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Banerjee T, Gosai A, Yousefi N, Garibay OO, Seal S, Balasubramanian G. Examining sialic acid derivatives as potential inhibitors of SARS-CoV-2 spike protein receptor binding domain. J Biomol Struct Dyn 2024; 42:6342-6358. [PMID: 37424217 DOI: 10.1080/07391102.2023.2234044] [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: 05/02/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) has been the primary reason behind the COVID-19 global pandemic which has affected millions of lives worldwide. The fundamental cause of the infection is the molecular binding of the viral spike protein receptor binding domain (SP-RBD) with the human cell angiotensin-converting enzyme 2 (ACE2) receptor. The infection can be prevented if the binding of RBD-ACE2 is resisted by utilizing certain inhibitors or drugs that demonstrate strong binding affinity towards the SP RBD. Sialic acid based glycans found widely in human cells and tissues have notable propensity of binding to viral proteins of the coronaviridae family. Recent experimental literature have used N-acetyl neuraminic acid (Sialic acid) to create diagnostic sensors for SARS-CoV-2, but a detailed interrogation of the underlying molecular mechanisms is warranted. Here, we perform all atom molecular dynamics (MD) simulations for the complexes of certain Sialic acid-based molecules with that of SP RBD of SARS CoV-2. Our results indicate that Sialic acid not only reproduces a binding affinity comparable to the RBD-ACE2 interactions, it also assumes the longest time to dissociate completely from the protein binding pocket of SP RBD. Our predictions corroborate that a combination of electrostatic and van der Waals energies as well the polar hydrogen bond interactions between the RBD residues and the inhibitors influence free energy of binding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tanumoy Banerjee
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA, USA
| | | | - Niloofar Yousefi
- Industrial Engineering and Management Systems, University of Central Florida, Orlando, FL, USA
| | - Ozlem Ozmen Garibay
- Industrial Engineering and Management Systems, University of Central Florida, Orlando, FL, USA
| | - Sudipta Seal
- College of Medicine, Bionix Cluster, University of Central Florida, Orlando, FL, USA
- Advanced Materials Processing and Analysis Center, Dept. of Materials Science and Engineering, University of Central Florida, Orlando, FL, USA
| | - Ganesh Balasubramanian
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA, USA
- Institute of Functional Materials & Devices and College of Health, Lehigh University, Bethlehem, PA, USA
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2
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Verzino SJ, Priyev SA, Sánchez Estrada VA, Crowley GX, Rutkowski A, Lam AC, Nazginov ES, Kotemelo P, Bacelo A, Sukhram DT, Vázquez FX, Juárez JF. Expanding salivary biomarker detection by creating a synthetic neuraminic acid sensor via chimeragenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598939. [PMID: 38915506 PMCID: PMC11195194 DOI: 10.1101/2024.06.13.598939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Accurate and timely diagnosis of oral squamous cell carcinoma (OSCC) is crucial in preventing its progression to advanced stages with a poor prognosis. As such, the construction of sensors capable of detecting previously established disease biomarkers for the early and non-invasive diagnosis of this and many other conditions has enormous therapeutic potential. In this work, we apply synthetic biology techniques for the development of a whole-cell biosensor (WCB) that leverages the physiology of engineered bacteria in vivo to promote the expression of an observable effector upon detection of a soluble molecule. To this end, we have constructed a bacterial strain expressing a novel chimeric transcription factor (Sphnx) for the detection of N-acetylneuraminic acid (Neu5Ac), a salivary biomolecule correlated with the onset of OSCC. This WCB serves as the proof-of-concept of a platform that can eventually be applied to clinical screening panels for a multitude of oral and systemic medical conditions whose biomarkers are present in saliva.
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3
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Thomas J, Ghosh A, Ranjan S, Satija J. Cheminformatics approach to identify andrographolide derivatives as dual inhibitors of methyltransferases (nsp14 and nsp16) of SARS-CoV-2. Sci Rep 2024; 14:9801. [PMID: 38684706 PMCID: PMC11058777 DOI: 10.1038/s41598-024-58532-7] [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: 12/22/2023] [Accepted: 04/01/2024] [Indexed: 05/02/2024] Open
Abstract
The Covid-19 pandemic outbreak has accelerated tremendous efforts to discover a therapeutic strategy that targets severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to control viral infection. Various viral proteins have been identified as potential drug targets, however, to date, no specific therapeutic cure is available against the SARS-CoV-2. To address this issue, the present work reports a systematic cheminformatic approach to identify the potent andrographolide derivatives that can target methyltransferases of SARS-CoV-2, i.e. nsp14 and nsp16 which are crucial for the replication of the virus and host immune evasion. A consensus of cheminformatics methodologies including virtual screening, molecular docking, ADMET profiling, molecular dynamics simulations, free-energy landscape analysis, molecular mechanics generalized born surface area (MM-GBSA), and density functional theory (DFT) was utilized. Our study reveals two new andrographolide derivatives (PubChem CID: 2734589 and 138968421) as natural bioactive molecules that can form stable complexes with both proteins via hydrophobic interactions, hydrogen bonds and electrostatic interactions. The toxicity analysis predicts class four toxicity for both compounds with LD50 value in the range of 500-700 mg/kg. MD simulation reveals the stable formation of the complex for both the compounds and their average trajectory values were found to be lower than the control inhibitor and protein alone. MMGBSA analysis corroborates the MD simulation result and showed the lowest energy for the compounds 2734589 and 138968421. The DFT and MEP analysis also predicts the better reactivity and stability of both the hit compounds. Overall, both andrographolide derivatives exhibit good potential as potent inhibitors for both nsp14 and nsp16 proteins, however, in-vitro and in vivo assessment would be required to prove their efficacy and safety in clinical settings. Moreover, the drug discovery strategy aiming at the dual target approach might serve as a useful model for inventing novel drug molecules for various other diseases.
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Affiliation(s)
- Jobin Thomas
- Centre for Nanobiotechnology (CNBT), Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Anupam Ghosh
- NanoBio Research Lab, School of Nano Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721301, India
| | - Shivendu Ranjan
- NanoBio Research Lab, School of Nano Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721301, India
| | - Jitendra Satija
- Centre for Nanobiotechnology (CNBT), Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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4
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Scheim DE, Parry PI, Rabbolini DJ, Aldous C, Yagisawa M, Clancy R, Borody TJ, Hoy WE. Back to the Basics of SARS-CoV-2 Biochemistry: Microvascular Occlusive Glycan Bindings Govern Its Morbidities and Inform Therapeutic Responses. Viruses 2024; 16:647. [PMID: 38675987 PMCID: PMC11054389 DOI: 10.3390/v16040647] [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: 03/14/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Consistent with the biochemistry of coronaviruses as well established over decades, SARS-CoV-2 makes its initial attachment to host cells through the binding of its spike protein (SP) to sialylated glycans (containing the monosaccharide sialic acid) on the cell surface. The virus can then slide over and enter via ACE2. SARS-CoV-2 SP attaches particularly tightly to the trillions of red blood cells (RBCs), platelets and endothelial cells in the human body, each cell very densely coated with sialic acid surface molecules but having no ACE2 or minimal ACE2. These interlaced attachments trigger the blood cell aggregation, microvascular occlusion and vascular damage that underlie the hypoxia, blood clotting and related morbidities of severe COVID-19. Notably, the two human betacoronaviruses that express a sialic acid-cleaving enzyme are benign, while the other three-SARS, SARS-CoV-2 and MERS-are virulent. RBC aggregation experimentally induced in several animal species using an injected polysaccharide caused most of the same morbidities of severe COVID-19. This glycan biochemistry is key to disentangling controversies that have arisen over the efficacy of certain generic COVID-19 treatment agents and the safety of SP-based COVID-19 vaccines. More broadly, disregard for the active physiological role of RBCs yields unreliable or erroneous reporting of pharmacokinetic parameters as routinely obtained for most drugs and other bioactive agents using detection in plasma, with whole-blood levels being up to 30-fold higher. Appreciation of the active role of RBCs can elucidate the microvascular underpinnings of other health conditions, including cardiovascular disease, and therapeutic opportunities to address them.
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Affiliation(s)
- David E. Scheim
- US Public Health Service, Commissioned Corps, Inactive Reserve, Blacksburg, VA 24060, USA
| | - Peter I. Parry
- Children’s Health Research Clinical Unit, Faculty of Medicine, The University of Queensland, South Brisbane, QLD 4101, Australia;
- Department of Psychiatry, Flinders University, Bedford Park, SA 5042, Australia
| | - David J. Rabbolini
- Kolling Institute, Faculty of Medicine and Health, The University of Sydney, St Leonards, NSW 2064, Australia
| | - Colleen Aldous
- College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa;
| | - Morimasa Yagisawa
- Satoshi Omura Memorial Research Institute, Kitasato University, Tokyo 108-8641, Japan
- Louis Pasteur Center for Medical Research, Kyoto 606-8225, Japan
| | - Robert Clancy
- Emeritus Professor, School of Medicine and Public Health, University of Newcastle, Newcastle, NE1 7RU, Australia
| | | | - Wendy E. Hoy
- Emeritus Professor of Medicine, University of Queensland, Herston, QLD 4029, Australia
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5
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Fedurek P, Asiimwe C, Rice GK, Akankwasa WJ, Reynolds V, Hobaiter C, Kityo R, Muhanguzi G, Zuberbühler K, Crockford C, Cer RZ, Bennett AJ, Rothman JM, Bishop-Lilly KA, Goldberg TL. Selective deforestation and exposure of African wildlife to bat-borne viruses. Commun Biol 2024; 7:470. [PMID: 38649441 PMCID: PMC11035629 DOI: 10.1038/s42003-024-06139-z] [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: 05/23/2023] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Proposed mechanisms of zoonotic virus spillover often posit that wildlife transmission and amplification precede human outbreaks. Between 2006 and 2012, the palm Raphia farinifera, a rich source of dietary minerals for wildlife, was nearly extirpated from Budongo Forest, Uganda. Since then, chimpanzees, black-and-white colobus, and red duiker were observed feeding on bat guano, a behavior not previously observed. Here we show that guano consumption may be a response to dietary mineral scarcity and may expose wildlife to bat-borne viruses. Videos from 2017-2019 recorded 839 instances of guano consumption by the aforementioned species. Nutritional analysis of the guano revealed high concentrations of sodium, potassium, magnesium and phosphorus. Metagenomic analyses of the guano identified 27 eukaryotic viruses, including a novel betacoronavirus. Our findings illustrate how "upstream" drivers such as socioeconomics and resource extraction can initiate elaborate chains of causation, ultimately increasing virus spillover risk.
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Affiliation(s)
- Pawel Fedurek
- Division of Psychology, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
- Budongo Conservation Field Station, PO Box 362, Masindi, Uganda
| | | | - Gregory K Rice
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, 21702, USA
- Leidos, 1750 Presidents St, Reston, VA, 20190, USA
| | | | - Vernon Reynolds
- Budongo Conservation Field Station, PO Box 362, Masindi, Uganda
- School of Anthropology, University of Oxford, 51/53 Banbury Road, Oxford, OX2 6PE, UK
| | - Catherine Hobaiter
- Budongo Conservation Field Station, PO Box 362, Masindi, Uganda
- School of Psychology and Neuroscience, University of St Andrews; St Mary's Quad, South Street, St Andrews, KY16 9JP, UK
| | - Robert Kityo
- Department of Zoology, Entomology & Fisheries Sciences, Makerere University, PO Box 7062, Kampala, Uganda
| | | | - Klaus Zuberbühler
- Budongo Conservation Field Station, PO Box 362, Masindi, Uganda
- School of Psychology and Neuroscience, University of St Andrews; St Mary's Quad, South Street, St Andrews, KY16 9JP, UK
- Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000, Neuchâtel, Switzerland
| | - Catherine Crockford
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
- Institut des Sciences Cognitives, 67 Bd Pinel, 69500, Bron, France
| | - Regina Z Cer
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, 21702, USA
| | - Andrew J Bennett
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, 21702, USA
- Leidos, 1750 Presidents St, Reston, VA, 20190, USA
| | - Jessica M Rothman
- Department of Anthropology, Hunter College of the City University of New York, 695 Park Avenue, New York, NY, 10065, USA
| | - Kimberly A Bishop-Lilly
- Biological Defense Research Directorate, Naval Medical Research Command, Fort Detrick, MD, 21702, USA
| | - Tony L Goldberg
- School of Veterinary Medicine, Department of Pathobiological Sciences, University of Wisconsin-Madison, 1656 Linden Drive, Madison, WI, USA.
