1
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Nakayoshi T, Kato K, Kurimoto E, Takano Y, Oda A. Predicting Reaction Mechanisms for the Threonine-Residue Stereoinversion Catalyzed by a Dihydrogen Phosphate Ion. ACS OMEGA 2022; 7:18306-18314. [PMID: 35694452 PMCID: PMC9178615 DOI: 10.1021/acsomega.2c00372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
The stereoinversion of amino acid residues in proteins is considered to trigger various age-related diseases. Serine (Ser) residues are relatively prone to stereoinversion. It is assumed that threonine (Thr) residues also undergo stereoinversion, which results in the formation of the d-allo-Thr residue, by the same mechanisms as those for Ser-residue stereoinversion; however, d-allo-Thr residues have not been detected in vivo. To date, although Ser-residue stereoinversion has been suggested to progress via enolization, plausible reaction mechanisms for Thr-residue stereoinversion have not been proposed. In this study, we investigated the pathway of Thr-residue enolization and successfully identified the three types of plausible reaction pathways of Thr-residue stereoinversion catalyzed by a dihydrogen phosphate ion. The geometries of reactant complexes, transition states, and enolized product complexes were optimized using B3LYP density functional methods, and single-point calculations were performed for all optimized geometries using Møller-Plesset perturbation theory to obtain reliable energies. As a result, the calculated activation energies of Thr-residue stereoinversion were 105-106 kJ mol-1, which were comparable with those of Ser-residue stereoinversion reported previously. The infrequency of Thr-residue stereoinversion may be due to other factors, such as the hydrophobicity and/or the steric hindrance of the γ-methyl group, rather than the high activation energies.
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Affiliation(s)
- Tomoki Nakayoshi
- Graduate
School of Information Sciences, Hiroshima
City University, 3-4-1 Ozukahigashi, Asaminami-ku, Hiroshima, Hiroshima 731-3194, Japan
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Institute
of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Koichi Kato
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Faculty
of Pharmaceutical Sciences, Shonan University
of Medical Sciences, 16-48 Kamishinano, Totsuka-ku, Yokohama, Kanagawa 244-0806, Japan
- College
of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Eiji Kurimoto
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Yu Takano
- Graduate
School of Information Sciences, Hiroshima
City University, 3-4-1 Ozukahigashi, Asaminami-ku, Hiroshima, Hiroshima 731-3194, Japan
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Akifumi Oda
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Institute
of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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2
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Kato K, Nakayoshi T, Ishikawa Y, Kurimoto E, Oda A. Computational Analysis of the Mechanism of Nonenzymatic Peptide Bond Cleavage at the C-Terminal Side of an Asparagine Residue. ACS OMEGA 2021; 6:30078-30084. [PMID: 34778679 PMCID: PMC8582265 DOI: 10.1021/acsomega.1c04821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
The nonenzymatic peptide bond cleavage at the C-terminal side of Asn residues is a protein post-translational modification that occurs under physiological conditions. This reaction proceeds much slower than the deamidation of the Asn side chain and causes denaturation and hypofunction of proteins. The peptide bond cleavage of Asn is detected primarily in crystallins and aquaporin 0 in the eye lens. Therefore, cleavage is thought to be involved in age-related cataracts. In this study, to clarify the mechanism underlying succinimide formation for the peptide bond cleavage of the Asn residue, we performed quantum chemical calculations on the model compound Ace-Asn-Gly-Nme (Ace = acetyl and Nme = methylamino). The density functional theory with the B3LYP/6-31+G(d,p) level of theory was used to obtain optimized geometries. The results suggested that the reaction proceeds through two steps, cyclization and C-terminal fragment release, and the required proton transfers can be mediated by H2PO4 - and HCO3 - ions. The conformational change of the main chain on the N-terminal side of Asn was needed for the C-terminal fragmentation step, and a separate conformational change at the C-terminal side was required for the cyclization step. Furthermore, the calculated activation barriers of the reactions catalyzed by the H2PO4 - ion (130 kJ mol-1) and the HCO3 - ion (123 kJ mol-1) were sufficiently low for the reactions to occur under normal physiological conditions.
