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Contardi C, Rubes D, Serra M, Dorati R, Dattilo M, Mavliutova L, Patrini M, Guglielmann R, Sellergren B, De Lorenzi E. Affinity Capillary Electrophoresis as a Tool To Characterize Molecularly Imprinted Nanogels in Solution. Anal Chem 2024. [PMID: 38284411 DOI: 10.1021/acs.analchem.3c04912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
In this work, an innovative and accurate affinity capillary electrophoresis (ACE) method was set up to monitor the complexation of aqueous MIP nanogels (NGs) with model cancer-related antigens. Using α2,6'- and α2,3'-sialyllactose as oversimplified cancer biomarker-mimicking templates, NGs were synthesized and characterized in terms of size, polydispersity, and overall charge. A stability study was also carried out in order to select the best storage conditions and to ensure product quality. After optimization of capillary electrophoresis conditions, injection of MIP NGs resulted in a single, sharp, and efficient peak. The mobility shift approach was applied to quantitatively estimate binding affinity, in this case resulting in an association constant of K ≈ 106 M-1. The optimized polymers further displayed a pronounced discrimination between the two sialylated sugars. The newly developed ACE protocol has the potential to become a very effective method for nonconstrained affinity screening of NG in solution, especially during the NG development phase and/or for a final accurate quantitation of the observed binding.
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Affiliation(s)
- Cecilia Contardi
- Department of Drug Sciences, University of Pavia, 27100 Pavia, PV, Italy
| | - Davide Rubes
- Department of Drug Sciences, University of Pavia, 27100 Pavia, PV, Italy
| | - Massimo Serra
- Department of Drug Sciences, University of Pavia, 27100 Pavia, PV, Italy
| | - Rossella Dorati
- Department of Drug Sciences, University of Pavia, 27100 Pavia, PV, Italy
| | - Marco Dattilo
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, CS, Italy
| | - Liliia Mavliutova
- Biofilms Research Center for Biointerfaces, Department of Biomedical Sciences, Faculty of Health and Society, Malmö University, 21432 Malmö, Sweden
| | | | | | - Börje Sellergren
- Biofilms Research Center for Biointerfaces, Department of Biomedical Sciences, Faculty of Health and Society, Malmö University, 21432 Malmö, Sweden
| | - Ersilia De Lorenzi
- Department of Drug Sciences, University of Pavia, 27100 Pavia, PV, Italy
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Stutz H. Advances and applications of electromigration methods in the analysis of therapeutic and diagnostic recombinant proteins – A Review. J Pharm Biomed Anal 2022; 222:115089. [DOI: 10.1016/j.jpba.2022.115089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/29/2022]
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Mancuso F, Angeli A, De Luca V, Bucolo F, De Luca L, Capasso C, Supuran CT, Gitto R. Synthesis and biological evaluation of sulfonamide-based compounds as inhibitors of carbonic anhydrase from Vibrio cholerae. Arch Pharm (Weinheim) 2022; 355:e2200070. [PMID: 35739618 DOI: 10.1002/ardp.202200070] [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: 02/10/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/06/2022]
Abstract
This study reports our continued efforts to identify inhibitors capable of targeting carbonic anhydrases (CAs) expressed in bacteria. Based on previously identified chemotypes, we designed and synthesized new analogs that were screened toward the α, β, and γ classes encoded in Vibrio cholerae (Vch). The Ki values measured in the stopped-flow hydrase assay revealed that very simple structural modifications might induce a relevant impact on the inhibitory effects as well as the selectivity profile over ubiquitous human isozymes (hCA I/II). Unfortunately, the best active VchCA inhibitors demonstrated a dramatic loss of hCA II selectivity when compared to previously reported compounds. Among the new series of sulfonamides, several molecules proved to be about sevenfold more potent against VchCAγ than the reference compound acetazolamide, thus furnishing new insights for further development of inhibitors targeting CAs expressed in bacteria.
