1
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Emam MH, Elezaby RS, Swidan SA, Hathout RM. Nanofiberous facemasks as protectives against pandemic respiratory viruses. Expert Rev Respir Med 2024:1-17. [PMID: 38753449 DOI: 10.1080/17476348.2024.2356601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 05/14/2024] [Indexed: 05/18/2024]
Abstract
INTRODUCTION Wearing protective face masks and respirators has been a necessity to reduce the transmission rate of respiratory viruses since the outbreak of the coronavirus (COVID-19) disease. Nevertheless, the outbreak has revealed the need to develop efficient air filter materials and innovative anti-microbial protectives. Nanofibrous facemasks, either loaded with antiviral nanoparticles or not, are very promising personal protective equipment (PPE) against pandemic respiratory viruses. AREAS COVERED In this review, multiple types of face masks and respirators are discussed as well as filtration mechanisms of particulates. In this regard, the limitations of traditional face masks were summarized and the advancement of nanotechnology in developing nanofibrous masks and air filters was discussed. Different methods of preparing nanofibers were explained. The various approaches used for enhancing nanofibrous face masks were covered. EXPERT OPINION Although wearing conventional face masks can limit viral infection spread to some extent, the world is in great need for more protective face masks. Nanofibers can block viral particles efficiently and can be incorporated into face masks in order to enhance their filtration efficiency. Also, we believe that other modifications such as addition of antiviral nanoparticles can significantly increase the protection power of facemasks.
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Affiliation(s)
- Merna H Emam
- Nanotechnology Research Center (NTRC), The British University in Egypt, Cairo, Egypt
| | - Reham S Elezaby
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Shady A Swidan
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
- The Centre for Drug Research and Development (CDRD), Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - Rania M Hathout
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
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2
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Kalashnyk O, Lykhmus O, Sullivan R, Komisarenko S, Skok M. Agonists or positive allosteric modulators of α7 nicotinic acetylcholine receptor prevent interaction of SARS-Cov-2 receptor-binding domain with astrocytoma cells. Biochem Biophys Res Commun 2024; 709:149825. [PMID: 38537599 DOI: 10.1016/j.bbrc.2024.149825] [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: 03/04/2024] [Accepted: 03/24/2024] [Indexed: 04/13/2024]
Abstract
SARS-Cov-2, the virus causing COVID-19, penetrates host target cells via the receptor of angiotensin-converting enzyme 2 (ACE2). Disrupting the virus interaction with ACE2 affords a plausible mechanism for prevention of cell penetration and inhibiting dissemination of the virus. Our studies demonstrate that ACE2 interaction with the receptor binding domain of SARS-Cov-2 spike protein (RBD) can be impaired by modulating the α7 nicotinic acetylcholine receptor (α7 nAChR) contiguous with ACE2. U373 cells of human astrocytoma origin were shown to bind both ACE2-specific antibody and recombinant RBD in Cell-ELISA. ACE2 was found to interact with α7 nAChR in U373 cell lysates studied by Sandwich ELISA. Our studies demonstrate that inhibition of RBD binding to ACE2-expressing U373 cells were defined with α7 nAChR agonists choline and PNU282987, but not a competitive antagonist methyllicaconitine (MLA). Additionally, the type 2 positive allosteric modulator (PAM2) PNU120596 and hydroxyurea (HU) also inhibited the binding. Our studies demonstrate that activation of α7 AChRs has efficacy in inhibiting the SARS-Cov-2 interaction with the ACE2 receptor and in such a way can prevent virus target cell penetration. These studies also help to clarify the consistent efficacy and positive outcomes for utilizing HU in treating COVID-19.
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Affiliation(s)
- Olena Kalashnyk
- Palladin Institute of Biochemistry, NAS of Ukraine, 9, Leontovycha Str., 01054, Kyiv, Ukraine.
| | - Olena Lykhmus
- Palladin Institute of Biochemistry, NAS of Ukraine, 9, Leontovycha Str., 01054, Kyiv, Ukraine.
| | | | - Serhiy Komisarenko
- Palladin Institute of Biochemistry, NAS of Ukraine, 9, Leontovycha Str., 01054, Kyiv, Ukraine.
| | - Maryna Skok
- Palladin Institute of Biochemistry, NAS of Ukraine, 9, Leontovycha Str., 01054, Kyiv, Ukraine.
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3
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Brinkkemper M, Poniman M, Siteur-van Rijnstra E, Iddouch WA, Bijl TP, Guerra D, Tejjani K, Grobben M, Bhoelan F, Bemelman D, Kempers R, van Gils MJ, Sliepen K, Stegmann T, van der Velden YU, Sanders RW. A spike virosome vaccine induces pan-sarbecovirus antibody responses in mice. iScience 2024; 27:109719. [PMID: 38706848 PMCID: PMC11068555 DOI: 10.1016/j.isci.2024.109719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/08/2024] [Accepted: 04/08/2024] [Indexed: 05/07/2024] Open
Abstract
Zoonotic events by sarbecoviruses have sparked an epidemic (severe acute respiratory syndrome coronavirus [SARS-CoV]) and a pandemic (SARS-CoV-2) in the past two decades. The continued risk of spillovers from animals to humans is an ongoing threat to global health and a pan-sarbecovirus vaccine would be an important contribution to pandemic preparedness. Here, we describe multivalent virosome-based vaccines that present stabilized spike proteins from four sarbecovirus strains, one from each clade. A cocktail of four monovalent virosomes or a mosaic virosome preparation induced broad sarbecovirus binding and neutralizing antibody responses in mice. Pre-existing immunity against SARS-CoV-2 and extending the intervals between immunizations enhanced antibody responses. These results should inform the development of a pan-sarbecovirus vaccine, as part of our efforts to prepare for and/or avoid a next pandemic.
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Affiliation(s)
- Mitch Brinkkemper
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Meliawati Poniman
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Esther Siteur-van Rijnstra
- Amsterdam UMC, location University of Amsterdam, Department of Experimental Immunology, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Widad Ait Iddouch
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Tom P.L. Bijl
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Denise Guerra
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Khadija Tejjani
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Marloes Grobben
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Farien Bhoelan
- Mymetics BV, JH Oortweg 21, CH 2333 Leiden, the Netherlands
| | | | - Ronald Kempers
- Mymetics BV, JH Oortweg 21, CH 2333 Leiden, the Netherlands
| | - Marit J. van Gils
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Kwinten Sliepen
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Toon Stegmann
- Mymetics BV, JH Oortweg 21, CH 2333 Leiden, the Netherlands
| | - Yme U. van der Velden
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Rogier W. Sanders
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA
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4
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Zhai Y, Li S, Wang H, Shan Y. Revealing the dynamic mechanism of cell-penetrating peptides across cell membranes at the single-molecule level. J Mater Chem B 2024. [PMID: 38741568 DOI: 10.1039/d4tb00522h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Cell-penetrating peptides (CPPs) have gained prominence in cellular drug delivery due to their extremely low toxicity and rapid cell internalization properties. Understanding the effect of CPPs' physicochemical properties on trans-membrane behavior will provide a better screening scheme for designing effective CPP-conjugated nano-drugs. Herein, the efficiency of the CPPs interacting with the cell membrane and the subsequent trans-membrane is revealed at the single-molecule level using single-molecule force spectroscopy (SMFS) and force tracing technique based on atomic force spectroscopy (AFM). The dynamic force spectroscopy (DFS) analysis indicates that cationic TAT48-60 and amphipathic MAP are more effective during the interaction with cell membrane due to the strong electrostatic interaction between CPPs and cell membrane. However, for the subsequent trans-membrane process, the hydrophobicity of Pep-7 plays a key role, showing a higher trans-membrane speed at the single-molecule level. Meanwhile, Pep-7 shows lower trans-membrane speed and probability on normal cells (Vero), which makes it more suitable as a peptide-based nano-drug to treat tumors avoiding harming normal cells. The dynamic parameters obtained in this study offer guidance for screening and modifying effective CPPs, targeting specific cell lines or tissues during the nano-drug design.
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Affiliation(s)
- Yuhang Zhai
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China.
| | - Siying Li
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China.
| | - Hui Wang
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China.
| | - Yuping Shan
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China.
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5
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Santisteban Celis IC, Matoba N. Lectibodies as antivirals. Antiviral Res 2024; 227:105901. [PMID: 38734211 DOI: 10.1016/j.antiviral.2024.105901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/02/2024] [Accepted: 05/05/2024] [Indexed: 05/13/2024]
Abstract
Growing concerns regarding the emergence of highly transmissible viral diseases highlight the urgent need to expand the repertoire of antiviral therapeutics. For this reason, new strategies for neutralizing and inhibiting these viruses are necessary. A promising approach involves targeting the glycans present on the surfaces of enveloped viruses. Lectins, known for their ability to recognize specific carbohydrate molecules, offer the potential for glycan-targeted antiviral strategies. Indeed, numerous studies have reported the antiviral effects of various lectins of both endogenous and exogenous origins. However, many lectins in their natural forms, are not suitable for use as antiviral therapeutics due to toxicity, other unfavorable pharmacological effects, and/or unreliable manufacturing sources. Therefore, improvements are crucial for employing lectins as effective antiviral therapeutics. A novel approach to enhance lectins' suitability as pharmaceuticals could be the generation of recombinant lectin-Fc fusion proteins, termed "lectibodies." In this review, we discuss the scientific rationale behind lectin-based antiviral strategies and explore how lectibodies could facilitate the development of new antiviral therapeutics. We will also share our perspective on the potential of these molecules to transcend their potential use as antiviral agents.
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Affiliation(s)
- Ian Carlosalberto Santisteban Celis
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY, USA; Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville School of Medicine, Louisville, KY, USA
| | - Nobuyuki Matoba
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY, USA; Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville School of Medicine, Louisville, KY, USA; UofL Health - Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY, USA.
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6
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Huang Y, Chen T, Chen X, Chen X, Zhang J, Liu S, Lu M, Chen C, Ding X, Yang C, Huang R, Song Y. Decoding Biomechanical Cues Based on DNA Sensors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310330. [PMID: 38185740 DOI: 10.1002/smll.202310330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/18/2023] [Indexed: 01/09/2024]
Abstract
Biological systems perceive and respond to mechanical forces, generating mechanical cues to regulate life processes. Analyzing biomechanical forces has profound significance for understanding biological functions. Therefore, a series of molecular mechanical techniques have been developed, mainly including single-molecule force spectroscopy, traction force microscopy, and molecular tension sensor systems, which provide indispensable tools for advancing the field of mechanobiology. DNA molecules with a programmable structure and well-defined mechanical characteristics have attached much attention to molecular tension sensors as sensing elements, and are designed for the study of biomechanical forces to present biomechanical information with high sensitivity and resolution. In this work, a comprehensive overview of molecular mechanical technology is presented, with a particular focus on molecular tension sensor systems, specifically those based on DNA. Finally, the future development and challenges of DNA-based molecular tension sensor systems are looked upon.
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Affiliation(s)
- Yihao Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Ting Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Xiaodie Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Ximing Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Jialu Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Sinong Liu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Menghao Lu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Chong Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Xiangyu Ding
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
- Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Ruiyun Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
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7
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Ray A, Minh Tran TT, Santos Natividade RD, Moreira RA, Simpson JD, Mohammed D, Koehler M, L Petitjean SJ, Zhang Q, Bureau F, Gillet L, Poma AB, Alsteens D. Single-Molecule Investigation of the Binding Interface Stability of SARS-CoV-2 Variants with ACE2. ACS NANOSCIENCE AU 2024; 4:136-145. [PMID: 38644967 PMCID: PMC11027127 DOI: 10.1021/acsnanoscienceau.3c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 04/23/2024]
Abstract
The SARS-CoV-2 pandemic spurred numerous research endeavors to comprehend the virus and mitigate its global severity. Understanding the binding interface between the virus and human receptors is pivotal to these efforts and paramount to curbing infection and transmission. Here we employ atomic force microscopy and steered molecular dynamics simulation to explore SARS-CoV-2 receptor binding domain (RBD) variants and angiotensin-converting enzyme 2 (ACE2), examining the impact of mutations at key residues upon binding affinity. Our results show that the Omicron and Delta variants possess strengthened binding affinity in comparison to the Mu variant. Further, using sera from individuals either vaccinated or with acquired immunity following Delta strain infection, we assess the impact of immunity upon variant RBD/ACE2 complex formation. Single-molecule force spectroscopy analysis suggests that vaccination before infection may provide stronger protection across variants. These results underscore the need to monitor antigenic changes in order to continue developing innovative and effective SARS-CoV-2 abrogation strategies.
