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Gamov G, Kiselev A, Zavalishin M, Yarullin D. Formation and hydrolysis of pyridoxal-5’-phosphate hydrazones and Schiff bases: Prediction of equilibrium and rate constants. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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2
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Yamabe S, Tsuchida N, Yamazaki S. A DFT study of the active role of the phosphate group of an internal aldimine in a transamination reaction. Org Biomol Chem 2022; 20:5334-5341. [PMID: 35748359 DOI: 10.1039/d2ob00913g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A transamination reaction from an internal aldimine ([PLP]) and (S)-alanine to pyridoxamine phosphate (PMP) and pyruvic acid was investigated by DFT calculations. As [PLP], a model where the lysine (-Lys) part was approximated by -CH[-NH-C(O)-CH3]-C(O)-NH-CH3 was adopted. (H2O)4 was also included to trace reaction paths involving proton transfers. 13 elementary processes were obtained. For (the external aldimine → quinoid), (quinoid → ketimine) and (ketimine → carbinol amine) processes, the water dimer was found to connect a phosphate-group oxygen with the moving proton. The connection promoted the Grotthuss-type proton transfer in transition states. It was revealed that the phosphate group is not a mere substituent but has the central role in the transfer.
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Affiliation(s)
- Shinichi Yamabe
- Department of Chemistry, Nara University of Education, Takabatake-cho, Nara 630-8528, Japan.
| | - Noriko Tsuchida
- Department of Liberal Arts, Faculty of Medicine, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Shoko Yamazaki
- Department of Chemistry, Nara University of Education, Takabatake-cho, Nara 630-8528, Japan.
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3
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Omidinia R, Ali Beyramabadi S, Allameh S, Morsali A, Pordel M. Synthesis, characterization, DFT and antibacterial studies of a novel vitamin B6 Schiff base and its Cu(II) and Zn(II) complexes. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131452] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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4
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Soniya K, Chandra A. Free Energy Landscape and Proton Transfer Pathways of the Transimination Reaction at the Active site of the Serine Hydroxymethyltransferase Enzyme in Aqueous Medium. J Phys Chem B 2021; 125:11848-11856. [PMID: 34696588 DOI: 10.1021/acs.jpcb.1c05864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Serine hydroxymethyltransferase (SHMT) is a ubiquitous enzyme belonging to the fold type I or aspartate aminotransferase (AspAT) family of the pyridoxal 5'-phosphate (PLP)-dependent enzymes. Like other PLP-dependent enzymes, SHMT also undergoes the so-called transimination reaction before exhibiting its enzymatic activity. The transimination process constitutes an important pre-step for all PLP-dependent enzymes, where an internal aldimine of the PLP-enzyme complex gets converted to an external aldimine of the substrate-PLP complex at the active site of the enzyme. In case of the transimination reaction involving SHMT, the PLP molecule bound to the active site lysine residue of SHMT (internal aldimine) gets detached from the enzyme by a serine substrate to produce an external aldimine complex, where the PLP is now bound to the serine substrate. In the current study, the free energy surfaces and reaction pathways of different steps of the transimination reaction at the active site of SHMT are investigated by employing hybrid quantum mechanical/molecular mechanical (QM/MM) simulations combined with metadynamics methods of rare event sampling. It is found that the process of transimination involving serine and PLP at the active site of the SHMT enzyme takes place through different elementary steps such as the formation of the first geminal diamine intermediate (GDI1), transfer of a proton from the substrate serine to the phenolic oxygen of PLP, followed by another proton transfer from PLP to the amine nitrogen of lysine with the formation of the second geminal diamine intermediate (GDI2), and finally, detachment of the active site lysine residue from PLP to produce the external aldimine.
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Affiliation(s)
- Kumari Soniya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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5
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Li Z, Zhang L, Pu M, Lei M. Mechanistic Understanding of Base‐Catalyzed Aldimine/Ketoamine Condensations: An Old Story and A New Model. ASIAN J ORG CHEM 2021. [DOI: 10.1002/ajoc.202000700] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Zhe‐wei Li
- State Key Laboratory of Chemical Resource Engineering Institute of Computational Chemistry College of Chemistry Beijing University of Chemical Technology Beijing 100029 P. R. China
| | - Lin Zhang
- State Key Laboratory of Chemical Resource Engineering Institute of Computational Chemistry College of Chemistry Beijing University of Chemical Technology Beijing 100029 P. R. China
| | - Min Pu
- State Key Laboratory of Chemical Resource Engineering Institute of Computational Chemistry College of Chemistry Beijing University of Chemical Technology Beijing 100029 P. R. China
| | - Ming Lei
- State Key Laboratory of Chemical Resource Engineering Institute of Computational Chemistry College of Chemistry Beijing University of Chemical Technology Beijing 100029 P. R. China
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6
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Complexes of Copper and Iron with Pyridoxamine, Ascorbic Acid, and a Model Amadori Compound: Exploring Pyridoxamine's Secondary Antioxidant Activity. Antioxidants (Basel) 2021; 10:antiox10020208. [PMID: 33535448 PMCID: PMC7912584 DOI: 10.3390/antiox10020208] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 01/23/2021] [Accepted: 01/26/2021] [Indexed: 12/28/2022] Open
Abstract
The thermodynamic stability of 11 complexes of Cu(II) and 26 complexes of Fe(III) is studied, comprising the ligands pyridoxamine (PM), ascorbic acid (ASC), and a model Amadori compound (AMD). In addition, the secondary antioxidant activity of PM is analyzed when chelating both Cu(II) and Fe(III), relative to the rate constant of the first step of the Haber-Weiss cycle, in the presence of the superoxide radical anion (O2•-) or ascorbate (ASC-). Calculations are performed at the M05(SMD)/6-311+G(d,p) level of theory. The aqueous environment is modeled by making use of the SMD solvation method in all calculations. This level of theory accurately reproduces the experimental data available. When put in perspective with the stability of various complexes of aminoguanidine (AG) (which we have previously studied), the following stability trends can be found for the Cu(II) and Fe(III) complexes, respectively: ASC < AG < AMD < PM and AG < ASC < AMD < PM. The most stable complex of Cu(II) with PM (with two bidentate ligands) presents a ΔGf0 value of -35.8 kcal/mol, whereas the Fe(III) complex with the highest stability (with three bidentate ligands) possesses a ΔGf0 of -58.9 kcal/mol. These complexes can significantly reduce the rate constant of the first step of the Haber-Weiss cycle with both O2•- and ASC-. In the case of the copper-containing reaction, the rates are reduced up to 9.70 × 103 and 4.09 × 1013 times, respectively. With iron, the rates become 1.78 × 103 and 4.45 × 1015 times smaller, respectively. Thus, PM presents significant secondary antioxidant activity since it is able to inhibit the production of ·OH radicals. This work concludes a series of studies on secondary antioxidant activity and allows potentially new glycation inhibitors to be investigated and compared relative to both PM and AG.
