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Kumari S, Mistry H, Bihani SC, Mukherjee SP, Gupta GD. Unveiling potential inhibitors targeting the nucleocapsid protein of SARS-CoV-2: Structural insights into their binding sites. Int J Biol Macromol 2024; 273:133167. [PMID: 38885868 DOI: 10.1016/j.ijbiomac.2024.133167] [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: 04/05/2024] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Abstract
The Nucleocapsid (N) protein of SARS-CoV-2 plays a crucial role in viral replication and pathogenesis, making it an attractive target for developing antiviral therapeutics. In this study, we used differential scanning fluorimetry to establish a high-throughput screening method for identifying high-affinity ligands of N-terminal domain of the N protein (N-NTD). We screened an FDA-approved drug library of 1813 compounds and identified 102 compounds interacting with N-NTD. The screened compounds were further investigated for their ability to inhibit the nucleic-acid binding activity of the N protein using electrophoretic mobility-shift assays. We have identified three inhibitors, Ceftazidime, Sennoside A, and Tannic acid, that disrupt the N protein's interaction with RNA probe. Ceftazidime and Sennoside A exhibited nano-molar range binding affinities with N protein, determined through surface plasmon resonance. The binding sites of Ceftazidime and Sennoside A were investigated using [1H, 15N]-heteronuclear single quantum coherence (HSQC) NMR spectroscopy. Ceftazidime and Sennoside A bind to the putative RNA binding site of the N protein, thus providing insights into the inhibitory mechanism of these compounds. These findings will contribute to the development of novel antiviral agents targeting the N protein of SARS-CoV-2.
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Affiliation(s)
- Shweta Kumari
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Hiral Mistry
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Subhash C Bihani
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Sulakshana P Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha 760003, India
| | - Gagan D Gupta
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India.
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2
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Cheng S, Feng Y, Li W, Liu T, Lv X, Tong X, Xi G, Ye X, Li X. Development of novel antivrial agents that induce the degradation of the main protease of human-infecting coronaviruses. Eur J Med Chem 2024; 275:116629. [PMID: 38941718 DOI: 10.1016/j.ejmech.2024.116629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 06/30/2024]
Abstract
The family of human-infecting coronaviruses (HCoVs) poses a serious threat to global health and includes several highly pathogenic strains that cause severe respiratory illnesses. It is essential that we develop effective broad-spectrum anti-HCoV agents to prepare for future outbreaks. In this study, we used PROteolysis TArgeting Chimera (PROTAC) technology focused on degradation of the HCoV main protease (Mpro), a conserved enzyme essential for viral replication and pathogenicity. By adapting the Mpro inhibitor GC376, we produced two novel PROTACs, P2 and P3, which showed relatively broad-spectrum activity against the human-infecting CoVs HCoV-229E, HCoV-OC43, and SARS-CoV-2. The concentrations of these PROTACs that reduced virus replication by 50 % ranged from 0.71 to 4.6 μM, and neither showed cytotoxicity at 100 μM. Furthermore, mechanistic binding studies demonstrated that P2 and P3 effectively targeted HCoV-229E, HCoV-OC43, and SARS-CoV-2 by degrading Mpro within cells in vitro. This study highlights the potential of PROTAC technology in the development of broad-spectrum anti-HCoVs agents, presenting a novel approach for dealing with future viral outbreaks, particularly those stemming from CoVs.
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Affiliation(s)
- Shuihong Cheng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China.
| | - Yong Feng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Wei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
| | - Tong Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China
| | - Xun Lv
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China
| | - Xiaomei Tong
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Gan Xi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China
| | - Xin Ye
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China
| | - Xuebing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China.
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3
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Han L, Wang B, Sun K, Sitara M, Li M, Wang P, Chen N, Yu XA, Tian J. A SARS-CoV-2 M pro fluorescent sensor for exploring pharmacodynamic substances from traditional Chinese medicine. Analyst 2024; 149:3585-3595. [PMID: 38767148 DOI: 10.1039/d4an00372a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The main protease of SARS-CoV-2 (SARS-CoV-2 Mpro) plays a critical role in the replication and life cycle of the virus. Currently, how to screen SARS-CoV-2 Mpro inhibitors from complex traditional Chinese medicine (TCM) is the bottleneck for exploring the pharmacodynamic substances of TCM against SARS-CoV-2. In this study, a simple, cost-effective, rapid, and selective fluorescent sensor (TPE-S-TLG sensor) was designed with an AIE (aggregation-induced emission) probe (TPE-Ph-In) and the SARS-CoV-2 Mpro substrate (S-TLG). The TPE-S-TLG sensor was characterized using UV-Vis absorption spectroscopy, fluorescence spectroscopy, dynamic light scattering (DLS), transmission electron microscopy (TEM), zeta potential, and Fourier transform infrared (FTIR) spectroscopy techniques. The limit of detection of this method to detect SARS-CoV-2 Mpro was measured to be 5 ng mL-1. Furthermore, the TPE-S-TLG sensor was also successfully applied to screen Mpro inhibitors from Xuebijing injection using the separation and collection of the HPLC-fully automatic partial fraction collector (HPLC-FC). Six active compounds, including protocatechualdehyde, chlorogenic acid, hydroxysafflower yellow A, caffeic acid, isoquercetin, and pentagalloylglucose, were identified using UHPLC-Q-TOF/MS that could achieve 90% of the Mpro inhibition rate for the Xuebijing injection. Accordingly, the strategy can be broadly applied in the detection of disease-related proteases as well as screening active substances from TCM.
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Affiliation(s)
- Lei Han
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China.
| | - Bing Wang
- NMPA Key Laboratory for Quality Research and Evaluation of Traditional Chinese Medicine, Shenzhen Institute for Drug Control, Shenzhen, 518057, People's Republic of China.
| | - Kunhui Sun
- NMPA Key Laboratory for Quality Research and Evaluation of Traditional Chinese Medicine, Shenzhen Institute for Drug Control, Shenzhen, 518057, People's Republic of China.
| | - Muqadas Sitara
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China.
| | - Meifang Li
- NMPA Key Laboratory for Quality Research and Evaluation of Traditional Chinese Medicine, Shenzhen Institute for Drug Control, Shenzhen, 518057, People's Republic of China.
| | - Ping Wang
- NMPA Key Laboratory for Quality Research and Evaluation of Traditional Chinese Medicine, Shenzhen Institute for Drug Control, Shenzhen, 518057, People's Republic of China.
| | - Ning Chen
- NMPA Key Laboratory for Quality Research and Evaluation of Traditional Chinese Medicine, Shenzhen Institute for Drug Control, Shenzhen, 518057, People's Republic of China.
| | - Xie-An Yu
- NMPA Key Laboratory for Quality Research and Evaluation of Traditional Chinese Medicine, Shenzhen Institute for Drug Control, Shenzhen, 518057, People's Republic of China.
| | - Jiangwei Tian
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China.
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4
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Khachatryan H, Matevosyan M, Harutyunyan V, Gevorgyan S, Shavina A, Tirosyan I, Gabrielyan Y, Ayvazyan M, Bozdaganyan M, Fakhar Z, Gharaghani S, Zakaryan H. Computational evaluation and benchmark study of 342 crystallographic holo-structures of SARS-CoV-2 Mpro enzyme. Sci Rep 2024; 14:14255. [PMID: 38902397 PMCID: PMC11189913 DOI: 10.1038/s41598-024-65228-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 06/18/2024] [Indexed: 06/22/2024] Open
Abstract
The coronavirus disease 19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global health crisis with millions of confirmed cases and related deaths. The main protease (Mpro) of SARS-CoV-2 is crucial for viral replication and presents an attractive target for drug development. Despite the approval of some drugs, the search for effective treatments continues. In this study, we systematically evaluated 342 holo-crystal structures of Mpro to identify optimal conformations for structure-based virtual screening (SBVS). Our analysis revealed limited structural flexibility among the structures. Three docking programs, AutoDock Vina, rDock, and Glide were employed to assess the efficiency of virtual screening, revealing diverse performances across selected Mpro structures. We found that the structures 5RHE, 7DDC, and 7DPU (PDB Ids) consistently displayed the lowest EF, AUC, and BEDROCK scores. Furthermore, these structures demonstrated the worst pose prediction results in all docking programs. Two structural differences contribute to variations in docking performance: the absence of the S1 subsite in 7DDC and 7DPU, and the presence of a subpocket in the S2 subsite of 7DDC, 7DPU, and 5RHE. These findings underscore the importance of selecting appropriate Mpro conformations for SBVS, providing valuable insights for advancing drug discovery efforts.
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Affiliation(s)
- Hamlet Khachatryan
- Denovo Sciences Inc, 0060, Yerevan, Armenia.
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia.
| | - Mher Matevosyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Vardan Harutyunyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Smbat Gevorgyan
- Denovo Sciences Inc, 0060, Yerevan, Armenia
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Anastasiya Shavina
- Denovo Sciences Inc, 0060, Yerevan, Armenia
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Irina Tirosyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Yeva Gabrielyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | - Marusya Ayvazyan
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia
| | | | - Zeynab Fakhar
- Laboratory of Bioinformatics and Drug Design (LBD), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Sajjad Gharaghani
- Laboratory of Bioinformatics and Drug Design (LBD), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Hovakim Zakaryan
- Denovo Sciences Inc, 0060, Yerevan, Armenia.
- Laboratory of Antiviral Drug Discovery, Institute of Molecular Biology of NAS, Hasratyan 7, 0014, Yerevan, Armenia.
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5
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Sokolinskaya EL, Ivanova ON, Fedyakina IT, Ivanov AV, Lukyanov KA. Natural-Target-Mimicking Translocation-Based Fluorescent Sensor for Detection of SARS-CoV-2 PLpro Protease Activity and Virus Infection in Living Cells. Int J Mol Sci 2024; 25:6635. [PMID: 38928340 PMCID: PMC11203561 DOI: 10.3390/ijms25126635] [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: 05/11/2024] [Revised: 06/13/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
Papain-like protease PLpro, a domain within a large polyfunctional protein, nsp3, plays key roles in the life cycle of SARS-CoV-2, being responsible for the first events of cleavage of a polyprotein into individual proteins (nsp1-4) as well as for the suppression of cellular immunity. Here, we developed a new genetically encoded fluorescent sensor, named PLpro-ERNuc, for detection of PLpro activity in living cells using a translocation-based readout. The sensor was designed as follows. A fragment of nsp3 protein was used to direct the sensor on the cytoplasmic surface of the endoplasmic reticulum (ER) membrane, thus closely mimicking the natural target of PLpro. The fluorescent part included two bright fluorescent proteins-red mScarlet I and green mNeonGreen-separated by a linker with the PLpro cleavage site. A nuclear localization signal (NLS) was attached to ensure accumulation of mNeonGreen into the nucleus upon cleavage. We tested PLpro-ERNuc in a model of recombinant PLpro expressed in HeLa cells. The sensor demonstrated the expected cytoplasmic reticular network in the red and green channels in the absence of protease, and efficient translocation of the green signal into nuclei in the PLpro-expressing cells (14-fold increase in the nucleus/cytoplasm ratio). Then, we used PLpro-ERNuc in a model of Huh7.5 cells infected with the SARS-CoV-2 virus, where it showed robust ER-to-nucleus translocation of the green signal in the infected cells 24 h post infection. We believe that PLpro-ERNuc represents a useful tool for screening PLpro inhibitors as well as for monitoring virus spread in a culture.
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Affiliation(s)
- Elena L. Sokolinskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
| | - Olga N. Ivanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (O.N.I.); (A.V.I.)
| | - Irina T. Fedyakina
- Gamaleya National Research Centre for Epidemiology and Microbiology of the Ministry of Russia, 132098 Moscow, Russia;
| | - Alexander V. Ivanov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (O.N.I.); (A.V.I.)
| | - Konstantin A. Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia;
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6
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Furukawa H, Nakamura S, Mizuta R, Sakamoto K, Inaba H, Sawada SI, Sasaki Y, Akiyoshi K, Matsuura K. Enveloped Viral Replica Equipped with Spike Protein Derived from SARS-CoV-2. ACS Synth Biol 2024. [PMID: 38885191 DOI: 10.1021/acssynbio.4c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Synthetic viral nanostructures are useful as materials for analyzing the biological behavior of natural viruses and as vaccine materials. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped virus embedding a spike (S) protein involved in host cell infection. Although nanomaterials modified with an S protein without an envelope membrane have been developed, they are considered unsuitable for stability and functionality. We previously constructed an enveloped viral replica complexed with a cationic lipid bilayer and an anionic artificial viral capsid self-assembled from β-annulus peptides. In this study, we report the first example of an enveloped viral replica equipped with an S protein derived from SARS-CoV-2. Interestingly, even the S protein equipped on the enveloped viral replica bound strongly to the free angiotensin-converting enzyme 2 (ACE2) receptor as well as ACE2 localized on the cell membrane.