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Affiliation(s)
- Ankita Ray
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Thu Thi Minh Tran
- Faculty
of Materials Science and Technology, University
of Science—VNU HCM, 227 Nguyen Van Cu Street, District 5, 700000 Ho Chi Minh City, Vietnam
- Vietnam
National University, 700000 Ho Chi Minh City, Vietnam
| | - Rita dos Santos Natividade
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Rodrigo A. Moreira
- Basque
Center for Applied Mathematics, Mazarredo 14, 48009 Bilbao, Spain
| | - Joshua D. Simpson
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Danahe Mohammed
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Melanie Koehler
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Simon J. L Petitjean
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Qingrong Zhang
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Fabrice Bureau
- Laboratory
of Cellular and Molecular Immunology, GIGA Institute, Liège University, 4000 Liège, Belgium
| | - Laurent Gillet
- Immunology-Vaccinology
Lab of the Faculty of Veterinary Medicine, Liège University, 4000 Liège, Belgium
| | - Adolfo B. Poma
- Institute
of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland
| | - David Alsteens
- Louvain
Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
- WELBIO
department, WEL Research Institute, 1300 Wavre, Belgium
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8
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Nguyen HL, Nguyen TQ, Li MS. SARS-CoV-2 Omicron Subvariants Do Not Differ Much in Binding Affinity to Human ACE2: A Molecular Dynamics Study. J Phys Chem B 2024; 128:3340-3349. [PMID: 38564480 PMCID: PMC11017248 DOI: 10.1021/acs.jpcb.3c06270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/12/2024] [Accepted: 03/12/2024] [Indexed: 04/04/2024]
Abstract
The emergence of the variant of concern Omicron (B.1.1.529) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exacerbates the COVID-19 pandemic due to its high contagious ability. Studies have shown that the Omicron binds human ACE2 more strongly than the wild type. The prevalence of Omicron in new cases of COVID-19 promotes novel lineages with improved receptor binding affinity and immune evasion. To shed light on this open problem, in this work, we investigated the binding free energy of the receptor binding domain of the Omicron lineages BA.2, BA.2.3.20, BA.3, BA4/BA5, BA.2.75, BA.2.75.2, BA.4.6, XBB.1, XBB.1.5, BJ.1, BN.1, BQ.1.1, and CH.1.1 to human ACE2 using all-atom molecular dynamics simulation and the molecular mechanics Poisson-Boltzmann surface area method. The results show that these lineages have increased binding affinity compared to the BA.1 lineage, and BA.2.75 and BA.2.75.2 subvariants bind ACE2 more strongly than others. However, in general, the binding affinities of the Omicron lineages do not differ significantly from each other. The electrostatic force dominates over the van der Waals force in the interaction between Omicron lineages and human cells. Based on our results, we argue that viral evolution does not further improve the affinity of SARS-CoV-2 for ACE2 but may increase immune evasion.
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Affiliation(s)
- Hoang Linh Nguyen
- Institute
of Fundamental and Applied Sciences, Duy
Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty
of Environmental and Natural Sciences, Duy
Tan University, Da Nang 550000, Vietnam
| | - Thai Quoc Nguyen
- Faculty
of Physics, VNU University of Science, Vietnam
National University, 334 Nguyen Trai, Hanoi 100000, Vietnam
- Dong
Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh
City, Dong Thap 81000, Vietnam
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, Warsaw 02-668, Poland
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9
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Ivanusic D, Maier J, Icli S, Falcone V, Bernauer H, Bannert N. tANCHOR-cell-based assay for monitoring of SARS-CoV-2 neutralizing antibodies rapidly adaptive to various receptor-binding domains. iScience 2024; 27:109123. [PMID: 38380248 PMCID: PMC10877956 DOI: 10.1016/j.isci.2024.109123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 10/24/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
Conventional neutralizing enzyme-linked immunosorbent assay (ELISA) systems for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mimic the protein-protein interaction between angiotensin-converting enzyme 2 (ACE2) and the receptor-binding domain (RBD). However, an easy and rapidly adaptative ELISA-based system for testing neutralizing antibodies against upcoming SARS-CoV-2 variants is urgently needed. In this study, we closed this gap by developing a tANCHOR-cell-based RBD neutralization assay that avoids time-consuming protein expression and purification followed by coating on ELISA plates. This cell-based assay can be rapidly adopted to monitor neutralizing antibodies (NAbs) against upcoming SARS-CoV-2 variants. We show that the results obtained with the tANCHOR-cell-based assay system strongly correlate with commercially available surrogate assays for testing NAbs. Moreover, this technique can directly measure binding between cell-surface-exposed RBDs and soluble ACE2. With this technique, the degree of antibody escape elicited by emerging SARS-CoV-2 variants in current vaccination regimens can be determined rapidly and reliably.
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Affiliation(s)
- Daniel Ivanusic
- Sexually transmitted bacterial pathogens and HIV (FG18), Robert Koch-Institute, 13353 Berlin, Germany
| | - Josef Maier
- ATG:biosynthetics GmbH, 79249 Merzhausen, Germany
| | - Suheda Icli
- Sexually transmitted bacterial pathogens and HIV (FG18), Robert Koch-Institute, 13353 Berlin, Germany
| | - Valeria Falcone
- Freiburg University Medical Center, Faculty of Medicine, Institute of Virology, University of Freiburg, 79104 Freiburg, Germany
| | | | - Norbert Bannert
- Sexually transmitted bacterial pathogens and HIV (FG18), Robert Koch-Institute, 13353 Berlin, Germany
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10
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Wang Z, Hu S, Popowski KD, Liu S, Zhu D, Mei X, Li J, Hu Y, Dinh PUC, Wang X, Cheng K. Inhalation of ACE2-expressing lung exosomes provides prophylactic protection against SARS-CoV-2. Nat Commun 2024; 15:2236. [PMID: 38472181 DOI: 10.1038/s41467-024-45628-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/24/2024] [Indexed: 03/14/2024] Open
Abstract
Continued emergence of SARS-CoV-2 variants of concern that are capable of escaping vaccine-induced immunity highlights the urgency of developing new COVID-19 therapeutics. An essential mechanism for SARS-CoV-2 infection begins with the viral spike protein binding to the human ACE2. Consequently, inhibiting this interaction becomes a highly promising therapeutic strategy against COVID-19. Herein, we demonstrate that ACE2-expressing human lung spheroid cells (LSC)-derived exosomes (LSC-Exo) could function as a prophylactic agent to bind and neutralize SARS-CoV-2, protecting the host against SARS-CoV-2 infection. Inhalation of LSC-Exo facilitates its deposition and biodistribution throughout the whole lung in a female mouse model. We show that LSC-Exo blocks the interaction of SARS-CoV-2 with host cells in vitro and in vivo by neutralizing the virus. LSC-Exo treatment protects hamsters from SARS-CoV-2-induced disease and reduced viral loads. Furthermore, LSC-Exo intercepts the entry of multiple SARS-CoV-2 variant pseudoviruses in female mice and shows comparable or equal potency against the wild-type strain, demonstrating that LSC-Exo may act as a broad-spectrum protectant against existing and emerging virus variants.
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Affiliation(s)
- Zhenzhen Wang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, 511442, P.R. China.
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, 27606, USA.
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, and North Carolina State University, Raleigh, NC, 27606, USA.
| | - Shiqi Hu
- Department of Biomedical Engineering, Columbia University, New York, New York, 10032, USA
| | - Kristen D Popowski
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, 27606, USA
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, and North Carolina State University, Raleigh, NC, 27606, USA
| | - Shuo Liu
- Department of Biomedical Engineering, Columbia University, New York, New York, 10032, USA
| | - Dashuai Zhu
- Department of Biomedical Engineering, Columbia University, New York, New York, 10032, USA
| | - Xuan Mei
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, 27606, USA
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, and North Carolina State University, Raleigh, NC, 27606, USA
| | - Junlang Li
- Xsome Biotech Inc., Raleigh, North Carolina, 27607, USA
| | - Yilan Hu
- Department of Biomedical Engineering, Columbia University, New York, New York, 10032, USA
| | - Phuong-Uyen C Dinh
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC, 27606, USA
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, and North Carolina State University, Raleigh, NC, 27606, USA
| | - Xiaojie Wang
- School of Pharmacy, Wenzhou Medical University, Wenzhou, 325035, P.R. China.
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, P.R. China.
| | - Ke Cheng
- Department of Biomedical Engineering, Columbia University, New York, New York, 10032, USA.
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11
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Bauer MS, Gruber S, Hausch A, Melo MCR, Gomes PSFC, Nicolaus T, Milles LF, Gaub HE, Bernardi RC, Lipfert J. Single-molecule force stability of the SARS-CoV-2-ACE2 interface in variants-of-concern. NATURE NANOTECHNOLOGY 2024; 19:399-405. [PMID: 38012274 DOI: 10.1038/s41565-023-01536-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 09/26/2023] [Indexed: 11/29/2023]
Abstract
Mutations in SARS-CoV-2 have shown effective evasion of population immunity and increased affinity to the cellular receptor angiotensin-converting enzyme 2 (ACE2). However, in the dynamic environment of the respiratory tract, forces act on the binding partners, which raises the question of whether not only affinity but also force stability of the SARS-CoV-2-ACE2 interaction might be a selection factor for mutations. Using magnetic tweezers, we investigate the impact of amino acid substitutions in variants of concern (Alpha, Beta, Gamma and Delta) and on force-stability and bond kinetic of the receptor-binding domain-ACE2 interface at a single-molecule resolution. We find a higher affinity for all of the variants of concern (>fivefold) compared with the wild type. In contrast, Alpha is the only variant of concern that shows higher force stability (by 17%) compared with the wild type. Using molecular dynamics simulations, we rationalize the mechanistic molecular origins of this increase in force stability. Our study emphasizes the diversity of contributions to the transmissibility of variants and establishes force stability as one of the several factors for fitness. Understanding fitness advantages opens the possibility for the prediction of probable mutations, allowing a rapid adjustment of therapeutics, vaccines and intervention measures.
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Affiliation(s)
- Magnus S Bauer
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Sophia Gruber
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
| | - Adina Hausch
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
- Center for Protein Assemblies, TUM School of Natural Sciences, Technical University of Munich, Munich, Germany
| | | | | | - Thomas Nicolaus
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
| | - Lukas F Milles
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hermann E Gaub
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
| | | | - Jan Lipfert
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany.
- Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.
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12
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Sun H, Liao F, Tian Y, Lei Y, Fu Y, Wang J. Molecular-Scale Investigations Reveal the Effect of Natural Polyphenols on BAX/Bcl-2 Interactions. Int J Mol Sci 2024; 25:2474. [PMID: 38473728 DOI: 10.3390/ijms25052474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
Apoptosis signaling controls the cell cycle through the protein-protein interactions (PPIs) of its major B-cell lymphoma 2-associated x protein (BAX) and B-cell lymphoma 2 protein (Bcl-2). Due to the antagonistic function of both proteins, apoptosis depends on a properly tuned balance of the kinetics of BAX and Bcl-2 activities. The utilization of natural polyphenols to regulate the binding process of PPIs is feasible. However, the mechanism of this modulation has not been studied in detail. Here, we utilized atomic force microscopy (AFM) to evaluate the effects of polyphenols (kaempferol, quercetin, dihydromyricetin, baicalin, curcumin, rutin, epigallocatechin gallate, and gossypol) on the BAX/Bcl-2 binding mechanism. We demonstrated at the molecular scale that polyphenols quantitatively affect the interaction forces, kinetics, thermodynamics, and structural properties of BAX/Bcl-2 complex formation. We observed that rutin, epigallocatechin gallate, and baicalin reduced the binding affinity of BAX/Bcl-2 by an order of magnitude. Combined with surface free energy and molecular docking, the results revealed that polyphenols are driven by multiple forces that affect the orientation freedom of PPIs, with hydrogen bonding, hydrophobic interactions, and van der Waals forces being the major contributors. Overall, our work provides valuable insights into how molecules tune PPIs to modulate their function.
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Affiliation(s)
- Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Fenghui Liao
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Yichen Tian
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Yongrong Lei
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Yuna Fu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
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13
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Alam I, Boonkoom T, Pitakjakpipop H, Boonbanjong P, Loha K, Saeyang T, Vanichtanankul J, Japrung D. Single-Molecule Analysis of SARS-CoV-2 Double-Stranded Polynucleotides Using Solid-State Nanopore with AI-Assisted Detection and Classification: Implications for Understanding Disease Severity. ACS APPLIED BIO MATERIALS 2024; 7:1017-1027. [PMID: 38194666 DOI: 10.1021/acsabm.3c00998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
This study utilized solid-state nanopores, combined with artificial intelligence (AI), to analyze the double-stranded polynucleotides encoding angiotensin-converting enzyme 2, receptor-binding domain, and N protein, important parts of SARS-CoV-2 infection. By examining ionic current signals during DNA translocation, we revealed the dynamic interactions and structural characteristics of these nucleotide sequences and also quantified their abundance. Nanopores of sizes 3 and 10 nm were efficiently fabricated and characterized, ensuring an optimal experimental approach. Our results showed a clear relationship between DNA capture rates and concentration, proving our method's effectiveness. Notably, longer DNA sequences had higher capture rates, suggesting their importance for potential disease marker analysis. The 3 nm nanopore demonstrated superior performance in our DNA analysis. Using dwell time measurements and excluded currents, we were able to distinguish the longer DNA fragments, paving the way for a DNA length-based analysis. Overall, our research underscores the potential of nanopore technology, enhanced with AI, in analyzing COVID-19-related DNA and its implications for understanding disease severity. This provides insight into innovative diagnostic and treatment strategies.