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Affiliation(s)
| | - Andrea Angeli
- NEUROFARBA Department, University of Florence, Florence, Italy
| | - Viviana De Luca
- Institute of Biosciences and Bioresources, National Research Council (CNR), Naples, Italy
| | - Federica Bucolo
- CHIBIOFARAM Department, University of Messina, Messina, Italy
| | - Laura De Luca
- CHIBIOFARAM Department, University of Messina, Messina, Italy
| | - Clemente Capasso
- Institute of Biosciences and Bioresources, National Research Council (CNR), Naples, Italy
| | | | - Rosaria Gitto
- CHIBIOFARAM Department, University of Messina, Messina, Italy
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Bitan G. Disease-modifying therapy for proteinopathies: Can the exception become the rule? PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 168:277-287. [PMID: 31699321 DOI: 10.1016/bs.pmbts.2019.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Disease-modifying therapies for proteinopathies are urgently needed yet clinical trials for the major neurodegenerative diseases, Alzheimer's and Parkinson's, have been failing at an alarming rate leaving patients and caregivers scrambling for any sign of hope. At the same time, for one family of proteinopathies, the rare TTR amyloidoses, disease-modifying therapy has existed for almost 3 decades and two new types of disease-modifying therapy have become available more recently. In this chapter, I discuss those therapies, examine to what extent they can be generalized for other diseases, and consider what we may learn from their relative success.
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Affiliation(s)
- Gal Bitan
- Department of Neurology, David Geffen School of Medicine, Brain Research Institute, and Molecular Biology Institute, University of California, Los Angeles, CA, United States.
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Liu T, Marcinko TM, Kiefer PA, Vachet RW. Using Covalent Labeling and Mass Spectrometry To Study Protein Binding Sites of Amyloid Inhibiting Molecules. Anal Chem 2017; 89:11583-11591. [PMID: 29028328 PMCID: PMC5677544 DOI: 10.1021/acs.analchem.7b02915] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Amyloid aggregates are associated with several debilitating diseases, and there are numerous efforts to develop small molecule treatments against these diseases. One challenge associated with these efforts is determining protein binding site information for potential therapeutics because amyloid-forming proteins rapidly form oligomers and aggregates, making traditional protein structural analysis techniques challenging. Using β-2-microglobulin (β2m) as a model amyloid-forming protein along with two recently identified small molecule amyloid inhibitors (i.e., rifamycin SV and doxycycline), we demonstrate that covalent labeling and mass spectrometry (MS) can be used to map small-molecule binding sites for a rapidly aggregating protein. Specifically, three different covalent labeling reagents, namely diethylpyrocarbonate, 2,3-butanedione, and the reagent pair EDC/GEE, are used together to pinpoint the binding sites of rifamycin SV, doxycycline, and another molecule, suramin, which binds but does not inhibit Cu(II)-induced β2m amyloid formation. The labeling results reveal binding sites that are consistent with the known effects of these molecules on β2m amyloid formation and are in general agreement with molecular docking results. We expect that this combined covalent labeling approach will be applicable to other protein/small molecule systems that are difficult to study by traditional means.
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Affiliation(s)
- Tianying Liu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Tyler M. Marcinko
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Patrick A. Kiefer
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Richard W. Vachet
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
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Marcinko TM, Dong J, LeBlanc R, Daborowski KV, Vachet RW. Small molecule-mediated inhibition of β-2-microglobulin-based amyloid fibril formation. J Biol Chem 2017; 292:10630-10638. [PMID: 28468825 DOI: 10.1074/jbc.m116.774083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 05/02/2017] [Indexed: 12/26/2022] Open
Abstract
In dialysis patients, β-2 microglobulin (β2m) can aggregate and eventually form amyloid fibrils in a condition known as dialysis-related amyloidosis, which deleteriously affects joint and bone function. Recently, several small molecules have been identified as potential inhibitors of β2m amyloid formation in vitro Here we investigated whether these molecules are more broadly applicable inhibitors of β2m amyloid formation by studying their effect on Cu(II)-induced β2m amyloid formation. Using a variety of biophysical techniques, we also examined their inhibitory mechanisms. We found that two molecules, doxycycline and rifamycin SV, can inhibit β2m amyloid formation in vitro by causing the formation of amorphous, redissolvable aggregates. Rather than interfering with β2m amyloid formation at the monomer stage, we found that doxycycline and rifamycin SV exert their effect by binding to oligomeric species both in solution and in gas phase. Their binding results in a diversion of the expected Cu(II)-induced progression of oligomers toward a heterogeneous collection of oligomers, including trimers and pentamers, that ultimately matures into amorphous aggregates. Using ion mobility mass spectrometry, we show that both inhibitors promote the compaction of the initially formed β2m dimer, which causes the formation of other off-pathway and amyloid-incompetent oligomers that are isomeric with amyloid-competent oligomers in some cases. Overall, our results suggest that doxycycline and rifamycin are general inhibitors of Cu(II)-induced β2m amyloid formation. Interestingly, the putative mechanism of their activity is different depending on how amyloid formation is initiated with β2m, which underscores the complexity of how these structures assemble in vitro.
