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Bržezická T, Mlčochová H, Glatz Z, Kohútová L. Contactless conductivity detector as a tool for improving universality and sensitivity of capillary electrophoresis-frontal analysis: Proof of concept. J Sep Sci 2024; 47:e2300667. [PMID: 38234025 DOI: 10.1002/jssc.202300667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/13/2023] [Accepted: 12/05/2023] [Indexed: 01/19/2024]
Abstract
Drug binding to plasma proteins influences processes such as liberation, adsorption, disposition, metabolism, and elimination of drugs, which are thus one of the key steps of a new drug development. As a result, the characterization of drug-protein interactions is an essential part of these time- and money-consuming processes. It is important to determine not only the binding strength and the stoichiometry of interaction, but also the binding site of a drug on a protein molecule, because two drugs with the same binding site can mutually affect free drug concentration. Capillary electrophoresis-frontal analysis with mobility shift affinity capillary electrophoresis is one of the most used affinity capillary electrophoresis methods for the characterization of these interactions. In this study, a well-known sensitivity problem of most capillary electrophoresis-frontal analyses using ultraviolet detection is solved by its combination with contactless conductivity detection, which provided sixfold lower limits of quantitation and detection. Binding parameters of the human serum albumin-salicylic acid model affinity pair were evaluated by this newly developed approach and by the classical approach with ultraviolet detection primarily used for their mutual comparison. The results of both approaches agreed well and are also in agreement with literature data obtained using different techniques.
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Affiliation(s)
- Taťána Bržezická
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Hana Mlčochová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zdeněk Glatz
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lenka Kohútová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
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2
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Bržezická T, Glatz Z, Kohútová L. Sensitivity enhancement of capillary electrophoresis-frontal analysis-based method for characterization of drug-protein interactions using on-line sample preconcentration. J Sep Sci 2023; 46:e2300152. [PMID: 37386816 DOI: 10.1002/jssc.202300152] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/31/2023] [Accepted: 06/10/2023] [Indexed: 07/01/2023]
Abstract
Capillary electrophoresis-frontal analysis is one of the most frequently used approaches for the study of plasma protein-drug interactions as a substantial part of new drug development. However, the capillary electrophoresis-frontal analysis typically combined with ultraviolet-visible detection suffers from insufficient concentration sensitivity, particularly for substances with limited solubility and low molar absorption coefficient. The sensitivity problem has been solved in this work by its combination with an on-line sample preconcentration. According to the knowledge of the authors this combination has never been used to characterize plasma protein-drug binding. It resulted in a fully automated and versatile methodology for the characterization of binding interactions. Further, the validated method minimalizes the experimental errors due to a reduction in the manipulation of samples. Moreover, employing an on-line preconcentration strategy with capillary electrophoresis-frontal analysis using human serum albumin-salicylic acid as a model system improves the drug concentration sensitivity 17-fold compared to the conventional method. The value of binding constant (1.51 ± 0.63) · 104 L/mol obtained by this new capillary electrophoresis-frontal analysis modification is in agreement with the value (1.13 ± 0.28) ·104 L/mol estimated by a conventional variant of capillary electrophoresis-frontal analysis without the preconcentration step, as well as with literature data obtained using different techniques.
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Affiliation(s)
- Taťána Bržezická
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zdeněk Glatz
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lenka Kohútová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
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3
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Escobedo-González RG, Moyers-Montoya ED, Martínez-Pérez CA, García-Casillas PE, Miranda-Ruvalcaba R, Nicolás-Vázquez MIN. In Silico Study of Novel Cyclodextrin Inclusion Complexes of Polycaprolactone and Its Correlation with Skin Regeneration. Int J Mol Sci 2023; 24:ijms24108932. [PMID: 37240276 DOI: 10.3390/ijms24108932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/26/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Three novel biomaterials obtained via inclusion complexes of β-cyclodextrin, 6-deoxi-6-amino-β-cyclodextrin and epithelial growth factor grafted to 6-deoxi-6-amino-β-cyclodextrin with polycaprolactone. Furthermore, some physicochemical, toxicological and absorption properties were predicted using bioinformatics tools. The electronic, geometrical and spectroscopical calculated properties agree with the properties obtained via experimental methods, explaining the behaviors observed in each case. The interaction energy was obtained, and its values were -60.6, -20.9 and -17.1 kcal/mol for β-cyclodextrin/polycaprolactone followed by the 6-amino-β-cyclodextrin-polycaprolactone complex and finally the complex of epithelial growth factor anchored to 6-deoxy-6-amino-β-cyclodextrin/polycaprolactone. Additionally, the dipolar moments were calculated, achieving values of 3.2688, 5.9249 and 5.0998 Debye, respectively, and in addition the experimental wettability behavior of the studied materials has also been explained. It is important to note that the toxicological predictions suggested no mutagenic, tumorigenic or reproductive effects; moreover, an anti-inflammatory effect has been shown. Finally, the improvement in the cicatricial effect of the novel materials has been conveniently explained by comparing the poly-caprolactone data obtained in the experimental assessments.