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Affiliation(s)
- Koichi Kato
- Faculty
of Pharmaceutical Sciences, Shonan University
of Medical Sciences, 16-48 Kamishinano, Totsuka-ku, Yokohama, Kanagawa 244-0806, Japan
- College
of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Tomoki Nakayoshi
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Graduate
School of Information Sciences, Hiroshima
City University, 3-4-1 Ozukahigasi, Asaminami-ku, Hiroshima, Hiroshima 731-3194, Japan
| | - Yoshinobu Ishikawa
- Faculty
of Pharmaceutical Sciences, Shonan University
of Medical Sciences, 16-48 Kamishinano, Totsuka-ku, Yokohama, Kanagawa 244-0806, Japan
| | - Eiji Kurimoto
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Akifumi Oda
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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3
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Nakayoshi T, Wanita K, Kato K, Kurimoto E, Oda A. Computational analysis of nonenzymatic deamidation of asparagine residues catalysed by acetic acid. Mol Phys 2021. [DOI: 10.1080/00268976.2020.1827176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Tomoki Nakayoshi
- Graduate School of Pharmacy, Meijo University, Nagoya, Japan
- Institute of Medical, Pharmaceutical and Health Science, Kanazawa University, Kanazawa, Japan
| | - Kota Wanita
- Graduate School of Pharmacy, Meijo University, Nagoya, Japan
| | - Koichi Kato
- Graduate School of Pharmacy, Meijo University, Nagoya, Japan
- Department of Pharmacy, Kinjo Gakuin University, Nagoya, Japan
| | - Eiji Kurimoto
- Graduate School of Pharmacy, Meijo University, Nagoya, Japan
| | - Akifumi Oda
- Graduate School of Pharmacy, Meijo University, Nagoya, Japan
- Institute of Medical, Pharmaceutical and Health Science, Kanazawa University, Kanazawa, Japan
- Institute for Protein Research, Suita, Japan
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4
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Zhu L, Ding Z, Li X, Wei H, Chen Y. Research Progress of Radiolabeled Asn-Gly-Arg (NGR) Peptides for Imaging and Therapy. Mol Imaging 2021; 19:1536012120934957. [PMID: 32862776 PMCID: PMC7466889 DOI: 10.1177/1536012120934957] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Asn-Gly-Arg (NGR) motifs have vasculature-homing properties via interactions with the aminopeptidase N (CD13) expressed on tumor neovasculature. Numerous NGR peptides with different molecular scaffolds have been exploited for targeted delivery of different compounds for imaging and therapy. When conjugated with NGR, complexes recognize the CD13 receptor expressed on the tumor vasculature, which improves the specificity to tumor and avoids systematic toxic reactions. Both preclinical and clinical studies performed with these products suggest that NGR-mediated vascular targeting is an effective strategy for delivering bioactive amounts of cytokines to tumor endothelial cells. For molecular imaging, radiolabeled peptides have been the most successful approach and have been translated into clinic. This review describes current data on radiolabeled tumor vasculature-homing NGR peptides for imaging and therapy.
