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Libera V, Fasolato C, Ripanti F, Catalini S, Bertini L, Petrillo C, Schirò G, D'Amico F, Rossi B, Paciaroni A, Comez L. Molecular mechanisms behind BRACO19 and human telomeric G-quadruplex interaction. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 322:124684. [PMID: 38981290 DOI: 10.1016/j.saa.2024.124684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/12/2024] [Accepted: 06/18/2024] [Indexed: 07/11/2024]
Abstract
Human telomeres (HTs) can form DNA G-quadruplex (G4), an attractive target for anticancer and antiviral drugs. HT-G4s exhibit inherent structural polymorphism, posing challenges for understanding their specific recognition by ligands. Here, we aim to explore the impact of different topologies within a small segment of the HT (Tel22) on its interaction with BRACO19, a rationally designed G4 ligand with high quadruplex affinity, already employed in in-vivo treatments. Our multi-technique approach is based on the combined use of a set of contactless spectroscopic tools. Circular dichroism and UV resonance Raman spectroscopy probe ligand-induced conformational changes in the G4 sequence, while UV-visible absorption, coupled with steady-state fluorescence spectroscopy, provides further insights into the electronic features of the complex, exploiting the photoresponsive properties of BRACO19. Overall, we find that modifying the topology of the unbound Tel22 through cations (K+ or Na+), serves as a critical determinant for ligand interactions and binding modes, thus influencing the HT-G4's assembly capabilities. Furthermore, we show how fluorescence serves as a valuable probe for recognizing cation-driven multimeric structures, which may be present in living organisms, giving rise to pathological forms.
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Affiliation(s)
- Valeria Libera
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123, Perugia, Italy.
| | - Claudia Fasolato
- Institute for Complex System, National Research Council (ISC-CNR), Piazzale Aldo Moro, 5, 00185, Roma, Italy
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123, Perugia, Italy
| | - Sara Catalini
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123, Perugia, Italy; European Laboratory for Non-Linear Spectroscopy (LENS), via Nello Carrara 1, 50019, Sesto Fiorentino (FI), Italy; National Research Council-National Institute of Optics (CNR-INO), Largo Fermi 6, 50125, Florence, Italy
| | - Luca Bertini
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123, Perugia, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123, Perugia, Italy
| | - Giorgio Schirò
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Francesco D'Amico
- Elettra - Sincrotrone Trieste S.C.p.A, s.s. 14 km 163, 500 in Area Science Park, 34149, Trieste, Italy
| | - Barbara Rossi
- Elettra - Sincrotrone Trieste S.C.p.A, s.s. 14 km 163, 500 in Area Science Park, 34149, Trieste, Italy
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123, Perugia, Italy
| | - Lucia Comez
- CNR-IOM - Istituto Officina dei Materiali, Via Alessandro Pascoli, 06123, Perugia, Italy.
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Ye H, Zhang H, Xiang J, Shen G, Yang F, Wang F, Wang J, Tang Y. Advances and prospects of natural dietary polyphenols as G-quadruplex stabilizers in biomedical applications. Int J Biol Macromol 2024; 254:127825. [PMID: 37926317 DOI: 10.1016/j.ijbiomac.2023.127825] [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: 07/19/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
G-quadruplexes (G4s) have arrested continuous interest in cancer research, and targeting G4s with small molecules has become an ideal approach for drug development. Plant-based dietary polyphenols have attracted much attention for their remarkable anti-cancer effects. Studies have suggested that polyphenols exhibit interesting scaffolds to bind G4s, which can effectively downregulate the proto-oncogenes by stabilizing those G4 structures. Therefore, this review not only summarizes studies on natural dietary polyphenols (including analogs) as G4 stabilizers, but also reveals their anti-cancer activities. Furthermore, the structural and antioxidant insights of polyphenols with G4s are discussed, and future development is proposed. These insights may pave the way for the development of the next generation of anti-cancer drugs targeting nucleic acids.
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Affiliation(s)
- Huanfeng Ye
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Hong Zhang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; Beijing National Laboratory for Molecular Sciences (BNLMS), PR China.
| | - Junfeng Xiang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Gang Shen
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; Beijing National Laboratory for Molecular Sciences (BNLMS), PR China
| | - Fengmin Yang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; Beijing National Laboratory for Molecular Sciences (BNLMS), PR China
| | - Fangfang Wang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jie Wang
- Department of Cardiology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, PR China.
| | - Yalin Tang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Beijing National Laboratory for Molecular Sciences (BNLMS), PR China.
