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Yamada CAO, de Paula Oliveira Santos B, Lemos RP, Batista ACS, da Conceição IMCA, de Paula Sabino A, E Lima LMTDR, de Magalhães MTQ. Applications of Mass Spectrometry in the Characterization, Screening, Diagnosis, and Prognosis of COVID-19. Adv Exp Med Biol 2024; 1443:33-61. [PMID: 38409415 DOI: 10.1007/978-3-031-50624-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Mass spectrometry (MS) is a powerful analytical technique that plays a central role in modern protein analysis and the study of proteostasis. In the field of advanced molecular technologies, MS-based proteomics has become a cornerstone that is making a significant impact in the post-genomic era and as precision medicine moves from the research laboratory to clinical practice. The global dissemination of COVID-19 has spurred collective efforts to develop effective diagnostics, vaccines, and therapeutic interventions. This chapter highlights how MS seamlessly integrates with established methods such as RT-PCR and ELISA to improve viral identification and disease progression assessment. In particular, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) takes the center stage, unraveling intricate details of SARS-CoV-2 proteins, revealing modifications such as glycosylation, and providing insights critical to formulating therapies and assessing prognosis. However, high-throughput analysis of MALDI data presents challenges in manual interpretation, which has driven the development of programmatic pipelines and specialized packages such as MALDIquant. As we move forward, it becomes clear that integrating proteomic data with various omic findings is an effective strategy to gain a comprehensive understanding of the intricate biology of COVID-19 and ultimately develop targeted therapeutic paradigms.
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Affiliation(s)
- Camila Akemi Oliveira Yamada
- Laboratory for Macromolecular Biophysics - LBM, Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Bruno de Paula Oliveira Santos
- Laboratory for Macromolecular Biophysics - LBM, Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rafael Pereira Lemos
- Laboratory for Macromolecular Biophysics - LBM, Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ana Carolina Silva Batista
- Laboratory for Macromolecular Biophysics - LBM, Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Adriano de Paula Sabino
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratory of Clinical and Molecular Hematology - Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Mariana T Q de Magalhães
- Laboratory for Macromolecular Biophysics - LBM, Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
- Biochemistry and Immunology Postgraduate Program, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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Mahmoudi Azar L, Öncel MM, Karaman E, Soysal LF, Fatima A, Choi SB, Eyupoglu AE, Erman B, Khan AM, Uysal S. Human ACE2 orthologous peptide sequences show better binding affinity to SARS-CoV-2 RBD domain: Implications for drug design. Comput Struct Biotechnol J 2023; 21:4096-4109. [PMID: 37671240 PMCID: PMC10475354 DOI: 10.1016/j.csbj.2023.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 09/07/2023] Open
Abstract
Computational methods coupled with experimental validation play a critical role in the identification of novel inhibitory peptides that interact with viral antigenic determinants. The interaction between the receptor binding domain (RBD) of SARS-CoV-2 spike protein and the helical peptide of human angiotensin-converting enzyme-2 (ACE2) is a necessity for the initiation of viral infection. Herein, natural orthologs of human ACE2 helical peptide were evaluated for competitive inhibitory binding to the viral RBD by use of a computational approach, which was experimentally validated. A total of 624 natural ACE2 orthologous 32-amino acid long peptides were identified through a similarity search. Molecular docking was used to virtually screen and rank the peptides based on binding affinity metrics, benchmarked against human ACE2 peptide docked to the RBD. Molecular dynamics (MD) simulations were done for the human reference and the Nipponia nippon peptide as it exhibited the highest binding affinity (Gibbs free energy; -14 kcal/mol) predicted from the docking results. The MD simulation confirmed the stability of the assessed peptide in the complex (-12.3 kcal/mol). The top three docked-peptides (from Chitinophaga sancti, Nipponia nippon, and Mus musculus) and the human reference were experimentally validated by use of surface plasmon resonance technology. The human reference exhibited the weakest binding affinity (Kd of 318-441 pM) among the peptides tested, in agreement with the docking prediction, while the peptide from Nipponia nippon was the best, with 267-538-fold higher affinity than the reference. The validated peptides merit further investigation. This work showcases that the approach herein can aid in the identification of inhibitory biosimilar peptides for other viruses.
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Affiliation(s)
- Lena Mahmoudi Azar
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Istanbul 34820, Turkiye
| | - Muhammed Miran Öncel
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Istanbul 34820, Turkiye
| | - Elif Karaman
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Istanbul 34820, Turkiye
- Department of Biotechnology, Institute of Health Sciences, Bezmialem Vakif University, Istanbul 34093, Turkiye
| | - Levent Faruk Soysal
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Istanbul 34820, Turkiye
| | - Ayesha Fatima
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Istanbul 34820, Turkiye
| | - Sy Bing Choi
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Kuala Lumpur 50490, Malaysia
| | - Alp Ertunga Eyupoglu
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul 34450 Turkiye
| | - Batu Erman
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, Istanbul 34450 Turkiye
| | - Asif M. Khan
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Istanbul 34820, Turkiye
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Kuala Lumpur 50490, Malaysia
| | - Serdar Uysal
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Istanbul 34820, Turkiye
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Santos FRDS, de Azevedo MSP, Bielavsky M, da Costa HHM, Ribeiro DG, Nascimento GGD, Marcondes GMP, de Castro BP, de Lima Neto DF, Prudencio CR. Mutational profile confers increased stability of SARS-CoV-2 spike protein in Brazilian isolates. J Biomol Struct Dyn 2022; 40:13184-13189. [PMID: 34633892 DOI: 10.1080/07391102.2021.1982775] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Spike (S) protein has been recognized as a promising molecular target for diagnostic, vaccines and antiviral drugs development for COVID-19. In this study, we analyzed the most predominant mutations in the S protein of Brazilian isolates and predicted the effect of these amino acid alterations to protein conformation. A total of 25,924 sequences were obtained from GISAID for five regions of Brazilian territory (Midwest, North, Northeast, South, and Southeast), according to exclusion criteria. Most of the SARS-CoV-2 isolates belongs to the G clade and showed a large occurrence of D614G, N501Y and L18F substitutions. Prediction effects of these amino acid substitutions on the structure dynamics of the spike protein indicated a positive ΔΔG values and negative ΔΔSVib in most cases which is associated to structural stabilization and flexibility reduction of the S protein. Mutations E484K, N501Y and K417N belong to several SARS-CoV-2 variants of concern such as Alpha, Beta, Gamma and Delta, and showed high incidence among Brazilian isolates. These mutations have been described to increase RBD affinity to ACE-2 host and abolishment of RBD affinity to potent neutralizing ant-RBD. The increase in rates of infection and reinfection requires continuous genomic surveillance studies in order to characterize emerging mutations and monitor vaccine efficacy, and thus consideration structural data and dynamics in the observed phenotypes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Monica Bielavsky
- Laboratory of Immunotechnology, Center of Immunology, Adolfo Lutz Institute, São Paulo, SP, Brazil
| | | | - Daniela Gomes Ribeiro
- Laboratory of Immunotechnology, Center of Immunology, Adolfo Lutz Institute, São Paulo, SP, Brazil
| | | | | | | | - Daniel Ferreira de Lima Neto
- Coordenação-Geral de Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil.,Laboratório de Termodinâmica de Proteínas, Departamento de Bioquímica, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Carlos Roberto Prudencio
- Laboratory of Immunotechnology, Center of Immunology, Adolfo Lutz Institute, São Paulo, SP, Brazil
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Kowalczyk A, Kasprzak A, Ruzycka-Ayoush M, Podsiadły E, Demkow U, Grudzinski IP, Nowicka AM. Ultrasensitive voltammetric detection of SARS-CoV-2 in clinical samples. Sens Actuators B Chem 2022; 371:132539. [PMID: 36033923 PMCID: PMC9395233 DOI: 10.1016/j.snb.2022.132539] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
In every pandemic, it is critical to test as many people as possible and keep track of the number of new cases of infection. Therefore, there is a need for novel, fast and unambiguous testing methods. In this study, we designed a sandwich-type voltammetric immunosensor based on unlabeled- and labeled with a redox probe antibodies against virus spike protein for fast and ultrasensitive detection of SARS-CoV-2. The process of the preparation of the sensor layer included chemisorption of cysteamine layer and covalent anchoring of antibody specific for the S1 subunit of the S protein. The source of the voltametric signal was the antibody labeled with the redox probe, which was introduced onto biosensor surface only after the recognition of the virus. This easy-to-handle immunosensor was characterized by a wide analytical range (2.0·10-7 to 0.20 mg·L-1) and low detection limit (8.0·10-8 mg·L-1 ≡ 0.08 pg·mL-1 ≡ 4 virions·μL-1). The utility of the designed device was also evidenced by the detection of SARS-CoV-2 in the clinical samples. Moreover, the main advantage and a huge novelty of the developed device, compared to those already existing, is the moment of generating the analytical signal of the redox probe that appears only after the virus recognition. Thus, our diagnostic innovation may considerably contribute to controlling the COVID-19 pandemic. The as-developed immunosensor may well offer a novel alternative approach for viral detection that could complement or even replace the existing methods.