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Affiliation(s)
- René Gerardo Escobedo-González
- Department of Industrial Maintenance, Technological University of the City of Juárez, Av. Universidad Tecnológica No. 3051, Col. Lote Bravo II, Ciudad Juárez 32695, Mexico
| | - Edgar Daniel Moyers-Montoya
- Institute of Engineering and Technology, Autonomous University of the City of Juárez (UACJ), Ave. Del Charro 450 Norte, Ciudad Juárez 32310, Mexico
| | - Carlos Alberto Martínez-Pérez
- Institute of Engineering and Technology, Autonomous University of the City of Juárez (UACJ), Ave. Del Charro 450 Norte, Ciudad Juárez 32310, Mexico
| | - Perla Elvia García-Casillas
- Institute of Engineering and Technology, Autonomous University of the City of Juárez (UACJ), Ave. Del Charro 450 Norte, Ciudad Juárez 32310, Mexico
- Applied Chemistry Research Center, Blvd. Enrique Reyna Hermosillo No. 140, Saltillo 25294, Mexico
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4
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Ohmuro-Matsuyama Y, Gomi K, Shimoda T, Yamaji H, Ueda H. Improving the Stability of Protein-Protein Interaction Assay FlimPIA Using a Thermostabilized Firefly Luciferase. Front Bioeng Biotechnol 2021; 9:778120. [PMID: 34858964 PMCID: PMC8631863 DOI: 10.3389/fbioe.2021.778120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
The protein–protein interaction assay is a key technology in various fields, being applicable in drug screening as well as in diagnosis and inspection, wherein the stability of assays is important. In a previous study, we developed a unique protein–protein interaction assay “FlimPIA” based on the functional complementation of mutant firefly luciferases (Fluc). The catalytic step of Fluc was divided into two half steps: D-luciferin was adenylated in the first step, while adenylated luciferin was oxidized in the second step. We constructed two mutants of Fluc from Photinus pyralis (Ppy); one mutant named Donor is defective in the second half reaction, while the other mutant named Acceptor exhibited low activity in the first half reaction. To date, Ppy has been used in the system; however, its thermostability is low. In this study, to improve the stability of the system, we applied Fluc from thermostabilized Luciola lateralis to FlimPIA. We screened suitable mutants as probes for FlimPIA and obtained Acceptor and Donor candidates. We detected the interaction of FKBP12-FRB with FlimPIA using these candidates. Furthermore, after the incubation of the probes at 37°C for 1 h, the luminescence signal of the new system was 2.4-fold higher than that of the previous system, showing significant improvement in the stability of the assay.
