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Ouyang L, Wang N, Irudayaraj J, Majima T. Virus on surfaces: Chemical mechanism, influence factors, disinfection strategies, and implications for virus repelling surface design. Adv Colloid Interface Sci 2023; 320:103006. [PMID: 37778249 DOI: 10.1016/j.cis.2023.103006] [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: 05/29/2023] [Revised: 09/07/2023] [Accepted: 09/22/2023] [Indexed: 10/03/2023]
Abstract
While SARS-CoV-2 is generally under control, the question of variants and infections still persists. Fundamental information on how the virus interacts with inanimate surfaces commonly found in our daily life and when in contact with the skin will be helpful in developing strategies to inhibit the spread of the virus. Here in, a critically important review of current understanding of the interaction between virus and surface is summarized from chemistry point-of-view. The Derjaguin-Landau-Verwey-Overbeek and extended Derjaguin-Landau-Verwey-Overbeek theories to model virus attachments on surfaces are introduced, along with the interaction type and strength, and quantification of each component. The virus survival and transfer are affected by a combination of biological, physical, and chemical parameters, as well as environmental parameters. The surface properties for virus and virus survival on typical surfaces such as metals, plastics, and glass are summarized. Attention is also paid to the transfer of virus to/from surfaces and skin. Typical virus disinfection strategies utilizing heat, light, chemicals, and ozone are discussed together with their disinfection mechanism. In the last section, design principles for virus repelling surface chemistry such as surperhydrophobic or surperhydrophilic surfaces are also introduced, to demonstrate how the integration of surface property control and advanced material fabrication can lead to the development of functional surfaces for mitigating the effect of viral infection upon contact.
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Affiliation(s)
- Lei Ouyang
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Nan Wang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Joseph Irudayaraj
- Department of Bioengineering, College of Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
| | - Tetsuro Majima
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China; The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Ibaraki, Osaka 567-0047, Japan
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Frenkel R, Tribby D, Boumajny B, Larson N, Sampson M, Barney C, Bergelson S, Sosic Z, Yeung B. ACUVRA: Anion-Exchange Chromatography UV-Ratio Analysis-A QC-Friendly Method for Monitoring Adeno-Associated Virus Empty Capsid Content To Support Process Development and GMP Release Testing. AAPS J 2022; 25:3. [PMID: 36414847 DOI: 10.1208/s12248-022-00768-0] [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: 07/06/2022] [Accepted: 10/28/2022] [Indexed: 11/24/2022] Open
Abstract
The genome content of adeno-associated virus (AAV) vectors is critical to the safety and potency of AAV-based gene therapy products. Empty capsids are considered a product-related impurity and a critical quality attribute (CQA) of the drug product, thus requiring characterization throughout the production process to demonstrate they are controlled to acceptable levels in the final drug product. Anion exchange chromatography has been used to achieve separation between empty and full capsids, but requires method development and gradient optimization for different serotypes and formulations. Here, we describe an alternative approach to quantitation that does not rely on achieving separation between empty and full capsids, but instead uses the well-established relationship between absorbance at UV A260/A280 and relation to DNA/protein content, in combination with anion-exchange chromatography to allow one to calculate the relative proportion of empty and full capsids in AAV samples from a single peak. We call this approach ACUVRA: Anion-exchange Chromatography UV-Ratio Analysis, and show the applicability of the method through a case study with recombinant AAV2 (rAAV2) process intermediates and drug substance. Method qualification and GMP validation in a quality control (QC) laboratory results show that ACUVRA is a fit-for-purpose method for process development support and characterization, while also being a QC-friendly option for GMP release testing at all stages of clinical development. Graphical abstract.
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Affiliation(s)
- Ruth Frenkel
- Department of Gene Therapy Analytical Development, Biogen Inc, 255 Binney St, Cambridge, Massachusetts, 02142, USA.
