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Rafiepour P, Mortazavi SMJ, Sihver L. A Critical Look at Heavy Ion Beam Irradiation for Vaccine Development. J Biomed Phys Eng 2024; 14:315-318. [PMID: 39027708 PMCID: PMC11252548 DOI: 10.31661/jbpe.v0i0.2405-1765] [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: 05/14/2024] [Accepted: 05/26/2024] [Indexed: 07/20/2024]
Abstract
Recent studies offer valuable insights into viral inactivation for vaccine development. Schulze et al. have demonstrated the potential of heavy ion beam irradiation to create effective vaccines, which is particularly relevant in the context of airborne pandemics. Notably, the success in immunizing mice via intranasal administration with the inactivated influenza virus is encouraging, especially given the genetic similarities between influenza and SARS-CoV-2. However, the study raises important considerations. While heavy ion treatment shows advantages, there are concerns about viral inactivation completeness and the potential for surviving viruses, albeit at extremely low levels. Prolonged irradiation times and the risk of selective pressure leading to the evolution of resistant variants are highlighted. Biosafety concerns regarding accidental lab escape of resistant strains are crucial, emphasizing the need for caution during experiments. Moreover, limitations in Monte Carlo simulations of virus irradiation are discussed, pointing out the need for more comprehensive studies to assess the impact of secondary particles on virus inactivation under realistic irradiation conditions. Given these considerations, while the study presents a promising approach for vaccine development, further research is essential to address potential drawbacks and optimize the method for safe and effective application.
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Affiliation(s)
- Payman Rafiepour
- Department of Nuclear Engineering, School of Mechanical Engineering, Shiraz University, Shiraz, Iran
| | - Seyed Mohammad Javad Mortazavi
- Ionizing and Non-ionizing Radiation Protection Research Center (INIRPRC), Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medical Physics and Engineering, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Lembit Sihver
- Department of Radiation Physics, Technische Universität Wien, Atominstitut, 1040 Vienna, Austria
- Department of Chemistry and Chemical Engineering, Royal Military College of Canada, Kingston, ON, Canada
- Department of Physics, East Carolina University, Greenville, NC 27858, USA
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2
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Rafiepour P, Sina S, Amoli ZA, Shekarforoush SS, Farajzadeh E, Mortazavi SMJ. A mechanistic simulation of induced DNA damage in a bacterial cell by X- and gamma rays: a parameter study. Phys Eng Sci Med 2024:10.1007/s13246-024-01424-x. [PMID: 38652348 DOI: 10.1007/s13246-024-01424-x] [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: 08/27/2023] [Accepted: 04/07/2024] [Indexed: 04/25/2024]
Abstract
Mechanistic Monte Carlo simulations calculating DNA damage caused by ionizing radiation are highly dependent on the simulation parameters. In the present study, using the Geant4-DNA toolkit, the impact of different parameters on DNA damage induced in a bacterial cell by X- and gamma-ray irradiation was investigated. Three geometry configurations, including the simple (without DNA details), the random (a random multiplication of identical DNA segments), and the fractal (a regular replication of DNA segments using fractal Hilbert curves), were simulated. Also, three physics constructors implemented in Geant4-DNA, i.e., G4EmDNAPhysics_option2, G4EmDNAPhysics_option4, and G4EmDNAPhysics_option6, with two energy thresholds of 17.5 eV and 5-37.5 eV were compared for direct DNA damage calculations. Finally, a previously developed mathematical model of cell repair called MEDRAS (Mechanistic DNA Repair and Survival) was employed to compare the impact of physics constructors on the cell survival curve. The simple geometry leads to undesirable results compared to the random and fractal ones, highlighting the importance of simulating complex DNA structures in mechanistic simulation studies. Under the same conditions, the DNA damage calculated in the fractal geometry was more consistent with the experimental data. All physics constructors can be used alternatively with the fractal geometry, provided that an energy threshold of 17.5 eV is considered for recording direct DNA damage. All physics constructors represent a similar behavior in generating cell survival curves, although the slopes of the curves are different. Since the inverse of the slope of a bacterial cell survival curve (i.e., the D10-value) is highly sensitive to the simulation parameters, it is not logical to determine an optimal set of parameters for calculating the D10-value by Monte Carlo simulation.