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Affiliation(s)
- Ibrar Alam
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
| | - Thitikorn Boonkoom
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
| | - Harit Pitakjakpipop
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
| | - Poramin Boonbanjong
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Kawin Loha
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Thanaya Saeyang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
| | - Jarunee Vanichtanankul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
| | - Deanpen Japrung
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
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14
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Schobesberger S, Thumfart H, Selinger F, Spitz S, Gonzalez C, Pei L, Poglitsch M, Ertl P. Application of a Biomimetic Nanoparticle-Based Mock Virus to Determine SARS-CoV-2 Neutralizing Antibody Levels in Blood Samples Using a Lateral Flow Assay. Anal Chem 2024. [PMID: 38334364 PMCID: PMC10882572 DOI: 10.1021/acs.analchem.3c04372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
The presence of neutralizing antibodies against SARS-CoV-2 in blood, acquired through previous infection or vaccination, is known to prevent the (re)occurrence of outbreaks unless the virus mutates. Therefore, the measurement of neutralizing antibodies constitutes an indispensable tool in assessing an individual's and a population's immunity against SARS-CoV-2. For this reason, we have developed an innovative lateral flow assay (LFA) capable of detecting blood-derived neutralizing antibodies using a biomimetic SARS-CoV-2 mock virus system. Here, functionalized gold nanoparticles (AuNPs) featuring the trimeric spike (S) protein at its surface imitate the virus's structure and are applied to monitor the presence and efficacy of neutralizing antibodies in blood samples. The detection principle relies on the interaction between mock virus and the immobilized angiotensin-converting enzyme 2 (ACE2) receptor, which is inhibited when neutralizing antibodies are present. To further enhance the sensitivity of our competitive assay and identify low titers of neutralizing antibodies, an additional mixing pad is embedded into the device to increase the interaction time between mock virus and neutralizing antibodies. The developed LFA is benchmarked against the WHO International Standard (21/338) and demonstrated reliable quantification of neutralizing antibodies that inhibit ACE2 binding events down to a detection limit of an antibody titer of 59 IU/mL. Additional validation using whole blood and plasma samples showed reproducible results and good comparability to a laboratory-based reference test, thus highlighting its applicability for point-of-care testing.
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Affiliation(s)
| | - Helena Thumfart
- TU Wien, Faculty of Technical Chemistry, Getreidemarkt 9, 1060 Vienna, Austria
| | - Florian Selinger
- TU Wien, Faculty of Technical Chemistry, Getreidemarkt 9, 1060 Vienna, Austria
| | - Sarah Spitz
- TU Wien, Faculty of Technical Chemistry, Getreidemarkt 9, 1060 Vienna, Austria
| | | | - Lei Pei
- Covirabio GmbH, Brehmstraße 14a, 1110 Vienna, Austria
| | | | - Peter Ertl
- TU Wien, Faculty of Technical Chemistry, Getreidemarkt 9, 1060 Vienna, Austria
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15
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Lan PD, Nissley DA, O'Brien EP, Nguyen TT, Li MS. Deciphering the free energy landscapes of SARS-CoV-2 wild type and Omicron variant interacting with human ACE2. J Chem Phys 2024; 160:055101. [PMID: 38310477 DOI: 10.1063/5.0188053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 01/08/2024] [Indexed: 02/05/2024] Open
Abstract
The binding of the receptor binding domain (RBD) of the SARS-CoV-2 spike protein to the host cell receptor angiotensin-converting enzyme 2 (ACE2) is the first step in human viral infection. Therefore, understanding the mechanism of interaction between RBD and ACE2 at the molecular level is critical for the prevention of COVID-19, as more variants of concern, such as Omicron, appear. Recently, atomic force microscopy has been applied to characterize the free energy landscape of the RBD-ACE2 complex, including estimation of the distance between the transition state and the bound state, xu. Here, using a coarse-grained model and replica-exchange umbrella sampling, we studied the free energy landscape of both the wild type and Omicron subvariants BA.1 and XBB.1.5 interacting with ACE2. In agreement with experiment, we find that the wild type and Omicron subvariants have similar xu values, but Omicron binds ACE2 more strongly than the wild type, having a lower dissociation constant KD.
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Affiliation(s)
- Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Daniel A Nissley
- Department of Statistics, University of Oxford, Oxford Protein Bioinformatics Group, Oxford OX1 2JD, United Kingdom
| | - Edward P O'Brien
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, USA
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA
- Institute for Computational and Data Sciences, Penn State University, University Park, Pennsylvania 16802, USA
| | - Toan T Nguyen
- Key Laboratory for Multiscale Simulation of Complex Systems and Department of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University - Hanoi, 334 Nguyen Trai Street, Thanh Xuan District, Hanoi 11400, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
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16
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Ravichandran KA, Heneka MT. Inflammasomes in neurological disorders - mechanisms and therapeutic potential. Nat Rev Neurol 2024; 20:67-83. [PMID: 38195712 DOI: 10.1038/s41582-023-00915-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2023] [Indexed: 01/11/2024]
Abstract
Inflammasomes are molecular scaffolds that are activated by damage-associated and pathogen-associated molecular patterns and form a key element of innate immune responses. Consequently, the involvement of inflammasomes in several diseases that are characterized by inflammatory processes, such as multiple sclerosis, is widely appreciated. However, many other neurological conditions, including Alzheimer disease, Parkinson disease, amyotrophic lateral sclerosis, stroke, epilepsy, traumatic brain injury, sepsis-associated encephalopathy and neurological sequelae of COVID-19, all involve persistent inflammation in the brain, and increasing evidence suggests that inflammasome activation contributes to disease progression in these conditions. Understanding the biology and mechanisms of inflammasome activation is, therefore, crucial for the development of inflammasome-targeted therapies for neurological conditions. In this Review, we present the current evidence for and understanding of inflammasome activation in neurological diseases and discuss current and potential interventional strategies that target inflammasome activation to mitigate its pathological consequences.
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Affiliation(s)
- Kishore Aravind Ravichandran
- Department of Neuroinflammation, Institute of innate immunity, University of Bonn Medical Center Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Michael T Heneka
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Esch-sur-Alzette, Luxembourg.
- Department of Infectious Diseases and Immunology, University of Massachusetts Medical School, North Worcester, MA, USA.
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17
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Song MS, Lee DK, Lee CY, Park SC, Yang J. Host Subcellular Organelles: Targets of Viral Manipulation. Int J Mol Sci 2024; 25:1638. [PMID: 38338917 PMCID: PMC10855258 DOI: 10.3390/ijms25031638] [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: 01/04/2024] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
Viruses have evolved sophisticated mechanisms to manipulate host cell processes and utilize intracellular organelles to facilitate their replication. These complex interactions between viruses and cellular organelles allow them to hijack the cellular machinery and impair homeostasis. Moreover, viral infection alters the cell membrane's structure and composition and induces vesicle formation to facilitate intracellular trafficking of viral components. However, the research focus has predominantly been on the immune response elicited by viruses, often overlooking the significant alterations that viruses induce in cellular organelles. Gaining a deeper understanding of these virus-induced cellular changes is crucial for elucidating the full life cycle of viruses and developing potent antiviral therapies. Exploring virus-induced cellular changes could substantially improve our understanding of viral infection mechanisms.
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Affiliation(s)
- Min Seok Song
- Department of Physiology and Convergence Medical Science, Institute of Medical Science, College of Medicine, Gyeongsang National University, Jinju 52727, Republic of Korea
| | - Dong-Kun Lee
- Department of Physiology and Convergence Medical Science, Institute of Medical Science, College of Medicine, Gyeongsang National University, Jinju 52727, Republic of Korea
| | - Chung-Young Lee
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Sang-Cheol Park
- Artificial Intelligence and Robotics Laboratory, Myongji Hospital, Goyang 10475, Republic of Korea
| | - Jinsung Yang
- Department of Biochemistry and Convergence Medical Science, Institute of Medical Science, College of Medicine, Gyeongsang National University, Jinju 52727, Republic of Korea
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18
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Duman ET, Tuna G, Ak E, Avsar G, Pir P. Optimized network based natural language processing approach to reveal disease comorbidities in COVID-19. Sci Rep 2024; 14:2325. [PMID: 38282038 PMCID: PMC10822845 DOI: 10.1038/s41598-024-52819-5] [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: 03/23/2023] [Accepted: 01/24/2024] [Indexed: 01/30/2024] Open
Abstract
A novel virus emerged from Wuhan, China, at the end of 2019 and quickly evolved into a pandemic, significantly impacting various industries, especially healthcare. One critical lesson from COVID-19 is the importance of understanding and predicting underlying comorbidities to better prioritize care and pharmacological therapies. Factors like age, race, and comorbidity history are crucial in determining disease mortality. While clinical data from hospitals and cohorts have led to the identification of these comorbidities, traditional approaches often lack a mechanistic understanding of the connections between them. In response, we utilized a deep learning approach to integrate COVID-19 data with data from other diseases, aiming to detect comorbidities with mechanistic insights. Our modified algorithm in the mpDisNet package, based on word-embedding deep learning techniques, incorporates miRNA expression profiles from SARS-CoV-2 infected cell lines and their target transcription factors. This approach is aligned with the emerging field of network medicine, which seeks to define diseases based on distinct pathomechanisms rather than just phenotypes. The main aim is discovery of possible unknown comorbidities by connecting the diseases by their miRNA mediated regulatory interactions. The algorithm can predict the majority of COVID-19's known comorbidities, as well as several diseases that have yet to be discovered to be comorbid with COVID-19. These potentially comorbid diseases should be investigated further to raise awareness and prevention, as well as informing the comorbidity research for the next possible outbreak.
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Affiliation(s)
- Emre Taylan Duman
- Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey.
- NGS-Core Unit for Integrative Genomics, Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany.
| | - Gizem Tuna
- Department of Molecular Biology, Gebze Technical University, Kocaeli, Turkey
| | - Enes Ak
- Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey
| | - Gülben Avsar
- Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey
| | - Pinar Pir
- Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey
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19
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Cummings SE, Delaney SP, St-Denis Bissonnette F, Stalker A, Muradia G, Mehic J, Graber TE, Alain T, Lavoie JR. SARS-CoV-2 antigen-carrying extracellular vesicles activate T cell responses in a human immunogenicity model. iScience 2024; 27:108708. [PMID: 38226155 PMCID: PMC10788222 DOI: 10.1016/j.isci.2023.108708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 10/16/2023] [Accepted: 12/08/2023] [Indexed: 01/17/2024] Open
Abstract
Extracellular vesicles (EVs) are entering the clinical arena as novel biologics for infectious diseases, potentially serving as the immunogenic components of next generation vaccines. However, relevant human assays to evaluate the immunogenicity of EVs carrying viral antigens are lacking, contributing to challenges in translating rodent studies to human clinical trials. Here, we engineered EVs to carry SARS-CoV-2 Spike to evaluate the immunogenicity of antigen-carrying EVs using human peripheral blood mononuclear cells (PBMCs). Delivery of Spike EVs to PBMCs resulted in specific immune cell activation as assessed through T cell activation marker expression. Further, Spike EVs were taken up largely by antigen-presenting cells (monocytes, dendritic cells and B cells). Taken together, this human PBMC-based system models physiologically relevant pathways of antigen delivery, uptake and presentation. In summary, the current study highlights the suitability of using human PBMCs for evaluating the immunogenicity of EVs engineered to carry antigens for infectious disease therapeutics.
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Affiliation(s)
- Sarah E. Cummings
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Sean P. Delaney
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Frederic St-Denis Bissonnette
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Andrew Stalker
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON, Canada
| | - Gauri Muradia
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON, Canada
| | - Jelica Mehic
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON, Canada
| | - Tyson E. Graber
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, 401 Smyth Road, Ottawa, ON K1H 8L1 Canada
| | - Tommy Alain
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, 401 Smyth Road, Ottawa, ON K1H 8L1 Canada
| | - Jessie R. Lavoie
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
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20
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Yang X, Yang Y, Zhang Z, Li M. Deep Learning Image Recognition-Assisted Atomic Force Microscopy for Single-Cell Efficient Mechanics in Co-culture Environments. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:837-852. [PMID: 38154137 DOI: 10.1021/acs.langmuir.3c03046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
Atomic force microscopy (AFM)-based force spectroscopy assay has become an important method for characterizing the mechanical properties of single living cells under aqueous conditions, but a disadvantage is its reliance on manual operation and experience as well as the resulting low throughput. Particularly, providing a capacity to accurately identify the type of the cell grown in co-culture environments without the need of fluorescent labeling will further facilitate the applications of AFM in life sciences. Here, we present a study of deep learning image recognition-assisted AFM, which not only enables fluorescence-independent recognition of the identity of single co-cultured cells but also allows efficient downstream AFM force measurements of the identified cells. With the use of the deep learning-based image recognition model, the viability and type of individual cells grown in co-culture environments were identified directly from the optical bright-field images, which were confirmed by the following cell growth and fluorescent labeling results. Based on the image recognition results, the positional relationship between the AFM probe and the targeted cell was automatically determined, allowing the precise movement of the AFM probe to the target cell to perform force measurements. The experimental results show that the presented method was applicable not only to the conventional (microsphere-modified) AFM probe used in AFM indentation assay for measuring the Young's modulus of single co-cultured cells but also to the single-cell probe used in AFM-based single-cell force spectroscopy (SCFS) assay for measuring the adhesion forces of single co-cultured cells. The study illustrates deep learning imaging recognition-assisted AFM as a promising approach for label-free and high-throughput detection of single-cell mechanics under co-culture conditions, which will facilitate unraveling the mechanical cues involved in cell-cell interactions in their native states at the single-cell level and will benefit the field of mechanobiology.
