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Tomris I, Unione L, Nguyen L, Zaree P, Bouwman KM, Liu L, Li Z, Fok JA, Ríos Carrasco M, van der Woude R, Kimpel ALM, Linthorst MW, Verpalen ECJM, Caniels TG, Sanders RW, Heesters BA, Pieters RJ, Jiménez-Barbero J, Klassen JS, Boons GJ, de Vries RP. The SARS-CoV-2 spike N-terminal domain engages 9- O -acetylated α2-8-linked sialic acids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.09.14.507904. [PMID: 36263070 PMCID: PMC9580382 DOI: 10.1101/2022.09.14.507904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
SARS-CoV-2 viruses engage ACE2 as a functional receptor with their spike protein. The S1 domain of the spike protein contains a C-terminal receptor-binding domain (RBD) and an N-terminal domain (NTD). The NTD of other coronaviruses includes a glycan-binding cleft. However, for the SARS-CoV-2 NTD protein-glycan binding was only observed weakly for sialic acids with highly sensitive methods. Amino acid changes in the NTD of Variants of Concern (VoC) shows antigenic pressure, which can be an indication of NTD-mediated receptor binding. Trimeric NTD proteins of SARS-CoV-2, Alpha, Beta, Delta, and Omicron did not reveal a receptor binding capability. Unexpectedly, the SARS-CoV-2 Beta subvariant strain (501Y.V2-1) NTD binding to Vero E6 cells was sensitive to sialidase pretreatment. Glycan microarray analyses identified a putative 9- O -acetylated sialic acid as a ligand, which was confirmed by catch-and-release ESI-MS, STD-NMR analyses, and a graphene-based electrochemical sensor. The Beta (501Y.V2-1) variant attained an enhanced glycan binding modality in the NTD with specificity towards 9- O -acetylated structures, suggesting a dual-receptor functionality of the SARS-CoV-2 S1 domain, which was quickly selected against. These results indicate that SARS-CoV-2 can probe additional evolutionary space, allowing binding to glycan receptors on the surface of target cells. Graphical abstract Synopsis Coronaviruses utilize their N-terminal domain (NTD) for initial reversible low-affinity interaction to (sialylated) glycans. This initial low-affinity/high-avidity engagement enables viral surfing on the target membrane, potentially followed by a stronger secondary receptor interaction. Several coronaviruses, such as HKU1 and OC43, possess a hemagglutinin-esterase for viral release after sialic acid interaction, thus allowing viral dissemination. Other coronaviruses, such as MERS-CoV, do not possess a hemagglutinin-esterase, but interact reversibly to sialic acids allowing for viral surfing and dissemination. The early 501Y.V2-1 subvariant of the Beta SARS-CoV-2 Variant of Concern has attained a receptor-binding functionality towards 9- O -acetylated sialic acid using its NTD. This binding functionality was selected against rapidly, most likely due to poor dissemination. Ablation of sialic acid binding in more recent SARS-CoV-2 Variants of Concern suggests a fine balance of sialic acid interaction of SARS-CoV-2 is required for infection and/or transmission.
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Singh R, Kumar A, Rane JS, Khan R, Tripathi G, Ajay AK, Prakash A, Ray S. Arylcoumarin perturbs SARS-CoV-2 pathogenesis by targeting the S-protein/ACE2 interaction. Sci Rep 2022; 12:17038. [PMID: 36220880 PMCID: PMC9552724 DOI: 10.1038/s41598-022-20759-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 09/19/2022] [Indexed: 12/29/2022] Open
Abstract
The vaccination drive against COVID-19 worldwide was quite successful. However, the second wave of infections was even more disastrous. There was a rapid increase in reinfections and human deaths due to the appearance of new SARS-CoV-2 variants. The viral genome mutations in the variants were acquired while passing through different human hosts that could escape antibodies in convalescent or vaccinated individuals. The treatment was based on oxygen supplements and supportive protocols due to the lack of a specific drug. In this study, we identified three lead inhibitors of arylated coumarin derivatives 4,6,8-tri(naphthalen-2-yl)-2H-chromen-2-one (NF1), 8-(4-hydroxyphenyl)-4,6-di(naphthalen-2-yl)-2H-chromen-2-one (NF12) and 8-(4-hydroxyphenyl)-3,6-di(naphthalen-2-yl)-2H-chromen-2-one (NF-13) that showed higher binding affinity towards the junction of SARS-CoV-2 spike glycoprotein (S-protein) and human angiotensin-converting enzyme 2 (ACE2) receptor. Using molecular docking analysis, we identified the putative binding sites of these potent inhibitors. Notably, molecular dynamics (MD) simulation and MM-PBSA studies confirmed that these inhibitors have the potential ability to bind Spike-protein/ACE2 protein complex with minimal energy. Further, the two major concerns are an adaptive mutation of spike proteins- N501Y and D614G which displayed strong affinity towards NF-13 in docking analysis. Additionally, in vitro and in vivo studies are required to confirm the above findings and develop the inhibitors as potential drugs against SARS-CoV-2.
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Affiliation(s)
- Ruhar Singh
- grid.10706.300000 0004 0498 924XSchool of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Abhijeet Kumar
- Department of Chemistry, Mahatma Gandhi Central University, Motihari, 845401 India
| | - Jitendra Subhash Rane
- grid.417971.d0000 0001 2198 7527Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076 India
| | - Rajni Khan
- grid.464629.b0000 0004 1775 2698Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Hajipur, 844102 India
| | - Garima Tripathi
- grid.265038.a0000 0000 9895 3045Department of Chemistry, T.N.B. College, Bhagalpur, Tilka Manjhi Bhagalpur University, Bhagalpur, 812007 India
| | - Amrendra K. Ajay
- grid.38142.3c000000041936754XRenal Division, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115 USA
| | - Amresh Prakash
- grid.444644.20000 0004 1805 0217Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon, 122413 India
| | - Shashikant Ray
- Department of Biotechnology, Mahatma Gandhi Central University, Motihari, 845401 India
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Mohammadi M, Antoine D, Vitt M, Dickie JM, Sultana Jyoti S, Wall JG, Johnson PA, Wawrousek KE. A fast, ultrasensitive SERS immunoassay to detect SARS-CoV-2 in saliva. Anal Chim Acta 2022; 1229:340290. [PMID: 36156215 PMCID: PMC9395977 DOI: 10.1016/j.aca.2022.340290] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/11/2022] [Accepted: 08/17/2022] [Indexed: 01/13/2023]
Abstract
The COVID-19 pandemic has emphasized the need for accurate, rapid, point-of-care diagnostics to control disease transmission. We have developed a simple, ultrasensitive single-particle surface-enhanced Raman spectroscopy (SERS) immunoassay to detect the SARS-CoV-2 spike protein in saliva. This assay relies on the use of single chain Fv (scFv) recombinant antibody expressed in E. coli to bind the SARS-CoV-2 spike protein. Recombinant scFv labeled with a SERS-active dye in solution is mixed with unlabeled scFv conjugated to gold-coated magnetic nanoparticles and a sample to be tested. In the presence of the SARS-CoV-2 spike protein, immunocomplexes form and concentrate the labeled scFv close to the gold surface of the nanoparticles, causing an increased SERS signal. The assay detects inactivated SARS-CoV-2 virus and spike protein in saliva at concentrations of 1.94 × 103 genomes mL-1 and 4.7 fg mL-1, respectively, making this direct detection antigen test only 2-3 times less sensitive than some qRT-PCR tests. All tested SARS-CoV-2 spike proteins, including those from alpha, beta, gamma, delta, and omicron variants, were detected without recognition of the closely related SARS and MERS spike proteins. This 30 min, no-wash assay requires only mixing, a magnetic separation step, and signal measurements using a hand-held, battery-powered Raman spectrometer, making this assay ideal for ultrasensitive detection of the SARS-CoV-2 virus at the point-of-care.
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Affiliation(s)
- Moein Mohammadi
- Chemical Engineering, University of Wyoming, 1000 E. University Ave. Dept. 3295, Laramie, WY, 82071, USA
| | - Delphine Antoine
- Microbiology, School of Biological and Chemical Sciences, and SFI Centre for Medical Devices (CÚRAM), University of Galway, Galway H91 TK33, Ireland
| | - Madison Vitt
- Chemical Engineering, University of Wyoming, 1000 E. University Ave. Dept. 3295, Laramie, WY, 82071, USA
| | - Julia Marie Dickie
- Chemical Engineering, University of Wyoming, 1000 E. University Ave. Dept. 3295, Laramie, WY, 82071, USA
| | - Sharmin Sultana Jyoti
- Chemical Engineering, University of Wyoming, 1000 E. University Ave. Dept. 3295, Laramie, WY, 82071, USA
| | - J Gerard Wall
- Microbiology, School of Biological and Chemical Sciences, and SFI Centre for Medical Devices (CÚRAM), University of Galway, Galway H91 TK33, Ireland
| | - Patrick A Johnson
- Chemical Engineering, University of Wyoming, 1000 E. University Ave. Dept. 3295, Laramie, WY, 82071, USA
| | - Karen E Wawrousek
- Chemical Engineering, University of Wyoming, 1000 E. University Ave. Dept. 3295, Laramie, WY, 82071, USA.
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Quinteros JA, Noormohammadi AH, Lee SW, Browning GF, Diaz‐Méndez A. Genomics and pathogenesis of the avian coronavirus infectious bronchitis virus. Aust Vet J 2022; 100:496-512. [PMID: 35978541 PMCID: PMC9804484 DOI: 10.1111/avj.13197] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 04/25/2022] [Accepted: 05/02/2022] [Indexed: 01/05/2023]
Abstract
Infectious bronchitis virus (IBV) is a member of the family Coronaviridae, together with viruses such as SARS-CoV, MERS-CoV and SARS-CoV-2 (the causative agent of the COVID-19 global pandemic). In this family of viruses, interspecies transmission has been reported, so understanding their pathobiology could lead to a better understanding of the emergence of new serotypes. IBV possesses a single-stranded, non-segmented RNA genome about 27.6 kb in length that encodes several non-structural and structural proteins. Most functions of these proteins have been confirmed in IBV, but some other proposed functions have been based on research conducted on other members of the family Coronaviridae. IBV has variable tissue tropism depending on the strain, and can affect the respiratory, reproductive, or urinary tracts; however, IBV can also replicate in other organs. Additionally, the pathogenicity of IBV is also variable, with some strains causing only mild clinical signs, while infection with others results in high mortality rates in chickens. This paper extensively and comprehensibly reviews general aspects of coronaviruses and, more specifically, IBV, with emphasis on protein functions and pathogenesis. The pathogenicity of the Australian strains of IBV is also reviewed, describing the variability between the different groups of strains, from the classical to the novel and recombinant strains. Reverse genetic systems, cloning and cell culture growth techniques applicable to IBV are also reviewed.
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Affiliation(s)
- JA Quinteros
- Asia‐Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVictoriaAustralia,Present address:
Escuela de Ciencias Agrícolas y VeterinariasUniversidad Viña del Mar, Agua Santa 7055 2572007Viña del MarChile
| | - AH Noormohammadi
- Asia‐Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneWerribeeVictoriaAustralia
| | - SW Lee
- Asia‐Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVictoriaAustralia,College of Veterinary MedicineKonkuk UniversitySeoulRepublic of Korea
| | - GF Browning
- Asia‐Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVictoriaAustralia
| | - A Diaz‐Méndez
- Asia‐Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVictoriaAustralia
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Islam A, Ferdous J, Islam S, Sayeed MA, Rahman MK, Saha O, Hassan MM, Shirin T. Transmission dynamics and susceptibility patterns of SARS-CoV-2 in domestic, farmed and wild animals: Sustainable One Health surveillance for conservation and public health to prevent future epidemics and pandemics. Transbound Emerg Dis 2022; 69:2523-2543. [PMID: 34694705 PMCID: PMC8662162 DOI: 10.1111/tbed.14356] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/14/2021] [Accepted: 10/17/2021] [Indexed: 12/11/2022]
Abstract
The exact origin of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and source of introduction into humans has not been established yet, though it might be originated from animals. Therefore, we conducted a study to understand the putative reservoirs, transmission dynamics, and susceptibility patterns of SARS-CoV-2 in animals. Rhinolophus bats are presumed to be natural progenitors of SARS-CoV-2-related viruses. Initially, pangolin was thought to be the source of spillover to humans, but they might be infected by human or other animal species. So, the virus spillover pathways to humans remain unknown. Human-to-animal transmission has been testified in pet, farmed, zoo and free-ranging wild animals. Infected animals can transmit the virus to other animals in natural settings like mink-to-mink and mink-to-cat transmission. Animal-to-human transmission is not a persistent pathway, while mink-to-human transmission continues to be illuminated. Multiple companions and captive wild animals were infected by an emerging alpha variant of concern (B.1.1.7 lineage) whereas Asiatic lions were infected by delta variant, (B.1.617.2). To date, multiple animal species - cat, ferrets, non-human primates, hamsters and bats - showed high susceptibility to SARS-CoV-2 in the experimental condition, while swine, poultry, cattle showed no susceptibility. The founding of SARS-CoV-2 in wild animal reservoirs can confront the control of the virus in humans and might carry a risk to the welfare and conservation of wildlife as well. We suggest vaccinating pets and captive animals to stop spillovers and spillback events. We recommend sustainable One Health surveillance at the animal-human-environmental interface to detect and prevent future epidemics and pandemics by Disease X.
