title: Succinimide Formation from an NGR-Containing Cyclic Peptide: Computational Evidence for Catalytic Roles of Phosphate Buffer and the Arginine Side Chain.
abstract: The Asn-Gly-Arg (NGR) motif and its deamidation productisoAsp-Gly-Arg (isoDGR) have recently attracted considerable attention as tumor-targeting ligands. Because an NGR-containing peptide and the correspondingisoDGR-containing peptide target different receptors, the spontaneous NGR deamidation can be used in dual targeting strategies. It is well known that the Asn deamidation proceeds via a succinimide derivative. In the present study, we computationally investigated the mechanism of succinimide formation from a cyclic peptide, c[CH₂CO-NGRC]-NH₂, which has recently been shown to undergo rapid deamidation in a phosphate buffer. An H₂PO₄-ion was explicitly included in the calculations. We employed the density functional theory using the B3LYP functional. While geometry optimizations were performed in the gas phase, hydration Gibbs energies were calculated by the SM8 (solvation model 8) continuum model. We have found a pathway leading to the five-membered ring tetrahedral intermediate in which both the H₂PO₄-ion and the Arg side chain act as catalyst. This intermediate, once protonated at the NH₂ group on the five-membered ring, was shown to easily undergo NH₃ elimination leading to the succinimide formation. This study is the first to propose a possible catalytic role for the Arg side chain in the NGR deamidation.
authors.affiliation: Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan. kirikoshi@tokoku-mpu.ac.jp.
authors.forename: Ryota
authors.initials: R
authors.lastname: Kirikoshi
authors.affiliation: Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan. manabe@tohoku-mpu.ac.jp.
authors.forename: Noriyoshi
authors.initials: N
authors.lastname: Manabe
authors.affiliation: Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan. ohgi@tohoku-mpu.ac.jp.
authors.forename: Ohgi
authors.initials: O
authors.lastname: Takahashi
mesh_terms: D001120:Arginine / Q000737:chemistry; D002021:Buffers; D002384:Catalysis; D008958:Models, Molecular; D008968:Molecular Conformation; D009842:Oligopeptides / Q000737:chemistry*; D010710:Phosphates / Q000737:chemistry; D013388:Succinimides / Q000737:chemistry*
chemical_list: D002021:Buffers; C526428:NGR peptide; D009842:Oligopeptides; D010710:Phosphates; D013388:Succinimides; D001120:Arginine
keywords: Asn-Gly-Arg (NGR) motif; computational chemistry; deamidation; density functional theory; intramolecular catalysis; isoAsp-Gly-Arg (isoDGR) motif; nonenzymatic reaction; phosphate buffer catalysis; succinimide intermediate; tumor-targeting ligands