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Duarte T, Omage FB, Rieder GS, Rocha JBT, Dalla Corte CL. Investigating SARS-CoV-2 virus-host interactions and mRNA expression: Insights using three models of D. melanogaster. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167324. [PMID: 38925484 DOI: 10.1016/j.bbadis.2024.167324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/22/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
Responsible for COVID-19, SARS-CoV-2 is a coronavirus in which contagious variants continue to appear. Therefore, some population groups have demonstrated greater susceptibility to contagion and disease progression. For these reasons, several researchers have been studying the SARS-CoV-2/human interactome to understand the pathophysiology of COVID-19 and develop new pharmacological strategies. D. melanogaster is a versatile animal model with approximately 90 % human protein orthology related to SARS-CoV-2/human interactome and is widely used in metabolic studies. In this context, our work assessed the potential interaction between human proteins (ZNF10, NUP88, BCL2L1, UBC9, and RBX1) and their orthologous proteins in D. melanogaster (gl, Nup88, Buffy, ubc9, and Rbx1a) with proteins from SARS-CoV-2 (nsp3, nsp9, E, ORF7a, N, and ORF10) using computational approaches. Our results demonstrated that all the proteins have the potential to interact, and we compared the binding sites between humans and fruit flies. The stability and consistency in the structure of the gl_nsp3 complex, specifically, could be crucial for its specific biological functions. Lastly, to enhance the understanding of the influence of host factors on coronavirus infection, we also analyse the mRNA expression of the five genes (mbo, gl, lwr, Buffy, and Roc1a) responsible for encoding the fruit fly proteins. Briefly, we demonstrated that those genes were differentially regulated according to diets, sex, and age. Two groups showed higher positive gene regulation than others: females in the HSD group and males in the aging group, which could imply a higher virus-host susceptibility. Overall, while preliminary, our work contributes to the understanding of host defense mechanisms and potentially identifies candidate proteins and genes for in vivo viral studies against SARS-CoV-2.
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Affiliation(s)
- Tâmie Duarte
- Laboratory of Experimental Biochemistry and Toxicology, Department of Biochemistry and Molecular Biology, Center of Natural and Exact Sciences, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil; Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil
| | - Folorunsho Bright Omage
- Biological Chemistry Laboratory, Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, SP, Brazil; Computational Biology Research Group, Embrapa Agricultural Informatics, Campinas, SP, Brazil
| | - Guilherme Schmitt Rieder
- Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil
| | - João B T Rocha
- Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil
| | - Cristiane Lenz Dalla Corte
- Laboratory of Experimental Biochemistry and Toxicology, Department of Biochemistry and Molecular Biology, Center of Natural and Exact Sciences, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil; Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil.
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Sultana N, Nagesha SN, Reddy CNL, Ramesh BN, Shyamalamma S, Shashidhara KS, Satish KM, Pradeep C, Vidyadhar GD. Computational analysis of affinity dynamics between the variants of SARS-CoV-2 spike protein (RBD) and human ACE-2 receptor. Virol J 2024; 21:88. [PMID: 38641844 PMCID: PMC11031966 DOI: 10.1186/s12985-024-02365-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/13/2024] [Indexed: 04/21/2024] Open
Abstract
The novel coronavirus SARS-CoV-2 resulted in a significant worldwide health emergency known as the COVID-19 pandemic. This crisis has been marked by the widespread of various variants, with certain ones causing notable apprehension. In this study, we harnessed computational techniques to scrutinize these Variants of Concern (VOCs), including various Omicron subvariants. Our approach involved the use of protein structure prediction algorithms and molecular docking techniques, we have investigated the effects of mutations within the Receptor Binding Domain (RBD) of SARS-CoV-2 and how these mutations influence its interactions with the human angiotensin-converting enzyme 2 (hACE-2) receptor. Further we have predicted the structural alterations in the RBD of naturally occurring SARS-CoV-2 variants using the tr-Rosetta algorithm. Subsequent docking and binding analysis employing HADDOCK and PRODIGY illuminated crucial interactions occurring at the Receptor-Binding Motif (RBM). Our findings revealed a hierarchy of increased binding affinity between the human ACE2 receptor and the various RBDs, in the order of wild type (Wuhan-strain) < Beta < Alpha < Gamma < Omicron-B.1.1.529 < Delta < Omicron-BA.2.12.1 < Omicron-BA.5.2.1 < Omicron-BA.1.1. Notably, Omicron-BA.1.1 demonstrated the highest binding affinity of -17.4 kcal mol-1 to the hACE2 receptor when compared to all the mutant complexes. Additionally, our examination indicated that mutations occurring in active residues of the Receptor Binding Domain (RBD) consistently improved the binding affinity and intermolecular interactions in all mutant complexes. Analysis of the differences among variants has laid a foundation for the structure-based drug design targeting the RBD region of SARS-CoV-2.
