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Drozd M, Kobylska E, Żmieńko M, Chudy M. Sensitive and label-free SPR biosensing platforms for high-throughput screening of plasma membrane receptors interactions with insulin-like targets of hypoglycaemic activity. Talanta 2024; 274:125914. [PMID: 38537356 DOI: 10.1016/j.talanta.2024.125914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 05/04/2024]
Abstract
Progress in medical sciences aims for tailored therapy of civilization diseases like diabetes. Preclinical screening of new medicines superior to insulin should include the verification of their affinity to the membrane receptors naturally stimulated by this hormone: insulin receptor isoforms A and B and insulin-like growth factor receptor. Considering that the affinity constants obtained using different experimental conditions are incomparable, it is essential to develop a robust and reliable method to analyze these interactions. The versatile SPR platform developed in this study enables the evaluation of the bioactivity of hypoglycaemic molecules. Thanks to the comprehensive characterization of miscellaneous aspects of the analytical platform, including the design of the SPR biosensor receptor layer, ensuring interaction specificity, as well as the quality control of the standards used (human insulin, HI; long-acting insulin analog: glargine, Gla), the feasibility of the method of equilibrium and kinetic constants determination for insulin-like targets was confirmed. SPR assays constructed in the direct format using IR-A, IR-B, and IGF1-R receptor proteins show high sensitivities and low detection limits towards insulin and glargine detection in the range of 18.3-53.3 nM with no signs of mass transport limitations. The improved analytical performance and stability of SPR biosensors favor the acquisition of good-quality kinetic data, while preservation of receptors activity after binding to long-chain carboxymethyldextran, combined with spontaneous regeneration, results in stability and long shelf life of the biosensor, which makes it useful for label-free insulin analogs biosensing and thus extensive screening in diabetic drugs discovery.
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Affiliation(s)
- Marcin Drozd
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664, Warsaw, Poland; Centre for Advanced Materials and Technologies CEZAMAT, Poleczki 19, 02-822, Warsaw, Poland
| | - Ewa Kobylska
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664, Warsaw, Poland; Łukasiewicz - Industrial Chemistry Institute, Rydygiera 8, 01-793, Warsaw, Poland
| | - Małgorzata Żmieńko
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664, Warsaw, Poland
| | - Michał Chudy
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664, Warsaw, Poland.
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Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. Mol Biol Cell 2024; 35:mr1. [PMID: 38117593 PMCID: PMC10916857 DOI: 10.1091/mbc.e23-07-0289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 12/22/2023] Open
Abstract
The assembly of biomolecular condensate in eukaryotic cells and the accumulation of amyloid deposits in neurons are processes involving the nucleation and growth (NAG) of new protein phases. To therapeutically target protein phase separation, drug candidates are tested in in vitro assays that monitor the increase in the mass or size of the new phase. Limited mechanistic insight is, however, provided if empirical or untestable kinetic models are fitted to these progress curves. Here we present the web server NAGPKin that quantifies NAG rates using mass-based or size-based progress curves as the input data. A report is generated containing the fitted NAG parameters and elucidating the phase separation mechanisms at play. The NAG parameters can be used to predict particle size distributions of, for example, protein droplets formed by liquid-liquid phase separation (LLPS) or amyloid fibrils formed by protein aggregation. Because minimal intervention is required from the user, NAGPKin is a good platform for standardized reporting of LLPS and protein self-assembly data. NAGPKin is useful for drug discovery as well as for fundamental studies on protein phase separation. NAGPKin is freely available (no login required) at https://nagpkin.i3s.up.pt.
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Affiliation(s)
- Zsuzsa Sárkány
- Biomolecular Structure and Function Group, IBMC – Instituto de Biologia Molecular e Celular, Porto 4200-135, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde da Universidade do Porto, Porto 4200-135, Portugal
| | - Francisco Figueiredo
- Biomolecular Structure and Function Group, IBMC – Instituto de Biologia Molecular e Celular, Porto 4200-135, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde da Universidade do Porto, Porto 4200-135, Portugal
| | - Sandra Macedo-Ribeiro
- Biomolecular Structure and Function Group, IBMC – Instituto de Biologia Molecular e Celular, Porto 4200-135, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde da Universidade do Porto, Porto 4200-135, Portugal
| | - Pedro M. Martins
- Biomolecular Structure and Function Group, IBMC – Instituto de Biologia Molecular e Celular, Porto 4200-135, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde da Universidade do Porto, Porto 4200-135, Portugal
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3
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Panda C, Kumar S, Gupta S, Pandey LM. Structural, kinetic, and thermodynamic aspects of insulin aggregation. Phys Chem Chem Phys 2023; 25:24195-24213. [PMID: 37674360 DOI: 10.1039/d3cp03103a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Given the significance of protein aggregation in proteinopathies and the development of therapeutic protein pharmaceuticals, revamped interest in assessing and modelling the aggregation kinetics has been observed. Quantitative analysis of aggregation includes data of gradual monomeric depletion followed by the formation of subvisible particles. Kinetic and thermodynamic studies are essential to gain key insights into the aggregation process. Despite being the medical marvel in the world of diabetes, insulin suffers from the challenge of aggregation. Physicochemical stresses are experienced by insulin during industrial formulation, storage, delivery, and transport, considerably impacting product quality, efficacy, and effectiveness. The present review briefly describes the pathways, mathematical kinetic models, and thermodynamics of protein misfolding and aggregation. With a specific focus on insulin, further discussions include the structural heterogeneity and modifications of the intermediates incurred during insulin fibrillation. Finally, different model equations to fit the kinetic data of insulin fibrillation are discussed. We believe that this review will shed light on the conditions that induce structural changes in insulin during the lag phase of fibrillation and will motivate scientists to devise strategies to block the initialization of the aggregation cascade. Subsequent abrogation of insulin fibrillation during bioprocessing will ensure stable and globally accessible insulin for efficient management of diabetes.