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Affiliation(s)
- Payman Rafiepour
- Department of Nuclear Engineering, School of Mechanical Engineering, Shiraz University, Shiraz, Iran
| | - Sedigheh Sina
- Department of Nuclear Engineering, School of Mechanical Engineering, Shiraz University, Shiraz, Iran.
- Radiation research center, School of Mechanical Engineering, Shiraz University, Shiraz, Iran.
| | - Zahra Alizadeh Amoli
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Seyed Shahram Shekarforoush
- Department of Food Hygiene and Public Health, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Ebrahim Farajzadeh
- Secondary Standard Dosimetry Laboratory (SSDL), Pars Isotope Co, Karaj, Iran
| | - Seyed Mohammad Javad Mortazavi
- Ionizing and Non-ionizing Radiation Protection Research Center (INIRPRC), Shiraz University of Medical Sciences, Shiraz, Iran
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3
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Schulze K, Weber U, Schuy C, Durante M, Guzmán CA. Influenza Virus Inactivated by Heavy Ion Beam Irradiation Stimulates Antigen-Specific Immune Responses. Pharmaceutics 2024; 16:465. [PMID: 38675126 PMCID: PMC11054185 DOI: 10.3390/pharmaceutics16040465] [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: 02/21/2024] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/28/2024] Open
Abstract
The COVID-19 pandemic has made clear the need for effective and rapid vaccine development methods. Conventional inactivated virus vaccines, together with new technologies like vector and mRNA vaccines, were the first to be rolled out. However, the traditional methods used for virus inactivation can affect surface-exposed antigen, thereby reducing vaccine efficacy. Gamma rays have been used in the past to inactivate viruses. We recently proposed that high-energy heavy ions may be more suitable as an inactivation method because they increase the damage ratio between the viral nucleic acid and surface proteins. Here, we demonstrate that irradiation of the influenza virus using heavy ion beams constitutes a suitable method to develop effective vaccines, since immunization of mice by the intranasal route with the inactivated virus resulted in the stimulation of strong antigen-specific humoral and cellular immune responses.
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Affiliation(s)
- Kai Schulze
- Department of Vaccinology and Applied Microbiology, Helmholtz Zentrum für Infektionsforschung (HZI), 38124 Braunschweig, Germany;
| | - Ulrich Weber
- Biophysics Department, GSI Helmholtzzentrum für Schwerionenforschung, 64291 Darmstadt, Germany; (U.W.); (C.S.); (M.D.)
- Fachbereich Mathematik, Naturwissenschaften und Informatik, Technische Hochschule Mittelhessen, 35390 Gießen, Germany
| | - Christoph Schuy
- Biophysics Department, GSI Helmholtzzentrum für Schwerionenforschung, 64291 Darmstadt, Germany; (U.W.); (C.S.); (M.D.)
| | - Marco Durante
- Biophysics Department, GSI Helmholtzzentrum für Schwerionenforschung, 64291 Darmstadt, Germany; (U.W.); (C.S.); (M.D.)