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Affiliation(s)
- Agata Kowalczyk
- Faculty of Chemistry, University of Warsaw, Pasteura 1 Str., PL 02-093 Warsaw, Poland
| | - Artur Kasprzak
- Faculty of Chemistry, Warsaw University of Technology, Nowakowskiego 3 Str., PL 00-664 Warsaw, Poland
| | - Monika Ruzycka-Ayoush
- Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Str., PL 02-097 Warsaw, Poland
| | - Edyta Podsiadły
- Department of Pharmaceutical Microbiology, Centre for Preclinical Research, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1B Str., PL 02-097 Warsaw, Poland
| | - Urszula Demkow
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Medical University of Warsaw, Zwirki i Wigury 63 A Str., PL 02-091 Warsaw, Poland
| | - Ireneusz P Grudzinski
- Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Str., PL 02-097 Warsaw, Poland
| | - Anna M Nowicka
- Faculty of Chemistry, University of Warsaw, Pasteura 1 Str., PL 02-093 Warsaw, Poland
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Huang YX, Li NF, Li CY, Zheng FP, Yao XY, Lin BH, Huang XZ, Zhao NJ, Yang JY, Chen QM, Zhang MM, Yi LT, Chen XQ. Clinical features and effectiveness of Chinese medicine in patients with COVID-19 from overseas: A retrospective study in Xiamen, China. Front Public Health 2022; 10:1038017. [PMID: 36353282 PMCID: PMC9638095 DOI: 10.3389/fpubh.2022.1038017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 09/29/2022] [Indexed: 01/29/2023] Open
Abstract
COVID-19, referred to as new coronary pneumonia, is an acute infectious disease caused by a new type of coronavirus SARS-CoV-2. To evaluate the effect of integrated Chinese medicine and Western medicine in patients with COVID-19 from overseas. Data were collected from 178 COVID-19 patients overseas at First Affiliated Hospital of Xiamen University from April 1, 2021 to July 31, 2021. These patients received therapy of integrated Chinese medicine and western medicine. Demographic data and clinical characteristics were extracted and analyzed. In addition, the prescription which induced less length of PCR positive days and hospitalization days than the median value was obtained. The top 4 frequently used Chinese medicine and virus-related genes were analyzed by network pharmacology and bioinformatics analysis. According to the chest computed tomography (CT) measurement, abnormal lung findings were observed in 145 subjects. The median length of positive PCR/hospitalization days was 7/7 days for asymptomatic subjects, 14/24 days for mild subjects, 10/15 days for moderate subjects, and 14/20 days for severe subjects. The most frequently used Chinese medicine were Scutellaria baicalensis (Huangqin), Glycyrrhiza uralensis (Gancao), Bupleurum chinense (Chaihu), and Pinellia ternata (Banxia). The putative active ingredients were baicalin, stigmasterol, sigmoidin-B, cubebin, and troxerutin. ACE, SARS-CoV-2 3CL, SARS-CoV-2 Spike, SARS-CoV-2 ORF7a, and caspase-6 showed good binding properties to active ingredients. In conclusion, the clinical results showed that integrated Chinese medicine and Western medicine are effective in treating COVID-19 patients from overseas. Based on the clinical outcomes, the putative ingredients from Chinese medicine and the potential targets of SARS-CoV-2 were provided, which could provide a reference for the clinical application of Chinese medicine in treating COVID-19 worldwide.
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Affiliation(s)
- Yu-Xuan Huang
- The First Affiliated Hospital of Xiamen University, Xiamen, China,Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Na-Fen Li
- The First Affiliated Hospital of Xiamen University, Xiamen, China,Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Chen-Yao Li
- The First Affiliated Hospital of Xiamen University, Xiamen, China,Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Fang-Ping Zheng
- Department of Traditional Chinese Medicine, Xiamen Maluan Wan Hospital, Xiamen, China
| | - Xiang-Yang Yao
- Xinglin Branch of the First Hospital of Xiamen University, Designated Hospital for Treatment of Novel Coronavirus Pneumonia in Xiamen, Xiamen, China
| | - Bao-Hua Lin
- Xinglin Branch of the First Hospital of Xiamen University, Designated Hospital for Treatment of Novel Coronavirus Pneumonia in Xiamen, Xiamen, China
| | - Xian-Zhong Huang
- The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Neng-Jiang Zhao
- The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Jia-Yong Yang
- The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Qiu-Min Chen
- Xinglin Branch of the First Hospital of Xiamen University, Designated Hospital for Treatment of Novel Coronavirus Pneumonia in Xiamen, Xiamen, China
| | - Man-Man Zhang
- Department of Chemical and Pharmaceutical Engineering, Huaqiao University, Xiamen, China
| | - Li-Tao Yi
- Department of Chemical and Pharmaceutical Engineering, Huaqiao University, Xiamen, China,Li-Tao Yi
| | - Xue-Qin Chen
- The First Affiliated Hospital of Xiamen University, Xiamen, China,*Correspondence: Xue-Qin Chen
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Shahanshah MFH, Anvitha D, Gupta V. In-silico screening to delineate novel antagonists to SARS-CoV-2 nucleocapsid protein. Phys Chem Earth (2002) 2022; 127:103188. [PMID: 35757560 PMCID: PMC9212792 DOI: 10.1016/j.pce.2022.103188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 06/07/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Since its inception, SARS-CoV-2 has crossed all borders and continues rampaging around the globe, causing profound economic damage and heavy burden on the scientific community and the healthcare fraternity and facilities. With the emergence of new variants, the global pandemic has prolonged and raised concerns regarding the existing therapies. Most of the identified mutants have the potential to exacerbate the already existing crisis. In line with the urgent need for promising antivirals against the novel coronavirus, we conducted an in-silico drug docking study using SeeSAR and other bioinformatics tools and identified prospective molecules that target the nucleocapsid protein of SARS-CoV-2. The highly conserved N protein plays a crucial role in viral assembly and pathogenicity by interacting with the host ribosomal subunits and suppressing nonsense mediated decay (NMD) of viral mRNA by the host cell. In the current study, FDA approved drugs were docked into pockets created within the N protein including the crucial conserved residues and analyzed for their affinity. The docked compounds give us novel plausible models that can be inspected further and paves way for the development of potent therapeutics against SARS-CoV-2.
