Structural Insights into the Design of Nonpeptidic Isothiazolidinone-containing Inhibitors of Protein-tyrosine Phosphatase 1B

Abstract

Structural analyses of the protein-tyrosine phosphatase 1B (PTP1B) active site and inhibitor complexes have aided in optimization of a peptide inhibitor containing the novel (S)-isothiazolidinone (IZD) phosphonate mimetic. Potency and permeability were simultaneously improved by replacing the polar peptidic backbone of the inhibitor with nonpeptidic moieties. The C-terminal primary amide was replaced with a benzimidazole ring, which hydrogen bonds to the carboxylate of Asp 48 , and the N terminus of the peptide was replaced with an aryl sulfonamide, which hydrogen bonds to Asp 48 and the backbone NH of Arg 47 via a water molecule. Although both substituents retain the favorable hydrogen bonding network of the peptide scaffold, their aryl rings interact weakly with the protein. The aryl ring of benzimidazole is partially solvent exposed and only participates in van der Waals interactions with Phe 182 of the flap. The aryl ring of aryl sulfonamide adopts an unexpected conformation and only participates in intramolecular -stacking interactions with the benzimidazole ring. These results explain the flat SAR for substitutions on both rings and the reason why unsubstituted moieties were selected as candidates. Finally, substituents ortho to the IZD heterocycle on the aryl ring of the IZD-phenyl moiety bind in a small narrow site adjacent to the primary phosphate binding pocket. The crystal structure of an o-chloro derivative reveals that chlorine interacts extensively with residues in the small site. The structural insights that have led to the discovery of potent benzimidazole aryl sulfonamide o-substituted derivatives are discussed in detail.Type II diabetes, also known as non-insulin-dependent diabetes mellitus, is characterized by a deficiency in insulin signaling despite normal or greatly elevated levels of insulin. Although the cause of insulin resistance is unknown, inhibiting enzymes that negatively regulate the signaling pathway may restore insulin responsiveness. Protein-tyrosine phosphatase 1B (PTP1B), 2 a key negative regulator of insulin signaling, has emerged as an attractive target for the treatment of type II diabetes. PTP1B directly inactivates the insulin receptor (IR) by dephosphorylating tyrosine residues in the regulatory domain (1, 2) and its overexpression inhibits IR signaling (3). The most convincing evidence for its potential use as a therapeutic target, however, is that PTP1B knock-out mice (4) and those injected with an antisense oligonucleotide (5, 6) displayed increased insulin sensitivity.A number of PTP1B inhibitors containing highly charged non-hydrolyzable phosphonate mimetics have been reported (7-13). Poor membrane permeability, however, has limited their development as drug candidates. The lack of inhibitors with suitable physicochemical properties can be attributed to the need to interact with the highly positively charged primary phosphate binding pocket and the surrounding flat, solventexposed region.We have recently reported the structure-based design of a novel isothiazolidino...

Inhibition protein tyrosine phosphatases by an oxovanadium glutamate complex, Na2[VO(Glu)2(CH3OH)](Glu = glutamate)

“…PTP1B gene knockout or antisense studies in normal and diabetic mice have shown lowered blood glucose levels and improved insulin responsiveness through enhanced IR signaling in peripheral tissues (Elchebly et al 1999;Klaman et al 2000;Zinker et al 2002). Therefore, PTP1B inhibitors have been pursued to develop novel anti-diabetic drugs (Xie and Seto 2007;Na et al 2006;Alal et al 2006;Shrestha et al 2007;Sparks et al 2007;Maccari et al 2007;Winter et al 2005).…”

Protein tyrosine phosphatase 1B inhibitory activity of alkaloids from Rhizoma Coptidis and their molecular docking studies

“…Therefore, PTP1B inhibitors are potential therapeutic candidates to restore insulin sensitivity and treat T2DM. A series of PTP1B inhibitors containing highly charged, nonhydrolyzable phosphonate mimetic have been reported such as, difluoromethylene phosphonate, 2-carbomethoxybenzoic acid, and 2-oxalylaminobenzic acids (Ala et al, 2006;Johnson et al, 2002 due to poor cell membrane permeability, low oral bioavailability, and the difficulty in balancing the IR tyrosine kinase that is involved in downstream insulin signal phosphatases, such as PTP1B, that are required to shut down these signals. Therefore, small molecular and lipophilic PTP1B inhibitors with selectivity, bioavailability and acceptable pharmacokinetic properties have emerged as novel PTP1B drugs (Combs, 2010).…”

The design strategy of selective PTP1B inhibitors over TCPTP

“…Due to lack of binding determinants, the C site to be less suitable than the A and B sites for structure-based design techniques, which often require accurate predictions of bound conformations of substituents. 18 The D site is a small narrow pocket, partially shielded from solvent and lined with polar and charged residues (Lys120, Lys116, Asp181, and Ser216, Fig. 1).…”

“…1). 18 As this disordered site is positioned fairly close to the active site of PTP1B, it is possible to increase potency and elicit selectivity with only a small increase in molecular weight. 19 …”