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Department of Physics “Ettore Pancini”, University Federico II, 80138 Naples, Italy
| | - Carlos Alberto Guzmán
- Department of Vaccinology and Applied Microbiology, Helmholtz Zentrum für Infektionsforschung (HZI), 38124 Braunschweig, Germany;
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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Rafiepour P, Sina S, Mortazavi SMJ. Inactivation of SARS-CoV-2 by charged particles for Future Vaccine Production Applications: A Monte Carlo study. Radiat Phys Chem Oxf Engl 1993 2022; 198:110265. [PMID: 35663798 PMCID: PMC9142867 DOI: 10.1016/j.radphyschem.2022.110265] [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: 10/13/2021] [Revised: 01/25/2022] [Accepted: 05/24/2022] [Indexed: 11/01/2022]
Abstract
The world is still suffering from the SARS-CoV-2 pandemic, and the number of infected people is still growing in many countries in 2022. Although great strides have been made to produce effective vaccines, efforts in this field should be accelerated, particularly due to the emergence of new variants. Using inactivated viruses is a conventional method of vaccine production. High levels of ionizing radiation can effectively inactivate viruses. Recently, studies on SARS-CoV-2 irradiation using low-LET radiations (e.g., gamma rays) have been performed. However, there are insufficient studies on the impact of charged particles on the inactivation of this virus. In this study, a realistic structure of SARS-CoV-2 is simulated by using Geant4 Monte Carlo toolkit, and the effect of electrons, protons, alphas, C-12, and Fe-56 ions on the inactivation of SARS-CoV-2 is investigated. The simulation results indicated that densely ionizing (high-LET) particles have the advantage of minimum number of damaged spike proteins per single RNA break. The RNA breaks induced by hydroxyl radicals produced in the surrounding water medium were significant only for electron beam radiation. Hence, indirect RNA breaks induced by densely ionizing particles is negligible. From a simulation standpoint, alpha particles (with energies up to 30 MeV) as well as C-12 ions (with energies up to 80 MeV/n), and Fe-56 ions (with any energy) can be introduced as particles of choice for effective SARS-CoV-2 inactivation.
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Affiliation(s)
- Payman Rafiepour
- Department of Nuclear Engineering, School of Mechanical Engineering, Shiraz University, Shiraz, Iran
| | - Sedigheh Sina
- Department of Nuclear Engineering, School of Mechanical Engineering, Shiraz University, Shiraz, Iran.,Radiation Research Center, School of Mechanical Engineering, Shiraz University, Shiraz, Iran
| | - Seyed Mohammad Javad Mortazavi
- Department of Medical Physics and Engineering, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.,Ionizing and Non-ionizing Radiation Protection Research Center (INIRPRC), Shiraz University of Medical Sciences, Shiraz, Iran
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Villagomez-Bernabe B, Chan SW, Coulter JA, Roseman AM, Currell FJ. Fast Ion-Beam Inactivation of Viruses, Where Radiation Track Structure Meets RNA Structural Biology. Radiat Res 2022; 198:68-80. [PMID: 35436347 DOI: 10.1667/rade-21-00133.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 03/17/2022] [Indexed: 11/03/2022]
Abstract
Here we show an interplay between the structures present in ionization tracks and nucleocapsid RNA structural biology, using fast ion-beam inactivation of the severe acute respiratory syndrome coronavirus (SARS-CoV) virion as an example. This interplay could be a key factor in predicting dose-inactivation curves for high-energy ion-beam inactivation of virions. We also investigate the adaptation of well-established cross-section data derived from radiation interactions with water to the interactions involving the components of a virion, going beyond the density-scaling approximation developed previously. We conclude that solving one of the grand challenges of structural biology - the determination of RNA tertiary/quaternary structure - is linked to predicting ion-beam inactivation of viruses and that the two problems can be mutually informative. Indeed, our simulations show that fast ion beams have a key role to play in elucidating RNA tertiary/quaternary structure.