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Affiliation(s)
| | - D Anvitha
- Ram Lal Anand College, University of Delhi, New Delhi, India
| | - Vandana Gupta
- Ram Lal Anand College, University of Delhi, New Delhi, India
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Debnath P, Khan U, Khan MS. Characterization and Structural Prediction of Proteins in SARS-CoV-2 Bangladeshi Variant Through Bioinformatics. Microbiol Insights 2022; 15:11786361221115595. [PMID: 35966939 PMCID: PMC9373114 DOI: 10.1177/11786361221115595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/30/2022] [Indexed: 11/15/2022] Open
Abstract
The renowned respiratory disease induced by the severe acute respiratory
syndrome-coronavirus-2 (SARS-CoV-2) has become a global epidemic in just less
than a year by the first half of 2020. The subsequent efficient human-to-human
transmission of this virus eventually affected millions of people worldwide. The
most devastating thing is that the infection rate is continuously uprising and
resulting in significant mortality especially among the older age population and
those with health co-morbidities. This enveloped, positive-sense RNA virus is
chiefly responsible for the infection of the upper respiratory system. The
virulence of the SARS-CoV-2 is mostly regulated by its proteins such as entry to
the host cell through fusion mechanism, fusion of infected cells with
neighboring uninfected cells to spread virus, inhibition of host gene
expression, cellular differentiation, apoptosis, mitochondrial biogenesis, etc.
But very little is known about the protein structures and functionalities.
Therefore, the main purpose of this study is to learn more about these proteins
through bioinformatics approaches. In this study, ORF10, ORF7b, ORF7a, ORF6,
membrane glycoprotein, and envelope protein have been selected from a
Bangladeshi Corona-virus strain G039392 and a number of bioinformatics tools
(MEGA-X-V10.1.7, PONDR, ProtScale, ProtParam, SCRIBER, NetSurfP v2.0, IntFOLD,
UCSF Chimera, and PyMol) and strategies were implemented for multiple sequence
alignment and phylogeny analysis with 9 different variants, predicting
hydropathicity, amino acid compositions, protein-binding propensity, protein
disorders, and 2D and 3D protein modeling. Selected proteins were characterized
as highly flexible, structurally and electrostatically extremely stable,
ordered, biologically active, hydrophobic, and closely related to proteins of
different variants. This detailed information regarding the characterization and
structure of proteins of SARS-CoV-2 Bangladeshi variant was performed for the
first time ever to unveil the deep mechanism behind the virulence features. And
this robust appraisal also paves the future way for molecular docking, vaccine
development targeting these characterized proteins.
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Affiliation(s)
- Pinky Debnath
- Chemical Biotechnology Department, Technical University of Munich, Straubing, Germany
| | - Umama Khan
- Biotechnology and Genetic Engineering Discipline, Khulna University, Bangladesh
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Rashid F, Xie Z, Suleman M, Shah A, Khan S, Luo S. Roles and functions of SARS-CoV-2 proteins in host immune evasion. Front Immunol 2022; 13:940756. [PMID: 36003396 PMCID: PMC9394213 DOI: 10.3389/fimmu.2022.940756] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/07/2022] [Indexed: 12/27/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evades the host immune system through a variety of regulatory mechanisms. The genome of SARS-CoV-2 encodes 16 non-structural proteins (NSPs), four structural proteins, and nine accessory proteins that play indispensable roles to suppress the production and signaling of type I and III interferons (IFNs). In this review, we discussed the functions and the underlying mechanisms of different proteins of SARS-CoV-2 that evade the host immune system by suppressing the IFN-β production and TANK-binding kinase 1 (TBK1)/interferon regulatory factor 3 (IRF3)/signal transducer and activator of transcription (STAT)1 and STAT2 phosphorylation. We also described different viral proteins inhibiting the nuclear translocation of IRF3, nuclear factor-κB (NF-κB), and STATs. To date, the following proteins of SARS-CoV-2 including NSP1, NSP6, NSP8, NSP12, NSP13, NSP14, NSP15, open reading frame (ORF)3a, ORF6, ORF8, ORF9b, ORF10, and Membrane (M) protein have been well studied. However, the detailed mechanisms of immune evasion by NSP5, ORF3b, ORF9c, and Nucleocapsid (N) proteins are not well elucidated. Additionally, we also elaborated the perspectives of SARS-CoV-2 proteins.
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Affiliation(s)
- Farooq Rashid
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Zhixun Xie
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
- *Correspondence: Zhixun Xie,
| | - Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Abdullah Shah
- Department of Biotechnology, Shaheed Benazir Bhutto University, Sheringal, Pakistan
| | - Suliman Khan
- Department of Medical Lab Technology, The University of Haripur, Haripur, Pakistan
| | - Sisi Luo
- Department of Biotechnology, Guangxi Veterinary Research Institute, Nanning, China
- Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, China
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Vassilaki N, Papadimitriou K, Ioannidis A, Papandreou NC, Milona RS, Iconomidou VA, Chatzipanagiotou S. SARS-CoV-2 Amino Acid Mutations Detection in Greek Patients Infected in the First Wave of the Pandemic. Microorganisms 2022; 10:microorganisms10071430. [PMID: 35889149 PMCID: PMC9322066 DOI: 10.3390/microorganisms10071430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel virus that belongs to the Coronoviridae family, emerged in December 2019, causing the COVID-19 pandemic in March 2020. Unlike previous SARS and Middle East respiratory syndrome (MERS) outbreaks, this virus has a higher transmissibility rate, albeit a lower case fatality rate, which results in accumulation of a significant number of mutations and a faster evolution rate. Genomic studies on the mutation rate of the virus, as well as the identification of mutations that prevail and their impact on disease severity, are of great importance for pandemic surveillance and vaccine and drug development. Here, we aim to identify mutations on the SARS-CoV-2 viral genome and their effect on the proteins they are located in, in Greek patients infected in the first wave of the pandemic. To this end, we perform SARS-CoV-2 amplicon-based NGS sequencing on nasopharyngeal swab samples from Greek patients and bioinformatic analysis of the results. Although SARS-CoV-2 is considered genetically stable, we discover a variety of mutations on the viral genome. In detail, 18 mutations are detected in total on 10 SARS-CoV-2 isolates. The mutations are located on ORF1ab, S protein, M protein, ORF3a and ORF7a. Sixteen are also detected in patients from other regions around the world, and two are identified for the first time in the present study. Most of them result in amino acid substitutions. These substitutions are analyzed using computational tools, and the results indicate minor or major impact on the proteins’ structural stability, which could probably affect viral transmissibility and pathogenesis. The correlation of these variations with the viral load levels is examined, and their implication for disease severity and the biology of the virus are discussed.