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Affiliation(s)
- Xuliang Yang
- School of Artificial Intelligence, Shenyang University of Technology, Shenyang 110870, China
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China
| | - Yanqi Yang
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihui Zhang
- School of Artificial Intelligence, Shenyang University of Technology, Shenyang 110870, China
| | - Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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21
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Gressett TE, Hossen ML, Talkington G, Volic M, Perez H, Tiwari PB, Chapagain P, Bix G. Molecular interactions between perlecan LG3 and the SARS-CoV-2 spike protein receptor binding domain. Protein Sci 2024; 33:e4843. [PMID: 37996967 PMCID: PMC10731540 DOI: 10.1002/pro.4843] [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: 06/18/2023] [Revised: 10/14/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused a global health crisis with significant clinical morbidity and mortality. While angiotensin-converting enzyme 2 (ACE2) is the primary receptor for viral entry, other cell surface and extracellular matrix proteins may also bind to the viral receptor binding domain (RBD) within the SARS-CoV-2 spike protein. Recent studies have implicated heparan sulfate proteoglycans, specifically perlecan LG3, in facilitating SARS-CoV-2 binding to ACE2. However, the role of perlecan LG3 in SARS-CoV-2 pathophysiology is not well understood. In this study, we investigated the binding interactions between the SARS-CoV-2 spike protein RBD and perlecan LG3 through molecular modeling simulations and surface plasmon resonance (SPR) experiments. Our results indicate stable binding between LG3 and SARS-CoV-2 spike protein RBD, which may potentially enhance RBD-ACE2 interactions. These findings shed light on the role of perlecan LG3 in SARS-CoV-2 infection and provide insight into SARS-CoV-2 pathophysiology and potential therapeutic strategy for COVID-19.
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Affiliation(s)
- Timothy E. Gressett
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
- Tulane Brain InstituteTulane UniversityNew OrleansLouisianaUSA
| | - Md Lokman Hossen
- Department of PhysicsFlorida International UniversityMiamiFloridaUSA
- Department of PhysicsUniversity of BarishalKornokathiBangladesh
| | - Grant Talkington
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
- Tulane Brain InstituteTulane UniversityNew OrleansLouisianaUSA
| | - Milla Volic
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
| | - Hugo Perez
- Department of PhysicsFlorida International UniversityMiamiFloridaUSA
| | | | - Prem Chapagain
- Department of PhysicsFlorida International UniversityMiamiFloridaUSA
- Biomolecular Sciences InstituteFlorida International UniversityMiamiFloridaUSA
| | - Gregory Bix
- Department of Neurosurgery, Clinical Neuroscience Research CenterTulane University School of MedicineNew OrleansLouisianaUSA
- Tulane Brain InstituteTulane UniversityNew OrleansLouisianaUSA
- Department of NeurologyTulane University School of MedicineNew OrleansLouisianaUSA
- Department of Microbiology and ImmunologyTulane University School of MedicineNew OrleansLouisianaUSA
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22
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Mohammadi A, Chiang S, Li F, Wei F, Lau CS, Aziz M, Ibarrondo FJ, Fulcher JA, Yang OO, Chia D, Kim Y, Wong DT. Direct Detection of 4-Dimensions of SARS-CoV-2: Infection (vRNA), Infectivity (Antigen), Binding Antibody, and Functional Neutralizing Antibody in Saliva. RESEARCH SQUARE 2023:rs.3.rs-3745787. [PMID: 38234820 PMCID: PMC10793499 DOI: 10.21203/rs.3.rs-3745787/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
We developed a 4-parameter clinical assay using Electric Field Induced Release and Measurement (EFIRM) technology to simultaneously assess SARS-CoV-2 RNA (vRNA), nucleocapsid antigen, host binding (BAb) and neutralizing antibody (NAb) levels from a drop of saliva with performance that equals or surpasses current EUA-approved tests. The vRNA and antigen assays achieved lower limit of detection (LOD) of 100 copies/reaction and 3.5 TCID₅₀/mL, respectively. The vRNA assay differentiated between acutely infected (n=10) and infection-naïve patients (n=33) with an AUC of 0.9818, sensitivity of 90%, and specificity of 100%. The antigen assay similarly differentiated these patient populations with an AUC of 1.000. The BAb assay detected BAbs with an LOD of 39 pg/mL and distinguished acutely infected (n=35), vaccinated with prior infection (n=13), and vaccinated infection-naïve patients (n=13) from control (n=81) with AUC of 0.9481, 1.000, and 0.9962, respectively. The NAb assay detected NAbs with an LOD of 31.6 Unit/mL and differentiated between COVID-19 recovered or vaccinated patients (n=31) and pre-pandemic controls (n=60) with an AUC 0.923, sensitivity of 87.10%, and specificity of 86.67%. Our multiparameter assay represents a significant technological advancement to simultaneously address SARS-CoV-2 infection and immunity, and it lays the foundation for tackling potential future pandemics.
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Affiliation(s)
- Aida Mohammadi
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Samantha Chiang
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Feng Li
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Fang Wei
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Mohammad Aziz
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Francisco J. Ibarrondo
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jennifer A. Fulcher
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Otto O. Yang
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - David Chia
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Yong Kim
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
| | - David T.W. Wong
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
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23
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Petitjean SJL, Eeckhout S, Delguste M, Zhang Q, Durlet K, Alsteens D. Heparin-Induced Allosteric Changes in SARS-CoV-2 Spike Protein Facilitate ACE2 Binding and Viral Entry. NANO LETTERS 2023; 23:11678-11684. [PMID: 38055954 DOI: 10.1021/acs.nanolett.3c03550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Understanding the entry of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) into host cells is crucial in the battle against COVID-19. Using atomic force microscopy (AFM), we probed the interaction between the virus's spike protein and heparan sulfate (HS) as a potential attachment factor. Our AFM studies revealed a moderate-affinity interaction between the spike protein and HS on both model surfaces and living cells, highlighting HS's role in early viral attachment. Remarkably, we observed an interplay between HS and the host cell receptor angiotensin-converting enzyme 2 (ACE2), with HS engagement resulting in enhanced ACE2 binding and subsequent viral entry. Our research furthers our understanding of SARS-CoV-2 infection mechanisms and reveals potential interventions targeting viral entry. These insights are valuable as we navigate the evolving landscape of viral threats and seek effective strategies to combat emerging infectious diseases.
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Affiliation(s)
- Simon J L Petitjean
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - Savannah Eeckhout
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - Martin Delguste
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - Qingrong Zhang
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - Kimberley Durlet
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
- WELBIO Department, WEL Research Institute, Wavre, Walloon Brabant 1300, Belgium
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24
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Len JS, Koh CWT, Chan KR. The Functional Roles of MDSCs in Severe COVID-19 Pathogenesis. Viruses 2023; 16:27. [PMID: 38257728 PMCID: PMC10821470 DOI: 10.3390/v16010027] [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: 11/17/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Severe COVID-19 is a major cause of morbidity and mortality worldwide, especially among those with co-morbidities, the elderly, and the immunocompromised. However, the molecular determinants critical for severe COVID-19 progression remain to be fully elucidated. Meta-analyses of transcriptomic RNAseq and single-cell sequencing datasets comparing severe and mild COVID-19 patients have demonstrated that the early expansion of myeloid-derived suppressor cells (MDSCs) could be a key feature of severe COVID-19 progression. Besides serving as potential early prognostic biomarkers for severe COVID-19 progression, several studies have also indicated the functional roles of MDSCs in severe COVID-19 pathogenesis and possibly even long COVID. Given the potential links between MDSCs and severe COVID-19, we examine the existing literature summarizing the characteristics of MDSCs, provide evidence of MDSCs in facilitating severe COVID-19 pathogenesis, and discuss the potential therapeutic avenues that can be explored to reduce the risk and burden of severe COVID-19. We also provide a web app where users can visualize the temporal changes in specific genes or MDSC-related gene sets during severe COVID-19 progression and disease resolution, based on our previous study.
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Affiliation(s)
- Jia Soon Len
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore;
| | - Clara W. T. Koh
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore;
| | - Kuan Rong Chan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore;
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25
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Almazán NM, Rahbar A, Carlsson M, Hoffman T, Kolstad L, Rönnberg B, Pantalone MR, Fuchs IL, Nauclér A, Ohlin M, Sacharczuk M, Religa P, Amér S, Molnár C, Lundkvist Å, Susrud A, Sörensen B, Söderberg-Nauclér C. Influenza-A mediated pre-existing immunity levels to SARS-CoV-2 could predict early COVID-19 outbreak dynamics. iScience 2023; 26:108441. [PMID: 38144451 PMCID: PMC10746369 DOI: 10.1016/j.isci.2023.108441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/14/2023] [Accepted: 11/09/2023] [Indexed: 12/26/2023] Open
Abstract
Susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is highly variable and could be mediated by a cross-protective pre-immunity. We identified 14 cross-reactive peptides between SARS-CoV-2 and influenza A H1N1, H3N2, and human herpesvirus (HHV)-6A/B with potential relevance. The H1N1 peptide NGVEGF was identical to a peptide in the most critical receptor binding motif in SARS-CoV-2 spike protein that interacts with the angiotensin converting enzyme 2 receptor. About 62%-73% of COVID-19-negative blood donors in Stockholm had antibodies to this peptide in the early pre-vaccination phase of the pandemic. Seasonal flu vaccination enhanced neutralizing capacity to SARS-CoV-2 and T cell immunity to this peptide. Mathematical modeling taking the estimated pre-immunity levels to flu into account could fully predict pre-Omicron SARS-CoV-2 outbreaks in Stockholm and India. This cross-immunity provides mechanistic explanations to the epidemiological observation that influenza vaccination protected people against early SARS-CoV-2 infections and implies that flu-mediated cross-protective immunity significantly dampened the first SARS-CoV-2 outbreaks.
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Affiliation(s)
- Nerea Martín Almazán
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, 141 86 Huddinge Stockholm, Sweden
| | - Afsar Rahbar
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
| | - Marcus Carlsson
- Centre for the Mathematical Sciences, Lund University, 223 62 Lund, Sweden
| | - Tove Hoffman
- Zoonosis Science Center (ZSC), Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, 1477 Uppsala, Sweden
| | - Linda Kolstad
- Zoonosis Science Center (ZSC), Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, 1477 Uppsala, Sweden
| | - Bengt Rönnberg
- Zoonosis Science Center (ZSC), Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, 1477 Uppsala, Sweden
| | - Mattia Russel Pantalone
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
| | - Ilona Lewensohn Fuchs
- Department of Labortory Medicine, Division of Clinical Microbiology, Karolinska Institutet, 141 86 Huddinge Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, 141 86 Huddinge Stockholm, Sweden
| | - Anna Nauclér
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
| | - Mats Ohlin
- Department of Immunotechnology and SciLifeLab Human Antibody Therapeutics Infrastructure Unit, Lund University, 223 62 Lund, Sweden
| | - Mariusz Sacharczuk
- Faculty of Pharmacy with the Laboratory Medicine Division, Department of Pharmacodynamics, Medical University of Warsaw, Centre for Preclinical Research and Technology, Banacha 1B, 02-091 Warsaw, Poland
- Department of Experimental Genomics, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Postępu 36A, 05-552 Magdalenka, Poland
| | - Piotr Religa
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
- Department of Experimental Genomics, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Postępu 36A, 05-552 Magdalenka, Poland
| | - Stefan Amér
- Familjeläkarna Saltsjöbaden, 133 34 Saltsjöbaden, Sweden
| | - Christian Molnár
- Familjeläkarna Saltsjöbaden, 133 34 Saltsjöbaden, Sweden
- Department of Neurobiology, Care Sciences and Society, NVS, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Åke Lundkvist
- Zoonosis Science Center (ZSC), Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, 1477 Uppsala, Sweden
| | | | | | - Cecilia Söderberg-Nauclér
- Department of Medicine, Unit for Microbial Pathogenesis, Karolinska Institutet, 17164 Solna, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, 171 76 Solna Stockholm, Sweden
- Institute of Biomedicine, Unit for Infection and Immunology, MediCity Research Laboratory, University of Turku, FI-20014 Turku, Finland
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26
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Stewart H, Palmulli R, Johansen KH, McGovern N, Shehata OM, Carnell GW, Jackson HK, Lee JS, Brown JC, Burgoyne T, Heeney JL, Okkenhaug K, Firth AE, Peden AA, Edgar JR. Tetherin antagonism by SARS-CoV-2 ORF3a and spike protein enhances virus release. EMBO Rep 2023; 24:e57224. [PMID: 37818801 PMCID: PMC10702813 DOI: 10.15252/embr.202357224] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/23/2023] [Accepted: 09/21/2023] [Indexed: 10/13/2023] Open
Abstract
The antiviral restriction factor, tetherin, blocks the release of several different families of enveloped viruses, including the Coronaviridae. Tetherin is an interferon-induced protein that forms parallel homodimers between the host cell and viral particles, linking viruses to the surface of infected cells and inhibiting their release. We demonstrate that SARS-CoV-2 infection causes tetherin downregulation and that tetherin depletion from cells enhances SARS-CoV-2 viral titres. We investigate the potential viral proteins involved in abrogating tetherin function and find that SARS-CoV-2 ORF3a reduces tetherin localisation within biosynthetic organelles where Coronaviruses bud, and increases tetherin localisation to late endocytic organelles via reduced retrograde recycling. We also find that expression of Spike protein causes a reduction in cellular tetherin levels. Our results confirm that tetherin acts as a host restriction factor for SARS-CoV-2 and highlight the multiple distinct mechanisms by which SARS-CoV-2 subverts tetherin function.