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Gajardo-Parra N, Meneses L, Duarte ARC, Paiva A, Held C. Assessing the Influence of Betaine-Based Natural Deep Eutectic Systems on Horseradish Peroxidase. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2022; 10:12873-12881. [PMID: 36573121 PMCID: PMC9783073 DOI: 10.1021/acssuschemeng.2c04045] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/26/2022] [Indexed: 06/02/2023]
Abstract
To validate the use of horseradish peroxidase (HRP) in natural deep eutectic systems (NADES), five different betaine-based NADES were characterized in terms of water content, water activity, density, and viscosity experimentally and by thermodynamic modeling. The results show that the NADES under study have a water activity of about 0.4 at 37 °C for water contents between 14 and 22 wt %. The densities of the studied NADES had values between 1.2 and 1.3 g.cm-3 at 20 °C. The density was modeled with a state-of-the-art equation of state; an excellent agreement with the experimental density data was achieved, allowing reasonable predictions for water activities. The system betaine:glycerol (1:2) was found to be the most viscous with a dynamic viscosity of ∼600 mPa.s at 40 °C, while all the other systems had viscosities <350 mPa.s at 40 °C. The impact of the NADES on the enzymatic activity, as well as on, conformational and thermal stability was assessed. The system betaine/sorbitol:water (1:1:3) showed the highest benefit for enzymatic activity, increasing it by two-folds. Moreover, upon NADES addition, thermal stability was increased followed by an increment in a-helix secondary structure content.
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Affiliation(s)
- Nicolás
F. Gajardo-Parra
- Laboratory
of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany
| | - Liane Meneses
- LAQV-REQUIMTE,
Department of Chemistry, School of Science and Technology, NOVA University Lisbon, 2825-149 Caparica, Portugal
| | - Ana Rita C. Duarte
- LAQV-REQUIMTE,
Department of Chemistry, School of Science and Technology, NOVA University Lisbon, 2825-149 Caparica, Portugal
| | - Alexandre Paiva
- LAQV-REQUIMTE,
Department of Chemistry, School of Science and Technology, NOVA University Lisbon, 2825-149 Caparica, Portugal
| | - Christoph Held
- Laboratory
of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Str. 70, 44227 Dortmund, Germany
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Stolzke T, Krieg F, Peng T, Zhang H, Häusler O, Brandenbusch C. Hydroxylpropyl-β-cyclodextrin as Potential Excipient to Prevent Stress-Induced Aggregation in Liquid Protein Formulations. Molecules 2022; 27:molecules27165094. [PMID: 36014329 PMCID: PMC9414600 DOI: 10.3390/molecules27165094] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 11/22/2022] Open
Abstract
Due to the growing demand for patient-friendly subcutaneous dosage forms, the ability to increasing protein solubility and stability in formulations to deliver on the required high protein concentrations is crucial. A common approach to ensure protein solubility and stability in high concentration protein formulations is the addition of excipients such as sugars, amino acids, surfactants, approved by the Food and Drug Administration. In a best-case scenario, these excipients fulfil multiple demands simultaneously, such as increasing long-term stability of the formulation, reducing protein adsorption on surfaces/interfaces, and stabilizing the protein against thermal or mechanical stress. 2-Hydroxylpropyl-β-cyclodextrin (derivative of β-cyclodextrin) holds this potential, but has not yet been sufficiently investigated for use in protein formulations. Within this work, we have systematically investigated the relevant molecular interactions to identify the potential of Kleptose®HPB (2-hydroxylpropyl-β-cyclodextrin from Roquette Freres, Lestrem, France) as “multirole” excipient within liquid protein formulations. Based on our results three factors determine the influence of Kleptose®HPB on protein formulation stability: (1) concentration of Kleptose®HPB, (2) protein type and protein concentration, and (3) quality of the protein formulation. Our results not only contribute to the understanding of the relevant interactions but also enable the target-oriented use of Kleptose®HPB within formulation design.
