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Dixit H, Upadhyay V, Kulharia M, Verma SK. The Study of Metalloproteome of DNA Viruses: Identification, Functional Annotation, and Diversity Analysis of Viral Metal-Binding Proteins. J Proteome Res 2024; 23:4014-4026. [PMID: 39134029 DOI: 10.1021/acs.jproteome.4c00358] [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] [Indexed: 09/07/2024]
Abstract
Metalloproteins are fundamental to diverse biological processes but still lack extensive investigation in viral contexts. This study reveals the prevalence and functional diversity of metal-binding proteins in DNA viruses. Among a subset of 1432 metalloproteins, zinc and magnesium-binding proteins are notably abundant, indicating their importance in viral biology. Furthermore, significant numbers of proteins binding to iron, manganese, copper, nickel, mercury, and cadmium were also detected. Human-infecting viral proteins displayed a rich landscape of metalloproteins, with MeBiPred (964 proteins) and Pfam (666) yielding the highest numbers. Interestingly, many essential viral proteins exhibited metal-binding capabilities, including polymerases, DNA binding proteins, helicases, dUPTase, thymidine kinase, and various structural and accessory proteins. This study sheds light on the ubiquitous presence of metalloproteins, their functional signatures, subcellular placements, and metal-utilization patterns, providing valuable insights into viral biology. A similar metal utilization pattern was observed in similar functional proteins across the various DNA viruses. Furthermore, these findings provide a foundation for identifying potential drug targets for combating viral infections.
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Affiliation(s)
- Himisha Dixit
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, 176206, Himachal Pradesh, India
| | - Vipin Upadhyay
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, 176206, Himachal Pradesh, India
| | - Mahesh Kulharia
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, 176206, Himachal Pradesh, India
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Ferreira JC, Fadl S, Cardoso THS, Andrade BS, Melo TS, Silva EMDA, Agarwal A, Turville SJ, Saksena NK, Rabeh WM. Boosting immunity: synergistic antiviral effects of luteolin, vitamin C, magnesium and zinc against SARS-CoV-2 3CLpro. Biosci Rep 2024; 44:BSR20240617. [PMID: 39045772 PMCID: PMC11327220 DOI: 10.1042/bsr20240617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/10/2024] [Accepted: 07/23/2024] [Indexed: 07/25/2024] Open
Abstract
SARS-CoV-2 was first discovered in 2019 and has disseminated throughout the globe to pandemic levels, imposing significant health and economic burdens. Although vaccines against SARS-CoV-2 have been developed, their long-term efficacy and specificity have not been determined, and antiviral drugs remain necessary. Flavonoids, which are commonly found in plants, fruits, and vegetables and are part of the human diet, have attracted considerable attention as potential therapeutic agents due to their antiviral and antimicrobial activities and effects on other biological activities, such as inflammation. The present study uses a combination of biochemical, cellular, molecular dynamics, and molecular docking experiments to provide compelling evidence that the flavonoid luteolin (2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one) has antiviral activity against SARS-CoV-2 3-chymotrypsin-like protease (3CLpro) that is synergistically enhanced by magnesium, zinc, and vitamin C. The IC50 of luteolin against 2 µM 3CLpro is 78 µM and decreases 10-fold to 7.6 µM in the presence of zinc, magnesium, and vitamin C. Thermodynamic stability analyses revealed that luteolin has minimal effects on the structure of 3CLpro, whereas metal ions and vitamin C significantly alter the thermodynamic stability of the protease. Interactome analysis uncovered potential host-virus interactions and functional clusters associated with luteolin activity, supporting the relevance of this flavone for combating SARS-CoV-2 infection. This comprehensive investigation sheds light on luteolin's therapeutic potential and provides insights into its mechanisms of action against SARS-CoV-2. The novel formulation of luteolin, magnesium, zinc, and vitamin C may be an effective avenue for treating COVID-19 patients.