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Affiliation(s)
- Hazel Stewart
- Department of PathologyUniversity of CambridgeCambridgeUK
| | | | - Kristoffer H Johansen
- Department of PathologyUniversity of CambridgeCambridgeUK
- Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
| | - Naomi McGovern
- Department of PathologyUniversity of CambridgeCambridgeUK
| | - Ola M Shehata
- Department of Biomedical ScienceUniversity of Sheffield, Firth CourtSheffieldUK
| | - George W Carnell
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | | | - Jin S Lee
- Department of PathologyUniversity of CambridgeCambridgeUK
| | | | - Thomas Burgoyne
- Royal Brompton HospitalGuy's and St Thomas' NHS Foundation TrustLondonUK
- UCL Institute of OphthalmologyUniversity College LondonLondonUK
| | | | | | - Andrew E Firth
- Department of PathologyUniversity of CambridgeCambridgeUK
| | - Andrew A Peden
- Department of Biomedical ScienceUniversity of Sheffield, Firth CourtSheffieldUK
| | - James R Edgar
- Department of PathologyUniversity of CambridgeCambridgeUK
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27
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Loi LK, Yang CC, Lin YC, Su YF, Juan YC, Chen YH, Chang HC. Decoy peptides effectively inhibit the binding of SARS-CoV-2 to ACE2 on oral epithelial cells. Heliyon 2023; 9:e22614. [PMID: 38107325 PMCID: PMC10724569 DOI: 10.1016/j.heliyon.2023.e22614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 12/19/2023] Open
Abstract
The entry of SARS-CoV-2 into host cells involves the interaction between the viral spike protein and the human angiotensin-converting enzyme 2 (ACE2) receptor. Given that the spike protein evolves rapidly to evade host immunity, therapeutics that block ACE2 accessibility, such as spike decoys, could serve as an alternative strategy for attenuating viral infection. Here, we constructed a drug screening platform based on oral epithelial cells to rapidly identify peptides or compounds capable of blocking the spike-ACE2 interaction. We engineered short decoy peptides, 8 to 14 amino acids in length, using the spike protein's receptor-binding motif (RBM) and demonstrated that these peptides can effectively inhibit virus attachment to host cells. Additionally, we discovered that diminazene aceturate (DIZE), an ACE2 activator, similarly inhibited virus binding. Our research thus validates the potential of decoy peptides as a new therapeutic strategy against SARS-CoV-2 infections, opening avenues for further development and study.
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Affiliation(s)
- Lai-Keng Loi
- Department of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Cheng-Chieh Yang
- Department of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Stomatology, Oral & Maxillofacial Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yu-Cheng Lin
- Department of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yee-Fun Su
- iStat Biomedical Co., Ltd, New Taipei City, Taiwan
| | - Yi-Chen Juan
- iStat Biomedical Co., Ltd, New Taipei City, Taiwan
| | - Yi-Hsin Chen
- Institute of Oral Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hsiu-Chuan Chang
- Institute of Oral Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
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28
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Parikh C, Upadhyay H, Patel S, Sundararajan R, Shah D, Anand A, Baraskar B, Bhatt T, Verma D, Agrawal S, Mittal A, Gupta S. Nephrotic syndrome following COVID-19 vaccination: a systematic review. J Nephrol 2023; 36:2431-2440. [PMID: 37505405 DOI: 10.1007/s40620-023-01710-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 infection has caused significant morbidity and mortality. Vaccines produced against this virus have proven highly effective. However, adverse events following vaccination have also been reported. One of them is nephrotic syndrome, that can be associated with different pathologic pictures. This review aims to provide a wider understanding of incidence, etiopathogenesis, and management of nephrotic syndrome following vaccination against SARS-CoV-2. METHODS AND RESULTS A literature search was undertaken using appropriate keywords in various databases like PubMed, Google Scholar, Europe PMC, and Science Direct. Twenty-one articles were included following qualitative assessment. Data of 74 patients from these articles were included. DISCUSSION The pathogenesis of nephrotic syndrome following COVID vaccination has been widely attributed to the activation of angiotensin-converting enzyme-2 receptors, leading to podocyte effacement. Relapses have also been reported in patients with prior history of nephrotic syndrome following COVID-19 vaccination. A renal biopsy is necessary to identify the histopathological picture. Management of COVID-19 vaccine-induced nephrotic syndrome was mainly reported as successfully attainable with corticosteroids and supportive management. CONCLUSION Further investigations will help in establishing an early diagnosis and salvaging kidney function.
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Affiliation(s)
- Charmy Parikh
- Pramukhswami Medical College, Anand, Gujarat, India.
- Carle BroMenn Medical Center, Normal, Illinois, USA.
| | | | - Suyog Patel
- B.J. Medical College, Ahmedabad, Gujarat, India
| | - Ramaswamy Sundararajan
- JSS Medical College (JSS Academy of Higher Education and Research), Mysore, Karnataka, India
| | | | - Ayush Anand
- BP Koirala Institute of Health Sciences, Dharan, Nepal
| | - Bhavana Baraskar
- Index Medical College Hospital and Research Centre, Indore, Madhya Pradesh, India
| | - Tulsi Bhatt
- Pramukhswami Medical College, Anand, Gujarat, India
| | | | | | - Amol Mittal
- Westchester Medical Center, Valhalla, USA
- New York Medical College, Valhalla, USA
| | - Sanjeev Gupta
- Westchester Medical Center, Valhalla, USA
- New York Medical College, Valhalla, USA
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29
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Greenwald MA, Namin S, Zajdowicz J, Jones AL, Fritts L, Kuehnert MJ, Miller CJ, Ray G. Testing of tissue specimens obtained from SARS-CoV-2 nasopharyngeal swab-positive donors. Cell Tissue Bank 2023:10.1007/s10561-023-10119-8. [PMID: 37995051 DOI: 10.1007/s10561-023-10119-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]
Abstract
Risk for transmission of SARS-CoV-2 through allogeneic human tissue transplantation is unknown. To further evaluate the risk of virus transmission, tissues were obtained from deceased donors who had tested positive for SARS-CoV-2 RNA via nasopharyngeal swab. This study evaluated an array of human tissues recovered for transplantation, including bone, tendon, skin, fascia lata, vascular tissues, and heart valves. Tissue samples and plasma or serum samples, if available, were tested for viral RNA (vRNA) using a real time PCR system for the presence of virus RNA. All samples were tested in quadruplicate for both subgenomic (sgRNA) and genomic (gRNA) RNA encoding the SARS-CoV-2 nucleocapsid gene. Amplification of a cellular housekeeping gene served as the positive control for every sample. A total of 47 tissue samples from 17 donors were tested for SARS-CoV-2 RNA. Four donors had plasma or serum available for paired testing. SARS-CoV-2 RNA was not detected from any tissue or plasma/serum sample tested. Based on these findings, risk of transmission through the transplantation of tissue types studied from SARS-CoV-2 infected donors is likely to be low.
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Affiliation(s)
- Melissa A Greenwald
- Donor Alliance, Denver, CO, USA.
- Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
| | | | | | | | | | - Matthew J Kuehnert
- MTF Biologics, Edison, NJ, USA
- Hackensack Meridian School of Medicine, Hackensack, NJ, USA
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Mohammad Faizal NDF, Ramli NA, Mat Rani NNI, Shaibie NA, Aarti, Poonsawas P, Sharma SK, Mohd Amin MCI. Leveraging immunoliposomes as nanocarriers against SARS-CoV-2 and its emerging variants. Asian J Pharm Sci 2023; 18:100855. [PMID: 38125653 PMCID: PMC10730353 DOI: 10.1016/j.ajps.2023.100855] [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: 06/03/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 12/23/2023] Open
Abstract
The global COVID-19 pandemic arising from SARS-CoV-2 has impacted many lives, gaining interest worldwide ever since it was first identified in December 2019. Till 2023, 752 million cumulative cases and 6.8 million deaths were documented globally. COVID-19 has been rapidly evolving, affecting virus transmissibility and properties and contributing to increased disease severity. The Omicron is the most circulating variant of concern. Although success in its treatment has indicated progress in tackling the virus, limitations in delivering the current antiviral agents in battling emerging variants remain remarkable. With the latest advancements in nanotechnology for controlling infectious diseases, liposomes have the potential to counteract SARS-CoV-2 because of their ability to employ different targeting strategies, incorporating monoclonal antibodies for the active and passive targeting of infected patients. This review will present a concise summary of the possible strategies for utilizing immunoliposomes to improve current treatment against the occurrence of SARS-CoV-2 and its variants.
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Affiliation(s)
- Nur Dini Fatini Mohammad Faizal
- Centre for Drug Delivery Technology and Vaccine (CENTRIC), Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
| | - Nurul Afina Ramli
- Centre for Drug Delivery Technology and Vaccine (CENTRIC), Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
| | - Nur Najihah Izzati Mat Rani
- Faculty of Pharmacy, University Royal College of Medicine Perak (UniKL RCMP) No.3, Jalan Greentown, Ipoh 30450, Perak, Malaysia
| | - Nur Adania Shaibie
- Centre for Drug Delivery Technology and Vaccine (CENTRIC), Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
| | - Aarti
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | | | - Sunil K. Sharma
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Mohd Cairul Iqbal Mohd Amin
- Centre for Drug Delivery Technology and Vaccine (CENTRIC), Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
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Derafsh E, Ebrahimzadeh F, Kahrizi MS, Kayedi M, Shojaei N, Rahimi S, Alesaeidi S, Ghafouri K. The therapeutic effects of mesenchymal stem cell (MSCs) exosomes in covid-19 disease; Focusing on dexamethasone therapy. Pathol Res Pract 2023; 251:154815. [PMID: 37797382 DOI: 10.1016/j.prp.2023.154815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/05/2023] [Accepted: 09/08/2023] [Indexed: 10/07/2023]
Abstract
The study of diseases, specifically their aetiologies, their step-by-step progressions (pathogenesis), and their impact on normal structure and function, is the focus of pathology, a branch of science and medicine. In therapeutic fields, it is critical to decrease significantly elevated levels of proinflammatory cytokines. The immunomodulatory drugs such as dexamethasone have been used in several of inflammatory diseases such as Covid-19. The use of dexamethasone alone or in combination with other drugs or method such as mesenchymal stem cell (MSC) is one of the most up-to-date discussions about Covid-19. In this review, we first examined the effects of dexamethasone as monotherapy on inflammatory cytokines and then examined studies that used combination therapy of dexamethasone and other drugs such as Baricitinib, Tofacitinib and tocilizumab. Also, therapeutic aspects of MSCs are examined in this review.
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Affiliation(s)
- Ehsan Derafsh
- Department of Basic Medical Science, Windsor University School of Medicine, Brighton's Estate, Cayton, Saint Kitts and Nevis
| | - Farnoosh Ebrahimzadeh
- Department of Internal Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, lran
| | | | - Mehrdad Kayedi
- Department of radiology. Shiraz university of medical sciences, Shiraz, iran
| | - Niloofar Shojaei
- School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Shiva Rahimi
- School of medicine,fasa university of medical sciences,Fasa, Iran
| | - Samira Alesaeidi
- Department of Internal medicine and rheumatology, ⁎Rheumatology Research Center⁎, Tehran University of Medical Sciences, Tehran, Iran.
| | - Kimia Ghafouri
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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Mclaughlin M, Sanal-Hayes NEM, Hayes LD, Berry EC, Sculthorpe NF. People with Long COVID and Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Exhibit Similarly Impaired Vascular Function. Am J Med 2023:S0002-9343(23)00609-5. [PMID: 37832757 DOI: 10.1016/j.amjmed.2023.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND This study aimed to compare flow-mediated dilation values between individuals with long COVID, individuals with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), and healthy age-matched controls to assess the potential implications for clinical management and long-term health outcomes. METHODS A case-case-control approach was employed, and flow-mediated dilation measurements were obtained from 51 participants (17 long COVID patients, 17 ME/CFS patients, and 17 healthy age-matched controls). Flow-mediated dilation values were analyzed using 1-way analysis of variance for between-group comparisons. RESULTS Results revealed significantly impaired endothelial function in both long COVID and ME/CFS groups compared with healthy age-matched controls as determined by maximum % brachial artery diameter post-occlusion compared with pre-occlusion resting diameter (6.99 ± 4.33% and 6.60 ± 3.48% vs 11.30 ± 4.44%, respectively, both P < .05). Notably, there was no difference in flow-mediated dilation between long COVID and ME/CFS groups (P = .949), despite significantly longer illness duration in the ME/CFS group (ME/CFS: 16 ± 11.15 years vs long COVID: 1.36 ± 0.51 years, P < .0001). CONCLUSION The study demonstrates that both long COVID and ME/CFS patients exhibit similarly impaired endothelial function, indicating potential vascular involvement in the pathogenesis of these post-viral illnesses. The significant reduction in flow-mediated dilation values suggests an increased cardiovascular risk in these populations, warranting careful monitoring and the development of targeted interventions to improve endothelial function and mitigate long-term health implications.
