Research Article: Screening and identification of potential PTP1B allosteric inhibitors using in silico and in vitro approaches

Date Published: June 18, 2018

Publisher: Public Library of Science

Author(s): Ranajit Nivrutti Shinde, G. Siva Kumar, Shahbaz Eqbal, M. Elizabeth Sobhia, Freddie Salsbury.

http://doi.org/10.1371/journal.pone.0199020

Abstract

Protein tyrosine phosphatase 1B (PTP1B) is a validated therapeutic target for Type 2 diabetes due to its specific role as a negative regulator of insulin signaling pathways. Discovery of active site directed PTP1B inhibitors is very challenging due to highly conserved nature of the active site and multiple charge requirements of the ligands, which makes them non-selective and non-permeable. Identification of the PTP1B allosteric site has opened up new avenues for discovering potent and selective ligands for therapeutic intervention. Interactions made by potent allosteric inhibitor in the presence of PTP1B were studied using Molecular Dynamics (MD). Computationally optimized models were used to build separate pharmacophore models of PTP1B and TCPTP, respectively. Based on the nature of interactions the target residues offered, a receptor based pharmacophore was developed. The pharmacophore considering conformational flexibility of the residues was used for the development of pharmacophore hypothesis to identify potentially active inhibitors by screening large compound databases. Two pharmacophore were successively used in the virtual screening protocol to identify potential selective and permeable inhibitors of PTP1B. Allosteric inhibition mechanism of these molecules was established using molecular docking and MD methods. The geometrical criteria values confirmed their ability to stabilize PTP1B in an open conformation. 23 molecules that were identified as potential inhibitors were screened for PTP1B inhibitory activity. After screening, 10 molecules which have good permeability values were identified as potential inhibitors of PTP1B. This study confirms that selective and permeable inhibitors can be identified by targeting allosteric site of PTP1B.

Partial Text

Protein tyrosine phosphatases (PTPs) are a group of 107 enzymes that dephosphorylate phosphotyrosine residues of the protein substrates.[1,2] These enzymes are the key regulatory components in cellular functions and signal transduction pathways.[3,4] The PTP superfamily has a highly conserved active site motif C(X)5R, commonly known as PTP signature motif.[5] Protein tyrosine phosphatase 1B (PTP1B) is a representative member of this superfamily. PTP1B is a widely expressed cytosolic soluble protein with a molecular weight around 50 kD. In the native form, PTP1B consists of 435 amino-acid residues that are divided into three regions: N-terminal catalytic region or PTP domain (Residues 1–300), regulatory region (residues 300–400) and C-terminal membrane localization region (residues 400 to 435).[6,7] Activity of PTP1B is regulated by a variety of post-translational mechanisms, including phosphorylation of serine and tyrosine residues at various sites within of catalytic and transmembrane domains, oxidation of Cys215 due to reactive oxygen species, and spatial separation from its plasma membrane-localized substrates. It is involved in multiple signal transduction pathways acting as protein dephosphorylating enzyme.[8]. It has been established as a key enzyme in the negative regulation of insulin signalling pathway.[9–11]

 

Source:

http://doi.org/10.1371/journal.pone.0199020

 

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