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Affiliation(s)
- Nishad Sultana
- Department of Plant Biotechnology, University of Agricultural Sciences, GKVK, Bangalore, 560 065, India
| | - S N Nagesha
- Department of Plant Biotechnology, College of Agriculture, Hassan, UAS, Bangalore, 573 225, India.
| | | | - B N Ramesh
- ICAR-PHT, UAS, GKVK, Bangalore, 560 065, India
| | - S Shyamalamma
- Department of Plant Biotechnology, University of Agricultural Sciences, GKVK, Bangalore, 560 065, India
| | - K S Shashidhara
- Department of Genetics and Plant Breeding, College of Agriculture, Hassan, UAS, Bangalore, 573 225, India
| | - K M Satish
- Department Biotechnology, KSNUAHS, Shivamogga, 577 412, India
| | - C Pradeep
- Department of Plant Biotechnology, University of Agricultural Sciences, GKVK, Bangalore, 560 065, India
| | - G D Vidyadhar
- Department of Plant Biotechnology, University of Agricultural Sciences, GKVK, Bangalore, 560 065, India
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Son L, Kost V, Maiorov V, Sukhov D, Arkhangelskaya P, Ivanov I, Kudryavtsev D, Siniavin A, Utkin Y, Kasheverov I. Efficient Expression in Leishmania tarentolae (LEXSY) of the Receptor-Binding Domain of the SARS-CoV-2 S-Protein and the Acetylcholine-Binding Protein from Lymnaea stagnalis. Molecules 2024; 29:943. [PMID: 38474455 DOI: 10.3390/molecules29050943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/31/2024] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
Leishmania tarentolae (LEXSY) system is an inexpensive and effective expression approach for various research and medical purposes. The stated advantages of this system are the possibility of obtaining the soluble product in the cytoplasm, a high probability of correct protein folding with a full range of post-translational modifications (including uniform glycosylation), and the possibility of expressing multi-subunit proteins. In this paper, a LEXSY expression system has been employed for obtaining the receptor binding domain (RBD) of the spike-protein of the SARS-CoV-2 virus and the homopentameric acetylcholine-binding protein (AChBP) from Lymnaea stagnalis. RBD is actively used to obtain antibodies against the virus and in various scientific studies on the molecular mechanisms of the interaction of the virus with host cell targets. AChBP represents an excellent structural model of the ligand-binding extracellular domain of all subtypes of nicotinic acetylcholine receptors (nAChRs). Both products were obtained in a soluble glycosylated form, and their structural and functional characteristics were compared with those previously described.
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Affiliation(s)
- Lina Son
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Vladimir Kost
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Valery Maiorov
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Dmitry Sukhov
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Polina Arkhangelskaya
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Igor Ivanov
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Denis Kudryavtsev
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Andrei Siniavin
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Ivanovsky Institute of Virology, N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Yuri Utkin
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Igor Kasheverov
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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Srivastava M, Dukeshire MR, Mir Q, Omoru OB, Manzourolajdad A, Janga SC. Experimental and computational methods for studying the dynamics of RNA-RNA interactions in SARS-COV2 genomes. Brief Funct Genomics 2024; 23:46-54. [PMID: 36752040 PMCID: PMC10799312 DOI: 10.1093/bfgp/elac050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/24/2022] [Accepted: 11/11/2022] [Indexed: 02/09/2023] Open
Abstract
Long-range ribonucleic acid (RNA)-RNA interactions (RRI) are prevalent in positive-strand RNA viruses, including Beta-coronaviruses, and these take part in regulatory roles, including the regulation of sub-genomic RNA production rates. Crosslinking of interacting RNAs and short read-based deep sequencing of resulting RNA-RNA hybrids have shown that these long-range structures exist in severe acute respiratory syndrome coronavirus (SARS-CoV)-2 on both genomic and sub-genomic levels and in dynamic topologies. Furthermore, co-evolution of coronaviruses with their hosts is navigated by genetic variations made possible by its large genome, high recombination frequency and a high mutation rate. SARS-CoV-2's mutations are known to occur spontaneously during replication, and thousands of aggregate mutations have been reported since the emergence of the virus. Although many long-range RRIs have been experimentally identified using high-throughput methods for the wild-type SARS-CoV-2 strain, evolutionary trajectory of these RRIs across variants, impact of mutations on RRIs and interaction of SARS-CoV-2 RNAs with the host have been largely open questions in the field. In this review, we summarize recent computational tools and experimental methods that have been enabling the mapping of RRIs in viral genomes, with a specific focus on SARS-CoV-2. We also present available informatics resources to navigate the RRI maps and shed light on the impact of mutations on the RRI space in viral genomes. Investigating the evolution of long-range RNA interactions and that of virus-host interactions can contribute to the understanding of new and emerging variants as well as aid in developing improved RNA therapeutics critical for combating future outbreaks.