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Affiliation(s)
- Marie Mclaughlin
- Sport and Physical Activity Research Institute, School of Health and Life Sciences, University of the West of Scotland, Glasgow, United Kingdom; School of Sport, Exercise & Rehabilitation Sciences, Faculty of Health Sciences, University of Hull, United Kingdom.
| | - Nilihan E M Sanal-Hayes
- Sport and Physical Activity Research Institute, School of Health and Life Sciences, University of the West of Scotland, Glasgow, United Kingdom; School of Health and Society, University of Salford, United Kingdom
| | - Lawrence D Hayes
- Sport and Physical Activity Research Institute, School of Health and Life Sciences, University of the West of Scotland, Glasgow, United Kingdom
| | - Ethan C Berry
- Sport and Physical Activity Research Institute, School of Health and Life Sciences, University of the West of Scotland, Glasgow, United Kingdom
| | - Nicholas F Sculthorpe
- Sport and Physical Activity Research Institute, School of Health and Life Sciences, University of the West of Scotland, Glasgow, United Kingdom
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Chen F, Matsuda A, Budinger GRS, Sporn PHS, Casalino-Matsuda SM. Hypercapnia increases ACE2 expression and pseudo-SARS-CoV-2 entry in bronchial epithelial cells by augmenting cellular cholesterol. Front Immunol 2023; 14:1251120. [PMID: 37901225 PMCID: PMC10600497 DOI: 10.3389/fimmu.2023.1251120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Patients with chronic lung disease, obesity, and other co-morbid conditions are at increased risk of severe illness and death when infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Hypercapnia, the elevation of CO2 in blood and tissue, commonly occurs in patients with severe acute and chronic lung disease, including those with pulmonary infections, and is also associated with high mortality risk. We previously reported that hypercapnia increases viral replication and mortality of influenza A virus infection in mice. We have also shown that culture in elevated CO2 upregulates expression of cholesterol synthesis genes in primary human bronchial epithelial cells. Interestingly, factors that increase the cholesterol content of lipid rafts and lipid droplets, platforms for viral entry and assembly, enhance SARS-CoV-2 infection. In the current study, we investigated the effects of hypercapnia on ACE2 expression and entry of SARS-CoV-2 pseudovirus (p-SARS-CoV-2) into airway epithelial cells. We found that hypercapnia increased ACE2 expression and p-SARS-CoV-2 uptake by airway epithelium in mice, and in cultured VERO and human bronchial epithelial cells. Hypercapnia also increased total cellular and lipid raft-associated cholesterol in epithelial cells. Moreover, reducing cholesterol synthesis with inhibitors of sterol regulatory element binding protein 2 (SREBP2) or statins, and depletion of cellular cholesterol, each blocked the hypercapnia-induced increases in ACE2 expression and p-SARS-CoV-2 entry into epithelial cells. Cigarette smoke extract (CSE) also increased ACE2 expression, p-SARS-CoV-2 entry and cholesterol accumulation in epithelial cells, an effect not additive to that of hypercapnia, but also inhibited by statins. These findings reveal a mechanism that may account, in part, for poor clinical outcomes of SARS-CoV-2 infection in patients with advanced lung disease and hypercapnia, and in those who smoke cigarettes. Further, our results suggest the possibility that cholesterol-lowering therapies may be of particular benefit in patients with hypercapnia when exposed to or infected with SARS-CoV-2.
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Affiliation(s)
- Fei Chen
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Aiko Matsuda
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - G. R. Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, IL, United States
| | - Peter H. S. Sporn
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
- Research Service, Jesse Brown Veterans Affairs Medical Center, Chicago, IL, United States
| | - S. Marina Casalino-Matsuda
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
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Murali M, Nair B, Vishnu VR, Aneesh TP, Nath LR. 2,4-Dihydroxycinnamic acid as spike ACE2 inhibitor and apigenin as RdRp inhibitor in Nimbamritadi Panchatiktam Kashayam against COVID-19: an in silico and in vitro approach. Mol Divers 2023; 27:2353-2363. [PMID: 36357813 PMCID: PMC9648999 DOI: 10.1007/s11030-022-10552-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/17/2022] [Indexed: 11/12/2022]
Abstract
Nimbamritadi Panchatiktam Kashayam (NPK) is an ayurvedic formulation composed of ingredients with potent anti-viral activities. We studied the interaction energy of 144 phytoconstituents present in NPK against spike receptor-binding domain (RBD) complexed with ACE2 protein (PDB ID: 6LZG) and RNA-dependent RNA polymerase protein (PDB ID: 7BTF) using Biovia Drug Discovery studio. The result indicated that 2,4-hydroxycinnamic acid exerts more significant binding affinities (28.43 kcal/mol) than Umifenovir (21.24 kcal/mol) against spike ACE2. Apigenin exhibited the highest binding affinities (54.63 kcal/mol) compared with Remdesivir (24.52 kcal/mol) against RdRp. An in vitro analysis showed a reduction in the number of lentiviral particles on transfected HEK293T-hACE2 cells as assessed by pseudovirus inhibition assay. At the same time, the tested compounds showed non-toxic up to 100 µg/ml in normal cells by MTT assay. The study highlights the plausible clinical utility of this traditional medicine against SARS CoV2.
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Affiliation(s)
- Maneesha Murali
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India
- Department of Pharmacology, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India
| | - Bhagyalakshmi Nair
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India
- Department of Pharmacology, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India
| | - V R Vishnu
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India
| | - T P Aneesh
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India.
| | - Lekshmi R Nath
- Department of Pharmacognosy, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, 682 041, India.
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Hou D, Cao W, Kim S, Cui X, Ziarnik M, Im W, Zhang XF. Biophysical investigation of interactions between SARS-CoV-2 spike protein and neuropilin-1. Protein Sci 2023; 32:e4773. [PMID: 37656811 PMCID: PMC10510470 DOI: 10.1002/pro.4773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/19/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
Recent studies have suggested that neuropilin-1 (NRP1) may serve as a potential receptor in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, the biophysical characteristics of interactions between NRP1 and SARS-CoV-2 remain unclear. In this study, we examined the interactions between NRP1 and various SARS-CoV-2 spike (S) fragments, including the receptor-binding domain (RBD) and the S protein trimer in a soluble form or expressed on pseudovirions, using atomic force microscopy and structural modeling. Our measurements shows that NRP1 interacts with the RBD and trimer at a higher binding frequency (BF) compared to ACE2. This NRP1-RBD interaction has also been predicted and simulated via AlphaFold2 and molecular dynamics simulations, and the results indicate that their binding patterns are very similar to RBD-ACE2 interactions. Additionally, under similar loading rates, the most probable unbinding forces between NRP1 and S trimer (both soluble form and on pseudovirions) are larger than the forces between NRP1 and RBD and between trimer and ACE2. Further analysis indicates that NRP1 has a stronger binding affinity to the SARS-CoV-2 S trimer with a dissociation rate of 0.87 s-1 , four times lower than the dissociation rate of 3.65 s-1 between NRP1 and RBD. Moreover, additional experiments show that RBD-neutralizing antibodies can significantly reduce the BF for both ACE2 and NRP1. Together, the study suggests that NRP1 can be an alternative receptor for SARS-CoV-2 attachment to human cells, and the neutralizing antibodies targeting SARS-CoV-2 RBD can reduce the binding between SARS-CoV-2 and NRP1.
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Affiliation(s)
- Decheng Hou
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
- Department of Biomedical EngineeringUniversity of Massachusetts AmherstAmherstMassachusettsUSA
| | - Wenpeng Cao
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Seonghan Kim
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Xinyu Cui
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
- Department of Biomedical EngineeringUniversity of Massachusetts AmherstAmherstMassachusettsUSA
| | - Matthew Ziarnik
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
| | - Wonpil Im
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
- Departments of Biological Sciences, Chemistry, and Computer Science and EngineeringLehigh UniversityBethlehemUSA
| | - X. Frank Zhang
- Department of BioengineeringLehigh UniversityBethlehemPennsylvaniaUSA
- Department of Biomedical EngineeringUniversity of Massachusetts AmherstAmherstMassachusettsUSA
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36
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Barlang LA, Mohl BP, Blaurock C, Harder S, Breithaupt A, Merkel OM, Balkema-Buschmann A, Popp A. SARS-CoV-2 induced changes in the glycosylation pattern in the respiratory tract of Golden Syrian hamsters. Acta Histochem 2023; 125:152077. [PMID: 37523787 DOI: 10.1016/j.acthis.2023.152077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 08/02/2023]
Abstract
Even after more than two years of intensive research, not all of the pathophysiological processes of Coronavirus Disease 2019 (COVID-19), induced by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection, have been fully elucidated. The initial virus-host interaction at the respiratory epithelium plays a crucial role in the course and progression of the infection, and is highly dependent on the glycosylation pattern of the host cell and of the secreted mucins. Glycans are polysaccharides that can be attached to proteins and thereby add to their stability and functionality. Lectins are glycan-binding proteins that recognize specific glycan motifs, and lectin histochemistry is a suitable tool to visualize and examine glycosylation pattern changes in tissues. In this study we used lectins with different glycan-specificities for the visualization of glycosylation pattern changes in the respiratory tract of SARS-CoV-2 infected Golden Syrian hamsters. While some lectins (LEL, STL) enable the visualization of the damage to alveolar type 1 pneumocytes, other lectins, e.g., GSLI, visualized the loss and subsequent hyperplasia of type 2 pneumocytes. UEAI staining was co-localized with KI67, a proliferation marker. Double staining of lectins LEL, STL and WGA with specific immune cell markers (Iba1, CD68) showed co-localization and the dominant infiltration of monocyte-derived macrophages into infected alveolar tissue. The elucidation of the glycosylation pattern of the respiratory tract cells in uninfected and infected Golden Syrian hamsters revealed physiological and pathological aspects of the disease that may open new possibilities for therapeutic development.
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Affiliation(s)
- Lea-Adriana Barlang
- Preclinical Safety, AbbVie Deutschland GmbH & Co. KG, Knollstraße, 67061 Ludwigshafen, Germany; Department of Pharmacy, Pharmaceutical Technology and Biopharmacy, Ludwig-Maximilians-University, Butenandtstraße 5-13, 8133 Munich, Germany.
| | - Björn-Patrick Mohl
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Suedufer 10, 17493 Greifswald, Insel Riems, Germany
| | - Claudia Blaurock
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Suedufer 10, 17493 Greifswald, Insel Riems, Germany
| | - Sophia Harder
- Preclinical Safety, AbbVie Deutschland GmbH & Co. KG, Knollstraße, 67061 Ludwigshafen, Germany
| | - Angele Breithaupt
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Suedufer 10, 17493 Greifswald, Insel Riems, Germany
| | - Olivia M Merkel
- Department of Pharmacy, Pharmaceutical Technology and Biopharmacy, Ludwig-Maximilians-University, Butenandtstraße 5-13, 8133 Munich, Germany
| | - Anne Balkema-Buschmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Suedufer 10, 17493 Greifswald, Insel Riems, Germany
| | - Andreas Popp
- Preclinical Safety, AbbVie Deutschland GmbH & Co. KG, Knollstraße, 67061 Ludwigshafen, Germany
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Li Y, Touret F, de Lamballerie X, Nguyen M, Laurent M, Benoit-Vical F, Robert A, Liu Y, Meunier B. Hybrid molecules based on an emodin scaffold. Synthesis and activity against SARS-CoV-2 and Plasmodium. Org Biomol Chem 2023; 21:7382-7394. [PMID: 37655748 DOI: 10.1039/d3ob01122d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Since the Covid-19 epidemic, it has been clear that the availability of small and affordable drugs that are able to efficiently control viral infections in humans is still a challenge in medicinal chemistry. The synthesis and biological activities of a series of hybrid molecules that combine an emodin moiety and other structural moieties expected to act as possible synergistic pharmacophores in a single molecule were studied. Emodin has been reported to block the entry of the SARS-CoV-2 virus into human cells and might also inhibit cytokine production, resulting in the reduction of pulmonary injury induced by SARS-CoV-2. The pharmacophore associated with emodin was either a polyamine residue (emodin-PA series), a choice driven by the fact that a natural alkyl PA like spermine and spermidine play regulatory roles in immune cell functions, or a diphenylmethylpiperazine derivative of the norchlorcyclizine series (emoxyzine series). In fact, diphenylmethylpiperazine antagonists of the H1 histamine receptor display activity against several viruses by multiple interrelated mechanisms. In the emoxyzine series, the most potent drug against SARS-CoV-2 was (R)-emoxyzine-2, with an EC50 value = 1.9 μM, which is in the same range as that of the reference drug remdesivir. However, the selectivity index was rather low, indicating that the dissociation of antiviral potency and cytotoxicity remains a challenge. In addition, since emodin was also reported to be a relatively high-affinity inhibitor of the virulence regulator FIKK kinase from the malaria parasite Plasmodium vivax, the antimalarial activity of the synthesized hybrid compounds has been evaluated. However, these molecules cannot efficiently compete with the currently used antimalarial drugs.
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Affiliation(s)
- Youzhi Li
- Education Mega Center, Guangdong University of Technology, School of Chemical Engineering and Light Industry, No. 100 Waihuan Xi Road, Guangzhou, P. R. China.
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France.
- New Antimalarial Molecules and Pharmacological Approaches, MAAP, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France
| | - Franck Touret
- Unité des Virus Émergents (UVE), Aix Marseille Univ, IRD 190, Inserm 1207, 27 Boulevard Jean Moulin, 13005 Marseille Cedex 05, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE), Aix Marseille Univ, IRD 190, Inserm 1207, 27 Boulevard Jean Moulin, 13005 Marseille Cedex 05, France
| | - Michel Nguyen
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France.
- New Antimalarial Molecules and Pharmacological Approaches, MAAP, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France
| | - Marion Laurent
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France.
