Structural insights and molecular dynamics into the inhibitory mechanism of a Kunitz-type trypsin inhibitor from Tamarindus indica L

Abstract

Trypsin inhibitors from tamarind seed have been studied in vitro and in preclinical studies for the treatment of obesity, its complications and associated comorbidities. It is still necessary to fully understand the structure and behaviour of these molecules. We purifed this inhibitor, sequenced de novo by MALDI-TOF/ TOF, performed its homology modelling, and assessed the interaction with the trypsin enzyme through molecular dynamics (MD) simulation under physiological conditions. We identified additional 75 amino acid residues, reaching approximately 72% of total coverage. The four best conformations of the best homology modelling were submitted to the MD. The conformation n 287 was selected considering the RMSD analysis and interaction energy (-301.0128 kcal.mol À1 ). Residues Ile (54), Pro (57), Arg (59), Arg (63), and Glu (78) of pTTI presented the highest interactions with trypsin, and arginine residues were mainly involved in its binding mechanism. The results favour bioprospecting of this protein for pharmaceutical health applications.

An Insulin Receptor-Binding Multifunctional Protein from Tamarindus indica L. Presents a Hypoglycemic Effect in a Diet-Induced Type 2 Diabetes—Preclinical Study

“…Thus, as the structural conformation of TTIp was already known, along with the model that best adjusted to the parameters of molecular dynamics simulation (TTIp 56/287) interacting with trypsin [ 19 ], the knowledge of these characteristics allowed the bioprospection of a possible interaction between TTIp 56/287 and the IR (PDB ID 4OGA). In this study, using molecular docking, it was possible to observe the interaction between the two structural models, TTIp 56/287 and insulin, with the IR (PDB ID 4OGA), the latter being the same presented in the study by Menting et al [ 13 ].…”

“…In the present study, the potential of TTIp 56/287 as a ligand of the IR (PDB ID 4OGA) was revealed. Medeiros et al [ 19 ], when performing the molecular dynamics simulations analysis between TTIp 56/287 and trypsin, identified that the IPE between these two molecules was −301.0128 kcal mol −1 and that the amino acid residues isoleucine (54), proline (57), arginine (59), arginine (63) and glutamine (78) from TTIp 56/287 had the strongest interactions with trypsin, especially the residues of arginine, an amino acid of a basic nature, so these authors infer that the active site of trypsin presented a negative character in the interaction with TTIp 56/287.…”

“…In this study, we used the three-dimensional structure of TTIp, model number 56, and conformation number 287 (TTIp 56/287), according to Medeiros et al [ 19 ]. The three-dimensional structure of the insulin receptor (IR) with insulin with a resolution of 3.50 Å used in this study was obtained from the RCSB Protein Database [ 32 ], with the code PDB ID: 4OGA, according to Menting et al [ 13 ].…”

“…The purified TTI (TTIp) was recently characterized, sequenced and had its molecular arrangement and conformation estimated [ 18 , 19 ]. Sequencing the molecule and its modeled structural conformation is safe, and can evaluate its pharmacological potential [ 15 , 18 , 19 , 20 ] as a ligand in the active site (pocket) of another molecule (receptor), hand as great relevance for a better understanding of its action on specific metabolic pathways, including those mediated by insulin.…”

“…The purified TTI (TTIp) was recently characterized, sequenced and had its molecular arrangement and conformation estimated [ 18 , 19 ]. Sequencing the molecule and its modeled structural conformation is safe, and can evaluate its pharmacological potential [ 15 , 18 , 19 , 20 ] as a ligand in the active site (pocket) of another molecule (receptor), hand as great relevance for a better understanding of its action on specific metabolic pathways, including those mediated by insulin. In silico studies have been considered a valuable tool with which to determine the potential of a particular biological activity and provide information about the possible interactions exhibited by the most diverse peptides [ 21 , 22 , 23 , 24 ].…”