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Affiliation(s)
- Ariful Islam
- EcoHealth AllianceNew YorkUnited States
- Centre for Integrative Ecology, School of Life and Environmental ScienceDeakin UniversityVictoriaAustralia
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
| | - Jinnat Ferdous
- EcoHealth AllianceNew YorkUnited States
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
| | - Shariful Islam
- EcoHealth AllianceNew YorkUnited States
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
| | - Md. Abu Sayeed
- EcoHealth AllianceNew YorkUnited States
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
| | - Md. Kaisar Rahman
- EcoHealth AllianceNew YorkUnited States
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
| | - Otun Saha
- EcoHealth AllianceNew YorkUnited States
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
- Department of MicrobiologyUniversity of DhakaDhakaBangladesh
| | - Mohammad Mahmudul Hassan
- Faculty of Veterinary MedicineChattogram Veterinary and Animal Sciences UniversityChattogramBangladesh
| | - Tahmina Shirin
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
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Lubinski B, Frazier LE, Phan MVT, Bugembe DL, Cunningham JL, Tang T, Daniel S, Cotten M, Jaimes JA, Whittaker GR. Spike Protein Cleavage-Activation in the Context of the SARS-CoV-2 P681R Mutation: an Analysis from Its First Appearance in Lineage A.23.1 Identified in Uganda. Microbiol Spectr 2022; 10:e0151422. [PMID: 35766497 PMCID: PMC9430374 DOI: 10.1128/spectrum.01514-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/06/2022] [Indexed: 11/20/2022] Open
Abstract
Based on its predicted ability to affect transmissibility and pathogenesis, surveillance studies have highlighted the role of a specific mutation (P681R) in the S1/S2 furin cleavage site of the SARS-CoV-2 spike protein. Here we analyzed A.23.1, first identified in Uganda, as a P681R-containing virus several months prior to the emergence of B.1.617.2 (Delta variant). We performed assays using peptides mimicking the S1/S2 from A.23.1 and B.1.617 and observed significantly increased cleavability with furin compared to both an original B lineage (Wuhan-Hu1) and B.1.1.7 (Alpha variant). We also performed cell-cell fusion and functional infectivity assays using pseudotyped particles and observed an increase in activity for A.23.1 compared to an original B lineage spike. However, these changes in activity were not reproduced in the B lineage spike bearing only the P681R substitution. Our findings suggest that while A.23.1 has increased furin-mediated cleavage linked to the P681R substitution, this substitution needs to occur on the background of other spike protein changes to enable its functional consequences. IMPORTANCE During the course of the SARS-CoV-2 pandemic, viral variants have emerged that often contain notable mutations in the spike gene. Mutations that encode changes in the spike S1/S2 (furin) activation site have been considered especially impactful. The S1/S2 change from proline to arginine at position 681 (P681R) first emerged in the A.23.1 variant in Uganda, and subsequently occurred in the more widely transmitted Delta variant. We show that the A.23.1 spike is more readily activated by the host cell protease furin, but that this is not reproduced in an original SARS-CoV-2 spike containing the P681R mutation. Changes to the S1/S2 (furin) activation site play a role in SARS-CoV-2 infection and spread, but successful viruses combine these mutations with other less well identified changes, occurring as part of natural selection.
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Affiliation(s)
- Bailey Lubinski
- Graduate Program in Biological & Biomedical Sciences, Cornell University, Ithaca, New York, USA
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Laura E. Frazier
- Graduate Program in Biological & Biomedical Sciences, Cornell University, Ithaca, New York, USA
| | - My V. T. Phan
- MRC/UVRI and London School of Hygiene and Tropical Medicine – Uganda Research Unit, Entebbe, Uganda
| | - Daniel L. Bugembe
- MRC/UVRI and London School of Hygiene and Tropical Medicine – Uganda Research Unit, Entebbe, Uganda
| | - Jessie L. Cunningham
- Graduate Program in Biological & Biomedical Sciences, Cornell University, Ithaca, New York, USA
| | - Tiffany Tang
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA
| | - Susan Daniel
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA
| | - Matthew Cotten
- MRC/UVRI and London School of Hygiene and Tropical Medicine – Uganda Research Unit, Entebbe, Uganda
- MRC Centre of Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Javier A. Jaimes
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Gary R. Whittaker
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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Garg P, Vanamamalai VK, Jali I, Sharma S. In silico prediction of the animal susceptibility and virtual screening of natural compounds against SARS-CoV-2: Molecular dynamics simulation based analysis. Front Genet 2022; 13:906955. [PMID: 36110222 PMCID: PMC9468858 DOI: 10.3389/fgene.2022.906955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
COVID-19 is an infectious disease caused by the SARS-CoV-2 virus. It has six open reading frames (orf1ab, orf3a, orf6, orf7a, orf8, and orf10), a spike protein, a membrane protein, an envelope small membrane protein, and a nucleocapsid protein, out of which, orf1ab is the largest ORF coding different important non-structural proteins. In this study, an effort was made to evaluate the susceptibility of different animals against SARS-CoV-2 by analyzing the interactions of Spike and ACE2 proteins of the animals and propose a list of potential natural compounds binding to orf1ab of SARS-CoV-2. Here, we analyzed structural interactions between spike proteins of SARS-CoV-2 and the ACE2 receptor of 16 different hosts. A simulation for 50 ns was performed on these complexes. Based on post-simulation analysis, Chelonia mydas was found to have a more stable complex, while Bubalus bubalis, Aquila chrysaetos chrysaetos, Crocodylus porosus, and Loxodonta africana were found to have the least stable complexes with more fluctuations than all other organisms. Apart from that, we performed domain assignment of orf1ab of SARS-CoV-2 and identified 14 distinct domains. Out of these, Domain 3 (DNA/RNA polymerases) was selected as a target, as it showed no similarities with host proteomes and was validated in silico. Then, the top 10 molecules were selected from the virtual screening of ∼1.8 lakh molecules from the ZINC database, based on binding energy, and validated for ADME and toxicological properties. Three molecules were selected and analyzed further. The structural analysis showed that these molecules were residing within the pocket of the receptor. Finally, a simulation for 200 ns was performed on complexes with three selected molecules. Based on post-simulation analysis (RMSD, RMSF, Rg, SASA, and energies), the molecule ZINC000103666966 was found as the most suitable inhibitory compound against Domain 3. As this is an in silico prediction, further experimental studies could unravel the potential of the proposed molecule against SARS-CoV-2.
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Abstract
Despite effective spike-based vaccines and monoclonal antibodies, the SARS-CoV-2 pandemic continues more than two and a half years post-onset. Relentless investigation has outlined a causative dynamic between host-derived antibodies and reciprocal viral subversion. Integration of this paradigm into the architecture of next generation antiviral strategies, predicated on a foundational understanding of the virology and immunology of SARS-CoV-2, will be critical for success. This review aims to serve as a primer on the immunity endowed by antibodies targeting SARS-CoV-2 spike protein through a structural perspective. We begin by introducing the structure and function of spike, polyclonal immunity to SARS-CoV-2 spike, and the emergence of major SARS-CoV-2 variants that evade immunity. The remainder of the article comprises an in-depth dissection of all major epitopes on SARS-CoV-2 spike in molecular detail, with emphasis on the origins, neutralizing potency, mechanisms of action, cross-reactivity, and variant resistance of representative monoclonal antibodies to each epitope.
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Affiliation(s)
- John M Errico
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, United States
| | - Lucas J Adams
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, United States
| | - Daved H Fremont
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, United States; Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, United States; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, United States.
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Sequence Similarity Network Analysis Provides Insight into the Temporal and Geographical Distribution of Mutations in SARS-CoV-2 Spike Protein. Viruses 2022; 14:v14081672. [PMID: 36016294 PMCID: PMC9413517 DOI: 10.3390/v14081672] [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: 06/15/2022] [Revised: 07/28/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022] Open
Abstract
Severe acute respiratory syndrome-related coronavirus (SARS-CoV-2), which still infects hundreds of thousands of people globally each day despite various countermeasures, has been mutating rapidly. Mutations in the spike (S) protein seem to play a vital role in viral stability, transmission, and adaptability. Therefore, to control the spread of the virus, it is important to gain insight into the evolution and transmission of the S protein. This study deals with the temporal and geographical distribution of mutant S proteins from sequences gathered across the US over a period of 19 months in 2020 and 2021. The S protein sequences are studied using two approaches: (i) multiple sequence alignment is used to identify prominent mutations and highly mutable regions and (ii) sequence similarity networks are subsequently employed to gain further insight and study mutation profiles of concerning variants across the defined time periods and states. Additionally, we tracked the variants using visualizations on geographical maps. The visualizations produced using the Directed Weighted All Nearest Neighbors (DiWANN) networks and maps provided insights into the transmission of the virus that reflect well the statistics reported for the time periods studied. We found that the networks created using DiWANN are superior to commonly used approximate distance networks created using BLAST bitscores. The study offers a richer computational approach to analyze the transmission profile of the prominent S protein mutations in SARS-CoV-2 and can be extended to other proteins and viruses.
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Lubinski B, Jaimes JA, Whittaker GR. Intrinsic furin-mediated cleavability of the spike S1/S2 site from SARS-CoV-2 variant B.1.1.529 (Omicron). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.04.20.488969. [PMID: 35923311 PMCID: PMC9347273 DOI: 10.1101/2022.04.20.488969] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The ability of SARS-CoV-2 to be primed for viral entry by the host cell protease furin has become one of the most investigated of the numerous transmission and pathogenicity features of the virus. SARS-CoV-2 The variant B.1.1.529 (Omicron) emerged in late 2020 and has continued to evolve and is now present in several distinct sub-variants. Here, we analyzed the "furin cleavage site" of the spike protein of SARS-CoV-2 B.1.1.529 (Omicron variant) in vitro, to assess the role of two key mutations (spike, N679K and P681H) that are common across all subvariants compared to the ancestral B.1 virus and other notable lineages. We observed significantly increased intrinsic cleavability with furin compared to an original B lineage virus (Wuhan-Hu1), as well as to two variants, B.1.1.7 (Alpha) and B.1.617 (Delta) that subsequently had wide circulation. Increased furin-mediated cleavage was attributed to the N679K mutation, which lies outside the conventional furin binding pocket. Our findings suggest that B.1.1.529 (Omicron variant) has gained genetic features linked to intrinsic furin cleavability, in line with its evolution within the population as the COVID-19 pandemic has proceeded.
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Affiliation(s)
- Bailey Lubinski
- Graduate Field of Biological & Biomedical Sciences, Cornell University, Ithaca NY, 14853, USA
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca NY, 14853, USA
| | - Javier A. Jaimes
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca NY, 14853, USA
| | - Gary R. Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca NY, 14853, USA
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Appraisal of SARS-CoV-2 mutations and their impact on vaccination efficacy: an overview. J Diabetes Metab Disord 2022; 21:1763-1783. [PMID: 35891981 PMCID: PMC9305048 DOI: 10.1007/s40200-022-01002-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/07/2022] [Indexed: 12/02/2022]
Abstract
With the unexpected emergence of the novel 2019 Wuhan coronavirus, the world was faced with a sudden uproar that quickly shifted into a serious life-threatening pandemic. Affecting the lives of the global population and leaving drastic damage in various sections and systems, several measures have been constantly taken to tackle down this crisis. For instance, numerous vaccines have been developed in the past two years, some of which have been granted emergency use, thus providing sufficient immunity to the vaccinated individuals. However, the appearance of newly emerged SARS-CoV-2 variants with accelerated transmission and fatality has led the world towards another pandemic. Having undergone various mutations in genomic and/or amino acid profiles, some of the emerged variants of concern (VOCs) including Alpha, Beta, Gamma, and Delta have displayed immune evasion and pathogenicity even in the vaccinated population, hence raising concerns regarding the efficacy of current vaccines against new VOCs of COVID-19. Therefore, genomic investigations of SARS-CoV-2 mutations are expected to provide valuable insight into the evolution of SARS-CoV-2, while also determining the impact of different mutations on infection severity. This study was constructed with the aim of shining light on recent advances regarding mutations in major COVID-19 VOCs, as well as vaccination efficacy against those VOCs.
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62
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Matsoukas JM, Gadanec LK, Zulli A, Apostolopoulos V, Kelaidonis K, Ligielli I, Moschovou K, Georgiou N, Plotas P, Chasapis CT, Moore G, Ridgway H, Mavromoustakos T. Diminazene Aceturate Reduces Angiotensin II Constriction and Interacts with the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2. Biomedicines 2022; 10:biomedicines10071731. [PMID: 35885036 PMCID: PMC9312513 DOI: 10.3390/biomedicines10071731] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/27/2022] [Accepted: 07/05/2022] [Indexed: 12/15/2022] Open
Abstract
Diminazene aceturate (DIZE) is a putative angiotensin-converting enzyme 2 (ACE2) activator and angiotensin type 1 receptor antagonist (AT1R). Its simple chemical structure possesses a negatively charged triazene segment that is homologous to the tetrazole of angiotensin receptor blockers (ARB), which explains its AT1R antagonistic activity. Additionally, the activation of ACE2 by DIZE converts the toxic octapeptide angiotensin II (AngII) to the heptapeptides angiotensin 1–7 and alamandine, which promote vasodilation and maintains homeostatic balance. Due to DIZE’s protective cardiovascular and pulmonary effects and its ability to target ACE2 (the predominant receptor utilized by severe acute respiratory syndrome coronavirus 2 to enter host cells), it is a promising treatment for coronavirus 2019 (COVID-19). To determine DIZE’s ability to inhibit AngII constriction, in vitro isometric tension analysis was conducted on rabbit iliac arteries incubated with DIZE or candesartan and constricted with cumulative doses of AngII. In silico docking and ligand interaction studies were performed to investigate potential interactions between DIZE and other ARBs with AT1R and the spike protein/ACE2 complex. DIZE, similar to the other ARBs investigated, was able to abolish vasoconstriction in response to AngII and exhibited a binding affinity for the spike protein/ACE2 complex (PDB 6LZ6). These results support the potential of DIZE as a treatment for COVID-19.
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Affiliation(s)
- John M. Matsoukas
- NewDrug PC, Patras Science Park, 26500 Patras, Greece;
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (A.Z.); (V.A.)
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Correspondence: (J.M.M.); (T.M.)
| | - Laura Kate Gadanec
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (A.Z.); (V.A.)
| | - Anthony Zulli
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (A.Z.); (V.A.)
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (A.Z.); (V.A.)
- Immunology Program, Australian Institute for Musculoskeletal Science, Melbourne, VIC 3021, Australia
| | | | - Irene Ligielli
- Department of Chemistry National and Kapodistrian, University of Athens, Zographou, 15784 Athens, Greece; (I.L.); (K.M.); (N.G.)
| | - Kalliopi Moschovou
- Department of Chemistry National and Kapodistrian, University of Athens, Zographou, 15784 Athens, Greece; (I.L.); (K.M.); (N.G.)
| | - Nikitas Georgiou
- Department of Chemistry National and Kapodistrian, University of Athens, Zographou, 15784 Athens, Greece; (I.L.); (K.M.); (N.G.)
| | - Panagiotis Plotas
- Laboratory of Primary Health Care, School of Health Rehabilitation Sciences, University of Patras, 26504 Patras, Greece;
| | - Christos T. Chasapis
- NMR Facility, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, 26504 Patras, Greece;
- Institute of Chemical Engineering Sciences, Foundation for Research and Technology, Hellas (FORTH/ICE-HT), 26504 Patras, Greece
| | - Graham Moore
- Pepmetics Incorporated, 772 Murphy Pace, Victoria, BC V8Y 3H4, Canada;
| | - Harry Ridgway
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, VIC 8001, Australia;
- AquaMem Consultants, Rodeo, NM 88056, USA
| | - Thomas Mavromoustakos
- Department of Chemistry National and Kapodistrian, University of Athens, Zographou, 15784 Athens, Greece; (I.L.); (K.M.); (N.G.)
- Correspondence: (J.M.M.); (T.M.)