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Affiliation(s)
- Juliana C Ferreira
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Thyago H S Cardoso
- G42 Healthcare Omics Excellence Center, Masdar City, Abu Dhabi, United Arabes Emirates
| | - Bruno Silva Andrade
- UESB - Universidade Estatudal Do Sudoeste da Bahia. Deparmento de Ciencias Biologicas
| | - Tarcisio S Melo
- UESB - Universidade Estatudal Do Sudoeste da Bahia. Deparmento de Ciencias Biologicas
| | | | | | | | - Nitin K Saksena
- Victoria University, Footscray Park Campus, Melbourne, VIC, 3134, Australia
- Aegros Therapeutics Pty Ltd, 5-6 Eden Park Drive, Macquarie Park, NSW 2113, Australia
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
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Dixit H, Kulharia M, Verma SK. Metal-binding proteins and proteases in RNA viruses: unravelling functional diversity and expanding therapeutic horizons. J Virol 2023; 97:e0139923. [PMID: 37982624 PMCID: PMC10734521 DOI: 10.1128/jvi.01399-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 10/18/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE Metal-binding proteins are pivotal components with diverse functions in organisms, including viruses. Despite their significance, many metalloproteins in viruses remain uncharacterized, posing challenges to understanding viral systems. This study addresses this knowledge gap by identifying and analyzing metal-binding proteins and proteases in RNA viruses. The findings emphasize the prevalence of these proteins as essential functional classes within viruses and shed light on the role of metal ions and metalloproteins in viral replication and pathogenesis. Moreover, this research serves as a crucial foundation for further investigations in this field, offering the potential for developing innovative antiviral strategies. Additionally, the study enhances our understanding of the distribution and evolutionary patterns of metal-binding proteases in major human viruses. Continually exploring metal-binding proteomes across diverse viruses will deepen our knowledge of metal-dependent biological processes and provide valuable insights for combating viral infections, including respiratory viruses and other life-threatening diseases.
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Affiliation(s)
- Himisha Dixit
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, India
| | - Mahesh Kulharia
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, India
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Zhou Y, Yuan S, Xiao F, Li H, Ye Z, Cheng T, Luo C, Tang K, Cai J, Situ J, Sridhar S, Chu WM, Tam AR, Chu H, Che CM, Jin L, Hung IFN, Lu L, Chan JFW, Sun H. Metal-coding assisted serological multi-omics profiling deciphers the role of selenium in COVID-19 immunity. Chem Sci 2023; 14:10570-10579. [PMID: 37799995 PMCID: PMC10548515 DOI: 10.1039/d3sc03345g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 08/02/2023] [Indexed: 10/07/2023] Open
Abstract
Uncovering how host metal(loid)s mediate the immune response against invading pathogens is critical for better understanding the pathogenesis mechanism of infectious disease. Clinical data show that imbalance of host metal(loid)s is closely associated with the severity and mortality of COVID-19. However, it remains elusive how metal(loid)s, which are essential elements for all forms of life and closely associated with multiple diseases if dysregulated, are involved in COVID-19 pathophysiology and immunopathology. Herein, we built up a metal-coding assisted multiplexed serological metallome and immunoproteome profiling system to characterize the links of metallome with COVID-19 pathogenesis and immunity. We found distinct metallome features in COVID-19 patients compared with non-infected control subjects, which may serve as a biomarker for disease diagnosis. Moreover, we generated the first correlation network between the host metallome and immunity mediators, and unbiasedly uncovered a strong association of selenium with interleukin-10 (IL-10). Supplementation of selenium to immune cells resulted in enhanced IL-10 expression in B cells and reduced induction of proinflammatory cytokines in B and CD4+ T cells. The selenium-enhanced IL-10 production in B cells was confirmed to be attributable to the activation of ERK and Akt pathways. We further validated our cellular data in SARS-CoV-2-infected K18-hACE2 mice, and found that selenium supplementation alleviated SARS-CoV-2-induced lung damage characterized by decreased alveolar inflammatory infiltrates through restoration of virus-repressed selenoproteins to alleviate oxidative stress. Our approach can be readily extended to other diseases to understand how the host defends against invading pathogens through regulation of metallome.