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Affiliation(s)
- Mansi Srivastava
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
- Department of Biology, Indiana University, 1001 East 3 St, Bloomington, Indiana 47405, USA
| | - Matthew R Dukeshire
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
| | - Quoseena Mir
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
| | - Okiemute Beatrice Omoru
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
| | - Amirhossein Manzourolajdad
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
- Department of Computer Science, Colgate University, Hamilton, NY, USA
| | - Sarath Chandra Janga
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, Indiana 46202, USA
- Centre for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, Indiana 46202, USA
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Queirós-Reis L, Mesquita JR, Brancale A, Bassetto M. Exploring the Fatty Acid Binding Pocket in the SARS-CoV-2 Spike Protein - Confirmed and Potential Ligands. J Chem Inf Model 2023; 63:7282-7298. [PMID: 37991468 DOI: 10.1021/acs.jcim.3c00803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Severe Acute Respiratory syndrome 2 (SARS-CoV-2) is a respiratory virus responsible for coronavirus disease 19 (COVID-19) and the still ongoing and unprecedented global pandemic. The key viral protein for cell infection is the spike glycoprotein, a surface-exposed fusion protein that both recognizes and mediates entry into host cells. Within the spike glycoprotein, a fatty acid binding pocket (FABP) was confirmed, with the crystallization of linoleic acid (LA) occupying a well-defined site. Importantly, when the pocket is occupied by a fatty acid, an inactive conformation is stabilized, and cell recognition is hindered. In this review, we discuss ligands reported so far for this site, correlating their activity predicted through in silico studies with antispike experimental activity, assessed by either binding assays or cell-infection assays. LA was the first confirmed ligand, cocrystallized in a cryo-EM structure of the spike protein, resulting in increased stability of the inactive conformation of the spike protein. The next identified ligand, lifitegrast, was also experimentally confirmed as a ligand with antiviral activity, suggesting the potential for diverse chemical scaffolds to bind this site. Finally, SPC-14 was also confirmed as a ligand, although no inhibition assays were performed. In this review, we identified 20 studies describing small-molecule compounds predicted to bind the pocket in in silico studies and with confirmed binding or in vitro activity, either inhibitory activity against the spike-ACE2 interaction or antiviral activity in cell-based assays. When considering all ligands confirmed with in vitro assays, a good overall occupation of the pocket should be complemented with the ability to make direct interactions, both hydrophilic and hydrophobic, with key amino acid residues defining the pocket surface. Among the active compounds, long flexible carbon chains are recurrent, with retinoids capable of binding the FABP, although bulkier systems are also capable of affecting viral fitness. Compounds able to bind this site with high affinity have the potential to stabilize the inactive conformation of the SARS-CoV-2 spike protein and therefore reduce the virus's ability to infect new cells. Since this pocket is conserved in highly pathogenic human coronaviruses, including MERS-CoV and SARS-CoV, this effect could be exploited for the development of new antiviral agents, with broad-spectrum anticoronavirus activity.
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Affiliation(s)
- Luís Queirós-Reis
- Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - João R Mesquita
- Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Epidemiology Research Unit (EPIunit), Institute of Public Health, University of Porto, 4050-091 Porto, Portugal
| | - Andrea Brancale
- University of Chemistry and Technology, Prague, 166 28 Praha, Czechia
| | - Marcella Bassetto
- School of Pharmacy and Pharmaceutical Sciences, College of Biomedical and Life Sciences, Cardiff University, Cardiff CF10 3BN, U.K
- Department of Chemistry, Faculty of Science and Engineering, Swansea University, Swansea SA2 8PP, U.K
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Mesquita JR. From Spike to Symptom: A Contribution to Decoding the Molecular Mechanisms Underlying SARS-CoV-2 Transmission, Infection, and Disease Pathology. Int J Mol Sci 2023; 24:12294. [PMID: 37569670 PMCID: PMC10418666 DOI: 10.3390/ijms241512294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
In December 2019, a novel coronavirus, SARS-CoV-2, was identified in Wuhan, China, from patients with severe pneumonia of unknown origin [...].
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Affiliation(s)
- João R. Mesquita
- ICBAS-School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal; ; Tel.: +351-220428000
- Epidemiology Research Unit (EPIunit), Institute of Public Health, Porto University, 4050-600 Porto, Portugal
- Laboratório para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), 4050-600 Porto, Portugal
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Kharlamova MV, Kramberger C. Electrochemistry of Carbon Materials: Progress in Raman Spectroscopy, Optical Absorption Spectroscopy, and Applications. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:640. [PMID: 36839009 PMCID: PMC9961505 DOI: 10.3390/nano13040640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
This paper is dedicated to the discussion of applications of carbon material in electrochemistry. The paper starts with a general discussion on electrochemical doping. Then, investigations by spectroelectrochemistry are discussed. The Raman spectroscopy experiments in different electrolyte solutions are considered. This includes aqueous solutions and acetonitrile and ionic fluids. The investigation of carbon nanotubes on different substrates is considered. The optical absorption experiments in different electrolyte solutions and substrate materials are discussed. The chemical functionalization of carbon nanotubes is considered. Finally, the application of carbon materials and chemically functionalized carbon nanotubes in batteries, supercapacitors, sensors, and nanoelectronic devices is presented.