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63
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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64
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Sanyal D, Banerjee S, Bej A, Chowdhury VR, Uversky VN, Chowdhury S, Chattopadhyay K. An integrated understanding of the evolutionary and structural features of the SARS-CoV-2 spike receptor binding domain (RBD). Int J Biol Macromol 2022; 217:492-505. [PMID: 35841961 PMCID: PMC9278002 DOI: 10.1016/j.ijbiomac.2022.07.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 12/23/2022]
Abstract
Conventional drug development strategies typically use pocket in protein structures as drug-target sites. They overlook the plausible effects of protein evolvability and resistant mutations on protein structure which in turn may impair protein-drug interaction. In this study, we used an integrated evolution and structure guided strategy to develop potential evolutionary-escape resistant therapeutics using receptor binding domain (RBD) of SARS-CoV-2 spike-protein/S-protein as a model. Deploying an ensemble of sequence space exploratory tools including co-evolutionary analysis and deep mutational scans we provide a quantitative insight into the evolutionarily constrained subspace of the RBD sequence-space. Guided by molecular simulation and structure network analysis we highlight regions inside the RBD, which are critical for providing structural integrity and conformational flexibility. Using fuzzy C-means clustering we combined evolutionary and structural features of RBD and identified a critical region. Subsequently, we used computational drug screening using a library of 1615 small molecules and identified one lead molecule, which is expected to target the identified region, critical for evolvability and structural stability of RBD. This integrated evolution-structure guided strategy to develop evolutionary-escape resistant lead molecules have potential general applications beyond SARS-CoV-2.
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Affiliation(s)
- Dwipanjan Sanyal
- Protein Folding and Dynamics Group, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Suharto Banerjee
- Protein Folding and Dynamics Group, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Aritra Bej
- Protein Folding and Dynamics Group, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Vaidehi Roy Chowdhury
- Protein Folding and Dynamics Group, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow region 142290, Russia
| | - Sourav Chowdhury
- Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Krishnananda Chattopadhyay
- Protein Folding and Dynamics Group, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
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65
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Nikitin PA, DiMuzio JM, Dowling JP, Patel NB, Bingaman-Steele JL, Heimbach BC, Henriquez N, Nicolescu C, Polley A, Sikorski EL, Howanski RJ, Nath M, Shukla H, Scheaffer SM, Finn JP, Liang LF, Smith T, Storm N, McKay LGA, Johnson RI, Malsick LE, Honko AN, Griffiths A, Diamond MS, Sarma P, Geising DH, Morin MJ, Robinson MK. IMM-BCP-01, a patient-derived anti-SARS-CoV-2 antibody cocktail, is active across variants of concern including Omicron BA.1 and BA.2. Sci Immunol 2022; 7:eabl9943. [PMID: 35771946 PMCID: PMC9273042 DOI: 10.1126/sciimmunol.abl9943] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Monoclonal antibodies are an efficacious therapy against SARS-CoV-2. However, rapid viral mutagenesis, led to escape from most of these therapies, outlining the need for an antibody cocktail with a broad neutralizing potency. Using an unbiased interrogation of the memory B cell repertoire of convalescent COVID-19 patients, we identified human antibodies with broad antiviral activity in vitro and efficacy in vivo against all tested SARS-CoV-2 variants of concern, including Delta, Omicron BA.1 and BA.2. Here, we describe an antibody cocktail IMM-BCP-01, that consists of three patient-derived broadly neutralizing antibodies directed at non-overlapping surfaces on the SARS-CoV-2 spike protein. Two antibodies, IMM20184 and IMM20190, directly blocked Spike binding to the ACE2 receptor. Binding of the third antibody, IMM20253, to its cryptic epitope on the outer surface of RBD, altered the conformation of the Spike Trimer, promoting release of Spike monomers. These antibodies decreased Omicron SARS-CoV-2 infection in the lungs of Syrian golden hamsters in vivo, and potently induced antiviral effector response in vitro, including phagocytosis, ADCC, and complement pathway activation. Our pre-clinical data demonstrated that the three antibody cocktail IMM-BCP-01 could be a promising means for preventing or treating infection of SARS-CoV-2 variants of concern, including Omicron BA.1 and BA.2, in susceptible individuals.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Suzanne M Scheaffer
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | | | | | - Nadia Storm
- Department of Microbiology, Boston University School of Medicine and National Emerging Infectious Diseases Laboratories, Boston, MA, USA
| | - Lindsay G A McKay
- Department of Microbiology, Boston University School of Medicine and National Emerging Infectious Diseases Laboratories, Boston, MA, USA
| | - Rebecca I Johnson
- Department of Microbiology, Boston University School of Medicine and National Emerging Infectious Diseases Laboratories, Boston, MA, USA
| | - Lauren E Malsick
- Department of Microbiology, Boston University School of Medicine and National Emerging Infectious Diseases Laboratories, Boston, MA, USA
| | - Anna N Honko
- Department of Microbiology, Boston University School of Medicine and National Emerging Infectious Diseases Laboratories, Boston, MA, USA
| | - Anthony Griffiths
- Department of Microbiology, Boston University School of Medicine and National Emerging Infectious Diseases Laboratories, Boston, MA, USA
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
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66
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Identification, virtual screening and molecular dynamic analysis of novel TMPRSS2 inhibitors from natural compound database as potential entry-blocking agents in SARS-CoV-2 therapy. Struct Chem 2022; 33:1609-1617. [PMID: 35754942 PMCID: PMC9210338 DOI: 10.1007/s11224-022-01991-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/04/2022] [Indexed: 11/28/2022]
Abstract
Scientific insights gained from the severe acute respiratory syndrome (SARS) and middle east respiratory syndrome (MERS) outbreaks have been assisting scientists and researchers in the quest of antiviral drug discovery process against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Coronaviruses and influenza viruses both rely on the host type 2 transmembrane serine protease, TMPRSS2, for entry and propagation. Recent studies report SARS-CoV-2 also uses TMPRSS2 to enter cells. In the current study, we employed structure-based virtual screening of 1,82,651 natural compounds downloaded from the zin database against the homology model of the TMPRSS2 protein, followed by a molecular dynamics-based simulation to identify potential TMPRSS2 hits. The virtual screening yielded 110 hits with docking scores ranging from −8.654 to −6.775 and glide energies ranging from −55.714 to −29.065 kcal/mol. The binding mode analysis revealed that the hit molecules made H-bond, Pi-Pi stacking and salt bridge contacts with the TMPRSS2 active site residues. MD simulations of the top two hits (ZINC000095912839 and ZINC000085597504) revealed to form a stable complex with TMPRSS2, with a minimal RMSD and RMSF fluctuation. Both the hit structures interacted strongly with the Asp180, Gln183, Gly184, Ser186, Gly207 and Gly209, as predicted by Glide XP docking, and formed a significant H-bond interaction with Ser181 in MD simulation. Among these two, ZINC000095912839 was having the most stable binding interaction with TMPRSS2 of the two molecules. The present study successfully identified TMPRSS2 ligands from a database of zinc natural molecules as potential leads for novel SARs-CoV-2 treatment.
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67
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Kastenhuber ER, Johnson JL, Yaron TM, Mercadante M, Cantley LC. Evolution of host protease interactions among SARS-CoV-2 variants of concern and related coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.06.16.496428. [PMID: 35734085 PMCID: PMC9216717 DOI: 10.1101/2022.06.16.496428] [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] [Indexed: 11/24/2022]
Abstract
Previously, we showed that coagulation factors directly cleave SARS-CoV-2 spike and promote viral entry (Kastenhuber et al., 2022). Here, we show that substitutions in the S1/S2 cleavage site observed in SARS-CoV-2 variants of concern (VOCs) exhibit divergent interactions with host proteases, including factor Xa and furin. Nafamostat remains effective to block coagulation factor-mediated cleavage of variant spike sequences. Furthermore, host protease usage has likely been a selection pressure throughout coronavirus evolution, and we observe convergence of distantly related coronaviruses to attain common host protease interactions, including coagulation factors. Interpretation of genomic surveillance of emerging SARS-CoV-2 variants and future zoonotic spillover is supported by functional characterization of recurrent emerging features.
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Affiliation(s)
- Edward R. Kastenhuber
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Jared L. Johnson
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Tomer M. Yaron
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Marisa Mercadante
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Lewis C. Cantley
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Dana Farber Cancer Institute, Boston, MA, USA
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68
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Cicaloni V, Costanti F, Pasqui A, Bianchini M, Niccolai N, Bongini P. A Bioinformatics Approach to Investigate Structural and Non-Structural Proteins in Human Coronaviruses. Front Genet 2022; 13:891418. [PMID: 35774504 PMCID: PMC9237418 DOI: 10.3389/fgene.2022.891418] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Recent studies confirmed that people unexposed to SARS-CoV-2 have preexisting reactivity, probably due to previous exposure to widely circulating common cold coronaviruses. Such preexistent reactivity against SARS-CoV-2 comes from memory T cells that can specifically recognize a SARS-CoV-2 epitope of structural and non-structural proteins and the homologous epitopes from common cold coronaviruses. Therefore, it is important to understand the SARS-CoV-2 cross-reactivity by investigating these protein sequence similarities with those of different circulating coronaviruses. In addition, the emerging SARS-CoV-2 variants lead to an intense interest in whether mutations in proteins (especially in the spike) could potentially compromise vaccine effectiveness. Since it is not clear that the differences in clinical outcomes are caused by common cold coronaviruses, a deeper investigation on cross-reactive T-cell immunity to SARS-CoV-2 is crucial to examine the differential COVID-19 symptoms and vaccine performance. Therefore, the present study can be a starting point for further research on cross-reactive T cell recognition between circulating common cold coronaviruses and SARS-CoV-2, including the most recent variants Delta and Omicron. In the end, a deep learning approach, based on Siamese networks, is proposed to accurately and efficiently calculate a BLAST-like similarity score between protein sequences.
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Affiliation(s)
| | - Filippo Costanti
- Department of Information Engineering and Mathematics, University of Siena, Siena, Italy
| | | | - Monica Bianchini
- Department of Information Engineering and Mathematics, University of Siena, Siena, Italy
| | - Neri Niccolai
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Siena, Italy
| | - Pietro Bongini
- Department of Information Engineering and Mathematics, University of Siena, Siena, Italy
- Department of Information Engineering, University of Florence, Firenze, Italy
- *Correspondence: Pietro Bongini,
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69
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Translocating Peptides of Biomedical Interest Obtained from the Spike (S) Glycoprotein of the SARS-CoV-2. MEMBRANES 2022; 12:membranes12060600. [PMID: 35736307 PMCID: PMC9229458 DOI: 10.3390/membranes12060600] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 02/01/2023]
Abstract
At the beginning of 2020, the pandemic caused by the SARS-CoV-2 virus led to the fast sequencing of its genome to facilitate molecular engineering strategies to control the pathogen’s spread. The spike (S) glycoprotein has been identified as the leading therapeutic agent due to its role in localizing the ACE2 receptor in the host’s pulmonary cell membrane, binding, and eventually infecting the cells. Due to the difficulty of delivering bioactive molecules to the intracellular space, we hypothesized that the S protein could serve as a source of membrane translocating peptides. AHB-1, AHB-2, and AHB-3 peptides were identified and analyzed on a membrane model of DPPC (dipalmitoylphosphatidylcholine) using molecular dynamics (MD) simulations. An umbrella sampling approach was used to quantify the energy barrier necessary to cross the boundary (13.2 to 34.9 kcal/mol), and a flat-bottom pulling helped to gain a deeper understanding of the membrane’s permeation dynamics. Our studies revealed that the novel peptide AHB-1 exhibited comparable penetration potential of already known potent cell-penetrating peptides (CPPs) such as TP2, Buforin II, and Frenatin 2.3s. Results were confirmed by in vitro analysis of the peptides conjugated to chitosan nanoparticles, demonstrating its ability to reach the cytosol and escape endosomes, while maintaining high biocompatibility levels according to standardized assays.
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70
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Bondar AN. Graphs of Hydrogen-Bond Networks to Dissect Protein Conformational Dynamics. J Phys Chem B 2022; 126:3973-3984. [PMID: 35639610 DOI: 10.1021/acs.jpcb.2c00200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Dynamic hydrogen bonds and hydrogen-bond networks are ubiquitous in proteins and protein complexes. Functional roles that have been assigned to hydrogen-bond networks include structural plasticity for protein function, allosteric conformational coupling, long-distance proton transfers, and transient storage of protons. Advances in structural biology provide invaluable insights into architectures of large proteins and protein complexes of direct interest to human physiology and disease, including G Protein Coupled Receptors (GPCRs) and the SARS-Covid-19 spike protein S, and give rise to the challenge of how to identify those interactions that are more likely to govern protein dynamics. This Perspective discusses applications of graph-based algorithms to dissect dynamical hydrogen-bond networks of protein complexes, with illustrations for GPCRs and spike protein S. H-bond graphs provide an overview of sites in GPCR structures where hydrogen-bond dynamics would be required to assemble longer-distance networks between functionally important motifs. In the case of spike protein S, graphs identify regions of the protein where hydrogen bonds rearrange during the reaction cycle and where local hydrogen-bond networks likely change in a virus variant of concern.
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Affiliation(s)
- Ana-Nicoleta Bondar
- University of Bucharest, Faculty of Physics, Str. Atomiştilor 405, 077125 Bucharest-Măgurele, Romania.,Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany
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71
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Kashani NR, Azadbakht J, Ehteram H, Kashani HH, Rajabi-Moghadam H, Ahmad E, Nikzad H, Hosseini ES. Molecular and Clinical Investigation of COVID-19: From Pathogenesis and Immune Responses to Novel Diagnosis and Treatment. Front Mol Biosci 2022; 9:770775. [PMID: 35664675 PMCID: PMC9161360 DOI: 10.3389/fmolb.2022.770775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 04/04/2022] [Indexed: 01/08/2023] Open
Abstract
The coronavirus-related severe acute respiratory syndrome (SARS-CoV) in 2002/2003, the Middle East respiratory syndrome (MERS-CoV) in 2012/2013, and especially the current 2019/2021 severe acute respiratory syndrome-2 (SARS-CoV-2) negatively affected the national health systems worldwide. Different SARS-CoV-2 variants, including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and recently Omicron (B.1.1.529), have emerged resulting from the high rate of genetic recombination and S1-RBD/S2 mutation/deletion in the spike protein that has an impact on the virus activity. Furthermore, genetic variability in certain genes involved in the immune system might impact the level of SARS-CoV-2 recognition and immune response against the virus among different populations. Understanding the molecular mechanism and function of SARS-CoV-2 variants and their different epidemiological outcomes is a key step for effective COVID-19 treatment strategies, including antiviral drug development and vaccine designs, which can immunize people with genetic variabilities against various strains of SARS-CoV-2. In this review, we center our focus on the recent and up-to-date knowledge on SARS-CoV-2 (Alpha to Omicron) origin and evolution, structure, genetic diversity, route of transmission, pathogenesis, new diagnostic, and treatment strategies, as well as the psychological and economic impact of COVID-19 pandemic on individuals and their lives around the world.