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Affiliation(s)
- Yuki Ohmuro-Matsuyama
- Laboratory of Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.,Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan.,Technology Research Laboratory, Shimadzu Corporation, Kyoto, Japan
| | | | - Takuya Shimoda
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Hideki Yamaji
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Hiroshi Ueda
- Laboratory of Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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5
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Davoine C, Fillet M, Pochet L. Capillary electrophoresis as a fragment screening tool to cross-validate hits from chromogenic assay: Application to FXIIa. Talanta 2021; 226:122163. [PMID: 33676706 DOI: 10.1016/j.talanta.2021.122163] [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: 10/11/2020] [Revised: 12/20/2020] [Accepted: 01/25/2021] [Indexed: 10/22/2022]
Abstract
In this study, a partial-filling affinity capillary electrophoresis (pf-ACE) method was developed for the cross-validation of fragment hits revealed by chromogenic factor XIIa (FXIIa) assay. Chromogenic assay produces false positives, mainly due to spectrophotometric interferences and sample purity issues. pf-ACE was selected as counter-screening technology because of its separative character and the fact that the target does not have to be attached or tagged. The effects of protein plug length, applied voltage and composition of the running buffer were examined and optimized. Detection limit in terms of dissociation constant was estimated at 400 μM. The affinity evaluation was performed close to physiological conditions (pH 7.4, ionic strength 0.13 mol L-1) in a poly (ethylene oxide)-coated capillary of 75 μm internal diameter x 33 cm length with an applied voltage of 3 kV. This method uncovered chromogenic assay's false positives due to zinc contamination. Moreover, pf-ACE supported the evaluation of compounds absorbing at 405 nm.
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Affiliation(s)
- C Davoine
- Namur Medicine & Drug Innovation Center (NAMEDIC - NARILIS), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium; Laboratory for the Analysis of Medicines (LAM), Department of Pharmacy, CIRM, University of Liege, Place du 20 Août 7, 4000, Liège, Belgium
| | - M Fillet
- Laboratory for the Analysis of Medicines (LAM), Department of Pharmacy, CIRM, University of Liege, Place du 20 Août 7, 4000, Liège, Belgium
| | - L Pochet
- Namur Medicine & Drug Innovation Center (NAMEDIC - NARILIS), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium.
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Chang M, Wilson CJ, Karunatilleke NC, Moselhy MH, Karttunen M, Choy WY. Exploring the Conformational Landscape of the Neh4 and Neh5 Domains of Nrf2 Using Two Different Force Fields and Circular Dichroism. J Chem Theory Comput 2021; 17:3145-3156. [PMID: 33861593 DOI: 10.1021/acs.jctc.0c01243] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The nuclear factor erythroid 2-related factor 2 (Nrf2)-ARE transcriptional response pathway plays a critical role in protecting the cell from oxidative stresses via the upregulation of cytoprotective genes. Aberrant activation of Nrf2 in cancer cells can confer this cytoprotectivity, thereby reducing the efficacy of both chemotherapeutics and radiotherapies. Key to this antioxidant pathway is the interaction between Nrf2 and CREB binding protein (CBP), mediated by the Neh4 and Neh5 domains of Nrf2. Disruption of this interaction via small-molecule therapeutics could negate the effects of aberrant Nrf2 upregulation. Due to the disordered nature of these domains, there remains no three-dimensional structure of Neh4 or Neh5, making structure-based drug design a challenge. Here, we performed 48 μs of unbiased molecular dynamics (MD) simulations with the Amber99SB*-ILDNP and CHARMM36m force fields and circular dichroism (CD) spectropolarimetry experiments to elucidate the free-state structures of these domains; no previous data regarding their conformational landscapes exists. There are two main findings: First, we find Neh5 to be markedly more disordered than Neh4, which has nine residues in the middle of the domain showing α-helical propensity, thus pointing to Neh4 and Neh5 having different binding mechanisms. Second, the two force fields show strong differences for the glutamic acid-rich Neh5 peptide but are in reasonable agreement for Neh4, which has no glutamic acid. The CHARMM36m force field agrees more closely with the CD results.