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Affiliation(s)
- Marianna V. Kharlamova
- Centre for Advanced Materials Application (CEMEA) of Slovak Academy of Sciences, Dúbravská cesta 5807/9, 845 11 Bratislava, Slovakia
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Self-Emulsifying Micellization of Crude Extracts from Apple (Malus domestica cv. Anna), Plum ( Prunus domestica cv. Satsuma), and Guava ( Psidium guajava L.) Fruits. Molecules 2023; 28:molecules28031297. [PMID: 36770962 PMCID: PMC9921913 DOI: 10.3390/molecules28031297] [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: 12/16/2022] [Revised: 01/13/2023] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
Micellar microemulsions are thermodynamically stable self-emulsifying systems that have been used to successfully improve the low oral bioavailability of several bioactive phytochemicals, such as antioxidant polyphenols. However, most studies have reported the micellization of single-compounds or purified chemical fractions; thus, the stability, phytochemical-loading efficiency, and bioactivity of complex crude extracts remain largely unexplored. In this study, we evaluated the effects of micellar emulsification of tropical apple (Malus domestica cv. Anna), plum (Prunus domestica cv. Satsuma), and guava (Psidium guajava L.) extracts regarding particle size and stability, polyphenol-loading efficiency, antioxidant capacity, and cytotoxic activity in human and murine cells. Simple food-grade extraction protocols were implemented to obtain apple, plum, and guava extracts. Total polyphenols, flavonoids, and antioxidant activity (DPPH) were determined in the fruit extracts, and their polyphenol profile was further characterized by liquid chromatography (HPLC-DAD). The dried extracts were mixed into a food-grade, self-emulsifying system, and their cytotoxicity in human and murine cell lines was compared. Our research showed that complex fruit matrixes were successfully emulsified into thermodynamically stable polysorbate-based nanometric micelles with uniform size distribution and consistent pH stability, with potential applications in food and biomedical industries.
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Lucini D, Pagani E, Capria F, Galiano M, Marchese M, Cribellati S, Parati G. Age Influences on Lifestyle and Stress Perception in the Working Population. Nutrients 2023; 15:nu15020399. [PMID: 36678269 PMCID: PMC9865201 DOI: 10.3390/nu15020399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Workplace health promotion programs and services offered by insurers may play a fundamental role to foster health/well-being and to prevent chronic diseases. To this end, they should be tailored to companies/employees’ requirements and characteristics. In particular, age needs to be taken into account, considering both that young age workers are generally healthy, and that young age is the best period in lifespan to address prevention and instilling healthy behaviors. We employed an anonymous, simple web-based questionnaire (filled out by 1305 employees) which furnishes data regarding lifestyle (nutrition, exercise, smoking, stress, sleep, etc.), some of which were used to build a unique descriptor (Lifestyle Index; 0−100 higher scores being healthier). We considered three subgroups accordingly to age: ≤30; between 30 and 50; >50 years. This study showed age influences lifestyle and stress perception in the working population: the youngest employees (both men and women) presented the worst lifestyle index, particularly in its stress component. This observation may potentially be useful to tailor workplace health promotion programs and to personalize insurance protocols and services offered to employees. The practical message of our study is that in healthy young people focusing only on medical parameters (frequently within normal ranges in this cohort), albeit important, may be not sufficient to foster proactive actions to prevent chronic non-communicable diseases in adult life. Vice versa, driving their attention on current behaviors might elicit their proactive role to improve lifestyle, getting immediate advantages such as well-being improvement and the possibility to best manage stress.