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Affiliation(s)
- Chinmaya Panda
- Bio-interface & Environmental Engineering Lab Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, 781039, India.
| | - Sachin Kumar
- Viral Immunology Lab Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, 781039, India
| | - Sharad Gupta
- Neurodegeneration and Peptide Engineering Research Lab Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Gujarat, 382355, India
| | - Lalit M Pandey
- Bio-interface & Environmental Engineering Lab Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, 781039, India.
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Figueiredo F, Sárkány Z, Silva A, Vilasboas-Campos D, Maciel P, Teixeira-Castro A, Martins PM, Macedo-Ribeiro S. Drug repurposing of dopaminergic drugs to inhibit ataxin-3 aggregation. Biomed Pharmacother 2023; 165:115258. [PMID: 37549460 DOI: 10.1016/j.biopha.2023.115258] [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: 05/24/2023] [Revised: 07/24/2023] [Accepted: 07/29/2023] [Indexed: 08/09/2023] Open
Abstract
The accumulation of mutant ataxin-3 (Atx3) in neuronal nuclear inclusions is a pathological hallmark of Machado-Joseph disease (MJD), also known as Spinocerebellar Ataxia Type 3. Decreasing the protein aggregation burden is a possible disease-modifying strategy to tackle MJD and other neurodegenerative disorders for which only symptomatic treatments are currently available. We performed a drug repurposing screening to identify inhibitors of Atx3 aggregation with known toxicological and pharmacokinetic profiles. Interestingly, dopamine hydrochloride and other catecholamines are among the most potent inhibitors of Atx3 aggregation in vitro. Our results indicate that low micromolar concentrations of dopamine markedly delay the formation of mature amyloid fibrils of mutant Atx3 through the inhibition of the earlier oligomerization steps. Although dopamine itself does not cross the blood-brain barrier, dopamine levels in the brain can be increased by low doses of dopamine precursors and dopamine agonists commonly used to treat Parkinsonian symptoms. In agreement, treatment with levodopa ameliorated motor symptoms in a C. elegans model of MJD. These findings suggest a possible application of dopaminergic drugs to halt or reduce Atx3 accumulation in the brains of MJD patients.
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Affiliation(s)
- Francisco Figueiredo
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Zsuzsa Sárkány
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Alexandra Silva
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Daniela Vilasboas-Campos
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Patrícia Maciel
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Andreia Teixeira-Castro
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Pedro M Martins
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal.
| | - Sandra Macedo-Ribeiro
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal.
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5
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Sárkány Z, Rocha F, Bratek‐Skicki A, Tompa P, Macedo‐Ribeiro S, Martins PM. Quantification of Surface Tension Effects and Nucleation-and-Growth Rates during Self-Assembly of Biological Condensates. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301501. [PMID: 37279376 PMCID: PMC10427409 DOI: 10.1002/advs.202301501] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/12/2023] [Indexed: 06/08/2023]
Abstract
Liquid-solid and liquid-liquid phase separation (PS) drives the formation of functional and disease-associated biological assemblies. Principles of phase equilibrium are here employed to derive a general kinetic solution that predicts the evolution of the mass and size of biological assemblies. Thermodynamically, protein PS is determined by two measurable concentration limits: the saturation concentration and the critical solubility. Due to surface tension effects, the critical solubility can be higher than the saturation concentration for small, curved nuclei. Kinetically, PS is characterized by the primary nucleation rate constant and a combined rate constant accounting for growth and secondary nucleation. It is demonstrated that the formation of a limited number of large condensates is possible without active mechanisms of size control and in the absence of coalescence phenomena. The exact analytical solution can be used to interrogate how the elementary steps of PS are affected by candidate drugs.