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7
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Nasrabadi M, Morsali A, Beyramabadi SA. An applied quantum-chemical model for genipin-crosslinked chitosan (GCS) nanocarrier. Int J Biol Macromol 2020; 165:1229-1240. [PMID: 33038394 DOI: 10.1016/j.ijbiomac.2020.10.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/23/2020] [Accepted: 10/01/2020] [Indexed: 12/17/2022]
Abstract
The genipin-crosslinked chitosan (GCS) nanocarrier has received a lot of attention due to its unique biological and chemical properties as an effective drug delivery system. GCS was modeled by considering two chitosan (CS) polymer sequences with six monomer units that are crosslinked by genipin. To investigate the characteristics of this model, we considered it as a nanocarrier of the anti-cancer drug cladribine (2CdA). Seven configurations of GCS and 2CdA (GCS/2CdA1-7) were optimized at M06-2X/6-31G(d,p) in aqueous solution. The average binding energy above 100 kJ mol-1 indicates a high drug loading amount. The high adsorption of the drug on GCS is due to the hydrogen bonds that were investigated by AIM analysis. Hydrogen bonds also allow the drug to be released more slowly. These results were confirmed by experimental evidence and the comparison of this model with the simple model of one polymer chain. Also, the mechanism of GCS formation was investigated by calculating the activation parameters, which indicates that solvent (H2O) molecules are explicitly involved in the formation of GCS.
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Affiliation(s)
- Marjan Nasrabadi
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran; Research Center for Animal Development Applied Biology, Mashhad Branch, Islamic Azad University, Mashhad 917568, Iran
| | - Ali Morsali
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran; Research Center for Animal Development Applied Biology, Mashhad Branch, Islamic Azad University, Mashhad 917568, Iran.
| | - S Ali Beyramabadi
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran; Research Center for Animal Development Applied Biology, Mashhad Branch, Islamic Azad University, Mashhad 917568, Iran
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8
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García-Díez G, Mora-Diez N. Theoretical Study of the Iron Complexes with Aminoguanidine: Investigating Secondary Antioxidant Activity. Antioxidants (Basel) 2020; 9:E756. [PMID: 32824195 PMCID: PMC7463863 DOI: 10.3390/antiox9080756] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/02/2020] [Accepted: 08/11/2020] [Indexed: 12/27/2022] Open
Abstract
A thorough analysis of the thermodynamic stability of various complexes of aminoguanidine (AG) with Fe(III) at a physiological pH is presented. Moreover, the secondary antioxidant activity of AG is studied with respect to its kinetic role in the Fe(III) reduction to Fe(II) when reacting with the superoxide radical anion or ascorbate. Calculations are performed at the M05(SMD)/6-311+G(d,p) level of theory. Solvent effects (water) are taken into account in both geometry optimizations and frequency calculations employing the SMD solvation method. Even though the results of this study show that AG can form an extensive number of stable complexes with Fe(III), none of these can reduce the rate constant of the initial step of the Haber-Weiss cycle when the reducing agent is O2•-. However, when the reductant is the ascorbate anion, AG is capable of reducing the rate constant of this reaction significantly, to the point of inhibiting the production of •OH radicals. In fact, the most stable complex of Fe(III) with AG, having a ∆Gf° of -37.9 kcal/mol, can reduce the rate constant of this reaction by 7.9 × 105 times. Thus, AG possesses secondary antioxidant activity relative to the Fe(III)/Fe(II) reduction with ascorbate, but not with O2•-. Similar results have also been found for AG relative to the Cu(II)/Cu(I) reduction, in agreement with experimental results.
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Affiliation(s)
| | - Nelaine Mora-Diez
- Department of Chemistry, Thompson Rivers University, Kamloops, BC V2C 0C8, Canada;
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9
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García-Díez G, Ramis R, Mora-Diez N. Theoretical Study of the Copper Complexes with Aminoguanidine: Investigating Secondary Antioxidant Activity. ACS OMEGA 2020; 5:14502-14512. [PMID: 32596588 PMCID: PMC7315568 DOI: 10.1021/acsomega.0c01175] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
A systematic study of the thermodynamic stability of various Cu(II) complexes with aminoguanidine (AG) is performed, together with the study of its secondary antioxidant activity. Calculations have been carried out at the M05(SMD)/6-311+G(d,p) level of theory using water as the solvent. The results obtained indicate that AG is capable of forming a wide array of stable coordination compounds with Cu(II) under physiological pH conditions, and it possesses some degree of secondary antioxidant activity when coordinating to copper. The most thermodynamically stable complex can slow down 2.8 times the first step of the Haber-Weiss cycle (from 7.71 × 109 to 2.80 × 109 M-1 s-1) and slightly reduce the potential damage that the formation of •OH radicals can cause. The results of this research add to previous knowledge on this molecule, which could be used as a potential glycation inhibitor.