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Affiliation(s)
- Narjes Riahi Kashani
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
- Gametogenesis Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Javid Azadbakht
- Department of Radiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Hassan Ehteram
- Department of Pathology, School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Hamed Haddad Kashani
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
- Gametogenesis Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Hassan Rajabi-Moghadam
- Department of Cardiovascular Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Ejaz Ahmad
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Hossein Nikzad
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
- Gametogenesis Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Elahe Seyed Hosseini
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
- Gametogenesis Research Center, Kashan University of Medical Sciences, Kashan, Iran
- *Correspondence: Elahe Seyed Hosseini,
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72
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Murugavel S, Vasudevan P, Chandrasekaran R, Archana V, Ponnuswany A. Synthesis, crystal structure elucidation,
DFT
analysis, drug‐likeness and
ADMET
evaluation and molecular docking studies of triazole derivatives: Binary inhibition of spike protein and
ACE2
receptor protein of
COVID
‐19. J CHIN CHEM SOC-TAIP 2022; 69:884-900. [PMID: 35941959 PMCID: PMC9347919 DOI: 10.1002/jccs.202200140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/13/2022] [Accepted: 05/01/2022] [Indexed: 12/13/2022]
Abstract
The recent incidence of terrible acute respiratory syndrome coronavirus 2 (SARS CoV‐2) has presently experienced some noteworthy mutations since its discovery in 2019 in Wuhan, China. The present research work focuses on the synthesis of three triazole derivatives (BMTPP, BMTTP, and BMTIP) and their inhibition activities against SARS‐Cov‐2 spike and ACE2 receptor proteins. The crystal structure for BMTTP was determined by the SCXRD method and optimized geometrical parameters for the three triazole derivatives were obtained by DFT calculations. HOMO‐LUMO, Global reactive descriptors [GRD], and Molecular electrostatic potential (MEP) investigations exposed that all three compounds have biological properties. The drug‐likeness ability of the synthesized compounds was examined using Molinspiration and a pre‐ADMET online Server. Further, to explore the binding nature of three synthesized compounds with SARS‐Cov‐2 spike proteins/ACE2 receptor molecular docking studies were executed. The outcomes we obtained from molecular docking simulation studies suggest that the synthesized triazole derivatives may be well utilized as curing medicines against COVID‐19. Ultimately, animal tests and precise clinical tests are required to prove the potent nature of these compounds against COVID‐19. Finally, the present outcomes must be proved to utilize in‐vitro and in‐vivo antiviral methods.
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Affiliation(s)
- Saminathan Murugavel
- Department of Physics Thanthai Periyar Government Institute of Technology Vellore Tamil Nadu India
| | - Perumal Vasudevan
- Department of Physics Thanthai Periyar Government Institute of Technology Vellore Tamil Nadu India
| | - RaviKumar Chandrasekaran
- Department of Physics Thanthai Periyar EVR Government Polytechnic College Vellore Tamil Nadu India
| | - Vellingiri Archana
- Department of Chemistry School of Physical Sciences and Computational Sciences, Avinashilingam Institute for Home Science and Higher Education for Women Coimbatore Tamil Nadu India
| | - Alagusundaram Ponnuswany
- Department of Organic chemistry School of chemistry, Madurai Kamaraj University Madurai Tamil Nadu India
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73
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Ridgway H, Chasapis CT, Kelaidonis K, Ligielli I, Moore GJ, Gadanec LK, Zulli A, Apostolopoulos V, Mavromoustakos T, Matsoukas JM. Understanding the Driving Forces That Trigger Mutations in SARS-CoV-2: Mutational Energetics and the Role of Arginine Blockers in COVID-19 Therapy. Viruses 2022; 14:v14051029. [PMID: 35632769 PMCID: PMC9143829 DOI: 10.3390/v14051029] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/20/2022] [Accepted: 04/24/2022] [Indexed: 12/27/2022] Open
Abstract
SARS-CoV-2 is a global challenge due to its ability to mutate into variants that spread more rapidly than the wild-type virus. Because the molecular biology of this virus has been studied in such great detail, it represents an archetypal paradigm for research into new antiviral drug therapies. The rapid evolution of SARS-CoV-2 in the human population is driven, in part, by mutations in the receptor-binding domain (RBD) of the spike (S-) protein, some of which enable tighter binding to angiotensin-converting enzyme (ACE2). More stable RBD-ACE2 association is coupled with accelerated hydrolysis of furin and 3CLpro cleavage sites that augment infection. Non-RBD and non-interfacial mutations assist the S-protein in adopting thermodynamically favorable conformations for stronger binding. The driving forces of key mutations for Alpha, Beta, Gamma, Delta, Kappa, Lambda and Omicron variants, which stabilize the RBD-ACE2 complex, are investigated by free-energy computational approaches, as well as equilibrium and steered molecular dynamic simulations. Considered also are the structural hydropathy traits of the residues in the interface between SARS-CoV-2 RBD and ACE2 protein. Salt bridges and π-π interactions are critical forces that create stronger complexes between the RBD and ACE2. The trend of mutations is the replacement of non-polar hydrophobic interactions with polar hydrophilic interactions, which enhance binding of RBD with ACE2. However, this is not always the case, as conformational landscapes also contribute to a stronger binding. Arginine, the most polar and hydrophilic among the natural amino acids, is the most aggressive mutant amino acid for stronger binding. Arginine blockers, such as traditional sartans that bear anionic tetrazoles and carboxylates, may be ideal candidate drugs for retarding viral infection by weakening S-protein RBD binding to ACE2 and discouraging hydrolysis of cleavage sites. Based on our computational results it is suggested that a new generation of “supersartans”, called “bisartans”, bearing two anionic biphenyl-tetrazole pharmacophores, are superior to carboxylates in terms of their interactions with viral targets, suggesting their potential as drugs in the treatment of COVID-19. In Brief: This in silico study reviews our understanding of molecular driving forces that trigger mutations in the SARS-CoV-2 virus. It also reports further studies on a new class of “supersartans” referred to herein as “bisartans”, bearing two anionic biphenyltetrazole moieties that show potential in models for blocking critical amino acids of mutants, such as arginine, in the Delta variant. Bisartans may also act at other targets essential for viral infection and replication (i.e., ACE2, furin cleavage site and 3CLpro), rendering them potential new drugs for additional experimentation and translation to human clinical trials.
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Affiliation(s)
- Harry Ridgway
- AquaMem Consultants, Rodeo, New Mexico, NM 88056, USA
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, VIC 3030, Australia
- Correspondence: (H.R.); (J.M.M.)
| | - Christos T. Chasapis
- NMR Facility, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, 26504 Patras, Greece;
- Institute of Chemical Engineering Sciences, Foundation for Research and Technology, Hellas (FORTH/ICE-HT), 26504 Patras, Greece
| | | | - Irene Ligielli
- Department of Chemistry, National and Kapodistrian University of Athens, 15784 Athens, Greece; (I.L.); (T.M.)
| | - Graham J. Moore
- Pepmetics Inc., 772 Murphy Place, Victoria, BC V6Y 3H4, Canada;
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Laura Kate Gadanec
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (A.Z.); (V.A.)
| | - Anthony Zulli
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (A.Z.); (V.A.)
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (A.Z.); (V.A.)
- Immunology Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
| | - Thomas Mavromoustakos
- Department of Chemistry, National and Kapodistrian University of Athens, 15784 Athens, Greece; (I.L.); (T.M.)
| | - John M. Matsoukas
- NewDrug PC, Patras Science Park, 26504 Patras, Greece;
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (L.K.G.); (A.Z.); (V.A.)
- Correspondence: (H.R.); (J.M.M.)
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74
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Sonnleitner ST, Prelog M, Sonnleitner S, Hinterbichler E, Halbfurter H, Kopecky DBC, Almanzar G, Koblmüller S, Sturmbauer C, Feist L, Horres R, Posch W, Walder G. Cumulative SARS-CoV-2 mutations and corresponding changes in immunity in an immunocompromised patient indicate viral evolution within the host. Nat Commun 2022; 13:2560. [PMID: 35538074 PMCID: PMC9090742 DOI: 10.1038/s41467-022-30163-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 04/19/2022] [Indexed: 01/07/2023] Open
Abstract
Different scenarios explaining the emergence of novel variants of concern (VOC) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported, including their evolution in scarcely monitored populations, in animals as alternative hosts, or in immunocompromised individuals. Here we report SARS-CoV-2 immune escape mutations over a period of seven months in an immunocompromised patient with prolonged viral shedding. Signs of infection, viral shedding and mutation events are periodically analyzed using RT-PCR and next-generation sequencing based on naso-pharyngeal swabs, with the results complemented by immunological diagnostics to determine humoral and T cell immune responses. Throughout the infection course, 17 non-synonymous intra-host mutations are noted, with 15 (88.2%) having been previously described as prominent immune escape mutations (S:E484K, S:D950N, S:P681H, S:N501Y, S:del(9), N:S235F and S:H655Y) in VOCs. The high frequency of these non-synonymous mutations is consistent with multiple events of convergent evolution. Thus, our results suggest that specific mutations in the SARS-CoV-2 genome may represent positions with a fitness advantage, and may serve as targets in future vaccine and therapeutics development for COVID-19. Variants of concerns arise from SARS-CoV-2 mutations poise as severe public health threats. Here the authors chronicle SARS-CoV-2 mutations onset and immune parameters in an immunocompromised patient with continuous virus-shedding, thereby hinting potential intra-host viral evolution and escape facilitated by ineffective T cell immunity.
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Affiliation(s)
- Sissy Therese Sonnleitner
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria. .,Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020, Innsbruck, Austria.
| | - Martina Prelog
- Pediatric Rheumatology/Special Immunology, Department of Pediatrics, University Hospital Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, Germany
| | - Stefanie Sonnleitner
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Eva Hinterbichler
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Hannah Halbfurter
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Dominik B C Kopecky
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Giovanni Almanzar
- Pediatric Rheumatology/Special Immunology, Department of Pediatrics, University Hospital Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, Germany
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Leonard Feist
- GenXPro GmbH, Altenhoeferallee 3, 60438, Frankfurt am Main, Germany
| | - Ralf Horres
- GenXPro GmbH, Altenhoeferallee 3, 60438, Frankfurt am Main, Germany
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Gernot Walder
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
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75
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Strohl WR, Ku Z, An Z, Carroll SF, Keyt BA, Strohl LM. Passive Immunotherapy Against SARS-CoV-2: From Plasma-Based Therapy to Single Potent Antibodies in the Race to Stay Ahead of the Variants. BioDrugs 2022; 36:231-323. [PMID: 35476216 PMCID: PMC9043892 DOI: 10.1007/s40259-022-00529-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 12/15/2022]
Abstract
The COVID-19 pandemic is now approaching 2 years old, with more than 440 million people infected and nearly six million dead worldwide, making it the most significant pandemic since the 1918 influenza pandemic. The severity and significance of SARS-CoV-2 was recognized immediately upon discovery, leading to innumerable companies and institutes designing and generating vaccines and therapeutic antibodies literally as soon as recombinant SARS-CoV-2 spike protein sequence was available. Within months of the pandemic start, several antibodies had been generated, tested, and moved into clinical trials, including Eli Lilly's bamlanivimab and etesevimab, Regeneron's mixture of imdevimab and casirivimab, Vir's sotrovimab, Celltrion's regdanvimab, and Lilly's bebtelovimab. These antibodies all have now received at least Emergency Use Authorizations (EUAs) and some have received full approval in select countries. To date, more than three dozen antibodies or antibody combinations have been forwarded into clinical trials. These antibodies to SARS-CoV-2 all target the receptor-binding domain (RBD), with some blocking the ability of the RBD to bind human ACE2, while others bind core regions of the RBD to modulate spike stability or ability to fuse to host cell membranes. While these antibodies were being discovered and developed, new variants of SARS-CoV-2 have cropped up in real time, altering the antibody landscape on a moving basis. Over the past year, the search has widened to find antibodies capable of neutralizing the wide array of variants that have arisen, including Alpha, Beta, Gamma, Delta, and Omicron. The recent rise and dominance of the Omicron family of variants, including the rather disparate BA.1 and BA.2 variants, demonstrate the need to continue to find new approaches to neutralize the rapidly evolving SARS-CoV-2 virus. This review highlights both convalescent plasma- and polyclonal antibody-based approaches as well as the top approximately 50 antibodies to SARS-CoV-2, their epitopes, their ability to bind to SARS-CoV-2 variants, and how they are delivered. New approaches to antibody constructs, including single domain antibodies, bispecific antibodies, IgA- and IgM-based antibodies, and modified ACE2-Fc fusion proteins, are also described. Finally, antibodies being developed for palliative care of COVID-19 disease, including the ramifications of cytokine release syndrome (CRS) and acute respiratory distress syndrome (ARDS), are described.
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Affiliation(s)
| | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Sciences Center, Houston, TX USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Sciences Center, Houston, TX USA
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76
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Renaudineau Y, Abravanel F, Izopet J, Bost C, Treiner E, Congy N, Blancher A. Novel T cell interferon gamma release assay (IGRA) using spike recombinant protein for COVID19 vaccine response and Nucleocapsid for SARS-Cov2 response. Clin Immunol 2022; 237:108979. [PMID: 35301104 PMCID: PMC8920083 DOI: 10.1016/j.clim.2022.108979] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 02/08/2022] [Accepted: 03/08/2022] [Indexed: 01/04/2023]
Abstract
We explored the performance of a whole blood interferon gamma release assay (IGRA) based on the stimulation of SARS-Cov2-specific T cells by purified recombinant proteins. Twenty volunteers vaccinated with BNT162b2 were selected first for T cell response evaluation using an in-house IGRA, a commercial IGRA, and ELISpot showing a S2 > S1 poly-epitopic response. Next, 64 vaccinated and 103 non-vaccinated individuals were tested for humoral and T cell response (IGRA-Spike/-nucleocapsid recombinant proteins). Following the second vaccine injection, humoral (100%) and IGRA-Spike T cell (95.3%) responses took place irrespective of sex, age, and vaccine type. The humoral response declined first, followed by IGRA-Spike T cell response after the second vaccine injection. Altogether, this study confirms the utility of the IGRA-Spike/-nucleocapsid assay to complement serology in COVID19 vaccinated individuals and those who have recovered from SARS-Cov2.
