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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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Bayani F, Hashkavaei NS, Arjmand S, Rezaei S, Uskoković V, Alijanianzadeh M, Uversky VN, Ranaei Siadat SO, Mozaffari-Jovin S, Sefidbakht Y. An overview of the vaccine platforms to combat COVID-19 with a focus on the subunit vaccines. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 178:32-49. [PMID: 36801471 PMCID: PMC9938630 DOI: 10.1016/j.pbiomolbio.2023.02.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/21/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging virus that has caused the recent coronavirus disease (COVID-19) global pandemic. The current approved COVID-19 vaccines have shown considerable efficiency against hospitalization and death. However, the continuation of the pandemic for more than two years and the likelihood of new strain emergence despite the global rollout of vaccination highlight the immediate need for the development and improvement of vaccines. mRNA, viral vector, and inactivated virus vaccine platforms were the first members of the worldwide approved vaccine list. Subunit vaccines. which are vaccines based on synthetic peptides or recombinant proteins, have been used in lower numbers and limited countries. The unavoidable advantages of this platform, including safety and precise immune targeting, make it a promising vaccine with wider global use in the near future. This review article summarizes the current knowledge on different vaccine platforms, focusing on the subunit vaccines and their clinical trial advancements against COVID-19.
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Affiliation(s)
- Fatemeh Bayani
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | | | - Sareh Arjmand
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Shokouh Rezaei
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Vuk Uskoković
- Department of Mechanical Engineering, San Diego State University, San Diego, CA, 92182, USA; TardigradeNano LLC, Irvine, CA, 92604, USA
| | - Mahdi Alijanianzadeh
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
| | | | - Sina Mozaffari-Jovin
- Department of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Yahya Sefidbakht
- Protein Research Center, Shahid Beheshti University, Tehran, Iran.
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Comparison of the Immune Response in Vaccinated People Positive and Negative to SARS-CoV-2 Employing FTIR Spectroscopy. Cells 2022; 11:cells11233884. [PMID: 36497139 PMCID: PMC9740721 DOI: 10.3390/cells11233884] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/21/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
Various immunopathological events characterize the systemic acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Moreover, it has been reported that coronavirus disease 2019 (COVID-19) vaccination and infection by SARS-CoV-2 induce humoral immunity mediated by B-cell-derived antibodies and cellular immunity mediated by T cells and memory B cells. Immunoglobulins, cytokines, and chemokines play an important role in shaping immunity in response to infection and vaccination. Furthermore, different vaccines have been developed to prevent COVID-19. Therefore, this research aimed to analyze and compare Fourier-transform infrared (FTIR) spectra of vaccinated people with a positive (V-COVID-19 group) or negative (V-Healthy group) real-time quantitative reverse transcription-polymerase chain reaction (RT-qPCR) test, evaluating the immunoglobulin and cytokine content as an immunological response through FTIR spectroscopy. Most individuals that integrated the V-Healthy group (88.1%) were asymptomatic; on the contrary, only 28% of the V-COVID-19 group was asymptomatic. Likewise, 68% of the V-COVID-19 group had at least one coexisting illness. Regarding the immunological response analyzed through FTIR spectroscopy, the V-COVID-19 group showed a greater immunoglobulins G, A, and M (IgG, IgA, and IgM) content, as well as the analyzed cytokines interferon-gamma (IFN-γ), tumor necrosis factor-alpha (TNF-ɑ), and interleukins 1β, 6, and 10 (IL-1β, IL-6, and IL-10). Therefore, we can state that it was possible to detect biochemical changes through FTIR spectroscopy associated with COVID-19 immune response in vaccinated people.