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Affiliation(s)
- Niki Vassilaki
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece; (N.V.); (R.S.M.)
| | - Konstantinos Papadimitriou
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece;
| | - Anastasios Ioannidis
- Department of Nursing, Faculty of Health Sciences, University of Peloponnese, Sehi Area, 22100 Tripoli, Greece;
| | - Nikos C. Papandreou
- Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (N.C.P.); (V.A.I.)
| | - Raphaela S. Milona
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece; (N.V.); (R.S.M.)
| | - Vassiliki A. Iconomidou
- Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (N.C.P.); (V.A.I.)
| | - Stylianos Chatzipanagiotou
- Department of Medical Biopathology, Eginition Hospital, Athens Medical School, National and Kapodistrian University of Athens, 72–74 Vasilissis Sofias Avenue, 11528 Athens, Greece
- Correspondence:
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Sirin S, Nigdelioglu Dolanbay S, Aslim B. The relationship of early- and late-onset Alzheimer’s disease genes with COVID-19. J Neural Transm (Vienna) 2022; 129:847-859. [PMID: 35429259 PMCID: PMC9012910 DOI: 10.1007/s00702-022-02499-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/02/2022] [Indexed: 12/13/2022]
Abstract
Individuals with Alzheimer’s disease and other neurodegenerative diseases have been exposed to excess risk by the COVID-19 pandemic. COVID-19’s main manifestations include high body temperature, dry cough, and exhaustion. Nevertheless, some affected individuals may have an atypical presentation at diagnosis but suffer neurological signs and symptoms as the first disease manifestation. These findings collectively show the neurotropic nature of SARS-CoV-2 virus and its ability to involve the central nervous system. In addition, Alzheimer’s disease and COVID-19 has a number of common risk factors and comorbid conditions including age, sex, hypertension, diabetes, and the expression of APOE ε4. Until now, a plethora of studies have examined the COVID-19 disease but only a few studies has yet examined the relationship of COVID-19 and Alzheimer’s disease as risk factors of each other. This review emphasizes the recently published evidence on the role of the genes of early- or late-onset Alzheimer’s disease in the susceptibility of individuals currently suffering or recovered from COVID-19 to Alzheimer’s disease or in the susceptibility of individuals at risk of or with Alzheimer’s disease to COVID-19 or increased COVID-19 severity and mortality. Furthermore, the present review also draws attention to other uninvestigated early- and late-onset Alzheimer’s disease genes to elucidate the relationship between this multifactorial disease and COVID-19.
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11
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Fang E, Liu X, Li M, Zhang Z, Song L, Zhu B, Wu X, Liu J, Zhao D, Li Y. Advances in COVID-19 mRNA vaccine development. Signal Transduct Target Ther 2022; 7:94. [PMID: 35322018 PMCID: PMC8940982 DOI: 10.1038/s41392-022-00950-y] [Citation(s) in RCA: 141] [Impact Index Per Article: 70.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/10/2022] [Accepted: 03/03/2022] [Indexed: 12/15/2022] Open
Abstract
To date, the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has determined 399,600,607 cases and 5,757,562 deaths worldwide. COVID-19 is a serious threat to human health globally. The World Health Organization (WHO) has declared COVID-19 pandemic a major public health emergency. Vaccination is the most effective and economical intervention for controlling the spread of epidemics, and consequently saving lives and protecting the health of the population. Various techniques have been employed in the development of COVID-19 vaccines. Among these, the COVID-19 messenger RNA (mRNA) vaccine has been drawing increasing attention owing to its great application prospects and advantages, which include short development cycle, easy industrialization, simple production process, flexibility to respond to new variants, and the capacity to induce better immune response. This review summarizes current knowledge on the structural characteristics, antigen design strategies, delivery systems, industrialization potential, quality control, latest clinical trials and real-world data of COVID-19 mRNA vaccines as well as mRNA technology. Current challenges and future directions in the development of preventive mRNA vaccines for major infectious diseases are also discussed.
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Affiliation(s)
- Enyue Fang
- National Institute for Food and Drug Control, Beijing, 102629, China
- Wuhan Institute of Biological Products, Co., Ltd., Wuhan, 430207, China
| | - Xiaohui Liu
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Miao Li
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Zelun Zhang
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Lifang Song
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Baiyu Zhu
- Texas A&M University, College Station, TX, 77843, USA
| | - Xiaohong Wu
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Jingjing Liu
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Danhua Zhao
- National Institute for Food and Drug Control, Beijing, 102629, China
| | - Yuhua Li
- National Institute for Food and Drug Control, Beijing, 102629, China.
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12
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Zhao L, Li S, Zhong W. Mechanism of Action of Small-Molecule Agents in Ongoing Clinical Trials for SARS-CoV-2: A Review. Front Pharmacol 2022; 13:840639. [PMID: 35281901 PMCID: PMC8916227 DOI: 10.3389/fphar.2022.840639] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/28/2022] [Indexed: 01/18/2023] Open
Abstract
Since the first reports from December 2019, COVID-19 caused an overwhelming global pandemic that has affected 223 countries, seriously endangering public health and creating an urgent need for effective drugs to treat SARS-CoV-2 infection. Currently, there is a lack of safe, effective, and specific therapeutic drugs for COVID-19, with mainly supportive and symptomatic treatments being administered to patients. The preferred option for responding to an outbreak of acute infectious disease is through drug repurposing, saving valuable time that would otherwise be lost in preclinical and clinical research, hastening clinical introduction, and lowering treatment costs. Alternatively, researchers seek to design and discover novel small-molecule candidate drugs targeting the key proteins in the life cycle of SARS-CoV-2 through an in-depth study of the infection mechanism, thus obtaining a number of candidate compounds with favorable antiviral effects in preclinical and clinical settings. There is an urgent need to further elucidate the efficacy and mechanism of action of potential anti-SARS-CoV-2 small-molecule drugs. Herein, we review the candidate small-molecule anti-SARS-CoV-2 drugs in ongoing clinical trials, with a major focus on their mechanisms of action in an attempt to provide useful insight for further research and development of small-molecule compounds against SARS-CoV-2 infection.
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Affiliation(s)
- Lei Zhao
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
- Beijing Sunho Pharmaceutical Co., Ltd., Beijing, China
| | - Song Li
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Wu Zhong
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, China
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13
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Tian Y, Zhang G, Liu H, Ding P, Jia R, Zhou J, Chen Y, Qi Y, Du J, Liang C, Zhu X, Wang A. Screening and identification of B cell epitope of the nucleocapsid protein in SARS-CoV-2 using the monoclonal antibodies. Appl Microbiol Biotechnol 2022; 106:1151-1164. [PMID: 35037999 PMCID: PMC8762450 DOI: 10.1007/s00253-022-11769-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 12/10/2021] [Accepted: 01/07/2022] [Indexed: 11/02/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes the coronavirus disease (COVID-19). It is confirmed that nucleocapsid (N) protein is closely related to viral pathogenesis, modulation of host immune response, RNA transcription, and replication and virus packaging. Therefore, the N protein is a preponderant antigen target for virus detection. The codon-optimized N gene was designed according to the encoding characteristics of insect cells and inserted into pFastBacTM1 vector with 6 × His-tag-fused N protein for expression in insect sf21 cells. Six anti-N mAbs (4G3, 5B3, 12B6, 18C7-A2, 21H10-A3, 21H10-E9) were prepared by recombinant N protein. The mAbs showed high titers, antibody affinity, and reactivity with the SARS-CoV-2 N protein. Then, fourteen overlapped peptides that covered the intact N protein were synthesized (N1-N14). Peptide N14 was identified as the main linear B-cell epitope region via peptide-ELISA and dot-blot assay, and this region was truncated gradually until mapping the peptide 401-DFSKQLQQ-408. Simultaneously, compared with the sequence of variants of concern (VOCs) and variants of interest (VOIs) strains among the several countries, epitope 401-DFSKQLQQ-408 is very conservative among them. The findings provide new guidance for the design and detection of COVID-19 targets. KEY POINTS: • The N protein was optimized according to the insect cell codon preference and was highly expressed. • The monoclonal antibodies prepared in this study were shown high antibody titers and high affinity. • Monoclonal antibodies were used to map the epitope 401-408 amino acids of N protein for the first time in this study.