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Affiliation(s)
- Ying Zhou
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
- Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital Shenzhen Guangdong China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park Hong Kong SAR China
| | - Fan Xiao
- Department of Pathology, Shenzhen Institute of Research and Innovation, The University of Hong Kong Hong Kong SAR China
| | - Hongyan Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Ziwei Ye
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Tianfan Cheng
- Faculty of Dentistry, The University of Hong Kong Pokfulam Hong Kong SAR Hong Kong China
| | - Cuiting Luo
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Kaiming Tang
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Jianpiao Cai
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Jianwen Situ
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Siddharth Sridhar
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
- Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital Shenzhen Guangdong China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park Hong Kong SAR China
- Department of Microbiology, Queen Mary Hospital Pokfulam Hong Kong SAR China
| | - Wing-Ming Chu
- Division of Infectious Diseases, Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Anthony Raymond Tam
- Division of Infectious Diseases, Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Chi-Ming Che
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Lijian Jin
- Faculty of Dentistry, The University of Hong Kong Pokfulam Hong Kong SAR Hong Kong China
| | - Ivan Fan-Ngai Hung
- Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital Shenzhen Guangdong China
- Division of Infectious Diseases, Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
| | - Liwei Lu
- Department of Pathology, Shenzhen Institute of Research and Innovation, The University of Hong Kong Hong Kong SAR China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong Pokfulam Hong Kong SAR China
- Department of Infectious Diseases and Microbiology, The University of Hong Kong-Shenzhen Hospital Shenzhen Guangdong China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park Hong Kong SAR China
- Department of Microbiology, Queen Mary Hospital Pokfulam Hong Kong SAR China
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, The University of Hong Kong Pokfulam Hong Kong SAR China
- Guangzhou Laboratory Guangdong Province China
| | - Hongzhe Sun
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Pokfulam Hong Kong SAR China
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Suzuki E, Kuronuma K, Murai R, Fujiya Y, Saito A, Chiba H, Takahashi S. Serum Testosterone Is Associated With the Severity of COVID-19. In Vivo 2023; 37:2314-2319. [PMID: 37652515 PMCID: PMC10500529 DOI: 10.21873/invivo.13334] [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: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 09/02/2023]
Abstract
BACKGROUND/AIM Coronavirus disease 2019 (COVID-19) is more likely to be severe in men than in women. Its association with sex hormones as an aggravating factor for male patients has been attracting attention. This study aimed to investigate whether serum testosterone is associated with the aggravation of COVID-19. PATIENTS AND METHODS Serum testosterone concentrations in 116 male patients with COVID-19 and residual serum were measured and examined upon their admission to Sapporo Medical University Hospital between February 1, 2020 and March 31, 2021. RESULTS Blood samples collected from these patients with COVID-19 were analyzed. The serum testosterone levels were 2.19±1.35, 1.29±0.88, and 0.75±0.58 ng/ml in mild, moderate, and severe groups, respectively. Patients with severe COVID-19 on admission had lower testosterone levels (p<0.001). At a cutoff level of 1.31 ng/ml, the area under the curve for the comparison of severe with non-severe cases was 0.825. Furthermore, serum testosterone levels negatively correlated with C-reactive protein and serum amyloid A levels but positively correlated with calcium, zinc, C3, and C4. CONCLUSION In male patients with COVID-19, low serum testosterone levels correlated with disease severity, accompanied by a strong inflammatory reaction and proportion of complement consumption.