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Affiliation(s)
- Hiroto Furukawa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Sosuke Nakamura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Ryosuke Mizuta
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kentarou Sakamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
| | - Shin-Ichi Sawada
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Synergy Institute for Futuristic Mucosal Vaccine Research and Development, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Yoshihiro Sasaki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kazunari Akiyoshi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Department of Immunology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
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7
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Takada K, Orba Y, Kida Y, Wu J, Ono C, Matsuura Y, Nakagawa S, Sawa H, Watanabe T. Genes involved in the limited spread of SARS-CoV-2 in the lower respiratory airways of hamsters may be associated with adaptive evolution. J Virol 2024; 98:e0178423. [PMID: 38624229 PMCID: PMC11092350 DOI: 10.1128/jvi.01784-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/17/2024] [Indexed: 04/17/2024] Open
Abstract
Novel respiratory viruses can cause a pandemic and then evolve to coexist with humans. The Omicron strain of severe acute respiratory syndrome coronavirus 2 has spread worldwide since its emergence in late 2021, and its sub-lineages are now established in human society. Compared to previous strains, Omicron is markedly less invasive in the lungs and causes less severe disease. One reason for this is that humans are acquiring immunity through previous infection and vaccination, but the nature of the virus itself is also changing. Using our newly established low-volume inoculation system, which reflects natural human infection, we show that the Omicron strain spreads less efficiently into the lungs of hamsters compared with an earlier Wuhan strain. Furthermore, by characterizing chimeric viruses with the Omicron gene in the Wuhan strain genetic background and vice versa, we found that viral genes downstream of ORF3a, but not the S gene, were responsible for the limited spread of the Omicron strain in the lower airways of the virus-infected hamsters. Moreover, molecular evolutionary analysis of SARS-CoV-2 revealed a positive selection of genes downstream of ORF3a (M and E genes). Our findings provide insight into the adaptive evolution of the virus in humans during the pandemic convergence phase.IMPORTANCEThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has spread worldwide since its emergence in late 2021, and its sub-lineages are established in human society. Compared to previous strains, the Omicron strain is less invasive in the lower respiratory tract, including the lungs, and causes less severe disease; however, the mechanistic basis for its restricted replication in the lower airways is poorly understood. In this study, using a newly established low-volume inoculation system that reflects natural human infection, we demonstrated that the Omicron strain spreads less efficiently into the lungs of hamsters compared with an earlier Wuhan strain and found that viral genes downstream of ORF3a are responsible for replication restriction in the lower respiratory tract of Omicron-infected hamsters. Furthermore, we detected a positive selection of genes downstream of ORF3a (especially the M and E genes) in SARS-CoV-2, suggesting that these genes may undergo adaptive changes in humans.
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Grants
- 16H06429, 16K21723, 16H06434, JP22H02521 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21H02736 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP16K21723, JP16H06432 MEXT | Japan Society for the Promotion of Science (JSPS)
- 22K15469, 21J01036 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP20fk0108281, JP19fk0108113, JP20pc0101047 Japan Agency for Medical Research and Development (AMED)
- JP20fk0108401, JP21fk0108493 Japan Agency for Medical Research and Development (AMED)
- JP23wm0125008, JP223fa627005 Japan Agency for Medical Research and Development (AMED)
- JP19fk018113, JP223fa627002h, 22gm1610010h0001 Japan Agency for Medical Research and Development (AMED)
- JPMJMS2025 MEXT | Japan Science and Technology Agency (JST)
- JPMJCR20H6 MEXT | Japan Science and Technology Agency (JST)
- Takeda Science Foundation (TSF)
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Affiliation(s)
- Kosuke Takada
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yurie Kida
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Jiaqi Wu
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Chikako Ono
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - Yoshiharu Matsuura
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hirofumi Sawa
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Hokkaido, Japan
- Global Virus Network, Baltimore, Maryland, USA
| | - Tokiko Watanabe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Suita, Osaka, Japan
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8
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Gori Savellini G, Anichini G, Manetti F, Trivisani CI, Cusi MG. Deletion of 82-85 N-Terminal Residues in SARS-CoV-2 Nsp1 Restricts Virus Replication. Viruses 2024; 16:689. [PMID: 38793572 PMCID: PMC11125901 DOI: 10.3390/v16050689] [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: 04/03/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Non-structural protein 1 (Nsp1) represents one of the most crucial SARS-CoV-2 virulence factors by inhibiting the translation of host mRNAs and promoting their degradation. We selected naturally occurring virus lineages with specific Nsp1 deletions located at both the N- and C-terminus of the protein. Our data provide new insights into how Nsp1 coordinates these functions on host and viral mRNA recognition. Residues 82-85 in the N-terminal part of Nsp1 likely play a role in docking the 40S mRNA entry channel, preserving the inhibition of host gene expression without affecting cellular mRNA decay. Furthermore, this domain prevents viral mRNAs containing the 5'-leader sequence to escape translational repression. These findings support the presence of distinct domains within the Nsp1 protein that differentially modulate mRNA recognition, translation and turnover. These insights have implications for the development of drugs targeting viral proteins and provides new evidences of how specific mutations in SARS-CoV-2 Nsp1 could attenuate the virus.
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Affiliation(s)
| | - Gabriele Anichini
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy;
| | - Fabrizio Manetti
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy (C.I.T.)
| | | | - Maria Grazia Cusi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy;
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Lv X, Chen R, Liang T, Peng H, Fang Q, Xiao S, Liu S, Hu M, Yu F, Cao L, Zhang Y, Pan T, Xi Z, Ding Y, Feng L, Zeng T, Huang W, Zhang H, Ma X. NSP6 inhibits the production of ACE2-containing exosomes to promote SARS-CoV-2 infectivity. mBio 2024; 15:e0335823. [PMID: 38303107 PMCID: PMC10936183 DOI: 10.1128/mbio.03358-23] [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: 12/14/2023] [Accepted: 01/04/2024] [Indexed: 02/03/2024] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has triggered a global pandemic, which severely endangers public health. Our and others' works have shown that the angiotensin-converting enzyme 2 (ACE2)-containing exosomes (ACE2-exos) have superior antiviral efficacies, especially in response to emerging variants. However, the mechanisms of how the virus counteracts the host and regulates ACE2-exos remain unclear. Here, we identified that SARS-CoV-2 nonstructural protein 6 (NSP6) inhibits the production of ACE2-exos by affecting the protein level of ACE2 as well as tetraspanin-CD63 which is a key factor for exosome biogenesis. We further found that the protein stability of CD63 and ACE2 is maintained by the deubiquitination of proteasome 26S subunit, non-ATPase 12 (PSMD12). NSP6 interacts with PSMD12 and counteracts its function, consequently promoting the degradation of CD63 and ACE2. As a result, NSP6 diminishes the antiviral efficacy of ACE2-exos and facilitates the virus to infect healthy bystander cells. Overall, our study provides a valuable target for the discovery of promising drugs for the treatment of coronavirus disease 2019. IMPORTANCE The outbreak of coronavirus disease 2019 (COVID-19) severely endangers global public health. The efficacy of vaccines and antibodies declined with the rapid emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutants. Angiotensin-converting enzyme 2-containing exosomes (ACE2-exos) therapy exhibits a broad neutralizing activity, which could be used against various viral mutations. Our study here revealed that SARS-CoV-2 nonstructural protein 6 inhibited the production of ACE2-exos, thereby promoting viral infection to the adjacent bystander cells. The identification of a new target for blocking SARS-CoV-2 depends on fully understanding the virus-host interaction networks. Our study sheds light on the mechanism by which the virus resists the host exosome defenses, which would facilitate the study and design of ACE2-exos-based therapeutics for COVID-19.
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Affiliation(s)
- Xi Lv
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Ran Chen
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Taizhen Liang
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
| | - Haojie Peng
- Department of Breast Surgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Qiannan Fang
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Shiqi Xiao
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
| | - Sen Liu
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
| | - Meilin Hu
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
- Department of Breast Surgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Fei Yu
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Lixue Cao
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Yiwen Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ting Pan
- Center for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Zhihui Xi
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Yao Ding
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Linyuan Feng
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Tao Zeng
- Department of Breast Surgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wenjing Huang
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Hui Zhang
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiancai Ma
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
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10
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Mahgoub RE, Mohamed FE, Ali BR, Ferreira J, Rabeh WM, Atatreh N, Ghattas MA. Discovery of pyrimidoindol and benzylpyrrolyl inhibitors targeting SARS-CoV-2 main protease (M pro) through pharmacophore modelling, covalent docking, and biological evaluation. J Mol Graph Model 2024; 127:108672. [PMID: 37992552 DOI: 10.1016/j.jmgm.2023.108672] [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: 09/15/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
The main protease (Mpro) enzyme has an imperative function in disease progression and the life cycle of the SARS-CoV-2 virus. Although the orally active drug nirmatrelvir (co-administered with ritonavir as paxlovid) has been approved for emergency use as the frontline antiviral agent, there are a number of limitations that necessitate the discovery of new drug scaffolds, such as poor pharmacokinetics and susceptibility to proteolytic degradation due to its peptidomimetic nature. This study utilized a novel virtual screening workflow that combines pharmacophore modelling, multiple-receptor covalent docking, and biological evaluation in order to find new Mpro inhibitors. After filtering and analysing ∼66,000 ligands from three different electrophilic libraries, 29 compounds were shortlisted for experimental testing, and two of them exhibited ≥20% inhibition at 100 μM. Our top candidate, GF04, is a benzylpyrrolyl compound that exhibited the highest inhibition activity of 38.3%, with a relatively small size (<350 Da) and leadlike character. Interestingly, our approach also identified another hit, DR07, a pyrimidoindol with a non-peptide character, and a molecular weight of 438.9 Da, reporting an inhibition of 26.3%. The established approach detailed in this study, in conjunction with the discovered inhibitors, has the capacity to yield novel perspectives for devising covalent inhibitors targeting the COVID-19 Mpro enzyme and other comparable targets.
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Affiliation(s)
- Radwa E Mahgoub
- College of Pharmacy, Al Ain University, Abu Dhabi, 112612, United Arab Emirates; AAU Health and Biomedical Research Centre, Al Ain University, Abu Dhabi, 112612, United Arab Emirates
| | - Feda E Mohamed
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, 15551, United Arab Emirates; Zayed Centre for Health Sciences, United Arab Emirates University, Al-Ain, 15551, United Arab Emirates
| | - Juliana Ferreira
- Science Division, New York University Abu Dhabi, Abu Dhabi, 129188, United Arab Emirates
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, Abu Dhabi, 129188, United Arab Emirates
| | - Noor Atatreh
- College of Pharmacy, Al Ain University, Abu Dhabi, 112612, United Arab Emirates; AAU Health and Biomedical Research Centre, Al Ain University, Abu Dhabi, 112612, United Arab Emirates
| | - Mohammad A Ghattas
- College of Pharmacy, Al Ain University, Abu Dhabi, 112612, United Arab Emirates; AAU Health and Biomedical Research Centre, Al Ain University, Abu Dhabi, 112612, United Arab Emirates.
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11
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Albani S, Costanzi E, Hoang GL, Kuzikov M, Frings M, Ansari N, Demitri N, Nguyen TT, Rizzi V, Schulz JB, Bolm C, Zaliani A, Carloni P, Storici P, Rossetti G. Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease. J Chem Inf Model 2024; 64:892-904. [PMID: 38051605 PMCID: PMC10865365 DOI: 10.1021/acs.jcim.3c01497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/07/2023]
Abstract
Many homodimeric enzymes tune their functions by exploiting either negative or positive cooperativity between subunits. In the SARS-CoV-2 Main protease (Mpro) homodimer, the latter has been suggested by symmetry in most of the 500 reported protease/ligand complex structures solved by macromolecular crystallography (MX). Here we apply the latter to both covalent and noncovalent ligands in complex with Mpro. Strikingly, our experiments show that the occupation of both active sites of the dimer originates from an excess of ligands. Indeed, cocrystals obtained using a 1:1 ligand/protomer stoichiometry lead to single occupation only. The empty binding site exhibits a catalytically inactive geometry in solution, as suggested by molecular dynamics simulations. Thus, Mpro operates through negative cooperativity with the asymmetric activity of the catalytic sites. This allows it to function with a wide range of substrate concentrations, making it resistant to saturation and potentially difficult to shut down, all properties advantageous for the virus' adaptability and resistance.