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Affiliation(s)
- Daniela Lucini
- BIOMETRA Department, University of Milan, 20129 Milan, Italy
- Exercise Medicine Unit, Istituto Auxologico Italiano, IRCCS, 20135 Milan, Italy
- Correspondence: ; Tel.: +39-02-619112808
| | - Eleonora Pagani
- Department of Psychology, Catholic University of the Sacred Hearth, 20123 Milan, Italy
| | | | | | | | | | - Gianfranco Parati
- Department of Medicine and Surgery, University of Milano-Bicocca, 20126 Milan, Italy
- Department of Cardiology, Istituto Auxologico Italiano, IRCCS, 20149 Milan, Italy
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Kerch G. Severe COVID-19-A Review of Suggested Mechanisms Based on the Role of Extracellular Matrix Stiffness. Int J Mol Sci 2023; 24:1187. [PMID: 36674700 PMCID: PMC9861790 DOI: 10.3390/ijms24021187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The severity of COVID-19 commonly depends on age-related tissue stiffness. The aim was to review publications that explain the effect of microenvironmental extracellular matrix stiffness on cellular processes. Platelets and endothelial cells are mechanosensitive. Increased tissue stiffness can trigger cytokine storm with the upregulated expression of pro-inflammatory cytokines, such as tumor necrosis factor alpha and interleukin IL-6, and tissue integrity disruption, leading to enhanced virus entry and disease severity. Increased tissue stiffness in critically ill COVID-19 patients triggers platelet activation and initiates plague formation and thrombosis development. Cholesterol content in cell membrane increases with aging and further enhances tissue stiffness. Membrane cholesterol depletion decreases virus entry to host cells. Membrane cholesterol lowering drugs, such as statins or novel chitosan derivatives, have to be further developed for application in COVID-19 treatment. Statins are also known to decrease arterial stiffness mitigating cardiovascular diseases. Sulfated chitosan derivatives can be further developed for potential use in future as anticoagulants in prevention of severe COVID-19. Anti-TNF-α therapies as well as destiffening therapies have been suggested to combat severe COVID-19. The inhibition of the nuclear factor kappa-light-chain-enhancer of activated B cells pathway must be considered as a therapeutic target in the treatment of severe COVID-19 patients. The activation of mechanosensitive platelets by higher matrix stiffness increases their adhesion and the risk of thrombus formation, thus enhancing the severity of COVID-19.
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Affiliation(s)
- Garry Kerch
- Faculty of Materials Science and Applied Chemistry, Riga Technical University, 1048 Riga, Latvia
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Singh DD, Han I, Choi EH, Yadav DK. A Clinical Update on SARS-CoV-2: Pathology and Development of Potential Inhibitors. Curr Issues Mol Biol 2023; 45:400-433. [PMID: 36661514 PMCID: PMC9857284 DOI: 10.3390/cimb45010028] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/29/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
SARS-CoV-2 (severe acute respiratory syndrome) is highly infectious and causes severe acute respiratory distress syndrome (SARD), immune suppression, and multi-organ failure. For SARS-CoV-2, only supportive treatment options are available, such as oxygen supportive therapy, ventilator support, antibiotics for secondary infections, mineral and fluid treatment, and a significant subset of repurposed effective drugs. Viral targeted inhibitors are the most suitable molecules, such as ACE2 (angiotensin-converting enzyme-2) and RBD (receptor-binding domain) protein-based inhibitors, inhibitors of host proteases, inhibitors of viral proteases 3CLpro (3C-like proteinase) and PLpro (papain-like protease), inhibitors of replicative enzymes, inhibitors of viral attachment of SARS-CoV-2 to the ACE2 receptor and TMPRSS2 (transmembrane serine proteinase 2), inhibitors of HR1 (Heptad Repeat 1)-HR2 (Heptad Repeat 2) interaction at the S2 protein of the coronavirus, etc. Targeting the cathepsin L proteinase, peptide analogues, monoclonal antibodies, and protein chimaeras as RBD inhibitors interferes with the spike protein's ability to fuse to the membrane. Targeting the cathepsin L proteinase, peptide analogues, monoclonal antibodies, and protein chimaeras as RBD inhibitors interferes with the spike protein's ability to fuse to the membrane. Even with the tremendous progress made, creating effective drugs remains difficult. To develop COVID-19 treatment alternatives, clinical studies are examining a variety of therapy categories, including antibodies, antivirals, cell-based therapy, repurposed diagnostic medicines, and more. In this article, we discuss recent clinical updates on SARS-CoV-2 infection, clinical characteristics, diagnosis, immunopathology, the new emergence of variant, SARS-CoV-2, various approaches to drug development and treatment options. The development of therapies has been complicated by the global occurrence of many SARS-CoV-2 mutations. Discussion of this manuscript will provide new insight into drug pathophysiology and drug development.
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Affiliation(s)
- Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Ihn Han
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea
- Correspondence: (I.H.); (D.K.Y.); Tel.: +82-2-597-0365 (I.H. & D.K.Y.)
| | - Eun-Ha Choi
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Dharmendra Kumar Yadav
- Department of R&D Center, Arontier Co., Seoul 06735, Republic of Korea
- Correspondence: (I.H.); (D.K.Y.); Tel.: +82-2-597-0365 (I.H. & D.K.Y.)
