209 and the imidazole ring of HIS126. Some other favorable interactions include hydrophilic interaction of acidic group (COOH) of GLU205 with the carbonyl group of primidone ring of ANK4, while VAL657 was having hydrophobic interaction with phenyl ring of ANK4. The pi-pi interactions were showed by TRY547 and PHE357 with the benzylamine ring of ANK4. Further, a detail investigation on ANK4 is needed to explore it as a potential DPP-4 inhibitor.

CONFLICT OF INTEREST:

The authors declare that they have no conflict of interests.

Acknowledgment:

Authors are thankful to second International Conference of Pharmacy, held by School of Pharmaceutical Sciences, Lovely Professional University on September 13-14, 2019 to fund the publication of this manuscript.

References:

1. Walker, R.; Whittlesea, C. Clinical pharmacy and therapeutics. Churchill Livingstone: Edinburg, 2007.

2. Baggio, L.; Drucker, D. Incretin hormones in the treatment of type 2 diabetes: Therapeutic applications of DPP-IV inhibitors. Medscape Diabetes Endocrinol 2006, 8, 1-5.

3. Seshadri, K.; Kirubha, M. Gliptins: A new class of oral antidiabetic agents. Indian J Pharm Sci 2009, 71, 608–614.

4. Drucker, D. J.; Nauck, M. A. The incretin system: glucagon-like peptide-1 receptor agonists and dipeptidyl peptidase-4 inhibitors in type 2 diabetes. Lancet 2006, 368, 1696-1705.

5. Mentlein, R. Dipeptidyl-peptidase IV (CD26)-role in the inactivation of regulatory peptides. Regul Pept 1999, 85, 9-24.

6. Mentlein, R.; Gallwitz, B.; Schmidt, W. E. Dipeptidyl‐peptidase IV hydrolyses gastric inhibitory polypeptide, glucagon‐like peptide‐1 (7–36) amide, peptide histidine methionine and is responsible for their degradation in human serum. Eur J Biochem 1993, 214, 829-835.

7. Vilsbøll, T.; Agersø, H.; Krarup, T.; Holst, J. J. Similar elimination rates of glucagon-like peptide-1 in obese type 2 diabetic patients and healthy subjects. J Clin Endocrinol Metab 2003, 88, 220-224.

8. Holst, J. J.; Deacon, C. F. Inhibition of the activity of dipeptidyl-peptidase IV as a treatment for type 2 diabetes. Diabetes 1998, 47, 1663-1670.

9. Gupta, V.; Kalra, S. Choosing a gliptin. Indian J Endocrinol Metab 2011, 15, 298–308.

10. Scheen, A. J. Dipeptidylpeptidase-4 inhibitors (gliptins). Clin Pharmacokinet 2010, 49, 573-588.

11. Garber, A.; Foley, J.; Banerji, M.; Ebeling, P.; Gudbjörnsdottir, S.; Camisasca, R. P.; Couturier, A.; Baron, M. Effects of vildagliptin on glucose control in patients with type 2 diabetes inadequately controlled with a sulphonylurea. Diabetes Obes Metab 2008, 10, 1047-1056.

12. Kodimuthali, A.; Prasunamba, P. L.; Pal, M. Synthesis of a novel analogue of DPP-4 inhibitor Alogliptin: Introduction of a spirocyclic moiety on the piperidine ring. Beilstein J Org Chem 2010, 6, doi:10.3762/bjoc.6.71.

13. Lai, Z.-W.; Li, C.; Liu, J.; Kong, L.; Wen, X.; Sun, H. Discovery of highly potent DPP-4 inhibitors by hybrid compound design based on linagliptin and alogliptin. Eur J Med Chem 2014, 83, 547-560.

14. Li, N.; Wang, L.-J.; Jiang, B.; Guo, S.-J.; Li, X.-Q.; Chen, X.-C.; Luo, J.; Li, C.; Wang, Y.; Shi, D.-Y. Design, synthesis and biological evaluation of novel pyrimidinedione derivatives as DPP-4 inhibitors. Bioorg Med Chem Lett 2018, 28, 2131-2135.

15. Deng, X.; Shen, J.; Zhu, H.; Xiao, J.; Sun, R.; Xie, F.; Lam, C.; Wang, J.; Qiao, Y.; Tavallaie, M. S. Surrogating and redirection of pyrazolo [1, 5-a] pyrimidin-7 (4H)-one core, a novel class of potent and selective DPP-4 inhibitors. Bioorg Med Chem 2018, 26, 903-912.