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Affiliation(s)
- Tyler M Marcinko
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Jia Dong
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Raquel LeBlanc
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Kate V Daborowski
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Richard W Vachet
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
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Bertoletti L, Schappler J, Colombo R, Rudaz S, Haselberg R, Domínguez-Vega E, Raimondi S, Somsen GW, De Lorenzi E. Evaluation of capillary electrophoresis-mass spectrometry for the analysis of the conformational heterogeneity of intact proteins using beta 2-microglobulin as model compound. Anal Chim Acta 2016; 945:102-109. [PMID: 27968711 DOI: 10.1016/j.aca.2016.10.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 10/07/2016] [Accepted: 10/09/2016] [Indexed: 10/20/2022]
Abstract
In this work we explored the feasibility of different CE-ESI-MS set-ups for the analysis of conformational states of an intact protein. By using the same background electrolyte at quasi physiological conditions (50 mM ammonium bicarbonate, pH 7.4) a sequential optimization was carried out, initially by evaluating a sheath-liquid interface with both a single quadrupole (SQ) and a time-of-flight (TOF) mass spectrometer; then a sheathless interface coupled with high-resolution QTOF MS was considered. Beta2-microglobulin has been taken as a model, as it is an amyloidogenic protein and its conformational changes are strictly connected to the onset of a disease. The separation of two conformers at dynamic equilibrium is achieved all the way down to the MS detection. Notably, the equilibrium ratio of the protein conformers is maintained in the electrospray source after CE separation. Strengths and weaknesses of each optimized set-up are emphasized and their feasibility in unfolding studies is evaluated. In particular, ESI-TOF MS can assign protein forms that differ by 1 Da only and sheathless interfacing is best suited to preserve protein structure integrity. This demonstrates the CE-ESI-MS performance in terms of separation, detection and characterization of conformational species that co-populate a protein solution.
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Affiliation(s)
- Laura Bertoletti
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy.
| | - Julie Schappler
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, CMU, Rue Michel Servet 1, 1211, Geneva 4, Switzerland.
| | - Raffaella Colombo
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy.
| | - Serge Rudaz
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, CMU, Rue Michel Servet 1, 1211, Geneva 4, Switzerland.
| | - Rob Haselberg
- Division of BioAnalytical Chemistry, AIMMS Research Group BioMolecular Analysis, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
| | - Elena Domínguez-Vega
- Division of BioAnalytical Chemistry, AIMMS Research Group BioMolecular Analysis, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
| | - Sara Raimondi
- Department of Molecular Medicine, Institute of Biochemistry, University of Pavia, Viale Taramelli 3b, 27100, Pavia, Italy.
| | - Govert W Somsen
- Division of BioAnalytical Chemistry, AIMMS Research Group BioMolecular Analysis, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
| | - Ersilia De Lorenzi
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy.
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Bertoletti L, Bisceglia F, Colombo R, Giorgetti S, Raimondi S, Mangione PP, De Lorenzi E. Capillary electrophoresis analysis of different variants of the amyloidogenic protein β2 -microglobulin as a simple tool for misfolding and stability studies. Electrophoresis 2015; 36:2465-72. [PMID: 26084573 DOI: 10.1002/elps.201500148] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/13/2015] [Accepted: 05/21/2015] [Indexed: 11/07/2022]
Abstract
Free solution capillary electrophoresis with UV detection is here used to retrieve information on the conformational changes of wild-type β2 -microglobulin and a series of naturally and artificially created variants known to have different stability and amyloidogenic potential. Under nondenaturing conditions, the resolution of at least two folding conformers at equilibrium is obtained and a third species is detected for the less stable isoforms. Partial denaturation by using chaotropic agents such as acetonitrile or trifluoroethanol reveals that the separated peaks are at equilibrium, as the presence of less structured species is either enhanced or induced at the expenses of the native form. Reproducible CE data allow to obtain an interesting semiquantitative correlation between the peak areas observed and the protein stability. Thermal unfolding over the range 25-42°C is induced inside the capillary for the two pathogenic proteins (wtβ2 -microglobulin and D76N variant): the large differences observed upon small temperature variation draw attention on the robustness of analytical methods when dealing with proteins prone to misfolding and aggregation.