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Affiliation(s)
- Megan Chang
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada
| | - Carter J Wilson
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada.,Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Nadun Chanaka Karunatilleke
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada
| | - Mohamed Hesham Moselhy
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada.,Department of Computer Science, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Mikko Karttunen
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada.,Centre for Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada
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7
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Lou C, Ye X, Chen G, Zhu J, Kang J. Screening inhibitors for blocking UHRF1-methylated DNA interaction with capillary electrophoresis. J Chromatogr A 2020; 1636:461790. [PMID: 33340746 DOI: 10.1016/j.chroma.2020.461790] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/27/2020] [Accepted: 12/04/2020] [Indexed: 11/19/2022]
Abstract
Epigenetic inheritance in mammals relies in part on propagation of DNA methylation patterns throughout development. UHRF1 (ubiquitin-like containing PHD and RING finger domains 1) is required for maintenance the methylation pattern. It was reported that UHRF1 is overexpressed in a number of cancer types, and its depletion has been established to inhibit growth and invasion of cancer cells. It has been considered as a new therapeutic target for cancer. In the present work, we described a method for screening inhibitors for blocking the formation of UHRF1-methylated DNA (mDNA) complex by using nonequilibrium capillary electrophoresis of the equilibrium mixture (NECEEM). A recombinant UHRF1 with the SRA domain (residues 408-643), a fluorescently labeled double strand mDNA (12 mer) and a known inhibitor mitoxantrone were employed for proof of concept. The method allows to measure the dissociation constant (Kd) of the UHRF1-mDNA complex as well as the rate kinetic constant for complex formation (kon) and dissociation (koff). A small chemical library composed of 60 natural compounds were used to validate the method. Sample pooling strategy was employed to improve the screening throughput. The merit of the method was confirmed by the discovery of two natural products proanthocyanidins and baicalein as the new inhibitors for blocking the formation of UHRF1-mDNA complex. Our work demonstrated that CE represents a straightforward and robust technique for studying UHRF1-mDNA interaction and screening of the inhibitors.
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Affiliation(s)
- Chunli Lou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; School of physical science and technology, ShanghaiTech University, Haike Road 100, Shanghai, 200120, China; University of Chinese Academy of Sciences
| | - Xiongzhen Ye
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; School of physical science and technology, ShanghaiTech University, Haike Road 100, Shanghai, 200120, China; University of Chinese Academy of Sciences
| | - Ge Chen
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 26 Qiuyue Road, Shanghai 201210, China
| | - Jidong Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 26 Qiuyue Road, Shanghai 201210, China
| | - Jingwu Kang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; School of physical science and technology, ShanghaiTech University, Haike Road 100, Shanghai, 200120, China.
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8
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Gao K, Oerlemans R, Groves MR. Theory and applications of differential scanning fluorimetry in early-stage drug discovery. Biophys Rev 2020; 12:85-104. [PMID: 32006251 PMCID: PMC7040159 DOI: 10.1007/s12551-020-00619-2] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
Differential scanning fluorimetry (DSF) is an accessible, rapid, and economical biophysical technique that has seen many applications over the years, ranging from protein folding state detection to the identification of ligands that bind to the target protein. In this review, we discuss the theory, applications, and limitations of DSF, including the latest applications of DSF by ourselves and other researchers. We show that DSF is a powerful high-throughput tool in early drug discovery efforts. We place DSF in the context of other biophysical methods frequently used in drug discovery and highlight their benefits and downsides. We illustrate the uses of DSF in protein buffer optimization for stability, refolding, and crystallization purposes and provide several examples of each. We also show the use of DSF in a more downstream application, where it is used as an in vivo validation tool of ligand-target interaction in cell assays. Although DSF is a potent tool in buffer optimization and large chemical library screens when it comes to ligand-binding validation and optimization, orthogonal techniques are recommended as DSF is prone to false positives and negatives.
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Affiliation(s)
- Kai Gao
- Structure Biology in Drug Design, Drug Design Group XB20, Departments of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Rick Oerlemans
- Structure Biology in Drug Design, Drug Design Group XB20, Departments of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Matthew R Groves
- Structure Biology in Drug Design, Drug Design Group XB20, Departments of Pharmacy, University of Groningen, Groningen, The Netherlands.
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9
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Takayanagi T, Mine M, Mizuguchi H. Capillary Electrophoresis/Dynamic Frontal Analysis for the Enzyme Assay of 4-Nitrophenyl Phosphate with Alkaline Phosphatase. ANAL SCI 2020; 36:829-834. [PMID: 31956161 DOI: 10.2116/analsci.19p471] [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] [Indexed: 11/23/2022]
Abstract
A substrate of 4-nitrophenyl phosphate was enzymatically hydrolyzed by alkaline phosphatase (ALP) in a capillary tube, while an injected zone of the substrate was electrophoretically migrating in the separation buffer containing the enzyme by capillary electrophoresis (CE). During CE migration of the substrate from the start time of the electrophoresis to the detection time of the substrate, the substrate was continuously hydrolyzed by ALP to form a product of 4-nitrophenolate, and a plateau signal of 4-nitrophenolate was detected as a result of the zero-order kinetic reaction. The height of the plateau signal was directly related to the reaction rate, and it was used for the determination of a Michaelis-Menten constant through Lineweaver-Burk plots. Since the plateau signal is attributed to the dynamic formation of the product by the enzymatic reaction in CE, this analysis method is named as capillary electrophoresis/dynamic frontal analysis (CE/DFA). In CE/DFA, the CE separation is included on detecting the plateau signal, and the hydrolysis product before the sample injection is resolved from the dynamically and continuously formed product. The inhibition of the enzyme with the product is also eliminated in CE/DFA by the CE separation.