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Affiliation(s)
- Liqin Zhu
- Department of Nuclear Medicine, 556508The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Zhikai Ding
- Department of Nuclear Medicine, 556508The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Xingliang Li
- Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang, Sichuan, People's Republic of China.,Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou, Sichuan, People's Republic of China
| | - Hongyuan Wei
- Department of Nuclear Medicine, 556508The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang, Sichuan, People's Republic of China.,Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou, Sichuan, People's Republic of China
| | - Yue Chen
- Department of Nuclear Medicine, 556508The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou, Sichuan, People's Republic of China
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5
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Dénes N, Kis A, Szabó JP, Jószai I, Hajdu I, Arató V, Enyedi KN, Mező G, Hunyadi J, Trencsényi G, Kertész I. In vivo preclinical assessment of novel 68Ga-labelled peptides for imaging of tumor associated angiogenesis using positron emission tomography imaging. Appl Radiat Isot 2021; 174:109778. [PMID: 34004593 DOI: 10.1016/j.apradiso.2021.109778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/27/2021] [Accepted: 05/07/2021] [Indexed: 11/28/2022]
Abstract
Formation and growth of metastases require a new vascular network. Angiogenesis plays an essential role in the expansion and progression of most malignancies. A high number of molecular pathways regulate angiogenesis, including vascular endothelial growth factor (VEGF), αvβ3 integrin, matrix metalloproteinases (MMPs), or aminopeptidase N. The aim of this study is to involve new, easily accessible peptide sequences into the of neo-angiogenesis in malignant processes. Labelling of these peptide ligands with 68Ga enable PET imaging of neo-vascularization.
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Affiliation(s)
- Noémi Dénes
- Division of Nuclear Medicine and Translational Imaging, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, Nagyerdei St. 98, H-4032, Debrecen, Hungary; Gyula Petrányi Doctoral School of Allergy and Clinical Immunology, Faculty of Medicine, University of Debrecen, Nagyerdei St. 98, H-4032, Debrecen, Hungary
| | - Adrienn Kis
- Division of Nuclear Medicine and Translational Imaging, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, Nagyerdei St. 98, H-4032, Debrecen, Hungary; Doctoral School of Clinical Medicine, Faculty of Medicine, University of Debrecen, Nagyerdei St. 98, H-4032, Debrecen, Hungary
| | - Judit P Szabó
- Division of Nuclear Medicine and Translational Imaging, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, Nagyerdei St. 98, H-4032, Debrecen, Hungary; Doctoral School of Clinical Medicine, Faculty of Medicine, University of Debrecen, Nagyerdei St. 98, H-4032, Debrecen, Hungary
| | - István Jószai
- Division of Nuclear Medicine and Translational Imaging, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, Nagyerdei St. 98, H-4032, Debrecen, Hungary
| | - István Hajdu
- Division of Nuclear Medicine and Translational Imaging, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, Nagyerdei St. 98, H-4032, Debrecen, Hungary
| | - Viktória Arató
- Division of Nuclear Medicine and Translational Imaging, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, Nagyerdei St. 98, H-4032, Debrecen, Hungary
| | - Kata Nóra Enyedi
- Eötvös Loránd University, Faculty of Science, Institute of Chemistry, Budapest, Hungary
| | - Gábor Mező
- Eötvös Loránd University, Faculty of Science, Institute of Chemistry, Budapest, Hungary; MTA-ELTE, Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös L. University, Budapest, Hungary
| | - János Hunyadi
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Nagyerdei St. 98, H-4032, Debrecen, Hungary
| | - György Trencsényi
- Division of Nuclear Medicine and Translational Imaging, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, Nagyerdei St. 98, H-4032, Debrecen, Hungary; Gyula Petrányi Doctoral School of Allergy and Clinical Immunology, Faculty of Medicine, University of Debrecen, Nagyerdei St. 98, H-4032, Debrecen, Hungary; Doctoral School of Clinical Medicine, Faculty of Medicine, University of Debrecen, Nagyerdei St. 98, H-4032, Debrecen, Hungary
| | - István Kertész
- Division of Nuclear Medicine and Translational Imaging, Department of Medical Imaging, Faculty of Medicine, University of Debrecen, Nagyerdei St. 98, H-4032, Debrecen, Hungary.