16. Kaur, K.; Kaur, P.; Mittal, A.; Nayak, S.; Khatik, G. Design and molecular docking studies of novel antimicrobial peptides using Autodock molecular docking software. Asian J Pharm Clin Res 2017, Sept, 28-31.

17. Kaur, P.; Khatik, G. L. Identification of novel 5-styryl- 1,2,4-oxadiazole/Triazole derivatives as the potential antiandrogens. through molecular docking study. Int J Pharm Pharm Sci 2016, 8, 72-77.

18. 3g0b accessed from https://www.rcsb.org/structure/3g0b=. Accessed on 10 oct 2018.

19. Trott, O.; Olson, A. J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 2010, 31, 455-461.

20. Energy minimizations were performed MM2 Interface program on ChemBio3D Ultra 12.0, and structures were drawn by ChemBioDrwa Ultra 12.0 (CambridgeSoft).

21. Bashary, R. and Khatik, G.L. Design, and facile synthesis of 1, 3 diaryl-3-(arylamino) propan-1-one derivatives as the potential alpha-amylase inhibitors and antioxidants. Bioorg Chem 2018, 82, 156-162.

22. Kaur, P., Mittal, A., Nayak, S.K., Vyas, M., Mishra, V., Khatik, G.L. Current Strategies and Drug Targets in the Management of Type 2 Diabetes Mellitus. Curr Drug Targets 2018, 19(15), 1738-1766.

23. Osanyinpeju, O.S., Bashary, R., Mittal, A., Mittal, Vyas, M., Nayak, S.K., Khatik, G.L. A comparative study of stereochemical effects of anti-prostate agents by molecular docking. Asian J Pharm Clin Res 2018, 11(2), 76-80.

24. Ramjith U.S., Muhammed S. Molecular Docking Study of Novel Imidazo[2,1-b]-1,3,4 thiadiazole derivatives. Research J. Pharm. and Tech 2013, 6(6), 688-694.

25. Sravani, M., Duganath, N., Gade, D.R., Reddy R.C.H. Insilico Analysis and Docking of Imatinib Derivatives Targeting BCR-ABL Oncoprotein for Chronic Myeloid Leukemia. Asian J. Research Chem. 2012, 5(1), 153-158.

26. Chauhan, R., Singh, N., Abraham, J. Bioactivity and Molecular Docking of Secondary Metabolites produced by Streptomyces xanthochromogenes JAR5. Research J. Pharm. and Tech. 2015, 8(3), 300-309.

27. Shanmugapriya, E., Ravichandiran, V., Aanandhi, M.V. Molecular docking studies on naturally occurring selected flavones against protease enzyme of Dengue virus. Research J. Pharm. and Tech. 2016, 9(7), 929-932.

28. Dhananjayan, K., Sumathy, A., Palanisamy, S. Molecular Docking Studies and in-vitro Acetylcholinesterase Inhibition by Terpenoids and Flavonoids. Asian J. Research Chem. 2013, 6(11), 1011-1017.

29. Reddy, N.V.L.S., Anarthe S.J., Raju, G.M, Akhila, M, Raj, P.G.B.. Molecular docking studies of isolated compounds from Cassia fistula on HMG-COA reductase. Asian J. Research Chem. 2019, 12(2), 89-93.

30. Napoleon, A.A., Sharma, V. Molecular Docking and In-vitro anti-inflammatory evaluation of Novel Isochromen-1-one analogues from Etodolac. Research J. Pharm. and Tech. 2017, 10(8), 2446-2450.

31. Suganya, J., Viswanathan T., Radha, M., Marimuthu, N. In silico Molecular Docking studies to investigate interactions of natural Camptothecin molecule with diabetic enzymes. Research J. Pharm. and Tech. 2017, 10(9), 2917-2922.

32. Hemalatha, K., Girija K. Evaluation of Drug Candidature of some Benzimidazole Derivatives as Biotin Carboxylase Inhibitors: Molecular docking and Insilico studies. Asian J. Res. Pharm. Sci. 2016, 6(1), 15-20.

33. Hemalatha, K., Selvin, J., Girija, K. Synthesis, In silico Molecular Docking Study and Anti-bacterial Evaluation of some Novel 4-Anilino Quinazolines. Asian J. Pharm. Res. 2018, 8(3), 125-132.

Received on 20.11.2019           Modified on 04.01.2020

Accepted on 18.02.2020         © RJPT All right reserved

Research J. Pharm. and Tech. 2020; 13(11):5257-5262.

DOI: 10.5958/0974-360X.2020.00919.1