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Singh A, Jangid K, Nehul S, Dhaka P, Rani R, Pareek A, Sharma GK, Kumar P, Tomar S. Structural and Mechanistic Insights into the Main Protease (Mpro) Dimer Interface Destabilization Inhibitor: Unveiling New Therapeutic Avenues against SARS-CoV-2. Biochemistry 2025; 64:1589-1605. [PMID: 39882595 DOI: 10.1021/acs.biochem.4c00535] [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: 01/31/2025]
Abstract
SARS-CoV-2 variant recurrence has emphasized the imperative prerequisite for effective antivirals. The main protease (Mpro) of SARS-CoV-2 is crucial for viral replication, making it one of the prime and promising antiviral targets. Mpro features several druggable sites, including active sites and allosteric sites near the dimerization interface, that regulate its catalytic activity. This study identified six highly efficacious antiviral SARS-CoV-2 compounds (WIN-62577, KT185, bexarotene, ledipasvir, diacerein, and simepervir) using structure-based virtual screening of compound libraries against Mpro. Using SPR and ITC, the binding of selected inhibitory compounds to the target Mpro was validated. The FRET-based protease assay demonstrated that the identified molecules effectively inhibit Mpro with IC50 values in the range from 0.64 to 11.98 μM. Additionally, in vitro cell-based antiviral assays showed high efficacy with EC50 values in the range of 1.51 to 18.92 μM. The crystal structure of the Mpro-minocycline complex detailed the possible inhibition mechanism of minocycline, an FDA-approved antibiotic. Minocycline binds to an allosteric site, revealing residues critical for the loss of protease activity due to destabilization of molecular interactions at the dimeric interface, which are crucial for the proteolytic activity of Mpro. The study suggests that the binding of minocycline to the allosteric site may play a role in Mpro dimer destabilization and direct the rational design of minocycline derivatives as antiviral drugs.
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Affiliation(s)
- Ankur Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Kuldeep Jangid
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Sanketkumar Nehul
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Preeti Dhaka
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Ruchi Rani
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Akshay Pareek
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Gaurav Kumar Sharma
- Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India
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Dhaka P, Mahto JK, Singh A, Kumar P, Tomar S. Structural insights into the RNA binding inhibitors of the C-terminal domain of the SARS-CoV-2 nucleocapsid. J Struct Biol 2025; 217:108197. [PMID: 40113149 DOI: 10.1016/j.jsb.2025.108197] [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: 10/09/2024] [Revised: 01/26/2025] [Accepted: 03/13/2025] [Indexed: 03/22/2025]
Abstract
The SARS-CoV-2 nucleocapsid (N) protein is an essential structural element of the virion, playing a crucial role in enclosing the viral genome into a ribonucleoprotein (RNP) assembly, as well as viral replication and transmission. The C-terminal domain of the N-protein (N-CTD) is essential for encapsidation, contributing to the stabilization of the RNP complex. In a previous study, three inhibitors (ceftriaxone, cefuroxime, and ampicillin) were screened for their potential to disrupt the RNA packaging process by targeting the N-protein. However, the binding efficacy, mechanism of RNA binding inhibition, and molecular insights of binding with N-CTD remain unclear. In this study, we evaluated the binding efficacy of these inhibitors using isothermal titration calorimetry (ITC), revealing the affinity of ceftriaxone (18 ± 1.3 μM), cefuroxime (55 ± 4.2 μM), and ampicillin (28 ± 1.2 μM) with the N-CTD. Further inhibition assay and fluorescence polarisation assay demonstrated RNA binding inhibition, with IC50 ranging from ∼ 12 to 18 μM and KD values between 24 μM to 32 μM for the inhibitors, respectively. Additionally, we also determined the inhibitor-bound complex crystal structures of N-CTD-Ceftriaxone (2.0 Å) and N-CTD-Ampicillin (2.2 Å), along with the structure of apo N-CTD (1.4 Å). These crystal structures revealed previously unobserved interaction sites involving residues K261, K266, R293, Q294, and W301 at the oligomerization interface and the predicted RNA-binding region of N-CTD. These findings provide valuable molecular insights into the inhibition of N-CTD, highlighting its potential as an underexplored but promising target for the development of novel antiviral agents against coronaviruses.