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6
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Kato K, Nakayoshi T, Kurimoto E, Oda A. Mechanisms of Deamidation of Asparagine Residues and Effects of Main-Chain Conformation on Activation Energy. Int J Mol Sci 2020; 21:ijms21197035. [PMID: 32987875 PMCID: PMC7582646 DOI: 10.3390/ijms21197035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/19/2020] [Accepted: 09/22/2020] [Indexed: 12/14/2022] Open
Abstract
Deamidation of asparagine (Asn) residues is a nonenzymatic post-translational modification of proteins. Asn deamidation is associated with pathogenesis of age-related diseases and hypofunction of monoclonal antibodies. Deamidation rate is known to be affected by the residue following Asn on the carboxyl side and by secondary structure. Information about main-chain conformation of Asn residues is necessary to accurately predict deamidation rate. In this study, the effect of main-chain conformation of Asn residues on deamidation rate was computationally investigated using molecular dynamics (MD) simulations and quantum chemical calculations. The results of MD simulations for γS-crystallin suggested that frequently deamidated Asn residues have common main-chain conformations on the N-terminal side. Based on the simulated structure, initial structures for the quantum chemical calculations were constructed and optimized geometries were obtained using the B3LYP density functional method. Structures that were frequently deamidated had a lower activation energy barrier than that of the little deamidated structure. We also showed that dihydrogen phosphate and bicarbonate ions are important catalysts for deamidation of Asn residues.
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Affiliation(s)
- Koichi Kato
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan; (T.N.); (E.K.); (A.O.)
- Correspondence: ; Tel.: +81-527-980-180
| | - Tomoki Nakayoshi
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan; (T.N.); (E.K.); (A.O.)
| | - Eiji Kurimoto
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan; (T.N.); (E.K.); (A.O.)
| | - Akifumi Oda
- Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan; (T.N.); (E.K.); (A.O.)
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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7
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Nakayoshi T, Kato K, Kurimoto E, Oda A. Computational Studies on the Mechanisms of Nonenzymatic Intramolecular Cyclization of the Glutamine Residues Located at N-Termini Catalyzed by Inorganic Phosphate Species. ACS OMEGA 2020; 5:9162-9170. [PMID: 32363268 PMCID: PMC7191561 DOI: 10.1021/acsomega.9b04384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/02/2020] [Indexed: 05/13/2023]
Abstract
Glutamine (Gln) residues located at N-termini undergo spontaneous intramolecular cyclization, causing the formation of pyroglutamic acid (pGlu) residues. pGlu residues have been detected at the N-termini in various peptides and proteins. The formation of pGlu residues during the fermentation and purification processes of antibody drugs is one of the concerns in the design and formulation of these drugs and has been reported to proceed rapidly in a phosphate buffer. In this study, we have examined the phosphate-catalyzed mechanisms of the pGlu residue formation from N-terminal Gln residues via quantum chemical calculations using B3LYP density functional methods. Single-point energies were calculated using the second-order Møller-Plesset perturbation theory. We performed the calculations for the model compound in which an uncharged N-terminal Gln residue is capped with a methyl amino group on the C-terminal. The activation energy of the formation of pGlu residues was calculated as 83.8 kJ mol-1, which was lower than that of the typical nonenzymatic reaction of amino acid residues. In addition, the computational results indicate that the flexibility of the main and side chains in N-terminal Gln residues was necessary for the formation of pGlu residues to proceed. In the obtained pathway, inorganic phosphate species act as the catalyst by mediating the proton transfer.