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Affiliation(s)
- Guillermo García-Díez
- Department
of Chemistry, Thompson Rivers University, Kamloops, British Columbia V2C 0C8, Canada
| | - Rafael Ramis
- Departament
de Química, Universitat de les Illes
Balears, Palma de Mallorca 07122, Spain
| | - Nelaine Mora-Diez
- Department
of Chemistry, Thompson Rivers University, Kamloops, British Columbia V2C 0C8, Canada
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10
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Vitamin B6 and Diabetes: Relationship and Molecular Mechanisms. Int J Mol Sci 2020; 21:ijms21103669. [PMID: 32456137 PMCID: PMC7279184 DOI: 10.3390/ijms21103669] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/14/2022] Open
Abstract
Vitamin B6 is a cofactor for approximately 150 reactions that regulate the metabolism of glucose, lipids, amino acids, DNA, and neurotransmitters. In addition, it plays the role of antioxidant by counteracting the formation of reactive oxygen species (ROS) and advanced glycation end-products (AGEs). Epidemiological and experimental studies indicated an evident inverse association between vitamin B6 levels and diabetes, as well as a clear protective effect of vitamin B6 on diabetic complications. Interestingly, by exploring the mechanisms that govern the relationship between this vitamin and diabetes, vitamin B6 can be considered both a cause and effect of diabetes. This review aims to report the main evidence concerning the role of vitamin B6 in diabetes and to examine the underlying molecular and cellular mechanisms. In addition, the relationship between vitamin B6, genome integrity, and diabetes is examined. The protective role of this vitamin against diabetes and cancer is discussed.
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11
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Quantum chemical studies of chitosan nanoparticles as effective drug delivery systems for 5-fluorouracil anticancer drug. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112495] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Mueser TC, Drago V, Kovalevsky A, Dajnowicz S. Pyridoxal 5'-phosphate dependent reactions: Analyzing the mechanism of aspartate aminotransferase. Methods Enzymol 2020; 634:333-359. [PMID: 32093839 DOI: 10.1016/bs.mie.2020.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzyme catalysis is the primary activity in energy and information metabolism and enzyme cofactors are key to the catalytic ability of most enzymes. Pyridoxal 5'-phosphate (PLP) cofactor, derived from Vitamin B6, is widely distributed in nature and has significant latitude in catalytic diversity. X-ray crystallography has revealed the structures of diverse PLP dependent enzymes from multiple families. But these structures are incomplete, lacking the positions of protons essential for understanding enzymatic mechanisms. Here, we review the diversity of PLP and discuss the use of neutron crystallography and joint X-ray/neutron refinement of Fold Type I aspartate aminotransferase to visualize the positions of protons in both the internal and external aldimine forms. Strategies used to prepare extremely large crystals required for neutron diffraction and the approach to data refinement including the PLP cofactor are discussed. The observed positions of protons, including one located in a previously unknown low-barrier hydrogen bond, have been used to create more accurate models for computational analysis. The results revealed a new mechanism for the transaminase reaction where hyperconjugation is key to reducing the energy barrier which finally provides a clear explanation of the Dunathan alignment.
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Affiliation(s)
- Timothy C Mueser
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH, United States.
| | - Victoria Drago
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH, United States
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Steven Dajnowicz
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH, United States; Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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13
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Ramis R, Ortega-Castro J, Caballero C, Casasnovas R, Cerrillo A, Vilanova B, Adrover M, Frau J. How Does Pyridoxamine Inhibit the Formation of Advanced Glycation End Products? The Role of Its Primary Antioxidant Activity. Antioxidants (Basel) 2019; 8:E344. [PMID: 31480509 PMCID: PMC6770850 DOI: 10.3390/antiox8090344] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/16/2019] [Accepted: 08/22/2019] [Indexed: 12/28/2022] Open
Abstract
Pyridoxamine, one of the natural forms of vitamin B6, is known to be an effective inhibitor of the formation of advanced glycation end products (AGEs), which are closely related to various human diseases. Pyridoxamine forms stable complexes with metal ions that catalyze the oxidative reactions taking place in the advanced stages of the protein glycation cascade. It also reacts with reactive carbonyl compounds generated as byproducts of protein glycation, thereby preventing further protein damage. We applied Density Functional Theory to study the primary antioxidant activity of pyridoxamine towards three oxygen-centered radicals (•OOH, •OOCH3 and •OCH3) to find out whether this activity may also play a crucial role in the context of protein glycation inhibition. Our results show that, at physiological pH, pyridoxamine can trap the •OCH3 radical, in both aqueous and lipidic media, with rate constants in the diffusion limit (>1.0 × 108 M - 1 s - 1 ). The quickest pathways involve the transfer of the hydrogen atoms from the protonated pyridine nitrogen, the protonated amino group or the phenolic group. Its reactivity towards •OOH and •OOCH3 is smaller, but pyridoxamine can still scavenge them with moderate rate constants in aqueous media. Since reactive oxygen species are also involved in the formation of AGEs, these results highlight that the antioxidant capacity of pyridoxamine is also relevant to explain its inhibitory role on the glycation process.
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Affiliation(s)
- Rafael Ramis
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d'Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Joaquín Ortega-Castro
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.