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Affiliation(s)
- Ema Suzuki
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
| | - Koji Kuronuma
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, Japan;
| | - Ryosei Murai
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
| | - Yoshihiro Fujiya
- Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Atsushi Saito
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hirofumi Chiba
- Department of Respiratory Medicine and Allergology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Satoshi Takahashi
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Sapporo, Japan
- Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
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Dixit H, Kulharia M, Verma SK. Metalloproteome of human-infective RNA viruses: a study towards understanding the role of metal ions in virology. Pathog Dis 2023; 81:ftad020. [PMID: 37653445 DOI: 10.1093/femspd/ftad020] [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: 06/22/2023] [Revised: 08/07/2023] [Accepted: 08/29/2023] [Indexed: 09/02/2023] Open
Abstract
Metalloproteins and metal-based inhibitors have been shown to effectively combat infectious diseases, particularly those caused by RNA viruses. In this study, a diverse set of bioinformatics methods was employed to identify metal-binding proteins of human RNA viruses. Seventy-three viral proteins with a high probability of being metal-binding proteins were identified. These proteins included 40 zinc-, 47 magnesium- and 14 manganese-binding proteins belonging to 29 viral species and eight significant viral families, including Coronaviridae, Flaviviridae and Retroviridae. Further functional characterization has revealed that these proteins play a critical role in several viral processes, including viral replication, fusion and host viral entry. They fall under the essential categories of viral proteins, including polymerase and protease enzymes. Magnesium ion is abundantly predicted to interact with these viral enzymes, followed by zinc. In addition, this study also examined the evolutionary aspects of predicted viral metalloproteins, offering essential insights into the metal utilization patterns among different viral species. The analysis indicates that the metal utilization patterns are conserved within the functional classes of the proteins. In conclusion, the findings of this study provide significant knowledge on viral metalloproteins that can serve as a valuable foundation for future research in this area.
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Affiliation(s)
- Himisha Dixit
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra 176206, Himachal Pradesh, India
| | - Mahesh Kulharia
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra 176206, Himachal Pradesh, India
| | - Shailender Kumar Verma
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra 176206, Himachal Pradesh, India
- Department of Environmental Studies, University of Delhi 110007, Delhi, India
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Dixit H, Upadhyay V, Kulharia M, Verma SK. The putative metal-binding proteome of the Coronaviridae family. METALLOMICS : INTEGRATED BIOMETAL SCIENCE 2023; 15:6969429. [PMID: 36610727 DOI: 10.1093/mtomcs/mfad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/28/2022] [Indexed: 01/09/2023]
Abstract
Metalloproteins are well-known for playing various physicochemical processes in all life forms, including viruses. Some life-threatening viruses (such as some members of the Coronaviridae family of viruses) are emerged and remerged frequently and are rapidly transmitted throughout the globe. This study aims to identify and characterize the metal-binding proteins (MBPs) of the Coronaviridae family of viruses and further provides insight into the MBP's role in sustaining and propagating viruses inside a host cell and in the outer environment. In this study, the available proteome of the Coronaviridae family was exploited. Identified potential MBPs were analyzed for their functional domains, structural aspects, and subcellular localization. We also demonstrate phylogenetic aspects of all predicted MBPs among other Coronaviridae family members to understand the evolutionary trend among their respective hosts. A total of 256 proteins from 51 different species of coronaviruses are predicted as MBPs. These MBPs perform various key roles in the replication and survival of viruses within the host cell. Cysteine, aspartic acid, threonine, and glutamine are key amino acid residues interacting with respective metal ions. Our observations also indicate that the metalloproteins of this family of viruses circulated and evolved in different hosts, which supports the zoonotic nature of coronaviruses. The comprehensive information on MBPs of the Coronaviridae family may be further helpful in designing novel therapeutic metalloprotein targets. Moreover, the study of viral MBPs can also help to understand the roles of MBPs in virus pathogenesis and virus-host interactions.
