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Roohi A, Gharagozlou S. Vitamin D supplementation and calcium: Many-faced gods or nobody in fighting against Corona Virus Disease 2019. Clin Nutr ESPEN 2024; 62:172-184. [PMID: 38901939 DOI: 10.1016/j.clnesp.2024.05.015] [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: 11/15/2023] [Revised: 05/07/2024] [Accepted: 05/22/2024] [Indexed: 06/22/2024]
Abstract
In December 2019, Corona Virus Disease 2019 (COVID-19) was first identified and designated as a pandemic in March 2020 due to rapid spread of the virus globally. At the beginning of the pandemic, only a few treatment options, mainly focused on supportive care and repurposing medications, were available. Due to its effects on immune system, vitamin D was a topic of interest during the pandemic, and researchers investigated its potential impact on COVID-19 outcomes. However, the results of studies about the impact of vitamin D on the disease are inconclusive. In the present narrative review, different roles of vitamin D regarding the COVID-19 have been discussed to show that vitamin D supplementation should be recommended carefully.
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Affiliation(s)
- Azam Roohi
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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2
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Guarnieri JW, Haltom JA, Albrecht YES, Lie T, Olali AZ, Widjaja GA, Ranshing SS, Angelin A, Murdock D, Wallace DC. SARS-CoV-2 mitochondrial metabolic and epigenomic reprogramming in COVID-19. Pharmacol Res 2024; 204:107170. [PMID: 38614374 DOI: 10.1016/j.phrs.2024.107170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/15/2024]
Abstract
To determine the effects of SARS-CoV-2 infection on cellular metabolism, we conducted an exhaustive survey of the cellular metabolic pathways modulated by SARS-CoV-2 infection and confirmed their importance for SARS-CoV-2 propagation by cataloging the effects of specific pathway inhibitors. This revealed that SARS-CoV-2 strongly inhibits mitochondrial oxidative phosphorylation (OXPHOS) resulting in increased mitochondrial reactive oxygen species (mROS) production. The elevated mROS stabilizes HIF-1α which redirects carbon molecules from mitochondrial oxidation through glycolysis and the pentose phosphate pathway (PPP) to provide substrates for viral biogenesis. mROS also induces the release of mitochondrial DNA (mtDNA) which activates innate immunity. The restructuring of cellular energy metabolism is mediated in part by SARS-CoV-2 Orf8 and Orf10 whose expression restructures nuclear DNA (nDNA) and mtDNA OXPHOS gene expression. These viral proteins likely alter the epigenome, either by directly altering histone modifications or by modulating mitochondrial metabolite substrates of epigenome modification enzymes, potentially silencing OXPHOS gene expression and contributing to long-COVID.
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Affiliation(s)
- Joseph W Guarnieri
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jeffrey A Haltom
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yentli E Soto Albrecht
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Timothy Lie
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arnold Z Olali
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Gabrielle A Widjaja
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sujata S Ranshing
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alessia Angelin
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Deborah Murdock
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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3
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Cubisino SAM, Milenkovic S, Conti-Nibali S, Musso N, Bonacci P, De Pinto V, Ceccarelli M, Reina S. Electrophysiological properties and structural prediction of the SARS-CoV-2 viroprotein E. Front Mol Biosci 2024; 11:1334819. [PMID: 38606285 PMCID: PMC11007222 DOI: 10.3389/fmolb.2024.1334819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/15/2024] [Indexed: 04/13/2024] Open
Abstract
COVID-19, the infectious disease caused by the most recently discovered coronavirus SARS- CoV-2, has caused millions of sick people and thousands of deaths all over the world. The viral positive-sense single-stranded RNA encodes 31 proteins among which the spike (S) is undoubtedly the best known. Recently, protein E has been reputed as a potential pharmacological target as well. It is essential for the assembly and release of the virions in the cell. Literature describes protein E as a voltage-dependent channel with preference towards monovalent cations whose intracellular expression, though, alters Ca2+ homeostasis and promotes the activation of the proinflammatory cascades. Due to the extremely high sequence identity of SARS-CoV-2 protein E (E-2) with the previously characterized E-1 (i.e., protein E from SARS-CoV) many data obtained for E-1 were simply adapted to the other. Recent solid state NMR structure revealed that the transmembrane domain (TMD) of E-2 self-assembles into a homo-pentamer, albeit the oligomeric status has not been validated with the full-length protein. Prompted by the lack of a common agreement on the proper structural and functional features of E-2, we investigated the specific mechanism/s of pore-gating and the detailed molecular structure of the most cryptic protein of SARS-CoV-2 by means of MD simulations of the E-2 structure and by expressing, refolding and analyzing the electrophysiological activity of the transmembrane moiety of the protein E-2, in its full length. Our results show a clear agreement between experimental and predictive studies and foresee a mechanism of activity based on Ca2+ affinity.