- Institut d'Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain.
| | - Carmen Caballero
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d'Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Rodrigo Casasnovas
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d'Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Antonia Cerrillo
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d'Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Bartolomé Vilanova
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d'Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Miquel Adrover
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d'Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Juan Frau
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d'Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
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14
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Soniya K, Awasthi S, Nair NN, Chandra A. Transimination Reaction at the Active Site of Aspartate Aminotransferase: A Proton Hopping Mechanism through Pyridoxal 5′-Phosphate. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00834] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kumari Soniya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Shalini Awasthi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Nisanth N. Nair
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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15
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Reactions of aldehyde with collagen: a DFT study. Struct Chem 2018. [DOI: 10.1007/s11224-018-1131-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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16
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Kaya Y. Density Functional Study of the Reaction Mechanism of Two Oxiimine Alcohol Formations and Their Novel Rearrangements. Helv Chim Acta 2016. [DOI: 10.1002/hlca.201500155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yunus Kaya
- Department of Chemistry; Faculty of Arts and Sciences; Uludag University; TR-16059 Bursa Turkey
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17
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Monitoring utilizations of amino acids and vitamins in culture media and Chinese hamster ovary cells by liquid chromatography tandem mass spectrometry. J Pharm Biomed Anal 2016; 117:163-72. [DOI: 10.1016/j.jpba.2015.08.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 08/24/2015] [Accepted: 08/27/2015] [Indexed: 11/21/2022]
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18
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Ding YQ, Cui YZ, Li TD. New views on the reaction of primary amine and aldehyde from DFT study. J Phys Chem A 2015; 119:4252-60. [PMID: 25859816 DOI: 10.1021/acs.jpca.5b02186] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A general theoretical investigation on the reaction of primary amine with aldehyde was carried out by density functional theory. The calculation systems involve three kinds of primary amines (methylamine, vinylamine, and phenylamine) and three kinds of aldehydes (formaldehyde, acetaldehyde, and acrylaldehyde). The steric and electronic inductive effects on the reaction mechanism were studied. Results reveal that the nucleophilic attack of primary amine on aldehyde under neutral conditions leads to carbinolamines, rather than Schiff bases. The nucleophilic attack on the protonated aldehyde produces the protonated Schiff base. The steric hindrance of the aldehyde slows down the nucleophilic attack but allows enough time to abstract a H; consequently, the formation of the protonated Schiff base is preferred. During the carbinolamine protonation, the H(+) preferably locates on the amine nitrogen and then is abstracted by the hydroxyl oxygen over an energy barrier, leaving protonated Schiff base after timely water liberation. The formation of a prereaction potential energy well obviously softens the steric and electronic inductive effects on the active barrier for different reactants.
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Affiliation(s)
- Yun-qiao Ding
- Shandong Provincial Key Laboratory of Fine Chemicals, School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology, 250353, Jinan, Shandong China
| | - Yue-zhi Cui
- Shandong Provincial Key Laboratory of Fine Chemicals, School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology, 250353, Jinan, Shandong China
| | - Tian-duo Li
- Shandong Provincial Key Laboratory of Fine Chemicals, School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology, 250353, Jinan, Shandong China
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19
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Solís-Calero C, Ortega-Castro J, Frau J, Muñoz F. Nonenzymatic Reactions above Phospholipid Surfaces of Biological Membranes: Reactivity of Phospholipids and Their Oxidation Derivatives. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2015; 2015:319505. [PMID: 25977746 PMCID: PMC4419266 DOI: 10.1155/2015/319505] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 01/03/2023]
Abstract
Phospholipids play multiple and essential roles in cells, as components of biological membranes. Although phospholipid bilayers provide the supporting matrix and surface for many enzymatic reactions, their inherent reactivity and possible catalytic role have not been highlighted. As other biomolecules, phospholipids are frequent targets of nonenzymatic modifications by reactive substances including oxidants and glycating agents which conduct to the formation of advanced lipoxidation end products (ALEs) and advanced glycation end products (AGEs). There are some theoretical studies about the mechanisms of reactions related to these processes on phosphatidylethanolamine surfaces, which hypothesize that cell membrane phospholipids surface environment could enhance some reactions through a catalyst effect. On the other hand, the phospholipid bilayers are susceptible to oxidative damage by oxidant agents as reactive oxygen species (ROS). Molecular dynamics simulations performed on phospholipid bilayers models, which include modified phospholipids by these reactions and subsequent reactions that conduct to formation of ALEs and AGEs, have revealed changes in the molecular interactions and biophysical properties of these bilayers as consequence of these reactions. Then, more studies are desirable which could correlate the biophysics of modified phospholipids with metabolism in processes such as aging and diseases such as diabetes, atherosclerosis, and Alzheimer's disease.
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Affiliation(s)
- Christian Solís-Calero
- Institut d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Instituto de Investigación Sanitaria de Palma, 07010 Palma, Spain
| | - Joaquín Ortega-Castro
- Institut d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Instituto de Investigación Sanitaria de Palma, 07010 Palma, Spain
| | - Juan Frau
- Institut d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Instituto de Investigación Sanitaria de Palma, 07010 Palma, Spain
| | - Francisco Muñoz
- Institut d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Instituto de Investigación Sanitaria de Palma, 07010 Palma, Spain
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20
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Solís-Calero C, Ortega-Castro J, Frau J, Muñoz F. Scavenger mechanism of methylglyoxal by metformin. A DFT study. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1649-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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21
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Solís-Calero C, Ortega-Castro J, Hernández-Laguna A, Frau J, Muñoz F. A DFT study of the carboxymethyl-phosphatidylethanolamine formation from glyoxal and phosphatidylethanolamine surface. Comparison with the formation of N(ε)-(carboxymethyl)lysine from glyoxal and l-lysine. Phys Chem Chem Phys 2015; 17:8210-22. [DOI: 10.1039/c4cp05360e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mechanisms of the generation of CML and CM-PE from the reactions between glyoxal and l-lysine, and glyoxal and phosphatidylethanolamine (PE) were studied using the DFT method.