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Affiliation(s)
- Tomoki Nakayoshi
- Graduate
School of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Institute
of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Koichi Kato
- Graduate
School of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Department
of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Eiji Kurimoto
- Graduate
School of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Akifumi Oda
- Graduate
School of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Institute
of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka,
Suita, Osaka 565-0871, Japan
- . Phone: +81-52-832-1151
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8
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Nakayoshi T, Kato K, Kurimoto E, Oda A. Computational studies on nonenzymatic pyroglutamylation mechanism of N-terminal glutamic acid residues in aqueous conditions*. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1702727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Tomoki Nakayoshi
- Graduate School of Pharmacy, Meijo University, Nagoya, Japan
- Institute of Medical, Pharmaceutical and Health Science, Kanazawa University, Kanazawa, Japan
| | - Koichi Kato
- Graduate School of Pharmacy, Meijo University, Nagoya, Japan
- Department of Pharmacy, Kinjo Gakuin University, Nagoya, Japan
| | - Eiji Kurimoto
- Graduate School of Pharmacy, Meijo University, Nagoya, Japan
| | - Akifumi Oda
- Graduate School of Pharmacy, Meijo University, Nagoya, Japan
- Institute of Medical, Pharmaceutical and Health Science, Kanazawa University, Kanazawa, Japan
- Institute for Protein Research, Osaka, Japan
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9
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Tripodi AAP, Ranđelović I, Biri-Kovács B, Szeder B, Mező G, Tóvári J. In Vivo Tumor Growth Inhibition and Antiangiogenic Effect of Cyclic NGR Peptide-Daunorubicin Conjugates Developed for Targeted Drug Delivery. Pathol Oncol Res 2019; 26:1879-1892. [PMID: 31820302 PMCID: PMC7297862 DOI: 10.1007/s12253-019-00773-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/22/2019] [Indexed: 01/09/2023]
Abstract
Among various homing devices, peptides containing the NGR tripeptide sequence represent a promising approach to selectively recognize CD13 receptor isoforms on the surface of tumor cells. They have been successfully used for the delivery of various chemotherapeutic drugs to tumor vessels. Here, we report on the murine plasma stability, in vitro and in vivo antitumor activity of our recently described bioconjugates containing daunorubicin as payload. Furthermore, CD13 expression of KS Kaposi’s Sarcoma cell line and HT-29 human colon carcinoma cell line was investigated. Flow cytometry studies confirm the fast cellular uptake resulting in the rapid delivery of the active metabolite Dau = Aoa-Gly-OH to tumor cells. The increased in vitro antitumor effect might be explained by the faster rearrangement from NGR to isoDGR in case of conjugate 2 (Dau = Aoa-GFLGK(c[NleNGRE]-GG)-NH2) in comparison with conjugate 1 (Dau = Aoa-GFLGK(c[KNGRE]-GG)-NH2). Nevertheless, results indicated that both conjugates showed significant effect on inhibition of proliferation in the primary tumor and also on blood vessel formation making them a potential candidate for targeting angiogenesis processes in tumors where CD13 and integrins are involved.
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Affiliation(s)
- Andrea Angelo Pierluigi Tripodi
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, Budapest, Hungary.,Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Ivan Ranđelović
- Department of Experimental Pharmacology, National Institute of Oncology, Budapest, Hungary
| | - Beáta Biri-Kovács
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, Budapest, Hungary.,Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Bálint Szeder
- Research Centre for Natural Sciences, Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
| | - Gábor Mező
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, Budapest, Hungary.,Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - József Tóvári
- Department of Experimental Pharmacology, National Institute of Oncology, Budapest, Hungary.
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10
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Kato K, Nakayoshi T, Kurimoto E, Oda A. Computational Studies on the Nonenzymatic Deamidation Mechanisms of Glutamine Residues. ACS OMEGA 2019; 4:3508-3513. [PMID: 31459565 PMCID: PMC6648516 DOI: 10.1021/acsomega.8b03199] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/22/2019] [Indexed: 05/16/2023]
Abstract
The nonenzymatic deamidation reactions of asparagine (Asn) and glutamine (Gln) residues in proteins are associated with protein turnover and age-related diseases. The reactions are also believed to provide a molecular clock for biological processes. Although Gln deamidation is assumed to occur through the glutarimide intermediate, the mechanisms for this are unclear because under normal physiological conditions, Gln deamidation occurs relatively less frequently and at a lower rate than Asn deamidation. We investigate the mechanisms underlying glutarimide formation from Gln residues, which proceeds in two steps (cyclization and deammoniation) catalyzed by phosphate and carbonate. We also compare these reactions with noncatalytic mechanisms and water-catalyzed mechanisms. The calculations were performed on the model compound Ace-Gln-Nme (Ace = acetyl, Nme = methylamino) using the density functional theory with the B3LYP/6-31+G(d,p) level of theory. Our results suggest that all the catalysts used in our study can mediate the proton relays required for glutarimide formation. We further determined that the calculated activation barriers of the reactions catalyzed by phosphate ions (115 kJ mol-1) and carbonate ions (112 kJ mol-1) are sufficiently low for the reactions to occur under normal physiological conditions. We also show that nucleophilic enhancement of Nme nitrogen is essential for the cyclization of Gln residues.