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Affiliation(s)
- Simone Albani
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- Faculty
of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, Aachen 52062, Germany
| | - Elisa Costanzi
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Gia Linh Hoang
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
| | - Maria Kuzikov
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
- Constructor University, School of Science, Campus Ring 1, Bremen 28759, Germany
| | - Marcus Frings
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Narjes Ansari
- Atomistic
Simulations, Italian Institute of Technology, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Nicola Demitri
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Toan T. Nguyen
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Valerio Rizzi
- School
of Pharmaceutical Sciences, University of
Geneva, Rue Michel Servet 1, 1206 Genève, Switzerland
| | - Jörg B. Schulz
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
| | - Carsten Bolm
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Andrea Zaliani
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg 22525, Germany
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
| | - Paolo Carloni
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Paola Storici
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Giulia Rossetti
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
- Jülich
Supercomputing Center (JSC), Forschungszentrum
Jülich, Jülich 52425, Germany
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12
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Zhang D, Kukkar D, Kim KH, Bhatt P. A comprehensive review on immunogen and immune-response proteins of SARS-CoV-2 and their applications in prevention, diagnosis, and treatment of COVID-19. Int J Biol Macromol 2024; 259:129284. [PMID: 38211928 DOI: 10.1016/j.ijbiomac.2024.129284] [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: 09/06/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/13/2024]
Abstract
Exposure to severe acute respiratory syndrome-corona virus-2 (SARS-CoV-2) prompts humoral immune responses in the human body. As the auxiliary diagnosis of a current infection, the existence of viral proteins can be checked from specific antibodies (Abs) induced by immunogenic viral proteins. For people with a weakened immune system, Ab treatment can help neutralize viral antigens to resist and treat the disease. On the other hand, highly immunogenic viral proteins can serve as effective markers for detecting prior infections. Additionally, the identification of viral particles or the presence of antibodies may help establish an immune defense against the virus. These immunogenic proteins rather than SARS-CoV-2 can be given to uninfected people as a vaccination to improve their coping ability against COVID-19 through the generation of memory plasma cells. In this work, we review immunogenic and immune-response proteins derived from SARS-CoV-2 with regard to their classification, origin, and diverse applications (e.g., prevention (vaccine development), diagnostic testing, and treatment (via neutralizing Abs)). Finally, advanced immunization strategies against COVID-19 are discussed along with the contemporary circumstances and future challenges.
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Affiliation(s)
- Daohong Zhang
- College of Food Engineering, Ludong University, Yantai 264025, Shandong, China; Bio-Nanotechnology Research Institute, Ludong University, Yantai 264025, Shandong, China
| | - Deepak Kukkar
- Department of Biotechnology, Chandigarh University, Gharuan, Mohali 140413, Punjab, India; University Center for Research and Development, Chandigarh University, Gharuan, Mohali 140413, Punjab, India
| | - Ki-Hyun Kim
- Department of Civil & Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763, Republic of Korea.
| | - Poornima Bhatt
- Department of Biotechnology, Chandigarh University, Gharuan, Mohali 140413, Punjab, India; University Center for Research and Development, Chandigarh University, Gharuan, Mohali 140413, Punjab, India
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13
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Zhou B, Chen D, Zhang T, Song C, Zhang X, Lin L, Huang J, Peng X, Liu Y, Wu G, Li J, Chen W. Recent advancements in the discovery of small-molecule non-nucleoside inhibitors targeting SARS-CoV-2 RdRp. Biomed Pharmacother 2024; 171:116180. [PMID: 38266622 DOI: 10.1016/j.biopha.2024.116180] [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: 10/27/2023] [Revised: 01/14/2024] [Accepted: 01/16/2024] [Indexed: 01/26/2024] Open
Abstract
The RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 plays a pivotal role in the life cycle of the novel coronavirus and stands as a significant and promising target for anti-SARS-CoV-2 drugs. Non-nucleoside inhibitors (NNIs), as a category of compounds directed against SARS-CoV-2 RdRp, exhibit a unique and highly effective mechanism, effectively overcoming various factors contributing to drug resistance against nucleoside inhibitors (NIs). This review investigates various NNIs, including both natural and synthetic inhibitors, that closely interacting with the SARS-CoV-2 RdRp with valid evidences from in vitro and in silico studies.
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Affiliation(s)
- Bangdi Zhou
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, PR China; The First School of Clinical Medicine, Gannan Medical University, Ganzhou 341000, PR China
| | - Dianming Chen
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, PR China; School of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, PR China
| | - Tingyan Zhang
- School of Nusing, Gannan Medical University, Ganzhou 341000, PR China
| | - Chenggui Song
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou 341000, PR China
| | - Xianwu Zhang
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou 341000, PR China
| | - Leying Lin
- School of Basic Medicine, Gannan Medical University, Ganzhou 341000, PR China
| | - Jiuzhong Huang
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, PR China; School of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, PR China
| | - Xiaopeng Peng
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, PR China; School of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, PR China
| | - Yuanchang Liu
- School of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, PR China
| | - Gaorong Wu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, PR China; School of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, PR China
| | - Jingyuan Li
- School of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, PR China
| | - Weiming Chen
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, PR China; School of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, PR China.
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14
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Waqas M, Ullah S, Halim SA, Rehman NU, Ali A, Jan A, Muhsinah AB, Khan A, Al-Harrasi A. Targeting papain-like protease by natural products as novel therapeutic potential SARS-CoV-2. Int J Biol Macromol 2024; 258:128812. [PMID: 38114011 DOI: 10.1016/j.ijbiomac.2023.128812] [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: 10/31/2023] [Revised: 11/27/2023] [Accepted: 12/12/2023] [Indexed: 12/21/2023]
Abstract
The highly infectious respiratory illness 'COVID-19' was caused by SARS-CoV-2 and is responsible for millions of deaths. SARS-single-stranded viral RNA genome encodes several structural and nonstructural proteins, including papain-like protease (PLpro), which is essential for viral replication and immune evasion and serve as a potential therapeutic target. Multiple computational techniques were used to search the natural compounds that may block the protease and deubiquitinase activities of PLpro. Five compounds showed strong interactions and binding energy (ranges between -8.18 to -8.69 Kcal/mol) in our in-silico studies. Interestingly, those molecules strongly bind in the PLpro active site and form a stable complex, as shown by microscale molecular dynamic simulations (MD). The dynamic movements indicate that PLpro acquires closed conformation by the attachment of these molecules, thereby changing its normal function. In the in-vitro evaluation, compound COMP4 showed the most potent inhibitory potential for PLpro (protease activity: 2.24 ± 0.17 μM and deubiquitinase activity: 1.43 ± 0.14 μM), followed by COMP1, 2, 3, and 5. Furthermore, the cytotoxic effect of COMP1-COMP5 on a human BJ cell line revealed that these compounds demonstrate negligible cytotoxicity at a dosage of 30 μM. The results suggest that these entities bear therapeutic efficacy for SARS-CoV-2 PLpro.
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Affiliation(s)
- Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 2100, Pakistan
| | - Saeed Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Najeeb Ur Rehman
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 2100, Pakistan.
| | - Afnan Jan
- Department of Biochemistry, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Abdullatif Bin Muhsinah
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman.
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15
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Sievers BL, Cheng MTK, Csiba K, Meng B, Gupta RK. SARS-CoV-2 and innate immunity: the good, the bad, and the "goldilocks". Cell Mol Immunol 2024; 21:171-183. [PMID: 37985854 PMCID: PMC10805730 DOI: 10.1038/s41423-023-01104-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
An ancient conflict between hosts and pathogens has driven the innate and adaptive arms of immunity. Knowledge about this interplay can not only help us identify biological mechanisms but also reveal pathogen vulnerabilities that can be leveraged therapeutically. The humoral response to SARS-CoV-2 infection has been the focus of intense research, and the role of the innate immune system has received significantly less attention. Here, we review current knowledge of the innate immune response to SARS-CoV-2 infection and the various means SARS-CoV-2 employs to evade innate defense systems. We also consider the role of innate immunity in SARS-CoV-2 vaccines and in the phenomenon of long COVID.
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Affiliation(s)
| | - Mark T K Cheng
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kata Csiba
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
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16
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Tofaute M, Weller B, Graß C, Halder H, Dohai B, Falter-Braun P, Krappmann D. SARS-CoV-2 NSP14 MTase activity is critical for inducing canonical NF-κB activation. Biosci Rep 2024; 44:BSR20231418. [PMID: 38131452 PMCID: PMC10776897 DOI: 10.1042/bsr20231418] [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: 08/14/2023] [Revised: 12/07/2023] [Accepted: 12/21/2023] [Indexed: 12/23/2023] Open
Abstract
Upon SARS-CoV-2 infection, patients with severe forms of COVID-19 often suffer from a dysregulated immune response and hyperinflammation. Aberrant expression of cytokines and chemokines is associated with strong activation of the immunoregulatory transcription factor NF-κB, which can be directly induced by the SARS-CoV-2 protein NSP14. Here, we use NSP14 mutants and generated cells with host factor knockouts (KOs) in the NF-κB signaling pathways to characterize the molecular mechanism of NSP14-induced NF-κB activation. We demonstrate that full-length NSP14 requires methyltransferase (MTase) activity to drive NF-κB induction. NSP14 WT, but not an MTase-defective mutant, is poorly expressed and inherent post-translational instability is mediated by proteasomal degradation. Binding of SARS-CoV-2 NSP10 or addition of the co-factor S-adenosylmethionine (SAM) stabilizes NSP14 and augments its potential to activate NF-κB. Using CRISPR/Cas9-engineered KO cells, we demonstrate that NSP14 stimulation of canonical NF-κB activation relies on NF-κB factor p65/RELA downstream of the NEMO/IKK complex, while c-Rel or non-canonical RelB are not required to induce NF-κB transcriptional activity. However, NSP14 overexpression is unable to induce canonical IκB kinase β (IKKβ)/NF-κB signaling and in co-immunoprecipitation assays we do not detect stable associations between NSP14 and NEMO or p65, suggesting that NSP14 activates NF-κB indirectly through its methyltransferase activity. Taken together, our data provide a framework how NSP14 can augment basal NF-κB activation, which may enhance cytokine expression in SARS-CoV-2 infected cells.
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Affiliation(s)
- Marie J. Tofaute
- Research Unit Signaling and Translation, Group Signaling and Immunity, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Benjamin Weller
- Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
| | - Carina Graß
- Research Unit Signaling and Translation, Group Signaling and Immunity, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Hridi Halder
- Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
| | - Bushra Dohai
- Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
| | - Pascal Falter-Braun
- Institute of Network Biology (INET), Molecular Targets and Therapeutics Center (MTTC), Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-Universität (LMU) München, Planegg-Martinsried, Germany
| | - Daniel Krappmann
- Research Unit Signaling and Translation, Group Signaling and Immunity, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
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17
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Wang Q, Lu X, Jia R, Yan X, Wang J, Zhao L, Zhong R, Sun G. Recent advances in chemometric modelling of inhibitors against SARS-CoV-2. Heliyon 2024; 10:e24209. [PMID: 38293468 PMCID: PMC10826659 DOI: 10.1016/j.heliyon.2024.e24209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
The outbreak of the novel coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused great harm to all countries worldwide. This disease can be prevented by vaccination and managed using various treatment methods, including injections, oral medications, or aerosol therapies. However, the selection of suitable compounds for the research and development of anti-SARS-CoV-2 drugs is a daunting task because of the vast databases of available compounds. The traditional process of drug research and development is time-consuming, labour-intensive, and costly. The application of chemometrics can significantly expedite drug R&D. This is particularly necessary and important for drug development against pandemic public emergency diseases, such as COVID-19. Through various chemometric techniques, such as quantitative structure-activity relationship (QSAR) modelling, molecular docking, and molecular dynamics (MD) simulations, compounds with inhibitory activity against SARS-CoV-2 can be quickly screened, allowing researchers to focus on the few prioritised candidates. In addition, the ADMET properties of the screened candidate compounds should be further explored to promote the successful discovery of anti-SARS-CoV-2 drugs. In this case, considerable time and economic costs can be saved while minimising the need for extensive animal experiments, in line with the 3R principles. This paper focuses on recent advances in chemometric modelling studies of COVID-19-related inhibitors, highlights current limitations, and outlines potential future directions for development.
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Affiliation(s)
- Qianqian Wang
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Xinyi Lu
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Runqing Jia
- Department of Biology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Xinlong Yan
- Department of Biology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Jianhua Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Translational Medicine Laboratory, Capital Institute of Pediatrics, Beijing 100124, PR China
| | - Lijiao Zhao
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Rugang Zhong
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
| | - Guohui Sun
- Beijing Key Laboratory of Environmental and Viral Oncology, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, PR China
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Minatel VM, Prudencio CR, Barraviera B, Ferreira RS. Nanobodies: a promising approach to treatment of viral diseases. Front Immunol 2024; 14:1303353. [PMID: 38322011 PMCID: PMC10844482 DOI: 10.3389/fimmu.2023.1303353] [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: 09/29/2023] [Accepted: 12/12/2023] [Indexed: 02/08/2024] Open
Abstract
Since their discovery in the 1990s, heavy chain antibodies have garnered significant interest in the scientific community. These antibodies, found in camelids such as llamas and alpacas, exhibit distinct characteristics from conventional antibodies due to the absence of a light chain in their structure. Furthermore, they possess a single antigen-binding domain known as VHH or Nanobody (Nb). With a small size of approximately 15 kDa, these Nbs demonstrate improved characteristics compared to conventional antibodies, including greater physicochemical stability and enhanced biodistribution, enabling them to bind inaccessible epitopes more effectively. As a result, Nbs have found numerous applications in various medical and veterinary fields, particularly in diagnostics and therapeutics. Advances in biotechnology have made the production of recombinant antibodies feasible and compatible with large-scale manufacturing. Through the construction of immune phage libraries that display VHHs and subsequent selection through biopanning, it has become possible to isolate specific Nbs targeting pharmaceutical targets of interest, such as viruses. This review describes the processes involved in nanobody production, from hyperimmunization to purification, with the aim of their application in the pharmaceutical industry.