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Wang X, Hu M, Liu B, Xu H, Jin Y, Wang B, Zhao Y, Wu J, Yue J, Ren H. Evaluating the effect of SARS-CoV-2 spike mutations with a linear doubly robust learner. Front Cell Infect Microbiol 2023; 13:1161445. [PMID: 37153142 PMCID: PMC10154619 DOI: 10.3389/fcimb.2023.1161445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/03/2023] [Indexed: 05/09/2023] Open
Abstract
Driven by various mutations on the viral Spike protein, diverse variants of SARS-CoV-2 have emerged and prevailed repeatedly, significantly prolonging the pandemic. This phenomenon necessitates the identification of key Spike mutations for fitness enhancement. To address the need, this manuscript formulates a well-defined framework of causal inference methods for evaluating and identifying key Spike mutations to the viral fitness of SARS-CoV-2. In the context of large-scale genomes of SARS-CoV-2, it estimates the statistical contribution of mutations to viral fitness across lineages and therefore identifies important mutations. Further, identified key mutations are validated by computational methods to possess functional effects, including Spike stability, receptor-binding affinity, and potential for immune escape. Based on the effect score of each mutation, individual key fitness-enhancing mutations such as D614G and T478K are identified and studied. From individual mutations to protein domains, this paper recognizes key protein regions on the Spike protein, including the receptor-binding domain and the N-terminal domain. This research even makes further efforts to investigate viral fitness via mutational effect scores, allowing us to compute the fitness score of different SARS-CoV-2 strains and predict their transmission capacity based solely on their viral sequence. This prediction of viral fitness has been validated using BA.2.12.1, which is not used for regression training but well fits the prediction. To the best of our knowledge, this is the first research to apply causal inference models to mutational analysis on large-scale genomes of SARS-CoV-2. Our findings produce innovative and systematic insights into SARS-CoV-2 and promotes functional studies of its key mutations, serving as reliable guidance about mutations of interest.
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Affiliation(s)
| | | | | | | | | | | | | | - Jun Wu
- *Correspondence: Hongguang Ren, ; Junjie Yue, ; Jun Wu,
| | - Junjie Yue
- *Correspondence: Hongguang Ren, ; Junjie Yue, ; Jun Wu,
| | - Hongguang Ren
- *Correspondence: Hongguang Ren, ; Junjie Yue, ; Jun Wu,
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13
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Panorama of Breakthrough Infection Caused by SARS-CoV-2: A Review. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:medicina58121733. [PMID: 36556935 PMCID: PMC9784755 DOI: 10.3390/medicina58121733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022]
Abstract
Since the outbreak of the novel coronavirus disease 2019 (COVID-19) in 2019, many countries have successively developed a variety of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, with the continuous spread of SARS-CoV-2, it has evolved several variants; as a result, prevention and control of the pandemic of SARS-CoV-2 has become more important. Among these variants, the Omicron variant has higher transmissibility and immune escape ability and is the main variant causing a large number of COVID-19 breakthrough infection, thus, presenting new challenges to pandemic prevention and control. Hence, we review the biological characteristics of the Omicron variant and discuss the current status and possible mechanism of breakthrough infection caused by the Omicron variant in order to provide insights into the prevention and control of the pandemic of SARS-CoV-2.
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14
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Mesquita JR. Molecular Advances in SARS-CoV-2: A Brief Update on Transmission, Infection, and Pathology Aspects. Int J Mol Sci 2022; 23:ijms232214250. [PMID: 36430725 PMCID: PMC9692546 DOI: 10.3390/ijms232214250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
It all started back in late 2019 with a virus making a leap, crossing the barrier of species from an animal reservoir to a human and quickly spreading around the world [...].
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Affiliation(s)
- João R. Mesquita
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; ; Tel.: +351-220-428-000
- Epidemiology Research Unit (EPIUnit), Instituto de Saúde Pública da Universidade do Porto (ISPUP), 4050-313 Porto, Portugal
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15
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Candido KL, Eich CR, de Fariña LO, Kadowaki MK, da Conceição Silva JL, Maller A, Simão RDCG. Spike protein of SARS-CoV-2 variants: a brief review and practical implications. Braz J Microbiol 2022; 53:1133-1157. [PMID: 35397075 PMCID: PMC8994061 DOI: 10.1007/s42770-022-00743-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/21/2022] [Indexed: 12/24/2022] Open
Abstract
The scientific community has been alarmed by the possible immunological evasion, higher infectivity, and severity of disease caused by the newest variants of SARS-CoV-2. The spike protein has an important role in the cellular invasion of viruses and is the target of several vaccines and therapeutic resources, such as monoclonal antibodies. In addition, some of the most relevant mutations in the different variants are on the spike (S) protein gene sequence that leads to structural alterations in the predicted protein, thus causing concern about the protection mediated by vaccines against these new strains. The present review highlights the most recent knowledge about COVID-19 and vaccines, emphasizing the different spike protein structures of SARS-CoV-2 and updating the reader about the emerging viral variants and their classifications, the more common viral mutations described and their distribution in Brazil. It also compiles a table with the most recent knowledge about all of the Omicron spike mutations.