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Affiliation(s)
- Koichi Kato
- College
of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- E-mail: . Phone: +81-52-798-7474 (K.K.)
| | - Tomoki Nakayoshi
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Eiji Kurimoto
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Akifumi Oda
- Faculty
of Pharmacy, Meijo University, 150 Yagotoyama,
Tempaku-ku, Nagoya, Aichi 468-8503, Japan
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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11
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Lu X, Nobrega RP, Lynaugh H, Jain T, Barlow K, Boland T, Sivasubramanian A, Vásquez M, Xu Y. Deamidation and isomerization liability analysis of 131 clinical-stage antibodies. MAbs 2018; 11:45-57. [PMID: 30526254 PMCID: PMC6343770 DOI: 10.1080/19420862.2018.1548233] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Contemporary in vivo and in vitro discovery platform technologies greatly increase the odds of identifying high-affinity monoclonal antibodies (mAbs) towards essentially any desired biologically relevant epitope. Lagging discovery throughput is the ability to select for highly developable mAbs with drug-like properties early in the process. Upstream consideration of developability metrics should reduce the frequency of failures in later development stages. As the field moves towards incorporating biophysical screening assays in parallel to discovery processes, similar approaches should also be used to ensure robust chemical stability. Optimization of chemical stability in the early stages of discovery has the potential to reduce complications in formulation development and improve the potential for successful liquid formulations. However, at present, our knowledge of the chemical stability characteristics of clinical-stage therapeutic mAbs is fragmented and lacks comprehensive comparative assessment. To address this knowledge gap, we produced 131 mAbs with amino acid sequences corresponding to the variable regions of clinical-stage mAbs, subjected these to low and high pH stresses and identified the resulting modifications at amino acid-level resolution via tryptic peptide mapping. Among this large set of mAbs, relatively high frequencies of asparagine deamidation events were observed in CDRs H2 and L1, while CDRs H3, H2 and L1 contained relatively high frequencies of instances of aspartate isomerization.
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Affiliation(s)
- Xiaojun Lu
- a Protein Analytics , Adimab , Lebanon , NH , USA
| | | | | | - Tushar Jain
- b Computational Biology , Adimab , Palo Alto , CA , USA
| | - Kyle Barlow
- b Computational Biology , Adimab , Palo Alto , CA , USA
| | - Todd Boland
- b Computational Biology , Adimab , Palo Alto , CA , USA
| | | | | | - Yingda Xu
- a Protein Analytics , Adimab , Lebanon , NH , USA
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12
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Kirikoshi R, Manabe N, Takahashi O. Phosphate-Catalyzed Succinimide Formation from an NGR-Containing Cyclic Peptide: A Novel Mechanism for Deammoniation of the Tetrahedral Intermediate. Molecules 2018; 23:E2217. [PMID: 30200364 PMCID: PMC6225186 DOI: 10.3390/molecules23092217] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/15/2018] [Accepted: 08/30/2018] [Indexed: 01/23/2023] Open
Abstract
Spontaneous deamidation in the Asn-Gly-Arg (NGR) motif that yields an isoAsp-Gly-Arg (isoDGR) sequence has recently attracted considerable attention because of the possibility of application to dual tumor targeting. It is well known that Asn deamidation reactions in peptide chains occur via the five-membered ring succinimide intermediate. Recently, we computationally showed by the B3LYP density functional theory method, that inorganic phosphate and the Arg side chain can catalyze the NGR deamidation using a cyclic peptide, c[CH₂CO⁻NGRC]⁻NH₂. In this previous study, the tetrahedral intermediate of the succinimide formation was assumed to be readily protonated at the nitrogen originating from the Asn side chain by the solvent water before the release of an NH₃ molecule. In the present study, we found a new mechanism for the decomposition of the tetrahedral intermediate that does not require the protonation by an external proton source. The computational method is the same as in the previous study. In the new mechanism, the release of an NH₃ molecule occurs after a proton exchange between the peptide and the phosphate and conformational changes. The rate-determining step of the overall reaction course is the previously reported first step, i.e., the cyclization to form the tetrahedral intermediate.