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Affiliation(s)
- Toshio Takayanagi
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University
| | - Masanori Mine
- Graduate School of Advanced Technology and Science, Tokushima University
| | - Hitoshi Mizuguchi
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University
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10
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Determining the affinity of anti-mitotic compounds binding to colchicine binding site of tubulin by affinity probe capillary electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1121:66-71. [DOI: 10.1016/j.jchromb.2019.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 05/05/2019] [Accepted: 05/12/2019] [Indexed: 11/19/2022]
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11
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Wang W, Yang J. Advances in screening enzyme inhibitors by capillary electrophoresis. Electrophoresis 2019; 40:2075-2083. [DOI: 10.1002/elps.201900013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/06/2019] [Accepted: 05/19/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Wei‐Feng Wang
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources Key Laboratory for Natural Medicine of Gansu Province Lanzhou Institute of Chemical Physics Chinese Academy of Sciences Lanzhou P. R. China
| | - Jun‐Li Yang
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources Key Laboratory for Natural Medicine of Gansu Province Lanzhou Institute of Chemical Physics Chinese Academy of Sciences Lanzhou P. R. China
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12
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Zhang R, Wu H, He M, Zhang W, Xu W. Mobility Capillary Electrophoresis-Restrained Modeling Method for Protein Structure Analysis in Mixtures. J Phys Chem B 2019; 123:2335-2341. [PMID: 30807169 DOI: 10.1021/acs.jpcb.9b01148] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein stereostructure analysis in mixtures still remains challenging, especially large-scale analysis such as in proteomics. With the capability of measuring the hydrodynamic radius of ions in the liquid phase, mobility capillary electrophoresis (MCE) has been applied to study the structure of peptides. In this study, MCE was extended for protein mixture separation and their corresponding hydrodynamic radius analyses. After ellipsoid approximation, the results obtained by MCE experiments were then used as a restraint in molecular dynamics simulations to predict the most probable structure of each protein. Besides a three-protein mixture, a mixture of disulfide bond reduced insulin was also studied by this MCE-restrained modeling method. The results obtained by this method agree with literature studies, and mass spectrometry experiments were also carried out to confirm our findings.
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Affiliation(s)
- Rongkai Zhang
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , China
| | - Haimei Wu
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , China
| | - Muyi He
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , China
| | - Wenjing Zhang
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , China
| | - Wei Xu
- School of Life Science , Beijing Institute of Technology , Beijing 100081 , China
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13
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Nevídalová H, Michalcová L, Glatz Z. Capillary electrophoresis-based approaches for the study of affinity interactions combined with various sensitive and nontraditional detection techniques. Electrophoresis 2019; 40:625-642. [PMID: 30600537 DOI: 10.1002/elps.201800367] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/20/2018] [Accepted: 12/20/2018] [Indexed: 12/17/2022]
Abstract
Nearly all processes in living organisms are controlled and regulated by the synergy of many biomolecule interactions involving proteins, peptides, nucleic acids, nucleotides, saccharides, and small molecular weight ligands. There is growing interest in understanding them, not only for the purposes of interactomics as an essential part of system biology, but also in their further elucidation in disease pathology, diagnostics, and treatment. The necessity of detailed investigation of these interactions leads to the requirement of laboratory methods characterized by high efficiency and sensitivity. As a result, many instrumental approaches differing in their fundamental principles have been developed, including those based on capillary electrophoresis. Although capillary electrophoresis offers numerous advantages for such studies, it still has one serious limitation, its poor concentration sensitivity with the most commonly used detection method-ultraviolet-visible spectrometry. However, coupling capillary electrophoresis with a more sensitive detector fulfils the above-mentioned requirement. In this review, capillary electrophoresis combined with fluorescence, mass spectrometry, and several nontraditional detection techniques in affinity interaction studies are summarized and discussed, together with the possibility of conducting these measurements in microchip format.