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Affiliation(s)
- C. Solís-Calero
- Institut d’Investigació en Ciències de la Salut (IUNICS)
- Departament de Química
- Universitat de les Illes Balears
- E-07122 Palma de Mallorca
- Spain
| | - J. Ortega-Castro
- Institut d’Investigació en Ciències de la Salut (IUNICS)
- Departament de Química
- Universitat de les Illes Balears
- E-07122 Palma de Mallorca
- Spain
| | | | - J. Frau
- Institut d’Investigació en Ciències de la Salut (IUNICS)
- Departament de Química
- Universitat de les Illes Balears
- E-07122 Palma de Mallorca
- Spain
| | - F. Muñoz
- Institut d’Investigació en Ciències de la Salut (IUNICS)
- Departament de Química
- Universitat de les Illes Balears
- E-07122 Palma de Mallorca
- Spain
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22
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Pandey S, Garg P, Lee S, Choung HW, Choung YH, Choung PH, Chung JH. Nucleotide biosynthesis arrest by silencing SHMT1 function via vitamin B6-coupled vector and effects on tumor growth inhibition. Biomaterials 2014; 35:9332-42. [PMID: 25132602 DOI: 10.1016/j.biomaterials.2014.07.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 07/23/2014] [Indexed: 01/15/2023]
Abstract
Serine hydroxymethyltransferase isoforms (SHMT1 & SHMT2α), which serve as scaffold protein for the formation of a multi-enzyme complex and generate one-carbon unit for the de novo thymidylate biosynthesis pathway during DNA synthesis, are vitamin B6 (VB6)-dependent enzyme. Cancer cells with high proliferation intensity need increased SHMT activation which enforces the facilitated-diffusion of VB6 for the continuous functioning of thymidylate synthase cycle. Therefore, SHMT knockdown presents an alternative approach to prevent DNA synthesis in cancer cells; however, its potential to inhibit cancer growth remains unknown so far. Here we demonstrated that VB6 coupled to poly(ester amine) (VBPEA) enforces a high level of VTC (VB6-transporting membrane carriers)-mediated endocytosis of the complexed SHMT1 siRNA (siSHMT1) to interrupt the thymidylate biosynthesis pathway of cancer cells. The detrimental effect of SHMT1 knockdown on the disintegration of multi-enzyme complex resulted in cell cycle arrest and a decrease in cell's genomic DNA content, leading to enhanced apoptotic events in cancer cells. A reduction in tumor size was observed with constant SHMT1 suppression in xenograft mice. This study illustrates how silencing the SHMT1 expression inhibits cancer growth and the increased VB6 channeling for sustenance of cancer cells promotes VB6-coupled vector to elicit enhanced delivery of siSHMT1.
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Affiliation(s)
- Shambhavi Pandey
- Department of Biosystems & Biomaterials Science and Engineering, Seoul National University, Seoul 151-921, Republic of Korea
| | - Pankaj Garg
- Department of Biosystems & Biomaterials Science and Engineering, Seoul National University, Seoul 151-921, Republic of Korea
| | - Somin Lee
- Laboratory of Toxicology, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Republic of Korea
| | - Han-Wool Choung
- Department of Oral and Maxillofacial Surgery and Dental Research Institute, School of Dentistry, Seoul National University, Seoul 110-774, Republic of Korea
| | - Yun-Hoon Choung
- Department of Otalaryngology, Ajou University School of Medicine, Suwon 443-749, Republic of Korea
| | - Pill-Hoon Choung
- Department of Oral and Maxillofacial Surgery and Dental Research Institute, School of Dentistry, Seoul National University, Seoul 110-774, Republic of Korea.
| | - Jong Hoon Chung
- Department of Biosystems & Biomaterials Science and Engineering, Seoul National University, Seoul 151-921, Republic of Korea; Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
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23
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Gökcan H, Konuklar FAS. Stereoelectronic explanations for the mechanistic details of transimination and HF elimination reactions. J Mol Graph Model 2014; 51:173-83. [PMID: 24929816 DOI: 10.1016/j.jmgm.2014.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 11/26/2022]
Abstract
The β-fluoroamines are commonly used as substrate analogs to determine the mechanistic details of enzymatic reactions. Presence of fluorine atom gives rise to the alterations in the electronic profile and the pKa of molecules which results in mechanistic deviations. The fluorine-substituted mechanism-based substrate analogs are widely used in the inactivation of pyridoxal 5'-phosphate (PLP)-dependent enzymes. The presence of fluorine atom also alters the sequence of reactions taking place in PLP-dependent enzymes where the HF elimination reaction appears in between the transimination and inactivation reactions. Despite the amount of the works on β-fluoroamines, the effect of stereoelectronic differences on the transimination and HF elimination reactions taking place in PLP-dependent enzymes has not been investigated yet. A density functional theory study is conducted to elucidate mechanistic details of the reactions occurring in PLP-dependent enzymes. In order to understand the mechanistic insights of different isomers and the effect of the fluorine atom, 4-amino-3-fluorobutanoic acid (3-F-GABA) enantiomers are chosen to be investigated besides 4-aminobutanoic acid (GABA), which is the natural substrate for γ-aminobutyric acid aminotransferase (GABA-AT). The investigated β-fluoroamines are the experimentally proposed potential inhibitors of PLP-dependent enzyme GABA-AT.