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6
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Xie Y, Butler M. N-glycomic profiling of capsid proteins from Adeno-Associated Virus serotypes. Glycobiology 2024; 34:cwad074. [PMID: 37774344 PMCID: PMC10950483 DOI: 10.1093/glycob/cwad074] [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: 05/01/2023] [Revised: 09/14/2023] [Accepted: 09/23/2023] [Indexed: 10/01/2023] Open
Abstract
Adeno-associated virus (AAV) vector has become the leading platform for gene delivery. Each serotype exhibits a different tissue tropism, immunogenicity, and in vivo transduction performance. Therefore, selecting the most suitable AAV serotype is critical for efficient gene delivery to target cells or tissues. Genome divergence among different serotypes is due mainly to the hypervariable regions of the AAV capsid proteins. However, the heterogeneity of capsid glycosylation is largely unexplored. In the present study, the N-glycosylation profiles of capsid proteins of AAV serotypes 1 to 9 have been systemically characterized and compared using a previously developed high-throughput and high-sensitivity N-glycan profiling platform. The results showed that all 9 investigated AAV serotypes were glycosylated, with comparable profiles. The most conspicuous feature was the high abundance mannosylated N-glycans, including FM3, M5, M6, M7, M8, and M9, that dominated the chromatograms within a range of 74 to 83%. Another feature was the relatively lower abundance of fucosylated and sialylated N-glycan structures, in the range of 23%-40% and 10%-17%, respectively. However, the exact N-glycan composition differed. These differences may be utilized to identify potential structural relationships between the 9 AAV serotypes. The current research lays the foundation for gaining better understanding of the importance of N-glycans on the AAV capsid surface that may play a significant role in tissue tropism, interaction with cell surface receptors, cellular uptake, and intracellular processing.
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Affiliation(s)
- Yongjing Xie
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland
| | - Michael Butler
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, A94 X099, Ireland
- School of Chemical and Bioprocess Engineering, University College Dublin (UCD), Belfield, Dublin 4, D04 V1W8, Ireland
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7
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Thomas J, Kumar S, Satija J. Integrated molecular and quantum mechanical approach to identify novel potent natural bioactive compound against 2'-O-methyltransferase (nsp16) of SARS-CoV-2. J Biomol Struct Dyn 2024; 42:1999-2012. [PMID: 37129206 DOI: 10.1080/07391102.2023.2206287] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 04/09/2023] [Indexed: 05/03/2023]
Abstract
With the advent of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak, efforts are still in progress to find out a functional cure for the infection. Among the various protein targets, nsp16 capping protein is one of the vital targets for drug development as it protects the virus against the host cell nucleases and evading innate immunity. The nsp16 protein forms a heterodimer with a co-factor nsp10 and triggers 2'-O-methyltransferase activity which catalyzes the conversion of S-adenosyl methionine into S-adenosyl homocysteine. The free methyl group is transferred to the 2'-O position on ribose sugar at the 5' end of mRNA to form the cap-1 structure which is essential for replication of the virus and evading the innate immunity of the host. In this study, we identify a potential lead natural bioactive compound against nsp16 protein by systematic cheminformatic analysis of more than 144k natural compounds. Virtual screening, molecular docking interactions, ADMET profiling, molecular dynamics (MD) simulations, molecular mechanics-generalized born surface area (MM-GBSA), free energy analysis and density functional theory analysis were used to discover the potential lead compound. Our investigation revealed that ZINC8952607 (methyl-[(6-methyl-2,3,4,9-tetrahydro-1H-carbazol-1-yl)aminomethyl]BLAHone) has the greatest binding affinity and best pharmacokinetic parameters due to presence of carbazol and BLAHone (biaryl moiety). Further, time-dependent MD simulation analysis substantiates the stability and rigidness of nsp16 protein even after interaction with the lead compound. We believe that the compound ZINC8952607 might establish as a novel natural drug candidate against CoVID-19 infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jobin Thomas
- Centre for Nanobiotechnology (CNBT), Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Sanjit Kumar
- Centre for Bio-Separation and Technology (CBST), Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Jitendra Satija
- Centre for Nanobiotechnology (CNBT), Vellore Institute of Technology, Vellore, Tamil Nadu, India
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8
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Gonzalez-Garcia P, Fiorillo Moreno O, Zarate Peñata E, Calderon-Villalba A, Pacheco Lugo L, Acosta Hoyos A, Villarreal Camacho JL, Navarro Quiroz R, Pacheco Londoño L, Aroca Martinez G, Moares N, Gabucio A, Fernandez-Ponce C, Garcia-Cozar F, Navarro Quiroz E. From Cell to Symptoms: The Role of SARS-CoV-2 Cytopathic Effects in the Pathogenesis of COVID-19 and Long COVID. Int J Mol Sci 2023; 24:ijms24098290. [PMID: 37175995 PMCID: PMC10179575 DOI: 10.3390/ijms24098290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) infection triggers various events from molecular to tissue level, which in turn is given by the intrinsic characteristics of each patient. Given the molecular diversity characteristic of each cellular phenotype, the possible cytopathic, tissue and clinical effects are difficult to predict, which determines the heterogeneity of COVID-19 symptoms. The purpose of this article is to provide a comprehensive review of the cytopathic effects of SARS-CoV-2 on various cell types, focusing on the development of COVID-19, which in turn may lead, in some patients, to a persistence of symptoms after recovery from the disease, a condition known as long COVID. We describe the molecular mechanisms underlying virus-host interactions, including alterations in protein expression, intracellular signaling pathways, and immune responses. In particular, the article highlights the potential impact of these cytopathies on cellular function and clinical outcomes, such as immune dysregulation, neuropsychiatric disorders, and organ damage. The article concludes by discussing future directions for research and implications for the management and treatment of COVID-19 and long COVID.
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Affiliation(s)
| | - Ornella Fiorillo Moreno
- Clínica Iberoamerica, Barranquilla 080001, Colombia
- Life Science Research Center, Universidad Simon Bolívar, Barranquilla 080001, Colombia
| | - Eloina Zarate Peñata
- Life Science Research Center, Universidad Simon Bolívar, Barranquilla 080001, Colombia
| | | | - Lisandro Pacheco Lugo
- Life Science Research Center, Universidad Simon Bolívar, Barranquilla 080001, Colombia
| | - Antonio Acosta Hoyos
- Life Science Research Center, Universidad Simon Bolívar, Barranquilla 080001, Colombia
| | | | - Roberto Navarro Quiroz
- Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona, Spanish National Research Council, 08028 Barcelona, Spain
| | | | - Gustavo Aroca Martinez
- Life Science Research Center, Universidad Simon Bolívar, Barranquilla 080001, Colombia
- School of Medicine, Universidad del Norte, Barranquilla 080001, Colombia
| | - Noelia Moares
- Department of Biomedicine, Biotechnology and Public Health, Faculty of Medicine, University of Cadiz, 11003 Cádiz, Spain
| | - Antonio Gabucio
- Department of Biomedicine, Biotechnology and Public Health, Faculty of Medicine, University of Cadiz, 11003 Cádiz, Spain
| | - Cecilia Fernandez-Ponce
- Institute of Biomedical Research Cadiz (INIBICA), 11009 Cádiz, Spain
- Department of Biomedicine, Biotechnology and Public Health, Faculty of Medicine, University of Cadiz, 11003 Cádiz, Spain
| | - Francisco Garcia-Cozar
- Institute of Biomedical Research Cadiz (INIBICA), 11009 Cádiz, Spain
- Department of Biomedicine, Biotechnology and Public Health, Faculty of Medicine, University of Cadiz, 11003 Cádiz, Spain
| | - Elkin Navarro Quiroz
- Life Science Research Center, Universidad Simon Bolívar, Barranquilla 080001, Colombia
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Erten M, Acharya MR, Kamath AP, Sampathila N, Bairy GM, Aydemir E, Barua PD, Baygin M, Tuncer I, Dogan S, Tuncer T. Hamlet-Pattern-Based Automated COVID-19 and Influenza Detection Model Using Protein Sequences. Diagnostics (Basel) 2022; 12:diagnostics12123181. [PMID: 36553188 PMCID: PMC9777168 DOI: 10.3390/diagnostics12123181] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 and Influenza-A can present similar symptoms. Computer-aided diagnosis can help facilitate screening for the two conditions, and may be especially relevant and useful in the current COVID-19 pandemic because seasonal Influenza-A infection can still occur. We have developed a novel text-based classification model for discriminating between the two conditions using protein sequences of varying lengths. We downloaded viral protein sequences of SARS-CoV-2 and Influenza-A with varying lengths (all 100 or greater) from the NCBI database and randomly selected 16,901 SARS-CoV-2 and 19,523 Influenza-A sequences to form a two-class study dataset. We used a new feature extraction function based on a unique pattern, HamletPat, generated from the text of Shakespeare's Hamlet, and a signum function to extract local binary pattern-like bits from overlapping fixed-length (27) blocks of the protein sequences. The bits were converted to decimal map signals from which histograms were extracted and concatenated to form a final feature vector of length 1280. The iterative Chi-square function selected the 340 most discriminative features to feed to an SVM with a Gaussian kernel for classification. The model attained 99.92% and 99.87% classification accuracy rates using hold-out (75:25 split ratio) and five-fold cross-validations, respectively. The excellent performance of the lightweight, handcrafted HamletPat-based classification model suggests that it can be a valuable tool for screening protein sequences to discriminate between SARS-CoV-2 and Influenza-A infections.
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Affiliation(s)
- Mehmet Erten
- Laboratory of Medical Biochemistry, Malatya Training and Research Hospital, 44000 Malatya, Turkey
| | - Madhav R Acharya
- Department of Biomedical Engineering, Manipal Academy of Higher Education, Manipal 04478, India
| | - Aditya P Kamath
- Center for Biomedical Engineering, Brown University, Providence, RI 02912, USA
| | - Niranjana Sampathila
- Department of Biomedical Engineering, Manipal Academy of Higher Education, Manipal 04478, India
| | - G Muralidhar Bairy
- Department of Biomedical Engineering, Manipal Academy of Higher Education, Manipal 04478, India
| | - Emrah Aydemir
- Department of Management Information, College of Management, Sakarya University, 54050 Sakarya, Turkey
| | - Prabal Datta Barua
- School of Management & Enterprise, University of Southern Queensland, Toowoomba, QLD 4350, Australia
- Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Mehmet Baygin
- Department of Computer Engineering, Faculty of Engineering, Ardahan University, 75000 Ardahan, Turkey
| | - Ilknur Tuncer
- Elazig Governorship, Interior Ministry, 23119 Elazig, Turkey
| | - Sengul Dogan
- Department of Digital Forensics Engineering, Technology Faculty, Firat University, 23119 Elazig, Turkey
| | - Turker Tuncer
- Department of Digital Forensics Engineering, Technology Faculty, Firat University, 23119 Elazig, Turkey
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10
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dos Santos AAC, Rodrigues LE, Alecrim-Zeza AL, de Araújo Ferreira L, Trettel CDS, Gimenes GM, da Silva AF, Sousa-Filho CPB, Serdan TDA, Levada-Pires AC, Hatanaka E, Borges FT, de Barros MP, Cury-Boaventura MF, Bertolini GL, Cassolla P, Marzuca-Nassr GN, Vitzel KF, Pithon-Curi TC, Masi LN, Curi R, Gorjao R, Hirabara SM. Molecular and cellular mechanisms involved in tissue-specific metabolic modulation by SARS-CoV-2. Front Microbiol 2022; 13:1037467. [PMID: 36439786 PMCID: PMC9684198 DOI: 10.3389/fmicb.2022.1037467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/26/2022] [Indexed: 09/09/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is triggered by the SARS-CoV-2, which is able to infect and cause dysfunction not only in lungs, but also in multiple organs, including central nervous system, skeletal muscle, kidneys, heart, liver, and intestine. Several metabolic disturbances are associated with cell damage or tissue injury, but the mechanisms involved are not yet fully elucidated. Some potential mechanisms involved in the COVID-19-induced tissue dysfunction are proposed, such as: (a) High expression and levels of proinflammatory cytokines, including TNF-α IL-6, IL-1β, INF-α and INF-β, increasing the systemic and tissue inflammatory state; (b) Induction of oxidative stress due to redox imbalance, resulting in cell injury or death induced by elevated production of reactive oxygen species; and (c) Deregulation of the renin-angiotensin-aldosterone system, exacerbating the inflammatory and oxidative stress responses. In this review, we discuss the main metabolic disturbances observed in different target tissues of SARS-CoV-2 and the potential mechanisms involved in these changes associated with the tissue dysfunction.