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Affiliation(s)
- Tanja Stolzke
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
| | - Franziska Krieg
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
| | - Tao Peng
- Roquette Asia Pacific Pte. Ltd., Singapore 138588, Singapore
| | - Hailong Zhang
- Roquette Asia Pacific Pte. Ltd., Singapore 138588, Singapore
| | | | - Christoph Brandenbusch
- Laboratory of Thermodynamics, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany
- Correspondence:
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5
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Interface of G-quadruplex with both stabilizing and destabilizing ligands for targeting various diseases. Int J Biol Macromol 2022; 219:414-427. [DOI: 10.1016/j.ijbiomac.2022.07.248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/22/2022] [Accepted: 07/29/2022] [Indexed: 11/19/2022]
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Stolzke T, Brandenbusch C. Simplified choice of suitable excipients within biologics formulation design using protein-protein interaction- and water activity-maps. Eur J Pharm Biopharm 2022; 176:153-167. [DOI: 10.1016/j.ejpb.2022.05.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 01/17/2023]
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Boosting the kinetic efficiency of formate dehydrogenase by combining the effects of temperature, high pressure and co-solvent mixtures. Colloids Surf B Biointerfaces 2021; 208:112127. [PMID: 34626897 DOI: 10.1016/j.colsurfb.2021.112127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 10/20/2022]
Abstract
The application of co-solvents and high pressure has been shown to be an efficient means to modify the kinetics of enzyme-catalyzed reactions without compromising enzyme stability, which is often limited by temperature modulation. In this work, the high-pressure stopped-flow methodology was applied in conjunction with fast UV/Vis detection to investigate kinetic parameters of formate dehydrogenase reaction (FDH), which is used in biotechnology for cofactor recycling systems. Complementary FTIR spectroscopic and differential scanning fluorimetric studies were performed to reveal pressure and temperature effects on the structure and stability of the FDH. In neat buffer solution, the kinetic efficiency increases by one order of magnitude by increasing the temperature from 25° to 45 °C and the pressure from ambient up to the kbar range. The addition of particular co-solvents further doubled the kinetic efficiency of the reaction, in particular the compatible osmolyte trimethylamine-N-oxide and its mixtures with the macromolecular crowding agent dextran. The thermodynamic model PC-SAFT was successfully applied within a simplified activity-based Michaelis-Menten framework to predict the effects of co-solvents on the kinetic efficiency by accounting for interactions involving substrate, co-solvent, water, and FDH. Especially mixtures of the co-solvents at high concentrations were beneficial for the kinetic efficiency and for the unfolding temperature.
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Wessner M, Bommarius B, Brandenbusch C, Bommarius AS. Purification of chimeric amine dehydrogenase using a tailor-made aqueous two-phase system - A case study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114991] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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9
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Wessner M, Nowaczyk M, Brandenbusch C. Rapid identification of tailor-made aqueous two-phase systems for the extractive purification of high-value biomolecules. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113655] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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10
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Wen J, Lord H, Knutson N, Wikström M. Nano differential scanning fluorimetry for comparability studies of therapeutic proteins. Anal Biochem 2020; 593:113581. [PMID: 31935356 DOI: 10.1016/j.ab.2020.113581] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/07/2020] [Accepted: 01/10/2020] [Indexed: 01/26/2023]
Abstract
Differential scanning calorimetry (DSC) has been extensively used in the biopharmaceutical industry to characterize protein thermal stability and domain folding integrity. Recently, nano differential scanning fluorimetry (nanoDSF) has emerged as a powerful tool for thermal stability analysis and studies of protein domain unfolding. Due to increased interests in the qualification of characterization methods, we are in this study presenting the qualification results for the comparability studies of thermal stability analysis using nanoDSF. The results show that nanoDSF is able to detect thermal transition signals for mAbs, BiTE® molecules, and cytokines at a wide concentration range with high precision, clearly indicating that nanoDSF is suitable for characterization including comparability studies of therapeutic proteins. Compared to the current recognized industry standard DSC, the nanoDSF method enables thermal stability analysis over a much wider concentration range, consumes considerably less materials, and provides significantly higher throughput.
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Affiliation(s)
- Jie Wen
- Higher Order Structure, Attribute Sciences, Thousand Oaks, CA, 91320, United States.
| | - Harrison Lord
- Higher Order Structure, Attribute Sciences, Thousand Oaks, CA, 91320, United States
| | - Nicholas Knutson
- Higher Order Structure, Attribute Sciences, Thousand Oaks, CA, 91320, United States
| | - Mats Wikström
- Higher Order Structure, Attribute Sciences, Thousand Oaks, CA, 91320, United States.
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