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Affiliation(s)
- Vitória Meneghetti Minatel
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP—Univ Estadual Paulista), Botucatu, São Paulo, Brazil
| | | | - Benedito Barraviera
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP—Univ Estadual Paulista), Botucatu, São Paulo, Brazil
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), São Paulo State University (UNESP—Univ Estadual Paulista), Botucatu, São Paulo, Brazil
| | - Rui Seabra Ferreira
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP—Univ Estadual Paulista), Botucatu, São Paulo, Brazil
- Graduate Program in Tropical Diseases, Botucatu Medical School (FMB), São Paulo State University (UNESP—Univ Estadual Paulista), Botucatu, São Paulo, Brazil
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Tian L, Qiang T, Yang X, Gao Y, Zhai X, Kang K, Du C, Lu Q, Gao H, Zhang D, Xie X, Liang C. Development of de-novo coronavirus 3-chymotrypsin-like protease (3CL pro) inhibitors since COVID-19 outbreak: A strategy to tackle challenges of persistent virus infection. Eur J Med Chem 2024; 264:115979. [PMID: 38048696 DOI: 10.1016/j.ejmech.2023.115979] [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: 09/18/2023] [Revised: 10/30/2023] [Accepted: 11/18/2023] [Indexed: 12/06/2023]
Abstract
Although no longer a public health emergency of international concern, COVID-19 remains a persistent and critical health concern. The development of effective antiviral drugs could serve as the ultimate piece of the puzzle to curbing this global crisis. 3-chymotrypsin-like protease (3CLpro), with its substrate specificity mirroring that of the main picornavirus 3C protease and conserved across various coronaviruses, emerges as an ideal candidate for broad-spectrum antiviral drug development. Moreover, it holds the potential as a reliable contingency option to combat emerging SARS-CoV-2 variants. In this light, the approved drugs, promising candidates, and de-novo small molecule therapeutics targeting 3CLpro since the COVID-19 outbreak in 2020 are discussed. Emphasizing the significance of diverse structural characteristics in inhibitors, be they peptidomimetic or nonpeptidic, with a shared mission to minimize the risk of cross-resistance. Moreover, the authors propose an innovative optimization strategy for 3CLpro reversible covalent PROTACs, optimizing pharmacodynamics and pharmacokinetics to better prepare for potential future viral outbreaks.
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Affiliation(s)
- Lei Tian
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Taotao Qiang
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China.
| | - Xiuding Yang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Yue Gao
- College of Pharmacy, Jinan University, Guangzhou, 511436, PR China
| | - Xiaopei Zhai
- Department of Pharmaceutics, School of Pharmacy, Air Force Medical University, Xi'an, 710032, PR China
| | - Kairui Kang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Cong Du
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Qi Lu
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Hong Gao
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Shaanxi Pioneer Biotech Co., Ltd., Xi'an, 710021, PR China
| | - Dezhu Zhang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Shaanxi Panlong Pharmaceutical Group Co., Ltd., Xi'an, 710025, PR China
| | - Xiaolin Xie
- Shaanxi Panlong Pharmaceutical Group Co., Ltd., Xi'an, 710025, PR China
| | - Chengyuan Liang
- Key Laboratory for Antiviral and Antimicrobial-Resistant Bacteria Research of Xi'an, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; School of Biological and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an, 710021, PR China.
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20
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Drobysh M, Liustrovaite V, Kanetski Y, Brasiunas B, Zvirbliene A, Rimkute A, Gudas D, Kucinskaite-Kodze I, Simanavicius M, Ramanavicius S, Slibinskas R, Ciplys E, Plikusiene I, Ramanavicius A. Electrochemical biosensing based comparative study of monoclonal antibodies against SARS-CoV-2 nucleocapsid protein. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168154. [PMID: 37923263 DOI: 10.1016/j.scitotenv.2023.168154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
In this study, we are reporting an electrochemical biosensor for the determination of three different clones of monoclonal antibodies (mAbs) against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recombinant nucleocapsid protein (rN). The nucleocapsid protein was chosen as a system component identifying and discriminating antibodies that occur after virus infection instead of S protein used in serological tests to measure antibodies raised after vaccination and infection. The sensing platform was based on a screen-printed carbon electrode (SPCE) covered with gold nanoparticles (AuNP) and subsequently modified with a self-assembled monolayer (SAM) to ensure the covalent immobilization of the rN. The interaction between the protein and three clones of mAbs against SARS-CoV-2 rN with clone numbers 4G6, 7F10, and 1A6, were electrochemically registered in the range of concentrations. Three techniques, cyclic voltammetry (CV), differential pulse voltammetry (DPV), and pulse amperometric detection (PAD) were used for the detection. A gradual change in the responses with an increase in mAbs concentration for all techniques was observed. To assess the performance of the developed electrochemical biosensor, 'complexation constant' (KC), limit of detection (LOD), and limit of quantification (LOQ) were calculated for all assessed clones of mAbs and all used techniques. Our results indicated that DPV possessing higher fitting accuracy illustrated more significant differences in KC constants and LOD/LOQ values. According to the DPV results, 7F10 clone was characterized with the highest KC value of 1.47 ± 0.07 μg/mL while the lowest LOD and LOQ values belonged to the 4G6 clone and equaled 0.08 ± 0.01 and 0.25 ± 0.01 μg/mL, respectively. Overall, these results demonstrate the potential of electrochemical techniques for the detection and distinguishing of different clones of mAbs against SARS-CoV-2 nucleocapsid protein.
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Affiliation(s)
- Maryia Drobysh
- State Research Institute Center for Physical and Technological Sciences, Sauletekio ave. 3, Vilnius, Lithuania; Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, 03225 Vilnius, Lithuania
| | - Viktorija Liustrovaite
- Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, 03225 Vilnius, Lithuania
| | - Yahor Kanetski
- Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, 03225 Vilnius, Lithuania
| | - Benediktas Brasiunas
- Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, 03225 Vilnius, Lithuania
| | - Aurelija Zvirbliene
- Life Sciences Center, Vilnius University, Sauletekio ave. 7, Vilnius, Lithuania
| | - Agne Rimkute
- Life Sciences Center, Vilnius University, Sauletekio ave. 7, Vilnius, Lithuania
| | - Dainius Gudas
- Life Sciences Center, Vilnius University, Sauletekio ave. 7, Vilnius, Lithuania
| | | | | | - Simonas Ramanavicius
- State Research Institute Center for Physical and Technological Sciences, Sauletekio ave. 3, Vilnius, Lithuania; Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, 03225 Vilnius, Lithuania
| | - Rimantas Slibinskas
- Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, 03225 Vilnius, Lithuania; Life Sciences Center, Vilnius University, Sauletekio ave. 7, Vilnius, Lithuania
| | - Evaldas Ciplys
- Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, 03225 Vilnius, Lithuania; Life Sciences Center, Vilnius University, Sauletekio ave. 7, Vilnius, Lithuania
| | - Ieva Plikusiene
- Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, 03225 Vilnius, Lithuania
| | - Arunas Ramanavicius
- State Research Institute Center for Physical and Technological Sciences, Sauletekio ave. 3, Vilnius, Lithuania; Department of Physical Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 24, 03225 Vilnius, Lithuania.
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21
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Borba JRBDM, de Araújo LP, Veloso MP, da Silveira NJF. Applying the bioisosterism strategy to obtain lead compounds against SARS-CoV-2 cysteine proteases: An in-silico approach. J Comput Chem 2024; 45:35-46. [PMID: 37641955 DOI: 10.1002/jcc.27217] [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: 05/31/2023] [Revised: 07/17/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023]
Abstract
SARS-CoV-2 cysteine proteases are essential nonstructural proteins due to their role in the formation of the virus multiple enzyme replication-transcription complex. As a result, those functional proteins are extremely relevant targets in the development of a new drug candidate to fight COVID-19. Based on this fact and guided by the bioisosterism strategy, the present work has selected 126 out of 1050 ligands from DrugBank website. Subsequently, 831 chemical analogs containing bioisosteres, some of which became structurally simplified, were created using the MB-Isoster software, and molecular docking simulations were performed using AutoDock Vina. Finally, a study of physicochemical properties, along with pharmacokinetic profiles, was carried out through SwissADME and ADMETlab 2.0 platforms. The promising results obtained with the molecules encoded as DB00549_BI_005, DB04868_BI_003, DB11984_BI_002, DB12364_BI_006 and DB12805_BI_004 must be confirmed by molecular dynamics studies, followed by in vitro and in vivo empirical tests that ratify the advocated in-silico results.
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Affiliation(s)
- João Ricardo Bueno de Morais Borba
- João Ricardo Bueno de Morais Borba, Laboratory of Molecular Modeling and Computer Simulation - MolMod-CS, Institute of Chemistry, Federal University of Alfenas - UNIFAL-MG, Alfenas, Brazil
| | - Leonardo Pereira de Araújo
- Leonardo Pereira de Araújo, Laboratory of Molecular Modeling and Computer Simulation - MolMod-CS, Institute of Chemistry, Federal University of Alfenas - UNIFAL-MG, Alfenas, Brazil
| | - Marcia Paranho Veloso
- Marcia Paranho Veloso, Laboratory of Molecular Modeling and Computer Simulation - MolMod-CS, Institute of Chemistry, Federal University of Alfenas - UNIFAL-MG, Alfenas, Brazil
| | - Nelson José Freitas da Silveira
- Nelson José Freitas da Silveira, Laboratory of Molecular Modeling and Computer Simulation - MolMod-CS, Institute of Chemistry, Federal University of Alfenas - UNIFAL-MG, Alfenas, Brazil
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22
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Chatterjee S, Zaia J. Proteomics-based mass spectrometry profiling of SARS-CoV-2 infection from human nasopharyngeal samples. MASS SPECTROMETRY REVIEWS 2024; 43:193-229. [PMID: 36177493 PMCID: PMC9538640 DOI: 10.1002/mas.21813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 05/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the on-going global pandemic of coronavirus disease 2019 (COVID-19) that continues to pose a significant threat to public health worldwide. SARS-CoV-2 encodes four structural proteins namely membrane, nucleocapsid, spike, and envelope proteins that play essential roles in viral entry, fusion, and attachment to the host cell. Extensively glycosylated spike protein efficiently binds to the host angiotensin-converting enzyme 2 initiating viral entry and pathogenesis. Reverse transcriptase polymerase chain reaction on nasopharyngeal swab is the preferred method of sample collection and viral detection because it is a rapid, specific, and high-throughput technique. Alternate strategies such as proteomics and glycoproteomics-based mass spectrometry enable a more detailed and holistic view of the viral proteins and host-pathogen interactions and help in detection of potential disease markers. In this review, we highlight the use of mass spectrometry methods to profile the SARS-CoV-2 proteome from clinical nasopharyngeal swab samples. We also highlight the necessity for a comprehensive glycoproteomics mapping of SARS-CoV-2 from biological complex matrices to identify potential COVID-19 markers.
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Affiliation(s)
- Sayantani Chatterjee
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass SpectrometryBoston University School of MedicineBostonMassachusettsUSA
- Bioinformatics ProgramBoston University School of MedicineBostonMassachusettsUSA
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23
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Song L, Gao S, Ye B, Yang M, Cheng Y, Kang D, Yi F, Sun JP, Menéndez-Arias L, Neyts J, Liu X, Zhan P. Medicinal chemistry strategies towards the development of non-covalent SARS-CoV-2 M pro inhibitors. Acta Pharm Sin B 2024; 14:87-109. [PMID: 38239241 PMCID: PMC10792984 DOI: 10.1016/j.apsb.2023.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/10/2023] [Accepted: 08/02/2023] [Indexed: 01/22/2024] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is an attractive target in anti-COVID-19 therapy for its high conservation and major role in the virus life cycle. The covalent Mpro inhibitor nirmatrelvir (in combination with ritonavir, a pharmacokinetic enhancer) and the non-covalent inhibitor ensitrelvir have shown efficacy in clinical trials and have been approved for therapeutic use. Effective antiviral drugs are needed to fight the pandemic, while non-covalent Mpro inhibitors could be promising alternatives due to their high selectivity and favorable druggability. Numerous non-covalent Mpro inhibitors with desirable properties have been developed based on available crystal structures of Mpro. In this article, we describe medicinal chemistry strategies applied for the discovery and optimization of non-covalent Mpro inhibitors, followed by a general overview and critical analysis of the available information. Prospective viewpoints and insights into current strategies for the development of non-covalent Mpro inhibitors are also discussed.