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Affiliation(s)
- Himisha Dixit
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra176206, India
| | - Vipin Upadhyay
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra176206, India
| | - Mahesh Kulharia
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra176206, India
| | - Shailender Kumar Verma
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra176206, India.,Department of Environmental Studies, University of Delhi, Delhi110007, India
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Stamoula E, Sarantidi E, Dimakopoulos V, Ainatzoglou A, Dardalas I, Papazisis G, Kontopoulou K, Anagnostopoulos AK. Serum Proteome Signatures of Anti-SARS-CoV-2 Vaccinated Healthcare Workers in Greece Associated with Their Prior Infection Status. Int J Mol Sci 2022; 23:ijms231710153. [PMID: 36077551 PMCID: PMC9456361 DOI: 10.3390/ijms231710153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Over the course of the pandemic, proteomics, being in the frontline of anti-COVID-19 research, has massively contributed to the investigation of molecular pathogenic properties of the virus. However, data on the proteome on anti-SARS-CoV-2 vaccinated individuals remain scarce. This study aimed to identify the serum proteome characteristics of anti-SARS-CoV-2 vaccinated individuals who had previously contracted the virus and comparatively assess them against those of virus-naïve vaccine recipients. Blood samples of n = 252 individuals, out of whom n = 35 had been previously infected, were collected in the "G. Gennimatas" General Hospital of Thessaloniki, from 4 January 2021 to 31 August 2021. All participants received the BNT162b2 mRNA COVID-19 vaccine (Pfizer/BioNTech). A label-free quantitative proteomics LC-MS/MS approach was undertaken, and the identified proteins were analyzed using the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes) databases as well as processed by bioinformatics tools. Titers of total RBD-specific IgGs against SARS-CoV-2 were also determined using the SARS-CoV-2 IgG II Quant assay. A total of 47 proteins were significantly differentially expressed, the majority of which were down-regulated in sera of previously infected patients compared to virus-naïve controls. Several pathways were affected supporting the crucial role of the humoral immune response in the protection against SARS-CoV-2 infection provided by COVID-19 vaccination. Overall, our comprehensive proteome profiling analysis contributes novel knowledge of the mechanisms of immune response induced by anti-SARS-CoV-2 vaccination and identified protein signatures reflecting the immune status of vaccine recipients.
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Affiliation(s)
- Eleni Stamoula
- Department of Biotechnology, Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- Department of Clinical Pharmacology, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Eleana Sarantidi
- Department of Biotechnology, Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Vasilis Dimakopoulos
- Department of Biotechnology, Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Alexandra Ainatzoglou
- Department of Clinical Pharmacology, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Ioannis Dardalas
- Department of Clinical Pharmacology, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Georgios Papazisis
- Department of Clinical Pharmacology, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
- Clinical Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | | | - Athanasios K. Anagnostopoulos
- Department of Biotechnology, Centre of Systems Biology, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
- Correspondence:
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Andreini C, Rosato A. Structural Bioinformatics and Deep Learning of Metalloproteins: Recent Advances and Applications. Int J Mol Sci 2022; 23:7684. [PMID: 35887033 PMCID: PMC9323969 DOI: 10.3390/ijms23147684] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023] Open
Abstract
All living organisms require metal ions for their energy production and metabolic and biosynthetic processes. Within cells, the metal ions involved in the formation of adducts interact with metabolites and macromolecules (proteins and nucleic acids). The proteins that require binding to one or more metal ions in order to be able to carry out their physiological function are called metalloproteins. About one third of all protein structures in the Protein Data Bank involve metalloproteins. Over the past few years there has been tremendous progress in the number of computational tools and techniques making use of 3D structural information to support the investigation of metalloproteins. This trend has been boosted by the successful applications of neural networks and machine/deep learning approaches in molecular and structural biology at large. In this review, we discuss recent advances in the development and availability of resources dealing with metalloproteins from a structure-based perspective. We start by addressing tools for the prediction of metal-binding sites (MBSs) using structural information on apo-proteins. Then, we provide an overview of the methods for and lessons learned from the structural comparison of MBSs in a fold-independent manner. We then move to describing databases of metalloprotein/MBS structures. Finally, we summarizing recent ML/DL applications enhancing the functional interpretation of metalloprotein structures.
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Affiliation(s)
- Claudia Andreini
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
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