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Affiliation(s)
| | - Luiz Eduardo Rodrigues
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brazil
| | - Amanda Lins Alecrim-Zeza
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brazil
| | - Liliane de Araújo Ferreira
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brazil
| | - Caio dos Santos Trettel
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brazil
| | - Gabriela Mandú Gimenes
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brazil
| | - Adelson Fernandes da Silva
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brazil
| | | | - Tamires Duarte Afonso Serdan
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brazil
- Department of Molecular Pathobiology, University of New York, New York, NY, United States
| | - Adriana Cristina Levada-Pires
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brazil
| | - Elaine Hatanaka
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brazil
| | - Fernanda Teixeira Borges
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brazil
- Divisão de Nefrologia, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Marcelo Paes de Barros
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brazil
| | - Maria Fernanda Cury-Boaventura
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brazil
| | - Gisele Lopes Bertolini
- Department of Physiological Sciences, Biological Science Center, State University of Londrina, Londrina, PR, Brazil
| | - Priscila Cassolla
- Department of Physiological Sciences, Biological Science Center, State University of Londrina, Londrina, PR, Brazil
| | | | - Kaio Fernando Vitzel
- School of Health Sciences, College of Health, Massey University, Auckland, New Zealand
| | - Tania Cristina Pithon-Curi
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brazil
| | - Laureane Nunes Masi
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brazil
| | - Rui Curi
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brazil
- Instituto Butantan, São Paulo, Brazil
| | - Renata Gorjao
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brazil
| | - Sandro Massao Hirabara
- Programa de Pós-graduação Interdisciplinar em Ciências da Saúde, Universidade Cruzeiro do Sul, São Paulo, São Paulo, Brazil
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11
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Al-Humaidi JY, Shaaban MM, Rezki N, Aouad MR, Zakaria M, Jaremko M, Hagar M, Elwakil BH. 1,2,3-Triazole-Benzofused Molecular Conjugates as Potential Antiviral Agents against SARS-CoV-2 Virus Variants. Life (Basel) 2022; 12:life12091341. [PMID: 36143380 PMCID: PMC9502539 DOI: 10.3390/life12091341] [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: 07/08/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 and its variants, especially the Omicron variant, remain a great threat to human health. The need to discover potent compounds that may control the SARS-CoV-2 virus pandemic and the emerged mutants is rising. A set of 1,2,3-triazole and/or 1,2,4-triazole was synthesized either from benzimidazole or isatin precursors. Molecular docking studies and in vitro enzyme activity revealed that most of the investigated compounds demonstrated promising binding scores against the SARS-CoV-2 and Omicron spike proteins, in comparison to the reference drugs. In particular, compound 9 has the highest scoring affinity against the SARS-CoV-2 and Omicron spike proteins in vitro with its IC50 reaching 75.98 nM against the Omicron spike protein and 74.51 nM against the SARS-CoV-2 spike protein. The possible interaction between the synthesized triazoles and the viral spike proteins was by the prevention of the viral entry into the host cells, which led to a reduction in viral reproduction and infection. A cytopathic inhibition assay in the human airway epithelial cell line (Vero E6) infected with SARS-CoV-2 revealed the effectiveness and safety of the synthesized compound (compound 9) (EC50 and CC50 reached 80.4 and 1028.28 µg/mL, respectively, with a selectivity index of 12.78). Moreover, the antiinflammatory effect of the tested compound may pave the way to reduce the reported SARS-CoV-2-induced hyperinflammation.
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Affiliation(s)
- Jehan Y. Al-Humaidi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Marwa M. Shaaban
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Nadjet Rezki
- Department of Chemistry, College of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia
| | - Mohamed R. Aouad
- Department of Chemistry, College of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia
| | - Mohamed Zakaria
- Department of Chemistry, Faculty of Science, Alexandria University, Alexandria 21321, Egypt
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Mohamed Hagar
- Department of Chemistry, Faculty of Science, Alexandria University, Alexandria 21321, Egypt
- Correspondence: (M.H.); (B.H.E.)
| | - Bassma H. Elwakil
- Department of Medical Laboratory Technology, Faculty of Applied Health Sciences Technology, Pharos University in Alexandria, Alexandria 21521, Egypt
- Correspondence: (M.H.); (B.H.E.)
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12
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Hamdy R, Soliman SSM. Response to the letter, entitled 'Haemagglutinin, neuraminidase and haemagglutinin esterase on the surface of SARS-CoV-2?'. Rev Med Virol 2022; 32:e2387. [PMID: 36029483 PMCID: PMC9538454 DOI: 10.1002/rmv.2387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Rania Hamdy
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
| | - Sameh S M Soliman
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE.,College of Pharmacy, University of Sharjah, Sharjah, UAE
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13
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The Influence of Viral Infections on Iron Homeostasis and the Potential for Lactoferrin as a Therapeutic in the Age of the SARS-CoV-2 Pandemic. Nutrients 2022; 14:nu14153090. [PMID: 35956266 PMCID: PMC9370565 DOI: 10.3390/nu14153090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
The association of hyperinflammation and hyperferritinemia with adverse outcomes in SARS-CoV-2-infected patients suggests an integral role for iron homeostasis in pathogenesis, a commonly described symptom of respiratory viral infections. This dysregulated iron homeostasis results in viral-induced lung injury, often lasting long after the acute viral infection; however, much remains to be understood mechanistically. Lactoferrin is a multipurpose glycoprotein with key immunomodulatory, antimicrobial, and antiviral functions, which can be found in various secreted fluids, but is most abundantly characterized in milk from all mammalian species. Lactoferrin is found at its highest concentrations in primate colostrum; however, the abundant availability of bovine-dairy-derived lactoferrin (bLf) has led to the use of bLf as a functional food. The recent research has demonstrated the potential value of bovine lactoferrin as a therapeutic adjuvant against SARS-CoV-2, and herein this research is reviewed and the potential mechanisms of therapeutic targeting are considered.
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14
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An Overview of Systematic Reviews of the Role of Vitamin D on Inflammation in Patients with Diabetes and the Potentiality of Its Application on Diabetic Patients with COVID-19. Int J Mol Sci 2022; 23:ijms23052873. [PMID: 35270015 PMCID: PMC8911457 DOI: 10.3390/ijms23052873] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/25/2022] [Accepted: 02/25/2022] [Indexed: 02/04/2023] Open
Abstract
Almost two years have passed since the outbreak reported for the first time in Wuhan of coronavirus disease 2019 (COVID-19), due to severe acute respiratory syndrome (SARS)-CoV-2 coronavirus, rapidly evolved into a pandemic. This infectious disease has stressed global health care systems. The mortality rate is higher, particularly in elderly population and in patients with comorbidities such as hypertension, diabetes mellitus, cardiovascular disease, chronic lung disease, chronic renal disease, and malignancy. Among them, subjects with diabetes have a high risk of developing severe form of COVID-19 and show increased mortality. How diabetes contributes to COVID-19 severity remains unclear. It has been hypothesized that it may be correlated with the effects of hyperglycemia on systemic inflammatory responses and immune system dysfunction. Vitamin D (VD) is a modulator of immune-response. Data from literature showed that vitamin D deficiency in COVID-19 patients increases COVID-19 severity, likely because of its negative impact on immune and inflammatory responses. Therefore, the use of vitamin D might play a role in some aspects of the infection, particularly the inflammatory state and the immune system function of patients. Moreover, a piece of evidence highlighted a link among vitamin D deficiency, obesity and diabetes, all factors associated with COVID-19 severity. Given this background, we performed an overview of the systematic reviews to assess the association between vitamin D supplementation and inflammatory markers in patients with diabetes; furthermore, vitamin D’s possible role in COVID-19 patients was assessed as well. Three databases, namely MEDLINE, PubMed Central and the Cochrane Library of Systematic Reviews, were reviewed to retrieve the pertinent data. The aim of this review is to provide insight into the recent advances about the molecular basis of the relationship between vitamin D, immune response, inflammation, diabetes and COVID-19.
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15
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Cavezzi A, Menicagli R, Troiani E, Corrao S. COVID-19, Cation Dysmetabolism, Sialic Acid, CD147, ACE2, Viroporins, Hepcidin and Ferroptosis: A Possible Unifying Hypothesis. F1000Res 2022; 11:102. [PMID: 35340277 PMCID: PMC8921693 DOI: 10.12688/f1000research.108667.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/17/2022] [Indexed: 12/15/2022] Open
Abstract
Background: iron and calcium dysmetabolism, with hyperferritinemia, hypoferremia, hypocalcemia and anemia have been documented in the majority of COVID-19 patients at later/worse stages. Furthermore, complementary to ACE2, both sialic acid (SA) molecules and CD147 proved relevant host receptors for SARS-CoV-2 entry, which explains the viral attack to multiple types of cells, including erythrocytes, endothelium and neural tissue. Several authors advocated that cell ferroptosis may be the core and final cell degenerative mechanism. Methods: a literature research was performed in several scientific search engines, such as PubMed Central, Cochrane Library, Chemical Abstract Service. More than 500 articles were retrieved until mid-December 2021, to highlight the available evidence about the investigated issues. Results: based on COVID-19 literature data, we have highlighted a few pathophysiological mechanisms, associated with virus-based cation dysmetabolism, multi-organ attack, mitochondria degeneration and ferroptosis. Our suggested elucidated pathological sequence is: a) spike protein subunit S1 docking with sialylated membrane glycoproteins/receptors (ACE2, CD147), and S2 subunit fusion with the lipid layer; b) cell membrane morpho-functional changes due to the consequent electro-chemical variations and viroporin action, which induce an altered ion channel function and intracellular cation accumulation; c) additional intracellular iron concentration due to a deregulated hepcidin-ferroportin axis, with higher hepcidin levels. Viral invasion may also affect erythrocytes/erythroid precursors, endothelial cells and macrophages, through SA and CD147 receptors, with relative hemoglobin and iron/calcium dysmetabolism. AB0 blood group, hemochromatosis, or environmental elements may represent possible factors which affect individual susceptibility to COVID-19. Conclusions: our literature analysis confirms the combined role of SA molecules, ACE2, CD147, viroporins and hepcidin in determining the cation dysmetabolism and final ferroptosis in the cells infected by SARS-CoV-2. The altered ion channels and electrochemical gradients of the cell membrane have a pivotal role in the virus entry and cell dysmetabolism, with subsequent multi-organ immune-inflammatory degeneration and erythrocyte/hemoglobin alterations.
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Affiliation(s)
- Attilio Cavezzi
- Eurocenter Venalinfa, San Benedetto del Tronto, AP, 63074, Italy
| | | | - Emidio Troiani
- Cardiology Unit, Social Security Institute, State Hospital, Cailungo, 47893, San Marino
| | - Salvatore Corrao
- Department of Clinical Medicine, Internal Medicine Division,, ARNAS Civico Di Cristina Benfratelli Hospital Trust, Palermo, Italy
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16
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Robson B. Towards faster response against emerging epidemics and prediction of variants of concern. INFORMATICS IN MEDICINE UNLOCKED 2022; 31:100966. [PMID: 35611320 PMCID: PMC9119712 DOI: 10.1016/j.imu.2022.100966] [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: 03/23/2022] [Revised: 05/05/2022] [Accepted: 05/11/2022] [Indexed: 01/11/2023] Open
Abstract
The author, the journal, Computers in Biology and Medicine (CBM), and Elsevier Press more generally, played a helpful very early role in responding to COVID-19. Within a few days of the appearance of the "Wuhan Seafood isolate" genome on GenBank, a bioinformatics study was posted by the present author in ResearchGate in January 2020, "Preliminary Bioinformatics Studies on the Design of Synthetic Vaccines and Preventative Peptidomimetic Antagonists against the Wuhan Seafood Market Coronavirus. Possible Importance of the KRSFIEDLLFNKV Motif" DOI: 10.13140/RG.2.2.18275.09761. On February 2nd, 2020, a more thorough analysis was submitted to CBM, e-published on February 26, and formally published in April 2020, at about the same time as the virus named as 2019n-CoV was identified as essentially SARS and renames SARS-COV-2. This was followed by four further papers describing in more detail some previously unreported aspects of the early investigation. The speed of research and writing of the papers was made possible by knowledge-gathering tools. Based on this and earlier experiences with fast responses to emerging epidemics such as HIV and Mad Cow Disease, it is possible to envisage the nature of a speedier response to emerging epidemics and new variants of concern in established epidemics.
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Affiliation(s)
- B Robson
- Ingine Inc., Cleveland, Ohio, USA.,The Dirac Foundation, Oxfordshire, UK
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17
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Yang Q, Jian X, Syed AAS, Fahira A, Zheng C, Zhu Z, Wang K, Zhang J, Wen Y, Li Z, Pan D, Lu T, Wang Z, Shi Y. Structural Comparison and Drug Screening of Spike Proteins of Ten SARS-CoV-2 Variants. RESEARCH (WASHINGTON, D.C.) 2022; 2022:9781758. [PMID: 35198984 PMCID: PMC8829538 DOI: 10.34133/2022/9781758] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/30/2021] [Indexed: 12/14/2022]
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) has evolved many variants with stronger infectivity and immune evasion than the original strain, including Alpha, Beta, Gamma, Delta, Epsilon, Kappa, Iota, Lambda, and 21H strains. Amino acid mutations are enriched in the spike protein of SARS-CoV-2, which plays a crucial role in cell infection. However, the impact of these mutations on protein structure and function is unclear. Understanding the pathophysiology and pandemic features of these SARS-CoV-2 variants requires knowledge of the spike protein structures. Here, we obtained the spike protein structures of 10 main globally endemic SARS-CoV-2 strains using AlphaFold2. The clustering analysis based on structural similarity revealed the unique features of the mainly pandemic SARS-CoV-2 Delta variants, indicating that structural clusters can reflect the current characteristics of the epidemic more accurately than those based on the protein sequence. The analysis of the binding affinities of ACE2-RBD, antibody-NTD, and antibody-RBD complexes in the different variants revealed that the recognition of antibodies against S1 NTD and RBD was decreased in the variants, especially the Delta variant compared with the original strain, which may induce the immune evasion of SARS-CoV-2 variants. Furthermore, by virtual screening the ZINC database against a high-accuracy predicted structure of Delta spike protein and experimental validation, we identified multiple compounds that target S1 NTD and RBD, which might contribute towards the development of clinical anti-SARS-CoV-2 medicines. Our findings provided a basic foundation for future in vitro and in vivo investigations that might speed up the development of potential therapies for the SARS-CoV-2 variants.