| | - Dana Tribby
- Department of Gene Therapy Analytical Development, Biogen Inc, 255 Binney St, Cambridge, Massachusetts, 02142, USA
| | - Boris Boumajny
- Department of Gene Therapy Analytical Development, Biogen Inc, 255 Binney St, Cambridge, Massachusetts, 02142, USA
| | - Nicholas Larson
- Department of Gene Therapy Analytical Development, Biogen Inc, 255 Binney St, Cambridge, Massachusetts, 02142, USA
| | - Matthew Sampson
- Department of Quality Control-Analytical Technology, Biogen Inc, 5000 Davis Dr, Durham, North Carolina, 27709, USA
| | - Christopher Barney
- Department of Quality Control-Analytical Technology, Biogen Inc, 5000 Davis Dr, Durham, North Carolina, 27709, USA
| | - Svetlana Bergelson
- Department of Gene Therapy Analytical Development, Biogen Inc, 255 Binney St, Cambridge, Massachusetts, 02142, USA
| | - Zoran Sosic
- Department of Gene Therapy Analytical Development, Biogen Inc, 255 Binney St, Cambridge, Massachusetts, 02142, USA
| | - Bernice Yeung
- Department of Gene Therapy Analytical Development, Biogen Inc, 255 Binney St, Cambridge, Massachusetts, 02142, USA
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Armanious A, Mezzenga R. A Roadmap for Building Waterborne Virus Traps. JACS AU 2022; 2:2205-2221. [PMID: 36311831 PMCID: PMC9597599 DOI: 10.1021/jacsau.2c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/18/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Outbreaks of waterborne viruses pose a massive threat to human health, claiming the lives of hundreds of thousands of people every year. Adsorption-based filtration offers a promising facile and environmentally friendly approach to help provide safe drinking water to a world population of almost 8 billion people, particularly in communities that lack the infrastructure for large-scale facilities. The search for a material that can effectively trap viruses has been mainly driven by a top-down approach, in which old and new materials have been tested for this purpose. Despite substantial advances, finding a material that achieves this crucial goal and meets all associated challenges remains elusive. We suggest that the road forward should strongly rely on a complementary bottom-up approach based on our fundamental understanding of virus interactions at interfaces. We review the state-of-the-art physicochemical knowledge of the forces that drive the adsorption of viruses at solid-water interfaces. Compared to other nanometric colloids, viruses have heterogeneous surface chemistry and diverse morphologies. We advocate that advancing our understanding of virus interactions would require describing their physicochemical properties using novel descriptors that reflect their heterogeneity and diversity. Several other related topics are also addressed, including the effect of coadsorbates on virus adsorption, virus inactivation at interfaces, and experimental considerations to ensure well-grounded research results. We finally conclude with selected examples of materials that made notable advances in the field.
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Affiliation(s)
- Antonius Armanious
- Department
of Health Sciences and Technology, ETH Zurich, Zurich8092, Switzerland
| | - Raffaele Mezzenga
- Department
of Health Sciences and Technology, ETH Zurich, Zurich8092, Switzerland
- Department
of Materials, ETH Zurich, Zurich8093, Switzerland
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Ghasabi F, Hashempour A, Khodadad N, Bemani S, Keshani P, Shekiba MJ, Hasanshahi Z. First report of computational protein-ligand docking to evaluate susceptibility to HIV integrase inhibitors in HIV-infected Iranian patients. Biochem Biophys Rep 2022; 30:101254. [PMID: 35368742 PMCID: PMC8968007 DOI: 10.1016/j.bbrep.2022.101254] [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: 01/15/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 12/04/2022] Open
Abstract
Background Iran has recently included integrase (INT) inhibitors (INTIs) in the first-line treatment regimen in human immunodeficiency virus (HIV)-infected patients. However, there is no bioinformatics data to elaborate the impact of resistance-associated mutations (RAMs) and naturally occurring polymorphisms (NOPs) on INTIs treatment outcome in Iranian patients. Method In this cross-sectional survey, 850 HIV-1-infected patients enrolled; of them, 78 samples had successful sequencing results for INT gene. Several analyses were performed including docking screening, genotypic resistance, secondary/tertiary structures, post-translational modification (PTM), immune epitopes, etc. Result The average docking energy (E value) of different samples with elvitegravir (EVG) and raltegravir (RAL) was more than other INTIs. Phylogenetic tree analysis and Stanford HIV Subtyping program revealed HIV-1 CRF35-AD was the predominant subtype (94.9%) in our cases; in any event, online subtyping tools confirmed A1 as the most frequent subtype. For the first time, CRF-01B and BF were identified as new subtypes in Iran. Decreased CD4 count was associated with several factors: poor or unstable adherence, naïve treatment, and drug user status. Conclusion As the first bioinformatic report on HIV-integrase from Iran, this study indicates that EVG and RAL are the optimal INTIs in first-line antiretroviral therapy (ART) in Iranian patients. Some conserved motifs and specific amino acids in INT-protein binding sites have characterized that mutation(s) in them may disrupt INT-drugs interaction and cause a significant loss in susceptibility to INTIs. Good adherence, treatment of naïve patients, and monitoring injection drug users are fundamental factors to control HIV infection in Iran effectively.