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Affiliation(s)
- Yves Renaudineau
- Immunology department laboratory, Institut Fédératif de Biologie, Toulouse University Hospital Center, France,INFINITy, Toulouse Institute for Infectious and Inflammatory Diseases, INSERM U1291, CNRS U5051, University Toulouse III, Toulouse, France,Corresponding authors at: Institut Fédératif de Biologie, Laboratoire d'immunologie, CHU Purpan, 330 avenue de Grande Bretagne, 31000 Toulouse, France
| | - Florence Abravanel
- INFINITy, Toulouse Institute for Infectious and Inflammatory Diseases, INSERM U1291, CNRS U5051, University Toulouse III, Toulouse, France,Virology department laboratory, Institut Fédératif de Biologie, Toulouse University Hospital Center, France
| | - Jacques Izopet
- INFINITy, Toulouse Institute for Infectious and Inflammatory Diseases, INSERM U1291, CNRS U5051, University Toulouse III, Toulouse, France,Virology department laboratory, Institut Fédératif de Biologie, Toulouse University Hospital Center, France
| | - Chloé Bost
- Immunology department laboratory, Institut Fédératif de Biologie, Toulouse University Hospital Center, France,INFINITy, Toulouse Institute for Infectious and Inflammatory Diseases, INSERM U1291, CNRS U5051, University Toulouse III, Toulouse, France
| | - Emmanuel Treiner
- Immunology department laboratory, Institut Fédératif de Biologie, Toulouse University Hospital Center, France,INFINITy, Toulouse Institute for Infectious and Inflammatory Diseases, INSERM U1291, CNRS U5051, University Toulouse III, Toulouse, France
| | - Nicolas Congy
- Immunology department laboratory, Institut Fédératif de Biologie, Toulouse University Hospital Center, France
| | - Antoine Blancher
- Immunology department laboratory, Institut Fédératif de Biologie, Toulouse University Hospital Center, France,INFINITy, Toulouse Institute for Infectious and Inflammatory Diseases, INSERM U1291, CNRS U5051, University Toulouse III, Toulouse, France,Corresponding authors at: Institut Fédératif de Biologie, Laboratoire d'immunologie, CHU Purpan, 330 avenue de Grande Bretagne, 31000 Toulouse, France
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77
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Mehmood A, Nawab S, Wang Y, Chandra Kaushik A, Wei DQ. Discovering potent inhibitors against the Mpro of the SARS-CoV-2. A medicinal chemistry approach. Comput Biol Med 2022; 143:105235. [PMID: 35123137 PMCID: PMC8789387 DOI: 10.1016/j.compbiomed.2022.105235] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 11/17/2022]
Abstract
The global pandemic caused by a single-stranded RNA (ssRNA) virus known as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still at its peak, with new cases being reported daily. Although the vaccines have been administered on a massive scale, the frequent mutations in the viral gene and resilience of the future strains could be more problematic. Therefore, new compounds are always needed to be available for therapeutic approaches. We carried out the present study to discover potential drug compounds against the SARS-CoV-2 main protease (Mpro). A total of 16,000 drug-like small molecules from the ChemBridge database were virtually screened to obtain the top hits. As a result, 1032 hits were selected based on their docking scores. Next, these structures were prepared for molecular docking, and each small molecule was docked into the active site of the Mpro. Only compounds with solid interactions with the active site residues and the highest docking score were subjected to molecular dynamics (MD) simulation. The post-simulation analyses were carried out using the in-built GROMACS tools to gauge the stability, flexibility, and compactness. Principal component analysis (PCA) and hydrogen bonding were also calculated to observe trends and affinity of the drugs towards the target. Among the five top compounds, C1, C3, and C6 revealed strong interaction with the target's active site and remained highly stable throughout the simulation. We believe the predicted compounds in this study could be potential inhibitors in the natural system and can be utilized in designing therapeutic strategies against the SARS-CoV-2.
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Affiliation(s)
- Aamir Mehmood
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; Peng Cheng Laboratory, Shenzhen, Guangdong, 518055, China
| | - Sadia Nawab
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, PR China
| | - Yanjing Wang
- Engineering Research Center of Cell & Therapeutic Antibody , School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Aman Chandra Kaushik
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; Peng Cheng Laboratory, Shenzhen, Guangdong, 518055, China.
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78
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Noorabad Ghahroodi F, Khalili S, Rasaee MJ. Recombinant subunits of SARS‐CoV‐2 spike protein as vaccine candidates to elicit neutralizing antibodies. J Clin Lab Anal 2022; 36:e24328. [PMID: 35349744 PMCID: PMC9102496 DOI: 10.1002/jcla.24328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/24/2022] [Accepted: 02/07/2022] [Indexed: 11/30/2022] Open
Abstract
Objectives The spike protein has been reported as one of the most critical targets for vaccine design strategies against the SARS‐CoV‐2 infection. Hence, we have designed, produced, and evaluated the potential use of three truncated recombinant proteins derived from spike protein as vaccine candidates capable of neutralizing SARS‐CoV‐2 virus. Methods In silico tools were used to design spike‐based subunit recombinant proteins (RBD (P1), fusion peptide (P2), and S1/S2 cleavage site (P3)). These proteins were checked for their ability to be identified by the anti‐SARS‐CoV‐2 antibodies by exposing them to COVID‐19 serum samples. The proteins were also injected into mice and rabbit, and the antibody titers were measured for 390 days to assess their neutralization efficiency. Results The antibodies that existed in the serum of COVID‐19 patients were identified by designed proteins. The anti‐spike antibody titer was increased in the animals injected with recombinant proteins. The VNT results revealed that the produced antibodies could neutralize the cultured live virus. Conclusion Truncated subunit vaccines could also be considered as robust tools for effective vaccination against COVID‐19. Using a combination of in silico, in vitro, and in vivo experiments, it was shown that the injection of spike‐based truncated recombinant proteins could stimulate long‐lasting and neutralizing antibody responses.
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Affiliation(s)
- Faezeh Noorabad Ghahroodi
- Department of Clinical Biochemistry Faculty of Medical Sciences Tarbiat Modares University Tehran Iran
| | - Saeed Khalili
- Department of Biology Sciences Shahid Rajaee Teacher Training University Tehran Iran
| | - Mohammad Javad Rasaee
- Department of Clinical Biochemistry Faculty of Medical Sciences Tarbiat Modares University Tehran Iran
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Lubinski B, Frazier LE, Phan MV, Bugembe DL, Cunningham JL, Tang T, Daniel S, Cotten M, Jaimes JA, Whittaker GR. Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.06.30.450632. [PMID: 34230931 PMCID: PMC8259907 DOI: 10.1101/2021.06.30.450632] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The African continent like all other parts of the world with high infection/low vaccination rates can, and will, be a source of novel SARS-CoV-2 variants. The A.23 viral lineage, characterized by three spike mutations F157L, V367F and Q613H, was first identified in COVID-19 cases from a Ugandan prison in July 2020, and then was identified in the general population with additional spike mutations (R102I, L141F, E484K and P681R) to comprise lineage A.23.1 by September 2020, with this virus being designated a variant of interest (VOI) in Africa and with subsequent spread to 26 other countries. The P681R spike substitution of the A.23.1 VOI is of note as it increases the number of basic residues in the sub-optimal SARS-CoV-2 spike protein furin cleavage site; as such, this substitution may affect viral replication, transmissibility or pathogenic properties. The same P681R substitution has also appeared in B.1.617 variants, including B.1.617.2 (Delta). Here, we performed assays using fluorogenic peptides mimicking the S1/S2 sequence from A.23.1 and B.1.617.2 and observed significantly increased cleavability with furin, compared to sequences derived from the original Wuhan-Hu1 S1/S2. We performed functional infectivity assays using pseudotyped MLV particles harboring SARS-CoV-2 spike proteins and observed an increase in transduction for A.23.1-pseudotyped particles compared to Wuhan-Hu-1 in Vero-TMPRSS2 and Calu-3 cells (with a presumed early entry pathway), although lowered infection in Vero E6 cells (with a presumed late entry pathway). However, these changes in infectivity were not reproduced in the original Wuhan-Hu-1 spike bearing only the P681R substitution. Our findings suggest that while A.23.1 has increased furin-mediated cleavage linked to the P681R substitution, which may affect viral infection and transmissibility, this substitution alone is not sufficient and needs to occur on the background of other spike protein changes to enable its full functional consequences.
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Affiliation(s)
- Bailey Lubinski
- Graduate Program in Biological & Biomedical Sciences, Cornell University, Ithaca, NY, 14853, USA
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Laura E. Frazier
- Graduate Program in Biological & Biomedical Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - My V.T. Phan
- MRC/UVRI & London School of Hygiene and Tropical Medicine – Uganda Research Unit, Entebbe, Uganda
| | - Daniel L. Bugembe
- MRC/UVRI & London School of Hygiene and Tropical Medicine – Uganda Research Unit, Entebbe, Uganda
| | - Jessie L. Cunningham
- Graduate Program in Biological & Biomedical Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Tiffany Tang
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Susan Daniel
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew Cotten
- MRC/UVRI & London School of Hygiene and Tropical Medicine – Uganda Research Unit, Entebbe, Uganda
- MRC Centre of Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Javier A. Jaimes
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gary R. Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Master of Public Health Program, Cornell University, Ithaca, NY, 14853, USA
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van der Straten K, van Gils MJ, de Taeye SW, de Bree GJ. Optimization of Anti-SARS-CoV-2 Neutralizing Antibody Therapies: Roadmap to Improve Clinical Effectiveness and Implementation. FRONTIERS IN MEDICAL TECHNOLOGY 2022; 4:867982. [PMID: 35419561 PMCID: PMC8996231 DOI: 10.3389/fmedt.2022.867982] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/07/2022] [Indexed: 12/11/2022] Open
Abstract
One of the major breakthroughs to combat the current Coronavirus Disease 2019 (COVID-19) pandemic has been the development of highly effective vaccines against the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Still, alternatives are needed for individuals who are at high risk of developing severe COVID-19 and are not protected by vaccination. Monoclonal antibodies against the spike protein of SARS-CoV-2 have been shown to be effective as prophylaxis and treatment against COVID-19. However, the emergence of variants of concern (VOCs) challenges the efficacy of antibody therapies. This review describes the neutralization resistance of the clinically-approved monoclonal antibody therapies against the Alpha (B.1.1.7), Beta (B.1.351), Gamma (P1), Delta (B.1.617.2), and the Omicron (B.1.1.529) variants. To guide the development of monoclonal antibody therapies and to anticipate on the continuous evolution of SARS-CoV-2, we highlight different strategies to broaden the antibody activity by targeting more conserved epitopes and/or simultaneously targeting multiple sites of vulnerability of the virus. This review further describes the contribution of antibody Fc effector functions to optimize the antibody efficacy. In addition, the main route of SARS-CoV-2 antibody administration is currently intravenously and dictates a monthly injection when used as prophylactic. Therefore, we discusses the concept of long-acting antibodies (LAABs) and non-intravenously routes of antibody administration in order to broaden the clinical applicability of antibody therapies.
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Affiliation(s)
- Karlijn van der Straten
- Department of Medical Microbiology and Infection Prevention, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Internal Medicine, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Marit J. van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Steven W. de Taeye
- Department of Medical Microbiology and Infection Prevention, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Godelieve J. de Bree
- Department of Internal Medicine, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- *Correspondence: Godelieve J. de Bree
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81
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Manandhar S, Pai KSR, Krishnamurthy PT, Kiran AVVVR, Kumari GK. Identification of novel TMPRSS2 inhibitors against SARS-CoV-2 infection: a structure-based virtual screening and molecular dynamics study. Struct Chem 2022; 33:1529-1541. [PMID: 35345416 PMCID: PMC8941836 DOI: 10.1007/s11224-022-01921-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/13/2022] [Indexed: 12/27/2022]
Abstract
The scientific insights gained from the severe acute respiratory syndrome (SARS) and the middle east respiratory syndrome (MERS) outbreaks are helping scientists to fast-track the antiviral drug discovery process against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Coronaviruses, as well as influenza viruses, depend on host type 2 transmembrane serine protease, TMPRSS2, for entry and propagation in the human cell. Recent studies show that SARS-CoV-2 also uses TMPRSS2 for its cell entry. In the present study, a structure-based virtual screening of 52,337, protease ligands downloaded from the Zinc database was carried out against the homology model of TMPRSS2 protein followed by the molecular dynamics-based simulation to identify potential TMPRSS2 hits. The virtual screening has identified 13 hits with a docking score range of -10.447 to -9.863 and glide energy range of -60.737 to -40.479 kcal/mol. The binding mode analysis shows that the hit molecules form H-bond (Asp180, Gly184 & Gly209), Pi-Pi stacking (His41), and salt bridge (Asp180) type of contacts with the active site residues of TMPRSS2. In the MD simulation of ZINC000013444414, ZINC000137976768, and ZINC000143375720 hits show that these molecules form a stable complex with TMPRSS2. The complex equilibrates well with a minimal RMSD and RMSF fluctuation. All three structures, as predicted in Glide XP docking, show a prominent interaction with the Asp180, Gly184, Gly209, and His41. Further, MD simulation also identifies a notable H-bond interaction with Ser181 for all three hits. Among these hits, ZINC000143375720 shows the most stable binding interaction with TMPRSS2. The present study is successful in identifying TMPRSS2 ligands from zinc data base for a possible application in the treatment of COVID-19.
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Affiliation(s)
- Suman Manandhar
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576 104 India
| | - K Sreedhara Ranganath Pai
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576 104 India
| | - Praveen T Krishnamurthy
- Department of Pharmacology, JSS College of Pharmacy (JSS Academy of Higher Education & Research), Ooty, The Nilgiris, 643 001 Tamil Nadu India
| | - Ammu V V V Ravi Kiran
- Department of Pharmacology, JSS College of Pharmacy (JSS Academy of Higher Education & Research), Ooty, The Nilgiris, 643 001 Tamil Nadu India
| | - Garikapati Kusuma Kumari
- Department of Pharmacology, JSS College of Pharmacy (JSS Academy of Higher Education & Research), Ooty, The Nilgiris, 643 001 Tamil Nadu India
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82
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Khuntia BK, Sharma V, Wadhawan M, Chhabra V, Kidambi B, Rathore S, Agrawal A, Ram A, Qazi S, Ahmad S, Raza K, Sharma G. Antiviral Potential of Indian Medicinal Plants Against Influenza and SARS-CoV: A Systematic Review. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221086988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The COVID-19 pandemic has posed a significant threat to human health due to the lack of drugs that can potentially act against SARS-CoV -2. Also, even after the emergency approval of WHO, the vaccines’ efficacy is still a question, and people are getting reinfections. Previous studies have demonstrated the efficacy of traditional medicinal plants against influenza and SARS coronavirus. The present article aims to review potential phytochemicals from Indian medicinal plants that may be used against SARS-CoV-2. Articles published in the English language between 1992 and 2021 were retrieved from Embase, PubMed, and Google scholar using relevant keywords, and the scientific literature on efficacies of Indian medicinal plants against SARS-CoV and influenza virus were analyzed. The initial search revealed 1304 studies, but, on subsequent screening, 115 eligible studies were reported. Twenty research articles investigating traditional medicinal plant extracts and metabolites against SARS-CoV and influenza A virus in in vitro and in vivo systems satisfied the search criteria. The studies reported that plant extracts and active compounds such as glycyrrhizin, 14-α-lipoyl andrographolide, and curcumin from medicinal plants such as Yashtimadhu ( Glycyrrhiza glabra), Bhunimba ( Andrographis paniculata), and Haridra ( Curcuma longa) are effective against the various phases of the virus life cycle, viz., virus-host cell attachment, viral replication, 3CL protease activity, neuraminidase activity, adsorption and penetration of the virus. As per ancient Indian literature, plants in Ayurveda possess Rasayana (revitalizing) and Jwara hara (antipyretic, anti-inflammatory) properties. This evidence may be used to conduct experimental and clinical trials to study the underlying mechanisms and efficacy of antiviral properties of Indian medicinal plants against SARS-CoV-2.