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Affiliation(s)
- Qiangzhen Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Xuemin Jian
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Ali Alamdar Shah Syed
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Aamir Fahira
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Chenxiang Zheng
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Zijia Zhu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Ke Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Jinmai Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Yanqin Wen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Zhiqiang Li
- Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao 266003, China
| | - Dun Pan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Tingting Lu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Zhuo Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, China
- Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao 266003, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Department of Psychiatry, First Teaching Hospital of Xinjiang Medical University, Urumqi 830046, China
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18
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Robson B, Boray S, Weisman J. Mining real-world high dimensional structured data in medicine and its use in decision support. Some different perspectives on unknowns, interdependency, and distinguishability. Comput Biol Med 2021; 141:105118. [PMID: 34971979 DOI: 10.1016/j.compbiomed.2021.105118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/18/2021] [Accepted: 12/02/2021] [Indexed: 11/03/2022]
Abstract
There are many difficulties in extracting and using knowledge for medical analytic and predictive purposes from Real-World Data, even when the data is already well structured in the manner of a large spreadsheet. Preparative curation and standardization or "normalization" of such data involves a variety of chores but underlying them is an interrelated set of fundamental problems that can in part be dealt with automatically during the datamining and inference processes. These fundamental problems are reviewed here and illustrated and investigated with examples. They concern the treatment of unknowns, the need to avoid independency assumptions, and the appearance of entries that may not be fully distinguished from each other. Unknowns include errors detected as implausible (e.g., out of range) values that are subsequently converted to unknowns. These problems are further impacted by high dimensionality and problems of sparse data that inevitably arise from high-dimensional datamining even if the data is extensive. All these considerations are different aspects of incomplete information, though they also relate to problems that arise if care is not taken to avoid or ameliorate consequences of including the same information twice or more, or if misleading or inconsistent information is combined. This paper addresses these aspects from a slightly different perspective using the Q-UEL language and inference methods based on it by borrowing some ideas from the mathematics of quantum mechanics and information theory. It takes the view that detection and correction of probabilistic elements of knowledge subsequently used in inference need only involve testing and correction so that they satisfy certain extended notions of coherence between probabilities. This is by no means the only possible view, and it is explored here and later compared with a related notion of consistency.
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Affiliation(s)
- Barry Robson
- Ingine Inc, Ohio, USA; The Dirac Foundation, Oxfordshire, UK.
| | | | - J Weisman
- The Dirac Foundation, Oxfordshire, UK.
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Haroun RAH, Osman WH, Eessa AM. Evaluation of serum total sialic acid in moderate COVID-19 patients with and without gastrointestinal tract manifestations. Tissue Cell 2021; 74:101679. [PMID: 34801789 PMCID: PMC8598396 DOI: 10.1016/j.tice.2021.101679] [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: 09/27/2021] [Revised: 10/31/2021] [Accepted: 11/09/2021] [Indexed: 12/15/2022]
Abstract
Background It is known that SARS-CoV-2 mostly infects the respiratory system causing pneumonia; although it can also affect the gastrointestinal tract (GIT), which covered with a bi-layer of mucus rich in glycosylated proteins that terminated by sialic acid. Therefore; this study aimed to evaluate serum total sialic acid (TSA) in moderate COVID-19 patients with and without GIT manifestations. Methods A total of 161 moderate COVID-19 patients without and with GIT manifestations and 50 controls were enrolled into our study. Serum electrolytes levels were measured by using colorimetric or turbidmetric commercial assay kits, while the level of serum TSA was measured by using a commercial ELISA kit. Results Our results showed that serum TSA level was highly significantly increased in moderate COVID-19 patients with GIT manifestations (81.43 ± 8.91) when compared with controls (61.24 ± 6.41) or even moderate COVID-19 patients without GIT manifestations (69.46 ± 7.03). ROC curve analysis showed that AUC for TSA is 0.84 with 76.2 % sensitivity and 73.7 % specificity in discrimination between moderate COVID-19 patients with and without GIT manifestations. Serum potassium and sodium levels were highly significantly decreased in moderate COVID-19 patients with GIT manifestations when compared with controls or even moderate COVID-19 patients without GIT manifestations; while serum calcium level was found to be significantly decreased in moderate COVID-19 patients with GIT manifestations when compared with controls. Conclusion Finally, we can conclude that SA plays a crucial role in the pathogenesis of GIT complications associated with COVID-19 and could be a potential biomarker for the COVID-19 gastrointestinal complications.
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Affiliation(s)
| | - Waleed H Osman
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Asmaa M Eessa
- Department of Geriatric Medicine and Gerontology, Faculty of Medicine, Port-Said University, Port-Said, Egypt
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20
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Alzahrani AY, Shaaban MM, Elwakil BH, Hamed MT, Rezki N, Aouad MR, Zakaria MA, Hagar M. Anti-COVID-19 activity of some benzofused 1,2,3-triazolesulfonamide hybrids using in silico and in vitro analyses. CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS : AN INTERNATIONAL JOURNAL SPONSORED BY THE CHEMOMETRICS SOCIETY 2021; 217:104421. [PMID: 34538993 PMCID: PMC8434689 DOI: 10.1016/j.chemolab.2021.104421] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/14/2021] [Accepted: 09/06/2021] [Indexed: 05/26/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a pandemic fatal infection with no known treatment. The severity of the disease and the fast viral mutations forced the scientific community to search for potential solution. Here in the present manuscript, some benzofused1,2,3triazolesulfonamide hybrids were synthesized and evaluated for their anti- SARS-CoV-2 activity using in silico prediction then the most potent compounds were assessed using in-Vitro analysis. The in-Silico study was assessed against RNA dependent RNA polymerase, Spike protein S1, Main protease (3CLpro) and 2'-O-methyltransferase (nsp16). It was found that 4b and 4c showed high binding scores against RNA dependent RNA polymerase reached -8.40 and -8.75 kcal/mol, respectively compared to the approved antiviral (remdesivir -6.77 kcal/mol). Upon testing the binding score with SARS-CoV-2 Spike protein it was revealed that 4c exhibited the highest score (-7.22 kcal/mol) compared to the reference antibacterial drug Ceftazidime (-6.36 kcal/mol). Surprisingly, the two compounds 4b and 4c showed the highest binding scores against SARS-CoV-2 3CLpro (-8.75, -8.48 kcal/mol, respectively) and nsp16 (- 8.84 and - 8.89 kcal/mol, respectively) displaying many types of interaction with all the enzymes binding sites. The derivatives 4b and 4c were examined in vitro for their potential anti-SARS-CoV-2 and it was revealed that 4c was the most promising compound with IC50 reached 758.8108 mM and complete (100%) inhibition of the binding of SARS-CoV-2 virus to human ACE2 can be accomplished by using 0.01 mg.
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Affiliation(s)
- Abdullah Y Alzahrani
- Department of Chemistry, Faculty of Science and Arts, King Khalid University, Mohail, Assir, Saudi Arabia
| | - Marwa M Shaaban
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt
| | - Bassma H Elwakil
- Department of Medical Laboratory Technology, Faculty of Applied Health Sciences Technology, Pharos University in Alexandria, Alexandria, Egypt
| | - Moaaz T Hamed
- Industrial Microbiology and Applied Chemistry Program, Department of Botany & Microbiology, Faculty of Science, Alexandria University, Alexandria, 21568, Egypt
| | - Nadjet Rezki
- Department of Chemistry, College of Science, Taibah University, Al-Madinah Al-Munawarah, 30002, Saudi Arabia
| | - Mohamed R Aouad
- Department of Chemistry, College of Science, Taibah University, Al-Madinah Al-Munawarah, 30002, Saudi Arabia
| | - Mohamed A Zakaria
- Department of Chemistry, College of Sciences, Taibah University, Yanbu, 30799, Saudi Arabia
| | - Mohamed Hagar
- Department of Chemistry, College of Sciences, Taibah University, Yanbu, 30799, Saudi Arabia
- Department of Chemistry, Faculty of Science, Alexandria University, Alexandria, 21321, Egypt
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21
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Robson B. Testing machine learning techniques for general application by using protein secondary structure prediction. A brief survey with studies of pitfalls and benefits using a simple progressive learning approach. Comput Biol Med 2021; 138:104883. [PMID: 34598067 DOI: 10.1016/j.compbiomed.2021.104883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/05/2021] [Accepted: 09/17/2021] [Indexed: 01/05/2023]
Abstract
Many researchers have recently used the prediction of protein secondary structure (local conformational states of amino acid residues) to test advances in predictive and machine learning technology such as Neural Net Deep Learning. Protein secondary structure prediction continues to be a helpful tool in research in biomedicine and the life sciences, but it is also extremely enticing for testing predictive methods such as neural nets that are intended for different or more general purposes. A complication is highlighted here for researchers testing their methods for other applications. Modern protein databases inevitably contain important clues to the answer, so-called "strong buried clues", though often obscurely; they are hard to avoid. This is because most proteins or parts of proteins in a modern protein data base are related to others by biological evolution. For researchers developing machine learning and predictive methods, this can overstate and so confuse understanding of the true quality of a predictive method. However, for researchers using the algorithms as tools, understanding strong buried clues is of great value, because they need to make maximum use of all information available. A simple method related to the GOR methods but with some features of neural nets in the sense of progressive learning of large numbers of weights, is used to explore this. It can acquire tens of millions and hence gigabytes of weights, but they are learned stably by exhaustive sampling. The significance of the findings is discussed in the light of promising recent results from AlphaFold using Google's DeepMind.
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Affiliation(s)
- Barry Robson
- Ingine Inc. Ohio, USA and the Dirac Foundation Oxfordshire, UK.
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22
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Lechuga GC, Souza-Silva F, Sacramento CQ, Trugilho MRO, Valente RH, Napoleão-Pêgo P, Dias SSG, Fintelman-Rodrigues N, Temerozo JR, Carels N, Alves CR, Pereira MCS, Provance DW, Souza TML, De-Simone SG. SARS-CoV-2 Proteins Bind to Hemoglobin and Its Metabolites. Int J Mol Sci 2021; 22:9035. [PMID: 34445741 PMCID: PMC8396565 DOI: 10.3390/ijms22169035] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/28/2021] [Accepted: 08/10/2021] [Indexed: 01/19/2023] Open
Abstract
(1) Background: coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been linked to hematological dysfunctions, but there are little experimental data that explain this. Spike (S) and Nucleoprotein (N) proteins have been putatively associated with these dysfunctions. In this work, we analyzed the recruitment of hemoglobin (Hb) and other metabolites (hemin and protoporphyrin IX-PpIX) by SARS-Cov2 proteins using different approaches. (2) Methods: shotgun proteomics (LC-MS/MS) after affinity column adsorption identified hemin-binding SARS-CoV-2 proteins. The parallel synthesis of the peptides technique was used to study the interaction of the receptor bind domain (RBD) and N-terminal domain (NTD) of the S protein with Hb and in silico analysis to identify the binding motifs of the N protein. The plaque assay was used to investigate the inhibitory effect of Hb and the metabolites hemin and PpIX on virus adsorption and replication in Vero cells. (3) Results: the proteomic analysis by LC-MS/MS identified the S, N, M, Nsp3, and Nsp7 as putative hemin-binding proteins. Six short sequences in the RBD and 11 in the NTD of the spike were identified by microarray of peptides to interact with Hb and tree motifs in the N protein by in silico analysis to bind with heme. An inhibitory effect in vitro of Hb, hemin, and PpIX at different levels was observed. Strikingly, free Hb at 1mM suppressed viral replication (99%), and its interaction with SARS-CoV-2 was localized into the RBD region of the spike protein. (4) Conclusions: in this study, we identified that (at least) five proteins (S, N, M, Nsp3, and Nsp7) of SARS-CoV-2 recruit Hb/metabolites. The motifs of the RDB of SARS-CoV-2 spike, which binds Hb, and the sites of the heme bind-N protein were disclosed. In addition, these compounds and PpIX block the virus's adsorption and replication. Furthermore, we also identified heme-binding motifs and interaction with hemin in N protein and other structural (S and M) and non-structural (Nsp3 and Nsp7) proteins.