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Affiliation(s)
| | | | - Stefano Conti-Nibali
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Nicolò Musso
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Paolo Bonacci
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Vito De Pinto
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- We.MitoBiotech S.R.L, Catania, Italy
| | | | - Simona Reina
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
- We.MitoBiotech S.R.L, Catania, Italy
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4
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Surya W, Tavares-Neto E, Sanchis A, Queralt-Martín M, Alcaraz A, Torres J, Aguilella VM. The Complex Proteolipidic Behavior of the SARS-CoV-2 Envelope Protein Channel: Weak Selectivity and Heterogeneous Oligomerization. Int J Mol Sci 2023; 24:12454. [PMID: 37569828 PMCID: PMC10420310 DOI: 10.3390/ijms241512454] [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: 07/07/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
The envelope (E) protein is a small polypeptide that can form ion channels in coronaviruses. In SARS coronavirus 2 (SARS-CoV-2), the agent that caused the recent COVID-19 pandemic, and its predecessor SARS-CoV-1, E protein is found in the endoplasmic reticulum-Golgi intermediate compartment (ERGIC), where virion budding takes place. Several reports claim that E protein promotes the formation of "cation-selective channels". However, whether this term represents specificity to certain ions (e.g., potassium or calcium) or the partial or total exclusion of anions is debatable. Herein, we discuss this claim based on the available data for SARS-CoV-1 and -2 E and on new experiments performed using the untagged full-length E protein from SARS-CoV-2 in planar lipid membranes of different types, including those that closely mimic the ERGIC membrane composition. We provide evidence that the selectivity of the E-induced channels is very mild and depends strongly on lipid environment. Thus, despite past and recent claims, we found no indication that the E protein forms cation-selective channels that prevent anion transport, and even less that E protein forms bona fide specific calcium channels. In fact, the E channel maintains its multi-ionic non-specific neutral character even in concentrated solutions of Ca2+ ions. Also, in contrast to previous studies, we found no evidence that SARS-CoV-2 E channel activation requires a particular voltage, high calcium concentrations or low pH, in agreement with available data from SARS-CoV-1 E. In addition, sedimentation velocity experiments suggest that the E channel population is mostly pentameric, but very dynamic and probably heterogeneous, consistent with the broad distribution of conductance values typically found in electrophysiological experiments. The latter has been explained by the presence of proteolipidic channel structures.
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Affiliation(s)
- Wahyu Surya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore;
| | - Ernesto Tavares-Neto
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12080 Castellon, Spain; (E.T.-N.); (M.Q.-M.); (A.A.)
| | - Andrea Sanchis
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12080 Castellon, Spain; (E.T.-N.); (M.Q.-M.); (A.A.)
| | - María Queralt-Martín
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12080 Castellon, Spain; (E.T.-N.); (M.Q.-M.); (A.A.)
| | - Antonio Alcaraz
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12080 Castellon, Spain; (E.T.-N.); (M.Q.-M.); (A.A.)
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore;
| | - Vicente M. Aguilella
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12080 Castellon, Spain; (E.T.-N.); (M.Q.-M.); (A.A.)