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Affiliation(s)
- Letian Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Shenghua Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518057, China
| | - Bing Ye
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Mianling Yang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Yusen Cheng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Fan Yi
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan 250012, China
| | - Jin-Peng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Luis Menéndez-Arias
- Centro de Biología Molecular “Severo Ochoa” (Consejo Superior de Investigaciones Científicas & Autonomous University of Madrid), Madrid 28049, Spain
| | - Johan Neyts
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven 3000, Belgium
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
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24
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Bae M, Choi S, Kim J, Seo G, Lee YW. Temperature-insensitive label-free SARS-CoV-2 spike protein detection based on complementary refractive index and temperature dependence of multi-mode interference and grating resonance. Talanta 2024; 266:125091. [PMID: 37625291 DOI: 10.1016/j.talanta.2023.125091] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/12/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023]
Abstract
We demonstrated temperature-insensitive, label-free detection of SARS-CoV-2 spike protein (SSP) by harnessing the complementary refractive index and temperature dependence of multi-mode interference (MMI) created by a no-core fiber (NCF) and phase-matched resonance generated by a long-period fiber grating (LPFG). To combine MMI and grating resonance, primarily sensitive to the surrounding medium refractive index (SMRI) and ambient temperature, respectively, a fiber-optic transducer was fabricated by splicing an NCF segment with an LPFG inscribed on double-clad fiber. The transducer was functionalized with human ACE2 receptors to selectively capture SSP. The functionalized sensor head exhibited high SSP selectivity, with overall average wavelength displacements of ∼253.33 and ∼160.00 pm in PBS and saliva, respectively, for SSP with concentrations ranging from 1 to 104 ng/mL. These spectral shifts are associated with localized SMRI modulations on the sensor surface induced by specific binding between SSP and ACE2. We also examined the cross-reactivity of the sensor head for MERS-CoV spike protein to confirm its SSP specificity. Moreover, we proved the capability of temperature-independent SSP detection and ambient temperature measurement by scrutinizing the temperature effect on the sensor performance. Our functionalized fiber transducer showed great promise as a temperature-insensitive and portable platform for rapid SSP detection.
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Affiliation(s)
- Minchan Bae
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan, 48513, Republic of Korea
| | - Sungwook Choi
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan, 48513, Republic of Korea
| | - Jihoon Kim
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan, 48513, Republic of Korea
| | - Giwan Seo
- Research Center for Bioconvergence, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea; Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
| | - Yong Wook Lee
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan, 48513, Republic of Korea; School of Electrical Engineering, Pukyong National University, Busan, 48513, Republic of Korea.
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25
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Zhao Z, Zhu Q, Zhou X, Li W, Yin X, Li J. Structural Basis for the Inhibition of SARS-CoV-2 M pro D48N Mutant by Shikonin and PF-07321332. Viruses 2023; 16:65. [PMID: 38257765 PMCID: PMC10818409 DOI: 10.3390/v16010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/24/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Preventing the spread of SARS-CoV-2 and its variants is crucial in the fight against COVID-19. Inhibition of the main protease (Mpro) of SARS-CoV-2 is the key to disrupting viral replication, making Mpro a promising target for therapy. PF-07321332 and shikonin have been identified as effective broad-spectrum inhibitors of SARS-CoV-2 Mpro. The crystal structures of SARS-CoV-2 Mpro bound to PF-07321332 and shikonin have been resolved in previous studies. However, the exact mechanism regarding how SARS-CoV-2 Mpro mutants impact their binding modes largely remains to be investigated. In this study, we expressed a SARS-CoV-2 Mpro mutant, carrying the D48N substitution, representing a class of mutations located near the active sites of Mpro. The crystal structures of Mpro D48N in complex with PF-07321332 and shikonin were solved. A detailed analysis of the interactions between Mpro D48N and two inhibitors provides key insights into the binding pattern and its structural determinants. Further, the binding patterns of the two inhibitors to Mpro D48N mutant and wild-type Mpro were compared in detail. This study illustrates the possible conformational changes when the Mpro D48N mutant is bound to inhibitors. Structural insights derived from this study will inform the development of new drugs against novel coronaviruses.
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Affiliation(s)
- Zhenyu Zhao
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China; (Z.Z.); (X.Z.); (W.L.)
| | - Qinyao Zhu
- Applied Biology Laboratory, College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang 110142, China;
| | - Xuelan Zhou
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China; (Z.Z.); (X.Z.); (W.L.)
| | - Wenwen Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China; (Z.Z.); (X.Z.); (W.L.)
| | - Xiushan Yin
- Applied Biology Laboratory, College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, Shenyang 110142, China;
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China; (Z.Z.); (X.Z.); (W.L.)
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Srivastava R, Panda SK, Sen Gupta PS, Chaudhary A, Naaz F, Yadav AK, Ram NK, Rana MK, Singh RK, Srivastava R. In silico evaluation of S-adenosyl-L-homocysteine analogs as inhibitors of nsp14-viral cap N7 methyltranferase and PLpro of SARS-CoV-2: synthesis, molecular docking, physicochemical data, ADMET and molecular dynamics simulations studies. J Biomol Struct Dyn 2023:1-18. [PMID: 38147408 DOI: 10.1080/07391102.2023.2297005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023]
Abstract
A series of S-adenosyl-L-homosysteine (SAH) analogs, with modification in the base and sugar moiety, have been designed, synthesized and screened as nsp14 and PLpro inhibitors of severe acute respiratory syndrome corona virus (SARS-CoV-2). The outcomes of ADMET (Adsorption, Distribution, Metabolism, Excretion, and Toxicity) studies demonstrated that the physicochemical properties of all analogs were permissible for development of these SAH analogs as antiviral agents. All molecules were screened against different SARS-CoV-2 targets using molecular docking. The docking results revealed that the SAH analogs interacted well in the active site of nsp14 protein having H-bond interactions with the amino acid residues Arg289, Val290, Asn388, Arg400, Phe401 and π-alkyl interactions with Arg289, Val290 and Phe426 of Nsp14-MTase site. These analogs also formed stable H-bonds with Leu163, Asp165, Arg167, Ser246, Gln270, Tyr274 and Asp303 residues of PLpro proteins and found to be quite stable complexes therefore behaved as probable nsp14 and PLpro inhibitors. Interestingly, analog 3 showed significant in silico activity against the nsp14 N7 methyltransferase of SARS-CoV-2. The molecular dynamics (MD) and post-MD results of analog 3 unambiguously established the higher stability of the nsp14 (N7 MTase):3 complex and also indicated its behavior as probable nsp14 inhibitor like the reference sinefungin. The docking and MD simulations studies also suggested that sinefungin did act as SARS-CoV-2 PLpro inhibitor as well. This study's findings not only underscore the efficacy of the designed SAH analogs as potent inhibitors against crucial SARS-CoV-2 proteins but also pinpoint analog 3 as a particularly promising candidate. All the study provides valuable insights, paving the way for potential advancements in antiviral drug development against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ritika Srivastava
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Odisha, India
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, India
| | - Saroj Kumar Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Odisha, India
| | - Parth Sarthi Sen Gupta
- School of Biosciences and Bioengineering, D Y Patil International University, Akurdi, India
| | - Anvita Chaudhary
- Department of Applied Chemistry, Delhi Technological University, Delhi, India
| | - Farha Naaz
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, India
| | - Aditya K Yadav
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, India
| | - Nand Kumar Ram
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Odisha, India
| | - Ramendra K Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, India
| | - Richa Srivastava
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, India
- Department of Applied Chemistry, Delhi Technological University, Delhi, India
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Parsons RJ, Acharya P. Evolution of the SARS-CoV-2 Omicron spike. Cell Rep 2023; 42:113444. [PMID: 37979169 PMCID: PMC10782855 DOI: 10.1016/j.celrep.2023.113444] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/21/2023] [Accepted: 10/30/2023] [Indexed: 11/20/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern, first identified in November 2021, rapidly spread worldwide and diversified into several subvariants. The Omicron spike (S) protein accumulated an unprecedented number of sequence changes relative to previous variants. In this review, we discuss how Omicron S protein structural features modulate host cell receptor binding, virus entry, and immune evasion and highlight how these structural features differentiate Omicron from previous variants. We also examine how key structural properties track across the still-evolving Omicron subvariants and the importance of continuing surveillance of the S protein sequence evolution over time.
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Affiliation(s)
- Ruth J Parsons
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Biochemistry, Durham, NC 27710, USA.
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Biochemistry, Durham, NC 27710, USA; Duke University, Department of Surgery, Durham, NC 27710, USA.
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28
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Dhaka P, Singh A, Choudhary S, Peddinti RK, Kumar P, Sharma GK, Tomar S. Mechanistic and thermodynamic characterization of antiviral inhibitors targeting nucleocapsid N-terminal domain of SARS-CoV-2. Arch Biochem Biophys 2023; 750:109820. [PMID: 37956938 DOI: 10.1016/j.abb.2023.109820] [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: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/21/2023]
Abstract
The nucleocapsid (N) protein of SARS-CoV-2 plays a pivotal role in encapsulating the viral genome. Developing antiviral treatments for SARS-CoV-2 is imperative due to the diminishing immunity of the available vaccines. This study targets the RNA-binding site located in the N-terminal domain (NTD) of the N-protein to identify the potential antiviral molecules against SARS-CoV-2. A structure-based repurposing approach identified the twelve high-affinity molecules from FDA-approved drugs, natural products, and the LOPAC1280 compound libraries that precisely bind to the RNA binding site within the NTD. The interaction of these potential antiviral agents with the purified NTD protein was thermodynamically characterized using isothermal titration calorimetry (ITC). A fluorescence-based plate assay to assess the RNA binding inhibitory activity of small molecules against the NTD has been employed, and the selected compounds exhibited significant RNA binding inhibition with calculated IC50 values ranging from 8.8 μM to 15.7 μM. Furthermore, the antiviral efficacy of these compounds was evaluated using in vitro cell-based assays targeting the replication of SARS-CoV-2. Remarkably, two compounds, Telmisartan and BMS-189453, displayed potential antiviral activity against SARS-CoV-2, with EC50 values of approximately 1.02 μM and 0.98 μM, and a notable selective index of >98 and > 102, respectively. This study gives valuable insight into developing therapeutic interventions against SARS-CoV-2 by targeting the N-protein, a significant effort given the global public health concern posed due to the virus re-emergence and long COVID-19 disease.
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Affiliation(s)
- Preeti Dhaka
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Ankur Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Shweta Choudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Rama Krishna Peddinti
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.
| | - Gaurav Kumar Sharma
- Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India.
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India.
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29
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Arya R, Tripathi P, Nayak K, Ganesh J, Bihani SC, Ghosh B, Prashar V, Kumar M. Insights into the evolution of mutations in SARS-CoV-2 non-spike proteins. Microb Pathog 2023; 185:106460. [PMID: 37995880 DOI: 10.1016/j.micpath.2023.106460] [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: 06/12/2023] [Revised: 10/16/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023]
Abstract
The COVID-19 pandemic has been driven by the emergence of SARS-CoV-2 variants with mutations across all the viral proteins. Although mutations in the spike protein have received significant attention, understanding the prevalence and potential impact of mutations in other viral proteins is essential for comprehending the evolution of SARS-CoV-2. Here, we conducted a comprehensive analysis of approximately 14 million sequences of SARS-CoV-2 deposited in the GISAID database until December 2022 to identify prevalent mutations in the non-spike proteins at the global and country levels. Additionally, we evaluated the energetics of each mutation to better understand their impact on protein stability. While the consequences of many mutations remain unclear, we discuss potential structural and functional significance of some mutations. Our study highlights the ongoing evolutionary process of SARS-CoV-2 and underscores the importance of understanding changes in non-spike proteins.
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Affiliation(s)
- Rimanshee Arya
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Preeti Tripathi
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Karthik Nayak
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; School of Chemical Sciences, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidyanagari, Mumbai, 400098, India
| | - Janani Ganesh
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Subhash C Bihani
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Biplab Ghosh
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India; Beamline Development & Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Vishal Prashar
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
| | - Mukesh Kumar
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
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30
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Chan LC, Mat Yassim AS, Ahmad Fuaad AAH, Leow TC, Sabri S, Radin Yahaya RS, Abu Bakar AMS. Inhibition of SARS-CoV-2 3CL protease by the anti-viral chimeric protein RetroMAD1. Sci Rep 2023; 13:20178. [PMID: 37978223 PMCID: PMC10656507 DOI: 10.1038/s41598-023-47511-z] [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: 03/20/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
COVID-19 results from SARS-CoV-2, which mutates frequently, challenging current treatments. Therefore, it is critical to develop new therapeutic drugs against this disease. This study explores the interaction between SARS-CoV-2 3CLpro and RetroMAD1, a well-characterized coronavirus protein and potential drug target, using in-silico methods. The analysis through the HDOCK server showed stable complex formation with a binding energy of -12.3, the lowest among reference drugs. The RetroMAD1-3CLpro complex underwent a 100 ns molecular dynamics simulation (MDS) in an explicit solvation system, generating various trajectories, including RMSD, RMSF, hydrogen bonding, radius of gyration, and ligand binding energy. MDS results confirmed intact interactions within the RetroMAD1-3CLpro complex during simulations. In vitro experiments validated RetroMAD1's ability to inhibit 3CLpro enzyme activity and prevent SARS-CoV-2 infection in human bronchial cells. RetroMAD1 exhibited antiviral efficacy comparable to Remdesivir without cytotoxicity at effective concentrations. These results suggest RetroMAD1 as a potential drug candidate against SARS-CoV-2, warranting further in vivo and clinical studies to assess its efficiency.
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Affiliation(s)
- Lee-Chin Chan
- Biovalence Sdn. Bhd., 22, Jalan SS 25/34, Taman Mayang, 47301, Petaling Jaya, Selangor, Malaysia
- Biovalence Technologies Pte. Ltd., #06-307 The Plaza, 7500A Beach Road, Singapore, 199591, Singapore
| | - Aini Syahida Mat Yassim
- Biovalence Sdn. Bhd., 22, Jalan SS 25/34, Taman Mayang, 47301, Petaling Jaya, Selangor, Malaysia.