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Affiliation(s)
- Guilherme C. Lechuga
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
- Laboratory of Celular Ultrastructure, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Franklin Souza-Silva
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
- Biology and Heath Science Faculty, Iguaçu University, Nova Iguaçu 26260-045, RJ, Brazil
| | - Carolina Q. Sacramento
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
- Laboratory of Immunopharmacology, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Monique R. O. Trugilho
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
- Laboratory of Toxinology, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Richard H. Valente
- Laboratory of Toxinology, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Paloma Napoleão-Pêgo
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
| | - Suelen S. G. Dias
- Laboratory of Immunopharmacology, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Natalia Fintelman-Rodrigues
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
- Laboratory of Immunopharmacology, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Jairo R. Temerozo
- Laboratory of Thymus Research, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
- FIOCRUZ, National Institute for Science and Technology on Neuroimmunomodulation (INCT/NIM), Rio de Janeiro 21040-900, RJ, Brazil
| | - Nicolas Carels
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
- Biology and Heath Science Faculty, Iguaçu University, Nova Iguaçu 26260-045, RJ, Brazil
| | - Carlos R. Alves
- Laboratory of Molecular Biology and Endemic Diseases, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Mirian C. S. Pereira
- Laboratory of Celular Ultrastructure, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
| | - David W. Provance
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
| | - Thiago M. L. Souza
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
- Laboratory of Immunopharmacology, FIOCRUZ, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, RJ, Brazil;
| | - Salvatore G. De-Simone
- FIOCRUZ, Center for Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Population Diseases (INCT-IDPN), Rio de Janeiro 21040-900, RJ, Brazil; (G.C.L.); (F.S.-S.); (C.Q.S.); (M.R.O.T.); (P.N.-P.); (N.F.-R.); (N.C.); (D.W.P.J.); (T.M.L.S.)
- Department of Cellular and Molecular Biology, Biology Institute, Federal Fluminense University, Niterói 24020-141, RJ, Brazil
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23
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Abstract
Selective pressures drive adaptive changes in the coronavirus spike proteins directing virus-cell entry. These changes are concentrated in the amino-terminal domains (NTDs) and the receptor-binding domains (RBDs) of complex modular spike protein trimers. The impact of this hypervariability on virus entry is often unclear, particularly with respect to sarbecovirus NTD variations. Therefore, we constructed indels and substitutions within hypervariable NTD regions and used severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus-like particles and quantitative virus-cell entry assays to elucidate spike structures controlling this initial infection stage. We identified NTD variations that increased SARS-CoV-2 spike protein-mediated membrane fusion and cell entry. Increased cell entry correlated with greater presentation of RBDs to ACE2 receptors. This revealed a significant allosteric effect, in that changes within the NTDs can orient RBDs for effective virus-cell binding. Yet, those NTD changes elevating receptor binding and membrane fusion also reduced interdomain associations, leaving spikes on virus-like particles susceptible to irreversible inactivation. These findings parallel those obtained decades ago, in which comparisons of murine coronavirus spike protein variants established inverse relationships between membrane fusion potential and virus stability. Considerable hypervariability in the SARS-CoV-2 spike protein NTDs also appear to be driven by counterbalancing pressures for effective virus-cell entry and durable extracellular virus infectivity. These forces may selectively amplify SARS-CoV-2 variants of concern.
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24
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García-Ayllón MS, Moreno-Pérez O, García-Arriaza J, Ramos-Rincón JM, Cortés-Gómez MÁ, Brinkmalm G, Andrés M, León-Ramírez JM, Boix V, Gil J, Zetterberg H, Esteban M, Merino E, Sáez-Valero J. Plasma ACE2 species are differentially altered in COVID-19 patients. FASEB J 2021; 35:e21745. [PMID: 34191346 PMCID: PMC8441911 DOI: 10.1096/fj.202100051r] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/24/2021] [Accepted: 06/07/2021] [Indexed: 12/20/2022]
Abstract
Studies are needed to identify useful biomarkers to assess the severity and prognosis of COVID-19 disease, caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2) virus. Here, we examine the levels of various plasma species of the SARS-CoV-2 host receptor, the angiotensin-converting enzyme 2 (ACE2), in patients at different phases of the infection. Human plasma ACE2 species were characterized by immunoprecipitation and western blotting employing antibodies against the ectodomain and the C-terminal domain, using a recombinant human ACE2 protein as control. In addition, changes in the cleaved and full-length ACE2 species were also examined in serum samples derived from humanized K18-hACE2 mice challenged with a lethal dose of SARS-CoV-2. ACE2 immunoreactivity was present in human plasma as several molecular mass species that probably comprise truncated (70 and 75 kDa) and full-length forms (95, 100, 130, and 170 kDa). COVID-19 patients in the acute phase of infection (n = 46) had significantly decreased levels of ACE2 full-length species, while a truncated 70-kDa form was marginally higher compared with non-disease controls (n = 26). Levels of ACE2 full-length species were in the normal range in patients after a recovery period with an interval of 58-70 days (n = 29), while the 70-kDa species decreased. Levels of the truncated ACE2 species served to discriminate between individuals infected by SARS-CoV-2 and those infected with influenza A virus (n = 17). In conclusion, specific plasma ACE2 species are altered in patients with COVID-19 and these changes normalize during the recovery phase. Alterations in ACE2 species following SARS-CoV-2 infection warrant further investigation regarding their potential usefulness as biomarkers for the disease process and to asses efficacy during vaccination.
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Affiliation(s)
- María-Salud García-Ayllón
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-CSIC, San Juan de Alicante, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.,Unidad de Investigación, Hospital General Universitario de Elche, FISABIO, Elche, Spain
| | - Oscar Moreno-Pérez
- Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain.,Endocrinology and Nutrition Department, Alicante General University Hospital, Alicante, Spain.,Clinical Medicine Department, Universidad Miguel Hernández, Elche, Spain
| | - Juan García-Arriaza
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - José-Manuel Ramos-Rincón
- Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain.,Clinical Medicine Department, Universidad Miguel Hernández, Elche, Spain.,Internal Medicine Department, Alicante General University Hospital, Alicante, Spain
| | - María-Ángeles Cortés-Gómez
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-CSIC, San Juan de Alicante, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.,Unidad de Investigación, Hospital General Universitario de Elche, FISABIO, Elche, Spain
| | - Gunnar Brinkmalm
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Mariano Andrés
- Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain.,Clinical Medicine Department, Universidad Miguel Hernández, Elche, Spain.,Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Rheumatology Department, Alicante General University Hospital Alicante, Alicante, Spain
| | - José-Manuel León-Ramírez
- Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain.,Pneumology Department, Alicante General University Hospital, Alicante, Spain
| | - Vicente Boix
- Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain.,Clinical Medicine Department, Universidad Miguel Hernández, Elche, Spain.,Unit of Infectious Diseases, Alicante General University Hospital, Alicante, Spain
| | - Joan Gil
- Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain.,Pneumology Department, Alicante General University Hospital, Alicante, Spain
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.,Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, UK.,UK Dementia Research Institute, UCL, London, UK
| | - Mariano Esteban
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Esperanza Merino
- Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain.,Unit of Infectious Diseases, Alicante General University Hospital, Alicante, Spain
| | - Javier Sáez-Valero
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-CSIC, San Juan de Alicante, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.,Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
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25
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Oikonomou KG, Papamichalis P, Zafeiridis T, Xanthoudaki M, Papapostolou E, Valsamaki A, Bouliaris K, Papamichalis M, Karvouniaris M, Vlachostergios PJ, Skoura AL, Komnos A. Gastroenterology and liver disease during COVID-19 and in anticipation of post-COVID-19 era: Current practice and future directions. World J Clin Cases 2021; 9:4918-4938. [PMID: 34307544 PMCID: PMC8283616 DOI: 10.12998/wjcc.v9.i19.4918] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/10/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as a major threat to global public health. The virus causes the clinical syndrome known as coronavirus disease 2019 (COVID-19), in which multiple organs can get affected. Apart from manifestations of the respiratory system, which predominate, its clinical presentation is frequently accompanied by symptoms of the gastro-intestinal (GI) tract and liver abnormalities. The correlation of symptoms and abnormalities with disease severity is discussed, leading to ambiguous results from international literature. Moreover, the disease infects patients with co-existing liver and GI disorders affecting both their health status and the availability of healthcare services provided to them. The risk of transmission of the disease during aerosol-generating procedures has changed the diagnostic approach and follow-up algorithms for liver and GI diseases. For the safety of both doctors and patients, telemedicine and distant evaluation have become everyday practice, whereas several routines and emergency visits at outpatient and emergency departments have been postponed or delayed. Vaccination against SARS-CoV-2 is underway, providing hope to humanity and the expectation that the post-COVID-19 era is near. This review aims to update knowledge about the manifestations of COVID-19 related to liver and GI diseases and the effect of the pandemic on the diagnostic and therapeutic procedures for these diseases with a special focus on how current practices have changed and what changes will possibly remain in the future.
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Affiliation(s)
- Katerina G Oikonomou
- Intensive Care Unit, General Hospital of Larissa, Larissa 41221, Thessaly, Greece
| | | | | | - Maria Xanthoudaki
- Intensive Care Unit, General Hospital of Larissa, Larissa 41221, Thessaly, Greece
| | | | - Asimina Valsamaki
- Intensive Care Unit, General Hospital of Larissa, Larissa 41221, Thessaly, Greece
| | | | - Michail Papamichalis
- Department of Cardiology, University Hospital of Larissa, Larissa 41110, Thessaly, Greece
| | - Marios Karvouniaris
- Intensive Care Unit, University Hospital of Larissa, Larissa 41110, Thessaly, Greece
| | - Panagiotis J Vlachostergios
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, United States
| | - Apostolia-Lemonia Skoura
- Intensive Care Unit, University Hospital of Larissa, Larissa 41110, Thessaly, Greece
- Transfusion Medicine Department, University Hospital of Larissa, Larissa 41110, Thessaly, Greece
| | - Apostolos Komnos
- Intensive Care Unit, General Hospital of Larissa, Larissa 41221, Thessaly, Greece
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26
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Di Gaetano S, Capasso D, Delre P, Pirone L, Saviano M, Pedone E, Mangiatordi GF. More Is Always Better Than One: The N-Terminal Domain of the Spike Protein as Another Emerging Target for Hampering the SARS-CoV-2 Attachment to Host Cells. Int J Mol Sci 2021; 22:6462. [PMID: 34208755 PMCID: PMC8235207 DOI: 10.3390/ijms22126462] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/13/2021] [Accepted: 06/14/2021] [Indexed: 12/31/2022] Open
Abstract
Although the approved vaccines are proving to be of utmost importance in containing the Coronavirus disease 2019 (COVID-19) threat, they will hardly be resolutive as new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, a single-stranded RNA virus) variants might be insensitive to the immune response they induce. In this scenario, developing an effective therapy is still a dire need. Different targets for therapeutic antibodies and diagnostics have been identified, among which the SARS-CoV-2 spike (S) glycoprotein, particularly its receptor-binding domain, has been defined as crucial. In this context, we aim to focus attention also on the role played by the S N-terminal domain (S1-NTD) in the virus attachment, already recognized as a valuable target for neutralizing antibodies, in particular, building on a cavity mapping indicating the presence of two druggable pockets and on the recent literature hypothesizing the presence of a ganglioside-binding domain. In this perspective, we aim at proposing S1-NTD as a putative target for designing small molecules hopefully able to hamper the SARS-CoV-2 attachment to host cells.
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Affiliation(s)
- Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, CNR, 80134 Naples, Italy; (S.D.G.); (L.P.)
- CIRPEB, University of Naples “Federico II”, 80134 Naples, Italy; (D.C.); (M.S.)
| | - Domenica Capasso
- CIRPEB, University of Naples “Federico II”, 80134 Naples, Italy; (D.C.); (M.S.)
- CESTEV, University of Naples “Federico II”, 80145 Naples, Italy
| | - Pietro Delre
- Institute of Crystallography, CNR, 70126 Bari, Italy; (P.D.); (G.F.M.)
- Chemistry Department, University of Bari, 70121 Bari, Italy
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging, CNR, 80134 Naples, Italy; (S.D.G.); (L.P.)
| | - Michele Saviano
- CIRPEB, University of Naples “Federico II”, 80134 Naples, Italy; (D.C.); (M.S.)
- Institute of Crystallography, CNR, 70126 Bari, Italy; (P.D.); (G.F.M.)
| | - Emilia Pedone
- Institute of Biostructures and Bioimaging, CNR, 80134 Naples, Italy; (S.D.G.); (L.P.)
- CIRPEB, University of Naples “Federico II”, 80134 Naples, Italy; (D.C.); (M.S.)