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Zhou S, Lv P, Li M, Chen Z, Xin H, Reilly S, Zhang X. SARS-CoV-2 E protein: Pathogenesis and potential therapeutic development. Biomed Pharmacother 2023; 159:114242. [PMID: 36652729 PMCID: PMC9832061 DOI: 10.1016/j.biopha.2023.114242] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a devastating global pandemic, which has seriously affected human health worldwide. The discovery of therapeutic agents is extremely urgent, and the viral structural proteins are particularly important as potential drug targets. SARS-CoV-2 envelope (E) protein is one of the main structural proteins of the virus, which is involved in multiple processes of the virus life cycle and is directly related to pathogenesis process. In this review, we present the amino acid sequence of the E protein and compare it with other two human coronaviruses. We then explored the role of E protein in the viral life cycle and discussed the pathogenic mechanisms that E protein may be involved in. Next, we summarize the potential drugs against E protein discovered in the current studies. Finally, we described the possible effects of E protein mutation on virus and host. This established a knowledge system of E protein to date, aiming to provide theoretical insights for mitigating the current COVID-19 pandemic and potential future coronavirus outbreaks.
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Affiliation(s)
- Shilin Zhou
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
| | - Panpan Lv
- Clinical Laboratory, Minhang Hospital, Fudan University, Shanghai, China.
| | - Mingxue Li
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
| | - Zihui Chen
- School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Hong Xin
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
| | - Svetlana Reilly
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
| | - Xuemei Zhang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China.
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6
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Guarnieri JW, Angelin A, Murdock DG, Schaefer P, Portluri P, Lie T, Huang J, Wallace DC. SARS-COV-2 viroporins activate the NLRP3-inflammasome by the mitochondrial permeability transition pore. Front Immunol 2023; 14:1064293. [PMID: 36891303 PMCID: PMC9986324 DOI: 10.3389/fimmu.2023.1064293] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/30/2023] [Indexed: 02/22/2023] Open
Abstract
Background Compared to healthy controls, severe COVID19 patients display increased levels of activated NLRP3-inflammasome (NLRP3-I) and interleukin (IL)-1β. SARS-CoV-2 encodes viroporin proteins E and Orf3a(2-E+2-3a) with homologs to SARS-CoV-1, 1-E+1-3a, which elevate NLRP3-I activation; by an unknown mechanism. Thus, we investigated how 2-E+2-3a activates the NLRP3-I to better understand the pathophysiology of severe COVID-19. Methods We generated a polycistronic expression-vector co-expressing 2-E+2-3a from a single transcript. To elucidate how 2-E+2-3a activates the NLRP3-I, we reconstituted the NLRP3-I in 293T cells and used THP1-derived macrophages to monitor the secretion of mature IL-1β. Mitochondrial physiology was assessed using fluorescent microscopy and plate reader assays, and the release of mitochondrial DNA (mtDNA) was detected from cytosolic-enriched fractions using Real-Time PCR. Results Expression of 2-E+2-3a in 293T cells increased cytosolic Ca++ and elevated mitochondrial Ca++, taken up through the MCUi11-sensitive mitochondrial calcium uniporter. Increased mitochondrial Ca++ stimulated NADH, mitochondrial reactive oxygen species (mROS) production and the release of mtDNA into the cytosol. Expression of 2-E+2-3a in NLRP3-I reconstituted 293T cells and THP1-derived macrophages displayed increased secretion of IL-1β. Increasing mitochondrial antioxidant defenses via treatment with MnTBAP or genetic expression of mCAT abolished 2-E+2-3a elevation of mROS, cytosolic mtDNA levels, and secretion of NLRP3-activated-IL-1β. The 2-E+2-3a-induced release of mtDNA and the secretion of NLRP3-activated-IL-1β were absent in cells lacking mtDNA and blocked in cells treated with the mitochondrial-permeability-pore(mtPTP)-specific inhibitor NIM811. Conclusion Our findings revealed that mROS activates the release of mitochondrial DNA via the NIM811-sensitive mitochondrial-permeability-pore(mtPTP), activating the inflammasome. Hence, interventions targeting mROS and the mtPTP may mitigate the severity of COVID-19 cytokine storms.