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Affiliation(s)
- B Villagomez-Bernabe
- The Dalton Cumbrian Facility and the Department of Chemistry, The University of Manchester, Westlakes Science & Technology Park, Moor Row, Cumbria, CA24 3HA, United Kingdom
| | - S W Chan
- School of Biological Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester Academic Health Science Centre, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PL, United Kingdom
| | - J A Coulter
- School of Pharmacy, Queen's University Belfast, Belfast, BT9 7BL
| | - A M Roseman
- School of Biological Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester Academic Health Science Centre, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PL, United Kingdom
| | - F J Currell
- The Dalton Cumbrian Facility and the Department of Chemistry, The University of Manchester, Westlakes Science & Technology Park, Moor Row, Cumbria, CA24 3HA, United Kingdom
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Erdogan RT, Alkhaled M, Kaynak BE, Alhmoud H, Pisheh HS, Kelleci M, Karakurt I, Yanik C, Şen ZB, Sari B, Yagci AM, Özkul A, Hanay MS. Atmospheric Pressure Mass Spectrometry of Single Viruses and Nanoparticles by Nanoelectromechanical Systems. ACS NANO 2022; 16:3821-3833. [PMID: 35785967 DOI: 10.1021/acsnano.1c08423] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mass spectrometry of intact nanoparticles and viruses can serve as a potent characterization tool for material science and biophysics. Inaccessible by widespread commercial techniques, the mass of single nanoparticles and viruses (>10MDa) can be readily measured by nanoelectromechanical systems (NEMS)-based mass spectrometry, where charged and isolated analyte particles are generated by electrospray ionization (ESI) in air and transported onto the NEMS resonator for capture and detection. However, the applicability of NEMS as a practical solution is hindered by their miniscule surface area, which results in poor limit-of-detection and low capture efficiency values. Another hindrance is the necessity to house the NEMS inside complex vacuum systems, which is required in part to focus analytes toward the miniscule detection surface of the NEMS. Here, we overcome both limitations by integrating an ion lens onto the NEMS chip. The ion lens is composed of a polymer layer, which charges up by receiving part of the ions incoming from the ESI tip and consequently starts to focus the analytes toward an open window aligned with the active area of the NEMS electrostatically. With this integrated system, we have detected the mass of gold and polystyrene nanoparticles under ambient conditions and with two orders-of-magnitude improvement in capture efficiency compared to the state-of-the-art. We then applied this technology to obtain the mass spectrum of SARS-CoV-2 and BoHV-1 virions. With the increase in analytical throughput, the simplicity of the overall setup, and the operation capability under ambient conditions, the technique demonstrates that NEMS mass spectrometry can be deployed for mass detection of engineered nanoparticles and biological samples efficiently.
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Affiliation(s)
| | | | | | | | | | | | | | - Cenk Yanik
- Sabancı University, SUNUM Nanotechnology Research and Application Center, 34956 Istanbul, Turkey
| | | | - Burak Sari
- Faculty of Engineering and Natural Sciences, Sabancı University, 34956 Istanbul, Turkey
| | | | - Aykut Özkul
- Faculty of Veterinary Medicine, Department of Virology, Ankara University, 06110 Ankara, Turkey
- Biotechnology Institute, Ankara University, 06135 Ankara, Turkey
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Durante M. Failla Memorial Lecture: The Many Facets of Heavy-Ion Science. Radiat Res 2021; 195:403-411. [PMID: 33979440 DOI: 10.1667/rade-21-00029.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 02/22/2021] [Indexed: 11/03/2022]
Abstract
Heavy ions are riveting in radiation biophysics, particularly in the areas of radiotherapy and space radiation protection. Accelerated charged particles can indeed penetrate deeply in the human body to sterilize tumors, exploiting the favorable depth-dose distribution of ions compared to conventional X rays. Conversely, the high biological effectiveness in inducing late effects presents a hazard for manned space exploration. Even after half a century of accelerator-based experiments, clinical applications and flight research, these two topics remain both fascinating and baffling. Heavy-ion therapy is very expensive, and despite the clinical success it remains controversial. Research on late radiation morbidity in spaceflight led to a reduction in uncertainty, but also pointed to new risks previously underestimated, such as possible damage to the central nervous system. Recently, heavy ions have also been used in other, unanticipated biomedical fields, such as treatment of heart arrhythmia or inactivation of viruses for vaccine development. Heavy-ion science nicely merges physics and biology and remains an extraordinary research field for the 21st century.
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Affiliation(s)
- Marco Durante
- Biophysics Department, GSI Helmholtzzentrum für Schwerionenforschung, 64291 Darmstadt, Germany; and Technische Universität Darmstadt, Institute of Condensed Matter Physics, 64289 Darmstadt, Germany
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