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27
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Mahnam K, Lotfi M, Shapoorabadi FA. Examining the interactions scorpion venom peptides (HP1090, Meucin-13, and Meucin-18) with the receptor binding domain of the coronavirus spike protein to design a mutated therapeutic peptide. J Mol Graph Model 2021; 107:107952. [PMID: 34119951 PMCID: PMC8174010 DOI: 10.1016/j.jmgm.2021.107952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 11/30/2022]
Abstract
The spike protein of SARS-CoV-2 (Severe Acute Respiratory Syndrome coronavirus 2) interacts with the ACE2 receptor in human cells and starts the infection of COVID-19 disease. Given the importance of spike protein's interaction with ACE2 receptor, we selected some antiviral peptides of venom scorpion such as HP1090, meucin-13, and meucin-18 and performed docking and molecular docking analysis of them with the RBD domain of spike protein. The results showed that meucin-18 (FFGHLFKLATKIIPSLFQ) had better interaction with the RBD domain of spike protein than other peptides. We also designed some mutations in meucin-18 and investigated their interactions with the RBD domain. The results revealed that the A9T mutation had more effective interaction with the RBD domain than the meucin-18 and was able to inhibit spike protein's interaction with ACE2 receptor. Hence, peptide “FFGHLFKLTTKIIPSLFQ” can be considered as the potential drug for the treatment of COVID-19 disease.
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Affiliation(s)
- Karim Mahnam
- Biology Department, Faculty of Science, Shahrekord University, Shahrekord, Iran; Nanotechnology Research Center, Shahrekord University, 8818634141, Shahrekord, Iran.
| | - Maryam Lotfi
- Biotechnology Department, Faculty of Agriculture, Payame Noor University, Esfahan, Iran
| | - Farzaneh Ahmadi Shapoorabadi
- Biotechnology Department, Faculty of Biological Science and Technology, Shahid Ashrafi Esfahani University, Esfahan, Iran
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28
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Tada A, Senpuku H. The Impact of Oral Health on Respiratory Viral Infection. Dent J (Basel) 2021; 9:43. [PMID: 33924596 PMCID: PMC8069613 DOI: 10.3390/dj9040043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/14/2022] Open
Abstract
Influenza virus and severe acute respiratory syndrome coronavirus (SARS-CoV-2) have caused respiratory diseases worldwide. Coronavirus disease 2019 (COVID-19) is now a global health concern requiring emergent measures. These viruses enter the human body through the oral cavity and infect respiratory cells. Since the oral cavity has a complex microbiota, influence of oral bacteria on respiratory virus infection is considered. Saliva has immune molecules which work as the front line in the biophylactic mechanism and has considerable influence on the incidence and progression of respiratory viral infection. Salivary scavenger molecules, such as gp340 and sialic acid, have been reported to exert anti-influenza virus activity. Salivary secretory immunoglobulin A (SIgA) has potential to acquire immunity against these viruses. Biological features of the oral cavity are thought to affect viral infection in respiratory organs in various ways. In this review, we reviewed the literature addressing the impact of oral conditions on respiratory infectious diseases caused by viruses.
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Affiliation(s)
- Akio Tada
- Department of Health Science, Hyogo University, Kakogawa 675-0195, Japan
| | - Hidenobu Senpuku
- Department of Bacteriology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan;
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Zhao X, Chen H, Wang H. Glycans of SARS-CoV-2 Spike Protein in Virus Infection and Antibody Production. Front Mol Biosci 2021; 8:629873. [PMID: 33928117 PMCID: PMC8076860 DOI: 10.3389/fmolb.2021.629873] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/22/2021] [Indexed: 12/18/2022] Open
Abstract
Viral protein glycosylation represents a successful strategy employed by the parasite to take advantage of host-cell machinery for modification of its own proteins. The resulting glycans have unneglectable roles in viral infection and immune response. The spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which presents on the surface of matured virion and mediates viral entry into the host, also undergoes extensive glycosylation to shield it from the human defense system. It is believed that the ongoing COVID-19 pandemic with more than 90,000,000 infections and 1,900,000 deaths is partly due to its successful glycosylation strategy. On the other hand, while glycan patches on S protein have been reported to shield the host immune response by masking "nonself" viral peptides with "self-glycans," the epitopes are also important in eliciting neutralizing antibodies. In this review, we will summarize the roles of S protein glycans in mediating virus-receptor interactions, and in antibody production, as well as indications for vaccine development.
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Affiliation(s)
| | | | - Hongliang Wang
- Department of Pathogen Biology and Immunology, Xi’an Jiaotong University Health Science Center, Xi’an, China
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Miotto M, Di Rienzo L, Bò L, Boffi A, Ruocco G, Milanetti E. Molecular Mechanisms Behind Anti SARS-CoV-2 Action of Lactoferrin. Front Mol Biosci 2021; 8:607443. [PMID: 33659275 PMCID: PMC7917183 DOI: 10.3389/fmolb.2021.607443] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/11/2021] [Indexed: 12/15/2022] Open
Abstract
Despite the huge effort to contain the infection, the novel SARS-CoV-2 coronavirus has rapidly become pandemic, mainly due to its extremely high human-to-human transmission capability, and a surprisingly high viral charge of symptom-less people. While the seek for a vaccine is still ongoing, promising results have been obtained with antiviral compounds. In particular, lactoferrin is regarded to have beneficial effects both in preventing and soothing the infection. Here, we explore the possible molecular mechanisms with which lactoferrin interferes with SARS-CoV-2 cell invasion, preventing attachment and/or entry of the virus. To this aim, we search for possible interactions lactoferrin may have with virus structural proteins and host receptors. Representing the molecular iso-electron surface of proteins in terms of 2D-Zernike descriptors, we 1) identified putative regions on the lactoferrin surface able to bind sialic acid present on the host cell membrane, sheltering the cell from the virus attachment; 2) showed that no significant shape complementarity is present between lactoferrin and the ACE2 receptor, while 3) two high complementarity regions are found on the N- and C-terminal domains of the SARS-CoV-2 spike protein, hinting at a possible competition between lactoferrin and ACE2 for the binding to the spike protein.
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Affiliation(s)
- Mattia Miotto
- Department of Physics, University of Rome `La Sapienza', Rome, Italy
- Istituto Italiano di Tecnologia (IIT), Center for Life Nano Science, Rome, Italy
| | - Lorenzo Di Rienzo
- Istituto Italiano di Tecnologia (IIT), Center for Life Nano Science, Rome, Italy
| | - Leonardo Bò
- Istituto Italiano di Tecnologia (IIT), Center for Life Nano Science, Rome, Italy
| | - Alberto Boffi
- Istituto Italiano di Tecnologia (IIT), Center for Life Nano Science, Rome, Italy
- Department of Biochemical Sciences “A. Rossi Fanelli” Sapienza University, Rome, Italy
| | - Giancarlo Ruocco
- Department of Physics, University of Rome `La Sapienza', Rome, Italy
- Istituto Italiano di Tecnologia (IIT), Center for Life Nano Science, Rome, Italy
| | - Edoardo Milanetti
- Department of Physics, University of Rome `La Sapienza', Rome, Italy
- Istituto Italiano di Tecnologia (IIT), Center for Life Nano Science, Rome, Italy
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Cuéllar-Cruz M. The histo-blood group antigens of the host cell may determine the binding of different viruses such as SARS-CoV-2. Future Microbiol 2021; 16:107-118. [PMID: 33459559 PMCID: PMC7842250 DOI: 10.2217/fmb-2020-0158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Viruses have caused the death of millions of people worldwide. Specifically, human viruses are grouped into 21 families, including the family of coronaviruses (CoVs). In December 2019, in Wuhan, China, a new human CoV was identified, SARS-CoV-2. The first step of the infection mechanism of the SARS-CoV-2 in the human host is adhesion, which occurs through the S glycoprotein that is found in diverse human organs. Another way through which SARS-CoV-2 could possibly attach to the host's cells is by means of the histo-blood group antigens. In this work, we have reviewed the mechanisms by which some viruses bind to the histo-blood group antigens, which could be related to the susceptibility of the individual and are dependent on the histo-blood group.
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Affiliation(s)
- Mayra Cuéllar-Cruz
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Noria Alta S/N, Col. Noria Alta, C.P. 36050, Guanajuato, Guanajuato, México
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Bò L, Miotto M, Di Rienzo L, Milanetti E, Ruocco G. Exploring the Association Between Sialic Acid and SARS-CoV-2 Spike Protein Through a Molecular Dynamics-Based Approach. FRONTIERS IN MEDICAL TECHNOLOGY 2021; 2:614652. [PMID: 35047894 PMCID: PMC8757799 DOI: 10.3389/fmedt.2020.614652] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/03/2020] [Indexed: 12/19/2022] Open
Abstract
Recent experimental evidence demonstrated the capability of SARS-CoV-2 Spike protein to bind sialic acid molecules, which was a trait not present in SARS-CoV and could shed light on the molecular mechanism used by the virus for the cell invasion. This peculiar feature has been successfully predicted by in-silico studies comparing the sequence and structural characteristics that SARS-CoV-2 shares with other sialic acid-binding viruses, like MERS-CoV. Even if the region of the binding has been identified in the N-terminal domain of Spike protein, so far no comprehensive analyses have been carried out on the spike-sialic acid conformations once in the complex. Here, we addressed this aspect performing an extensive molecular dynamics simulation of a system composed of the N-terminal domain of the spike protein and a sialic acid molecule. We observed several short-lived binding events, reconnecting to the avidic nature of the binding, interestingly occurring in the surface Spike region where several insertions are present with respect to the SARS-CoV sequence. Characterizing the bound configurations via a clustering analysis on the Principal Component of the motion, we identified different possible binding conformations and discussed their dynamic and structural properties. In particular, we analyze the correlated motion between the binding residues and the binding effect on the stability of atomic fluctuation, thus proposing regions with high binding propensity with sialic acid.
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Affiliation(s)
- Leonardo Bò
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
| | - Mattia Miotto
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
- Department of Physics, Sapienza University, Rome, Italy
| | - Lorenzo Di Rienzo
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
| | - Edoardo Milanetti
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
- Department of Physics, Sapienza University, Rome, Italy
| | - Giancarlo Ruocco
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Rome, Italy
- Department of Physics, Sapienza University, Rome, Italy
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Oommen A, Cunningham S, Joshi L. Transcriptomic Analysis of Respiratory Tissue and Cell Line Models to Examine Glycosylation Machinery during SARS-CoV-2 Infection. Viruses 2021; 13:v13010082. [PMID: 33435561 PMCID: PMC7827443 DOI: 10.3390/v13010082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023] Open
Abstract
Glycosylation, being the most abundant post-translational modification, plays a profound role affecting expression, localization and function of proteins and macromolecules in immune response to infection. Presented are the findings of a transcriptomic analysis performed using high-throughput functional genomics data from public repository to examine the altered transcription of the human glycosylation machinery in response to SARS-CoV-2 stimulus and infection. In addition to the conventional in silico functional enrichment analysis methods we also present results from the manual analysis of biomedical literature databases to bring about the biological significance of glycans and glycan-binding proteins in modulating the host immune response during SARS-CoV-2 infection. Our analysis revealed key immunomodulatory lectins, proteoglycans and glycan epitopes implicated in exerting both negative and positive downstream inflammatory signaling pathways, in addition to its vital role as adhesion receptors for SARS-CoV-2 pathogen. A hypothetical correlation of the differentially expressed human glycogenes with the altered host inflammatory response and the cytokine storm-generated in response to SARS-CoV-2 pathogen is proposed. These markers can provide novel insights into the diverse roles and functioning of glycosylation pathways modulated by SARS-CoV-2, provide avenues of stratification, treatment, and targeted approaches for COVID-19 immunity and other viral infectious agents.
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Affiliation(s)
- Anup Oommen
- Advanced Glycoscience Research Cluster (AGRC), National University of Ireland Galway, H91 TK33 Galway, Ireland; (A.O.); (S.C.)
- Centre for Research in Medical Devices (CURAM), National University of Ireland Galway, H91 TK33 Galway, Ireland
| | - Stephen Cunningham
- Advanced Glycoscience Research Cluster (AGRC), National University of Ireland Galway, H91 TK33 Galway, Ireland; (A.O.); (S.C.)
- Centre for Research in Medical Devices (CURAM), National University of Ireland Galway, H91 TK33 Galway, Ireland
| | - Lokesh Joshi
- Advanced Glycoscience Research Cluster (AGRC), National University of Ireland Galway, H91 TK33 Galway, Ireland; (A.O.); (S.C.)
- Centre for Research in Medical Devices (CURAM), National University of Ireland Galway, H91 TK33 Galway, Ireland
- Correspondence:
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Murillo J, Villegas LM, Ulloa-Murillo LM, Rodríguez AR. Recent trends on omics and bioinformatics approaches to study SARS-CoV-2: A bibliometric analysis and mini-review. Comput Biol Med 2021; 128:104162. [PMID: 33310371 PMCID: PMC7710474 DOI: 10.1016/j.compbiomed.2020.104162] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND The successful sequencing of SARS-CoV-2 cleared the way for the use of omics technologies and integrative biology research for combating the COVID-19 pandemic. Currently, many research groups have slowed down their respective projects to concentrate efforts in the study of the biology of SARS-CoV-2. In this bibliometric analysis and mini-review, we aimed to describe how computational methods or omics approaches were used during the first months of the COVID-19 pandemic. METHODS We analyzed bibliometric data from Scopus, BioRxiv, and MedRxiv (dated June 19th, 2020) using quantitative and knowledge mapping approaches. We complemented our analysis with a manual process of carefully reading the selected articles to identify either the omics or bioinformatic tools used and their purpose. RESULTS From a total of 184 articles, we found that metagenomics and transcriptomics were the main sources of data to perform phylogenetic analysis aimed at corroborating zoonotic transmission, identifying the animal origin and taxonomic allocation of SARS-CoV-2. Protein sequence analysis, immunoinformatics and molecular docking were used to give insights about SARS-CoV-2 targets for drug and vaccine development. Most of the publications were from China and USA. However, China, Italy and India covered the top 10 most cited papers on this topic. CONCLUSION We found an abundance of publications using omics and bioinformatics approaches to establish the taxonomy and animal origin of SARS-CoV-2. We encourage the growing community of researchers to explore other lesser-known aspects of COVID-19 such as virus-host interactions and host response.