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Affiliation(s)
- Bharat Krushna Khuntia
- Centre for Integrative Medicine and Research (CIMR), All India Institute of MedicalSciences (AIIMS), New Delhi, India
| | - Vandna Sharma
- Centre for Integrative Medicine and Research (CIMR), All India Institute of MedicalSciences (AIIMS), New Delhi, India
| | - Mohit Wadhawan
- Centre for Integrative Medicine and Research (CIMR), All India Institute of MedicalSciences (AIIMS), New Delhi, India
| | - Varun Chhabra
- Centre for Integrative Medicine and Research (CIMR), All India Institute of MedicalSciences (AIIMS), New Delhi, India
| | - Bharatraj Kidambi
- Department of Cardiology, Centre for Integrative Medicine and Research, All India Institute of Medical Sciences, New Delhi, India
| | - Shubhangi Rathore
- Centre for Integrative Medicine and Research (CIMR), All India Institute of MedicalSciences (AIIMS), New Delhi, India
| | - Aman Agrawal
- Centre for Integrative Medicine and Research (CIMR), All India Institute of MedicalSciences (AIIMS), New Delhi, India
| | - Amirtha Ram
- Centre for Integrative Medicine and Research (CIMR), All India Institute of MedicalSciences (AIIMS), New Delhi, India
| | - Sahar Qazi
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Shaban Ahmad
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Gautam Sharma
- Department of Cardiology, Centre for Integrative Medicine and Research, All India Institute of Medical Sciences, New Delhi, India
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83
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Kastenhuber ER, Mercadante M, Nilsson-Payant B, Johnson JL, Jaimes JA, Muecksch F, Weisblum Y, Bram Y, Whittaker GR, tenOever BR, Schwartz RE, Chandar V, Cantley L. Coagulation factors directly cleave SARS-CoV-2 spike and enhance viral entry. eLife 2022; 11:77444. [PMID: 35294338 PMCID: PMC8942469 DOI: 10.7554/elife.77444] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Coagulopathy is a significant aspect of morbidity in COVID-19 patients. The clotting cascade is propagated by a series of proteases, including factor Xa and thrombin. While certain host proteases, including TMPRSS2 and furin, are known to be important for cleavage activation of SARS-CoV-2 spike to promote viral entry in the respiratory tract, other proteases may also contribute. Using biochemical and cell-based assays, we demonstrate that factor Xa and thrombin can also directly cleave SARS-CoV-2 spike, enhancing infection at the stage of viral entry. Coagulation factors increased SARS-CoV-2 infection in human lung organoids. A drug-repurposing screen identified a subset of protease inhibitors that promiscuously inhibited spike cleavage by both transmembrane serine proteases and coagulation factors. The mechanism of the protease inhibitors nafamostat and camostat may extend beyond inhibition of TMPRSS2 to coagulation-induced spike cleavage. Anticoagulation is critical in the management of COVID-19, and early intervention could provide collateral benefit by suppressing SARS-CoV-2 viral entry. We propose a model of positive feedback whereby infection-induced hypercoagulation exacerbates SARS-CoV-2 infectivity.
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Affiliation(s)
| | - Marisa Mercadante
- Department of Medicine, Weill Cornell Medical College, New York, United States
| | - Benjamin Nilsson-Payant
- Institute of Experimental Virology, TWINCORE Zentrum für Experimentelle und Klinische Infektionsforschung GmbH, Hannover, Germany
| | - Jared L Johnson
- Department of Medicine, Weill Cornell Medical College, New York, United States
| | - Javier A Jaimes
- Department of Microbiology and Immunology, Cornell University, Ithaca, United States
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, United States
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, United States
| | - Yaron Bram
- Department of Medicine, Weill Cornell Medicine, New York, United States
| | - Gary R Whittaker
- Department of Microbiology and Immunology, Cornell University, Ithaca, United States
| | - Benjamin R tenOever
- Department of Microbiology, New York University Langone Medical Center, New York, United States
| | - Robert E Schwartz
- Department of Medicine, Weill Cornell Medicine, New York, United States
| | - Vasuretha Chandar
- Department of Medicine, Weill Cornell Medicine, New York, United States
| | - Lewis Cantley
- Department of Medicine, Weill Cornell Medical College, New York, United States
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84
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Espinoza C, Alarcón M. The Immune Response to SARS-CoV-2: Mechanisms, Aging, Sequelae and Vaccines. Mini Rev Med Chem 2022; 22:2166-2185. [PMID: 35249484 DOI: 10.2174/1389557522666220304231537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/28/2021] [Accepted: 12/08/2021] [Indexed: 11/22/2022]
Abstract
This review seeks to clarify the factors involved in the various immune responses to SARS-CoV-2 infection and the mechanisms that influence the development of COVID-19 with severe evolution. The innate immune response that evolves against SARS-CoV-2 in a complex way is highlighted, integrating multiple pathways by coronaviruses to evade it, in addition to characterizing the adaptive immune response, which can lead to an effective immune response or can contribute to immunopathological imbalance. In turn, host-dependent biomarkers such as age, gender, ABO blood group, and risk factors that contribute to the critical and varied progress of COVID-19 immunopathogenesis were analyzed. Finally, the potential vaccine candidates are presented, capable of generating immune protection with humoral and/or cellular neutralizing responses, in favor of blocking and destroying both the new human coronavirus and its variants, which cause the current pandemic.
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Affiliation(s)
- Carolina Espinoza
- Department of Clinical Biochemistry and Immunohaematology, Faculty of Health Sciences, Universidad de Talca, Talca, Chile
- Thrombosis Research Center, Universidad de Talca, Talca, Chile
| | - Marcelo Alarcón
- Department of Clinical Biochemistry and Immunohaematology, Faculty of Health Sciences, Universidad de Talca, Talca, Chile
- Thrombosis Research Center, Universidad de Talca, Talca, Chile
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85
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Niehues RV, Wozniak J, Wiersch F, Lilienthal E, Tacken N, Schumertl T, Garbers C, Ludwig A, Düsterhöft S. The collectrin-like part of the SARS-CoV-1 and -2 receptor ACE2 is shed by the metalloproteinases ADAM10 and ADAM17. FASEB J 2022; 36:e22234. [PMID: 35199397 PMCID: PMC9111296 DOI: 10.1096/fj.202101521r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/04/2022] [Accepted: 02/14/2022] [Indexed: 12/13/2022]
Abstract
The transmembrane protease angiotensin converting enzyme 2 (ACE2) is a protective regulator within the renin angiotensin system and additionally represents the cellular receptor for SARS‐CoV. The release of soluble ACE2 (sACE2) from the cell surface is hence believed to be a crucial part of its (patho)physiological functions, as both, ACE2 protease activity and SARS‐CoV binding ability, are transferred from the cell membrane to body fluids. Yet, the molecular sources of sACE2 are still not completely investigated. In this study, we show different sources and prerequisites for the release of sACE2 from the cell membrane. By using inhibitors as well as CRISPR/Cas9‐derived cells, we demonstrated that, in addition to the metalloprotease ADAM17, also ADAM10 is an important novel shedding protease of ACE2. Moreover, we observed that ACE2 can also be released in extracellular vesicles. The degree of either ADAM10‐ or ADAM17‐mediated ACE2 shedding is dependent on stimulatory conditions and on the expression level of the pro‐inflammatory ADAM17 regulator iRhom2. Finally, by using structural analysis and in vitro verification, we determined for the first time that the susceptibility to ADAM10‐ and ADAM17‐mediated shedding is mediated by the collectrin‐like part of ACE2. Overall, our findings give novel insights into sACE2 release by several independent molecular mechanisms.
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Affiliation(s)
- Rabea Victoria Niehues
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Justyna Wozniak
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Florian Wiersch
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Eva Lilienthal
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Nikola Tacken
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Tim Schumertl
- Department of Pathology, Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Christoph Garbers
- Department of Pathology, Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Andreas Ludwig
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Stefan Düsterhöft
- Institute of Molecular Pharmacology, Medical Faculty, RWTH Aachen University, Aachen, Germany
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86
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Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a serious threat to global public health, underscoring the urgency of developing effective therapies. Therapeutics and, more specifically, direct-acting antiviral development are still very much in their infancy. Here, we report that two hepatitis C virus (HCV) fusion inhibitors identified in our previous study, dichlorcyclizine and fluoxazolevir, broadly block human coronavirus entry into various cell types. Both compounds were effective against various human-pathogenic CoVs in multiple assays based on vesicular stomatitis virus (VSV) pseudotyped with the spike protein and spike-mediated syncytium formation. The antiviral effects were confirmed in SARS-CoV-2 infection systems. These compounds were equally effective against recently emerged variants, including the delta variant. Cross-linking experiments and structural modeling suggest that the compounds bind to a hydrophobic pocket near the fusion peptide of S protein, consistent with their potential mechanism of action as fusion inhibitors. In summary, these fusion inhibitors have broad-spectrum antiviral activities and may be promising leads for treatment of SARS-CoV-2, its variants, and other pathogenic CoVs. IMPORTANCE SARS-CoV-2 is an enveloped virus that requires membrane fusion for entry into host cells. Since the fusion process is relatively conserved among enveloped viruses, we tested our HCV fusion inhibitors, dichlorcyclizine and fluoxazolevir, against SARS-CoV-2. We performed in vitro assays and demonstrated their effective antiviral activity against SARS-CoV-2 and its variants. Cross-linking experiments and structural modeling suggest that the compounds bind to a hydrophobic pocket in spike protein to exert their inhibitory effect on the fusion step. These data suggest that both dichlorcyclizine and fluoxazolevir are promising candidates for further development as treatment for SARS-CoV-2.
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87
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Capturing a Crucial ‘Disorder-to-Order Transition’ at the Heart of the Coronavirus Molecular Pathology—Triggered by Highly Persistent, Interchangeable Salt-Bridges. Vaccines (Basel) 2022; 10:vaccines10020301. [PMID: 35214759 PMCID: PMC8875383 DOI: 10.3390/vaccines10020301] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/27/2022] [Accepted: 02/05/2022] [Indexed: 02/05/2023] Open
Abstract
The COVID-19 origin debate has greatly been influenced by genome comparison studies of late, revealing the emergence of the Furin-like cleavage site at the S1/S2 junction of the SARS-CoV-2 Spike (FLCSSpike) containing its 681PRRAR685 motif, absent in other related respiratory viruses. Being the rate-limiting (i.e., the slowest) step, the host Furin cleavage is instrumental in the abrupt increase in transmissibility in COVID-19, compared to earlier onsets of respiratory viral diseases. In such a context, the current paper entraps a ‘disorder-to-order transition’ of the FLCSSpike (concomitant to an entropy arrest) upon binding to Furin. The interaction clearly seems to be optimized for a more efficient proteolytic cleavage in SARS-CoV-2. The study further shows the formation of dynamically interchangeable and persistent networks of salt-bridges at the Spike–Furin interface in SARS-CoV-2 involving the three arginines (R682, R683, R685) of the FLCSSpike with several anionic residues (E230, E236, D259, D264, D306) coming from Furin, strategically distributed around its catalytic triad. Multiplicity and structural degeneracy of plausible salt-bridge network archetypes seem to be the other key characteristic features of the Spike–Furin binding in SARS-CoV-2, allowing the system to breathe—a trademark of protein disorder transitions. Interestingly, with respect to the homologous interaction in SARS-CoV (2002/2003) taken as a baseline, the Spike–Furin binding events, generally, in the coronavirus lineage, seems to have preference for ionic bond formation, even with a lesser number of cationic residues at their potentially polybasic FLCSSpike patches. The interaction energies are suggestive of characteristic metastabilities attributed to Spike–Furin interactions, generally to the coronavirus lineage, which appears to be favorable for proteolytic cleavages targeted at flexible protein loops. The current findings not only offer novel mechanistic insights into the coronavirus molecular pathology and evolution, but also add substantially to the existing theories of proteolytic cleavages.
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88
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Zou J, Li L, Zheng P, Liang W, Hu S, Zhou S, Wang Y, Zhao J, Yuan D, Liu L, Wu D, Xu M, Zhang F, Zhu M, Wu Z, Cao X, Ni M, Ling X, Wu Y, Kuang Z, Hu M, Li J, Li X, Guo X, Xu T, Jiang H, Gao C, Yu M, Liu J, Zhong N, Zhou J, Huang JA, Jin T, He J. Ultrapotent neutralizing antibodies against SARS-CoV-2 with a high degree of mutation resistance. J Clin Invest 2022; 132:154987. [PMID: 35108220 PMCID: PMC8843702 DOI: 10.1172/jci154987] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/04/2022] [Indexed: 12/16/2022] Open
Abstract
Many SARS-CoV-2 neutralizing antibodies (nAbs) lose potency against variants of concern. In this study, we developed 2 strategies to produce mutation-resistant antibodies. First, a yeast library expressing mutant receptor binding domains (RBDs) of the spike protein was utilized to screen for potent nAbs that are least susceptible to viral escape. Among the candidate antibodies, P5-22 displayed ultrahigh potency for virus neutralization as well as an outstanding mutation resistance profile. Additionally, P14-44 and P15-16 were recognized as mutation-resistant antibodies with broad betacoronavirus neutralization properties. P15-16 has only 1 binding hotspot, which is K378 in the RBD of SARS-CoV-2. The crystal structure of the P5-22, P14-44, and RBD ternary complex clarified the unique mechanisms that underlie the excellent mutation resistance profiles of these antibodies. Secondly, polymeric IgG enhanced antibody avidity by eliminating P5-22’s only hotspot, residue F486 in the RBD, thereby potently blocking cell entry by mutant viruses. Structural and functional analyses of antibodies screened using both potency assays and the yeast RBD library revealed rare, ultrapotent, mutation-resistant nAbs against SARS-CoV-2.