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Affiliation(s)
- Hatice Gökcan
- Istanbul Technical University, Informatics Institute, Computational Science and Engineering Division, Ayazağa Campus, 34496 Maslak, Istanbul, Turkey
| | - F Aylin Sungur Konuklar
- Istanbul Technical University, Informatics Institute, Computational Science and Engineering Division, Ayazağa Campus, 34496 Maslak, Istanbul, Turkey.
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24
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Solís-Calero C, Ortega-Castro J, Hernández-Laguna A, Muñoz F. DFT study of the mechanism of the reaction of aminoguanidine with methylglyoxal. J Mol Model 2014; 20:2202. [PMID: 24705776 DOI: 10.1007/s00894-014-2202-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/04/2014] [Indexed: 11/28/2022]
Abstract
We have studied the mechanism of the reaction between aminoguanidine (AG) and methylglyoxal (MG) by carrying out Dmol3/DFT calculations, obtaining intermediates, transition-state structures, and free-energy profiles for all of the elementary steps of the reaction. Designed models included explicit water solvent, which forms hydrogen-bond networks around the reactants and intermediate molecules, facilitating intramolecular proton transfer in some steps of the reaction mechanism. The reaction take place in four steps, namely: (1) formation of a guanylhydrazone-acetylcarbinol adduct by condensation of AG and MG; (2) dehydration of the adduct; (3) formation of an 1,2,4-triazine derivative by ring closure; and (4) dehydration with the formation of 5-methyl 3-amino-1,2,4-triazine as the final product. From a microkinetic point of view, the first dehydration step was found to be the rate-determining step for the reaction, with the reaction having an apparent activation energy of 12.65 kcal mol⁻¹. Additionally, some analogous structures of intermediates and transition states for the reaction between AG and 2,3-dicarbonyl-phosphatidylethanolamine, a possible intermediate in Amadori-glycated phosphatidylethanolamine (Amadori-PE) autooxidation, were obtained to evaluate the reaction above a phosphatidylethanolamine (PE) surface. Our results are in agreement with experimental results obtaining by other authors, showing that AG is efficient at trapping dicarbonyl compounds such as methylglyoxal, and by extension these compounds joined to biomolecules such as PE in environments such as surfaces and their aqueous surroundings.
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Affiliation(s)
- Christian Solís-Calero
- Departament de Química, Institut d'Investigació en Ciències de la Salut (IUNICS), Universitat de les Illes Balears, E-07122, Palma de Mallorca, Spain
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25
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Asadi M, Torabi S, Mohammadi K. Synthesis, characterization, and thermodynamics of some new unsymmetrical Schiff bases of salicylaldehyde with 3,4-diaminopyridine and their cobalt(III) complexes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 122:676-681. [PMID: 24342295 DOI: 10.1016/j.saa.2013.09.098] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 09/08/2013] [Accepted: 09/26/2013] [Indexed: 06/03/2023]
Abstract
Some new Schiff bases derived from 3,4-diaminopyridine (3,4-DAP) and their new unsymmetrical Co(III) five coordinate complexes described as [Co(Chel)(L)]ClO4⋅H2O where (Chel) is the deprotonated form of a series of unsymmetric ligands containing 3,4-diaminopyridine (3,4-DAP) and substituted salicylaldehyde moieties and a new Co(III) six coordinate Co(III) complex, were synthesized and characterized by (1)H NMR, IR, UV-Vis, and elemental analysis. For the new synthesized five coordinate complexes, the formation constants of the interaction of the Co(III) Schiff bases with various donors were measured spectrophotometrically. The trend of the formation constants of the five coordinate Co(III) Schiff base complexes toward a given phosphine is as follow: 5-H>5-Br and the formation constants trend of these donors are as follow: PBu3>PPh2Me. Furthermore the adduct formation of the five coordinate [Co(3,4-Salpyr)(PBu3)] ClO4⋅H2O, with aromatic amines shows the following binding trend: Im>2-MeIm>2-EtIm>BzIm. The trend of the formation constants of Co(III) Schiff base complexes toward a given donor according to the phosphine axial ligand is as follow: PBu3>PPh2Me.
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Affiliation(s)
- Mozaffar Asadi
- Chemistry Department, College of Sciences, Shiraz University, Shiraz 71454, Islamic Republic of Iran.
| | - Susan Torabi
- Chemistry Department, College of Sciences, Shiraz University, Shiraz 71454, Islamic Republic of Iran; International Branch, Shiraz University of Medical Sciences, Shiraz, Islamic Republic of Iran
| | - Khosro Mohammadi
- Chemistry Department, Faculty of Sciences, Persian Gulf University, Bushehr 75169, Islamic Republic of Iran
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26
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Xia H, Mathew B, John T, Hegab H, Feng J. Microfluidic based immunosensor for detection and purification of carbonylated proteins. Biomed Microdevices 2014; 15:519-30. [PMID: 23471602 DOI: 10.1007/s10544-013-9751-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A microchip has been developed on the basis of immno-precipitation approach for fast and sensitive enrichment of low abundant carbonylated proteins. This microfluidic method could enrich molecular biomarkers, which could be further analyzed in the proteomic study of age-related diseases and therapeutic development. In this study, an immunoaffinity-based PDMS micro-device was designed, fabricated, and chemically modified to specifically trap DNP-labeled PTM proteins of low abundance from a complex protein mixture. Carbonylated protein is selected as a representative PTM protein to illustrate the wide application of this immuno-based microchip for other PTMs which could be readily labeled by different antibody groups. Surface characterization methods such as atomic force microscopy and fluorescence microscopy were used to evaluate the construction of glutaraldehyde- and antibody- terminated PDMS substrates in the device fabrication. Quantitative study was also applied to study the target protein capture and elution efficiency of the device. In a testing mixture consisting of smaller amount of test model-In Vitro oxidized cytochrome c and large blocking protein BSA, a high sensitivity and specificity for only carbonylated protein biomarkers was demonstrated using this on-chip immnuoaffinity based extraction/enrichment. For this highly dense 193-post arrays μ-chip, a low abundance of 159 ng of standard in vitro test model- cytochrome c was enriched at flow speed of 5 μL/min within 110 min. We demonstrated that this nascent micro-immunoprecipitation (μ-IP) method is capable for enrichment of biomarkers in protein post-translation modification related diseases and promise great advance in early disease detection.