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Key Words
- Antiretroviral therapy, ART
- Behavioral Diseases Consultation Center, BDCC
- Bictegravir, BIC
- C-terminal domain, CTD
- CRF35-AD
- Cabotegravir, CBT
- Catalytic core domain, CCD
- Dolutegravir, DTG
- Drug resistance
- Elvitegravir, EVG
- Grand average hydropathy, GRAVY
- HIV
- Human immunodeficiency virus, HIV
- INT, Integrase
- INTIs, Integrase inhibitors (INTIs)
- Injecting drug users, IDUs
- Integrase
- Integrase inhibitors
- Molecular docking
- N-terminal domain, NTD
- Naturally occurring polymorphisms, NOPs
- Post-translational modification, PTM
- Raltegravir, RAL
- Resistance-associated mutations, RAMs
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Affiliation(s)
- Farzane Ghasabi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ava Hashempour
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nastaran Khodadad
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Soudabeh Bemani
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Parisa Keshani
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohamad Javad Shekiba
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Hasanshahi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
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Hasanshahi Z, Hashempour A, Ghasabi F, Moayedi J, Musavi Z, Dehghani B, Sharafi H, Joulaei H. First report on molecular docking analysis and drug resistance substitutions to approved HCV NS5A and NS5B inhibitors amongst Iranian patients. BMC Gastroenterol 2021; 21:443. [PMID: 34819046 PMCID: PMC8612383 DOI: 10.1186/s12876-021-01988-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 10/22/2021] [Indexed: 12/13/2022] Open
Abstract
Background NS5A and NS5B proteins of hepatitis C virus (HCV) are the main targets of compounds that directly inhibit HCV infections. However, the emergence of resistance-associated substitutions (RASs) may cause substantial reductions in susceptibility to inhibitors. Methods Viral load and genotyping were determined in eighty-seven naïve HCV-infected patients, and the amplified NS5A and NS5B regions were sequenced by Sanger sequencing. In addition, physicochemical properties, structural features, immune epitopes, and inhibitors-protein interactions of sequences were analyzed using several bioinformatics tools. Results Several amino acid residue changes were found in NS5A and NS5B proteins; however, we did not find any mutations related to resistance to the treatment in NS5B. Different phosphorylation and few glycosylation sites were assessed. Disulfide bonds were identified in both proteins that had a significant effect on the function and structure of HCV proteins. Applying reliable software to predict B-cell epitopes, 3 and 5 regions were found for NS5A and NS5B, respectively, representing a considerable potential to induce the humoral immune system. Docking analysis determined amino acids involved in the interaction of inhibitors and mentioned proteins may not decrease the drug efficiency. Conclusions Strong interactions between inhibitors, NS5A and NS5B proteins and the lack of efficient drug resistance mutations in the analyzed sequences may confirm the remarkable ability of NS5A and NS5B inhibitors to control HCV infection amongst Iranian patients. The results of bioinformatics analysis could unveil all features of both proteins, which can be beneficial for further investigations on HCV drug resistance and designing novel vaccines. Supplementary Information The online version contains supplementary material available at 10.1186/s12876-021-01988-y.
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Affiliation(s)
- Zahra Hasanshahi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ava Hashempour
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Farzane Ghasabi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Javad Moayedi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Musavi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Behzad Dehghani
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Heidar Sharafi
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Middle East Liver Diseases (MELD) Center, Tehran, Iran
| | - Hassan Joulaei
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
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Single-Particle Characterization of SARS-CoV-2 Isoelectric Point and Comparison to Variants of Interest. Microorganisms 2021; 9:microorganisms9081606. [PMID: 34442686 PMCID: PMC8401476 DOI: 10.3390/microorganisms9081606] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2, the cause of COVID-19, is a new, highly pathogenic coronavirus, which is the third coronavirus to emerge in the past 2 decades and the first to become a global pandemic. The virus has demonstrated itself to be extremely transmissible and deadly. Recent data suggest that a targeted approach is key to mitigating infectivity. Due to the proliferation of cataloged protein and nucleic acid sequences in databases, the function of the nucleic acid, and genetic encoded proteins, we make predictions by simply aligning sequences and exploring their homology. Thus, similar amino acid sequences in a protein usually confer similar biochemical function, even from distal or unrelated organisms. To understand viral transmission and adhesion, it is key to elucidate the structural, surface, and functional properties of each viral protein. This is typically first modeled in highly pathogenic species by exploring folding, hydrophobicity, and isoelectric point (IEP). Recent evidence from viral RNA sequence modeling and protein crystals have been inadequate, which prevent full understanding of the IEP and other viral properties of SARS-CoV-2. We have thus experimentally determined the IEP of SARS-CoV-2. Our findings suggest that for enveloped viruses, such as SARS-CoV-2, estimates of IEP by the amino acid sequence alone may be unreliable. We compared the experimental IEP of SARS-CoV-2 to variants of interest (VOIs) using their amino acid sequence, thus providing a qualitative comparison of the IEP of VOIs.