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Affiliation(s)
- Ryota Kirikoshi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
| | - Noriyoshi Manabe
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
| | - Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
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13
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Tripodi AAP, Tóth S, Enyedi KN, Schlosser G, Szakács G, Mező G. Development of novel cyclic NGR peptide-daunomycin conjugates with dual targeting property. Beilstein J Org Chem 2018; 14:911-918. [PMID: 29765472 PMCID: PMC5942373 DOI: 10.3762/bjoc.14.78] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 04/13/2018] [Indexed: 01/03/2023] Open
Abstract
Cyclic NGR peptides as homing devices are good candidates for the development of drug conjugates for targeted tumor therapy. In our previous study we reported that the Dau=Aoa-GFLGK(c[KNGRE]-GG-)-NH2 conjugate has a significant antitumor activity against both CD13+ HT-1080 human fibrosarcoma and CD13- but integrin positive HT-29 human colon adenocarcinoma cells. However, it seems that the free ε-amino group of Lys in the cycle is not necessary for the biological activity. Therefore, we developed novel cyclic NGR peptide-daunomycin conjugates in which Lys was replaced by different amino acids (Ala, Leu, Nle, Pro, Ser). The exchange of the Lys residue in the cycle simplified the cyclization step and resulted in a higher yield. The new conjugates showed lower chemostability against deamidation of Asn than the control compound, thus they had lower selectivity to CD13+ cells. However, the cellular uptake and cytotoxic effect of Dau=Aoa-GFLGK(c[NleNGRE]-GG-)-NH2 was higher in comparison to the control especially on HT-29 cells. Therefore, this conjugate is more suitable for drug targeting with dual targeting property.
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Affiliation(s)
- Andrea Angelo Pierluigi Tripodi
- Eötvös Loránd University, Faculty of Science, Institute of Chemistry, Pázmány P. stny. 1/A, H-1117 Budapest, Hungary.,MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, Pázmány P. stny. 1/A, H-1117 Budapest, Hungary
| | - Szilárd Tóth
- Institute of Enzimology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | - Kata Nóra Enyedi
- Eötvös Loránd University, Faculty of Science, Institute of Chemistry, Pázmány P. stny. 1/A, H-1117 Budapest, Hungary.,MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, Pázmány P. stny. 1/A, H-1117 Budapest, Hungary
| | - Gitta Schlosser
- Eötvös Loránd University, Faculty of Science, Institute of Chemistry, Pázmány P. stny. 1/A, H-1117 Budapest, Hungary.,MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, Pázmány P. stny. 1/A, H-1117 Budapest, Hungary
| | - Gergely Szakács
- Institute of Enzimology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary.,Institute of Cancer Research, Medical University Vienna, Borschkegasse 8a, A-1090 Vienna, Austria
| | - Gábor Mező
- Eötvös Loránd University, Faculty of Science, Institute of Chemistry, Pázmány P. stny. 1/A, H-1117 Budapest, Hungary.,MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös Loránd University, Pázmány P. stny. 1/A, H-1117 Budapest, Hungary
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14