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Affiliation(s)
- Yuanyuan Tian
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Gaiping Zhang
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Hongliang Liu
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Peiyang Ding
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Rui Jia
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Jingming Zhou
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Yumei Chen
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Yanhua Qi
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Jinran Du
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Chao Liang
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Xifang Zhu
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China
| | - Aiping Wang
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, People's Republic of China.
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14
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Martí S, Arafet K, Lodola A, Mulholland AJ, Świderek K, Moliner V. Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 M pro Explored by QM/MM Simulations. ACS Catal 2022; 12:698-708. [PMID: 35036042 PMCID: PMC8751016 DOI: 10.1021/acscatal.1c04661] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/17/2021] [Indexed: 12/18/2022]
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus-2, SARS-CoV-2, shows the need for effective antiviral treatments. Here, we present a simulation study of the inhibition of the SARS-CoV-2 main protease (Mpro), a cysteine hydrolase essential for the life cycle of the virus. The free energy landscape for the mechanism of the inhibition process is explored by QM/MM umbrella sampling and free energy perturbation simulations at the M06-2X/MM level of theory for two proposed peptidyl covalent inhibitors that share the same recognition motif but feature distinct cysteine-targeting warheads. Regardless of the intrinsic reactivity of the modeled inhibitors, namely a Michael acceptor and a hydroxymethyl ketone activated carbonyl, our results confirm that the inhibitory process takes place by means of a two-step mechanism, in which the formation of an ion pair C145/H41 dyad precedes the protein-inhibitor covalent bond formation. The nature of this second step is strongly dependent on the functional groups in the warhead: while the nucleophilic attack of the C145 sulfur atom on the Cα of the double bond of the Michael acceptor takes place concertedly with the proton transfer from H41 to Cβ, in the compound with an activated carbonyl, the sulfur attacks the carbonyl carbon concomitant with a proton transfer from H41 to the carbonyl oxygen via the hydroxyl group. An analysis of the free energy profiles, structures along the reaction path, and interactions between the inhibitors and the different pockets of the active site on the protein shows a measurable effect of the warhead on the kinetics and thermodynamics of the process. These results and QM/MM methods can be used as a guide to select warheads to design efficient irreversible and reversible inhibitors of SARS-CoV-2 Mpro.
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Affiliation(s)
- Sergio Martí
- BioComp
Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain
| | - Kemel Arafet
- BioComp
Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, I-43124 Parma, Italy
| | - Alessio Lodola
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, I-43124 Parma, Italy
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Katarzyna Świderek
- BioComp
Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain
| | - Vicent Moliner
- BioComp
Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain
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15
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Mathew BJ, Gupta S, Nema RK, Vyas AK, Khare P, Biswas D, Singh AK. Genomic, proteomic and metabolomic profiling of severe acute respiratory syndrome-Coronavirus-2. Computational Approaches for Novel Therapeutic and Diagnostic Designing to Mitigate SARS-CoV-2 Infection 2022. [DOI: 10.1016/b978-0-323-91172-6.00019-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2) is one of the worst human health problems faced by humanity in recent centuries. An end to this health crisis relies on our ability to monitor viral transmission dynamics to check spread, develop therapeutics and preventatives for treatment of SARS-CoV-2 infection and understand the pathophysiology of the disease for better management of the patients. Omics technologies have played a crucial part in understanding the different aspects of COVID-19 disease. While whole-genome sequencing of SARS-CoV-2 isolates from across the globe has aided in the development of molecular diagnostic assays and informed about the viral evolution, knowledge of structure and function of viral proteome fueled the development of small molecule and biologicals therapeutics as well as vaccines. Concurrently, metabolomic profiling of samples from COVID-19 patients experiencing a varying level of disease severity has provided a snapshot of the pathophysiology of the disease helping device effective treatment regimen. This chapter deals with genomic, proteomic, and metabolomic profiling of SRAS-CoV-2.
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16
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Gupta D, Sharma P, Singh M, Kumar M, Ethayathulla AS, Kaur P. Structural and functional insights into the spike protein mutations of emerging SARS-CoV-2 variants. Cell Mol Life Sci 2021; 78:7967-89. [PMID: 34731254 DOI: 10.1007/s00018-021-04008-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 02/07/2023]
Abstract
Since the emergence of the first case of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2), the viral genome has constantly undergone rapid mutations for better adaptation in the host system. These newer mutations have given rise to several lineages/ variants of the virus that have resulted in high transmission and virulence rates compared to the previously circulating variants. Owing to this, the overall caseload and related mortality have tremendously increased globally to > 233 million infections and > 4.7 million deaths as of Sept. 28th, 2021. SARS-CoV-2, Spike (S) protein binds to host cells by recognizing human angiotensin-converting enzyme 2 (hACE2) receptor. The viral S protein contains S1 and S2 domains that constitute the binding and fusion machinery, respectively. Structural analysis of viral S protein reveals that the virus undergoes conformational flexibility and dynamicity to interact with the hACE2 receptor. The SARS-CoV-2 variants and mutations might be associated with affecting the conformational plasticity of S protein, potentially linked to its altered affinity, infectivity, and immunogenicity. This review focuses on the current circulating variants of SARS-CoV-2 and the structure-function analysis of key S protein mutations linked with increased affinity, higher infectivity, enhanced transmission rates, and immune escape against this infection.
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17
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Berdowska I, Matusiewicz M. Cathepsin L, transmembrane peptidase/serine subfamily member 2/4, and other host proteases in COVID-19 pathogenesis – with impact on gastrointestinal tract. World J Gastroenterol 2021; 27:6590-6600. [PMID: 34754154 PMCID: PMC8554394 DOI: 10.3748/wjg.v27.i39.6590] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/28/2021] [Accepted: 09/19/2021] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) seems to employ two routes of entrance to the host cell; via membrane fusion (with the cells expressing both angiotensin converting enzyme 2 (ACE2) and transmembrane peptidase/serine subfamily member 2/4 (TMPRSS2/4)) or via receptor-mediated endocytosis (to the target cells expressing only ACE2). The second mode is associated with cysteine cathepsins (probably cathepsin L) involvement in the virus spike protein (S protein) proteolytic activation. Also furin might activate the virus S protein enabling it to enter cells. Gastrointestinal tract (GIT) involvement in SARS-CoV-2 infection is evident in a subset of coronavirus disease 2019 (COVID-19) patients exhibiting GIT symptoms, such as diarrhea, and presenting viral-shedding in feces. Considering the abundance and co-localization of ACE2 and TMPRSS2 in the lower GIT (especially brush-border enterocytes), these two receptors seem to be mainly involved in SARS-CoV-2 invasion of the digestive tract. Additionally, in vitro studies have demonstrated the virions capability of infection and replication in the human epithelial cells lining GIT. However, also furin and cysteine cathepsins (cathepsin L) might participate in the activation of SARS-CoV-2 spike protein contributing to the virus invasiveness within GIT. Moreover, cathepsin L (due to its involvement in extracellular matrix components degradation and remodeling, the processes enhanced during SARS-CoV-2-induced inflammation) might be responsible for the dysregulation of absorption/ digestion functions of GIT, thus adding to the observed in some COVID-19 patients symptoms such as diarrhea.