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Heffron J, Bork M, Mayer BK, Skwor T. A Comparison of Porphyrin Photosensitizers in Photodynamic Inactivation of RNA and DNA Bacteriophages. Viruses 2021; 13:v13030530. [PMID: 33807067 PMCID: PMC8005208 DOI: 10.3390/v13030530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 12/22/2022] Open
Abstract
Effective broad-spectrum antiviral treatments are in dire need as disinfectants and therapeutic alternatives. One such method of disinfection is photodynamic inactivation, which involves the production of reactive oxygen species from dissolved oxygen in response to light-stimulated photosensitizers. This study evaluated the efficacy of functionalized porphyrin compounds for photodynamic inactivation of bacteriophages as human virus surrogates. A blue-light light emitting diode (LED) lamp was used to activate porphyrin compounds in aqueous solution (phosphate buffer). The DNA bacteriophages ΦX174 and P22 were more resistant to porphyrin TMPyP photodynamic inactivation than RNA bacteriophage fr, with increasing rates of inactivation in the order: ΦX174 << P22 << fr. Bacteriophage ΦX174 was therefore considered a resistant virus suitable for the evaluation of three additional porphyrins. These porphyrins were synthesized from TMPyP by inclusion of a central palladium ion (PdT4) and/or the addition of a hydrophobic C14 chain (PdC14 or C14). While the inactivation rate of bacteriophage ΦX174 via TMPyP was similar to previous reports of resistant viruses, ΦX174 inactivation increased by a factor of approximately 2.5 using the metalloporphyrins PdT4 and PdC14. The order of porphyrin effectiveness was TMPyP < C14 < PdT4 < PdC14, indicating that both Pd2+ ligation and C14 functionalization aided virus inactivation.
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Affiliation(s)
- Joe Heffron
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 W. Wisconsin Ave, Milwaukee, WI 53233, USA; (J.H.); (B.K.M.)
| | - Matthew Bork
- Department of Chemical and Biological Sciences, Rockford University, 5050 E. State St., Rockford, IL 61108, USA;
| | - Brooke K. Mayer
- Department of Civil, Construction and Environmental Engineering, Marquette University, 1637 W. Wisconsin Ave, Milwaukee, WI 53233, USA; (J.H.); (B.K.M.)
| | - Troy Skwor
- Department of Biomedical Sciences, University of Wisconsin–Milwaukee, 2400 E. Hartford Ave., Milwaukee, WI 53211, USA
- Correspondence:
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Virus Isoelectric Point Estimation: Theories and Methods. Appl Environ Microbiol 2021; 87:AEM.02319-20. [PMID: 33188001 DOI: 10.1128/aem.02319-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Much of virus fate, both in the environment and in physical/chemical treatment, is dependent on electrostatic interactions. Developing an accurate means of predicting virion isoelectric point (pI) would help to understand and anticipate virus fate and transport, especially for viruses that are not readily propagated in the lab. One simple approach to predicting pI estimates the pH at which the sum of charges from ionizable amino acids in capsid proteins approaches zero. However, predicted pIs based on capsid charges frequently deviate by several pH units from empirically measured pIs. Recently, the discrepancy between empirical and predicted pI was attributed to the electrostatic neutralization of predictable polynucleotide-binding regions (PBRs) of the capsid interior. In this paper, we review models presupposing (i) the influence of the viral polynucleotide on surface charge or (ii) the contribution of only exterior residues to surface charge. We then compare these models to the approach of excluding only PBRs and hypothesize a conceptual electrostatic model that aligns with this approach. The PBR exclusion method outperformed methods based on three-dimensional (3D) structure and accounted for major discrepancies in predicted pIs without adversely affecting pI prediction for a diverse range of viruses. In addition, the PBR exclusion method was determined to be the best available method for predicting virus pI, since (i) PBRs are predicted independently of the impact on pI, (ii) PBR prediction relies on proteome sequences rather than detailed structural models, and (iii) PBR exclusion was successfully demonstrated on a diverse set of viruses. These models apply to nonenveloped viruses only. A similar model for enveloped viruses is complicated by a lack of data on enveloped virus pI, as well as uncertainties regarding the influence of the phospholipid envelope on charge and ion gradients.
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