title: Understanding the molecular dynamics of type-2 diabetes drug target DPP-4 and its interaction with Sitagliptin and inhibitor Diprotin-A.
abstract: The occurrence of type 2 diabetes (T2D) accounts for 90-95 % of all diabetes. Intestine hormone glucagon-like peptide-1 (GLP-1) has an antidiabetic role that enhances insulin secretion and pancreatic β-cell proliferation. GLP-1 is degraded by the enzyme dipeptidyl peptidase-4 (DPP-4) rapidly. Hence, the DPP-4 inhibition has been preferred not only for the treatment but also as a major drug target. Sitagliptin and Diprotin-A are antihyperglycemic agents for the treatment of T2D. However, little is known on the molecular dynamics of DPP-4 and the interaction properties with its ligands, namely Sitagliptin and Diprotin-A. This study has used the latest bioinformatic tools to understand the molecular dynamics and its interaction properties of DPP-4. This study has explored the number of α helices, β strands, β hairpins, Ψ loop, β bulges, β turns, and ϒ turns and they were 19, 46, 25, 1, 14, 70, and 4, respectively. The highest number of H-bonds was recorded in α helix of domain-1, and the lowest number H-bonds were noted in α helix of domain-2. During interaction between residues, in A- and B-chain, 47 and 48 residues are involved for interaction, and interaction interface area was more in A-Chain (2176 Å(2)). From DPP-4 and Sitagliptin interaction, three residues in active sites such as Try226, Glu205, and Glu206 were involved in three H-bond formation, while 10 other amino acids (Try547, Try667, Asn710, Val711, His740, Ser630, Ser209, Arg358, Phe357, and Val207) were involved in hydrophobic interactions. In this review, we have shown the importance of bioinformatics as an excellent tool for a rapid method to assess the molecular dynamics and its interaction properties of DPP-4. Our predictions highlighted in this review will help researchers to understand the interaction properties and recognition of interactive sites to design more DPP-4 inhibitors for the treatment of T2D and drug discovery.
authors.affiliation: School of Computer and Information Sciences, Galgotias University, Greater Noida, India.
authors.forename: Chiranjib
authors.initials: C
authors.lastname: Chakraborty
authors.forename: Minna J
authors.initials: MJ
authors.lastname: Hsu
authors.forename: Govindasamy
authors.initials: G
authors.lastname: Agoramoorthy
mesh_terms: D000595:Amino Acid Sequence; D017124:Conserved Sequence; D003924:Diabetes Mellitus, Type 2 / Q000188:drug therapy*; D018819:Dipeptidyl Peptidase 4 / Q000737:chemistry / Q000378:metabolism*; D054873:Dipeptidyl-Peptidase IV Inhibitors / Q000378:metabolism* / Q000494:pharmacology / Q000627:therapeutic use; D006801:Humans; D006860:Hydrogen Bonding; D007004:Hypoglycemic Agents / Q000378:metabolism* / Q000494:pharmacology / Q000627:therapeutic use; D008024:Ligands; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000378:metabolism* / Q000494:pharmacology / Q000627:therapeutic use; D011485:Protein Binding; D011499:Protein Processing, Post-Translational; D017433:Protein Structure, Secondary; D021122:Protein Subunits / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D011719:Pyrazines / Q000378:metabolism* / Q000494:pharmacology / Q000627:therapeutic use; D000068900:Sitagliptin Phosphate; D013499:Surface Properties; D014230:Triazoles / Q000378:metabolism* / Q000494:pharmacology / Q000627:therapeutic use
chemical_list: D054873:Dipeptidyl-Peptidase IV Inhibitors; D007004:Hypoglycemic Agents; D008024:Ligands; D009842:Oligopeptides; D021122:Protein Subunits; D011719:Pyrazines; D014230:Triazoles; C041445:diprotin A; D018819:Dipeptidyl Peptidase 4; D000068900:Sitagliptin Phosphate