- New Antimalarial Molecules and Pharmacological Approaches, MAAP, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France
| | - Françoise Benoit-Vical
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France.
- New Antimalarial Molecules and Pharmacological Approaches, MAAP, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France
| | - Anne Robert
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France.
- New Antimalarial Molecules and Pharmacological Approaches, MAAP, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France
| | - Yan Liu
- Education Mega Center, Guangdong University of Technology, School of Chemical Engineering and Light Industry, No. 100 Waihuan Xi Road, Guangzhou, P. R. China.
| | - Bernard Meunier
- Education Mega Center, Guangdong University of Technology, School of Chemical Engineering and Light Industry, No. 100 Waihuan Xi Road, Guangzhou, P. R. China.
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France.
- New Antimalarial Molecules and Pharmacological Approaches, MAAP, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France
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Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023; 52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Mateusz Sikora
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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Pagis A, Alfi O, Kinreich S, Yilmaz A, Hamdan M, Gadban A, Panet A, Wolf DG, Benvenisty N. Genome-wide loss-of-function screen using human pluripotent stem cells to study virus-host interactions for SARS-CoV-2. Stem Cell Reports 2023; 18:1766-1774. [PMID: 37703821 PMCID: PMC10545482 DOI: 10.1016/j.stemcr.2023.07.003] [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: 12/13/2022] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 09/15/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019, has become a global health concern. Therefore, there is an immense need to understand the network of virus-host interactions by using human disease-relevant cells. We have thus conducted a loss-of-function genome-wide screen using haploid human embryonic stem cells (hESCs) to identify genes involved in SARS-CoV-2 infection. Although the undifferentiated hESCs are resistant to SARS-CoV-2, their differentiated definitive endoderm (DE) progenies, which express high levels of ACE2, are highly sensitive to the virus. Our genetic screening was able to identify the well-established entry receptor ACE2 as a host factor, along with additional potential novel modulators of SARS-CoV-2. Two such novel screen hits, the transcription factor MAFG and the transmembrane protein TMEM86A, were further validated as conferring resistance against SARS-CoV-2 by using CRISPR-mediated mutagenesis in hESCs, followed by differentiation of mutant lines into DE cells and infection by SARS-CoV-2. Our genome-wide genetic screening investigated SARS-CoV-2 host factors in non-cancerous human cells with endogenous ACE2 expression, providing a unique platform to identify novel modulators of SARS-CoV-2 cytopathology in human cells.
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Affiliation(s)
- Ariel Pagis
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Or Alfi
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel; Lautenberg Center for General and Tumor Immunology, The Hebrew University, Jerusalem 91121, Israel
| | - Shay Kinreich
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Atilgan Yilmaz
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; Leuven Stem Cell Institute, Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
| | - Marah Hamdan
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Aseel Gadban
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Amos Panet
- Department of Biochemistry, Faculty of Medicine, The Hebrew University, Jerusalem 91121, Israel
| | - Dana G Wolf
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel; Lautenberg Center for General and Tumor Immunology, The Hebrew University, Jerusalem 91121, Israel.
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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40
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Gasparello J, Marzaro G, Papi C, Gentili V, Rizzo R, Zurlo M, Scapoli C, Finotti A, Gambari R. Effects of Sulforaphane on SARS‑CoV‑2 infection and NF‑κB dependent expression of genes involved in the COVID‑19 'cytokine storm'. Int J Mol Med 2023; 52:76. [PMID: 37477130 PMCID: PMC10555481 DOI: 10.3892/ijmm.2023.5279] [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: 12/30/2022] [Accepted: 06/09/2023] [Indexed: 07/22/2023] Open
Abstract
Since its spread at the beginning of 2020, the coronavirus disease 2019 (COVID‑19) pandemic represents one of the major health problems. Despite the approval, testing, and worldwide distribution of anti‑severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) vaccines, the development of specific antiviral agents targeting the SARS‑CoV‑2 life cycle with high efficiency, and/or interfering with the associated 'cytokine storm', is highly required. A recent study, conducted by the authors' group indicated that sulforaphane (SFN) inhibits the expression of IL‑6 and IL‑8 genes induced by the treatment of IB3‑1 bronchial cells with a recombinant spike protein of SARS‑CoV‑2. In the present study, the ability of SFN to inhibit SARS‑CoV‑2 replication and the expression of pro‑inflammatory genes encoding proteins of the COVID‑19 'cytokine storm' was evaluated. SARS‑CoV‑2 replication was assessed in bronchial epithelial Calu‑3 cells. Moreover, SARS‑CoV‑2 replication and expression of pro‑inflammatory genes was evaluated by reverse transcription quantitative droplet digital PCR. The effects on the expression levels of NF‑κB were assessed by western blotting. Molecular dynamics simulations of NF‑kB/SFN interactions were conducted with Gromacs 2021.1 software under the Martini 2 CG force field. Computational studies indicated that i) SFN was stably bound with the NF‑κB monomer; ii) a ternary NF‑kB/SFN/DNA complex was formed; iii) the SFN interacted with both the protein and the nucleic acid molecules modifying the binding mode of the latter, and impairing the full interaction between the NF‑κB protein and the DNA molecule. This finally stabilized the inactive complex. Molecular studies demonstrated that SFN i) inhibits the SARS‑CoV‑2 replication in infected Calu‑3 cells, decreasing the production of the N‑protein coding RNA sequences, ii) decreased NF‑κB content in SARS‑CoV‑2 infected cells and inhibited the expression of NF‑kB‑dependent IL‑1β and IL‑8 gene expression. The data obtained in the present study demonstrated inhibitory effects of SFN on the SARS‑CoV‑2 life cycle and on the expression levels of the pro‑inflammatory genes, sustaining the possible use of SFN in the management of patients with COVID‑19.
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Affiliation(s)
- Jessica Gasparello
- Department of Life Sciences and Biotechnology, University of Ferrara, I-44121 Ferrara
| | - Giovanni Marzaro
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, I-35131 Padova
| | - Chiara Papi
- Department of Life Sciences and Biotechnology, University of Ferrara, I-44121 Ferrara
| | - Valentina Gentili
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, I-44121 Ferrara, Italy
| | - Roberta Rizzo
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, I-44121 Ferrara, Italy
| | - Matteo Zurlo
- Department of Life Sciences and Biotechnology, University of Ferrara, I-44121 Ferrara
| | - Chiara Scapoli
- Department of Life Sciences and Biotechnology, University of Ferrara, I-44121 Ferrara
| | - Alessia Finotti
- Department of Life Sciences and Biotechnology, University of Ferrara, I-44121 Ferrara
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, University of Ferrara, I-44121 Ferrara
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Lee YB, Jung M, Kim J, Charles A, Christ W, Kang J, Kang MG, Kwak C, Klingström J, Smed-Sörensen A, Kim JS, Mun JY, Rhee HW. Super-resolution proximity labeling reveals anti-viral protein network and its structural changes against SARS-CoV-2 viral proteins. Cell Rep 2023; 42:112835. [PMID: 37478010 DOI: 10.1016/j.celrep.2023.112835] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 05/31/2023] [Accepted: 07/05/2023] [Indexed: 07/23/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates in human cells by interacting with host factors following infection. To understand the virus and host interactome proximity, we introduce a super-resolution proximity labeling (SR-PL) method with a "plug-and-playable" PL enzyme, TurboID-GBP (GFP-binding nanobody protein), and we apply it for interactome mapping of SARS-CoV-2 ORF3a and membrane protein (M), which generates highly perturbed endoplasmic reticulum (ER) structures. Through SR-PL analysis of the biotinylated interactome, 224 and 272 peptides are robustly identified as ORF3a and M interactomes, respectively. Within the ORF3a interactome, RNF5 co-localizes with ORF3a and generates ubiquitin modifications of ORF3a that can be involved in protein degradation. We also observe that the SARS-CoV-2 infection rate is efficiently reduced by the overexpression of RNF5 in host cells. The interactome data obtained using the SR-PL method are presented at https://sarscov2.spatiomics.org. We hope that our method will contribute to revealing virus-host interactions of other viruses in an efficient manner.
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Affiliation(s)
- Yun-Bin Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Minkyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Jeesoo Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea
| | - Afandi Charles
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, 17164 Stockholm, Sweden
| | - Wanda Christ
- Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 14183 Stockholm, Sweden
| | - Jiwoong Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Chulhwan Kwak
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Jonas Klingström
- Centre for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 14183 Stockholm, Sweden; Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
| | - Anna Smed-Sörensen
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, 17164 Stockholm, Sweden
| | - Jong-Seo Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea.
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea.
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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42
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Rasizadeh R, Aghbash PS, Nahand JS, Entezari-Maleki T, Baghi HB. SARS-CoV-2-associated organs failure and inflammation: a focus on the role of cellular and viral microRNAs. Virol J 2023; 20:179. [PMID: 37559103 PMCID: PMC10413769 DOI: 10.1186/s12985-023-02152-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 08/04/2023] [Indexed: 08/11/2023] Open
Abstract
SARS-CoV-2 has been responsible for the recent pandemic all over the world, which has caused many complications. One of the hallmarks of SARS-CoV-2 infection is an induced immune dysregulation, in some cases resulting in cytokine storm syndrome, acute respiratory distress syndrome and many organs such as lungs, brain, and heart that are affected during the SARS-CoV-2 infection. Several physiological parameters are altered as a result of infection and cytokine storm. Among them, microRNAs (miRNAs) might reflect this poor condition since they play a significant role in immune cellular performance including inflammatory responses. Both host and viral-encoded miRNAs are crucial for the successful infection of SARS-CoV-2. For instance, dysregulation of miRNAs that modulate multiple genes expressed in COVID-19 patients with comorbidities (e.g., type 2 diabetes, and cerebrovascular disorders) could affect the severity of the disease. Therefore, altered expression levels of circulating miRNAs might be helpful to diagnose this illness and forecast whether a COVID-19 patient could develop a severe state of the disease. Moreover, a number of miRNAs could inhibit the expression of proteins, such as ACE2, TMPRSS2, spike, and Nsp12, involved in the life cycle of SARS-CoV-2. Accordingly, miRNAs represent potential biomarkers and therapeutic targets for this devastating viral disease. In the current study, we investigated modifications in miRNA expression and their influence on COVID-19 disease recovery, which may be employed as a therapy strategy to minimize COVID-19-related disorders.
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Affiliation(s)
- Reyhaneh Rasizadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parisa Shiri Aghbash
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javid Sadri Nahand
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, 5166/15731, Iran
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Taher Entezari-Maleki
- Cardiovascular Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Clinical Pharmacy, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Bannazadeh Baghi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, 5166/15731, Iran.
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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43
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Sharma T, Gerstman B, Chapagain P. Distinctive Features of the XBB.1.5 and XBB.1.16 Spike Protein Receptor-Binding Domains and Their Roles in Conformational Changes and Angiotensin-Converting Enzyme 2 Binding. Int J Mol Sci 2023; 24:12586. [PMID: 37628766 PMCID: PMC10454900 DOI: 10.3390/ijms241612586] [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: 07/10/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The emergence and the high transmissibility of the XBB.1.5 and XBB.1.16 subvariants of the SARS-CoV-2 omicron has reignited concerns over the potential impact on vaccine efficacy for these and future variants. We investigated the roles of the XBB.1.5 and XBB.1.16 mutations on the structure of the spike protein's receptor-binding domain (RBD) and its interactions with the host cell receptor ACE2. To bind to ACE2, the RBD must transition from the closed-form to the open-form configuration. We found that the XBB variants have less stable closed-form structures that may make the transition to the open-form easier. We found that the mutations enhance the RBD-ACE2 interactions in XBB.1.16 compared to XBB.1.5. We observed significant structural changes in the loop and motif regions of the RBD, altering well-known antibody-binding sites and potentially rendering primary RBD-specific antibodies ineffective. Our findings elucidate how subtle structural changes and interactions contribute to the subvariants' fitness over their predecessors.
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Affiliation(s)
- Tej Sharma
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Bernard Gerstman
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
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44
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Cardoso-Lima R, Santos-Oliveira R, Souza PFN, Barbosa LRS, Wuite GJL, Alencar LMR. Physical virology: how physics is enabling a better understanding of recent viral invaders. Biophys Rev 2023; 15:611-623. [PMID: 37681101 PMCID: PMC10480132 DOI: 10.1007/s12551-023-01075-4] [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: 04/11/2023] [Accepted: 06/04/2023] [Indexed: 09/09/2023] Open
Abstract
The world is frequently afflicted by several viral outbreaks that bring diseases and health crises. It is vital to comprehend how viral assemblies' fundamental components work to counteract them. Determining the ultrastructure and nanomechanical characteristics of viruses from a physical standpoint helps categorize their mechanical characteristics, offers insight into new treatment options, and/or shows weak spots that can clarify methods for medication targeting. This study compiles the findings from studies on the ultrastructure and nanomechanical behavior of SARS-CoV-2, ZIKV (Zika virus), and CHIKV (Chikungunya virus) viral particles. With results that uncovered aspects of the organization and the spatial distribution of the proteins on the surface of the viral particle as well as the deformation response of the particles when applied a recurring loading force, this review aims to provide further discussion on the mechanical properties of viral particles at the nanoscale, offering new prospects that could be employed for designing strategies for the prevention and treatment of viral diseases. Supplementary Information The online version contains supplementary material available at 10.1007/s12551-023-01075-4.