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Affiliation(s)
- Jia Zou
- Guangzhou Laboratory, Guangzhou International Biotech Island, Guangzhou, China.,Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Li Li
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Peiyi Zheng
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wenhua Liang
- Guangzhou Laboratory, Guangzhou International Biotech Island, Guangzhou, China
| | - Siyi Hu
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Shuaixiang Zhou
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Yanqun Wang
- Guangzhou Laboratory, Guangzhou International Biotech Island, Guangzhou, China.,State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jincun Zhao
- Guangzhou Laboratory, Guangzhou International Biotech Island, Guangzhou, China.,State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Daopeng Yuan
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Lu Liu
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Dongdong Wu
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Mengqiu Xu
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Fangfang Zhang
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Mengzhu Zhu
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Zhihai Wu
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Xiaochao Cao
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Meng Ni
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Xiaomin Ling
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Yue Wu
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Zhihui Kuang
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Moyan Hu
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Jianfeng Li
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Xue Li
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Xiling Guo
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Tianmin Xu
- Department of Infectious Diseases, The Third People's Hospital of Changzhou, Changzhou, China
| | - Haiping Jiang
- Department of Medical Oncology, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Changshou Gao
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Michael Yu
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Junjian Liu
- Innovent Biologics (Suzhou) Co., Ltd., Suzhou, Jiangsu, China
| | - Nanshan Zhong
- Guangzhou Laboratory, Guangzhou International Biotech Island, Guangzhou, China.,State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Guangzhou Institute of Respiratory Health, Guangzhou, China
| | - Jianfeng Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jian-An Huang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Tengchuan Jin
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Jianxing He
- Guangzhou Laboratory, Guangzhou International Biotech Island, Guangzhou, China.,Guangzhou Institute of Respiratory Health, Guangzhou, China.,Department of Thoracic Oncology and Surgery, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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89
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Brazaca LC, Imamura AH, Gomes NO, Almeida MB, Scheidt DT, Raymundo-Pereira PA, Oliveira ON, Janegitz BC, Machado SAS, Carrilho E. Electrochemical immunosensors using electrodeposited gold nanostructures for detecting the S proteins from SARS-CoV and SARS-CoV-2. Anal Bioanal Chem 2022; 414:5507-5517. [PMID: 35169906 PMCID: PMC8853172 DOI: 10.1007/s00216-022-03956-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/29/2022] [Accepted: 02/01/2022] [Indexed: 12/29/2022]
Abstract
This paper reports the development of a low-cost (< US$ 0.03 per device) immunosensor based on gold-modified screen-printed carbon electrodes (SPCEs). As a proof of concept, the immunosensor was tested for a fast and sensitive determination of S proteins from both SARS-CoV and SARS-CoV-2, by a single disposable device. Gold nanoparticles were electrochemically deposited via direct reduction of gold ions on the electrode using amperometry. Capture antibodies from spike (S) protein were covalently immobilized on carboxylic groups of self-assembled monolayers (SAM) of mercaptoacetic acid (MAA) attached to the gold nanoparticles. Label-free detection of S proteins from both SARS-CoV and SARS-CoV-2 was performed with electrochemical impedance spectroscopy (EIS). The immunosensor fabricated with 9 s gold deposition had a high performance in terms of selectivity, sensitivity, and low limit of detection (LOD) (3.16 pmol L-1), thus permitting the direct determination of the target proteins in spiked saliva samples. The complete analysis can be carried out within 35 min using a simple one-step assay protocol with small sample volumes (10 µL). With such features, the immunoplatform presented here can be deployed for mass testing in point-of-care settings.
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Affiliation(s)
- Laís Canniatti Brazaca
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, 13566-590, Brazil. .,Instituto Nacional de Ciência e Tecnologia de Bioanalítica-INCTBio, Campinas, SP, 13083-970, Brazil.
| | - Amanda Hikari Imamura
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, 13566-590, Brazil.,Instituto Nacional de Ciência e Tecnologia de Bioanalítica-INCTBio, Campinas, SP, 13083-970, Brazil
| | - Nathalia Oezau Gomes
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, 13566-590, Brazil
| | - Mariana Bortholazzi Almeida
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, 13566-590, Brazil.,Instituto Nacional de Ciência e Tecnologia de Bioanalítica-INCTBio, Campinas, SP, 13083-970, Brazil
| | - Desirée Tamara Scheidt
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, 13566-590, Brazil.,Instituto Nacional de Ciência e Tecnologia de Bioanalítica-INCTBio, Campinas, SP, 13083-970, Brazil
| | | | - Osvaldo N Oliveira
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, 13566-590, Brazil
| | - Bruno Campos Janegitz
- Departamento de Ciências da Natureza, Matemática e Educação, Universidade Federal de São Carlos, Araras, SP, 13600-970, Brazil
| | | | - Emanuel Carrilho
- Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, 13566-590, Brazil. .,Instituto Nacional de Ciência e Tecnologia de Bioanalítica-INCTBio, Campinas, SP, 13083-970, Brazil.
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90
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Staufer O, Gupta K, Hernandez Bücher JE, Kohler F, Sigl C, Singh G, Vasileiou K, Yagüe Relimpio A, Macher M, Fabritz S, Dietz H, Cavalcanti Adam EA, Schaffitzel C, Ruggieri A, Platzman I, Berger I, Spatz JP. Synthetic virions reveal fatty acid-coupled adaptive immunogenicity of SARS-CoV-2 spike glycoprotein. Nat Commun 2022; 13:868. [PMID: 35165285 PMCID: PMC8844029 DOI: 10.1038/s41467-022-28446-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/24/2022] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 infection is a major global public health concern with incompletely understood pathogenesis. The SARS-CoV-2 spike (S) glycoprotein comprises a highly conserved free fatty acid binding pocket (FABP) with unknown function and evolutionary selection advantage1,2. Deciphering FABP impact on COVID-19 progression is challenged by the heterogenous nature and large molecular variability of live virus. Here we create synthetic minimal virions (MiniVs) of wild-type and mutant SARS-CoV-2 with precise molecular composition and programmable complexity by bottom-up assembly. MiniV-based systematic assessment of S free fatty acid (FFA) binding reveals that FABP functions as an allosteric regulatory site enabling adaptation of SARS-CoV-2 immunogenicity to inflammation states via binding of pro-inflammatory FFAs. This is achieved by regulation of the S open-to-close equilibrium and the exposure of both, the receptor binding domain (RBD) and the SARS-CoV-2 RGD motif that is responsible for integrin co-receptor engagement. We find that the FDA-approved drugs vitamin K and dexamethasone modulate S-based cell binding in an FABP-like manner. In inflammatory FFA environments, neutralizing immunoglobulins from human convalescent COVID-19 donors lose neutralization activity. Empowered by our MiniV technology, we suggest a conserved mechanism by which SARS-CoV-2 dynamically couples its immunogenicity to the host immune response. Staufer et al. provide a protocol for preparation of synthetic minimal virions (MiniV) of SARS-CoV-2, mimicking viral structure and allowing for precise investigation of receptor binding mechanism. They find that the highly conserved free fatty acid binding pocket (FABP) can function as an allosteric regulator, enabling adaptation of immunogenicity via binding of proinflammatory free fatty acids and mediating the spike open to-closed equilibrium.
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91
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Mansy SS, AbouSamra MM. Electron microscopy overview of SARS-COV2 and its clinical impact. Ultrastruct Pathol 2022; 46:1-17. [PMID: 35139747 DOI: 10.1080/01913123.2022.2035475] [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: 10/19/2022]
Abstract
Research centers around the world are competing to develop therapeutic and prophylactic agents to provide new intervention strategies that could halt or even help slow the progression of the COVID19 pandemic. This requires a deep understanding of the biology and cytopathology of the interaction of SARS-CoV-2 with the cell. This review highlights the importance of electron microscopy (EM) in better understanding the morphology, the subcellular morphogenesis, and pathogenesis of SARS-CoV-2, given its nanometric dimensions. The study also underscores the value of cryo-electron microscopy for analyzing the structure of viral protein complex at atomic resolution in its native state and the development of novel antibodies, vaccines, and therapies targeting the trimeric S spike proteins and the viral replication organelles. This review highlighted the emergence in a short period of time of several viral variants of concern with enhanced transmissibility and increased infectivity. This is due to the elevated affinity of the host receptor with acquired adaptive mutations in the spike protein gene of the virus.Subsequently, to the technical improvement of EM resolutions and the recent promising results with SARS-CoV2 variant structure determination, antibodies production, and vaccine development, it is necessary to maximize our investigations regarding the potential occurrence of immune pressure and viral adaptation secondary to repeated infection and vaccination.
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Affiliation(s)
- Soheir Saiid Mansy
- Electron Microscopy Research Department, Theodor Bilharz Research Institute, Egypt
| | - Mona Mahmoud AbouSamra
- Pharmaceutical Technology Department, Pharmaceutical and Drug Industries Institute, National Research Centre, Cairo, Egypt
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92
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Ghorbani A, Samarfard S, Jajarmi M, Bagheri M, Karbanowicz TP, Afsharifar A, Eskandari MH, Niazi A, Izadpanah K. Highlight of potential impact of new viral genotypes of SARS-CoV-2 on vaccines and anti-viral therapeutics. GENE REPORTS 2022; 26:101537. [PMID: 35128175 PMCID: PMC8808475 DOI: 10.1016/j.genrep.2022.101537] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/10/2021] [Accepted: 12/02/2021] [Indexed: 12/23/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of the coronavirus disease (COVID-19) pandemic, has infected millions of people globally. Genetic variation and selective pressures lead to the accumulation of single nucleotide polymorphism (SNP) within the viral genome that may affect virulence, transmission rate, viral recognition and the efficacy of prophylactic and interventional measures. To address these concerns at the genomic level, we assessed the phylogeny and SNPs of the SARS-CoV-2 mutant population collected to date in Iran in relation to globally reported variants. Phylogenetic analysis of mutant strains revealed the occurrence of the variants known as B.1.1.7 (Alpha), B.1.525 (Eta), and B.1.617 (Delta) that appear to have delineated independently in Iran. SNP analysis of the Iranian sequences revealed that the mutations were predominantly positioned within the S protein-coding region, with most SNPs localizing to the S1 subunit. Seventeen S1-localizing SNPs occurred in the RNA binding domain that interacts with ACE2 of the host cell. Importantly, many of these SNPs are predicted to influence the binding of antibodies and anti-viral therapeutics, indicating that the adaptive host response appears to be imposing a selective pressure that is driving the evolution of the virus in this closed population through enhancing virulence. The SNPs detected within these mutant cohorts are addressed with respect to current prophylactic measures and therapeutic interventions.
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Key Words
- ACE2, Angiotensin-converting enzyme 2
- Antiviral drugs
- Bioinformatics
- CSSE, Center for Systems Science and Engineering
- E, Envelope
- FP, Fusion peptide
- HR1, Heptad repeat 1
- HR2, Heptad repeat 2
- IC, Intracellular domain
- JHU, Johns Hopkins University
- M, Membrane
- Mutation detection
- N, Nucleocapsid
- NAG, N-acetylglucosamine
- NSP, Non-structural proteins
- NTD, N-terminal domain
- Phylogenetic analysis
- RBD, Receptor-binding domain
- S, Spike glycoprotein
- SARS-CoV-2
- SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2;
- SD1, Subdomain 1
- SD2, Subdomain 2
- SNP, Single nucleotide polymorphism
- SP, Structural proteins
- TM, Transmembrane region
- UTRs, Untranslated regions
- Viral vaccines
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Affiliation(s)
- Abozar Ghorbani
- Plant Virology Research Centre, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Samira Samarfard
- Berrimah Veterinary Laboratory, Department of Primary Industry and Resources, Berrimah, NT 0828 Australia
| | - Maziar Jajarmi
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mahboube Bagheri
- Department of Food Science and Technology, Bardsir Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | | | - Alireza Afsharifar
- Plant Virology Research Centre, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Mohammad Hadi Eskandari
- Department of Food Science and Technology, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Ali Niazi
- Institute of Biotechnology, College of Agriculture, Shiraz University, Shiraz, Iran
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93
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Butnariu AB, Look A, Grillo M, Tabish TA, McGarvey MJ, Pranjol MZI. SARS-CoV-2-host cell surface interactions and potential antiviral therapies. Interface Focus 2022; 12:20200081. [PMID: 34956606 PMCID: PMC8662392 DOI: 10.1098/rsfs.2020.0081] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 10/13/2021] [Indexed: 12/13/2022] Open
Abstract
In this review, we reveal the latest developments at the interface between SARS-CoV-2 and the host cell surface. In particular, we evaluate the current and potential mechanisms of binding, fusion and the conformational changes of the spike (S) protein to host cell surface receptors, especially the human angiotensin-converting enzyme 2 (ACE2) receptor. For instance, upon the initial attachment, the receptor binding domain of the S protein forms primarily hydrogen bonds with the protease domain of ACE2 resulting in conformational changes within the secondary structure. These surface interactions are of paramount importance and have been therapeutically exploited for antiviral design, such as monoclonal antibodies. Additionally, we provide an insight into novel therapies that target viral non-structural proteins, such as viral RNA polymerase. An example of which is remdesivir which has now been approved for use in COVID-19 patients by the US Food and Drug Administration. Establishing further understanding of the molecular details at the cell surface will undoubtably aid the development of more efficacious and selectively targeted therapies to reduce the burden of COVID-19.
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Affiliation(s)
| | - Alex Look
- School of Life Sciences, University of Sussex, Falmer, UK
| | - Marta Grillo
- School of Life Sciences, University of Sussex, Falmer, UK
| | - Tanveer A. Tabish
- Faculty of Engineering, Department of Materials, Royal School of Mines, Imperial College London, London, UK
| | - Michael J. McGarvey
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
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94
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Sarubbo F, El Haji K, Vidal-Balle A, Bargay Lleonart J. Neurological consequences of COVID-19 and brain related pathogenic mechanisms: A new challenge for neuroscience. Brain Behav Immun Health 2022; 19:100399. [PMID: 34870247 PMCID: PMC8629776 DOI: 10.1016/j.bbih.2021.100399] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 12/15/2022] Open
Abstract
Due to the infection by the SARS-CoV-2 virus (COVID-19) there were also reported neurological symptoms, being the most frequent and best cited those that affect the cerebrovascular, sensorial, cognitive and motor functions, together with the neurological diffuse symptoms as for examples headache or dizziness. Besides, some of them behave high risk of mortality. Consequently, it is crucial to elucidate the mechanisms of action in brain of SARS-CoV-2 virus in order to create new therapeutic targets to fight against this new disease. Since now the mechanisms of arrival to the brain seems to be related with the following processes: blood brain barrier (BBB) disruption together with nervous or axonal transport of the virus by the trigeminal nerve, the vagus nerve, or the brain-gut-axis. Being two the mechanisms of brain affectation most cited: a direct affectation of the virus in the brain through neuroinvasion and an indirect mechanism of action due to the effects of the systemic infection. Both processes include the triggering of inflammation, hypoxia and the increased likelihood of secondary infections. This topic supposes a major novel challenge for neuroscience. Therefore, the aim of this review is to provide summarized information about the neurological symptomatology and the brain pathogenic mechanisms involved and reported in COVID-19.