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Affiliation(s)
- Hana Nevídalová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lenka Michalcová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zdeněk Glatz
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
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14
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Frontal analysis capillary electrophoresis: recent advances and future perspectives. Bioanalysis 2018; 10:1143-1159. [DOI: 10.4155/bio-2018-0051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The developments on frontal analysis capillary electrophoresis (FACE) from 2012 to 2017 to study interactions of simple and complex systems are reviewed. Most research papers focused on therapeutic drug-related studies; however, other studies include chemical sensing, drug delivery, inhibitor screening and capillary coating. New ligand–substrate systems such as template-molecularly imprinted polymer systems were reported. Comparison of FACE with other analytical techniques used to investigate binding interaction, and the determination of binding parameters using different isotherm models are also covered. In 2017, eight research papers were reported including new detection by ESI–MS. Future research direction of FACE may include high sensitivity detection and throughput screening of drugs, natural products and biomarkers for clinical diagnosis.
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15
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Li QQ, Li SY, Wang FQ, Chen H, Hu Y, Xia ZN, Yang FQ. Evaluation of the Interactions Between Platelets and Alkaloids by Frontal Analysis Capillary Electrophoresis Using Polyvinyl Alcohol-Coated Capillary. Chromatographia 2018. [DOI: 10.1007/s10337-018-3476-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Zhang X, Hu H. Investigating and characterizing the binding activity of the immobilized calmodulin to calmodulin-dependent protein kinase I binding domain with atomic force microscopy. Chem Cent J 2017; 11:128. [PMID: 29214517 PMCID: PMC5718999 DOI: 10.1186/s13065-017-0360-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/30/2017] [Indexed: 12/03/2022] Open
Abstract
Protein–protein interactions are responsible for many biological processes, and the study of how proteins undergo a conformational change induced by other proteins in the immobilized state can help us to understand a protein’s function and behavior, empower the current knowledge on molecular etiology of disease, as well as the discovery of putative protein targets of therapeutic interest. In this study, a bottom-up approach was utilized to fabricate micro/nanometer-scale protein patterns. One cysteine mutated calmodulin (CaM), as a model protein, was immobilized on thiol-terminated pattern surfaces. Atomic Force Microscopy (AFM) was then employed as a tool to investigate the interactions between CaM and CaM kinase I binding domain, and show that the immobilized CaM retains its activity to interact with its target protein. Our work demonstrate the potential of employing AFM to the research and assay works evolving surface-based protein–protein interactions biosensors, bioelectronics or drug screening.
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Affiliation(s)
- Xiaoning Zhang
- College of Biotechnology, Southwest University, Chongqing, 400715, China.
| | - Hongmei Hu
- Key Laboratory of Mariculture and Enhancement of Zhejiang Province, Marine Fishery Institute of Zhejiang Province, Zhoushan, 316021, China
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Kašička V. Recent developments in capillary and microchip electroseparations of peptides (2015-mid 2017). Electrophoresis 2017; 39:209-234. [PMID: 28836681 DOI: 10.1002/elps.201700295] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 12/17/2022]
Abstract
The review brings a comprehensive overview of recent developments and applications of high performance capillary and microchip electroseparation methods (zone electrophoresis, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography) to analysis, microscale isolation, purification, and physicochemical and biochemical characterization of peptides in the years 2015, 2016, and ca. up to the middle of 2017. Advances in the investigation of electromigration properties of peptides and in the methodology of their analysis (sample preseparation, preconcentration and derivatization, adsorption suppression and EOF control, and detection) are described. New developments in particular CE and CEC methods are presented and several types of their applications to peptide analysis are reported: qualitative and quantitative analysis, determination in complex (bio)matrices, monitoring of chemical and enzymatical reactions and physical changes, amino acid, sequence and chiral analysis, and peptide mapping of proteins. Some micropreparative peptide separations are shown and capabilities of CE and CEC methods to provide important physicochemical characteristics of peptides are demonstrated.