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Affiliation(s)
- Preeti Dhaka
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Jai Krishna Mahto
- 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
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India.
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India.
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Handa T, Saha A, Narayanan A, Ronzier E, Kumar P, Singla J, Tomar S. Structural Virology: The Key Determinants in Development of Antiviral Therapeutics. Viruses 2025; 17:417. [PMID: 40143346 PMCID: PMC11945554 DOI: 10.3390/v17030417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2025] [Revised: 03/07/2025] [Accepted: 03/10/2025] [Indexed: 03/28/2025] Open
Abstract
Structural virology has emerged as the foundation for the development of effective antiviral therapeutics. It is pivotal in providing crucial insights into the three-dimensional frame of viruses and viral proteins at atomic-level or near-atomic-level resolution. Structure-based assessment of viral components, including capsids, envelope proteins, replication machinery, and host interaction interfaces, is instrumental in unraveling the multiplex mechanisms of viral infection, replication, and pathogenesis. The structural elucidation of viral enzymes, including proteases, polymerases, and integrases, has been essential in combating viruses like HIV-1 and HIV-2, SARS-CoV-2, and influenza. Techniques including X-ray crystallography, Nuclear Magnetic Resonance spectroscopy, Cryo-electron Microscopy, and Cryo-electron Tomography have revolutionized the field of virology and significantly aided in the discovery of antiviral therapeutics. The ubiquity of chronic viral infections, along with the emergence and reemergence of new viral threats necessitate the development of novel antiviral strategies and agents, while the extensive structural diversity of viruses and their high mutation rates further underscore the critical need for structural analysis of viral proteins to aid antiviral development. This review highlights the significance of structure-based investigations for bridging the gap between structure and function, thus facilitating the development of effective antiviral therapeutics, vaccines, and antibodies for tackling emerging viral threats.
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Affiliation(s)
- Tanuj Handa
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India; (T.H.); (A.S.); (P.K.); (J.S.)
| | - Ankita Saha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India; (T.H.); (A.S.); (P.K.); (J.S.)
| | - Aarthi Narayanan
- Department of Biology, College of Science, George Mason University, Fairfax, VA 22030, USA;
| | - Elsa Ronzier
- Biomedical Research Laboratory, Institute for Biohealth Innovation, George Mason University, Fairfax, VA 22030, USA;
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India; (T.H.); (A.S.); (P.K.); (J.S.)
| | - Jitin Singla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India; (T.H.); (A.S.); (P.K.); (J.S.)
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, India; (T.H.); (A.S.); (P.K.); (J.S.)
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Saha A, Choudhary S, Walia P, Kumar P, Tomar S. Transformative approaches in SARS-CoV-2 management: Vaccines, therapeutics and future direction. Virology 2025; 604:110394. [PMID: 39889481 DOI: 10.1016/j.virol.2025.110394] [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: 10/15/2024] [Revised: 12/24/2024] [Accepted: 12/28/2024] [Indexed: 02/03/2025]
Abstract
The global healthcare and economic challenges caused by the pandemic of COVID-19 reinforced the urgent demand for quick and effective therapeutic and preventative interventions. While vaccines served as the frontline of defense, antivirals emerged as adjunctive countermeasures, especially for people who developed infection, were immunocompromised, or were reluctant to be vaccinated. Beyond the serious complications of SARS-CoV-2 infection, the threats of long-COVID and the potential for zoonotic spillover continue to be significant health concerns that cannot be overlooked. Moreover, the incessant viral evolution, clinical safety issues, waning immune responses, and the emergence of drug-resistant variants pinpoint towards more severe viral threats in the future and call for broad-spectrum innovative therapies as a pre-pandemic preparedness measure. The present review provides a comprehensive up-to-date overview of the strategies utilized in the development of classical and next-generation vaccines against SARS-CoV-2, the clinical and experimental data obtained from clinical trials, while addressing safety risks that may arise. Besides vaccines, the review also covers recent breakthroughs in anti-SARS-CoV-2 drug discovery, emphasizing druggable viral and host targets, virus- and host-targeting antivirals, and highlighting mechanistically representative molecules that are either approved or are under clinical investigation. In conclusion, the integration of both vaccines and antiviral therapies, along with swift innovative strategies to address viral evolution and drug resistance is crucial to strengthen our preparedness against future viral outbreaks.