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Mastrangeli R, D'amici F, D'Acunto CW, Fiumi S, Rossi M, Terlizzese M, Palinsky W, Bierau H. A deamidated interferon-β variant binds to integrin αvβ3. Cytokine 2018; 104:38-41. [PMID: 29414325 DOI: 10.1016/j.cyto.2018.01.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/25/2018] [Accepted: 01/30/2018] [Indexed: 12/25/2022]
Abstract
Human type I interferons are a family of pleiotropic cytokines with antiviral, anti-proliferative and immunomodulatory activities. They signal through the same cell surface receptors IFNAR1 and IFNAR2 yet evoking markedly different physiological effects. One differentiating factor of interferon-beta (IFN-β) from other type I interferons is the presence of theAsn-Gly-Arg (NGR) sequence motif, which, upon deamidation, converts to Asp-Gly-Arg (DGR) and iso-Asp-Gly-Arg (iso-DGR) motifs. In other proteins, the NGR and iso-DGR motifs are reported as CD13- and αvβ3, αvβ5, αvβ6, αvβ8 and α5β1 integrin-binding motifs, respectively. The scope of this study was to perform exploratory surface plasmon resonance (SPR) experiments to assess the binding properties of a deamidated IFN-β variant to integrins. For this purpose, integrin αvβ3 was selected as a reference model within the iso-DGR- integrin binding members. The obtained results show that deamidated IFN-β binds integrin αvβ3 with nanomolar affinity and that the response was dependent on the deamidation extent. Based on these results, it can be expected that deamidated IFN-β also binds to other integrin family members that are able to bind to the iso-DGR binding motif. The novel binding properties could help elucidate specific IFN-β attributes that under physiological conditions may be modulated by the deamidation.
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Affiliation(s)
- Renato Mastrangeli
- Biotech Development Programme, CMC Science & Intelligence, Merck Serono S.p.A. (an affiliate of Merck KGaA, Darmstadt, Germany), Via Luigi Einaudi, 11, 00012 Guidonia Montecelio (Roma), Italy
| | - Fabio D'amici
- Pharmaceutical & Analytical Development Biotech Products, Merck Serono S.p.A. (an affiliate of Merck KGaA, Darmstadt, Germany), Via Luigi Einaudi, 11, 00012 Guidonia Montecelio (Roma), Italy
| | - Cosimo-Walter D'Acunto
- Pharmaceutical & Analytical Development Biotech Products, Merck Serono S.p.A. (an affiliate of Merck KGaA, Darmstadt, Germany), Via Luigi Einaudi, 11, 00012 Guidonia Montecelio (Roma), Italy
| | - Sabrina Fiumi
- Pharmaceutical & Analytical Development Biotech Products, Merck Serono S.p.A. (an affiliate of Merck KGaA, Darmstadt, Germany), Via Luigi Einaudi, 11, 00012 Guidonia Montecelio (Roma), Italy
| | - Mara Rossi
- Pharmaceutical & Analytical Development Biotech Products, Merck Serono S.p.A. (an affiliate of Merck KGaA, Darmstadt, Germany), Via Luigi Einaudi, 11, 00012 Guidonia Montecelio (Roma), Italy
| | - Mariagrazia Terlizzese
- Pharmaceutical & Analytical Development Biotech Products, Merck Serono S.p.A. (an affiliate of Merck KGaA, Darmstadt, Germany), Via Luigi Einaudi, 11, 00012 Guidonia Montecelio (Roma), Italy
| | - Wolf Palinsky
- Biotech Development Programme, Merck Biopharma (an affiliate of Merck KGaA, Darmstadt, Germany), Zone Industrielle de l'Ouriettaz, Aubonne 1170, Switzerland
| | - Horst Bierau
- Biotech Development Programme, CMC Science & Intelligence, Merck Serono S.p.A. (an affiliate of Merck KGaA, Darmstadt, Germany), Via Luigi Einaudi, 11, 00012 Guidonia Montecelio (Roma), Italy.
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