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Cuoghi S, Caraffi R, Anderlini A, Baraldi C, Enzo E, Vandelli MA, Tosi G, Ruozi B, Duskey JT, Ottonelli I. Challenges of enzyme therapy: Why two players are better than one. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2024; 16:e1979. [PMID: 38955512 DOI: 10.1002/wnan.1979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/29/2024] [Accepted: 05/28/2024] [Indexed: 07/04/2024]
Abstract
Enzyme-based therapy has garnered significant attention for its current applications in various diseases. Despite the notable advantages associated with the use of enzymes as therapeutic agents, that could have high selectivity, affinity, and specificity for the target, their application faces challenges linked to physico-chemical and pharmacological properties. These limitations can be addressed through the encapsulation of enzymes in nanoplatforms as a comprehensive solution to mitigate their degradation, loss of activity, off-target accumulation, and immunogenicity, thus enhancing bioavailability, therapeutic efficacy, and circulation time, thereby reducing the number of administrations, and ameliorating patient compliance. The exploration of novel nanomedicine-based enzyme therapeutics for the treatment of challenging diseases stands as a paramount goal in the contemporary scientific landscape, but even then it is often not enough. Combining an enzyme with another therapeutic (e.g., a small molecule, another enzyme or protein, a monoclonal antibody, or a nucleic acid) within a single nanocarrier provides innovative multidrug-integrated therapy and ensures that both the actives arrive at the target site and exert their therapeutic effect, leading to synergistic action and superior therapeutic efficacy. Moreover, this strategic approach could be extended to gene therapy, a field that nowadays has gained increasing attention, as enzymes acting at genomic level and nucleic acids may be combined for synergistic therapy. This multicomponent therapeutic approach opens opportunities for promising future developments. This article is categorized under: Therapeutic Approaches and Drug Discovery > Nanomedicine for Neurological Disease Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease Therapeutic Approaches and Drug Discovery > Emerging Technologies.
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Affiliation(s)
- Sabrina Cuoghi
- Nanotech Lab, Te.Far.T.I., Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Riccardo Caraffi
- Nanotech Lab, Te.Far.T.I., Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Clinical and Experimental Medicine PhD Program, Department of Biomedical, Metabolic, and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Alessandro Anderlini
- Nanotech Lab, Te.Far.T.I., Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Cecilia Baraldi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Elena Enzo
- Centre for Regenerative Medicine "Stefano Ferrari", University of Modena and Reggio Emilia, Modena, Italy
| | - Maria Angela Vandelli
- Nanotech Lab, Te.Far.T.I., Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Giovanni Tosi
- Nanotech Lab, Te.Far.T.I., Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Barbara Ruozi
- Nanotech Lab, Te.Far.T.I., Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Jason Thomas Duskey
- Nanotech Lab, Te.Far.T.I., Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Ilaria Ottonelli
- Nanotech Lab, Te.Far.T.I., Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
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Dantu SC, Khalil M, Bria M, Saint-Pierre C, Orio M, Gasparutto D, Sicoli G. Cleaving DNA with DNA: Cooperative Tuning of Structure and Reactivity Driven by Copper Ions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306710. [PMID: 38419268 DOI: 10.1002/advs.202306710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/15/2024] [Indexed: 03/02/2024]
Abstract
A copper-dependent self-cleaving DNA (DNAzyme or deoyxyribozyme) previously isolated by in vitro selection has been analyzed by a combination of Molecular Dynamics (MD) simulations and advanced Electron Paramagnetic Resonance (Electron Spin Resonance) EPR/ESR spectroscopy, providing insights on the structural and mechanistic features of the cleavage reaction. The modeled 46-nucleotide deoxyribozyme in MD simulations forms duplex and triplex sub-structures that flank a highly conserved catalytic core. The DNA self-cleaving construct can also form a bimolecular complex that has a distinct substrate and enzyme domains. The highly dynamic structure combined with an oxidative site-specific cleavage of the substrate are two key-aspects to elucidate. By combining EPR/ESR spectroscopy with selectively isotopically labeled nucleotides it has been possible to overcome the major drawback related to the "metal-soup" scenario, also known as "super-stoichiometric" ratios of cofactors versus substrate, conventionally required for the DNA cleavage reaction within those nucleic acids-based enzymes. The focus on the endogenous paramagnetic center (Cu2+) here described paves the way for analysis on mixtures where several different cofactors are involved. Furthermore, the insertion of cleavage reaction within more complex architectures is now a realistic perspective towards the applicability of EPR/ESR spectroscopic studies.
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Affiliation(s)
- Sarath Chandra Dantu
- Department of Computer Science, Brunel University London, Kingston Lane, Uxbridge, UB8 3PH, UK
| | - Mahdi Khalil
- LASIRE, CNRS UMR 8516, University of Lille, C4 building, Avenue Paul Langevin, Villeneuve d'Ascq, F-59655, France
| | - Marc Bria
- Michle-Eugène Chevreul Institute, FR 2638, Avenue Paul Langevin, Villeneuve d'Ascq, F-59655, France
| | - Christine Saint-Pierre
- Université Grenoble Alpes, CEA, CNRS, UMR 5819 SyMMES-CREAB, Avenue des Martyrs, Grenoble, F-38000, France
| | - Maylis Orio
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, UMR CNRS 7313, Marseille, 13397, France
| | - Didier Gasparutto
- Université Grenoble Alpes, CEA, CNRS, UMR 5819 SyMMES-CREAB, Avenue des Martyrs, Grenoble, F-38000, France
| | - Giuseppe Sicoli
- LASIRE, CNRS UMR 8516, University of Lille, C4 building, Avenue Paul Langevin, Villeneuve d'Ascq, F-59655, France
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Characterization of a DNA-hydrolyzing DNAzyme for generation of PCR strands of unequal length. Biochimie 2020; 179:181-189. [PMID: 33022314 DOI: 10.1016/j.biochi.2020.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/13/2020] [Accepted: 10/01/2020] [Indexed: 11/21/2022]
Abstract
I-R3 DNAzyme is a small, highly active catalytic DNA for DNA hydrolysis. In here, we designed two cis-structure DNAzymes (I-R3N and I-R3S) based on the different locates of the joint linker between I-R3 and its substrate. Data demonstrated that both DNAzymes were highly dependent on Zn2+, and worked at a narrow range around pH 7.0. They exhibited strong anti-interference with Mg2+ and Ca2+, but inhibited by Na+ and K+. Moreover, single and multiple-site mutations were generated within the catalytic core to carry out a comprehensive mutational study of I-R3 motif, in which most nucleotides were highly conserved and the nucleotides A5, T11 and T8 were identified as the mutational hotspots. Furthermore, an efficient variant A5G was obtained and its reaction condition was optimized. Finally, we constructed A5G to the 3' end of a single-stranded DNA (ssDNA) and applied it for asymmetrical PCR amplification to produce a single and double-stranded DNA mixture, in which A5G within ssDNA can self-cleave to generate a shorter desired ssDNA by denaturing gel separation. This would provide a new non-chemical modification approach for preparation of the expected ssDNA for in vitro selection of DNAzymes.
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