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Popovic M, Pantović Pavlović M, Pavlović M. Ghosts of the past: Elemental composition, biosynthesis reactions and thermodynamic properties of Zeta P.2, Eta B.1.525, Theta P.3, Kappa B.1.617.1, Iota B.1.526, Lambda C.37 and Mu B.1.621 variants of SARS-CoV-2. MICROBIAL RISK ANALYSIS 2023; 24:100263. [PMID: 37234934 PMCID: PMC10199755 DOI: 10.1016/j.mran.2023.100263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/07/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023]
Abstract
From the perspectives of molecular biology, genetics and biothermodynamics, SARS-CoV-2 is the among the best characterized viruses. Research on SARS-CoV-2 has shed a new light onto driving forces and molecular mechanisms of viral evolution. This paper reports results on empirical formulas, biosynthesis reactions and thermodynamic properties of biosynthesis (multiplication) for the Zeta P.2, Eta B.1.525, Theta P.3, Kappa B.1.617.1, Iota B.1.526, Lambda C.37 and Mu B.1.621 variants of SARS-CoV-2. Thermodynamic analysis has shown that the physical driving forces for evolution of SARS-CoV-2 are Gibbs energy of biosynthesis and Gibbs energy of binding. The driving forces have led SARS-CoV-2 through the evolution process from the original Hu-1 to the newest variants in accordance with the expectations of the evolution theory.
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Affiliation(s)
- Marko Popovic
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, 11000 Belgrade, Serbia
| | - Marijana Pantović Pavlović
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, 11000 Belgrade, Serbia
- University of Belgrade, Centre of Excellence in Chemistry and Environmental Engineering - ICTM, Belgrade, Serbia
| | - Miroslav Pavlović
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, 11000 Belgrade, Serbia
- University of Belgrade, Centre of Excellence in Chemistry and Environmental Engineering - ICTM, Belgrade, Serbia
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Gomari MM, Tarighi P, Choupani E, Abkhiz S, Mohamadzadeh M, Rostami N, Sadroddiny E, Baammi S, Uversky VN, Dokholyan NV. Structural evolution of Delta lineage of SARS-CoV-2. Int J Biol Macromol 2023; 226:1116-1140. [PMID: 36435470 PMCID: PMC9683856 DOI: 10.1016/j.ijbiomac.2022.11.227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
One of the main obstacles in prevention and treatment of COVID-19 is the rapid evolution of the SARS-CoV-2 Spike protein. Given that Spike is the main target of common treatments of COVID-19, mutations occurring at this virulent factor can affect the effectiveness of treatments. The B.1.617.2 lineage of SARS-CoV-2, being characterized by many Spike mutations inside and outside of its receptor-binding domain (RBD), shows high infectivity and relative resistance to existing cures. Here, utilizing a wide range of computational biology approaches, such as immunoinformatics, molecular dynamics (MD), analysis of intrinsically disordered regions (IDRs), protein-protein interaction analyses, residue scanning, and free energy calculations, we examine the structural and biological attributes of the B.1.617.2 Spike protein. Furthermore, the antibody design protocol of Rosetta was implemented for evaluation the stability and affinity improvement of the Bamlanivimab (LY-CoV55) antibody, which is not capable of interactions with the B.1.617.2 Spike. We observed that the detected mutations in the Spike of the B1.617.2 variant of concern can cause extensive structural changes compatible with the described variation in immunogenicity, secondary and tertiary structure, oligomerization potency, Furin cleavability, and drug targetability. Compared to the Spike of Wuhan lineage, the B.1.617.2 Spike is more stable and binds to the Angiotensin-converting enzyme 2 (ACE2) with higher affinity.