- Biovalence Technologies Pte. Ltd., #06-307 The Plaza, 7500A Beach Road, Singapore, 199591, Singapore.
- School of Health Science, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.
| | - Abdullah Al Hadi Ahmad Fuaad
- Centre of Fundamental and Frontier Sciences in Self-Assembly (FSSA), Department of Chemistry, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Thean Chor Leow
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Suriana Sabri
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Radin Shafierul Radin Yahaya
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Awang Muhammad Sagaf Abu Bakar
- Jabatan Perkhidmatan Veterinar Sabah, Aras 3, Blok B, Wisma Pertanian Sabah, Jalan Tasik, Luyang (Off Jln Maktab Gaya), Beg Berkunci 2051, 88999, Kota Kinabalu, Sabah, Malaysia.
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31
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de Almeida MT, Barbosa AP, Bomfim CG, Visnardi AB, Vinces TC, Ceroni A, Durigon EL, Guzzo CR. Obtaining a high titer of polyclonal antibodies from rats to the SARS-CoV-2 nucleocapsid protein and its N- and C-terminal domains for diagnostic test development. J Immunol Methods 2023; 522:113558. [PMID: 37704125 DOI: 10.1016/j.jim.2023.113558] [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: 04/18/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is an enveloped, plus-stranded RNA virus responsible for the Coronavirus Disease 2019 (COVID-19). Patients infected with COVID-19 may be asymptomatic or have symptoms ranging from mild manifestations to severe cases of the disease that could lead to death. The SARS-CoV-2 genome encodes 4 structural proteins, including the Spike protein (S), the Nucleocapsid protein (N), Membrane protein (M) and, the Envelope protein (E). The N protein forms a major component of the ribonucleoprotein complex within the virus particle and play a vital role in its transcription and replication. Nevertheless, the S protein was the most important protein in the development of vaccines against COVID-19. However, the decrease in number of registered immunizations against the disease and the rapid drop in neutralizing antibody titers together with looser preventive measures for virus transmission, favored the rapid appearance of new variants of concerns (VOCs) that primarily show mutations in the S protein. This fact makes the N protein a good candidate for the development of diagnostic tests, due to its stability, amino acid conservation, high immunogenicity, and the smaller likelihood of mutation. With the aim of developing a new diagnostic kit based on the N protein, we evaluated the humoral response in female Wistar rats against this target. Three constructions of the N protein were used to inoculate the animals: the full-length protein (Cfull), the N- (NTD), and the C-terminal (CTD) portion of the protein. The immunizations induced the animal's immune response, with specific polyclonal IgG antibodies against the Cfull protein and its fragments. There were not non-specific bind to the protein used as negative control. Anti-Cfull antibodies demonstrated high efficiency in binding to the NTD protein and the antibodies present in the anti-CTD and anti-NTD sera have recognized the Cfull protein, but they were not able to recognize the NTD and CTD proteins, respectively. Our results indicate an efficient protocol for obtaining high antibody titers against the N recombinant protein of SARS-CoV-2 and its fragments highlighting the Cfull protein, which can be used in the development of new diagnostic kits.
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Affiliation(s)
| | - Ana Paula Barbosa
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Camila Gasque Bomfim
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Aline Biazola Visnardi
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Tania Churasacari Vinces
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alexandre Ceroni
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Edison Luiz Durigon
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Scientific Platform Pasteur USP, São Paulo, Brazil
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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32
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Grand RJ. SARS-CoV-2 and the DNA damage response. J Gen Virol 2023; 104:001918. [PMID: 37948194 PMCID: PMC10768691 DOI: 10.1099/jgv.0.001918] [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: 09/01/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
The recent coronavirus disease 2019 (COVID-19) pandemic was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is characterized by respiratory distress, multiorgan dysfunction and, in some cases, death. The virus is also responsible for post-COVID-19 condition (commonly referred to as 'long COVID'). SARS-CoV-2 is a single-stranded, positive-sense RNA virus with a genome of approximately 30 kb, which encodes 26 proteins. It has been reported to affect multiple pathways in infected cells, resulting, in many cases, in the induction of a 'cytokine storm' and cellular senescence. Perhaps because it is an RNA virus, replicating largely in the cytoplasm, the effect of SARS-Cov-2 on genome stability and DNA damage responses (DDRs) has received relatively little attention. However, it is now becoming clear that the virus causes damage to cellular DNA, as shown by the presence of micronuclei, DNA repair foci and increased comet tails in infected cells. This review considers recent evidence indicating how SARS-CoV-2 causes genome instability, deregulates the cell cycle and targets specific components of DDR pathways. The significance of the virus's ability to cause cellular senescence is also considered, as are the implications of genome instability for patients suffering from long COVID.
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Affiliation(s)
- Roger J. Grand
- Institute for Cancer and Genomic Science, The Medical School, University of Birmingham, Birmingham, UK
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33
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Prasad R, Ajith H, Kumar Chandrakumaran N, Dnyaneshwar Khangar P, Mohan A, Nelson-Sathi S. In silico study identifies peptide inhibitors that negate the effect of non-synonymous mutations in major drug targets of SARS-CoV-2 variants. J Biomol Struct Dyn 2023; 41:9551-9561. [PMID: 36377464 DOI: 10.1080/07391102.2022.2143426] [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: 09/15/2022] [Accepted: 10/29/2022] [Indexed: 11/16/2022]
Abstract
Since its advent in December 2019, SARS-CoV-2 has diverged into multiple variants with differing levels of virulence owing to the accumulation of mutations in its genome. The structural changes induced by non-synonymous mutations in major drug targets of the virus are known to alter the binding of potential antagonistic inhibitors. Here, we analyzed the effects of non-synonymous mutations in major targets of SARS-CoV-2 in response to potential peptide inhibitors. We screened 12 peptides reported to have anti-viral properties against RBD and 5 peptides against Mpro of SARS-CoV-2 variants using molecular docking and simulation approaches. The mutational landscape of RBD among SARS-CoV-2 variants had 21 non-synonymous mutations across 18 distinct sites. Among these, 14 mutations were present in the RBM region directly interacting with the hACE2 receptor. However, Only 3 non-synonymous mutations were observed in Mpro. We found that LCB1 - a de novo-synthesized peptide has the highest binding affinity to RBD despite non-synonymous mutations in variants and engages key residues of RBD-hACE2 interaction such as K417, E484, N487, and N501. Similarly, an antimicrobial peptide; 2JOS, was identified against Mpro with high binding affinity as it interacts with key residues in dimerization sites such as E166 and F140 crucial for viral replication. MD simulations affirm the stability of RBD-LCB1 and Mpro-2JOS complexes with an average RMSD of 1.902 and 2.476 respectively. We ascertain that LCB1 and 2JOS peptides are promising inhibitors to combat emerging variants of SARS-CoV-2 and thus warrant further investigations using in-vitro and in-vivo analysis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Roshny Prasad
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Harikrishnan Ajith
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | | | | | - Anand Mohan
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Shijulal Nelson-Sathi
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
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Alzyoud L, Mahgoub RE, Mohamed FE, Ali BR, Ferreira J, Rabeh WM, Atatreh N, Ghattas MA. The Discovery of Novel Small Oxindole-Based Inhibitors Targeting the SARS-CoV-2 Main Protease (M pro ). Chem Biodivers 2023; 20:e202301176. [PMID: 37861105 DOI: 10.1002/cbdv.202301176] [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: 08/07/2023] [Revised: 10/14/2023] [Accepted: 10/18/2023] [Indexed: 10/21/2023]
Abstract
With the potential for coronaviruses to re-emerge and trigger future pandemics, the urgent development of antiviral inhibitors against SARS-CoV-2 is essential. The Mpro enzyme is crucial for disease progression and the virus's life cycle. It possesses allosteric sites that can hinder its catalytic activity, with some of these sites located at or near the dimerization interface. Among them, sites #2 and #5 possess druggable pockets and are predicted to bind drug-like molecules. Consequently, a commercially available ligand library containing ~7 million ligands was used to target site #2 via structure-based virtual screening. After extensive filtering, docking, and post-docking analyses, 53 compounds were chosen for biological testing. An oxindole derivative was identified as a Mpro non-competitive reversible inhibitor with a Ki of 115 μM and an IC50 of 101.9 μM. Throughout the 200 ns-long MD trajectories, our top hit has shown a very stable binding mode, forming several interactions with residues in sites #2 and #5. Moreover, derivatives of our top hit were acquired for biological testing to gain deeper insights into their structure-activity relationship. To sum up, drug-like allosteric inhibitors seem promising and can provide us with an additional weapon in our war against the recent pandemic, and possibly other coronaviruses-caused diseases.
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Affiliation(s)
- Lara Alzyoud
- College of Pharmacy, Al Ain University, Abu, Dhabi, 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, 64141, United Arab Emirates
| | - Radwa E Mahgoub
- College of Pharmacy, Al Ain University, Abu, Dhabi, 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, 64141, United Arab Emirates
| | - Feda E Mohamed
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, 15551, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, 15551, United Arab Emirates
- Zayed Centre for Health Sciences, United Arab Emirates University, Al-Ain, 15551, United Arab Emirates
| | - Juliana Ferreira
- Science Division, New York University Abu Dhabi, Abu Dhabi, 129188, United Arab Emirates
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, Abu Dhabi, 129188, United Arab Emirates
| | - Noor Atatreh
- College of Pharmacy, Al Ain University, Abu, Dhabi, 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, 64141, United Arab Emirates
| | - Mohammad A Ghattas
- College of Pharmacy, Al Ain University, Abu, Dhabi, 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, 64141, United Arab Emirates
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35
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Miura K, Suzuki Y, Ishida K, Arakawa M, Wu H, Fujioka Y, Emi A, Maeda K, Hamajima R, Nakano T, Tenno T, Hiroaki H, Morita E. Distinct motifs in the E protein are required for SARS-CoV-2 virus particle formation and lysosomal deacidification in host cells. J Virol 2023; 97:e0042623. [PMID: 37830820 PMCID: PMC10617393 DOI: 10.1128/jvi.00426-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/18/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), has caused a global public health crisis. The E protein, a structural protein found in this virus particle, is also known to be a viroporin. As such, it forms oligomeric ion channels or pores in the host cell membrane. However, the relationship between these two functions is poorly understood. In this study, we showed that the roles of E protein in virus particle and viroporin formation are distinct. This study contributes to the development of drugs that inhibit SARS-CoV-2 virus particle formation. Additionally, we designed a highly sensitive and high-throughput virus-like particle detection system using the HiBiT tag, which is a useful tool for studying the release of SARS-CoV-2.
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Affiliation(s)
- Koya Miura
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
| | - Youichi Suzuki
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Kotaro Ishida
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
| | - Masashi Arakawa
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
| | - Hong Wu
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Yoshihiko Fujioka
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Akino Emi
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Koki Maeda
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
| | - Ryusei Hamajima
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi, Japan
| | - Takashi Nakano
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Takeshi Tenno
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi, Japan
- BeCellBar LLC, Nagoya, Aichi, Japan
| | - Hidekazu Hiroaki
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi, Japan
- BeCellBar LLC, Nagoya, Aichi, Japan
| | - Eiji Morita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
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Oyola S. Characterization of SARS-CoV-2 genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population. RESEARCH SQUARE 2023:rs.3.rs-3457875. [PMID: 37961584 PMCID: PMC10635312 DOI: 10.21203/rs.3.rs-3457875/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Vaccination is a key control measure of COVID-19 by preventing severe effects of disease outcomes, reducing hospitalization rates and death, and increasing herd immunity. However, vaccination can affect the evolution and adaptation of SARS-CoV-2, largely through vaccine-induced immune pressure. Here we investigated the recombination events and single nucleotide polymorphisms (SNPs) on SARS-CoV-2 genome in non-vaccinated and vaccinated patients in the Kenyan population. We identified recombination hotspots in the S, N, and ORF1a/b genes and showed the genetic evolution landscape of SARS-CoV-2 by comparing within-wave and inter-wave recombination events from the beginning of the pandemic (June 2020) to (October 2022) in Kenya. An in-depth analysis of (SNPs) on the S, ORf1a/b, and N genes identified previously unreported mutations. We detected a minority variant in non-vaccinated patients in Kenya, that contained immune escape mutation S255F of the spike gene and showing a differential recombination pattern within the non-vaccinated patients. Detailed analysis of recombination between waves suggested an association between increased population immunity and declining risk of emergence of variants of concern. Overall, this work identified unique mutations in SARS-CoV-2 which could have significant implications for virus evolution, virulence, and immune escape.