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Affiliation(s)
- Václav Kašička
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague, Czech Republic
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Farcaş E, Bouckaert C, Servais AC, Hanson J, Pochet L, Fillet M. Partial filling affinity capillary electrophoresis as a useful tool for fragment-based drug discovery: A proof of concept on thrombin. Anal Chim Acta 2017; 984:211-222. [DOI: 10.1016/j.aca.2017.06.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 06/13/2017] [Accepted: 06/25/2017] [Indexed: 01/19/2023]
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Escobedo-González R, Vargas-Requena CL, Moyers-Montoya E, Aceves-Hernández JM, Nicolás-Vázquez MI, Miranda-Ruvalcaba R. In silico Study of the Pharmacologic Properties and Cytotoxicity Pathways in Cancer Cells of Various Indolylquinone Analogues of Perezone. Molecules 2017; 22:E1060. [PMID: 28672837 PMCID: PMC6152338 DOI: 10.3390/molecules22071060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 12/23/2022] Open
Abstract
Several indolylquinone analogues of perezone, a natural sesquiterpene quinone, were characterized in this work by theoretical methods. In addition, some physicochemical, toxicological and metabolic properties were predicted using bioinformatics software. The predicted physicochemical properties are in agreement with the solubility and cLogP values, the penetration across the cell membrane, and absorption values, as well as with a possible apoptosis-activated mechanism of cytotoxic action. The toxicological predictions suggest no mutagenic, tumorigenic or reproductive effects of the four target molecules. Complementarily, the results of a performed docking study show high scoring values and hydrogen bonding values in agreement with the cytotoxicity IC50 value ranking, i.e: indolylmenadione > indolylperezone > indolylplumbagine > indolylisoperezone. Consequently, it is possible to suggest an appropriate apoptotic pathway for each compound. Finally, potential metabolic pathways of the molecules were proposed.
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Affiliation(s)
- René Escobedo-González
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli, Estado de México, C.P. 54740, México.
| | - Claudia Lucia Vargas-Requena
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Henry Dunant #4600, Ciudad Juárez 32310, México.
| | - Edgar Moyers-Montoya
- Instituto de Ingeniería y tecnología, Universidad Autónoma de Ciudad Juárez, Ave. Del Charro 450 Norte, Ciudad Juárez 32310, México.
| | - Juan Manuel Aceves-Hernández
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli, Estado de México, C.P. 54740, México.
| | - María Inés Nicolás-Vázquez
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli, Estado de México, C.P. 54740, México.
| | - René Miranda-Ruvalcaba
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli, Estado de México, C.P. 54740, México.
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Ouimet CM, D’Amico CI, Kennedy RT. Advances in capillary electrophoresis and the implications for drug discovery. Expert Opin Drug Discov 2017; 12:213-224. [PMID: 27911223 PMCID: PMC5521262 DOI: 10.1080/17460441.2017.1268121] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Many screening platforms are prone to assay interferences that can be avoided by directly measuring the target or enzymatic product. Capillary electrophoresis (CE) and microchip electrophoresis (MCE) have been applied in a variety of formats to drug discovery. CE provides direct detection of the product allowing for the identification of some forms of assay interference. The high efficiency, rapid separations, and low volume requirements make CE amenable to drug discovery. Areas covered: This article describes advances in capillary electrophoresis throughput, sample introduction, and target assays as they pertain to drug discovery and screening. Instrumental advances discussed include integrated droplet microfluidics platforms and multiplexed arrays. Applications of CE to assays of diverse drug discovery targets, including enzymes and affinity interactions are also described. Expert opinion: Current screening with CE does not fully take advantage of the throughputs or low sample volumes possible with CE and is most suitable as a secondary screening method or for screens that are inaccessible with more common platforms. With further development, droplet microfluidics coupled to MCE could take advantage of the low sample requirements by performing assays on the nanoliter scale at high throughput.
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Affiliation(s)
- Claire M. Ouimet
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI, 48109, United States
| | - Cara I. D’Amico
- Department of Pharmacology, University of Michigan, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109, United States
| | - Robert T. Kennedy
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI, 48109, United States
- Department of Pharmacology, University of Michigan, 1150 W. Medical Center Dr., Ann Arbor, MI, 48109, United States
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