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Affiliation(s)
- Fiorella Sarubbo
- Research Unit, University Hospital Son Llàtzer, Health Research Institute of the Balearic Islands (IdISBa), Crta, Manacor Km 4, 07198, Palma, Spain
- University of the Balearic Islands (UIB), Biology Department, Mallorca, Spain
- University of the Balearic Islands (UIB), Medicine Faculty, Mallorca, Spain
| | - Khaoulah El Haji
- Research Unit, University Hospital Son Llàtzer, Health Research Institute of the Balearic Islands (IdISBa), Crta, Manacor Km 4, 07198, Palma, Spain
| | - Aina Vidal-Balle
- Research Unit, University Hospital Son Llàtzer, Health Research Institute of the Balearic Islands (IdISBa), Crta, Manacor Km 4, 07198, Palma, Spain
| | - Joan Bargay Lleonart
- Research Unit, University Hospital Son Llàtzer, Health Research Institute of the Balearic Islands (IdISBa), Crta, Manacor Km 4, 07198, Palma, Spain
- University of the Balearic Islands (UIB), Medicine Faculty, Mallorca, Spain
- Hematology Department, University Hospital Son Llàtzer, Crta, Manacor Km 4, 07198, Palma, Spain
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95
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Parra-Lucares A, Segura P, Rojas V, Pumarino C, Saint-Pierre G, Toro L. Emergence of SARS-CoV-2 Variants in the World: How Could This Happen? Life (Basel) 2022; 12:194. [PMID: 35207482 PMCID: PMC8879166 DOI: 10.3390/life12020194] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic has had a significant global impact, with more than 280,000,000 people infected and 5,400,000 deaths. The use of personal protective equipment and the anti-SARS-CoV-2 vaccination campaigns have reduced infection and death rates worldwide. However, a recent increase in infection rates has been observed associated with the appearance of SARS-CoV-2 variants, including the more recently described lineage B.1.617.2 (Delta variant) and lineage B.1.1.529/BA.1 (Omicron variant). These new variants put the effectiveness of international vaccination at risk, with the appearance of new outbreaks of COVID-19 throughout the world. This emergence of new variants has been due to multiple predisposing factors, including molecular characteristics of the virus, geographic and environmental conditions, and the impact of social determinants of health that favor the genetic diversification of SARS-CoV-2. We present a literature review on the most recent information available on the emergence of new variants of SARS-CoV-2 in the world. We analyzed the biological, geographical, and sociocultural factors that favor the development of these variants. Finally, we evaluate the surveillance strategies for the early detection of new variants and prevent their distribution outside these regions.
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Affiliation(s)
- Alfredo Parra-Lucares
- Division of Critical Care Medicine, Department of Medicine, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile; (A.P.-L.); (V.R.)
| | - Paula Segura
- Department of Anatomic Pathology, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile;
| | - Verónica Rojas
- Division of Critical Care Medicine, Department of Medicine, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile; (A.P.-L.); (V.R.)
- Centro de Investigación Clínica Avanzada, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile
| | - Catalina Pumarino
- School of Medicine, Faculty of Medicine, Universidad de Chile, 8380456 Santiago, Chile;
| | - Gustavo Saint-Pierre
- Microbiology Unit, Clinical Laboratory, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile;
| | - Luis Toro
- Centro de Investigación Clínica Avanzada, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile
- Division of Nephrology, Department of Medicine, Hospital Clínico Universidad de Chile, 8380456 Santiago, Chile
- Critical Care Unit, Clínica Las Condes, 7591047 Santiago, Chile
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96
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Lubinski B, Fernandes MH, Frazier L, Tang T, Daniel S, Diel DG, Jaimes JA, Whittaker GR. Functional evaluation of the P681H mutation on the proteolytic activation of the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. iScience 2022; 25:103589. [PMID: 34909610 PMCID: PMC8662955 DOI: 10.1016/j.isci.2021.103589] [Citation(s) in RCA: 95] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/15/2021] [Accepted: 12/07/2021] [Indexed: 12/27/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent causing the COVID-19 pandemic. SARS-CoV-2 B.1.1.7 (Alpha), a WHO variant of concern first identified in the United Kingdom in late 2020, contains several mutations including P681H in the spike S1/S2 cleavage site, which is predicted to increase cleavage by furin, potentially impacting the viral cell entry. Here, we studied the role of the P681H mutation in B.1.1.7 cell entry. We performed assays using fluorogenic peptides mimicking the Wuhan-Hu-1 and B.1.1.7 S1/S2 sequence and observed no significant difference in furin cleavage. Functional assays using pseudoparticles harboring SARS-CoV-2 spikes and cell-to-cell fusion assays demonstrated no differences between Wuhan-Hu-1, B.1.1.7, or a P681H point mutant. Likewise, we observed no differences in viral growth between USA-WA1/2020 and a B.1.1.7 isolate in cell culture. Our findings suggest that, although the B.1.1.7 P681H mutation may slightly increase S1/S2 cleavage, this does not significantly impact viral entry or cell-cell spread.
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Affiliation(s)
- Bailey Lubinski
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, 618 Tower Road, Ithaca, NY 14853, USA
| | - Maureen H.V. Fernandes
- Department of Population Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Laura Frazier
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, 618 Tower Road, Ithaca, NY 14853, USA
| | - Tiffany Tang
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Susan Daniel
- Robert Frederick Smith School of Chemical & Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Diego G. Diel
- Department of Population Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Javier A. Jaimes
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, 618 Tower Road, Ithaca, NY 14853, USA
| | - Gary R. Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, 618 Tower Road, Ithaca, NY 14853, USA
- Master of Public Health Program, Cornell University, Ithaca, NY 14853, USA
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97
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Abstract
The spike protein (S-protein) of SARS-CoV-2, the protein that enables the virus to infect human cells, is the basis for many vaccines and a hotspot of concerning virus evolution. Here, we discuss the outstanding progress in structural characterization of the S-protein and how these structures facilitate analysis of virus function and evolution. We emphasize the differences in reported structures and that analysis of structure-function relationships is sensitive to the structure used. We show that the average residue solvent exposure in nearly complete structures is a good descriptor of open vs closed conformation states. Because of structural heterogeneity of functionally important surface-exposed residues, we recommend using averages of a group of high-quality protein structures rather than a single structure before reaching conclusions on specific structure-function relationships. To illustrate these points, we analyze some significant chemical tendencies of prominent S-protein mutations in the context of the available structures. In the discussion of new variants, we emphasize the selectivity of binding to ACE2 vs prominent antibodies rather than simply the antibody escape or ACE2 affinity separately. We note that larger chemical changes, in particular increased electrostatic charge or side-chain volume of exposed surface residues, are recurring in mutations of concern, plausibly related to adaptation to the negative surface potential of human ACE2. We also find indications that the fixated mutations of the S-protein in the main variants are less destabilizing than would be expected on average, possibly pointing toward a selection pressure on the S-protein. The richness of available structures for all of these situations provides an enormously valuable basis for future research into these structure-function relationships.
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Affiliation(s)
- Rukmankesh Mehra
- Department of Chemistry, Indian Institute
of Technology Bhilai, Sejbahar, Raipur 492015, Chhattisgarh,
India
| | - Kasper P. Kepp
- DTU Chemistry, Technical University of
Denmark, Building 206, 2800 Kongens Lyngby,
Denmark
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98
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Ranjbar M, Asadi M, Nourigorji M, Sarkari B, Mostafavi‐Pour Z, Zomorodian K, Shabaninejad Z, Taheri‐Anganeh M, Maleksabet A, Moghadami M, Savardashtaki A. Development of a recombinant nucleocapsid protein-based ELISA for the detection of IgM and IgG antibodies to SARS-CoV-2. Biotechnol Appl Biochem 2022; 69:2592-2598. [PMID: 34965611 PMCID: PMC9011413 DOI: 10.1002/bab.2308] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/19/2021] [Indexed: 12/27/2022]
Abstract
Coronavirus 2019 (COVID-19) is a global concern for public health. Thus, early and accurate diagnosis is a critical step in management of this infectious disease. Currently, RT-PCR is routine diagnosis test for COVID-19, but it has some limitations and false negative results. enzyme-linked immunosorbent assay (ELISA) against SARS-CoV-2 antigens seems to be an appropriate approach for serodiagnosis of COVID-19. In the current study, an ELISA system, using a recombinant nucleocapsid (N) protein, was developed for the detection of IgM and IgG antibodies to SARS-CoV-2. The related protein was expressed, purified, and used in an ELISA system. Sera samples (67) for COVID-19 patients, as well as sera samples from healthy volunteers (112), along with sera samples from non-COVID-19 patients were examined by the ELISA system. The expression and purity of the recombinant N protein were approved by SDS-PAGE and Western blotting. The sensitivity of ELISA system was 91.04 and 92.53% for the detection of IgG and IgM antibodies, respectively. Moreover, the specificity of the developed ELISA system for IgG and IgM were 98.21 and 97.32%, respectively. Our developed ELISA system showed satisfactory sensitivity and specificity for the detection of antiSARS-CoV-2 IgM and IgG antibodies and could be used as a complementary approach for proper diagnosis of COVID-19.
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Affiliation(s)
- Maryam Ranjbar
- Department of Medical Biotechnology, School of Advanced Medical Sciences and TechnologiesShiraz University of Medical SciencesShirazIran
| | - Marzieh Asadi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and TechnologiesShiraz University of Medical SciencesShirazIran
| | - Marjan Nourigorji
- Health Research InstituteBabol University of Medical SciencesBabolIran
| | - Bahador Sarkari
- Department of Parasitology and Mycology, School of MedicineShiraz University of Medical SciencesShirazIran,Basic Sciences in Infectious Diseases Research CenterShiraz University of Medical SciencesShirazIran
| | - Zohreh Mostafavi‐Pour
- Recombinant Protein Laboratory, Department of Biochemistry, School of MedicineShiraz University of Medical SciencesShirazIran,Autophagy Research CenterShiraz University of Medical SciencesShirazIran
| | - Kamiar Zomorodian
- Department of Parasitology and Mycology, School of MedicineShiraz University of Medical SciencesShirazIran,Basic Sciences in Infectious Diseases Research CenterShiraz University of Medical SciencesShirazIran
| | - Zahra Shabaninejad
- Department of Nanobiotechnology, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran,Pharmaceutical Sciences Research CenterShiraz University of Medical SciencesShirazIran
| | - Mortaza Taheri‐Anganeh
- Department of Medical Biotechnology, School of Advanced Medical Sciences and TechnologiesShiraz University of Medical SciencesShirazIran
| | - Amir Maleksabet
- Department of Medical Biotechnology, School of Advanced Technologies in MedicineMazandaran University of Medical SciencesSariIran
| | - Mohsen Moghadami
- Department of Internal Medicine, School of MedicineShiraz University of Medical SciencesShirazIran,Health Policy Research CenterShiraz University of Medical SciencesShirazIran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and TechnologiesShiraz University of Medical SciencesShirazIran,Infertility Research CenterShiraz University of Medical SciencesShirazIran
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99
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Escobedo RA, Kaushal D, Singh DK. Insights Into the Changing Landscape of Coronavirus Disease 2019. Front Cell Infect Microbiol 2022; 11:761521. [PMID: 35083164 PMCID: PMC8784834 DOI: 10.3389/fcimb.2021.761521] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a highly contagious, infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which emerged in late 2019 in Wuhan China. A year after the World Health Organization declared COVID-19 a global pandemic, over 215 million confirmed cases and approximately 5 million deaths have been reported worldwide. In this multidisciplinary review, we summarize important insights for COVID-19, ranging from its origin, pathology, epidemiology, to clinical manifestations and treatment. More importantly, we also highlight the foundational connection between genetics and the development of personalized medicine and how these aspects have an impact on disease treatment and management in the dynamic landscape of this pandemic.
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Affiliation(s)
- Ruby A. Escobedo
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
- The Integrated Biomedical Sciences (IBMS) Graduate Program, University of Texas Health Sciences Center at San Antonio, San Antonio, TX, United States
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Dhiraj K. Singh
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
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Mutational landscape and in silico structure models of SARS-CoV-2 spike receptor binding domain reveal key molecular determinants for virus-host interaction. BMC Mol Cell Biol 2022; 23:2. [PMID: 34991443 PMCID: PMC8736301 DOI: 10.1186/s12860-021-00403-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 12/23/2021] [Indexed: 12/15/2022] Open
Abstract
Background SARS-CoV-2, the causative agent of COVID-19 pandemic is a RNA virus prone to mutations. Formation of a stable binding interface between the Receptor Binding Domain (RBD) of SARS-CoV-2 Spike (S) protein and Angiotensin-Converting Enzyme 2 (ACE2) of host is pivotal for viral entry. RBD has been shown to mutate frequently during pandemic. Although, a few mutations in RBD exhibit enhanced transmission rates leading to rise of new variants of concern, most RBD mutations show sustained ACE2 binding and virus infectivity. Yet, how all these mutations make the binding interface constantly favourable for virus remain enigmatic. This study aims to delineate molecular rearrangements in the binding interface of SARS-CoV-2 RBD mutants. Results Here, we have generated a mutational and structural landscape of SARS-CoV-2 RBD in first six months of the pandemic. We analyzed 31,403 SARS-CoV-2 genomes randomly across the globe, and identified 444 non-synonymous mutations in RBD that cause 49 distinct amino acid substitutions in contact and non-contact amino acid residues. Molecular phylogenetic analysis suggested independent emergence of RBD mutants. Structural mapping of these mutations on the SARS-CoV-2 Wuhan reference strain RBD and structural comparison with RBDs from bat-CoV, SARS-CoV, and pangolin-CoV, all bound to human or mouse ACE2, revealed several changes in the interfacial interactions in all three binding clusters. Interestingly, interactions mediated via N487 residue in cluster-I and Y449, G496, T500, G502 residues in cluster-III remained largely unchanged in all RBD mutants. Further analysis showed that these interactions are evolutionarily conserved in sarbecoviruses which use ACE2 for entry. Importantly, despite extensive changes in the interface, RBD-ACE2 stability and binding affinities were maintained in all the analyzed mutants. Taken together, these findings reveal how SARS-CoV-2 uses its RBD residues to constantly remodel the binding interface. Conclusion Our study broadly signifies understanding virus-host binding interfaces and their alterations during pandemic. Our findings propose a possible interface remodelling mechanism used by SARS-CoV-2 to escape deleterious mutations. Future investigations will focus on functional validation of in-silico findings and on investigating interface remodelling mechanisms across sarbecoviruses. Thus, in long run, this study may provide novel clues to therapeutically target RBD-ACE2 interface for pan-sarbecovirus infections. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-021-00403-4.
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