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Affiliation(s)
- Izabela Berdowska
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, Wroclaw 50-368, Lower Silesia, Poland
| | - Malgorzata Matusiewicz
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, Wroclaw 50-368, Lower Silesia, Poland
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18
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Prahlad J, Struble LR, Lutz WE, Wallin SA, Khurana S, Schnaubelt A, Broadhurst MJ, Bayles KW, Borgstahl GEO. CyDisCo production of functional recombinant SARS-CoV-2 spike receptor binding domain. Protein Sci 2021; 30:1983-1990. [PMID: 34191362 PMCID: PMC8376421 DOI: 10.1002/pro.4152] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/14/2021] [Accepted: 06/22/2021] [Indexed: 01/05/2023]
Abstract
The COVID‐19 pandemic caused by SARS‐CoV‐2 has applied significant pressure on overtaxed healthcare around the world, underscoring the urgent need for rapid diagnosis and treatment. We have developed a bacterial strategy for the expression and purification of a SARS‐CoV‐2 spike protein receptor binding domain (RBD) that includes the SD1 domain. Bacterial cytoplasm is a reductive environment, which is problematic when the recombinant protein of interest requires complicated folding and/or processing. The use of the CyDisCo system (cytoplasmic disulfide bond formation in E. coli) bypasses this issue by pre‐expressing a sulfhydryl oxidase and a disulfide isomerase, allowing the recombinant protein to be correctly folded with disulfide bonds for protein integrity and functionality. We show that it is possible to quickly and inexpensively produce an active RBD in bacteria that is capable of recognizing and binding to the ACE2 (angiotensin‐converting enzyme) receptor as well as antibodies in COVID‐19 patient sera.
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Affiliation(s)
- Janani Prahlad
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Lucas R Struble
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - William E Lutz
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Savanna A Wallin
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, Maryland, USA
| | - Andy Schnaubelt
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Mara J Broadhurst
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Kenneth W Bayles
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Gloria E O Borgstahl
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA.,Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
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19
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Matsuo T. Viewing SARS-CoV-2 Nucleocapsid Protein in Terms of Molecular Flexibility. Biology (Basel) 2021; 10:454. [PMID: 34064163 PMCID: PMC8224284 DOI: 10.3390/biology10060454] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 12/23/2022]
Abstract
The latest coronavirus SARS-CoV-2, which causes coronavirus disease 2019 (COVID-19) pneumonia leading to the pandemic, contains 29 proteins. Among them, nucleocapsid protein (NCoV2) is one of the abundant proteins and shows multiple functions including packaging the RNA genome during the infection cycle. It has also emerged as a potential drug target. In this review, the current status of the research of NCoV2 is described in terms of molecular structure and dynamics. NCoV2 consists of two domains, i.e., the N-terminal domain (NTD) and the C-terminal domain (CTD) with a disordered region between them. Recent simulation studies have identified several potential drugs that can bind to NTD or CTD with high affinity. Moreover, it was shown that the degree of flexibility in the disordered region has a large effect on drug binding rate, suggesting the importance of molecular flexibility for the NCoV2 function. Molecular flexibility has also been shown to be integral to the formation of droplets, where NCoV2, RNA and/or other viral proteins gather through liquid-liquid phase separation and considered important for viral replication. Finally, as one of the future research directions, a strategy for obtaining the structural and dynamical information on the proteins contained in droplets is presented.
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Affiliation(s)
- Tatsuhito Matsuo
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1106, Japan;
- Laboratoire Interdisciplinaire de Physique (LiPhy), Grenoble-Alpes University, 140 Rue de la Physique, 38402 Saint Martin d’Hères, France
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, CEDEX 9, 38042 Grenoble, France
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20
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Yamamoto N, Yamamoto R, Ariumi Y, Mizokami M, Shimotohno K, Yoshikura H. Does Genetic Predisposition Contribute to the Exacerbation of COVID-19 Symptoms in Individuals with Comorbidities and Explain the Huge Mortality Disparity between the East and the West? Int J Mol Sci 2021; 22:5000. [PMID: 34066804 DOI: 10.3390/ijms22095000] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/25/2021] [Accepted: 05/06/2021] [Indexed: 12/15/2022] Open
Abstract
The elderly and patients with several comorbidities experience more severe cases of coronavirus disease 2019 (COVID-19) than healthy patients without underlying medical conditions. However, it is unclear why these people are prone to developing alveolar pneumonia, rapid exacerbations, and death. Therefore, we hypothesized that people with comorbidities may have a genetic predisposition that makes them more vulnerable to various factors; for example, they are likely to become more severely ill when infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To test this hypothesis, we searched the literature extensively. Polymorphisms of genes, such as those that encode angiotensin-converting enzyme 1 (ACE1), have been associated with numerous comorbidities, such as cardiovascular disease, hypertension, diabetes, chronic kidney disease, and obesity, and there are potential mechanisms to explain these associations (e.g., DD-type carriers have greater ACE1 activity, and patients with a genetic alpha-1 anti-trypsin (AAT) deficiency lack control over inflammatory mediators). Since comorbidities are associated with chronic inflammation and are closely related to the renin–angiotensin–aldosterone system (RAAS), these individuals may already have a mild ACE1/ACE2 imbalance before viral infection, which increases their risk for developing severe cases of COVID-19. However, there is still much debate about the association between ACE1 D/I polymorphism and comorbidities. The best explanation for this discrepancy could be that the D allele and DD subtypes are associated with comorbidities, but the DD genotype alone does not have an exceptionally large effect. This is also expected since the ACE1 D/I polymorphism is only an intron marker. We also discuss how polymorphisms of AAT and other genes are involved in comorbidities and the severity of SARS-CoV-2 infection. Presumably, a combination of multiple genes and non-genetic factors is involved in the establishment of comorbidities and aggravation of COVID-19.
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21
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Fogeron ML, Lecoq L, Cole L, Harbers M, Böckmann A. Easy Synthesis of Complex Biomolecular Assemblies: Wheat Germ Cell-Free Protein Expression in Structural Biology. Front Mol Biosci 2021; 8:639587. [PMID: 33842544 PMCID: PMC8027086 DOI: 10.3389/fmolb.2021.639587] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/20/2021] [Indexed: 12/18/2022] Open
Abstract
Cell-free protein synthesis (CFPS) systems are gaining more importance as universal tools for basic research, applied sciences, and product development with new technologies emerging for their application. Huge progress was made in the field of synthetic biology using CFPS to develop new proteins for technical applications and therapy. Out of the available CFPS systems, wheat germ cell-free protein synthesis (WG-CFPS) merges the highest yields with the use of a eukaryotic ribosome, making it an excellent approach for the synthesis of complex eukaryotic proteins including, for example, protein complexes and membrane proteins. Separating the translation reaction from other cellular processes, CFPS offers a flexible means to adapt translation reactions to protein needs. There is a large demand for such potent, easy-to-use, rapid protein expression systems, which are optimally serving protein requirements to drive biochemical and structural biology research. We summarize here a general workflow for a wheat germ system providing examples from the literature, as well as applications used for our own studies in structural biology. With this review, we want to highlight the tremendous potential of the rapidly evolving and highly versatile CFPS systems, making them more widely used as common tools to recombinantly prepare particularly challenging recombinant eukaryotic proteins.