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Affiliation(s)
- Joseph W Guarnieri
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Alessia Angelin
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Deborah G Murdock
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Patrick Schaefer
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Prasanth Portluri
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Timothy Lie
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Department of biology, University of Pennsylvania, Philadelphia, PA, United States
| | - Jessica Huang
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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7
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Perini DA, Parra-Ortiz E, Varó I, Queralt-Martín M, Malmsten M, Alcaraz A. Surface-Functionalized Polystyrene Nanoparticles Alter the Transmembrane Potential via Ion-Selective Pores Maintaining Global Bilayer Integrity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:14837-14849. [PMID: 36417698 PMCID: PMC9974068 DOI: 10.1021/acs.langmuir.2c02487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Although nanoplastics have well-known toxic effects toward the environment and living organisms, their molecular toxicity mechanisms, including the nature of nanoparticle-cell membrane interactions, are still under investigation. Here, we employ dynamic light scattering, quartz crystal microbalance with dissipation monitoring, and electrophysiology to investigate the interaction between polystyrene nanoparticles (PS NPs) and phospholipid membranes. Our results show that PS NPs adsorb onto lipid bilayers creating soft inhomogeneous films that include disordered defects. PS NPs form an integral part of the generated channels so that the surface functionalization and charge of the NP determine the pore conductive properties. The large difference in size between the NP diameter and the lipid bilayer thickness (∼60 vs ∼5 nm) suggests a particular and complex lipid-NP assembly that is able to maintain overall membrane integrity. In view of this, we suggest that NP-induced toxicity in cells could operate in more subtle ways than membrane disintegration, such as inducing lipid reorganization and transmembrane ionic fluxes that disrupt the membrane potential.
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Affiliation(s)
- D. Aurora Perini
- Laboratory
of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071Castellón, Spain
| | - Elisa Parra-Ortiz
- Department
of Pharmacy, University of Copenhagen, DK-2100Copenhagen, Denmark
| | - Inmaculada Varó
- Institute
of Aquaculture Torre de la Sal (IATS-CSIC), Ribera de Cabanes, 12595Castellón, Spain
| | - María Queralt-Martín
- Laboratory
of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071Castellón, Spain
| | - Martin Malmsten
- Department
of Pharmacy, University of Copenhagen, DK-2100Copenhagen, Denmark
- Department
of Physical Chemistry 1, University of Lund, SE-22100Lund, Sweden
| | - Antonio Alcaraz
- Laboratory
of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071Castellón, Spain
- . Tel.: +34 964 72 8044
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8
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Kolocouris A, Arkin I, Glykos NM. A proof-of-concept study of the secondary structure of influenza A, B M2 and MERS- and SARS-CoV E transmembrane peptides using folding molecular dynamics simulations in a membrane mimetic solvent. Phys Chem Chem Phys 2022; 24:25391-25402. [PMID: 36239696 DOI: 10.1039/d2cp02881f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Here, we have carried out a proof-of-concept molecular dynamics (MD) simulation with adaptive tempering in a membrane mimetic environment to study the folding of single-pass membrane peptides. We tested the influenza A M2 viroporin, influenza B M2 viroporin, and protein E from coronaviruses MERS-Cov-2 and SARS-CoV-2 peptides with known experimental secondary structures in membrane bilayers. The two influenza-derived peptides are significantly different in the peptide sequence and secondary structure and more polar than the two coronavirus-derived peptides. Through a total of more than 50 μs of simulation time that could be accomplished in trifluoroethanol (TFE), as a membrane model, we characterized comparatively the folding behavior, helical stability, and helical propensity of these transmembrane peptides that match perfectly their experimental secondary structures, and we identified common motifs that reflect their quaternary organization and known (or not) biochemical function. We showed that BM2 is organized into two structurally distinct parts: a significantly more stable N-terminal half, and a fast-converting C-terminal half that continuously folds and unfolds between α-helical structures and non-canonical structures, which are mostly turns. In AM2, both the N-terminal half and C-terminal half are very flexible. In contrast, the two coronavirus-derived transmembrane peptides are much more stable and fast helix-formers when compared with the influenza ones. In particular, the SARS-derived peptide E appears to be the fastest and most stable helix-former of all the four viral peptides studied, with a helical structure that persists almost without disruption for the whole of its 10 μs simulation. By comparing the results with experimental observations, we benchmarked TFE in studying the conformation of membrane and hydrophobic peptides. This work provided accurate results suggesting a methodology to run long MD simulations and predict structural properties of biologically important membrane peptides.
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Affiliation(s)
- Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, 15771, Greece.
| | - Isaiah Arkin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, 91904, Israel
| | - Nicholas M Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Alexandroupolis, 68100, Greece.