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Affiliation(s)
| | | | | | - Sofia Giorgetti
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Sara Raimondi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - P Patrizia Mangione
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.,Centre for Amyloidosis and Acute Phase Proteins, University College London, London, UK
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Bertoletti L, Regazzoni L, Aldini G, Colombo R, Abballe F, Caccialanza G, De Lorenzi E. Separation and characterisation of beta2-microglobulin folding conformers by ion-exchange liquid chromatography and ion-exchange liquid chromatography–mass spectrometry. Anal Chim Acta 2013; 771:108-14. [DOI: 10.1016/j.aca.2013.01.058] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 01/29/2013] [Accepted: 01/31/2013] [Indexed: 01/07/2023]
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Abstract
Dialysis-related amyloidosis (DRA) is a clinical syndrome of pain, loss of function and other symptoms due to the deposition of amyloid consisting of β(2)-microglobulin (β(2)m) in the musculoskeletal system. The condition is seen in patients who suffer from chronic kidney disease and are treated with hemodialysis for a long time. Even though β(2)m easily can be manipulated to form amyloid in laboratory experiments under non-physiological conditions the precise mechanisms involved in the formation of β(2)m-amyloid in patients with DRA have been difficult to unravel. The current knowledge which is reviewed here indicates that conformational fluctuations centered around the D-strand, the DE-loop, and around the cis-configured Pro32 peptide bond are involved in β(2)m amyloidosis. Also required are highly increased concentrations of circulating β(2)m and possibly various post-translational modifications mediated by the pro-inflammatory environment in uremic blood, together with the influence of divalent metal ions (specifically Cu(2 +)), uremic toxins, and dialysis-enhanced redox-processes. It seems plausible that domain-swapped β(2)m dimers act as building blocks of β-spine cross-β -sheet fibrils consisting of otherwise globular, roughly natively folded protein. An activated complement system and cellular activation perpetuate these reactions which due to the affinity of β(2)m-amyloid for the collagen of synovial surfaces result in the DRA syndrome.
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Affiliation(s)
- Dorthe B Corlin
- Department of Clinical Biochemistry and Immunology, Division of Microbiology and Diagnostics, Statens Serum Institut, Bldg. 85/240, Artillerivej 5, 2300, Copenhagen S, Denmark,
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Abstract
In this chapter we provided the overall background to the subject of protein aggregation and fibrillogenesis in amyloidogenesis, with introduction and brief discussion of the various topics that are included with the coming chapters. The division of the book into basic science and clinical science sections enables correlation of the topics to be made. The many proteins and peptides that have currently been found to undergo fibrillogenesis are tabulated. A broad technical survey is made, to indicate the vast array of techniques currently available to study aspects of protein oligomerization, aggregation and fibrillogenesis. These are split into three groups and tabulated, as the microscopical techniques, the analytical and biophysical methods, and the biochemical and cellular techniques. A few techniques are discussed, but in most cases only a link to relevant recent literature is provided.
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Chen Q, Li N, Zhang W, Chen J, Chen Z. Simultaneous determination of vinblastine and its monomeric precursors vindoline and catharanthine in Catharanthus roseus by capillary electrophoresis-mass spectrometry. J Sep Sci 2011; 34:2885-92. [PMID: 21735550 DOI: 10.1002/jssc.201100359] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/02/2011] [Accepted: 06/02/2011] [Indexed: 11/09/2022]
Abstract
Catharanthus roseus is an important dicotyledonous medicinal plant that contains various anticancer components, such as vinblastine (VLB) and its monomeric precursors (vindoline and catharanthine). A capillary electrophoresis-mass spectrometry (CE-MS) approach for the simultaneous determination of three components was developed in this work. Baseline separation for three components was achieved by using a running buffer consisting of 20 mM ammonium acetate and 1.5% acetic acid in <20 min. Quantification of three components was assigned in positive-ion mode at a protonated molecular ion [M+H](+). The CE-MS method was validated for linearity, sensitivity, accuracy and precision, and then used to determine the content of the above components. The detection limits of VLB, catharanthine and vindoline are 0.8, 0.1 and 0.1 μg/mL, respectively. The precision was not more than 4.54% and the mean recovery of the analytes was 95.04-97.04%. The CE-MS method was successfully applied to determine VLB and its monomeric precursors in real sample C. roseus.
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Affiliation(s)
- Qinhua Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan, PR China
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