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Zheng Y, Song K, Cai K, Liu L, Tang D, Long W, Zhai B, Chen J, Tao Y, Zhao Y, Liang S, Huang Q, Liu Q, Zhang Q, Chen Y, Liu Y, Li H, Wang P, Lan K, Liu H, Xu K. B-Cell-Epitope-Based Fluorescent Quantum Dot Biosensors for SARS-CoV-2 Enable Highly Sensitive COVID-19 Antibody Detection. Viruses 2022; 14:v14051031. [PMID: 35632772 PMCID: PMC9145955 DOI: 10.3390/v14051031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/11/2022] [Accepted: 05/06/2022] [Indexed: 12/21/2022] Open
Abstract
A new antibody diagnostic assay with more rapid and robust properties is demanded to quantitatively evaluate anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunity in a large population. Here, we developed a nanometer-scale fluorescent biosensor system consisting of CdSe-ZnS quantum dots (QDs) coupled with the highly sensitive B-cell epitopes of SARS-CoV-2 that could remarkably identify the corresponding antibody with a detection limit of 100 pM. Intriguingly, we found that fluorescence quenching of QDs was stimulated more obviously when coupled with peptides than the corresponding proteins, indicating that the energy transfer between QDs and peptides was more effective. Compared to the traditional enzyme-linked immunosorbent assay (ELISA), the B-cell-epitope-based QD-biosensor could robustly distinguish coronavirus disease 2019 (COVID-19) antibody-positive patients from uninfected individuals with a higher sensitivity (92.3–98.1% positive rates by QD-biosensor vs. 78.3–83.1% positive rates by ELISAs in 207 COVID-19 patients’ sera) in a more rapid (5 min) and labor-saving manner. Taken together, the ‘QD-peptides’ biosensor provided a novel real-time, quantitative, and high-throughput method for clinical diagnosis and home-use tests.
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Affiliation(s)
- Yucheng Zheng
- State Key Laboratory of Virology, Institute for Vaccine Research, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.Z.); (K.S.); (D.T.); (S.L.); (Q.L.); (Q.Z.); (Y.C.); (Y.L.); (K.L.)
| | - Kun Song
- State Key Laboratory of Virology, Institute for Vaccine Research, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.Z.); (K.S.); (D.T.); (S.L.); (Q.L.); (Q.Z.); (Y.C.); (Y.L.); (K.L.)
| | - Kun Cai
- Hubei Provincial Center for Diseases Control and Prevention, Wuhan 430079, China; (K.C.); (L.L.)
| | - Linlin Liu
- Hubei Provincial Center for Diseases Control and Prevention, Wuhan 430079, China; (K.C.); (L.L.)
| | - Dixiao Tang
- State Key Laboratory of Virology, Institute for Vaccine Research, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.Z.); (K.S.); (D.T.); (S.L.); (Q.L.); (Q.Z.); (Y.C.); (Y.L.); (K.L.)
| | - Wenbo Long
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Optics Valley Laboratory, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China; (W.L.); (B.Z.); (Y.T.); (Y.Z.); (Q.H.); (H.L.)
| | - Bohui Zhai
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Optics Valley Laboratory, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China; (W.L.); (B.Z.); (Y.T.); (Y.Z.); (Q.H.); (H.L.)
| | - Jianjun Chen
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, China;
| | - Yanbing Tao
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Optics Valley Laboratory, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China; (W.L.); (B.Z.); (Y.T.); (Y.Z.); (Q.H.); (H.L.)
| | - Yunong Zhao
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Optics Valley Laboratory, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China; (W.L.); (B.Z.); (Y.T.); (Y.Z.); (Q.H.); (H.L.)
| | - Simeng Liang
- State Key Laboratory of Virology, Institute for Vaccine Research, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.Z.); (K.S.); (D.T.); (S.L.); (Q.L.); (Q.Z.); (Y.C.); (Y.L.); (K.L.)
| | - Qing Huang
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Optics Valley Laboratory, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China; (W.L.); (B.Z.); (Y.T.); (Y.Z.); (Q.H.); (H.L.)
| | - Qianyun Liu
- State Key Laboratory of Virology, Institute for Vaccine Research, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.Z.); (K.S.); (D.T.); (S.L.); (Q.L.); (Q.Z.); (Y.C.); (Y.L.); (K.L.)
| | - Qi Zhang
- State Key Laboratory of Virology, Institute for Vaccine Research, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.Z.); (K.S.); (D.T.); (S.L.); (Q.L.); (Q.Z.); (Y.C.); (Y.L.); (K.L.)
| | - Yu Chen
- State Key Laboratory of Virology, Institute for Vaccine Research, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.Z.); (K.S.); (D.T.); (S.L.); (Q.L.); (Q.Z.); (Y.C.); (Y.L.); (K.L.)
- Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University, Wuhan 430072, China
| | - Yingle Liu
- State Key Laboratory of Virology, Institute for Vaccine Research, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.Z.); (K.S.); (D.T.); (S.L.); (Q.L.); (Q.Z.); (Y.C.); (Y.L.); (K.L.)
- Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University, Wuhan 430072, China
| | - Huayao Li
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Optics Valley Laboratory, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China; (W.L.); (B.Z.); (Y.T.); (Y.Z.); (Q.H.); (H.L.)
| | - Ping Wang
- Department of Clinical Laboratory, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, China;
| | - Ke Lan
- State Key Laboratory of Virology, Institute for Vaccine Research, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.Z.); (K.S.); (D.T.); (S.L.); (Q.L.); (Q.Z.); (Y.C.); (Y.L.); (K.L.)
- Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University, Wuhan 430072, China
| | - Huan Liu
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Optics Valley Laboratory, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China; (W.L.); (B.Z.); (Y.T.); (Y.Z.); (Q.H.); (H.L.)
- Correspondence: (H.L.); (K.X.); Tel.: +86-27-87793936 (H.L.); +86-27-68756997 (K.X.); Fax: +86-27-68754592 (K.X.)
| | - Ke Xu
- State Key Laboratory of Virology, Institute for Vaccine Research, College of Life Sciences, Wuhan University, Wuhan 430072, China; (Y.Z.); (K.S.); (D.T.); (S.L.); (Q.L.); (Q.Z.); (Y.C.); (Y.L.); (K.L.)
- Institute for Vaccine Research, Animal Biosafety Level 3 Laboratory, Wuhan University, Wuhan 430072, China
- Correspondence: (H.L.); (K.X.); Tel.: +86-27-87793936 (H.L.); +86-27-68756997 (K.X.); Fax: +86-27-68754592 (K.X.)
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5
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Jung BK, An YH, Jang JJ, Jeon JH, Jang SH, Jang H. The human ACE-2 receptor binding domain of SARS-CoV-2 express on the viral surface of the Newcastle disease virus as a non-replicating viral vector vaccine candidate. PLoS One 2022; 17:e0263684. [PMID: 35134091 PMCID: PMC8824364 DOI: 10.1371/journal.pone.0263684] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 01/24/2022] [Indexed: 12/24/2022] Open
Abstract
Since the SARS-CoV-2 infection was identified in December 2019, SARS-CoV-2 infection has rapidly spread worldwide and has become a significant pandemic disease. In addition, human death and serious health problem caused by SARS-CoV-2 infection, the socio-economic impact has been very serious. Here, we describe the development of the viral vector vaccine, which is the receptor-binding domain (RBD) of SARS-CoV-2 expressed on the surface of Newcastle disease virus (LVP-K1-RBD19). The RBD protein concentrations on the viral surface were measured by the sandwich ELISA method. 106.7 TCID50/ml of LVP-K1-RBD19 has a 0.17 μg of RBD protein. Optical density (OD) values of mouse sera inoculated with 10 μg of RBD protein expressed on the surface of LVP-K1-RBD19 generated 1.78-fold higher RBD-specific antibody titers than mice inoculated with 10 μg RBD protein with alum at 28 dpi. Moreover, mice inoculated with 10 μg of RBD protein expressed on the surface of LVP-K1-RBD19 virus showed more than 80% neutralization at 1:256 against the SARS-CoV-2 pseudovirus. These results demonstrated that inactivated LVP-K1-RBD19 virus produces neutralizing antibodies against SARS-CoV-2 in a short period and could be elect protective immunity in humans and LVP-K1-RBD19 will be a good candidate for the COVID-19 vaccine.