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9
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Yang R, Wu S, Wang S, Rubino G, Nickels JD, Cheng X. Refinement of SARS-CoV-2 envelope protein structure in a native-like environment by molecular dynamics simulations. Front Mol Biosci 2022; 9:1027223. [PMID: 36299297 PMCID: PMC9589232 DOI: 10.3389/fmolb.2022.1027223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
COVID-19 has become an unprecedented threat to human health. The SARS-CoV-2 envelope (E) protein plays a critical role in the viral maturation process and pathogenesis. Despite intensive investigation, its structure in physiological conditions remains mysterious: no high-resolution full-length structure is available and only an NMR structure of the transmembrane (TM) region has been determined. Here, we present a refined E protein structure, using molecular dynamics (MD) simulations to investigate its structure and dynamics in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer system. Our initial homology model based upon the SARS-CoV E protein structure is shown to be unstable in the lipid bilayer, and the H3 helices tend to move away from the membrane center to the membrane-water interface. A more stable model was developed by replacing all H3 helices with the fully equilibrated H3 structure sampled in the MD simulations. This refined model exhibited more favorable contacts with lipids and water than the original homology model and induced local membrane curvature, decreasing local lipid order. Interestingly, the pore radius profiles showed that the channel in both homology and refined models remained in a closed state throughout the simulations. We also demonstrated the utility of this structure to develop anti-SARS-CoV-2 drugs by docking a library of FDA-approved, investigational, and experimental drugs to the refined E protein structure, identifying 20 potential channel blockers. This highlights the power of MD simulations to refine low-resolution structures of membrane proteins in a native-like membrane environment, shedding light on the structural features of the E protein and providing a platform for the development of novel antiviral treatments.
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Affiliation(s)
- Rui Yang
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Sijin Wu
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, United States
- *Correspondence: Sijin Wu, ; Jonathan D. Nickels, ; Xiaolin Cheng,
| | - Shen Wang
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Grace Rubino
- Department of Chemical and Biomolecular Engineering, College of Engineering, The Ohio State University, Columbus, OH, United States
| | - Jonathan D. Nickels
- Department of Chemical and Environmental Engineering, The University of Cincinnati, Cincinnati, OH, United States
- *Correspondence: Sijin Wu, ; Jonathan D. Nickels, ; Xiaolin Cheng,
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, United States
- Translational Data Analytics Institute (TDAI), The Ohio State University, Columbus, OH, United States
- *Correspondence: Sijin Wu, ; Jonathan D. Nickels, ; Xiaolin Cheng,
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10
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Kannan L, Raj R, Rhoad W, Akella R, Jacob A. Immobilization-Induced Hypercalcemia in COVID-19 With a Prolonged Intensive Care Unit Stay. Cureus 2022; 14:e24081. [PMID: 35573518 PMCID: PMC9098108 DOI: 10.7759/cureus.24081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2022] [Indexed: 11/16/2022] Open
Abstract
Immobilization is an uncommon etiology of hypercalcemia. It is usually seen in conditions associated with limited movements such as spinal cord injuries, vascular events, or following prolonged hospitalization. Hereby, we present a case of a young patient who had prolonged hospitalization following infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). During her prolonged and complicated hospital stay, she developed severe hypercalcemia secondary to immobilization, which was resistant to treatment with hydration, calcitonin, and denosumab. One dose of zoledronic acid was used, although the patient was on hemodialysis, with adequate response in calcium levels. This case illustrates that patients with COVID-19-related hospitalization are at increased risk of immobilization-induced hypercalcemia, likely due to prolonged hospital stay due to critical illness and lack of early physical therapy during hospitalization.