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Affiliation(s)
- Mohammad Mahmoudi Gomari
- Student Research Committee, Iran University of Medical Sciences, Tehran 1449614535, Iran,Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Parastoo Tarighi
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Edris Choupani
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Shadi Abkhiz
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Masoud Mohamadzadeh
- Department of Chemistry, Faculty of Sciences, University of Hormozgan, Bandar Abbas 7916193145, Iran
| | - Neda Rostami
- Department of Chemical Engineering, Faculty of Engineering, Arak University, Arak 3848177584, Iran
| | - Esmaeil Sadroddiny
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran 1417613151, Iran
| | - Soukayna Baammi
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir 43150, Morocco
| | - 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 33620, USA,Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia,Correspondence to: V.N. Uversky, Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA
| | - Nikolay V. Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 16802, USA,Corresponding author
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Sriwijitalai W, Wiwanitkit V. Reactive synovitis of the knee joint and COVID-19 vaccination: Commentary. Int J Rheum Dis 2023; 26:168. [PMID: 36263659 PMCID: PMC9874906 DOI: 10.1111/1756-185x.14461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 01/27/2023]
Affiliation(s)
| | - Viroj Wiwanitkit
- Joseph Ayobabalola UniversityIkeji‐ArakejiNigeria,Dr DY Patil UniversityPuneIndia,Hainan Medical UniversityHaikouChina,Faculty of MedicineUniversity of NisNisSerbia,Department of Eastern MedicineGovernment College University FaisalabadFaisalabadPakistan
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Alexopoulou L. Nucleic acid-sensing toll-like receptors: Important players in Sjögren’s syndrome. Front Immunol 2022; 13:980400. [PMID: 36389822 PMCID: PMC9659959 DOI: 10.3389/fimmu.2022.980400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/12/2022] [Indexed: 11/30/2022] Open
Abstract
Sjögren’s syndrome (SS) is a chronic systemic autoimmune disease that affects the salivary and lacrimal glands, as well as other organ systems like the lungs, kidneys and nervous system. SS can occur alone or in combination with another autoimmune disease, such as systemic lupus erythematosus (SLE) or rheumatoid arthritis. The etiology of SS is unknown but recent studies have revealed the implication of the activation of innate immune receptors, including Toll-like receptors (TLRs), mainly through the detection of endogenous nucleic acids, in the pathogenesis of systemic autoimmune diseases. Studies on SS mouse models suggest that TLRs and especially TLR7 that detects single-stranded RNA of microbial or endogenous origin can drive the development of SS and findings in SS patients corroborate those in mouse models. In this review, we will give an overview of the function and signaling of nucleic acid-sensing TLRs, the interplay of TLR7 with TLR8 and TLR9 in the context of autoimmunity, summarize the evidence for the critical role of TLR7 in the pathogenesis of SS and present a possible connection between SARS-CoV-2 and SS.
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Design and Analysis of Highly Sensitive LSPR-Based Metal–Insulator–Metal Nano-Discs as a Biosensor for Fast Detection of SARS-CoV-2. PHOTONICS 2022. [DOI: 10.3390/photonics9080542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
For over 2 years, the coronavirus has been the most urgent challenge to humanity, and the development of rapid and accurate detection methods is crucial to control these viruses. Here, a 3D FDTD simulation of Au/SiO2/Au metal–insulator–metal (MIM) nanostructures as a biosensor was performed. The strong coupling between the two plasmonic interfaces in the Au/SiO2/Au cavity helped us to obtain relatively higher sensitivity. The attachment of SARS-CoV-2 changed the refractive index, which was used to detect SARS-CoV-2. Due to the higher overlapping of plasmonic mode with the environment of nano-discs, a higher sensitivity of 312.8 nm/RIU was obtained. The peak wavelength of the proposed structure shifted by approximately 47 nm when the surrounding medium refractive index changed from 1.35 (no binding) to 1.5 (full binding). Consequently, the SPR peak intensity variation can be used as another sensing mechanism to detect SARS-CoV-2. Finally, the previously reported refractive index changes for various concentrations of the SARS-CoV-2 S-glycoprotein solution were used to evaluate the performance of the designed biosensor.
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Iliescu FS, Ionescu AM, Gogianu L, Simion M, Dediu V, Chifiriuc MC, Pircalabioru GG, Iliescu C. Point-of-Care Testing-The Key in the Battle against SARS-CoV-2 Pandemic. MICROMACHINES 2021; 12:1464. [PMID: 34945314 PMCID: PMC8708595 DOI: 10.3390/mi12121464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 12/11/2022]
Abstract
The deleterious effects of the coronavirus disease 2019 (COVID-19) pandemic urged the development of diagnostic tools to manage the spread of disease. Currently, the "gold standard" involves the use of quantitative real-time polymerase chain reaction (qRT-PCR) for SARS-CoV-2 detection. Even though it is sensitive, specific and applicable for large batches of samples, qRT-PCR is labour-intensive, time-consuming, requires trained personnel and is not available in remote settings. This review summarizes and compares the available strategies for COVID-19: serological testing, Point-of-Care Testing, nanotechnology-based approaches and biosensors. Last but not least, we address the advantages and limitations of these methods as well as perspectives in COVID-19 diagnostics. The effort is constantly focused on understanding the quickly changing landscape of available diagnostic testing of COVID-19 at the clinical levels and introducing reliable and rapid screening point of care testing. The last approach is key to aid the clinical decision-making process for infection control, enhancing an appropriate treatment strategy and prompt isolation of asymptomatic/mild cases. As a viable alternative, Point-of-Care Testing (POCT) is typically low-cost and user-friendly, hence harbouring tremendous potential for rapid COVID-19 diagnosis.
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Affiliation(s)
- Florina Silvia Iliescu
- National Institute for Research and Development in Microtechnologies, IMT-Bucharest, 077190 Bucharest, Romania; (F.S.I.); (A.M.I.); (L.G.); (M.S.); (V.D.)
| | - Ana Maria Ionescu
- National Institute for Research and Development in Microtechnologies, IMT-Bucharest, 077190 Bucharest, Romania; (F.S.I.); (A.M.I.); (L.G.); (M.S.); (V.D.)