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Affiliation(s)
| | - Yong Hee An
- Libentech Co. LTD, Daejeon, Republic of Korea
| | - Jin-Ju Jang
- Libentech Co. LTD, Daejeon, Republic of Korea
| | | | - Sung Hoon Jang
- Department of Biological Sciences, College of Natural Sciences, Inha University, Incheon, Republic of Korea
| | - Hyun Jang
- Libentech Co. LTD, Daejeon, Republic of Korea
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Kaul R, Paul P, Kumar S, Büsselberg D, Dwivedi VD, Chaari A. Promising Antiviral Activities of Natural Flavonoids against SARS-CoV-2 Targets: Systematic Review. Int J Mol Sci 2021; 22:11069. [PMID: 34681727 PMCID: PMC8539743 DOI: 10.3390/ijms222011069] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/08/2021] [Accepted: 10/10/2021] [Indexed: 12/13/2022] Open
Abstract
The ongoing COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) became a globally leading public health concern over the past two years. Despite the development and administration of multiple vaccines, the mutation of newer strains and challenges to universal immunity has shifted the focus to the lack of efficacious drugs for therapeutic intervention for the disease. As with SARS-CoV, MERS-CoV, and other non-respiratory viruses, flavonoids present themselves as a promising therapeutic intervention given their success in silico, in vitro, in vivo, and more recently, in clinical studies. This review focuses on data from in vitro studies analyzing the effects of flavonoids on various key SARS-CoV-2 targets and presents an analysis of the structure-activity relationships for the same. From 27 primary papers, over 69 flavonoids were investigated for their activities against various SARS-CoV-2 targets, ranging from the promising 3C-like protease (3CLpro) to the less explored nucleocapsid (N) protein; the most promising were quercetin and myricetin derivatives, baicalein, baicalin, EGCG, and tannic acid. We further review promising in silico studies featuring activities of flavonoids against SARS-CoV-2 and list ongoing clinical studies involving the therapeutic potential of flavonoid-rich extracts in combination with synthetic drugs or other polyphenols and suggest prospects for the future of flavonoids against SARS-CoV-2.
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Affiliation(s)
- Ridhima Kaul
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha 24144, Qatar; (R.K.); (P.P.)
| | - Pradipta Paul
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha 24144, Qatar; (R.K.); (P.P.)
| | - Sanjay Kumar
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida 201308, India; (S.K.); (V.D.D.)
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Dietrich Büsselberg
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha 24144, Qatar;
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida 201308, India; (S.K.); (V.D.D.)
| | - Ali Chaari
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha 24144, Qatar; (R.K.); (P.P.)
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KOCABAŞ F, USLU M. The current state of validated small molecules inhibiting SARS-CoV-2 nonstructural proteins. Turk J Biol 2021; 45:469-483. [PMID: 34803448 PMCID: PMC8573838 DOI: 10.3906/biy-2106-42] [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: 08/20/2021] [Accepted: 08/06/2021] [Indexed: 11/03/2022] Open
Abstract
The current COVID-19 outbreak has had a profound influence on public health and daily life. Despite all restrictions and vaccination programs, COVID-19 still can lead to fatality due to a lack of COVID-19-specific treatments. A number of studies have demonstrated the feasibility to develop therapeutics by targeting underlying components of the viral proteome. Here we reviewed recently developed and validated small molecule inhibitors of SARS-CoV-2's nonstructural proteins. We described the validation level of identified compounds specific for SARS-CoV-2 in the presence of in vitro and in vivo supporting data. The mechanisms of pharmacological activity, as well as approaches for developing improved SARS-CoV-2 NSP inhibitors have been emphasized.
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Affiliation(s)
- Fatih KOCABAŞ
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, İstanbulTurkey
| | - Merve USLU
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, İstanbulTurkey
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