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Affiliation(s)
- Ankita Saha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, 247667, India
| | - Shweta Choudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, 247667, India
| | - Priyanshu Walia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, 247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, 247667, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, 247667, India.
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Dhaka P, Singh A, Nehul S, Choudhary S, Panda PK, Sharma GK, Kumar P, Tomar S. Disruption of Molecular Interactions between the G3BP1 Stress Granule Host Protein and the Nucleocapsid (NTD-N) Protein Impedes SARS-CoV-2 Virus Replication. Biochemistry 2025; 64:823-840. [PMID: 39708056 DOI: 10.1021/acs.biochem.4c00536] [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: 12/23/2024]
Abstract
The Ras GTPase-activating protein SH3-domain-binding protein 1 (G3BP1) serves as a formidable barrier to viral replication by generating stress granules (SGs) in response to viral infections. Interestingly, viruses, including SARS-CoV-2, have evolved defensive mechanisms to hijack SG proteins like G3BP1 for the dissipation of SGs that lead to the evasion of the host's immune responses. Previous research has demonstrated that the interaction between the NTF2-like domain of G3BP1 (G3BP1NTF-2) and the intrinsically disordered N-terminal domain (NTD-N1-25) of the N-protein plays a crucial role in regulating viral replication and pathogenicity. Interestingly, the current study identified an additional upstream stretch of residues (128KDGIIWVATEG138) (N128-138) within the N-terminal domain of the N-protein (NTD-N41-174) that also forms molecular contacts with the G3BP1 protein, as revealed through in silico analysis, site-directed mutagenesis, and biochemical analysis. Remarkably, WIN-62577, and fluspirilene, the small molecules targeting the conserved peptide-binding pocket in G3BP1NTF-2, not only disrupted the protein-protein interactions (PPIs) between NTD-N41-174 and G3BP1NTF-2 but also exhibited significant antiviral efficacy against SARS-CoV-2 replication with EC50 values of ∼1.8 and ∼1.3 μM, respectively. The findings of this study, validated by biophysical thermodynamics and biochemical investigations, advance the potential of developing therapeutics targeting the SG host protein against SARS-CoV-2, which may also serve as a broad-spectrum antiviral target.
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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
| | - Sanketkumar Nehul
- 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
| | - Prasan Kumar Panda
- Department of Medicine, All India Institute of Medical Sciences (AIIMS), Rishikesh 249203, India
| | - Gaurav Kumar Sharma
- Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
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Dhaka P, Singh A, Nehul S, Choudhary S, Panda PK, Sharma GK, Kumar P, Tomar S. Disruption of molecular interactions between G3BP1 stress granule host protein and nucleocapsid (NTD-N) protein impedes SARS-CoV-2 virus replication.. [DOI: 10.1101/2024.10.27.620470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2025]
Abstract
ABSTRACTThe Ras GTPase-activating protein SH3-domain-binding protein 1 (G3BP1) serves as a formidable barrier to viral replication by generating stress granules (SGs) in response to viral infections. Interestingly, viruses, including SARS-CoV-2, have evolved defensive mechanisms to hijack SG proteins like G3BP1 for the dissipation of SGs that lead to the evasion of host’s immune responses. Previous research has demonstrated that the interaction between the NTF2-like domain of G3BP1 (G3BP1NTF-2) and the intrinsically disordered N-terminal domain (NTD-N1-25) of the N protein plays a crucial role in regulating viral replication and pathogenicity. Interestingly, the current study identified an additional upstream stretch of residues (128KDGIIWVATEG138) (N128-138) within the N-terminal domain of the N protein (NTD-N41-174) that also forms molecular contacts with the G3BP1 protein, as revealed throughin silicoanalysis, site-directed mutagenesis and biochemical analysis. Remarkably, WIN-62577, and fluspirilene, the small molecules targeting the conserved peptide binding pocket in G3BP1NTF-2,not only disrupted the protein-protein interactions (PPIs) between the NTD-N41-174and G3BP1NTF-2but also exhibited significant antiviral efficacy against SARS-CoV-2 replication with EC50values of ∼1.8 µM and ∼1.3 µM, respectively. The findings of this study, validated by biophysical thermodynamics and biochemical investigations, advance the potential of developing therapeutics targeting the SG host protein against SARS-CoV-2, which may also serve as a broad-spectrum antiviral target.