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Affiliation(s)
- Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Matthias Harbers
- CellFree Sciences, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
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22
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Abstract
The Coronavirus disease-19 (COVID-19) pandemic is still devastating the world causing significant social, economic, and political chaos. Corresponding to the absence of globally approved antiviral drugs for treatment and vaccines for controlling the pandemic, the number of cases and/or mortalities are still rising. Current patient management relies on supportive treatment and the use of repurposed drugs as an indispensable option. Of a crucial role in the viral life cycle, ongoing studies are looking for potential inhibitors to the main protease (Mpro) of severe acute respiratory syndrome Coronavirus -2 (SARS-CoV-2) to tackle the pandemic. Although promising results have been achieved in searching for drugs inhibiting the Mpro, work remains to be done on designing structure-based improved drugs. This review discusses the structural basis of potential inhibitors targeting SARS-CoV-2 Mpro, identifies gaps, and provides future directions. Further, compounds with potential Mpro based antiviral activity are highlighted.
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Affiliation(s)
- Hylemariam Mihiretie Mengist
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- 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
- Department of Medical Laboratory Science, College of Health Science, Debre Markos University, Debre Markos, Ethiopia
| | - Tebelay Dilnessa
- Department of Medical Laboratory Science, College of Health Science, Debre Markos University, Debre Markos, Ethiopia
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- 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
- CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Science, Shanghai, China
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23
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Gao T, Gao Y, Liu X, Nie Z, Sun H, Lin K, Peng H, Wang S. Identification and functional analysis of the SARS-COV-2 nucleocapsid protein. BMC Microbiol 2021; 21:58. [PMID: 33618668 PMCID: PMC7898026 DOI: 10.1186/s12866-021-02107-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/27/2021] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND A severe form of pneumonia, named coronavirus disease 2019 (COVID-19) by the World Health Organization is widespread on the whole world. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was proved to be the main agent of COVID-19. In the present study, we conducted an in depth analysis of the SARS-COV-2 nucleocapsid to identify potential targets that may allow identification of therapeutic targets. METHODS The SARS-COV-2 N protein subcellular localization and physicochemical property was analyzed by PSORT II Prediction and ProtParam tool. Then SOPMA tool and swiss-model was applied to analyze the structure of N protein. Next, the biological function was explored by mass spectrometry analysis and flow cytometry. At last, its potential phosphorylation sites were analyzed by NetPhos3.1 Server and PROVEAN PROTEIN. RESULTS SARS-COV-2 N protein composed of 419 aa, is a 45.6 kDa positively charged unstable hydrophobic protein. It has 91 and 49% similarity to SARS-CoV and MERS-CoV and is predicted to be predominantly a nuclear protein. It mainly contains random coil (55.13%) of which the tertiary structure was further determined with high reliability (95.76%). Cells transfected with SARS-COV-2 N protein usually show a G1/S phase block company with an increased expression of TUBA1C, TUBB6. At last, our analysis of SARS-COV-2 N protein predicted a total number of 12 phosphorylated sites and 9 potential protein kinases which would significantly affect SARS-COV-2 N protein function. CONCLUSION In this study, we report the physicochemical properties, subcellular localization, and biological function of SARS-COV-2 N protein. The 12 phosphorylated sites and 9 potential protein kinase sites in SARS-COV-2 N protein may serve as promising targets for drug discovery and development for of a recombinant virus vaccine.
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Affiliation(s)
- Tianyi Gao
- Department of clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China
| | - Yingdong Gao
- Department of clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China
| | - Xiangxiang Liu
- Central Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China
| | - Zhenlin Nie
- Department of clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China
| | - Huilin Sun
- Central Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China
| | - Kang Lin
- Department of clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China
| | - Hongxin Peng
- Department of clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China
| | - Shukui Wang
- Department of clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China. .,Central Laboratory, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China. .,Jiangsu Collaborative Innovation Center on Cancer Personalized Medicine, Nanjing Medical University, 68 Changle Road, Nanjing, 210006, Jiangsu, China.
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24
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Freidel MR, Armen RS. Mapping major SARS-CoV-2 drug targets and assessment of druggability using computational fragment screening: Identification of an allosteric small-molecule binding site on the Nsp13 helicase. PLoS One 2021; 16:e0246181. [PMID: 33596235 DOI: 10.1371/journal.pone.0246181] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/14/2021] [Indexed: 01/18/2023] Open
Abstract
The 2019 emergence of, SARS-CoV-2 has tragically taken an immense toll on human life and far reaching impacts on society. There is a need to identify effective antivirals with diverse mechanisms of action in order to accelerate preclinical development. This study focused on five of the most established drug target proteins for direct acting small molecule antivirals: Nsp5 Main Protease, Nsp12 RNA-dependent RNA polymerase, Nsp13 Helicase, Nsp16 2'-O methyltransferase and the S2 subunit of the Spike protein. A workflow of solvent mapping and free energy calculations was used to identify and characterize favorable small-molecule binding sites for an aromatic pharmacophore (benzene). After identifying the most favorable sites, calculated ligand efficiencies were compared utilizing computational fragment screening. The most favorable sites overall were located on Nsp12 and Nsp16, whereas the most favorable sites for Nsp13 and S2 Spike had comparatively lower ligand efficiencies relative to Nsp12 and Nsp16. Utilizing fragment screening on numerous possible sites on Nsp13 helicase, we identified a favorable allosteric site on the N-terminal zinc binding domain (ZBD) that may be amenable to virtual or biophysical fragment screening efforts. Recent structural studies of the Nsp12:Nsp13 replication-transcription complex experimentally corroborates ligand binding at this site, which is revealed to be a functional Nsp8:Nsp13 protein-protein interaction site in the complex. Detailed structural analysis of Nsp13 ZBD conformations show the role of induced-fit flexibility in this ligand binding site and identify which conformational states are associated with efficient ligand binding. We hope that this map of over 200 possible small-molecule binding sites for these drug targets may be of use for ongoing discovery, design, and drug repurposing efforts. This information may be used to prioritize screening efforts or aid in the process of deciphering how a screening hit may bind to a specific target protein.