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Bodakuntla S, Kuhn CC, Biertümpfel C, Mizuno N. Cryo-electron microscopy in the fight against COVID-19-mechanism of virus entry. Front Mol Biosci 2023; 10:1252529. [PMID: 37867557 PMCID: PMC10587472 DOI: 10.3389/fmolb.2023.1252529] [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: 07/03/2023] [Accepted: 09/20/2023] [Indexed: 10/24/2023] Open
Abstract
Cryogenic electron microscopy (cryo-EM) and electron tomography (cryo-ET) have become a critical tool for studying viral particles. Cryo-EM has enhanced our understanding of viral assembly and replication processes at a molecular resolution. Meanwhile, in situ cryo-ET has been used to investigate how viruses attach to and invade host cells. These advances have significantly contributed to our knowledge of viral biology. Particularly, prompt elucidations of structures of the SARS-CoV-2 spike protein and its variants have directly impacted the development of vaccines and therapeutic measures. This review discusses the progress made by cryo-EM based technologies in comprehending the severe acute respiratory syndrome coronavirus-2 (SARS-Cov-2), the virus responsible for the devastating global COVID-19 pandemic in 2020 with focus on the SARS-CoV-2 spike protein and the mechanisms of the virus entry and replication.
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Affiliation(s)
- Satish Bodakuntla
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Christopher Cyrus Kuhn
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Christian Biertümpfel
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Naoko Mizuno
- Laboratory of Structural Cell Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States
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Duarte LF, Vázquez Y, Diethelm-Varela B, Pavez V, Berríos-Rojas R, Méndez C, Riedel CA, White JA, Kalergis AM, Bueno SM, González PA. Differential Severe Acute Respiratory Syndrome Coronavirus 2-Specific Humoral Response in Inactivated Virus-Vaccinated, Convalescent, and Breakthrough-Infected Subjects. J Infect Dis 2023; 228:857-867. [PMID: 37572355 PMCID: PMC10547456 DOI: 10.1093/infdis/jiad320] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/26/2023] [Accepted: 08/11/2023] [Indexed: 08/14/2023] Open
Abstract
BACKGROUND We sought to identify potential antigens for discerning between humoral responses elicited after vaccination with CoronaVac (a severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2] inactivated vaccine), natural infection, or breakthrough infection. METHODS Serum samples obtained from volunteers immunized with CoronaVac (2 and 3 doses), breakthrough case patients, and from convalescent individuals were analyzed to determine the immunoglobulin (Ig) G responses against 3 structural and 8 nonstructural SARS-CoV-2 antigens. RESULTS Immunization with CoronaVac induced higher levels of antibodies against the viral membrane (M) protein compared with convalescent subjects both after primary vaccination and after a booster dose. Individuals receiving a booster dose displayed equivalent levels of IgG antibodies against the nucleocapsid (N) protein, similar to convalescent subjects. Breakthrough case patients produced the highest antibody levels against the N and M proteins. Antibodies against nonstructural viral proteins were present in >50% of the convalescent subjects. CONCLUSIONS Vaccinated individuals elicited a different humoral response compared to convalescent subjects. The analysis of particular SARS-CoV-2 antigens could be used as biomarkers for determining infection in subjects previously vaccinated with CoronaVac.
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Affiliation(s)
- Luisa F Duarte
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Yaneisi Vázquez
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Benjamín Diethelm-Varela
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Valentina Pavez
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Roslye Berríos-Rojas
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Constanza Méndez
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudia A Riedel
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | | | - Alexis M Kalergis
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Susan M Bueno
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo A González
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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Tan M, Xia J, Luo H, Meng G, Zhu Z. Applying the digital data and the bioinformatics tools in SARS-CoV-2 research. Comput Struct Biotechnol J 2023; 21:4697-4705. [PMID: 37841328 PMCID: PMC10568291 DOI: 10.1016/j.csbj.2023.09.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/29/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023] Open
Abstract
Bioinformatics has been playing a crucial role in the scientific progress to fight against the pandemic of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The advances in novel algorithms, mega data technology, artificial intelligence and deep learning assisted the development of novel bioinformatics tools to analyze daily increasing SARS-CoV-2 data in the past years. These tools were applied in genomic analyses, evolutionary tracking, epidemiological analyses, protein structure interpretation, studies in virus-host interaction and clinical performance. To promote the in-silico analysis in the future, we conducted a review which summarized the databases, web services and software applied in SARS-CoV-2 research. Those digital resources applied in SARS-CoV-2 research may also potentially contribute to the research in other coronavirus and non-coronavirus viruses.
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Affiliation(s)
- Meng Tan
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Jiaxin Xia
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Haitao Luo
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Geng Meng
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhenglin Zhu
- School of Life Sciences, Chongqing University, Chongqing, China
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40
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Shin J, Shimomura I. COVID-19, Obesity, and GRP78: Unraveling the Pathological Link. J Obes Metab Syndr 2023; 32:183-196. [PMID: 37752707 PMCID: PMC10583770 DOI: 10.7570/jomes23053] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 09/28/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, driven by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to an unprecedented global surge in infections and fatalities. Notably, obesity has emerged as an important susceptibility factor for COVID-19; however, the pathological mechanisms for this remain poorly understood. Recent studies proposed a role for glucose-regulated protein 78 (GRP78), a protein implicated in both obesity and metabolic syndrome, which may function as a binding partner and/or co-receptor for SARS-CoV-2. Given its crucial involvement in diverse biological processes, GRP78 likely plays a major role in multiple facets of the viral life cycle and the pathology of COVID-19. This perspective review discusses the potential contributions of GRP78 to the dynamics of SARS-CoV-2 infection and pathology, particularly in the context of obesity. The primary objective is to facilitate a deeper understanding of the pathogenesis of COVID-19. Through this exploration, we aim to illuminate the complex interactions underpinning the nexus of COVID-19, obesity, and GRP78, ultimately paving the way for informed therapeutic strategies and preventive measures.
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Affiliation(s)
- Jihoon Shin
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Diabetes Care Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Iichiro Shimomura
- Department of Metabolic Medicine, Graduate School of Medicine, Osaka University, Suita, Japan
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Shafqat A, Omer MH, Albalkhi I, Alabdul Razzak G, Abdulkader H, Abdul Rab S, Sabbah BN, Alkattan K, Yaqinuddin A. Neutrophil extracellular traps and long COVID. Front Immunol 2023; 14:1254310. [PMID: 37828990 PMCID: PMC10565006 DOI: 10.3389/fimmu.2023.1254310] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023] Open
Abstract
Post-acute COVID-19 sequelae, commonly known as long COVID, encompasses a range of systemic symptoms experienced by a significant number of COVID-19 survivors. The underlying pathophysiology of long COVID has become a topic of intense research discussion. While chronic inflammation in long COVID has received considerable attention, the role of neutrophils, which are the most abundant of all immune cells and primary responders to inflammation, has been unfortunately overlooked, perhaps due to their short lifespan. In this review, we discuss the emerging role of neutrophil extracellular traps (NETs) in the persistent inflammatory response observed in long COVID patients. We present early evidence linking the persistence of NETs to pulmonary fibrosis, cardiovascular abnormalities, and neurological dysfunction in long COVID. Several uncertainties require investigation in future studies. These include the mechanisms by which SARS-CoV-2 brings about sustained neutrophil activation phenotypes after infection resolution; whether the heterogeneity of neutrophils seen in acute SARS-CoV-2 infection persists into the chronic phase; whether the presence of autoantibodies in long COVID can induce NETs and protect them from degradation; whether NETs exert differential, organ-specific effects; specifically which NET components contribute to organ-specific pathologies, such as pulmonary fibrosis; and whether senescent cells can drive NET formation through their pro-inflammatory secretome in long COVID. Answering these questions may pave the way for the development of clinically applicable strategies targeting NETs, providing relief for this emerging health crisis.
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Affiliation(s)
- Areez Shafqat
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Mohamed H. Omer
- School of Medicine, Cardiff University, Cardiff, United Kingdom
| | | | | | | | | | | | - Khaled Alkattan
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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Vernia F, Ashktorab H, Cesaro N, Monaco S, Faenza S, Sgamma E, Viscido A, Latella G. COVID-19 and Gastrointestinal Tract: From Pathophysiology to Clinical Manifestations. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1709. [PMID: 37893427 PMCID: PMC10608106 DOI: 10.3390/medicina59101709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/10/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023]
Abstract
Background: Since its first report in Wuhan, China, in December 2019, COVID-19 has become a pandemic, affecting millions of people worldwide. Although the virus primarily affects the respiratory tract, gastrointestinal symptoms are also common. The aim of this narrative review is to provide an overview of the pathophysiology and clinical manifestations of gastrointestinal COVID-19. Methods: We conducted a systematic electronic search of English literature up to January 2023 using Medline, Scopus, and the Cochrane Library, focusing on papers that analyzed the role of SARS-CoV-2 in the gastrointestinal tract. Results: Our review highlights that SARS-CoV-2 directly infects the gastrointestinal tract and can cause symptoms such as diarrhea, nausea/vomiting, abdominal pain, anorexia, loss of taste, and increased liver enzymes. These symptoms result from mucosal barrier damage, inflammation, and changes in the microbiota composition. The exact mechanism of how the virus overcomes the acid gastric environment and leads to the intestinal damage is still being studied. Conclusions: Although vaccination has increased the prevalence of less severe symptoms, the long-term interaction with SARS-CoV-2 remains a concern. Understanding the interplay between SARS-CoV-2 and the gastrointestinal tract is essential for future management of the virus.
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Affiliation(s)
- Filippo Vernia
- Gastroenterology Unit, Division of Gastroenterology, Hepatology, and Nutrition, Department of Life, Health and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Hassan Ashktorab
- Department of Medicine, Gastroenterology Division, Howard University College of Medicine, Washington, DC 20060, USA
| | - Nicola Cesaro
- Gastroenterology Unit, Division of Gastroenterology, Hepatology, and Nutrition, Department of Life, Health and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Sabrina Monaco
- Gastroenterology Unit, Division of Gastroenterology, Hepatology, and Nutrition, Department of Life, Health and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Susanna Faenza
- Gastroenterology Unit, Division of Gastroenterology, Hepatology, and Nutrition, Department of Life, Health and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Emanuele Sgamma
- Gastroenterology Unit, Division of Gastroenterology, Hepatology, and Nutrition, Department of Life, Health and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Angelo Viscido
- Gastroenterology Unit, Division of Gastroenterology, Hepatology, and Nutrition, Department of Life, Health and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Giovanni Latella
- Gastroenterology Unit, Division of Gastroenterology, Hepatology, and Nutrition, Department of Life, Health and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
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Tamayo-Ordóñez MC, Rosas-García NM, Ayil-Gutiérrez BA, Bello-López JM, Tamayo-Ordóñez FA, Anguebes-Franseschi F, Damas-Damas S, Tamayo-Ordóñez YDJ. Non-Structural Proteins (Nsp): A Marker for Detection of Human Coronavirus Families. Pathogens 2023; 12:1185. [PMID: 37764993 PMCID: PMC10537875 DOI: 10.3390/pathogens12091185] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/06/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
SARS-CoV-2 was the cause of the global pandemic that caused a total of 14.9 million deaths during the years 2020 and 2021, according to the WHO. The virus presents a mutation rate between 10-5 and 10-3 substitutions per nucleotide site per cell infection (s/n/c). Due to this, studies aimed at knowing the evolution of this virus could help us to foresee (through the future development of new detection strategies and vaccines that prevent the infection of this virus in human hosts) that a pandemic caused by this virus will be generated again. In this research, we performed a functional annotation and identification of changes in Nsp (non-structural proteins) domains in the coronavirus genome. The comparison of the 13 selected coronavirus pangenomes demonstrated a total of 69 protein families and 57 functions associated with the structural domain's differentials between genomes. A marked evolutionary conservation of non-structural proteins was observed. This allowed us to identify and classify highly pathogenic human coronaviruses into alpha, beta, gamma, and delta groups. The designed Nsp cluster provides insight into the trajectory of SARS-CoV-2, demonstrating that it continues to evolve rapidly. An evolutionary marker allows us to discriminate between phylogenetically divergent groups, viral genotypes, and variants between the alpha and betacoronavirus genera. These types of evolutionary studies provide a window of opportunity to use these Nsp as targets of viral therapies.