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Affiliation(s)
- Kattlyn Laryssa Candido
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Caio Ricardo Eich
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Luciana Oliveira de Fariña
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Marina Kimiko Kadowaki
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - José Luis da Conceição Silva
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Alexandre Maller
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Rita de Cássia Garcia Simão
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
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16
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Pondé RAA. Physicochemical effect of the N501Y, E484K/Q, K417N/T, L452R and T478K mutations on the SARS-CoV-2 spike protein RBD and its influence on agent fitness and on attributes developed by emerging variants of concern. Virology 2022; 572:44-54. [PMID: 35580380 PMCID: PMC9096574 DOI: 10.1016/j.virol.2022.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/26/2022] [Accepted: 05/06/2022] [Indexed: 01/17/2023]
Abstract
The spike protein comprises one of the main structural components of SARS-CoV-2 because it is directly involved in the infection process and viral transmission, and also because of its immunogenic properties, as an inducer of the protective antibodies production and as a vaccine component. The occurrence of mutations in this region or in other the virus genome regions, comprises a natural phenomenon in its evolution. However, they also occur due to the selective immune pressure, to which the agent is continuously subjected, especially in the spike protein immunodominant regions, such as the RBD. Mutations in the spike protein can change the virus' fitness, increasing its affinity for target cells, its transmissibility and its virulence. In addition, these mutations can giving it the potential ability to evade the protective antibodies action obtained from convalescent sera or vaccine origin, as well as those used in therapy, which may favor the virus expansion and compromise the infection control. Five mutations N501Y, E484K/Q, K417N/T, L452R and T478K, located in the spike protein RBD, have had a greater impact because they are associated with new attributes developed by the virus, which characterize the emerging variants of concern (VOCs) of SARS-Cov-2 identified so far. The occurrence of these mutations induces complex physicochemical effects that can alter the spike protein's structure and its function, which in turn, lead to changes in the agents' fitness. This manuscript discusses the attributes of VOCs associated with the physicochemical effects caused by the aforementioned mutations.
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Affiliation(s)
- R A A Pondé
- State Department of Health SES/Superintendence of Health Surveillance SUVISA/GO, Management of Epidemiological Surveillance-GVE/Coordination of Analysis and Research-CAP, Goiânia, Goiás, Brazil; Laboratory of Human Virology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil.
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17
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Tsai MS, Shih WT, Yang YH, Lin YS, Chang GH, Hsu CM, Yeh RA, Shu LH, Cheng YC, Liu HT, Wu YH, Wu YH, Shen RC, Wu CY. Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Biomed Pharmacother 2022; 149:112802. [PMID: 35279013 PMCID: PMC8906167 DOI: 10.1016/j.biopha.2022.112802] [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: 01/25/2022] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 11/02/2022] Open
Abstract
At the time of writing, more than 440 million confirmed coronavirus disease 2019 (COVID-19) cases and more than 5.97 million COVID-19 deaths worldwide have been reported by the World Health Organization since the start of the outbreak of the pandemic in Wuhan, China. During the COVID-19 pandemic, many variants of SARS-CoV-2 have arisen because of high mutation rates. N501Y, E484K, K417N, K417T, L452R and T478K in the receptor binding domain (RBD) region may increase the infectivity in several variants of SARS-CoV-2. In this study, we discovered that GB-1, developed from Chiehyuan herbal formula which obtained from Tian Shang Sheng Mu of Chiayi Puzi Peitian Temple, can inhibit the binding between ACE2 and RBD with Wuhan type, K417N-E484K-N501Y and L452R-T478K mutation. In addition, GB-1 inhibited the binding between ACE2 and RBD with a single mutation (E484K or N501Y), except the K417N mutation. In the compositions of GB-1, glycyrrhizic acid can inhibit the binding between ACE2 and RBD with Wuhan type, except K417N-E484K-N501Y mutation. Our results suggest that GB-1 could be a potential candidate for the prophylaxis of different variants of SARS-CoV-2 infection because of its inhibition of binding between ACE2 and RBD with different mutations (L452R-T478K, K417N-E484K-N501Y, N501Y or E484K).