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Affiliation(s)
- Zsuzsa Sárkány
- IBMC − Instituto de Biologia Molecular e CelularUniversidade do PortoPorto4150–180Portugal
- i3S − Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPorto4150–180Portugal
| | - Fernando Rocha
- LEPABE − Laboratory for Process Engineering Environment Biotechnology and EnergyFaculdade de Engenharia da Universidade do PortoPorto4200‐465Portugal
| | - Anna Bratek‐Skicki
- Jerzy Haber Institute of Catalysis and Surface ChemistryPolish Academy of SciencesNiezapominajek 8KrakowPL30239Poland
- VIB‐VUB Center for Structural BiologyVlaams Instituut voor BiotechnologyBrussels1050 IxellesBelgium
- Structural Biology Brussels (SBB)Bioengineering Sciences DepartmentVrije Universiteit Brussel (VUB)BrusselsB‐1050Belgium
| | - Peter Tompa
- VIB‐VUB Center for Structural BiologyVlaams Instituut voor BiotechnologyBrussels1050 IxellesBelgium
- Structural Biology Brussels (SBB)Bioengineering Sciences DepartmentVrije Universiteit Brussel (VUB)BrusselsB‐1050Belgium
- Institute of EnzymologyResearch Centre for Natural SciencesBudapest1117Hungary
| | - Sandra Macedo‐Ribeiro
- IBMC − Instituto de Biologia Molecular e CelularUniversidade do PortoPorto4150–180Portugal
- i3S − Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPorto4150–180Portugal
| | - Pedro M. Martins
- IBMC − Instituto de Biologia Molecular e CelularUniversidade do PortoPorto4150–180Portugal
- i3S − Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPorto4150–180Portugal
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Martins PM, Navarro S, Silva A, Pinto MF, Sárkány Z, Figueiredo F, Pereira PJB, Pinheiro F, Bednarikova Z, Burdukiewicz M, Galzitskaya OV, Gazova Z, Gomes CM, Pastore A, Serpell LC, Skrabana R, Smirnovas V, Ziaunys M, Otzen DE, Ventura S, Macedo-Ribeiro S. MIRRAGGE - Minimum Information Required for Reproducible AGGregation Experiments. Front Mol Neurosci 2020; 13:582488. [PMID: 33328883 PMCID: PMC7729192 DOI: 10.3389/fnmol.2020.582488] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
Reports on phase separation and amyloid formation for multiple proteins and aggregation-prone peptides are recurrently used to explore the molecular mechanisms associated with several human diseases. The information conveyed by these reports can be used directly in translational investigation, e.g., for the design of better drug screening strategies, or be compiled in databases for benchmarking novel aggregation-predicting algorithms. Given that minute protocol variations determine different outcomes of protein aggregation assays, there is a strong urge for standardized descriptions of the different types of aggregates and the detailed methods used in their production. In an attempt to address this need, we assembled the Minimum Information Required for Reproducible Aggregation Experiments (MIRRAGGE) guidelines, considering first-principles and the established literature on protein self-assembly and aggregation. This consensus information aims to cover the major and subtle determinants of experimental reproducibility while avoiding excessive technical details that are of limited practical interest for non-specialized users. The MIRRAGGE table (template available in Supplementary Information) is useful as a guide for the design of new studies and as a checklist during submission of experimental reports for publication. Full disclosure of relevant information also enables other researchers to reproduce results correctly and facilitates systematic data deposition into curated databases.
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Affiliation(s)
- Pedro M Martins
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Susanna Navarro
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Alexandra Silva
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Maria F Pinto
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Zsuzsa Sárkány
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Francisco Figueiredo
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal.,International Iberian Nanotechnology Laboratory - Department of Atomic Structure - Composition of Materials, Braga, Portugal
| | - Pedro José Barbosa Pereira
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Francisca Pinheiro
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Zuzana Bednarikova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Kosice, Slovakia
| | - Michał Burdukiewicz
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Zuzana Gazova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Kosice, Slovakia
| | - Cláudio M Gomes
- Biosystems and Integrative Sciences Institute and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Annalisa Pastore
- UK-DRI Centre at King's College London, the Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
| | - Louise C Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Rostislav Skrabana
- Department of Neuroimmunology, Axon Neuroscience R&D Services SE, Bratislava, Slovakia.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Sandra Macedo-Ribeiro
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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Sárkány Z, Rocha F, Damas AM, Macedo-Ribeiro S, Martins PM. Chemical Kinetic Strategies for High-Throughput Screening of Protein Aggregation Modulators. Chem Asian J 2019; 14:500-508. [DOI: 10.1002/asia.201801703] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/11/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Zsuzsa Sárkány
- LEPABE-Departamento de Engenharia Química; Faculdade de Engenharia da Universidade do Porto; Rua Dr. Roberto Frias 4200-465 Porto Portugal
| | - Fernando Rocha
- LEPABE-Departamento de Engenharia Química; Faculdade de Engenharia da Universidade do Porto; Rua Dr. Roberto Frias 4200-465 Porto Portugal
| | - Ana M. Damas
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar; Universidade do Porto; 4050-313 Porto Portugal
| | - Sandra Macedo-Ribeiro
- IBMC-Instituto de Biologia Molecular e Celular; Universidade do Porto; 4200-135 Porto Portugal
- Instituto de Investigação e Inovação em Saúde; Universidade do Porto; 4200-135 Porto Portugal
| | - Pedro M. Martins
- IBMC-Instituto de Biologia Molecular e Celular; Universidade do Porto; 4200-135 Porto Portugal
- Instituto de Investigação e Inovação em Saúde; Universidade do Porto; 4200-135 Porto Portugal
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar; Universidade do Porto; 4050-313 Porto Portugal
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