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25
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何 文, 陈 清. [Progress in source tracking of SARS-CoV-2]. Nan Fang Yi Ke Da Xue Xue Bao 2020; 40:1838-1842. [PMID: 33380405 PMCID: PMC7835685 DOI: 10.12122/j.issn.1673-4254.2020.12.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Indexed: 12/15/2022]
Abstract
Coronavirus disease 2019 (COVID-19) pandemic has caused a total of 55 928 327 confirmed cases and 1 344 003 deaths as of November 19, 2020. But so far the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes this pandemic has remained undetermined. The purpose of this study is to review the current research of SARS-CoV-2 and the existing problems therein, which may provide inspiration for further researches. Existing evidence suggested that SARS-CoV-2 may be derived from bat coronavirus 40-70 years ago. During the evolution, this virus underwent extensive variations in the process of mutations and natural selection. Different genomic regions of SARS-CoV-2 may have different selection pressures, but all of which increase the difficulty of tracing the origin of this virus. A wide variety of animals have been considered as potential hosts of SARS-CoV-2, including cats, lions, tigers, dogs and minks. SARS-CoV-2 has a chance to transmit from humans to animals and can be transmitted among animals. Current research evidence has shown that China is not the original source of SARS-CoV-2. It is still unclear how the virus spreads to human, and efforts are still need to be made to explore the origin of SARS-CoV-2, its hosts and intermediate hosts, and the mechanism of its transmission across different species of animals.
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Affiliation(s)
- 文巧 何
- />南方医科大学公共卫生学院流行病学系,广东 广州 510515Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou 510515, China
| | - 清 陈
- />南方医科大学公共卫生学院流行病学系,广东 广州 510515Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou 510515, China
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26
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Neumaier F, Zlatopolskiy BD, Neumaier B. Nuclear Medicine in Times of COVID-19: How Radiopharmaceuticals Could Help to Fight the Current and Future Pandemics. Pharmaceutics 2020; 12:E1247. [PMID: 33371500 PMCID: PMC7767508 DOI: 10.3390/pharmaceutics12121247] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
The emergence and global spread of COVID-19, an infectious disease caused by the novel coronavirus SARS-CoV-2, has resulted in a continuing pandemic threat to global health. Nuclear medicine techniques can be used for functional imaging of (patho)physiological processes at the cellular or molecular level and for treatment approaches based on targeted delivery of therapeutic radionuclides. Ongoing development of radiolabeling methods has significantly improved the accessibility of radiopharmaceuticals for in vivo molecular imaging or targeted radionuclide therapy, but their use for biosafety threats such as SARS-CoV-2 is restricted by the contagious nature of these agents. Here, we highlight several potential uses of nuclear medicine in the context of SARS-CoV-2 and COVID-19, many of which could also be performed in laboratories without dedicated containment measures. In addition, we provide a broad overview of experimental or repurposed SARS-CoV-2-targeting drugs and describe how radiolabeled analogs of these compounds could facilitate antiviral drug development and translation to the clinic, reduce the incidence of late-stage failures and possibly provide the basis for radionuclide-based treatment strategies. Based on the continuing threat by emerging coronaviruses and other pathogens, it is anticipated that these applications of nuclear medicine will become a more important part of future antiviral drug development and treatment.
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Affiliation(s)
- Felix Neumaier
- Forschungszentrum Jülich GmbH, Institute of Neuroscience and Medicine, Nuclear Chemistry (INM-5), Wilhelm-Johnen-Str., 52428 Jülich, Germany; (B.D.Z.); (B.N.)
- Institute of Radiochemistry and Experimental Molecular Imaging, Faculty of Medicine and University Hospital Cologne, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Boris D. Zlatopolskiy
- Forschungszentrum Jülich GmbH, Institute of Neuroscience and Medicine, Nuclear Chemistry (INM-5), Wilhelm-Johnen-Str., 52428 Jülich, Germany; (B.D.Z.); (B.N.)
- Institute of Radiochemistry and Experimental Molecular Imaging, Faculty of Medicine and University Hospital Cologne, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Max Planck Institute for Metabolism Research, 50931 Cologne, Germany
| | - Bernd Neumaier
- Forschungszentrum Jülich GmbH, Institute of Neuroscience and Medicine, Nuclear Chemistry (INM-5), Wilhelm-Johnen-Str., 52428 Jülich, Germany; (B.D.Z.); (B.N.)
- Institute of Radiochemistry and Experimental Molecular Imaging, Faculty of Medicine and University Hospital Cologne, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
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27
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Halder A, Anto A, Subramanyan V, Bhattacharyya M, Vishveshwara S, Vishveshwara S. Surveying the Side-Chain Network Approach to Protein Structure and Dynamics: The SARS-CoV-2 Spike Protein as an Illustrative Case. Front Mol Biosci 2020; 7:596945. [PMID: 33392257 PMCID: PMC7775578 DOI: 10.3389/fmolb.2020.596945] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/04/2020] [Indexed: 02/04/2023] Open
Abstract
Network theory-based approaches provide valuable insights into the variations in global structural connectivity between different dynamical states of proteins. Our objective is to review network-based analyses to elucidate such variations, especially in the context of subtle conformational changes. We present technical details of the construction and analyses of protein structure networks, encompassing both the non-covalent connectivity and dynamics. We examine the selection of optimal criteria for connectivity based on the physical concept of percolation. We highlight the advantages of using side-chain-based network metrics in contrast to backbone measurements. As an illustrative example, we apply the described network approach to investigate the global conformational changes between the closed and partially open states of the SARS-CoV-2 spike protein. These conformational changes in the spike protein is crucial for coronavirus entry and fusion into human cells. Our analysis reveals global structural reorientations between the two states of the spike protein despite small changes between the two states at the backbone level. We also observe some differences at strategic locations in the structures, correlating with their functions, asserting the advantages of the side-chain network analysis. Finally, we present a view of allostery as a subtle synergistic-global change between the ligand and the receptor, the incorporation of which would enhance drug design strategies.
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Affiliation(s)
- Anushka Halder
- Department of Pharmacology, Yale University, New Haven, CT, United States
| | - Arinnia Anto
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Varsha Subramanyan
- Department of Physics, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | | | - Smitha Vishveshwara
- Department of Physics, University of Illinois at Urbana-Champaign, Champaign, IL, United States
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28
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Arafet K, Serrano-Aparicio N, Lodola A, Mulholland AJ, González FV, Świderek K, Moliner V. Mechanism of inhibition of SARS-CoV-2 M pro by N3 peptidyl Michael acceptor explained by QM/MM simulations and design of new derivatives with tunable chemical reactivity. Chem Sci 2020; 12:1433-1444. [PMID: 34163906 PMCID: PMC8179034 DOI: 10.1039/d0sc06195f] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The SARS-CoV-2 main protease (Mpro) is essential for replication of the virus responsible for the COVID-19 pandemic, and one of the main targets for drug design. Here, we simulate the inhibition process of SARS-CoV-2 Mpro with a known Michael acceptor (peptidyl) inhibitor, N3. The free energy landscape for the mechanism of the formation of the covalent enzyme-inhibitor product is computed with QM/MM molecular dynamics methods. The simulations show a two-step mechanism, and give structures and calculated barriers in good agreement with experiment. Using these results and information from our previous investigation on the proteolysis reaction of SARS-CoV-2 Mpro, we design two new, synthetically accessible N3-analogues as potential inhibitors, in which the recognition and warhead motifs are modified. QM/MM modelling of the mechanism of inhibition of Mpro by these novel compounds indicates that both may be promising candidates as drug leads against COVID-19, one as an irreversible inhibitor and one as a potential reversible inhibitor.
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Affiliation(s)
- Kemel Arafet
- Departament de Química Física i Analítica, Universitat Jaume I 12071 Castelló Spain
| | | | - Alessio Lodola
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma Italy
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol UK
| | - Florenci V González
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I 12071 Castelló Spain
| | - Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I 12071 Castelló Spain
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I 12071 Castelló Spain
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