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11
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Breitinger U, Farag NS, Sticht H, Breitinger HG. Viroporins: Structure, function, and their role in the life cycle of SARS-CoV-2. Int J Biochem Cell Biol 2022; 145:106185. [PMID: 35219876 PMCID: PMC8868010 DOI: 10.1016/j.biocel.2022.106185] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022]
Abstract
Viroporins are indispensable for viral replication. As intracellular ion channels they disturb pH gradients of organelles and allow Ca2+ flux across ER membranes. Viroporins interact with numerous intracellular proteins and pathways and can trigger inflammatory responses. Thus, they are relevant targets in the search for antiviral drugs. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) underlies the world-wide pandemic of COVID-19, where an effective therapy is still lacking despite impressive progress in the development of vaccines and vaccination campaigns. Among the 29 proteins of SARS-CoV-2, the E- and ORF3a proteins have been identified as viroporins that contribute to the massive release of inflammatory cytokines observed in COVID-19. Here, we describe structure and function of viroporins and their role in inflammasome activation and cellular processes during the virus replication cycle. Techniques to study viroporin function are presented, with a focus on cellular and electrophysiological assays. Contributions of SARS-CoV-2 viroporins to the viral life cycle are discussed with respect to their structure, channel function, binding partners, and their role in viral infection and virus replication. Viroporin sequences of new variants of concern (α–ο) of SARS-CoV-2 are briefly reviewed as they harbour changes in E and 3a proteins that may affect their function.
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Affiliation(s)
- Ulrike Breitinger
- Department of Biochemistry, German University in Cairo, New Cairo, Egypt
| | - Noha S Farag
- Department of Microbiology and Immunology, German University in Cairo, New Cairo, Egypt
| | - Heinrich Sticht
- Division of Bioinformatics, Institute for Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
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Monje-Galvan V, Voth GA. Molecular interactions of the M and E integral membrane proteins of SARS-CoV-2. Faraday Discuss 2021; 232:49-67. [PMID: 34543372 PMCID: PMC8712422 DOI: 10.1039/d1fd00031d] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Specific lipid-protein interactions are key for cellular processes, and even more so for the replication of pathogens. The COVID-19 pandemic has drastically changed our lives and caused the death of nearly four million people worldwide, as of this writing. SARS-CoV-2 is the virus that causes the disease and has been at the center of scientific research over the past year. Most of the research on the virus is focused on key players during its initial attack and entry into the cellular host; namely the S protein, its glycan shield, and its interactions with the ACE2 receptors of human cells. As cases continue to rise around the globe, and new mutants are identified, there is an urgent need to understand the mechanisms of this virus during different stages of its life cycle. Here, we consider two integral membrane proteins of SARS-CoV-2 known to be important for viral assembly and infectivity. We have used microsecond-long all-atom molecular dynamics to examine the lipid-protein and protein-protein interactions of the membrane (M) and envelope (E) structural proteins of SARS-CoV-2 in a complex membrane model. We contrast the two proposed protein complexes for each of these proteins, and quantify their effect on their local lipid environment. This ongoing work also aims to provide molecular-level understanding of the mechanisms of action of this virus to possibly aid in the design of novel treatments.
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Affiliation(s)
- Viviana Monje-Galvan
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and The James Franck Institute, The University of Chicago, Chicago, Illinois, 60637, USA.
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and The James Franck Institute, The University of Chicago, Chicago, Illinois, 60637, USA.
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Monje-Galvan V, Voth GA. Molecular interactions of the M and E integral membrane proteins of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33948595 DOI: 10.1101/2021.04.29.442018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Specific lipid-protein interactions are key for cellular processes, and even more so for the replication of pathogens. The COVID-19 pandemic has drastically changed our lives and cause the death of nearly three million people worldwide, as of this writing. SARS-CoV-2 is the virus that causes the disease and has been at the center of scientific research over the past year. Most of the research on the virus is focused on key players during its initial attack and entry into the cellular host; namely the S protein, its glycan shield, and its interactions with the ACE2 receptors of human cells. As cases continue to raise around the globe, and new mutants are identified, there is an urgent need to understand the mechanisms of this virus during different stages of its life cycle. Here, we consider two integral membrane proteins of SARS-CoV-2 known to be important for viral assembly and infectivity. We have used microsecond-long all-atom molecular dynamics to examine the lipid-protein and protein-protein interactions of the membrane (M) and envelope (E) structural proteins of SARS-CoV-2 in a complex membrane model. We contrast the two proposed protein complexes for each of these proteins, and quantify their effect on their local lipid environment. This ongoing work also aims to provide molecular-level understanding of the mechanisms of action of this virus to possibly aid in the design of novel treatments.
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