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Affiliation(s)
- Julieth Murillo
- Faculty of Engineering, Pontificia Universidad Javeriana-Cali, Cali, Colombia.
| | | | - Leidy Marcela Ulloa-Murillo
- Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Czech Republic.
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Rahul M, Tewari N, Mathur V, Goel S, Jain G. Evidence mapping and quality analysis of published dental literature on COVID-19 - A systematic review. Natl J Maxillofac Surg 2021; 12:139-161. [PMID: 34483571 PMCID: PMC8386272 DOI: 10.4103/njms.njms_237_20] [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: 10/27/2020] [Accepted: 02/12/2021] [Indexed: 12/14/2022] Open
Abstract
A large number of scientific articles have been published regarding impact of COVID-19 infection on dental practice, dental professionals, and the mode of spread of infection via dental procedures. The present systematic review was planned with an aim of evidence mapping and quality analysis of published research on the dental aspects of COVID-19 infection. The protocol was registered at https://share.osf.io/registration/46221-C87-BA8. The search was performed in Scopus, PubMed, Cochrane, and Embase databases till 15th July 2020. There was no restriction of year of publication and language. All types of published articles related to Dentistry, Dentist, Dental practice, and Oral health education on COVID-19 were included. The Joanna Briggs Institute's (JBI) Critical Appraisal Tools were used for the risk of bias analysis of included studies. A total of 393 articles were short-listed and were checked for eligibility and finally, 380 articles were included. Among the 380 research articles published (till July 15, 2020), the majority of the included articles belonged to the lowermost strata of the evidence pyramid. There were 54 original research articles with no randomized clinical trial, systematic review or, meta-analysis pertaining to the dental perspective of COVID-19 infection. The level of available evidence about dentistry and COVID-19 infection is very low with a lack of researches of highest quality. The guidelines/recommendations for dental professionals, proposed by the different scientific organizations/societies regarding COVID-19 infection are only consensus-based necessitating the need to formulate evidence-based guidelines. There is a need to identify essential research questions and strengthen the study designs in most of the aspects related to the dentistry and COVID-19 pandemic.
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Affiliation(s)
- Morankar Rahul
- Division of Pedodontics and Preventive Dentistry, Centre for Dental Education and Research, AIIMS, New Delhi, India,Address for correspondence: Dr. Morankar Rahul, Division of Pedodontics and Preventive Dentistry, Centre for Dental Education and Research, AIIMS, New Delhi, India. E-mail:
| | - Nitesh Tewari
- Division of Pedodontics and Preventive Dentistry, Centre for Dental Education and Research, AIIMS, New Delhi, India
| | - Vijay Mathur
- Division of Pedodontics and Preventive Dentistry, Centre for Dental Education and Research, AIIMS, New Delhi, India
| | - Shubhi Goel
- Division of Pedodontics and Preventive Dentistry, Centre for Dental Education and Research, AIIMS, New Delhi, India
| | - Gunjar Jain
- Department of Orthopaedics, AIIMS, New Delhi, India
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36
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Bernard I, Limonta D, Mahal LK, Hobman TC. Endothelium Infection and Dysregulation by SARS-CoV-2: Evidence and Caveats in COVID-19. Viruses 2020; 13:E29. [PMID: 33375371 PMCID: PMC7823949 DOI: 10.3390/v13010029] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/16/2020] [Accepted: 12/25/2020] [Indexed: 02/06/2023] Open
Abstract
The ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by the acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) poses a persistent threat to global public health. Although primarily a respiratory illness, extrapulmonary manifestations of COVID-19 include gastrointestinal, cardiovascular, renal and neurological diseases. Recent studies suggest that dysfunction of the endothelium during COVID-19 may exacerbate these deleterious events by inciting inflammatory and microvascular thrombotic processes. Although controversial, there is evidence that SARS-CoV-2 may infect endothelial cells by binding to the angiotensin-converting enzyme 2 (ACE2) cellular receptor using the viral Spike protein. In this review, we explore current insights into the relationship between SARS-CoV-2 infection, endothelial dysfunction due to ACE2 downregulation, and deleterious pulmonary and extra-pulmonary immunothrombotic complications in severe COVID-19. We also discuss preclinical and clinical development of therapeutic agents targeting SARS-CoV-2-mediated endothelial dysfunction. Finally, we present evidence of SARS-CoV-2 replication in primary human lung and cardiac microvascular endothelial cells. Accordingly, in striving to understand the parameters that lead to severe disease in COVID-19 patients, it is important to consider how direct infection of endothelial cells by SARS-CoV-2 may contribute to this process.
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Affiliation(s)
- Isabelle Bernard
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada;
| | - Daniel Limonta
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada;
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Lara K. Mahal
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada;
| | - Tom C. Hobman
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada;
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada;
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Women & Children’s Health Research Institute, University of Alberta, Edmonton, AB T6G 1C9, Canada
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Gasbarri M, V’kovski P, Torriani G, Thiel V, Stellacci F, Tapparel C, Cagno V. SARS-CoV-2 Inhibition by Sulfonated Compounds. Microorganisms 2020; 8:E1894. [PMID: 33265927 PMCID: PMC7760145 DOI: 10.3390/microorganisms8121894] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 12/15/2022] Open
Abstract
Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) depends on angiotensin converting enzyme 2 (ACE2) for cellular entry, but it might also rely on attachment receptors such as heparan sulfates. Several groups have recently demonstrated an affinity of the SARS-CoV2 spike protein for heparan sulfates and a reduced binding to cells in the presence of heparin or heparinase treatment. Here, we investigated the inhibitory activity of several sulfated and sulfonated molecules, which prevent interaction with heparan sulfates, against vesicular stomatitis virus (VSV)-pseudotyped-SARS-CoV-2 and the authentic SARS-CoV-2. Sulfonated cyclodextrins and nanoparticles that have recently shown broad-spectrum non-toxic virucidal activity against many heparan sulfates binding viruses showed inhibitory activity in the micromolar and nanomolar ranges, respectively. In stark contrast with the mechanisms that these compounds present for these other viruses, the inhibition against SARS-CoV-2 was found to be simply reversible.
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Affiliation(s)
- Matteo Gasbarri
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; (M.G.); (F.S.)
| | - Philip V’kovski
- Institute of Virology and Immunology (IVI), Länggassstrasse 122, 3012 Bern, Switzerland; (P.V.); (V.T.)
- Institute for Infectious Diseases, University of Bern, Hochschulstrasse 6, 3012 Bern, Switzerland
| | - Giulia Torriani
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneve, Switzerland; (G.T.); (C.T.)
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Länggassstrasse 122, 3012 Bern, Switzerland; (P.V.); (V.T.)
- Institute for Infectious Diseases, University of Bern, Hochschulstrasse 6, 3012 Bern, Switzerland
| | - Francesco Stellacci
- Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; (M.G.); (F.S.)
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Caroline Tapparel
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneve, Switzerland; (G.T.); (C.T.)
| | - Valeria Cagno
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneve, Switzerland; (G.T.); (C.T.)
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Robson B. Techniques assisting peptide vaccine and peptidomimetic design. Sidechain exposure in the SARS-CoV-2 spike glycoprotein. Comput Biol Med 2020; 128:104124. [PMID: 33276271 PMCID: PMC7679524 DOI: 10.1016/j.compbiomed.2020.104124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 01/15/2023]
Abstract
The aim of the present study is to discuss the design of peptide vaccines and peptidomimetics against SARS-COV-2, to develop and apply a method of protein structure analysis that is particularly appropriate to applying and discussing such design, and also to use that method to summarize some important features of the SARS-COV-2 spike protein sequence. A tool for assessing sidechain exposure in the SARS-CoV-2 spike glycoprotein is described. It extends to assessing accessibility of sidechains by considering several different three-dimensional structure determinations of SARS-CoV-2 and SARS-CoV-1 spike protein. The method is designed to be insensitive to a distance limit for counting neighboring atoms and the results are in good agreement with the physical chemical properties and exposure trends of the 20 naturally occurring sidechains. The spike protein sequence is analyzed with comment regarding exposable character. It includes studies of complexes with antibody elements and ACE2. These indicate changes in exposure at sites remote to those at which the antibody binds. They are of interest concerning design of synthetic peptide vaccines, and for peptidomimetics as a basis of drug discovery. The method was also developed in order to provide linear (one-dimensional) information that can be used along with other bioinformatics data of this kind in data mining and machine learning, potentially as genomic data regarding protein polymorphisms to be combined with more traditional clinical data. Bioinformatics studies are carried out on SARS-CoV-2 spike, studying solvent exposure. The methods are particularly suited for synthetic vaccines and d-amino acid peptidomimetics. Methods of generating d-amino acid peptidomimetics are described and reviewed. The effect of antibody binding in stabilizing loop conformation and exposing remote sites is noted.
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Affiliation(s)
- B Robson
- Ingine Inc. Cleveland Ohio USA and the Dirac Foundation, Oxfordshire, UK.
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39
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Habashy NH, Abu-Serie MM. The potential antiviral effect of major royal jelly protein2 and its isoform X1 against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): Insight on their sialidase activity and molecular docking. J Funct Foods 2020; 75:104282. [PMID: 33199981 PMCID: PMC7656998 DOI: 10.1016/j.jff.2020.104282] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/03/2020] [Accepted: 11/07/2020] [Indexed: 12/01/2022] Open
Abstract
Major royal jelly protein 2 and its isoform X1 are two predicted inhibitors of SARS-CoV-2. Major royal jelly protein 2 and its isoform X1 have sialidase activity. Major royal jelly protein 2 and its isoform X1 might inhibit SARS-CoV-2 entry and replication. Major royal jelly protein 2 and its isoform X1 might inhibit SARS-CoV-2-induced hypoxia.
Severe acute respiratory syndrome-coronavirus (SARS-CoV)-2 is a newly emerging type of CoV. We evaluated the predicted anti-SARS-CoV-2 effect of major royal jelly protein (MRJP)2 and MRJP2 isoform X1, which recently showed high efficacy against other enveloped RNA-viruses (HCV and HIV). Some in-silico analyses have been performed to predict the impact of these proteins on viral entry, replication, and complications. These proteins have shown a high potency in sialic acid hydrolysis from the lung cells (WI-38) surface. Docking analysis showed that these proteins have a high binding affinity to viral receptor-binding sites in the receptor-binding domain, causing attachment prevention. Moreover, MRJPs can exert an inhibitory influence, via different mechanisms, for SARS-CoV-2 non-structural proteins (main and papain proteases, RNA replicase, RNA-dependent RNA polymerase, and methyltransferase). Also, they can bind to hemoglobin-binding sites on viral-nsps and prevent their hemoglobin attack. Thus, MRJP2 and MRJP2 X1 can be a promising therapy for SARS-CoV-2 infection.
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Affiliation(s)
- Noha H Habashy
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria 21511, Egypt
| | - Marwa M Abu-Serie
- Department of Medical Biotechnology, Genetic Engineering, and Biotechnology Research Institute, City for Scientific Research and Technology Applications (SRTA-City), New Borg EL-Arab 21934, Alexandria, Egypt
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Abstract
The pandemic of novel coronavirus disease (COVID-19) caused by the Severe Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) creates an immense menace to public health worldwide. Currently, the World Health Organization (WHO) has recognized the novel coronavirus as the main cause of global pandemic. Patients infected with this virus generally show fever, nausea, and respiratory illness, while some patients also manifest gastrointestinal symptoms such as abdominal pain, vomiting, and diarrhea. Traces of SARS-CoV-2 RNA have been found in gastrointestinal cells. Further angiotensin converting enzyme 2 (ACE2) the known receptor for the virus is extensively expressed in these cells. This implies that gastrointestinal tract can be infected and can also present them as a replication site for SARS-CoV-2, but since this infection may lead to multiple organ failure, therefore identification of another receptor is a plausible choice. This review aims to provide comprehensive information about probable receptors such as sialic acid and CD147 which may facilitate the virus entry. Several potential targets are mentioned which can be used as a therapeutic approach for COVID-19 and associated GI disorders. The gut microbiomes are responsible for high levels of interferon-gamma which causes hyper-inflammation and exacerbates the severity of the disease. Briefly, this article highlights the gut microbiome’s relation and provides potential diagnostic approaches like RDT and LC-MS for sensitive and specific identification of viral proteins. Altogether, this article reviews epidemiology, probable receptors and put forward the tentative ideas of the therapeutic targets and diagnostic methods for COVID-19 with gastrointestinal aspect of disease.