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Affiliation(s)
- Hui Xia
- Department of Biomedical Engineering, Louisiana Tech University, Ruston, USA
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27
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The efficiency of membrane transport of vitamin B6 coupled to poly(ester amine) gene transporter and transfection in cancer cells. Biomaterials 2013; 34:3716-28. [DOI: 10.1016/j.biomaterials.2013.01.098] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Accepted: 01/30/2013] [Indexed: 11/22/2022]
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28
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C–H Activation in Pyridoxal-5′-phosphate and Pyridoxamine-5′-phosphate Schiff Bases: Effect of Metal Chelation. A Computational Study. J Phys Chem B 2013; 117:2339-47. [DOI: 10.1021/jp311861p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Casasnovas R, Ortega-Castro J, Donoso J, Frau J, Muñoz F. Theoretical calculations of stability constants and pKa values of metal complexes in solution: application to pyridoxamine–copper(ii) complexes and their biological implications in AGE inhibition. Phys Chem Chem Phys 2013; 15:16303-13. [DOI: 10.1039/c3cp50840d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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30
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Xiao X, Liu M, Rong C, Xue F, Li S, Xie Y, Shi Y. An Efficient Asymmetric Biomimetic Transamination of α-Keto Esters to Chiral α-Amino Esters. Org Lett 2012; 14:5270-3. [DOI: 10.1021/ol302427d] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiao Xiao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Mao Liu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Chao Rong
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Fazhen Xue
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Songlei Li
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Ying Xie
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Yian Shi
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
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31
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Casasnovas R, Adrover M, Ortega-Castro J, Frau J, Donoso J, Muñoz F. C–H Activation in Pyridoxal-5′-phosphate Schiff Bases: The Role of the Imine Nitrogen. A Combined Experimental and Computational Study. J Phys Chem B 2012; 116:10665-75. [DOI: 10.1021/jp303678n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rodrigo Casasnovas
- Institut
d’Investigació en Ciènces de la Salut (IUNICS),
Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Miquel Adrover
- Institut
d’Investigació en Ciènces de la Salut (IUNICS),
Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Joaquin Ortega-Castro
- Institut
d’Investigació en Ciènces de la Salut (IUNICS),
Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Juan Frau
- Institut
d’Investigació en Ciènces de la Salut (IUNICS),
Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Josefa Donoso
- Institut
d’Investigació en Ciènces de la Salut (IUNICS),
Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
| | - Francisco Muñoz
- Institut
d’Investigació en Ciènces de la Salut (IUNICS),
Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
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32
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A comparative DFT study of the Schiff base formation from acetaldehyde and butylamine, glycine and phosphatidylethanolamine. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1263-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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33
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Xue F, Xiao X, Wang H, Shi Y. The effect of benzyl amine on the efficiency of the base-catalyzed transamination of α-keto esters. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.06.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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34
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Gökcan H, Konuklar FAS. Theoretical study on HF elimination and aromatization mechanisms: a case of pyridoxal 5' phosphate-dependent enzyme. J Org Chem 2012; 77:5533-43. [PMID: 22646918 DOI: 10.1021/jo3005815] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyridoxal 5-phosphate (PLP), the phosphorylated and the oxidized form of vitamin B6 is an organic cofactor. PLP forms a Schiff base with the ϵ-amino group of a lysine residue of PLP-dependent enzymes. γ-Aminobutyric acid (GABA) aminotransferase is a PLP-dependent enzyme that degrades GABA to succinic semialdehyde, while reduction of GABA concentration in the brain causes convolution besides several neurological diseases. The fluorine-containing substrate analogues for the inactivation of the GABA-AT are synthesized extensively in cases where the inactivation mechanisms involve HF elimination. Although two proposed mechanisms are present for the HF elimination, the details of the base-induced HF elimination are not well identified. In this density functional theory (DFT) study, fluorine-containing substrate analogue, 5-amino-2-fluorocyclohex-3-enecarboxylic acid, is particularly chosen in order to explain the details of the HF elimination reactions. On the other hand, the experimental studies revealed that aromatization competes with Michael addition mechanism in the presence of 5-amino-2-fluorocyclohex-3-enecarboxylic acid. The results allowed us to draw a conclusion for the nature of HF elimination, besides the elucidation of the mechanism preference for the inactivation mechanism. Furthermore, the solvent phase calculations carried out in this study ensure that the proton transfer steps should be assisted either by a water molecule or a base for lower activation energy barriers.
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Affiliation(s)
- Hatice Gökcan
- Informatics Institute, Computational Science and Engineering Programme, Istanbul Technical University, Ayazağa Campus 34469, Maslak, Istanbul, Turkey
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35
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Ortega-Castro J, Frau J, Casasnovas R, Fernández D, Donoso J, Muñoz F. High- and low-spin Fe(III) complexes of various AGE inhibitors. J Phys Chem A 2012; 116:2961-71. [PMID: 22369344 DOI: 10.1021/jp210188w] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Density functional theory calculations [CPCM/UM06/6-31+G(d,p)] were used to elucidate the structures and relative stability of Fe(III) complexes with various ligands that inhibit the formation of advanced glycation end products (AGEs) or iron overloaded disease (viz. aminoguanidine, pyridoxamine, LR-74, Amadori compounds, and ascorbic acid). EDTA was used as the free energy reference ligand. The distorted neutral octahedral complex containing one iron atom and three molecules of pyridoxamine [Fe(PM)(3)] was found to be the most stable. The stability of the complexes decreases in the following chelate sequence: pyridoxamine, Amadori complex, aminoguanidine, LR inhibitor, and ascorbic acid.