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Affiliation(s)
- María Concepción Tamayo-Ordóñez
- Laboratorio de Ingeniería Genética, Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Saltillo 25280, Coahuila, Mexico;
| | - Ninfa María Rosas-García
- Laboratorio de Biotecnología Ambiental del Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Tamaulipas, Mexico
| | - Benjamín Abraham Ayil-Gutiérrez
- CONAHCYT-Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Biotecnología Vegetal, Reynosa 88710, Tamaulipas, Mexico
| | - Juan Manuel Bello-López
- División de Investigación, Hospital Juárez de México, Ciudad de México 07760, Campeche, Mexico
| | - Francisco Alberto Tamayo-Ordóñez
- Facultad de Química, Universidad Autónoma del Carmen, Calle 56 N. 4, Av. Concordia Col. Benito Juárez, Ciudad del Carmen 24180, Campeche, Mexico (S.D.-D.)
| | - Francisco Anguebes-Franseschi
- Facultad de Química, Universidad Autónoma del Carmen, Calle 56 N. 4, Av. Concordia Col. Benito Juárez, Ciudad del Carmen 24180, Campeche, Mexico (S.D.-D.)
| | - Siprian Damas-Damas
- Facultad de Química, Universidad Autónoma del Carmen, Calle 56 N. 4, Av. Concordia Col. Benito Juárez, Ciudad del Carmen 24180, Campeche, Mexico (S.D.-D.)
| | - Yahaira de Jesús Tamayo-Ordóñez
- Laboratorio de Biotecnología Ambiental del Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Tamaulipas, Mexico
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44
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Yuan C, Ma Z, Xie J, Li W, Su L, Zhang G, Xu J, Wu Y, Zhang M, Liu W. The role of cell death in SARS-CoV-2 infection. Signal Transduct Target Ther 2023; 8:357. [PMID: 37726282 PMCID: PMC10509267 DOI: 10.1038/s41392-023-01580-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/09/2023] [Accepted: 07/31/2023] [Indexed: 09/21/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), showing high infectiousness, resulted in an ongoing pandemic termed coronavirus disease 2019 (COVID-19). COVID-19 cases often experience acute respiratory distress syndrome, which has caused millions of deaths. Apart from triggering inflammatory and immune responses, many viral infections can cause programmed cell death in infected cells. Cell death mechanisms have a vital role in maintaining a suitable environment to achieve normal cell functionality. Nonetheless, these processes are dysregulated, potentially contributing to disease pathogenesis. Over the past decades, multiple cell death pathways are becoming better understood. Growing evidence suggests that the induction of cell death by the coronavirus may significantly contributes to viral infection and pathogenicity. However, the interaction of SARS-CoV-2 with cell death, together with its associated mechanisms, is yet to be elucidated. In this review, we summarize the existing evidence concerning the molecular modulation of cell death in SARS-CoV-2 infection as well as viral-host interactions, which may shed new light on antiviral therapy against SARS-CoV-2.
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Affiliation(s)
- Cui Yuan
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Zhenling Ma
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Jiufeng Xie
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wenqing Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Lijuan Su
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Guozhi Zhang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Jun Xu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yaru Wu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Min Zhang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Wei Liu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China.
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45
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Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023; 52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Mateusz Sikora
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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46
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Mihalič F, Benz C, Kassa E, Lindqvist R, Simonetti L, Inturi R, Aronsson H, Andersson E, Chi CN, Davey NE, Överby AK, Jemth P, Ivarsson Y. Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets. Nat Commun 2023; 14:5636. [PMID: 37704626 PMCID: PMC10499821 DOI: 10.1038/s41467-023-41312-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 08/30/2023] [Indexed: 09/15/2023] Open
Abstract
The virus life cycle depends on host-virus protein-protein interactions, which often involve a disordered protein region binding to a folded protein domain. Here, we used proteomic peptide phage display (ProP-PD) to identify peptides from the intrinsically disordered regions of the human proteome that bind to folded protein domains encoded by the SARS-CoV-2 genome. Eleven folded domains of SARS-CoV-2 proteins were found to bind 281 peptides from human proteins, and affinities of 31 interactions involving eight SARS-CoV-2 protein domains were determined (KD ∼ 7-300 μM). Key specificity residues of the peptides were established for six of the interactions. Two of the peptides, binding Nsp9 and Nsp16, respectively, inhibited viral replication. Our findings demonstrate how high-throughput peptide binding screens simultaneously identify potential host-virus interactions and peptides with antiviral properties. Furthermore, the high number of low-affinity interactions suggest that overexpression of viral proteins during infection may perturb multiple cellular pathways.
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Affiliation(s)
- Filip Mihalič
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Caroline Benz
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eszter Kassa
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Richard Lindqvist
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187, Umeå, Sweden
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Raviteja Inturi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Hanna Aronsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Celestine N Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Anna K Överby
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187, Umeå, Sweden
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden.
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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47
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Aleebrahim-Dehkordi E, Ghoshouni H, Koochaki P, Esmaili-Dehkordi M, Aleebrahim E, Chichagi F, Jafari A, Hanaei S, Heidari-Soureshjani E, Rezaei N. Targeting the vital non-structural proteins (NSP12, NSP7, NSP8 and NSP3) from SARS-CoV-2 and inhibition of RNA polymerase by natural bioactive compound naringenin as a promising drug candidate against COVID-19. J Mol Struct 2023; 1287:135642. [PMID: 37131962 PMCID: PMC10131750 DOI: 10.1016/j.molstruc.2023.135642] [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: 04/24/2022] [Revised: 04/16/2023] [Accepted: 04/21/2023] [Indexed: 05/04/2023]
Abstract
The prevalence of SARS-CoV-2-induced respiratory infections is now a major challenge worldwide. There is currently no specific antiviral drug to prevent or treat this disease. Infection with COVID-19 seriously needs to find effective therapeutic agents. In the present study, naringenin, as a potential inhibitor candidate for RNA Polymerase SARS-CoV-2 was compared with remdesivir (FDA-approved drug) and GS-441,524 (Derivative of the drug remdesivir) by screening with wild-type and mutant SARS-CoV-2 NSP12 (NSP7-NSP8) and NSP3 interfaces, then complexes were simulated by molecular dynamics (MD) simulations to gain their stabilities. The docking results displayed scores of -3.45 kcal/mol and -4.32 kcal/mol against NSP12 and NSP3, respectively. Our results showed that naringenin had ΔG values more negative than the ΔG values of Remdesivir (RDV) and GS-441,524. Hence, naringenin was considered to be a potential inhibitor. Also, the number of hydrogen bonds of naringenin with NSP3 and later NSP12 are more than Remdesivir and its derivative. In this research, Mean root mean square deviation (RMSD) values of NSP3 and NSP12with naringenin ligand (5.55±1.58 nm to 3.45±0.56 nm and 0.238±0.01 to 0.242±0.021 nm, respectively showed stability in the presence of ligand. The root mean square fluctuations (RMSF) values of NSP3 and NSP12 amino acid units in the presence of naringenin in were 1.5 ± 0.31 nm and 0.118±0.058, respectively. Pharmacokinetic properties and prediction of absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of naringenin and RDV showed that these two compounds had no potential cytotoxicity.
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Affiliation(s)
- Elahe Aleebrahim-Dehkordi
- Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Nutritional Health Team (NHT), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Hamed Ghoshouni
- Medical student, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Pooneh Koochaki
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - Elham Aleebrahim
- PhD Student in Food Sciences and Engineering, Islamic Azad University, Tehran North Branch, Tehran, Iran
| | - Fatemeh Chichagi
- Research Development Center, Sina Hospital, Tehran University of Medical Science, Tehran, Iran
| | - Ali Jafari
- Nutritional Health Team (NHT), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Student Research Committee, Department of Nutrition, School of Health, Golestan University of Medical Sciences, Gorgan, Iran
- Golestan Research Center of Gastroenterology and Hepatology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Sara Hanaei
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Ehsan Heidari-Soureshjani
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box. 115, Iran
- Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Nima Rezaei
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
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48
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Nguyen HL, Thai NQ, Li MS. Identifying inhibitors of NSP16-NSP10 of SARS-CoV-2 from large databases. J Biomol Struct Dyn 2023; 41:7045-7054. [PMID: 36002258 DOI: 10.1080/07391102.2022.2114941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/14/2022] [Indexed: 12/15/2022]
Abstract
The COVID-19 pandemic, which has already claimed millions of lives, continues to pose a serious threat to human health, requiring the development of new effective drugs. Non-structural proteins of SARS-CoV-2 play an important role in viral replication and infection. Among them, NSP16 (non-structured protein 16) and its cofactor NSP10 (non-structured protein 10) perform C2'-O methylation at the 5' end of the viral RNA, which promotes efficient virus replication. Therefore, the NSP16-NSP10 complex becomes an attractive target for drug development. Using a multi-step virtual screening protocol which includes Lipinski's rule, docking, steered molecular dynamics and umbrella sampling, we searched for potential inhibitors from the PubChem and anti-HIV databases. It has been shown that CID 135566620 compound from PubChem is the best candidate with an inhibition constant in the sub-μM range. The Van der Waals interaction was found to be more important than the electrostatic interaction in the binding affinity of this compound to NSP16-NSP10. Further in vitro and in vivo studies are needed to test the activity of the identified compound against COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hoang Linh Nguyen
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung, Software City, Ho Chi Minh City, Vietnam
- Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | | | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
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49
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Leonard RA, Rao VN, Bartlett A, Froggatt HM, Luftig MA, Heaton BE, Heaton NS. A low-background, fluorescent assay to evaluate inhibitors of diverse viral proteases. J Virol 2023; 97:e0059723. [PMID: 37578235 PMCID: PMC10506478 DOI: 10.1128/jvi.00597-23] [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: 04/20/2023] [Accepted: 06/11/2023] [Indexed: 08/15/2023] Open
Abstract
Multiple coronaviruses (CoVs) can cause respiratory diseases in humans. While prophylactic vaccines designed to prevent infection are available for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), incomplete vaccine efficacy, vaccine hesitancy, and the threat of other pathogenic CoVs for which vaccines do not exist have highlighted the need for effective antiviral therapies. While antiviral compounds targeting the viral polymerase and protease are already in clinical use, their sensitivity to potential resistance mutations as well as their breadth against the full range of human and preemergent CoVs remain incompletely defined. To begin to fill that gap in knowledge, we report here the development of an improved, noninfectious, cell-based fluorescent assay with high sensitivity and low background that reports on the activity of viral proteases, which are key drug targets. We demonstrate that the assay is compatible with not only the SARS-CoV-2 Mpro protein but also orthologues from a range of human and nonhuman CoVs as well as clinically reported SARS-CoV-2 drug-resistant Mpro variants. We then use this assay to define the breadth of activity of two clinically used protease inhibitors, nirmatrelvir and ensitrelvir. Continued use of this assay will help define the strengths and limitations of current therapies and may also facilitate the development of next-generation protease inhibitors that are broadly active against both currently circulating and preemergent CoVs. IMPORTANCE Coronaviruses (CoVs) are important human pathogens with the ability to cause global pandemics. Working in concert with vaccines, antivirals specifically limit viral disease in people who are actively infected. Antiviral compounds that target CoV proteases are already in clinical use; their efficacy against variant proteases and preemergent zoonotic CoVs, however, remains incompletely defined. Here, we report an improved, noninfectious, and highly sensitive fluorescent method of defining the sensitivity of CoV proteases to small molecule inhibitors. We use this approach to assay the activity of current antiviral therapies against clinically reported SARS-CoV-2 protease mutants and a panel of highly diverse CoV proteases. Additionally, we show this system is adaptable to other structurally nonrelated viral proteases. In the future, this assay can be used to not only better define the strengths and limitations of current therapies but also help develop new, broadly acting inhibitors that more broadly target viral families.
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Affiliation(s)
- Rebecca A. Leonard
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Vishwas N. Rao
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Medical Scientist Training Program, Duke University School of Medicine, Durham, North Carolina, USA
| | - Alexandria Bartlett
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Heather M. Froggatt
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Micah A. Luftig
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Brook E. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
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50
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Zeng Z, Geng X, Wen X, Chen Y, Zhu Y, Dong Z, Hao L, Wang T, Yang J, Zhang R, Zheng K, Sun Z, Zhang Y. Novel receptor, mutation, vaccine, and establishment of coping mode for SARS-CoV-2: current status and future. Front Microbiol 2023; 14:1232453. [PMID: 37645223 PMCID: PMC10461067 DOI: 10.3389/fmicb.2023.1232453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/25/2023] [Indexed: 08/31/2023] Open
Abstract
Since the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its resultant pneumonia in December 2019, the cumulative number of infected people worldwide has exceeded 670 million, with over 6.8 million deaths. Despite the marketing of multiple series of vaccines and the implementation of strict prevention and control measures in many countries, the spread and prevalence of SARS-CoV-2 have not been completely and effectively controlled. The latest research shows that in addition to angiotensin converting enzyme II (ACE2), dozens of protein molecules, including AXL, can act as host receptors for SARS-CoV-2 infecting human cells, and virus mutation and immune evasion never seem to stop. To sum up, this review summarizes and organizes the latest relevant literature, comprehensively reviews the genome characteristics of SARS-CoV-2 as well as receptor-based pathogenesis (including ACE2 and other new receptors), mutation and immune evasion, vaccine development and other aspects, and proposes a series of prevention and treatment opinions. It is expected to provide a theoretical basis for an in-depth understanding of the pathogenic mechanism of SARS-CoV-2 along with a research basis and new ideas for the diagnosis and classification, of COVID-19-related disease and for drug and vaccine research and development.
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Affiliation(s)
- Zhaomu Zeng
- Department of Neurosurgery, Jiangxi Provincial People’s Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
- Department of Neurosurgery, Xiangya Hospital Jiangxi Hospital of Central South University, National Regional Medical Center for Nervous System Diseases, Nanchang, China
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Xiuchao Geng
- Department of Nursing, School of Medicine, Taizhou University, Taizhou, China
| | - Xichao Wen
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Yueyue Chen
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
| | - Yixi Zhu
- Department of Pharmacy, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zishu Dong
- Department of Zoology, Advanced Research Institute, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Liangchao Hao
- Department of Plastic Surgery, Shaoxing People’s Hospital, Shaoxing, China
| | - Tingting Wang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Jifeng Yang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Ruobing Zhang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Kebin Zheng
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Zhiwei Sun
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing, China
| | - Yuhao Zhang
- Cancer Center, Department of Neurosurgery, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, China
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