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Cao Z, Ling X, Haseeb A, Sun P, Zhang H, Yin W, Fan K, Yang H, Zhang Z, Zhong J, Sun Y, Sun N, Li H. Analysis of the anti-PCV2 mechanism of Lactobacillus acidophilus based on non-target metabolomics and high-throughput molecular docking. Front Microbiol 2024; 15:1416235. [PMID: 38860222 PMCID: PMC11163031 DOI: 10.3389/fmicb.2024.1416235] [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: 04/12/2024] [Accepted: 05/13/2024] [Indexed: 06/12/2024] Open
Abstract
Our previous studies have revealed that L. acidophilus possesses inhibitory effects on PCV2 proliferation in vivo, although the underlying mechanisms remain elusive. Probiotics like L. acidophilus are known to exert antiviral through their metabolites. Therefore, in this study, non-targeted metabolomics was used to detect the changes in metabolites of L. acidophilus after 24 h of proliferation. Subsequently, high-throughput molecular docking was utilized to analyze the docking scores of these metabolites with PCV2 Cap and Rep, aiming to identify compounds with potential anti-PCV2 effects. The results demonstrated that 128 compounds such as Dl-lactate were significantly increased. The results of high-throughput molecular docking indicated that compounds such as ergocristine, and telmisartan formed complexes with Cap and Rep, suggesting their potential anti-PCV2 properties. Furthermore, compounds like vitamin C, exhibit pharmacological effects consistent with L. acidophilus adding credence to the idea that L. acidophilus may exert pharmacological effects through its metabolites. These results will provide a foundation for the study of L. acidophilus.
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Affiliation(s)
- Zhigang Cao
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Xiaoya Ling
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Abdul Haseeb
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Panpan Sun
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Hua Zhang
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Wei Yin
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Kuohai Fan
- Laboratory Animal Center, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Huizhen Yang
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Zhenbiao Zhang
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Jia Zhong
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Yaogui Sun
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Na Sun
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Hongquan Li
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi, China
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Choudhary S, Nehul S, Singh A, Panda PK, Kumar P, Sharma GK, Tomar S. Unraveling antiviral efficacy of multifunctional immunomodulatory triterpenoids against SARS-COV-2 targeting main protease and papain-like protease. IUBMB Life 2024; 76:228-241. [PMID: 38059400 DOI: 10.1002/iub.2793] [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: 03/15/2023] [Accepted: 10/20/2023] [Indexed: 12/08/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may be over, but its variants continue to emerge, and patients with mild symptoms having long COVID is still under investigation. SARS-CoV-2 infection leading to elevated cytokine levels and suppressed immune responses set off cytokine storm, fatal systemic inflammation, tissue damage, and multi-organ failure. Thus, drug molecules targeting the SARS-CoV-2 virus-specific proteins or capable of suppressing the host inflammatory responses to viral infection would provide an effective antiviral therapy against emerging variants of concern. Evolutionarily conserved papain-like protease (PLpro) and main protease (Mpro) play an indispensable role in the virus life cycle and immune evasion. Direct-acting antivirals targeting both these viral proteases represent an attractive antiviral strategy that is also expected to reduce viral inflammation. The present study has evaluated the antiviral and anti-inflammatory potential of natural triterpenoids: azadirachtin, withanolide_A, and isoginkgetin. These molecules inhibit the Mpro and PLpro proteolytic activities with half-maximal inhibitory concentrations (IC50) values ranging from 1.42 to 32.7 μM. Isothermal titration calorimetry (ITC) analysis validated the binding of these compounds to Mpro and PLpro. As expected, the two compounds, withanolide_A and azadirachtin, exhibit potent anti-SARS-CoV-2 activity in cell-based assays, with half-maximum effective concentration (EC50) values of 21.73 and 31.19 μM, respectively. The anti-inflammatory roles of azadirachtin and withanolide_A when assessed using HEK293T cells, were found to significantly reduce the levels of CXCL10, TNFα, IL6, and IL8 cytokines, which are elevated in severe cases of COVID-19. Interestingly, azadirachtin and withanolide_A were also found to rescue the decreased type-I interferon response (IFN-α1). The results of this study clearly highlight the role of triterpenoids as effective antiviral molecules that target SARS-CoV-2-specific enzymes and also host immune pathways involved in virus-mediated inflammation.