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Affiliation(s)
- J Ortega-Castro
- Institut d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
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36
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Vilanova B, Gallardo JM, Caldés C, Adrover M, Ortega-Castro J, Muñoz F, Donoso J. Formation of Schiff Bases of O-Phosphorylethanolamine and O-Phospho-d,l-serine with Pyridoxal 5′-Phosphate. Experimental and Theoretical Studies. J Phys Chem A 2012; 116:1897-905. [DOI: 10.1021/jp2116033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bartolomé Vilanova
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
| | - Jessica M. Gallardo
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
| | - Catalina Caldés
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
| | - Miquel Adrover
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
| | - Joaquín Ortega-Castro
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
| | - Francisco Muñoz
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
| | - Josefa Donoso
- Institut
Universitari d’Investigació
en Ciències de la Salut (IUNICS), Departament de
Química, Universitat de les Illes Balears, Ctra Valldemosa km 7.5, E-07122 Palma de Mallorca,
Spain
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37
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Ultra sensitive affinity chromatography on avidin-functionalized PMMA microchip for low abundant post-translational modified protein enrichment. Biomed Microdevices 2011; 14:67-81. [DOI: 10.1007/s10544-011-9586-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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38
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Studies on molecular structure and tautomerism of a vitamin B6 analog with density functional theory. J Mol Model 2011; 18:1993-2001. [PMID: 21877155 DOI: 10.1007/s00894-011-1214-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 08/07/2011] [Indexed: 10/17/2022]
Abstract
This work presents a computational study on the molecular structure and tautomeric equilibria of a novel Schiff base L derived from pyridoxal (PL) and o-phenylenediamine by using the density functional method B3LYP with basis sets 6-31 G(d,p), 6-31++G(d,p), 6-311 G(d,p) and 6-311++G(d,p). The optimized geometrical parameters obtained by B3LYP/6-31 G(d,p) method showed the best agreement with the experimental values. Tautomeric stability study of L inferred that the enolimine form is more stable than its ketoenamine form in both gas phase and solution. However, protonation of the pyridoxal nitrogen atom (LH) have accelerated the formation of ketoenamine form, and therefore, both ketoenamine and enolimine forms could be present in acidic media.
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Caldés C, Vilanova B, Adrover M, Muñoz F, Donoso J. Understanding non-enzymatic aminophospholipid glycation and its inhibition. Polar head features affect the kinetics of Schiff base formation. Bioorg Med Chem 2011; 19:4536-43. [DOI: 10.1016/j.bmc.2011.06.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 06/01/2011] [Accepted: 06/08/2011] [Indexed: 02/02/2023]
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Cerqueira NMFSA, Fernandes PA, Ramos MJ. Computational Mechanistic Studies Addressed to the Transimination Reaction Present in All Pyridoxal 5′-Phosphate-Requiring Enzymes. J Chem Theory Comput 2011; 7:1356-68. [DOI: 10.1021/ct1002219] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- N. M. F. S. A. Cerqueira
- REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - P. A. Fernandes
- REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - M. J. Ramos
- REQUIMTE, Faculdade de Ciências, Universidade do Porto, Rua Campo Alegre, s/n, 4169-007 Porto, Portugal
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Bruno A, Amori L, Costantino G. Addressing the Conformational Flexibility of Serine Racemase by Combining Targeted Molecular Dynamics, Conformational Sampling and Docking Studies. Mol Inform 2011; 30:317-28. [DOI: 10.1002/minf.201000162] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 12/22/2010] [Indexed: 11/06/2022]
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Durak AT, Gökcan H, Konuklar FAS. Theoretical studies on the inactivation mechanism of γ-aminobutyric acid aminotransferase. Org Biomol Chem 2011; 9:5162-71. [DOI: 10.1039/c1ob05146f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Solís-Calero C, Ortega-Castro J, Muñoz F. Reactivity of a phospholipid monolayer model under periodic boundary conditions: a density functional theory study of the Schiff base formation between phosphatidylethanolamine and acetaldehyde. J Phys Chem B 2010; 114:15879-85. [PMID: 21077587 DOI: 10.1021/jp1088367] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A mechanism for the formation of the Schiff base between an acetaldehyde and an amine-phospholipid monolayer model based on Dmol3/density functional theory calculations under periodic boundary conditions was constructed. This is the first time such a system has been modeled to examine its chemical reactivity at this computation level. Each unit cell contains two phospholipid molecules, one acetaldehyde molecule, and nine water molecules. One of the amine-phospholipid molecules in the cell possesses a neutral amino group that is used to model the nucleophilic attack on the carboxyl group of acetaldehyde, whereas the other has a charged amino group acting as a proton donor. The nine water molecules form a hydrogen bond network along the polar heads of the phospholipids that facilitates very fast proton conduction at the interface. Using periodic boundary conditions afforded proton transfer between different cells. The reaction takes place in two steps, namely, (1) formation of a carbinolamine and (2) its dehydration to the Schiff base. The carbinolamine is the primary reaction intermediate, and dehydration is the rate-determining step of the process, consistent with available experimental evidence for similar reactions. On the basis of the results, the cell membrane surface environment may boost phospholipid glycation via a neighboring catalyst effect.
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Affiliation(s)
- Christian Solís-Calero
- Institut d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain
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