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Affiliation(s)
- Ruana Cardoso-Lima
- Physics Department, Laboratory of Biophysics and Nanosystems, Federal University of Maranhão, São Luís, MA Brazil
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Ralph Santos-Oliveira
- Brazilian Nuclear Energy Commission, Nuclear Engineering Institute, Rio de Janeiro, 21941906 Brazil
- Laboratory of Nanoradiopharmacy, Rio de Janeiro State University, Rio de Janeiro, 23070200 Brazil
| | - Pedro Filho Noronha Souza
- Department of Biochemistry, Federal University of Ceará, Fortaleza, CE Brazil
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, CE Brazil
| | - Leandro R. S. Barbosa
- Department of General Physics, Institute of Physics, University of São Paulo, São Paulo, SP 05508-000 Brazil
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP 13083-100 Brazil
| | - Gijs J. L. Wuite
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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45
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Kumru OS, Bajoria S, Kaur K, Hickey JM, Van Slyke G, Doering J, Berman K, Richardson C, Lien H, Kleanthous H, Mantis NJ, Joshi SB, Volkin DB. Effects of aluminum-salt, CpG and emulsion adjuvants on the stability and immunogenicity of a virus-like particle displaying the SARS-CoV-2 receptor-binding domain (RBD). Hum Vaccin Immunother 2023; 19:2264594. [PMID: 37932241 PMCID: PMC10760504 DOI: 10.1080/21645515.2023.2264594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/25/2023] [Indexed: 11/08/2023] Open
Abstract
Second-generation COVID-19 vaccines with improved immunogenicity (e.g., breadth, duration) and availability (e.g., lower costs, refrigerator stable) are needed to enhance global coverage. In this work, we formulated a clinical-stage SARS-CoV-2 receptor-binding domain (RBD) virus-like particle (VLP) vaccine candidate (IVX-411) with widely available adjuvants. Specifically, we assessed the in vitro storage stability and in vivo mouse immunogenicity of IVX-411 formulated with aluminum-salt adjuvants (Alhydrogel™, AH and Adjuphos™, AP), without or with the TLR-9 agonist CpG-1018™ (CpG), and compared these profiles to IVX-411 adjuvanted with an oil-in-water nano-emulsion (AddaVax™, AV). Although IVX-411 bound both AH and AP, lower binding strength of antigen to AP was observed by Langmuir binding isotherms. Interestingly, AH- and AP-adsorbed IVX-411 had similar storage stability profiles as measured by antigen-binding assays (competitive ELISAs), but the latter displayed higher pseudovirus neutralizing titers (pNT) in mice, at levels comparable to titers elicited by AV-adjuvanted IVX-411. CpG addition to alum (AP or AH) resulted in a marginal trend of improved pNTs in stressed samples only, yet did not impact the storage stability profiles of IVX-411. In contrast, previous work with AH-formulations of a monomeric RBD antigen showed greatly improved immunogenicity and decreased stability upon CpG addition to alum. At elevated temperatures (25, 37°C), IVX-411 formulated with AH or AP displayed decreased in vitro stability compared to AV-formulated IVX-411and this rank-ordering correlated with in vivo performance (mouse pNT values). This case study highlights the importance of characterizing antigen-adjuvant interactions to develop low cost, aluminum-salt adjuvanted recombinant subunit vaccine candidates.
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Affiliation(s)
- Ozan S. Kumru
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Sakshi Bajoria
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Kawaljit Kaur
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - John M. Hickey
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - Greta Van Slyke
- Division of Infectious Disease, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Jennifer Doering
- Division of Infectious Disease, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Katherine Berman
- Division of Infectious Disease, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | | | | | - Harry Kleanthous
- Discovery & Translational Sciences, Global Health, Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Nicholas J. Mantis
- Division of Infectious Disease, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Sangeeta B. Joshi
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
| | - David B. Volkin
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS, USA
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46
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Zheng B, Xiao Y, Tong B, Mao Y, Ge R, Tian F, Dong X, Zheng P. S373P Mutation Stabilizes the Receptor-Binding Domain of the Spike Protein in Omicron and Promotes Binding. JACS AU 2023; 3:1902-1910. [PMID: 37502147 PMCID: PMC10369413 DOI: 10.1021/jacsau.3c00142] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 07/29/2023]
Abstract
A cluster of several newly occurring mutations on Omicron is found at the β-core region of the spike protein's receptor-binding domain (RBD), where mutation rarely happened before. Notably, the binding of SARS-CoV-2 to human receptor ACE2 via RBD happens in a dynamic airway environment, where mechanical force caused by coughing or sneezing occurs. Thus, we used atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to measure the stability of RBDs and found that the mechanical stability of Omicron RBD increased by ∼20% compared with the wild type. Molecular dynamics (MD) simulations revealed that Omicron RBD showed more hydrogen bonds in the β-core region due to the closing of the α-helical motif caused primarily by the S373P mutation. In addition to a higher unfolding force, we showed a higher dissociation force between Omicron RBD and ACE2. This work reveals the mechanically stabilizing effect of the conserved mutation S373P for Omicron and the possible evolution trend of the β-core region of RBD.
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Affiliation(s)
- Bin Zheng
- State
Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine
Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yuelong Xiao
- State
Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine
Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Bei Tong
- Institute
of Botany, Jiangsu Province and Chinese
Academy of Sciences, Nanjing, Jiangsu 210014, China
| | - Yutong Mao
- State
Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine
Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Rui Ge
- State
Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine
Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Fang Tian
- State
Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine
Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xianchi Dong
- State
Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
- Engineering
Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, Jiangsu 210023, China
| | - Peng Zheng
- State
Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine
Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
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47
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Chen YJ, Huang JC, Yang CP, Hsu KF, Liu HF. A Comprehensive Phylogenetic Analysis of SARS-CoV-2: Utilizing a Novel and Convenient In-House RT-PCR Method for Characterization without Virus Culture and BSL-3 Facilities. Viruses 2023; 15:1562. [PMID: 37515248 PMCID: PMC10383548 DOI: 10.3390/v15071562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
We developed a convenient method for amplifying the complete SARS-CoV-2 sequence using in-house RT-PCR without virus culture. Forty-one stored throat swabs and blood specimens were collected from eight SARS-CoV-2 infections at multiple time points. Total RNA was extracted using the QIAamp viral RNA mini kit and pooled for higher RNA levels. Only those positive specimens by commercial real-time RT-PCR (RT-qPCR) were selected and amplified by in-house RT-PCR for complete sequences, followed by sequencing. Phylogenetic trees and exploratory analyses were performed using MEGA 11 and Simplot 3.5.1 software. Swab samples had significantly higher total RNA concentrations than plasma (p < 0.01). Positive results were found mainly in swabs, but one was found in plasma. Successful gene amplification depended on Ct values (Ct < 38). A non-synonymous substitution was found in ORF1ab/Nsp3 (at NC045512.2 position 6312, C to A) and most spike protein mutations occurred in the S1 subunit (residues 14-685). The proposed method is time-saving and reliable for rapid genomic analysis. Increasing sample volume and pooling them for RNA extraction increases RNA concentration without culture. Combining nucleotide sequences from specific variable regions of the genome is more efficient than conventional methods.
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Affiliation(s)
- Yen-Ju Chen
- Research Assistant Center, Tainan Municipal Hospital (Managed by Show Chwan Medical Care Corporation), Tainan 701033, Taiwan
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Jason C Huang
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Ching-Ping Yang
- Department of Medical Technology, Jenteh Junior College of Medicine, Nursing and Management, Miaoli 356006, Taiwan
| | - Kuo-Feng Hsu
- Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 114202, Taiwan
| | - Hsin-Fu Liu
- Department of Medical Research, MacKay Memorial Hospital, Taipei 25169, Taiwan
- Institute of Biomedical Sciences, MacKay Medical College, New Taipei City 252005, Taiwan
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48
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Deptuła P, Fiedoruk K, Wasilewska M, Suprewicz Ł, Cieśluk M, Żeliszewska P, Oćwieja M, Adamczyk Z, Pogoda K, Bucki R. Physicochemical Nature of SARS-CoV-2 Spike Protein Binding to Human Vimentin. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37413693 PMCID: PMC10360031 DOI: 10.1021/acsami.3c03347] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Vimentin, a protein that builds part of the cytoskeleton and is involved in many aspects of cellular function, was recently identified as a cell surface attachment site for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The present study investigated the physicochemical nature of the binding between the SARS-CoV-2 S1 glycoprotein receptor binding domain (S1 RBD) and human vimentin using atomic force microscopy and a quartz crystal microbalance. The molecular interactions of S1 RBD and vimentin proteins were quantified using vimentin monolayers attached to the cleaved mica or a gold microbalance sensor as well as in its native extracellular form present on the live cell surface. The presence of specific interactions between vimentin and S1 RBD was also confirmed using in silico studies. This work provides new evidence that cell-surface vimentin (CSV) functions as a site for SARS-CoV-2 virus attachment and is involved in the pathogenesis of Covid-19, providing a potential target for therapeutic countermeasures.
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Affiliation(s)
- Piotr Deptuła
- Independent Laboratory of Nanomedicine, Medical University of Bialystok, PL-15222 Białystok, Poland
| | - Krzysztof Fiedoruk
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Białystok, Poland
| | - Monika Wasilewska
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Łukasz Suprewicz
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Białystok, Poland
| | - Mateusz Cieśluk
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Białystok, Poland
| | - Paulina Żeliszewska
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Magdalena Oćwieja
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Zbigniew Adamczyk
- J. Haber Institute of Catalysis and Surface Chemistry Polish Academy of Science, Niezapominajek 8, PL-30239 Krakow, Poland
| | - Katarzyna Pogoda
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31342 Krakow, Poland
| | - Robert Bucki
- Department of Medical Microbiology and Nanobiomedical Engineering, Medical University of Bialystok, PL-15222 Białystok, Poland
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49
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Xie E, Ahmad S, Smyth RP, Sieben C. Advanced fluorescence microscopy in respiratory virus cell biology. Adv Virus Res 2023; 116:123-172. [PMID: 37524480 DOI: 10.1016/bs.aivir.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Respiratory viruses are a major public health burden across all age groups around the globe, and are associated with high morbidity and mortality rates. They can be transmitted by multiple routes, including physical contact or droplets and aerosols, resulting in efficient spreading within the human population. Investigations of the cell biology of virus replication are thus of utmost importance to gain a better understanding of virus-induced pathogenicity and the development of antiviral countermeasures. Light and fluorescence microscopy techniques have revolutionized investigations of the cell biology of virus infection by allowing the study of the localization and dynamics of viral or cellular components directly in infected cells. Advanced microscopy including high- and super-resolution microscopy techniques available today can visualize biological processes at the single-virus and even single-molecule level, thus opening a unique view on virus infection. We will highlight how fluorescence microscopy has supported investigations on virus cell biology by focusing on three major respiratory viruses: respiratory syncytial virus (RSV), Influenza A virus (IAV) and SARS-CoV-2. We will review our current knowledge of virus replication and highlight how fluorescence microscopy has helped to improve our state of understanding. We will start by introducing major imaging and labeling modalities and conclude the chapter with a perspective discussion on remaining challenges and potential opportunities.
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Affiliation(s)
- Enyu Xie
- Nanoscale Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Shazeb Ahmad
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany; Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Christian Sieben
- Nanoscale Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany; Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany.
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50
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Razi O, Teixeira AM, Tartibian B, Zamani N, Knechtle B. Respiratory issues in patients with multiple sclerosis as a risk factor during SARS-CoV-2 infection: a potential role for exercise. Mol Cell Biochem 2023; 478:1533-1559. [PMID: 36411399 PMCID: PMC9684932 DOI: 10.1007/s11010-022-04610-1] [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: 01/27/2022] [Accepted: 11/04/2022] [Indexed: 11/23/2022]
Abstract
Coronavirus disease-2019 (COVID-19) is associated with cytokine storm and is characterized by acute respiratory distress syndrome (ARDS) and pneumonia problems. The respiratory system is a place of inappropriate activation of the immune system in people with multiple sclerosis (MS), and this may cause damage to the lung and worsen both MS and infections.The concerns for patients with multiple sclerosis are because of an enhance risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The MS patients pose challenges in this pandemic situation, because of the regulatory defect of autoreactivity of the immune system and neurological and respiratory tract symptoms. In this review, we first indicate respiratory issues associated with both diseases. Then, the main mechanisms inducing lung damages and also impairing the respiratory muscles in individuals with both diseases is discussed. At the end, the leading role of physical exercise on mitigating respiratory issues inducing mechanisms is meticulously evaluated.
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Affiliation(s)
- Omid Razi
- Department of Exercise Physiology, Faculty of Physical Education and Sport Sciences, Razi University, Kermanshah, Iran
| | - Ana Maria Teixeira
- Research Center for Sport and Physical Activity, Faculty of Sport Sciences and Physical Education, University of Coimbra, Coimbra, Portugal
| | - Bakhtyar Tartibian
- Department of Exercise Physiology, Faculty of Physical Education and Sports Sciences, Allameh Tabataba’i University, Tehran, Iran
| | - Nastaran Zamani
- Department of Biology, Faculty of Science, Payame-Noor University, Tehran, Iran
| | - Beat Knechtle
- Institute of Primary Care, University of Zurich, Zurich, Switzerland
- Medbase St. Gallen Am Vadianplatz, Vadianstrasse 26, 9001 St. Gallen, Switzerland
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