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Affiliation(s)
- Ming-Shao Tsai
- Department of Otolaryngology, Chang Gung Memorial Hospital, Chiayi, Taiwan; Faculty of Medicine, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | - Wei-Tai Shih
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Yao-Hsu Yang
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan; School of Chinese Medicine, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | - Yu-Shih Lin
- Department of Pharmacy, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Geng-He Chang
- Department of Otolaryngology, Chang Gung Memorial Hospital, Chiayi, Taiwan; Faculty of Medicine, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan; Health Information and Epidemiology Laboratory, Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Cheng-Ming Hsu
- Department of Otolaryngology, Chang Gung Memorial Hospital, Chiayi, Taiwan; Faculty of Medicine, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | - Reming-Albert Yeh
- Department of Otolaryngology, Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Li-Hsin Shu
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Yu-Ching Cheng
- Department of Otolaryngology, Chang Gung Memorial Hospital, Chiayi, Taiwan; Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Hung-Te Liu
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Yu-Huei Wu
- Department of Biomedical Sciences, Chang Gung University, Tao-Yuan, Taiwan
| | - Yu-Heng Wu
- Department of Electrical Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Rou-Chen Shen
- Department of Otolaryngology, Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Ching-Yuan Wu
- Department of Chinese Medicine, Chiayi Chang Gung Memorial Hospital, Chiayi, Taiwan; School of Chinese Medicine, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan; Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan.
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Omotuyi O, Olubiyi O, Nash O, Afolabi E, Oyinloye B, Fatumo S, Femi-Oyewo M, Bogoro S. SARS-CoV-2 Omicron spike glycoprotein receptor binding domain exhibits super-binder ability with ACE2 but not convalescent monoclonal antibody. Comput Biol Med 2022; 142:105226. [PMID: 35066447 PMCID: PMC8739363 DOI: 10.1016/j.compbiomed.2022.105226] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/28/2021] [Accepted: 01/05/2022] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2, the causative virus for COVID-19 has now super-mutated into the Omicron (Om) variant. On its spike (S) glycoprotein alone, more than 30 substitutions have been characterized with 15 within the receptor binding domain (RBD); It therefore calls to question the transmissibility and antibody escapability of Omicron. This study was setup to investigate the Omicron RBD's interaction with ACE2 (host receptor) and a SARS-CoV-2 neutralizing monoclonal antibody (mAb). In-silico mutagenesis was used to generate the Om-RBD in complex with ACE2 or mAb from the wildtype. HDOCK server was used to redock and score the mAbs in Om-RBD bound state relative to the wildtype. Stability of interaction between all complexes were investigated using all-atom molecular dynamics (MD). Analyses of trajectories showed that Om-RBD has evolved into an efficient ACE2 binder, via pi-pi (Om-RBD-Y501/ACE2-Y41) and salt-bridge (Om-RBD-K493/ACE2-Y41) interactions. Conversely, in binding mAb, it has become less efficient (Center of mass distance of RBD from mAb complex, wildtype ≈ 30 Å, Omicron ≈ 41 Å). Disruption of Om-RBD/mAb complex resulted from loose interaction between Om-RBD and the light chain complementarity-determining region residues. Omicron is expected to be better transmissible and less efficiently interacting with neutralizing convalescent mAbs with consequences on transmissibility provided other mutations within the S protein similarly promote cell fusion and viral entry.
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Affiliation(s)
- Olaposi Omotuyi
- Institute for Drug Research and Development, S.E. Bogoro Center, Afe Babalola University, Ado Ekiti, Nigeria; Molecular Biology and Molecular Simulation Center (Mols&Sims), Ado Ekiti, Nigeria.
| | - Olujide Olubiyi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria
| | - Oyekanmi Nash
- Centre for Genomics Research and Innovation, National Biotechnology Agency, Nigeria
| | - Elizabeth Afolabi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria
| | - Babatunji Oyinloye
- Institute for Drug Research and Development, S.E. Bogoro Center, Afe Babalola University, Ado Ekiti, Nigeria
| | - Segun Fatumo
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Mbang Femi-Oyewo
- Department of Pharmaceutical Chemistry, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria
| | - Suleiman Bogoro
- Institute for Drug Research and Development, S.E. Bogoro Center, Afe Babalola University, Ado Ekiti, Nigeria
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Omicron SARS-CoV-2 Variant Spike Protein Shows an Increased Affinity to the Human ACE2 Receptor: An In Silico Analysis. Pathogens 2021; 11:pathogens11010045. [PMID: 35055993 PMCID: PMC8779645 DOI: 10.3390/pathogens11010045] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 12/20/2022] Open
Abstract
The rise of SARS-CoV-2 variants, with changes that could be related to an increased virus pathogenicity, have received the interest of the scientific and medical community. In this study, we evaluated the changes that occurred in the viral spike of the SARS-CoV-2 Omicron variant and whether these changes modulate the interactions with the angiotensin-converting enzyme 2 (ACE2) host receptor. The mutations associated with the Omicron variant were retrieved from the GISAID and covariants.org databases, and a structural model was built using the SWISS-Model server. The interaction between the spike and the human ACE2 was evaluated using two different docking software, Zdock and Haddock. We found that the binding free energy was lower for the Omicron variant as compared to the WT spike. In addition, the Omicron spike protein showed an increased number of electrostatic interactions with ACE2 than the WT spike, especially the interactions related to charged residues. This study contributes to a better understanding of the changes in the interaction between the Omicron spike and the human host ACE2 receptor.
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