- Department of Biochemical Engineering, University College London, Bernard Katz Building, London WC1E 6BT, UK
| | - Larisa Gogianu
- National Institute for Research and Development in Microtechnologies, IMT-Bucharest, 077190 Bucharest, Romania; (F.S.I.); (A.M.I.); (L.G.); (M.S.); (V.D.)
| | - Monica Simion
- National Institute for Research and Development in Microtechnologies, IMT-Bucharest, 077190 Bucharest, Romania; (F.S.I.); (A.M.I.); (L.G.); (M.S.); (V.D.)
| | - Violeta Dediu
- National Institute for Research and Development in Microtechnologies, IMT-Bucharest, 077190 Bucharest, Romania; (F.S.I.); (A.M.I.); (L.G.); (M.S.); (V.D.)
| | - Mariana Carmen Chifiriuc
- Research Institute of University of Bucharest, University of Bucharest, 050095 Bucharest, Romania;
- The Romanian Academy, 25, Calea Victoriei, Sector 1, 010071 Bucharest, Romania
| | | | - Ciprian Iliescu
- National Institute for Research and Development in Microtechnologies, IMT-Bucharest, 077190 Bucharest, Romania; (F.S.I.); (A.M.I.); (L.G.); (M.S.); (V.D.)
- Academy of Romanian Scientists, 010071 Bucharest, Romania
- Faculty of Applied Chemistry and Material Science, University “Politehnica” of Bucharest, 011061 Bucharest, Romania
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Gudowska-Sawczuk M, Mroczko B. The Role of Neuropilin-1 (NRP-1) in SARS-CoV-2 Infection: Review. J Clin Med 2021; 10:2772. [PMID: 34202613 PMCID: PMC8267897 DOI: 10.3390/jcm10132772] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 12/14/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), discovered in 2019, is responsible for the global coronavirus disease 19 (COVID-19) pandemic. The main protein that interacts with the host cell receptor is the Spike-1 (S1) subunit of the coronavirus. This subunit binds with receptors present on the host cell membrane. It has been identified from several studies that neuropilin-1 (NRP-1) is one of the co-receptors for SARS-CoV-2 entry. Therefore, in this review, we focus on the significance of NRP-1 in SARS-CoV-2 infection. MEDLINE/PubMed database was used for a search of available literature. In the current review, we report that NRP-1 plays many important functions, including angiogenesis, neuronal development, and the regulation of immune responses. Additionally, the presence of this glycoprotein on the host cell membrane significantly augments the infection and spread of SARS-CoV-2. Literature data suggest that NRP-1 facilitates entry of the virus into the central nervous system through the olfactory epithelium of the nasal cavity. Moreover, published findings show that interfering with VEGF-A/NRP-1 using NRP-1 inhibitors may produce an analgesic effect. The review describes an association between NRP-1, SARS-CoV-2 and, inter alia, pathological changes in the retina. Based on the published findings, we suggest that NRP-1 is a very important mediator implicated in, inter alia, neurological manifestations of SARS-CoV-2 infection. Additionally, it appears that the use of NRP-1 inhibitors is a promising therapeutic strategy for the treatment of SARS-CoV-2 infection.
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Affiliation(s)
- Monika Gudowska-Sawczuk
- Department of Biochemical Diagnostics, Medical University of Bialystok, Waszyngtona 15A St., 15-269 Bialystok, Poland
| | - Barbara Mroczko
- Department of Biochemical Diagnostics, Medical University of Bialystok, Waszyngtona 15A St., 15-269 Bialystok, Poland
- Department of Neurodegeneration Diagnostics, Medical University of Bialystok, Waszyngtona 15A St., 15-269 Bialystok, Poland
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Signorini C, Pignatti P, Coccini T. How Do Inflammatory Mediators, Immune Response and Air Pollution Contribute to COVID-19 Disease Severity? A Lesson to Learn. Life (Basel) 2021; 11:182. [PMID: 33669011 PMCID: PMC7996623 DOI: 10.3390/life11030182] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/16/2021] [Accepted: 02/21/2021] [Indexed: 02/07/2023] Open
Abstract
Inflammatory and immune processes are defensive mechanisms that aim to remove harmful agents. As a response to infections, inflammation and immune response contribute to the pathophysiological mechanisms of diseases. Coronavirus disease 2019 (COVID-19), whose underlying mechanisms remain not fully elucidated, has posed new challenges for the knowledge of pathophysiology. Chiefly, the inflammatory process and immune response appear to be unique features of COVID-19 that result in developing a hyper-inflammatory syndrome, and air pollution, the world's largest health risk factor, may partly explain the behaviour and fate of COVID-19. Understanding the mechanisms involved in the progression of COVID-19 is of fundamental importance in order to avoid the late stage of the disease, associated with a poor prognosis. Here, the role of the inflammatory and immune mediators in COVID-19 pathophysiology is discussed.
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Affiliation(s)
- Cinzia Signorini
- Department of Molecular and Developmental Medicine, University of Siena, Via Aldo Moro, 53100 Siena, Italy
| | - Patrizia Pignatti
- Allergy and Immunology Unit, Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy;
| | - Teresa Coccini
- Laboratory of Clinical and Experimental Toxicology, Pavia Poison Centre, National Toxicology Information Centre, Toxicology Unit, Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy;
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