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41
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Robson B. The use of knowledge management tools in viroinformatics. Example study of a highly conserved sequence motif in Nsp3 of SARS-CoV-2 as a therapeutic target. Comput Biol Med 2020; 125:103963. [PMID: 32828990 PMCID: PMC7424310 DOI: 10.1016/j.compbiomed.2020.103963] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 12/16/2022]
Abstract
Knowledge management tools that assist in systematic review and exploration of scientific knowledge generally are of obvious potential importance in evidence based medicine in general, but also to the design of therapeutics based on the protein subsequences and fold motifs of virus proteins as considered here. Rapid access to bundles (clusters) of related elements of knowledge gathered from diverse sources on the Internet and from growing knowledge repositories seem particularly helpful when exploring less obvious therapeutic targets in viruses (for which knowledge new to the researcher is important), and when using the following concept. Subsequences of amino acid residue sequences of proteins that are conserved across strains and species are (a) more likely to be important targets and (b) less likely to exhibit escape mutations that would make them resistant to vaccines and therapeutic agents. However, the terms "conserved" and even "highly conserved" used by authors are matters of degree, depending on how distant from SARS-CoV-2 they wished to go in comparing other sequences. The binding site to the human ACE2 protein as virus receptor and human antibody CR3022 binding site on the spike glycoprotein are rather variable by the criteria used in the present and preceding studies. To look for more strongly conserved targets, open reading frames of SARS-CoV-2 were examined for extremely highly conserved regions, meaning recognizable across many viruses and organisms. Most prominent is a motif found in SARS-CoV-2 non-structural protein 3 (Nsp3). It relates to a fold called type called the macro domain and has remarkably wide distribution across organisms including humans with significant homologies involving three especially conserved subsequences (a) VVVNAANVYLKHGGGVAGALNK, (b) LHVVGPNVNKG, and (c) PLLSAGIFG. Careful study of the variations of these and of the more variable sequences between and around them might provide a finer "scalpel" to ensure inhibition of a vital function of the virus without impairing the functions of related host macro domains.
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Affiliation(s)
- B. Robson
- Ingine Inc., Cleveland, OH, USA,The Dirac Foundation, Oxfordshire, UK
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Caniglia JL, Asuthkar S, Tsung AJ, Guda MR, Velpula KK. Immunopathology of galectin-3: an increasingly promising target in COVID-19. F1000Res 2020; 9:1078. [PMID: 33082935 PMCID: PMC7536583 DOI: 10.12688/f1000research.25979.2] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/09/2020] [Indexed: 01/18/2023] Open
Abstract
The pandemic brought on by the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) has become a global health crisis, with over 22 million confirmed cases and 777,000 fatalities due to coronavirus disease 2019 (COVID-19) reported worldwide. The major cause of fatality in infected patients, now referred to as the "Cytokine Storm Syndrome" (CSS), is a direct result of aberrant immune activation following SARS-CoV2 infection and results in excess release of inflammatory cytokines, such as interleukin (IL)-1, tumor necrosis factor α (TNF-α), and IL-6, by macrophages, monocytes, and dendritic cells. Single cell analysis has also shown significantly elevated levels of galectin 3 (Gal-3) in macrophages, monocytes, and dendritic cells in patients with severe COVID-19 as compared to mild disease. Inhibition of Gal-3 reduces the release of IL-1, IL-6, and TNF-α from macrophages in vitro, and as such may hold promise in reducing the incidence of CSS. In addition, Gal-3 inhibition shows promise in reducing transforming growth factor ß (TGF-ß) mediated pulmonary fibrosis, likely to be a major consequence in survivors of severe COVID-19. Finally, a key domain in the spike protein of SARS-CoV2 has been shown to bind N-acetylneuraminic acid (Neu5Ac), a process that may be essential to cell entry by the virus. This Neu5Ac-binding domain shares striking morphological, sequence, and functional similarities with human Gal-3. Here we provide an updated review of the literature linking Gal-3 to COVID-19 pathogenesis. Dually targeting galectins and the Neu5Ac-binding domain of SARS-CoV2 shows tentative promise in several stages of the disease: preventing viral entry, modulating the host immune response, and reducing the post-infectious incidence of pulmonary fibrosis.
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Affiliation(s)
- John L. Caniglia
- Departments of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Swapna Asuthkar
- Departments of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Andrew J. Tsung
- Departments of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
- Department of Neurosurgery, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
- Illinois Neurological Institute, Peoria, IL, USA
| | - Maheedhara R. Guda
- Departments of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Kiran K. Velpula
- Departments of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
- Department of Neurosurgery, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
- Department of Pediatrics, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
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Caniglia JL, Asuthkar S, Tsung AJ, Guda MR, Velpula KK. Immunopathology of galectin-3: an increasingly promising target in COVID-19. F1000Res 2020; 9:1078. [PMID: 33082935 PMCID: PMC7536583 DOI: 10.12688/f1000research.25979.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/25/2020] [Indexed: 01/11/2024] Open
Abstract
The pandemic brought on by the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) has become a global health crisis, with over 22 million confirmed cases and 777,000 fatalities due to coronavirus disease 2019 (COVID-19) reported worldwide. The major cause of fatality in infected patients, now referred to as the "Cytokine Storm Syndrome" (CSS), is a direct result of aberrant immune activation following SARS-CoV2 infection and results in excess release of inflammatory cytokines, such as interleukin (IL)-1, tumor necrosis factor α (TNF-α), and IL-6, by macrophages, monocytes, and dendritic cells. Single cell analysis has also shown significantly elevated levels of galectin 3 (Gal-3) in macrophages, monocytes, and dendritic cells in patients with severe COVID-19 as compared to mild disease. Inhibition of Gal-3 reduces the release of IL-1, IL-6, and TNF-α from macrophages in vitro, and as such may hold promise in reducing the incidence of CSS. In addition, Gal-3 inhibition shows promise in reducing transforming growth factor ß (TGF-ß) mediated pulmonary fibrosis, likely to be a major consequence in survivors of severe COVID-19. Finally, a key domain in the spike protein of SARS-CoV2 has been shown to bind N-acetylneuraminic acid (Neu5Ac), a process that may be essential to cell entry by the virus. This Neu5Ac-binding domain shares striking morphological, sequence, and functional similarities with human Gal-3. Here we provide an updated review of the literature linking Gal-3 to COVID-19 pathogenesis. Dually targeting galectins and the Neu5Ac-binding domain of SARS-CoV2 shows tentative promise in several stages of the disease: preventing viral entry, modulating the host immune response, and reducing the post-infectious incidence of pulmonary fibrosis.
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Affiliation(s)
- John L. Caniglia
- Departments of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Swapna Asuthkar
- Departments of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Andrew J. Tsung
- Departments of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
- Department of Neurosurgery, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
- Illinois Neurological Institute, Peoria, IL, USA
| | - Maheedhara R. Guda
- Departments of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Kiran K. Velpula
- Departments of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
- Department of Neurosurgery, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
- Department of Pediatrics, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
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Sulzer D, Antonini A, Leta V, Nordvig A, Smeyne RJ, Goldman JE, Al-Dalahmah O, Zecca L, Sette A, Bubacco L, Meucci O, Moro E, Harms AS, Xu Y, Fahn S, Ray Chaudhuri K. COVID-19 and possible links with Parkinson's disease and parkinsonism: from bench to bedside. NPJ Parkinsons Dis 2020; 6:18. [PMID: 32885037 PMCID: PMC7441399 DOI: 10.1038/s41531-020-00123-0] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/20/2020] [Indexed: 02/08/2023] Open
Abstract
This Viewpoint discusses insights from basic science and clinical perspectives on coronavirus disease 2019 (COVID-19)/severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection in the brain, with a particular focus on Parkinson's disease. Major points include that neuropathology studies have not answered the central issue of whether the virus enters central nervous system neurons, astrocytes or microglia, and the brain vascular cell types that express virus have not yet been identified. Currently, there is no clear evidence for human neuronal or astrocyte expression of angiotensin-converting enzyme 2 (ACE2), the major receptor for viral entry, but ACE2 expression may be activated by inflammation, and a comparison of healthy and infected brains is important. In contrast to the 1918 influenza pandemic and avian flu, reports of encephalopathy in COVID-19 have been slow to emerge, and there are so far no documented reports of parkinsonism apart from a single case report. We recommend consensus guidelines for the clinical treatment of Parkinson's patients with COVID-19. While a role for the virus in causing or exacerbating Parkinson's disease appears unlikely at this time, aggravation of specific motor and non-motor symptoms has been reported, and it will be important to monitor subjects after recovery, particularly for those with persisting hyposmia.
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Affiliation(s)
- David Sulzer
- Departments of Psychiatry, Neurology, Pharmacology, Columbia University Medical Center, New York State Psychiatric Institute, New York, NY 10032 USA
| | - Angelo Antonini
- Department of Neuroscience, Parkinson and Movement Disorders Unit, University of Padua, Padua, Italy
| | - Valentina Leta
- King’s College London, Institute of Psychiatry, Psychology & Neuroscience, De Crespigny Park, London, SE5 8AF UK
- Parkinson’s Foundation Centre of Excellence, King’s College Hospital, Denmark Hill, London, SE5 9RS UK
| | - Anna Nordvig
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY 10032 USA
| | - Richard J. Smeyne
- Department of Neurosciences, Thomas Jefferson University, Philadelphia, PA 19107 USA
| | - James E. Goldman
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY 10032 USA
| | - Osama Al-Dalahmah
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY 10032 USA
| | - Luigi Zecca
- Institute of Biomedical Technologies, National Research Council of Italy, Segrate, Milan, Italy
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92093 USA
- Department of Medicine, University of California, San Diego, CA 92093 USA
| | - Luigi Bubacco
- Department of Biology, University of Padova, Padova, Italy
| | - Olimpia Meucci
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102 USA
- Center of Neuroimmunology and CNS Therapeutics, Institute of Molecular Medicine and Infectious Diseases, Drexel University College of Medicine, Philadelphia, PA 19102 USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102 USA
| | - Elena Moro
- Department of Neurology, Grenoble Alpes University Hospital, Grenoble, France
- Grenoble Institute of Neurosciences GIN-INSERM U1216/CEA/UGA, Grenoble, France
- Grenoble Alpes University, Grenoble, France
| | - Ashley S. Harms
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Yaqian Xu
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - Stanley Fahn
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY 10032 USA
| | - K. Ray Chaudhuri
- King’s College London, Institute of Psychiatry, Psychology & Neuroscience, De Crespigny Park, London, SE5 8AF UK
- Parkinson’s Foundation Centre of Excellence, King’s College Hospital, Denmark Hill, London, SE5 9RS UK
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Awasthi M, Gulati S, Sarkar DP, Tiwari S, Kateriya S, Ranjan P, Verma SK. The Sialoside-Binding Pocket of SARS-CoV-2 Spike Glycoprotein Structurally Resembles MERS-CoV. Viruses 2020; 12:E909. [PMID: 32825063 PMCID: PMC7551769 DOI: 10.3390/v12090909] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022] Open
Abstract
COVID-19 novel coronavirus (CoV) disease caused by severe acquired respiratory syndrome (SARS)-CoV-2 manifests severe lethal respiratory illness in humans and has recently developed into a worldwide pandemic. The lack of effective treatment strategy and vaccines against the SARS-CoV-2 poses a threat to human health. An extremely high infection rate and multi-organ secondary infection within a short period of time makes this virus more deadly and challenging for therapeutic interventions. Despite high sequence similarity and utilization of common host-cell receptor, human angiotensin-converting enzyme-2 (ACE2) for virus entry, SARS-CoV-2 is much more infectious than SARS-CoV. Structure-based sequence comparison of the N-terminal domain (NTD) of the spike protein of Middle East respiratory syndrome (MERS)-CoV, SARS-CoV, and SARS-CoV-2 illustrate three divergent loop regions in SARS-CoV-2, which is reminiscent of MERS-CoV sialoside binding pockets. Comparative binding analysis with host sialosides revealed conformational flexibility of SARS-CoV-2 divergent loop regions to accommodate diverse glycan-rich sialosides. These key differences with SARS-CoV and similarity with MERS-CoV suggest an evolutionary adaptation of SARS-CoV-2 spike glycoprotein reciprocal interaction with host surface sialosides to infect host cells with wide tissue tropism.
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Affiliation(s)
- Mayanka Awasthi
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA;
| | | | - Debi P. Sarkar
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021, India;
| | - Swasti Tiwari
- Department of Molecular Medicine & Biotechnology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India;
| | - Suneel Kateriya
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India;
| | - Peeyush Ranjan
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA;
| | - Santosh Kumar Verma
- Department of Molecular Medicine & Biotechnology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India;
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