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Affiliation(s)
- Shweta Choudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Sanketkumar Nehul
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Ankur Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Prasan Kumar Panda
- Department of Internal Medicine (Division of Infectious diseases), All India Institute of Medical Sciences (AIIMS), Rishikesh, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Gaurav Kumar Sharma
- Centre for Animal Disease Research and Diagnosis (CADRAD), Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
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Choudhary S, Nehul S, Singh A, Panda PK, Kumar P, Sharma GK, Tomar S. Unraveling antiviral efficacy of multifunctional immunomodulatory triterpenoids against SARS‐COV‐2 targeting main protease and papain‐like protease. IUBMB Life 2024; 76:228-241. [DOI: 10.1002/iub.2793 | pmid: 38059400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/20/2023] [Indexed: 05/15/2025]
Abstract
AbstractThe coronavirus disease 2019 (COVID‐19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) may be over, but its variants continue to emerge, and patients with mild symptoms having long COVID is still under investigation. SARS‐CoV‐2 infection leading to elevated cytokine levels and suppressed immune responses set off cytokine storm, fatal systemic inflammation, tissue damage, and multi‐organ failure. Thus, drug molecules targeting the SARS‐CoV‐2 virus‐specific proteins or capable of suppressing the host inflammatory responses to viral infection would provide an effective antiviral therapy against emerging variants of concern. Evolutionarily conserved papain‐like protease (PLpro) and main protease (Mpro) play an indispensable role in the virus life cycle and immune evasion. Direct‐acting antivirals targeting both these viral proteases represent an attractive antiviral strategy that is also expected to reduce viral inflammation. The present study has evaluated the antiviral and anti‐inflammatory potential of natural triterpenoids: azadirachtin, withanolide_A, and isoginkgetin. These molecules inhibit the Mpro and PLpro proteolytic activities with half‐maximal inhibitory concentrations (IC50) values ranging from 1.42 to 32.7 μM. Isothermal titration calorimetry (ITC) analysis validated the binding of these compounds to Mpro and PLpro. As expected, the two compounds, withanolide_A and azadirachtin, exhibit potent anti‐SARS‐CoV‐2 activity in cell‐based assays, with half‐maximum effective concentration (EC50) values of 21.73 and 31.19 μM, respectively. The anti‐inflammatory roles of azadirachtin and withanolide_A when assessed using HEK293T cells, were found to significantly reduce the levels of CXCL10, TNFα, IL6, and IL8 cytokines, which are elevated in severe cases of COVID‐19. Interestingly, azadirachtin and withanolide_A were also found to rescue the decreased type‐I interferon response (IFN‐α1). The results of this study clearly highlight the role of triterpenoids as effective antiviral molecules that target SARS‐CoV‐2‐specific enzymes and also host immune pathways involved in virus‐mediated inflammation.
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Affiliation(s)
- Shweta Choudhary
- Department of Biosciences and Bioengineering Indian Institute of Technology Roorkee Roorkee India
| | - Sanketkumar Nehul
- Department of Biosciences and Bioengineering Indian Institute of Technology Roorkee Roorkee India
| | - Ankur Singh
- Department of Biosciences and Bioengineering Indian Institute of Technology Roorkee Roorkee India
| | - Prasan Kumar Panda
- Department of Internal Medicine (Division of Infectious diseases) All India Institute of Medical Sciences (AIIMS) Rishikesh India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering Indian Institute of Technology Roorkee Roorkee India
| | - Gaurav Kumar Sharma
- Centre for Animal Disease Research and Diagnosis (CADRAD) Indian Veterinary Research Institute Bareilly Uttar Pradesh India
| | - Shailly Tomar
- Department of Biosciences and Bioengineering Indian Institute of Technology Roorkee Roorkee India
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